diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 5a67c547df16487a9f70f6041059ce1a3735df54..3ff672a05d3ffba38dace3c11ecb3b98270cfeef 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -68,7 +68,8 @@ How quickly your contribution will be integrated depends largely on how much eff Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list. * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI. -* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers outside of , STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included ( instead of , or instead of ). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. +* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included ( instead of , or instead of ). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. +* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'. * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `.cpp` and `.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. diff --git a/bench/POTENTIALS/CH.airebo b/bench/POTENTIALS/CH.airebo deleted file mode 100644 index 3be02a9d8c9c5daa3ef948f5a836b900de63ee15..0000000000000000000000000000000000000000 --- a/bench/POTENTIALS/CH.airebo +++ /dev/null @@ -1,37592 +0,0 @@ -# AI-REBO Brenner/Stuart potential -# need to cite the appropriate papers here - -1.7 rcmin_CC -1.3 rcmin_CH -1.1 rcmin_HH -2.0 rcmax_CC -1.8 rcmax_CH -1.7 rcmax_HH -2.0 rcmaxp_CC -1.6 rcmaxp_CH -1.7 rcmaxp_HH -0.1 smin -2.0 Nmin -3.0 Nmax -3.2 NCmin -3.7 NCmax -0.31346 Q_CC -0.340776 Q_CH -0.370471 Q_HH -4.7465391 alpha_CC -4.1025498 alpha_CH -3.5362986 alpha_HH -10953.544 A_CC -149.94099 A_CH -32.817356 A_HH -12388.792 BIJc_CC1 -17.567065 BIJc_CC2 -30.714932 BIJc_CC3 -32.355187 BIJc_CH1 -0.0 BIJc_CH2 -0.0 BIJc_CH3 -29.632593 BIJc_HH1 -0.0 BIJc_HH2 -0.0 BIJc_HH3 -4.7204523 Beta_CC1 -1.4332132 Beta_CC2 -1.3826913 Beta_CC3 -1.4344581 Beta_CH1 -0.0 Beta_CH2 -0.0 Beta_CH3 -1.7158922 Beta_HH1 -0.0 Beta_HH2 -0.0 Beta_HH3 -0.0 rho_CC -1.09 rho_CH -0.7415887 rho_HH -3.4 rcLJmin_CC -3.025 rcLJmin_CH -2.65 rcLJmin_HH -3.816370964 rcLJmax_CC -3.395447696 rcLJmax_CH -2.974524428 rcLJmax_HH -0.77 bLJmin_CC -0.75 bLJmin_CH -0.32 bLJmin_HH -0.81 bLJmax_CC -0.9 bLJmax_CH -0.42 bLJmax_HH -0.00284 epsilon_CC -0.0020639767 epsilon_CH -0.0015 epsilon_HH -3.4 sigma_CC -3.025 sigma_CH -2.65 sigma_HH -0.3079 epsilonT_CCCC -0.1787 epsilonT_CCCH -0.125 epsilonT_HCCH - -# gC1 and gC2 - -5 --1.0 --0.6666666667 --0.5 --0.3333333333 -1.0 - - 0.2816950000 - 1.0627430000 - 2.1363075000 - 2.5334145000 - 1.5544035000 - 0.3862485000 - 0.2827390000 - 1.0718770000 - 2.1681365000 - 2.5885710000 - 1.6019100000 - 0.4025160000 - 0.6900250000 - 5.4601600000 - 23.0108000000 - 54.9086400000 - 68.6124000000 - 34.7051520000 - 0.2718560918 - 0.4892740137 - -0.4328177539 - -0.5616817383 - 1.2708702246 - -0.0375008379 - - 0.2816950000 - 1.0627430000 - 2.1363075000 - 2.5334145000 - 1.5544035000 - 0.3862485000 - 0.2827390000 - 1.0718770000 - 2.1681365000 - 2.5885710000 - 1.6019100000 - 0.4025160000 - 0.6900250000 - 5.4601600000 - 23.0108000000 - 54.9086400000 - 68.6124000000 - 34.7051520000 - 0.3754514434 - 1.4072691309 - 2.2551320117 - 2.0288747461 - 1.4269207324 - 0.5063519355 - -# gH - -4 --1.0 --0.8333333333 --0.5 -1.0 - - 270.4568000026 - 1549.6358000143 - 3781.7719000316 - 4582.1544000348 - 2721.4308000191 - 630.6336000042 - 16.9534406250 - -21.0823875000 - -102.4683000000 - -210.6432299999 - -229.8471299999 - -94.9946400000 - 19.0650249321 - 2.0177562840 - -2.5664219198 - 3.2913322346 - -2.6535615062 - 0.8376699753 - -# pCC - -4 -0.0 -4.0 -0.0 -4.0 - - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - -0.0986400000 - 0.0657600000 - 0.0000000000 - 0.0000000000 - 0.0657600000 - -0.0438400000 - -0.0025000000 - 0.0060000000 - -0.0045000000 - 0.0010000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.2339100000 - -0.6402960000 - 0.4802220000 - -0.1067160000 - -0.1559400000 - 0.4268640000 - -0.3201480000 - 0.0711440000 - 0.4650000000 - -0.5985000000 - 0.2493750000 - -0.0332500000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - -1.9074060000 - 2.4787080000 - -1.0327950000 - 0.1377060000 - 1.2716040000 - -1.6524720000 - 0.6885300000 - -0.0918040000 - -1.2900000000 - 1.1610000000 - -0.3386250000 - 0.0322500000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 3.8700000000 - -3.4830000000 - 1.0158750000 - -0.0967500000 - -2.5800000000 - 2.3220000000 - -0.6772500000 - 0.0645000000 - -0.1380150000 - 0.0000000000 - 0.5932650000 - -0.3955100000 - 0.3312360000 - 0.0000000000 - -1.5027480000 - 1.0018320000 - -0.2484270000 - 0.0000000000 - 1.1270610000 - -0.7513740000 - 0.0552060000 - 0.0000000000 - -0.2504580000 - 0.1669720000 - -0.3654800000 - 1.0205280000 - -0.7653960000 - 0.1700880000 - 1.0582800000 - -2.9471040000 - 2.2103280000 - -0.4911840000 - -0.7937100000 - 2.2103280000 - -1.6577460000 - 0.3683880000 - 0.1763800000 - -0.4911840000 - 0.3683880000 - -0.0818640000 - 0.6832080000 - -0.9109440000 - 0.3795600000 - -0.0506080000 - -2.0496240000 - 2.7328320000 - -1.1386800000 - 0.1518240000 - 1.5372180000 - -2.0496240000 - 0.8540100000 - -0.1138680000 - -0.3416040000 - 0.4554720000 - -0.1897800000 - 0.0253040000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 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0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - -# PCH - -4 -0.0 -4.0 -0.0 -4.0 - - 0.0000000000 - 0.0000000000 - 0.6280110000 - -0.4186740000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0300000000 - 0.0000000000 - -3.1001400000 - 2.0667600000 - -0.0200000000 - 0.0000000000 - 2.0667600000 - -1.3778400000 - -1.1595980000 - 3.2854440000 - -2.4640830000 - 0.5475740000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.4966950000 - -3.6001800000 - 2.7001350000 - -0.6000300000 - -0.3311300000 - 2.4001200000 - -1.8000900000 - 0.4000200000 - -6.7698340000 - 8.6212080000 - -3.5921700000 - 0.4789560000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 44.5208070000 - -58.1453640000 - 24.2272350000 - -3.2302980000 - -29.6805380000 - 38.7635760000 - -16.1514900000 - 2.1535320000 - 24.3142400000 - -21.8828160000 - 6.3824880000 - -0.6078560000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - -72.9427200000 - 65.6484480000 - -19.1474640000 - 1.8235680000 - 48.6284800000 - -43.7656320000 - 12.7649760000 - -1.2157120000 - -0.6502100000 - 0.0000000000 - -1.0558290000 - 0.7038860000 - 1.5845040000 - 0.0000000000 - 1.5611040000 - -1.0407360000 - -1.1883780000 - 0.0000000000 - -1.1708280000 - 0.7805520000 - 0.2640840000 - 0.0000000000 - 0.2601840000 - -0.1734560000 - 9.9867120000 - -26.3732760000 - 19.7799570000 - -4.3955460000 - -26.3537880000 - 68.3007840000 - -51.2255880000 - 11.3834640000 - 19.7653410000 - -51.2255880000 - 38.4191910000 - -8.5375980000 - -4.3922980000 - 11.3834640000 - -8.5375980000 - 1.8972440000 - -32.2817400000 - 43.0423200000 - -17.9343000000 - 2.3912400000 - 96.8452200000 - -129.1269600000 - 53.8029000000 - -7.1737200000 - -72.6339150000 - 96.8452200000 - -40.3521750000 - 5.3802900000 - 16.1408700000 - -21.5211600000 - 8.9671500000 - -1.1956200000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 0.0000000000 - 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1.4418444610242331e-02 1.4132134584901757e-02 1.3853612084676337e-02 1.3582507369821917e-02 1.3318475216818060e-02 - 1.3061193172097418e-02 1.2810359927147186e-02 1.2565693807050415e-02 1.2326931365025051e-02 1.2093826075940506e-02 - 1.1866147122233661e-02 1.1643678266026136e-02 1.1426216801644407e-02 1.1213572583084475e-02 1.1005567121320226e-02 - 1.0802032746662471e-02 1.0602811831688208e-02 1.0407756070544782e-02 1.0216725810699157e-02 1.0029589433467268e-02 - 9.8462227798860602e-03 9.6665086187306404e-03 9.4903361536790021e-03 9.3176005668363371e-03 9.1482025960089031e-03 - 8.9820481433065535e-03 8.8190479128032462e-03 8.6591170751522117e-03 8.5021749571883021e-03 8.3481447546937537e-03 - 8.1969532666261724e-03 8.0485306492223962e-03 7.9028101885199598e-03 7.7597280899136256e-03 7.6192232834934315e-03 - 7.4812372439735375e-03 7.3457138241272979e-03 7.2125991007052359e-03 7.0818412319012813e-03 6.9533903254870300e-03 - 6.8271983168139705e-03 6.7032188559211503e-03 6.5814072030662141e-03 6.4617201320263939e-03 6.3441158405819764e-03 - 6.2285538676237207e-03 6.1149950163802147e-03 6.0034012832899109e-03 5.8937357920846312e-03 5.7859627326801166e-03 - 5.6800473044990030e-03 5.5759556638887986e-03 5.4736548753111791e-03 5.3731128660109428e-03 5.2742983838981461e-03 - 5.1771809583849582e-03 5.0817308639591330e-03 4.9879190862693046e-03 4.8957172905357560e-03 4.8050977921015592e-03 - 4.7160335289582467e-03 4.6284980360953021e-03 4.5424654215287241e-03 4.4579103438822931e-03 4.3748079913988880e-03 - 4.2931340622749670e-03 4.2128647462132407e-03 4.1339767071033873e-03 4.0564470667446839e-03 3.9802533895282599e-03 - 3.9053736680121076e-03 3.8317863093158128e-03 3.7594701222811860e-03 3.6884043053326127e-03 3.6185684349951674e-03 - 3.5499424550168301e-03 3.4825066660512660e-03 3.4162417158645347e-03 3.3511285900229004e-03 3.2871486030347646e-03 - 3.2242833899080170e-03 3.1625148980992668e-03 3.1018253798278661e-03 3.0421973847258310e-03 2.9836137528083811e-03 - 2.9260576077371064e-03 2.8695123503632708e-03 2.8139616525287708e-03 2.7593894511106498e-03 2.7057799422959966e-03 - 2.6531175760685227e-03 2.6013870509009052e-03 2.5505733086344240e-03 2.5006615295404683e-03 2.4516371275501436e-03 - 2.4034857456453340e-03 2.3561932514012535e-03 2.3097457326723414e-03 2.2641294934160616e-03 2.2193310496436136e-03 - 2.1753371254977782e-03 2.1321346494441173e-03 2.0897107505768314e-03 2.0480527550303662e-03 2.0071481824917164e-03 - 1.9669847428123305e-03 1.9275503327108034e-03 1.8888330325659355e-03 1.8508211032951805e-03 1.8135029833145980e-03 - 1.7768672855772646e-03 1.7409027946878666e-03 1.7055984640891586e-03 1.6709434133182904e-03 1.6369269253308227e-03 - 1.6035384438881917e-03 1.5707675710093030e-03 1.5386040644797400e-03 1.5070378354209296e-03 1.4760589459142243e-03 - 1.4456576066784674e-03 1.4158241748004133e-03 1.3865491515145517e-03 1.3578231800324136e-03 1.3296370434173130e-03 - 1.3019816625059188e-03 1.2748480938728074e-03 1.2482275278369870e-03 1.2221112865106742e-03 1.1964908218862064e-03 - 1.1713577139624703e-03 1.1467036689077198e-03 1.1225205172586891e-03 1.0988002121543120e-03 1.0755348276031765e-03 - 1.0527165567835728e-03 1.0303377103750150e-03 1.0083907149206553e-03 9.8686811121878604e-04 9.6576255274356815e-04 - 9.4506680409354657e-04 9.2477373946662708e-04 9.0487634116191706e-04 8.8536769810608137e-04 8.6624100440530968e-04 - 8.4748955791986991e-04 8.2910675886310736e-04 8.1108610842155551e-04 7.9342120739794852e-04 7.7610575487466887e-04 - 7.5913354689786591e-04 7.4249847518158968e-04 7.2619452583109687e-04 7.1021577808524222e-04 6.9455640307671332e-04 - 6.7921066261025093e-04 6.6417290795844214e-04 6.4943757867335500e-04 6.3499920141575628e-04 6.2085238879914031e-04 - 6.0699183824991856e-04 5.9341233088238896e-04 5.8010873038847818e-04 5.6707598194186137e-04 5.5430911111587280e-04 - 5.4180322281523891e-04 5.2955350022104025e-04 5.1755520374872563e-04 5.0580367001857793e-04 4.9429431083891986e-04 - 4.8302261220136561e-04 4.7198413328763435e-04 4.6117450548847222e-04 4.5058943143359842e-04 4.4022468403297037e-04 - 4.3007610552883886e-04 4.2013960655883260e-04 4.1041116522908330e-04 4.0088682619821882e-04 3.9156269977118005e-04 - 3.8243496100300207e-04 3.7349984881274514e-04 3.6475366510662147e-04 3.5619277391102898e-04 3.4781360051482253e-04 - 3.3961263062063513e-04 3.3158640950565685e-04 3.2373154119109092e-04 3.1604468762060252e-04 3.0852256784754707e-04 - 3.0116195723081836e-04 2.9395968663908575e-04 2.8691264166377101e-04 2.8001776184017647e-04 2.7327203987681688e-04 - 2.6667252089326854e-04 2.6021630166557681e-04 2.5390052988028163e-04 2.4772240339593181e-04 2.4167916951265550e-04 - 2.3576812424967210e-04 2.2998661163024531e-04 2.2433202297460642e-04 2.1880179620031078e-04 2.1339341513026532e-04 - 2.0810440880823181e-04 2.0293235082175821e-04 1.9787485863260665e-04 1.9292959291436311e-04 1.8809425689761319e-04 - 1.8336659572205580e-04 1.7874439579616125e-04 1.7422548416372047e-04 1.6980772787763936e-04 1.6548903338088530e-04 - 1.6126734589430591e-04 1.5714064881157744e-04 1.5310696310104604e-04 1.4916434671449329e-04 1.4531089400280153e-04 - 1.4154473513841234e-04 1.3786403554466153e-04 1.3426699533172857e-04 1.3075184873951283e-04 1.2731686358694039e-04 - 1.2396034072819674e-04 1.2068061351527565e-04 1.1747604726729168e-04 1.1434503874632306e-04 1.1128601563955686e-04 - 1.0829743604811193e-04 1.0537778798212988e-04 1.0252558886227753e-04 9.9739385027582898e-05 9.7017751249615057e-05 - 9.4359290252773662e-05 9.1762632240957511e-05 8.9226434430383569e-05 8.6749380588361721e-05 8.4330180578390864e-05 - 8.1967569911181246e-05 7.9660309301724484e-05 7.7407184232279429e-05 7.5207004521348451e-05 7.3058603898526649e-05 - 7.0960839585107720e-05 6.8912591880629977e-05 6.6912763755002085e-05 6.4960280446513426e-05 6.3054089065330086e-05 - 6.1193158202771814e-05 5.9376477546041213e-05 5.7603057498502742e-05 5.5871928805544500e-05 5.4182142185708361e-05 - 5.2532767967318744e-05 5.0922895730446966e-05 4.9351633954125953e-05 4.7818109668823321e-05 4.6321468114150300e-05 - 4.4860872401664663e-05 4.3435503182825573e-05 4.2044558321957873e-05 4.0687252574273750e-05 3.9362817268785450e-05 - 3.8070499996214428e-05 3.6809564301621984e-05 3.5579289382025496e-05 3.4378969788611451e-05 3.3207915133769052e-05 - 3.2065449802711312e-05 3.0950912669766876e-05 2.9863656819185611e-05 2.8803049270468119e-05 2.7768470708167169e-05 - 2.6759315216115260e-05 2.5774990015931323e-05 2.4814915209964844e-05 2.3878523528387922e-05 2.2965260080560611e-05 - 2.2074582110528148e-05 2.1205958756658535e-05 2.0358870815317476e-05 1.9532810508535560e-05 1.8727281255713447e-05 - 1.7941797449145505e-05 1.7175884233475961e-05 1.6429077288930018e-05 1.5700922618341645e-05 1.4990976337865471e-05 - 1.4298804471386687e-05 1.3623982748522034e-05 1.2966096406226424e-05 1.2324739993882115e-05 1.1699517181902770e-05 - 1.1090040573734860e-05 1.0495931521266495e-05 9.9168199435395021e-06 9.3523441487842465e-06 8.8021506596591475e-06 - 8.2658940417265321e-06 7.7432367350197678e-06 7.2338488887770244e-06 6.7374081991923703e-06 6.2535997501888662e-06 - 5.7821158571569505e-06 5.3226559136389283e-06 4.8749262408651290e-06 4.4386399401326240e-06 4.0135167480073166e-06 - 3.5992828942305738e-06 3.1956709623667747e-06 2.8024197531120341e-06 2.4192741502208947e-06 2.0459849890155880e-06 - 1.6823089274468580e-06 1.3280083196495871e-06 9.8285109196557868e-07 6.4661062138351467e-07 3.1906561636122974e-07 - 0. 0. 0. 0. 0. - - diff --git a/bench/POTENTIALS/Cu_u3.eam b/bench/POTENTIALS/Cu_u3.eam new file mode 120000 index 0000000000000000000000000000000000000000..892d592f813d2e99866298871f3226f11c3503d0 --- /dev/null +++ b/bench/POTENTIALS/Cu_u3.eam @@ -0,0 +1 @@ +../../potentials/Cu_u3.eam \ No newline at end of file diff --git a/bench/POTENTIALS/Ni.adp b/bench/POTENTIALS/Ni.adp deleted file mode 100644 index 7cc301c678bda705c8a88109d63f8736fd4edf71..0000000000000000000000000000000000000000 --- a/bench/POTENTIALS/Ni.adp +++ /dev/null @@ -1,43007 +0,0 @@ -Nickel ADP potential: Mishin et al. Acta Mater 2005 pp 4029 -Data below r=1.5 A is extrapolated -F(rho) data not extrapolated -1 Ni -3001 9.7054386687161695E-04 10000 5.1685168516851690E-04 5.1680000000000001E+00 -28 58.690000 3.520000 bcc -0.0000000000000000E+00 --3.0290737299999999E-02 --5.0634721479999999E-02 --6.9797312240000006E-02 --8.8564051170000005E-02 --1.0717802630000001E-01 --1.2573466940000000E-01 --1.4427463460000001E-01 --1.6281478960000001E-01 --1.8136070720000000E-01 --1.9991233659999999E-01 --2.1846679510000000E-01 --2.3701981929999999E-01 --2.5556654820000002E-01 --2.7410195389999997E-01 --2.9262107840000001E-01 --3.1111916309999998E-01 --3.2959171329999998E-01 --3.4803452779999999E-01 --3.6644370580000002E-01 --3.8481564250000000E-01 --4.0314701679999998E-01 --4.2143477629999998E-01 --4.3967611990000000E-01 --4.5786848019999998E-01 --4.7600950640000000E-01 --4.9409704809999999E-01 --5.1212913940000004E-01 --5.3010398489999999E-01 --5.4801994549999999E-01 --5.6587552679999997E-01 --5.8366936719999996E-01 --6.0140022810000004E-01 --6.1906698350000000E-01 --6.3666861190000001E-01 --6.5420418790000001E-01 --6.7167287529999997E-01 --6.8907391990000000E-01 --7.0640664360000005E-01 --7.2367043900000005E-01 --7.4086476369999998E-01 --7.5798913580000005E-01 --7.7504312980000001E-01 --7.9202637200000003E-01 --8.0893853729999998E-01 --8.2577934590000002E-01 --8.4254855930000006E-01 --8.5924597840000005E-01 --8.7587144029999997E-01 --8.9242481610000002E-01 --9.0890600820000000E-01 --9.2531494839999995E-01 --9.4165159590000003E-01 --9.5791593580000001E-01 --9.7410797689999995E-01 --9.9022775019999998E-01 --1.0062753080000000E+00 --1.0222507210000000E+00 --1.0381540800000000E+00 --1.0539854900000001E+00 --1.0697450749999999E+00 --1.0854329720000000E+00 --1.1010493330000000E+00 --1.1165943210000000E+00 --1.1320681130000001E+00 --1.1474708970000000E+00 --1.1628028710000000E+00 --1.1780642440000000E+00 --1.1932552329999999E+00 --1.2083760649999999E+00 --1.2234269739999999E+00 --1.2384082009999999E+00 --1.2533199970000000E+00 --1.2681626150000000E+00 --1.2829363170000001E+00 --1.2976413720000000E+00 --1.3122780510000001E+00 --1.3268466230000000E+00 --1.3413473300000001E+00 --1.3557803710000000E+00 --1.3701459140000001E+00 --1.3844440910000000E+00 --1.3986750180000000E+00 --1.4128387830000000E+00 --1.4269354599999999E+00 --1.4409651070000000E+00 --1.4549277709999999E+00 --1.4688234890000000E+00 --1.4826522929999999E+00 --1.4964142090000001E+00 --1.5101092580000000E+00 --1.5237374640000001E+00 --1.5372988460000001E+00 --1.5507934280000000E+00 --1.5642212350000000E+00 --1.5775822930000001E+00 --1.5908766360000000E+00 --1.6041043010000000E+00 --1.6172653290000001E+00 --1.6303597679999999E+00 --1.6433876740000000E+00 --1.6563491070000000E+00 --1.6692441370000000E+00 --1.6820728410000001E+00 --1.6948353009999999E+00 --1.7075316100000000E+00 --1.7201618670000001E+00 --1.7327261800000000E+00 --1.7452246659999999E+00 --1.7576574469999999E+00 --1.7700246570000000E+00 --1.7823264360000000E+00 --1.7945629320000001E+00 --1.8067343020000000E+00 --1.8188407110000000E+00 --1.8308823310000000E+00 --1.8428593400000000E+00 --1.8547719279999999E+00 --1.8666202890000001E+00 --1.8784046260000000E+00 --1.8901251480000001E+00 --1.9017820710000000E+00 --1.9133756200000001E+00 --1.9249060240000000E+00 --1.9363735179999999E+00 --1.9477783479999999E+00 --1.9591207589999999E+00 --1.9704010100000000E+00 --1.9816193580000001E+00 --1.9927760720000001E+00 --2.0038714230000001E+00 --2.0149056879999998E+00 --2.0258791480000000E+00 --2.0367920900000001E+00 --2.0476448060000001E+00 --2.0584375929999998E+00 --2.0691707490000000E+00 --2.0798445810000001E+00 --2.0904593960000000E+00 --2.1010155089999998E+00 --2.1115132330000002E+00 --2.1219528880000000E+00 --2.1323347990000001E+00 --2.1426592900000001E+00 --2.1529266909999998E+00 --2.1631373350000000E+00 --2.1732915560000001E+00 --2.1833896920000000E+00 --2.1934320820000002E+00 --2.2034190680000001E+00 --2.2133509960000000E+00 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--1.8394040639416483E-07 --1.7970186636971915E-07 --1.7553657120934498E-07 --1.7144368586409230E-07 --1.6742237822370230E-07 --1.6347182008918821E-07 --1.5959118607361577E-07 --1.5577966030216672E-07 --1.5203642961887040E-07 --1.4836068679752336E-07 --1.4475162858072309E-07 --1.4120845439505123E-07 --1.3773036821721508E-07 --1.3431657632178286E-07 --1.3096629423619672E-07 --1.2767874069059649E-07 --1.2445313978825279E-07 --1.2128872025401995E-07 --1.1818471326019451E-07 --1.1514035521244997E-07 --1.1215488451769189E-07 --1.0922754824265955E-07 --1.0635759722683983E-07 --1.0354428717223641E-07 --1.0078687915200324E-07 --9.8084636397994985E-08 --9.5436827807157803E-08 --9.2842724202280293E-08 --9.0301604456946776E-08 --8.7812751915926455E-08 --8.5375454164323255E-08 --8.2989004787548316E-08 --8.0652699329342564E-08 --7.8365839359754679E-08 --7.6127728516170878E-08 --7.3937677718265837E-08 --7.1795003071114345E-08 --6.9699024327251605E-08 --6.7649067812870524E-08 --6.5644461714697754E-08 --6.3684540406085333E-08 --6.1768640667970903E-08 --5.9896105732860628E-08 --5.8066284734382320E-08 --5.6278529907678729E-08 --5.4532200516303043E-08 --5.2826657716173464E-08 --5.1161268828395195E-08 --4.9535404090844922E-08 --4.7948439335204572E-08 --4.6399756969035914E-08 --4.4888742046300438E-08 --4.3414786953307868E-08 --4.1977286145102631E-08 --4.0575640051610707E-08 --3.9209252656388163E-08 --3.7877532693359062E-08 --3.6579896067242194E-08 --3.5315761007868847E-08 --3.4084553194099595E-08 --3.2885700706981924E-08 --3.1718637266734964E-08 --3.0582800870761919E-08 --2.9477633477044601E-08 --2.8402584690591421E-08 --2.7357106285703514E-08 --2.6340657405740641E-08 --2.5352700085148896E-08 --2.4392701535596197E-08 --2.3460134004192362E-08 --2.2554473007610634E-08 --2.1675202046275195E-08 --2.0821806804722712E-08 --1.9993780074536437E-08 --1.9190618150830800E-08 --1.8411821962823177E-08 --1.7656898224886286E-08 --1.6925356366920838E-08 --1.6216713966422522E-08 --1.5530490974154429E-08 --1.4866214033824219E-08 --1.4223413993515892E-08 --1.3601625751322447E-08 --1.3000390679644334E-08 --1.2419252490600745E-08 --1.1857763011146499E-08 --1.1315476808619242E-08 --1.0791954599677132E-08 --1.0286762051513243E-08 --9.7994683074129686E-09 --9.3296495784861910E-09 --8.8768842354633953E-09 --8.4407585245141295E-09 --8.0208619557496970E-09 --7.6167895630817633E-09 --7.2281420904837388E-09 --6.8545232349760602E-09 --6.4955442050555536E-09 --6.1508183849660006E-09 --5.8199666338722945E-09 --5.5026137187817486E-09 --5.1983892543797646E-09 --4.9069292867461168E-09 --4.6278723979633209E-09 --4.3608649466215645E-09 --4.1055556793654406E-09 --3.8616002800722149E-09 --3.6286590616325362E-09 --3.4063965046082363E-09 --3.1944841626415147E-09 --2.9925958610998772E-09 --2.8004132501180830E-09 --2.6176207741868601E-09 --2.4439091723227222E-09 --2.2789745698618595E-09 --2.1225166208134801E-09 --1.9742425760555375E-09 --1.8338618682468397E-09 --1.7010915898259416E-09 --1.5756521986997543E-09 --1.4572697390043510E-09 --1.3456763938851140E-09 --1.2406073222362054E-09 --1.1418056470454685E-09 --1.0490167649383810E-09 --9.6199338384017097E-10 --8.8049227003083141E-10 --8.0427504250002919E-10 --7.3311016287488540E-10 --6.6676864961636898E-10 --6.0502965934625762E-10 --5.4767490229679998E-10 --4.9449289774138324E-10 --4.4527699284214277E-10 --3.9982467175762660E-10 --3.5794087314491195E-10 --3.1943284875747906E-10 --2.8411594159965001E-10 --2.5180851434792234E-10 --2.2233511707284062E-10 --1.9552592807064303E-10 --1.7121460860159049E-10 --1.4924275740892149E-10 --1.2945422976277375E-10 --1.1170072186078897E-10 --9.5837568309496897E-11 --8.1725593636869548E-11 --6.9232035143674366E-11 --5.8227065979996797E-11 --4.8589113817898478E-11 --4.0198998019636638E-11 --3.2944955130422726E-11 --2.6719588764544600E-11 --2.1420266312769912E-11 --1.6951489990687653E-11 --1.3220303816900579E-11 --1.0142115692954298E-11 --7.6350564157245434E-12 --5.6241182526454802E-12 --4.0394621565471332E-12 --2.8152841090332069E-12 --1.8934873635463345E-12 --1.2183351879044278E-12 --7.4250779871519885E-13 --4.2196259985249582E-13 --2.1839191798943897E-13 --9.9035346821695661E-14 --3.5381277322081621E-14 --9.3397035389237926E-15 --4.4862118882457237E-15 --4.3963887862075566E-15 diff --git a/bench/POTENTIALS/Ni.adp b/bench/POTENTIALS/Ni.adp new file mode 120000 index 0000000000000000000000000000000000000000..1c4f62174768775378fd57fd82c37de946c7ba87 --- /dev/null +++ b/bench/POTENTIALS/Ni.adp @@ -0,0 +1 @@ +../../potentials/Ni.adp \ No newline at end of file diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 91fb930be28ba1c9f83fcf605c0045efba6b3079..ddad6c2626991c197f7b70de9e0f9db923452d7c 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -52,8 +52,15 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR}) include(CheckCCompilerFlag) include(CheckIncludeFileCXX) -if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") +if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict -std=c++11") +endif() + +option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF) +if(DISABLE_CXX11_REQUIREMENT) + add_definitions(-DLAMMPS_CXX98) +# else() +# set(CMAKE_CXX_STANDARD 11) endif() # GNU compiler features @@ -241,6 +248,7 @@ if(BUILD_OMP) endif() if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) + enable_language(C) find_package(LAPACK) find_package(BLAS) if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) @@ -315,13 +323,14 @@ endif() include(Packages/KSPACE) include(Packages/PYTHON) include(Packages/VORONOI) -include(Packages/USER-SCAFACOS) -include(Packages/USER-PLUMED) +include(Packages/USER-COLVARS) include(Packages/USER-MOLFILE) include(Packages/USER-NETCDF) -include(Packages/USER-SMD) -include(Packages/USER-QUIP) +include(Packages/USER-PLUMED) include(Packages/USER-QMMM) +include(Packages/USER-QUIP) +include(Packages/USER-SCAFACOS) +include(Packages/USER-SMD) include(Packages/USER-VTK) include(Packages/KIM) include(Packages/LATTE) @@ -411,8 +420,7 @@ endforeach() ############################################## # add lib sources of (simple) enabled packages ############################################ -foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD - USER-QMMM) +foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM) if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) @@ -426,10 +434,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include) elseif(PKG_LIB STREQUAL h5md) target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS}) - elseif(PKG_LIB STREQUAL colvars) - target_compile_options(colvars PRIVATE -DLEPTON) - target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include) - target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars) else() target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}) endif() diff --git a/cmake/Modules/FindKIM-API.cmake b/cmake/Modules/FindKIM-API.cmake index 5108b0f98c42acfc2a3fcec2a4fc7e557470148c..17c195e62f515752d893118cd9a0d08e0ad8ae58 100644 --- a/cmake/Modules/FindKIM-API.cmake +++ b/cmake/Modules/FindKIM-API.cmake @@ -37,6 +37,26 @@ # KIM-API-CMAKE_Fortran_COMPILER # +function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr) + if(NOT EXISTS ${_version_hdr}) + message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)") + endif() + foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH) + file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+") + if(_contents) + string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}") + if(${_${_var}} STREQUAL "") + message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!") + elseif(NOT ${_${_var}} MATCHES "^[0-9]+$") + message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!") + endif() + else() + message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}") + endif() + endforeach() + set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE) +endfunction() + if(KIM-API_FIND_QUIETLY) set(REQ_OR_QUI "QUIET") else() @@ -54,6 +74,12 @@ if(KIM-API_FOUND) pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER) endif() +if(KIM-API_INCLUDEDIR) + _KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h) +else() + set(KIM-API_VERSION 0) +endif() + # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE # if all listed variables are TRUE -find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES) +find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION) diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake index 43f95125c874e32fd6ed10b54ade877fa7f8a067..8d172257600317ba4964f3ca167430cbd223476d 100644 --- a/cmake/Modules/Packages/KIM.cmake +++ b/cmake/Modules/Packages/KIM.cmake @@ -1,4 +1,5 @@ if(PKG_KIM) + set(KIM-API_MIN_VERSION 2.1) find_package(CURL) if(CURL_FOUND) include_directories(${CURL_INCLUDE_DIRS}) @@ -7,10 +8,17 @@ if(PKG_KIM) endif() find_package(KIM-API QUIET) if(KIM-API_FOUND) - set(DOWNLOAD_KIM_DEFAULT OFF) + if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION}) + if ("${DOWNLOAD_KIM}" STREQUAL "") + message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\". Default behavior set to download and build our own.") + endif() + set(DOWNLOAD_KIM_DEFAULT ON) + else() + set(DOWNLOAD_KIM_DEFAULT OFF) + endif() else() - if (NOT DOWNLOAD_KIM) - message(WARNING "KIM-API package not found. We will download and build our own") + if ("${DOWNLOAD_KIM}" STREQUAL "") + message(WARNING "KIM-API package not found. Default behavior set to download and build our own") endif() set(DOWNLOAD_KIM_DEFAULT ON) endif() @@ -42,7 +50,7 @@ if(PKG_KIM) set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}) list(APPEND LAMMPS_DEPS kim_build) else() - find_package(KIM-API REQUIRED) + find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED) endif() list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}") include_directories(${KIM-API_INCLUDE_DIRS}) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index 2f7d40180201b37f0fab715b5e396324044766ec..428588ec9d06e860f3535cf6b8de619fc896a67d 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -1,15 +1,24 @@ if(PKG_KOKKOS) - set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) - set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos) + # TODO: this option needs to be documented when this works with a + # regular release version of KOKKOS, and a version compatibility check + # of external KOKKOS lib versus what the KOKKOS package needs is required. + option(EXTERNAL_KOKKOS "Build against external kokkos library") + if(EXTERNAL_KOKKOS) + find_package(Kokkos REQUIRED) + list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos) + else() + set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) + set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos) + add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR}) + + set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src + ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src + ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src + ${LAMMPS_LIB_KOKKOS_BIN_DIR}) + include_directories(${Kokkos_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS kokkos) + endif() add_definitions(-DLMP_KOKKOS) - add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR}) - - set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src - ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src - ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src - ${LAMMPS_LIB_KOKKOS_BIN_DIR}) - include_directories(${Kokkos_INCLUDE_DIRS}) - list(APPEND LAMMPS_LINK_LIBS kokkos) set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS) set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp @@ -17,12 +26,15 @@ if(PKG_KOKKOS) ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp + ${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp) @@ -38,6 +50,7 @@ if(PKG_KOKKOS) # register kokkos-only styles RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h) + RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h) if(PKG_USER-DPD) get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES) diff --git a/cmake/Modules/Packages/MESSAGE.cmake b/cmake/Modules/Packages/MESSAGE.cmake index 3c1bdde855c366fbf74374c08d8bcb6f88eb1d24..aff9c2964adecf9088dcd1e23463f1fc36bb7bc9 100644 --- a/cmake/Modules/Packages/MESSAGE.cmake +++ b/cmake/Modules/Packages/MESSAGE.cmake @@ -1,4 +1,7 @@ if(PKG_MESSAGE) + if(LAMMPS_SIZES STREQUAL BIGBIG) + message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG") + endif() option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF) file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c diff --git a/cmake/Modules/Packages/USER-COLVARS.cmake b/cmake/Modules/Packages/USER-COLVARS.cmake new file mode 100644 index 0000000000000000000000000000000000000000..b7fb91917cc32595dfd589adf779c26ac3af28bf --- /dev/null +++ b/cmake/Modules/Packages/USER-COLVARS.cmake @@ -0,0 +1,42 @@ +if(PKG_USER-COLVARS) + + set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars) + + file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp) + + # Build Lepton by default + set(COLVARS_LEPTON_DEFAULT ON) + # but not if C++11 is disabled per user request + if(DEFINED DISABLE_CXX11_REQUIREMENT) + if(DISABLE_CXX11_REQUIREMENT) + set(COLVARS_LEPTON_DEFAULT OFF) + endif() + endif() + + option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT}) + + # Verify that the user's choice is consistent + if(DEFINED DISABLE_CXX11_REQUIREMENT) + if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON)) + message(FATAL_ERROR "Building the Lepton library requires C++11 or later.") + endif() + endif() + + if(COLVARS_LEPTON) + set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton) + file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp) + add_library(lepton STATIC ${LEPTON_SOURCES}) + target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include) + endif() + + add_library(colvars STATIC ${COLVARS_SOURCES}) + target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars) + list(APPEND LAMMPS_LINK_LIBS colvars) + + if(COLVARS_LEPTON) + list(APPEND LAMMPS_LINK_LIBS lepton) + target_compile_options(colvars PRIVATE -DLEPTON) + target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include) + endif() + +endif() diff --git a/cmake/Modules/Packages/USER-MOLFILE.cmake b/cmake/Modules/Packages/USER-MOLFILE.cmake index 16ffc349940eb3b5a58b1eab4f73b4154523a075..b8c4234d265dbc2381ae4bfcc57aec00a2ee7407 100644 --- a/cmake/Modules/Packages/USER-MOLFILE.cmake +++ b/cmake/Modules/Packages/USER-MOLFILE.cmake @@ -1,4 +1,8 @@ if(PKG_USER-MOLFILE) + if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library + message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later") + endif() + set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers") add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 5c35e13bda33bd3b7592581694964b35fdc5482a..bf5c502d84bbe9421c6e37518ea519fcb3f97dbb 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -49,8 +49,8 @@ if(PKG_USER-PLUMED) message(STATUS "PLUMED download requested - we will build our own") include(ExternalProject) ExternalProject_Add(plumed_build - URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz - URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a + URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz + URL_MD5 de30d6e7c2dcc0973298e24a6da24286 BUILD_IN_SOURCE 1 CONFIGURE_COMMAND /configure --prefix= ${CONFIGURE_REQUEST_PIC} diff --git a/cmake/README.md b/cmake/README.md index 01b6f6a60e805425c178f2f83ee95aa962540dbf..6255307ef32f36120eaefe6c1fea097cdab50824 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -1798,6 +1798,32 @@ Requires installation of the Voro++ library +### USER-COLVARS Package + +Requires a C++11 compiler to compile with the Lepton library included. + + + + + + + + + + + + + + + +
OptionDescriptionValues
COLVARS_LEPTONEnable the use of the Lepton library inside the Colvars library. + +
+
on (default)
+
off
+
+
+ ### USER-LATTE Package Requires installation of the LATTE library diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 35ad7ba55c688d4bdc371e8ff5a715f8c94a0f78..eed560b995dd0dbd64e2082689ec3e1270649adf 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -4,10 +4,10 @@ set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI - PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI + PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESO - USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC + USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF) foreach(PKG ${ALL_PACKAGES}) diff --git a/doc/Makefile b/doc/Makefile index 3b9d25694d2520daa4f5d7d0e779aabf3c7ad425..72c03929a1c5f971cfbd3c10b41b388078738b4c 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -71,6 +71,7 @@ html: $(OBJECTS) $(ANCHORCHECK) sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ echo "############################################" ;\ doc_anchor_check src/*.txt ;\ + env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\ echo "############################################" ;\ deactivate ;\ ) diff --git a/doc/lammps.1 b/doc/lammps.1 index ac19749dd69295103e6ccc6b0ee2b6b25d868ccb..ec31d19b740cf24dfff2bac5c8ecdf0e31a5a74d 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "7 August 2019" "2019-08-07" +.TH LAMMPS "30 October 2019" "2019-10-30" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index 04e11009afc9c3121f60d0f537c8ca5aff8b29d0..cde1055419a799e47060f25092d77acd7d7c5169 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -51,7 +51,7 @@ Serial build (see src/MAKE/Makefile.serial): MPI_INC = -I../STUBS MPI_PATH = -L../STUBS -MPI_LIB = -lmpi_stubs :pre +MPI_LIB = -lmpi_stubs :pre For a parallel build, if MPI is installed on your system in the usual place (e.g. under /usr/local), you do not need to specify the 3 @@ -183,17 +183,17 @@ want. Parallel build (see src/MAKE/Makefile.mpi): -CC = mpicxx -CCFLAGS = -g -O3 -LINK = mpicxx -LINKFLAGS = -g -O :pre +CC = mpicxx +CCFLAGS = -g -O3 +LINK = mpicxx +LINKFLAGS = -g -O :pre Serial build (see src/MAKE/Makefile.serial): -CC = g++ -CCFLAGS = -g -O3 -LINK = g++ -LINKFLAGS = -g -O :pre +CC = g++ +CCFLAGS = -g -O3 +LINK = g++ +LINKFLAGS = -g -O :pre The "compiler/linker settings" section of a Makefile.machine lists compiler and linker settings for your C++ compiler, including diff --git a/doc/src/Build_development.txt b/doc/src/Build_development.txt index 16a3d3d20e97ef95d53582f3dc0d3f6afc1c84df..bd3897fba61133959164428ebf6adc6088f2cd1c 100644 --- a/doc/src/Build_development.txt +++ b/doc/src/Build_development.txt @@ -50,7 +50,7 @@ Code Coverage and Testing :h4,link(testing) We do extensive regression testing of the LAMMPS code base on a continuous basis. Some of the logic to do this has been added to the CMake build so -developers can run the tests directly on their workstation. +developers can run the tests directly on their workstation. NOTE: this is incomplete and only represents a small subset of tests that we run diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index b0bf0c9cd6335a4d9e4c1fc2b9b797f6d4e495ca..b315e244c59724f4ba4ebbed6742261b952723aa 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -302,7 +302,7 @@ files. KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper -CC = mpicxx :pre +CC = mpicxx :pre :line @@ -642,30 +642,61 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre USER-COLVARS package :h4,link(user-colvars) +This package includes into the LAMMPS distribution the Colvars library, which +can be built for the most part with all major versions of the C++ language. + +A few of the most recent features require C++11 support. In particular, the +library is optionally built together with the +"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also +included in the LAMMPS distribution. Lepton implements the +"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction +feature, and requires C++11 support. + +See "here"_https://colvars.github.io/README-c++11.html for a detailed list of +C++11-only features. + [CMake build]: -No additional settings are needed besides "-D PKG_USER-COLVARS=yes". +This is the recommended build recipe: no additional settings are normally +needed besides "-D PKG_USER-COLVARS=yes". + +Building and linking of Lepton (or other C++11-only features) is enabled +automatically when compilation is carried out with C++11 support, and disabled +otherwise. Optionally, Lepton build may be manually controlled with the flag +"-D COLVARS_LEPTON=yes|no". [Traditional make]: -Before building LAMMPS, you must build the COLVARS library in -lib/colvars. You can do this manually if you prefer; follow the -instructions in lib/colvars/README. You can also do it in one step -from the lammps/src dir, using a command like these, which simply -invoke the lib/colvars/Install.py script with the specified args: +Before building LAMMPS, one must build the Colvars library in lib/colvars. + +This can be done manually in the same folder by using or adapting one of the +provided Makefiles: for example, Makefile.g++ for the GNU compiler. + +In general, it is safer to use build setting consistent with the rest of +LAMMPS. This is best carried out from the LAMMPS src directory using a +command like these, which simply invoke the lib/colvars/Install.py script with +the specified args: make lib-colvars # print help message make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre -The build should produce two files: lib/colvars/libcolvars.a and -lib/colvars/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to build LAMMPS with the -COLVARS library (though typically the settings are just blank). If -necessary, you can edit/create a new lib/colvars/Makefile.machine file -for your system, which should define an EXTRAMAKE variable to specify -a corresponding Makefile.lammps.machine file. +The "machine" argument of the "-m" flag is used to find a Makefile.machine to +use as build recipe. If it does not already exist in lib/colvars, it will be +auto-generated by using compiler flags consistent with those parsed from the +core LAMMPS makefiles. + +Optional flags may be specified as environment variables: + +COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) +COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) + +The build should produce two files: the library lib/colvars/libcolvars.a +(which also includes Lepton objects if enabled) and the specification file +lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does +not need to be edited. + :line @@ -802,7 +833,7 @@ dir, using a command like these, which simply invoke the lib/h5md/Install.py script with the specified args: make lib-h5md # print help message -make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre +make lib-h5md args="-m h5cc" # build with h5cc compiler :pre The build should produce two files: lib/h5md/libch5md.a and lib/h5md/Makefile.lammps. The latter is copied from an existing @@ -849,15 +880,15 @@ additional information. For CPUs: OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) +CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) +LINKFLAGS = -g -qopenmp $(OPTFLAGS) LIB = -ltbbmalloc :pre For KNLs: OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) +CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) +LINKFLAGS = -g -qopenmp $(OPTFLAGS) LIB = -ltbbmalloc :pre :line diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index 287cd39ff6ab914be895cb0e5e7c703200553b19..730d779d63a0afb9bafcd89a26ef65fddd666e2c 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -12,6 +12,7 @@ Optional build settings :h3 LAMMPS can be built with several optional settings. Each sub-section explain how to do this for building both with CMake and make. +"C++11 standard compliance test"_#cxx11 when building all of LAMMPS "FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command "Size of LAMMPS data types"_#size "Read or write compressed files"_#gzip @@ -23,6 +24,33 @@ explain how to do this for building both with CMake and make. :line +C++11 standard compliance test :h4,link(cxx11) + +The LAMMPS developers plan to transition to make the C++11 standard the +minimum requirement for compiling LAMMPS. Currently this only applies to +some packages like KOKKOS while the rest aims to be compatible with the C++98 +standard. Most currently used compilers are compatible with C++11; some need +to set extra flags to switch. To determine the impact of requiring C++11, +we have added a simple compliance test to the source code, that will cause +the compilation to abort, if C++11 compliance is not available or enabled. +To bypass this check, you need to change a setting in the makefile or +when calling CMake. + +[CMake variable]: + +-D DISABLE_CXX11_REQUIREMENT=yes :pre + +You can set additional C++ compiler flags (beyond those selected by CMake) +through the CMAKE_CXX_FLAGS variable. Example for CentOS 7: + +-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" :pre + +[Makefile.machine setting]: + +LMP_INC = -DLAMMPS_CXX98 :pre + +:line + FFT library :h4,link(fft) When the KSPACE package is included in a LAMMPS build, the diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index d0d7657c07250f6400572ea514a2aaf7e7f7c37e..ecd21e42e7ad9586f22759e11dc10daa8701dcfe 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -124,6 +124,7 @@ An alphabetic list of all general LAMMPS commands. "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, +"third_order"_third_order.html, "timer"_timer.html, "timestep"_timestep.html, "uncompute"_uncompute.html, diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index 40c2d0283a489c49574361d725e90d80c0cd9c2b..aecbf4cca0252c31ad89bc363685387df96064d3 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -108,7 +108,7 @@ OPT. "class2 (ko)"_dihedral_class2.html, "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, "fourier (io)"_dihedral_fourier.html, -"harmonic (io)"_dihedral_harmonic.html, +"harmonic (iko)"_dihedral_harmonic.html, "helix (o)"_dihedral_helix.html, "multi/harmonic (o)"_dihedral_multi_harmonic.html, "nharmonic (o)"_dihedral_nharmonic.html, diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 47d4c40d8ed71e2bbd767ced9d05fb24d74412b6..e6ebd219879f38e0972ac883eaaf7122a89266db 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -166,6 +166,7 @@ OPT. "lj/smooth/linear (o)"_pair_lj_smooth_linear.html, "lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html, "lj96/cut (go)"_pair_lj96.html, +"local/density"_pair_local_density.html, "lubricate (o)"_pair_lubricate.html, "lubricate/poly (o)"_pair_lubricate.html, "lubricateU"_pair_lubricateU.html, diff --git a/doc/src/Eqs/fix_bond_react.jpg b/doc/src/Eqs/fix_bond_react.jpg new file mode 100644 index 0000000000000000000000000000000000000000..d63b983230c0c26a7bf9c50b38593bdd65196a35 Binary files /dev/null and b/doc/src/Eqs/fix_bond_react.jpg differ diff --git a/doc/src/Eqs/fix_bond_react.tex b/doc/src/Eqs/fix_bond_react.tex new file mode 100644 index 0000000000000000000000000000000000000000..94006560387be13465638cfbe2a1aee294f5707f --- /dev/null +++ b/doc/src/Eqs/fix_bond_react.tex @@ -0,0 +1,9 @@ +\documentstyle[12pt]{article} +\pagestyle{empty} +\begin{document} + +\begin{eqnarray*} + k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}} +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/norm_inf.jpg b/doc/src/Eqs/norm_inf.jpg new file mode 100644 index 0000000000000000000000000000000000000000..42a2afb3d299b7ef031d9def8fe7eb1de0b7d931 Binary files /dev/null and b/doc/src/Eqs/norm_inf.jpg differ diff --git a/doc/src/Eqs/norm_inf.tex b/doc/src/Eqs/norm_inf.tex new file mode 100644 index 0000000000000000000000000000000000000000..b97a9f88f7a3d388f3015171c9bcf15df1653cfe --- /dev/null +++ b/doc/src/Eqs/norm_inf.tex @@ -0,0 +1,15 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + || \vec{F} ||_{inf} + = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, + |F_N^1|, |F_N^2|, |F_N^3|\right) + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/norm_max.jpg b/doc/src/Eqs/norm_max.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c10db9a53144cb3e889eb3c4315352d2ef0c85e8 Binary files /dev/null and b/doc/src/Eqs/norm_max.jpg differ diff --git a/doc/src/Eqs/norm_max.tex b/doc/src/Eqs/norm_max.tex new file mode 100644 index 0000000000000000000000000000000000000000..3b2198bdf0e3487b5215fdfb07d7a60217d37562 --- /dev/null +++ b/doc/src/Eqs/norm_max.tex @@ -0,0 +1,15 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + % \left| \left| \vec{F} \right| \right|_2 + || \vec{F} ||_{max} + = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/norm_two.jpg b/doc/src/Eqs/norm_two.jpg new file mode 100644 index 0000000000000000000000000000000000000000..5554de32f96a3a16f855b7e5011aa999d3c2819c Binary files /dev/null and b/doc/src/Eqs/norm_two.jpg differ diff --git a/doc/src/Eqs/norm_two.tex b/doc/src/Eqs/norm_two.tex new file mode 100644 index 0000000000000000000000000000000000000000..d428081a496cd16511dba1b3b6f5048afd612fa1 --- /dev/null +++ b/doc/src/Eqs/norm_two.tex @@ -0,0 +1,15 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + % \left| \left| \vec{F} \right| \right|_2 + || \vec{F} ||_{2} + = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N} + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_local_density_energy.jpg b/doc/src/Eqs/pair_local_density_energy.jpg new file mode 100644 index 0000000000000000000000000000000000000000..68e44ce9d95ec0592ddc3236076f0067e7cc981c Binary files /dev/null and b/doc/src/Eqs/pair_local_density_energy.jpg differ diff --git a/doc/src/Eqs/pair_local_density_energy.tex b/doc/src/Eqs/pair_local_density_energy.tex new file mode 100644 index 0000000000000000000000000000000000000000..a77b51305106ec0e2d2ce91e741570713f15fa04 --- /dev/null +++ b/doc/src/Eqs/pair_local_density_energy.tex @@ -0,0 +1,11 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + U_{LD} = \sum_i F(\rho_i) +$$ + + +\end{document} +~ diff --git a/doc/src/Eqs/pair_local_density_energy_implement.jpg b/doc/src/Eqs/pair_local_density_energy_implement.jpg new file mode 100644 index 0000000000000000000000000000000000000000..bd1f65d5424eedcbc4aaa57125a2cda0f8104c92 Binary files /dev/null and b/doc/src/Eqs/pair_local_density_energy_implement.jpg differ diff --git a/doc/src/Eqs/pair_local_density_energy_implement.tex b/doc/src/Eqs/pair_local_density_energy_implement.tex new file mode 100644 index 0000000000000000000000000000000000000000..4b1f1c3df2b5e424145670a9be9acc89dda6ad53 --- /dev/null +++ b/doc/src/Eqs/pair_local_density_energy_implement.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_local_density_energy_multi.jpg b/doc/src/Eqs/pair_local_density_energy_multi.jpg new file mode 100644 index 0000000000000000000000000000000000000000..df9dbfa5c82b24e491275c21aaac682f065be945 Binary files /dev/null and b/doc/src/Eqs/pair_local_density_energy_multi.jpg differ diff --git a/doc/src/Eqs/pair_local_density_energy_multi.tex b/doc/src/Eqs/pair_local_density_energy_multi.tex new file mode 100644 index 0000000000000000000000000000000000000000..4ca0b7e8b9d777651a640beb22b37e57f461ae63 --- /dev/null +++ b/doc/src/Eqs/pair_local_density_energy_multi.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +U_{LD} = \sum_i a_\alpha F(\rho_i) +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_local_density_indicator_func.jpg b/doc/src/Eqs/pair_local_density_indicator_func.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e038b2884d004d115ae30456c126c2492600665c Binary files /dev/null and b/doc/src/Eqs/pair_local_density_indicator_func.jpg differ diff --git a/doc/src/Eqs/pair_local_density_indicator_func.tex b/doc/src/Eqs/pair_local_density_indicator_func.tex new file mode 100644 index 0000000000000000000000000000000000000000..aa595c96dcf9306c4b3729e8831e0d82b84d8f1d --- /dev/null +++ b/doc/src/Eqs/pair_local_density_indicator_func.tex @@ -0,0 +1,16 @@ +\documentclass[12pt]{article} +\usepackage[utf8]{inputenc} +\usepackage{amsmath} +\usepackage{amsfonts} + +\begin{document} +\[ + \varphi(r) = + \begin{cases} + 1 & r \le R_1 \\ + c_0 + c_2r^2 + c_4r^4 + c_6r^6 & r \in (R_1, R_2) \\ + 0 & r \ge R_2 + \end{cases} +\] + +\end{document} diff --git a/doc/src/Eqs/pair_local_density_ld.jpg b/doc/src/Eqs/pair_local_density_ld.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9e6a8e1b72315b32b783bcba6a5c190f62689413 Binary files /dev/null and b/doc/src/Eqs/pair_local_density_ld.jpg differ diff --git a/doc/src/Eqs/pair_local_density_ld.tex b/doc/src/Eqs/pair_local_density_ld.tex new file mode 100644 index 0000000000000000000000000000000000000000..1affa67cd31a8ca17b36fe04af1341149a1274a0 --- /dev/null +++ b/doc/src/Eqs/pair_local_density_ld.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + + +$$ +\rho_i = \sum_{j \neq i} \varphi(r_{ij}) +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_local_density_ld_implement.jpg b/doc/src/Eqs/pair_local_density_ld_implement.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e8b98125a2b9f4cb3532792431ceded0b74ce9f4 Binary files /dev/null and b/doc/src/Eqs/pair_local_density_ld_implement.jpg differ diff --git a/doc/src/Eqs/pair_local_density_ld_implement.tex b/doc/src/Eqs/pair_local_density_ld_implement.tex new file mode 100644 index 0000000000000000000000000000000000000000..85ee8bad21a905b7faeee92c4c2176ee514a33b4 --- /dev/null +++ b/doc/src/Eqs/pair_local_density_ld_implement.tex @@ -0,0 +1,10 @@ +\documentstyle[12pt]{article} + +\begin{document} + + +$$ +\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij}) +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_local_density_ld_multi.jpg b/doc/src/Eqs/pair_local_density_ld_multi.jpg new file mode 100644 index 0000000000000000000000000000000000000000..feef991d498dca5d2ab0e8fa5ee54b275c7b73d9 Binary files /dev/null and b/doc/src/Eqs/pair_local_density_ld_multi.jpg differ diff --git a/doc/src/Eqs/pair_local_density_ld_multi.tex b/doc/src/Eqs/pair_local_density_ld_multi.tex new file mode 100644 index 0000000000000000000000000000000000000000..c441288c5dae8aa767db88d46427b4abad55fdb8 --- /dev/null +++ b/doc/src/Eqs/pair_local_density_ld_multi.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + + +$$ +\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij}) +$$ + +\end{document} diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index c131b10ec6b983004623c0cd51caadbbd53aa9f2..33593d4d5327d209de278da18b93325af49c185a 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -4791,6 +4791,22 @@ Self-explanatory. :dd This fix option cannot be used with point particles. :dd +{Fix langevin gjf and respa are not compatible} :dt + +Self-explanatory. :dd + +{Fix langevin gjf cannot have period equal to dt/2} :dt + +If the period is equal to dt/2 then division by zero will happen. :dd + +{Fix langevin gjf should come before fix nve} :dt + +Self-explanatory. :dd + +{Fix langevin gjf with tbias is not yet implemented with kokkos} :dt + +This option is not yet available. :dd + {Fix langevin omega is not yet implemented with kokkos} :dt This option is not yet available. :dd diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 9f346ba8c136bfedb48bfd95aef6f3fb307a1189..06474e1bb37fe378ad038394502857184249fc52 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -47,6 +47,11 @@ too far away. :dd Self-explanatory. :dd +{Angles are defined but no angle style is set} :dt + +The topology contains angles, but there are no angle forces computed +since there was no angle_style command. :dd + {Atom style in data file differs from currently defined atom style} :dt Self-explanatory. :dd @@ -73,6 +78,11 @@ short or the bond has blown apart and an atom is too far away. :dd Self-explanatory. :dd +{Bonds are defined but no bond style is set} :dt + +The topology contains bonds, but there are no bond forces computed +since there was no bond_style command. :dd + {Bond/angle/dihedral extent > half of periodic box length} :dt This is a restriction because LAMMPS can be confused about which image @@ -186,6 +196,11 @@ to check your simulation geometry. :dd Self-explanatory. :dd +{Dihedrals are defined but no dihedral style is set} :dt + +The topology contains dihedrals, but there are no dihedral forces computed +since there was no dihedral_style command. :dd + {Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt If the fix changes the timestep, the dump dcd file will not @@ -248,6 +263,10 @@ included one or more of the following: kspace, triclinic, a hybrid pair style, an eam pair style, or no "single" function for the pair style. :dd +{Fix langevin gjf using random gaussians is not implemented with kokkos} :dt + +This will most likely cause errors in kinetic fluctuations. + {Fix property/atom mol or charge w/out ghost communication} :dt A model typically needs these properties defined for ghost atoms. :dd @@ -348,6 +367,11 @@ to check your simulation geometry. :dd Self-explanatory. :dd +{Impropers are defined but no improper style is set} :dt + +The topology contains impropers, but there are no improper forces computed +since there was no improper_style command. :dd + {Inconsistent image flags} :dt The image flags for a pair on bonded atoms appear to be inconsistent. @@ -366,6 +390,11 @@ have fully consistent image flags, since some bonds will cross periodic boundaries and connect two atoms with the same image flag. :dd +{Increasing communication cutoff for GPU style} :dt + +The pair style has increased the communication cutoff to be consistent with +the communication cutoff requirements for this pair style when run on the GPU. :dd + {KIM Model does not provide 'energy'; Potential energy will be zero} :dt Self-explanatory. :dd @@ -403,6 +432,30 @@ This library function cannot be used if atom IDs are not defined or are not consecutively numbered, or if no atom map is defined. See the atom_modify command for details about atom maps. :dd +{Likewise 1-2 special neighbor interactions != 1.0} :dt + +The topology contains bonds, but there is no bond style defined +and a 1-2 special neighbor scaling factor was not 1.0. This +means that pair style interactions may have scaled or missing +pairs in the neighbor list in expectation of interactions for +those pairs being computed from the bond style. :dd + +{Likewise 1-3 special neighbor interactions != 1.0} :dt + +The topology contains angles, but there is no angle style defined +and a 1-3 special neighbor scaling factor was not 1.0. This +means that pair style interactions may have scaled or missing +pairs in the neighbor list in expectation of interactions for +those pairs being computed from the angle style. :dd + +{Likewise 1-4 special neighbor interactions != 1.0} :dt + +The topology contains dihedrals, but there is no dihedral style defined +and a 1-4 special neighbor scaling factor was not 1.0. This +means that pair style interactions may have scaled or missing +pairs in the neighbor list in expectation of interactions for +those pairs being computed from the dihedral style. :dd + {Lost atoms via change_box: original %ld current %ld} :dt The command options you have used caused atoms to be lost. :dd diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index 36d0ac86f9f644fd5c43f312ecd75fe76c4bb944..86617e13dfd24c02fc07975266b9e0cf379e0728 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -141,6 +141,7 @@ HEAT: compute thermal conductivity for LJ and water via fix ehex KAPPA: compute thermal conductivity via several methods MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system SPIN: examples for features of the SPIN package +UNITS: examples that run the same simulation in lj, real, metal units USER: examples for USER packages and USER-contributed commands VISCOSITY: compute viscosity via several methods :tb(s=:) diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt index e29cf13167dd2e131794d41643cd9201217f1f2d..ef9b49f87c4092f2783ba694b94d6c6ffeffc5a2 100644 --- a/doc/src/Howto_chunk.txt +++ b/doc/src/Howto_chunk.txt @@ -136,7 +136,9 @@ The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command spreads per-chunk values to each atom in the chunk, producing per-atom values as its output. This can be useful for outputting per-chunk values to a per-atom "dump file"_dump.html. Or for using an atom's -associated chunk value in an "atom-style variable"_variable.html. +associated chunk value in an "atom-style variable"_variable.html. Or +as input to the "fix ave/chunk"_fix_ave_chunk.html command to +spatially average per-chunk values calculated by a per-chunk compute. The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a peratom value across the atoms in each chunk to produce a value per @@ -184,12 +186,20 @@ compute cc1 all chunk/atom c_cluster compress yes compute size all property/chunk cc1 count fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre -(6) An example of using a per-chunk value to apply per-atom forces to +(6) An example for using a per-chunk value to apply per-atom forces to compress individual polymer chains (molecules) in a mixture, is explained on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html command doc page. -(7) An example of using one set of per-chunk values for molecule +(7) An example for using one set of per-chunk values for molecule chunks, to create a 2nd set of micelle-scale chunks (clustered molecules, due to hydrophobicity), is explained on the "compute chunk/reduce"_compute_reduce_chunk.html command doc page. + +(8) An example for using one set of per-chunk values (dipole moment +vectors) for molecule chunks, spreading the values to each atom in +each chunk, then defining a second set of chunks as spatial bins, and +using the "fix ave/chunk"_fix_ave_chunk.html command to calculate an +average dipole moment vector for each bin. This example is explained +on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html +command doc page. diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt index 80b2a54fe4cb8a34b61819af34f6521b1181d3a0..c4bdc502ce1c8fc2b004750ad68b4157a22110e2 100644 --- a/doc/src/Howto_spins.txt +++ b/doc/src/Howto_spins.txt @@ -43,19 +43,19 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate the thermal energy of the Langevin thermostat, or to perform a relaxation of the magnetic configuration toward an equilibrium state. -The command "fix setforce/spin"_fix_setforce.html allows to set the -components of the magnetic precession vectors (while erasing and -replacing the previously computed magnetic precession vectors on -the atom). -This command can be used to freeze the magnetic moment of certain -atoms in the simulation by zeroing their precession vector. +The command "fix setforce/spin"_fix_setforce.html allows to set the +components of the magnetic precession vectors (while erasing and +replacing the previously computed magnetic precession vectors on +the atom). +This command can be used to freeze the magnetic moment of certain +atoms in the simulation by zeroing their precession vector. The command "fix nve/spin"_fix_nve_spin.html can be used to -perform a symplectic integration of the combined dynamics of spins +perform a symplectic integration of the combined dynamics of spins and atomic motions. The minimization style "min/spin"_min_spin.html can be applied -to the spins to perform a minimization of the spin configuration. +to the spins to perform a minimization of the spin configuration. All the computed magnetic properties can be output by two main diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index ee070eba58711f3787a03812bef5830a5dc44345..c87c8a3b8409b457c9b04f9349f9a371e31d2cff 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -83,7 +83,7 @@ variable d equal $p*$s # dump interval :pre # convert from LAMMPS real units to SI :pre -variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann +variable kB equal 1.3806504e-23 # \[J/K\] Boltzmann variable atm2Pa equal 101325.0 variable A2m equal 1.0e-10 variable fs2s equal 1.0e-15 diff --git a/doc/src/JPG/dynamical_matrix_dynmat.jpg b/doc/src/JPG/dynamical_matrix_dynmat.jpg new file mode 100644 index 0000000000000000000000000000000000000000..6c6adae72c2205d646c490036c1e64483334483c Binary files /dev/null and b/doc/src/JPG/dynamical_matrix_dynmat.jpg differ diff --git a/doc/src/JPG/dynamical_matrix_force_constant.jpg b/doc/src/JPG/dynamical_matrix_force_constant.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e1a0e50d14fa9325b32c7647a0edb33443189583 Binary files /dev/null and b/doc/src/JPG/dynamical_matrix_force_constant.jpg differ diff --git a/doc/src/JPG/dynamical_matrix_phonons.jpg b/doc/src/JPG/dynamical_matrix_phonons.jpg new file mode 100644 index 0000000000000000000000000000000000000000..2a6d3a36d77afac80ed4ac990eeb0b4cf4e5c16c Binary files /dev/null and b/doc/src/JPG/dynamical_matrix_phonons.jpg differ diff --git a/doc/src/JPG/third_order_force_constant.png b/doc/src/JPG/third_order_force_constant.png new file mode 100644 index 0000000000000000000000000000000000000000..f6171ccf097e9df5fee54241d1bc2f142de2d398 Binary files /dev/null and b/doc/src/JPG/third_order_force_constant.png differ diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index c63137ef6fd2ef303fb14ca50e0a9c93fd3488c9..041a481547cd5a3e6e8ce948508487037568bc17 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -7 Aug 2019 version :c,h2 +30 Oct 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/doc/src/PDF/pair_gayberne_extra.pdf b/doc/src/PDF/pair_gayberne_extra.pdf index c82233992d48be53584344510152bd8f5173d87a..5ac8bd051bd371b5b6580ea8b67f03a0f3662afe 100644 Binary files a/doc/src/PDF/pair_gayberne_extra.pdf and b/doc/src/PDF/pair_gayberne_extra.pdf differ diff --git a/doc/src/PDF/pair_gayberne_extra.tex b/doc/src/PDF/pair_gayberne_extra.tex index 5f0d97d7abb7862caba14ada74d108cd7fa5efe0..0568b54dcf195f6390b540def95767e268741439 100644 --- a/doc/src/PDF/pair_gayberne_extra.tex +++ b/doc/src/PDF/pair_gayberne_extra.tex @@ -48,8 +48,8 @@ $$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 + \mathbf{G}_2. $$ Let the relative energy matrices $\mathbf{E}_i = \mbox{diag} -(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by -the relative well depths (dimensionless energy scales +(\epsilon_{ia}^{-1/\mu}, \epsilon_{ib}^{-1/\mu}, \epsilon_{ic}^{-1/\mu})$ +be given by the relative well depths (dimensionless energy scales inversely proportional to the well-depths of the respective orthogonal configurations of the interacting molecules). The $\chi$ orientation-dependent energy based on the user-specified @@ -62,8 +62,8 @@ $$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$ and -$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 + -\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 + +$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 + +\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 = \mathbf{B}_1 + \mathbf{B}_2. $$ Here, we use the distance of closest approach approximation given by the @@ -131,7 +131,7 @@ and $$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i -\times \mathbf{\iota} ). $$ +\times \mathbf{\iota} ) \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu}. $$ For the derivative of the $\eta$ term, we were unable to find a matrix expression due to the determinant. Let $a_{mi}$ be the mth row of the diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index eead133add1a131cfc201f88b636baec98a39a0b..fc30c045cf14618a766e5fe99a1d182f2bb418bf 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1746,11 +1746,12 @@ USER-PHONON package :link(PKG-USER-PHONON),h4 A "fix phonon"_fix_phonon.html command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. -And a "dynamical_matrix" command to compute the dynamical matrix -from finite differences. +And a "dynamical_matrix"_dynamical_matrix.html as well as a +"third_order"_third_order.html command to compute the dynamical matrix +and third order tensor from finite differences. [Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" -and Charlie Sievers (UC Davis) for "dynamical_matrix" +and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" [Supporting info:] @@ -1759,6 +1760,7 @@ src/USER-PHONON: filenames -> commands src/USER-PHONON/README "fix phonon"_fix_phonon.html "dynamical_matrix"_dynamical_matrix.html +"third_order"_third_order.html examples/USER/phonon :ul :line diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index 87b272a866d541d72d65fea293dfc0b1c07c3b73..df1a57421a6ac12e8f0857f8ab1890391f4638b4 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -126,9 +126,10 @@ are intended for computational work like running LAMMPS. By default Ng = 1 and Ns is not set. Depending on which flavor of MPI you are running, LAMMPS will look for -one of these 3 environment variables +one of these 4 environment variables SLURM_LOCALID (various MPI variants compiled with SLURM support) +MPT_LRANK (HPE MPI) MV2_COMM_WORLD_LOCAL_RANK (Mvapich) OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index 99d29864dcac85d0eb3153f53778fbbb3a424823..66f8fab8d9fdfb60b43175d52f4dd486ce77717f 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -46,14 +46,14 @@ software version 7.5 or later must be installed on your system. See the discussion for the "GPU package"_Speed_gpu.html for details of how to check and do this. -NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library -is CUDA-aware. This is not always the case, especially when using -pre-compiled MPI libraries provided by a Linux distribution. This is not -a problem when using only a single GPU with a single MPI rank. When -running with multiple MPI ranks, you may see segmentation faults without -CUDA-aware MPI support. These can be avoided by adding the flags "-pk -kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by -using the command "package kokkos cuda/aware off"_package.html in the +NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library +is CUDA-aware. This is not always the case, especially when using +pre-compiled MPI libraries provided by a Linux distribution. This is not +a problem when using only a single GPU with a single MPI rank. When +running with multiple MPI ranks, you may see segmentation faults without +CUDA-aware MPI support. These can be avoided by adding the flags "-pk +kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by +using the command "package kokkos cuda/aware off"_package.html in the input file. [Building LAMMPS with the KOKKOS package:] @@ -110,10 +110,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP back end (i.e. Makefile.kokkos_omp) because some of the overhead to make the code thread-safe is removed. -NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to -change the default "package kokkos"_package.html options. See its doc -page for details and default settings. Experimenting with its options -can provide a speed-up for specific calculations. For example: +NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to +change the default "package kokkos"_package.html options. See its doc +page for details and default settings. Experimenting with its options +can provide a speed-up for specific calculations. For example: mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre @@ -183,15 +183,15 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of threads/task as Nt. The product of these two values should be N, i.e. 256 or 264. -NOTE: The default for the "package kokkos"_package.html command when -running on KNL is to use "half" neighbor lists and set the Newton flag -to "on" for both pairwise and bonded interactions. This will typically -be best for many-body potentials. For simpler pair-wise potentials, it -may be faster to use a "full" neighbor list with Newton flag to "off". -Use the "-pk kokkos" "command-line switch"_Run_options.html to change -the default "package kokkos"_package.html options. See its doc page for -details and default settings. Experimenting with its options can provide -a speed-up for specific calculations. For example: +NOTE: The default for the "package kokkos"_package.html command when +running on KNL is to use "half" neighbor lists and set the Newton flag +to "on" for both pairwise and bonded interactions. This will typically +be best for many-body potentials. For simpler pair-wise potentials, it +may be faster to use a "full" neighbor list with Newton flag to "off". +Use the "-pk kokkos" "command-line switch"_Run_options.html to change +the default "package kokkos"_package.html options. See its doc page for +details and default settings. Experimenting with its options can provide +a speed-up for specific calculations. For example: mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj # Newton off, full neighbor list, non-threaded comm :pre @@ -206,19 +206,19 @@ supports. [Running on GPUs:] -Use the "-k" "command-line switch"_Run_options.html to specify the -number of GPUs per node. Typically the -np setting of the mpirun command -should set the number of MPI tasks/node to be equal to the number of -physical GPUs on the node. You can assign multiple MPI tasks to the same -GPU with the KOKKOS package, but this is usually only faster if some -portions of the input script have not been ported to use Kokkos. In this -case, also packing/unpacking communication buffers on the host may give -speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS +Use the "-k" "command-line switch"_Run_options.html to specify the +number of GPUs per node. Typically the -np setting of the mpirun command +should set the number of MPI tasks/node to be equal to the number of +physical GPUs on the node. You can assign multiple MPI tasks to the same +GPU with the KOKKOS package, but this is usually only faster if some +portions of the input script have not been ported to use Kokkos. In this +case, also packing/unpacking communication buffers on the host may give +speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS is recommended in this scenario. -Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be -avoided by using "-pk kokkos cuda/aware no"_package.html. As above for -multi-core CPUs (and no GPU), if N is the number of physical cores/node, +Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be +avoided by using "-pk kokkos cuda/aware no"_package.html. As above for +multi-core CPUs (and no GPU), if N is the number of physical cores/node, then the number of MPI tasks/node should not exceed N. -k on g Ng :pre @@ -229,18 +229,18 @@ one or more nodes, each with two GPUs: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre -NOTE: The default for the "package kokkos"_package.html command when -running on GPUs is to use "full" neighbor lists and set the Newton flag -to "off" for both pairwise and bonded interactions, along with threaded -communication. When running on Maxwell or Kepler GPUs, this will -typically be best. For Pascal GPUs, using "half" neighbor lists and -setting the Newton flag to "on" may be faster. For many pair styles, -setting the neighbor binsize equal to twice the CPU default value will -give speedup, which is the default when running on GPUs. Use the "-pk -kokkos" "command-line switch"_Run_options.html to change the default -"package kokkos"_package.html options. See its doc page for details and -default settings. Experimenting with its options can provide a speed-up -for specific calculations. For example: +NOTE: The default for the "package kokkos"_package.html command when +running on GPUs is to use "full" neighbor lists and set the Newton flag +to "off" for both pairwise and bonded interactions, along with threaded +communication. When running on Maxwell or Kepler GPUs, this will +typically be best. For Pascal GPUs, using "half" neighbor lists and +setting the Newton flag to "on" may be faster. For many pair styles, +setting the neighbor binsize equal to twice the CPU default value will +give speedup, which is the default when running on GPUs. Use the "-pk +kokkos" "command-line switch"_Run_options.html to change the default +"package kokkos"_package.html options. See its doc page for details and +default settings. Experimenting with its options can provide a speed-up +for specific calculations. For example: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index eb7b6d81b880e95126608b593fbc7955f83891c0..dccdf77dee2f18714367ae4f5518fb1eb1296577 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -76,9 +76,10 @@ Post-processing tools :h3 "pymol_asphere"_#pymol, "python"_#pythontools, "reax"_#reax_tool, +"replica"_#replica, "smd"_#smd, "spin"_#spin, -"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) +"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) Miscellaneous tools :h3 @@ -86,6 +87,7 @@ Miscellaneous tools :h3 "emacs"_#emacs, "i-pi"_#ipi, "kate"_#kate, +"singularity"_#singularity_tool, "vim"_#vim :tb(c=5,ea=c,a=l) :line @@ -485,6 +487,21 @@ README for more info on Pizza.py and how to use these scripts. :line +replica tool :h4,link(replica) + +The tools/replica directory contains the reorder_remd_traj python script which +can be used to reorder the replica trajectories (resulting from the use of the +temper command) according to temperature. This will produce discontinuous +trajectories with all frames at the same temperature in each trajectory. +Additional options can be used to calculate the canonical configurational +log-weight for each frame at each temperature using the pymbar package. See +the README.md file for further details. Try out the peptide example provided. + +This tool was written by (and is maintained by) Tanmoy Sanyal, +while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) + +:line + reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alone codes that can @@ -515,17 +532,26 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). spin tool :h4,link(spin) The spin sub-directory contains a C file interpolate.c which can -be compiled and used to perform a cubic polynomial interpolation of +be compiled and used to perform a cubic polynomial interpolation of the MEP following a GNEB calculation. See the README file in tools/spin/interpolate_gneb for more details. This tool was written by the SPIN package author, Julien -Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei +Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei Ivanov, at University of Iceland (ali5 at hi.is). :line +singularity tool :h4,link(singularity_tool) + +The singularity sub-directory contains container definitions files +that can be used to build container images for building and testing +LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io +container software. Contributions for additional variants are welcome. + +:line + vim tool :h4,link(vim) The files in the tools/vim directory are add-ons to the VIM editor @@ -549,3 +575,4 @@ simulation. See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) + diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 5f03636c1db240c439d9cee6256a715926588faf..9a792f6cc6047334eb7a165b584f911cc598a993 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -40,11 +40,12 @@ coordinates and other properties are exchanged between neighboring processors and stored as properties of ghost atoms. NOTE: These options apply to the currently defined comm style. When -you specify a "comm_style"_comm_style.html command, all communication -settings are restored to their default values, including those +you specify a "comm_style"_comm_style.html or +"read_restart"_read_restart.html command, all communication settings +are restored to their default or stored values, including those previously reset by a comm_modify command. Thus if your input script -specifies a comm_style command, you should use the comm_modify command -after it. +specifies a comm_style or read_restart command, you should use the +comm_modify command after it. The {mode} keyword determines whether a single or multiple cutoff distances are used to determine which atoms to communicate. diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index a5c9b568edb8f871a57b6f073c0735a1c730b5f1..714aedefedf1010e3ec96b053243d244c954e4d0 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -108,6 +108,7 @@ Commands :h1 thermo thermo_modify thermo_style + third_order timer timestep uncompute diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 214fbdefc442538feabdc05d944c31583730fbf8..b54d2d2e7b432d199d73a4e19fee03da92f25461 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -244,7 +244,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor "pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates -"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field +"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays @@ -284,7 +284,7 @@ compute"_Commands_compute.html doc page are followed by one or more of "stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes "stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes "stress/tally"_compute_tally.html - -"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle +"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 6055d28770add3d07c77fe41232cfe373e65faea..889741753a83678335c97be00e90f2f149ecd403 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -15,10 +15,11 @@ compute ID group-ID bond/local value1 value2 ... keyword args ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l bond/local = style name of this compute command :l one or more values may be appended :l -value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l +value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l {dist} = bond distance {engpot} = bond potential energy {force} = bond force :pre + {fx},{fy},{fz} = components of bond force {engvib} = bond kinetic energy of vibration {engrot} = bond kinetic energy of rotation {engtrans} = bond kinetic energy of translation @@ -38,6 +39,7 @@ keyword = {set} :l compute 1 all bond/local engpot compute 1 all bond/local dist engpot force :pre +compute 1 all bond/local dist fx fy fz :pre compute 1 all angle/local dist v_distsq set dist d :pre [Description:] @@ -59,6 +61,9 @@ based on the current separation of the pair of atoms in the bond. The value {force} is the magnitude of the force acting between the pair of atoms in the bond. +The values {fx}, {fy}, and {fz} are the xyz components of +{force} between the pair of atoms in the bond. + The remaining properties are all computed for motion of the two atoms relative to the center of mass (COM) velocity of the 2 atoms in the bond. diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt index 4afb62683eaf84be70b98310252827b15ab1cf31..c84fe679eefa54575c34562d87078e775b7f60cb 100644 --- a/doc/src/compute_chunk_spread_atom.txt +++ b/doc/src/compute_chunk_spread_atom.txt @@ -30,11 +30,18 @@ compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre [Description:] Define a calculation that "spreads" one or more per-chunk values to -each atom in the chunk. This can be useful for creating a "dump -file"_dump.html where each atom lists info about the chunk it is in, -e.g. for post-processing purposes. It can also be used in "atom-style -variables"_variable.html that need info about the chunk each atom is -in. Examples are given below. +each atom in the chunk. This can be useful in several scenarios: + +For creating a "dump file"_dump.html where each atom lists info about +the chunk it is in, e.g. for post-processing purposes. :ulb,l + +To access chunk value in "atom-style variables"_variable.html that +need info about the chunk each atom is in. :l + +To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially +average per-chunk values calculated by a per-chunk compute. :l,ule + +Examples are given below. In LAMMPS, chunks are collections of atoms defined by a "compute chunk/atom"_compute_chunk_atom.html command, which assigns each atom @@ -148,6 +155,28 @@ thermo_style custom step etotal press v_ave :pre :line +Here is an example for using one set of chunks, defined for molecules, +to compute the dipole moment vector for each chunk. E.g. for water +molecules. Then spreading those values to each atom in each chunk. +Then defining a second set of chunks based on spatial bins. And +finally, using the "fix ave/chunk"_fix_ave_chunk.html command to +calculate an average dipole moment vector per spatial bin. + +compute cmol all chunk/atom molecule +compute dipole all dipole/chunk cmol +compute spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\] +compute cspatial all chunk/atom bin/1d z lower 0.1 units reduced +fix ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre + +Note that the "fix ave/chunk"_fix_ave_chunk.html command requires +per-atom values as input. That is why the compute chunk/spread/atom +command is used to assign per-chunk values to each atom in the chunk. +If a molecule straddles bin boundaries, each of its atoms contributes +in a weighted manner to the average dipole moment of the spatial bin +it is in. + +:line + [Output info:] This compute calculates a per-atom vector or array, which can be diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index af0be4be562fdd4633bac50d142830fe15880897..e4d57a5dc5e79a70f803b3127d9237f76f09bf6a 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -47,7 +47,7 @@ neighboring atoms, unless selected by type, type range, or group option, are included in the coordination number tally. The optional {group} keyword allows to specify from which group atoms -contribute to the coordination number. Default setting is group 'all'. +contribute to the coordination number. Default setting is group 'all'. The {typeN} keywords allow specification of which atom types contribute to each coordination number. One coordination number is diff --git a/doc/src/compute_gyration_shape.txt b/doc/src/compute_gyration_shape.txt index 7c428aea8ad86d6bab938491b188915889c73f2c..5be09686cdc5a5b18af4f2217d2bb45b89185dc3 100644 --- a/doc/src/compute_gyration_shape.txt +++ b/doc/src/compute_gyration_shape.txt @@ -24,7 +24,7 @@ compute 1 molecule gyration/shape pe :pre Define a computation that calculates the eigenvalues of the gyration tensor of a group of atoms and three shape parameters. The computation includes all effects -due to atoms passing thru periodic boundaries. +due to atoms passing through periodic boundaries. The three computed shape parameters are the asphericity, b, the acylindricity, c, and the relative shape anisotropy, k: @@ -84,3 +84,6 @@ package"_Build_package.html doc page for more info. :link(Theodorou) [(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985). +:link(Mattice) +[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994. + diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index 4ab355abd77f0f82a707a94a50480853394af9a5..289138eaa8a901f3757b2ad8981dc46117cbeb9a 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -34,7 +34,7 @@ compute 2 all hma 1 u cv :pre Define a computation that calculates the properties of a solid (potential energy, pressure or heat capacity), using the harmonically-mapped averaging -(HMA) method. +(HMA) method. This command yields much higher precision than the equivalent compute commands ("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.) commands during a canonical simulation of an atomic crystal. Specifically, @@ -52,7 +52,7 @@ restricted to simulations in the NVT ensemble. While this compute may be used with any potential in LAMMPS, it will provide inaccurate results for potentials that do not go to 0 at the truncation distance; "pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should -work fine, while "pair_lj"_pair_lj.html will perform poorly unless +work fine, while "pair_lj"_pair_lj.html will perform poorly unless the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large. Furthermore, computation of the heat capacity with this compute is restricted to those that implement the single_hessian method in Pair. Implementing single_hessian in additional pair styles is simple. @@ -64,8 +64,8 @@ the list of pair styles that currently implement pair_hessian: :ule In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble -averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination -by noise produced by the already-known harmonic behavior. +averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination +by noise produced by the already-known harmonic behavior. A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula: \begin\{equation\} @@ -74,9 +74,9 @@ A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa) where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's constant, \(T\) is the temperature, \(d\) is the -dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the -atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of -pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. +dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the +atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of +pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies. The pressure is computed by the formula: @@ -118,30 +118,30 @@ When using this keyword, the compute must be first active (it must be included via a "thermo_style custom"_thermo_style.html command) while the atoms are still at their lattice sites (before equilibration). -The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or -Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat -("fix langevin"_fix_langevin.html) -should be avoided as its extra forces interfere with the HMA implementation. +The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or +Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat +("fix langevin"_fix_langevin.html) +should be avoided as its extra forces interfere with the HMA implementation. - -NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites. + +NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites. The simulation should not be started before this command has been used in the input script. The following example illustrates the placement of this command in the input script: -min_style cg -minimize 1e-35 1e-15 50000 500000 +min_style cg +minimize 1e-35 1e-15 50000 500000 compute 1 all hma thermostatid u -fix thermostatid all nvt temp 600.0 600.0 100.0 :pre +fix thermostatid all nvt temp 600.0 600.0 100.0 :pre NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation. - + NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command. An example input script that uses this compute is included in @@ -180,5 +180,5 @@ this compute. :line :link(hma-Moustafa) -[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation}, +[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation}, "Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303 diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 7327a7b1d333a5375d033d5d8f88b9e74efc6237..d59033f17988894b7345c47b5f097787fc5772f2 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} {cutoff} value = distance cutoff {nnn} value = number of nearest neighbors {degrees} values = nlvalues, l1, l2,... + {wl} value = yes or no + {wl/hat} value = yes or no {components} value = ldegree :pre :ule @@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components} compute 1 all orientorder/atom compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 -compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre +compute 1 all orientorder/atom wl/hat yes +compute 1 all orientorder/atom components 6 :pre [Description:] @@ -48,7 +51,7 @@ neighbors of the central atom. The angles theta and phi are the standard spherical polar angles defining the direction of the bond vector {rij}. The second equation defines {Ql}, which is a -rotationally invariant scalar quantity obtained by summing +rotationally invariant non-negative amplitude obtained by summing over all the components of degree {l}. The optional keyword {cutoff} defines the distance cutoff @@ -63,7 +66,7 @@ specified distance cutoff are used. The optional keyword {degrees} defines the list of order parameters to be computed. The first argument {nlvalues} is the number of order -parameters. This is followed by that number of integers giving the +parameters. This is followed by that number of non-negative integers giving the degree of each order parameter. Because {Q}2 and all odd-degree order parameters are zero for atoms in cubic crystals (see "Steinhardt"_#Steinhardt), the default order parameters are {Q}4, @@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see = sqrt(7/3)/8 = 0.19094.... The numerical values of all order parameters up to {Q}12 for a range of commonly encountered high-symmetry structures are given in Table I of "Mickel et -al."_#Mickel. +al."_#Mickel, and these can be reproduced with this compute + +The optional keyword {wl} will output the third-order invariants {Wl} +(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as +for the {Ql} parameters. For the FCC crystal with {nnn} =12, +{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136... + +The optional keyword {wl/hat} will output the normalized third-order +invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt) +for the same degrees as for the {Ql} parameters. For the FCC crystal +with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical +values of {Wlhat} for a range of commonly encountered high-symmetry +structures are given in Table I of "Steinhardt"_#Steinhardt, and these +can be reproduced with this keyword. The optional keyword {components} will output the components of the normalized complex vector {Ybar_lm} of degree {ldegree}, which must be @@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2. The value of {Ql} is set to zero for atoms not in the specified compute group, as well as for atoms that have less than -{nnn} neighbors within the distance cutoff. +{nnn} neighbors within the distance cutoff, unless {nnn} is NULL. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms @@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns, giving the {Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1. +If the keyword {wl} is set to yes, then the {Wl} values for each +atom will be added to the output array, which are real numbers. + +If the keyword {wl/hat} is set to yes, then the {Wl_hat} +values for each atom will be added to the output array, which are real numbers. + If the keyword {components} is set, then the real and imaginary parts of each component of (normalized) {Ybar_lm} will be added to the output array in the following order: Re({Ybar_-m}) Im({Ybar_-m}) @@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html [Default:] The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, -{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. +{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12, +{wl} = no, {wl/hat} = no, and {components} off :line diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index 1460ba18a5b1ffbadfce39cae346872c16866dd0..10ff68958210b2a1274f80f51e0b7271fcc991da 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -64,6 +64,23 @@ which calculate the tangential force between two particles and return its components and magnitude acting on atom I for N = 1,2,3,4. See individual pair styles for details. +When using {pN} with pair style {hybrid}, the output will be the Nth +quantity from the sub-style that computes the pairwise interaction +(based on atom types). If that sub-style does not define a {pN}, +the output will be 0.0. The maximum allowed N is the maximum number +of quantities provided by any sub-style. + +When using {pN} with pair style {hybrid/overlay} the quantities +from all sub-styles that provide them are concatenated together +into one long list. For example, if there are 3 sub-styles and +2 of them have additional output (with 3 and 4 quantities, +respectively), then 7 values ({p1} up to {p7}) are defined. +The values {p1} to {p3} refer to quantities defined by the first +of the two sub-styles. Values {p4} to {p7} refer to quantities +from the second of the two sub-styles. If the referenced {pN} +is not computed for the specific pairwise interaction (based on +atom types), then the output will be 0.0. + The value {dist} will be in distance "units"_units.html. The value {eng} will be in energy "units"_units.html. The values {force}, {fx}, {fy}, and {fz} will be in force "units"_units.html. The values {pN} @@ -126,7 +143,7 @@ options. The output for {dist} will be in distance "units"_units.html. The output for {eng} will be in energy "units"_units.html. The output for {force}, {fx}, {fy}, and {fz} will be in force "units"_units.html. -The outpur for {pN} will be in whatever units the pair style defines. +The output for {pN} will be in whatever units the pair style defines. [Restrictions:] none diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 518d28aec9519d274b2254e6e907ffb652af95d4..eab32d8757255e1c100b4e6b60ae190290d25ea7 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -196,7 +196,7 @@ for j1 in range(0,twojmax+1): if (j>=j1): print j1/2.,j2/2.,j/2. :pre NOTE: the {diagonal} keyword allowing other possible choices -for the number of bispectrum components was removed in 2019, +for the number of bispectrum components was removed in 2019, since all potentials use the value of 3, corresponding to the above set of bispectrum components. diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt index d27e402972e881c5896f675e3e0f32eb5fac8ade..0824a70dd02b6f4ca0cbdb6534cf9ded54a8ef26 100644 --- a/doc/src/compute_spin.txt +++ b/doc/src/compute_spin.txt @@ -40,14 +40,14 @@ The simplest way to output the results of the compute spin calculation is to define some of the quantities as variables, and to use the thermo and thermo_style commands, for example: -compute out_mag all spin :pre +compute out_mag all spin :pre -variable mag_z equal c_out_mag\[3\] -variable mag_norm equal c_out_mag\[4\] -variable temp_mag equal c_out_mag\[6\] :pre +variable mag_z equal c_out_mag\[3\] +variable mag_norm equal c_out_mag\[4\] +variable temp_mag equal c_out_mag\[6\] :pre -thermo 10 -thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre +thermo 10 +thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre This series of commands evaluates the total magnetization along z, the norm of the total magnetization, and the magnetic temperature. Three variables are diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index abd1959e81d6d0d94747746b42682228448ed300..9c073b6c552432fd4493bcf31cd8c2f5d52be3f1 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -23,11 +23,14 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l btype = bond type of new bond batom1,batom2 = atom IDs for two atoms in bond {single/angle} args = atype aatom1 aatom2 aatom3 - atype = bond type of new angle + atype = angle type of new angle aatom1,aatom2,aatom3 = atom IDs for three atoms in angle {single/dihedral} args = dtype datom1 datom2 datom3 datom4 - dtype = bond type of new dihedral - datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre + dtype = dihedral type of new dihedral + datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral + {single/improper} args = itype iatom1 iatom2 iatom3 iatom4 + itype = improper type of new improper + iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper :pre zero or more keyword/value pairs may be appended :l keyword = {special} :l {special} value = {yes} or {no} :pre @@ -38,51 +41,54 @@ keyword = {special} :l create_bonds many all all 1 1.0 1.2 create_bonds many surf solvent 3 2.0 2.4 create_bonds single/bond 1 1 2 -create_bonds single/angle 5 52 98 107 special no :pre +create_bonds single/angle 5 52 98 107 special no +create_bonds single/dihedral 2 4 19 27 101 +create_bonds single/improper 3 23 26 31 57 :pre [Description:] Create bonds between pairs of atoms that meet a specified distance -criteria. Or create a single bond, angle, or dihedral between 2, 3, +criteria. Or create a single bond, angle, dihedral or improper between 2, 3, or 4 specified atoms. -The new bond (angle, dihedral) interactions will then be computed -during a simulation by the bond (angle, dihedral) potential defined by +The new bond (angle, dihedral, improper) interactions will then be computed +during a simulation by the bond (angle, dihedral, improper) potential defined by the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html, "angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html, "dihedral_style"_dihedral_style.html, -"dihedral_coeff"_dihedral_coeff.html commands. +"dihedral_coeff"_dihedral_coeff.html, "improper_style"_improper_style.html, +"improper_coeff"_improper_coeff.html commands. The {many} style is useful for adding bonds to a system, e.g. between nearest neighbors in a lattice of atoms, without having to enumerate all the bonds in the data file read by the "read_data"_read_data.html command. -The {single} styles are useful for adding bonds, angles, dihedrals +The {single} styles are useful for adding bonds, angles, dihedrals, impropers to a system incrementally, then continuing a simulation. -Note that this command does not auto-create any angle or dihedral +Note that this command does not auto-create any angle, dihedral or improper interactions when a bond is added. Nor does it auto-create any bonds -when an angle or dihedral is added. Or auto-create any angles when a -dihedral is added. Thus the flexibility of this command is limited. +when an angle, dihedral or improper is added. Or auto-create any angles when a +dihedral or improper is added. Thus the flexibility of this command is limited. It can be used several times to create different types of bond at different distances. But it cannot typically auto-create all the -bonds or angles or dihedral that would normally be defined in a data -file for a complex system of molecules. +bonds or angles or dihedrals or impropers that would normally be defined in a +data file for a complex system of molecules. -NOTE: If the system has no bonds (angles, dihedrals) to begin with, or -if more bonds per atom are being added than currently exist, then you +NOTE: If the system has no bonds (angles, dihedrals, impropers) to begin with, +or if more bonds per atom are being added than currently exist, then you must insure that the number of bond types and the maximum number of bonds per atom are set to large enough values. And similarly for -angles and dihedrals. Otherwise an error may occur when too many -bonds (angles, dihedrals) are added to an atom. If the +angles, dihedrals and impropers. Otherwise an error may occur when too many +bonds (angles, dihedrals, impropers) are added to an atom. If the "read_data"_read_data.html command is used to define the system, these parameters can be set via the "bond types" and "extra bond per atom" fields in the header section of the data file. If the "create_box"_create_box.html command is used to define the system, these 2 parameters can be set via its optional "bond/types" and -"extra/bond/per/atom" arguments. And similarly for angles and -dihedrals. See the doc pages for these 2 commands for details. +"extra/bond/per/atom" arguments. And similarly for angles, dihedrals and +impropers. See the doc pages for these 2 commands for details. :line @@ -137,18 +143,25 @@ ordered linearly within the angle; the central atom is {aatom2}. {Atype} must be a value between 1 and the number of angle types defined. -The {single/dihedral} style creates a single dihedral of type {btype} -between two atoms with IDs {batom1} and {batom2}. The ordering of the -atoms is the same as in the {Dihedrals} section of a data file read by -the "read_data"_read_data.html command. I.e. the 4 atoms are ordered -linearly within the dihedral. {Dtype} must be a value between 1 and +The {single/dihedral} style creates a single dihedral of type {dtype} +between four atoms with IDs {datom1}, {datom2}, {datom3}, and {datom4}. The +ordering of the atoms is the same as in the {Dihedrals} section of a data file +read by the "read_data"_read_data.html command. I.e. the 4 atoms are ordered +linearly within the dihedral. {dtype} must be a value between 1 and the number of dihedral types defined. +The {single/improper} style creates a single improper of type {itype} +between four atoms with IDs {iatom1}, {iatom2}, {iatom3}, and {iatom4}. The +ordering of the atoms is the same as in the {Impropers} section of a data file +read by the "read_data"_read_data.html command. I.e. the 4 atoms are ordered +linearly within the improper. {itype} must be a value between 1 and +the number of improper types defined. + :line The keyword {special} controls whether an internal list of special -bonds is created after one or more bonds, or a single angle or -dihedral is added to the system. +bonds is created after one or more bonds, or a single angle, dihedral or +improper is added to the system. The default value is {yes}. A value of {no} cannot be used with the {many} style. @@ -161,16 +174,16 @@ see the "special_bonds"_special_bonds.html command for details. Thus if you are adding a few bonds or a large list of angles all at the same time, by using this command repeatedly, it is more efficient to only trigger the internal list to be created once, after the last -bond (or angle, or dihedral) is added: +bond (or angle, or dihedral, or improper) is added: create_bonds single/bond 5 52 98 special no -create_bonds single/bond 5 73 74 special no +create_bonds single/bond 5 73 74 special no ... create_bonds single/bond 5 17 386 special no create_bonds single/bond 4 112 183 special yes :pre Note that you MUST insure the internal list is re-built after the last -bond (angle, dihedral) is added, before performing a simulation. +bond (angle, dihedral, improper) is added, before performing a simulation. Otherwise pairwise interactions will not be properly excluded or weighted. LAMMPS does NOT check that you have done this correctly. diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index 27bc04f9df6d05cf8774270a2900a5fb96cf1d4c..b4071c863c01075a6823d0c8f381581360ee3c89 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -8,6 +8,7 @@ dihedral_style harmonic command :h3 dihedral_style harmonic/intel command :h3 +dihedral_style harmonic/kk command :h3 dihedral_style harmonic/omp command :h3 [Syntax:] diff --git a/doc/src/dump.txt b/doc/src/dump.txt index ff1b2dc3a64b9b9f9915c1f5f0b991f83e8536aa..0d08fdf471a851e74a1c936dd0a684c34ed91ffb 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre ID = user-assigned name for the dump :ulb,l group-ID = ID of the group of atoms to be dumped :l -style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l +style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or +{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l N = dump every this many timesteps :l file = name of file to write dump info to :l args = list of arguments for a particular style :l diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 6be0d26463f86062ca079f7c1349bd7842d10418..63a3476d300999690da4d544cb2ea2d595252fb1 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre dump-ID = ID of dump to modify :ulb,l one or more keyword/value pairs may be appended :l these keywords apply to various dump styles :l -keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l +keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {pbc} or {precision} or {region} or {refresh} or {scale} or {sfactor} or {sort} or {tfactor} or {thermo} or {thresh} or {time} or {units} or {unwrap} :l {append} arg = {yes} or {no} {at} arg = N N = index of frame written upon first dump @@ -30,10 +30,10 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi {fileper} arg = Np Np = write one file for every this many processors {first} arg = {yes} or {no} + {flush} arg = {yes} or {no} {format} args = {line} string, {int} string, {float} string, M string, or {none} string = C-style format string M = integer from 1 to N, where N = # of per-atom quantities being output - {flush} arg = {yes} or {no} {image} arg = {yes} or {no} {label} arg = string string = character string (e.g. BONDS) to use in header of dump local file @@ -48,18 +48,20 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi {refresh} arg = c_ID = compute ID that supports a refresh operation {scale} arg = {yes} or {no} {sfactor} arg = coordinate scaling factor (> 0.0) - {thermo} arg = {yes} or {no} - {tfactor} arg = time scaling factor (> 0.0) {sort} arg = {off} or {id} or N or -N off = no sorting of per-atom lines within a snapshot id = sort per-atom lines by atom ID N = sort per-atom lines in ascending order by the Nth column -N = sort per-atom lines in descending order by the Nth column + {tfactor} arg = time scaling factor (> 0.0) + {thermo} arg = {yes} or {no} + {time} arg = {yes} or {no} {thresh} args = attribute operator value attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding + {units} arg = {yes} or {no} {unwrap} arg = {yes} or {no} :pre these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l @@ -620,6 +622,37 @@ threshold criterion is met. Otherwise it is not met. :line +The {time} keyword only applies to the dump {atom}, {custom}, and +{local} styles (and their COMPRESS package versions {atom/gz}, +{custom/gz} and {local/gz}). If set to {yes}, each frame will will +contain two extra lines before the "ITEM: TIMESTEP" entry: + +ITEM: TIME +\ :pre + +This will output the current elapsed simulation time in current +time units equivalent to the "thermo keyword"_thermo_style.html {time}. +This is to simplify post-processing of trajectories using a variable time +step, e.g. when using "fix dt/reset"_fix_dt_reset.html. +The default setting is {no}. + +:line + +The {units} keyword only applies to the dump {atom}, {custom}, and +{local} styles (and their COMPRESS package versions {atom/gz}, +{custom/gz} and {local/gz}). If set to {yes}, each individual dump +file will contain two extra lines at the very beginning with: + +ITEM: UNITS +\ :pre + +This will output the current selected "units"_units.html style +to the dump file and thus allows visualization and post-processing +tools to determine the choice of units of the data in the dump file. +The default setting is {no}. + +:line + The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles. If set to {yes}, coordinates will be written "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has passed through @@ -924,6 +957,7 @@ scale = yes sort = off for dump styles {atom}, {custom}, {cfg}, and {local} sort = id for dump styles {dcd}, {xtc}, and {xyz} thresh = none +units = no unwrap = no :ul acolor = * red/green/blue/yellow/aqua/cyan diff --git a/doc/src/dynamical_matrix.txt b/doc/src/dynamical_matrix.txt index 6291bdec520b59596d9a2978e54fbf4d0b7d0aea..2d9b256694074b6eebfa823ce06c95992364cce5 100644 --- a/doc/src/dynamical_matrix.txt +++ b/doc/src/dynamical_matrix.txt @@ -30,14 +30,29 @@ dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre [Description:] -Calculate the dynamical matrix of the selected group. +Calculate the dynamical matrix by finite difference of the selected group, -[Restrictions:] +:c,image(JPG/dynamical_matrix_dynmat.jpg) + +where D is the dynamical matrix and Phi is the force constant matrix defined by + +:c,image(JPG/dynamical_matrix_force_constant.jpg). + +The output for the dynamical matrix is printed three elements at a time. The +three elements are the three beta elements for a respective i/alpha/j combination. +Each line is printed in order of j increasing first, alpha second, and i last. -The command collects the entire dynamical matrix a single MPI rank, -so the memory requirements can be very significant for large systems. +If the style eskm is selected, the dynamical matrix will be in units of inverse squared +femtoseconds. These units will then conveniently leave frequencies in THz, where +frequencies, represented as omega, can be calculated from + +:c, image(Eqs/dynamical_matrix_phonons.jpg) + +[Restrictions:] -This command assumes a periodic system. +The command collects an array of nine times the number of atoms in a group +on every single MPI rank, so the memory requirements can be very significant +for large systems. This command is part of the USER-PHONON package. It is only enabled if LAMMPS was built with that package. See the "Build @@ -52,4 +67,4 @@ provided by Pair's single_hessian. [Default:] -The default settings are file = "dynmat.dyn", binary = no +The default settings are file = "dynmat.dyn", binary = no diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 1dd9cc9f1b37b419cc609964f95a6a97a363ec13..fd281bce83b98d1ed7fcf0096f60ac74377765cf 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -188,7 +188,7 @@ accelerated styles exist. "box/relax"_fix_box_relax.html - relax box size during energy minimization "client/md"_fix_client_md.html - MD client for client/server simulations "cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field -"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library +"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library "controller"_fix_controller.html - apply control loop feedback mechanism "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface @@ -221,7 +221,7 @@ accelerated styles exist. "heat"_fix_heat.html - add/subtract momentum-conserving heat "hyper/global"_fix_hyper_global.html - global hyperdynamics "hyper/local"_fix_hyper_local.html - local hyperdynamics -"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol +"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol "indent"_fix_indent.html - impose force due to an indenter "ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations "langevin"_fix_langevin.html - Langevin temperature control @@ -327,7 +327,7 @@ accelerated styles exist. "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration "rx"_fix_rx.html - -"saed/vtk"_fix_saed_vtk.html - +"saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles "shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 3f428e2103b3f067e31a45e1623ad236c49a0963..d729f09b5469f47340b1c4c242933c54598cc3fb 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -186,20 +186,25 @@ reacting atoms. Some atoms in the pre-reacted template that are not reacting may have missing topology with respect to the simulation. For example, the -pre-reacted template may contain an atom that would connect to the -rest of a long polymer chain. These are referred to as edge atoms, and -are also specified in the map file. When the pre-reaction template -contains edge atoms, not all atoms, bonds, charges, etc. specified in -the reaction templates will be updated. Specifically, topology that -involves only atoms that are 'too near' to template edges will not be -updated. The definition of 'too near the edge' depends on which -interactions are defined in the simulation. If the simulation has -defined dihedrals, atoms within two bonds of edge atoms are considered -'too near the edge.' If the simulation defines angles, but not -dihedrals, atoms within one bond of edge atoms are considered 'too -near the edge.' If just bonds are defined, only edge atoms are +pre-reacted template may contain an atom that, in the simulation, is +currently connected to the rest of a long polymer chain. These are +referred to as edge atoms, and are also specified in the map file. All +pre-reaction template atoms should be linked to a bonding atom, via at +least one path that does not involve edge atoms. When the pre-reaction +template contains edge atoms, not all atoms, bonds, charges, etc. +specified in the reaction templates will be updated. Specifically, +topology that involves only atoms that are 'too near' to template +edges will not be updated. The definition of 'too near the edge' +depends on which interactions are defined in the simulation. If the +simulation has defined dihedrals, atoms within two bonds of edge atoms +are considered 'too near the edge.' If the simulation defines angles, +but not dihedrals, atoms within one bond of edge atoms are considered +'too near the edge.' If just bonds are defined, only edge atoms are considered 'too near the edge.' +NOTE: Small molecules, i.e. ones that have all their atoms contained +within the reaction templates, never have edge atoms. + Note that some care must be taken when a building a molecule template for a given simulation. All atom types in the pre-reacted template must be the same as those of a potential reaction site in the @@ -261,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the discussion of the 'update_edges' keyword. The fourth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, -there is one type of constraint available, as discussed below. +there are three types of constraints available, as discussed below. A sample map file is given below: @@ -295,17 +300,47 @@ Equivalences :pre :line Any number of additional constraints may be specified in the -Constraints section of the map file. Currently there is one type of -additional constraint, of type 'distance', whose syntax is as follows: +Constraints section of the map file. The constraint of type 'distance' +has syntax as follows: distance {ID1} {ID2} {rmin} {rmax} :pre where 'distance' is the required keyword, {ID1} and {ID2} are pre-reaction atom IDs, and these two atoms must be separated by a -distance between {rmin} and {rmax} for the reaction to occur. This +distance between {rmin} and {rmax} for the reaction to occur. + +The constraint of type 'angle' has the following syntax: + +angle {ID1} {ID2} {ID3} {amin} {amax} :pre + +where 'angle' is the required keyword, {ID1}, {ID2} and {ID3} are +pre-reaction atom IDs, and these three atoms must form an angle +between {amin} and {amax} for the reaction to occur (where {ID2} is +the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. +The constraint of type 'arrhenius' imposes an additional reaction +probability according to the temperature-dependent Arrhenius equation: + +:c,image(Eqs/fix_bond_react.jpg) + +The Arrhenius constraint has the following syntax: + +arrhenius {A} {n} {E_a} {seed} :pre + +where 'arrhenius' is the required keyword, {A} is the pre-exponential +factor, {n} is the exponent of the temperature dependence, {E_a} is +the activation energy ("units"_units.html of energy), and {seed} is a +random number seed. The temperature is defined as the instantaneous +temperature averaged over all atoms in the reaction site, and is +calculated in the same manner as for example +"compute_temp_chunk"_compute_temp_chunk.html. Currently, there are no +options for additional temperature averaging or velocity-biased +temperature calculations. A uniform random number between 0 and 1 is +generated using {seed}; if this number is less than the result of the +Arrhenius equation above, the reaction is permitted to occur. + Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the post-reacted molecule template. All force fields with fixed bonds, @@ -381,7 +416,7 @@ will apply to all reactions. Computationally, each timestep this fix operates, it loops over neighbor lists (for bond-forming reactions) and computes distances between pairs of atoms in the list. It also communicates between -neighboring processors to coordinate which bonds are created and/or +neighboring processors to coordinate which bonds are created and/or removed. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently. @@ -392,10 +427,11 @@ local command. [Restart, fix_modify, output, run start/stop, minimize info:] -No information about this fix is written to "binary restart -files"_restart.html, aside from internally-created per-atom -properties. None of the "fix_modify"_fix_modify.html options are -relevant to this fix. +Cumulative reaction counts for each reaction are written to "binary +restart files"_restart.html. These values are associated with the +reaction name (react-ID). Additionally, internally-created per-atom +properties are stored to allow for smooth restarts. None of the +"fix_modify"_fix_modify.html options are relevant to this fix. This fix computes one statistic for each {react} argument that it stores in a global vector, of length 'number of react arguments', that @@ -406,8 +442,8 @@ These is 1 quantity for each react argument: (1) cumulative # of reactions occurred :ul -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +No parameter of this fix can be used with the {start/stop} keywords +of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. When fix bond/react is 'unfixed,' all internally-created groups are @@ -417,18 +453,20 @@ all other fixes that use any group created by fix bond/react. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. +LAMMPS was built with that package. See the +"Build package"_Build_package.html doc page for more info. [Related commands:] -"fix bond/create"_fix_bond_create.html, "fix -bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, +"fix bond/create"_fix_bond_create.html, +"fix bond/break"_fix_bond_break.html, +"fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] -The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none +The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, +update_edges = none :line diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index 7458f1bcfa015985158cbb3a1148fe625eb964e4..45eb646b8e5f4e639f21f6bd2c40150bb51ac4fc 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -31,7 +31,6 @@ cvar = name of control variable :l [Examples:] - fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 861eed4a6fc9a4eb08aa4dc5954797e178c0b260..49ecf96ff61f60508a29e269dc8b0b28ce074258 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -24,9 +24,10 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l {angmom} value = {no} or factor {no} = do not thermostat rotational degrees of freedom via the angular momentum factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below - {gjf} value = {no} or {yes} + {gjf} value = {no} or {vfull} or {vhalf} {no} = use standard formulation - {yes} = use Gronbech-Jensen/Farago formulation + {vfull} = use Gronbech-Jensen/Farago formulation + {vhalf} = use 2GJ formulation {omega} value = {no} or {yes} {no} = do not thermostat rotational degrees of freedom via the angular velocity {yes} = do thermostat rotational degrees of freedom via the angular velocity @@ -217,6 +218,10 @@ the particles. As described below, this energy can then be printed out or added to the potential energy of the system to monitor energy conservation. +NOTE: this accumulated energy does NOT include kinetic energy removed +by the {zero} flag. LAMMPS will print a warning when both options are +active. + The keyword {zero} can be used to eliminate drift due to the thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix @@ -232,29 +237,24 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago described in the papers cited below, the purpose of this method is to enable longer timesteps to be used (up to the numerical stability limit of the integrator), while still producing the correct Boltzmann -distribution of atom positions. It is implemented within LAMMPS, by -changing how the random force is applied so that it is composed of -the average of two random forces representing half-contributions from -the previous and current time intervals. - -In common with all methods based on Verlet integration, the -discretized velocities generated by this method in conjunction with -velocity-Verlet time integration are not exactly conjugate to the -positions. As a result the temperature (computed from the discretized -velocities) will be systematically lower than the target temperature, -by a small amount which grows with the timestep. Nonetheless, the -distribution of atom positions will still be consistent with the +distribution of atom positions. + +The current implementation provides the user with the option to output +the velocity in one of two forms: {vfull} or {vhalf}, which replaces +the outdated option {yes}. The {gjf} option {vfull} outputs the on-site +velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity +is shown to be systematically lower than the target temperature by a small +amount, which grows quadratically with the timestep. +The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in +"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; for linear systems, +this velocity is shown to not have any statistical errors for any stable time step. +An overview of statistically correct Boltzmann and Maxwell-Boltzmann +sampling of true on-site and true half-step velocities is given in +"Gronbech-Jensen"_#1Gronbech-Jensen. +Regardless of the choice of output velocity, the sampling of the configurational +distribution of atom positions is the same, and linearly consistent with the target temperature. -As an example of using the {gjf} keyword, for molecules containing C-H -bonds, configurational properties generated with dt = 2.5 fs and tdamp -= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity -distribution systematically decreases with increasing timestep, the -method should not be used to generate properties that depend on the -velocity distribution, such as the velocity auto-correlation function -(VACF). In this example, the velocity distribution at dt = 2.5fs -generates an average temperature of 220 K, instead of 300 K. - :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are @@ -312,7 +312,10 @@ This fix can ramp its target temperature over multiple runs, using the This fix is not invoked during "energy minimization"_minimize.html. -[Restrictions:] none +[Restrictions:] + +For {gjf} do not choose damp=dt/2. {gjf} is not compatible +with run_style respa. [Related commands:] @@ -335,5 +338,10 @@ types, tally = no, zero = no, gjf = no. :link(Gronbech-Jensen) [(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983 -(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, -185, 524 (2014) +(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014) + +:link(2Gronbech-Jensen) +[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019) + +:link(1Gronbech-Jensen) +[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506 diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt index e4065adad54375a1b5b922f36d4c7073b2414496..e5dccc5e572e7dfb622ba68624bdd148b16c6ad8 100644 --- a/doc/src/fix_langevin_spin.txt +++ b/doc/src/fix_langevin_spin.txt @@ -50,7 +50,7 @@ As an example: fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 fix 2 all langevin/spin 300.0 0.01 21 -fix 3 all nve/spin lattice yes :pre +fix 3 all nve/spin lattice moving :pre is correct, but defining a force/spin command after the langevin/spin command would give an error message. diff --git a/doc/src/fix_neb_spin.txt b/doc/src/fix_neb_spin.txt index 89420f451ca793260a306b5ea60a556fd1968291..e62d2972709aba063210ce4b456d0ab96302f0e7 100644 --- a/doc/src/fix_neb_spin.txt +++ b/doc/src/fix_neb_spin.txt @@ -24,18 +24,18 @@ fix 1 active neb/spin 1.0 [Description:] Add nudging forces to spins in the group for a multi-replica -simulation run via the "neb/spin"_neb_spin.html command to perform a -geodesic nudged elastic band (GNEB) calculation for finding the +simulation run via the "neb/spin"_neb_spin.html command to perform a +geodesic nudged elastic band (GNEB) calculation for finding the transition state. -Hi-level explanations of GNEB are given with the -"neb/spin"_neb_spin.html command and on the -"Howto replica"_Howto_replica.html doc page. -The fix neb/spin command must be used with the "neb/spin" command and -defines how inter-replica nudging forces are computed. A GNEB -calculation is divided in two stages. In the first stage n replicas -are relaxed toward a MEP until convergence. In the second stage, the -climbing image scheme is enabled, so that the replica having the highest -energy relaxes toward the saddle point (i.e. the point of highest energy +Hi-level explanations of GNEB are given with the +"neb/spin"_neb_spin.html command and on the +"Howto replica"_Howto_replica.html doc page. +The fix neb/spin command must be used with the "neb/spin" command and +defines how inter-replica nudging forces are computed. A GNEB +calculation is divided in two stages. In the first stage n replicas +are relaxed toward a MEP until convergence. In the second stage, the +climbing image scheme is enabled, so that the replica having the highest +energy relaxes toward the saddle point (i.e. the point of highest energy along the MEP), and a second relaxation is performed. The nudging forces are calculated as explained in diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt index 7b382bb6adc66a96fd9953e71807f80a20f3cce6..8e6284639b3203905f1a892636dc3cd50c6294c2 100644 --- a/doc/src/fix_nve_spin.txt +++ b/doc/src/fix_nve_spin.txt @@ -15,22 +15,26 @@ fix ID group-ID nve/spin keyword values :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l nve/spin = style name of this fix command :l keyword = {lattice} :l - {lattice} value = {no} or {yes} :pre + {lattice} value = {moving} or {frozen} + moving = integrate both spin and atomic degress of freedom + frozen = integrate spins on a fixed lattice :pre :ule [Examples:] -fix 3 all nve/spin lattice yes -fix 1 all nve/spin lattice no :pre +fix 3 all nve/spin lattice moving +fix 1 all nve/spin lattice frozen :pre [Description:] Perform a symplectic integration for the spin or spin-lattice system. The {lattice} keyword defines if the spins are integrated on a lattice -of fixed atoms (lattice = no), or if atoms are moving (lattice = yes). - -By default (lattice = yes), a spin-lattice integration is performed. +of fixed atoms (lattice = frozen), or if atoms are moving +(lattice = moving). +The first case corresponds to a spin dynamics calculation, and +the second to a spin-lattice calculation. +By default a spin-lattice integration is performed (lattice = moving). The {nve/spin} fix applies a Suzuki-Trotter decomposition to the equations of motion of the spin lattice system, following the scheme: @@ -63,7 +67,9 @@ instead of "array" is also valid. "atom_style spin"_atom_style.html, "fix nve"_fix_nve.html -[Default:] none +[Default:] + +The option default is lattice = moving. :line diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt index 708b2bd7aad2e120827548195ff1634fd0baa11d..040a3086d39ab2df15ed6f3877b2e2d04df4dbc4 100644 --- a/doc/src/fix_precession_spin.txt +++ b/doc/src/fix_precession_spin.txt @@ -21,7 +21,7 @@ style = {zeeman} or {anisotropy} or {cubic} :l {anisotropy} args = K x y z K = intensity of the magnetic anisotropy (in eV) x y z = vector direction of the anisotropy :pre - {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z + {cubic} args = K1 K2c n1x n1y n1x n2x n2y n2z n3x n3y n3z K1 and K2c = intensity of the magnetic anisotropy (in eV) n1x to n3z = three direction vectors of the cubic anisotropy :pre :ule @@ -55,24 +55,24 @@ with n defining the direction of the anisotropy, and K (in eV) its intensity. If K>0, an easy axis is defined, and if K<0, an easy plane is defined. Style {cubic} is used to simulate a cubic anisotropy, with three -possible easy axis for the magnetic spins in the defined group: +possible easy axis for the magnetic spins in the defined group: :c,image(Eqs/fix_spin_cubic.jpg) -with K1 and K2c (in eV) the intensity coefficients and +with K1 and K2c (in eV) the intensity coefficients and n1, n2 and n3 defining the three anisotropic directions -defined by the command (from n1x to n3z). -For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an +defined by the command (from n1x to n3z). +For n1 = (100), n2 = (010), and n3 = (001), K1 < 0 defines an iron type anisotropy (easy axis along the (001)-type cube edges), and K1 > 0 defines a nickel type anisotropy (easy axis -along the (111)-type cube diagonals). +along the (111)-type cube diagonals). K2^c > 0 also defines easy axis along the (111)-type cube diagonals. See chapter 2 of "(Skomski)"_#Skomski1 for more details on cubic anisotropies. In all cases, the choice of (x y z) only imposes the vector -directions for the forces. Only the direction of the vector is +directions for the forces. Only the direction of the vector is important; it's length is ignored (the entered vectors are normalized). diff --git a/doc/src/fix_rigid_meso.txt b/doc/src/fix_rigid_meso.txt index 0819fdb2fbf6a39dbfb2fe80937bef44fbb9a824..a9c68b2c049bde31ddfb85f2d45a7728c707ca19 100644 --- a/doc/src/fix_rigid_meso.txt +++ b/doc/src/fix_rigid_meso.txt @@ -44,7 +44,7 @@ fix 1 rods rigid/meso molecule fix 1 spheres rigid/meso single force 1 off off on fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off :pre - + [Description:] Treat one or more sets of mesoscopic SPH/SDPD particles as independent diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index 63713d87c289bd140bccbdfdc0942b0d61bc5179..5ee289ec5cacb7e0b024b8d5c7fd002d133de4f1 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -67,15 +67,15 @@ to it. :line -Style {spin} suffix sets the components of the magnetic precession -vectors instead of the mechanical forces. This also erases all -previously computed magnetic precession vectors on the atom, though +Style {spin} suffix sets the components of the magnetic precession +vectors instead of the mechanical forces. This also erases all +previously computed magnetic precession vectors on the atom, though additional magnetic fixes could add new forces. -This command can be used to freeze the magnetic moment of certain -atoms in the simulation by zeroing their precession vector. +This command can be used to freeze the magnetic moment of certain +atoms in the simulation by zeroing their precession vector. -All options defined above remain valid, they just apply to the magnetic +All options defined above remain valid, they just apply to the magnetic precession vectors instead of the forces. :line @@ -132,7 +132,7 @@ forces to any value besides zero when performing a minimization. Use the "fix addforce"_fix_addforce.html command if you want to apply a non-zero force to atoms during a minimization. -[Restrictions:] +[Restrictions:] The fix {setforce/spin} only makes sense when LAMMPS was built with the SPIN package. diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt index 1b569b38946b8746c1e6692959ae5af76640cf0a..f4f59ed6366c88552b45caa793d44aeb24477e5e 100644 --- a/doc/src/improper_fourier.txt +++ b/doc/src/improper_fourier.txt @@ -16,7 +16,7 @@ improper_style fourier :pre [Examples:] improper_style fourier -improper_coeff 1 100.0 180.0 :pre +improper_coeff 1 100.0 0.0 1.0 0.5 1 :pre [Description:] @@ -24,12 +24,12 @@ The {fourier} improper style uses the following potential: :c,image(Eqs/improper_fourier.jpg) -where K is the force constant and omega is the angle between the IL -axis and the IJK plane: +where K is the force constant, C0, C1, C2 are dimensionless coefficients, +and omega is the angle between the IL axis and the IJK plane: :c,image(JPG/umbrella.jpg) -If all parameter (see bellow) is not zero, the all the three possible angles will taken in account. +If all parameter (see below) is not zero, the all the three possible angles will taken in account. The following coefficients must be defined for each improper type via the "improper_coeff"_improper_coeff.html command as in the example @@ -38,10 +38,10 @@ above, or in the data file or restart files read by the commands: K (energy) -C0 (real) -C1 (real) -C2 (real) -all (integer >= 0) :ul +C0 (unitless) +C1 (unitless) +C2 (unitless) +all (0 or 1, optional) :ul :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 98ec1e64e6284bad5204884d8457e80457f02d78..04b845acaac816d789ee2edc09737bccb7cdcdd8 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -116,10 +116,10 @@ used without a cutoff, i.e. they become full long-range potentials. The {ewald/disp} style can also be used with point-dipoles, see "(Toukmaji)"_#Toukmaji. -The {ewald/dipole} style adds long-range standard Ewald summations +The {ewald/dipole} style adds long-range standard Ewald summations for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji. -The {ewald/dipole/spin} style adds long-range standard Ewald +The {ewald/dipole/spin} style adds long-range standard Ewald summations for magnetic dipole-dipole interactions between magnetic spins. @@ -142,11 +142,11 @@ The optional {smallq} argument defines the cutoff for the absolute charge value which determines whether a particle is considered charged or not. Its default value is 1.0e-5. -The {pppm/dipole} style invokes a particle-particle particle-mesh solver +The {pppm/dipole} style invokes a particle-particle particle-mesh solver for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008. -The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver -for magnetic dipole-dipole interactions between magnetic spins. +The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver +for magnetic dipole-dipole interactions between magnetic spins. The {pppm/tip4p} style is identical to the {pppm} style except that it adds a charge at the massless 4th site in each TIP4P water molecule. diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 3c856bde19f519153e9f18aabb4fcc2d95986888..eec7520fdc936c71536122a5a79b9d6443597f5e 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -217,6 +217,7 @@ temper_npt.html thermo.html thermo_modify.html thermo_style.html +third_order.html timer.html timestep.html uncompute.html @@ -611,6 +612,7 @@ pair_lj_smooth.html pair_lj_smooth_linear.html pair_fep_soft.html pair_lj_switch3_coulgauss.html +pair_local_density.html pair_lubricate.html pair_lubricateU.html pair_mdf.html diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt index d342e8bf0184a7f5d8eb2eea251949dd399cc48e..c23ca67852ec0eb10c59bd953e6a7a810e589b54 100644 --- a/doc/src/min_modify.txt +++ b/doc/src/min_modify.txt @@ -13,11 +13,15 @@ min_modify command :h3 min_modify keyword values ... :pre one or more keyword/value pairs may be listed :ulb,l -keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor} +keyword = {dmax} or {line} or {norm} or {alpha_damp} or {discrete_factor} {dmax} value = max max = maximum distance for line search to move (distance units) - {line} value = {backtrack} or {quadratic} or {forcezero} - backtrack,quadratic,forcezero = style of linesearch to use + {line} value = {backtrack} or {quadratic} or {forcezero} or {spin_cubic} or {spin_none} + backtrack,quadratic,forcezero,spin_cubic,spin_none = style of linesearch to use + {norm} value = {two} or {max} + two = Euclidean two-norm (length of 3N vector) + inf = max force component across all 3-vectors + max = max force norm across all 3-vectors {alpha_damp} value = damping damping = fictitious Gilbert damping for spin minimization (adim) {discrete_factor} value = factor @@ -69,18 +73,54 @@ difference of two large values (energy before and energy after) and that difference may be smaller than machine epsilon even if atoms could move in the gradient direction to reduce forces further. +The choice of a norm can be modified for the min styles {cg}, {sd}, +{quickmin}, {fire}, {spin}, {spin/cg} and {spin/lbfgs} using +the {norm} keyword. +The default {two} norm computes the 2-norm (Euclidean length) of the +global force vector: + +:c,image(Eqs/norm_two.jpg) + +The {max} norm computes the length of the 3-vector force +for each atom (2-norm), and takes the maximum value of those across +all atoms + +:c,image(Eqs/norm_max.jpg) + +The {inf} norm takes the maximum component across the forces of +all atoms in the system: + +:c,image(Eqs/norm_inf.jpg) + +For the min styles {spin}, {spin/cg} and {spin/lbfgs}, the force +norm is replaced by the spin-torque norm. + Keywords {alpha_damp} and {discrete_factor} only make sense when -a "min_spin"_min_spin.html command is declared. +a "min_spin"_min_spin.html command is declared. Keyword {alpha_damp} defines an analog of a magnetic Gilbert damping. It defines a relaxation rate toward an equilibrium for -a given magnetic system. +a given magnetic system. Keyword {discrete_factor} defines a discretization factor for the -adaptive timestep used in the {spin} minimization. +adaptive timestep used in the {spin} minimization. See "min_spin"_min_spin.html for more information about those quantities. -Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0. -[Restrictions:] none +The choice of a line search algorithm for the {spin/cg} and +{spin/lbfgs} styles can be specified via the {line} keyword. +The {spin_cubic} and {spin_none} only make sense when one of those +two minimization styles is declared. +The {spin_cubic} performs the line search based on a cubic interpolation +of the energy along the search direction. The {spin_none} keyword +deactivates the line search procedure. +The {spin_none} is a default value for {line} keyword for both {spin/lbfgs} +and {spin/cg}. Convergence of {spin/lbfgs} can be more robust if +{spin_cubic} line search is used. + +[Restrictions:] + +For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used +when styles {spin/cg} and {spin/lbfgs} are employed. +See "neb/spin"_neb_spin.html for more explanation. [Related commands:] @@ -88,4 +128,8 @@ Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0. [Default:] -The option defaults are dmax = 0.1 and line = quadratic. +The option defaults are dmax = 0.1, line = quadratic and norm = two. + +For the {spin}, {spin/cg} and {spin/lbfgs} styles, the +option defaults are alpha_damp = 1.0, discrete_factor = 10.0, +line = spin_none, and norm = euclidean. diff --git a/doc/src/min_spin.txt b/doc/src/min_spin.txt index 890e324aca41842471c3040838ab3e44fea5ef28..89766891c84534a57ac9c3149ab219058470be4f 100644 --- a/doc/src/min_spin.txt +++ b/doc/src/min_spin.txt @@ -6,14 +6,19 @@ :line min_style spin command :h3 +min_style spin/cg command :h3 +min_style spin/lbfgs command :h3 [Syntax:] -min_style spin :pre +min_style spin +min_style spin/cg +min_style spin/lbfgs :pre [Examples:] -min_style spin :pre +min_style spin/lbfgs +min_modify line spin_cubic discrete_factor 10.0 :pre [Description:] @@ -27,28 +32,57 @@ timestep, according to: with lambda a damping coefficient (similar to a Gilbert damping). -Lambda can be defined by setting the {alpha_damp} keyword with the -"min_modify"_min_modify.html command. +Lambda can be defined by setting the {alpha_damp} keyword with the +"min_modify"_min_modify.html command. The minimization procedure solves this equation using an -adaptive timestep. The value of this timestep is defined -by the largest precession frequency that has to be solved in the +adaptive timestep. The value of this timestep is defined +by the largest precession frequency that has to be solved in the system: :c,image(Eqs/min_spin_timestep.jpg) with {|omega|_{max}} the norm of the largest precession frequency in the system (across all processes, and across all replicas if a -spin/neb calculation is performed). +spin/neb calculation is performed). -Kappa defines a discretization factor {discrete_factor} for the -definition of this timestep. +Kappa defines a discretization factor {discrete_factor} for the +definition of this timestep. {discrete_factor} can be defined with the "min_modify"_min_modify.html command. -NOTE: The {spin} style replaces the force tolerance by a torque +Style {spin/cg} defines an orthogonal spin optimization +(OSO) combined to a conjugate gradient (CG) algorithm. +The "min_modify"_min_modify.html command can be used to +couple the {spin/cg} to a line search procedure, and to modify the +discretization factor {discrete_factor}. +By default, style {spin/cg} does not employ the line search procedure +and uses the adaptive time-step technique in the same way as style {spin}. + +Style {spin/lbfgs} defines an orthogonal spin optimization +(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno +(L-BFGS) algorithm. +By default, style {spin/lbfgs} does not employ line search procedure. +If the line search procedure is not used then the discrete factor defines +the maximum root mean squared rotation angle of spins by equation {pi/(5*Kappa)}. +The default value for Kappa is 10. +The {spin_cubic} line search can improve the convergence of the +{spin/lbfgs} algorithm. + +The "min_modify"_min_modify.html command can be used to +activate the line search procedure, and to modify the +discretization factor {discrete_factor}. + +For more information about styles {spin/cg} and {spin/lbfgs}, +see their implementation reported in "(Ivanov)"_#Ivanov1. + +NOTE: All the {spin} styles replace the force tolerance by a torque tolerance. See "minimize"_minimize.html for more explanation. +NOTE: The {spin/cg} and {spin/lbfgs} styles can be used +for magnetic NEB calculations only if the line search procedure +is deactivated. See "neb/spin"_neb_spin.html for more explanation. + [Restrictions:] This minimization procedure is only applied to spin degrees of @@ -56,10 +90,15 @@ freedom for a frozen lattice configuration. [Related commands:] -"min_style"_min_style.html, "minimize"_minimize.html, +"min_style"_min_style.html, "minimize"_minimize.html, "min_modify"_min_modify.html [Default:] -The option defaults are {alpha_damp} = 1.0 and {discrete_factor} = -10.0. +The option defaults are {alpha_damp} = 1.0, {discrete_factor} = +10.0, {line} = spin_none and {norm} = euclidean. + +:line + +:link(Ivanov1) +[(Ivanov)] Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019). diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt index c46c1492b48223fbd7f6f5fa68ac25f2bb88e180..8816d62ffa579c9f29ed9d4c79a755d09e8c4c3e 100644 --- a/doc/src/min_style.txt +++ b/doc/src/min_style.txt @@ -11,7 +11,7 @@ min_style command :h3 min_style style :pre -style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul +style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} or {spin/cg} or {spin/lbfgs} :ul [Examples:] @@ -62,21 +62,60 @@ the velocity non-parallel to the current force vector. The velocity of each atom is initialized to 0.0 by this style, at the beginning of a minimization. -Style {spin} is a damped spin dynamics with an adaptive +Style {spin} is a damped spin dynamics with an adaptive timestep. -See the "min/spin"_min_spin.html doc page for more information. + +Style {spin/cg} uses an orthogonal spin optimization (OSO) +combined to a conjugate gradient (CG) approach to minimize spin +configurations. + +Style {spin/lbfgs} uses an orthogonal spin optimization (OSO) +combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno +(LBFGS) approach to minimize spin configurations. + +See the "min/spin"_min_spin.html doc page for more information +about the {spin}, {spin/cg} and {spin/lbfgs} styles. Either the {quickmin} and {fire} styles are useful in the context of nudged elastic band (NEB) calculations via the "neb"_neb.html command. +Either the {spin}, {spin/cg} and {spin/lbfgs} styles are useful +in the context of magnetic geodesic nudged elastic band (GNEB) calculations +via the "neb/spin"_neb_spin.html command. + NOTE: The damped dynamic minimizers use whatever timestep you have defined via the "timestep"_timestep.html command. Often they will converge more quickly if you use a timestep about 10x larger than you would normally use for dynamics simulations. -NOTE: The {quickmin}, {fire}, and {hftn} styles do not yet support the -use of the "fix box/relax"_fix_box_relax.html command or minimizations -involving the electron radius in "eFF"_pair_eff.html models. +NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet +support the use of the "fix box/relax"_fix_box_relax.html command or +minimizations involving the electron radius in "eFF"_pair_eff.html +models. + +:line + +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + +:line [Restrictions:] none diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index ecf1ad0fcffbb65cc9fcb320ff3285cdd6bcac14..da203c7d2d6db2e842f92f1f07373ae40c0550b8 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -7,6 +7,7 @@ :line minimize command :h3 +minimize/kk command :h3 [Syntax:] @@ -103,12 +104,13 @@ the line search fails because the step distance backtracks to 0.0 the number of outer iterations or timesteps exceeds {maxiter} the number of total force evaluations exceeds {maxeval} :ul -NOTE: the "minimization style"_min_style.html {spin} replaces +NOTE: the "minimization style"_min_style.html {spin}, +{spin/cg}, and {spin/lbfgs} replace the force tolerance {ftol} by a torque tolerance. -The minimization procedure stops if the 2-norm (length) of the -global torque vector (defined as the cross product between the -spins and their precession vectors omega) is less than {ftol}, -or if any of the other criteria are met. +The minimization procedure stops if the 2-norm (length) of the torque vector on atom +(defined as the cross product between the +atomic spin and its precession vectors omega) is less than {ftol}, +or if any of the other criteria are met. Torque have the same units as the energy. NOTE: You can also use the "fix halt"_fix_halt.html command to specify a general criterion for exiting a minimization, that is a calculation @@ -256,6 +258,28 @@ info in the Restrictions section below. :line +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. + +These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the "Build +package"_Build_package.html doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Run_options.html when you invoke LAMMPS, or you can use the +"suffix"_suffix.html command in your input script. + +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. + +:line + [Restrictions:] Features that are not yet implemented are listed here, in case someone diff --git a/doc/src/neb_spin.txt b/doc/src/neb_spin.txt index 7dbd924cd249e099e33718b17eeeda18dd9331f2..217606289f3c546871b1415cec2ac6b4e0bd58c9 100644 --- a/doc/src/neb_spin.txt +++ b/doc/src/neb_spin.txt @@ -45,7 +45,7 @@ and last are the end points of the transition path. GNEB is a method for finding both the spin configurations and height of the energy barrier associated with a transition state, e.g. spins to perform a collective rotation from one energy basin to -another. +another. The implementation in LAMMPS follows the discussion in the following paper: "(BessarabA)"_#BessarabA. @@ -59,35 +59,35 @@ performance speed-up you would see with one or more physical processors per replica. See the "Howto replica"_Howto_replica.html doc page for further discussion. -NOTE: As explained below, a GNEB calculation performs a damped dynamics -minimization across all the replicas. The "spin"_min_spin.html -style minimizer has to be defined in your input script. +NOTE: As explained below, a GNEB calculation performs a +minimization across all the replicas. One of the "spin"_min_spin.html +style minimizers has to be defined in your input script. When a GNEB calculation is performed, it is assumed that each replica is running the same system, though LAMMPS does not check for this. -I.e. the simulation domain, the number of magnetic atoms, the -interaction potentials, and the starting configuration when the neb +I.e. the simulation domain, the number of magnetic atoms, the +interaction potentials, and the starting configuration when the neb command is issued should be the same for every replica. In a GNEB calculation each replica is connected to other replicas by inter-replica nudging forces. These forces are imposed by the "fix -neb/spin"_fix_neb_spin.html command, which must be used in conjunction -with the neb command. +neb/spin"_fix_neb_spin.html command, which must be used in conjunction +with the neb command. The group used to define the fix neb/spin command defines the -GNEB magnetic atoms which are the only ones that inter-replica springs -are applied to. +GNEB magnetic atoms which are the only ones that inter-replica springs +are applied to. If the group does not include all magnetic atoms, then non-GNEB -magnetic atoms have no inter-replica springs and the torques they feel -and their precession motion is computed in the usual way due only -to other magnetic atoms within their replica. -Conceptually, the non-GNEB atoms provide a background force field for -the GNEB atoms. -Their magnetic spins can be allowed to evolve during the GNEB +magnetic atoms have no inter-replica springs and the torques they feel +and their precession motion is computed in the usual way due only +to other magnetic atoms within their replica. +Conceptually, the non-GNEB atoms provide a background force field for +the GNEB atoms. +Their magnetic spins can be allowed to evolve during the GNEB minimization procedure. The initial spin configuration for each of the replicas can be specified in different manners via the {file-style} setting, as -discussed below. Only atomic spins whose initial coordinates should +discussed below. Only atomic spins whose initial coordinates should differ from the current configuration need to be specified. Conceptually, the initial and final configurations for the first @@ -106,21 +106,21 @@ closer to the MEP and read them in. :line For a {file-style} setting of {final}, a filename is specified which -contains atomic and spin coordinates for zero or more atoms, in the -format described below. -For each atom that appears in the file, the new coordinates are -assigned to that atom in the final replica. Each intermediate replica -also assigns a new spin to that atom in an interpolated manner. -This is done by using the current direction of the spin at the starting -point and the read-in direction as the final point. -The "angular distance" between them is calculated, and the new direction +contains atomic and spin coordinates for zero or more atoms, in the +format described below. +For each atom that appears in the file, the new coordinates are +assigned to that atom in the final replica. Each intermediate replica +also assigns a new spin to that atom in an interpolated manner. +This is done by using the current direction of the spin at the starting +point and the read-in direction as the final point. +The "angular distance" between them is calculated, and the new direction is assigned to be a fraction of the angular distance. -NOTE: The "angular distance" between the starting and final point is -evaluated in the geodesic sense, as described in -"(BessarabA)"_#BessarabA. +NOTE: The "angular distance" between the starting and final point is +evaluated in the geodesic sense, as described in +"(BessarabA)"_#BessarabA. -NOTE: The angular interpolation between the starting and final point +NOTE: The angular interpolation between the starting and final point is achieved using Rodrigues formula: :c,image(Eqs/neb_spin_rodrigues_formula.jpg) @@ -130,7 +130,7 @@ omega_i^nu is a rotation angle defined as: :c,image(Eqs/neb_spin_angle.jpg) -with nu the image number, Q the total number of images, and +with nu the image number, Q the total number of images, and omega_i the total rotation between the initial and final spins. k_i defines a rotation axis such as: @@ -139,16 +139,16 @@ k_i defines a rotation axis such as: if the initial and final spins are not aligned. If the initial and final spins are aligned, then their cross product is null, and the expression above does not apply. -If they point toward the same direction, the intermediate images +If they point toward the same direction, the intermediate images conserve the same orientation. If the initial and final spins are aligned, but point toward opposite directions, an arbitrary rotation vector belonging to -the plane perpendicular to initial and final spins is chosen. +the plane perpendicular to initial and final spins is chosen. In this case, a warning message is displayed. For a {file-style} setting of {each}, a filename is specified which is -assumed to be unique to each replica. -See the "neb"_neb.html documentation page for more information about this +assumed to be unique to each replica. +See the "neb"_neb.html documentation page for more information about this option. For a {file-style} setting of {none}, no filename is specified. Each @@ -170,9 +170,10 @@ command is issued. :line A NEB calculation proceeds in two stages, each of which is a -minimization procedure, performed via damped dynamics. To enable -this, you must first define a damped spin dynamics -"min_style"_min_style.html, using the {spin} style (see +minimization procedure. To enable +this, you must first define a +"min_style"_min_style.html, using either the {spin}, +{spin/cg}, or {spin/lbfgs} style (see "min_spin"_min_spin.html for more information). The other styles cannot be used, since they relax the lattice degrees of freedom instead of the spins. @@ -195,9 +196,9 @@ damped dynamics is like a single timestep in a dynamics replica and its normalized distance along the reaction path (reaction coordinate RD) will be printed to the screen and log file every {Nevery} timesteps. The RD is 0 and 1 for the first and last replica. -For intermediate replicas, it is the cumulative angular distance -(normalized by the total cumulative angular distance) between adjacent -replicas, where "distance" is defined as the length of the 3N-vector of +For intermediate replicas, it is the cumulative angular distance +(normalized by the total cumulative angular distance) between adjacent +replicas, where "distance" is defined as the length of the 3N-vector of the geodesic distances in spin coordinates, with N the number of GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA). These outputs allow you to monitor NEB's progress in @@ -207,11 +208,11 @@ of {Nevery}. In the first stage of GNEB, the set of replicas should converge toward a minimum energy path (MEP) of conformational states that transition over a barrier. The MEP for a transition is defined as a sequence of -3N-dimensional spin states, each of which has a potential energy -gradient parallel to the MEP itself. -The configuration of highest energy along a MEP corresponds to a saddle -point. The replica states will also be roughly equally spaced along -the MEP due to the inter-replica nudging force added by the +3N-dimensional spin states, each of which has a potential energy +gradient parallel to the MEP itself. +The configuration of highest energy along a MEP corresponds to a saddle +point. The replica states will also be roughly equally spaced along +the MEP due to the inter-replica nudging force added by the "fix neb"_fix_neb.html command. In the second stage of GNEB, the replica with the highest energy is @@ -234,12 +235,12 @@ An atom map must be defined which it is not by default for "atom_style atomic"_atom_style.html problems. The "atom_modify map"_atom_modify.html command can be used to do this. -An initial value can be defined for the timestep. Although, the {spin} -minimization algorithm is an adaptive timestep methodology, so that -this timestep is likely to evolve during the calculation. +An initial value can be defined for the timestep. Although, the {spin} +minimization algorithm is an adaptive timestep methodology, so that +this timestep is likely to evolve during the calculation. The minimizers in LAMMPS operate on all spins in your system, even -non-GNEB atoms, as defined above. +non-GNEB atoms, as defined above. :line @@ -257,7 +258,7 @@ ID2 g2 x2 y2 z2 sx2 sy2 sz2 ... IDN gN yN zN sxN syN szN :pre -The fields are the atom ID, the norm of the associated magnetic spin, +The fields are the atom ID, the norm of the associated magnetic spin, followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates. The lines can be listed in any order. Additional trailing information on the line is OK, such as a comment. @@ -290,22 +291,22 @@ reaction coordinate and potential energy of each replica. The "maximum torque per replica" is the two-norm of the 3N-length vector given by the cross product of a spin by its -precession vector omega, in each replica, maximized across replicas, +precession vector omega, in each replica, maximized across replicas, which is what the {ttol} setting is checking against. In this case, N is all the atoms in each replica. The "maximum torque per atom" is the maximum torque component of any atom in any replica. The potential -gradients are the two-norm of the 3N-length magnetic precession vector -solely due to the interaction potential i.e. without adding in -inter-replica forces, and projected along the path tangent (as detailed +gradients are the two-norm of the 3N-length magnetic precession vector +solely due to the interaction potential i.e. without adding in +inter-replica forces, and projected along the path tangent (as detailed in Appendix D of "(BessarabA)"_#BessarabA). The "reaction coordinate" (RD) for each replica is the two-norm of the 3N-length vector of geodesic distances between its spins and the preceding -replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to -the RD of the preceding replica. The RD of the first replica RD1 = 0.0; -the RD of the final replica RDN = RDT, the total reaction coordinate. -The normalized RDs are divided by RDT, so that they form a monotonically -increasing sequence from zero to one. When computing RD, N only includes +replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to +the RD of the preceding replica. The RD of the first replica RD1 = 0.0; +the RD of the final replica RDN = RDT, the total reaction coordinate. +The normalized RDs are divided by RDT, so that they form a monotonically +increasing sequence from zero to one. When computing RD, N only includes the spins being operated on by the fix neb/spin command. The forward (reverse) energy barrier is the potential energy of the @@ -313,17 +314,17 @@ highest replica minus the energy of the first (last) replica. Supplementary information for all replicas can be printed out to the screen and master log.lammps file by adding the verbose keyword. This -information include the following. -The "GradVidottan" are the projections of the potential gradient for -the replica i on its tangent vector (as detailed in Appendix D of +information include the following. +The "GradVidottan" are the projections of the potential gradient for +the replica i on its tangent vector (as detailed in Appendix D of "(BessarabA)"_#BessarabA). -The "DNi" are the non normalized geodesic distances (see equation (13) -of "(BessarabA)"_#BessarabA), between a replica i and the next replica +The "DNi" are the non normalized geodesic distances (see equation (13) +of "(BessarabA)"_#BessarabA), between a replica i and the next replica i+1. For the last replica, this distance is not defined and a "NAN" -value is the corresponding output. +value is the corresponding output. When a NEB calculation does not converge properly, the supplementary -information can help understanding what is going wrong. +information can help understanding what is going wrong. When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a @@ -346,9 +347,9 @@ restart the calculation from an intermediate point with altered parameters. A c file script in provided in the tool/spin/interpolate_gneb -directory, that interpolates the MEP given the information provided +directory, that interpolates the MEP given the information provided by the verbose output option (as detailed in Appendix D of -"(BessarabA)"_#BessarabA). +"(BessarabA)"_#BessarabA). :line @@ -358,6 +359,9 @@ This command can only be used if LAMMPS was built with the SPIN package. See the "Build package"_Build_package.html doc page for more info. +For magnetic GNEB calculations, only {spin_none} value for {line} keyword can be used +when styles {spin/cg} and {spin/lbfgs} are employed. + :line [Related commands:] diff --git a/doc/src/package.txt b/doc/src/package.txt index edd409a8426d6d7c7ca04d9caea7ee26471ed168..4ecb5d96d0a3f5e2abc1ca73f2bdb33539ab5d4e 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -423,115 +423,115 @@ processes/threads used for LAMMPS. :line -The {kokkos} style invokes settings associated with the use of the -KOKKOS package. - -All of the settings are optional keyword/value pairs. Each has a default -value as listed below. - -The {neigh} keyword determines how neighbor lists are built. A value of -{half} uses a thread-safe variant of half-neighbor lists, the same as -used by most pair styles in LAMMPS, which is the default when running on -CPUs (i.e. the Kokkos CUDA back end is not enabled). - -A value of {full} uses a full neighbor lists and is the default when -running on GPUs. This performs twice as much computation as the {half} -option, however that is often a win because it is thread-safe and -doesn't require atomic operations in the calculation of pair forces. For -that reason, {full} is the default setting for GPUs. However, when -running on CPUs, a {half} neighbor list is the default because it are -often faster, just as it is for non-accelerated pair styles. Similarly, -the {neigh/qeq} keyword determines how neighbor lists are built for "fix -qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of +The {kokkos} style invokes settings associated with the use of the +KOKKOS package. + +All of the settings are optional keyword/value pairs. Each has a default +value as listed below. + +The {neigh} keyword determines how neighbor lists are built. A value of +{half} uses a thread-safe variant of half-neighbor lists, the same as +used by most pair styles in LAMMPS, which is the default when running on +CPUs (i.e. the Kokkos CUDA back end is not enabled). + +A value of {full} uses a full neighbor lists and is the default when +running on GPUs. This performs twice as much computation as the {half} +option, however that is often a win because it is thread-safe and +doesn't require atomic operations in the calculation of pair forces. For +that reason, {full} is the default setting for GPUs. However, when +running on CPUs, a {half} neighbor list is the default because it are +often faster, just as it is for non-accelerated pair styles. Similarly, +the {neigh/qeq} keyword determines how neighbor lists are built for "fix +qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of {neigh/qeq} will match {neigh}. -If the {neigh/thread} keyword is set to {off}, then the KOKKOS package -threads only over atoms. However, for small systems, this may not expose -enough parallelism to keep a GPU busy. When this keyword is set to {on}, -the KOKKOS package threads over both atoms and neighbors of atoms. When -using {neigh/thread} {on}, a full neighbor list must also be used. Using -{neigh/thread} {on} may be slower for large systems, so this this option -is turned on by default only when there are 16K atoms or less owned by -an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled -potentials support this keyword yet, and only thread over atoms. Many -simple pair-wise potentials such as Lennard-Jones do support threading +If the {neigh/thread} keyword is set to {off}, then the KOKKOS package +threads only over atoms. However, for small systems, this may not expose +enough parallelism to keep a GPU busy. When this keyword is set to {on}, +the KOKKOS package threads over both atoms and neighbors of atoms. When +using {neigh/thread} {on}, a full neighbor list must also be used. Using +{neigh/thread} {on} may be slower for large systems, so this this option +is turned on by default only when there are 16K atoms or less owned by +an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled +potentials support this keyword yet, and only thread over atoms. Many +simple pair-wise potentials such as Lennard-Jones do support threading over both atoms and neighbors. -The {newton} keyword sets the Newton flags for pairwise and bonded -interactions to {off} or {on}, the same as the "newton"_newton.html -command allows. The default for GPUs is {off} because this will almost -always give better performance for the KOKKOS package. This means more -computation is done, but less communication. However, when running on -CPUs a value of {on} is the default since it can often be faster, just -as it is for non-accelerated pair styles - -The {binsize} keyword sets the size of bins used to bin atoms in -neighbor list builds. The same value can be set by the "neigh_modify -binsize"_neigh_modify.html command. Making it an option in the package -kokkos command allows it to be set from the command line. The default -value for CPUs is 0.0, which means the LAMMPS default will be used, -which is bins = 1/2 the size of the pairwise cutoff + neighbor skin -distance. This is fine when neighbor lists are built on the CPU. For GPU -builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin -is often faster, which is the default. Note that if you use a -longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction -of KSpace work with a "long-range Coulombic solver"_kspace_style.html -because the GPU is faster at performing pairwise interactions, then this -rule of thumb may give too large a binsize and the default should be -overridden with a smaller value. - -The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} -keywords determine whether the host or device performs the packing and -unpacking of data when communicating per-atom data between processors. -"Exchange" communication happens only on timesteps that neighbor lists -are rebuilt. The data is only for atoms that migrate to new processors. -"Forward" communication happens every timestep. "Reverse" communication -happens every timestep if the {newton} option is on. The data is for -atom coordinates and any other atom properties that needs to be updated +The {newton} keyword sets the Newton flags for pairwise and bonded +interactions to {off} or {on}, the same as the "newton"_newton.html +command allows. The default for GPUs is {off} because this will almost +always give better performance for the KOKKOS package. This means more +computation is done, but less communication. However, when running on +CPUs a value of {on} is the default since it can often be faster, just +as it is for non-accelerated pair styles + +The {binsize} keyword sets the size of bins used to bin atoms in +neighbor list builds. The same value can be set by the "neigh_modify +binsize"_neigh_modify.html command. Making it an option in the package +kokkos command allows it to be set from the command line. The default +value for CPUs is 0.0, which means the LAMMPS default will be used, +which is bins = 1/2 the size of the pairwise cutoff + neighbor skin +distance. This is fine when neighbor lists are built on the CPU. For GPU +builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin +is often faster, which is the default. Note that if you use a +longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction +of KSpace work with a "long-range Coulombic solver"_kspace_style.html +because the GPU is faster at performing pairwise interactions, then this +rule of thumb may give too large a binsize and the default should be +overridden with a smaller value. + +The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} +keywords determine whether the host or device performs the packing and +unpacking of data when communicating per-atom data between processors. +"Exchange" communication happens only on timesteps that neighbor lists +are rebuilt. The data is only for atoms that migrate to new processors. +"Forward" communication happens every timestep. "Reverse" communication +happens every timestep if the {newton} option is on. The data is for +atom coordinates and any other atom properties that needs to be updated for ghost atoms owned by each processor. -The {comm} keyword is simply a short-cut to set the same value for both +The {comm} keyword is simply a short-cut to set the same value for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords. -The value options for all 3 keywords are {no} or {host} or {device}. A -value of {no} means to use the standard non-KOKKOS method of -packing/unpacking data for the communication. A value of {host} means to -use the host, typically a multi-core CPU, and perform the -packing/unpacking in parallel with threads. A value of {device} means to -use the device, typically a GPU, to perform the packing/unpacking +The value options for all 3 keywords are {no} or {host} or {device}. A +value of {no} means to use the standard non-KOKKOS method of +packing/unpacking data for the communication. A value of {host} means to +use the host, typically a multi-core CPU, and perform the +packing/unpacking in parallel with threads. A value of {device} means to +use the device, typically a GPU, to perform the packing/unpacking operation. -The optimal choice for these keywords depends on the input script and -the hardware used. The {no} value is useful for verifying that the -Kokkos-based {host} and {device} values are working correctly. It is the +The optimal choice for these keywords depends on the input script and +the hardware used. The {no} value is useful for verifying that the +Kokkos-based {host} and {device} values are working correctly. It is the default when running on CPUs since it is usually the fastest. -When running on CPUs or Xeon Phi, the {host} and {device} values work -identically. When using GPUs, the {device} value is the default since it -will typically be optimal if all of your styles used in your input -script are supported by the KOKKOS package. In this case data can stay -on the GPU for many timesteps without being moved between the host and -GPU, if you use the {device} value. If your script uses styles (e.g. -fixes) which are not yet supported by the KOKKOS package, then data has -to be move between the host and device anyway, so it is typically faster -to let the host handle communication, by using the {host} value. Using -{host} instead of {no} will enable use of multiple threads to -pack/unpack communicated data. When running small systems on a GPU, -performing the exchange pack/unpack on the host CPU can give speedup +When running on CPUs or Xeon Phi, the {host} and {device} values work +identically. When using GPUs, the {device} value is the default since it +will typically be optimal if all of your styles used in your input +script are supported by the KOKKOS package. In this case data can stay +on the GPU for many timesteps without being moved between the host and +GPU, if you use the {device} value. If your script uses styles (e.g. +fixes) which are not yet supported by the KOKKOS package, then data has +to be move between the host and device anyway, so it is typically faster +to let the host handle communication, by using the {host} value. Using +{host} instead of {no} will enable use of multiple threads to +pack/unpack communicated data. When running small systems on a GPU, +performing the exchange pack/unpack on the host CPU can give speedup since it reduces the number of CUDA kernel launches. -The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When -this keyword is set to {on}, buffers in GPU memory are passed directly -through MPI send/receive calls. This reduces overhead of first copying -the data to the host CPU. However CUDA-aware MPI is not supported on all -systems, which can lead to segmentation faults and would require using a -value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not -available (currently only possible with OpenMPI v2.0.0 or later), then -the {cuda/aware} keyword is automatically set to {off} by default. When -the {cuda/aware} keyword is set to {off} while any of the {comm} -keywords are set to {device}, the value for these {comm} keywords will -be automatically changed to {host}. This setting has no effect if not -running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later +The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When +this keyword is set to {on}, buffers in GPU memory are passed directly +through MPI send/receive calls. This reduces overhead of first copying +the data to the host CPU. However CUDA-aware MPI is not supported on all +systems, which can lead to segmentation faults and would require using a +value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not +available (currently only possible with OpenMPI v2.0.0 or later), then +the {cuda/aware} keyword is automatically set to {off} by default. When +the {cuda/aware} keyword is set to {off} while any of the {comm} +keywords are set to {device}, the value for these {comm} keywords will +be automatically changed to {host}. This setting has no effect if not +running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu" flag is used. @@ -641,16 +641,16 @@ not used, you must invoke the package intel command in your input script or via the "-pk intel" "command-line switch"_Run_options.html. -For the KOKKOS package, the option defaults for GPUs are neigh = full, -neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default -value, comm = device, cuda/aware = on. When LAMMPS can safely detect -that CUDA-aware MPI is not available, the default value of cuda/aware -becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = -half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The -option neigh/thread = on when there are 16K atoms or less on an MPI -rank, otherwise it is "off". These settings are made automatically by -the required "-k on" "command-line switch"_Run_options.html. You can -change them by using the package kokkos command in your input script or +For the KOKKOS package, the option defaults for GPUs are neigh = full, +neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default +value, comm = device, cuda/aware = on. When LAMMPS can safely detect +that CUDA-aware MPI is not available, the default value of cuda/aware +becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = +half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The +option neigh/thread = on when there are 16K atoms or less on an MPI +rank, otherwise it is "off". These settings are made automatically by +the required "-k on" "command-line switch"_Run_options.html. You can +change them by using the package kokkos command in your input script or via the "-pk kokkos command-line switch"_Run_options.html. For the OMP package, the default is Nthreads = 0 and the option diff --git a/doc/src/pair_e3b.txt b/doc/src/pair_e3b.txt index 6d1f992ca15f33aab81c28c0e954f9723207e0d5..832b4719c361934f6f83ad04cfe6ee1b493db1d5 100644 --- a/doc/src/pair_e3b.txt +++ b/doc/src/pair_e3b.txt @@ -20,8 +20,8 @@ If the {preset} keyword is given, no others are needed. Otherwise, all are mandatory except for {neigh}. The {neigh} keyword is always optional. :l {preset} arg = {2011} or {2015} = which set of predefined parameters to use - 2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011 - 2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015 + 2011 = use the potential parameters from "(Tainter 2011)"_#Tainter2011 + 2015 = use the potential parameters from "(Tainter 2015)"_#Tainter2015 {Ea} arg = three-body energy for type A hydrogen bonding interactions (energy units) {Eb} arg = three-body energy for type B hydrogen bonding interactions (energy units) {Ec} arg = three-body energy for type C hydrogen bonding interactions (energy units) diff --git a/doc/src/pair_granular.txt b/doc/src/pair_granular.txt index f16cd9fe0bbfdf623021e3d85ea032aaeac02888..2091163e913299750679f7e8904fd82f71c0f7b1 100644 --- a/doc/src/pair_granular.txt +++ b/doc/src/pair_granular.txt @@ -100,7 +100,7 @@ on particle {i} due to contact with particle {j} is given by: \mathbf\{F\}_\{ne, Hooke\} = k_N \delta_\{ij\} \mathbf\{n\} \end\{equation\} -Where \(\delta = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle +Where \(\delta_\{ij\} = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle overlap, \(R_i, R_j\) are the particle radii, \(\mathbf\{r\}_\{ij\} = \mathbf\{r\}_i - \mathbf\{r\}_j\) is the vector separating the two particle centers (note the i-j ordering so that \(F_\{ne\}\) is @@ -177,7 +177,7 @@ following general form: \end\{equation\} Here, \(\mathbf\{v\}_\{n,rel\} = (\mathbf\{v\}_j - \mathbf\{v\}_i) -\cdot \mathbf\{n\}\) is the component of relative velocity along +\cdot \mathbf\{n\} \mathbf\{n\}\) is the component of relative velocity along \(\mathbf\{n\}\). The optional {damping} keyword to the {pair_coeff} command followed by @@ -299,8 +299,8 @@ the normal damping \(\eta_n\) (see above): \eta_t = -x_\{\gamma,t\} \eta_n \end\{equation\} -The normal damping prefactor \(\eta_n\) is determined by the choice of -the {damping} keyword, as discussed above. Thus, the {damping} +The normal damping prefactor \(\eta_n\) is determined by the choice +of the {damping} keyword, as discussed above. Thus, the {damping} keyword also affects the tangential damping. The parameter \(x_\{\gamma,t\}\) is a scaling coefficient. Several works in the literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009, @@ -308,10 +308,10 @@ literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009, tangential velocity at the point of contact is given by \(\mathbf\{v\}_\{t, rel\} = \mathbf\{v\}_\{t\} - (R_i\Omega_i + R_j\Omega_j) \times \mathbf\{n\}\), where \(\mathbf\{v\}_\{t\} = -\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\), \(\mathbf\{v\}_r = -\mathbf\{v\}_j - \mathbf\{v\}_i\). The direction of the applied force -is \(\mathbf\{t\} = -\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\). +\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\{n\}\), +\(\mathbf\{v\}_r = \mathbf\{v\}_j - \mathbf\{v\}_i\). +The direction of the applied force is \(\mathbf\{t\} = +\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\) . The normal force value \(F_\{n0\}\) used to compute the critical force depends on the form of the contact model. For non-cohesive models @@ -411,8 +411,8 @@ option by an additional factor of {a}, the radius of the contact region. The tan \mathbf\{F\}_t = -min(\mu_t F_\{n0\}, \|-k_t a \mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\} \end\{equation\} -Here, {a} is the radius of the contact region, given by \(a = \delta -R\) for all normal contact models, except for {jkr}, where it is given +Here, {a} is the radius of the contact region, given by \(a =\sqrt\{R\delta\}\) +for all normal contact models, except for {jkr}, where it is given implicitly by \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\), see discussion above. To match the Mindlin solution, one should set \(k_t = 8G\), where \(G\) is the shear modulus, related to Young's modulus @@ -680,7 +680,7 @@ The single() function of these pair styles returns 0.0 for the energy of a pairwise interaction, since energy is not conserved in these dissipative potentials. It also returns only the normal component of the pairwise interaction force. However, the single() function also -calculates 10 extra pairwise quantities. The first 3 are the +calculates 12 extra pairwise quantities. The first 3 are the components of the tangential force between particles I and J, acting on particle I. The 4th is the magnitude of this tangential force. The next 3 (5-7) are the components of the rolling torque acting on @@ -790,4 +790,4 @@ alternative contact force models during inelastic collisions. Powder Technology, 233, 30-46. :link(WaltonPC) -[(Otis R. Walton)] Walton, O.R., Personal Communication +[(Otis R. Walton)] Walton, O.R., Personal Communication diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 5a2623ed890e8a5d810fb757c262d5fd96c4d2bf..b42027aada76ea263da39a0a3fff3beaca29d4c7 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -43,8 +43,8 @@ when the tapper function is turned off. The formula of taper function can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. NOTE: This potential (ILP) is intended for interlayer interactions between two -different layers of graphene. To perform a realistic simulation, this potential -must be used in combination with intralayer potential, such as +different layers of graphene. To perform a realistic simulation, this potential +must be used in combination with intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential. To keep the intralayer properties unaffected, the interlayer interaction within the same layers should be avoided. Hence, each atom has to have a layer diff --git a/doc/src/pair_local_density.txt b/doc/src/pair_local_density.txt new file mode 100644 index 0000000000000000000000000000000000000000..4def63c5fc05c768234e41bccbe98c3ad0b1b803 --- /dev/null +++ b/doc/src/pair_local_density.txt @@ -0,0 +1,207 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style local/density command :h3 + +[Syntax:] + +pair_style style arg :pre + +style = {local/density} +arg = name of file containing tabulated values of local density and the potential :ul + +[Examples:] + +pair_style local/density benzene_water.localdensity.table :pre + +pair_style hybrid/overlay table spline 500 local/density +pair_coeff * * local/density benzene_water.localdensity.table :pre + +[Description:] + +The local density (LD) potential is a mean-field manybody potential, and, in some +sense,a generalization of embedded atom models (EAM). The name "local density +potential" arises from the fact that it assigns an energy to an atom depending +on the number of neighboring atoms of given type around it within a predefined +spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG) +literature suggests that such potentials can be widely useful in capturing +effective multibody forces in a computationally efficient manner so as to +improve the quality of CG models of implicit solvation"(Sanyal1)"_#Sanyal1 and +phase-segregation in liquid mixtures"(Sanyal2)"_#Sanyal2, and provide guidelines +to determine the extent of manybody correlations present in a CG +model."(Rosenberger)"_#Rosenberger The LD potential in LAMMPS is primarily +intended to be used as a corrective potential over traditional pair potentials +in bottom-up CG models, i.e., as a hybrid pair style with +other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). +Because the LD potential is not a pair potential per se, it is implemented +simply as a single auxiliary file with all specifications that will be read +upon initialization. + +NOTE: Thus when used as the only interaction in the system, there is no +corresponding pair_coeff command and when used with other pair styles using the +hybrid/overlay option, the corresponding pair_coeff command must be supplied +* * as placeholders for the atom types. + +:line + +[System with a single CG atom type:] + +A system of a single atom type (e.g., LJ argon) with a single local density (LD) +potential would have an energy given by: + +:c,image(Eqs/pair_local_density_energy.jpg) + +where rho_i is the LD at atom i and F(rho) is similar in spirit to the +embedding function used in EAM potentials. The LD at atom i is given by the sum + +:c,image(Eqs/pair_local_density_ld.jpg) + +where phi is an indicator function that is one at r=0 and zero beyond a cutoff +distance R2. The choice of the functional form of phi is somewhat arbitrary, +but the following piecewise cubic function has proven sufficiently general: +"(Sanyal1)"_#Sanyal1, "(Sanyal2)"_#Sanyal2 "(Rosenberger)"_#Rosenberger + +:c,image(Eqs/pair_local_density_indicator_func.jpg) + +The constants {c} are chosen so that the indicator function smoothly +interpolates between 1 and 0 between the distances R1 and R2, which are +called the inner and outer cutoffs, respectively. Thus phi satisfies +phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) = dphi/dr @ (r=R2) = 0. The embedding +function F(rho) may or may not have a closed-form expression. To maintain +generality, it is practically represented with a spline-interpolated table +over a predetermined range of rho. Outside of that range it simply adopts zero +values at the endpoints. + +It can be shown that the total force between two atoms due to the LD potential +takes the form of a pair force, which motivates its designation as a LAMMPS +pair style. Please see "(Sanyal1)"_#Sanyal1 for details of the derivation. + +:line + +[Systems with arbitrary numbers of atom types:] + +The potential is easily generalized to systems involving multiple atom types: + +:c,image(Eqs/pair_local_density_energy_multi.jpg) + +with the LD expressed as + +:c,image(Eqs/pair_local_density_ld_multi.jpg) + +where alpha gives the type of atom i, beta the type of atom j, and the +coefficients a and b filter for atom types as specified by the user. a is +called the central atom filter as it determines to which atoms the +potential applies; a_alpha = 1 if the LD potential applies to atom type alpha +else zero. On the other hand, b is called the neighbor atom filter because it +specifies which atom types to use in the calculation of the LD; b_beta = 1 if +atom type beta contributes to the LD and zero otherwise. + +NOTE: Note that the potentials need not be symmetric with respect to atom types, +which is the reason for two distinct sets of coefficients a and b. An atom type +may contribute to the LD but not the potential, or to the potential but not the +LD. Such decisions are made by the user and should (ideally) be motivated on +physical grounds for the problem at hand. + +:line + +[General form for implementation in LAMMPS:] + +Of course, a system with many atom types may have many different possible LD +potentials, each with their own atom type filters, cutoffs, and embedding +functions. The most general form of this potential as implemented in the +pair_style local/density is: + +:c,image(Eqs/pair_local_density_energy_implement.jpg) + +where, k is an index that spans the (arbitrary) number of applied LD potentials +N_LD. Each LD is calculated as before with: + +:c,image(Eqs/pair_local_density_ld_implement.jpg) + +The superscript on the indicator function phi simply indicates that it is +associated with specific values of the cutoff distances R1(k) and R2(k). In +summary, there may be N_LD distinct LD potentials. With each potential type (k), +one must specify: + +the inner and outer cutoffs as R1 and R2 +the central type filter a(k), where k = 1,2,...N_LD +the neighbor type filter b(k), where k = 1,2,...N_LD +the LD potential function F(k)(rho), typically as a table that is later spline-interpolated :ul + +:line + +[Tabulated input file format:] + +Line 1: comment or blank (ignored) +Line 2: comment or blank (ignored) +Line 3: N_LD N_rho (# of LD potentials and # of tabulated values, single space separated) +Line 4: blank (ignored) +Line 5: R1(k) R2(k) (lower and upper cutoffs, single space separated) +Line 6: central-types (central atom types, single space separated) +Line 7: neighbor-types (neighbor atom types single space separated) +Line 8: rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated) +Line 9: F(k)(rho_min + 0.drho) +Line 10: F(k)(rho_min + 1.drho) +Line 11: F(k)(rho_min + 2.drho) +... +Line 9+N_rho: F(k)(rho_min + N_rho . drho) +Line 10+N_rho: blank (ignored) :pre + +Block 2 :pre + +Block 3 :pre + +Block N_LD :pre + +Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated +(by blank lines) into N_LD blocks each representing a separate LD potential and +each specifying its own upper and lower cutoffs, central and neighbor atoms, +and potential. In general, blank lines anywhere are ignored. + +:line + +[Mixing, shift, table, tail correction, restart, info]: +This pair style does not support automatic mixing. For atom type pairs alpha, +beta and alpha != beta, even if LD potentials of type (alpha, alpha) and +(beta, beta) are provided, you will need to explicitly provide LD potential +types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha, +beta) means that alpha is the central atom to which the LD potential is applied +and beta is the neighbor atom which contributes to the LD potential on alpha). + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +The local/density pair style does not write its information to "binary restart +files"_restart.html, since it is stored in tabulated potential files. +Thus, you need to re-specify the pair_style and pair_coeff commands in +an input script that reads a restart file. + +:line + +[Restrictions:] + +The local/density pair style is a part of the USER-MISC package. It is only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + + +:link(Sanyal1) +[(Sanyal1)] Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109. +:link(Sanyal2) +[(Sanyal2)] Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693. + +:link(Rosenberger) +[(Rosenberger)] Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111. diff --git a/doc/src/pair_mm3_switch3_coulgauss.txt b/doc/src/pair_mm3_switch3_coulgauss.txt index 3e0e24150e2c1e2a8f11ee8eb085599797ebfc1c..86e6a0d1d986d77785547be99cd5e09b73374f6c 100644 --- a/doc/src/pair_mm3_switch3_coulgauss.txt +++ b/doc/src/pair_mm3_switch3_coulgauss.txt @@ -68,7 +68,7 @@ gamma (distance) :ul [Mixing, shift, table, tail correction, restart, rRESPA info]: -Mixing rules are fixed for this style as defined above. +Mixing rules are fixed for this style as defined above. Shifting the potential energy is not necessary because the switching function ensures that the potential is zero at the cut-off. diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index dfcd93c9a8dd6269c5adc5d91b43ce3187fb873f..8f3f9933e61f6aa46566a4faf6a741e2f22d8836 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -23,7 +23,7 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk} args = list of arguments for these particular styles :ul - {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 + {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) T = temperature (oxDNA units, 0.1 = 300 K) xi = temperature-independent coefficient in stacking strength @@ -36,7 +36,7 @@ args = list of arguments for these particular styles :ul pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -51,7 +51,10 @@ excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacki and coaxial stacking interaction {oxdna/coaxstk} as well as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported "(Sulc)"_#Sulc1. +are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using +more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. +This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +up and down along the backbone. The exact functional form of the pair styles is rather complex. The individual potentials consist of products of modulation factors, diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 3e462f384df006bd7046d3db6d6b9668d313be6f..64a686d5d9766c4c4d5b6ffb16c06ef8f8eb7b38 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -24,11 +24,11 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/ style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh} args = list of arguments for these particular styles :ul - {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 + {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) T = temperature (oxDNA units, 0.1 = 300 K) - xi = temperature-independent coefficient in stacking strength - kappa = coefficient of linear temperature dependence in stacking strength + xi = temperature-independent coefficient in stacking strength + kappa = coefficient of linear temperature dependence in stacking strength {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs) @@ -41,7 +41,7 @@ args = list of arguments for these particular styles :ul pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -57,7 +57,10 @@ excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stac and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh} as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported "(Sulc)"_#Sulc2. +are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using +more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. +This prevents the hybridization of in principle complementary bases within Ntypes/4 bases +up and down along the backbone. The exact functional form of the pair styles is rather complex. The individual potentials consist of products of modulation factors, diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index 1fba74a188b6424d2a50b86d83bb52afd7b49bb8..37d1a1ed18a3d5c49faf6f79f3672129e4160ba5 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -50,7 +50,7 @@ the SNAP potential files themselves. Only a single pair_coeff command is used with the {snap} style which specifies a SNAP coefficient file followed by a SNAP parameter file and then N additional arguments specifying the mapping of SNAP -elements to LAMMPS atom types, where N is the number of +elements to LAMMPS atom types, where N is the number of LAMMPS atom types: SNAP coefficient file @@ -79,7 +79,7 @@ The name of the SNAP coefficient file usually ends in the ".snapcoeff" extension. It may contain coefficients for many SNAP elements. The only requirement is that it contain at least those element names appearing in the -LAMMPS mapping list. +LAMMPS mapping list. The name of the SNAP parameter file usually ends in the ".snapparam" extension. It contains a small number of parameters that define the overall form of the SNAP potential. diff --git a/doc/src/pair_spin_dipole.txt b/doc/src/pair_spin_dipole.txt index 0d6471e07fc26bd961ed05ff0b93d74d7cb2be54..36bcd25d5ee2a136be99274b088936ed436a2e12 100644 --- a/doc/src/pair_spin_dipole.txt +++ b/doc/src/pair_spin_dipole.txt @@ -11,7 +11,7 @@ pair_style spin/dipole/long command :h3 [Syntax:] -pair_style spin/dipole/cut cutoff +pair_style spin/dipole/cut cutoff pair_style spin/dipole/long cutoff :pre cutoff = global cutoff for magnetic dipole energy and forces @@ -21,35 +21,34 @@ cutoff = global cutoff for magnetic dipole energy and forces [Examples:] pair_style spin/dipole/cut 10.0 -pair_coeff * * 10.0 +pair_coeff * * 10.0 pair_coeff 2 3 8.0 :pre pair_style spin/dipole/long 9.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5 -pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre +pair_coeff * * 10.0 +pair_coeff 2 3 6.0 :pre [Description:] Style {spin/dipole/cut} computes a short-range dipole-dipole -interaction between pairs of magnetic particles that each -have a magnetic spin. +interaction between pairs of magnetic particles that each +have a magnetic spin. The magnetic dipole-dipole interactions are computed by the -following formulas for the magnetic energy, magnetic precession +following formulas for the magnetic energy, magnetic precession vector omega and mechanical force between particles I and J. :c,image(Eqs/pair_spin_dipole.jpg) -where si and sj are the spin on two magnetic particles, -r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj| -is the direction vector between the two particles. +where si and sj are the spin on two magnetic particles, +r is their separation distance, and the vector e = (Ri - Rj)/|Ri - Rj| +is the direction vector between the two particles. Style {spin/dipole/long} computes long-range magnetic dipole-dipole interaction. A "kspace_style"_kspace_style.html must be defined to -use this pair style. Currently, "kspace_style +use this pair style. Currently, "kspace_style ewald/dipole/spin"_kspace_style.html and "kspace_style -pppm/dipole/spin"_kspace_style.html support long-range magnetic +pppm/dipole/spin"_kspace_style.html support long-range magnetic dipole-dipole interactions. :line @@ -68,8 +67,8 @@ to be specified in an input script that reads a restart file. [Restrictions:] The {spin/dipole/cut} and {spin/dipole/long} styles are part of -the SPIN package. They are only enabled if LAMMPS was built with that -package. See the "Build package"_Build_package.html doc page for more +the SPIN package. They are only enabled if LAMMPS was built with that +package. See the "Build package"_Build_package.html doc page for more info. Using dipole/spin pair styles with {electron} "units"_units.html is not diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt index 9ddff8a8dc850dbd5267a7229bee5878641cf159..cca20d1136870df6b882da9c4145b32c0352d230 100644 --- a/doc/src/pair_spin_dmi.txt +++ b/doc/src/pair_spin_dmi.txt @@ -15,11 +15,11 @@ pair_style spin/dmi cutoff :pre cutoff = global cutoff pair (distance in metal units) :ulb,l :ule - + [Examples:] pair_style spin/dmi 4.0 -pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0 +pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0 pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre [Description:] diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index 009ef7947d422b5e73ce0c56e47841530f338897..b255f23a09e8833dfd67df0b7b37c9e33135ff89 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -15,7 +15,7 @@ pair_style spin/neel cutoff :pre cutoff = global cutoff pair (distance in metal units) :ulb,l :ule - + [Examples:] pair_style spin/neel 4.0 diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 1b8e6d46ec308f138e0ba0b3e094aa580b5600f3..7ba982cd2dc05857cb1cf8672a1ae98f9b9c0092 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -228,6 +228,7 @@ accelerated styles exist. "lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential "lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential +"local/density"_pair_local_density.html - generalized basic local density potential "lubricate"_pair_lubricate.html - hydrodynamic lubrication forces "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt index b324003bd1ca252e6ecaa8a341219dfb11d521cd..def28b68560497c94d8883e20cd71a754cb6edcc 100644 --- a/doc/src/pair_zero.txt +++ b/doc/src/pair_zero.txt @@ -71,9 +71,8 @@ This pair style writes its information to "binary restart files"_restart.html, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. +This pair style supports the use of the {inner}, {middle}, +and {outer} keywords of the "run_style respa"_run_style.html command. :line diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index f36a87dea3c868fd0bc5fcb92462445aed07f3fc..1f8f130e48d429feca355647902e16d28ec27437 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -66,6 +66,7 @@ Pair Styles :h1 pair_lj_smooth pair_lj_smooth_linear pair_lj_switch3_coulgauss + pair_local_density pair_lubricate pair_lubricateU pair_mdf diff --git a/doc/src/temper.txt b/doc/src/temper.txt index edd578fbc93449e4d3eb3e0c4fb15dad6bad507f..6a61dfa6dd7f91946df8274b91645ca619098af3 100644 --- a/doc/src/temper.txt +++ b/doc/src/temper.txt @@ -110,7 +110,13 @@ the information from the log.lammps file. E.g. you could produce one dump file with snapshots at 300K (from all replicas), another with snapshots at 310K, etc. Note that these new dump files will not contain "continuous trajectories" for individual atoms, because two -successive snapshots (in time) may be from different replicas. +successive snapshots (in time) may be from different replicas. The +reorder_remd_traj python script can do the reordering for you +(and additionally also calculated configurational log-weights of +trajectory snapshots in the canonical ensemble). The script can be found +in the tools/replica directory while instructions on how to use it is +available in doc/Tools (in brief) and as a README file in tools/replica +(in detail). The last argument {index} in the temper command is optional and is used when restarting a tempering run from a set of restart files (one diff --git a/doc/src/third_order.txt b/doc/src/third_order.txt new file mode 100644 index 0000000000000000000000000000000000000000..9636ec830e8c0be6410ff337aa705819d5bfc022 --- /dev/null +++ b/doc/src/third_order.txt @@ -0,0 +1,62 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +third_order command :h3 + +[Syntax:] + +third_order group-ID style delta args keyword value ... :pre + +group-ID = ID of group of atoms to displace :ulb,l +style = {regular} or {eskm} :l +delta = finite different displacement length (distance units) :l +one or more keyword/arg pairs may be appended :l + keyword = {file} or {binary} + {file} name = name of output file for the third order tensor + {binary} arg = {yes} or {no} or {gzip} :pre +:ule + +[Examples:] + +third_order 1 regular 0.000001 +third_order 1 eskm 0.000001 +third_order 3 regular 0.00004 file third_order.dat +third_order 5 eskm 0.00000001 file third_order.dat binary yes :pre + +[Description:] + +Calculate the third order force constant tensor by finite difference of the selected group, + +:c,image(JPG/third_order_force_constant.png)) + +where Phi is the third order force constant tensor. + +The output of the command is the tensor, three elements at a time. The +three elements correspond to the three gamma elements for a specific i/alpha/j/beta/k. +The initial five numbers are i, alpha, j, beta, and k respectively. + +If the style eskm is selected, the tensor will be using energy units of 10 J/mol. +These units conform to eskm style from the dynamical_matrix command, which +will simplify operations using dynamical matrices with third order tensors. + +[Restrictions:] + +The command collects a 9 times the number of atoms in the group on every single MPI rank, +so the memory requirements can be very significant for large systems. + +This command is part of the USER-PHONON package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"fix phonon"_fix_phonon.html "dynamical_matrix"_dynamical_matrix.html + +[Default:] + +The default settings are file = "third_order.dat", binary = no diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py index 29de3af156395eb74cf17ac557a91f8d93e73045..727a5f76121f28084fbc61209c218039ffbb072e 100644 --- a/doc/utils/sphinx-config/conf.py +++ b/doc/utils/sphinx-config/conf.py @@ -30,7 +30,7 @@ import os # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.mathjax', + 'sphinx.ext.mathjax', 'sphinx.ext.imgmath' ] # 2017-12-07: commented out, since this package is broken with Sphinx 16.x # yet we can no longer use Sphinx 15.x, since that breaks with @@ -201,6 +201,11 @@ htmlhelp_basename = 'LAMMPSdoc' html_add_permalinks = '' +if 'epub' in sys.argv: + html_math_renderer = 'imgmath' +else: + html_math_renderer = 'mathjax' + # -- Options for LaTeX output --------------------------------------------- latex_elements = { diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 6d5112b4c735839fa37ac1ef723c2cdf608f6883..4028750fb55210c7b4d11cc36a92954703bdb1c0 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -71,6 +71,7 @@ AlO Alonso amap Amatrix +AMD amino Amirjalayer Amit @@ -108,6 +109,7 @@ Archlinux arcsin arg args +arrhenius Arun arXiv asin @@ -275,10 +277,12 @@ Broadwell Broglie brownian brownw +Broyden Bryantsev Btarget btype buckPlusAttr +builtin Bulatov Bureekaew burlywood @@ -305,6 +309,7 @@ Cavium Cawkwell cbecker ccache +ccachepiecewise ccmake ccNspecies CCu @@ -516,6 +521,7 @@ Dasgupta dashpot dat datafile +datatype datums Davidchack Daw @@ -622,6 +628,7 @@ Doye dpd DPD dpdTheta +dphi DPhil dr dR @@ -778,6 +785,7 @@ erotate Ertas ervel Espanol +eskm esu esub esw @@ -986,6 +994,7 @@ gmask Gmask gneb GNEB +Goldfarb googlemail Gordan GPa @@ -1403,6 +1412,7 @@ Laupretre lavenderblush lawngreen lB +lbfgs lbl LBtype lcbop @@ -1503,6 +1513,7 @@ logfreq logicals Lomdahl Lond +lookup lookups Lookups LoopVar @@ -1576,6 +1587,7 @@ Materias mathbf matlab matplotlib +Mattice Mattox Mattson maxangle @@ -2028,6 +2040,7 @@ openmp openmpi opls Oppelstrup +optimizations orangered organometallic orientational @@ -2039,12 +2052,12 @@ Orsi ortho orthonormal orthorhombic +oso ot Otype Ouldridge outfile outmost -outpur outputss Ouyang overlayed @@ -2124,6 +2137,7 @@ ph Phillpot phiphi phonon +phonons phophorous phosphide Phs @@ -2137,6 +2151,7 @@ picograms picosecond picoseconds pid +piecewise Pieniazek Pieter pimd @@ -2239,6 +2254,7 @@ Py pydir pylammps PyLammps +pymbar pymodule pymol pypar @@ -2269,6 +2285,7 @@ qoffload qopenmp qoverride qtb +quadratically quadrupolar Quant quartic @@ -2325,6 +2342,7 @@ reinit relink relTol remappings +remd Ren Rendon reneighbor @@ -2417,6 +2435,7 @@ Rodrigues Rohart Ronchetti Rosati +Rosenberger Rossky rosybrown rotationally @@ -2456,6 +2475,7 @@ Sandia sandybrown Sanitizer sanitizers +Sanyal sc scafacos SCAFACOS @@ -2476,10 +2496,12 @@ Schulten Schunk Schuring Schwen +screenshots Scripta sdk sdpd SDPD +se seagreen Secor sectoring @@ -2506,6 +2528,7 @@ setvel sfftw Sg Shan +Shanno shapex shapey shapez @@ -2573,6 +2596,7 @@ Snodin Sodani Soderlind solvated +solvation Sorensen soundspeed Souza @@ -2689,6 +2713,8 @@ Tajkhorshid Tamaskovics Tanaka tanh +tanmoy +Tanmoy Tartakovsky taskset taubi @@ -2931,6 +2957,7 @@ vectorial vectorization Vectorization vectorized +Vegt vel Verlag verlet diff --git a/examples/README b/examples/README index dbfdb3363b159cb29787ba9197a6a67fc92ad058..47463a85d8a03c9c9f57513aa7683c20cd4f8143 100644 --- a/examples/README +++ b/examples/README @@ -76,6 +76,7 @@ ellipse: ellipsoidal particles in spherical solvent, 2d system flow: Couette and Poiseuille flow in a 2d channel friction: frictional contact of spherical asperities between 2d surfaces gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command +gjf: use of fix langevin Gronbech-Jensen/Farago option granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics hyper: global and local hyperdynamics of diffusion on Pt surface @@ -99,12 +100,12 @@ pour: pouring of granular particles into a 3d box, then chute flow prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration -reax: RDX and TATB models using the ReaxFF +reax: RDX and TATB and several other models using ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void -snap: use of SNAP potential for Ta +snap: examples for using several bundled SNAP potentials srd: stochastic rotation dynamics (SRD) particles as solvent -snap: NVE dynamics for BCC tantalum crystal using SNAP potential +steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom streitz: Streitz-Mintmire potential for Al2O3 tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si threebody: regression test input for a variety of manybody potentials @@ -163,6 +164,12 @@ The MC directory has an example script for using LAMMPS as an energy-evaluation engine in a iterative Monte Carlo energy-relaxation loop. +The UNITS directory contains examples of input scripts modeling the +same Lennard-Jones liquid model, written in 3 different unit systems: +lj, real, and metal. So that you can see how to scale/unscale input +and output values read/written by LAMMPS to verify you are performing +the same simulation in different unit systems. + The USER directory contains subdirectories of user-provided example scripts for ser packages. See the README files in those directories for more info. See the doc/Section_start.html file for more info diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo index e3c88b0f0668a73073e72afd908dd647dc7ddbdc..2cd92001217a15e336b126a7614d221acbd66427 100644 --- a/examples/SPIN/bfo/in.spin.bfo +++ b/examples/SPIN/bfo/in.spin.bfo @@ -32,7 +32,7 @@ neigh_modify every 10 check yes delay 20 fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 fix 2 all langevin/spin 0.0 0.1 21 -fix 3 all nve/spin lattice no +fix 3 all nve/spin lattice frozen timestep 0.0002 diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc index ea98eeba94184b614add63f49a76991a5d907da4..9193faa798b822c4c2c342fed90a43b2f680d11a 100644 --- a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc +++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc @@ -35,7 +35,7 @@ fix_modify 1 energy yes fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp index 3f3483855368a19b10105471009c6bca7eb88e73..b9ede5f09cd722c15ba80eba72ff998cbd2d611d 100644 --- a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp +++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp @@ -37,7 +37,7 @@ neigh_modify every 10 check yes delay 20 fix 1 all precession/spin anisotropy 0.01 0.0 0.0 1.0 #fix 2 all langevin/spin 0.0 0.0 21 fix 2 all langevin/spin 0.0 0.1 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut b/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut index a409fe05639b07780db98a5b3e7affae56ee505e..34f7fea0d3961c9af442f9224c0fdaa96a01b9db 100644 --- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut +++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_cut @@ -33,7 +33,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1 fix_modify 1 energy yes fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald b/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald index 58b44b55fe0362a826ab7fccf1796f6403205026..f694bc5ddcead8a83879fefa2bc5a980d68d7369 100644 --- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald +++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald @@ -35,7 +35,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1 fix_modify 1 energy yes fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm b/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm index 28d7e4a4bc0bdac60778aba65e4833c5af4af917..4175038ade539d06f4d37945f234cefd7e673bfb 100644 --- a/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm +++ b/examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm @@ -36,7 +36,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1 fix_modify 1 energy yes fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron index bb1b0e1b4d4305d9fcb1c4d5eca4d86b4ba5efae..3468575493b280317d288cb0e8ddef132371cc1e 100644 --- a/examples/SPIN/iron/in.spin.iron +++ b/examples/SPIN/iron/in.spin.iron @@ -33,7 +33,7 @@ neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/iron/in.spin.iron_cubic b/examples/SPIN/iron/in.spin.iron_cubic index d4703a2959179a52699aa86ae6eed9d3d1351ca1..859d9df0fab2b70fc9ce8a3c4ac9f5ce69776a25 100644 --- a/examples/SPIN/iron/in.spin.iron_cubic +++ b/examples/SPIN/iron/in.spin.iron_cubic @@ -31,7 +31,7 @@ fix 1 all precession/spin cubic 0.001 0.0005 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1 fix_modify 1 energy yes fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel index 0ed2fac410d43cbdb87b464616383f3c9825bc24..caa1c940aed014b5193d112ef0755c5cc25f6f54 100644 --- a/examples/SPIN/nickel/in.spin.nickel +++ b/examples/SPIN/nickel/in.spin.nickel @@ -33,7 +33,7 @@ neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/nickel/in.spin.nickel_cubic b/examples/SPIN/nickel/in.spin.nickel_cubic index 3c97b284ae88d2d5b9e8a1eadbbf9cb487cde692..76ea23689af83a1fbee24a840f4dc8dabf386ac3 100644 --- a/examples/SPIN/nickel/in.spin.nickel_cubic +++ b/examples/SPIN/nickel/in.spin.nickel_cubic @@ -35,7 +35,7 @@ fix 1 all precession/spin cubic -0.0001 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1. fix_modify 1 energy yes fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # compute and output options diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data index a4504216990d1850bd2ef65eb9e769a6c1613f9d..e788ecf67eff4657a0cc7270178fd4fd59b0fddf 100644 --- a/examples/SPIN/read_restart/in.spin.read_data +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -20,7 +20,7 @@ neigh_modify every 1 check no delay 0 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # define outputs and computes diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart index 39157fdac42f8104a2c37bd4eff125925a43b158..ccce25b2544a664875c98ac4e1db1e666fe1eb49 100644 --- a/examples/SPIN/read_restart/in.spin.restart +++ b/examples/SPIN/read_restart/in.spin.restart @@ -24,7 +24,7 @@ neigh_modify every 1 check no delay 0 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 fix 2 all langevin/spin 0.0 0.0 21 -fix 3 all nve/spin lattice yes +fix 3 all nve/spin lattice moving timestep 0.0001 # define outputs diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart index 42f07fd316b61bb1989b4affa85007a85be6c13c..c1271010937f37f2051240e4055b831657ef2987 100644 --- a/examples/SPIN/read_restart/in.spin.write_restart +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -29,7 +29,7 @@ neigh_modify every 10 check yes delay 20 fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 fix 2 all langevin/spin 100.0 0.01 21 -fix 3 all nve/spin lattice no +fix 3 all nve/spin lattice frozen timestep 0.0001 # compute and output options diff --git a/examples/SPIN/setforce_spin/in.spinmin.setforce b/examples/SPIN/setforce_spin/in.spinmin.setforce index 10d4df66edd8968e79d831ad5bc4cd2a05a54232..822768e0efadb2e91246b3a72fa5bc66743ef101 100644 --- a/examples/SPIN/setforce_spin/in.spinmin.setforce +++ b/examples/SPIN/setforce_spin/in.spinmin.setforce @@ -35,7 +35,7 @@ fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 fix_modify 1 energy yes fix 2 fixed_spin setforce/spin 0.0 0.0 0.0 fix 3 all langevin/spin 0.0 0.1 21 -fix 4 all nve/spin lattice no +fix 4 all nve/spin lattice frozen timestep 0.0001 diff --git a/examples/SPIN/spinmin/in.spinmin_cg.bfo b/examples/SPIN/spinmin/in.spinmin_cg.bfo new file mode 100644 index 0000000000000000000000000000000000000000..9d57399a5652a84b0e9b90ffb8a393ddc568c0af --- /dev/null +++ b/examples/SPIN/spinmin/in.spinmin_cg.bfo @@ -0,0 +1,54 @@ +# bfo in a 3d periodic box + +units metal +dimension 3 +boundary p p f +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 1.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 1.0 +set group all spin/random 11 2.50 + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +# pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 +pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0 +pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix_modify 1 energy yes + +timestep 0.0001 + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 100 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +min_style spin/cg +# min_modify line spin_none discrete_factor 10.0 +minimize 1.0e-10 1.0e-10 10000 10000 diff --git a/examples/SPIN/spinmin/in.spinmin_lbfgs.bfo b/examples/SPIN/spinmin/in.spinmin_lbfgs.bfo new file mode 100644 index 0000000000000000000000000000000000000000..56cd6b8faed2ee43c8fe7056f924f1b8115e05d6 --- /dev/null +++ b/examples/SPIN/spinmin/in.spinmin_lbfgs.bfo @@ -0,0 +1,55 @@ +# bfo in a 3d periodic box + +units metal +dimension 3 +boundary p p f +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 1.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 1.0 +set group all spin/random 11 2.50 + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +#pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 +pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0 +pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix_modify 1 energy yes + +timestep 0.0001 + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 50 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +min_style spin/lbfgs +# min_modify line spin_cubic discrete_factor 10.0 +min_modify norm max +minimize 1.0e-15 1.0e-10 10000 1000 diff --git a/examples/UNITS/README b/examples/UNITS/README new file mode 100644 index 0000000000000000000000000000000000000000..3980b3868860944a76d7ce397756ba140ebb757f --- /dev/null +++ b/examples/UNITS/README @@ -0,0 +1,54 @@ +This directory has 3 scripts which show how to run the same problem +using the 3 most common units system used in LAMMPS: lj, real, and +metal units. As stated on the units command doc page: + +"Any simulation you perform for one choice of units can be duplicated +with any other unit setting LAMMPS supports. ... To perform the same +simulation in a different set of units you must change all the +unit-based input parameters in your input script and other input files +(data file, potential files, etc) correctly to the new units. And you +must correctly convert all output from the new units to the old units +when comparing to the original results. That is often not simple to +do." + +These examples are meant to illustrate how to do this for a simple +Lennard-Jones liquid (argon). All of the scripts have a set of +variables defined at the top which can be changed as command line +arguments (e.g. -v cutoff 3.0). All 3 scripts give identical output, +modulo round-offs due to the finite precision of the conversion +factors used, either internally in LAMMPS or in the scripts. If there +were run for a long time, the trajectories would diverge, but they +would still give statistically identical results. + +The LJ script is the simplest; it is similar to the bench/in.lj +script. + +The real and metal scripts each have a set of variables at the top +which define scale factors for converting quantities like distance, +energy, pressure from reduced LJ units to real or metal units. Once +these are defined the rest of the input script is very similar to the +LJ script. The approprate scale factor is applied to every input. +Output quantities are printed in both the native real/metal units and +unscaled back to LJ units. So that you can see the outputs are the +same if you examine the log files. Comments about this comparison +are at the bottom of the real and metal scripts. + +These 3 scripts are provided, because converting from lj reduced units +to physical units (e.g. real or metal) or vice versa is the trickiest +case. Converting input scripts between 2 sets of physical units +(e.g. reak <--> metal) is much easier. But you can use the same ideas +as in these scripts; just define a set of scale/unscale factors. + +See Allen & Tildesley's Computer Simulation of Liquids, Appendix B for +a nice discussion of reduced units. It will explain the conversion +formulas used in the real and metal scripts. + +Hopefully, if you study these scripts, you should be able to convert +an input script of your own, written in one set of units, to an +identical input script in an alternate set of units. Where +"identical" means it runs the same simulation in a statistical sense. + +You can find the full set of scale factors LAMMPS uses internally for +different unit systems it supports, at the top of the src/udpate.cpp +file. A couple of those values are used in the real and metal +scripts. diff --git a/examples/UNITS/in.ar.lj b/examples/UNITS/in.ar.lj new file mode 100644 index 0000000000000000000000000000000000000000..264ead8ab8ba03e33702a77903f094cd48207d17 --- /dev/null +++ b/examples/UNITS/in.ar.lj @@ -0,0 +1,43 @@ +# Ar in lj units + +# simulation params in reduced units +# settable from command line +# epsilon = sigma = mass = 1.0 + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# script + +units lj +atom_style atomic + +lattice fcc ${rhostar} +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +velocity all create ${tinitial} 12345 + +pair_style lj/cut ${cutoff} +pair_coeff 1 1 1.0 1.0 + +neighbor ${skin} bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep ${dt} + +thermo 10 + +run 100 diff --git a/examples/UNITS/in.ar.metal b/examples/UNITS/in.ar.metal new file mode 100644 index 0000000000000000000000000000000000000000..50f105530ec128785cdb7e94c2ab3ef9bd788758 --- /dev/null +++ b/examples/UNITS/in.ar.metal @@ -0,0 +1,98 @@ +# Ar in metal units + +# simulation params in reduced units +# settable from command line +# epsilon, sigma, mass set below + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# physical constants from update.cpp + +variable kb index 8.617343e-5 # kB in eV/K +variable avogadro index 6.02214129e23 # Avogadro's number + +# Ar properties in metal units + +variable epskb index 117.7 # LJ epsilon/kB in degrees K +variable sigma index 3.504 # LJ sigma in Angstroms +variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV +variable mass index 39.95 # mass in g/mole + +# scale factors + +# sigma = scale factor on distance, converts reduced distance to Angs +# epsilon = scale factor on energy, converts reduced energy to eV +# tmpscale = scale factor on temperature, converts reduced temp to degrees K +# tscale = scale factor on time, converts reduced time to ps +# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs +# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds +# pscale = scale factor on pressure, converts reduced pressure to bars +# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres +# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars + +variable eVtoJoule index 1.602e-19 # convert eV to Joules +variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars + +variable tmpscale equal ${epskb} +variable epsilonJ equal ${epsilon}*${eVtoJoule} +variable massKgAtom equal ${mass}/1000.0/${avogadro} +variable sigmaM equal ${sigma}/1.0e10 +variable sigmaMsq equal ${sigmaM}*${sigmaM} +variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq}) +variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} +variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ})) + +# variables +# alat = lattice constant in Angs (at reduced density rhostar) +# temp = reduced temperature for output +# epair,emol,etotal = reduced epair,emol,etotal energies for output +# press = reduced pressure for output + +variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable temp equal temp/${tmpscale} +variable epair equal epair/${epsilon} +variable emol equal emol/${epsilon} +variable etotal equal etotal/${epsilon} +variable press equal press/${pscale} + +# same script as in.ar.lj + +units metal +atom_style atomic + +lattice fcc ${alat} +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 ${mass} + +velocity all create $(v_tinitial*v_epskb) 12345 + +pair_style lj/cut $(v_cutoff*v_sigma) +pair_coeff 1 1 ${epsilon} ${sigma} + +neighbor $(v_skin*v_sigma) bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep $(v_dt*v_tscale) + +# columns 2,3,4 = temp,pe,press in metal units +# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj +# need to include metal unit output to enable use of reduced variables + +thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press +thermo_modify norm yes +thermo ${nthermo} + +run ${nsteps} diff --git a/examples/UNITS/in.ar.real b/examples/UNITS/in.ar.real new file mode 100644 index 0000000000000000000000000000000000000000..ea9670e5996219f844fd04ecb0ddcbd31b3314ac --- /dev/null +++ b/examples/UNITS/in.ar.real @@ -0,0 +1,98 @@ +# Ar in real units + +# simulation params in reduced units +# settable from command line +# epsilon, sigma, mass set below + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# physical constants from update.cpp + +variable kb index 0.0019872067 # kB in Kcal/mole/K +variable avogadro index 6.02214129e23 # Avogadro's number + +# Ar properties in real units + +variable epskb index 117.7 # LJ epsilon/kB in degrees K +variable sigma index 3.504 # LJ sigma in Angstroms +variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole +variable mass index 39.95 # mass in g/mole + +# scale factors + +# sigma = scale factor on distance, converts reduced distance to Angs +# epsilon = scale factor on energy, converts reduced energy to Kcal/mole +# tmpscale = scale factor on temperature, converts reduced temp to degrees K +# tscale = scale factor on time, converts reduced time to fs +# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs +# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds +# pscale = scale factor on pressure, converts reduced pressure to atmospheres +# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres +# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms + +variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules +variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres + +variable tmpscale equal ${epskb} +variable epsJmole equal ${epsilon}*${KcaltoJoule} +variable massKgmole equal ${mass}/1000.0 +variable sigmaM equal ${sigma}/1.0e10 +variable sigmaMsq equal ${sigmaM}*${sigmaM} +variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq}) +variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} +variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro})) + +# variables +# alat = lattice constant in Angs (at reduced density rhostar) +# temp = reduced temperature for output +# epair,emol,etotal = reduced epair,emol,etotal energies for output +# press = reduced pressure for output + +variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable temp equal temp/${tmpscale} +variable epair equal epair/${epsilon} +variable emol equal emol/${epsilon} +variable etotal equal etotal/${epsilon} +variable press equal press/${pscale} + +# same script as in.ar.lj + +units real +atom_style atomic + +lattice fcc ${alat} +region box block 0 $x 0 $y 0 $z +create_box 1 box +create_atoms 1 box +mass 1 ${mass} + +velocity all create $(v_tinitial*v_epskb) 12345 + +pair_style lj/cut $(v_cutoff*v_sigma) +pair_coeff 1 1 ${epsilon} ${sigma} + +neighbor $(v_skin*v_sigma) bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep $(v_dt*v_tscale) + +# columns 2,3,4 = temp,pe,press in real units +# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj +# need to include real unit output to enable use of reduced variables + +thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press +thermo_modify norm yes +thermo ${nthermo} + +run ${nsteps} diff --git a/examples/UNITS/log.ar.lj.8Oct19.g++.1 b/examples/UNITS/log.ar.lj.8Oct19.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..39c3143cf566e0626e144a70575fbe469ae8be65 --- /dev/null +++ b/examples/UNITS/log.ar.lj.8Oct19.g++.1 @@ -0,0 +1,109 @@ +LAMMPS (19 Sep 2019) +# Ar in lj units + +# simulation params in reduced units +# settable from command line +# epsilon = sigma = mass = 1.0 + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# script + +units lj +atom_style atomic + +lattice fcc ${rhostar} +lattice fcc 0.8842 +Lattice spacing in x,y,z = 1.65388 1.65388 1.65388 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.26938 8.26938 8.26938) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000547171 secs +mass 1 1.0 + +velocity all create ${tinitial} 12345 +velocity all create 1.0 12345 + +pair_style lj/cut ${cutoff} +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +neighbor ${skin} bin +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep ${dt} +timestep 0.005 + +thermo 10 + +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -7.1026383 0 -5.6056383 -5.1224757 + 10 0.74213042 -6.7245488 0 -5.6135795 -3.1363153 + 20 0.36167746 -6.1681704 0 -5.6267393 -0.40461854 + 30 0.4684512 -6.3315744 0 -5.630303 -1.0390065 + 40 0.46774191 -6.3308002 0 -5.6305906 -1.077533 + 50 0.48323399 -6.3533122 0 -5.6299109 -1.1506287 + 60 0.49569105 -6.3711644 0 -5.6291149 -1.2296104 + 70 0.5208333 -6.4096336 0 -5.6299462 -1.4483636 + 80 0.53708431 -6.4345933 0 -5.6305781 -1.5945708 + 90 0.52618946 -6.4185937 0 -5.6308881 -1.5264055 + 100 0.52862701 -6.4231724 0 -5.6318178 -1.5714077 +Loop time of 0.065218 on 1 procs for 100 steps with 500 atoms + +Performance: 662394.104 tau/day, 1533.320 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.053584 | 0.053584 | 0.053584 | 0.0 | 82.16 +Neigh | 0.0075939 | 0.0075939 | 0.0075939 | 0.0 | 11.64 +Comm | 0.0022638 | 0.0022638 | 0.0022638 | 0.0 | 3.47 +Output | 0.00021172 | 0.00021172 | 0.00021172 | 0.0 | 0.32 +Modify | 0.0011077 | 0.0011077 | 0.0011077 | 0.0 | 1.70 +Other | | 0.0004568 | | | 0.70 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1946 ave 1946 max 1946 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19572 ave 19572 max 19572 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19572 +Ave neighs/atom = 39.144 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/UNITS/log.ar.lj.8Oct19.g++.4 b/examples/UNITS/log.ar.lj.8Oct19.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..dba5ffb66a9c783439166a47fddd5c87c47da480 --- /dev/null +++ b/examples/UNITS/log.ar.lj.8Oct19.g++.4 @@ -0,0 +1,109 @@ +LAMMPS (19 Sep 2019) +# Ar in lj units + +# simulation params in reduced units +# settable from command line +# epsilon = sigma = mass = 1.0 + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# script + +units lj +atom_style atomic + +lattice fcc ${rhostar} +lattice fcc 0.8842 +Lattice spacing in x,y,z = 1.65388 1.65388 1.65388 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (8.26938 8.26938 8.26938) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000570774 secs +mass 1 1.0 + +velocity all create ${tinitial} 12345 +velocity all create 1.0 12345 + +pair_style lj/cut ${cutoff} +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +neighbor ${skin} bin +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep ${dt} +timestep 0.005 + +thermo 10 + +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -7.1026383 0 -5.6056383 -5.1224757 + 10 0.73621446 -6.7154544 0 -5.6133413 -3.089257 + 20 0.35775263 -6.1618707 0 -5.626315 -0.37875949 + 30 0.47139877 -6.3359656 0 -5.6302816 -1.1018761 + 40 0.46337135 -6.3247084 0 -5.6310415 -1.0985336 + 50 0.48738877 -6.360393 0 -5.630772 -1.2274707 + 60 0.50832261 -6.3913892 0 -5.6304302 -1.374293 + 70 0.50988271 -6.3936997 0 -5.6304053 -1.4112286 + 80 0.53931444 -6.4367444 0 -5.6293906 -1.6484686 + 90 0.55277272 -6.4563334 0 -5.6288326 -1.760598 + 100 0.54916776 -6.4507537 0 -5.6286495 -1.728837 +Loop time of 0.0237499 on 4 procs for 100 steps with 500 atoms + +Performance: 1818955.951 tau/day, 4210.546 timesteps/s +97.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0098808 | 0.011585 | 0.015043 | 1.9 | 48.78 +Neigh | 0.0015168 | 0.0017335 | 0.001997 | 0.4 | 7.30 +Comm | 0.005949 | 0.0097297 | 0.011739 | 2.3 | 40.97 +Output | 0.00019789 | 0.0002324 | 0.00032282 | 0.0 | 0.98 +Modify | 0.00021482 | 0.00025994 | 0.00031853 | 0.0 | 1.09 +Other | | 0.0002095 | | | 0.88 + +Nlocal: 125 ave 133 max 117 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 1099 ave 1107 max 1091 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 4909 ave 5493 max 4644 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 19636 +Ave neighs/atom = 39.272 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/UNITS/log.ar.metal.8Oct19.g++.1 b/examples/UNITS/log.ar.metal.8Oct19.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..8bcf54f6edae34b150c08f87c87d0963986700a5 --- /dev/null +++ b/examples/UNITS/log.ar.metal.8Oct19.g++.1 @@ -0,0 +1,197 @@ +LAMMPS (19 Sep 2019) +# Ar in metal units + +# simulation params in reduced units +# settable from command line +# epsilon, sigma, mass set below + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# physical constants from update.cpp + +variable kb index 8.617343e-5 # kB in eV/K +variable avogadro index 6.02214129e23 # Avogadro's number + +# Ar properties in metal units + +variable epskb index 117.7 # LJ epsilon/kB in degrees K +variable sigma index 3.504 # LJ sigma in Angstroms +variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV +variable epsilon equal 117.7*${kb} +variable epsilon equal 117.7*8.617343e-5 +variable mass index 39.95 # mass in g/mole + +# scale factors + +# sigma = scale factor on distance, converts reduced distance to Angs +# epsilon = scale factor on energy, converts reduced energy to eV +# tmpscale = scale factor on temperature, converts reduced temp to degrees K +# tscale = scale factor on time, converts reduced time to ps +# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs +# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds +# pscale = scale factor on pressure, converts reduced pressure to bars +# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres +# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars + +variable eVtoJoule index 1.602e-19 # convert eV to Joules +variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars + +variable tmpscale equal ${epskb} +variable tmpscale equal 117.7 +variable epsilonJ equal ${epsilon}*${eVtoJoule} +variable epsilonJ equal 0.010142612711*${eVtoJoule} +variable epsilonJ equal 0.010142612711*1.602e-19 +variable massKgAtom equal ${mass}/1000.0/${avogadro} +variable massKgAtom equal 39.95/1000.0/${avogadro} +variable massKgAtom equal 39.95/1000.0/6.02214129e23 +variable sigmaM equal ${sigma}/1.0e10 +variable sigmaM equal 3.504/1.0e10 +variable sigmaMsq equal ${sigmaM}*${sigmaM} +variable sigmaMsq equal 3.504e-10*${sigmaM} +variable sigmaMsq equal 3.504e-10*3.504e-10 +variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq}) +variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq}) +variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq}) +variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19) +variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10 +variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ})) +variable pscale equal 1e-05/(${sigmaM3}/(${epsilonJ})) +variable pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ})) +variable pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21)) + +# variables +# alat = lattice constant in Angs (at reduced density rhostar) +# temp = reduced temperature for output +# epair,emol,etotal = reduced epair,emol,etotal energies for output +# press = reduced pressure for output + +variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0) +variable temp equal temp/${tmpscale} +variable temp equal temp/117.7 +variable epair equal epair/${epsilon} +variable epair equal epair/0.010142612711 +variable emol equal emol/${epsilon} +variable emol equal emol/0.010142612711 +variable etotal equal etotal/${epsilon} +variable etotal equal etotal/0.010142612711 +variable press equal press/${pscale} +variable press equal press/377.676586146256 + +# same script as in.ar.lj + +units metal +atom_style atomic + +lattice fcc ${alat} +lattice fcc 5.79518437579763 +Lattice spacing in x,y,z = 5.79518 5.79518 5.79518 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000549078 secs +mass 1 ${mass} +mass 1 39.95 + +velocity all create $(v_tinitial*v_epskb) 12345 +velocity all create 117.70000000000000284 12345 + +pair_style lj/cut $(v_cutoff*v_sigma) +pair_style lj/cut 8.7599999999999997868 +pair_coeff 1 1 ${epsilon} ${sigma} +pair_coeff 1 1 0.010142612711 ${sigma} +pair_coeff 1 1 0.010142612711 3.504 + +neighbor $(v_skin*v_sigma) bin +neighbor 1.0511999999999999122 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep $(v_dt*v_tscale) +timestep 0.011194658410003900315 + +# columns 2,3,4 = temp,pe,press in metal units +# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj +# need to include metal unit output to enable use of reduced variables + +thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press +thermo_modify norm yes +thermo ${nthermo} +thermo 10 + +run ${nsteps} +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9.8112 + ghost atom cutoff = 9.8112 + binsize = 4.9056, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes +Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press + 0 117.7 -0.07203931 -1934.8523 1 -7.1026383 0 -5.6056383 -5.12304 + 10 87.345225 -0.06820404 -1184.5618 0.74210047 -6.724504 0 -5.6135796 -3.1364449 + 20 42.569809 -0.062561408 -152.82812 0.36168062 -6.1681748 0 -5.6267389 -0.40465341 + 30 55.137637 -0.064219154 -392.49645 0.46845911 -6.3316185 0 -5.6303352 -1.0392396 + 40 55.053014 -0.064210828 -406.99941 0.46774014 -6.3307976 0 -5.6305906 -1.07764 + 50 56.87723 -0.064439241 -434.61958 0.483239 -6.3533177 0 -5.6299089 -1.1507718 + 60 58.344019 -0.064620383 -464.4684 0.4957011 -6.3711772 0 -5.6291126 -1.2298046 + 70 61.30301 -0.065010529 -547.09852 0.5208412 -6.4096433 0 -5.629944 -1.44859 + 80 63.214836 -0.065263563 -602.29599 0.53708442 -6.4345909 0 -5.6305755 -1.5947401 + 90 61.931826 -0.065101194 -576.5342 0.52618374 -6.4185823 0 -5.6308852 -1.5265288 + 100 62.221816 -0.065148028 -593.59878 0.52864755 -6.4231998 0 -5.6318144 -1.5717119 +Loop time of 0.04864 on 1 procs for 100 steps with 500 atoms + +Performance: 1988.524 ns/day, 0.012 hours/ns, 2055.921 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.039802 | 0.039802 | 0.039802 | 0.0 | 81.83 +Neigh | 0.0057771 | 0.0057771 | 0.0057771 | 0.0 | 11.88 +Comm | 0.0015905 | 0.0015905 | 0.0015905 | 0.0 | 3.27 +Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.69 +Modify | 0.00077343 | 0.00077343 | 0.00077343 | 0.0 | 1.59 +Other | | 0.0003595 | | | 0.74 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1946 ave 1946 max 1946 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19572 ave 19572 max 19572 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19572 +Ave neighs/atom = 39.144 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/UNITS/log.ar.metal.8Oct19.g++.4 b/examples/UNITS/log.ar.metal.8Oct19.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..5a88231128f0e9f4447795e3a75980121b147f21 --- /dev/null +++ b/examples/UNITS/log.ar.metal.8Oct19.g++.4 @@ -0,0 +1,197 @@ +LAMMPS (19 Sep 2019) +# Ar in metal units + +# simulation params in reduced units +# settable from command line +# epsilon, sigma, mass set below + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# physical constants from update.cpp + +variable kb index 8.617343e-5 # kB in eV/K +variable avogadro index 6.02214129e23 # Avogadro's number + +# Ar properties in metal units + +variable epskb index 117.7 # LJ epsilon/kB in degrees K +variable sigma index 3.504 # LJ sigma in Angstroms +variable epsilon equal ${epskb}*${kb} # LJ epsilon in eV +variable epsilon equal 117.7*${kb} +variable epsilon equal 117.7*8.617343e-5 +variable mass index 39.95 # mass in g/mole + +# scale factors + +# sigma = scale factor on distance, converts reduced distance to Angs +# epsilon = scale factor on energy, converts reduced energy to eV +# tmpscale = scale factor on temperature, converts reduced temp to degrees K +# tscale = scale factor on time, converts reduced time to ps +# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs +# use epsilon (Joule), mass (kg/atom), sigma (meter) to get t in seconds +# pscale = scale factor on pressure, converts reduced pressure to bars +# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres +# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to bars + +variable eVtoJoule index 1.602e-19 # convert eV to Joules +variable NtMtoAtm equal 1.0e-5 # convert Nt/meter^2 to bars + +variable tmpscale equal ${epskb} +variable tmpscale equal 117.7 +variable epsilonJ equal ${epsilon}*${eVtoJoule} +variable epsilonJ equal 0.010142612711*${eVtoJoule} +variable epsilonJ equal 0.010142612711*1.602e-19 +variable massKgAtom equal ${mass}/1000.0/${avogadro} +variable massKgAtom equal 39.95/1000.0/${avogadro} +variable massKgAtom equal 39.95/1000.0/6.02214129e23 +variable sigmaM equal ${sigma}/1.0e10 +variable sigmaM equal 3.504/1.0e10 +variable sigmaMsq equal ${sigmaM}*${sigmaM} +variable sigmaMsq equal 3.504e-10*${sigmaM} +variable sigmaMsq equal 3.504e-10*3.504e-10 +variable tscale equal 1.0e12/sqrt(${epsilonJ}/${massKgAtom}/${sigmaMsq}) +variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/${massKgAtom}/${sigmaMsq}) +variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/${sigmaMsq}) +variable tscale equal 1.0e12/sqrt(1.6248465563022e-21/6.6338529895236e-26/1.2278016e-19) +variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10 +variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsilonJ})) +variable pscale equal 1e-05/(${sigmaM3}/(${epsilonJ})) +variable pscale equal 1e-05/(4.3022168064e-29/(${epsilonJ})) +variable pscale equal 1e-05/(4.3022168064e-29/(1.6248465563022e-21)) + +# variables +# alat = lattice constant in Angs (at reduced density rhostar) +# temp = reduced temperature for output +# epair,emol,etotal = reduced epair,emol,etotal energies for output +# press = reduced pressure for output + +variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0) +variable temp equal temp/${tmpscale} +variable temp equal temp/117.7 +variable epair equal epair/${epsilon} +variable epair equal epair/0.010142612711 +variable emol equal emol/${epsilon} +variable emol equal emol/0.010142612711 +variable etotal equal etotal/${epsilon} +variable etotal equal etotal/0.010142612711 +variable press equal press/${pscale} +variable press equal press/377.676586146256 + +# same script as in.ar.lj + +units metal +atom_style atomic + +lattice fcc ${alat} +lattice fcc 5.79518437579763 +Lattice spacing in x,y,z = 5.79518 5.79518 5.79518 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000674009 secs +mass 1 ${mass} +mass 1 39.95 + +velocity all create $(v_tinitial*v_epskb) 12345 +velocity all create 117.70000000000000284 12345 + +pair_style lj/cut $(v_cutoff*v_sigma) +pair_style lj/cut 8.7599999999999997868 +pair_coeff 1 1 ${epsilon} ${sigma} +pair_coeff 1 1 0.010142612711 ${sigma} +pair_coeff 1 1 0.010142612711 3.504 + +neighbor $(v_skin*v_sigma) bin +neighbor 1.0511999999999999122 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep $(v_dt*v_tscale) +timestep 0.011194658410003900315 + +# columns 2,3,4 = temp,pe,press in metal units +# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj +# need to include metal unit output to enable use of reduced variables + +thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press +thermo_modify norm yes +thermo ${nthermo} +thermo 10 + +run ${nsteps} +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9.8112 + ghost atom cutoff = 9.8112 + binsize = 4.9056, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes +Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press + 0 117.7 -0.07203931 -1934.8523 1 -7.1026383 0 -5.6056383 -5.12304 + 10 86.648851 -0.06811179 -1166.7855 0.73618395 -6.7154088 0 -5.6133414 -3.0893774 + 20 42.107954 -0.062497536 -143.06615 0.35775662 -6.1618774 0 -5.6263157 -0.37880598 + 30 55.484504 -0.064263032 -416.20245 0.47140615 -6.3359445 0 -5.6302495 -1.1020075 + 40 54.538222 -0.064148334 -414.88071 0.46336637 -6.3246361 0 -5.6309766 -1.0985079 + 50 57.367693 -0.064511259 -463.67683 0.48740606 -6.3604182 0 -5.6307714 -1.2277087 + 60 59.828794 -0.064824938 -519.05997 0.50831601 -6.3913451 0 -5.630396 -1.3743504 + 70 60.014616 -0.064848979 -533.07604 0.50989478 -6.3937154 0 -5.6304029 -1.4114617 + 80 63.47861 -0.065285885 -622.71073 0.53932549 -6.4367917 0 -5.6294215 -1.6487936 + 90 65.060881 -0.065484011 -664.99883 0.55276874 -6.4563257 0 -5.6288309 -1.7607627 + 100 64.637033 -0.065427467 -653.00765 0.54916765 -6.4507508 0 -5.6286468 -1.7290128 +Loop time of 0.0258265 on 4 procs for 100 steps with 500 atoms + +Performance: 3745.060 ns/day, 0.006 hours/ns, 3871.990 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0090213 | 0.012419 | 0.015494 | 2.1 | 48.09 +Neigh | 0.0013709 | 0.0018765 | 0.0022483 | 0.7 | 7.27 +Comm | 0.0071132 | 0.010597 | 0.014538 | 2.6 | 41.03 +Output | 0.00039983 | 0.00042897 | 0.00049567 | 0.0 | 1.66 +Modify | 0.00024104 | 0.00028801 | 0.00031543 | 0.0 | 1.12 +Other | | 0.0002173 | | | 0.84 + +Nlocal: 125 ave 133 max 117 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 1099 ave 1107 max 1091 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 4908.75 ave 5492 max 4644 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 19635 +Ave neighs/atom = 39.27 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/UNITS/log.ar.real.8Oct19.g++.1 b/examples/UNITS/log.ar.real.8Oct19.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..7c046ab965339cf8e0cf0c03b0ae5334e033c02b --- /dev/null +++ b/examples/UNITS/log.ar.real.8Oct19.g++.1 @@ -0,0 +1,197 @@ +LAMMPS (19 Sep 2019) +# Ar in real units + +# simulation params in reduced units +# settable from command line +# epsilon, sigma, mass set below + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# physical constants from update.cpp + +variable kb index 0.0019872067 # kB in Kcal/mole/K +variable avogadro index 6.02214129e23 # Avogadro's number + +# Ar properties in real units + +variable epskb index 117.7 # LJ epsilon/kB in degrees K +variable sigma index 3.504 # LJ sigma in Angstroms +variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole +variable epsilon equal 117.7*${kb} +variable epsilon equal 117.7*0.0019872067 +variable mass index 39.95 # mass in g/mole + +# scale factors + +# sigma = scale factor on distance, converts reduced distance to Angs +# epsilon = scale factor on energy, converts reduced energy to Kcal/mole +# tmpscale = scale factor on temperature, converts reduced temp to degrees K +# tscale = scale factor on time, converts reduced time to fs +# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs +# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds +# pscale = scale factor on pressure, converts reduced pressure to atmospheres +# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres +# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms + +variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules +variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres + +variable tmpscale equal ${epskb} +variable tmpscale equal 117.7 +variable epsJmole equal ${epsilon}*${KcaltoJoule} +variable epsJmole equal 0.23389422859*${KcaltoJoule} +variable epsJmole equal 0.23389422859*4.1868e3 +variable massKgmole equal ${mass}/1000.0 +variable massKgmole equal 39.95/1000.0 +variable sigmaM equal ${sigma}/1.0e10 +variable sigmaM equal 3.504/1.0e10 +variable sigmaMsq equal ${sigmaM}*${sigmaM} +variable sigmaMsq equal 3.504e-10*${sigmaM} +variable sigmaMsq equal 3.504e-10*3.504e-10 +variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq}) +variable tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq}) +variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq}) +variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19) +variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10 +variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro})) +variable pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro})) +variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro})) +variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro})) +variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23)) + +# variables +# alat = lattice constant in Angs (at reduced density rhostar) +# temp = reduced temperature for output +# epair,emol,etotal = reduced epair,emol,etotal energies for output +# press = reduced pressure for output + +variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0) +variable temp equal temp/${tmpscale} +variable temp equal temp/117.7 +variable epair equal epair/${epsilon} +variable epair equal epair/0.23389422859 +variable emol equal emol/${epsilon} +variable emol equal emol/0.23389422859 +variable etotal equal etotal/${epsilon} +variable etotal equal etotal/0.23389422859 +variable press equal press/${pscale} +variable press equal press/372.936366301003 + +# same script as in.ar.lj + +units real +atom_style atomic + +lattice fcc ${alat} +lattice fcc 5.79518437579763 +Lattice spacing in x,y,z = 5.79518 5.79518 5.79518 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000550985 secs +mass 1 ${mass} +mass 1 39.95 + +velocity all create $(v_tinitial*v_epskb) 12345 +velocity all create 117.70000000000000284 12345 + +pair_style lj/cut $(v_cutoff*v_sigma) +pair_style lj/cut 8.7599999999999997868 +pair_coeff 1 1 ${epsilon} ${sigma} +pair_coeff 1 1 0.23389422859 ${sigma} +pair_coeff 1 1 0.23389422859 3.504 + +neighbor $(v_skin*v_sigma) bin +neighbor 1.0511999999999999122 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep $(v_dt*v_tscale) +timestep 11.190297512378050371 + +# columns 2,3,4 = temp,pe,press in real units +# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj +# need to include real unit output to enable use of reduced variables + +thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press +thermo_modify norm yes +thermo ${nthermo} +thermo 10 + +run ${nsteps} +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9.8112 + ghost atom cutoff = 9.8112 + binsize = 4.9056, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes +Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press + 0 117.7 -1.6612661 -1909.5509 1 -7.1026383 0 -5.6056383 -5.1203128 + 10 87.369977 -1.5728967 -1169.6414 0.74231077 -6.7248204 0 -5.6135812 -3.1363029 + 20 42.567295 -1.4427006 -150.87379 0.36165926 -6.1681752 0 -5.6267713 -0.40455638 + 30 55.130978 -1.480902 -387.17817 0.46840253 -6.3315028 0 -5.6303042 -1.0381883 + 40 55.054202 -1.4807485 -401.72653 0.46775023 -6.3308469 0 -5.6306248 -1.0771986 + 50 56.873955 -1.4860029 -428.9126 0.48321117 -6.3533113 0 -5.6299442 -1.1500959 + 60 58.33701 -1.490161 -458.23636 0.49564154 -6.3710892 0 -5.6291138 -1.2287253 + 70 61.29671 -1.4991528 -539.72484 0.52078768 -6.4095331 0 -5.629914 -1.4472304 + 80 63.214984 -1.504992 -594.34987 0.53708567 -6.4344983 0 -5.630481 -1.5937032 + 90 61.936907 -1.5013008 -569.13985 0.5262269 -6.4187169 0 -5.6309552 -1.5261045 + 100 62.20662 -1.5023046 -585.49121 0.52851844 -6.4230083 0 -5.6318162 -1.5699494 +Loop time of 0.047307 on 1 procs for 100 steps with 500 atoms + +Performance: 2043.760 ns/day, 0.012 hours/ns, 2113.851 timesteps/s +98.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.038646 | 0.038646 | 0.038646 | 0.0 | 81.69 +Neigh | 0.0056832 | 0.0056832 | 0.0056832 | 0.0 | 12.01 +Comm | 0.0015347 | 0.0015347 | 0.0015347 | 0.0 | 3.24 +Output | 0.0003581 | 0.0003581 | 0.0003581 | 0.0 | 0.76 +Modify | 0.00075364 | 0.00075364 | 0.00075364 | 0.0 | 1.59 +Other | | 0.0003314 | | | 0.70 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1946 ave 1946 max 1946 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19572 ave 19572 max 19572 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19572 +Ave neighs/atom = 39.144 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/UNITS/log.ar.real.8Oct19.g++.4 b/examples/UNITS/log.ar.real.8Oct19.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..d5c01eb22d73b15e0a5680620d3b147c19d605be --- /dev/null +++ b/examples/UNITS/log.ar.real.8Oct19.g++.4 @@ -0,0 +1,197 @@ +LAMMPS (19 Sep 2019) +# Ar in real units + +# simulation params in reduced units +# settable from command line +# epsilon, sigma, mass set below + +variable x index 5 +variable y index 5 +variable z index 5 +variable rhostar index 0.8842 +variable dt index 0.005 +variable cutoff index 2.5 +variable skin index 0.3 +variable tinitial index 1.0 +variable nthermo index 10 +variable nsteps index 100 + +# physical constants from update.cpp + +variable kb index 0.0019872067 # kB in Kcal/mole/K +variable avogadro index 6.02214129e23 # Avogadro's number + +# Ar properties in real units + +variable epskb index 117.7 # LJ epsilon/kB in degrees K +variable sigma index 3.504 # LJ sigma in Angstroms +variable epsilon equal ${epskb}*${kb} # LJ epsilon in Kcal/mole +variable epsilon equal 117.7*${kb} +variable epsilon equal 117.7*0.0019872067 +variable mass index 39.95 # mass in g/mole + +# scale factors + +# sigma = scale factor on distance, converts reduced distance to Angs +# epsilon = scale factor on energy, converts reduced energy to Kcal/mole +# tmpscale = scale factor on temperature, converts reduced temp to degrees K +# tscale = scale factor on time, converts reduced time to fs +# formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs +# use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds +# pscale = scale factor on pressure, converts reduced pressure to atmospheres +# formula is P = P* / (sigma^3/epsilon), but need P in atmospheres +# use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms + +variable KcaltoJoule index 4.1868e3 # convert Kcals to Joules +variable NtMtoAtm equal 1.0/1.0135e5 # convert Nt/meter^2 to Atmospheres + +variable tmpscale equal ${epskb} +variable tmpscale equal 117.7 +variable epsJmole equal ${epsilon}*${KcaltoJoule} +variable epsJmole equal 0.23389422859*${KcaltoJoule} +variable epsJmole equal 0.23389422859*4.1868e3 +variable massKgmole equal ${mass}/1000.0 +variable massKgmole equal 39.95/1000.0 +variable sigmaM equal ${sigma}/1.0e10 +variable sigmaM equal 3.504/1.0e10 +variable sigmaMsq equal ${sigmaM}*${sigmaM} +variable sigmaMsq equal 3.504e-10*${sigmaM} +variable sigmaMsq equal 3.504e-10*3.504e-10 +variable tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq}) +variable tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq}) +variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq}) +variable tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19) +variable sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM} +variable sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10 +variable pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro})) +variable pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro})) +variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro})) +variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro})) +variable pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23)) + +# variables +# alat = lattice constant in Angs (at reduced density rhostar) +# temp = reduced temperature for output +# epair,emol,etotal = reduced epair,emol,etotal energies for output +# press = reduced pressure for output + +variable alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0) +variable alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0) +variable temp equal temp/${tmpscale} +variable temp equal temp/117.7 +variable epair equal epair/${epsilon} +variable epair equal epair/0.23389422859 +variable emol equal emol/${epsilon} +variable emol equal emol/0.23389422859 +variable etotal equal etotal/${epsilon} +variable etotal equal etotal/0.23389422859 +variable press equal press/${pscale} +variable press equal press/372.936366301003 + +# same script as in.ar.lj + +units real +atom_style atomic + +lattice fcc ${alat} +lattice fcc 5.79518437579763 +Lattice spacing in x,y,z = 5.79518 5.79518 5.79518 +region box block 0 $x 0 $y 0 $z +region box block 0 5 0 $y 0 $z +region box block 0 5 0 5 0 $z +region box block 0 5 0 5 0 5 +create_box 1 box +Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + create_atoms CPU = 0.000664949 secs +mass 1 ${mass} +mass 1 39.95 + +velocity all create $(v_tinitial*v_epskb) 12345 +velocity all create 117.70000000000000284 12345 + +pair_style lj/cut $(v_cutoff*v_sigma) +pair_style lj/cut 8.7599999999999997868 +pair_coeff 1 1 ${epsilon} ${sigma} +pair_coeff 1 1 0.23389422859 ${sigma} +pair_coeff 1 1 0.23389422859 3.504 + +neighbor $(v_skin*v_sigma) bin +neighbor 1.0511999999999999122 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +timestep $(v_dt*v_tscale) +timestep 11.190297512378050371 + +# columns 2,3,4 = temp,pe,press in real units +# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj +# need to include real unit output to enable use of reduced variables + +thermo_style custom step temp pe press v_temp v_epair v_emol v_etotal v_press +thermo_modify norm yes +thermo ${nthermo} +thermo 10 + +run ${nsteps} +run 100 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9.8112 + ghost atom cutoff = 9.8112 + binsize = 4.9056, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes +Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press + 0 117.7 -1.6612661 -1909.5509 1 -7.1026383 0 -5.6056383 -5.1203128 + 10 86.674156 -1.5707707 -1152.1077 0.73639895 -6.715731 0 -5.6133417 -3.0892877 + 20 42.104452 -1.4412091 -141.16344 0.35772687 -6.1617986 0 -5.6262815 -0.37851883 + 30 55.478223 -1.4819221 -410.58592 0.47135278 -6.3358644 0 -5.6302493 -1.1009544 + 40 54.54231 -1.4793231 -409.58446 0.4634011 -6.3247524 0 -5.631041 -1.098269 + 50 57.354168 -1.4876242 -457.34719 0.48729115 -6.3602431 0 -5.6307682 -1.2263411 + 60 59.835295 -1.4949249 -512.38519 0.50837124 -6.391457 0 -5.6304252 -1.3739212 + 70 60.005554 -1.4954174 -525.858 0.50981779 -6.3935625 0 -5.6303653 -1.4100475 + 80 63.469566 -1.505493 -614.29111 0.53924865 -6.4366403 0 -5.6293851 -1.6471741 + 90 65.064012 -1.5100983 -656.32951 0.55279535 -6.4563301 0 -5.6287955 -1.7598968 + 100 64.63774 -1.5088033 -644.51211 0.54917366 -6.4507932 0 -5.6286803 -1.7282093 +Loop time of 0.0285767 on 4 procs for 100 steps with 500 atoms + +Performance: 3383.318 ns/day, 0.007 hours/ns, 3499.350 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.012398 | 0.014826 | 0.016774 | 1.6 | 51.88 +Neigh | 0.001797 | 0.0021547 | 0.0025899 | 0.6 | 7.54 +Comm | 0.0079622 | 0.010444 | 0.013427 | 2.3 | 36.55 +Output | 0.00042987 | 0.00047708 | 0.00059676 | 0.0 | 1.67 +Modify | 0.00028896 | 0.00038844 | 0.00049448 | 0.0 | 1.36 +Other | | 0.0002864 | | | 1.00 + +Nlocal: 125 ave 133 max 117 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 1099 ave 1107 max 1091 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 4908.75 ave 5493 max 4644 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 19635 +Ave neighs/atom = 39.27 +Neighbor list builds = 5 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 index 34e17380afaef39952565afb4832da4a79a1dbe8..254c551f4e990f1934ba0dc91d64dc9987b7ee7f 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 @@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525 # oxDNA pair interactions pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..3a4b84bffd832e1eef7d157a9e618fe7f82f080d --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.1 @@ -0,0 +1,1166 @@ +LAMMPS (7 Aug 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 9.5e-05 secs + read_data CPU = 0.001865 secs + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.956 + ghost atom cutoff = 1.956 + binsize = 0.978, bins = 41 41 41 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685) +Per MPI rank memory allocation (min/avg/max) = 2.836 | 2.836 | 2.836 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 +1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 +2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 +3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 +4000 ekin = 0.0173888111295073 | erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436 +5000 ekin = 0.0264744514136619 | erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104 +6000 ekin = 0.0369277948556079 | erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875 +7000 ekin = 0.04839505571915 | erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172 +8000 ekin = 0.0604909336920643 | erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611 +9000 ekin = 0.0728137406440561 | erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514 +10000 ekin = 0.0849615563085878 | erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398 +11000 ekin = 0.0965486715045649 | erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229 +12000 ekin = 0.10722146628289 | erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598 +13000 ekin = 0.116672809719548 | erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627 +14000 ekin = 0.12465407373104 | erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151 +15000 ekin = 0.13098393968427 | erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544 +16000 ekin = 0.135553354544872 | erot = 0.669086028489761 | epot = -15.447072628815 | etot = -14.6424332457804 +17000 ekin = 0.138326263958247 | erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935 +18000 ekin = 0.139336096664052 | erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954 +19000 ekin = 0.138678360045177 | erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878 +20000 ekin = 0.136500074655373 | erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773 +21000 ekin = 0.132987065285671 | erot = 0.864912408452581 | epot = -15.6403327194916 | etot = -14.6424332457533 +22000 ekin = 0.128350288213556 | erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311 +23000 ekin = 0.122812385135508 | erot = 0.917661024683965 | epot = -15.6829066555277 | etot = -14.6424332457083 +24000 ekin = 0.116595521408284 | erot = 0.938759014332098 | epot = -15.6977877814267 | etot = -14.6424332456863 +25000 ekin = 0.109911323474816 | erot = 0.956471207347239 | epot = -15.7088157764882 | etot = -14.6424332456662 +26000 ekin = 0.102953426207644 | erot = 0.970893163953205 | epot = -15.7162798358091 | etot = -14.6424332456483 +27000 ekin = 0.0958928250746637 | erot = 0.982114250194058 | epot = -15.7204403209013 | etot = -14.6424332456325 +28000 ekin = 0.0888759410950343 | erot = 0.990219731539854 | epot = -15.7215289182535 | etot = -14.6424332456186 +29000 ekin = 0.0820250748773376 | erot = 0.995296041202929 | epot = -15.719754361686 | etot = -14.6424332456058 +30000 ekin = 0.0754407616839748 | erot = 0.997437949320997 | epot = -15.7153119565981 | etot = -14.6424332455932 +31000 ekin = 0.0692054432610605 | erot = 0.996756332762286 | epot = -15.7083950216035 | etot = -14.6424332455802 +32000 ekin = 0.0633878377978472 | erot = 0.993385345349225 | epot = -15.699206428713 | etot = -14.6424332455659 +33000 ekin = 0.0580474070871663 | erot = 0.987487973309971 | epot = -15.6879686259471 | etot = -14.64243324555 +34000 ekin = 0.0532383791888181 | erot = 0.979259192921751 | epot = -15.6749308176426 | etot = -14.642433245532 +35000 ekin = 0.0490128758307997 | erot = 0.968926197407229 | epot = -15.66037231875 | etot = -14.642433245512 +36000 ekin = 0.0454228081410748 | erot = 0.956745409625975 | epot = -15.6446014632576 | etot = -14.6424332454906 +37000 ekin = 0.0425203357176439 | erot = 0.942996238000726 | epot = -15.6279498191869 | etot = -14.6424332454685 +38000 ekin = 0.0403568280949571 | erot = 0.927971766616668 | epot = -15.6107618401582 | etot = -14.6424332454465 +39000 ekin = 0.0389804214212713 | erot = 0.911966804110017 | epot = -15.5933804709572 | etot = -14.642433245426 +40000 ekin = 0.0384324238856427 | erot = 0.895263959562923 | epot = -15.5761296288567 | etot = -14.6424332454081 +41000 ekin = 0.0387429860408528 | erot = 0.878118672838279 | epot = -15.5592949042733 | etot = -14.6424332453942 +42000 ekin = 0.0399266053637511 | erot = 0.860744395135508 | epot = -15.5431042458848 | etot = -14.6424332453855 +43000 ekin = 0.0419781561011213 | erot = 0.843299365355989 | epot = -15.52771076684 | etot = -14.6424332453829 +44000 ekin = 0.0448701894086714 | erot = 0.82587660331255 | epot = -15.5131800381078 | etot = -14.6424332453866 +45000 ekin = 0.0485521857411517 | erot = 0.808498758184885 | epot = -15.4994841893228 | etot = -14.6424332453968 +46000 ekin = 0.0529522094031971 | erot = 0.791119212186815 | epot = -15.4865046670025 | etot = -14.6424332454125 +47000 ekin = 0.0579809824236746 | erot = 0.773630265882156 | epot = -15.4740444937379 | etot = -14.6424332454321 +48000 ekin = 0.0635377846493077 | erot = 0.755878310836116 | epot = -15.4618493409392 | etot = -14.6424332454537 +49000 ekin = 0.069516912445729 | erot = 0.737684732482671 | epot = -15.4496348904037 | etot = -14.6424332454753 +50000 ekin = 0.0758129058454751 | erot = 0.718870126218106 | epot = -15.4371162775587 | etot = -14.6424332454952 +51000 ekin = 0.0823226638641914 | erot = 0.699278599518873 | epot = -15.4240345088949 | etot = -14.6424332455118 +52000 ekin = 0.0889431481334987 | erot = 0.678798807098492 | epot = -15.4101752007567 | etot = -14.6424332455248 +53000 ekin = 0.0955646689255783 | erot = 0.657379086770007 | epot = -15.3953770012299 | etot = -14.6424332455343 +54000 ekin = 0.102061477509349 | erot = 0.635035489168657 | epot = -15.3795302122191 | etot = -14.6424332455411 +55000 ekin = 0.108282960174 | erot = 0.611853171347175 | epot = -15.362569377067 | etot = -14.6424332455459 +56000 ekin = 0.114049426281782 | erot = 0.587982945924791 | epot = -15.344465617755 | etot = -14.6424332455484 +57000 ekin = 0.119155806186855 | erot = 0.56363525592402 | epot = -15.3252243076595 | etot = -14.6424332455486 +58000 ekin = 0.123384552305435 | erot = 0.539073355224031 | epot = -15.3048911530747 | etot = -14.6424332455452 +59000 ekin = 0.126526300954941 | erot = 0.514606324860987 | epot = -15.2835658713528 | etot = -14.6424332455369 +60000 ekin = 0.128404399836503 | erot = 0.490581338842511 | epot = -15.2614189842015 | etot = -14.6424332455224 +61000 ekin = 0.128898142362337 | erot = 0.467373892403714 | epot = -15.2387052802675 | etot = -14.6424332455015 +62000 ekin = 0.127959880290302 | erot = 0.445374820089113 | epot = -15.2157679458544 | etot = -14.6424332454749 +63000 ekin = 0.125622870624954 | erot = 0.424973765390048 | epot = -15.1930298814588 | etot = -14.6424332454438 +64000 ekin = 0.121999044843202 | erot = 0.406539918574853 | epot = -15.1709722088285 | etot = -14.6424332454104 +65000 ekin = 0.117268056619303 | erot = 0.390401831022836 | epot = -15.1501031330193 | etot = -14.6424332453771 +66000 ekin = 0.111660385257243 | erot = 0.376828594081003 | epot = -15.1309222246847 | etot = -14.6424332453465 +67000 ekin = 0.105437746905135 | erot = 0.366014539812687 | epot = -15.1138855320383 | etot = -14.6424332453205 +68000 ekin = 0.0988737375607857 | erot = 0.358069014156216 | epot = -15.0993759970176 | etot = -14.6424332453006 +69000 ekin = 0.0922368286502244 | erot = 0.353011948772493 | epot = -15.0876820227105 | etot = -14.6424332452877 +70000 ekin = 0.0857769015274457 | erot = 0.350775174164874 | epot = -15.0789853209744 | etot = -14.6424332452821 +71000 ekin = 0.0797156921642124 | erot = 0.35120884424483 | epot = -15.0733577816925 | etot = -14.6424332452834 +72000 ekin = 0.0742409440406404 | erot = 0.354092037745959 | epot = -15.0707662270775 | etot = -14.6424332452909 +73000 ekin = 0.069503749870144 | erot = 0.359146526959529 | epot = -15.0710835221333 | etot = -14.6424332453037 +74000 ekin = 0.0656184497423043 | erot = 0.36605276987658 | epot = -15.0741044649392 | etot = -14.6424332453203 +75000 ekin = 0.0626644690389273 | erot = 0.37446729003154 | epot = -15.07956500441 | etot = -14.6424332453395 +76000 ekin = 0.0606895535086071 | erot = 0.384040683400773 | epot = -15.0871634822692 | etot = -14.6424332453599 +77000 ekin = 0.0597139401235039 | erot = 0.394435495890113 | epot = -15.0965826813933 | etot = -14.6424332453797 +78000 ekin = 0.0597350629869167 | erot = 0.405343151479122 | epot = -15.1075114598641 | etot = -14.6424332453981 +79000 ekin = 0.0607324264355599 | erot = 0.416499017639979 | epot = -15.1196646894891 | etot = -14.6424332454136 +80000 ekin = 0.0626722904949853 | erot = 0.427694630236173 | epot = -15.1328001661567 | etot = -14.6424332454256 +81000 ekin = 0.0655118235328824 | erot = 0.438786127846776 | epot = -15.1467311968131 | etot = -14.6424332454334 +82000 ekin = 0.0692024020835959 | erot = 0.449698113828529 | epot = -15.1613337613492 | etot = -14.6424332454371 +83000 ekin = 0.0736917936906687 | erot = 0.460422490739007 | epot = -15.1765475298665 | etot = -14.6424332454368 +84000 ekin = 0.0789250526546792 | erot = 0.471012272293637 | epot = -15.1923705703818 | etot = -14.6424332454335 +85000 ekin = 0.0848440878750104 | erot = 0.481570908649218 | epot = -15.2088482419521 | etot = -14.6424332454279 +86000 ekin = 0.0913860133254689 | erot = 0.492238169205271 | epot = -15.226057427952 | etot = -14.6424332454213 +87000 ekin = 0.0984805441200107 | erot = 0.503174014616583 | epot = -15.2440878041518 | etot = -14.6424332454152 +88000 ekin = 0.106046830304303 | erot = 0.514542076496116 | epot = -15.2630221522109 | etot = -14.6424332454105 +89000 ekin = 0.113990204127989 | erot = 0.526494309539271 | epot = -15.2829177590758 | etot = -14.6424332454086 +90000 ekin = 0.122199339151899 | erot = 0.539158097285764 | epot = -15.3037906818476 | etot = -14.64243324541 +91000 ekin = 0.130544275971407 | erot = 0.552626637865788 | epot = -15.3256041592523 | etot = -14.6424332454151 +92000 ekin = 0.138875666148818 | erot = 0.566952900962214 | epot = -15.3482618125354 | etot = -14.6424332454244 +93000 ekin = 0.147025440614644 | erot = 0.58214693373749 | epot = -15.3716056197896 | etot = -14.6424332454375 +94000 ekin = 0.154808946847823 | erot = 0.598175891801268 | epot = -15.3954180841032 | etot = -14.6424332454541 +95000 ekin = 0.162028449602152 | erot = 0.6149659424539 | epot = -15.4194276375298 | etot = -14.6424332454737 +96000 ekin = 0.168477779667818 | erot = 0.632405154082103 | epot = -15.4433161792458 | etot = -14.6424332454959 +97000 ekin = 0.173947863026719 | erot = 0.6503466316284 | epot = -15.4667277401751 | etot = -14.64243324552 +98000 ekin = 0.178232875004241 | erot = 0.668611435746027 | epot = -15.4892775562957 | etot = -14.6424332455454 +99000 ekin = 0.181136831926352 | erot = 0.686991165056287 | epot = -15.5105612425543 | etot = -14.6424332455716 +100000 ekin = 0.182480533643596 | erot = 0.705250413407857 | epot = -15.5301641926494 | etot = -14.642433245598 +101000 ekin = 0.182108871451933 | erot = 0.723129571003271 | epot = -15.5476716880789 | etot = -14.6424332456237 +102000 ekin = 0.179898581170267 | erot = 0.740348571090405 | epot = -15.5626803979087 | etot = -14.642433245648 +103000 ekin = 0.175766517608083 | erot = 0.756612167825933 | epot = -15.5748119311038 | etot = -14.6424332456698 +104000 ekin = 0.169678431535444 | erot = 0.771617166851702 | epot = -15.5837288440751 | etot = -14.6424332456879 +105000 ekin = 0.161658036036865 | erot = 0.7850617429621 | epot = -15.5891530246999 | etot = -14.642433245701 +106000 ekin = 0.151795867650478 | erot = 0.796656613424693 | epot = -15.5908857267828 | etot = -14.6424332457076 +107000 ekin = 0.140257112952728 | erot = 0.806137449197324 | epot = -15.5888278078567 | etot = -14.6424332457066 +108000 ekin = 0.127287240201243 | erot = 0.813277564481201 | epot = -15.5829980503796 | etot = -14.6424332456971 +109000 ekin = 0.113214025490919 | erot = 0.817899691734526 | epot = -15.5735469629039 | etot = -14.6424332456785 +110000 ekin = 0.0984444823805245 | erot = 0.819885578054015 | epot = -15.5607633060855 | etot = -14.642433245651 +111000 ekin = 0.0834553769364607 | erot = 0.819182262545871 | epot = -15.5450708850979 | etot = -14.6424332456156 +112000 ekin = 0.0687764915871071 | erot = 0.815804215094497 | epot = -15.5270139522555 | etot = -14.6424332455739 +113000 ekin = 0.0549665904028951 | erot = 0.809830999844525 | epot = -15.5072308357758 | etot = -14.6424332455284 +114000 ekin = 0.0425830583120669 | erot = 0.801400700351035 | epot = -15.4864170041451 | etot = -14.642433245482 +115000 ekin = 0.032147280213268 | erot = 0.790699910049129 | epot = -15.4652804357002 | etot = -14.6424332454378 +116000 ekin = 0.0241087780345819 | erot = 0.777951546674794 | epot = -15.4444935701084 | etot = -14.642433245399 +117000 ekin = 0.0188117102728978 | erot = 0.763402004774129 | epot = -15.4246469604153 | etot = -14.6424332453683 +118000 ekin = 0.0164673894159088 | erot = 0.747309167857022 | epot = -15.4062098026202 | etot = -14.6424332453473 +119000 ekin = 0.0171359296532941 | erot = 0.72993256457545 | epot = -15.3895017395656 | etot = -14.6424332453369 +120000 ekin = 0.0207190822430537 | erot = 0.711526526250299 | epot = -15.3746788538304 | etot = -14.642433245337 +121000 ekin = 0.0269649552319852 | erot = 0.692336677373468 | epot = -15.3617348779521 | etot = -14.6424332453466 +122000 ekin = 0.035483922029777 | erot = 0.67259957021413 | epot = -15.3505167376078 | etot = -14.6424332453639 +123000 ekin = 0.0457738626451396 | erot = 0.652544850165462 | epot = -15.3407519581969 | etot = -14.6424332453863 +124000 ekin = 0.0572521324296494 | erot = 0.632399068066162 | epot = -15.3320844459073 | etot = -14.6424332454115 +125000 ekin = 0.069291373600259 | erot = 0.61239015618606 | epot = -15.324114775223 | etot = -14.6424332454366 +126000 ekin = 0.0812564128172871 | erot = 0.592751635109631 | epot = -15.3164412933861 | etot = -14.6424332454592 +127000 ekin = 0.0925398817823739 | erot = 0.573725774407947 | epot = -15.3086989016674 | etot = -14.642433245477 +128000 ekin = 0.102594692018531 | erot = 0.555565138943754 | epot = -15.3005930764508 | etot = -14.6424332454885 +129000 ekin = 0.110961953873463 | erot = 0.538532171478064 | epot = -15.2919273708439 | etot = -14.6424332454924 +130000 ekin = 0.117293279472126 | erot = 0.522896664453456 | epot = -15.2826231894135 | etot = -14.6424332454879 +131000 ekin = 0.121366644774015 | erot = 0.508931150171097 | epot = -15.2727310404202 | etot = -14.6424332454751 +132000 ekin = 0.123095155538849 | erot = 0.496904390905147 | epot = -15.2624327918983 | etot = -14.6424332454543 +133000 ekin = 0.122528239670492 | erot = 0.48707328299654 | epot = -15.2520347680937 | etot = -14.6424332454267 +134000 ekin = 0.119845042600695 | erot = 0.479673601169304 | epot = -15.2419518891638 | etot = -14.6424332453938 +135000 ekin = 0.115340171966309 | erot = 0.474910093714655 | epot = -15.2326835110385 | etot = -14.6424332453575 +136000 ekin = 0.10940241928465 | erot = 0.472946484072585 | epot = -15.2247821486776 | etot = -14.6424332453204 +137000 ekin = 0.102487634021819 | erot = 0.473895929917062 | epot = -15.2188168092236 | etot = -14.6424332452848 +138000 ekin = 0.0950874634047241 | erot = 0.477812435582801 | epot = -15.2153331442408 | etot = -14.6424332452533 +139000 ekin = 0.0876961121512828 | erot = 0.484683617748065 | epot = -15.2148129751279 | etot = -14.6424332452285 +140000 ekin = 0.0807775418431644 | erot = 0.494425108537532 | epot = -15.2176358955931 | etot = -14.6424332452124 +141000 ekin = 0.0747355681577843 | erot = 0.506876770807999 | epot = -15.2240455841725 | etot = -14.6424332452067 +142000 ekin = 0.0698891098450152 | erot = 0.521800821238859 | epot = -15.2341231762965 | etot = -14.6424332452126 +143000 ekin = 0.0664544171866109 | erot = 0.538881922424141 | epot = -15.2477695848412 | etot = -14.6424332452305 +144000 ekin = 0.0645355104692138 | erot = 0.557729316020268 | epot = -15.2646980717496 | etot = -14.6424332452601 +145000 ekin = 0.0641233595162975 | erot = 0.577881111412676 | epot = -15.2844377162296 | etot = -14.6424332453007 +146000 ekin = 0.065103607751526 | erot = 0.598810893851671 | epot = -15.3063477469538 | etot = -14.6424332453506 +147000 ekin = 0.067271957897368 | erot = 0.619936843681793 | epot = -15.3296420469867 | etot = -14.6424332454076 +148000 ekin = 0.070355749269213 | erot = 0.640633538190949 | epot = -15.3534225329294 | etot = -14.6424332454693 +149000 ekin = 0.0740398128642513 | erot = 0.660246523237734 | epot = -15.3767195816347 | etot = -14.6424332455327 +150000 ekin = 0.0779944201058762 | erot = 0.678109590376207 | epot = -15.398537256077 | etot = -14.6424332455949 +151000 ekin = 0.0819030604172403 | erot = 0.693564488648145 | epot = -15.4179007947184 | etot = -14.642433245653 +152000 ekin = 0.0854878938552698 | erot = 0.705982563003937 | epot = -15.4339037025634 | etot = -14.6424332457042 +153000 ekin = 0.0885310147328597 | erot = 0.714787575382121 | epot = -15.4457518358609 | etot = -14.6424332457459 +154000 ekin = 0.090890101288761 | erot = 0.719478762727545 | epot = -15.4528021097924 | etot = -14.6424332457761 +155000 ekin = 0.0925075703714592 | erot = 0.719653046097743 | epot = -15.4545938622626 | etot = -14.6424332457934 +156000 ekin = 0.0934129479728876 | erot = 0.715025243754007 | epot = -15.4508714375239 | etot = -14.642433245797 +157000 ekin = 0.093718743577964 | erot = 0.705445163946351 | epot = -15.4415971533109 | etot = -14.6424332457866 +158000 ekin = 0.0936106185393401 | erot = 0.690910554325733 | epot = -15.4269544186277 | etot = -14.6424332457627 +159000 ekin = 0.0933330174010976 | erot = 0.67157505165981 | epot = -15.407341314787 | etot = -14.6424332457261 +160000 ekin = 0.0931716565242302 | erot = 0.647750492120669 | epot = -15.3833553943233 | etot = -14.6424332456784 +161000 ekin = 0.093434329623141 | erot = 0.619903194016607 | epot = -15.3557707692612 | etot = -14.6424332456214 +162000 ekin = 0.0944314104804151 | erot = 0.588644098979629 | epot = -15.3255087550172 | etot = -14.6424332455572 +163000 ekin = 0.0964572425739466 | erot = 0.554712943453935 | epot = -15.293603431516 | etot = -14.6424332454881 +164000 ekin = 0.0997733472806099 | erot = 0.51895691856195 | epot = -15.2611635112594 | etot = -14.6424332454168 +165000 ekin = 0.104594102019908 | erot = 0.482304549422441 | epot = -15.2293318967882 | etot = -14.6424332453459 +166000 ekin = 0.111075276516248 | erot = 0.445735768512404 | epot = -15.1992442903064 | etot = -14.6424332452778 +167000 ekin = 0.119305597513578 | erot = 0.410249354728338 | epot = -15.1719881974571 | etot = -14.6424332452152 +168000 ekin = 0.129301354725085 | erot = 0.376829046178766 | epot = -15.1485636460642 | etot = -14.6424332451603 +169000 ekin = 0.141003965789751 | erot = 0.346409702527123 | epot = -15.129846913432 | etot = -14.6424332451151 +170000 ekin = 0.154280377439944 | erot = 0.319844892417983 | epot = -15.1165585149393 | etot = -14.6424332450814 +171000 ekin = 0.168926178621547 | erot = 0.29787722160694 | epot = -15.109236645289 | etot = -14.6424332450605 +172000 ekin = 0.184671319364516 | erot = 0.281112611137265 | epot = -15.1082171755549 | etot = -14.6424332450532 +173000 ekin = 0.201188345437126 | erot = 0.269999595570288 | epot = -15.1136211860671 | etot = -14.6424332450597 +174000 ekin = 0.218103052207045 | erot = 0.264814547402998 | epot = -15.1253508446899 | etot = -14.6424332450799 +175000 ekin = 0.235007413035636 | erot = 0.265653545950127 | epot = -15.1430942040986 | etot = -14.6424332451128 +176000 ekin = 0.25147453426793 | erot = 0.272431389432275 | epot = -15.1663391688573 | etot = -14.642433245157 +177000 ekin = 0.267075225143454 | erot = 0.284887984978814 | epot = -15.1943964553329 | etot = -14.6424332452106 +178000 ekin = 0.281395553895307 | erot = 0.302602030915426 | epot = -15.2264308300819 | etot = -14.6424332452711 +179000 ekin = 0.294054514411889 | erot = 0.325011526057921 | epot = -15.2614992858055 | etot = -14.6424332453357 +180000 ekin = 0.304720692896967 | erot = 0.351440214935869 | epot = -15.2985941532343 | etot = -14.6424332454015 +181000 ekin = 0.313126658918453 | erot = 0.381128639602711 | epot = -15.3366885439866 | etot = -14.6424332454655 +182000 ekin = 0.31907977582365 | erot = 0.413268071114184 | epot = -15.374781092463 | etot = -14.6424332455251 +183000 ekin = 0.322468290005793 | erot = 0.447035301736757 | epot = -15.4119368373208 | etot = -14.6424332455782 +184000 ekin = 0.323261947554702 | erot = 0.48162615508047 | epot = -15.4473213482582 | etot = -14.6424332456231 +185000 ekin = 0.321506983530858 | erot = 0.516285658867847 | epot = -15.4802258880574 | etot = -14.6424332456587 +186000 ekin = 0.317316057633713 | erot = 0.550333132629142 | epot = -15.5100824359478 | etot = -14.642433245685 +187000 ekin = 0.310854440590115 | erot = 0.583180936761995 | epot = -15.5364686230541 | etot = -14.642433245702 +188000 ekin = 0.302324329763978 | erot = 0.614346238385449 | epot = -15.55910381386 | etot = -14.6424332457106 +189000 ekin = 0.291949445197146 | erot = 0.643455779012842 | epot = -15.5778384699217 | etot = -14.6424332457117 +190000 ekin = 0.279961942768283 | erot = 0.670244185704452 | epot = -15.5926393741794 | etot = -14.6424332457066 +191000 ekin = 0.266593185653692 | erot = 0.694546781233374 | epot = -15.6035732125832 | etot = -14.6424332456962 +192000 ekin = 0.25206914162339 | erot = 0.716288088787003 | epot = -15.6107904760917 | etot = -14.6424332456813 +193000 ekin = 0.236610293254171 | erot = 0.73546730224254 | epot = -15.6145108411597 | etot = -14.642433245663 +194000 ekin = 0.220435149405134 | erot = 0.752141943027135 | epot = -15.615010338074 | etot = -14.6424332456418 +195000 ekin = 0.203765880093363 | erot = 0.766410799029957 | epot = -15.6126099247417 | etot = -14.6424332456184 +196000 ekin = 0.186834339037387 | erot = 0.778397083250795 | epot = -15.6076646678817 | etot = -14.6424332455935 +197000 ekin = 0.169886782294202 | erot = 0.788232586070606 | epot = -15.6005526139326 | etot = -14.6424332455678 +198000 ekin = 0.153185871078003 | erot = 0.796043434538988 | epot = -15.5916625511591 | etot = -14.6424332455421 +199000 ekin = 0.137008972987419 | erot = 0.801937915798975 | epot = -15.5813801343039 | etot = -14.6424332455175 +200000 ekin = 0.121642272364818 | erot = 0.80599667326165 | epot = -15.5700721911217 | etot = -14.6424332454952 +201000 ekin = 0.107370722656495 | erot = 0.808265456806725 | epot = -15.5580694249396 | etot = -14.6424332454764 +202000 ekin = 0.0944644042392259 | erot = 0.808750524309999 | epot = -15.5456481740113 | etot = -14.642433245462 +203000 ekin = 0.0831623790894052 | erot = 0.807416772443545 | epot = -15.5330123969864 | etot = -14.6424332454535 +204000 ekin = 0.0736556272335603 | erot = 0.804188725419786 | epot = -15.5202775981049 | etot = -14.6424332454515 +205000 ekin = 0.0660710401675988 | erot = 0.798954607355857 | epot = -15.50745889298 | etot = -14.6424332454565 +206000 ekin = 0.0604586317681712 | erot = 0.791573809424193 | epot = -15.4944656866606 | etot = -14.6424332454683 +207000 ekin = 0.0567840026883055 | erot = 0.781888054798429 | epot = -15.4811053029727 | etot = -14.642433245486 +208000 ekin = 0.0549275971601587 | erot = 0.769736381379669 | epot = -15.4670972240478 | etot = -14.6424332455079 +209000 ekin = 0.0546914447538068 | erot = 0.754973659533921 | epot = -15.4520983498196 | etot = -14.6424332455319 +210000 ekin = 0.0558130126775254 | erot = 0.737491764374774 | epot = -15.4357380226072 | etot = -14.6424332455549 +211000 ekin = 0.0579847210238465 | erot = 0.717241838880044 | epot = -15.417659805478 | etot = -14.6424332455741 +212000 ekin = 0.0608768356205403 | erot = 0.694255492639204 | epot = -15.3975655738466 | etot = -14.6424332455869 +213000 ekin = 0.0641610427083153 | erot = 0.66866247616333 | epot = -15.3752567644623 | etot = -14.6424332455907 +214000 ekin = 0.0675321043587494 | erot = 0.640702495517984 | epot = -15.3506678454611 | etot = -14.6424332455844 +215000 ekin = 0.070725533636796 | erot = 0.610729417267914 | epot = -15.3238881964721 | etot = -14.6424332455674 +216000 ekin = 0.0735300437834149 | erot = 0.579207054837064 | epot = -15.2951703441606 | etot = -14.6424332455401 +217000 ekin = 0.0757943994895872 | erot = 0.54669681320896 | epot = -15.2649244582023 | etot = -14.6424332455037 +218000 ekin = 0.0774290394184588 | erot = 0.513838451215604 | epot = -15.2337007360941 | etot = -14.6424332454601 +219000 ekin = 0.0784033323162054 | erot = 0.481325894960068 | epot = -15.2021624726878 | etot = -14.6424332454115 +220000 ekin = 0.0787395495628487 | erot = 0.449880299616969 | epot = -15.17105309454 | etot = -14.6424332453602 +221000 ekin = 0.0785046319692735 | erot = 0.420222425154563 | epot = -15.1411603024324 | etot = -14.6424332453086 +222000 ekin = 0.0778006814288913 | erot = 0.393045972165166 | epot = -15.113279898853 | etot = -14.642433245259 +223000 ekin = 0.0767549035403158 | erot = 0.368992968905282 | epot = -15.0881811176588 | etot = -14.6424332452132 +224000 ekin = 0.0755095293719617 | erot = 0.348631757026545 | epot = -15.0665745315715 | etot = -14.642433245173 +225000 ekin = 0.0742120885681049 | erot = 0.332437700423087 | epot = -15.0490830341314 | etot = -14.6424332451402 +226000 ekin = 0.0730063028703793 | erot = 0.320776497496347 | epot = -15.0362160454828 | etot = -14.642433245116 +227000 ekin = 0.072023814089001 | erot = 0.313889923623746 | epot = -15.0283469828147 | etot = -14.6424332451019 +228000 ekin = 0.0713769419944288 | erot = 0.311883945242982 | epot = -15.0256941323359 | etot = -14.6424332450985 +229000 ekin = 0.0711526728859999 | erot = 0.314719386436034 | epot = -15.0283053044286 | etot = -14.6424332451066 +230000 ekin = 0.0714080974064536 | erot = 0.322205638587354 | epot = -15.0360469811206 | etot = -14.6424332451268 +231000 ekin = 0.0721675361185164 | erot = 0.333998222200299 | epot = -15.0485990034776 | etot = -14.6424332451587 +232000 ekin = 0.0734216022897964 | erot = 0.349601270465511 | epot = -15.0654561179572 | etot = -14.6424332452019 +233000 ekin = 0.0751284397495126 | erot = 0.368376135876537 | epot = -15.0859378208814 | etot = -14.6424332452553 +234000 ekin = 0.0772173235430297 | erot = 0.389557254435315 | epot = -15.1092078232955 | etot = -14.6424332453172 +235000 ekin = 0.0795947059788122 | erot = 0.412276079792818 | epot = -15.134304031156 | etot = -14.6424332453844 +236000 ekin = 0.0821526186131207 | erot = 0.435593295650776 | epot = -15.1601791597182 | etot = -14.6424332454543 +237000 ekin = 0.0847791014223481 | erot = 0.458538653868279 | epot = -15.1857510008135 | etot = -14.6424332455229 +238000 ekin = 0.0873700423841474 | erot = 0.480156759890556 | epot = -15.2099600478608 | etot = -14.6424332455861 +239000 ekin = 0.0898415153120355 | erot = 0.499556095556555 | epot = -15.2318308565087 | etot = -14.6424332456401 +240000 ekin = 0.0921414623518661 | erot = 0.515957735404873 | epot = -15.250532443438 | etot = -14.6424332456813 +241000 ekin = 0.094259449012787 | erot = 0.528739776890155 | epot = -15.2654324716098 | etot = -14.6424332457068 +242000 ekin = 0.096233280586619 | erot = 0.537473606139462 | epot = -15.276140132441 | etot = -14.6424332457149 +243000 ekin = 0.0981515319325847 | erot = 0.5419487859829 | epot = -15.2825335636204 | etot = -14.642433245705 +244000 ekin = 0.100151482350113 | erot = 0.542184479376325 | epot = -15.2847692074041 | etot = -14.6424332456777 +245000 ekin = 0.102412491094949 | erot = 0.538426702319087 | epot = -15.283272439049 | etot = -14.6424332456349 +246000 ekin = 0.10514539554429 | erot = 0.531132085867033 | epot = -15.2787107269906 | etot = -14.6424332455793 +247000 ekin = 0.108578961411818 | erot = 0.520939994206916 | epot = -15.271952201133 | etot = -14.6424332455143 +248000 ekin = 0.112944688754722 | erot = 0.50863565229477 | epot = -15.2640135864931 | etot = -14.6424332454436 +249000 ekin = 0.118461348905716 | erot = 0.495107336752456 | epot = -15.2560019310293 | etot = -14.6424332453711 +250000 ekin = 0.12532051071417 | erot = 0.481300713195499 | epot = -15.2490544692103 | etot = -14.6424332453007 +251000 ekin = 0.133674056956426 | erot = 0.468173145421963 | epot = -15.2442804476139 | etot = -14.6424332452355 +252000 ekin = 0.143624355874462 | erot = 0.456650355971893 | epot = -15.2427079570251 | etot = -14.6424332451787 +253000 ekin = 0.155217400156355 | erot = 0.447587277163441 | epot = -15.2452379224524 | etot = -14.6424332451326 +254000 ekin = 0.168438906846642 | erot = 0.441734376015304 | epot = -15.2526065279605 | etot = -14.6424332450986 +255000 ekin = 0.183213121646742 | erot = 0.439710227351497 | epot = -15.2653565940763 | etot = -14.642433245078 +256000 ekin = 0.199403908834931 | erot = 0.441980689731482 | epot = -15.283817843638 | etot = -14.6424332450716 +257000 ekin = 0.216817638464837 | erot = 0.448844730303129 | epot = -15.3080956138476 | etot = -14.6424332450796 +258000 ekin = 0.235207399038858 | erot = 0.460426746273211 | epot = -15.3380673904137 | etot = -14.6424332451016 +259000 ekin = 0.254278151369372 | erot = 0.476675120646291 | epot = -15.3733865171527 | etot = -14.642433245137 +260000 ekin = 0.273692576680298 | erot = 0.497366691704061 | epot = -15.4134925135692 | etot = -14.6424332451849 +261000 ekin = 0.293077534076616 | erot = 0.522116767902342 | epot = -15.4576275472227 | etot = -14.6424332452438 +262000 ekin = 0.312031202024067 | erot = 0.550394247117877 | epot = -15.5048586944538 | etot = -14.6424332453119 +263000 ekin = 0.330131107619695 | erot = 0.581541281995867 | epot = -15.5541056350029 | etot = -14.6424332453873 +264000 ekin = 0.346943319973868 | erot = 0.614796773442828 | epot = -15.6041733388843 | etot = -14.6424332454676 +265000 ekin = 0.362033078258367 | erot = 0.649322794992396 | epot = -15.6537891188012 | etot = -14.6424332455505 +266000 ekin = 0.374977027500513 | erot = 0.684232889055324 | epot = -15.7016431621889 | etot = -14.6424332456331 +267000 ekin = 0.385377045185317 | erot = 0.718621072058556 | epot = -15.7464313629566 | etot = -14.6424332457127 +268000 ekin = 0.392875374680224 | erot = 0.75159036946148 | epot = -15.7868989899282 | etot = -14.6424332457865 +269000 ekin = 0.397170471139203 | erot = 0.782279784271994 | epot = -15.8218835012632 | etot = -14.642433245852 +270000 ekin = 0.39803266202809 | erot = 0.80988877167351 | epot = -15.8503546796086 | etot = -14.642433245907 +271000 ekin = 0.395318487598737 | erot = 0.833698516709663 | epot = -15.8714502502579 | etot = -14.6424332459495 +272000 ekin = 0.388982474352171 | erot = 0.853089551908401 | epot = -15.8845052722386 | etot = -14.6424332459781 +273000 ekin = 0.379085147931464 | erot = 0.867555470405014 | epot = -15.8890738643282 | etot = -14.6424332459917 +274000 ekin = 0.365796322193278 | erot = 0.876712662629274 | epot = -15.8849422308128 | etot = -14.6424332459903 +275000 ekin = 0.349393082921568 | erot = 0.880306121913762 | epot = -15.8721324508092 | etot = -14.6424332459739 +276000 ekin = 0.330252358905702 | erot = 0.878211432148943 | epot = -15.8508970369982 | etot = -14.6424332459435 +277000 ekin = 0.308838461220239 | erot = 0.870433084876928 | epot = -15.8217047919976 | etot = -14.6424332459005 +278000 ekin = 0.285686394604133 | erot = 0.857099294885134 | epot = -15.7852189353358 | etot = -14.6424332458465 +279000 ekin = 0.261382042766456 | erot = 0.838453513181018 | epot = -15.7422688017312 | etot = -14.6424332457837 +280000 ekin = 0.236540473325989 | erot = 0.814842890587939 | epot = -15.6938166096284 | etot = -14.6424332457145 +281000 ekin = 0.21178360260805 | erot = 0.78670403285838 | epot = -15.6409208811075 | etot = -14.6424332456411 +282000 ekin = 0.187718337271923 | erot = 0.754546508157667 | epot = -15.5846980909958 | etot = -14.6424332455662 +283000 ekin = 0.164916115090819 | erot = 0.71893470884518 | epot = -15.5262840694281 | etot = -14.6424332454921 +284000 ekin = 0.143894549221734 | erot = 0.680468811939341 | epot = -15.4667966065823 | etot = -14.6424332454212 +285000 ekin = 0.125101678372309 | erot = 0.639765701847639 | epot = -15.4073006255757 | etot = -14.6424332453557 +286000 ekin = 0.108903164107404 | erot = 0.597440790010452 | epot = -15.3487771994147 | etot = -14.6424332452969 +287000 ekin = 0.0955726645551871 | erot = 0.554091668604971 | epot = -15.2920975784065 | etot = -14.6424332452464 +288000 ekin = 0.0852855448006991 | erot = 0.510284456822087 | epot = -15.2380032468277 | etot = -14.6424332452049 +289000 ekin = 0.0781160413102893 | erot = 0.466543535623136 | epot = -15.1870928221065 | etot = -14.6424332451731 +290000 ekin = 0.0740379578618401 | erot = 0.42334512758908 | epot = -15.1398163306018 | etot = -14.6424332451509 +291000 ekin = 0.07292891006337 | erot = 0.381114879437427 | epot = -15.0964770346384 | etot = -14.6424332451376 +292000 ekin = 0.074578035792751 | erot = 0.340229271737877 | epot = -15.0572405526631 | etot = -14.6424332451324 +293000 ekin = 0.0786969407539187 | erot = 0.301020346548478 | epot = -15.0221505324364 | etot = -14.642433245134 +294000 ekin = 0.0849334564702348 | erot = 0.263782947588673 | epot = -14.9911496491996 | etot = -14.6424332451407 +295000 ekin = 0.0928875723607527 | erot = 0.228783448806945 | epot = -14.9641042663184 | etot = -14.6424332451507 +296000 ekin = 0.10212869750719 | erot = 0.19626884038739 | epot = -14.9408307830571 | etot = -14.6424332451625 +297000 ekin = 0.112213252496714 | erot = 0.166475068218874 | epot = -14.92112156589 | etot = -14.6424332451744 +298000 ekin = 0.122701527066799 | erot = 0.139633685446924 | epot = -14.9047684576991 | etot = -14.6424332451854 +299000 ekin = 0.133172792910571 | erot = 0.115976150690183 | epot = -14.8915821887951 | etot = -14.6424332451943 +300000 ekin = 0.14323783970709 | erot = 0.0957354521215423 | epot = -14.8814065370293 | etot = -14.6424332452007 +301000 ekin = 0.152548387988443 | erot = 0.0791450908732833 | epot = -14.8741267240661 | etot = -14.6424332452044 +302000 ekin = 0.16080318429946 | erot = 0.0664357608562006 | epot = -14.8696721903613 | etot = -14.6424332452056 +303000 ekin = 0.167750948486619 | erot = 0.0578302677257533 | epot = -14.868014461417 | etot = -14.6424332452046 +304000 ekin = 0.173190665587062 | erot = 0.0535373136372916 | epot = -14.8691612244265 | etot = -14.6424332452021 +305000 ekin = 0.176969952948875 | erot = 0.053744740290904 | epot = -14.8731479384385 | etot = -14.6424332451987 +306000 ekin = 0.17898236329054 | erot = 0.0586126977876512 | epot = -14.8800283062731 | etot = -14.6424332451949 +307000 ekin = 0.179164502944013 | erot = 0.0682670321056721 | epot = -14.8898647802412 | etot = -14.6424332451915 +308000 ekin = 0.177493763288032 | erot = 0.0827930029186384 | epot = -14.9027200113955 | etot = -14.6424332451889 +309000 ekin = 0.173987301150973 | erot = 0.102229291870626 | epot = -14.9186498382088 | etot = -14.6424332451872 +310000 ekin = 0.168702678647183 | erot = 0.126562162216031 | epot = -14.9376980860501 | etot = -14.6424332451869 +311000 ekin = 0.161740297008921 | erot = 0.155719593406505 | epot = -14.9598931356033 | etot = -14.6424332451879 +312000 ekin = 0.15324744012493 | erot = 0.189565237977707 | epot = -14.985245923293 | etot = -14.6424332451904 +313000 ekin = 0.143423389996968 | erot = 0.227892126760359 | epot = -15.0137487619517 | etot = -14.6424332451944 +314000 ekin = 0.132524706018471 | erot = 0.270416174780379 | epot = -15.0453741259986 | etot = -14.6424332451997 +315000 ekin = 0.120869409552547 | erot = 0.316769708289002 | epot = -15.0800723630487 | etot = -14.6424332452072 +316000 ekin = 0.108838546104732 | erot = 0.3664954379943 | epot = -15.117767229316 | etot = -14.642433245217 +317000 ekin = 0.0968734934277273 | erot = 0.419041536809115 | epot = -15.1583482754667 | etot = -14.6424332452299 +318000 ekin = 0.0854675378549808 | erot = 0.473758725764069 | epot = -15.2016595088657 | etot = -14.6424332452466 +319000 ekin = 0.0751507271451904 | erot = 0.529900497448209 | epot = -15.2474844698619 | etot = -14.6424332452685 +320000 ekin = 0.0664678443364339 | erot = 0.586627760739843 | epot = -15.2955288503729 | etot = -14.6424332452966 +321000 ekin = 0.0599504590563242 | erot = 0.643019202691524 | epot = -15.3454029070797 | etot = -14.6424332453318 +322000 ekin = 0.0560852142799999 | erot = 0.698088453267007 | epot = -15.3966069129217 | etot = -14.6424332453747 +323000 ekin = 0.0552815181248962 | erot = 0.750808639916083 | epot = -15.4485234034659 | etot = -14.6424332454249 +324000 ekin = 0.0578423255205682 | erot = 0.800144112657402 | epot = -15.5004196836594 | etot = -14.6424332454815 +325000 ekin = 0.0639414864634509 | erot = 0.845088070114915 | epot = -15.5514628021208 | etot = -14.6424332455424 +326000 ekin = 0.0736101694210092 | erot = 0.884703689967185 | epot = -15.6007471049934 | etot = -14.6424332456052 +327000 ekin = 0.0867333560897029 | erot = 0.918165419812939 | epot = -15.6473320215696 | etot = -14.642433245667 +328000 ekin = 0.103055779603997 | erot = 0.944796600223848 | epot = -15.6902856255527 | etot = -14.6424332457249 +329000 ekin = 0.122195446170794 | erot = 0.964099781594435 | epot = -15.7287284735416 | etot = -14.6424332457764 +330000 ekin = 0.143662406710256 | erot = 0.975776996237332 | epot = -15.7618726487672 | etot = -14.6424332458196 +331000 ekin = 0.166880785133597 | erot = 0.979738667517973 | epot = -15.7890526985047 | etot = -14.6424332458531 +332000 ekin = 0.191212923969949 | erot = 0.976101405902857 | epot = -15.8097475757491 | etot = -14.6424332458763 +333000 ekin = 0.215985355319607 | erot = 0.965176233539026 | epot = -15.8235948347474 | etot = -14.6424332458887 +334000 ekin = 0.24051665683118 | erot = 0.94744948511249 | epot = -15.8303993878336 | etot = -14.64243324589 +335000 ekin = 0.264146896086271 | erot = 0.923558676868031 | epot = -15.8301388188342 | etot = -14.6424332458799 +336000 ekin = 0.286267467754269 | erot = 0.894265184760613 | epot = -15.8229658983735 | etot = -14.6424332458586 +337000 ekin = 0.306349134750126 | erot = 0.860424939336685 | epot = -15.809207319913 | etot = -14.6424332458262 +338000 ekin = 0.323965497674733 | erot = 0.822957838322781 | epot = -15.7893565817813 | etot = -14.6424332457838 +339000 ekin = 0.338809250789021 | erot = 0.782816380150505 | epot = -15.7640588766724 | etot = -14.6424332457329 +340000 ekin = 0.350699444233775 | erot = 0.74095414130314 | epot = -15.7340868312126 | etot = -14.6424332456757 +341000 ekin = 0.359579293536528 | erot = 0.698295027831883 | epot = -15.7003075669831 | etot = -14.6424332456146 +342000 ekin = 0.365505462154955 | erot = 0.655704542035024 | epot = -15.6636432497426 | etot = -14.6424332455526 +343000 ekin = 0.36863083266141 | erot = 0.613964463465585 | epot = -15.6250285416196 | etot = -14.6424332454926 +344000 ekin = 0.369183369589239 | erot = 0.57375227308083 | epot = -15.5853688881069 | etot = -14.6424332454368 +345000 ekin = 0.367443732824309 | erot = 0.535626361233186 | epot = -15.5455033394448 | etot = -14.6424332453873 +346000 ekin = 0.363723933131786 | erot = 0.500017626276236 | epot = -15.5061748047535 | etot = -14.6424332453455 +347000 ekin = 0.35834870527769 | erot = 0.4672275854273 | epot = -15.468009536017 | etot = -14.642433245312 +348000 ekin = 0.351640582954847 | erot = 0.437432666908131 | epot = -15.4315064951499 | etot = -14.6424332452869 +349000 ekin = 0.34390902469482 | erot = 0.410693986169958 | epot = -15.3970362561344 | etot = -14.6424332452696 +350000 ekin = 0.335443435968795 | erot = 0.386971649880754 | epot = -15.3648483311092 | etot = -14.6424332452597 +351000 ekin = 0.326509584093778 | erot = 0.366142474251534 | epot = -15.3350853036005 | etot = -14.6424332452552 +352000 ekin = 0.317348699022206 | erot = 0.348019930401133 | epot = -15.3078018746784 | etot = -14.642433245255 +353000 ekin = 0.308178466648759 | erot = 0.332375117501959 | epot = -15.2829868294085 | etot = -14.6424332452578 +354000 ekin = 0.299195119854398 | erot = 0.318957598139 | epot = -15.2605859632553 | etot = -14.6424332452619 +355000 ekin = 0.290575888248861 | erot = 0.307515001370351 | epot = -15.2405241348854 | etot = -14.6424332452662 +356000 ekin = 0.282481160312499 | erot = 0.297810406217201 | epot = -15.2227248117992 | etot = -14.6424332452695 +357000 ekin = 0.275055828993794 | erot = 0.289636664277844 | epot = -15.2071257385429 | etot = -14.6424332452713 +358000 ekin = 0.268429427254947 | erot = 0.282827006912201 | epot = -15.1936896794382 | etot = -14.6424332452711 +359000 ekin = 0.262714810201774 | erot = 0.277261507857975 | epot = -15.1824095633287 | etot = -14.642433245269 +360000 ekin = 0.258005302569451 | erot = 0.272869227748628 | epot = -15.1733077755836 | etot = -14.6424332452655 +361000 ekin = 0.2543704006218 | erot = 0.26962613780198 | epot = -15.1664297836851 | etot = -14.6424332452613 +362000 ekin = 0.251850290178673 | erot = 0.267549186087919 | epot = -15.1618327215239 | etot = -14.6424332452573 +363000 ekin = 0.250449609862776 | erot = 0.266687109597444 | epot = -15.159569964715 | etot = -14.6424332452548 +364000 ekin = 0.250131041863364 | erot = 0.267108788857685 | epot = -15.1596730759762 | etot = -14.6424332452551 +365000 ekin = 0.250809442162096 | erot = 0.268890073927981 | epot = -15.1621327613494 | etot = -14.6424332452593 +366000 ekin = 0.252347318763382 | erot = 0.27210007300604 | epot = -15.1668806370379 | etot = -14.6424332452684 +367000 ekin = 0.254552520178544 | erot = 0.276787886819364 | epot = -15.1737736522811 | etot = -14.6424332452832 +368000 ekin = 0.25717899615333 | erot = 0.28297069952372 | epot = -15.1825829409812 | etot = -14.6424332453042 +369000 ekin = 0.259931424908739 | erot = 0.290624011143398 | epot = -15.1929886813831 | etot = -14.642433245331 +370000 ekin = 0.262474349326661 | erot = 0.299674631814961 | epot = -15.2045822265049 | etot = -14.6424332453633 +371000 ekin = 0.264446209428328 | erot = 0.309996869297309 | epot = -15.2168763241252 | etot = -14.6424332453996 +372000 ekin = 0.265478281861457 | erot = 0.321412142686622 | epot = -15.2293236699864 | etot = -14.6424332454383 +373000 ekin = 0.265218028290062 | erot = 0.333692059448684 | epot = -15.2413433332161 | etot = -14.6424332454774 +374000 ekin = 0.263355721247738 | erot = 0.346564809671242 | epot = -15.2523537764331 | etot = -14.6424332455141 +375000 ekin = 0.259652497500791 | erot = 0.359724567998139 | epot = -15.2618103110451 | etot = -14.6424332455462 +376000 ekin = 0.253967268934329 | erot = 0.372843454384676 | epot = -15.2692439688901 | etot = -14.6424332455711 +377000 ekin = 0.246279333497668 | erot = 0.385585491299172 | epot = -15.2742980703837 | etot = -14.6424332455868 +378000 ekin = 0.236703249874173 | erot = 0.397621906702945 | epot = -15.2767584021691 | etot = -14.642433245592 +379000 ekin = 0.225492756940715 | erot = 0.40864706693682 | epot = -15.2765730694637 | etot = -14.6424332455862 +380000 ekin = 0.213031377534926 | erot = 0.418394279001937 | epot = -15.2738589021068 | etot = -14.64243324557 +381000 ekin = 0.199808877311648 | erot = 0.426650676217097 | epot = -15.2688927990735 | etot = -14.6424332455448 +382000 ekin = 0.186384809014953 | erot = 0.433270396060973 | epot = -15.2620884505889 | etot = -14.642433245513 +383000 ekin = 0.173342616140324 | erot = 0.438185279055512 | epot = -15.2539611406731 | etot = -14.6424332454773 +384000 ekin = 0.161239700828068 | erot = 0.441412371407278 | epot = -15.2450853176757 | etot = -14.6424332454403 +385000 ekin = 0.15055995464472 | erot = 0.443057612556829 | epot = -15.2360508126064 | etot = -14.6424332454049 +386000 ekin = 0.141675129696858 | erot = 0.443315241526512 | epot = -15.2274236165962 | etot = -14.6424332453728 +387000 ekin = 0.134820015696242 | erot = 0.442462667351568 | epot = -15.219715928393 | etot = -14.6424332453452 +388000 ekin = 0.130083976412365 | erot = 0.440850813515941 | epot = -15.2133680352507 | etot = -14.6424332453224 +389000 ekin = 0.127418570237209 | erot = 0.438890246280336 | epot = -15.2087420618216 | etot = -14.6424332453041 +390000 ekin = 0.126658423092949 | erot = 0.437033702086702 | epot = -15.2061253704692 | etot = -14.6424332452896 +391000 ekin = 0.127550804261054 | erot = 0.435755902066146 | epot = -15.2057399516053 | etot = -14.6424332452781 +392000 ekin = 0.129788752936042 | erot = 0.435531744058158 | epot = -15.2077537422634 | etot = -14.6424332452692 +393000 ekin = 0.133043055316548 | erot = 0.436814065077171 | epot = -15.2122903656559 | etot = -14.6424332452622 +394000 ekin = 0.13698956146631 | erot = 0.440012156509963 | epot = -15.2194349632336 | etot = -14.6424332452574 +395000 ekin = 0.141329833042578 | erot = 0.445472096884894 | epot = -15.2292351751821 | etot = -14.6424332452547 +396000 ekin = 0.145804542777388 | erot = 0.453459767648299 | epot = -15.2416975556806 | etot = -14.6424332452549 +397000 ekin = 0.150200153188693 | erot = 0.464147173461362 | epot = -15.2567805719085 | etot = -14.6424332452585 +398000 ekin = 0.154350089766171 | erot = 0.477602441558455 | epot = -15.2743857765907 | etot = -14.642433245266 +399000 ekin = 0.158131920622385 | erot = 0.493783661155615 | epot = -15.2943488270562 | etot = -14.6424332452782 +400000 ekin = 0.161462056173815 | erot = 0.512536568006289 | epot = -15.3164318694755 | etot = -14.6424332452954 +401000 ekin = 0.164289301181092 | erot = 0.533595989002424 | epot = -15.3403185355012 | etot = -14.6424332453177 +402000 ekin = 0.166588323050712 | erot = 0.556590928839782 | epot = -15.3656124972355 | etot = -14.642433245345 +403000 ekin = 0.168353810379714 | erot = 0.581053183644432 | epot = -15.3918402394011 | etot = -14.642433245377 +404000 ekin = 0.169595821301209 | erot = 0.606429376023235 | epot = -15.4184584427372 | etot = -14.6424332454128 +405000 ekin = 0.170336578562032 | erot = 0.632096292540657 | epot = -15.444866116554 | etot = -14.6424332454513 +406000 ekin = 0.170608761978825 | erot = 0.65737934451492 | epot = -15.4704213519851 | etot = -14.6424332454913 +407000 ekin = 0.170455178567339 | erot = 0.681573854094692 | epot = -15.4944622781935 | etot = -14.6424332455315 +408000 ekin = 0.169929554809768 | erot = 0.703968692151365 | epot = -15.5163314925311 | etot = -14.64243324557 +409000 ekin = 0.169098093451402 | erot = 0.723871579521667 | epot = -15.5354029185781 | etot = -14.642433245605 +410000 ekin = 0.168041369040766 | erot = 0.740635137248604 | epot = -15.5511097519242 | etot = -14.6424332456348 +411000 ekin = 0.166856102809042 | erot = 0.753682569971378 | epot = -15.5629719184381 | etot = -14.6424332456577 +412000 ekin = 0.165656359033244 | erot = 0.762531725093222 | epot = -15.5706213297988 | etot = -14.6424332456723 +413000 ekin = 0.164573741711754 | erot = 0.766816218739629 | epot = -15.5738232061291 | etot = -14.6424332456777 +414000 ekin = 0.16375624095788 | erot = 0.76630237757158 | epot = -15.5724918642026 | etot = -14.6424332456731 +415000 ekin = 0.163365479945841 | erot = 0.760900920224475 | epot = -15.5666996458289 | etot = -14.6424332456586 +416000 ekin = 0.163572240094564 | erot = 0.750672586698962 | epot = -15.556678072428 | etot = -14.6424332456344 +417000 ekin = 0.164550286199959 | erot = 0.735827297890632 | epot = -15.5428108296923 | etot = -14.6424332456017 +418000 ekin = 0.166468663393417 | erot = 0.716716857299964 | epot = -15.5256187662552 | etot = -14.6424332455618 +419000 ekin = 0.169482781127086 | erot = 0.693821649098622 | epot = -15.5057376757421 | etot = -14.6424332455164 +420000 ekin = 0.173724722667741 | erot = 0.667732191682839 | epot = -15.4838901598183 | etot = -14.6424332454677 +421000 ekin = 0.179293310761204 | erot = 0.639126725581036 | epot = -15.4608532817599 | etot = -14.6424332454176 +422000 ekin = 0.186244514521543 | erot = 0.608746211198846 | epot = -15.4374239710891 | etot = -14.6424332453687 +423000 ekin = 0.19458279814717 | erot = 0.57736816557662 | epot = -15.4143842090468 | etot = -14.642433245323 +424000 ekin = 0.204253993032132 | erot = 0.545780680985193 | epot = -15.3924679192997 | etot = -14.6424332452824 +425000 ekin = 0.215140228919715 | erot = 0.514757766830946 | epot = -15.372331240999 | etot = -14.6424332452483 +426000 ekin = 0.227057395200036 | erot = 0.485036881514114 | epot = -15.3545275219361 | etot = -14.6424332452219 +427000 ekin = 0.239755526228613 | erot = 0.45729922156058 | epot = -15.3394879929935 | etot = -14.6424332452043 +428000 ekin = 0.252922416271937 | erot = 0.432153058133966 | epot = -15.3275087196017 | etot = -14.6424332451958 +429000 ekin = 0.26619066718155 | erot = 0.410120192007268 | epot = -15.318744104385 | etot = -14.6424332451962 +430000 ekin = 0.279148248287638 | erot = 0.391625457761839 | epot = -15.313206951255 | etot = -14.6424332452055 +431000 ekin = 0.291352495295118 | erot = 0.376989149810355 | epot = -15.310774890328 | etot = -14.6424332452226 +432000 ekin = 0.302347287571226 | erot = 0.366422254466054 | epot = -15.3112027872841 | etot = -14.6424332452468 +433000 ekin = 0.311682921771869 | erot = 0.360024429012261 | epot = -15.31414059606 | etot = -14.6424332452759 +434000 ekin = 0.318937954387437 | erot = 0.357784738270616 | epot = -15.3191559379665 | etot = -14.6424332453085 +435000 ekin = 0.323742037714879 | erot = 0.359585207272693 | epot = -15.3257604903309 | etot = -14.6424332453433 +436000 ekin = 0.325798554031361 | erot = 0.365207245305615 | epot = -15.3334390447156 | etot = -14.6424332453787 +437000 ekin = 0.324905697097351 | erot = 0.3743409223498 | epot = -15.3416798648587 | etot = -14.6424332454115 +438000 ekin = 0.320974589858406 | erot = 0.386596930160279 | epot = -15.3500047654589 | etot = -14.6424332454403 +439000 ekin = 0.314043077746411 | erot = 0.401520852185304 | epot = -15.3579971753956 | etot = -14.6424332454639 +440000 ekin = 0.304283988020589 | erot = 0.418609132213777 | epot = -15.3653263657149 | etot = -14.6424332454805 +441000 ekin = 0.292006859111662 | erot = 0.43732591619283 | epot = -15.3717660207935 | etot = -14.642433245489 +442000 ekin = 0.277652365815121 | erot = 0.457119792518649 | epot = -15.3772054038233 | etot = -14.6424332454895 +443000 ekin = 0.261778853590793 | erot = 0.477439412175561 | epot = -15.3816515112488 | etot = -14.6424332454825 +444000 ekin = 0.245040553434287 | erot = 0.497747053376211 | epot = -15.3852208522799 | etot = -14.6424332454694 +445000 ekin = 0.228157260420329 | erot = 0.517529408202232 | epot = -15.3881199140743 | etot = -14.6424332454517 +446000 ekin = 0.21187568172941 | erot = 0.536305196856337 | epot = -15.3906141240179 | etot = -14.6424332454322 +447000 ekin = 0.196923472681482 | erot = 0.553629632753198 | epot = -15.3929863508487 | etot = -14.642433245414 +448000 ekin = 0.183958277880817 | erot = 0.569096233370736 | epot = -15.3954877566523 | etot = -14.6424332454007 +449000 ekin = 0.173515771313228 | erot = 0.5823369471514 | epot = -15.3982859638601 | etot = -14.6424332453955 +450000 ekin = 0.165962361199431 | erot = 0.593021970145669 | epot = -15.4014175767459 | etot = -14.6424332454008 +451000 ekin = 0.161459280835244 | erot = 0.600860851249224 | epot = -15.4047533775022 | etot = -14.6424332454178 +452000 ekin = 0.159944578253892 | erot = 0.605606408076117 | epot = -15.4079842317756 | etot = -14.6424332454456 +453000 ekin = 0.16113765311534 | erot = 0.607062496367839 | epot = -15.410633394965 | etot = -14.6424332454818 +454000 ekin = 0.164567591513356 | erot = 0.605095779305886 | epot = -15.4120966163412 | etot = -14.642433245522 +455000 ekin = 0.169622334209554 | erot = 0.599650455421075 | epot = -15.4117060351916 | etot = -14.642433245561 +456000 ekin = 0.175611802350678 | erot = 0.590763702894336 | epot = -15.4088087508385 | etot = -14.6424332455934 +457000 ekin = 0.18183562198226 | erot = 0.578578749363001 | epot = -15.40284761696 | etot = -14.6424332456148 +458000 ekin = 0.187645727030885 | erot = 0.563352302649156 | epot = -15.3934312753017 | etot = -14.6424332456216 +459000 ekin = 0.192495880384903 | erot = 0.54545371714944 | epot = -15.380382843147 | etot = -14.6424332456127 +460000 ekin = 0.195973381637231 | erot = 0.525354597711837 | epot = -15.3637612249374 | etot = -14.6424332455883 +461000 ekin = 0.19781192099122 | erot = 0.503609203464113 | epot = -15.3438543700065 | etot = -14.6424332455512 +462000 ekin = 0.197887724919132 | erot = 0.48082756028462 | epot = -15.3211485307077 | etot = -14.642433245504 +463000 ekin = 0.196203198485173 | erot = 0.457644248438995 | epot = -15.2962806923752 | etot = -14.642433245451 +464000 ekin = 0.192863034125907 | erot = 0.434686220431767 | epot = -15.2699824999538 | etot = -14.6424332453961 +465000 ekin = 0.188047435822224 | erot = 0.412542760093908 | epot = -15.2430234412587 | etot = -14.6424332453426 +466000 ekin = 0.181986107552777 | erot = 0.391740010674779 | epot = -15.2161593635208 | etot = -14.6424332452933 +467000 ekin = 0.174935400197989 | erot = 0.372721626737635 | epot = -15.1900902721858 | etot = -14.6424332452502 +468000 ekin = 0.167159826102147 | erot = 0.355836258353843 | epot = -15.1654293296706 | etot = -14.6424332452146 +469000 ekin = 0.158918218022594 | erot = 0.341331890767393 | epot = -15.142683353977 | etot = -14.642433245187 +470000 ekin = 0.15045418565321 | erot = 0.329356584635604 | epot = -15.122244015456 | etot = -14.6424332451672 +471000 ekin = 0.141990180749419 | erot = 0.319964871778363 | epot = -15.1043882976826 | etot = -14.6424332451548 +472000 ekin = 0.133724353868213 | erot = 0.313128906246296 | epot = -15.0892865052631 | etot = -14.6424332451486 +473000 ekin = 0.125829398101872 | erot = 0.30875339232503 | epot = -15.0770160355745 | etot = -14.6424332451476 +474000 ekin = 0.118452666363189 | erot = 0.306693264414343 | epot = -15.0675791759279 | etot = -14.6424332451504 +475000 ekin = 0.111716976218893 | erot = 0.306773053291024 | epot = -15.0609232746654 | etot = -14.6424332451555 +476000 ekin = 0.105721655633223 | erot = 0.308806833537924 | epot = -15.0569617343329 | etot = -14.6424332451618 +477000 ekin = 0.100543523675712 | erot = 0.312617617130677 | epot = -15.0555943859742 | etot = -14.6424332451678 +478000 ekin = 0.0962376398644513 | erot = 0.318055055635923 | epot = -15.0567259406731 | etot = -14.6424332451728 +479000 ekin = 0.0928377950023785 | erot = 0.325010357031079 | epot = -15.0602813972093 | etot = -14.6424332451759 +480000 ekin = 0.090356854634411 | erot = 0.33342742776467 | epot = -15.0662175275758 | etot = -14.6424332451768 +481000 ekin = 0.0887871989354817 | erot = 0.343309423711643 | epot = -15.0745298678222 | etot = -14.6424332451751 +482000 ekin = 0.0881016191313876 | erot = 0.354720133059481 | epot = -15.0852549973622 | etot = -14.6424332451713 +483000 ekin = 0.0882551127429665 | erot = 0.367779908275322 | epot = -15.0984682661839 | etot = -14.6424332451656 +484000 ekin = 0.0891880440123839 | erot = 0.382656193510897 | epot = -15.1142774826821 | etot = -14.6424332451588 +485000 ekin = 0.0908310739090705 | erot = 0.399549033149946 | epot = -15.1328133522104 | etot = -14.6424332451514 +486000 ekin = 0.0931120890965814 | erot = 0.418672269927034 | epot = -15.154217604168 | etot = -14.6424332451444 +487000 ekin = 0.095965052636228 | erot = 0.440231422325024 | epot = -15.1786297200999 | etot = -14.6424332451386 +488000 ekin = 0.0993402613831294 | erot = 0.46439945138847 | epot = -15.2061729579066 | etot = -14.642433245135 +489000 ekin = 0.103214957393527 | erot = 0.491291775407073 | epot = -15.2369399779351 | etot = -14.6424332451345 +490000 ekin = 0.107602676592558 | erot = 0.520941965501705 | epot = -15.2709778872323 | etot = -14.6424332451381 +491000 ekin = 0.112559247659628 | erot = 0.553279563920015 | epot = -15.3082720567265 | etot = -14.6424332451469 +492000 ekin = 0.118183136718373 | erot = 0.588111425310959 | epot = -15.3487278071917 | etot = -14.6424332451624 +493000 ekin = 0.124608040121095 | erot = 0.625107908280837 | epot = -15.392149193588 | etot = -14.642433245186 +494000 ekin = 0.131986393307407 | erot = 0.663795156036258 | epot = -15.4382147945633 | etot = -14.6424332452196 +495000 ekin = 0.140463823895335 | erot = 0.703554605722134 | epot = -15.4864516748823 | etot = -14.6424332452649 +496000 ekin = 0.150146408031538 | erot = 0.743630741562818 | epot = -15.5362103949173 | etot = -14.642433245323 +497000 ekin = 0.16106457906771 | erot = 0.783147917316484 | epot = -15.5866457417788 | etot = -14.6424332453946 +498000 ekin = 0.17313921915462 | erot = 0.821136754970969 | epot = -15.6367092196046 | etot = -14.642433245479 +499000 ekin = 0.186156317831562 | erot = 0.856570103854254 | epot = -15.6851596672598 | etot = -14.642433245574 +500000 ekin = 0.199756195068111 | erot = 0.888407758271 | epot = -15.7305971990146 | etot = -14.6424332456755 +501000 ekin = 0.213441517837515 | erot = 0.91564807872929 | epot = -15.7715228423448 | etot = -14.642433245778 +502000 ekin = 0.226605416599129 | erot = 0.937383433645168 | epot = -15.8064220961188 | etot = -14.6424332458745 +503000 ekin = 0.238577508979587 | erot = 0.952855183120512 | epot = -15.833865938058 | etot = -14.6424332459579 +504000 ekin = 0.248682347019072 | erot = 0.961503066783608 | epot = -15.852618659824 | etot = -14.6424332460214 +505000 ekin = 0.256302488972932 | erot = 0.963003656361611 | epot = -15.8617393913938 | etot = -14.6424332460593 +506000 ekin = 0.260937583147984 | erot = 0.957293217915285 | epot = -15.8606640471316 | etot = -14.6424332460684 +507000 ekin = 0.262251679303336 | erot = 0.944571918253111 | epot = -15.849256843604 | etot = -14.6424332460476 +508000 ekin = 0.260103184115659 | erot = 0.925288564928836 | epot = -15.8278249950432 | etot = -14.6424332459987 +509000 ekin = 0.254554875284732 | erot = 0.900107536932193 | epot = -15.7970956581424 | etot = -14.6424332459255 +510000 ekin = 0.245864483352383 | erot = 0.869861717979723 | epot = -15.7581594471658 | etot = -14.6424332458337 +511000 ekin = 0.234458914530911 | erot = 0.835496660120876 | epot = -15.7123888203816 | etot = -14.6424332457298 +512000 ekin = 0.220896820243761 | erot = 0.798011684060442 | epot = -15.6613417499246 | etot = -14.6424332456204 +513000 ekin = 0.205824805091364 | erot = 0.758403224573062 | epot = -15.6066612751764 | etot = -14.642433245512 +514000 ekin = 0.189932244119323 | erot = 0.717614706855288 | epot = -15.5499801963845 | etot = -14.6424332454099 +515000 ekin = 0.17390874820257 | erot = 0.676495918867881 | epot = -15.4928379123889 | etot = -14.6424332453184 +516000 ekin = 0.158407108511426 | erot = 0.635773516021008 | epot = -15.4366138697731 | etot = -14.6424332452406 +517000 ekin = 0.14401335018595 | erot = 0.596033149114218 | epot = -15.3824797444788 | etot = -14.6424332451787 +518000 ekin = 0.131224514119687 | erot = 0.557712825685522 | epot = -15.3313705849381 | etot = -14.6424332451329 +519000 ekin = 0.120434042407135 | erot = 0.521106495594791 | epot = -15.283973783105 | etot = -14.6424332451031 +520000 ekin = 0.111924165177655 | erot = 0.486376443197342 | epot = -15.2407338534629 | etot = -14.6424332450879 +521000 ekin = 0.105864424816476 | erot = 0.453572806058521 | epot = -15.2018704759605 | etot = -14.6424332450855 +522000 ekin = 0.102315362067652 | erot = 0.422658367130085 | epot = -15.1674069742913 | etot = -14.6424332450936 +523000 ekin = 0.101236366465111 | erot = 0.393536647096003 | epot = -15.1372062586706 | etot = -14.6424332451095 +524000 ekin = 0.102496717236374 | erot = 0.366081244307575 | epot = -15.1110112066745 | etot = -14.6424332451305 +525000 ekin = 0.105888887335369 | erot = 0.340164343214287 | epot = -15.0884864757035 | etot = -14.6424332451539 +526000 ekin = 0.111143247849981 | erot = 0.315682368378401 | epot = -15.069258861406 | etot = -14.6424332451776 +527000 ekin = 0.117943398961218 | erot = 0.292576937806713 | epot = -15.0529535819675 | etot = -14.6424332451996 +528000 ekin = 0.12594147425438 | erot = 0.270849598243415 | epot = -15.0392243177162 | etot = -14.6424332452184 +529000 ekin = 0.134772916008765 | erot = 0.250569317238797 | epot = -15.0277754784806 | etot = -14.642433245233 +530000 ekin = 0.144070383401974 | erot = 0.231872340651149 | epot = -15.0183759692965 | etot = -14.6424332452434 +531000 ekin = 0.15347660196879 | erot = 0.214954741433796 | epot = -15.0108645886522 | etot = -14.6424332452496 +532000 ekin = 0.162656054077 | erot = 0.200058697647209 | epot = -15.0051479969762 | etot = -14.642433245252 +533000 ekin = 0.171305419079586 | erot = 0.187454143182299 | epot = -15.0011928075133 | etot = -14.6424332452514 +534000 ekin = 0.179162595538566 | erot = 0.177417842692211 | epot = -14.9990136834797 | etot = -14.6424332452489 +535000 ekin = 0.186014006484961 | erot = 0.170212094440673 | epot = -14.9986593461708 | etot = -14.6424332452451 +536000 ekin = 0.191699759238903 | erot = 0.166065149224394 | epot = -15.0001981537044 | etot = -14.6424332452411 +537000 ekin = 0.196116169930247 | erot = 0.165155084977408 | epot = -15.003704500145 | etot = -14.6424332452374 +538000 ekin = 0.199215220532698 | erot = 0.16759836456926 | epot = -15.0092468303366 | etot = -14.6424332452346 +539000 ekin = 0.201000709668931 | erot = 0.173443713615155 | epot = -15.0168776685175 | etot = -14.6424332452334 +540000 ekin = 0.201521164037735 | erot = 0.182671367030103 | epot = -15.0266257763018 | etot = -14.642433245234 +541000 ekin = 0.200859940141597 | erot = 0.195197211440054 | epot = -15.0384903968184 | etot = -14.6424332452368 +542000 ekin = 0.199123298889485 | erot = 0.210880936221537 | epot = -15.0524374803529 | etot = -14.6424332452419 +543000 ekin = 0.196427519384797 | erot = 0.229537017788178 | epot = -15.0683977824221 | etot = -14.6424332452491 +544000 ekin = 0.192886294946265 | erot = 0.250947202002037 | epot = -15.0862667422075 | etot = -14.6424332452592 +545000 ekin = 0.188599710888657 | erot = 0.274873110236047 | epot = -15.105906066396 | etot = -14.6424332452713 +546000 ekin = 0.183646045244013 | erot = 0.301067663120938 | epot = -15.1271469536504 | etot = -14.6424332452855 +547000 ekin = 0.178077473819967 | erot = 0.329284179376605 | epot = -15.1497948984979 | etot = -14.6424332453014 +548000 ekin = 0.171920510268461 | erot = 0.359282253787744 | epot = -15.1736360093748 | etot = -14.6424332453186 +549000 ekin = 0.165181670578861 | erot = 0.390829837836081 | epot = -15.1984447537512 | etot = -14.6424332453363 +550000 ekin = 0.157858408655945 | erot = 0.423701326923182 | epot = -15.2239929809331 | etot = -14.642433245354 +551000 ekin = 0.149954809005839 | erot = 0.457671882722358 | epot = -15.2500599370991 | etot = -14.6424332453709 +552000 ekin = 0.141500835822421 | erot = 0.492508662666581 | epot = -15.2764427438753 | etot = -14.6424332453863 +553000 ekin = 0.132573145480449 | erot = 0.527960055130409 | epot = -15.3029664460102 | etot = -14.6424332453994 +554000 ekin = 0.123314645146745 | erot = 0.563744383275535 | epot = -15.3294922738321 | etot = -14.6424332454099 +555000 ekin = 0.113949270900184 | erot = 0.599539792629149 | epot = -15.3559223089468 | etot = -14.6424332454175 +556000 ekin = 0.104788088804101 | erot = 0.634977129568617 | epot = -15.3821984637955 | etot = -14.6424332454228 +557000 ekin = 0.096223065473816 | erot = 0.669637513728817 | epot = -15.4082938246293 | etot = -14.6424332454266 +558000 ekin = 0.0887059614381205 | erot = 0.703055990484285 | epot = -15.4341951973531 | etot = -14.6424332454307 +559000 ekin = 0.0827118847691962 | erot = 0.734732129427077 | epot = -15.4598772596334 | etot = -14.6424332454371 +560000 ekin = 0.0786899547209169 | erot = 0.764147748401263 | epot = -15.4852709485701 | etot = -14.6424332454479 +561000 ekin = 0.0770067720584255 | erot = 0.790791153077886 | epot = -15.5102311706012 | etot = -14.6424332454649 +562000 ekin = 0.0778911706718282 | erot = 0.814186471630634 | epot = -15.5345108877914 | etot = -14.6424332454889 +563000 ekin = 0.0813901113631115 | erot = 0.83392592548433 | epot = -15.557749282367 | etot = -14.6424332455196 +564000 ekin = 0.0873448530183196 | erot = 0.849702302566903 | epot = -15.57948040114 | etot = -14.6424332455547 +565000 ekin = 0.0953935152513145 | erot = 0.861338569498428 | epot = -15.5991653303408 | etot = -14.6424332455911 +566000 ekin = 0.105001366117329 | erot = 0.868811531658717 | epot = -15.6162461434001 | etot = -14.642433245624 +567000 ekin = 0.115514789209051 | erot = 0.872266750929858 | epot = -15.6302147857878 | etot = -14.6424332456489 +568000 ekin = 0.126230320989268 | erot = 0.872022546763063 | epot = -15.6406861134137 | etot = -14.6424332456614 +569000 ekin = 0.136467575204541 | erot = 0.868561781940356 | epot = -15.6474626028035 | etot = -14.6424332456586 +570000 ekin = 0.14563482322856 | erot = 0.862511177265558 | epot = -15.6505792461336 | etot = -14.6424332456395 +571000 ekin = 0.153278250259509 | erot = 0.854608991359196 | epot = -15.6503204872237 | etot = -14.642433245605 +572000 ekin = 0.159109636953315 | erot = 0.84566291861986 | epot = -15.6472058011309 | etot = -14.6424332455578 +573000 ekin = 0.163011362016618 | erot = 0.836500892323047 | epot = -15.6419454998422 | etot = -14.6424332455025 +574000 ekin = 0.165021239079159 | erot = 0.827918058208187 | epot = -15.635372542732 | etot = -14.6424332454446 +575000 ekin = 0.165302195907322 | erot = 0.820623479706763 | epot = -15.6283589210038 | etot = -14.6424332453898 +576000 ekin = 0.164102988099574 | erot = 0.815190165400983 | epot = -15.621726398844 | etot = -14.6424332453435 +577000 ekin = 0.161716152385172 | erot = 0.812011817945883 | epot = -15.6161612156416 | etot = -14.6424332453106 +578000 ekin = 0.158438569369477 | erot = 0.811269345695122 | epot = -15.6121411603591 | etot = -14.6424332452945 +579000 ekin = 0.154538688866709 | erot = 0.812909695780285 | epot = -15.6098816299442 | etot = -14.6424332452972 +580000 ekin = 0.150232988451571 | erot = 0.816638977240369 | epot = -15.609305211011 | etot = -14.642433245319 +581000 ekin = 0.145672809811868 | erot = 0.821931135408533 | epot = -15.6100371905791 | etot = -14.6424332453587 +582000 ekin = 0.140941476788303 | erot = 0.828052590347458 | epot = -15.6114273125488 | etot = -14.6424332454131 +583000 ekin = 0.136060602595946 | erot = 0.834102246892096 | epot = -15.6125960949662 | etot = -14.6424332454781 +584000 ekin = 0.131003759893458 | erot = 0.839065139153303 | epot = -15.6125021445952 | etot = -14.6424332455484 +585000 ekin = 0.12571521648007 | erot = 0.841876757443486 | epot = -15.6100252195418 | etot = -14.6424332456182 +586000 ekin = 0.120131224766287 | erot = 0.841493945660819 | epot = -15.6040584161085 | etot = -14.6424332456814 +587000 ekin = 0.11420138056985 | erot = 0.836967317747627 | epot = -15.5936019440499 | etot = -14.6424332457324 +588000 ekin = 0.107907808224915 | erot = 0.827509595977126 | epot = -15.5778506499685 | etot = -14.6424332457665 +589000 ekin = 0.101280337908428 | erot = 0.812554260667712 | epot = -15.5562678443564 | etot = -14.6424332457802 +590000 ekin = 0.0944063548781052 | erot = 0.791799488415071 | epot = -15.5286390890649 | etot = -14.6424332457717 +591000 ekin = 0.0874345511050671 | erot = 0.765233519218362 | epot = -15.4951013160642 | etot = -14.6424332457407 +592000 ekin = 0.0805723392089649 | erot = 0.733139214280964 | epot = -15.4561447991789 | etot = -14.642433245689 +593000 ekin = 0.0740771594091136 | erot = 0.696077455345172 | epot = -15.4125878603738 | etot = -14.6424332456195 +594000 ekin = 0.0682423089615399 | erot = 0.654850963355347 | epot = -15.3655265178539 | etot = -14.642433245537 +595000 ekin = 0.0633782539034779 | erot = 0.610451848321571 | epot = -15.3162633476718 | etot = -14.6424332454467 +596000 ekin = 0.0597906540673611 | erot = 0.563997548399802 | epot = -15.2662214478219 | etot = -14.6424332453547 +597000 ekin = 0.0577565493650921 | erot = 0.516660644083595 | epot = -15.2168504387157 | etot = -14.642433245267 +598000 ekin = 0.0575003158564784 | erot = 0.469598294353525 | epot = -15.1695318553992 | etot = -14.6424332451892 +599000 ekin = 0.0591710965315349 | erot = 0.423886769451421 | epot = -15.125491111109 | etot = -14.6424332451261 +600000 ekin = 0.0628234356919278 | erot = 0.380465849282147 | epot = -15.0857225300552 | etot = -14.6424332450811 +601000 ekin = 0.0684027903404539 | erot = 0.340096852289996 | epot = -15.0509328876871 | etot = -14.6424332450566 +602000 ekin = 0.0757374499151871 | erot = 0.303336891509908 | epot = -15.0215075864782 | etot = -14.6424332450531 +603000 ekin = 0.0845381560125591 | erot = 0.27053072625361 | epot = -14.9975021273357 | etot = -14.6424332450695 +604000 ekin = 0.0944063594091915 | erot = 0.241820347964647 | epot = -14.9786599524771 | etot = -14.6424332451032 +605000 ekin = 0.104851562461362 | erot = 0.217171224792199 | epot = -14.9644560324035 | etot = -14.64243324515 +606000 ekin = 0.115317556390045 | erot = 0.196412930357212 | epot = -14.9541637319514 | etot = -14.6424332452042 +607000 ekin = 0.125216580352904 | erot = 0.179290709848448 | epot = -14.9469405354612 | etot = -14.6424332452598 +608000 ekin = 0.133969542489652 | erot = 0.165523445158619 | epot = -14.9419262329586 | etot = -14.6424332453103 +609000 ekin = 0.141049537027137 | erot = 0.154862582265986 | epot = -14.9383453646425 | etot = -14.6424332453493 +610000 ekin = 0.146025095174201 | erot = 0.147146040889238 | epot = -14.9356043814352 | etot = -14.6424332453717 +611000 ekin = 0.148599079333767 | erot = 0.142341118194411 | epot = -14.933373442902 | etot = -14.6424332453738 +612000 ekin = 0.148639027540153 | erot = 0.140571068728021 | epot = -14.9316433416219 | etot = -14.6424332453538 +613000 ekin = 0.146195193891304 | erot = 0.142121441396014 | epot = -14.9307498805999 | etot = -14.6424332453126 +614000 ekin = 0.141503544703229 | erot = 0.147424293659367 | epot = -14.931361083616 | etot = -14.6424332452534 +615000 ekin = 0.134972482668101 | erot = 0.157020849768253 | epot = -14.9344265776178 | etot = -14.6424332451814 +616000 ekin = 0.127153892886448 | erot = 0.171505679771477 | epot = -14.9410928177618 | etot = -14.6424332451039 +617000 ekin = 0.118700960496736 | erot = 0.191457667913385 | epot = -14.9525918734389 | etot = -14.6424332450288 +618000 ekin = 0.110316794782069 | erot = 0.217364584488849 | epot = -14.9701146242352 | etot = -14.6424332449643 +619000 ekin = 0.10269894266683 | erot = 0.249548776230041 | epot = -14.9946809638151 | etot = -14.6424332449182 +620000 ekin = 0.0964852203328795 | erot = 0.288101317489107 | epot = -15.0270197827187 | etot = -14.6424332448967 +621000 ekin = 0.0922059091544532 | erot = 0.332831044362015 | epot = -15.0674701984206 | etot = -14.6424332449041 +622000 ekin = 0.0902463647123495 | erot = 0.38323345185745 | epot = -15.1159130615123 | etot = -14.6424332449425 +623000 ekin = 0.0908226920728683 | erot = 0.438482716260395 | epot = -15.1717386533448 | etot = -14.6424332450115 +624000 ekin = 0.093971606254935 | erot = 0.497448307332334 | epot = -15.2338531586955 | etot = -14.6424332451083 +625000 ekin = 0.0995541611253139 | erot = 0.558735886776706 | epot = -15.3007232931298 | etot = -14.6424332452277 +626000 ekin = 0.107271859328534 | erot = 0.620750477448395 | epot = -15.3704555821401 | etot = -14.6424332453632 +627000 ekin = 0.116692826740249 | erot = 0.681778220893157 | epot = -15.4409042931398 | etot = -14.6424332455064 +628000 ekin = 0.127285245275924 | erot = 0.740081431761873 | epot = -15.5097999226864 | etot = -14.6424332456486 +629000 ekin = 0.138455039155856 | erot = 0.794000196763613 | epot = -15.5748884817005 | etot = -14.642433245781 +630000 ekin = 0.149584842938721 | erot = 0.842052640234425 | epot = -15.6340707290684 | etot = -14.6424332458952 +631000 ekin = 0.160071499854236 | erot = 0.883025442873649 | epot = -15.6855301887126 | etot = -14.6424332459847 +632000 ekin = 0.169359720293564 | erot = 0.91604650342356 | epot = -15.7278394697617 | etot = -14.6424332460446 +633000 ekin = 0.176970053692923 | erot = 0.940632922939441 | epot = -15.7600362227046 | etot = -14.6424332460723 +634000 ekin = 0.182519961289934 | erot = 0.956709735134031 | epot = -15.7816629424917 | etot = -14.6424332460677 +635000 ekin = 0.185737466035253 | erot = 0.964597760207907 | epot = -15.7927684722764 | etot = -14.6424332460332 +636000 ekin = 0.18646751930257 | erot = 0.964972204259268 | epot = -15.793872969535 | etot = -14.6424332459731 +637000 ekin = 0.184671774603444 | erot = 0.958796660380516 | epot = -15.7859016808771 | etot = -14.6424332458931 +638000 ekin = 0.18042282577675 | erot = 0.947239527077747 | epot = -15.7700955986542 | etot = -14.6424332457997 +639000 ekin = 0.173894119063336 | erot = 0.931581224201453 | epot = -15.7479085889647 | etot = -14.6424332456999 +640000 ekin = 0.165346701826116 | erot = 0.913120838758794 | epot = -15.7209007861851 | etot = -14.6424332456002 +641000 ekin = 0.155113786101916 | erot = 0.89309006009493 | epot = -15.690637091703 | etot = -14.6424332455061 +642000 ekin = 0.143583869242389 | erot = 0.87258071031098 | epot = -15.6585978249756 | etot = -14.6424332454222 +643000 ekin = 0.131182953687747 | erot = 0.852490168058439 | epot = -15.6261063670979 | etot = -14.6424332453517 +644000 ekin = 0.118356305759423 | erot = 0.833486853993461 | epot = -15.5942764050496 | etot = -14.6424332452967 +645000 ekin = 0.105550209083462 | erot = 0.815995971214927 | epot = -15.5639794255562 | etot = -14.6424332452578 +646000 ekin = 0.0931942744180316 | erot = 0.800204061932273 | epot = -15.5358315815851 | etot = -14.6424332452348 +647000 ekin = 0.0816850001788887 | erot = 0.786079744440846 | epot = -15.5101979898461 | etot = -14.6424332452264 +648000 ekin = 0.0713713598428991 | erot = 0.773407243192036 | epot = -15.4872118482655 | etot = -14.6424332452306 +649000 ekin = 0.0625431628711377 | erot = 0.761828976528719 | epot = -15.4668053846447 | etot = -14.6424332452448 +650000 ekin = 0.0554227735500933 | erot = 0.75089345341146 | epot = -15.4487494722279 | etot = -14.6424332452664 +651000 ekin = 0.0501605027659751 | erot = 0.740104978445454 | epot = -15.4326987265037 | etot = -14.6424332452922 +652000 ekin = 0.0468336713668763 | erot = 0.728972100417424 | epot = -15.4182390171038 | etot = -14.6424332453195 +653000 ekin = 0.0454490492582802 | erot = 0.717052285941716 | epot = -15.4049345805454 | etot = -14.6424332453455 +654000 ekin = 0.0459481524955786 | erot = 0.703990869780758 | epot = -15.392372267644 | etot = -14.6424332453677 +655000 ekin = 0.0482147495301334 | erot = 0.689552835103776 | epot = -15.3802008300181 | etot = -14.6424332453842 +656000 ekin = 0.0520838761279773 | erot = 0.673646332746782 | epot = -15.3681634542682 | etot = -14.6424332453934 +657000 ekin = 0.0573516620866903 | erot = 0.656337023113106 | epot = -15.3561219305943 | etot = -14.6424332453945 +658000 ekin = 0.0637853134946501 | erot = 0.637852348217965 | epot = -15.3440709070998 | etot = -14.6424332453872 +659000 ekin = 0.071132670288702 | erot = 0.618574815847019 | epot = -15.3321407315078 | etot = -14.6424332453721 +660000 ekin = 0.0791308828115974 | erot = 0.599023454708769 | epot = -15.3205875828708 | etot = -14.6424332453504 +661000 ekin = 0.0875139366244701 | erot = 0.579822939748188 | epot = -15.3097701216973 | etot = -14.6424332453246 +662000 ekin = 0.0960190004205403 | erot = 0.561660610348952 | epot = -15.3001128560671 | etot = -14.6424332452976 +663000 ekin = 0.104391848885285 | erot = 0.545232746056431 | epot = -15.2920578402148 | etot = -14.642433245273 +664000 ekin = 0.112391863389559 | erot = 0.531182949320054 | epot = -15.2860080579644 | etot = -14.6424332452547 +665000 ekin = 0.119797262719833 | erot = 0.520037124798717 | epot = -15.2822676327648 | etot = -14.6424332452462 +666000 ekin = 0.126411190061272 | erot = 0.512141060962375 | epot = -15.2809854962742 | etot = -14.6424332452505 +667000 ekin = 0.132069035722133 | erot = 0.507607681730257 | epot = -15.2821099627219 | etot = -14.6424332452695 +668000 ekin = 0.136646914538578 | erot = 0.50628131575487 | epot = -15.2853614755967 | etot = -14.6424332453033 +669000 ekin = 0.14007061600892 | erot = 0.507725566171504 | epot = -15.290229427531 | etot = -14.6424332453506 +670000 ekin = 0.142323740902298 | erot = 0.511239425097736 | epot = -15.2959964114079 | etot = -14.6424332454078 +671000 ekin = 0.143453306298631 | erot = 0.515903234043245 | epot = -15.3017897858122 | etot = -14.6424332454703 +672000 ekin = 0.143571012728183 | erot = 0.520652256715692 | epot = -15.3066565149759 | etot = -14.642433245532 +673000 ekin = 0.142848733833163 | erot = 0.524371563353989 | epot = -15.309653542774 | etot = -14.6424332455869 +674000 ekin = 0.141507613274597 | erot = 0.526002362927265 | epot = -15.3099432218308 | etot = -14.6424332456289 +675000 ekin = 0.139801302823325 | erot = 0.52464762902093 | epot = -15.3068821774981 | etot = -14.6424332456538 +676000 ekin = 0.137995095209364 | erot = 0.51966443903789 | epot = -15.3000927799057 | etot = -14.6424332456584 +677000 ekin = 0.136343677284965 | erot = 0.510732098514629 | epot = -15.2895090214414 | etot = -14.6424332456418 +678000 ekin = 0.135070664123434 | erot = 0.497888575253593 | epot = -15.275392484982 | etot = -14.6424332456049 +679000 ekin = 0.134352810446671 | erot = 0.481532294130257 | epot = -15.2583183501274 | etot = -14.6424332455504 +680000 ekin = 0.134310862658399 | erot = 0.462390968603737 | epot = -15.2391350767444 | etot = -14.6424332454823 +681000 ekin = 0.135007638926426 | erot = 0.441462941784009 | epot = -15.2189038261157 | etot = -14.6424332454053 +682000 ekin = 0.136452461528327 | erot = 0.419938865037714 | epot = -15.1988245718906 | etot = -14.6424332453245 +683000 ekin = 0.138609887401881 | erot = 0.399112293315981 | epot = -15.180155425963 | etot = -14.6424332452451 +684000 ekin = 0.141410065652151 | erot = 0.380287181763355 | epot = -15.1641304925875 | etot = -14.642433245172 +685000 ekin = 0.144758102725857 | erot = 0.364688846300657 | epot = -15.1518801941363 | etot = -14.6424332451098 +686000 ekin = 0.148540467122566 | erot = 0.353383275615777 | epot = -15.1443569878012 | etot = -14.6424332450628 +687000 ekin = 0.152627512101214 | erot = 0.347208212231946 | epot = -15.1422689693676 | etot = -14.6424332450344 +688000 ekin = 0.156872371009962 | erot = 0.34671840827179 | epot = -15.1460240243092 | etot = -14.6424332450275 +689000 ekin = 0.161107527975645 | erot = 0.352146941115415 | epot = -15.1556877141346 | etot = -14.6424332450435 +690000 ekin = 0.165141087380615 | erot = 0.363384304941253 | epot = -15.1709586374049 | etot = -14.642433245083 +691000 ekin = 0.16875504264815 | erot = 0.379976931154794 | epot = -15.1911652189476 | etot = -14.6424332451446 +692000 ekin = 0.171707649701913 | erot = 0.401146558394978 | epot = -15.2152874533223 | etot = -14.6424332452254 +693000 ekin = 0.173741393440548 | erot = 0.425831232784737 | epot = -15.242005871546 | etot = -14.6424332453207 +694000 ekin = 0.174597110621582 | erot = 0.452747528135183 | epot = -15.2697778841809 | etot = -14.6424332454241 +695000 ekin = 0.174033757468543 | erot = 0.480471830916593 | epot = -15.2969388339132 | etot = -14.6424332455281 +696000 ekin = 0.171852263360719 | erot = 0.507536398151815 | epot = -15.3218219071368 | etot = -14.6424332456242 +697000 ekin = 0.167921065286729 | erot = 0.532533688686105 | epot = -15.3428879996772 | etot = -14.6424332457043 +698000 ekin = 0.162200409472839 | erot = 0.554220619917834 | epot = -15.3588542751518 | etot = -14.6424332457611 +699000 ekin = 0.154762415711639 | erot = 0.571613361020687 | epot = -15.368809022521 | etot = -14.6424332457887 +700000 ekin = 0.145804230005146 | erot = 0.584063387080839 | epot = -15.3723008628696 | etot = -14.6424332457836 +701000 ekin = 0.13565226955545 | erot = 0.591306922714551 | epot = -15.3693924380152 | etot = -14.6424332457452 +702000 ekin = 0.124756460204928 | erot = 0.593482464342697 | epot = -15.3606721702232 | etot = -14.6424332456756 +703000 ekin = 0.113674325949402 | erot = 0.59111440185125 | epot = -15.3472219733801 | etot = -14.6424332455794 +704000 ekin = 0.103045675944469 | erot = 0.585064323191519 | epot = -15.3305432445998 | etot = -14.6424332454638 +705000 ekin = 0.0935593581959462 | erot = 0.576454826530277 | epot = -15.3124474300635 | etot = -14.6424332453373 +706000 ekin = 0.0859140824288432 | erot = 0.566573150252908 | epot = -15.2949204778911 | etot = -14.6424332452093 +707000 ekin = 0.0807756759568232 | erot = 0.55676342760618 | epot = -15.279972348653 | etot = -14.64243324509 +708000 ekin = 0.0787333622616465 | erot = 0.54831685528832 | epot = -15.2694834625381 | etot = -14.6424332449882 +709000 ekin = 0.0802577669172614 | erot = 0.542368667951201 | epot = -15.2650596797804 | etot = -14.642433244912 +710000 ekin = 0.0856633545554371 | erot = 0.539809747046566 | epot = -15.2679063464696 | etot = -14.6424332448676 +711000 ekin = 0.0950778519056249 | erot = 0.541219180888583 | epot = -15.2787302776533 | etot = -14.642433244859 +712000 ekin = 0.108420876625254 | erot = 0.546822307908553 | epot = -15.2976764294217 | etot = -14.6424332448878 +713000 ekin = 0.125393451698048 | erot = 0.556476834654628 | epot = -15.3243035313057 | etot = -14.642433244953 +714000 ekin = 0.145479367624672 | erot = 0.569687600116107 | epot = -15.3576002127918 | etot = -14.642433245051 +715000 ekin = 0.167958541120004 | erot = 0.585648522299775 | epot = -15.396040308596 | etot = -14.6424332451762 +716000 ekin = 0.191931735854258 | erot = 0.603308292528111 | epot = -15.4376732737035 | etot = -14.6424332453212 +717000 ekin = 0.216355400179739 | erot = 0.621454592033966 | epot = -15.4802432376909 | etot = -14.6424332454772 +718000 ekin = 0.240085056513045 | erot = 0.638810139728873 | epot = -15.5213284418766 | etot = -14.6424332456347 +719000 ekin = 0.261925698577652 | erot = 0.654132895984068 | epot = -15.5584918403458 | etot = -14.6424332457841 +720000 ekin = 0.280687969313521 | erot = 0.666312379865826 | epot = -15.5894335950958 | etot = -14.6424332459165 +721000 ekin = 0.295249345590636 | erot = 0.674454385927398 | epot = -15.6121369775414 | etot = -14.6424332460234 +722000 ekin = 0.304619886334687 | erot = 0.677947410255859 | epot = -15.6250005426882 | etot = -14.6424332460976 +723000 ekin = 0.308011983728321 | erot = 0.676505724572276 | epot = -15.6269509544342 | etot = -14.6424332461336 +724000 ekin = 0.304912667284023 | erot = 0.670186105902545 | epot = -15.6175320193137 | etot = -14.6424332461272 +725000 ekin = 0.295155116710468 | erot = 0.659377522493427 | epot = -15.5969658852801 | etot = -14.6424332460762 +726000 ekin = 0.278983134898227 | erot = 0.644765363163313 | epot = -15.5661817440425 | etot = -14.6424332459809 +727000 ekin = 0.257098790791736 | erot = 0.62727386036856 | epot = -15.5268058970048 | etot = -14.6424332458445 +728000 ekin = 0.230680158271606 | erot = 0.607992016186632 | epot = -15.4811054201315 | etot = -14.6424332456733 +729000 ekin = 0.201354496272774 | erot = 0.58808946404084 | epot = -15.4318772057915 | etot = -14.6424332454779 +730000 ekin = 0.171114103975002 | erot = 0.568729214722098 | epot = -15.3822765639698 | etot = -14.6424332452727 +731000 ekin = 0.142168923907796 | erot = 0.550984135076758 | epot = -15.33558630406 | etot = -14.6424332450754 +732000 ekin = 0.116742007096204 | erot = 0.535763349049472 | epot = -15.2949386010509 | etot = -14.6424332449052 +733000 ekin = 0.096829302753487 | erot = 0.523753647326654 | epot = -15.2630161948605 | etot = -14.6424332447804 +734000 ekin = 0.0839596135584424 | erot = 0.515379592342729 | epot = -15.2417724506162 | etot = -14.642433244715 +735000 ekin = 0.0789983701762927 | erot = 0.510784464199122 | epot = -15.2322160790918 | etot = -14.6424332447164 +736000 ekin = 0.0820355551920711 | erot = 0.509832642268435 | epot = -15.2343014422439 | etot = -14.6424332447834 +737000 ekin = 0.0923827123854171 | erot = 0.512132550856583 | epot = -15.2469485081483 | etot = -14.6424332449063 +738000 ekin = 0.108680448513047 | erot = 0.517077971027771 | epot = -15.2681916646097 | etot = -14.6424332450689 +739000 ekin = 0.12909371568261 | erot = 0.523904364926295 | epot = -15.2954313258598 | etot = -14.6424332452509 +740000 ekin = 0.151555277793257 | erot = 0.531755895778738 | epot = -15.325744419004 | etot = -14.642433245432 +741000 ekin = 0.174012721805987 | erot = 0.539758083452137 | epot = -15.3562040508521 | etot = -14.642433245594 +742000 ekin = 0.194640916830775 | erot = 0.54709054969783 | epot = -15.3841647122517 | etot = -14.6424332457231 +743000 ekin = 0.211995737397994 | erot = 0.55305412533586 | epot = -15.4074831085444 | etot = -14.6424332458105 +744000 ekin = 0.225100508722061 | erot = 0.557126762308091 | epot = -15.4246605168829 | etot = -14.6424332458528 +745000 ekin = 0.233469424485911 | erot = 0.559003260237678 | epot = -15.4349059305744 | etot = -14.6424332458508 +746000 ekin = 0.237079913464194 | erot = 0.558614810498956 | epot = -15.4381279697723 | etot = -14.6424332458091 +747000 ekin = 0.236308652984083 | erot = 0.556125790082259 | epot = -15.4348676888015 | etot = -14.6424332457352 +748000 ekin = 0.231845097887127 | erot = 0.551907079329901 | epot = -15.4261854228554 | etot = -14.6424332456383 +749000 ekin = 0.224593843483487 | erot = 0.5464873600296 | epot = -15.4135144490423 | etot = -14.6424332455292 +750000 ekin = 0.215574369391546 | erot = 0.540486233484958 | epot = -15.3984938482955 | etot = -14.6424332454189 +751000 ekin = 0.20582458342619 | erot = 0.53453535676443 | epot = -15.3827931855088 | etot = -14.6424332453181 +752000 ekin = 0.196313335741677 | erot = 0.52919581521799 | epot = -15.3679423961961 | etot = -14.6424332452364 +753000 ekin = 0.187866475787172 | erot = 0.524881252730799 | epot = -15.3551809736992 | etot = -14.6424332451812 +754000 ekin = 0.181110613625732 | erot = 0.521796491095835 | epot = -15.3453403498786 | etot = -14.642433245157 +755000 ekin = 0.176438042203831 | erot = 0.519900210804112 | epot = -15.338771498173 | etot = -14.6424332451651 +756000 ekin = 0.173994962646518 | erot = 0.518897676281033 | epot = -15.3353258841305 | etot = -14.642433245203 +757000 ekin = 0.173693190270087 | erot = 0.518265706177492 | epot = -15.3343921417126 | etot = -14.642433245265 +758000 ekin = 0.175243155014324 | erot = 0.517307659815626 | epot = -15.3349840601728 | etot = -14.6424332453429 +759000 ekin = 0.178203703092592 | erot = 0.515231902157781 | epot = -15.3358688506772 | etot = -14.6424332454268 +760000 ekin = 0.182042463548471 | erot = 0.511243837941775 | epot = -15.335719546997 | etot = -14.6424332455067 +761000 ekin = 0.186199747761037 | erot = 0.504639825540337 | epot = -15.3332728188748 | etot = -14.6424332455734 +762000 ekin = 0.190149235945093 | erot = 0.494891409026847 | epot = -15.3274738905913 | etot = -14.6424332456194 +763000 ekin = 0.193449921094621 | erot = 0.481710238280717 | epot = -15.3175934050151 | etot = -14.6424332456397 +764000 ekin = 0.195785552426502 | erot = 0.465087294345954 | epot = -15.3033060924046 | etot = -14.6424332456321 +765000 ekin = 0.196989678184887 | erot = 0.445303873487528 | epot = -15.2847267972695 | etot = -14.6424332455971 +766000 ekin = 0.19705591918301 | erot = 0.42291544028873 | epot = -15.2624046050093 | etot = -14.6424332455375 +767000 ekin = 0.196134076494091 | erot = 0.398712320920873 | epot = -15.2372796428729 | etot = -14.642433245458 +768000 ekin = 0.194513096652852 | erot = 0.373662938957262 | epot = -15.2106092809747 | etot = -14.6424332453646 +769000 ekin = 0.192592017627679 | erot = 0.348845887485153 | epot = -15.1838711503774 | etot = -14.6424332452645 +770000 ekin = 0.190840163686972 | erot = 0.325376840212764 | epot = -15.1586502490652 | etot = -14.6424332451654 +771000 ekin = 0.1897483972283 | erot = 0.304335529901141 | epot = -15.1365171722047 | etot = -14.6424332450753 +772000 ekin = 0.189774341851613 | erot = 0.286697153922667 | epot = -15.1189047407758 | etot = -14.6424332450016 +773000 ekin = 0.191286034501537 | erot = 0.27327185783823 | epot = -15.1069911372904 | etot = -14.6424332449506 +774000 ekin = 0.194510000609521 | erot = 0.264655458971911 | epot = -15.1015987045092 | etot = -14.6424332449277 +775000 ekin = 0.199490639679884 | erot = 0.261194193157477 | epot = -15.1031180777726 | etot = -14.6424332449353 +776000 ekin = 0.206067477066043 | erot = 0.262965803936856 | epot = -15.1114665259764 | etot = -14.6424332449735 +777000 ekin = 0.213875019086207 | erot = 0.269778568413728 | epot = -15.1260868325396 | etot = -14.6424332450396 +778000 ekin = 0.222366868965229 | erot = 0.281188790676708 | epot = -15.1459889047703 | etot = -14.6424332451284 +779000 ekin = 0.230862102269011 | erot = 0.296535944175866 | epot = -15.1698312916772 | etot = -14.6424332452323 +780000 ekin = 0.238608567019495 | erot = 0.314993169090641 | epot = -15.1960349814528 | etot = -14.6424332453427 +781000 ekin = 0.244855557741785 | erot = 0.335629445234115 | epot = -15.2229182484261 | etot = -14.6424332454502 +782000 ekin = 0.248927612478623 | erot = 0.357478674283284 | epot = -15.2488395323078 | etot = -14.6424332455459 +783000 ekin = 0.250291897529631 | erot = 0.379610269023857 | epot = -15.2723354121756 | etot = -14.6424332456221 +784000 ekin = 0.248613283253181 | erot = 0.401195731117766 | epot = -15.2922422600437 | etot = -14.6424332456728 +785000 ekin = 0.243793133450733 | erot = 0.421566090460907 | epot = -15.3077924696054 | etot = -14.6424332456938 +786000 ekin = 0.235989501852441 | erot = 0.440255905200996 | epot = -15.3186786527368 | etot = -14.6424332456834 +787000 ekin = 0.225617610784245 | erot = 0.457030673426574 | epot = -15.3250815298531 | etot = -14.6424332456423 +788000 ekin = 0.213330260901315 | erot = 0.471895861690424 | epot = -15.3276593681654 | etot = -14.6424332455737 +789000 ekin = 0.199978499676675 | erot = 0.485087183877963 | epot = -15.3274989290377 | etot = -14.6424332454831 +790000 ekin = 0.186553834702789 | erot = 0.497043141238414 | epot = -15.326030221319 | etot = -14.6424332453778 +791000 ekin = 0.174114766792182 | erot = 0.508362048566067 | epot = -15.3249100606251 | etot = -14.6424332452668 +792000 ekin = 0.163702420431755 | erot = 0.519746739177836 | epot = -15.3258824047693 | etot = -14.6424332451597 +793000 ekin = 0.156252224966481 | erot = 0.531940822987091 | epot = -15.3306262930197 | etot = -14.6424332450661 +794000 ekin = 0.152510350035455 | erot = 0.545660777313313 | epot = -15.3406043723436 | etot = -14.6424332449949 +795000 ekin = 0.152964251159066 | erot = 0.561528326979781 | epot = -15.3569258230916 | etot = -14.6424332449528 +796000 ekin = 0.15779574735844 | erot = 0.580007578777105 | epot = -15.3802365710801 | etot = -14.6424332449446 +797000 ekin = 0.16686245785925 | erot = 0.601351255568902 | epot = -15.4106469584001 | etot = -14.6424332449719 +798000 ekin = 0.179709603433403 | erot = 0.625560121844854 | epot = -15.447702970312 | etot = -14.6424332450337 +799000 ekin = 0.19560996606243 | erot = 0.652359247175797 | epot = -15.4904024583644 | etot = -14.6424332451262 +800000 ekin = 0.213626158791752 | erot = 0.681194021872627 | epot = -15.5372534259076 | etot = -14.6424332452433 +801000 ekin = 0.232687040193831 | erot = 0.711247726385194 | epot = -15.5863680119562 | etot = -14.6424332453772 +802000 ekin = 0.251669429106228 | erot = 0.741480919834361 | epot = -15.6355835944599 | etot = -14.6424332455193 +803000 ekin = 0.269477067858276 | erot = 0.770691008419008 | epot = -15.6826013219375 | etot = -14.6424332456602 +804000 ekin = 0.285110541457411 | erot = 0.797588259155916 | epot = -15.7251320464043 | etot = -14.642433245791 +805000 ekin = 0.297723982505673 | erot = 0.820882528796815 | epot = -15.7610397572057 | etot = -14.6424332459032 +806000 ekin = 0.30666638768647 | erot = 0.839373432910558 | epot = -15.7884730665871 | etot = -14.6424332459901 +807000 ekin = 0.311506975554916 | erot = 0.852035914442971 | epot = -15.8059761360442 | etot = -14.6424332460463 +808000 ekin = 0.312045176252063 | erot = 0.858093398525486 | epot = -15.8125718208464 | etot = -14.6424332460689 +809000 ekin = 0.30830664238606 | erot = 0.857071970756237 | epot = -15.8078118591993 | etot = -14.642433246057 +810000 ekin = 0.300527220558558 | erot = 0.848831113926852 | epot = -15.7917915804976 | etot = -14.6424332460122 +811000 ekin = 0.28912720441781 | erot = 0.833569138620822 | epot = -15.7651295889765 | etot = -14.6424332459379 +812000 ekin = 0.2746784275983 | erot = 0.811804116492284 | epot = -15.7289157899297 | etot = -14.6424332458392 +813000 ekin = 0.257866835579241 | erot = 0.784333459542523 | epot = -15.684633540844 | etot = -14.6424332457223 +814000 ekin = 0.23945308058914 | erot = 0.752176980196793 | epot = -15.63406330638 | etot = -14.6424332455941 +815000 ekin = 0.220233415146368 | erot = 0.716509170267457 | epot = -15.5791758308754 | etot = -14.6424332454616 +816000 ekin = 0.20100275104127 | erot = 0.678586569749112 | epot = -15.5220225661217 | etot = -14.6424332453314 +817000 ekin = 0.182521261074943 | erot = 0.639675603866084 | epot = -15.4646301101505 | etot = -14.6424332452094 +818000 ekin = 0.165485401522765 | erot = 0.600985363832454 | epot = -15.4089040104563 | etot = -14.642433245101 +819000 ekin = 0.150503789775692 | erot = 0.563608719249991 | epot = -15.3565457540359 | etot = -14.6424332450102 +820000 ekin = 0.138078032174242 | erot = 0.528474068972577 | epot = -15.308985346087 | etot = -14.6424332449401 +821000 ekin = 0.128588386726507 | erot = 0.496309093117288 | epot = -15.2673307247366 | etot = -14.6424332448928 +822000 ekin = 0.122284066133886 | erot = 0.467617125514411 | epot = -15.2323344365174 | etot = -14.6424332448691 +823000 ekin = 0.119278020922195 | erot = 0.44266622847641 | epot = -15.2043774942678 | etot = -14.6424332448692 +824000 ekin = 0.119546158602377 | erot = 0.42149068273525 | epot = -15.1834700862294 | etot = -14.6424332448917 +825000 ekin = 0.122931110514134 | erot = 0.403904342219283 | epot = -15.1692686976682 | etot = -14.6424332449348 +826000 ekin = 0.129150803764817 | erot = 0.389525074994505 | epot = -15.1611091237546 | etot = -14.6424332449952 +827000 ekin = 0.137812176400569 | erot = 0.377809252264071 | epot = -15.158054673734 | etot = -14.6424332450694 +828000 ekin = 0.148430331610645 | erot = 0.368094906955542 | epot = -15.1589584837187 | etot = -14.6424332451525 +829000 ekin = 0.160453205764771 | erot = 0.359651737504109 | epot = -15.162538188508 | etot = -14.6424332452391 +830000 ekin = 0.173291382900576 | erot = 0.351735589536987 | epot = -15.1674602177612 | etot = -14.6424332453236 +831000 ekin = 0.186352012967387 | erot = 0.343644456321394 | epot = -15.172429714689 | etot = -14.6424332454002 +832000 ekin = 0.199074924610329 | erot = 0.334772487912646 | epot = -15.1762806579866 | etot = -14.6424332454636 +833000 ekin = 0.210968084885631 | erot = 0.324658115180747 | epot = -15.1780594455754 | etot = -14.6424332455091 +834000 ekin = 0.221638757262098 | erot = 0.313022323434907 | epot = -15.1770943262305 | etot = -14.6424332455335 +835000 ekin = 0.230816330006855 | erot = 0.299793483319955 | epot = -15.1730430588624 | etot = -14.6424332455356 +836000 ekin = 0.238363132178622 | erot = 0.285116039954994 | epot = -15.1659124176498 | etot = -14.6424332455161 +837000 ekin = 0.244270841534611 | erot = 0.269341751254713 | epot = -15.1560458382673 | etot = -14.642433245478 +838000 ekin = 0.248642320238308 | erot = 0.253003904099878 | epot = -15.144079469764 | etot = -14.6424332454258 +839000 ekin = 0.25166156932901 | erot = 0.236776758984113 | epot = -15.1308715736783 | etot = -14.6424332453652 +840000 ekin = 0.253557306828157 | erot = 0.221424057159315 | epot = -15.11741460929 | etot = -14.6424332453026 +841000 ekin = 0.254567562695185 | erot = 0.207741475742172 | epot = -15.1047422836805 | etot = -14.6424332452432 +842000 ekin = 0.254912814680605 | erot = 0.196498262353501 | epot = -15.0938443222254 | etot = -14.6424332451913 +843000 ekin = 0.254783130761291 | erot = 0.18838292178676 | epot = -15.0855992976977 | etot = -14.6424332451496 +844000 ekin = 0.254340789692194 | erot = 0.183956927272137 | epot = -15.0807309620835 | etot = -14.6424332451192 +845000 ekin = 0.253734932885203 | erot = 0.183619247980828 | epot = -15.0797874259659 | etot = -14.6424332450999 +846000 ekin = 0.253120504189253 | erot = 0.187583282240151 | epot = -15.0831370315206 | etot = -14.6424332450911 +847000 ekin = 0.25267165008145 | erot = 0.195866742639383 | epot = -15.0909716378134 | etot = -14.6424332450925 +848000 ekin = 0.252580915304042 | erot = 0.208294222463338 | epot = -15.1033083828718 | etot = -14.6424332451044 +849000 ekin = 0.25303996684305 | erot = 0.224511555531943 | epot = -15.1199847675022 | etot = -14.6424332451272 +850000 ekin = 0.254204001794731 | erot = 0.244010590097857 | epot = -15.1406478370545 | etot = -14.6424332451619 +851000 ekin = 0.256148339024686 | erot = 0.26616256360269 | epot = -15.1647441478359 | etot = -14.6424332452085 +852000 ekin = 0.258829686440298 | erot = 0.290257858698357 | epot = -15.1915207904045 | etot = -14.6424332452658 +853000 ekin = 0.262064657830092 | erot = 0.315549558168062 | epot = -15.2200474613289 | etot = -14.6424332453308 +854000 ekin = 0.265534116125796 | erot = 0.341297947737011 | epot = -15.2492653092615 | etot = -14.6424332453987 +855000 ekin = 0.268815174658096 | erot = 0.366813004431933 | epot = -15.2780614245538 | etot = -14.6424332454637 +856000 ekin = 0.271435486960135 | erot = 0.391492007902975 | epot = -15.3053607403827 | etot = -14.6424332455196 +857000 ekin = 0.272939108069148 | erot = 0.414849750475493 | epot = -15.3302221041057 | etot = -14.642433245561 +858000 ekin = 0.272951155046116 | erot = 0.43653939069067 | epot = -15.3519237913208 | etot = -14.642433245584 +859000 ekin = 0.271229880682587 | erot = 0.456362750062525 | epot = -15.3700258763315 | etot = -14.6424332455864 +860000 ekin = 0.267698633839444 | erot = 0.474269718464337 | epot = -15.3844015978728 | etot = -14.642433245569 +861000 ekin = 0.262455001757546 | erot = 0.490347316011832 | epot = -15.395235563303 | etot = -14.6424332455336 +862000 ekin = 0.255758797180207 | erot = 0.504799761303166 | epot = -15.4029918039675 | etot = -14.6424332454841 +863000 ekin = 0.248003564343611 | erot = 0.517921532816755 | epot = -15.4083583425855 | etot = -14.6424332454251 +864000 ekin = 0.23967765558561 | erot = 0.530065823507455 | epot = -15.4121767244549 | etot = -14.6424332453618 +865000 ekin = 0.23132088944464 | erot = 0.541610953537996 | epot = -15.4153650882815 | etot = -14.6424332452989 +866000 ekin = 0.223481813674061 | erot = 0.552927233335028 | epot = -15.41884229225 | etot = -14.6424332452409 +867000 ekin = 0.216679174488308 | erot = 0.564346499434596 | epot = -15.4234589191144 | etot = -14.6424332451915 +868000 ekin = 0.211369750013263 | erot = 0.576136138940125 | epot = -15.4299391341069 | etot = -14.6424332451535 +869000 ekin = 0.207923502302183 | erot = 0.588478941151671 | epot = -15.4388356885827 | etot = -14.6424332451288 +870000 ekin = 0.206606152993329 | erot = 0.601459626889461 | epot = -15.4504990250012 | etot = -14.6424332451184 +871000 ekin = 0.207568796750739 | erot = 0.615058451103504 | epot = -15.4650604929769 | etot = -14.6424332451226 +872000 ekin = 0.210843969893675 | erot = 0.629151875756264 | epot = -15.4824290907906 | etot = -14.6424332451407 +873000 ekin = 0.216347593110829 | erot = 0.643519970829237 | epot = -15.5023008091114 | etot = -14.6424332451714 +874000 ekin = 0.223886305134919 | erot = 0.657859909725313 | epot = -15.5241794600729 | etot = -14.6424332452126 +875000 ekin = 0.233169807544942 | erot = 0.671804662204777 | epot = -15.5474077150118 | etot = -14.6424332452621 +876000 ekin = 0.243827877956003 | erot = 0.684945735793168 | epot = -15.5712068590658 | etot = -14.6424332453167 +877000 ekin = 0.255431632539201 | erot = 0.696858567347312 | epot = -15.5947234452596 | etot = -14.6424332453731 +878000 ekin = 0.267518408507603 | erot = 0.707128927381253 | epot = -15.6170805813169 | etot = -14.642433245428 +879000 ekin = 0.279619300254697 | erot = 0.715378495713559 | epot = -15.6374310414462 | etot = -14.642433245478 +880000 ekin = 0.291287955017646 | erot = 0.721287639191614 | epot = -15.6550088397293 | etot = -14.64243324552 +881000 ekin = 0.30212877846337 | erot = 0.724613422803328 | epot = -15.6691754468184 | etot = -14.6424332455517 +882000 ekin = 0.31182230406922 | erot = 0.725201068169744 | epot = -15.6794566178103 | etot = -14.6424332455713 +883000 ekin = 0.32014524378975 | erot = 0.722987481097383 | epot = -15.6855659704652 | etot = -14.6424332455781 +884000 ekin = 0.326982762202525 | erot = 0.71799612015275 | epot = -15.6874121279281 | etot = -14.6424332455729 +885000 ekin = 0.332330882217529 | erot = 0.710323349666018 | epot = -15.6850874774407 | etot = -14.6424332455572 +886000 ekin = 0.336287673337269 | erot = 0.700117442970509 | epot = -15.6788383618419 | etot = -14.6424332455341 +887000 ekin = 0.339032964158867 | erot = 0.687552454431532 | epot = -15.6690186640977 | etot = -14.6424332455073 +888000 ekin = 0.340797654552277 | erot = 0.672800100940224 | epot = -15.6560310009735 | etot = -14.642433245481 +889000 ekin = 0.341825106167264 | erot = 0.656003407097172 | epot = -15.6402617587239 | etot = -14.6424332454594 +890000 ekin = 0.34232834758349 | erot = 0.637256013160967 | epot = -15.6220176061905 | etot = -14.642433245446 +891000 ekin = 0.342447730500064 | erot = 0.616590618565621 | epot = -15.6014715945091 | etot = -14.6424332454435 +892000 ekin = 0.342214057419122 | erot = 0.593979026502071 | epot = -15.5786263293741 | etot = -14.6424332454529 +893000 ekin = 0.341522004916641 | erot = 0.569344767729577 | epot = -15.55330001812 | etot = -14.6424332454737 +894000 ekin = 0.34011793412299 | erot = 0.54258751991292 | epot = -15.5251386995396 | etot = -14.6424332455037 +895000 ekin = 0.337605044786632 | erot = 0.513616778977975 | epot = -15.4936550693037 | etot = -14.6424332455391 +896000 ekin = 0.333467462875063 | erot = 0.48239077517222 | epot = -15.4582914836221 | etot = -14.6424332455748 +897000 ekin = 0.327113397523359 | erot = 0.44895570900175 | epot = -15.4185023521299 | etot = -14.6424332456048 +898000 ekin = 0.31793601762133 | erot = 0.413480165458452 | epot = -15.3738494287026 | etot = -14.6424332456228 +899000 ekin = 0.305389123796087 | erot = 0.376280077469223 | epot = -15.3241024468879 | etot = -14.6424332456226 +900000 ekin = 0.289072881395307 | erot = 0.337830752319189 | epot = -15.2693368793129 | etot = -14.6424332455984 +901000 ekin = 0.268822686259832 | erot = 0.298764046957366 | epot = -15.2100199787633 | etot = -14.6424332455461 +902000 ekin = 0.244791653969177 | erot = 0.259850521117947 | epot = -15.1470754205501 | etot = -14.642433245463 +903000 ekin = 0.217514571462771 | erot = 0.2219680472104 | epot = -15.0819158640225 | etot = -14.6424332453494 +904000 ekin = 0.187939204411673 | erot = 0.186059692012536 | epot = -15.0164321416331 | etot = -14.6424332452089 +905000 ekin = 0.157410847731541 | erot = 0.153084564883788 | epot = -14.9529286576644 | etot = -14.642433245049 +906000 ekin = 0.127599356271593 | erot = 0.123965703545267 | epot = -14.8939983046982 | etot = -14.6424332448813 +907000 ekin = 0.100365589130959 | erot = 0.0995389863896934 | epot = -14.8423378202412 | etot = -14.6424332447206 +908000 ekin = 0.0775759855948257 | erot = 0.0805066337401618 | epot = -14.800515863918 | etot = -14.642433244583 +909000 ekin = 0.060887695003573 | erot = 0.0673982354567931 | epot = -14.7707191749444 | etot = -14.642433244484 +910000 ekin = 0.051538292299 | erot = 0.0605415547707063 | epot = -14.7545130915056 | etot = -14.6424332444358 +911000 ekin = 0.0501789452911415 | erot = 0.060044698962114 | epot = -14.7526568886979 | etot = -14.6424332444447 +912000 ekin = 0.0567846925755186 | erot = 0.0657906450223113 | epot = -14.7650085821073 | etot = -14.6424332445095 +913000 ekin = 0.0706603747974273 | erot = 0.0774445361857558 | epot = -14.7905381556057 | etot = -14.6424332446226 +914000 ekin = 0.0905398584141984 | erot = 0.0944735694284727 | epot = -14.8274466726133 | etot = -14.6424332447706 +915000 ekin = 0.114756144633711 | erot = 0.116178630204803 | epot = -14.8733680197762 | etot = -14.6424332449377 +916000 ekin = 0.141447043407485 | erot = 0.141736093135474 | epot = -14.9256163816503 | etot = -14.6424332451073 +917000 ekin = 0.168758535424653 | erot = 0.170247440484187 | epot = -14.9814392211744 | etot = -14.6424332452655 +918000 ekin = 0.195014913443802 | erot = 0.200793639363233 | epot = -15.0382417982084 | etot = -14.6424332454014 +919000 ekin = 0.218837422087009 | erot = 0.232490666330172 | epot = -15.093761333925 | etot = -14.6424332455079 +920000 ekin = 0.239206641026131 | erot = 0.26454226708574 | epot = -15.1461821536939 | etot = -14.642433245582 +921000 ekin = 0.255474577150064 | erot = 0.296286050795975 | epot = -15.1941938735697 | etot = -14.6424332456236 +922000 ekin = 0.267338631216169 | erot = 0.327229363199175 | epot = -15.2370012400502 | etot = -14.6424332456349 +923000 ekin = 0.274791412213632 | erot = 0.357072039931877 | epot = -15.2742966977651 | etot = -14.6424332456196 +924000 ekin = 0.278059017514887 | erot = 0.385714059427459 | epot = -15.3062063225249 | etot = -14.6424332455826 +925000 ekin = 0.277537405166048 | erot = 0.413247220090753 | epot = -15.333217870786 | etot = -14.6424332455292 +926000 ekin = 0.273733135235252 | erot = 0.439931173657219 | epot = -15.3560975543576 | etot = -14.6424332454651 +927000 ekin = 0.267211859637779 | erot = 0.466155363878472 | epot = -15.3758004689124 | etot = -14.6424332453961 +928000 ekin = 0.25855584753175 | erot = 0.492389553499223 | epot = -15.3933786463589 | etot = -14.6424332453279 +929000 ekin = 0.248330567887068 | erot = 0.519126582978688 | epot = -15.4098903961314 | etot = -14.6424332452656 +930000 ekin = 0.237059747160937 | erot = 0.54682171162893 | epot = -15.426314704004 | etot = -14.6424332452141 +931000 ekin = 0.225208144800282 | erot = 0.575833282920741 | epot = -15.4434746728982 | etot = -14.6424332451772 +932000 ekin = 0.213171319360079 | erot = 0.606369490848937 | epot = -15.4619740553667 | etot = -14.6424332451577 +933000 ekin = 0.20127172299004 | erot = 0.63844569037598 | epot = -15.4821506585232 | etot = -14.6424332451571 +934000 ekin = 0.189760460104316 | erot = 0.671856006696139 | epot = -15.5040497119762 | etot = -14.6424332451757 +935000 ekin = 0.178823941832674 | erot = 0.70616199658427 | epot = -15.527419183629 | etot = -14.6424332452121 +936000 ekin = 0.168594479109506 | erot = 0.740699865834002 | epot = -15.5517275902073 | etot = -14.6424332452638 +937000 ekin = 0.159163635629787 | erot = 0.774606336202774 | epot = -15.5762032171595 | etot = -14.6424332453269 +938000 ekin = 0.15059697191027 | erot = 0.806861786792913 | epot = -15.5998920041001 | etot = -14.6424332453969 +939000 ekin = 0.14294871162838 | erot = 0.836347883523471 | epot = -15.6217298406203 | etot = -14.6424332454684 +940000 ekin = 0.136274889167807 | erot = 0.861915676025906 | epot = -15.6406238107299 | etot = -14.6424332455362 +941000 ekin = 0.130643703196332 | erot = 0.882459199117971 | epot = -15.6555361479093 | etot = -14.642433245595 +942000 ekin = 0.126142088158943 | erot = 0.89698906517013 | epot = -15.6655643989695 | etot = -14.6424332456404 +943000 ekin = 0.122877886109216 | erot = 0.904700444357472 | epot = -15.6700115761356 | etot = -14.6424332456689 +944000 ekin = 0.120977407411876 | erot = 0.905030230236174 | epot = -15.6684408833264 | etot = -14.6424332456784 +945000 ekin = 0.120578563691194 | erot = 0.897699054745601 | epot = -15.6607108641049 | etot = -14.6424332456681 +946000 ekin = 0.121820103594628 | erot = 0.88273507092903 | epot = -15.6469884201622 | etot = -14.6424332456386 +947000 ekin = 0.124827761130735 | erot = 0.860477935597424 | epot = -15.6277389423202 | etot = -14.642433245592 +948000 ekin = 0.129698334170688 | erot = 0.831563037039339 | epot = -15.6036946167418 | etot = -14.6424332455318 +949000 ekin = 0.136482857560386 | erot = 0.796887554723775 | epot = -15.5758036577462 | etot = -14.6424332454621 +950000 ekin = 0.145170138933456 | erot = 0.757561255989872 | epot = -15.5451646403111 | etot = -14.6424332453878 +951000 ekin = 0.155672002997282 | erot = 0.714845916095117 | epot = -15.5129511644064 | etot = -14.642433245314 +952000 ekin = 0.167811650838071 | erot = 0.67008783325117 | epot = -15.480332729335 | etot = -14.6424332452457 +953000 ekin = 0.1813165794726 | erot = 0.62464809521225 | epot = -15.4483979198723 | etot = -14.6424332451874 +954000 ekin = 0.19581750070188 | erot = 0.57983508069521 | epot = -15.4180858265396 | etot = -14.6424332451425 +955000 ekin = 0.21085460687665 | erot = 0.536843219767247 | epot = -15.3901310717574 | etot = -14.6424332451135 +956000 ekin = 0.225892299836444 | erot = 0.496701376788955 | epot = -15.3650269217267 | etot = -14.6424332451013 +957000 ekin = 0.240343066496815 | erot = 0.460233438090351 | epot = -15.3430097496926 | etot = -14.6424332451055 +958000 ekin = 0.253600493836713 | erot = 0.428032849889673 | epot = -15.3240665888504 | etot = -14.642433245124 +959000 ekin = 0.26508043374484 | erot = 0.400452005453744 | epot = -15.3079656843521 | etot = -14.6424332451535 +960000 ekin = 0.274268068126469 | erot = 0.3776065494438 | epot = -15.2943078627599 | etot = -14.6424332451896 +961000 ekin = 0.280767177999005 | erot = 0.359393861243336 | epot = -15.2825942844696 | etot = -14.6424332452273 +962000 ekin = 0.284346484058609 | erot = 0.345524198810109 | epot = -15.2723039281299 | etot = -14.6424332452611 +963000 ekin = 0.284976816085041 | erot = 0.335562232322697 | epot = -15.2629722936944 | etot = -14.6424332452867 +964000 ekin = 0.282852494243525 | erot = 0.32897598649065 | epot = -15.2542617260345 | etot = -14.6424332453003 +965000 ekin = 0.278391086611735 | erot = 0.325189577593081 | epot = -15.2460139095051 | etot = -14.6424332453002 +966000 ekin = 0.272207924676681 | erot = 0.32363564014577 | epot = -15.2382768101091 | etot = -14.6424332452866 +967000 ekin = 0.265065367869008 | erot = 0.323803079983236 | epot = -15.2313016931137 | etot = -14.6424332452614 +968000 ekin = 0.25780129371369 | erot = 0.325275872287489 | epot = -15.2255104112296 | etot = -14.6424332452284 +969000 ekin = 0.251245661475409 | erot = 0.327759142573897 | epot = -15.2214380492417 | etot = -14.6424332451924 +970000 ekin = 0.246137008995692 | erot = 0.331089781179722 | epot = -15.2196600353337 | etot = -14.6424332451582 +971000 ekin = 0.243051319619915 | erot = 0.335230325664632 | epot = -15.2207148904151 | etot = -14.6424332451306 +972000 ekin = 0.242353409643559 | erot = 0.340246678804852 | epot = -15.2250333335614 | etot = -14.642433245113 +973000 ekin = 0.244176338167963 | erot = 0.346272190711359 | epot = -15.2328817739871 | etot = -14.6424332451077 +974000 ekin = 0.248428661663719 | erot = 0.353462430362792 | epot = -15.2443243371426 | etot = -14.6424332451161 +975000 ekin = 0.254824314808527 | erot = 0.361946299431624 | epot = -15.2592038593783 | etot = -14.6424332451381 +976000 ekin = 0.262926848825399 | erot = 0.371779749930863 | epot = -15.2771398439293 | etot = -14.6424332451731 +977000 ekin = 0.272199235334822 | erot = 0.382908123264924 | epot = -15.2975406038191 | etot = -14.6424332452194 +978000 ekin = 0.282052066854486 | erot = 0.395142048097982 | epot = -15.3196273602273 | etot = -14.6424332452748 +979000 ekin = 0.291885751915432 | erot = 0.408150081471576 | epot = -15.3424690787237 | etot = -14.6424332453367 +980000 ekin = 0.301125083790032 | erot = 0.421469125222411 | epot = -15.365027454414 | etot = -14.6424332454016 +981000 ekin = 0.309246535916151 | erot = 0.434531423655712 | epot = -15.3862112050375 | etot = -14.6424332454657 +982000 ekin = 0.315799497488435 | erot = 0.446704965615556 | epot = -15.4049377086287 | etot = -14.6424332455247 +983000 ekin = 0.320422573217695 | erot = 0.457342632742344 | epot = -15.4201984515349 | etot = -14.6424332455749 +984000 ekin = 0.322855465254384 | erot = 0.465834622597573 | epot = -15.4311233334643 | etot = -14.6424332456124 +985000 ekin = 0.322946302470594 | erot = 0.471658590972097 | epot = -15.4370381390772 | etot = -14.6424332456345 +986000 ekin = 0.32065391780096 | erot = 0.47442255658858 | epot = -15.437509720029 | etot = -14.6424332456394 +987000 ekin = 0.316044627357463 | erot = 0.473896755513782 | epot = -15.432374628498 | etot = -14.6424332456268 +988000 ekin = 0.309283477264372 | erot = 0.470032116943487 | epot = -15.421748839805 | etot = -14.6424332455972 +989000 ekin = 0.300620522165357 | erot = 0.462964620620384 | epot = -15.4060183883382 | etot = -14.6424332455525 +990000 ekin = 0.290373280688083 | erot = 0.453006262993474 | epot = -15.3858127891769 | etot = -14.6424332454953 +991000 ekin = 0.27890691570339 | erot = 0.440624526217875 | epot = -15.3619646873503 | etot = -14.642433245429 +992000 ekin = 0.266613826413786 | erot = 0.426413006889876 | epot = -15.3354600786606 | etot = -14.642433245357 +993000 ekin = 0.253894212446129 | erot = 0.411056197523116 | epot = -15.3073836552521 | etot = -14.6424332452828 +994000 ekin = 0.241138837000641 | erot = 0.3952913723868 | epot = -15.2788634545973 | etot = -14.6424332452098 +995000 ekin = 0.228714768908433 | erot = 0.379870207853254 | epot = -15.2510182219026 | etot = -14.6424332451409 +996000 ekin = 0.216954417472708 | erot = 0.365522282704992 | epot = -15.2249099452563 | etot = -14.6424332450786 +997000 ekin = 0.206147766459094 | erot = 0.352922066135596 | epot = -15.2015030776196 | etot = -14.6424332450249 +998000 ekin = 0.196537413161582 | erot = 0.342660495987547 | epot = -15.1816311541306 | etot = -14.6424332449815 +999000 ekin = 0.188315843917336 | erot = 0.335221830001114 | epot = -15.1659709188676 | etot = -14.6424332449491 +1000000 ekin = 0.1816243230724 | erot = 0.33096613964385 | epot = -15.155023707645 | etot = -14.6424332449287 + 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 +Loop time of 17.1797 on 1 procs for 1000000 steps with 10 atoms + +Performance: 50291.944 tau/day, 58208.268 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.871 | 13.871 | 13.871 | 0.0 | 80.74 +Bond | 0.52454 | 0.52454 | 0.52454 | 0.0 | 3.05 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.14987 | 0.14987 | 0.14987 | 0.0 | 0.87 +Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 +Modify | 2.4075 | 2.4075 | 2.4075 | 0.0 | 14.01 +Other | | 0.227 | | | 1.32 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 45 +Ave neighs/atom = 4.5 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:17 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..4616a7453aedc151066d9455380d6890b930643a --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.07Aug19.duplex1.g++.4 @@ -0,0 +1,1166 @@ +LAMMPS (7 Aug 2019) +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + special bonds CPU = 0.000216 secs + read_data CPU = 0.003061 secs + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.956 + ghost atom cutoff = 1.956 + binsize = 0.978, bins = 41 41 41 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685) +Per MPI rank memory allocation (min/avg/max) = 7.33 | 7.512 | 7.694 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 +1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 +2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 +3000 ekin = 0.00997964450840756 | erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892 +4000 ekin = 0.017388811129498 | erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436 +5000 ekin = 0.0264744514136422 | erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104 +6000 ekin = 0.0369277948555727 | erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875 +7000 ekin = 0.0483950557190949 | erot = 0.185086295692109 | epot = -14.8759145965832 | etot = -14.642433245172 +8000 ekin = 0.0604909336919856 | erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611 +9000 ekin = 0.0728137406439518 | erot = 0.288273694501615 | epot = -15.003520680497 | etot = -14.6424332453514 +10000 ekin = 0.0849615563084574 | erot = 0.343654369293589 | epot = -15.0710491710418 | etot = -14.6424332454398 +11000 ekin = 0.0965486715044103 | erot = 0.400187932108393 | epot = -15.1391698491357 | etot = -14.6424332455229 +12000 ekin = 0.107221466282716 | erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598 +13000 ekin = 0.116672809719361 | erot = 0.512877765427945 | epot = -15.27198382081 | etot = -14.6424332456627 +14000 ekin = 0.124654073730849 | erot = 0.567333962045501 | epot = -15.3344212814915 | etot = -14.6424332457151 +15000 ekin = 0.130983939684084 | erot = 0.619586028257145 | epot = -15.3930032136957 | etot = -14.6424332457544 +16000 ekin = 0.135553354544703 | erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804 +17000 ekin = 0.138326263958104 | erot = 0.715418858086098 | epot = -15.4961783678378 | etot = -14.6424332457936 +18000 ekin = 0.139336096663942 | erot = 0.758296324628463 | epot = -15.5400656670878 | etot = -14.6424332457954 +19000 ekin = 0.138678360045107 | erot = 0.797544234276633 | epot = -15.5786558401095 | etot = -14.6424332457878 +20000 ekin = 0.136500074655344 | erot = 0.833084204411832 | epot = -15.6120175248401 | etot = -14.642433245773 +21000 ekin = 0.13298706528568 | erot = 0.864912408453387 | epot = -15.6403327194924 | etot = -14.6424332457533 +22000 ekin = 0.128350288213599 | erot = 0.893077649558743 | epot = -15.6638611835035 | etot = -14.6424332457311 +23000 ekin = 0.122812385135574 | erot = 0.917661024684626 | epot = -15.6829066555285 | etot = -14.6424332457083 +24000 ekin = 0.116595521408358 | erot = 0.938759014332623 | epot = -15.6977877814273 | etot = -14.6424332456863 +25000 ekin = 0.109911323474882 | erot = 0.956471207347589 | epot = -15.7088157764886 | etot = -14.6424332456661 +26000 ekin = 0.102953426207684 | erot = 0.970893163953319 | epot = -15.7162798358093 | etot = -14.6424332456483 +27000 ekin = 0.0958928250746599 | erot = 0.982114250193934 | epot = -15.7204403209012 | etot = -14.6424332456326 +28000 ekin = 0.0888759410949697 | erot = 0.990219731539457 | epot = -15.721528918253 | etot = -14.6424332456186 +29000 ekin = 0.0820250748771988 | erot = 0.995296041202221 | epot = -15.7197543616852 | etot = -14.6424332456058 +30000 ekin = 0.0754407616837521 | erot = 0.997437949319969 | epot = -15.7153119565969 | etot = -14.6424332455932 +31000 ekin = 0.0692054432607507 | erot = 0.996756332760959 | epot = -15.708395021602 | etot = -14.6424332455803 +32000 ekin = 0.0633878377974527 | erot = 0.993385345347641 | epot = -15.6992064287111 | etot = -14.642433245566 +33000 ekin = 0.0580474070866972 | erot = 0.987487973308198 | epot = -15.6879686259451 | etot = -14.6424332455502 +34000 ekin = 0.0532383791882911 | erot = 0.979259192919845 | epot = -15.6749308176403 | etot = -14.6424332455322 +35000 ekin = 0.0490128758302368 | erot = 0.968926197405304 | epot = -15.6603723187477 | etot = -14.6424332455122 +36000 ekin = 0.0454228081405029 | erot = 0.9567454096241 | epot = -15.6446014632554 | etot = -14.6424332454908 +37000 ekin = 0.0425203357170925 | erot = 0.942996237999004 | epot = -15.6279498191848 | etot = -14.6424332454687 +38000 ekin = 0.0403568280944576 | erot = 0.927971766615168 | epot = -15.6107618401563 | etot = -14.6424332454467 +39000 ekin = 0.0389804214208548 | erot = 0.911966804108811 | epot = -15.5933804709558 | etot = -14.6424332454262 +40000 ekin = 0.0384324238853382 | erot = 0.89526395956208 | epot = -15.5761296288558 | etot = -14.6424332454084 +41000 ekin = 0.038742986040685 | erot = 0.878118672837852 | epot = -15.559294904273 | etot = -14.6424332453944 +42000 ekin = 0.0399266053637394 | erot = 0.860744395135542 | epot = -15.543104245885 | etot = -14.6424332453857 +43000 ekin = 0.0419781561012778 | erot = 0.843299365356476 | epot = -15.5277107668409 | etot = -14.6424332453831 +44000 ekin = 0.044870189409001 | erot = 0.825876603313475 | epot = -15.5131800381094 | etot = -14.6424332453869 +45000 ekin = 0.0485521857416515 | erot = 0.808498758186206 | epot = -15.4994841893249 | etot = -14.642433245397 +46000 ekin = 0.0529522094038557 | erot = 0.791119212188469 | epot = -15.486504667005 | etot = -14.6424332454127 +47000 ekin = 0.0579809824244727 | erot = 0.773630265884061 | epot = -15.4740444937409 | etot = -14.6424332454323 +48000 ekin = 0.063537784650219 | erot = 0.755878310838164 | epot = -15.4618493409424 | etot = -14.642433245454 +49000 ekin = 0.0695169124467211 | erot = 0.737684732484754 | epot = -15.4496348904071 | etot = -14.6424332454756 +50000 ekin = 0.0758129058465106 | erot = 0.71887012622011 | epot = -15.437116277562 | etot = -14.6424332454954 +51000 ekin = 0.0823226638652303 | erot = 0.699278599520668 | epot = -15.424034508898 | etot = -14.6424332455121 +52000 ekin = 0.0889431481345008 | erot = 0.678798807099979 | epot = -15.4101752007595 | etot = -14.642433245525 +53000 ekin = 0.0955646689265035 | erot = 0.657379086771082 | epot = -15.3953770012322 | etot = -14.6424332455346 +54000 ekin = 0.102061477510161 | erot = 0.635035489169246 | epot = -15.3795302122208 | etot = -14.6424332455414 +55000 ekin = 0.108282960174666 | erot = 0.611853171347221 | epot = -15.362569377068 | etot = -14.6424332455461 +56000 ekin = 0.114049426282278 | erot = 0.587982945924278 | epot = -15.3444656177552 | etot = -14.6424332455487 +57000 ekin = 0.119155806187163 | erot = 0.563635255922936 | epot = -15.3252243076589 | etot = -14.6424332455488 +58000 ekin = 0.123384552305545 | erot = 0.539073355222423 | epot = -15.3048911530734 | etot = -14.6424332455455 +59000 ekin = 0.126526300954853 | erot = 0.514606324858908 | epot = -15.2835658713509 | etot = -14.6424332455371 +60000 ekin = 0.128404399836228 | erot = 0.490581338840041 | epot = -15.261418984199 | etot = -14.6424332455227 +61000 ekin = 0.128898142361895 | erot = 0.467373892400967 | epot = -15.2387052802647 | etot = -14.6424332455018 +62000 ekin = 0.127959880289724 | erot = 0.445374820086214 | epot = -15.2157679458512 | etot = -14.6424332454752 +63000 ekin = 0.125622870624276 | erot = 0.424973765387136 | epot = -15.1930298814554 | etot = -14.642433245444 +64000 ekin = 0.121999044842464 | erot = 0.406539918572064 | epot = -15.1709722088251 | etot = -14.6424332454106 +65000 ekin = 0.117268056618549 | erot = 0.390401831020304 | epot = -15.1501031330161 | etot = -14.6424332453772 +66000 ekin = 0.111660385256518 | erot = 0.376828594078844 | epot = -15.1309222246819 | etot = -14.6424332453465 +67000 ekin = 0.105437746904479 | erot = 0.366014539811003 | epot = -15.1138855320359 | etot = -14.6424332453205 +68000 ekin = 0.0988737375602367 | erot = 0.358069014155073 | epot = -15.0993759970159 | etot = -14.6424332453006 +69000 ekin = 0.0922368286498106 | erot = 0.353011948771939 | epot = -15.0876820227094 | etot = -14.6424332452876 +70000 ekin = 0.085776901527188 | erot = 0.350775174164926 | epot = -15.0789853209741 | etot = -14.642433245282 +71000 ekin = 0.0797156921641233 | erot = 0.351208844245479 | epot = -15.0733577816928 | etot = -14.6424332452832 +72000 ekin = 0.0742409440407214 | erot = 0.354092037747167 | epot = -15.0707662270785 | etot = -14.6424332452906 +73000 ekin = 0.0695037498703868 | erot = 0.359146526961236 | epot = -15.0710835221349 | etot = -14.6424332453033 +74000 ekin = 0.0656184497426901 | erot = 0.366052769878701 | epot = -15.0741044649413 | etot = -14.6424332453199 +75000 ekin = 0.0626644690394278 | erot = 0.374467290033983 | epot = -15.0795650044125 | etot = -14.642433245339 +76000 ekin = 0.060689553509186 | erot = 0.384040683403435 | epot = -15.087163482272 | etot = -14.6424332453594 +77000 ekin = 0.0597139401241187 | erot = 0.39443549589289 | epot = -15.0965826813962 | etot = -14.6424332453792 +78000 ekin = 0.0597350629875202 | erot = 0.405343151481915 | epot = -15.107511459867 | etot = -14.6424332453976 +79000 ekin = 0.0607324264361026 | erot = 0.416499017642699 | epot = -15.1196646894919 | etot = -14.6424332454131 +80000 ekin = 0.0626722904954167 | erot = 0.42769463023874 | epot = -15.1328001661592 | etot = -14.6424332454251 +81000 ekin = 0.0655118235331535 | erot = 0.438786127849123 | epot = -15.1467311968152 | etot = -14.6424332454329 +82000 ekin = 0.0692024020836612 | erot = 0.449698113830619 | epot = -15.1613337613509 | etot = -14.6424332454367 +83000 ekin = 0.0736917936904891 | erot = 0.46042249074083 | epot = -15.1765475298676 | etot = -14.6424332454363 +84000 ekin = 0.0789250526542213 | erot = 0.471012272295178 | epot = -15.1923705703823 | etot = -14.6424332454329 +85000 ekin = 0.084844087874249 | erot = 0.481570908650499 | epot = -15.2088482419521 | etot = -14.6424332454274 +86000 ekin = 0.0913860133243872 | erot = 0.492238169206333 | epot = -15.2260574279515 | etot = -14.6424332454208 +87000 ekin = 0.0984805441186009 | erot = 0.503174014617464 | epot = -15.2440878041507 | etot = -14.6424332454146 +88000 ekin = 0.106046830302566 | erot = 0.514542076496851 | epot = -15.2630221522094 | etot = -14.64243324541 +89000 ekin = 0.113990204125935 | erot = 0.526494309539917 | epot = -15.2829177590739 | etot = -14.642433245408 +90000 ekin = 0.122199339149548 | erot = 0.539158097286353 | epot = -15.3037906818453 | etot = -14.6424332454094 +91000 ekin = 0.130544275968788 | erot = 0.552626637866356 | epot = -15.3256041592498 | etot = -14.6424332454146 +92000 ekin = 0.138875666145967 | erot = 0.566952900962782 | epot = -15.3482618125326 | etot = -14.6424332454239 +93000 ekin = 0.147025440611607 | erot = 0.582146933738072 | epot = -15.3716056197866 | etot = -14.642433245437 +94000 ekin = 0.154808946844651 | erot = 0.598175891801872 | epot = -15.3954180841001 | etot = -14.6424332454536 +95000 ekin = 0.162028449598904 | erot = 0.614965942454512 | epot = -15.4194276375267 | etot = -14.6424332454733 +96000 ekin = 0.168477779664558 | erot = 0.632405154082716 | epot = -15.4433161792427 | etot = -14.6424332454954 +97000 ekin = 0.173947863023514 | erot = 0.650346631629012 | epot = -15.466727740172 | etot = -14.6424332455195 +98000 ekin = 0.17823287500116 | erot = 0.668611435746641 | epot = -15.4892775562927 | etot = -14.6424332455449 +99000 ekin = 0.181136831923464 | erot = 0.686991165056919 | epot = -15.5105612425515 | etot = -14.6424332455712 +100000 ekin = 0.182480533640968 | erot = 0.70525041340853 | epot = -15.530164192647 | etot = -14.6424332455975 +101000 ekin = 0.182108871449626 | erot = 0.723129571004015 | epot = -15.5476716880769 | etot = -14.6424332456233 +102000 ekin = 0.179898581168333 | erot = 0.740348571091266 | epot = -15.5626803979072 | etot = -14.6424332456476 +103000 ekin = 0.175766517606564 | erot = 0.756612167826943 | epot = -15.5748119311029 | etot = -14.6424332456694 +104000 ekin = 0.169678431534366 | erot = 0.771617166852901 | epot = -15.5837288440747 | etot = -14.6424332456875 +105000 ekin = 0.16165803603624 | erot = 0.785061742963522 | epot = -15.5891530247003 | etot = -14.6424332457006 +106000 ekin = 0.1517958676503 | erot = 0.79665661342635 | epot = -15.5908857267839 | etot = -14.6424332457072 +107000 ekin = 0.140257112952973 | erot = 0.806137449199221 | epot = -15.5888278078584 | etot = -14.6424332457062 +108000 ekin = 0.12728724020187 | erot = 0.813277564483295 | epot = -15.5829980503819 | etot = -14.6424332456967 +109000 ekin = 0.113214025491873 | erot = 0.817899691736779 | epot = -15.5735469629067 | etot = -14.6424332456781 +110000 ekin = 0.098444482381739 | erot = 0.81988557805637 | epot = -15.5607633060887 | etot = -14.6424332456506 +111000 ekin = 0.0834553769378614 | erot = 0.819182262548248 | epot = -15.5450708851013 | etot = -14.6424332456151 +112000 ekin = 0.0687764915886159 | erot = 0.815804215096793 | epot = -15.5270139522589 | etot = -14.6424332455735 +113000 ekin = 0.0549665904044352 | erot = 0.809830999846637 | epot = -15.5072308357791 | etot = -14.642433245528 +114000 ekin = 0.0425830583135686 | erot = 0.801400700352864 | epot = -15.486417004148 | etot = -14.6424332454816 +115000 ekin = 0.032147280214672 | erot = 0.790699910050555 | epot = -15.4652804357027 | etot = -14.6424332454374 +116000 ekin = 0.0241087780358436 | erot = 0.777951546675731 | epot = -15.4444935701102 | etot = -14.6424332453986 +117000 ekin = 0.0188117102739906 | erot = 0.763402004774535 | epot = -15.4246469604164 | etot = -14.6424332453679 +118000 ekin = 0.0164673894168239 | erot = 0.747309167856823 | epot = -15.4062098026205 | etot = -14.6424332453469 +119000 ekin = 0.0171359296540405 | erot = 0.729932564574684 | epot = -15.3895017395652 | etot = -14.6424332453365 +120000 ekin = 0.0207190822436557 | erot = 0.711526526248979 | epot = -15.3746788538292 | etot = -14.6424332453366 +121000 ekin = 0.0269649552324791 | erot = 0.692336677371669 | epot = -15.3617348779504 | etot = -14.6424332453462 +122000 ekin = 0.0354839220302067 | erot = 0.67259957021192 | epot = -15.3505167376056 | etot = -14.6424332453635 +123000 ekin = 0.0457738626455522 | erot = 0.652544850162972 | epot = -15.3407519581945 | etot = -14.642433245386 +124000 ekin = 0.0572521324300914 | erot = 0.632399068063522 | epot = -15.3320844459048 | etot = -14.6424332454111 +125000 ekin = 0.0692913736007718 | erot = 0.612390156183436 | epot = -15.3241147752205 | etot = -14.6424332454363 +126000 ekin = 0.0812564128179042 | erot = 0.592751635107165 | epot = -15.3164412933838 | etot = -14.6424332454588 +127000 ekin = 0.0925398817831167 | erot = 0.573725774405778 | epot = -15.3086989016655 | etot = -14.6424332454767 +128000 ekin = 0.102594692019408 | erot = 0.555565138942016 | epot = -15.3005930764496 | etot = -14.6424332454881 +129000 ekin = 0.11096195387447 | erot = 0.538532171476867 | epot = -15.2919273708433 | etot = -14.642433245492 +130000 ekin = 0.117293279473245 | erot = 0.522896664452867 | epot = -15.2826231894136 | etot = -14.6424332454875 +131000 ekin = 0.121366644775215 | erot = 0.508931150171148 | epot = -15.2727310404211 | etot = -14.6424332454747 +132000 ekin = 0.123095155540091 | erot = 0.496904390905846 | epot = -15.2624327918999 | etot = -14.642433245454 +133000 ekin = 0.122528239671734 | erot = 0.487073282997867 | epot = -15.2520347680959 | etot = -14.6424332454263 +134000 ekin = 0.119845042601894 | erot = 0.479673601171197 | epot = -15.2419518891665 | etot = -14.6424332453934 +135000 ekin = 0.115340171967421 | erot = 0.474910093717031 | epot = -15.2326835110416 | etot = -14.6424332453571 +136000 ekin = 0.109402419285642 | erot = 0.472946484075328 | epot = -15.224782148681 | etot = -14.64243324532 +137000 ekin = 0.102487634022665 | erot = 0.473895929920059 | epot = -15.2188168092271 | etot = -14.6424332452844 +138000 ekin = 0.0950874634054126 | erot = 0.477812435585917 | epot = -15.2153331442443 | etot = -14.6424332452529 +139000 ekin = 0.0876961121518134 | erot = 0.484683617751174 | epot = -15.2148129751312 | etot = -14.6424332452282 +140000 ekin = 0.0807775418435475 | erot = 0.494425108540512 | epot = -15.2176358955961 | etot = -14.642433245212 +141000 ekin = 0.0747355681580414 | erot = 0.506876770810756 | epot = -15.2240455841751 | etot = -14.6424332452063 +142000 ekin = 0.0698891098451744 | erot = 0.521800821241298 | epot = -15.2341231762987 | etot = -14.6424332452123 +143000 ekin = 0.0664544171867047 | erot = 0.538881922426197 | epot = -15.247769584843 | etot = -14.6424332452301 +144000 ekin = 0.0645355104692778 | erot = 0.557729316021908 | epot = -15.2646980717509 | etot = -14.6424332452598 +145000 ekin = 0.0641233595163661 | erot = 0.577881111413867 | epot = -15.2844377162306 | etot = -14.6424332453003 +146000 ekin = 0.0651036077516285 | erot = 0.598810893852426 | epot = -15.3063477469543 | etot = -14.6424332453502 +147000 ekin = 0.0672719578975283 | erot = 0.619936843682121 | epot = -15.3296420469869 | etot = -14.6424332454073 +148000 ekin = 0.0703557492694452 | erot = 0.640633538190891 | epot = -15.3534225329293 | etot = -14.6424332454689 +149000 ekin = 0.0740398128645613 | erot = 0.66024652323733 | epot = -15.3767195816343 | etot = -14.6424332455324 +150000 ekin = 0.077994420106261 | erot = 0.678109590375523 | epot = -15.3985372560764 | etot = -14.6424332455946 +151000 ekin = 0.0819030604176878 | erot = 0.693564488647254 | epot = -15.4179007947176 | etot = -14.6424332456527 +152000 ekin = 0.08548789385576 | erot = 0.705982563002905 | epot = -15.4339037025625 | etot = -14.6424332457038 +153000 ekin = 0.0885310147333655 | erot = 0.714787575381006 | epot = -15.4457518358599 | etot = -14.6424332457455 +154000 ekin = 0.0908901012892495 | erot = 0.719478762726426 | epot = -15.4528021097914 | etot = -14.6424332457757 +155000 ekin = 0.0925075703718949 | erot = 0.719653046096655 | epot = -15.4545938622616 | etot = -14.642433245793 +156000 ekin = 0.0934129479732331 | erot = 0.71502524375301 | epot = -15.4508714375228 | etot = -14.6424332457966 +157000 ekin = 0.0937187435781837 | erot = 0.7054451639455 | epot = -15.4415971533099 | etot = -14.6424332457862 +158000 ekin = 0.0936106185394034 | erot = 0.690910554325068 | epot = -15.4269544186268 | etot = -14.6424332457623 +159000 ekin = 0.0933330174009798 | erot = 0.671575051659369 | epot = -15.4073413147861 | etot = -14.6424332457258 +160000 ekin = 0.0931716565239132 | erot = 0.647750492120475 | epot = -15.3833553943224 | etot = -14.6424332456781 +161000 ekin = 0.0934343296226144 | erot = 0.619903194016677 | epot = -15.3557707692603 | etot = -14.642433245621 +162000 ekin = 0.0944314104796785 | erot = 0.588644098979961 | epot = -15.3255087550165 | etot = -14.6424332455568 +163000 ekin = 0.0964572425730066 | erot = 0.554712943454524 | epot = -15.2936034315153 | etot = -14.6424332454878 +164000 ekin = 0.0997733472794833 | erot = 0.51895691856277 | epot = -15.2611635112587 | etot = -14.6424332454165 +165000 ekin = 0.104594102018619 | erot = 0.482304549423464 | epot = -15.2293318967876 | etot = -14.6424332453455 +166000 ekin = 0.111075276514824 | erot = 0.445735768513581 | epot = -15.1992442903059 | etot = -14.6424332452775 +167000 ekin = 0.119305597512052 | erot = 0.410249354729612 | epot = -15.1719881974565 | etot = -14.6424332452149 +168000 ekin = 0.12930135472349 | erot = 0.376829046180065 | epot = -15.1485636460635 | etot = -14.64243324516 +169000 ekin = 0.141003965788119 | erot = 0.346409702528372 | epot = -15.1298469134313 | etot = -14.6424332451148 +170000 ekin = 0.154280377438306 | erot = 0.319844892419105 | epot = -15.1165585149385 | etot = -14.6424332450811 +171000 ekin = 0.168926178619928 | erot = 0.297877221607854 | epot = -15.1092366452879 | etot = -14.6424332450601 +172000 ekin = 0.184671319362937 | erot = 0.281112611137901 | epot = -15.1082171755536 | etot = -14.6424332450527 +173000 ekin = 0.201188345435602 | erot = 0.269999595570589 | epot = -15.1136211860655 | etot = -14.6424332450593 +174000 ekin = 0.218103052205587 | erot = 0.264814547402911 | epot = -15.1253508446879 | etot = -14.6424332450794 +175000 ekin = 0.235007413034244 | erot = 0.265653545949627 | epot = -15.1430942040962 | etot = -14.6424332451123 +176000 ekin = 0.251474534266602 | erot = 0.272431389431356 | epot = -15.1663391688545 | etot = -14.6424332451566 +177000 ekin = 0.267075225142183 | erot = 0.284887984977502 | epot = -15.1943964553298 | etot = -14.6424332452101 +178000 ekin = 0.281395553894085 | erot = 0.302602030913778 | epot = -15.2264308300785 | etot = -14.6424332452706 +179000 ekin = 0.294054514410707 | erot = 0.325011526056011 | epot = -15.2614992858019 | etot = -14.6424332453351 +180000 ekin = 0.304720692895811 | erot = 0.351440214933808 | epot = -15.2985941532306 | etot = -14.6424332454009 +181000 ekin = 0.313126658917312 | erot = 0.381128639600623 | epot = -15.3366885439829 | etot = -14.6424332454649 +182000 ekin = 0.319079775822514 | erot = 0.413268071112208 | epot = -15.3747810924592 | etot = -14.6424332455245 +183000 ekin = 0.322468290004655 | erot = 0.447035301735044 | epot = -15.4119368373172 | etot = -14.6424332455775 +184000 ekin = 0.323261947553556 | erot = 0.481626155079162 | epot = -15.4473213482551 | etot = -14.6424332456224 +185000 ekin = 0.321506983529697 | erot = 0.516285658867075 | epot = -15.4802258880548 | etot = -14.642433245658 +186000 ekin = 0.317316057632531 | erot = 0.550333132629024 | epot = -15.5100824359458 | etot = -14.6424332456842 +187000 ekin = 0.310854440588904 | erot = 0.583180936762622 | epot = -15.5364686230528 | etot = -14.6424332457012 +188000 ekin = 0.30232432976273 | erot = 0.614346238386881 | epot = -15.5591038138594 | etot = -14.6424332457098 +189000 ekin = 0.291949445195852 | erot = 0.643455779015098 | epot = -15.5778384699219 | etot = -14.6424332457109 +190000 ekin = 0.279961942766932 | erot = 0.670244185707524 | epot = -15.5926393741803 | etot = -14.6424332457058 +191000 ekin = 0.266593185652274 | erot = 0.694546781237202 | epot = -15.6035732125848 | etot = -14.6424332456953 +192000 ekin = 0.252069141621896 | erot = 0.716288088791507 | epot = -15.6107904760939 | etot = -14.6424332456805 +193000 ekin = 0.2366102932526 | erot = 0.735467302247593 | epot = -15.6145108411624 | etot = -14.6424332456622 +194000 ekin = 0.220435149403491 | erot = 0.75214194303258 | epot = -15.6150103380771 | etot = -14.642433245641 +195000 ekin = 0.203765880091661 | erot = 0.766410799035626 | epot = -15.6126099247449 | etot = -14.6424332456176 +196000 ekin = 0.186834339035651 | erot = 0.778397083256526 | epot = -15.6076646678849 | etot = -14.6424332455927 +197000 ekin = 0.169886782292464 | erot = 0.788232586076187 | epot = -15.6005526139357 | etot = -14.642433245567 +198000 ekin = 0.153185871076301 | erot = 0.796043434544246 | epot = -15.5916625511619 | etot = -14.6424332455413 +199000 ekin = 0.137008972985795 | erot = 0.801937915803759 | epot = -15.5813801343063 | etot = -14.6424332455168 +200000 ekin = 0.121642272363314 | erot = 0.805996673265824 | epot = -15.5700721911236 | etot = -14.6424332454944 +201000 ekin = 0.107370722655147 | erot = 0.808265456810171 | epot = -15.5580694249409 | etot = -14.6424332454756 +202000 ekin = 0.0944644042380589 | erot = 0.808750524312638 | epot = -15.545648174012 | etot = -14.6424332454613 +203000 ekin = 0.0831623790884324 | erot = 0.807416772445363 | epot = -15.5330123969865 | etot = -14.6424332454527 +204000 ekin = 0.0736556272327789 | erot = 0.804188725420783 | epot = -15.5202775981043 | etot = -14.6424332454507 +205000 ekin = 0.066071040166988 | erot = 0.79895460735607 | epot = -15.5074588929788 | etot = -14.6424332454557 +206000 ekin = 0.0604586317676951 | erot = 0.79157380942372 | epot = -15.494465686659 | etot = -14.6424332454675 +207000 ekin = 0.0567840026879156 | erot = 0.781888054797388 | epot = -15.4811053029705 | etot = -14.6424332454852 +208000 ekin = 0.0549275971597975 | erot = 0.769736381378222 | epot = -15.4670972240452 | etot = -14.6424332455072 +209000 ekin = 0.054691444753414 | erot = 0.754973659532252 | epot = -15.4520983498168 | etot = -14.6424332455311 +210000 ekin = 0.0558130126770424 | erot = 0.737491764373083 | epot = -15.4357380226042 | etot = -14.6424332455541 +211000 ekin = 0.0579847210232219 | erot = 0.717241838878542 | epot = -15.4176598054751 | etot = -14.6424332455734 +212000 ekin = 0.0608768356197334 | erot = 0.694255492638095 | epot = -15.3975655738439 | etot = -14.642433245586 +213000 ekin = 0.0641610427072994 | erot = 0.66866247616279 | epot = -15.37525676446 | etot = -14.6424332455899 +214000 ekin = 0.0675321043575128 | erot = 0.64070249551818 | epot = -15.3506678454593 | etot = -14.6424332455836 +215000 ekin = 0.0707255336353422 | erot = 0.610729417268954 | epot = -15.3238881964709 | etot = -14.6424332455666 +216000 ekin = 0.0735300437817614 | erot = 0.579207054839019 | epot = -15.2951703441601 | etot = -14.6424332455393 +217000 ekin = 0.0757943994877641 | erot = 0.546696813211868 | epot = -15.2649244582025 | etot = -14.6424332455029 +218000 ekin = 0.0774290394165078 | erot = 0.51383845121943 | epot = -15.2337007360952 | etot = -14.6424332454593 +219000 ekin = 0.0784033323141758 | erot = 0.481325894964748 | epot = -15.2021624726897 | etot = -14.6424332454108 +220000 ekin = 0.0787395495607948 | erot = 0.449880299622387 | epot = -15.1710530945427 | etot = -14.6424332453595 +221000 ekin = 0.0785046319672525 | erot = 0.420222425160561 | epot = -15.1411603024357 | etot = -14.6424332453079 +222000 ekin = 0.0778006814269618 | erot = 0.393045972171563 | epot = -15.1132798988567 | etot = -14.6424332452582 +223000 ekin = 0.0767549035385332 | erot = 0.368992968911871 | epot = -15.0881811176628 | etot = -14.6424332452124 +224000 ekin = 0.0755095293703771 | erot = 0.348631757033118 | epot = -15.0665745315758 | etot = -14.6424332451723 +225000 ekin = 0.0742120885667612 | erot = 0.332437700429432 | epot = -15.0490830341357 | etot = -14.6424332451395 +226000 ekin = 0.0730063028693098 | erot = 0.320776497502258 | epot = -15.0362160454869 | etot = -14.6424332451153 +227000 ekin = 0.0720238140882299 | erot = 0.313889923629038 | epot = -15.0283469828185 | etot = -14.6424332451012 +228000 ekin = 0.0713769419939713 | erot = 0.311883945247486 | epot = -15.0256941323393 | etot = -14.6424332450978 +229000 ekin = 0.0711526728858612 | erot = 0.314719386439623 | epot = -15.0283053044314 | etot = -14.6424332451059 +230000 ekin = 0.0714080974066282 | erot = 0.32220563858993 | epot = -15.0360469811226 | etot = -14.6424332451261 +231000 ekin = 0.0721675361189904 | erot = 0.333998222201802 | epot = -15.0485990034788 | etot = -14.6424332451581 +232000 ekin = 0.073421602290549 | erot = 0.349601270465942 | epot = -15.0654561179577 | etot = -14.6424332452012 +233000 ekin = 0.0751284397505166 | erot = 0.368376135875933 | epot = -15.0859378208811 | etot = -14.6424332452547 +234000 ekin = 0.0772173235442522 | erot = 0.389557254433757 | epot = -15.1092078232945 | etot = -14.6424332453165 +235000 ekin = 0.0795947059802171 | erot = 0.412276079790421 | epot = -15.1343040311544 | etot = -14.6424332453838 +236000 ekin = 0.0821526186146683 | erot = 0.435593295647697 | epot = -15.160179159716 | etot = -14.6424332454537 +237000 ekin = 0.0847791014239972 | erot = 0.458538653864687 | epot = -15.1857510008109 | etot = -14.6424332455222 +238000 ekin = 0.087370042385855 | erot = 0.480156759886663 | epot = -15.209960047858 | etot = -14.6424332455854 +239000 ekin = 0.0898415153137564 | erot = 0.49955609555256 | epot = -15.2318308565057 | etot = -14.6424332456394 +240000 ekin = 0.0921414623535534 | erot = 0.515957735400968 | epot = -15.2505324434352 | etot = -14.6424332456807 +241000 ekin = 0.094259449014392 | erot = 0.528739776886534 | epot = -15.2654324716071 | etot = -14.6424332457062 +242000 ekin = 0.0962332805880934 | erot = 0.537473606136267 | epot = -15.2761401324386 | etot = -14.6424332457143 +243000 ekin = 0.0981515319338797 | erot = 0.541948785980249 | epot = -15.2825335636184 | etot = -14.6424332457043 +244000 ekin = 0.100151482351181 | erot = 0.542184479374293 | epot = -15.2847692074025 | etot = -14.642433245677 +245000 ekin = 0.102412491095747 | erot = 0.53842670231772 | epot = -15.2832724390477 | etot = -14.6424332456343 +246000 ekin = 0.105145395544779 | erot = 0.531132085866326 | epot = -15.2787107269898 | etot = -14.6424332455787 +247000 ekin = 0.108578961411965 | erot = 0.520939994206832 | epot = -15.2719522011324 | etot = -14.6424332455137 +248000 ekin = 0.112944688754503 | erot = 0.50863565229522 | epot = -15.2640135864927 | etot = -14.6424332454429 +249000 ekin = 0.118461348905117 | erot = 0.495107336753362 | epot = -15.256001931029 | etot = -14.6424332453705 +250000 ekin = 0.125320510713189 | erot = 0.48130071319677 | epot = -15.24905446921 | etot = -14.6424332453 +251000 ekin = 0.13367405695507 | erot = 0.468173145423505 | epot = -15.2442804476135 | etot = -14.6424332452349 +252000 ekin = 0.14362435587275 | erot = 0.456650355973621 | epot = -15.2427079570245 | etot = -14.6424332451781 +253000 ekin = 0.155217400154316 | erot = 0.447587277165273 | epot = -15.2452379224515 | etot = -14.6424332451319 +254000 ekin = 0.168438906844309 | erot = 0.441734376017195 | epot = -15.2526065279595 | etot = -14.642433245098 +255000 ekin = 0.183213121644152 | erot = 0.43971022735342 | epot = -15.265356594075 | etot = -14.6424332450774 +256000 ekin = 0.199403908832121 | erot = 0.441980689733431 | epot = -15.2838178436366 | etot = -14.642433245071 +257000 ekin = 0.216817638461841 | erot = 0.448844730305144 | epot = -15.308095613846 | etot = -14.642433245079 +258000 ekin = 0.235207399035704 | erot = 0.460426746275348 | epot = -15.3380673904121 | etot = -14.642433245101 +259000 ekin = 0.254278151366077 | erot = 0.476675120648602 | epot = -15.3733865171511 | etot = -14.6424332451364 +260000 ekin = 0.27369257667687 | erot = 0.497366691706637 | epot = -15.4134925135677 | etot = -14.6424332451842 +261000 ekin = 0.293077534073047 | erot = 0.522116767905255 | epot = -15.4576275472214 | etot = -14.6424332452431 +262000 ekin = 0.312031202020343 | erot = 0.550394247121191 | epot = -15.5048586944528 | etot = -14.6424332453112 +263000 ekin = 0.330131107615792 | erot = 0.58154128199962 | epot = -15.5541056350021 | etot = -14.6424332453866 +264000 ekin = 0.346943319969756 | erot = 0.61479677344706 | epot = -15.6041733388837 | etot = -14.6424332454669 +265000 ekin = 0.362033078254018 | erot = 0.649322794997101 | epot = -15.6537891188009 | etot = -14.6424332455498 +266000 ekin = 0.374977027495908 | erot = 0.684232889060489 | epot = -15.7016431621888 | etot = -14.6424332456324 +267000 ekin = 0.385377045180443 | erot = 0.718621072064117 | epot = -15.7464313629566 | etot = -14.642433245712 +268000 ekin = 0.392875374675087 | erot = 0.75159036946736 | epot = -15.7868989899283 | etot = -14.6424332457858 +269000 ekin = 0.397170471133826 | erot = 0.782279784278077 | epot = -15.8218835012632 | etot = -14.6424332458513 +270000 ekin = 0.39803266202252 | erot = 0.809888771679688 | epot = -15.8503546796085 | etot = -14.6424332459063 +271000 ekin = 0.395318487593041 | erot = 0.833698516715799 | epot = -15.8714502502577 | etot = -14.6424332459488 +272000 ekin = 0.388982474346436 | erot = 0.85308955191437 | epot = -15.8845052722382 | etot = -14.6424332459774 +273000 ekin = 0.379085147925793 | erot = 0.867555470410658 | epot = -15.8890738643275 | etot = -14.6424332459911 +274000 ekin = 0.365796322187783 | erot = 0.876712662634482 | epot = -15.8849422308119 | etot = -14.6424332459896 +275000 ekin = 0.349393082916365 | erot = 0.880306121918412 | epot = -15.872132450808 | etot = -14.6424332459733 +276000 ekin = 0.330252358900911 | erot = 0.878211432152944 | epot = -15.8508970369967 | etot = -14.6424332459429 +277000 ekin = 0.308838461215969 | erot = 0.87043308488023 | epot = -15.821704791996 | etot = -14.6424332458998 +278000 ekin = 0.285686394600485 | erot = 0.857099294887703 | epot = -15.7852189353341 | etot = -14.6424332458459 +279000 ekin = 0.26138204276351 | erot = 0.838453513182823 | epot = -15.7422688017294 | etot = -14.642433245783 +280000 ekin = 0.236540473323807 | erot = 0.814842890588987 | epot = -15.6938166096265 | etot = -14.6424332457138 +281000 ekin = 0.211783602606672 | erot = 0.786704032858688 | epot = -15.6409208811058 | etot = -14.6424332456404 +282000 ekin = 0.18771833727137 | erot = 0.754546508157259 | epot = -15.5846980909942 | etot = -14.6424332455655 +283000 ekin = 0.164916115091084 | erot = 0.718934708844117 | epot = -15.5262840694266 | etot = -14.6424332454914 +284000 ekin = 0.143894549222789 | erot = 0.680468811937684 | epot = -15.466796606581 | etot = -14.6424332454205 +285000 ekin = 0.125101678374108 | erot = 0.639765701845435 | epot = -15.4073006255745 | etot = -14.642433245355 +286000 ekin = 0.108903164109883 | erot = 0.597440790007762 | epot = -15.3487771994138 | etot = -14.6424332452962 +287000 ekin = 0.0955726645582656 | erot = 0.554091668601873 | epot = -15.2920975784058 | etot = -14.6424332452456 +288000 ekin = 0.0852855448042878 | erot = 0.51028445681865 | epot = -15.2380032468271 | etot = -14.6424332452042 +289000 ekin = 0.0781160413142908 | erot = 0.466543535619429 | epot = -15.187092822106 | etot = -14.6424332451723 +290000 ekin = 0.0740379578661526 | erot = 0.423345127585162 | epot = -15.1398163306014 | etot = -14.6424332451501 +291000 ekin = 0.07292891006789 | erot = 0.38111487943337 | epot = -15.0964770346382 | etot = -14.6424332451369 +292000 ekin = 0.0745780357973755 | erot = 0.340229271733751 | epot = -15.0572405526629 | etot = -14.6424332451317 +293000 ekin = 0.0786969407585494 | erot = 0.301020346544363 | epot = -15.0221505324362 | etot = -14.6424332451333 +294000 ekin = 0.0849334564747798 | erot = 0.263782947584644 | epot = -14.9911496491993 | etot = -14.6424332451399 +295000 ekin = 0.0928875723651302 | erot = 0.22878344880309 | epot = -14.9641042663181 | etot = -14.6424332451499 +296000 ekin = 0.102128697511331 | erot = 0.196268840383788 | epot = -14.9408307830568 | etot = -14.6424332451617 +297000 ekin = 0.11221325250056 | erot = 0.166475068215614 | epot = -14.9211215658898 | etot = -14.6424332451737 +298000 ekin = 0.122701527070309 | erot = 0.139633685444085 | epot = -14.904768457699 | etot = -14.6424332451846 +299000 ekin = 0.133172792913717 | erot = 0.115976150687844 | epot = -14.8915821887951 | etot = -14.6424332451935 +300000 ekin = 0.143237839709864 | erot = 0.0957354521197658 | epot = -14.8814065370295 | etot = -14.6424332451999 +301000 ekin = 0.152548387990851 | erot = 0.07914509087212 | epot = -14.8741267240666 | etot = -14.6424332452037 +302000 ekin = 0.160803184301524 | erot = 0.0664357608556835 | epot = -14.8696721903621 | etot = -14.6424332452049 +303000 ekin = 0.167750948488374 | erot = 0.0578302677258914 | epot = -14.8680144614182 | etot = -14.6424332452039 +304000 ekin = 0.173190665588555 | erot = 0.0535373136380679 | epot = -14.8691612244281 | etot = -14.6424332452015 +305000 ekin = 0.176969952950159 | erot = 0.0537447402922713 | epot = -14.8731479384405 | etot = -14.6424332451981 +306000 ekin = 0.178982363291678 | erot = 0.0586126977895342 | epot = -14.8800283062756 | etot = -14.6424332451944 +307000 ekin = 0.179164502945068 | erot = 0.0682670321079694 | epot = -14.8898647802439 | etot = -14.6424332451909 +308000 ekin = 0.177493763289069 | erot = 0.0827930029212249 | epot = -14.9027200113985 | etot = -14.6424332451882 +309000 ekin = 0.173987301152049 | erot = 0.10222929187336 | epot = -14.918649838212 | etot = -14.6424332451866 +310000 ekin = 0.168702678648352 | erot = 0.126562162218755 | epot = -14.9376980860534 | etot = -14.6424332451863 +311000 ekin = 0.161740297010225 | erot = 0.15571959340906 | epot = -14.9598931356066 | etot = -14.6424332451873 +312000 ekin = 0.153247440126399 | erot = 0.189565237979944 | epot = -14.9852459232961 | etot = -14.6424332451897 +313000 ekin = 0.143423389998623 | erot = 0.227892126762149 | epot = -15.0137487619545 | etot = -14.6424332451937 +314000 ekin = 0.132524706020311 | erot = 0.270416174781616 | epot = -15.045374126001 | etot = -14.6424332451991 +315000 ekin = 0.120869409554559 | erot = 0.31676970828961 | epot = -15.0800723630507 | etot = -14.6424332452065 +316000 ekin = 0.108838546106885 | erot = 0.366495437994255 | epot = -15.1177672293175 | etot = -14.6424332452163 +317000 ekin = 0.0968734934299726 | erot = 0.419041536808435 | epot = -15.1583482754675 | etot = -14.6424332452291 +318000 ekin = 0.0854675378572541 | erot = 0.473758725762824 | epot = -15.201659508866 | etot = -14.6424332452459 +319000 ekin = 0.0751507271474133 | erot = 0.529900497446511 | epot = -15.2474844698617 | etot = -14.6424332452678 +320000 ekin = 0.0664678443385179 | erot = 0.586627760737852 | epot = -15.2955288503723 | etot = -14.6424332452959 +321000 ekin = 0.0599504590581751 | erot = 0.643019202689424 | epot = -15.3454029070787 | etot = -14.6424332453311 +322000 ekin = 0.0560852142815241 | erot = 0.69808845326502 | epot = -15.3966069129205 | etot = -14.642433245374 +323000 ekin = 0.0552815181260046 | erot = 0.750808639914442 | epot = -15.4485234034646 | etot = -14.6424332454242 +324000 ekin = 0.0578423255211838 | erot = 0.800144112656325 | epot = -15.5004196836582 | etot = -14.6424332454807 +325000 ekin = 0.0639414864635107 | erot = 0.845088070114621 | epot = -15.5514628021198 | etot = -14.6424332455416 +326000 ekin = 0.0736101694204692 | erot = 0.884703689967839 | epot = -15.6007471049927 | etot = -14.6424332456044 +327000 ekin = 0.0867333560885398 | erot = 0.918165419814672 | epot = -15.6473320215695 | etot = -14.6424332456662 +328000 ekin = 0.103055779602205 | erot = 0.944796600226729 | epot = -15.690285625553 | etot = -14.6424332457241 +329000 ekin = 0.122195446168384 | erot = 0.964099781598493 | epot = -15.7287284735425 | etot = -14.6424332457756 +330000 ekin = 0.143662406707253 | erot = 0.975776996242511 | epot = -15.7618726487686 | etot = -14.6424332458188 +331000 ekin = 0.16688078513004 | erot = 0.979738667524168 | epot = -15.7890526985066 | etot = -14.6424332458524 +332000 ekin = 0.191212923965886 | erot = 0.976101405909884 | epot = -15.8097475757513 | etot = -14.6424332458756 +333000 ekin = 0.215985355315093 | erot = 0.965176233546684 | epot = -15.8235948347498 | etot = -14.642433245888 +334000 ekin = 0.240516656826274 | erot = 0.947449485120535 | epot = -15.830399387836 | etot = -14.6424332458892 +335000 ekin = 0.26414689608104 | erot = 0.923558676876203 | epot = -15.8301388188364 | etot = -14.6424332458792 +336000 ekin = 0.286267467748786 | erot = 0.89426518476866 | epot = -15.8229658983752 | etot = -14.6424332458578 +337000 ekin = 0.306349134744468 | erot = 0.860424939344321 | epot = -15.8092073199142 | etot = -14.6424332458254 +338000 ekin = 0.323965497668976 | erot = 0.822957838329794 | epot = -15.7893565817818 | etot = -14.642433245783 +339000 ekin = 0.338809250783254 | erot = 0.78281638015672 | epot = -15.7640588766721 | etot = -14.6424332457321 +340000 ekin = 0.35069944422809 | erot = 0.74095414130838 | epot = -15.7340868312114 | etot = -14.6424332456749 +341000 ekin = 0.359579293531018 | erot = 0.698295027836038 | epot = -15.7003075669809 | etot = -14.6424332456139 +342000 ekin = 0.365505462149712 | erot = 0.655704542038074 | epot = -15.6636432497397 | etot = -14.6424332455519 +343000 ekin = 0.368630832656515 | erot = 0.613964463467531 | epot = -15.6250285416158 | etot = -14.6424332454918 +344000 ekin = 0.369183369584766 | erot = 0.573752273081695 | epot = -15.5853688881025 | etot = -14.642433245436 +345000 ekin = 0.367443732820324 | erot = 0.535626361233062 | epot = -15.5455033394399 | etot = -14.6424332453865 +346000 ekin = 0.363723933128335 | erot = 0.500017626275246 | epot = -15.5061748047482 | etot = -14.6424332453447 +347000 ekin = 0.3583487052748 | erot = 0.467227585425602 | epot = -15.4680095360115 | etot = -14.6424332453111 +348000 ekin = 0.351640582952522 | erot = 0.437432666905881 | epot = -15.4315064951445 | etot = -14.6424332452861 +349000 ekin = 0.343909024693046 | erot = 0.41069398616734 | epot = -15.3970362561291 | etot = -14.6424332452687 +350000 ekin = 0.335443435967543 | erot = 0.386971649877949 | epot = -15.3648483311043 | etot = -14.6424332452588 +351000 ekin = 0.326509584093005 | erot = 0.366142474248723 | epot = -15.335085303596 | etot = -14.6424332452543 +352000 ekin = 0.317348699021852 | erot = 0.348019930398485 | epot = -15.3078018746744 | etot = -14.6424332452541 +353000 ekin = 0.30817846664876 | erot = 0.332375117499618 | epot = -15.2829868294052 | etot = -14.6424332452568 +354000 ekin = 0.299195119854683 | erot = 0.318957598137097 | epot = -15.2605859632527 | etot = -14.6424332452609 +355000 ekin = 0.290575888249358 | erot = 0.307515001368969 | epot = -15.2405241348835 | etot = -14.6424332452652 +356000 ekin = 0.282481160313138 | erot = 0.29781040621641 | epot = -15.222724811798 | etot = -14.6424332452685 +357000 ekin = 0.275055828994515 | erot = 0.289636664277668 | epot = -15.2071257385424 | etot = -14.6424332452703 +358000 ekin = 0.268429427255696 | erot = 0.282827006912643 | epot = -15.1936896794384 | etot = -14.6424332452701 +359000 ekin = 0.262714810202509 | erot = 0.277261507859007 | epot = -15.1824095633295 | etot = -14.642433245268 +360000 ekin = 0.258005302570141 | erot = 0.272869227750186 | epot = -15.1733077755848 | etot = -14.6424332452644 +361000 ekin = 0.254370400622431 | erot = 0.269626137803972 | epot = -15.1664297836866 | etot = -14.6424332452602 +362000 ekin = 0.251850290179243 | erot = 0.267549186090239 | epot = -15.1618327215257 | etot = -14.6424332452562 +363000 ekin = 0.250449609863295 | erot = 0.266687109599965 | epot = -15.159569964717 | etot = -14.6424332452537 +364000 ekin = 0.250131041863855 | erot = 0.267108788860278 | epot = -15.1596730759782 | etot = -14.642433245254 +365000 ekin = 0.250809442162592 | erot = 0.268890073930502 | epot = -15.1621327613513 | etot = -14.6424332452582 +366000 ekin = 0.252347318763925 | erot = 0.272100073008351 | epot = -15.1668806370397 | etot = -14.6424332452674 +367000 ekin = 0.254552520179183 | erot = 0.276787886821331 | epot = -15.1737736522827 | etot = -14.6424332452822 +368000 ekin = 0.257178996154117 | erot = 0.282970699525226 | epot = -15.1825829409825 | etot = -14.6424332453031 +369000 ekin = 0.25993142490973 | erot = 0.290624011144342 | epot = -15.1929886813841 | etot = -14.64243324533 +370000 ekin = 0.262474349327911 | erot = 0.299674631815262 | epot = -15.2045822265054 | etot = -14.6424332453622 +371000 ekin = 0.264446209429889 | erot = 0.309996869296908 | epot = -15.2168763241254 | etot = -14.6424332453986 +372000 ekin = 0.265478281863369 | erot = 0.321412142685491 | epot = -15.2293236699861 | etot = -14.6424332454373 +373000 ekin = 0.265218028292355 | erot = 0.333692059446813 | epot = -15.2413433332155 | etot = -14.6424332454763 +374000 ekin = 0.263355721250425 | erot = 0.346564809668647 | epot = -15.2523537764322 | etot = -14.6424332455131 +375000 ekin = 0.259652497503873 | erot = 0.359724567994869 | epot = -15.2618103110439 | etot = -14.6424332455452 +376000 ekin = 0.253967268937784 | erot = 0.372843454380806 | epot = -15.2692439688887 | etot = -14.6424332455701 +377000 ekin = 0.246279333501453 | erot = 0.385585491294785 | epot = -15.274298070382 | etot = -14.6424332455858 +378000 ekin = 0.236703249878221 | erot = 0.397621906698152 | epot = -15.2767584021673 | etot = -14.6424332455909 +379000 ekin = 0.225492756944939 | erot = 0.408647066931743 | epot = -15.2765730694618 | etot = -14.6424332455852 +380000 ekin = 0.213031377539219 | erot = 0.418394278996712 | epot = -15.2738589021049 | etot = -14.642433245569 +381000 ekin = 0.199808877315892 | erot = 0.426650676211857 | epot = -15.2688927990715 | etot = -14.6424332455438 +382000 ekin = 0.186384809019024 | erot = 0.433270396055851 | epot = -15.2620884505868 | etot = -14.642433245512 +383000 ekin = 0.173342616144098 | erot = 0.438185279050645 | epot = -15.253961140671 | etot = -14.6424332454763 +384000 ekin = 0.161239700831436 | erot = 0.441412371402807 | epot = -15.2450853176736 | etot = -14.6424332454394 +385000 ekin = 0.150559954647593 | erot = 0.443057612552847 | epot = -15.2360508126044 | etot = -14.6424332454039 +386000 ekin = 0.141675129699177 | erot = 0.443315241523115 | epot = -15.2274236165942 | etot = -14.6424332453719 +387000 ekin = 0.134820015697985 | erot = 0.442462667348824 | epot = -15.2197159283911 | etot = -14.6424332453443 +388000 ekin = 0.130083976413548 | erot = 0.440850813513903 | epot = -15.2133680352489 | etot = -14.6424332453215 +389000 ekin = 0.127418570237884 | erot = 0.43889024627901 | epot = -15.2087420618201 | etot = -14.6424332453032 +390000 ekin = 0.126658423093201 | erot = 0.437033702086081 | epot = -15.206125370468 | etot = -14.6424332452887 +391000 ekin = 0.127550804260996 | erot = 0.435755902066197 | epot = -15.2057399516044 | etot = -14.6424332452772 +392000 ekin = 0.129788752935801 | erot = 0.435531744058798 | epot = -15.2077537422629 | etot = -14.6424332452683 +393000 ekin = 0.133043055316258 | erot = 0.436814065078314 | epot = -15.2122903656559 | etot = -14.6424332452613 +394000 ekin = 0.136989561466103 | erot = 0.440012156511496 | epot = -15.219434963234 | etot = -14.6424332452564 +395000 ekin = 0.141329833042571 | erot = 0.445472096886692 | epot = -15.2292351751829 | etot = -14.6424332452537 +396000 ekin = 0.145804542777683 | erot = 0.453459767650238 | epot = -15.2416975556817 | etot = -14.6424332452538 +397000 ekin = 0.150200153189368 | erot = 0.464147173463313 | epot = -15.2567805719101 | etot = -14.6424332452574 +398000 ekin = 0.154350089767281 | erot = 0.477602441560301 | epot = -15.2743857765925 | etot = -14.6424332452649 +399000 ekin = 0.158131920623958 | erot = 0.493783661157258 | epot = -15.2943488270584 | etot = -14.6424332452772 +400000 ekin = 0.161462056175852 | erot = 0.512536568007644 | epot = -15.3164318694779 | etot = -14.6424332452944 +401000 ekin = 0.164289301183563 | erot = 0.533595989003439 | epot = -15.3403185355037 | etot = -14.6424332453167 +402000 ekin = 0.166588323053565 | erot = 0.556590928840414 | epot = -15.3656124972379 | etot = -14.642433245344 +403000 ekin = 0.168353810382881 | erot = 0.581053183644676 | epot = -15.3918402394035 | etot = -14.6424332453759 +404000 ekin = 0.169595821304602 | erot = 0.606429376023105 | epot = -15.4184584427394 | etot = -14.6424332454117 +405000 ekin = 0.17033657856555 | erot = 0.632096292540194 | epot = -15.4448661165559 | etot = -14.6424332454502 +406000 ekin = 0.170608761982357 | erot = 0.65737934451417 | epot = -15.4704213519868 | etot = -14.6424332454902 +407000 ekin = 0.170455178570774 | erot = 0.681573854093745 | epot = -15.4944622781949 | etot = -14.6424332455304 +408000 ekin = 0.169929554812993 | erot = 0.703968692150315 | epot = -15.5163314925321 | etot = -14.6424332455688 +409000 ekin = 0.169098093454308 | erot = 0.723871579520606 | epot = -15.5354029185787 | etot = -14.6424332456038 +410000 ekin = 0.168041369043254 | erot = 0.740635137247646 | epot = -15.5511097519244 | etot = -14.6424332456335 +411000 ekin = 0.166856102811026 | erot = 0.753682569970607 | epot = -15.562971918438 | etot = -14.6424332456564 +412000 ekin = 0.165656359034654 | erot = 0.762531725092731 | epot = -15.5706213297983 | etot = -14.642433245671 +413000 ekin = 0.164573741712539 | erot = 0.766816218739469 | epot = -15.5738232061283 | etot = -14.6424332456763 +414000 ekin = 0.163756240958007 | erot = 0.766302377571818 | epot = -15.5724918642016 | etot = -14.6424332456718 +415000 ekin = 0.163365479945299 | erot = 0.760900920225133 | epot = -15.5666996458276 | etot = -14.6424332456572 +416000 ekin = 0.163572240093361 | erot = 0.750672586700048 | epot = -15.5566780724264 | etot = -14.642433245633 +417000 ekin = 0.164550286198126 | erot = 0.735827297892139 | epot = -15.5428108296904 | etot = -14.6424332456002 +418000 ekin = 0.166468663391001 | erot = 0.716716857301867 | epot = -15.525618766253 | etot = -14.6424332455601 +419000 ekin = 0.169482781124152 | erot = 0.69382164910087 | epot = -15.5057376757396 | etot = -14.6424332455146 +420000 ekin = 0.173724722664366 | erot = 0.667732191685369 | epot = -15.4838901598155 | etot = -14.6424332454658 +421000 ekin = 0.179293310757479 | erot = 0.639126725583771 | epot = -15.4608532817569 | etot = -14.6424332454157 +422000 ekin = 0.186244514517565 | erot = 0.608746211201693 | epot = -15.4374239710859 | etot = -14.6424332453666 +423000 ekin = 0.194582798143041 | erot = 0.577368165579506 | epot = -15.4143842090433 | etot = -14.6424332453207 +424000 ekin = 0.204253993027957 | erot = 0.545780680988036 | epot = -15.392467919296 | etot = -14.64243324528 +425000 ekin = 0.215140228915595 | erot = 0.514757766833673 | epot = -15.372331240995 | etot = -14.6424332452458 +426000 ekin = 0.227057395196063 | erot = 0.485036881516669 | epot = -15.354527521932 | etot = -14.6424332452193 +427000 ekin = 0.239755526224872 | erot = 0.457299221562912 | epot = -15.3394879929894 | etot = -14.6424332452017 +428000 ekin = 0.252922416268501 | erot = 0.432153058136047 | epot = -15.3275087195977 | etot = -14.6424332451931 +429000 ekin = 0.266190667178472 | erot = 0.410120192009091 | epot = -15.318744104381 | etot = -14.6424332451935 +430000 ekin = 0.279148248284958 | erot = 0.391625457763427 | epot = -15.3132069512512 | etot = -14.6424332452028 +431000 ekin = 0.291352495292848 | erot = 0.37698914981175 | epot = -15.3107748903245 | etot = -14.6424332452199 +432000 ekin = 0.302347287569357 | erot = 0.36642225446733 | epot = -15.3112027872808 | etot = -14.6424332452441 +433000 ekin = 0.311682921770362 | erot = 0.360024429013509 | epot = -15.314140596057 | etot = -14.6424332452732 +434000 ekin = 0.318937954386234 | erot = 0.357784738271935 | epot = -15.3191559379639 | etot = -14.6424332453058 +435000 ekin = 0.323742037713894 | erot = 0.359585207274212 | epot = -15.3257604903287 | etot = -14.6424332453406 +436000 ekin = 0.325798554030488 | erot = 0.36520724530746 | epot = -15.3334390447139 | etot = -14.642433245376 +437000 ekin = 0.324905697096464 | erot = 0.374340922352109 | epot = -15.3416798648574 | etot = -14.6424332454088 +438000 ekin = 0.32097458985737 | erot = 0.386596930163185 | epot = -15.3500047654581 | etot = -14.6424332454376 +439000 ekin = 0.314043077745088 | erot = 0.401520852188919 | epot = -15.3579971753952 | etot = -14.6424332454612 +440000 ekin = 0.304283988018852 | erot = 0.418609132218188 | epot = -15.3653263657148 | etot = -14.6424332454778 +441000 ekin = 0.292006859109402 | erot = 0.437325916198087 | epot = -15.3717660207938 | etot = -14.6424332454863 +442000 ekin = 0.277652365812265 | erot = 0.457119792524783 | epot = -15.3772054038239 | etot = -14.6424332454868 +443000 ekin = 0.261778853587313 | erot = 0.477439412182564 | epot = -15.3816515112497 | etot = -14.6424332454798 +444000 ekin = 0.245040553430208 | erot = 0.497747053384035 | epot = -15.385220852281 | etot = -14.6424332454667 +445000 ekin = 0.228157260415726 | erot = 0.51752940821079 | epot = -15.3881199140755 | etot = -14.642433245449 +446000 ekin = 0.211875681724409 | erot = 0.536305196865493 | epot = -15.3906141240194 | etot = -14.6424332454295 +447000 ekin = 0.196923472676251 | erot = 0.553629632762795 | epot = -15.3929863508504 | etot = -14.6424332454113 +448000 ekin = 0.183958277875555 | erot = 0.569096233380591 | epot = -15.3954877566542 | etot = -14.642433245398 +449000 ekin = 0.17351577130814 | erot = 0.582336947161301 | epot = -15.3982859638623 | etot = -14.6424332453928 +450000 ekin = 0.165962361194715 | erot = 0.593021970155398 | epot = -15.4014175767483 | etot = -14.6424332453982 +451000 ekin = 0.161459280831074 | erot = 0.600860851258547 | epot = -15.4047533775047 | etot = -14.6424332454151 +452000 ekin = 0.159944578250399 | erot = 0.605606408084822 | epot = -15.4079842317782 | etot = -14.642433245443 +453000 ekin = 0.161137653112611 | erot = 0.607062496375706 | epot = -15.4106333949674 | etot = -14.6424332454791 +454000 ekin = 0.164567591511427 | erot = 0.605095779312731 | epot = -15.4120966163435 | etot = -14.6424332455193 +455000 ekin = 0.169622334208412 | erot = 0.59965045542677 | epot = -15.4117060351935 | etot = -14.6424332455583 +456000 ekin = 0.17561180235027 | erot = 0.590763702898776 | epot = -15.4088087508398 | etot = -14.6424332455907 +457000 ekin = 0.181835621982501 | erot = 0.578578749366117 | epot = -15.4028476169607 | etot = -14.6424332456121 +458000 ekin = 0.187645727031673 | erot = 0.563352302650952 | epot = -15.3934312753015 | etot = -14.6424332456189 +459000 ekin = 0.192495880386129 | erot = 0.545453717149971 | epot = -15.3803828431461 | etot = -14.64243324561 +460000 ekin = 0.195973381638787 | erot = 0.525354597711217 | epot = -15.3637612249357 | etot = -14.6424332455857 +461000 ekin = 0.197811920993003 | erot = 0.503609203462485 | epot = -15.343854370004 | etot = -14.6424332455485 +462000 ekin = 0.197887724921051 | erot = 0.480827560282181 | epot = -15.3211485307045 | etot = -14.6424332455013 +463000 ekin = 0.19620319848715 | erot = 0.457644248435948 | epot = -15.2962806923714 | etot = -14.6424332454483 +464000 ekin = 0.192863034127873 | erot = 0.434686220428325 | epot = -15.2699824999496 | etot = -14.6424332453934 +465000 ekin = 0.188047435824123 | erot = 0.412542760090272 | epot = -15.2430234412543 | etot = -14.6424332453399 +466000 ekin = 0.181986107554568 | erot = 0.391740010671155 | epot = -15.2161593635163 | etot = -14.6424332452906 +467000 ekin = 0.174935400199636 | erot = 0.372721626734198 | epot = -15.1900902721814 | etot = -14.6424332452475 +468000 ekin = 0.167159826103628 | erot = 0.355836258350725 | epot = -15.1654293296662 | etot = -14.6424332452119 +469000 ekin = 0.158918218023891 | erot = 0.341331890764694 | epot = -15.1426833539729 | etot = -14.6424332451843 +470000 ekin = 0.150454185654314 | erot = 0.329356584633373 | epot = -15.1222440154522 | etot = -14.6424332451645 +471000 ekin = 0.141990180750326 | erot = 0.319964871776615 | epot = -15.104388297679 | etot = -14.6424332451521 +472000 ekin = 0.133724353868926 | erot = 0.313128906245008 | epot = -15.0892865052598 | etot = -14.6424332451459 +473000 ekin = 0.125829398102403 | erot = 0.308753392324136 | epot = -15.0770160355714 | etot = -14.6424332451449 +474000 ekin = 0.118452666363553 | erot = 0.306693264413754 | epot = -15.0675791759249 | etot = -14.6424332451476 +475000 ekin = 0.111716976219115 | erot = 0.30677305329061 | epot = -15.0609232746625 | etot = -14.6424332451527 +476000 ekin = 0.105721655633337 | erot = 0.308806833537562 | epot = -15.0569617343299 | etot = -14.642433245159 +477000 ekin = 0.100543523675758 | erot = 0.312617617130229 | epot = -15.0555943859711 | etot = -14.6424332451651 +478000 ekin = 0.0962376398644811 | erot = 0.31805505563526 | epot = -15.0567259406697 | etot = -14.64243324517 +479000 ekin = 0.0928377950024532 | erot = 0.325010357030093 | epot = -15.0602813972057 | etot = -14.6424332451731 +480000 ekin = 0.0903568546345998 | erot = 0.333427427763264 | epot = -15.0662175275719 | etot = -14.642433245174 +481000 ekin = 0.0887871989358601 | erot = 0.343309423709768 | epot = -15.074529867818 | etot = -14.6424332451724 +482000 ekin = 0.0881016191320375 | erot = 0.354720133057113 | epot = -15.0852549973577 | etot = -14.6424332451685 +483000 ekin = 0.0882551127439699 | erot = 0.367779908272474 | epot = -15.0984682661793 | etot = -14.6424332451629 +484000 ekin = 0.0891880440138163 | erot = 0.382656193507622 | epot = -15.1142774826775 | etot = -14.642433245156 +485000 ekin = 0.0908310739109982 | erot = 0.399549033146323 | epot = -15.132813352206 | etot = -14.6424332451486 +486000 ekin = 0.0931120890990551 | erot = 0.41867226992318 | epot = -15.1542176041638 | etot = -14.6424332451416 +487000 ekin = 0.095965052639277 | erot = 0.440231422321074 | epot = -15.1786297200962 | etot = -14.6424332451358 +488000 ekin = 0.0993402613867534 | erot = 0.464399451384565 | epot = -15.2061729579035 | etot = -14.6424332451322 +489000 ekin = 0.103214957397693 | erot = 0.491291775403353 | epot = -15.2369399779327 | etot = -14.6424332451317 +490000 ekin = 0.107602676597199 | erot = 0.520941965498321 | epot = -15.2709778872308 | etot = -14.6424332451353 +491000 ekin = 0.112559247664636 | erot = 0.553279563917093 | epot = -15.3082720567258 | etot = -14.6424332451441 +492000 ekin = 0.11818313672361 | erot = 0.588111425308605 | epot = -15.3487278071918 | etot = -14.6424332451596 +493000 ekin = 0.124608040126391 | erot = 0.625107908279146 | epot = -15.3921491935888 | etot = -14.6424332451833 +494000 ekin = 0.131986393312571 | erot = 0.663795156035298 | epot = -15.4382147945647 | etot = -14.6424332452168 +495000 ekin = 0.140463823900169 | erot = 0.703554605721933 | epot = -15.4864516748842 | etot = -14.6424332452621 +496000 ekin = 0.150146408035849 | erot = 0.743630741563392 | epot = -15.5362103949194 | etot = -14.6424332453202 +497000 ekin = 0.161064579071324 | erot = 0.783147917317811 | epot = -15.586645741781 | etot = -14.6424332453918 +498000 ekin = 0.173139219157391 | erot = 0.821136754973018 | epot = -15.6367092196067 | etot = -14.6424332454763 +499000 ekin = 0.186156317833388 | erot = 0.856570103856968 | epot = -15.6851596672616 | etot = -14.6424332455712 +500000 ekin = 0.199756195068939 | erot = 0.888407758274321 | epot = -15.730597199016 | etot = -14.6424332456728 +501000 ekin = 0.213441517837342 | erot = 0.915648078733143 | epot = -15.7715228423457 | etot = -14.6424332457753 +502000 ekin = 0.226605416598005 | erot = 0.937383433649483 | epot = -15.8064220961193 | etot = -14.6424332458719 +503000 ekin = 0.238577508977599 | erot = 0.952855183125227 | epot = -15.8338659380581 | etot = -14.6424332459553 +504000 ekin = 0.248682347016338 | erot = 0.961503066788675 | epot = -15.8526186598237 | etot = -14.6424332460187 +505000 ekin = 0.256302488969596 | erot = 0.963003656366976 | epot = -15.8617393913932 | etot = -14.6424332460566 +506000 ekin = 0.260937583144194 | erot = 0.957293217920897 | epot = -15.8606640471307 | etot = -14.6424332460656 +507000 ekin = 0.262251679299244 | erot = 0.944571918258912 | epot = -15.849256843603 | etot = -14.6424332460448 +508000 ekin = 0.260103184111408 | erot = 0.925288564934742 | epot = -15.8278249950421 | etot = -14.6424332459959 +509000 ekin = 0.25455487528045 | erot = 0.900107536938111 | epot = -15.7970956581414 | etot = -14.6424332459228 +510000 ekin = 0.245864483348181 | erot = 0.869861717985596 | epot = -15.7581594471648 | etot = -14.642433245831 +511000 ekin = 0.234458914526881 | erot = 0.835496660126654 | epot = -15.7123888203807 | etot = -14.6424332457271 +512000 ekin = 0.220896820239973 | erot = 0.798011684066058 | epot = -15.6613417499238 | etot = -14.6424332456178 +513000 ekin = 0.205824805087872 | erot = 0.758403224578473 | epot = -15.6066612751758 | etot = -14.6424332455094 +514000 ekin = 0.189932244116162 | erot = 0.717614706860426 | epot = -15.5499801963839 | etot = -14.6424332454073 +515000 ekin = 0.173908748199766 | erot = 0.676495918872675 | epot = -15.4928379123882 | etot = -14.6424332453158 +516000 ekin = 0.158407108508993 | erot = 0.635773516025409 | epot = -15.4366138697724 | etot = -14.642433245238 +517000 ekin = 0.144013350183893 | erot = 0.59603314911818 | epot = -15.3824797444781 | etot = -14.642433245176 +518000 ekin = 0.131224514118005 | erot = 0.557712825688994 | epot = -15.3313705849372 | etot = -14.6424332451302 +519000 ekin = 0.120434042405824 | erot = 0.521106495597738 | epot = -15.283973783104 | etot = -14.6424332451004 +520000 ekin = 0.111924165176706 | erot = 0.486376443199764 | epot = -15.2407338534617 | etot = -14.6424332450853 +521000 ekin = 0.105864424815879 | erot = 0.453572806060429 | epot = -15.2018704759591 | etot = -14.6424332450828 +522000 ekin = 0.102315362067395 | erot = 0.422658367131502 | epot = -15.1674069742898 | etot = -14.6424332450909 +523000 ekin = 0.101236366465181 | erot = 0.393536647096984 | epot = -15.137206258669 | etot = -14.6424332451068 +524000 ekin = 0.102496717236757 | erot = 0.366081244308208 | epot = -15.1110112066728 | etot = -14.6424332451278 +525000 ekin = 0.105888887336051 | erot = 0.340164343214671 | epot = -15.0884864757019 | etot = -14.6424332451512 +526000 ekin = 0.111143247850943 | erot = 0.315682368378665 | epot = -15.0692588614045 | etot = -14.6424332451749 +527000 ekin = 0.117943398962438 | erot = 0.29257693780699 | epot = -15.0529535819665 | etot = -14.642433245197 +528000 ekin = 0.12594147425583 | erot = 0.270849598243837 | epot = -15.0392243177155 | etot = -14.6424332452158 +529000 ekin = 0.134772916010411 | erot = 0.250569317239496 | epot = -15.0277754784804 | etot = -14.6424332452305 +530000 ekin = 0.144070383403777 | erot = 0.231872340652232 | epot = -15.0183759692968 | etot = -14.6424332452408 +531000 ekin = 0.153476601970705 | erot = 0.214954741435346 | epot = -15.010864588653 | etot = -14.6424332452469 +532000 ekin = 0.162656054078974 | erot = 0.20005869764927 | epot = -15.0051479969776 | etot = -14.6424332452493 +533000 ekin = 0.171305419081562 | erot = 0.187454143184885 | epot = -15.0011928075152 | etot = -14.6424332452488 +534000 ekin = 0.179162595540481 | erot = 0.1774178426953 | epot = -14.9990136834821 | etot = -14.6424332452463 +535000 ekin = 0.186014006486751 | erot = 0.170212094444198 | epot = -14.9986593461735 | etot = -14.6424332452426 +536000 ekin = 0.191699759240504 | erot = 0.16606514922825 | epot = -15.0001981537073 | etot = -14.6424332452386 +537000 ekin = 0.1961161699316 | erot = 0.165155084981448 | epot = -15.0037045001479 | etot = -14.6424332452348 +538000 ekin = 0.199215220533753 | erot = 0.167598364573304 | epot = -15.0092468303391 | etot = -14.642433245232 +539000 ekin = 0.201000709669645 | erot = 0.173443713619011 | epot = -15.0168776685194 | etot = -14.6424332452308 +540000 ekin = 0.20152116403808 | erot = 0.182671367033565 | epot = -15.0266257763029 | etot = -14.6424332452312 +541000 ekin = 0.200859940141561 | erot = 0.195197211442919 | epot = -15.0384903968184 | etot = -14.642433245234 +542000 ekin = 0.199123298889081 | erot = 0.210880936223622 | epot = -15.0524374803517 | etot = -14.642433245239 +543000 ekin = 0.196427519384058 | erot = 0.229537017789335 | epot = -15.0683977824196 | etot = -14.6424332452462 +544000 ekin = 0.192886294945247 | erot = 0.250947202002153 | epot = -15.0862667422037 | etot = -14.6424332452563 +545000 ekin = 0.18859971088744 | erot = 0.274873110235068 | epot = -15.105906066391 | etot = -14.6424332452685 +546000 ekin = 0.183646045242699 | erot = 0.301067663118862 | epot = -15.1271469536444 | etot = -14.6424332452828 +547000 ekin = 0.178077473818675 | erot = 0.329284179373474 | epot = -15.149794898491 | etot = -14.6424332452988 +548000 ekin = 0.171920510267319 | erot = 0.359282253783652 | epot = -15.173636009367 | etot = -14.642433245316 +549000 ekin = 0.165181670578008 | erot = 0.390829837831177 | epot = -15.1984447537429 | etot = -14.6424332453337 +550000 ekin = 0.157858408655514 | erot = 0.42370132691765 | epot = -15.2239929809246 | etot = -14.6424332453514 +551000 ekin = 0.149954809005953 | erot = 0.457671882716406 | epot = -15.2500599370906 | etot = -14.6424332453683 +552000 ekin = 0.141500835823185 | erot = 0.492508662660431 | epot = -15.2764427438672 | etot = -14.6424332453836 +553000 ekin = 0.132573145481933 | erot = 0.527960055124278 | epot = -15.302966446003 | etot = -14.6424332453968 +554000 ekin = 0.123314645148986 | erot = 0.563744383269626 | epot = -15.3294922738258 | etot = -14.6424332454072 +555000 ekin = 0.113949270903175 | erot = 0.599539792623648 | epot = -15.3559223089416 | etot = -14.6424332454148 +556000 ekin = 0.104788088807786 | erot = 0.634977129563658 | epot = -15.3821984637915 | etot = -14.64243324542 +557000 ekin = 0.0962230654780946 | erot = 0.669637513724504 | epot = -15.4082938246265 | etot = -14.6424332454239 +558000 ekin = 0.0887059614428478 | erot = 0.70305599048067 | epot = -15.4341951973515 | etot = -14.642433245428 +559000 ekin = 0.082711884774194 | erot = 0.734732129424159 | epot = -15.4598772596328 | etot = -14.6424332454344 +560000 ekin = 0.0786899547259911 | erot = 0.764147748398984 | epot = -15.4852709485702 | etot = -14.6424332454453 +561000 ekin = 0.0770067720633791 | erot = 0.790791153076129 | epot = -15.5102311706017 | etot = -14.6424332454622 +562000 ekin = 0.0778911706764789 | erot = 0.814186471629281 | epot = -15.5345108877919 | etot = -14.6424332454862 +563000 ekin = 0.0813901113673084 | erot = 0.83392592548323 | epot = -15.5577492823674 | etot = -14.6424332455168 +564000 ekin = 0.0873448530219544 | erot = 0.849702302565905 | epot = -15.5794804011399 | etot = -14.642433245552 +565000 ekin = 0.0953935152543308 | erot = 0.861338569497384 | epot = -15.59916533034 | etot = -14.6424332455883 +566000 ekin = 0.105001366119722 | erot = 0.868811531657507 | epot = -15.6162461433985 | etot = -14.6424332456212 +567000 ekin = 0.11551478921087 | erot = 0.872266750928371 | epot = -15.6302147857853 | etot = -14.6424332456461 +568000 ekin = 0.126230320990598 | erot = 0.872022546761245 | epot = -15.6406861134104 | etot = -14.6424332456586 +569000 ekin = 0.1364675752055 | erot = 0.868561781938193 | epot = -15.6474626027995 | etot = -14.6424332456558 +570000 ekin = 0.145634823229284 | erot = 0.862511177263077 | epot = -15.650579246129 | etot = -14.6424332456367 +571000 ekin = 0.153278250260132 | erot = 0.854608991356468 | epot = -15.6503204872187 | etot = -14.6424332456021 +572000 ekin = 0.159109636953965 | erot = 0.845662918617004 | epot = -15.6472058011259 | etot = -14.6424332455549 +573000 ekin = 0.163011362017409 | erot = 0.836500892320213 | epot = -15.6419454998373 | etot = -14.6424332454997 +574000 ekin = 0.165021239080183 | erot = 0.82791805820557 | epot = -15.6353725427275 | etot = -14.6424332454418 +575000 ekin = 0.165302195908647 | erot = 0.820623479704516 | epot = -15.6283589210001 | etot = -14.6424332453869 +576000 ekin = 0.164102988101242 | erot = 0.815190165399292 | epot = -15.6217263988412 | etot = -14.6424332453406 +577000 ekin = 0.161716152387198 | erot = 0.812011817944906 | epot = -15.6161612156399 | etot = -14.6424332453078 +578000 ekin = 0.15843856937185 | erot = 0.811269345694985 | epot = -15.6121411603585 | etot = -14.6424332452916 +579000 ekin = 0.154538688869395 | erot = 0.812909695781084 | epot = -15.6098816299448 | etot = -14.6424332452944 +580000 ekin = 0.150232988454514 | erot = 0.816638977242154 | epot = -15.6093052110128 | etot = -14.6424332453162 +581000 ekin = 0.145672809814998 | erot = 0.82193113541131 | epot = -15.6100371905821 | etot = -14.6424332453558 +582000 ekin = 0.140941476791536 | erot = 0.828052590351175 | epot = -15.6114273125529 | etot = -14.6424332454102 +583000 ekin = 0.136060602599188 | erot = 0.834102246896661 | epot = -15.6125960949711 | etot = -14.6424332454752 +584000 ekin = 0.131003759896606 | erot = 0.839065139158589 | epot = -15.6125021446008 | etot = -14.6424332455456 +585000 ekin = 0.125715216483023 | erot = 0.841876757449347 | epot = -15.6100252195477 | etot = -14.6424332456153 +586000 ekin = 0.120131224768948 | erot = 0.841493945667052 | epot = -15.6040584161145 | etot = -14.6424332456785 +587000 ekin = 0.114201380572127 | erot = 0.836967317754023 | epot = -15.5936019440556 | etot = -14.6424332457295 +588000 ekin = 0.10790780822673 | erot = 0.827509595983478 | epot = -15.5778506499738 | etot = -14.6424332457636 +589000 ekin = 0.101280337909716 | erot = 0.812554260673813 | epot = -15.5562678443608 | etot = -14.6424332457773 +590000 ekin = 0.0944063548788227 | erot = 0.791799488420743 | epot = -15.5286390890684 | etot = -14.6424332457688 +591000 ekin = 0.0874345511051893 | erot = 0.765233519223455 | epot = -15.4951013160664 | etot = -14.6424332457378 +592000 ekin = 0.0805723392084907 | erot = 0.733139214285358 | epot = -15.4561447991799 | etot = -14.642433245686 +593000 ekin = 0.0740771594080655 | erot = 0.696077455348817 | epot = -15.4125878603734 | etot = -14.6424332456166 +594000 ekin = 0.0682423089599614 | erot = 0.654850963358217 | epot = -15.3655265178521 | etot = -14.642433245534 +595000 ekin = 0.0633782539014331 | erot = 0.610451848323659 | epot = -15.3162633476688 | etot = -14.6424332454437 +596000 ekin = 0.0597906540649347 | erot = 0.563997548401148 | epot = -15.2662214478178 | etot = -14.6424332453517 +597000 ekin = 0.0577565493623858 | erot = 0.516660644084273 | epot = -15.2168504387106 | etot = -14.642433245264 +598000 ekin = 0.0575003158536081 | erot = 0.469598294353632 | epot = -15.1695318553934 | etot = -14.6424332451862 +599000 ekin = 0.0591710965286251 | erot = 0.423886769451064 | epot = -15.1254911111027 | etot = -14.642433245123 +600000 ekin = 0.0628234356891045 | erot = 0.380465849281436 | epot = -15.0857225300487 | etot = -14.6424332450781 +601000 ekin = 0.0684027903378417 | erot = 0.340096852289044 | epot = -15.0509328876805 | etot = -14.6424332450536 +602000 ekin = 0.0757374499129008 | erot = 0.303336891508804 | epot = -15.0215075864718 | etot = -14.6424332450501 +603000 ekin = 0.0845381560106984 | erot = 0.270530726252426 | epot = -14.9975021273296 | etot = -14.6424332450665 +604000 ekin = 0.0944063594078355 | erot = 0.241820347963454 | epot = -14.9786599524715 | etot = -14.6424332451002 +605000 ekin = 0.104851562460566 | erot = 0.217171224791036 | epot = -14.9644560323985 | etot = -14.6424332451469 +606000 ekin = 0.115317556389835 | erot = 0.196412930356103 | epot = -14.954163731947 | etot = -14.6424332452011 +607000 ekin = 0.125216580353275 | erot = 0.179290709847405 | epot = -14.9469405354574 | etot = -14.6424332452567 +608000 ekin = 0.133969542490564 | erot = 0.165523445157646 | epot = -14.9419262329554 | etot = -14.6424332453072 +609000 ekin = 0.141049537028518 | erot = 0.15486258226509 | epot = -14.9383453646398 | etot = -14.6424332453462 +610000 ekin = 0.146025095175949 | erot = 0.147146040888439 | epot = -14.935604381433 | etot = -14.6424332453686 +611000 ekin = 0.148599079335757 | erot = 0.142341118193739 | epot = -14.9333734429002 | etot = -14.6424332453707 +612000 ekin = 0.148639027542241 | erot = 0.140571068727528 | epot = -14.9316433416205 | etot = -14.6424332453507 +613000 ekin = 0.146195193893338 | erot = 0.142121441395774 | epot = -14.9307498805986 | etot = -14.6424332453095 +614000 ekin = 0.141503544705058 | erot = 0.147424293659482 | epot = -14.9313610836148 | etot = -14.6424332452503 +615000 ekin = 0.134972482669589 | erot = 0.157020849768843 | epot = -14.9344265776168 | etot = -14.6424332451783 +616000 ekin = 0.127153892887477 | erot = 0.17150567977268 | epot = -14.9410928177609 | etot = -14.6424332451008 +617000 ekin = 0.118700960497215 | erot = 0.191457667915335 | epot = -14.9525918734382 | etot = -14.6424332450256 +618000 ekin = 0.110316794781948 | erot = 0.21736458449167 | epot = -14.9701146242348 | etot = -14.6424332449612 +619000 ekin = 0.102698942666097 | erot = 0.249548776233835 | epot = -14.994680963815 | etot = -14.6424332449151 +620000 ekin = 0.0964852203315631 | erot = 0.288101317493937 | epot = -15.0270197827191 | etot = -14.6424332448936 +621000 ekin = 0.0922059091526162 | erot = 0.332831044367888 | epot = -15.0674701984216 | etot = -14.6424332449011 +622000 ekin = 0.090246364710084 | erot = 0.383233451864307 | epot = -15.1159130615138 | etot = -14.6424332449395 +623000 ekin = 0.0908226920702867 | erot = 0.438482716268118 | epot = -15.1717386533468 | etot = -14.6424332450084 +624000 ekin = 0.0939716062521641 | erot = 0.497448307340739 | epot = -15.2338531586981 | etot = -14.6424332451052 +625000 ekin = 0.0995541611224816 | erot = 0.558735886785548 | epot = -15.3007232931327 | etot = -14.6424332452247 +626000 ekin = 0.107271859325762 | erot = 0.620750477457381 | epot = -15.3704555821432 | etot = -14.6424332453601 +627000 ekin = 0.116692826737646 | erot = 0.681778220901968 | epot = -15.440904293143 | etot = -14.6424332455034 +628000 ekin = 0.127285245273582 | erot = 0.740081431770171 | epot = -15.5097999226893 | etot = -14.6424332456456 +629000 ekin = 0.138455039153843 | erot = 0.794000196771077 | epot = -15.5748884817029 | etot = -14.6424332457779 +630000 ekin = 0.149584842937087 | erot = 0.84205264024076 | epot = -15.63407072907 | etot = -14.6424332458922 +631000 ekin = 0.160071499853009 | erot = 0.88302544287862 | epot = -15.6855301887133 | etot = -14.6424332459817 +632000 ekin = 0.169359720292754 | erot = 0.916046503426999 | epot = -15.7278394697613 | etot = -14.6424332460416 +633000 ekin = 0.176970053692527 | erot = 0.94063292294126 | epot = -15.7600362227031 | etot = -14.6424332460693 +634000 ekin = 0.182519961289934 | erot = 0.956709735134238 | epot = -15.7816629424889 | etot = -14.6424332460647 +635000 ekin = 0.185737466035627 | erot = 0.964597760206567 | epot = -15.7927684722724 | etot = -14.6424332460302 +636000 ekin = 0.186467519303287 | erot = 0.964972204256552 | epot = -15.79387296953 | etot = -14.6424332459701 +637000 ekin = 0.184671774604466 | erot = 0.958796660376671 | epot = -15.7859016808713 | etot = -14.6424332458901 +638000 ekin = 0.180422825778035 | erot = 0.947239527073052 | epot = -15.7700955986478 | etot = -14.6424332457967 +639000 ekin = 0.173894119064837 | erot = 0.931581224196235 | epot = -15.747908588958 | etot = -14.642433245697 +640000 ekin = 0.165346701827782 | erot = 0.91312083875339 | epot = -15.7209007861784 | etot = -14.6424332455972 +641000 ekin = 0.155113786103692 | erot = 0.893090060089671 | epot = -15.6906370916964 | etot = -14.6424332455031 +642000 ekin = 0.143583869244217 | erot = 0.872580710306169 | epot = -15.6585978249696 | etot = -14.6424332454192 +643000 ekin = 0.131182953689566 | erot = 0.852490168054334 | epot = -15.6261063670926 | etot = -14.6424332453487 +644000 ekin = 0.118356305761173 | erot = 0.833486853990269 | epot = -15.5942764050451 | etot = -14.6424332452937 +645000 ekin = 0.105550209085081 | erot = 0.815995971212791 | epot = -15.5639794255527 | etot = -14.6424332452548 +646000 ekin = 0.0931942744194625 | erot = 0.800204061931269 | epot = -15.5358315815826 | etot = -14.6424332452318 +647000 ekin = 0.0816850001800769 | erot = 0.786079744440999 | epot = -15.5101979898444 | etot = -14.6424332452233 +648000 ekin = 0.0713713598437978 | erot = 0.773407243193285 | epot = -15.4872118482646 | etot = -14.6424332452275 +649000 ekin = 0.0625431628717075 | erot = 0.761828976530965 | epot = -15.4668053846445 | etot = -14.6424332452418 +650000 ekin = 0.0554227735503044 | erot = 0.750893453414529 | epot = -15.4487494722282 | etot = -14.6424332452633 +651000 ekin = 0.0501605027658098 | erot = 0.74010497844913 | epot = -15.4326987265041 | etot = -14.6424332452892 +652000 ekin = 0.0468336713663308 | erot = 0.728972100421486 | epot = -15.4182390171043 | etot = -14.6424332453165 +653000 ekin = 0.0454490492573673 | erot = 0.717052285945908 | epot = -15.4049345805457 | etot = -14.6424332453424 +654000 ekin = 0.0459481524943306 | erot = 0.703990869784824 | epot = -15.3923722676438 | etot = -14.6424332453647 +655000 ekin = 0.048214749528602 | erot = 0.689552835107499 | epot = -15.3802008300172 | etot = -14.6424332453811 +656000 ekin = 0.0520838761262338 | erot = 0.673646332749968 | epot = -15.3681634542667 | etot = -14.6424332453905 +657000 ekin = 0.0573516620848271 | erot = 0.656337023115609 | epot = -15.356121930592 | etot = -14.6424332453915 +658000 ekin = 0.0637853134927773 | erot = 0.637852348219684 | epot = -15.3440709070967 | etot = -14.6424332453842 +659000 ekin = 0.0711326702869463 | erot = 0.618574815847903 | epot = -15.3321407315039 | etot = -14.642433245369 +660000 ekin = 0.0791308828100933 | erot = 0.59902345470884 | epot = -15.3205875828664 | etot = -14.6424332453475 +661000 ekin = 0.0875139366233532 | erot = 0.57982293974752 | epot = -15.3097701216927 | etot = -14.6424332453218 +662000 ekin = 0.096019000419939 | erot = 0.56166061034769 | epot = -15.3001128560625 | etot = -14.6424332452949 +663000 ekin = 0.104391848885312 | erot = 0.545232746054744 | epot = -15.2920578402104 | etot = -14.6424332452703 +664000 ekin = 0.1123918633903 | erot = 0.531182949318153 | epot = -15.2860080579606 | etot = -14.6424332452521 +665000 ekin = 0.119797262721338 | erot = 0.52003712479683 | epot = -15.2822676327618 | etot = -14.6424332452437 +666000 ekin = 0.126411190063547 | erot = 0.512141060960723 | epot = -15.2809854962723 | etot = -14.642433245248 +667000 ekin = 0.132069035725132 | erot = 0.507607681729055 | epot = -15.2821099627211 | etot = -14.6424332452669 +668000 ekin = 0.136646914542203 | erot = 0.506281315754288 | epot = -15.2853614755971 | etot = -14.6424332453006 +669000 ekin = 0.140070616013021 | erot = 0.50772556617166 | epot = -15.2902294275324 | etot = -14.6424332453477 +670000 ekin = 0.142323740906679 | erot = 0.511239425098687 | epot = -15.2959964114102 | etot = -14.6424332454048 +671000 ekin = 0.143453306303064 | erot = 0.515903234044996 | epot = -15.3017897858152 | etot = -14.6424332454671 +672000 ekin = 0.143571012732418 | erot = 0.520652256718186 | epot = -15.3066565149793 | etot = -14.6424332455287 +673000 ekin = 0.142848733836954 | erot = 0.524371563357074 | epot = -15.3096535427774 | etot = -14.6424332455834 +674000 ekin = 0.141507613277718 | erot = 0.526002362930759 | epot = -15.3099432218339 | etot = -14.6424332456254 +675000 ekin = 0.13980130282559 | erot = 0.524647629024632 | epot = -15.3068821775003 | etot = -14.6424332456501 +676000 ekin = 0.137995095210639 | erot = 0.519664439041565 | epot = -15.3000927799068 | etot = -14.6424332456546 +677000 ekin = 0.136343677285182 | erot = 0.510732098518056 | epot = -15.2895090214411 | etot = -14.6424332456378 +678000 ekin = 0.1350706641226 | erot = 0.49788857525657 | epot = -15.2753924849801 | etot = -14.6424332456009 +679000 ekin = 0.134352810444862 | erot = 0.481532294132637 | epot = -15.2583183501238 | etot = -14.6424332455463 +680000 ekin = 0.13431086265575 | erot = 0.462390968605425 | epot = -15.2391350767393 | etot = -14.6424332454781 +681000 ekin = 0.135007638923122 | erot = 0.441462941784965 | epot = -15.218903826109 | etot = -14.6424332454009 +682000 ekin = 0.136452461524589 | erot = 0.419938865037975 | epot = -15.1988245718825 | etot = -14.6424332453199 +683000 ekin = 0.138609887397947 | erot = 0.399112293315654 | epot = -15.1801554259539 | etot = -14.6424332452403 +684000 ekin = 0.141410065648264 | erot = 0.380287181762594 | epot = -15.1641304925779 | etot = -14.6424332451671 +685000 ekin = 0.144758102722244 | erot = 0.364688846299647 | epot = -15.1518801941267 | etot = -14.6424332451049 +686000 ekin = 0.14854046711943 | erot = 0.353383275614745 | epot = -15.144356987792 | etot = -14.6424332450578 +687000 ekin = 0.152627512098722 | erot = 0.347208212231136 | epot = -15.1422689693591 | etot = -14.6424332450292 +688000 ekin = 0.156872371008243 | erot = 0.346718408271441 | epot = -15.1460240243019 | etot = -14.6424332450222 +689000 ekin = 0.161107527974782 | erot = 0.352146941115747 | epot = -15.1556877141288 | etot = -14.6424332450382 +690000 ekin = 0.16514108738065 | erot = 0.363384304942447 | epot = -15.1709586374008 | etot = -14.6424332450777 +691000 ekin = 0.168755042649082 | erot = 0.379976931156971 | epot = -15.1911652189453 | etot = -14.6424332451393 +692000 ekin = 0.171707649703694 | erot = 0.401146558398203 | epot = -15.2152874533219 | etot = -14.64243324522 +693000 ekin = 0.173741393443093 | erot = 0.425831232789035 | epot = -15.2420058715475 | etot = -14.6424332453154 +694000 ekin = 0.174597110624773 | erot = 0.452747528140487 | epot = -15.2697778841841 | etot = -14.6424332454189 +695000 ekin = 0.174033757472237 | erot = 0.480471830922762 | epot = -15.2969388339179 | etot = -14.6424332455229 +696000 ekin = 0.171852263364752 | erot = 0.50753639815869 | epot = -15.3218219071425 | etot = -14.6424332456191 +697000 ekin = 0.167921065290924 | erot = 0.532533688693483 | epot = -15.3428879996837 | etot = -14.6424332456993 +698000 ekin = 0.162200409477016 | erot = 0.554220619925494 | epot = -15.3588542751586 | etot = -14.6424332457561 +699000 ekin = 0.154762415715625 | erot = 0.571613361028384 | epot = -15.3688090225278 | etot = -14.6424332457837 +700000 ekin = 0.14580423000878 | erot = 0.584063387088342 | epot = -15.3723008628759 | etot = -14.6424332457788 +701000 ekin = 0.135652269558589 | erot = 0.591306922721675 | epot = -15.3693924380207 | etot = -14.6424332457404 +702000 ekin = 0.124756460207458 | erot = 0.593482464349287 | epot = -15.3606721702276 | etot = -14.6424332456708 +703000 ekin = 0.11367432595124 | erot = 0.591114401857202 | epot = -15.3472219733832 | etot = -14.6424332455747 +704000 ekin = 0.10304567594557 | erot = 0.585064323196779 | epot = -15.3305432446014 | etot = -14.6424332454591 +705000 ekin = 0.093559358196298 | erot = 0.576454826534863 | epot = -15.3124474300637 | etot = -14.6424332453326 +706000 ekin = 0.0859140824284676 | erot = 0.566573150256884 | epot = -15.2949204778901 | etot = -14.6424332452047 +707000 ekin = 0.0807756759557719 | erot = 0.556763427609663 | epot = -15.2799723486508 | etot = -14.6424332450854 +708000 ekin = 0.0787333622599937 | erot = 0.548316855291462 | epot = -15.269483462535 | etot = -14.6424332449836 +709000 ekin = 0.0802577669150991 | erot = 0.542368667954137 | epot = -15.2650596797766 | etot = -14.6424332449074 +710000 ekin = 0.0856633545528662 | erot = 0.539809747049451 | epot = -15.2679063464654 | etot = -14.642433244863 +711000 ekin = 0.0950778519027508 | erot = 0.541219180891539 | epot = -15.2787302776488 | etot = -14.6424332448545 +712000 ekin = 0.10842087662218 | erot = 0.546822307911647 | epot = -15.2976764294171 | etot = -14.6424332448833 +713000 ekin = 0.125393451694867 | erot = 0.556476834657881 | epot = -15.3243035313012 | etot = -14.6424332449484 +714000 ekin = 0.145479367621472 | erot = 0.569687600119496 | epot = -15.3576002127874 | etot = -14.6424332450464 +715000 ekin = 0.167958541116859 | erot = 0.585648522303218 | epot = -15.3960403085917 | etot = -14.6424332451716 +716000 ekin = 0.191931735851232 | erot = 0.60330829253147 | epot = -15.4376732736993 | etot = -14.6424332453166 +717000 ekin = 0.216355400176894 | erot = 0.621454592037079 | epot = -15.4802432376866 | etot = -14.6424332454726 +718000 ekin = 0.24008505651044 | erot = 0.638810139731556 | epot = -15.521328441872 | etot = -14.64243324563 +719000 ekin = 0.261925698575349 | erot = 0.654132895986116 | epot = -15.558491840341 | etot = -14.6424332457795 +720000 ekin = 0.280687969311591 | erot = 0.666312379867061 | epot = -15.5894335950905 | etot = -14.6424332459119 +721000 ekin = 0.295249345589153 | erot = 0.674454385927668 | epot = -15.6121369775356 | etot = -14.6424332460188 +722000 ekin = 0.304619886333733 | erot = 0.67794741025506 | epot = -15.6250005426818 | etot = -14.642433246093 +723000 ekin = 0.308011983727977 | erot = 0.676505724570366 | epot = -15.6269509544273 | etot = -14.642433246129 +724000 ekin = 0.304912667284364 | erot = 0.670186105899516 | epot = -15.6175320193064 | etot = -14.6424332461225 +725000 ekin = 0.295155116711556 | erot = 0.659377522489347 | epot = -15.5969658852725 | etot = -14.6424332460716 +726000 ekin = 0.278983134900095 | erot = 0.644765363158316 | epot = -15.5661817440347 | etot = -14.6424332459763 +727000 ekin = 0.257098790794367 | erot = 0.627273860362841 | epot = -15.5268058969971 | etot = -14.6424332458399 +728000 ekin = 0.230680158274935 | erot = 0.607992016180396 | epot = -15.481105420124 | etot = -14.6424332456687 +729000 ekin = 0.201354496276678 | erot = 0.588089464034347 | epot = -15.4318772057843 | etot = -14.6424332454733 +730000 ekin = 0.171114103979303 | erot = 0.568729214715612 | epot = -15.382276563963 | etot = -14.6424332452681 +731000 ekin = 0.142168923912273 | erot = 0.55098413507054 | epot = -15.3355863040536 | etot = -14.6424332450708 +732000 ekin = 0.11674200710062 | erot = 0.535763349043798 | epot = -15.294938601045 | etot = -14.6424332449006 +733000 ekin = 0.096829302757611 | erot = 0.523753647321743 | epot = -15.263016194855 | etot = -14.6424332447757 +734000 ekin = 0.0839596135620853 | erot = 0.515379592338737 | epot = -15.2417724506111 | etot = -14.6424332447103 +735000 ekin = 0.0789983701793321 | erot = 0.510784464196176 | epot = -15.2322160790871 | etot = -14.6424332447116 +736000 ekin = 0.0820355551944618 | erot = 0.509832642266591 | epot = -15.2343014422397 | etot = -14.6424332447787 +737000 ekin = 0.0923827123871921 | erot = 0.51213255085583 | epot = -15.2469485081446 | etot = -14.6424332449015 +738000 ekin = 0.108680448514306 | erot = 0.517077971028045 | epot = -15.2681916646065 | etot = -14.6424332450641 +739000 ekin = 0.12909371568349 | erot = 0.523904364927467 | epot = -15.2954313258571 | etot = -14.6424332452461 +740000 ekin = 0.151555277793912 | erot = 0.531755895780646 | epot = -15.3257444190018 | etot = -14.6424332454272 +741000 ekin = 0.174012721806563 | erot = 0.539758083454575 | epot = -15.3562040508503 | etot = -14.6424332455892 +742000 ekin = 0.194640916831384 | erot = 0.547090549700596 | epot = -15.3841647122502 | etot = -14.6424332457182 +743000 ekin = 0.211995737398717 | erot = 0.553054125338761 | epot = -15.4074831085432 | etot = -14.6424332458057 +744000 ekin = 0.22510050872294 | erot = 0.557126762310943 | epot = -15.4246605168818 | etot = -14.6424332458479 +745000 ekin = 0.233469424486957 | erot = 0.559003260240344 | epot = -15.4349059305732 | etot = -14.6424332458459 +746000 ekin = 0.2370799134654 | erot = 0.558614810501353 | epot = -15.438127969771 | etot = -14.6424332458043 +747000 ekin = 0.236308652985431 | erot = 0.556125790084381 | epot = -15.4348676888002 | etot = -14.6424332457304 +748000 ekin = 0.231845097888603 | erot = 0.551907079331795 | epot = -15.426185422854 | etot = -14.6424332456336 +749000 ekin = 0.224593843485089 | erot = 0.546487360031397 | epot = -15.4135144490409 | etot = -14.6424332455244 +750000 ekin = 0.215574369393293 | erot = 0.540486233486826 | epot = -15.3984938482942 | etot = -14.6424332454141 +751000 ekin = 0.205824583428116 | erot = 0.534535356766581 | epot = -15.382793185508 | etot = -14.6424332453133 +752000 ekin = 0.196313335743831 | erot = 0.529195815220672 | epot = -15.367942396196 | etot = -14.6424332452315 +753000 ekin = 0.187866475789607 | erot = 0.524881252734243 | epot = -15.3551809737002 | etot = -14.6424332451763 +754000 ekin = 0.181110613628491 | erot = 0.521796491100216 | epot = -15.3453403498808 | etot = -14.6424332451521 +755000 ekin = 0.176438042206941 | erot = 0.519900210809565 | epot = -15.3387714981766 | etot = -14.6424332451601 +756000 ekin = 0.173994962649976 | erot = 0.518897676287607 | epot = -15.3353258841355 | etot = -14.642433245198 +757000 ekin = 0.173693190273855 | erot = 0.518265706185164 | epot = -15.334392141719 | etot = -14.6424332452599 +758000 ekin = 0.175243155018327 | erot = 0.517307659824269 | epot = -15.3349840601804 | etot = -14.6424332453378 +759000 ekin = 0.178203703096713 | erot = 0.515231902167182 | epot = -15.3358688506856 | etot = -14.6424332454217 +760000 ekin = 0.182042463552564 | erot = 0.511243837951639 | epot = -15.3357195470058 | etot = -14.6424332455016 +761000 ekin = 0.186199747764933 | erot = 0.504639825550332 | epot = -15.3332728188834 | etot = -14.6424332455682 +762000 ekin = 0.190149235948613 | erot = 0.494891409036607 | epot = -15.3274738905993 | etot = -14.6424332456141 +763000 ekin = 0.193449921097585 | erot = 0.481710238289879 | epot = -15.3175934050219 | etot = -14.6424332456345 +764000 ekin = 0.195785552428752 | erot = 0.465087294354156 | epot = -15.3033060924098 | etot = -14.6424332456268 +765000 ekin = 0.196989678186294 | erot = 0.445303873494492 | epot = -15.2847267972726 | etot = -14.6424332455918 +766000 ekin = 0.197055919183484 | erot = 0.422915440294251 | epot = -15.26240460501 | etot = -14.6424332455322 +767000 ekin = 0.19613407649359 | erot = 0.398712320924831 | epot = -15.2372796428711 | etot = -14.6424332454526 +768000 ekin = 0.194513096651386 | erot = 0.373662938959647 | epot = -15.2106092809703 | etot = -14.6424332453593 +769000 ekin = 0.192592017625304 | erot = 0.348845887486037 | epot = -15.1838711503705 | etot = -14.6424332452592 +770000 ekin = 0.190840163683791 | erot = 0.325376840212305 | epot = -15.1586502490562 | etot = -14.6424332451601 +771000 ekin = 0.189748397224452 | erot = 0.304335529899573 | epot = -15.136517172194 | etot = -14.64243324507 +772000 ekin = 0.189774341847263 | erot = 0.286697153920281 | epot = -15.1189047407638 | etot = -14.6424332449962 +773000 ekin = 0.191286034496866 | erot = 0.273271857835351 | epot = -15.1069911372776 | etot = -14.6424332449453 +774000 ekin = 0.194510000604709 | erot = 0.264655458968876 | epot = -15.101598704496 | etot = -14.6424332449224 +775000 ekin = 0.199490639675106 | erot = 0.261194193154614 | epot = -15.1031180777597 | etot = -14.64243324493 +776000 ekin = 0.206067477061454 | erot = 0.262965803934464 | epot = -15.1114665259641 | etot = -14.6424332449682 +777000 ekin = 0.213875019081943 | erot = 0.269778568412073 | epot = -15.1260868325284 | etot = -14.6424332450344 +778000 ekin = 0.222366868961404 | erot = 0.281188790675987 | epot = -15.1459889047605 | etot = -14.6424332451231 +779000 ekin = 0.230862102265719 | erot = 0.296535944176208 | epot = -15.169831291669 | etot = -14.6424332452271 +780000 ekin = 0.238608567016806 | erot = 0.31499316909211 | epot = -15.1960349814464 | etot = -14.6424332453374 +781000 ekin = 0.244855557739756 | erot = 0.335629445236695 | epot = -15.2229182484214 | etot = -14.6424332454449 +782000 ekin = 0.248927612477286 | erot = 0.357478674286886 | epot = -15.2488395323048 | etot = -14.6424332455406 +783000 ekin = 0.250291897528993 | erot = 0.379610269028342 | epot = -15.2723354121742 | etot = -14.6424332456169 +784000 ekin = 0.248613283253222 | erot = 0.401195731122937 | epot = -15.2922422600437 | etot = -14.6424332456676 +785000 ekin = 0.243793133451402 | erot = 0.421566090466529 | epot = -15.3077924696065 | etot = -14.6424332456886 +786000 ekin = 0.23598950185365 | erot = 0.44025590520682 | epot = -15.3186786527387 | etot = -14.6424332456782 +787000 ekin = 0.225617610785865 | erot = 0.457030673432359 | epot = -15.3250815298553 | etot = -14.6424332456371 +788000 ekin = 0.213330260903178 | erot = 0.471895861695948 | epot = -15.3276593681676 | etot = -14.6424332455685 +789000 ekin = 0.199978499678579 | erot = 0.485087183883026 | epot = -15.3274989290395 | etot = -14.6424332454779 +790000 ekin = 0.186553834704508 | erot = 0.49704314124288 | epot = -15.32603022132 | etot = -14.6424332453726 +791000 ekin = 0.174114766793481 | erot = 0.508362048569847 | epot = -15.3249100606249 | etot = -14.6424332452616 +792000 ekin = 0.163702420432414 | erot = 0.519746739180895 | epot = -15.3258824047679 | etot = -14.6424332451546 +793000 ekin = 0.156252224966309 | erot = 0.53194082298947 | epot = -15.3306262930168 | etot = -14.642433245061 +794000 ekin = 0.152510350034315 | erot = 0.545660777315094 | epot = -15.3406043723391 | etot = -14.6424332449897 +795000 ekin = 0.152964251156891 | erot = 0.5615283269811 | epot = -15.3569258230857 | etot = -14.6424332449477 +796000 ekin = 0.157795747355246 | erot = 0.580007578778131 | epot = -15.3802365710729 | etot = -14.6424332449395 +797000 ekin = 0.166862457855134 | erot = 0.601351255569813 | epot = -15.4106469583918 | etot = -14.6424332449668 +798000 ekin = 0.179709603428539 | erot = 0.62556012184583 | epot = -15.4477029703029 | etot = -14.6424332450285 +799000 ekin = 0.195609966057053 | erot = 0.652359247176983 | epot = -15.490402458355 | etot = -14.642433245121 +800000 ekin = 0.213626158786136 | erot = 0.68119402187417 | epot = -15.5372534258983 | etot = -14.642433245238 +801000 ekin = 0.232687040188266 | erot = 0.711247726387183 | epot = -15.5863680119474 | etot = -14.642433245372 +802000 ekin = 0.251669429100998 | erot = 0.741480919836821 | epot = -15.6355835944519 | etot = -14.642433245514 +803000 ekin = 0.269477067853637 | erot = 0.770691008421927 | epot = -15.6826013219306 | etot = -14.642433245655 +804000 ekin = 0.285110541453573 | erot = 0.797588259159231 | epot = -15.7251320463985 | etot = -14.6424332457857 +805000 ekin = 0.297723982502801 | erot = 0.820882528800413 | epot = -15.7610397572012 | etot = -14.6424332458979 +806000 ekin = 0.306666387684663 | erot = 0.839373432914301 | epot = -15.7884730665838 | etot = -14.6424332459848 +807000 ekin = 0.311506975554225 | erot = 0.852035914446659 | epot = -15.8059761360419 | etot = -14.642433246041 +808000 ekin = 0.312045176252483 | erot = 0.858093398528957 | epot = -15.812571820845 | etot = -14.6424332460636 +809000 ekin = 0.308306642387543 | erot = 0.857071970759347 | epot = -15.8078118591986 | etot = -14.6424332460517 +810000 ekin = 0.300527220561017 | erot = 0.848831113929473 | epot = -15.7917915804974 | etot = -14.6424332460069 +811000 ekin = 0.289127204421129 | erot = 0.833569138622877 | epot = -15.7651295889766 | etot = -14.6424332459326 +812000 ekin = 0.274678427602343 | erot = 0.811804116493732 | epot = -15.72891578993 | etot = -14.6424332458339 +813000 ekin = 0.257866835583857 | erot = 0.784333459543394 | epot = -15.6846335408442 | etot = -14.642433245717 +814000 ekin = 0.23945308059417 | erot = 0.752176980197134 | epot = -15.6340633063801 | etot = -14.6424332455888 +815000 ekin = 0.220233415151649 | erot = 0.716509170267373 | epot = -15.5791758308753 | etot = -14.6424332454563 +816000 ekin = 0.201002751046645 | erot = 0.678586569748774 | epot = -15.5220225661215 | etot = -14.6424332453261 +817000 ekin = 0.182521261080257 | erot = 0.639675603865673 | epot = -15.4646301101501 | etot = -14.6424332452042 +818000 ekin = 0.16548540152787 | erot = 0.600985363832187 | epot = -15.4089040104558 | etot = -14.6424332450958 +819000 ekin = 0.15050378978045 | erot = 0.563608719250084 | epot = -15.3565457540356 | etot = -14.642433245005 +820000 ekin = 0.138078032178526 | erot = 0.528474068973221 | epot = -15.3089853460867 | etot = -14.6424332449349 +821000 ekin = 0.1285883867302 | erot = 0.496309093118672 | epot = -15.2673307247365 | etot = -14.6424332448876 +822000 ekin = 0.12228406613689 | erot = 0.467617125516686 | epot = -15.2323344365175 | etot = -14.6424332448639 +823000 ekin = 0.119278020924427 | erot = 0.442666228479689 | epot = -15.204377494268 | etot = -14.6424332448639 +824000 ekin = 0.119546158603772 | erot = 0.421490682739598 | epot = -15.1834700862299 | etot = -14.6424332448865 +825000 ekin = 0.122931110514646 | erot = 0.403904342224695 | epot = -15.1692686976689 | etot = -14.6424332449295 +826000 ekin = 0.129150803764422 | erot = 0.389525075000924 | epot = -15.1611091237554 | etot = -14.64243324499 +827000 ekin = 0.137812176399265 | erot = 0.377809252271385 | epot = -15.1580546737348 | etot = -14.6424332450642 +828000 ekin = 0.148430331608458 | erot = 0.368094906963596 | epot = -15.1589584837193 | etot = -14.6424332451472 +829000 ekin = 0.160453205761757 | erot = 0.3596517375127 | epot = -15.1625381885084 | etot = -14.6424332452339 +830000 ekin = 0.173291382896823 | erot = 0.351735589545891 | epot = -15.1674602177611 | etot = -14.6424332453184 +831000 ekin = 0.186352012963015 | erot = 0.343644456330365 | epot = -15.1724297146884 | etot = -14.642433245395 +832000 ekin = 0.199074924605492 | erot = 0.334772487921431 | epot = -15.1762806579853 | etot = -14.6424332454584 +833000 ekin = 0.210968084880519 | erot = 0.324658115189106 | epot = -15.1780594455734 | etot = -14.6424332455038 +834000 ekin = 0.22163875725694 | erot = 0.313022323442632 | epot = -15.1770943262278 | etot = -14.6424332455283 +835000 ekin = 0.230816330001906 | erot = 0.299793483326875 | epot = -15.1730430588591 | etot = -14.6424332455304 +836000 ekin = 0.238363132174156 | erot = 0.285116039960992 | epot = -15.165912417646 | etot = -14.6424332455109 +837000 ekin = 0.244270841530906 | erot = 0.269341751259717 | epot = -15.1560458382634 | etot = -14.6424332454728 +838000 ekin = 0.248642320235629 | erot = 0.253003904103877 | epot = -15.1440794697601 | etot = -14.6424332454206 +839000 ekin = 0.251661569327587 | erot = 0.236776758987145 | epot = -15.1308715736748 | etot = -14.6424332453601 +840000 ekin = 0.253557306828163 | erot = 0.221424057161458 | epot = -15.117414609287 | etot = -14.6424332452974 +841000 ekin = 0.254567562696712 | erot = 0.207741475743549 | epot = -15.1047422836783 | etot = -14.642433245238 +842000 ekin = 0.254912814683648 | erot = 0.19649826235426 | epot = -15.093844322224 | etot = -14.6424332451861 +843000 ekin = 0.254783130765732 | erot = 0.18838292178705 | epot = -15.0855992976972 | etot = -14.6424332451444 +844000 ekin = 0.254340789697802 | erot = 0.183956927272122 | epot = -15.0807309620839 | etot = -14.642433245114 +845000 ekin = 0.253734932891637 | erot = 0.183619247980649 | epot = -15.079787425967 | etot = -14.6424332450947 +846000 ekin = 0.25312050419609 | erot = 0.187583282239926 | epot = -15.0831370315219 | etot = -14.6424332450859 +847000 ekin = 0.252671650088207 | erot = 0.195866742639201 | epot = -15.0909716378148 | etot = -14.6424332450873 +848000 ekin = 0.252580915310227 | erot = 0.208294222463247 | epot = -15.1033083828726 | etot = -14.6424332450991 +849000 ekin = 0.253039966848203 | erot = 0.224511555531949 | epot = -15.1199847675021 | etot = -14.642433245122 +850000 ekin = 0.254204001798466 | erot = 0.244010590097926 | epot = -15.1406478370531 | etot = -14.6424332451567 +851000 ekin = 0.25614833902674 | erot = 0.266162563602757 | epot = -15.1647441478328 | etot = -14.6424332452033 +852000 ekin = 0.258829686440543 | erot = 0.290257858698332 | epot = -15.1915207903994 | etot = -14.6424332452605 +853000 ekin = 0.262064657828545 | erot = 0.315549558167831 | epot = -15.2200474613219 | etot = -14.6424332453255 +854000 ekin = 0.265534116122616 | erot = 0.341297947736459 | epot = -15.2492653092525 | etot = -14.6424332453934 +855000 ekin = 0.26881517465356 | erot = 0.366813004430954 | epot = -15.2780614245429 | etot = -14.6424332454584 +856000 ekin = 0.2714354869546 | erot = 0.391492007901482 | epot = -15.3053607403704 | etot = -14.6424332455143 +857000 ekin = 0.272939108063026 | erot = 0.414849750473433 | epot = -15.3302221040922 | etot = -14.6424332455557 +858000 ekin = 0.272951155039827 | erot = 0.436539390688028 | epot = -15.3519237913065 | etot = -14.6424332455787 +859000 ekin = 0.27122988067654 | erot = 0.456362750059338 | epot = -15.370025876317 | etot = -14.6424332455811 +860000 ekin = 0.267698633834005 | erot = 0.474269718460678 | epot = -15.3844015978584 | etot = -14.6424332455637 +861000 ekin = 0.262455001753023 | erot = 0.490347316007822 | epot = -15.3952355632891 | etot = -14.6424332455283 +862000 ekin = 0.255758797176847 | erot = 0.504799761298972 | epot = -15.4029918039546 | etot = -14.6424332454788 +863000 ekin = 0.248003564341593 | erot = 0.517921532812577 | epot = -15.408358342574 | etot = -14.6424332454198 +864000 ekin = 0.239677655585047 | erot = 0.530065823503499 | epot = -15.412176724445 | etot = -14.6424332453565 +865000 ekin = 0.23132088944558 | erot = 0.541610953534477 | epot = -15.4153650882737 | etot = -14.6424332452936 +866000 ekin = 0.223481813676492 | erot = 0.552927233332167 | epot = -15.4188422922443 | etot = -14.6424332452356 +867000 ekin = 0.21667917449216 | erot = 0.564346499432584 | epot = -15.4234589191109 | etot = -14.6424332451862 +868000 ekin = 0.211369750018423 | erot = 0.576136138939141 | epot = -15.4299391341058 | etot = -14.6424332451482 +869000 ekin = 0.207923502308487 | erot = 0.588478941151825 | epot = -15.4388356885839 | etot = -14.6424332451236 +870000 ekin = 0.206606153000579 | erot = 0.601459626890824 | epot = -15.4504990250046 | etot = -14.6424332451132 +871000 ekin = 0.207568796758706 | erot = 0.615058451106102 | epot = -15.4650604929822 | etot = -14.6424332451174 +872000 ekin = 0.210843969902103 | erot = 0.629151875760072 | epot = -15.4824290907977 | etot = -14.6424332451355 +873000 ekin = 0.216347593119445 | erot = 0.643519970834179 | epot = -15.5023008091198 | etot = -14.6424332451662 +874000 ekin = 0.223886305143434 | erot = 0.657859909731246 | epot = -15.5241794600821 | etot = -14.6424332452075 +875000 ekin = 0.233169807553067 | erot = 0.671804662211551 | epot = -15.5474077150215 | etot = -14.6424332452569 +876000 ekin = 0.243827877963456 | erot = 0.684945735800616 | epot = -15.5712068590756 | etot = -14.6424332453115 +877000 ekin = 0.255431632545719 | erot = 0.696858567355222 | epot = -15.5947234452689 | etot = -14.642433245368 +878000 ekin = 0.267518408512945 | erot = 0.707128927389438 | epot = -15.6170805813253 | etot = -14.6424332454229 +879000 ekin = 0.279619300258663 | erot = 0.715378495721848 | epot = -15.6374310414535 | etot = -14.642433245473 +880000 ekin = 0.291287955020082 | erot = 0.721287639199831 | epot = -15.655008839735 | etot = -14.6424332455151 +881000 ekin = 0.302128778464172 | erot = 0.724613422811349 | epot = -15.6691754468222 | etot = -14.6424332455467 +882000 ekin = 0.311822304068348 | erot = 0.72520106817747 | epot = -15.6794566178122 | etot = -14.6424332455663 +883000 ekin = 0.32014524378723 | erot = 0.722987481104759 | epot = -15.6855659704652 | etot = -14.6424332455732 +884000 ekin = 0.326982762198449 | erot = 0.717996120159773 | epot = -15.6874121279262 | etot = -14.642433245568 +885000 ekin = 0.332330882212052 | erot = 0.710323349672674 | epot = -15.6850874774371 | etot = -14.6424332455524 +886000 ekin = 0.336287673330606 | erot = 0.700117442976865 | epot = -15.6788383618368 | etot = -14.6424332455294 +887000 ekin = 0.339032964151287 | erot = 0.687552454437637 | epot = -15.6690186640915 | etot = -14.6424332455026 +888000 ekin = 0.340797654544087 | erot = 0.672800100946149 | epot = -15.6560310009666 | etot = -14.6424332454764 +889000 ekin = 0.341825106158792 | erot = 0.656003407102967 | epot = -15.6402617587166 | etot = -14.6424332454548 +890000 ekin = 0.34232834757507 | erot = 0.637256013166648 | epot = -15.6220176061832 | etot = -14.6424332454415 +891000 ekin = 0.342447730492025 | erot = 0.616590618571196 | epot = -15.6014715945022 | etot = -14.642433245439 +892000 ekin = 0.342214057411764 | erot = 0.593979026507483 | epot = -15.5786263293677 | etot = -14.6424332454484 +893000 ekin = 0.341522004910226 | erot = 0.569344767734754 | epot = -15.5533000181142 | etot = -14.6424332454692 +894000 ekin = 0.340117934117732 | erot = 0.542587519917767 | epot = -15.5251386995347 | etot = -14.6424332454992 +895000 ekin = 0.337605044782691 | erot = 0.513616778982377 | epot = -15.4936550692997 | etot = -14.6424332455346 +896000 ekin = 0.333467462872541 | erot = 0.482390775176039 | epot = -15.4582914836189 | etot = -14.6424332455703 +897000 ekin = 0.327113397522298 | erot = 0.448955709004864 | epot = -15.4185023521275 | etot = -14.6424332456003 +898000 ekin = 0.317936017621705 | erot = 0.413480165460747 | epot = -15.3738494287008 | etot = -14.6424332456183 +899000 ekin = 0.305389123797813 | erot = 0.376280077470634 | epot = -15.3241024468866 | etot = -14.6424332456181 +900000 ekin = 0.289072881398238 | erot = 0.337830752319679 | epot = -15.2693368793119 | etot = -14.642433245594 +901000 ekin = 0.268822686263766 | erot = 0.298764046956941 | epot = -15.2100199787623 | etot = -14.6424332455416 +902000 ekin = 0.244791653973854 | erot = 0.259850521116686 | epot = -15.147075420549 | etot = -14.6424332454585 +903000 ekin = 0.217514571467877 | erot = 0.2219680472084 | epot = -15.0819158640211 | etot = -14.6424332453448 +904000 ekin = 0.187939204416865 | erot = 0.18605969200996 | epot = -15.016432141631 | etot = -14.6424332452042 +905000 ekin = 0.157410847736454 | erot = 0.153084564880819 | epot = -14.9529286576615 | etot = -14.6424332450442 +906000 ekin = 0.127599356275869 | erot = 0.123965703542124 | epot = -14.8939983046943 | etot = -14.6424332448764 +907000 ekin = 0.100365589134273 | erot = 0.0995389863865968 | epot = -14.8423378202365 | etot = -14.6424332447156 +908000 ekin = 0.0775759855969076 | erot = 0.0805066337373332 | epot = -14.8005158639122 | etot = -14.6424332445779 +909000 ekin = 0.060887695004245 | erot = 0.0673982354544352 | epot = -14.7707191749376 | etot = -14.6424332444789 +910000 ekin = 0.051538292298201 | erot = 0.0605415547689986 | epot = -14.7545130914979 | etot = -14.6424332444307 +911000 ekin = 0.0501789452889314 | erot = 0.0600446989611976 | epot = -14.7526568886895 | etot = -14.6424332444394 +912000 ekin = 0.0567846925720761 | erot = 0.0657906450222932 | epot = -14.7650085820985 | etot = -14.6424332445042 +913000 ekin = 0.0706603747930264 | erot = 0.0774445361866898 | epot = -14.7905381555969 | etot = -14.6424332446172 +914000 ekin = 0.0905398584091763 | erot = 0.0944735694303653 | epot = -14.8274466726047 | etot = -14.6424332447652 +915000 ekin = 0.114756144628428 | erot = 0.116178630207615 | epot = -14.8733680197682 | etot = -14.6424332449321 +916000 ekin = 0.141447043402292 | erot = 0.141736093139118 | epot = -14.9256163816431 | etot = -14.6424332451017 +917000 ekin = 0.168758535419861 | erot = 0.170247440488538 | epot = -14.9814392211683 | etot = -14.6424332452599 +918000 ekin = 0.195014913439662 | erot = 0.200793639368136 | epot = -15.0382417982035 | etot = -14.6424332453957 +919000 ekin = 0.218837422083706 | erot = 0.232490666335444 | epot = -15.0937613339213 | etot = -14.6424332455022 +920000 ekin = 0.239206641023781 | erot = 0.264542267091206 | epot = -15.1461821536913 | etot = -14.6424332455763 +921000 ekin = 0.255474577148722 | erot = 0.29628605080145 | epot = -15.1941938735681 | etot = -14.6424332456179 +922000 ekin = 0.26733863121584 | erot = 0.327229363204498 | epot = -15.2370012400495 | etot = -14.6424332456292 +923000 ekin = 0.274791412214288 | erot = 0.357072039936907 | epot = -15.2742966977651 | etot = -14.6424332456139 +924000 ekin = 0.278059017516471 | erot = 0.385714059432095 | epot = -15.3062063225254 | etot = -14.6424332455768 +925000 ekin = 0.277537405168489 | erot = 0.413247220094928 | epot = -15.3332178707869 | etot = -14.6424332455235 +926000 ekin = 0.273733135238468 | erot = 0.439931173660914 | epot = -15.3560975543588 | etot = -14.6424332454594 +927000 ekin = 0.26721185964169 | erot = 0.466155363881716 | epot = -15.3758004689138 | etot = -14.6424332453904 +928000 ekin = 0.258555847536273 | erot = 0.492389553502083 | epot = -15.3933786463605 | etot = -14.6424332453221 +929000 ekin = 0.248330567892114 | erot = 0.519126582981251 | epot = -15.4098903961332 | etot = -14.6424332452599 +930000 ekin = 0.237059747166417 | erot = 0.546821711631313 | epot = -15.4263147040061 | etot = -14.6424332452084 +931000 ekin = 0.225208144806099 | erot = 0.575833282923054 | epot = -15.4434746729006 | etot = -14.6424332451714 +932000 ekin = 0.213171319366128 | erot = 0.606369490851291 | epot = -15.4619740553693 | etot = -14.6424332451519 +933000 ekin = 0.201271722996209 | erot = 0.638445690378466 | epot = -15.482150658526 | etot = -14.6424332451513 +934000 ekin = 0.189760460110485 | erot = 0.671856006698808 | epot = -15.5040497119792 | etot = -14.6424332451699 +935000 ekin = 0.178823941838717 | erot = 0.706161996587126 | epot = -15.5274191836321 | etot = -14.6424332452063 +936000 ekin = 0.168594479115294 | erot = 0.740699865837039 | epot = -15.5517275902103 | etot = -14.6424332452579 +937000 ekin = 0.159163635635195 | erot = 0.774606336205919 | epot = -15.5762032171622 | etot = -14.6424332453211 +938000 ekin = 0.150596971915171 | erot = 0.806861786796075 | epot = -15.5998920041023 | etot = -14.6424332453911 +939000 ekin = 0.142948711632666 | erot = 0.836347883526529 | epot = -15.6217298406219 | etot = -14.6424332454627 +940000 ekin = 0.136274889171384 | erot = 0.861915676028721 | epot = -15.6406238107305 | etot = -14.6424332455304 +941000 ekin = 0.130643703199134 | erot = 0.882459199120404 | epot = -15.6555361479088 | etot = -14.6424332455893 +942000 ekin = 0.126142088160929 | erot = 0.896989065172066 | epot = -15.6655643989677 | etot = -14.6424332456347 +943000 ekin = 0.122877886110378 | erot = 0.904700444358843 | epot = -15.6700115761325 | etot = -14.6424332456633 +944000 ekin = 0.12097740741224 | erot = 0.905030230236918 | epot = -15.6684408833219 | etot = -14.6424332456728 +945000 ekin = 0.120578563690818 | erot = 0.897699054745715 | epot = -15.660710864099 | etot = -14.6424332456625 +946000 ekin = 0.121820103593603 | erot = 0.882735070928584 | epot = -15.6469884201552 | etot = -14.642433245633 +947000 ekin = 0.124827761129181 | erot = 0.860477935596529 | epot = -15.6277389423121 | etot = -14.6424332455864 +948000 ekin = 0.129698334168747 | erot = 0.831563037038142 | epot = -15.6036946167331 | etot = -14.6424332455262 +949000 ekin = 0.136482857558223 | erot = 0.796887554722467 | epot = -15.5758036577371 | etot = -14.6424332454564 +950000 ekin = 0.145170138931244 | erot = 0.757561255988665 | epot = -15.545164640302 | etot = -14.6424332453821 +951000 ekin = 0.155672002995198 | erot = 0.714845916094193 | epot = -15.5129511643977 | etot = -14.6424332453083 +952000 ekin = 0.167811650836288 | erot = 0.670087833250747 | epot = -15.4803327293271 | etot = -14.64243324524 +953000 ekin = 0.181316579471282 | erot = 0.62464809521251 | epot = -15.4483979198655 | etot = -14.6424332451817 +954000 ekin = 0.195817500701168 | erot = 0.579835080696309 | epot = -15.4180858265343 | etot = -14.6424332451368 +955000 ekin = 0.210854606876659 | erot = 0.536843219769282 | epot = -15.3901310717537 | etot = -14.6424332451077 +956000 ekin = 0.225892299837258 | erot = 0.49670137679197 | epot = -15.3650269217247 | etot = -14.6424332450955 +957000 ekin = 0.240343066498473 | erot = 0.460233438094331 | epot = -15.3430097496925 | etot = -14.6424332450997 +958000 ekin = 0.253600493839208 | erot = 0.428032849894538 | epot = -15.324066588852 | etot = -14.6424332451182 +959000 ekin = 0.26508043374811 | erot = 0.400452005459373 | epot = -15.3079656843552 | etot = -14.6424332451478 +960000 ekin = 0.274268068130398 | erot = 0.377606549450015 | epot = -15.2943078627643 | etot = -14.6424332451839 +961000 ekin = 0.280767178003419 | erot = 0.359393861249926 | epot = -15.2825942844748 | etot = -14.6424332452215 +962000 ekin = 0.284346484063279 | erot = 0.345524198816832 | epot = -15.2723039281355 | etot = -14.6424332452554 +963000 ekin = 0.284976816089691 | erot = 0.3355622323293 | epot = -15.2629722936999 | etot = -14.6424332452809 +964000 ekin = 0.282852494247854 | erot = 0.328975986496892 | epot = -15.2542617260392 | etot = -14.6424332452945 +965000 ekin = 0.278391086615428 | erot = 0.325189577598743 | epot = -15.2460139095086 | etot = -14.6424332452944 +966000 ekin = 0.272207924679439 | erot = 0.323635640150665 | epot = -15.2382768101109 | etot = -14.6424332452808 +967000 ekin = 0.265065367870575 | erot = 0.323803079987219 | epot = -15.2313016931133 | etot = -14.6424332452555 +968000 ekin = 0.257801293713888 | erot = 0.325275872290492 | epot = -15.2255104112269 | etot = -14.6424332452225 +969000 ekin = 0.251245661474162 | erot = 0.327759142575902 | epot = -15.2214380492365 | etot = -14.6424332451864 +970000 ekin = 0.24613700899304 | erot = 0.331089781180773 | epot = -15.2196600353261 | etot = -14.6424332451523 +971000 ekin = 0.243051319616021 | erot = 0.335230325664833 | epot = -15.2207148904054 | etot = -14.6424332451246 +972000 ekin = 0.242353409638695 | erot = 0.340246678804358 | epot = -15.22503333355 | etot = -14.6424332451069 +973000 ekin = 0.244176338162489 | erot = 0.346272190710356 | epot = -15.2328817739745 | etot = -14.6424332451017 +974000 ekin = 0.248428661658042 | erot = 0.353462430361478 | epot = -15.2443243371296 | etot = -14.6424332451101 +975000 ekin = 0.254824314803068 | erot = 0.361946299430202 | epot = -15.2592038593654 | etot = -14.6424332451321 +976000 ekin = 0.262926848820545 | erot = 0.371779749929518 | epot = -15.2771398439171 | etot = -14.642433245167 +977000 ekin = 0.27219923533091 | erot = 0.382908123263806 | epot = -15.297540603808 | etot = -14.6424332452133 +978000 ekin = 0.282052066851764 | erot = 0.395142048097211 | epot = -15.3196273602177 | etot = -14.6424332452688 +979000 ekin = 0.291885751914043 | erot = 0.408150081471225 | epot = -15.3424690787159 | etot = -14.6424332453306 +980000 ekin = 0.301125083790016 | erot = 0.421469125222495 | epot = -15.365027454408 | etot = -14.6424332453955 +981000 ekin = 0.309246535917451 | erot = 0.434531423656212 | epot = -15.3862112050333 | etot = -14.6424332454596 +982000 ekin = 0.315799497490911 | erot = 0.446704965616411 | epot = -15.404937708626 | etot = -14.6424332455187 +983000 ekin = 0.32042257322114 | erot = 0.457342632743475 | epot = -15.4201984515335 | etot = -14.6424332455688 +984000 ekin = 0.322855465258551 | erot = 0.465834622598882 | epot = -15.4311233334638 | etot = -14.6424332456063 +985000 ekin = 0.322946302475207 | erot = 0.47165859097348 | epot = -15.4370381390771 | etot = -14.6424332456284 +986000 ekin = 0.320653917805744 | erot = 0.474422556589946 | epot = -15.4375097200291 | etot = -14.6424332456334 +987000 ekin = 0.316044627362153 | erot = 0.473896755515053 | epot = -15.4323746284979 | etot = -14.6424332456207 +988000 ekin = 0.309283477268727 | erot = 0.470032116944613 | epot = -15.4217488398044 | etot = -14.6424332455911 +989000 ekin = 0.300620522169168 | erot = 0.462964620621354 | epot = -15.4060183883369 | etot = -14.6424332455464 +990000 ekin = 0.290373280691188 | erot = 0.453006262994313 | epot = -15.3858127891748 | etot = -14.6424332454893 +991000 ekin = 0.278906915705663 | erot = 0.440624526218637 | epot = -15.3619646873472 | etot = -14.6424332454229 +992000 ekin = 0.266613826415146 | erot = 0.426413006890641 | epot = -15.3354600786566 | etot = -14.6424332453509 +993000 ekin = 0.253894212446534 | erot = 0.411056197524004 | epot = -15.3073836552473 | etot = -14.6424332452767 +994000 ekin = 0.24113883700009 | erot = 0.395291372387941 | epot = -15.2788634545917 | etot = -14.6424332452037 +995000 ekin = 0.22871476890696 | erot = 0.379870207854789 | epot = -15.2510182218965 | etot = -14.6424332451348 +996000 ekin = 0.216954417470376 | erot = 0.365522282707067 | epot = -15.2249099452499 | etot = -14.6424332450725 +997000 ekin = 0.206147766455999 | erot = 0.352922066138332 | epot = -15.2015030776131 | etot = -14.6424332450188 +998000 ekin = 0.196537413157836 | erot = 0.342660495991062 | epot = -15.1816311541242 | etot = -14.6424332449753 +999000 ekin = 0.18831584391307 | erot = 0.335221830005501 | epot = -15.1659709188615 | etot = -14.642433244943 +1000000 ekin = 0.181624323067755 | erot = 0.330966139649165 | epot = -15.1550237076395 | etot = -14.6424332449226 + 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 +Loop time of 18.6281 on 4 procs for 1000000 steps with 10 atoms + +Performance: 46381.610 tau/day, 53682.419 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.50691 | 7.0285 | 12.641 | 197.6 | 37.73 +Bond | 0.081876 | 0.27627 | 0.44175 | 28.5 | 1.48 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.7692 | 2.0629 | 2.3468 | 17.0 | 11.07 +Output | 1.8e-05 | 2.625e-05 | 3e-05 | 0.0 | 0.00 +Modify | 0.17309 | 0.88362 | 1.5352 | 58.4 | 4.74 +Other | | 8.377 | | | 44.97 + +Nlocal: 2.5 ave 5 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 7.5 ave 10 max 5 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 18.5 ave 35 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 74 +Ave neighs/atom = 7.4 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:18 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 deleted file mode 100644 index 8b1c5c3807451c729cb70b95d3367e47860e276a..0000000000000000000000000000000000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1 +++ /dev/null @@ -1,1165 +0,0 @@ -LAMMPS (18 Jun 2019) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 5e-05 secs - read_data CPU = 0.001522 secs - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 -1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.0173888111295073 | erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136619 | erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948556079 | erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.04839505571915 | erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336920643 | erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406440561 | erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563085878 | erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398 -11000 ekin = 0.0965486715045649 | erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229 -12000 ekin = 0.10722146628289 | erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598 -13000 ekin = 0.116672809719548 | erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627 -14000 ekin = 0.12465407373104 | erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151 -15000 ekin = 0.13098393968427 | erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544 -16000 ekin = 0.135553354544872 | erot = 0.669086028489761 | epot = -15.447072628815 | etot = -14.6424332457804 -17000 ekin = 0.138326263958247 | erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935 -18000 ekin = 0.139336096664052 | erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954 -19000 ekin = 0.138678360045177 | erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878 -20000 ekin = 0.136500074655373 | erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773 -21000 ekin = 0.132987065285671 | erot = 0.864912408452581 | epot = -15.6403327194916 | etot = -14.6424332457533 -22000 ekin = 0.128350288213556 | erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311 -23000 ekin = 0.122812385135508 | erot = 0.917661024683964 | epot = -15.6829066555277 | etot = -14.6424332457083 -24000 ekin = 0.116595521408284 | erot = 0.938759014332096 | epot = -15.6977877814267 | etot = -14.6424332456863 -25000 ekin = 0.109911323474816 | erot = 0.956471207347236 | epot = -15.7088157764882 | etot = -14.6424332456662 -26000 ekin = 0.102953426207644 | erot = 0.970893163953198 | epot = -15.7162798358091 | etot = -14.6424332456483 -27000 ekin = 0.0958928250746637 | erot = 0.982114250194049 | epot = -15.7204403209013 | etot = -14.6424332456326 -28000 ekin = 0.0888759410950343 | erot = 0.990219731539835 | epot = -15.7215289182535 | etot = -14.6424332456186 -29000 ekin = 0.0820250748773376 | erot = 0.995296041202909 | epot = -15.719754361686 | etot = -14.6424332456058 -30000 ekin = 0.0754407616839748 | erot = 0.997437949320991 | epot = -15.7153119565981 | etot = -14.6424332455932 -31000 ekin = 0.0692054432610605 | erot = 0.996756332762285 | epot = -15.7083950216035 | etot = -14.6424332455802 -32000 ekin = 0.0633878377978472 | erot = 0.993385345349211 | epot = -15.699206428713 | etot = -14.6424332455659 -33000 ekin = 0.0580474070871663 | erot = 0.987487973309961 | epot = -15.6879686259471 | etot = -14.64243324555 -34000 ekin = 0.0532383791888181 | erot = 0.979259192921736 | epot = -15.6749308176426 | etot = -14.642433245532 -35000 ekin = 0.0490128758307997 | erot = 0.968926197407215 | epot = -15.66037231875 | etot = -14.642433245512 -36000 ekin = 0.0454228081410747 | erot = 0.95674540962595 | epot = -15.6446014632576 | etot = -14.6424332454906 -37000 ekin = 0.0425203357176436 | erot = 0.942996238000708 | epot = -15.6279498191869 | etot = -14.6424332454685 -38000 ekin = 0.0403568280949567 | erot = 0.92797176661665 | epot = -15.6107618401582 | etot = -14.6424332454466 -39000 ekin = 0.0389804214212708 | erot = 0.911966804110001 | epot = -15.5933804709572 | etot = -14.642433245426 -40000 ekin = 0.0384324238856422 | erot = 0.8952639595629 | epot = -15.5761296288567 | etot = -14.6424332454081 -41000 ekin = 0.0387429860408521 | erot = 0.878118672838247 | epot = -15.5592949042733 | etot = -14.6424332453942 -42000 ekin = 0.0399266053637504 | erot = 0.860744395135471 | epot = -15.5431042458848 | etot = -14.6424332453856 -43000 ekin = 0.0419781561011205 | erot = 0.843299365355946 | epot = -15.52771076684 | etot = -14.6424332453829 -44000 ekin = 0.0448701894086706 | erot = 0.825876603312506 | epot = -15.5131800381079 | etot = -14.6424332453867 -45000 ekin = 0.0485521857411509 | erot = 0.808498758184836 | epot = -15.4994841893228 | etot = -14.6424332453969 -46000 ekin = 0.0529522094031963 | erot = 0.791119212186772 | epot = -15.4865046670025 | etot = -14.6424332454125 -47000 ekin = 0.0579809824236739 | erot = 0.773630265882115 | epot = -15.4740444937379 | etot = -14.6424332454321 -48000 ekin = 0.063537784649307 | erot = 0.755878310836066 | epot = -15.4618493409392 | etot = -14.6424332454538 -49000 ekin = 0.0695169124457283 | erot = 0.737684732482629 | epot = -15.4496348904038 | etot = -14.6424332454754 -50000 ekin = 0.0758129058454745 | erot = 0.718870126218063 | epot = -15.4371162775588 | etot = -14.6424332454952 -51000 ekin = 0.082322663864191 | erot = 0.69927859951883 | epot = -15.4240345088949 | etot = -14.6424332455119 -52000 ekin = 0.0889431481334984 | erot = 0.67879880709845 | epot = -15.4101752007568 | etot = -14.6424332455248 -53000 ekin = 0.0955646689255781 | erot = 0.657379086769954 | epot = -15.3953770012299 | etot = -14.6424332455344 -54000 ekin = 0.102061477509349 | erot = 0.635035489168609 | epot = -15.3795302122192 | etot = -14.6424332455412 -55000 ekin = 0.108282960174 | erot = 0.611853171347129 | epot = -15.3625693770671 | etot = -14.6424332455459 -56000 ekin = 0.114049426281782 | erot = 0.58798294592476 | epot = -15.3444656177551 | etot = -14.6424332455485 -57000 ekin = 0.119155806186856 | erot = 0.563635255923989 | epot = -15.3252243076595 | etot = -14.6424332455486 -58000 ekin = 0.123384552305436 | erot = 0.539073355224011 | epot = -15.3048911530747 | etot = -14.6424332455453 -59000 ekin = 0.126526300954942 | erot = 0.514606324860975 | epot = -15.2835658713528 | etot = -14.6424332455369 -60000 ekin = 0.128404399836505 | erot = 0.490581338842491 | epot = -15.2614189842015 | etot = -14.6424332455225 -61000 ekin = 0.128898142362338 | erot = 0.46737389240369 | epot = -15.2387052802676 | etot = -14.6424332455016 -62000 ekin = 0.127959880290304 | erot = 0.445374820089083 | epot = -15.2157679458544 | etot = -14.642433245475 -63000 ekin = 0.125622870624957 | erot = 0.424973765390021 | epot = -15.1930298814589 | etot = -14.6424332454439 -64000 ekin = 0.121999044843205 | erot = 0.406539918574829 | epot = -15.1709722088285 | etot = -14.6424332454105 -65000 ekin = 0.117268056619305 | erot = 0.390401831022814 | epot = -15.1501031330194 | etot = -14.6424332453773 -66000 ekin = 0.111660385257246 | erot = 0.376828594080988 | epot = -15.1309222246848 | etot = -14.6424332453465 -67000 ekin = 0.105437746905138 | erot = 0.366014539812675 | epot = -15.1138855320384 | etot = -14.6424332453205 -68000 ekin = 0.0988737375607886 | erot = 0.3580690141562 | epot = -15.0993759970177 | etot = -14.6424332453007 -69000 ekin = 0.0922368286502271 | erot = 0.353011948772473 | epot = -15.0876820227105 | etot = -14.6424332452878 -70000 ekin = 0.085776901527448 | erot = 0.350775174164851 | epot = -15.0789853209745 | etot = -14.6424332452822 -71000 ekin = 0.0797156921642142 | erot = 0.351208844244805 | epot = -15.0733577816926 | etot = -14.6424332452835 -72000 ekin = 0.0742409440406418 | erot = 0.354092037745935 | epot = -15.0707662270776 | etot = -14.6424332452911 -73000 ekin = 0.0695037498701448 | erot = 0.359146526959505 | epot = -15.0710835221334 | etot = -14.6424332453038 -74000 ekin = 0.0656184497423043 | erot = 0.366052769876549 | epot = -15.0741044649392 | etot = -14.6424332453204 -75000 ekin = 0.0626644690389266 | erot = 0.374467290031506 | epot = -15.07956500441 | etot = -14.6424332453396 -76000 ekin = 0.0606895535086054 | erot = 0.384040683400738 | epot = -15.0871634822693 | etot = -14.64243324536 -77000 ekin = 0.0597139401235012 | erot = 0.394435495890075 | epot = -15.0965826813934 | etot = -14.6424332453798 -78000 ekin = 0.059735062986913 | erot = 0.405343151479082 | epot = -15.1075114598642 | etot = -14.6424332453982 -79000 ekin = 0.0607324264355555 | erot = 0.416499017639937 | epot = -15.1196646894892 | etot = -14.6424332454137 -80000 ekin = 0.06267229049498 | erot = 0.427694630236126 | epot = -15.1328001661568 | etot = -14.6424332454257 -81000 ekin = 0.0655118235328765 | erot = 0.438786127846728 | epot = -15.1467311968131 | etot = -14.6424332454335 -82000 ekin = 0.0692024020835893 | erot = 0.449698113828473 | epot = -15.1613337613493 | etot = -14.6424332454372 -83000 ekin = 0.0736917936906618 | erot = 0.460422490738957 | epot = -15.1765475298665 | etot = -14.6424332454369 -84000 ekin = 0.0789250526546722 | erot = 0.471012272293582 | epot = -15.1923705703818 | etot = -14.6424332454336 -85000 ekin = 0.0848440878750035 | erot = 0.481570908649162 | epot = -15.2088482419522 | etot = -14.642433245428 -86000 ekin = 0.0913860133254624 | erot = 0.492238169205216 | epot = -15.2260574279521 | etot = -14.6424332454214 -87000 ekin = 0.0984805441200046 | erot = 0.503174014616525 | epot = -15.2440878041518 | etot = -14.6424332454153 -88000 ekin = 0.106046830304297 | erot = 0.514542076496056 | epot = -15.263022152211 | etot = -14.6424332454106 -89000 ekin = 0.113990204127984 | erot = 0.526494309539207 | epot = -15.2829177590758 | etot = -14.6424332454087 -90000 ekin = 0.122199339151894 | erot = 0.539158097285698 | epot = -15.3037906818477 | etot = -14.6424332454101 -91000 ekin = 0.130544275971403 | erot = 0.552626637865723 | epot = -15.3256041592524 | etot = -14.6424332454152 -92000 ekin = 0.138875666148815 | erot = 0.566952900962156 | epot = -15.3482618125355 | etot = -14.6424332454245 -93000 ekin = 0.147025440614642 | erot = 0.582146933737432 | epot = -15.3716056197897 | etot = -14.6424332454376 -94000 ekin = 0.154808946847822 | erot = 0.598175891801207 | epot = -15.3954180841032 | etot = -14.6424332454542 -95000 ekin = 0.162028449602152 | erot = 0.614965942453837 | epot = -15.4194276375299 | etot = -14.6424332454739 -96000 ekin = 0.168477779667818 | erot = 0.632405154082029 | epot = -15.4433161792459 | etot = -14.642433245496 -97000 ekin = 0.17394786302672 | erot = 0.650346631628325 | epot = -15.4667277401752 | etot = -14.6424332455201 -98000 ekin = 0.178232875004242 | erot = 0.668611435745948 | epot = -15.4892775562957 | etot = -14.6424332455455 -99000 ekin = 0.181136831926353 | erot = 0.686991165056211 | epot = -15.5105612425543 | etot = -14.6424332455718 -100000 ekin = 0.182480533643598 | erot = 0.705250413407778 | epot = -15.5301641926495 | etot = -14.6424332455981 -101000 ekin = 0.182108871451935 | erot = 0.723129571003179 | epot = -15.547671688079 | etot = -14.6424332456239 -102000 ekin = 0.179898581170268 | erot = 0.740348571090314 | epot = -15.5626803979088 | etot = -14.6424332456482 -103000 ekin = 0.175766517608084 | erot = 0.756612167825837 | epot = -15.5748119311039 | etot = -14.64243324567 -104000 ekin = 0.169678431535445 | erot = 0.771617166851602 | epot = -15.5837288440751 | etot = -14.6424332456881 -105000 ekin = 0.161658036036865 | erot = 0.785061742962005 | epot = -15.5891530247 | etot = -14.6424332457012 -106000 ekin = 0.151795867650478 | erot = 0.796656613424597 | epot = -15.5908857267829 | etot = -14.6424332457078 -107000 ekin = 0.140257112952727 | erot = 0.806137449197231 | epot = -15.5888278078568 | etot = -14.6424332457068 -108000 ekin = 0.127287240201241 | erot = 0.813277564481104 | epot = -15.5829980503796 | etot = -14.6424332456973 -109000 ekin = 0.113214025490917 | erot = 0.817899691734432 | epot = -15.573546962904 | etot = -14.6424332456787 -110000 ekin = 0.0984444823805213 | erot = 0.819885578053921 | epot = -15.5607633060856 | etot = -14.6424332456512 -111000 ekin = 0.0834553769364569 | erot = 0.819182262545785 | epot = -15.545070885098 | etot = -14.6424332456157 -112000 ekin = 0.0687764915871027 | erot = 0.815804215094415 | epot = -15.5270139522555 | etot = -14.642433245574 -113000 ekin = 0.0549665904028903 | erot = 0.809830999844441 | epot = -15.5072308357759 | etot = -14.6424332455285 -114000 ekin = 0.0425830583120619 | erot = 0.801400700350953 | epot = -15.4864170041452 | etot = -14.6424332454821 -115000 ekin = 0.032147280213263 | erot = 0.790699910049051 | epot = -15.4652804357003 | etot = -14.642433245438 -116000 ekin = 0.024108778034577 | erot = 0.777951546674724 | epot = -15.4444935701085 | etot = -14.6424332453992 -117000 ekin = 0.0188117102728931 | erot = 0.763402004774069 | epot = -15.4246469604154 | etot = -14.6424332453684 -118000 ekin = 0.0164673894159043 | erot = 0.747309167856945 | epot = -15.4062098026203 | etot = -14.6424332453474 -119000 ekin = 0.0171359296532898 | erot = 0.729932564575393 | epot = -15.3895017395657 | etot = -14.642433245337 -120000 ekin = 0.0207190822430497 | erot = 0.711526526250247 | epot = -15.3746788538305 | etot = -14.6424332453372 -121000 ekin = 0.0269649552319816 | erot = 0.692336677373422 | epot = -15.3617348779522 | etot = -14.6424332453468 -122000 ekin = 0.0354839220297736 | erot = 0.672599570214091 | epot = -15.3505167376079 | etot = -14.642433245364 -123000 ekin = 0.0457738626451366 | erot = 0.652544850165416 | epot = -15.3407519581971 | etot = -14.6424332453865 -124000 ekin = 0.0572521324296466 | erot = 0.632399068066114 | epot = -15.3320844459074 | etot = -14.6424332454117 -125000 ekin = 0.0692913736002564 | erot = 0.612390156186006 | epot = -15.324114775223 | etot = -14.6424332454368 -126000 ekin = 0.0812564128172846 | erot = 0.592751635109578 | epot = -15.3164412933862 | etot = -14.6424332454593 -127000 ekin = 0.0925398817823717 | erot = 0.573725774407888 | epot = -15.3086989016675 | etot = -14.6424332454772 -128000 ekin = 0.102594692018529 | erot = 0.55556513894369 | epot = -15.3005930764509 | etot = -14.6424332454887 -129000 ekin = 0.110961953873462 | erot = 0.538532171478003 | epot = -15.291927370844 | etot = -14.6424332454925 -130000 ekin = 0.117293279472125 | erot = 0.52289666445339 | epot = -15.2826231894136 | etot = -14.642433245488 -131000 ekin = 0.121366644774014 | erot = 0.508931150171021 | epot = -15.2727310404203 | etot = -14.6424332454752 -132000 ekin = 0.123095155538848 | erot = 0.49690439090507 | epot = -15.2624327918984 | etot = -14.6424332454545 -133000 ekin = 0.122528239670491 | erot = 0.487073282996463 | epot = -15.2520347680938 | etot = -14.6424332454268 -134000 ekin = 0.119845042600695 | erot = 0.47967360116923 | epot = -15.2419518891638 | etot = -14.6424332453939 -135000 ekin = 0.115340171966309 | erot = 0.474910093714588 | epot = -15.2326835110385 | etot = -14.6424332453576 -136000 ekin = 0.10940241928465 | erot = 0.472946484072521 | epot = -15.2247821486777 | etot = -14.6424332453205 -137000 ekin = 0.102487634021818 | erot = 0.473895929917005 | epot = -15.2188168092237 | etot = -14.6424332452849 -138000 ekin = 0.0950874634047233 | erot = 0.477812435582745 | epot = -15.2153331442409 | etot = -14.6424332452534 -139000 ekin = 0.0876961121512815 | erot = 0.484683617748011 | epot = -15.2148129751279 | etot = -14.6424332452286 -140000 ekin = 0.0807775418431626 | erot = 0.494425108537478 | epot = -15.2176358955931 | etot = -14.6424332452125 -141000 ekin = 0.0747355681577817 | erot = 0.50687677080795 | epot = -15.2240455841725 | etot = -14.6424332452068 -142000 ekin = 0.0698891098450116 | erot = 0.521800821238808 | epot = -15.2341231762965 | etot = -14.6424332452127 -143000 ekin = 0.0664544171866063 | erot = 0.538881922424094 | epot = -15.2477695848413 | etot = -14.6424332452306 -144000 ekin = 0.0645355104692083 | erot = 0.557729316020225 | epot = -15.2646980717496 | etot = -14.6424332452602 -145000 ekin = 0.0641233595162911 | erot = 0.577881111412627 | epot = -15.2844377162297 | etot = -14.6424332453008 -146000 ekin = 0.0651036077515188 | erot = 0.598810893851628 | epot = -15.3063477469538 | etot = -14.6424332453507 -147000 ekin = 0.0672719578973601 | erot = 0.619936843681753 | epot = -15.3296420469868 | etot = -14.6424332454077 -148000 ekin = 0.0703557492692045 | erot = 0.640633538190902 | epot = -15.3534225329294 | etot = -14.6424332454693 -149000 ekin = 0.0740398128642427 | erot = 0.660246523237691 | epot = -15.3767195816347 | etot = -14.6424332455328 -150000 ekin = 0.0779944201058678 | erot = 0.678109590376156 | epot = -15.398537256077 | etot = -14.642433245595 -151000 ekin = 0.0819030604172323 | erot = 0.693564488648094 | epot = -15.4179007947185 | etot = -14.6424332456531 -152000 ekin = 0.0854878938552624 | erot = 0.705982563003889 | epot = -15.4339037025634 | etot = -14.6424332457043 -153000 ekin = 0.0885310147328532 | erot = 0.714787575382088 | epot = -15.4457518358609 | etot = -14.6424332457459 -154000 ekin = 0.0908901012887555 | erot = 0.719478762727528 | epot = -15.4528021097924 | etot = -14.6424332457761 -155000 ekin = 0.092507570371455 | erot = 0.719653046097721 | epot = -15.4545938622626 | etot = -14.6424332457934 -156000 ekin = 0.0934129479728847 | erot = 0.715025243753982 | epot = -15.4508714375239 | etot = -14.642433245797 -157000 ekin = 0.0937187435779626 | erot = 0.705445163946324 | epot = -15.4415971533109 | etot = -14.6424332457866 -158000 ekin = 0.0936106185393401 | erot = 0.690910554325706 | epot = -15.4269544186278 | etot = -14.6424332457627 -159000 ekin = 0.0933330174010987 | erot = 0.671575051659785 | epot = -15.4073413147871 | etot = -14.6424332457262 -160000 ekin = 0.0931716565242322 | erot = 0.647750492120645 | epot = -15.3833553943234 | etot = -14.6424332456785 -161000 ekin = 0.0934343296231438 | erot = 0.619903194016586 | epot = -15.3557707692612 | etot = -14.6424332456215 -162000 ekin = 0.0944314104804186 | erot = 0.588644098979611 | epot = -15.3255087550173 | etot = -14.6424332455572 -163000 ekin = 0.0964572425739502 | erot = 0.55471294345392 | epot = -15.2936034315161 | etot = -14.6424332454882 -164000 ekin = 0.0997733472806136 | erot = 0.518956918561936 | epot = -15.2611635112594 | etot = -14.6424332454169 -165000 ekin = 0.104594102019911 | erot = 0.482304549422426 | epot = -15.2293318967882 | etot = -14.6424332453459 -166000 ekin = 0.11107527651625 | erot = 0.445735768512381 | epot = -15.1992442903065 | etot = -14.6424332452778 -167000 ekin = 0.11930559751358 | erot = 0.410249354728318 | epot = -15.1719881974571 | etot = -14.6424332452152 -168000 ekin = 0.129301354725086 | erot = 0.37682904617874 | epot = -15.1485636460642 | etot = -14.6424332451604 -169000 ekin = 0.14100396578975 | erot = 0.346409702527097 | epot = -15.1298469134321 | etot = -14.6424332451152 -170000 ekin = 0.154280377439942 | erot = 0.319844892417961 | epot = -15.1165585149394 | etot = -14.6424332450815 -171000 ekin = 0.168926178621544 | erot = 0.297877221606916 | epot = -15.109236645289 | etot = -14.6424332450606 -172000 ekin = 0.184671319364511 | erot = 0.281112611137243 | epot = -15.108217175555 | etot = -14.6424332450532 -173000 ekin = 0.201188345437118 | erot = 0.269999595570268 | epot = -15.1136211860672 | etot = -14.6424332450598 -174000 ekin = 0.218103052207035 | erot = 0.264814547402982 | epot = -15.12535084469 | etot = -14.6424332450799 -175000 ekin = 0.235007413035623 | erot = 0.265653545950115 | epot = -15.1430942040986 | etot = -14.6424332451129 -176000 ekin = 0.251474534267915 | erot = 0.272431389432266 | epot = -15.1663391688573 | etot = -14.6424332451571 -177000 ekin = 0.267075225143436 | erot = 0.284887984978803 | epot = -15.1943964553329 | etot = -14.6424332452107 -178000 ekin = 0.281395553895287 | erot = 0.302602030915412 | epot = -15.2264308300819 | etot = -14.6424332452712 -179000 ekin = 0.294054514411866 | erot = 0.325011526057904 | epot = -15.2614992858055 | etot = -14.6424332453358 -180000 ekin = 0.304720692896942 | erot = 0.351440214935852 | epot = -15.2985941532343 | etot = -14.6424332454015 -181000 ekin = 0.313126658918426 | erot = 0.381128639602688 | epot = -15.3366885439866 | etot = -14.6424332454655 -182000 ekin = 0.319079775823621 | erot = 0.413268071114152 | epot = -15.374781092463 | etot = -14.6424332455252 -183000 ekin = 0.322468290005762 | erot = 0.447035301736728 | epot = -15.4119368373208 | etot = -14.6424332455783 -184000 ekin = 0.323261947554671 | erot = 0.48162615508044 | epot = -15.4473213482583 | etot = -14.6424332456231 -185000 ekin = 0.321506983530827 | erot = 0.516285658867815 | epot = -15.4802258880574 | etot = -14.6424332456588 -186000 ekin = 0.317316057633682 | erot = 0.550333132629112 | epot = -15.5100824359478 | etot = -14.642433245685 -187000 ekin = 0.310854440590084 | erot = 0.583180936761968 | epot = -15.5364686230541 | etot = -14.642433245702 -188000 ekin = 0.302324329763947 | erot = 0.614346238385429 | epot = -15.55910381386 | etot = -14.6424332457106 -189000 ekin = 0.291949445197116 | erot = 0.64345577901281 | epot = -15.5778384699217 | etot = -14.6424332457118 -190000 ekin = 0.279961942768254 | erot = 0.67024418570442 | epot = -15.5926393741794 | etot = -14.6424332457067 -191000 ekin = 0.266593185653664 | erot = 0.694546781233348 | epot = -15.6035732125832 | etot = -14.6424332456962 -192000 ekin = 0.252069141623363 | erot = 0.716288088786984 | epot = -15.6107904760917 | etot = -14.6424332456814 -193000 ekin = 0.236610293254145 | erot = 0.735467302242536 | epot = -15.6145108411597 | etot = -14.642433245663 -194000 ekin = 0.22043514940511 | erot = 0.75214194302714 | epot = -15.615010338074 | etot = -14.6424332456418 -195000 ekin = 0.20376588009334 | erot = 0.76641079902996 | epot = -15.6126099247417 | etot = -14.6424332456184 -196000 ekin = 0.186834339037366 | erot = 0.778397083250806 | epot = -15.6076646678817 | etot = -14.6424332455935 -197000 ekin = 0.169886782294183 | erot = 0.788232586070618 | epot = -15.6005526139326 | etot = -14.6424332455678 -198000 ekin = 0.153185871077985 | erot = 0.796043434538987 | epot = -15.5916625511591 | etot = -14.6424332455421 -199000 ekin = 0.137008972987403 | erot = 0.801937915798979 | epot = -15.581380134304 | etot = -14.6424332455176 -200000 ekin = 0.121642272364804 | erot = 0.805996673261661 | epot = -15.5700721911217 | etot = -14.6424332454953 -201000 ekin = 0.107370722656483 | erot = 0.808265456806726 | epot = -15.5580694249396 | etot = -14.6424332454764 -202000 ekin = 0.0944644042392164 | erot = 0.808750524310001 | epot = -15.5456481740113 | etot = -14.6424332454621 -203000 ekin = 0.0831623790893979 | erot = 0.807416772443554 | epot = -15.5330123969865 | etot = -14.6424332454535 -204000 ekin = 0.0736556272335549 | erot = 0.80418872541979 | epot = -15.5202775981049 | etot = -14.6424332454516 -205000 ekin = 0.0660710401675949 | erot = 0.79895460735586 | epot = -15.50745889298 | etot = -14.6424332454565 -206000 ekin = 0.0604586317681684 | erot = 0.791573809424189 | epot = -15.4944656866607 | etot = -14.6424332454683 -207000 ekin = 0.0567840026883034 | erot = 0.781888054798422 | epot = -15.4811053029728 | etot = -14.642433245486 -208000 ekin = 0.0549275971601569 | erot = 0.769736381379661 | epot = -15.4670972240478 | etot = -14.642433245508 -209000 ekin = 0.054691444753805 | erot = 0.754973659533912 | epot = -15.4520983498196 | etot = -14.6424332455319 -210000 ekin = 0.055813012677523 | erot = 0.737491764374765 | epot = -15.4357380226072 | etot = -14.6424332455549 -211000 ekin = 0.0579847210238433 | erot = 0.717241838880031 | epot = -15.417659805478 | etot = -14.6424332455742 -212000 ekin = 0.0608768356205362 | erot = 0.694255492639193 | epot = -15.3975655738466 | etot = -14.6424332455869 -213000 ekin = 0.06416104270831 | erot = 0.668662476163316 | epot = -15.3752567644624 | etot = -14.6424332455907 -214000 ekin = 0.0675321043587428 | erot = 0.64070249551798 | epot = -15.3506678454611 | etot = -14.6424332455844 -215000 ekin = 0.070725533636788 | erot = 0.610729417267909 | epot = -15.3238881964721 | etot = -14.6424332455674 -216000 ekin = 0.0735300437834057 | erot = 0.579207054837054 | epot = -15.2951703441606 | etot = -14.6424332455401 -217000 ekin = 0.0757943994895767 | erot = 0.546696813208958 | epot = -15.2649244582023 | etot = -14.6424332455037 -218000 ekin = 0.0774290394184473 | erot = 0.513838451215592 | epot = -15.2337007360942 | etot = -14.6424332454601 -219000 ekin = 0.0784033323161932 | erot = 0.481325894960063 | epot = -15.2021624726878 | etot = -14.6424332454116 -220000 ekin = 0.0787395495628362 | erot = 0.449880299616975 | epot = -15.1710530945401 | etot = -14.6424332453603 -221000 ekin = 0.0785046319692606 | erot = 0.420222425154575 | epot = -15.1411603024325 | etot = -14.6424332453087 -222000 ekin = 0.0778006814288784 | erot = 0.393045972165179 | epot = -15.1132798988531 | etot = -14.642433245259 -223000 ekin = 0.0767549035403029 | erot = 0.368992968905302 | epot = -15.0881811176588 | etot = -14.6424332452132 -224000 ekin = 0.0755095293719489 | erot = 0.348631757026569 | epot = -15.0665745315716 | etot = -14.6424332451731 -225000 ekin = 0.0742120885680923 | erot = 0.332437700423116 | epot = -15.0490830341315 | etot = -14.6424332451403 -226000 ekin = 0.0730063028703669 | erot = 0.320776497496383 | epot = -15.0362160454828 | etot = -14.6424332451161 -227000 ekin = 0.072023814088989 | erot = 0.313889923623787 | epot = -15.0283469828147 | etot = -14.642433245102 -228000 ekin = 0.0713769419944175 | erot = 0.31188394524302 | epot = -15.025694132336 | etot = -14.6424332450985 -229000 ekin = 0.0711526728859894 | erot = 0.314719386436074 | epot = -15.0283053044287 | etot = -14.6424332451066 -230000 ekin = 0.0714080974064438 | erot = 0.322205638587393 | epot = -15.0360469811206 | etot = -14.6424332451268 -231000 ekin = 0.0721675361185073 | erot = 0.333998222200335 | epot = -15.0485990034776 | etot = -14.6424332451588 -232000 ekin = 0.073421602289788 | erot = 0.349601270465542 | epot = -15.0654561179573 | etot = -14.6424332452019 -233000 ekin = 0.0751284397495051 | erot = 0.368376135876568 | epot = -15.0859378208814 | etot = -14.6424332452553 -234000 ekin = 0.0772173235430231 | erot = 0.389557254435346 | epot = -15.1092078232955 | etot = -14.6424332453172 -235000 ekin = 0.0795947059788063 | erot = 0.412276079792834 | epot = -15.1343040311561 | etot = -14.6424332453845 -236000 ekin = 0.0821526186131156 | erot = 0.435593295650787 | epot = -15.1601791597182 | etot = -14.6424332454543 -237000 ekin = 0.084779101422344 | erot = 0.458538653868273 | epot = -15.1857510008135 | etot = -14.6424332455229 -238000 ekin = 0.0873700423841441 | erot = 0.480156759890549 | epot = -15.2099600478608 | etot = -14.6424332455861 -239000 ekin = 0.0898415153120331 | erot = 0.499556095556538 | epot = -15.2318308565087 | etot = -14.6424332456401 -240000 ekin = 0.0921414623518645 | erot = 0.515957735404849 | epot = -15.2505324434381 | etot = -14.6424332456814 -241000 ekin = 0.0942594490127862 | erot = 0.528739776890127 | epot = -15.2654324716098 | etot = -14.6424332457069 -242000 ekin = 0.0962332805866192 | erot = 0.537473606139427 | epot = -15.276140132441 | etot = -14.6424332457149 -243000 ekin = 0.0981515319325858 | erot = 0.541948785982857 | epot = -15.2825335636204 | etot = -14.642433245705 -244000 ekin = 0.100151482350114 | erot = 0.542184479376275 | epot = -15.2847692074041 | etot = -14.6424332456777 -245000 ekin = 0.102412491094951 | erot = 0.538426702319034 | epot = -15.2832724390489 | etot = -14.642433245635 -246000 ekin = 0.105145395544293 | erot = 0.531132085866979 | epot = -15.2787107269906 | etot = -14.6424332455793 -247000 ekin = 0.108578961411821 | erot = 0.52093999420686 | epot = -15.271952201133 | etot = -14.6424332455143 -248000 ekin = 0.112944688754725 | erot = 0.50863565229471 | epot = -15.2640135864931 | etot = -14.6424332454436 -249000 ekin = 0.118461348905719 | erot = 0.495107336752391 | epot = -15.2560019310293 | etot = -14.6424332453712 -250000 ekin = 0.125320510714173 | erot = 0.481300713195434 | epot = -15.2490544692103 | etot = -14.6424332453007 -251000 ekin = 0.133674056956427 | erot = 0.468173145421896 | epot = -15.2442804476139 | etot = -14.6424332452356 -252000 ekin = 0.143624355874461 | erot = 0.456650355971834 | epot = -15.2427079570251 | etot = -14.6424332451788 -253000 ekin = 0.155217400156353 | erot = 0.447587277163379 | epot = -15.2452379224523 | etot = -14.6424332451326 -254000 ekin = 0.168438906846637 | erot = 0.441734376015244 | epot = -15.2526065279605 | etot = -14.6424332450987 -255000 ekin = 0.183213121646734 | erot = 0.439710227351439 | epot = -15.2653565940763 | etot = -14.6424332450781 -256000 ekin = 0.199403908834921 | erot = 0.441980689731424 | epot = -15.283817843638 | etot = -14.6424332450717 -257000 ekin = 0.216817638464824 | erot = 0.448844730303074 | epot = -15.3080956138475 | etot = -14.6424332450796 -258000 ekin = 0.235207399038843 | erot = 0.460426746273175 | epot = -15.3380673904137 | etot = -14.6424332451017 -259000 ekin = 0.254278151369354 | erot = 0.476675120646266 | epot = -15.3733865171527 | etot = -14.6424332451371 -260000 ekin = 0.273692576680278 | erot = 0.497366691704049 | epot = -15.4134925135692 | etot = -14.6424332451849 -261000 ekin = 0.293077534076593 | erot = 0.522116767902341 | epot = -15.4576275472227 | etot = -14.6424332452438 -262000 ekin = 0.312031202024041 | erot = 0.550394247117889 | epot = -15.5048586944538 | etot = -14.6424332453119 -263000 ekin = 0.330131107619666 | erot = 0.58154128199589 | epot = -15.5541056350029 | etot = -14.6424332453873 -264000 ekin = 0.346943319973835 | erot = 0.614796773442864 | epot = -15.6041733388843 | etot = -14.6424332454676 -265000 ekin = 0.36203307825833 | erot = 0.649322794992431 | epot = -15.6537891188012 | etot = -14.6424332455505 -266000 ekin = 0.374977027500473 | erot = 0.684232889055386 | epot = -15.7016431621889 | etot = -14.6424332456331 -267000 ekin = 0.385377045185273 | erot = 0.718621072058621 | epot = -15.7464313629566 | etot = -14.6424332457127 -268000 ekin = 0.392875374680177 | erot = 0.751590369461549 | epot = -15.7868989899282 | etot = -14.6424332457865 -269000 ekin = 0.397170471139152 | erot = 0.782279784272065 | epot = -15.8218835012632 | etot = -14.6424332458519 -270000 ekin = 0.398032662028036 | erot = 0.809888771673587 | epot = -15.8503546796086 | etot = -14.642433245907 -271000 ekin = 0.395318487598681 | erot = 0.833698516709737 | epot = -15.8714502502579 | etot = -14.6424332459495 -272000 ekin = 0.388982474352113 | erot = 0.853089551908481 | epot = -15.8845052722386 | etot = -14.642433245978 -273000 ekin = 0.379085147931406 | erot = 0.867555470405084 | epot = -15.8890738643282 | etot = -14.6424332459917 -274000 ekin = 0.36579632219322 | erot = 0.876712662629334 | epot = -15.8849422308128 | etot = -14.6424332459903 -275000 ekin = 0.349393082921511 | erot = 0.880306121913819 | epot = -15.8721324508092 | etot = -14.6424332459739 -276000 ekin = 0.330252358905648 | erot = 0.878211432148985 | epot = -15.8508970369982 | etot = -14.6424332459435 -277000 ekin = 0.308838461220188 | erot = 0.870433084876957 | epot = -15.8217047919976 | etot = -14.6424332459005 -278000 ekin = 0.285686394604086 | erot = 0.857099294885159 | epot = -15.7852189353358 | etot = -14.6424332458466 -279000 ekin = 0.261382042766412 | erot = 0.838453513181032 | epot = -15.7422688017312 | etot = -14.6424332457837 -280000 ekin = 0.23654047332595 | erot = 0.814842890587961 | epot = -15.6938166096284 | etot = -14.6424332457145 -281000 ekin = 0.211783602608016 | erot = 0.78670403285839 | epot = -15.6409208811076 | etot = -14.6424332456411 -282000 ekin = 0.187718337271894 | erot = 0.754546508157669 | epot = -15.5846980909958 | etot = -14.6424332455662 -283000 ekin = 0.164916115090795 | erot = 0.718934708845181 | epot = -15.5262840694281 | etot = -14.6424332454921 -284000 ekin = 0.143894549221715 | erot = 0.680468811939352 | epot = -15.4667966065823 | etot = -14.6424332454213 -285000 ekin = 0.125101678372295 | erot = 0.639765701847641 | epot = -15.4073006255757 | etot = -14.6424332453557 -286000 ekin = 0.108903164107394 | erot = 0.597440790010453 | epot = -15.3487771994148 | etot = -14.6424332452969 -287000 ekin = 0.0955726645551815 | erot = 0.554091668604978 | epot = -15.2920975784066 | etot = -14.6424332452464 -288000 ekin = 0.0852855448006968 | erot = 0.510284456822097 | epot = -15.2380032468277 | etot = -14.6424332452049 -289000 ekin = 0.07811604131029 | erot = 0.466543535623142 | epot = -15.1870928221065 | etot = -14.6424332451731 -290000 ekin = 0.0740379578618433 | erot = 0.423345127589082 | epot = -15.1398163306018 | etot = -14.6424332451509 -291000 ekin = 0.072928910063375 | erot = 0.381114879437431 | epot = -15.0964770346385 | etot = -14.6424332451377 -292000 ekin = 0.0745780357927571 | erot = 0.340229271737873 | epot = -15.0572405526631 | etot = -14.6424332451325 -293000 ekin = 0.0786969407539254 | erot = 0.301020346548472 | epot = -15.0221505324365 | etot = -14.6424332451341 -294000 ekin = 0.0849334564702411 | erot = 0.263782947588667 | epot = -14.9911496491996 | etot = -14.6424332451407 -295000 ekin = 0.0928875723607584 | erot = 0.228783448806939 | epot = -14.9641042663184 | etot = -14.6424332451507 -296000 ekin = 0.102128697507195 | erot = 0.19626884038738 | epot = -14.9408307830571 | etot = -14.6424332451625 -297000 ekin = 0.112213252496717 | erot = 0.166475068218863 | epot = -14.9211215658901 | etot = -14.6424332451745 -298000 ekin = 0.122701527066801 | erot = 0.139633685446912 | epot = -14.9047684576991 | etot = -14.6424332451854 -299000 ekin = 0.13317279291057 | erot = 0.115976150690173 | epot = -14.8915821887951 | etot = -14.6424332451943 -300000 ekin = 0.143237839707087 | erot = 0.0957354521215326 | epot = -14.8814065370293 | etot = -14.6424332452007 -301000 ekin = 0.152548387988438 | erot = 0.0791450908732747 | epot = -14.8741267240661 | etot = -14.6424332452044 -302000 ekin = 0.160803184299453 | erot = 0.0664357608561943 | epot = -14.8696721903613 | etot = -14.6424332452057 -303000 ekin = 0.167750948486611 | erot = 0.0578302677257495 | epot = -14.868014461417 | etot = -14.6424332452046 -304000 ekin = 0.173190665587053 | erot = 0.0535373136372916 | epot = -14.8691612244265 | etot = -14.6424332452022 -305000 ekin = 0.176969952948865 | erot = 0.0537447402909072 | epot = -14.8731479384385 | etot = -14.6424332451988 -306000 ekin = 0.178982363290529 | erot = 0.0586126977876584 | epot = -14.8800283062732 | etot = -14.642433245195 -307000 ekin = 0.179164502944002 | erot = 0.0682670321056827 | epot = -14.8898647802413 | etot = -14.6424332451916 -308000 ekin = 0.177493763288021 | erot = 0.0827930029186529 | epot = -14.9027200113955 | etot = -14.6424332451889 -309000 ekin = 0.173987301150961 | erot = 0.102229291870645 | epot = -14.9186498382089 | etot = -14.6424332451873 -310000 ekin = 0.168702678647172 | erot = 0.126562162216051 | epot = -14.9376980860502 | etot = -14.642433245187 -311000 ekin = 0.16174029700891 | erot = 0.155719593406526 | epot = -14.9598931356034 | etot = -14.642433245188 -312000 ekin = 0.15324744012492 | erot = 0.189565237977728 | epot = -14.985245923293 | etot = -14.6424332451904 -313000 ekin = 0.14342338999696 | erot = 0.227892126760383 | epot = -15.0137487619518 | etot = -14.6424332451944 -314000 ekin = 0.132524706018464 | erot = 0.270416174780403 | epot = -15.0453741259986 | etot = -14.6424332451998 -315000 ekin = 0.120869409552541 | erot = 0.31676970828902 | epot = -15.0800723630488 | etot = -14.6424332452072 -316000 ekin = 0.108838546104728 | erot = 0.366495437994318 | epot = -15.1177672293161 | etot = -14.642433245217 -317000 ekin = 0.0968734934277246 | erot = 0.419041536809129 | epot = -15.1583482754668 | etot = -14.6424332452299 -318000 ekin = 0.0854675378549793 | erot = 0.47375872576408 | epot = -15.2016595088657 | etot = -14.6424332452467 -319000 ekin = 0.0751507271451901 | erot = 0.529900497448216 | epot = -15.247484469862 | etot = -14.6424332452686 -320000 ekin = 0.0664678443364345 | erot = 0.586627760739854 | epot = -15.2955288503729 | etot = -14.6424332452966 -321000 ekin = 0.0599504590563252 | erot = 0.643019202691537 | epot = -15.3454029070798 | etot = -14.6424332453319 -322000 ekin = 0.0560852142800011 | erot = 0.698088453267024 | epot = -15.3966069129217 | etot = -14.6424332453747 -323000 ekin = 0.0552815181248971 | erot = 0.750808639916102 | epot = -15.4485234034659 | etot = -14.6424332454249 -324000 ekin = 0.057842325520568 | erot = 0.800144112657426 | epot = -15.5004196836595 | etot = -14.6424332454815 -325000 ekin = 0.0639414864634492 | erot = 0.845088070114938 | epot = -15.5514628021208 | etot = -14.6424332455424 -326000 ekin = 0.0736101694210054 | erot = 0.884703689967212 | epot = -15.6007471049934 | etot = -14.6424332456052 -327000 ekin = 0.0867333560896964 | erot = 0.91816541981297 | epot = -15.6473320215697 | etot = -14.642433245667 -328000 ekin = 0.103055779603987 | erot = 0.944796600223873 | epot = -15.6902856255527 | etot = -14.6424332457249 -329000 ekin = 0.12219544617078 | erot = 0.964099781594463 | epot = -15.7287284735416 | etot = -14.6424332457764 -330000 ekin = 0.143662406710238 | erot = 0.975776996237359 | epot = -15.7618726487672 | etot = -14.6424332458196 -331000 ekin = 0.166880785133575 | erot = 0.979738667517989 | epot = -15.7890526985047 | etot = -14.6424332458532 -332000 ekin = 0.191212923969923 | erot = 0.976101405902871 | epot = -15.8097475757491 | etot = -14.6424332458763 -333000 ekin = 0.215985355319577 | erot = 0.965176233539036 | epot = -15.8235948347474 | etot = -14.6424332458887 -334000 ekin = 0.240516656831147 | erot = 0.947449485112495 | epot = -15.8303993878336 | etot = -14.64243324589 -335000 ekin = 0.264146896086235 | erot = 0.923558676868035 | epot = -15.8301388188342 | etot = -14.6424332458799 -336000 ekin = 0.286267467754231 | erot = 0.894265184760612 | epot = -15.8229658983734 | etot = -14.6424332458586 -337000 ekin = 0.306349134750088 | erot = 0.860424939336672 | epot = -15.809207319913 | etot = -14.6424332458262 -338000 ekin = 0.323965497674696 | erot = 0.822957838322753 | epot = -15.7893565817813 | etot = -14.6424332457838 -339000 ekin = 0.338809250788985 | erot = 0.782816380150479 | epot = -15.7640588766724 | etot = -14.6424332457329 -340000 ekin = 0.35069944423374 | erot = 0.740954141303117 | epot = -15.7340868312125 | etot = -14.6424332456757 -341000 ekin = 0.359579293536495 | erot = 0.698295027831847 | epot = -15.700307566983 | etot = -14.6424332456147 -342000 ekin = 0.365505462154926 | erot = 0.655704542034982 | epot = -15.6636432497426 | etot = -14.6424332455527 -343000 ekin = 0.368630832661383 | erot = 0.613964463465552 | epot = -15.6250285416195 | etot = -14.6424332454926 -344000 ekin = 0.369183369589215 | erot = 0.573752273080787 | epot = -15.5853688881069 | etot = -14.6424332454369 -345000 ekin = 0.367443732824289 | erot = 0.535626361233146 | epot = -15.5455033394448 | etot = -14.6424332453874 -346000 ekin = 0.36372393313177 | erot = 0.500017626276193 | epot = -15.5061748047535 | etot = -14.6424332453455 -347000 ekin = 0.358348705277679 | erot = 0.467227585427262 | epot = -15.4680095360169 | etot = -14.642433245312 -348000 ekin = 0.351640582954838 | erot = 0.437432666908102 | epot = -15.4315064951499 | etot = -14.642433245287 -349000 ekin = 0.343909024694815 | erot = 0.410693986169929 | epot = -15.3970362561344 | etot = -14.6424332452696 -350000 ekin = 0.335443435968793 | erot = 0.386971649880727 | epot = -15.3648483311092 | etot = -14.6424332452597 -351000 ekin = 0.326509584093778 | erot = 0.366142474251511 | epot = -15.3350853036005 | etot = -14.6424332452552 -352000 ekin = 0.317348699022207 | erot = 0.34801993040111 | epot = -15.3078018746784 | etot = -14.6424332452551 -353000 ekin = 0.30817846664876 | erot = 0.332375117501944 | epot = -15.2829868294085 | etot = -14.6424332452578 -354000 ekin = 0.299195119854399 | erot = 0.318957598139001 | epot = -15.2605859632553 | etot = -14.6424332452619 -355000 ekin = 0.290575888248862 | erot = 0.307515001370356 | epot = -15.2405241348854 | etot = -14.6424332452662 -356000 ekin = 0.282481160312497 | erot = 0.29781040621721 | epot = -15.2227248117992 | etot = -14.6424332452695 -357000 ekin = 0.275055828993789 | erot = 0.289636664277857 | epot = -15.2071257385429 | etot = -14.6424332452713 -358000 ekin = 0.26842942725494 | erot = 0.282827006912222 | epot = -15.1936896794383 | etot = -14.6424332452711 -359000 ekin = 0.262714810201762 | erot = 0.277261507858003 | epot = -15.1824095633288 | etot = -14.642433245269 -360000 ekin = 0.258005302569436 | erot = 0.272869227748658 | epot = -15.1733077755836 | etot = -14.6424332452655 -361000 ekin = 0.254370400621781 | erot = 0.269626137802017 | epot = -15.1664297836851 | etot = -14.6424332452613 -362000 ekin = 0.251850290178651 | erot = 0.267549186087959 | epot = -15.1618327215239 | etot = -14.6424332452573 -363000 ekin = 0.250449609862751 | erot = 0.266687109597485 | epot = -15.159569964715 | etot = -14.6424332452548 -364000 ekin = 0.250131041863336 | erot = 0.267108788857729 | epot = -15.1596730759762 | etot = -14.6424332452551 -365000 ekin = 0.250809442162066 | erot = 0.268890073928026 | epot = -15.1621327613494 | etot = -14.6424332452593 -366000 ekin = 0.25234731876335 | erot = 0.272100073006091 | epot = -15.1668806370379 | etot = -14.6424332452684 -367000 ekin = 0.254552520178511 | erot = 0.276787886819413 | epot = -15.1737736522811 | etot = -14.6424332452832 -368000 ekin = 0.257178996153298 | erot = 0.282970699523766 | epot = -15.1825829409812 | etot = -14.6424332453042 -369000 ekin = 0.259931424908708 | erot = 0.29062401114344 | epot = -15.1929886813832 | etot = -14.642433245331 -370000 ekin = 0.262474349326632 | erot = 0.299674631814998 | epot = -15.2045822265049 | etot = -14.6424332453633 -371000 ekin = 0.264446209428301 | erot = 0.309996869297344 | epot = -15.2168763241253 | etot = -14.6424332453996 -372000 ekin = 0.265478281861433 | erot = 0.321412142686654 | epot = -15.2293236699864 | etot = -14.6424332454383 -373000 ekin = 0.265218028290041 | erot = 0.333692059448718 | epot = -15.2413433332161 | etot = -14.6424332454774 -374000 ekin = 0.26335572124772 | erot = 0.346564809671271 | epot = -15.2523537764331 | etot = -14.6424332455141 -375000 ekin = 0.259652497500777 | erot = 0.359724567998165 | epot = -15.2618103110451 | etot = -14.6424332455462 -376000 ekin = 0.253967268934319 | erot = 0.372843454384699 | epot = -15.2692439688902 | etot = -14.6424332455711 -377000 ekin = 0.246279333497663 | erot = 0.385585491299193 | epot = -15.2742980703837 | etot = -14.6424332455868 -378000 ekin = 0.236703249874173 | erot = 0.397621906702965 | epot = -15.2767584021691 | etot = -14.642433245592 -379000 ekin = 0.22549275694072 | erot = 0.408647066936832 | epot = -15.2765730694637 | etot = -14.6424332455862 -380000 ekin = 0.213031377534934 | erot = 0.418394279001949 | epot = -15.2738589021069 | etot = -14.64243324557 -381000 ekin = 0.19980887731166 | erot = 0.426650676217107 | epot = -15.2688927990735 | etot = -14.6424332455448 -382000 ekin = 0.186384809014969 | erot = 0.433270396060972 | epot = -15.2620884505889 | etot = -14.642433245513 -383000 ekin = 0.173342616140343 | erot = 0.4381852790555 | epot = -15.2539611406731 | etot = -14.6424332454773 -384000 ekin = 0.161239700828087 | erot = 0.441412371407271 | epot = -15.2450853176757 | etot = -14.6424332454403 -385000 ekin = 0.15055995464474 | erot = 0.443057612556821 | epot = -15.2360508126064 | etot = -14.6424332454049 -386000 ekin = 0.141675129696877 | erot = 0.443315241526503 | epot = -15.2274236165962 | etot = -14.6424332453728 -387000 ekin = 0.134820015696259 | erot = 0.442462667351556 | epot = -15.2197159283931 | etot = -14.6424332453452 -388000 ekin = 0.130083976412379 | erot = 0.44085081351593 | epot = -15.2133680352507 | etot = -14.6424332453224 -389000 ekin = 0.12741857023722 | erot = 0.43889024628032 | epot = -15.2087420618216 | etot = -14.6424332453041 -390000 ekin = 0.126658423092956 | erot = 0.43703370208669 | epot = -15.2061253704692 | etot = -14.6424332452895 -391000 ekin = 0.127550804261056 | erot = 0.435755902066133 | epot = -15.2057399516053 | etot = -14.6424332452781 -392000 ekin = 0.129788752936039 | erot = 0.435531744058152 | epot = -15.2077537422634 | etot = -14.6424332452692 -393000 ekin = 0.133043055316541 | erot = 0.43681406507717 | epot = -15.2122903656559 | etot = -14.6424332452622 -394000 ekin = 0.136989561466299 | erot = 0.440012156509965 | epot = -15.2194349632336 | etot = -14.6424332452574 -395000 ekin = 0.141329833042564 | erot = 0.445472096884898 | epot = -15.2292351751821 | etot = -14.6424332452547 -396000 ekin = 0.145804542777373 | erot = 0.45345976764831 | epot = -15.2416975556805 | etot = -14.6424332452548 -397000 ekin = 0.150200153188676 | erot = 0.464147173461378 | epot = -15.2567805719085 | etot = -14.6424332452585 -398000 ekin = 0.154350089766152 | erot = 0.477602441558481 | epot = -15.2743857765906 | etot = -14.642433245266 -399000 ekin = 0.158131920622366 | erot = 0.493783661155649 | epot = -15.2943488270562 | etot = -14.6424332452782 -400000 ekin = 0.161462056173796 | erot = 0.512536568006325 | epot = -15.3164318694755 | etot = -14.6424332452953 -401000 ekin = 0.164289301181072 | erot = 0.533595989002473 | epot = -15.3403185355012 | etot = -14.6424332453177 -402000 ekin = 0.166588323050693 | erot = 0.556590928839834 | epot = -15.3656124972355 | etot = -14.642433245345 -403000 ekin = 0.168353810379696 | erot = 0.581053183644485 | epot = -15.3918402394011 | etot = -14.6424332453769 -404000 ekin = 0.169595821301193 | erot = 0.606429376023291 | epot = -15.4184584427372 | etot = -14.6424332454127 -405000 ekin = 0.170336578562018 | erot = 0.63209629254071 | epot = -15.444866116554 | etot = -14.6424332454513 -406000 ekin = 0.170608761978812 | erot = 0.65737934451496 | epot = -15.4704213519851 | etot = -14.6424332454913 -407000 ekin = 0.170455178567329 | erot = 0.681573854094723 | epot = -15.4944622781935 | etot = -14.6424332455315 -408000 ekin = 0.169929554809759 | erot = 0.703968692151394 | epot = -15.5163314925311 | etot = -14.64243324557 -409000 ekin = 0.169098093451394 | erot = 0.723871579521683 | epot = -15.5354029185781 | etot = -14.6424332456051 -410000 ekin = 0.168041369040759 | erot = 0.740635137248624 | epot = -15.5511097519242 | etot = -14.6424332456348 -411000 ekin = 0.166856102809036 | erot = 0.753682569971393 | epot = -15.5629719184382 | etot = -14.6424332456577 -412000 ekin = 0.165656359033239 | erot = 0.762531725093238 | epot = -15.5706213297988 | etot = -14.6424332456724 -413000 ekin = 0.164573741711749 | erot = 0.766816218739624 | epot = -15.5738232061291 | etot = -14.6424332456777 -414000 ekin = 0.163756240957875 | erot = 0.766302377571564 | epot = -15.5724918642026 | etot = -14.6424332456732 -415000 ekin = 0.163365479945837 | erot = 0.76090092022446 | epot = -15.5666996458289 | etot = -14.6424332456586 -416000 ekin = 0.16357224009456 | erot = 0.750672586698944 | epot = -15.556678072428 | etot = -14.6424332456345 -417000 ekin = 0.164550286199954 | erot = 0.7358272978906 | epot = -15.5428108296923 | etot = -14.6424332456018 -418000 ekin = 0.166468663393413 | erot = 0.716716857299939 | epot = -15.5256187662552 | etot = -14.6424332455618 -419000 ekin = 0.169482781127082 | erot = 0.693821649098591 | epot = -15.5057376757421 | etot = -14.6424332455164 -420000 ekin = 0.173724722667737 | erot = 0.66773219168281 | epot = -15.4838901598182 | etot = -14.6424332454677 -421000 ekin = 0.179293310761201 | erot = 0.639126725581016 | epot = -15.4608532817598 | etot = -14.6424332454176 -422000 ekin = 0.18624451452154 | erot = 0.608746211198834 | epot = -15.437423971089 | etot = -14.6424332453687 -423000 ekin = 0.194582798147166 | erot = 0.577368165576623 | epot = -15.4143842090466 | etot = -14.6424332453228 -424000 ekin = 0.204253993032127 | erot = 0.545780680985215 | epot = -15.3924679192995 | etot = -14.6424332452822 -425000 ekin = 0.215140228919709 | erot = 0.514757766830984 | epot = -15.3723312409989 | etot = -14.6424332452482 -426000 ekin = 0.227057395200028 | erot = 0.485036881514174 | epot = -15.354527521936 | etot = -14.6424332452218 -427000 ekin = 0.239755526228602 | erot = 0.457299221560653 | epot = -15.3394879929934 | etot = -14.6424332452042 -428000 ekin = 0.252922416271923 | erot = 0.432153058134052 | epot = -15.3275087196016 | etot = -14.6424332451956 -429000 ekin = 0.266190667181531 | erot = 0.410120192007372 | epot = -15.3187441043849 | etot = -14.642433245196 -430000 ekin = 0.279148248287616 | erot = 0.391625457761957 | epot = -15.3132069512549 | etot = -14.6424332452053 -431000 ekin = 0.291352495295092 | erot = 0.376989149810484 | epot = -15.3107748903279 | etot = -14.6424332452223 -432000 ekin = 0.302347287571197 | erot = 0.366422254466197 | epot = -15.311202787284 | etot = -14.6424332452466 -433000 ekin = 0.311682921771834 | erot = 0.360024429012416 | epot = -15.3141405960599 | etot = -14.6424332452756 -434000 ekin = 0.318937954387398 | erot = 0.357784738270779 | epot = -15.3191559379664 | etot = -14.6424332453082 -435000 ekin = 0.323742037714837 | erot = 0.359585207272863 | epot = -15.3257604903308 | etot = -14.6424332453431 -436000 ekin = 0.325798554031316 | erot = 0.365207245305789 | epot = -15.3334390447156 | etot = -14.6424332453785 -437000 ekin = 0.324905697097303 | erot = 0.374340922349983 | epot = -15.3416798648586 | etot = -14.6424332454113 -438000 ekin = 0.320974589858357 | erot = 0.386596930160468 | epot = -15.3500047654588 | etot = -14.64243324544 -439000 ekin = 0.314043077746361 | erot = 0.401520852185505 | epot = -15.3579971753956 | etot = -14.6424332454637 -440000 ekin = 0.304283988020539 | erot = 0.41860913221399 | epot = -15.3653263657148 | etot = -14.6424332454802 -441000 ekin = 0.292006859111611 | erot = 0.437325916193047 | epot = -15.3717660207934 | etot = -14.6424332454888 -442000 ekin = 0.277652365815072 | erot = 0.457119792518877 | epot = -15.3772054038232 | etot = -14.6424332454893 -443000 ekin = 0.261778853590747 | erot = 0.477439412175799 | epot = -15.3816515112488 | etot = -14.6424332454822 -444000 ekin = 0.245040553434245 | erot = 0.497747053376455 | epot = -15.3852208522799 | etot = -14.6424332454692 -445000 ekin = 0.22815726042029 | erot = 0.517529408202492 | epot = -15.3881199140742 | etot = -14.6424332454515 -446000 ekin = 0.211875681729375 | erot = 0.536305196856599 | epot = -15.3906141240179 | etot = -14.6424332454319 -447000 ekin = 0.196923472681452 | erot = 0.553629632753464 | epot = -15.3929863508487 | etot = -14.6424332454138 -448000 ekin = 0.183958277880794 | erot = 0.569096233371 | epot = -15.3954877566523 | etot = -14.6424332454005 -449000 ekin = 0.173515771313211 | erot = 0.582336947151656 | epot = -15.3982859638601 | etot = -14.6424332453953 -450000 ekin = 0.16596236119942 | erot = 0.593021970145928 | epot = -15.4014175767459 | etot = -14.6424332454006 -451000 ekin = 0.161459280835239 | erot = 0.600860851249481 | epot = -15.4047533775022 | etot = -14.6424332454175 -452000 ekin = 0.159944578253891 | erot = 0.605606408076383 | epot = -15.4079842317757 | etot = -14.6424332454454 -453000 ekin = 0.161137653115343 | erot = 0.607062496368097 | epot = -15.410633394965 | etot = -14.6424332454815 -454000 ekin = 0.164567591513362 | erot = 0.605095779306141 | epot = -15.4120966163413 | etot = -14.6424332455218 -455000 ekin = 0.169622334209561 | erot = 0.599650455421321 | epot = -15.4117060351916 | etot = -14.6424332455607 -456000 ekin = 0.175611802350685 | erot = 0.590763702894581 | epot = -15.4088087508385 | etot = -14.6424332455932 -457000 ekin = 0.181835621982265 | erot = 0.578578749363229 | epot = -15.40284761696 | etot = -14.6424332456146 -458000 ekin = 0.187645727030889 | erot = 0.563352302649372 | epot = -15.3934312753016 | etot = -14.6424332456214 -459000 ekin = 0.192495880384907 | erot = 0.54545371714964 | epot = -15.380382843147 | etot = -14.6424332456124 -460000 ekin = 0.195973381637234 | erot = 0.525354597712022 | epot = -15.3637612249374 | etot = -14.6424332455881 -461000 ekin = 0.197811920991222 | erot = 0.503609203464283 | epot = -15.3438543700064 | etot = -14.6424332455509 -462000 ekin = 0.197887724919133 | erot = 0.480827560284776 | epot = -15.3211485307076 | etot = -14.6424332455037 -463000 ekin = 0.196203198485172 | erot = 0.457644248439133 | epot = -15.2962806923751 | etot = -14.6424332454508 -464000 ekin = 0.192863034125905 | erot = 0.434686220431894 | epot = -15.2699824999537 | etot = -14.6424332453959 -465000 ekin = 0.188047435822221 | erot = 0.412542760094015 | epot = -15.2430234412586 | etot = -14.6424332453423 -466000 ekin = 0.181986107552773 | erot = 0.39174001067487 | epot = -15.2161593635207 | etot = -14.642433245293 -467000 ekin = 0.174935400197984 | erot = 0.372721626737719 | epot = -15.1900902721857 | etot = -14.64243324525 -468000 ekin = 0.167159826102143 | erot = 0.355836258353913 | epot = -15.1654293296704 | etot = -14.6424332452144 -469000 ekin = 0.158918218022589 | erot = 0.34133189076746 | epot = -15.1426833539768 | etot = -14.6424332451868 -470000 ekin = 0.150454185653206 | erot = 0.329356584635659 | epot = -15.1222440154559 | etot = -14.642433245167 -471000 ekin = 0.141990180749416 | erot = 0.319964871778407 | epot = -15.1043882976824 | etot = -14.6424332451545 -472000 ekin = 0.13372435386821 | erot = 0.313128906246327 | epot = -15.089286505263 | etot = -14.6424332451484 -473000 ekin = 0.12582939810187 | erot = 0.308753392325055 | epot = -15.0770160355743 | etot = -14.6424332451474 -474000 ekin = 0.118452666363187 | erot = 0.306693264414364 | epot = -15.0675791759277 | etot = -14.6424332451502 -475000 ekin = 0.111716976218892 | erot = 0.306773053291038 | epot = -15.0609232746652 | etot = -14.6424332451553 -476000 ekin = 0.105721655633223 | erot = 0.308806833537935 | epot = -15.0569617343327 | etot = -14.6424332451616 -477000 ekin = 0.100543523675713 | erot = 0.312617617130682 | epot = -15.055594385974 | etot = -14.6424332451676 -478000 ekin = 0.0962376398644524 | erot = 0.31805505563592 | epot = -15.0567259406729 | etot = -14.6424332451726 -479000 ekin = 0.0928377950023796 | erot = 0.325010357031072 | epot = -15.0602813972091 | etot = -14.6424332451757 -480000 ekin = 0.0903568546344123 | erot = 0.333427427764652 | epot = -15.0662175275756 | etot = -14.6424332451766 -481000 ekin = 0.0887871989354825 | erot = 0.343309423711621 | epot = -15.074529867822 | etot = -14.6424332451749 -482000 ekin = 0.0881016191313879 | erot = 0.354720133059457 | epot = -15.085254997362 | etot = -14.6424332451711 -483000 ekin = 0.0882551127429667 | erot = 0.367779908275293 | epot = -15.0984682661837 | etot = -14.6424332451655 -484000 ekin = 0.0891880440123837 | erot = 0.382656193510863 | epot = -15.1142774826819 | etot = -14.6424332451586 -485000 ekin = 0.0908310739090695 | erot = 0.399549033149904 | epot = -15.1328133522102 | etot = -14.6424332451512 -486000 ekin = 0.0931120890965809 | erot = 0.418672269926982 | epot = -15.1542176041678 | etot = -14.6424332451442 -487000 ekin = 0.0959650526362282 | erot = 0.440231422324969 | epot = -15.1786297200997 | etot = -14.6424332451385 -488000 ekin = 0.09934026138313 | erot = 0.464399451388414 | epot = -15.2061729579063 | etot = -14.6424332451348 -489000 ekin = 0.103214957393528 | erot = 0.491291775407016 | epot = -15.2369399779348 | etot = -14.6424332451343 -490000 ekin = 0.107602676592561 | erot = 0.520941965501655 | epot = -15.2709778872321 | etot = -14.6424332451379 -491000 ekin = 0.112559247659633 | erot = 0.553279563919971 | epot = -15.3082720567263 | etot = -14.6424332451467 -492000 ekin = 0.118183136718381 | erot = 0.588111425310919 | epot = -15.3487278071915 | etot = -14.6424332451622 -493000 ekin = 0.124608040121107 | erot = 0.625107908280808 | epot = -15.3921491935878 | etot = -14.6424332451858 -494000 ekin = 0.131986393307421 | erot = 0.663795156036237 | epot = -15.4382147945631 | etot = -14.6424332452194 -495000 ekin = 0.140463823895351 | erot = 0.703554605722113 | epot = -15.4864516748821 | etot = -14.6424332452647 -496000 ekin = 0.150146408031555 | erot = 0.743630741562816 | epot = -15.5362103949171 | etot = -14.6424332453228 -497000 ekin = 0.161064579067727 | erot = 0.783147917316502 | epot = -15.5866457417786 | etot = -14.6424332453944 -498000 ekin = 0.173139219154636 | erot = 0.821136754971001 | epot = -15.6367092196045 | etot = -14.6424332454789 -499000 ekin = 0.186156317831577 | erot = 0.856570103854305 | epot = -15.6851596672597 | etot = -14.6424332455738 -500000 ekin = 0.199756195068125 | erot = 0.888407758271075 | epot = -15.7305971990145 | etot = -14.6424332456753 -501000 ekin = 0.213441517837528 | erot = 0.915648078729389 | epot = -15.7715228423447 | etot = -14.6424332457778 -502000 ekin = 0.226605416599141 | erot = 0.93738343364528 | epot = -15.8064220961188 | etot = -14.6424332458744 -503000 ekin = 0.238577508979596 | erot = 0.952855183120654 | epot = -15.833865938058 | etot = -14.6424332459578 -504000 ekin = 0.24868234701908 | erot = 0.961503066783773 | epot = -15.852618659824 | etot = -14.6424332460212 -505000 ekin = 0.256302488972939 | erot = 0.96300365636181 | epot = -15.8617393913938 | etot = -14.6424332460591 -506000 ekin = 0.26093758314799 | erot = 0.957293217915516 | epot = -15.8606640471316 | etot = -14.6424332460681 -507000 ekin = 0.262251679303339 | erot = 0.944571918253385 | epot = -15.8492568436041 | etot = -14.6424332460474 -508000 ekin = 0.260103184115661 | erot = 0.92528856492912 | epot = -15.8278249950432 | etot = -14.6424332459984 -509000 ekin = 0.254554875284732 | erot = 0.900107536932478 | epot = -15.7970956581425 | etot = -14.6424332459253 -510000 ekin = 0.245864483352381 | erot = 0.86986171798002 | epot = -15.7581594471659 | etot = -14.6424332458335 -511000 ekin = 0.234458914530907 | erot = 0.835496660121178 | epot = -15.7123888203816 | etot = -14.6424332457296 -512000 ekin = 0.220896820243755 | erot = 0.798011684060757 | epot = -15.6613417499247 | etot = -14.6424332456202 -513000 ekin = 0.205824805091356 | erot = 0.758403224573394 | epot = -15.6066612751765 | etot = -14.6424332455118 -514000 ekin = 0.189932244119312 | erot = 0.717614706855625 | epot = -15.5499801963846 | etot = -14.6424332454096 -515000 ekin = 0.173908748202557 | erot = 0.676495918868222 | epot = -15.4928379123889 | etot = -14.6424332453181 -516000 ekin = 0.158407108511411 | erot = 0.63577351602134 | epot = -15.4366138697731 | etot = -14.6424332452404 -517000 ekin = 0.144013350185933 | erot = 0.596033149114553 | epot = -15.3824797444789 | etot = -14.6424332451784 -518000 ekin = 0.131224514119668 | erot = 0.55771282568585 | epot = -15.3313705849382 | etot = -14.6424332451327 -519000 ekin = 0.120434042407116 | erot = 0.521106495595107 | epot = -15.2839737831051 | etot = -14.6424332451028 -520000 ekin = 0.111924165177635 | erot = 0.486376443197646 | epot = -15.240733853463 | etot = -14.6424332450877 -521000 ekin = 0.105864424816456 | erot = 0.453572806058813 | epot = -15.2018704759605 | etot = -14.6424332450853 -522000 ekin = 0.102315362067633 | erot = 0.422658367130362 | epot = -15.1674069742913 | etot = -14.6424332450933 -523000 ekin = 0.101236366465094 | erot = 0.393536647096269 | epot = -15.1372062586706 | etot = -14.6424332451092 -524000 ekin = 0.102496717236358 | erot = 0.366081244307823 | epot = -15.1110112066744 | etot = -14.6424332451302 -525000 ekin = 0.105888887335355 | erot = 0.340164343214516 | epot = -15.0884864757035 | etot = -14.6424332451536 -526000 ekin = 0.111143247849968 | erot = 0.315682368378613 | epot = -15.0692588614059 | etot = -14.6424332451774 -527000 ekin = 0.117943398961207 | erot = 0.292576937806905 | epot = -15.0529535819675 | etot = -14.6424332451994 -528000 ekin = 0.125941474254371 | erot = 0.270849598243589 | epot = -15.0392243177162 | etot = -14.6424332452183 -529000 ekin = 0.134772916008756 | erot = 0.250569317238961 | epot = -15.0277754784808 | etot = -14.642433245233 -530000 ekin = 0.144070383401965 | erot = 0.231872340651302 | epot = -15.0183759692967 | etot = -14.6424332452434 -531000 ekin = 0.153476601968781 | erot = 0.214954741433939 | epot = -15.0108645886523 | etot = -14.6424332452495 -532000 ekin = 0.162656054076991 | erot = 0.200058697647332 | epot = -15.0051479969763 | etot = -14.642433245252 -533000 ekin = 0.171305419079578 | erot = 0.18745414318241 | epot = -15.0011928075133 | etot = -14.6424332452513 -534000 ekin = 0.179162595538559 | erot = 0.177417842692309 | epot = -14.9990136834797 | etot = -14.6424332452488 -535000 ekin = 0.186014006484955 | erot = 0.17021209444076 | epot = -14.9986593461708 | etot = -14.6424332452451 -536000 ekin = 0.191699759238898 | erot = 0.166065149224471 | epot = -15.0001981537044 | etot = -14.642433245241 -537000 ekin = 0.196116169930243 | erot = 0.165155084977473 | epot = -15.003704500145 | etot = -14.6424332452373 -538000 ekin = 0.199215220532696 | erot = 0.167598364569312 | epot = -15.0092468303365 | etot = -14.6424332452345 -539000 ekin = 0.20100070966893 | erot = 0.173443713615195 | epot = -15.0168776685174 | etot = -14.6424332452333 -540000 ekin = 0.201521164037735 | erot = 0.182671367030132 | epot = -15.0266257763018 | etot = -14.6424332452339 -541000 ekin = 0.200859940141596 | erot = 0.195197211440065 | epot = -15.0384903968184 | etot = -14.6424332452368 -542000 ekin = 0.199123298889485 | erot = 0.210880936221535 | epot = -15.0524374803529 | etot = -14.6424332452419 -543000 ekin = 0.196427519384798 | erot = 0.229537017788165 | epot = -15.0683977824221 | etot = -14.6424332452492 -544000 ekin = 0.192886294946265 | erot = 0.25094720200201 | epot = -15.0862667422075 | etot = -14.6424332452593 -545000 ekin = 0.188599710888656 | erot = 0.274873110236005 | epot = -15.1059060663961 | etot = -14.6424332452715 -546000 ekin = 0.18364604524401 | erot = 0.301067663120887 | epot = -15.1271469536507 | etot = -14.6424332452858 -547000 ekin = 0.178077473819964 | erot = 0.329284179376543 | epot = -15.1497948984983 | etot = -14.6424332453018 -548000 ekin = 0.171920510268456 | erot = 0.359282253787671 | epot = -15.1736360093753 | etot = -14.6424332453191 -549000 ekin = 0.165181670578856 | erot = 0.390829837836003 | epot = -15.1984447537518 | etot = -14.6424332453369 -550000 ekin = 0.15785840865594 | erot = 0.423701326923092 | epot = -15.2239929809337 | etot = -14.6424332453547 -551000 ekin = 0.149954809005835 | erot = 0.457671882722257 | epot = -15.2500599370996 | etot = -14.6424332453715 -552000 ekin = 0.141500835822419 | erot = 0.492508662666464 | epot = -15.2764427438757 | etot = -14.6424332453869 -553000 ekin = 0.132573145480449 | erot = 0.527960055130273 | epot = -15.3029664460107 | etot = -14.6424332453999 -554000 ekin = 0.123314645146749 | erot = 0.563744383275372 | epot = -15.3294922738325 | etot = -14.6424332454104 -555000 ekin = 0.113949270900195 | erot = 0.599539792628959 | epot = -15.3559223089471 | etot = -14.642433245418 -556000 ekin = 0.104788088804118 | erot = 0.634977129568407 | epot = -15.3821984637958 | etot = -14.6424332454232 -557000 ekin = 0.0962230654738397 | erot = 0.669637513728588 | epot = -15.4082938246296 | etot = -14.6424332454272 -558000 ekin = 0.0887059614381524 | erot = 0.703055990484034 | epot = -15.4341951973535 | etot = -14.6424332454313 -559000 ekin = 0.0827118847692362 | erot = 0.734732129426798 | epot = -15.4598772596337 | etot = -14.6424332454377 -560000 ekin = 0.0786899547209647 | erot = 0.764147748400966 | epot = -15.4852709485704 | etot = -14.6424332454485 -561000 ekin = 0.0770067720584792 | erot = 0.790791153077553 | epot = -15.5102311706015 | etot = -14.6424332454654 -562000 ekin = 0.0778911706718854 | erot = 0.814186471630276 | epot = -15.5345108877916 | etot = -14.6424332454895 -563000 ekin = 0.0813901113631692 | erot = 0.833925925483943 | epot = -15.5577492823672 | etot = -14.6424332455201 -564000 ekin = 0.0873448530183735 | erot = 0.849702302566485 | epot = -15.5794804011401 | etot = -14.6424332455553 -565000 ekin = 0.0953935152513606 | erot = 0.861338569497979 | epot = -15.5991653303409 | etot = -14.6424332455915 -566000 ekin = 0.105001366117363 | erot = 0.868811531658242 | epot = -15.6162461434002 | etot = -14.6424332456246 -567000 ekin = 0.11551478920907 | erot = 0.872266750929345 | epot = -15.6302147857879 | etot = -14.6424332456494 -568000 ekin = 0.126230320989268 | erot = 0.872022546762513 | epot = -15.6406861134138 | etot = -14.642433245662 -569000 ekin = 0.13646757520452 | erot = 0.868561781939776 | epot = -15.6474626028035 | etot = -14.6424332456592 -570000 ekin = 0.145634823228517 | erot = 0.862511177264942 | epot = -15.6505792461335 | etot = -14.6424332456401 -571000 ekin = 0.153278250259444 | erot = 0.85460899135856 | epot = -15.6503204872235 | etot = -14.6424332456055 -572000 ekin = 0.159109636953228 | erot = 0.845662918619192 | epot = -15.6472058011307 | etot = -14.6424332455583 -573000 ekin = 0.163011362016512 | erot = 0.836500892322368 | epot = -15.6419454998419 | etot = -14.642433245503 -574000 ekin = 0.165021239079037 | erot = 0.827918058207513 | epot = -15.6353725427317 | etot = -14.6424332454451 -575000 ekin = 0.165302195907189 | erot = 0.820623479706097 | epot = -15.6283589210035 | etot = -14.6424332453902 -576000 ekin = 0.164102988099436 | erot = 0.815190165400348 | epot = -15.6217263988437 | etot = -14.642433245344 -577000 ekin = 0.161716152385033 | erot = 0.812011817945282 | epot = -15.6161612156414 | etot = -14.6424332453111 -578000 ekin = 0.158438569369342 | erot = 0.811269345694562 | epot = -15.6121411603589 | etot = -14.642433245295 -579000 ekin = 0.154538688866582 | erot = 0.812909695779756 | epot = -15.609881629944 | etot = -14.6424332452977 -580000 ekin = 0.150232988451456 | erot = 0.816638977239882 | epot = -15.6093052110108 | etot = -14.6424332453195 -581000 ekin = 0.145672809811769 | erot = 0.821931135408107 | epot = -15.610037190579 | etot = -14.6424332453591 -582000 ekin = 0.140941476788221 | erot = 0.828052590347089 | epot = -15.6114273125489 | etot = -14.6424332454136 -583000 ekin = 0.136060602595884 | erot = 0.834102246891801 | epot = -15.6125960949663 | etot = -14.6424332454786 -584000 ekin = 0.131003759893416 | erot = 0.839065139153076 | epot = -15.6125021445954 | etot = -14.6424332455489 -585000 ekin = 0.125715216480047 | erot = 0.841876757443314 | epot = -15.610025219542 | etot = -14.6424332456187 -586000 ekin = 0.120131224766283 | erot = 0.841493945660697 | epot = -15.6040584161089 | etot = -14.6424332456819 -587000 ekin = 0.114201380569862 | erot = 0.836967317747552 | epot = -15.5936019440503 | etot = -14.6424332457329 -588000 ekin = 0.107907808224941 | erot = 0.82750959597709 | epot = -15.577850649969 | etot = -14.642433245767 -589000 ekin = 0.101280337908465 | erot = 0.812554260667714 | epot = -15.5562678443569 | etot = -14.6424332457808 -590000 ekin = 0.0944063548781498 | erot = 0.791799488415112 | epot = -15.5286390890655 | etot = -14.6424332457722 -591000 ekin = 0.0874345511051164 | erot = 0.765233519218438 | epot = -15.4951013160648 | etot = -14.6424332457413 -592000 ekin = 0.0805723392090151 | erot = 0.733139214281057 | epot = -15.4561447991796 | etot = -14.6424332456895 -593000 ekin = 0.0740771594091624 | erot = 0.696077455345293 | epot = -15.4125878603745 | etot = -14.6424332456201 -594000 ekin = 0.0682423089615835 | erot = 0.654850963355498 | epot = -15.3655265178546 | etot = -14.6424332455375 -595000 ekin = 0.0633782539035135 | erot = 0.610451848321739 | epot = -15.3162633476725 | etot = -14.6424332454472 -596000 ekin = 0.0597906540673872 | erot = 0.563997548399991 | epot = -15.2662214478226 | etot = -14.6424332453552 -597000 ekin = 0.0577565493651072 | erot = 0.516660644083797 | epot = -15.2168504387165 | etot = -14.6424332452676 -598000 ekin = 0.0575003158564822 | erot = 0.469598294353737 | epot = -15.1695318554 | etot = -14.6424332451897 -599000 ekin = 0.0591710965315271 | erot = 0.423886769451641 | epot = -15.1254911111098 | etot = -14.6424332451266 -600000 ekin = 0.0628234356919084 | erot = 0.380465849282374 | epot = -15.085722530056 | etot = -14.6424332450817 -601000 ekin = 0.0684027903404234 | erot = 0.340096852290236 | epot = -15.0509328876879 | etot = -14.6424332450572 -602000 ekin = 0.0757374499151454 | erot = 0.303336891510158 | epot = -15.0215075864789 | etot = -14.6424332450536 -603000 ekin = 0.0845381560125067 | erot = 0.270530726253859 | epot = -14.9975021273365 | etot = -14.6424332450701 -604000 ekin = 0.0944063594091286 | erot = 0.241820347964902 | epot = -14.9786599524778 | etot = -14.6424332451038 -605000 ekin = 0.10485156246129 | erot = 0.217171224792453 | epot = -14.9644560324042 | etot = -14.6424332451505 -606000 ekin = 0.115317556389963 | erot = 0.19641293035746 | epot = -14.9541637319522 | etot = -14.6424332452047 -607000 ekin = 0.125216580352814 | erot = 0.179290709848685 | epot = -14.9469405354619 | etot = -14.6424332452604 -608000 ekin = 0.133969542489555 | erot = 0.165523445158836 | epot = -14.9419262329593 | etot = -14.6424332453109 -609000 ekin = 0.141049537027034 | erot = 0.154862582266178 | epot = -14.9383453646431 | etot = -14.6424332453499 -610000 ekin = 0.146025095174092 | erot = 0.1471460408894 | epot = -14.9356043814358 | etot = -14.6424332453723 -611000 ekin = 0.148599079333654 | erot = 0.142341118194537 | epot = -14.9333734429025 | etot = -14.6424332453743 -612000 ekin = 0.148639027540038 | erot = 0.140571068728109 | epot = -14.9316433416225 | etot = -14.6424332453543 -613000 ekin = 0.146195193891189 | erot = 0.14212144139606 | epot = -14.9307498806004 | etot = -14.6424332453132 -614000 ekin = 0.141503544703117 | erot = 0.147424293659367 | epot = -14.9313610836164 | etot = -14.6424332452539 -615000 ekin = 0.134972482667994 | erot = 0.157020849768205 | epot = -14.9344265776182 | etot = -14.642433245182 -616000 ekin = 0.127153892886345 | erot = 0.171505679771382 | epot = -14.9410928177621 | etot = -14.6424332451044 -617000 ekin = 0.118700960496639 | erot = 0.191457667913243 | epot = -14.9525918734392 | etot = -14.6424332450293 -618000 ekin = 0.110316794781978 | erot = 0.217364584488656 | epot = -14.9701146242355 | etot = -14.6424332449648 -619000 ekin = 0.102698942666746 | erot = 0.249548776229802 | epot = -14.9946809638153 | etot = -14.6424332449188 -620000 ekin = 0.0964852203328029 | erot = 0.28810131748882 | epot = -15.0270197827189 | etot = -14.6424332448972 -621000 ekin = 0.0922059091543824 | erot = 0.332831044361685 | epot = -15.0674701984207 | etot = -14.6424332449047 -622000 ekin = 0.0902463647122828 | erot = 0.383233451857076 | epot = -15.1159130615124 | etot = -14.6424332449431 -623000 ekin = 0.0908226920728038 | erot = 0.438482716259981 | epot = -15.1717386533448 | etot = -14.642433245012 -624000 ekin = 0.0939716062548715 | erot = 0.497448307331879 | epot = -15.2338531586956 | etot = -14.6424332451088 -625000 ekin = 0.0995541611252495 | erot = 0.55873588677621 | epot = -15.3007232931297 | etot = -14.6424332452283 -626000 ekin = 0.107271859328467 | erot = 0.620750477447864 | epot = -15.37045558214 | etot = -14.6424332453637 -627000 ekin = 0.116692826740179 | erot = 0.681778220892588 | epot = -15.4409042931397 | etot = -14.642433245507 -628000 ekin = 0.127285245275851 | erot = 0.740081431761277 | epot = -15.5097999226863 | etot = -14.6424332456492 -629000 ekin = 0.138455039155779 | erot = 0.794000196762996 | epot = -15.5748884817003 | etot = -14.6424332457815 -630000 ekin = 0.14958484293864 | erot = 0.842052640233787 | epot = -15.6340707290682 | etot = -14.6424332458958 -631000 ekin = 0.160071499854153 | erot = 0.883025442872994 | epot = -15.6855301887124 | etot = -14.6424332459852 -632000 ekin = 0.169359720293479 | erot = 0.916046503422886 | epot = -15.7278394697615 | etot = -14.6424332460451 -633000 ekin = 0.176970053692838 | erot = 0.940632922938759 | epot = -15.7600362227044 | etot = -14.6424332460728 -634000 ekin = 0.18251996128985 | erot = 0.956709735133355 | epot = -15.7816629424915 | etot = -14.6424332460683 -635000 ekin = 0.185737466035171 | erot = 0.964597760207225 | epot = -15.7927684722762 | etot = -14.6424332460338 -636000 ekin = 0.186467519302491 | erot = 0.964972204258569 | epot = -15.7938729695347 | etot = -14.6424332459737 -637000 ekin = 0.184671774603369 | erot = 0.958796660379843 | epot = -15.7859016808768 | etot = -14.6424332458936 -638000 ekin = 0.18042282577668 | erot = 0.947239527077098 | epot = -15.770095598654 | etot = -14.6424332458002 -639000 ekin = 0.173894119063272 | erot = 0.931581224200833 | epot = -15.7479085889646 | etot = -14.6424332457005 -640000 ekin = 0.165346701826059 | erot = 0.913120838758217 | epot = -15.720900786185 | etot = -14.6424332456007 -641000 ekin = 0.155113786101867 | erot = 0.893090060094414 | epot = -15.6906370917029 | etot = -14.6424332455066 -642000 ekin = 0.143583869242346 | erot = 0.872580710310524 | epot = -15.6585978249756 | etot = -14.6424332454227 -643000 ekin = 0.131182953687712 | erot = 0.85249016805802 | epot = -15.626106367098 | etot = -14.6424332453522 -644000 ekin = 0.118356305759397 | erot = 0.833486853993089 | epot = -15.5942764050497 | etot = -14.6424332452972 -645000 ekin = 0.105550209083444 | erot = 0.815995971214604 | epot = -15.5639794255564 | etot = -14.6424332452583 -646000 ekin = 0.0931942744180207 | erot = 0.800204061931992 | epot = -15.5358315815853 | etot = -14.6424332452353 -647000 ekin = 0.0816850001788838 | erot = 0.786079744440617 | epot = -15.5101979898464 | etot = -14.6424332452269 -648000 ekin = 0.0713713598428998 | erot = 0.773407243191854 | epot = -15.4872118482658 | etot = -14.6424332452311 -649000 ekin = 0.0625431628711437 | erot = 0.761828976528577 | epot = -15.466805384645 | etot = -14.6424332452453 -650000 ekin = 0.0554227735501042 | erot = 0.750893453411344 | epot = -15.4487494722283 | etot = -14.6424332452669 -651000 ekin = 0.0501605027659902 | erot = 0.740104978445366 | epot = -15.4326987265041 | etot = -14.6424332452927 -652000 ekin = 0.0468336713668948 | erot = 0.728972100417369 | epot = -15.4182390171042 | etot = -14.64243324532 -653000 ekin = 0.0454490492583012 | erot = 0.71705228594169 | epot = -15.4049345805459 | etot = -14.6424332453459 -654000 ekin = 0.0459481524956013 | erot = 0.703990869780751 | epot = -15.3923722676445 | etot = -14.6424332453682 -655000 ekin = 0.0482147495301563 | erot = 0.689552835103781 | epot = -15.3802008300186 | etot = -14.6424332453846 -656000 ekin = 0.052083876127999 | erot = 0.6736463327468 | epot = -15.3681634542687 | etot = -14.6424332453939 -657000 ekin = 0.0573516620867098 | erot = 0.656337023113139 | epot = -15.3561219305948 | etot = -14.6424332453949 -658000 ekin = 0.0637853134946659 | erot = 0.637852348218005 | epot = -15.3440709071003 | etot = -14.6424332453876 -659000 ekin = 0.0711326702887129 | erot = 0.618574815847064 | epot = -15.3321407315083 | etot = -14.6424332453725 -660000 ekin = 0.0791308828116024 | erot = 0.599023454708815 | epot = -15.3205875828713 | etot = -14.6424332453509 -661000 ekin = 0.0875139366244679 | erot = 0.579822939748233 | epot = -15.3097701216978 | etot = -14.6424332453251 -662000 ekin = 0.0960190004205311 | erot = 0.561660610348993 | epot = -15.3001128560677 | etot = -14.6424332452982 -663000 ekin = 0.104391848885269 | erot = 0.54523274605647 | epot = -15.2920578402154 | etot = -14.6424332452737 -664000 ekin = 0.112391863389534 | erot = 0.531182949320087 | epot = -15.286008057965 | etot = -14.6424332452554 -665000 ekin = 0.119797262719802 | erot = 0.520037124798746 | epot = -15.2822676327654 | etot = -14.6424332452468 -666000 ekin = 0.126411190061237 | erot = 0.512141060962394 | epot = -15.2809854962748 | etot = -14.6424332452511 -667000 ekin = 0.132069035722096 | erot = 0.507607681730268 | epot = -15.2821099627224 | etot = -14.64243324527 -668000 ekin = 0.13664691453854 | erot = 0.506281315754884 | epot = -15.2853614755972 | etot = -14.6424332453038 -669000 ekin = 0.140070616008884 | erot = 0.507725566171511 | epot = -15.2902294275315 | etot = -14.6424332453511 -670000 ekin = 0.142323740902266 | erot = 0.511239425097731 | epot = -15.2959964114084 | etot = -14.6424332454084 -671000 ekin = 0.143453306298606 | erot = 0.515903234043229 | epot = -15.3017897858128 | etot = -14.642433245471 -672000 ekin = 0.143571012728166 | erot = 0.520652256715664 | epot = -15.3066565149767 | etot = -14.6424332455328 -673000 ekin = 0.142848733833156 | erot = 0.52437156335394 | epot = -15.3096535427749 | etot = -14.6424332455878 -674000 ekin = 0.1415076132746 | erot = 0.526002362927187 | epot = -15.3099432218319 | etot = -14.6424332456301 -675000 ekin = 0.13980130282334 | erot = 0.524647629020819 | epot = -15.3068821774991 | etot = -14.6424332456549 -676000 ekin = 0.137995095209388 | erot = 0.519664439037725 | epot = -15.3000927799067 | etot = -14.6424332456596 -677000 ekin = 0.136343677284998 | erot = 0.510732098514415 | epot = -15.2895090214424 | etot = -14.642433245643 -678000 ekin = 0.135070664123473 | erot = 0.497888575253319 | epot = -15.2753924849829 | etot = -14.6424332456061 -679000 ekin = 0.134352810446714 | erot = 0.481532294129922 | epot = -15.2583183501282 | etot = -14.6424332455516 -680000 ekin = 0.134310862658442 | erot = 0.462390968603332 | epot = -15.2391350767452 | etot = -14.6424332454834 -681000 ekin = 0.135007638926465 | erot = 0.441462941783532 | epot = -15.2189038261164 | etot = -14.6424332454064 -682000 ekin = 0.136452461528359 | erot = 0.419938865037162 | epot = -15.1988245718911 | etot = -14.6424332453256 -683000 ekin = 0.138609887401901 | erot = 0.399112293315355 | epot = -15.1801554259633 | etot = -14.642433245246 -684000 ekin = 0.141410065652158 | erot = 0.380287181762659 | epot = -15.1641304925878 | etot = -14.642433245173 -685000 ekin = 0.144758102725849 | erot = 0.364688846299896 | epot = -15.1518801941367 | etot = -14.6424332451109 -686000 ekin = 0.148540467122542 | erot = 0.353383275614958 | epot = -15.1443569878014 | etot = -14.6424332450639 -687000 ekin = 0.152627512101174 | erot = 0.347208212231079 | epot = -15.1422689693677 | etot = -14.6424332450355 -688000 ekin = 0.156872371009907 | erot = 0.346718408270883 | epot = -15.1460240243093 | etot = -14.6424332450285 -689000 ekin = 0.161107527975576 | erot = 0.352146941114484 | epot = -15.1556877141346 | etot = -14.6424332450445 -690000 ekin = 0.165141087380535 | erot = 0.363384304940302 | epot = -15.1709586374048 | etot = -14.642433245084 -691000 ekin = 0.16875504264806 | erot = 0.379976931153832 | epot = -15.1911652189475 | etot = -14.6424332451456 -692000 ekin = 0.171707649701815 | erot = 0.401146558394006 | epot = -15.2152874533222 | etot = -14.6424332452264 -693000 ekin = 0.173741393440444 | erot = 0.425831232783773 | epot = -15.2420058715459 | etot = -14.6424332453217 -694000 ekin = 0.174597110621473 | erot = 0.452747528134232 | epot = -15.2697778841809 | etot = -14.6424332454252 -695000 ekin = 0.174033757468432 | erot = 0.480471830915669 | epot = -15.2969388339132 | etot = -14.6424332455291 -696000 ekin = 0.171852263360605 | erot = 0.507536398150921 | epot = -15.3218219071368 | etot = -14.6424332456253 -697000 ekin = 0.167921065286616 | erot = 0.532533688685243 | epot = -15.3428879996772 | etot = -14.6424332457054 -698000 ekin = 0.162200409472727 | erot = 0.55422061991701 | epot = -15.3588542751519 | etot = -14.6424332457621 -699000 ekin = 0.15476241571153 | erot = 0.5716133610199 | epot = -15.3688090225212 | etot = -14.6424332457897 -700000 ekin = 0.14580423000504 | erot = 0.584063387080082 | epot = -15.3723008628698 | etot = -14.6424332457847 -701000 ekin = 0.135652269555348 | erot = 0.591306922713837 | epot = -15.3693924380155 | etot = -14.6424332457463 -702000 ekin = 0.124756460204831 | erot = 0.59348246434204 | epot = -15.3606721702235 | etot = -14.6424332456766 -703000 ekin = 0.113674325949313 | erot = 0.591114401850656 | epot = -15.3472219733804 | etot = -14.6424332455805 -704000 ekin = 0.10304567594439 | erot = 0.585064323190966 | epot = -15.3305432446002 | etot = -14.6424332454648 -705000 ekin = 0.0935593581958762 | erot = 0.576454826529771 | epot = -15.3124474300639 | etot = -14.6424332453383 -706000 ekin = 0.0859140824287833 | erot = 0.566573150252444 | epot = -15.2949204778916 | etot = -14.6424332452103 -707000 ekin = 0.0807756759567746 | erot = 0.556763427605772 | epot = -15.2799723486536 | etot = -14.642433245091 -708000 ekin = 0.0787333622616091 | erot = 0.548316855287971 | epot = -15.2694834625388 | etot = -14.6424332449892 -709000 ekin = 0.0802577669172368 | erot = 0.542368667950884 | epot = -15.2650596797811 | etot = -14.642433244913 -710000 ekin = 0.0856633545554253 | erot = 0.539809747046289 | epot = -15.2679063464703 | etot = -14.6424332448686 -711000 ekin = 0.0950778519056264 | erot = 0.541219180888341 | epot = -15.2787302776541 | etot = -14.6424332448601 -712000 ekin = 0.108420876625267 | erot = 0.546822307908336 | epot = -15.2976764294225 | etot = -14.6424332448889 -713000 ekin = 0.125393451698069 | erot = 0.556476834654442 | epot = -15.3243035313066 | etot = -14.642433244954 -714000 ekin = 0.145479367624701 | erot = 0.569687600115953 | epot = -15.3576002127927 | etot = -14.642433245052 -715000 ekin = 0.167958541120038 | erot = 0.585648522299648 | epot = -15.3960403085969 | etot = -14.6424332451773 -716000 ekin = 0.191931735854292 | erot = 0.603308292527993 | epot = -15.4376732737045 | etot = -14.6424332453222 -717000 ekin = 0.216355400179768 | erot = 0.621454592033853 | epot = -15.4802432376918 | etot = -14.6424332454782 -718000 ekin = 0.240085056513064 | erot = 0.638810139728766 | epot = -15.5213284418775 | etot = -14.6424332456357 -719000 ekin = 0.261925698577658 | erot = 0.654132895983949 | epot = -15.5584918403468 | etot = -14.6424332457852 -720000 ekin = 0.280687969313511 | erot = 0.666312379865697 | epot = -15.5894335950967 | etot = -14.6424332459175 -721000 ekin = 0.295249345590605 | erot = 0.674454385927248 | epot = -15.6121369775423 | etot = -14.6424332460244 -722000 ekin = 0.304619886334631 | erot = 0.677947410255691 | epot = -15.625000542689 | etot = -14.6424332460987 -723000 ekin = 0.308011983728238 | erot = 0.676505724572098 | epot = -15.626950954435 | etot = -14.6424332461346 -724000 ekin = 0.304912667283913 | erot = 0.670186105902335 | epot = -15.6175320193145 | etot = -14.6424332461282 -725000 ekin = 0.295155116710332 | erot = 0.659377522493187 | epot = -15.5969658852808 | etot = -14.6424332460772 -726000 ekin = 0.278983134898071 | erot = 0.644765363163033 | epot = -15.5661817440431 | etot = -14.642433245982 -727000 ekin = 0.257098790791563 | erot = 0.627273860368268 | epot = -15.5268058970054 | etot = -14.6424332458455 -728000 ekin = 0.230680158271426 | erot = 0.607992016186298 | epot = -15.4811054201321 | etot = -14.6424332456743 -729000 ekin = 0.201354496272596 | erot = 0.588089464040467 | epot = -15.431877205792 | etot = -14.6424332454789 -730000 ekin = 0.171114103974836 | erot = 0.568729214721698 | epot = -15.3822765639703 | etot = -14.6424332452738 -731000 ekin = 0.142168923907651 | erot = 0.550984135076315 | epot = -15.3355863040605 | etot = -14.6424332450765 -732000 ekin = 0.116742007096091 | erot = 0.535763349049021 | epot = -15.2949386010514 | etot = -14.6424332449063 -733000 ekin = 0.0968293027534119 | erot = 0.523753647326195 | epot = -15.2630161948611 | etot = -14.6424332447815 -734000 ekin = 0.0839596135584089 | erot = 0.515379592342255 | epot = -15.2417724506168 | etot = -14.6424332447161 -735000 ekin = 0.0789983701762997 | erot = 0.510784464198618 | epot = -15.2322160790924 | etot = -14.6424332447175 -736000 ekin = 0.0820355551921124 | erot = 0.509832642267912 | epot = -15.2343014422445 | etot = -14.6424332447845 -737000 ekin = 0.092382712385484 | erot = 0.512132550856022 | epot = -15.246948508149 | etot = -14.6424332449075 -738000 ekin = 0.108680448513128 | erot = 0.517077971027173 | epot = -15.2681916646103 | etot = -14.64243324507 -739000 ekin = 0.129093715682691 | erot = 0.523904364925655 | epot = -15.2954313258603 | etot = -14.642433245252 -740000 ekin = 0.151555277793326 | erot = 0.531755895778055 | epot = -15.3257444190045 | etot = -14.6424332454331 -741000 ekin = 0.174012721806035 | erot = 0.539758083451399 | epot = -15.3562040508525 | etot = -14.6424332455951 -742000 ekin = 0.194640916830793 | erot = 0.547090549697037 | epot = -15.384164712252 | etot = -14.6424332457242 -743000 ekin = 0.211995737397977 | erot = 0.553054125335024 | epot = -15.4074831085446 | etot = -14.6424332458116 -744000 ekin = 0.225100508722008 | erot = 0.557126762307225 | epot = -15.4246605168831 | etot = -14.6424332458539 -745000 ekin = 0.233469424485825 | erot = 0.559003260236789 | epot = -15.4349059305745 | etot = -14.6424332458519 -746000 ekin = 0.23707991346408 | erot = 0.558614810498058 | epot = -15.4381279697723 | etot = -14.6424332458102 -747000 ekin = 0.236308652983949 | erot = 0.556125790081372 | epot = -15.4348676888016 | etot = -14.6424332457363 -748000 ekin = 0.231845097886983 | erot = 0.551907079329025 | epot = -15.4261854228555 | etot = -14.6424332456395 -749000 ekin = 0.224593843483339 | erot = 0.546487360028757 | epot = -15.4135144490424 | etot = -14.6424332455303 -750000 ekin = 0.215574369391403 | erot = 0.540486233484167 | epot = -15.3984938482956 | etot = -14.64243324542 -751000 ekin = 0.205824583426058 | erot = 0.534535356763698 | epot = -15.382793185509 | etot = -14.6424332453192 -752000 ekin = 0.196313335741561 | erot = 0.52919581521731 | epot = -15.3679423961964 | etot = -14.6424332452375 -753000 ekin = 0.187866475787076 | erot = 0.524881252730185 | epot = -15.3551809736995 | etot = -14.6424332451822 -754000 ekin = 0.181110613625657 | erot = 0.521796491095279 | epot = -15.345340349879 | etot = -14.6424332451581 -755000 ekin = 0.176438042203778 | erot = 0.519900210803623 | epot = -15.3387714981735 | etot = -14.6424332451661 -756000 ekin = 0.173994962646486 | erot = 0.518897676280608 | epot = -15.3353258841311 | etot = -14.642433245204 -757000 ekin = 0.173693190270073 | erot = 0.518265706177119 | epot = -15.3343921417132 | etot = -14.642433245266 -758000 ekin = 0.175243155014324 | erot = 0.517307659815294 | epot = -15.3349840601735 | etot = -14.6424332453439 -759000 ekin = 0.178203703092602 | erot = 0.515231902157482 | epot = -15.3358688506779 | etot = -14.6424332454278 -760000 ekin = 0.182042463548487 | erot = 0.51124383794149 | epot = -15.3357195469977 | etot = -14.6424332455077 -761000 ekin = 0.186199747761053 | erot = 0.50463982554006 | epot = -15.3332728188755 | etot = -14.6424332455744 -762000 ekin = 0.190149235945104 | erot = 0.494891409026585 | epot = -15.3274738905921 | etot = -14.6424332456204 -763000 ekin = 0.193449921094625 | erot = 0.481710238280476 | epot = -15.3175934050158 | etot = -14.6424332456407 -764000 ekin = 0.195785552426496 | erot = 0.465087294345703 | epot = -15.3033060924053 | etot = -14.6424332456331 -765000 ekin = 0.196989678184872 | erot = 0.445303873487263 | epot = -15.2847267972702 | etot = -14.6424332455981 -766000 ekin = 0.197055919182987 | erot = 0.422915440288454 | epot = -15.2624046050099 | etot = -14.6424332455385 -767000 ekin = 0.19613407649406 | erot = 0.398712320920584 | epot = -15.2372796428736 | etot = -14.6424332454589 -768000 ekin = 0.194513096652813 | erot = 0.37366293895697 | epot = -15.2106092809754 | etot = -14.6424332453656 -769000 ekin = 0.192592017627635 | erot = 0.348845887484862 | epot = -15.183871150378 | etot = -14.6424332452655 -770000 ekin = 0.190840163686923 | erot = 0.325376840212478 | epot = -15.1586502490658 | etot = -14.6424332451664 -771000 ekin = 0.189748397228249 | erot = 0.304335529900872 | epot = -15.1365171722054 | etot = -14.6424332450763 -772000 ekin = 0.18977434185156 | erot = 0.286697153922422 | epot = -15.1189047407765 | etot = -14.6424332450026 -773000 ekin = 0.191286034501482 | erot = 0.273271857838015 | epot = -15.1069911372911 | etot = -14.6424332449516 -774000 ekin = 0.194510000609465 | erot = 0.264655458971731 | epot = -15.1015987045099 | etot = -14.6424332449287 -775000 ekin = 0.199490639679827 | erot = 0.261194193157327 | epot = -15.1031180777734 | etot = -14.6424332449363 -776000 ekin = 0.206067477065984 | erot = 0.26296580393673 | epot = -15.1114665259772 | etot = -14.6424332449745 -777000 ekin = 0.213875019086146 | erot = 0.269778568413633 | epot = -15.1260868325404 | etot = -14.6424332450407 -778000 ekin = 0.222366868965164 | erot = 0.281188790676632 | epot = -15.1459889047712 | etot = -14.6424332451294 -779000 ekin = 0.230862102268941 | erot = 0.2965359441758 | epot = -15.1698312916782 | etot = -14.6424332452334 -780000 ekin = 0.238608567019415 | erot = 0.314993169090579 | epot = -15.1960349814538 | etot = -14.6424332453438 -781000 ekin = 0.244855557741695 | erot = 0.335629445234049 | epot = -15.222918248427 | etot = -14.6424332454513 -782000 ekin = 0.248927612478521 | erot = 0.357478674283205 | epot = -15.2488395323088 | etot = -14.642433245547 -783000 ekin = 0.250291897529516 | erot = 0.379610269023755 | epot = -15.2723354121766 | etot = -14.6424332456234 -784000 ekin = 0.248613283253053 | erot = 0.401195731117637 | epot = -15.2922422600447 | etot = -14.642433245674 -785000 ekin = 0.243793133450592 | erot = 0.421566090460737 | epot = -15.3077924696064 | etot = -14.6424332456951 -786000 ekin = 0.23598950185229 | erot = 0.440255905200772 | epot = -15.3186786527377 | etot = -14.6424332456846 -787000 ekin = 0.225617610784087 | erot = 0.457030673426299 | epot = -15.3250815298539 | etot = -14.6424332456436 -788000 ekin = 0.213330260901152 | erot = 0.471895861690097 | epot = -15.3276593681662 | etot = -14.642433245575 -789000 ekin = 0.19997849967651 | erot = 0.485087183877581 | epot = -15.3274989290384 | etot = -14.6424332454844 -790000 ekin = 0.186553834702627 | erot = 0.497043141237974 | epot = -15.3260302213197 | etot = -14.6424332453791 -791000 ekin = 0.174114766792028 | erot = 0.508362048565589 | epot = -15.3249100606257 | etot = -14.6424332452681 -792000 ekin = 0.163702420431615 | erot = 0.519746739177318 | epot = -15.3258824047698 | etot = -14.6424332451609 -793000 ekin = 0.156252224966357 | erot = 0.531940822986537 | epot = -15.3306262930203 | etot = -14.6424332450674 -794000 ekin = 0.152510350035351 | erot = 0.545660777312736 | epot = -15.3406043723442 | etot = -14.6424332449961 -795000 ekin = 0.152964251158983 | erot = 0.561528326979184 | epot = -15.3569258230923 | etot = -14.6424332449541 -796000 ekin = 0.157795747358379 | erot = 0.58000757877651 | epot = -15.3802365710807 | etot = -14.6424332449459 -797000 ekin = 0.166862457859208 | erot = 0.601351255568297 | epot = -15.4106469584007 | etot = -14.6424332449732 -798000 ekin = 0.179709603433377 | erot = 0.625560121844245 | epot = -15.4477029703127 | etot = -14.642433245035 -799000 ekin = 0.195609966062416 | erot = 0.65235924717518 | epot = -15.4904024583651 | etot = -14.6424332451275 -800000 ekin = 0.213626158791744 | erot = 0.681194021872009 | epot = -15.5372534259083 | etot = -14.6424332452445 -801000 ekin = 0.232687040193829 | erot = 0.711247726384584 | epot = -15.5863680119569 | etot = -14.6424332453785 -802000 ekin = 0.251669429106226 | erot = 0.741480919833726 | epot = -15.6355835944605 | etot = -14.6424332455205 -803000 ekin = 0.269477067858271 | erot = 0.77069100841835 | epot = -15.6826013219381 | etot = -14.6424332456615 -804000 ekin = 0.2851105414574 | erot = 0.797588259155217 | epot = -15.7251320464048 | etot = -14.6424332457922 -805000 ekin = 0.297723982505655 | erot = 0.82088252879607 | epot = -15.7610397572062 | etot = -14.6424332459044 -806000 ekin = 0.306666387686443 | erot = 0.839373432909784 | epot = -15.7884730665875 | etot = -14.6424332459913 -807000 ekin = 0.311506975554881 | erot = 0.852035914442116 | epot = -15.8059761360445 | etot = -14.6424332460475 -808000 ekin = 0.31204517625202 | erot = 0.858093398524567 | epot = -15.8125718208467 | etot = -14.6424332460701 -809000 ekin = 0.308306642386009 | erot = 0.857071970755237 | epot = -15.8078118591995 | etot = -14.6424332460582 -810000 ekin = 0.3005272205585 | erot = 0.848831113925777 | epot = -15.7917915804977 | etot = -14.6424332460134 -811000 ekin = 0.289127204417746 | erot = 0.83356913861968 | epot = -15.7651295889766 | etot = -14.6424332459392 -812000 ekin = 0.274678427598231 | erot = 0.811804116491095 | epot = -15.7289157899298 | etot = -14.6424332458404 -813000 ekin = 0.257866835579171 | erot = 0.784333459541309 | epot = -15.684633540844 | etot = -14.6424332457235 -814000 ekin = 0.23945308058907 | erot = 0.752176980195558 | epot = -15.63406330638 | etot = -14.6424332455953 -815000 ekin = 0.220233415146299 | erot = 0.716509170266206 | epot = -15.5791758308753 | etot = -14.6424332454628 -816000 ekin = 0.201002751041202 | erot = 0.678586569747871 | epot = -15.5220225661217 | etot = -14.6424332453326 -817000 ekin = 0.18252126107488 | erot = 0.639675603864852 | epot = -15.4646301101504 | etot = -14.6424332452107 -818000 ekin = 0.165485401522705 | erot = 0.600985363831257 | epot = -15.4089040104563 | etot = -14.6424332451023 -819000 ekin = 0.150503789775637 | erot = 0.563608719248849 | epot = -15.356545754036 | etot = -14.6424332450115 -820000 ekin = 0.138078032174191 | erot = 0.528474068971486 | epot = -15.3089853460871 | etot = -14.6424332449414 -821000 ekin = 0.128588386726458 | erot = 0.496309093116269 | epot = -15.2673307247368 | etot = -14.6424332448941 -822000 ekin = 0.122284066133841 | erot = 0.467617125513468 | epot = -15.2323344365177 | etot = -14.6424332448704 -823000 ekin = 0.119278020922153 | erot = 0.442666228475553 | epot = -15.2043774942682 | etot = -14.6424332448705 -824000 ekin = 0.119546158602336 | erot = 0.421490682734476 | epot = -15.1834700862298 | etot = -14.642433244893 -825000 ekin = 0.122931110514093 | erot = 0.403904342218594 | epot = -15.1692686976687 | etot = -14.6424332449361 -826000 ekin = 0.129150803764777 | erot = 0.389525074993895 | epot = -15.1611091237552 | etot = -14.6424332449966 -827000 ekin = 0.137812176400527 | erot = 0.377809252263535 | epot = -15.1580546737348 | etot = -14.6424332450707 -828000 ekin = 0.148430331610601 | erot = 0.368094906955077 | epot = -15.1589584837195 | etot = -14.6424332451538 -829000 ekin = 0.160453205764727 | erot = 0.359651737503703 | epot = -15.1625381885089 | etot = -14.6424332452404 -830000 ekin = 0.173291382900529 | erot = 0.351735589536635 | epot = -15.1674602177621 | etot = -14.642433245325 -831000 ekin = 0.186352012967339 | erot = 0.343644456321088 | epot = -15.17242971469 | etot = -14.6424332454015 -832000 ekin = 0.199074924610278 | erot = 0.334772487912379 | epot = -15.1762806579876 | etot = -14.6424332454649 -833000 ekin = 0.210968084885577 | erot = 0.324658115180513 | epot = -15.1780594455764 | etot = -14.6424332455103 -834000 ekin = 0.22163875726204 | erot = 0.313022323434694 | epot = -15.1770943262316 | etot = -14.6424332455348 -835000 ekin = 0.230816330006794 | erot = 0.299793483319765 | epot = -15.1730430588635 | etot = -14.6424332455369 -836000 ekin = 0.238363132178559 | erot = 0.285116039954826 | epot = -15.1659124176508 | etot = -14.6424332455174 -837000 ekin = 0.244270841534548 | erot = 0.269341751254572 | epot = -15.1560458382684 | etot = -14.6424332454793 -838000 ekin = 0.248642320238245 | erot = 0.253003904099761 | epot = -15.144079469765 | etot = -14.642433245427 -839000 ekin = 0.251661569328948 | erot = 0.236776758984022 | epot = -15.1308715736795 | etot = -14.6424332453665 -840000 ekin = 0.253557306828097 | erot = 0.221424057159249 | epot = -15.1174146092912 | etot = -14.6424332453038 -841000 ekin = 0.254567562695129 | erot = 0.20774147574213 | epot = -15.1047422836817 | etot = -14.6424332452444 -842000 ekin = 0.254912814680555 | erot = 0.196498262353486 | epot = -15.0938443222266 | etot = -14.6424332451926 -843000 ekin = 0.25478313076125 | erot = 0.188382921786766 | epot = -15.0855992976989 | etot = -14.6424332451509 -844000 ekin = 0.254340789692162 | erot = 0.183956927272162 | epot = -15.0807309620847 | etot = -14.6424332451204 -845000 ekin = 0.253734932885183 | erot = 0.183619247980868 | epot = -15.0797874259671 | etot = -14.6424332451011 -846000 ekin = 0.253120504189248 | erot = 0.187583282240197 | epot = -15.0831370315218 | etot = -14.6424332450923 -847000 ekin = 0.252671650081459 | erot = 0.195866742639432 | epot = -15.0909716378146 | etot = -14.6424332450937 -848000 ekin = 0.252580915304066 | erot = 0.208294222463377 | epot = -15.103308382873 | etot = -14.6424332451056 -849000 ekin = 0.253039966843089 | erot = 0.224511555531961 | epot = -15.1199847675035 | etot = -14.6424332451285 -850000 ekin = 0.254204001794782 | erot = 0.244010590097847 | epot = -15.1406478370558 | etot = -14.6424332451632 -851000 ekin = 0.256148339024743 | erot = 0.266162563602639 | epot = -15.1647441478372 | etot = -14.6424332452098 -852000 ekin = 0.258829686440357 | erot = 0.290257858698255 | epot = -15.1915207904057 | etot = -14.6424332452671 -853000 ekin = 0.262064657830147 | erot = 0.315549558167899 | epot = -15.2200474613301 | etot = -14.642433245332 -854000 ekin = 0.265534116125842 | erot = 0.341297947736774 | epot = -15.2492653092626 | etot = -14.6424332454 -855000 ekin = 0.268815174658127 | erot = 0.36681300443161 | epot = -15.2780614245547 | etot = -14.642433245465 -856000 ekin = 0.271435486960143 | erot = 0.391492007902569 | epot = -15.3053607403836 | etot = -14.6424332455209 -857000 ekin = 0.272939108069131 | erot = 0.414849750475003 | epot = -15.3302221041064 | etot = -14.6424332455623 -858000 ekin = 0.272951155046072 | erot = 0.436539390690098 | epot = -15.3519237913214 | etot = -14.6424332455852 -859000 ekin = 0.271229880682515 | erot = 0.456362750061876 | epot = -15.3700258763321 | etot = -14.6424332455877 -860000 ekin = 0.267698633839345 | erot = 0.474269718463609 | epot = -15.3844015978732 | etot = -14.6424332455702 -861000 ekin = 0.262455001757423 | erot = 0.490347316011031 | epot = -15.3952355633033 | etot = -14.6424332455349 -862000 ekin = 0.255758797180063 | erot = 0.504799761302306 | epot = -15.4029918039677 | etot = -14.6424332454854 -863000 ekin = 0.248003564343451 | erot = 0.517921532815844 | epot = -15.4083583425857 | etot = -14.6424332454264 -864000 ekin = 0.239677655585439 | erot = 0.530065823506495 | epot = -15.412176724455 | etot = -14.642433245363 -865000 ekin = 0.23132088944446 | erot = 0.541610953536998 | epot = -15.4153650882816 | etot = -14.6424332453002 -866000 ekin = 0.223481813673878 | erot = 0.552927233334005 | epot = -15.41884229225 | etot = -14.6424332452421 -867000 ekin = 0.216679174488124 | erot = 0.564346499433549 | epot = -15.4234589191144 | etot = -14.6424332451927 -868000 ekin = 0.211369750013082 | erot = 0.576136138939065 | epot = -15.4299391341069 | etot = -14.6424332451547 -869000 ekin = 0.207923502302006 | erot = 0.588478941150607 | epot = -15.4388356885827 | etot = -14.64243324513 -870000 ekin = 0.206606152993159 | erot = 0.601459626888393 | epot = -15.4504990250012 | etot = -14.6424332451197 -871000 ekin = 0.207568796750574 | erot = 0.615058451102447 | epot = -15.4650604929769 | etot = -14.6424332451239 -872000 ekin = 0.210843969893514 | erot = 0.629151875755212 | epot = -15.4824290907906 | etot = -14.6424332451419 -873000 ekin = 0.216347593110671 | erot = 0.643519970828197 | epot = -15.5023008091114 | etot = -14.6424332451726 -874000 ekin = 0.223886305134761 | erot = 0.65785990972427 | epot = -15.5241794600729 | etot = -14.6424332452139 -875000 ekin = 0.233169807544781 | erot = 0.671804662203727 | epot = -15.5474077150118 | etot = -14.6424332452633 -876000 ekin = 0.243827877955837 | erot = 0.684945735792129 | epot = -15.5712068590658 | etot = -14.6424332453179 -877000 ekin = 0.255431632539029 | erot = 0.69685856734628 | epot = -15.5947234452596 | etot = -14.6424332453743 -878000 ekin = 0.267518408507424 | erot = 0.707128927380235 | epot = -15.6170805813169 | etot = -14.6424332454292 -879000 ekin = 0.279619300254511 | erot = 0.715378495712557 | epot = -15.6374310414462 | etot = -14.6424332454792 -880000 ekin = 0.291287955017456 | erot = 0.721287639190631 | epot = -15.6550088397293 | etot = -14.6424332455213 -881000 ekin = 0.302128778463176 | erot = 0.724613422802369 | epot = -15.6691754468184 | etot = -14.6424332455529 -882000 ekin = 0.311822304069024 | erot = 0.725201068168812 | epot = -15.6794566178103 | etot = -14.6424332455725 -883000 ekin = 0.320145243789556 | erot = 0.722987481096488 | epot = -15.6855659704653 | etot = -14.6424332455793 -884000 ekin = 0.326982762202337 | erot = 0.717996120151906 | epot = -15.6874121279283 | etot = -14.642433245574 -885000 ekin = 0.332330882217347 | erot = 0.710323349665211 | epot = -15.6850874774409 | etot = -14.6424332455584 -886000 ekin = 0.336287673337102 | erot = 0.700117442969765 | epot = -15.6788383618422 | etot = -14.6424332455353 -887000 ekin = 0.33903296415872 | erot = 0.687552454430858 | epot = -15.6690186640981 | etot = -14.6424332455086 -888000 ekin = 0.340797654552155 | erot = 0.67280010093964 | epot = -15.6560310009741 | etot = -14.6424332454823 -889000 ekin = 0.341825106167166 | erot = 0.656003407096678 | epot = -15.6402617587246 | etot = -14.6424332454608 -890000 ekin = 0.342328347583419 | erot = 0.637256013160556 | epot = -15.6220176061914 | etot = -14.6424332454474 -891000 ekin = 0.342447730500021 | erot = 0.616590618565289 | epot = -15.6014715945102 | etot = -14.6424332454449 -892000 ekin = 0.342214057419104 | erot = 0.593979026501831 | epot = -15.5786263293753 | etot = -14.6424332454543 -893000 ekin = 0.34152200491664 | erot = 0.569344767729407 | epot = -15.5533000181212 | etot = -14.6424332454752 -894000 ekin = 0.340117934122997 | erot = 0.542587519912816 | epot = -15.525138699541 | etot = -14.6424332455052 -895000 ekin = 0.337605044786637 | erot = 0.513616778977938 | epot = -15.4936550693051 | etot = -14.6424332455405 -896000 ekin = 0.333467462875054 | erot = 0.48239077517223 | epot = -15.4582914836235 | etot = -14.6424332455762 -897000 ekin = 0.327113397523327 | erot = 0.448955709001807 | epot = -15.4185023521314 | etot = -14.6424332456062 -898000 ekin = 0.317936017621265 | erot = 0.413480165458539 | epot = -15.3738494287041 | etot = -14.6424332456243 -899000 ekin = 0.305389123795979 | erot = 0.376280077469313 | epot = -15.3241024468894 | etot = -14.6424332456241 -900000 ekin = 0.289072881395148 | erot = 0.337830752319287 | epot = -15.2693368793143 | etot = -14.6424332455999 -901000 ekin = 0.268822686259622 | erot = 0.298764046957452 | epot = -15.2100199787646 | etot = -14.6424332455475 -902000 ekin = 0.244791653968919 | erot = 0.259850521118035 | epot = -15.1470754205513 | etot = -14.6424332454644 -903000 ekin = 0.217514571462472 | erot = 0.221968047210473 | epot = -15.0819158640236 | etot = -14.6424332453507 -904000 ekin = 0.187939204411346 | erot = 0.186059692012592 | epot = -15.0164321416341 | etot = -14.6424332452102 -905000 ekin = 0.157410847731204 | erot = 0.153084564883822 | epot = -14.9529286576653 | etot = -14.6424332450503 -906000 ekin = 0.127599356271268 | erot = 0.123965703545286 | epot = -14.8939983046991 | etot = -14.6424332448825 -907000 ekin = 0.100365589130667 | erot = 0.0995389863896931 | epot = -14.8423378202422 | etot = -14.6424332447218 -908000 ekin = 0.0775759855945855 | erot = 0.0805066337401435 | epot = -14.800515863919 | etot = -14.6424332445842 -909000 ekin = 0.0608876950034 | erot = 0.0673982354567511 | epot = -14.7707191749454 | etot = -14.6424332444853 -910000 ekin = 0.0515382922989042 | erot = 0.0605415547706379 | epot = -14.7545130915067 | etot = -14.6424332444371 -911000 ekin = 0.0501789452911252 | erot = 0.0600446989620123 | epot = -14.7526568886991 | etot = -14.642433244446 -912000 ekin = 0.0567846925755769 | erot = 0.0657906450221707 | epot = -14.7650085821085 | etot = -14.6424332445108 -913000 ekin = 0.0706603747975489 | erot = 0.0774445361855688 | epot = -14.790538155607 | etot = -14.6424332446239 -914000 ekin = 0.0905398584143666 | erot = 0.0944735694282315 | epot = -14.8274466726145 | etot = -14.6424332447719 -915000 ekin = 0.114756144633904 | erot = 0.116178630204502 | epot = -14.8733680197774 | etot = -14.642433244939 -916000 ekin = 0.141447043407684 | erot = 0.141736093135102 | epot = -14.9256163816514 | etot = -14.6424332451087 -917000 ekin = 0.168758535424836 | erot = 0.170247440483737 | epot = -14.9814392211754 | etot = -14.6424332452668 -918000 ekin = 0.195014913443954 | erot = 0.200793639362701 | epot = -15.0382417982093 | etot = -14.6424332454026 -919000 ekin = 0.218837422087121 | erot = 0.232490666329554 | epot = -15.0937613339258 | etot = -14.6424332455091 -920000 ekin = 0.239206641026195 | erot = 0.264542267085039 | epot = -15.1461821536945 | etot = -14.6424332455832 -921000 ekin = 0.25547457715008 | erot = 0.296286050795184 | epot = -15.1941938735701 | etot = -14.6424332456248 -922000 ekin = 0.267338631216139 | erot = 0.327229363198297 | epot = -15.2370012400506 | etot = -14.6424332456361 -923000 ekin = 0.274791412213564 | erot = 0.357072039930916 | epot = -15.2742966977653 | etot = -14.6424332456208 -924000 ekin = 0.278059017514789 | erot = 0.385714059426418 | epot = -15.306206322525 | etot = -14.6424332455838 -925000 ekin = 0.277537405165931 | erot = 0.413247220089643 | epot = -15.333217870786 | etot = -14.6424332455304 -926000 ekin = 0.273733135235124 | erot = 0.439931173656047 | epot = -15.3560975543575 | etot = -14.6424332454664 -927000 ekin = 0.267211859637652 | erot = 0.466155363877246 | epot = -15.3758004689123 | etot = -14.6424332453974 -928000 ekin = 0.258555847531632 | erot = 0.492389553497958 | epot = -15.3933786463587 | etot = -14.6424332453291 -929000 ekin = 0.248330567886967 | erot = 0.519126582977394 | epot = -15.4098903961312 | etot = -14.6424332452668 -930000 ekin = 0.23705974716086 | erot = 0.546821711627624 | epot = -15.4263147040038 | etot = -14.6424332452153 -931000 ekin = 0.225208144800234 | erot = 0.575833282919438 | epot = -15.4434746728981 | etot = -14.6424332451784 -932000 ekin = 0.213171319360063 | erot = 0.606369490847652 | epot = -15.4619740553666 | etot = -14.6424332451589 -933000 ekin = 0.201271722990057 | erot = 0.638445690374705 | epot = -15.4821506585231 | etot = -14.6424332451583 -934000 ekin = 0.189760460104366 | erot = 0.67185600669489 | epot = -15.5040497119762 | etot = -14.6424332451769 -935000 ekin = 0.178823941832753 | erot = 0.706161996583042 | epot = -15.5274191836291 | etot = -14.6424332452133 -936000 ekin = 0.168594479109611 | erot = 0.74069986583281 | epot = -15.5517275902074 | etot = -14.642433245265 -937000 ekin = 0.159163635629916 | erot = 0.774606336201627 | epot = -15.5762032171597 | etot = -14.6424332453281 -938000 ekin = 0.150596971910416 | erot = 0.806861786791798 | epot = -15.5998920041003 | etot = -14.6424332453981 -939000 ekin = 0.142948711628538 | erot = 0.83634788352242 | epot = -15.6217298406206 | etot = -14.6424332454696 -940000 ekin = 0.136274889167971 | erot = 0.861915676024924 | epot = -15.6406238107303 | etot = -14.6424332455374 -941000 ekin = 0.130643703196498 | erot = 0.882459199117052 | epot = -15.6555361479098 | etot = -14.6424332455962 -942000 ekin = 0.126142088159105 | erot = 0.896989065169274 | epot = -15.66556439897 | etot = -14.6424332456417 -943000 ekin = 0.122877886109369 | erot = 0.904700444356692 | epot = -15.6700115761362 | etot = -14.6424332456702 -944000 ekin = 0.120977407412015 | erot = 0.905030230235472 | epot = -15.6684408833271 | etot = -14.6424332456797 -945000 ekin = 0.120578563691314 | erot = 0.897699054744981 | epot = -15.6607108641056 | etot = -14.6424332456693 -946000 ekin = 0.121820103594724 | erot = 0.882735070928503 | epot = -15.646988420163 | etot = -14.6424332456398 -947000 ekin = 0.124827761130805 | erot = 0.860477935596992 | epot = -15.6277389423211 | etot = -14.6424332455933 -948000 ekin = 0.129698334170726 | erot = 0.831563037038998 | epot = -15.6036946167428 | etot = -14.642433245533 -949000 ekin = 0.136482857560392 | erot = 0.796887554723542 | epot = -15.5758036577472 | etot = -14.6424332454633 -950000 ekin = 0.145170138933426 | erot = 0.757561255989732 | epot = -15.5451646403121 | etot = -14.642433245389 -951000 ekin = 0.155672002997215 | erot = 0.714845916095059 | epot = -15.5129511644075 | etot = -14.6424332453152 -952000 ekin = 0.167811650837965 | erot = 0.67008783325118 | epot = -15.480332729336 | etot = -14.6424332452469 -953000 ekin = 0.181316579472455 | erot = 0.624648095212333 | epot = -15.4483979198734 | etot = -14.6424332451886 -954000 ekin = 0.195817500701693 | erot = 0.579835080695355 | epot = -15.4180858265408 | etot = -14.6424332451437 -955000 ekin = 0.210854606876419 | erot = 0.536843219767442 | epot = -15.3901310717585 | etot = -14.6424332451147 -956000 ekin = 0.22589229983617 | erot = 0.496701376789191 | epot = -15.3650269217278 | etot = -14.6424332451025 -957000 ekin = 0.240343066496498 | erot = 0.460233438090612 | epot = -15.3430097496938 | etot = -14.6424332451067 -958000 ekin = 0.253600493836355 | erot = 0.428032849889929 | epot = -15.3240665888515 | etot = -14.6424332451252 -959000 ekin = 0.265080433744447 | erot = 0.400452005453988 | epot = -15.3079656843532 | etot = -14.6424332451548 -960000 ekin = 0.274268068126047 | erot = 0.37760654944402 | epot = -15.294307862761 | etot = -14.6424332451909 -961000 ekin = 0.280767177998564 | erot = 0.359393861243516 | epot = -15.2825942844706 | etot = -14.6424332452285 -962000 ekin = 0.284346484058158 | erot = 0.34552419881024 | epot = -15.2723039281308 | etot = -14.6424332452624 -963000 ekin = 0.284976816084592 | erot = 0.335562232322765 | epot = -15.2629722936953 | etot = -14.6424332452879 -964000 ekin = 0.282852494243092 | erot = 0.328975986490651 | epot = -15.2542617260353 | etot = -14.6424332453015 -965000 ekin = 0.278391086611333 | erot = 0.325189577593016 | epot = -15.2460139095058 | etot = -14.6424332453015 -966000 ekin = 0.272207924676324 | erot = 0.323635640145639 | epot = -15.2382768101098 | etot = -14.6424332452879 -967000 ekin = 0.265065367868708 | erot = 0.323803079983033 | epot = -15.2313016931144 | etot = -14.6424332452627 -968000 ekin = 0.257801293713459 | erot = 0.325275872287221 | epot = -15.2255104112304 | etot = -14.6424332452297 -969000 ekin = 0.251245661475255 | erot = 0.327759142573571 | epot = -15.2214380492424 | etot = -14.6424332451936 -970000 ekin = 0.246137008995617 | erot = 0.331089781179348 | epot = -15.2196600353345 | etot = -14.6424332451595 -971000 ekin = 0.243051319619918 | erot = 0.335230325664218 | epot = -15.220714890416 | etot = -14.6424332451318 -972000 ekin = 0.242353409643632 | erot = 0.340246678804405 | epot = -15.2250333335622 | etot = -14.6424332451142 -973000 ekin = 0.2441763381681 | erot = 0.346272190710886 | epot = -15.2328817739879 | etot = -14.642433245109 -974000 ekin = 0.248428661663904 | erot = 0.353462430362299 | epot = -15.2443243371435 | etot = -14.6424332451173 -975000 ekin = 0.254824314808745 | erot = 0.361946299431111 | epot = -15.2592038593792 | etot = -14.6424332451394 -976000 ekin = 0.26292684882563 | erot = 0.371779749930331 | epot = -15.2771398439303 | etot = -14.6424332451743 -977000 ekin = 0.27219923533505 | erot = 0.382908123264369 | epot = -15.29754060382 | etot = -14.6424332452206 -978000 ekin = 0.282052066854694 | erot = 0.395142048097406 | epot = -15.3196273602282 | etot = -14.6424332452761 -979000 ekin = 0.291885751915604 | erot = 0.408150081470976 | epot = -15.3424690787245 | etot = -14.6424332453379 -980000 ekin = 0.301125083790157 | erot = 0.421469125221772 | epot = -15.3650274544147 | etot = -14.6424332454028 -981000 ekin = 0.309246535916217 | erot = 0.434531423655031 | epot = -15.3862112050381 | etot = -14.6424332454669 -982000 ekin = 0.315799497488439 | erot = 0.446704965614828 | epot = -15.4049377086292 | etot = -14.642433245526 -983000 ekin = 0.320422573217629 | erot = 0.457342632741568 | epot = -15.4201984515353 | etot = -14.6424332455761 -984000 ekin = 0.322855465254252 | erot = 0.465834622596749 | epot = -15.4311233334646 | etot = -14.6424332456136 -985000 ekin = 0.322946302470394 | erot = 0.47165859097122 | epot = -15.4370381390773 | etot = -14.6424332456357 -986000 ekin = 0.320653917800696 | erot = 0.474422556587648 | epot = -15.437509720029 | etot = -14.6424332456406 -987000 ekin = 0.31604462735714 | erot = 0.473896755512796 | epot = -15.4323746284979 | etot = -14.642433245628 -988000 ekin = 0.309283477263999 | erot = 0.470032116942454 | epot = -15.4217488398048 | etot = -14.6424332455984 -989000 ekin = 0.300620522164939 | erot = 0.462964620619315 | epot = -15.406018388338 | etot = -14.6424332455537 -990000 ekin = 0.290373280687637 | erot = 0.453006262992374 | epot = -15.3858127891766 | etot = -14.6424332454965 -991000 ekin = 0.278906915702925 | erot = 0.440624526216757 | epot = -15.3619646873499 | etot = -14.6424332454302 -992000 ekin = 0.266613826413316 | erot = 0.42641300688875 | epot = -15.3354600786602 | etot = -14.6424332453582 -993000 ekin = 0.253894212445666 | erot = 0.411056197521998 | epot = -15.3073836552517 | etot = -14.6424332452841 -994000 ekin = 0.241138837000196 | erot = 0.395291372385701 | epot = -15.2788634545969 | etot = -14.642433245211 -995000 ekin = 0.228714768908018 | erot = 0.379870207852185 | epot = -15.2510182219023 | etot = -14.6424332451421 -996000 ekin = 0.216954417472331 | erot = 0.365522282703969 | epot = -15.2249099452561 | etot = -14.6424332450798 -997000 ekin = 0.206147766458768 | erot = 0.352922066134627 | epot = -15.2015030776195 | etot = -14.6424332450261 -998000 ekin = 0.196537413161314 | erot = 0.34266049598664 | epot = -15.1816311541306 | etot = -14.6424332449827 -999000 ekin = 0.188315843917132 | erot = 0.335221830000276 | epot = -15.1659709188677 | etot = -14.6424332449503 -1000000 ekin = 0.181624323072266 | erot = 0.330966139643081 | epot = -15.1550237076453 | etot = -14.6424332449299 - 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 -Loop time of 18.9591 on 1 procs for 1000000 steps with 10 atoms - -Performance: 45571.887 tau/day, 52745.239 timesteps/s -98.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 15.272 | 15.272 | 15.272 | 0.0 | 80.55 -Bond | 0.58511 | 0.58511 | 0.58511 | 0.0 | 3.09 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.19027 | 0.19027 | 0.19027 | 0.0 | 1.00 -Output | 8e-06 | 8e-06 | 8e-06 | 0.0 | 0.00 -Modify | 2.6225 | 2.6225 | 2.6225 | 0.0 | 13.83 -Other | | 0.2893 | | | 1.53 - -Nlocal: 10 ave 10 max 10 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 43 ave 43 max 43 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 43 -Ave neighs/atom = 4.3 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:18 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 deleted file mode 100644 index 59800043d3a50b4646114e0b61ceb997f8ffde90..0000000000000000000000000000000000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4 +++ /dev/null @@ -1,1165 +0,0 @@ -LAMMPS (18 Jun 2019) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - special bonds CPU = 0.000462 secs - read_data CPU = 0.004857 secs - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 2.5836586e-06 -1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450840756 | erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.017388811129498 | erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136422 | erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948555727 | erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.0483950557190949 | erot = 0.18508629569211 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336919856 | erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406439518 | erot = 0.288273694501614 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563084574 | erot = 0.343654369293588 | epot = -15.0710491710418 | etot = -14.6424332454398 -11000 ekin = 0.0965486715044103 | erot = 0.400187932108392 | epot = -15.1391698491357 | etot = -14.6424332455229 -12000 ekin = 0.107221466282716 | erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598 -13000 ekin = 0.116672809719361 | erot = 0.512877765427946 | epot = -15.27198382081 | etot = -14.6424332456627 -14000 ekin = 0.124654073730849 | erot = 0.567333962045503 | epot = -15.3344212814915 | etot = -14.6424332457151 -15000 ekin = 0.130983939684084 | erot = 0.619586028257146 | epot = -15.3930032136957 | etot = -14.6424332457544 -16000 ekin = 0.135553354544703 | erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804 -17000 ekin = 0.138326263958104 | erot = 0.715418858086103 | epot = -15.4961783678378 | etot = -14.6424332457936 -18000 ekin = 0.139336096663942 | erot = 0.758296324628468 | epot = -15.5400656670878 | etot = -14.6424332457954 -19000 ekin = 0.138678360045107 | erot = 0.797544234276629 | epot = -15.5786558401095 | etot = -14.6424332457878 -20000 ekin = 0.136500074655344 | erot = 0.83308420441182 | epot = -15.6120175248401 | etot = -14.642433245773 -21000 ekin = 0.13298706528568 | erot = 0.864912408453368 | epot = -15.6403327194924 | etot = -14.6424332457533 -22000 ekin = 0.128350288213599 | erot = 0.893077649558725 | epot = -15.6638611835035 | etot = -14.6424332457311 -23000 ekin = 0.122812385135574 | erot = 0.917661024684598 | epot = -15.6829066555285 | etot = -14.6424332457083 -24000 ekin = 0.116595521408358 | erot = 0.938759014332585 | epot = -15.6977877814273 | etot = -14.6424332456863 -25000 ekin = 0.109911323474882 | erot = 0.95647120734756 | epot = -15.7088157764886 | etot = -14.6424332456662 -26000 ekin = 0.102953426207684 | erot = 0.970893163953299 | epot = -15.7162798358093 | etot = -14.6424332456483 -27000 ekin = 0.0958928250746602 | erot = 0.982114250193902 | epot = -15.7204403209011 | etot = -14.6424332456326 -28000 ekin = 0.08887594109497 | erot = 0.990219731539409 | epot = -15.721528918253 | etot = -14.6424332456186 -29000 ekin = 0.0820250748771992 | erot = 0.995296041202176 | epot = -15.7197543616852 | etot = -14.6424332456058 -30000 ekin = 0.0754407616837525 | erot = 0.997437949319921 | epot = -15.7153119565969 | etot = -14.6424332455933 -31000 ekin = 0.0692054432607511 | erot = 0.996756332760935 | epot = -15.708395021602 | etot = -14.6424332455803 -32000 ekin = 0.0633878377974532 | erot = 0.993385345347625 | epot = -15.6992064287111 | etot = -14.6424332455661 -33000 ekin = 0.0580474070866977 | erot = 0.987487973308193 | epot = -15.6879686259451 | etot = -14.6424332455502 -34000 ekin = 0.0532383791882916 | erot = 0.979259192919847 | epot = -15.6749308176403 | etot = -14.6424332455322 -35000 ekin = 0.0490128758302373 | erot = 0.96892619740531 | epot = -15.6603723187477 | etot = -14.6424332455122 -36000 ekin = 0.0454228081405034 | erot = 0.956745409624112 | epot = -15.6446014632554 | etot = -14.6424332454908 -37000 ekin = 0.0425203357170931 | erot = 0.942996237999014 | epot = -15.6279498191848 | etot = -14.6424332454687 -38000 ekin = 0.0403568280944582 | erot = 0.927971766615185 | epot = -15.6107618401563 | etot = -14.6424332454467 -39000 ekin = 0.0389804214208553 | erot = 0.911966804108842 | epot = -15.5933804709559 | etot = -14.6424332454262 -40000 ekin = 0.0384324238853386 | erot = 0.89526395956212 | epot = -15.5761296288558 | etot = -14.6424332454083 -41000 ekin = 0.0387429860406854 | erot = 0.878118672837898 | epot = -15.559294904273 | etot = -14.6424332453944 -42000 ekin = 0.0399266053637397 | erot = 0.860744395135588 | epot = -15.543104245885 | etot = -14.6424332453857 -43000 ekin = 0.041978156101278 | erot = 0.84329936535652 | epot = -15.5277107668409 | etot = -14.6424332453831 -44000 ekin = 0.044870189409001 | erot = 0.825876603313516 | epot = -15.5131800381094 | etot = -14.6424332453868 -45000 ekin = 0.0485521857416513 | erot = 0.808498758186241 | epot = -15.4994841893249 | etot = -14.642433245397 -46000 ekin = 0.0529522094038552 | erot = 0.791119212188506 | epot = -15.486504667005 | etot = -14.6424332454127 -47000 ekin = 0.0579809824244721 | erot = 0.773630265884098 | epot = -15.4740444937409 | etot = -14.6424332454323 -48000 ekin = 0.0635377846502182 | erot = 0.755878310838203 | epot = -15.4618493409424 | etot = -14.6424332454539 -49000 ekin = 0.0695169124467202 | erot = 0.737684732484798 | epot = -15.4496348904071 | etot = -14.6424332454756 -50000 ekin = 0.0758129058465097 | erot = 0.718870126220151 | epot = -15.437116277562 | etot = -14.6424332454953 -51000 ekin = 0.0823226638652294 | erot = 0.699278599520714 | epot = -15.424034508898 | etot = -14.642433245512 -52000 ekin = 0.0889431481344998 | erot = 0.67879880710002 | epot = -15.4101752007595 | etot = -14.642433245525 -53000 ekin = 0.0955646689265025 | erot = 0.657379086771117 | epot = -15.3953770012321 | etot = -14.6424332455345 -54000 ekin = 0.10206147751016 | erot = 0.635035489169276 | epot = -15.3795302122208 | etot = -14.6424332455414 -55000 ekin = 0.108282960174665 | erot = 0.611853171347244 | epot = -15.362569377068 | etot = -14.6424332455461 -56000 ekin = 0.114049426282277 | erot = 0.587982945924297 | epot = -15.3444656177552 | etot = -14.6424332455486 -57000 ekin = 0.119155806187163 | erot = 0.563635255922951 | epot = -15.3252243076589 | etot = -14.6424332455488 -58000 ekin = 0.123384552305545 | erot = 0.539073355222428 | epot = -15.3048911530734 | etot = -14.6424332455454 -59000 ekin = 0.126526300954853 | erot = 0.514606324858911 | epot = -15.2835658713509 | etot = -14.6424332455371 -60000 ekin = 0.128404399836229 | erot = 0.490581338840044 | epot = -15.261418984199 | etot = -14.6424332455227 -61000 ekin = 0.128898142361897 | erot = 0.467373892400972 | epot = -15.2387052802646 | etot = -14.6424332455018 -62000 ekin = 0.127959880289726 | erot = 0.445374820086222 | epot = -15.2157679458511 | etot = -14.6424332454752 -63000 ekin = 0.125622870624277 | erot = 0.424973765387148 | epot = -15.1930298814554 | etot = -14.642433245444 -64000 ekin = 0.121999044842466 | erot = 0.406539918572074 | epot = -15.1709722088251 | etot = -14.6424332454105 -65000 ekin = 0.117268056618551 | erot = 0.390401831020312 | epot = -15.1501031330161 | etot = -14.6424332453772 -66000 ekin = 0.11166038525652 | erot = 0.376828594078856 | epot = -15.1309222246818 | etot = -14.6424332453464 -67000 ekin = 0.105437746904482 | erot = 0.366014539811009 | epot = -15.1138855320359 | etot = -14.6424332453204 -68000 ekin = 0.0988737375602389 | erot = 0.358069014155077 | epot = -15.0993759970158 | etot = -14.6424332453005 -69000 ekin = 0.0922368286498126 | erot = 0.353011948771943 | epot = -15.0876820227093 | etot = -14.6424332452876 -70000 ekin = 0.0857769015271899 | erot = 0.350775174164931 | epot = -15.078985320974 | etot = -14.6424332452819 -71000 ekin = 0.0797156921641249 | erot = 0.351208844245481 | epot = -15.0733577816927 | etot = -14.6424332452831 -72000 ekin = 0.0742409440407228 | erot = 0.354092037747166 | epot = -15.0707662270784 | etot = -14.6424332452906 -73000 ekin = 0.069503749870388 | erot = 0.359146526961232 | epot = -15.0710835221349 | etot = -14.6424332453033 -74000 ekin = 0.065618449742691 | erot = 0.366052769878692 | epot = -15.0741044649412 | etot = -14.6424332453199 -75000 ekin = 0.0626644690394284 | erot = 0.374467290033975 | epot = -15.0795650044124 | etot = -14.642433245339 -76000 ekin = 0.0606895535091863 | erot = 0.384040683403432 | epot = -15.087163482272 | etot = -14.6424332453594 -77000 ekin = 0.0597139401241188 | erot = 0.394435495892894 | epot = -15.0965826813962 | etot = -14.6424332453792 -78000 ekin = 0.0597350629875199 | erot = 0.405343151481916 | epot = -15.107511459867 | etot = -14.6424332453975 -79000 ekin = 0.0607324264361021 | erot = 0.4164990176427 | epot = -15.1196646894919 | etot = -14.6424332454131 -80000 ekin = 0.0626722904954161 | erot = 0.427694630238743 | epot = -15.1328001661592 | etot = -14.6424332454251 -81000 ekin = 0.0655118235331528 | erot = 0.438786127849131 | epot = -15.1467311968152 | etot = -14.6424332454329 -82000 ekin = 0.0692024020836604 | erot = 0.449698113830624 | epot = -15.1613337613509 | etot = -14.6424332454366 -83000 ekin = 0.0736917936904884 | erot = 0.460422490740831 | epot = -15.1765475298676 | etot = -14.6424332454363 -84000 ekin = 0.0789250526542207 | erot = 0.471012272295187 | epot = -15.1923705703823 | etot = -14.6424332454329 -85000 ekin = 0.0848440878742484 | erot = 0.481570908650517 | epot = -15.2088482419521 | etot = -14.6424332454273 -86000 ekin = 0.0913860133243867 | erot = 0.492238169206351 | epot = -15.2260574279515 | etot = -14.6424332454207 -87000 ekin = 0.0984805441186007 | erot = 0.503174014617495 | epot = -15.2440878041506 | etot = -14.6424332454146 -88000 ekin = 0.106046830302566 | erot = 0.514542076496893 | epot = -15.2630221522094 | etot = -14.6424332454099 -89000 ekin = 0.113990204125935 | erot = 0.526494309539958 | epot = -15.2829177590739 | etot = -14.642433245408 -90000 ekin = 0.122199339149549 | erot = 0.539158097286396 | epot = -15.3037906818453 | etot = -14.6424332454094 -91000 ekin = 0.130544275968789 | erot = 0.552626637866402 | epot = -15.3256041592497 | etot = -14.6424332454146 -92000 ekin = 0.138875666145969 | erot = 0.566952900962838 | epot = -15.3482618125326 | etot = -14.6424332454238 -93000 ekin = 0.14702544061161 | erot = 0.582146933738122 | epot = -15.3716056197866 | etot = -14.6424332454369 -94000 ekin = 0.154808946844654 | erot = 0.598175891801918 | epot = -15.3954180841001 | etot = -14.6424332454535 -95000 ekin = 0.162028449598908 | erot = 0.614965942454569 | epot = -15.4194276375267 | etot = -14.6424332454732 -96000 ekin = 0.168477779664562 | erot = 0.632405154082769 | epot = -15.4433161792427 | etot = -14.6424332454953 -97000 ekin = 0.173947863023519 | erot = 0.650346631629065 | epot = -15.466727740172 | etot = -14.6424332455194 -98000 ekin = 0.178232875001165 | erot = 0.668611435746703 | epot = -15.4892775562927 | etot = -14.6424332455449 -99000 ekin = 0.181136831923469 | erot = 0.686991165056991 | epot = -15.5105612425515 | etot = -14.6424332455711 -100000 ekin = 0.182480533640974 | erot = 0.705250413408614 | epot = -15.530164192647 | etot = -14.6424332455974 -101000 ekin = 0.182108871449632 | erot = 0.723129571004103 | epot = -15.5476716880769 | etot = -14.6424332456232 -102000 ekin = 0.179898581168339 | erot = 0.740348571091352 | epot = -15.5626803979071 | etot = -14.6424332456474 -103000 ekin = 0.17576651760657 | erot = 0.756612167827034 | epot = -15.5748119311029 | etot = -14.6424332456693 -104000 ekin = 0.169678431534372 | erot = 0.771617166852996 | epot = -15.5837288440748 | etot = -14.6424332456874 -105000 ekin = 0.161658036036246 | erot = 0.785061742963598 | epot = -15.5891530247003 | etot = -14.6424332457005 -106000 ekin = 0.151795867650305 | erot = 0.796656613426427 | epot = -15.5908857267839 | etot = -14.6424332457071 -107000 ekin = 0.140257112952978 | erot = 0.806137449199291 | epot = -15.5888278078584 | etot = -14.6424332457061 -108000 ekin = 0.127287240201874 | erot = 0.813277564483374 | epot = -15.5829980503819 | etot = -14.6424332456966 -109000 ekin = 0.113214025491877 | erot = 0.817899691736857 | epot = -15.5735469629067 | etot = -14.642433245678 -110000 ekin = 0.0984444823817425 | erot = 0.819885578056442 | epot = -15.5607633060887 | etot = -14.6424332456505 -111000 ekin = 0.0834553769378644 | erot = 0.819182262548316 | epot = -15.5450708851012 | etot = -14.6424332456151 -112000 ekin = 0.0687764915886182 | erot = 0.815804215096852 | epot = -15.5270139522588 | etot = -14.6424332455734 -113000 ekin = 0.0549665904044371 | erot = 0.809830999846678 | epot = -15.507230835779 | etot = -14.6424332455279 -114000 ekin = 0.04258305831357 | erot = 0.801400700352889 | epot = -15.486417004148 | etot = -14.6424332454815 -115000 ekin = 0.0321472802146729 | erot = 0.790699910050576 | epot = -15.4652804357026 | etot = -14.6424332454374 -116000 ekin = 0.0241087780358441 | erot = 0.77795154667576 | epot = -15.4444935701102 | etot = -14.6424332453986 -117000 ekin = 0.0188117102739907 | erot = 0.763402004774545 | epot = -15.4246469604164 | etot = -14.6424332453678 -118000 ekin = 0.0164673894168237 | erot = 0.747309167856841 | epot = -15.4062098026205 | etot = -14.6424332453468 -119000 ekin = 0.0171359296540399 | erot = 0.72993256457469 | epot = -15.3895017395652 | etot = -14.6424332453364 -120000 ekin = 0.0207190822436548 | erot = 0.711526526248979 | epot = -15.3746788538292 | etot = -14.6424332453366 -121000 ekin = 0.0269649552324778 | erot = 0.692336677371657 | epot = -15.3617348779503 | etot = -14.6424332453462 -122000 ekin = 0.0354839220302051 | erot = 0.672599570211917 | epot = -15.3505167376055 | etot = -14.6424332453634 -123000 ekin = 0.0457738626455503 | erot = 0.652544850162978 | epot = -15.3407519581944 | etot = -14.6424332453859 -124000 ekin = 0.0572521324300892 | erot = 0.632399068063538 | epot = -15.3320844459047 | etot = -14.6424332454111 -125000 ekin = 0.0692913736007693 | erot = 0.612390156183436 | epot = -15.3241147752204 | etot = -14.6424332454362 -126000 ekin = 0.0812564128179015 | erot = 0.592751635107163 | epot = -15.3164412933838 | etot = -14.6424332454587 -127000 ekin = 0.0925398817831139 | erot = 0.573725774405781 | epot = -15.3086989016655 | etot = -14.6424332454766 -128000 ekin = 0.102594692019405 | erot = 0.555565138942023 | epot = -15.3005930764495 | etot = -14.6424332454881 -129000 ekin = 0.110961953874467 | erot = 0.538532171476875 | epot = -15.2919273708433 | etot = -14.6424332454919 -130000 ekin = 0.117293279473242 | erot = 0.52289666445288 | epot = -15.2826231894136 | etot = -14.6424332454874 -131000 ekin = 0.121366644775211 | erot = 0.508931150171171 | epot = -15.272731040421 | etot = -14.6424332454746 -132000 ekin = 0.123095155540088 | erot = 0.496904390905875 | epot = -15.2624327918998 | etot = -14.6424332454539 -133000 ekin = 0.122528239671731 | erot = 0.487073282997897 | epot = -15.2520347680959 | etot = -14.6424332454262 -134000 ekin = 0.119845042601891 | erot = 0.47967360117123 | epot = -15.2419518891664 | etot = -14.6424332453933 -135000 ekin = 0.115340171967418 | erot = 0.474910093717058 | epot = -15.2326835110415 | etot = -14.642433245357 -136000 ekin = 0.109402419285639 | erot = 0.472946484075354 | epot = -15.2247821486809 | etot = -14.6424332453199 -137000 ekin = 0.102487634022662 | erot = 0.473895929920083 | epot = -15.218816809227 | etot = -14.6424332452843 -138000 ekin = 0.0950874634054098 | erot = 0.477812435585943 | epot = -15.2153331442442 | etot = -14.6424332452528 -139000 ekin = 0.0876961121518108 | erot = 0.484683617751208 | epot = -15.2148129751311 | etot = -14.6424332452281 -140000 ekin = 0.0807775418435451 | erot = 0.494425108540545 | epot = -15.217635895596 | etot = -14.6424332452119 -141000 ekin = 0.0747355681580393 | erot = 0.506876770810791 | epot = -15.2240455841751 | etot = -14.6424332452063 -142000 ekin = 0.0698891098451726 | erot = 0.521800821241339 | epot = -15.2341231762987 | etot = -14.6424332452121 -143000 ekin = 0.0664544171867034 | erot = 0.538881922426252 | epot = -15.247769584843 | etot = -14.64243324523 -144000 ekin = 0.064535510469277 | erot = 0.557729316021967 | epot = -15.2646980717509 | etot = -14.6424332452596 -145000 ekin = 0.0641233595163659 | erot = 0.577881111413926 | epot = -15.2844377162305 | etot = -14.6424332453002 -146000 ekin = 0.065103607751629 | erot = 0.598810893852487 | epot = -15.3063477469542 | etot = -14.6424332453501 -147000 ekin = 0.0672719578975296 | erot = 0.619936843682188 | epot = -15.3296420469869 | etot = -14.6424332454072 -148000 ekin = 0.0703557492694474 | erot = 0.64063353819095 | epot = -15.3534225329292 | etot = -14.6424332454688 -149000 ekin = 0.0740398128645644 | erot = 0.660246523237392 | epot = -15.3767195816342 | etot = -14.6424332455323 -150000 ekin = 0.0779944201062649 | erot = 0.67810959037558 | epot = -15.3985372560763 | etot = -14.6424332455945 -151000 ekin = 0.0819030604176924 | erot = 0.693564488647308 | epot = -15.4179007947176 | etot = -14.6424332456526 -152000 ekin = 0.0854878938557652 | erot = 0.705982563002958 | epot = -15.4339037025624 | etot = -14.6424332457037 -153000 ekin = 0.0885310147333713 | erot = 0.714787575381071 | epot = -15.4457518358598 | etot = -14.6424332457454 -154000 ekin = 0.0908901012892559 | erot = 0.719478762726488 | epot = -15.4528021097913 | etot = -14.6424332457756 -155000 ekin = 0.0925075703719017 | erot = 0.719653046096719 | epot = -15.4545938622615 | etot = -14.6424332457929 -156000 ekin = 0.0934129479732407 | erot = 0.715025243753081 | epot = -15.4508714375228 | etot = -14.6424332457965 -157000 ekin = 0.0937187435781918 | erot = 0.70544516394557 | epot = -15.4415971533099 | etot = -14.6424332457861 -158000 ekin = 0.093610618539412 | erot = 0.690910554325135 | epot = -15.4269544186267 | etot = -14.6424332457622 -159000 ekin = 0.093333017400989 | erot = 0.671575051659432 | epot = -15.4073413147861 | etot = -14.6424332457257 -160000 ekin = 0.0931716565239226 | erot = 0.647750492120542 | epot = -15.3833553943224 | etot = -14.642433245678 -161000 ekin = 0.0934343296226242 | erot = 0.619903194016743 | epot = -15.3557707692603 | etot = -14.6424332456209 -162000 ekin = 0.0944314104796886 | erot = 0.588644098980031 | epot = -15.3255087550164 | etot = -14.6424332455567 -163000 ekin = 0.0964572425730171 | erot = 0.554712943454593 | epot = -15.2936034315153 | etot = -14.6424332454877 -164000 ekin = 0.0997733472794941 | erot = 0.518956918562839 | epot = -15.2611635112587 | etot = -14.6424332454164 -165000 ekin = 0.10459410201863 | erot = 0.482304549423526 | epot = -15.2293318967876 | etot = -14.6424332453454 -166000 ekin = 0.111075276514836 | erot = 0.445735768513645 | epot = -15.1992442903058 | etot = -14.6424332452774 -167000 ekin = 0.119305597512064 | erot = 0.410249354729672 | epot = -15.1719881974565 | etot = -14.6424332452148 -168000 ekin = 0.129301354723501 | erot = 0.376829046180125 | epot = -15.1485636460635 | etot = -14.6424332451599 -169000 ekin = 0.141003965788129 | erot = 0.346409702528434 | epot = -15.1298469134313 | etot = -14.6424332451147 -170000 ekin = 0.154280377438315 | erot = 0.319844892419163 | epot = -15.1165585149384 | etot = -14.642433245081 -171000 ekin = 0.168926178619937 | erot = 0.297877221607912 | epot = -15.1092366452878 | etot = -14.64243324506 -172000 ekin = 0.184671319362945 | erot = 0.281112611137957 | epot = -15.1082171755535 | etot = -14.6424332450526 -173000 ekin = 0.201188345435608 | erot = 0.269999595570643 | epot = -15.1136211860654 | etot = -14.6424332450591 -174000 ekin = 0.218103052205593 | erot = 0.264814547402958 | epot = -15.1253508446879 | etot = -14.6424332450793 -175000 ekin = 0.235007413034248 | erot = 0.26565354594967 | epot = -15.1430942040961 | etot = -14.6424332451122 -176000 ekin = 0.251474534266605 | erot = 0.272431389431399 | epot = -15.1663391688545 | etot = -14.6424332451565 -177000 ekin = 0.267075225142185 | erot = 0.284887984977542 | epot = -15.1943964553297 | etot = -14.64243324521 -178000 ekin = 0.281395553894086 | erot = 0.302602030913814 | epot = -15.2264308300784 | etot = -14.6424332452705 -179000 ekin = 0.294054514410706 | erot = 0.325011526056047 | epot = -15.2614992858018 | etot = -14.642433245335 -180000 ekin = 0.304720692895809 | erot = 0.351440214933843 | epot = -15.2985941532305 | etot = -14.6424332454008 -181000 ekin = 0.31312665891731 | erot = 0.381128639600658 | epot = -15.3366885439828 | etot = -14.6424332454648 -182000 ekin = 0.319079775822511 | erot = 0.413268071112237 | epot = -15.3747810924591 | etot = -14.6424332455244 -183000 ekin = 0.322468290004652 | erot = 0.447035301735071 | epot = -15.4119368373172 | etot = -14.6424332455774 -184000 ekin = 0.323261947553553 | erot = 0.481626155079182 | epot = -15.447321348255 | etot = -14.6424332456223 -185000 ekin = 0.321506983529694 | erot = 0.516285658867092 | epot = -15.4802258880547 | etot = -14.6424332456579 -186000 ekin = 0.317316057632528 | erot = 0.55033313262905 | epot = -15.5100824359457 | etot = -14.6424332456841 -187000 ekin = 0.310854440588901 | erot = 0.583180936762646 | epot = -15.5364686230527 | etot = -14.6424332457011 -188000 ekin = 0.302324329762727 | erot = 0.614346238386904 | epot = -15.5591038138593 | etot = -14.6424332457097 -189000 ekin = 0.291949445195851 | erot = 0.643455779015123 | epot = -15.5778384699218 | etot = -14.6424332457108 -190000 ekin = 0.279961942766932 | erot = 0.670244185707557 | epot = -15.5926393741802 | etot = -14.6424332457057 -191000 ekin = 0.266593185652274 | erot = 0.694546781237238 | epot = -15.6035732125847 | etot = -14.6424332456952 -192000 ekin = 0.252069141621898 | erot = 0.716288088791539 | epot = -15.6107904760939 | etot = -14.6424332456804 -193000 ekin = 0.236610293252604 | erot = 0.735467302247627 | epot = -15.6145108411624 | etot = -14.6424332456621 -194000 ekin = 0.220435149403497 | erot = 0.752141943032621 | epot = -15.615010338077 | etot = -14.6424332456409 -195000 ekin = 0.203765880091669 | erot = 0.766410799035668 | epot = -15.6126099247448 | etot = -14.6424332456175 -196000 ekin = 0.18683433903566 | erot = 0.778397083256566 | epot = -15.6076646678848 | etot = -14.6424332455926 -197000 ekin = 0.169886782292475 | erot = 0.788232586076231 | epot = -15.6005526139356 | etot = -14.6424332455669 -198000 ekin = 0.153185871076313 | erot = 0.796043434544288 | epot = -15.5916625511618 | etot = -14.6424332455412 -199000 ekin = 0.137008972985806 | erot = 0.801937915803797 | epot = -15.5813801343063 | etot = -14.6424332455167 -200000 ekin = 0.121642272363325 | erot = 0.805996673265862 | epot = -15.5700721911235 | etot = -14.6424332454943 -201000 ekin = 0.107370722655158 | erot = 0.80826545681021 | epot = -15.5580694249408 | etot = -14.6424332454755 -202000 ekin = 0.0944644042380686 | erot = 0.808750524312687 | epot = -15.5456481740119 | etot = -14.6424332454612 -203000 ekin = 0.0831623790884404 | erot = 0.807416772445398 | epot = -15.5330123969864 | etot = -14.6424332454526 -204000 ekin = 0.0736556272327849 | erot = 0.80418872542083 | epot = -15.5202775981042 | etot = -14.6424332454506 -205000 ekin = 0.066071040166992 | erot = 0.798954607356127 | epot = -15.5074588929787 | etot = -14.6424332454556 -206000 ekin = 0.0604586317676969 | erot = 0.791573809423779 | epot = -15.4944656866589 | etot = -14.6424332454674 -207000 ekin = 0.0567840026879154 | erot = 0.781888054797448 | epot = -15.4811053029705 | etot = -14.6424332454851 -208000 ekin = 0.0549275971597956 | erot = 0.769736381378278 | epot = -15.4670972240452 | etot = -14.6424332455071 -209000 ekin = 0.0546914447534107 | erot = 0.754973659532307 | epot = -15.4520983498168 | etot = -14.642433245531 -210000 ekin = 0.0558130126770382 | erot = 0.737491764373139 | epot = -15.4357380226042 | etot = -14.642433245554 -211000 ekin = 0.0579847210232175 | erot = 0.717241838878594 | epot = -15.4176598054751 | etot = -14.6424332455733 -212000 ekin = 0.0608768356197291 | erot = 0.694255492638144 | epot = -15.3975655738438 | etot = -14.642433245586 -213000 ekin = 0.0641610427072956 | erot = 0.668662476162839 | epot = -15.37525676446 | etot = -14.6424332455898 -214000 ekin = 0.06753210435751 | erot = 0.640702495518234 | epot = -15.3506678454592 | etot = -14.6424332455835 -215000 ekin = 0.0707255336353407 | erot = 0.610729417269012 | epot = -15.3238881964708 | etot = -14.6424332455665 -216000 ekin = 0.0735300437817614 | erot = 0.579207054839078 | epot = -15.2951703441601 | etot = -14.6424332455392 -217000 ekin = 0.0757943994877656 | erot = 0.546696813211925 | epot = -15.2649244582025 | etot = -14.6424332455028 -218000 ekin = 0.0774290394165114 | erot = 0.51383845121948 | epot = -15.2337007360952 | etot = -14.6424332454592 -219000 ekin = 0.0784033323141814 | erot = 0.481325894964792 | epot = -15.2021624726897 | etot = -14.6424332454107 -220000 ekin = 0.0787395495608023 | erot = 0.449880299622429 | epot = -15.1710530945426 | etot = -14.6424332453594 -221000 ekin = 0.0785046319672615 | erot = 0.420222425160601 | epot = -15.1411603024356 | etot = -14.6424332453078 -222000 ekin = 0.0778006814269721 | erot = 0.39304597217159 | epot = -15.1132798988567 | etot = -14.6424332452581 -223000 ekin = 0.0767549035385447 | erot = 0.368992968911897 | epot = -15.0881811176628 | etot = -14.6424332452123 -224000 ekin = 0.0755095293703893 | erot = 0.348631757033145 | epot = -15.0665745315757 | etot = -14.6424332451722 -225000 ekin = 0.0742120885667742 | erot = 0.332437700429458 | epot = -15.0490830341357 | etot = -14.6424332451395 -226000 ekin = 0.073006302869323 | erot = 0.320776497502283 | epot = -15.0362160454868 | etot = -14.6424332451152 -227000 ekin = 0.0720238140882433 | erot = 0.313889923629061 | epot = -15.0283469828184 | etot = -14.6424332451011 -228000 ekin = 0.0713769419939847 | erot = 0.311883945247506 | epot = -15.0256941323392 | etot = -14.6424332450977 -229000 ekin = 0.0711526728858743 | erot = 0.314719386439641 | epot = -15.0283053044313 | etot = -14.6424332451058 -230000 ekin = 0.0714080974066408 | erot = 0.322205638589943 | epot = -15.0360469811226 | etot = -14.642433245126 -231000 ekin = 0.0721675361190023 | erot = 0.333998222201819 | epot = -15.0485990034788 | etot = -14.642433245158 -232000 ekin = 0.0734216022905603 | erot = 0.349601270465958 | epot = -15.0654561179576 | etot = -14.6424332452011 -233000 ekin = 0.0751284397505271 | erot = 0.368376135875951 | epot = -15.085937820881 | etot = -14.6424332452545 -234000 ekin = 0.0772173235442621 | erot = 0.389557254433776 | epot = -15.1092078232944 | etot = -14.6424332453164 -235000 ekin = 0.0795947059802265 | erot = 0.412276079790441 | epot = -15.1343040311543 | etot = -14.6424332453836 -236000 ekin = 0.0821526186146775 | erot = 0.43559329564772 | epot = -15.160179159716 | etot = -14.6424332454536 -237000 ekin = 0.0847791014240061 | erot = 0.458538653864716 | epot = -15.1857510008108 | etot = -14.6424332455221 -238000 ekin = 0.0873700423858637 | erot = 0.480156759886701 | epot = -15.2099600478579 | etot = -14.6424332455853 -239000 ekin = 0.0898415153137649 | erot = 0.499556095552604 | epot = -15.2318308565057 | etot = -14.6424332456393 -240000 ekin = 0.0921414623535621 | erot = 0.515957735401017 | epot = -15.2505324434351 | etot = -14.6424332456806 -241000 ekin = 0.0942594490144011 | erot = 0.528739776886579 | epot = -15.2654324716071 | etot = -14.6424332457061 -242000 ekin = 0.0962332805881029 | erot = 0.537473606136305 | epot = -15.2761401324386 | etot = -14.6424332457142 -243000 ekin = 0.0981515319338902 | erot = 0.541948785980292 | epot = -15.2825335636184 | etot = -14.6424332457042 -244000 ekin = 0.100151482351193 | erot = 0.542184479374338 | epot = -15.2847692074024 | etot = -14.6424332456769 -245000 ekin = 0.102412491095761 | erot = 0.538426702317763 | epot = -15.2832724390477 | etot = -14.6424332456342 -246000 ekin = 0.105145395544795 | erot = 0.531132085866374 | epot = -15.2787107269897 | etot = -14.6424332455785 -247000 ekin = 0.108578961411983 | erot = 0.520939994206881 | epot = -15.2719522011324 | etot = -14.6424332455135 -248000 ekin = 0.112944688754523 | erot = 0.508635652295277 | epot = -15.2640135864926 | etot = -14.6424332454428 -249000 ekin = 0.11846134890514 | erot = 0.495107336753422 | epot = -15.2560019310289 | etot = -14.6424332453704 -250000 ekin = 0.125320510713214 | erot = 0.48130071319683 | epot = -15.2490544692099 | etot = -14.6424332452999 -251000 ekin = 0.133674056955099 | erot = 0.468173145423569 | epot = -15.2442804476134 | etot = -14.6424332452347 -252000 ekin = 0.143624355872782 | erot = 0.456650355973676 | epot = -15.2427079570244 | etot = -14.6424332451779 -253000 ekin = 0.155217400154351 | erot = 0.447587277165331 | epot = -15.2452379224514 | etot = -14.6424332451318 -254000 ekin = 0.168438906844348 | erot = 0.441734376017242 | epot = -15.2526065279594 | etot = -14.6424332450978 -255000 ekin = 0.183213121644194 | erot = 0.43971022735347 | epot = -15.2653565940749 | etot = -14.6424332450772 -256000 ekin = 0.199403908832166 | erot = 0.441980689733479 | epot = -15.2838178436365 | etot = -14.6424332450708 -257000 ekin = 0.216817638461889 | erot = 0.448844730305189 | epot = -15.3080956138459 | etot = -14.6424332450788 -258000 ekin = 0.235207399035754 | erot = 0.460426746275392 | epot = -15.338067390412 | etot = -14.6424332451008 -259000 ekin = 0.254278151366129 | erot = 0.476675120648644 | epot = -15.373386517151 | etot = -14.6424332451362 -260000 ekin = 0.273692576676924 | erot = 0.49736669170667 | epot = -15.4134925135676 | etot = -14.642433245184 -261000 ekin = 0.293077534073102 | erot = 0.522116767905281 | epot = -15.4576275472213 | etot = -14.6424332452429 -262000 ekin = 0.312031202020399 | erot = 0.550394247121215 | epot = -15.5048586944527 | etot = -14.642433245311 -263000 ekin = 0.330131107615849 | erot = 0.581541281999657 | epot = -15.554105635002 | etot = -14.6424332453865 -264000 ekin = 0.346943319969814 | erot = 0.614796773447099 | epot = -15.6041733388837 | etot = -14.6424332454667 -265000 ekin = 0.362033078254078 | erot = 0.64932279499714 | epot = -15.6537891188008 | etot = -14.6424332455496 -266000 ekin = 0.374977027495969 | erot = 0.684232889060528 | epot = -15.7016431621888 | etot = -14.6424332456323 -267000 ekin = 0.385377045180505 | erot = 0.718621072064159 | epot = -15.7464313629565 | etot = -14.6424332457118 -268000 ekin = 0.392875374675151 | erot = 0.75159036946739 | epot = -15.7868989899282 | etot = -14.6424332457857 -269000 ekin = 0.397170471133891 | erot = 0.782279784278107 | epot = -15.8218835012631 | etot = -14.6424332458511 -270000 ekin = 0.398032662022584 | erot = 0.809888771679725 | epot = -15.8503546796085 | etot = -14.6424332459062 -271000 ekin = 0.395318487593106 | erot = 0.833698516715849 | epot = -15.8714502502576 | etot = -14.6424332459487 -272000 ekin = 0.3889824743465 | erot = 0.853089551914417 | epot = -15.8845052722381 | etot = -14.6424332459772 -273000 ekin = 0.379085147925856 | erot = 0.867555470410714 | epot = -15.8890738643275 | etot = -14.6424332459909 -274000 ekin = 0.365796322187845 | erot = 0.876712662634537 | epot = -15.8849422308118 | etot = -14.6424332459894 -275000 ekin = 0.349393082916426 | erot = 0.880306121918472 | epot = -15.872132450808 | etot = -14.6424332459731 -276000 ekin = 0.330252358900968 | erot = 0.878211432153003 | epot = -15.8508970369967 | etot = -14.6424332459427 -277000 ekin = 0.308838461216024 | erot = 0.870433084880285 | epot = -15.821704791996 | etot = -14.6424332458996 -278000 ekin = 0.285686394600537 | erot = 0.857099294887754 | epot = -15.785218935334 | etot = -14.6424332458457 -279000 ekin = 0.261382042763559 | erot = 0.838453513182875 | epot = -15.7422688017293 | etot = -14.6424332457829 -280000 ekin = 0.236540473323853 | erot = 0.814842890589049 | epot = -15.6938166096265 | etot = -14.6424332457136 -281000 ekin = 0.211783602606715 | erot = 0.786704032858738 | epot = -15.6409208811057 | etot = -14.6424332456403 -282000 ekin = 0.187718337271409 | erot = 0.754546508157302 | epot = -15.5846980909941 | etot = -14.6424332455654 -283000 ekin = 0.16491611509112 | erot = 0.718934708844168 | epot = -15.5262840694266 | etot = -14.6424332454913 -284000 ekin = 0.143894549222822 | erot = 0.680468811937736 | epot = -15.466796606581 | etot = -14.6424332454204 -285000 ekin = 0.125101678374138 | erot = 0.639765701845489 | epot = -15.4073006255745 | etot = -14.6424332453549 -286000 ekin = 0.108903164109909 | erot = 0.597440790007828 | epot = -15.3487771994138 | etot = -14.6424332452961 -287000 ekin = 0.0955726645582895 | erot = 0.554091668601936 | epot = -15.2920975784057 | etot = -14.6424332452455 -288000 ekin = 0.0852855448043095 | erot = 0.510284456818714 | epot = -15.2380032468271 | etot = -14.6424332452041 -289000 ekin = 0.0781160413143099 | erot = 0.466543535619487 | epot = -15.187092822106 | etot = -14.6424332451722 -290000 ekin = 0.0740379578661698 | erot = 0.423345127585219 | epot = -15.1398163306013 | etot = -14.6424332451499 -291000 ekin = 0.0729289100679055 | erot = 0.38111487943343 | epot = -15.0964770346381 | etot = -14.6424332451368 -292000 ekin = 0.07457803579739 | erot = 0.340229271733799 | epot = -15.0572405526628 | etot = -14.6424332451316 -293000 ekin = 0.0786969407585632 | erot = 0.301020346544403 | epot = -15.0221505324361 | etot = -14.6424332451332 -294000 ekin = 0.0849334564747931 | erot = 0.263782947584683 | epot = -14.9911496491992 | etot = -14.6424332451397 -295000 ekin = 0.0928875723651433 | erot = 0.228783448803118 | epot = -14.964104266318 | etot = -14.6424332451498 -296000 ekin = 0.102128697511344 | erot = 0.196268840383812 | epot = -14.9408307830567 | etot = -14.6424332451616 -297000 ekin = 0.112213252500573 | erot = 0.166475068215632 | epot = -14.9211215658898 | etot = -14.6424332451736 -298000 ekin = 0.122701527070322 | erot = 0.139633685444096 | epot = -14.9047684576989 | etot = -14.6424332451845 -299000 ekin = 0.133172792913731 | erot = 0.115976150687847 | epot = -14.891582188795 | etot = -14.6424332451934 -300000 ekin = 0.143237839709879 | erot = 0.0957354521197614 | epot = -14.8814065370294 | etot = -14.6424332451998 -301000 ekin = 0.152548387990868 | erot = 0.079145090872109 | epot = -14.8741267240665 | etot = -14.6424332452036 -302000 ekin = 0.160803184301541 | erot = 0.0664357608556664 | epot = -14.869672190362 | etot = -14.6424332452048 -303000 ekin = 0.167750948488392 | erot = 0.0578302677258683 | epot = -14.8680144614181 | etot = -14.6424332452038 -304000 ekin = 0.173190665588574 | erot = 0.053537313638039 | epot = -14.869161224428 | etot = -14.6424332452014 -305000 ekin = 0.17696995295018 | erot = 0.0537447402922378 | epot = -14.8731479384404 | etot = -14.642433245198 -306000 ekin = 0.178982363291699 | erot = 0.0586126977894969 | epot = -14.8800283062755 | etot = -14.6424332451943 -307000 ekin = 0.179164502945091 | erot = 0.0682670321079287 | epot = -14.8898647802439 | etot = -14.6424332451908 -308000 ekin = 0.177493763289092 | erot = 0.0827930029211812 | epot = -14.9027200113984 | etot = -14.6424332451881 -309000 ekin = 0.173987301152073 | erot = 0.102229291873313 | epot = -14.9186498382119 | etot = -14.6424332451865 -310000 ekin = 0.168702678648375 | erot = 0.126562162218708 | epot = -14.9376980860533 | etot = -14.6424332451862 -311000 ekin = 0.161740297010248 | erot = 0.155719593409014 | epot = -14.9598931356065 | etot = -14.6424332451872 -312000 ekin = 0.153247440126422 | erot = 0.189565237979898 | epot = -14.985245923296 | etot = -14.6424332451897 -313000 ekin = 0.143423389998644 | erot = 0.227892126762103 | epot = -15.0137487619544 | etot = -14.6424332451937 -314000 ekin = 0.132524706020331 | erot = 0.270416174781571 | epot = -15.0453741260009 | etot = -14.642433245199 -315000 ekin = 0.120869409554577 | erot = 0.316769708289568 | epot = -15.0800723630506 | etot = -14.6424332452064 -316000 ekin = 0.1088385461069 | erot = 0.366495437994219 | epot = -15.1177672293174 | etot = -14.6424332452162 -317000 ekin = 0.0968734934299854 | erot = 0.419041536808397 | epot = -15.1583482754675 | etot = -14.6424332452291 -318000 ekin = 0.0854675378572642 | erot = 0.473758725762781 | epot = -15.2016595088659 | etot = -14.6424332452459 -319000 ekin = 0.0751507271474209 | erot = 0.529900497446471 | epot = -15.2474844698617 | etot = -14.6424332452678 -320000 ekin = 0.0664678443385232 | erot = 0.586627760737817 | epot = -15.2955288503722 | etot = -14.6424332452959 -321000 ekin = 0.0599504590581789 | erot = 0.643019202689382 | epot = -15.3454029070786 | etot = -14.6424332453311 -322000 ekin = 0.0560852142815269 | erot = 0.698088453264983 | epot = -15.3966069129204 | etot = -14.6424332453739 -323000 ekin = 0.0552815181260071 | erot = 0.750808639914411 | epot = -15.4485234034645 | etot = -14.6424332454241 -324000 ekin = 0.057842325521187 | erot = 0.800144112656294 | epot = -15.5004196836582 | etot = -14.6424332454807 -325000 ekin = 0.063941486463515 | erot = 0.845088070114582 | epot = -15.5514628021197 | etot = -14.6424332455416 -326000 ekin = 0.0736101694204757 | erot = 0.8847036899678 | epot = -15.6007471049927 | etot = -14.6424332456044 -327000 ekin = 0.0867333560885493 | erot = 0.918165419814647 | epot = -15.6473320215694 | etot = -14.6424332456662 -328000 ekin = 0.103055779602218 | erot = 0.944796600226722 | epot = -15.690285625553 | etot = -14.642433245724 -329000 ekin = 0.122195446168401 | erot = 0.964099781598492 | epot = -15.7287284735425 | etot = -14.6424332457756 -330000 ekin = 0.143662406707274 | erot = 0.97577699624252 | epot = -15.7618726487685 | etot = -14.6424332458188 -331000 ekin = 0.166880785130066 | erot = 0.979738667524184 | epot = -15.7890526985066 | etot = -14.6424332458523 -332000 ekin = 0.191212923965916 | erot = 0.976101405909932 | epot = -15.8097475757513 | etot = -14.6424332458755 -333000 ekin = 0.215985355315126 | erot = 0.96517623354676 | epot = -15.8235948347498 | etot = -14.6424332458879 -334000 ekin = 0.240516656826312 | erot = 0.947449485120633 | epot = -15.8303993878361 | etot = -14.6424332458891 -335000 ekin = 0.264146896081082 | erot = 0.923558676876312 | epot = -15.8301388188364 | etot = -14.642433245879 -336000 ekin = 0.286267467748831 | erot = 0.894265184768772 | epot = -15.8229658983753 | etot = -14.6424332458577 -337000 ekin = 0.306349134744516 | erot = 0.86042493934443 | epot = -15.8092073199143 | etot = -14.6424332458253 -338000 ekin = 0.323965497669028 | erot = 0.822957838329898 | epot = -15.7893565817819 | etot = -14.642433245783 -339000 ekin = 0.338809250783309 | erot = 0.782816380156821 | epot = -15.7640588766722 | etot = -14.6424332457321 -340000 ekin = 0.350699444228147 | erot = 0.740954141308479 | epot = -15.7340868312114 | etot = -14.6424332456748 -341000 ekin = 0.359579293531077 | erot = 0.698295027836124 | epot = -15.700307566981 | etot = -14.6424332456138 -342000 ekin = 0.365505462149771 | erot = 0.65570454203815 | epot = -15.6636432497397 | etot = -14.6424332455518 -343000 ekin = 0.368630832656574 | erot = 0.613964463467596 | epot = -15.6250285416159 | etot = -14.6424332454917 -344000 ekin = 0.369183369584824 | erot = 0.573752273081762 | epot = -15.5853688881025 | etot = -14.6424332454359 -345000 ekin = 0.367443732820381 | erot = 0.535626361233121 | epot = -15.5455033394399 | etot = -14.6424332453864 -346000 ekin = 0.363723933128391 | erot = 0.500017626275295 | epot = -15.5061748047483 | etot = -14.6424332453446 -347000 ekin = 0.358348705274855 | erot = 0.467227585425635 | epot = -15.4680095360116 | etot = -14.6424332453111 -348000 ekin = 0.351640582952574 | erot = 0.437432666905905 | epot = -15.4315064951445 | etot = -14.642433245286 -349000 ekin = 0.343909024693095 | erot = 0.41069398616735 | epot = -15.3970362561291 | etot = -14.6424332452687 -350000 ekin = 0.335443435967589 | erot = 0.386971649877954 | epot = -15.3648483311043 | etot = -14.6424332452587 -351000 ekin = 0.326509584093047 | erot = 0.366142474248719 | epot = -15.335085303596 | etot = -14.6424332452542 -352000 ekin = 0.31734869902189 | erot = 0.348019930398469 | epot = -15.3078018746744 | etot = -14.642433245254 -353000 ekin = 0.308178466648795 | erot = 0.332375117499601 | epot = -15.2829868294052 | etot = -14.6424332452568 -354000 ekin = 0.299195119854714 | erot = 0.318957598137068 | epot = -15.2605859632527 | etot = -14.6424332452609 -355000 ekin = 0.290575888249386 | erot = 0.307515001368932 | epot = -15.2405241348834 | etot = -14.6424332452651 -356000 ekin = 0.282481160313163 | erot = 0.297810406216367 | epot = -15.222724811798 | etot = -14.6424332452684 -357000 ekin = 0.275055828994536 | erot = 0.289636664277623 | epot = -15.2071257385424 | etot = -14.6424332452702 -358000 ekin = 0.268429427255716 | erot = 0.2828270069126 | epot = -15.1936896794383 | etot = -14.64243324527 -359000 ekin = 0.262714810202527 | erot = 0.277261507858961 | epot = -15.1824095633294 | etot = -14.6424332452679 -360000 ekin = 0.258005302570158 | erot = 0.272869227750137 | epot = -15.1733077755847 | etot = -14.6424332452644 -361000 ekin = 0.254370400622446 | erot = 0.269626137803926 | epot = -15.1664297836866 | etot = -14.6424332452602 -362000 ekin = 0.251850290179257 | erot = 0.267549186090192 | epot = -15.1618327215256 | etot = -14.6424332452562 -363000 ekin = 0.250449609863309 | erot = 0.266687109599918 | epot = -15.1595699647169 | etot = -14.6424332452537 -364000 ekin = 0.250131041863869 | erot = 0.267108788860229 | epot = -15.1596730759781 | etot = -14.642433245254 -365000 ekin = 0.250809442162608 | erot = 0.268890073930453 | epot = -15.1621327613513 | etot = -14.6424332452583 -366000 ekin = 0.252347318763942 | erot = 0.272100073008303 | epot = -15.1668806370396 | etot = -14.6424332452674 -367000 ekin = 0.254552520179202 | erot = 0.276787886821285 | epot = -15.1737736522826 | etot = -14.6424332452822 -368000 ekin = 0.257178996154138 | erot = 0.282970699525187 | epot = -15.1825829409824 | etot = -14.6424332453031 -369000 ekin = 0.259931424909754 | erot = 0.290624011144305 | epot = -15.192988681384 | etot = -14.64243324533 -370000 ekin = 0.262474349327938 | erot = 0.299674631815232 | epot = -15.2045822265054 | etot = -14.6424332453622 -371000 ekin = 0.264446209429919 | erot = 0.30999686929688 | epot = -15.2168763241253 | etot = -14.6424332453985 -372000 ekin = 0.265478281863403 | erot = 0.321412142685467 | epot = -15.2293236699861 | etot = -14.6424332454372 -373000 ekin = 0.265218028292392 | erot = 0.333692059446794 | epot = -15.2413433332155 | etot = -14.6424332454763 -374000 ekin = 0.263355721250465 | erot = 0.346564809668633 | epot = -15.2523537764321 | etot = -14.642433245513 -375000 ekin = 0.259652497503914 | erot = 0.35972456799486 | epot = -15.2618103110439 | etot = -14.6424332455451 -376000 ekin = 0.253967268937827 | erot = 0.372843454380799 | epot = -15.2692439688887 | etot = -14.6424332455701 -377000 ekin = 0.246279333501497 | erot = 0.385585491294786 | epot = -15.274298070382 | etot = -14.6424332455857 -378000 ekin = 0.236703249878266 | erot = 0.397621906698155 | epot = -15.2767584021673 | etot = -14.6424332455909 -379000 ekin = 0.225492756944983 | erot = 0.408647066931749 | epot = -15.2765730694618 | etot = -14.6424332455851 -380000 ekin = 0.213031377539262 | erot = 0.418394278996725 | epot = -15.2738589021049 | etot = -14.6424332455689 -381000 ekin = 0.199808877315933 | erot = 0.42665067621188 | epot = -15.2688927990715 | etot = -14.6424332455437 -382000 ekin = 0.186384809019062 | erot = 0.433270396055884 | epot = -15.2620884505868 | etot = -14.6424332455119 -383000 ekin = 0.173342616144133 | erot = 0.438185279050674 | epot = -15.2539611406711 | etot = -14.6424332454762 -384000 ekin = 0.161239700831467 | erot = 0.441412371402834 | epot = -15.2450853176736 | etot = -14.6424332454393 -385000 ekin = 0.15055995464762 | erot = 0.44305761255288 | epot = -15.2360508126044 | etot = -14.6424332454039 -386000 ekin = 0.1416751296992 | erot = 0.443315241523152 | epot = -15.2274236165942 | etot = -14.6424332453718 -387000 ekin = 0.134820015698004 | erot = 0.442462667348858 | epot = -15.2197159283911 | etot = -14.6424332453442 -388000 ekin = 0.130083976413563 | erot = 0.440850813513923 | epot = -15.2133680352489 | etot = -14.6424332453214 -389000 ekin = 0.127418570237896 | erot = 0.438890246279034 | epot = -15.20874206182 | etot = -14.6424332453031 -390000 ekin = 0.126658423093211 | erot = 0.437033702086108 | epot = -15.2061253704679 | etot = -14.6424332452886 -391000 ekin = 0.127550804261002 | erot = 0.435755902066214 | epot = -15.2057399516043 | etot = -14.6424332452771 -392000 ekin = 0.129788752935804 | erot = 0.435531744058807 | epot = -15.2077537422628 | etot = -14.6424332452682 -393000 ekin = 0.13304305531626 | erot = 0.436814065078312 | epot = -15.2122903656558 | etot = -14.6424332452612 -394000 ekin = 0.136989561466103 | erot = 0.440012156511487 | epot = -15.2194349632339 | etot = -14.6424332452563 -395000 ekin = 0.14132983304257 | erot = 0.44547209688668 | epot = -15.2292351751828 | etot = -14.6424332452536 -396000 ekin = 0.145804542777681 | erot = 0.453459767650225 | epot = -15.2416975556816 | etot = -14.6424332452537 -397000 ekin = 0.150200153189366 | erot = 0.464147173463303 | epot = -15.25678057191 | etot = -14.6424332452573 -398000 ekin = 0.154350089767278 | erot = 0.477602441560288 | epot = -15.2743857765924 | etot = -14.6424332452648 -399000 ekin = 0.158131920623957 | erot = 0.49378366115725 | epot = -15.2943488270583 | etot = -14.6424332452771 -400000 ekin = 0.161462056175852 | erot = 0.512536568007638 | epot = -15.3164318694777 | etot = -14.6424332452942 -401000 ekin = 0.164289301183564 | erot = 0.533595989003432 | epot = -15.3403185355036 | etot = -14.6424332453166 -402000 ekin = 0.16658832305357 | erot = 0.556590928840415 | epot = -15.3656124972378 | etot = -14.6424332453438 -403000 ekin = 0.168353810382888 | erot = 0.581053183644666 | epot = -15.3918402394033 | etot = -14.6424332453758 -404000 ekin = 0.169595821304612 | erot = 0.606429376023098 | epot = -15.4184584427392 | etot = -14.6424332454115 -405000 ekin = 0.170336578565562 | erot = 0.63209629254019 | epot = -15.4448661165559 | etot = -14.6424332454501 -406000 ekin = 0.170608761982373 | erot = 0.657379344514174 | epot = -15.4704213519868 | etot = -14.6424332454903 -407000 ekin = 0.170455178570794 | erot = 0.681573854093766 | epot = -15.494462278195 | etot = -14.6424332455304 -408000 ekin = 0.169929554813017 | erot = 0.703968692150334 | epot = -15.5163314925322 | etot = -14.6424332455689 -409000 ekin = 0.169098093454334 | erot = 0.723871579520639 | epot = -15.5354029185788 | etot = -14.6424332456039 -410000 ekin = 0.168041369043284 | erot = 0.740635137247676 | epot = -15.5511097519246 | etot = -14.6424332456336 -411000 ekin = 0.16685610281106 | erot = 0.753682569970645 | epot = -15.5629719184382 | etot = -14.6424332456565 -412000 ekin = 0.165656359034691 | erot = 0.762531725092763 | epot = -15.5706213297985 | etot = -14.6424332456711 -413000 ekin = 0.16457374171258 | erot = 0.766816218739503 | epot = -15.5738232061285 | etot = -14.6424332456764 -414000 ekin = 0.163756240958051 | erot = 0.766302377571847 | epot = -15.5724918642017 | etot = -14.6424332456718 -415000 ekin = 0.163365479945346 | erot = 0.760900920225164 | epot = -15.5666996458277 | etot = -14.6424332456572 -416000 ekin = 0.16357224009341 | erot = 0.75067258670007 | epot = -15.5566780724265 | etot = -14.642433245633 -417000 ekin = 0.164550286198177 | erot = 0.735827297892157 | epot = -15.5428108296905 | etot = -14.6424332456002 -418000 ekin = 0.166468663391054 | erot = 0.71671685730188 | epot = -15.5256187662531 | etot = -14.6424332455602 -419000 ekin = 0.169482781124205 | erot = 0.69382164910088 | epot = -15.5057376757398 | etot = -14.6424332455147 -420000 ekin = 0.17372472266442 | erot = 0.667732191685371 | epot = -15.4838901598156 | etot = -14.6424332454658 -421000 ekin = 0.179293310757533 | erot = 0.639126725583772 | epot = -15.460853281757 | etot = -14.6424332454157 -422000 ekin = 0.18624451451762 | erot = 0.608746211201687 | epot = -15.437423971086 | etot = -14.6424332453667 -423000 ekin = 0.194582798143094 | erot = 0.577368165579487 | epot = -15.4143842090434 | etot = -14.6424332453208 -424000 ekin = 0.204253993028008 | erot = 0.545780680988006 | epot = -15.392467919296 | etot = -14.64243324528 -425000 ekin = 0.215140228915644 | erot = 0.514757766833632 | epot = -15.3723312409951 | etot = -14.6424332452459 -426000 ekin = 0.22705739519611 | erot = 0.485036881516617 | epot = -15.3545275219322 | etot = -14.6424332452194 -427000 ekin = 0.239755526224917 | erot = 0.457299221562847 | epot = -15.3394879929896 | etot = -14.6424332452018 -428000 ekin = 0.252922416268543 | erot = 0.432153058135964 | epot = -15.3275087195978 | etot = -14.6424332451933 -429000 ekin = 0.266190667178511 | erot = 0.410120192008996 | epot = -15.3187441043811 | etot = -14.6424332451936 -430000 ekin = 0.279148248284993 | erot = 0.391625457763317 | epot = -15.3132069512512 | etot = -14.6424332452029 -431000 ekin = 0.291352495292879 | erot = 0.376989149811629 | epot = -15.3107748903245 | etot = -14.64243324522 -432000 ekin = 0.302347287569384 | erot = 0.366422254467196 | epot = -15.3112027872808 | etot = -14.6424332452442 -433000 ekin = 0.311682921770386 | erot = 0.360024429013363 | epot = -15.314140596057 | etot = -14.6424332452733 -434000 ekin = 0.318937954386255 | erot = 0.357784738271778 | epot = -15.3191559379639 | etot = -14.6424332453059 -435000 ekin = 0.323742037713914 | erot = 0.359585207274041 | epot = -15.3257604903287 | etot = -14.6424332453407 -436000 ekin = 0.325798554030506 | erot = 0.365207245307274 | epot = -15.3334390447139 | etot = -14.6424332453761 -437000 ekin = 0.324905697096481 | erot = 0.374340922351912 | epot = -15.3416798648573 | etot = -14.642433245409 -438000 ekin = 0.320974589857387 | erot = 0.38659693016297 | epot = -15.350004765458 | etot = -14.6424332454377 -439000 ekin = 0.314043077745106 | erot = 0.401520852188694 | epot = -15.3579971753951 | etot = -14.6424332454613 -440000 ekin = 0.304283988018871 | erot = 0.418609132217954 | epot = -15.3653263657147 | etot = -14.6424332454779 -441000 ekin = 0.292006859109421 | erot = 0.437325916197858 | epot = -15.3717660207937 | etot = -14.6424332454864 -442000 ekin = 0.277652365812285 | erot = 0.457119792524558 | epot = -15.3772054038237 | etot = -14.6424332454869 -443000 ekin = 0.261778853587334 | erot = 0.477439412182338 | epot = -15.3816515112496 | etot = -14.6424332454799 -444000 ekin = 0.245040553430229 | erot = 0.497747053383812 | epot = -15.3852208522809 | etot = -14.6424332454669 -445000 ekin = 0.228157260415745 | erot = 0.517529408210577 | epot = -15.3881199140755 | etot = -14.6424332454491 -446000 ekin = 0.211875681724426 | erot = 0.536305196865301 | epot = -15.3906141240194 | etot = -14.6424332454296 -447000 ekin = 0.196923472676264 | erot = 0.553629632762624 | epot = -15.3929863508503 | etot = -14.6424332454114 -448000 ekin = 0.183958277875564 | erot = 0.569096233380439 | epot = -15.3954877566541 | etot = -14.6424332453981 -449000 ekin = 0.173515771308145 | erot = 0.582336947161166 | epot = -15.3982859638623 | etot = -14.6424332453929 -450000 ekin = 0.165962361194716 | erot = 0.593021970155278 | epot = -15.4014175767483 | etot = -14.6424332453983 -451000 ekin = 0.161459280831071 | erot = 0.600860851258448 | epot = -15.4047533775048 | etot = -14.6424332454152 -452000 ekin = 0.159944578250394 | erot = 0.605606408084745 | epot = -15.4079842317782 | etot = -14.6424332454431 -453000 ekin = 0.161137653112604 | erot = 0.607062496375647 | epot = -15.4106333949675 | etot = -14.6424332454792 -454000 ekin = 0.164567591511419 | erot = 0.605095779312697 | epot = -15.4120966163436 | etot = -14.6424332455194 -455000 ekin = 0.169622334208404 | erot = 0.599650455426745 | epot = -15.4117060351936 | etot = -14.6424332455584 -456000 ekin = 0.175611802350263 | erot = 0.590763702898767 | epot = -15.4088087508399 | etot = -14.6424332455909 -457000 ekin = 0.181835621982496 | erot = 0.578578749366124 | epot = -15.4028476169608 | etot = -14.6424332456122 -458000 ekin = 0.18764572703167 | erot = 0.563352302650977 | epot = -15.3934312753017 | etot = -14.6424332456191 -459000 ekin = 0.192495880386128 | erot = 0.545453717150014 | epot = -15.3803828431463 | etot = -14.6424332456101 -460000 ekin = 0.19597338163879 | erot = 0.525354597711273 | epot = -15.3637612249358 | etot = -14.6424332455858 -461000 ekin = 0.197811920993009 | erot = 0.503609203462558 | epot = -15.3438543700042 | etot = -14.6424332455486 -462000 ekin = 0.19788772492106 | erot = 0.480827560282267 | epot = -15.3211485307047 | etot = -14.6424332455014 -463000 ekin = 0.196203198487162 | erot = 0.457644248436047 | epot = -15.2962806923717 | etot = -14.6424332454485 -464000 ekin = 0.192863034127886 | erot = 0.434686220428428 | epot = -15.2699824999498 | etot = -14.6424332453935 -465000 ekin = 0.188047435824139 | erot = 0.412542760090385 | epot = -15.2430234412545 | etot = -14.64243324534 -466000 ekin = 0.181986107554585 | erot = 0.391740010671268 | epot = -15.2161593635165 | etot = -14.6424332452907 -467000 ekin = 0.174935400199653 | erot = 0.372721626734306 | epot = -15.1900902721816 | etot = -14.6424332452476 -468000 ekin = 0.167159826103645 | erot = 0.355836258350829 | epot = -15.1654293296665 | etot = -14.642433245212 -469000 ekin = 0.158918218023908 | erot = 0.341331890764793 | epot = -15.1426833539731 | etot = -14.6424332451844 -470000 ekin = 0.15045418565433 | erot = 0.32935658463347 | epot = -15.1222440154524 | etot = -14.6424332451646 -471000 ekin = 0.141990180750341 | erot = 0.319964871776709 | epot = -15.1043882976792 | etot = -14.6424332451522 -472000 ekin = 0.133724353868939 | erot = 0.313128906245089 | epot = -15.08928650526 | etot = -14.642433245146 -473000 ekin = 0.125829398102414 | erot = 0.308753392324214 | epot = -15.0770160355716 | etot = -14.642433245145 -474000 ekin = 0.118452666363562 | erot = 0.306693264413826 | epot = -15.0675791759251 | etot = -14.6424332451477 -475000 ekin = 0.111716976219122 | erot = 0.306773053290683 | epot = -15.0609232746627 | etot = -14.6424332451529 -476000 ekin = 0.10572165563334 | erot = 0.308806833537627 | epot = -15.0569617343301 | etot = -14.6424332451591 -477000 ekin = 0.100543523675759 | erot = 0.312617617130285 | epot = -15.0555943859712 | etot = -14.6424332451652 -478000 ekin = 0.0962376398644792 | erot = 0.31805505563531 | epot = -15.0567259406699 | etot = -14.6424332451701 -479000 ekin = 0.0928377950024481 | erot = 0.325010357030128 | epot = -15.0602813972058 | etot = -14.6424332451732 -480000 ekin = 0.0903568546345918 | erot = 0.33342742776329 | epot = -15.066217527572 | etot = -14.6424332451741 -481000 ekin = 0.0887871989358495 | erot = 0.343309423709778 | epot = -15.0745298678181 | etot = -14.6424332451725 -482000 ekin = 0.0881016191320247 | erot = 0.354720133057113 | epot = -15.0852549973578 | etot = -14.6424332451687 -483000 ekin = 0.0882551127439553 | erot = 0.367779908272464 | epot = -15.0984682661794 | etot = -14.642433245163 -484000 ekin = 0.0891880440138003 | erot = 0.382656193507601 | epot = -15.1142774826776 | etot = -14.6424332451562 -485000 ekin = 0.0908310739109808 | erot = 0.399549033146284 | epot = -15.1328133522061 | etot = -14.6424332451488 -486000 ekin = 0.0931120890990374 | erot = 0.418672269923129 | epot = -15.1542176041639 | etot = -14.6424332451417 -487000 ekin = 0.0959650526392593 | erot = 0.440231422321011 | epot = -15.1786297200963 | etot = -14.642433245136 -488000 ekin = 0.0993402613867364 | erot = 0.464399451384487 | epot = -15.2061729579036 | etot = -14.6424332451324 -489000 ekin = 0.103214957397678 | erot = 0.491291775403258 | epot = -15.2369399779328 | etot = -14.6424332451318 -490000 ekin = 0.107602676597184 | erot = 0.520941965498208 | epot = -15.2709778872308 | etot = -14.6424332451354 -491000 ekin = 0.112559247664622 | erot = 0.553279563916956 | epot = -15.3082720567259 | etot = -14.6424332451443 -492000 ekin = 0.118183136723597 | erot = 0.588111425308452 | epot = -15.3487278071918 | etot = -14.6424332451598 -493000 ekin = 0.12460804012638 | erot = 0.62510790827898 | epot = -15.3921491935888 | etot = -14.6424332451834 -494000 ekin = 0.131986393312561 | erot = 0.663795156035111 | epot = -15.4382147945646 | etot = -14.6424332452169 -495000 ekin = 0.140463823900159 | erot = 0.703554605721736 | epot = -15.4864516748841 | etot = -14.6424332452622 -496000 ekin = 0.15014640803584 | erot = 0.743630741563187 | epot = -15.5362103949193 | etot = -14.6424332453203 -497000 ekin = 0.161064579071316 | erot = 0.783147917317585 | epot = -15.5866457417809 | etot = -14.642433245392 -498000 ekin = 0.173139219157384 | erot = 0.821136754972775 | epot = -15.6367092196065 | etot = -14.6424332454764 -499000 ekin = 0.186156317833383 | erot = 0.856570103856722 | epot = -15.6851596672614 | etot = -14.6424332455713 -500000 ekin = 0.199756195068936 | erot = 0.888407758274067 | epot = -15.7305971990159 | etot = -14.6424332456729 -501000 ekin = 0.21344151783734 | erot = 0.915648078732879 | epot = -15.7715228423456 | etot = -14.6424332457754 -502000 ekin = 0.226605416598004 | erot = 0.937383433649205 | epot = -15.8064220961192 | etot = -14.642433245872 -503000 ekin = 0.238577508977599 | erot = 0.952855183124955 | epot = -15.833865938058 | etot = -14.6424332459554 -504000 ekin = 0.248682347016341 | erot = 0.961503066788411 | epot = -15.8526186598236 | etot = -14.6424332460188 -505000 ekin = 0.256302488969601 | erot = 0.963003656366721 | epot = -15.8617393913931 | etot = -14.6424332460567 -506000 ekin = 0.260937583144201 | erot = 0.957293217920631 | epot = -15.8606640471306 | etot = -14.6424332460658 -507000 ekin = 0.262251679299254 | erot = 0.944571918258648 | epot = -15.8492568436029 | etot = -14.642433246045 -508000 ekin = 0.260103184111419 | erot = 0.925288564934488 | epot = -15.827824995042 | etot = -14.6424332459961 -509000 ekin = 0.254554875280464 | erot = 0.90010753693787 | epot = -15.7970956581413 | etot = -14.642433245923 -510000 ekin = 0.245864483348196 | erot = 0.869861717985383 | epot = -15.7581594471648 | etot = -14.6424332458312 -511000 ekin = 0.234458914526896 | erot = 0.835496660126456 | epot = -15.7123888203806 | etot = -14.6424332457273 -512000 ekin = 0.22089682023999 | erot = 0.798011684065881 | epot = -15.6613417499238 | etot = -14.642433245618 -513000 ekin = 0.205824805087888 | erot = 0.758403224578321 | epot = -15.6066612751757 | etot = -14.6424332455095 -514000 ekin = 0.189932244116178 | erot = 0.717614706860286 | epot = -15.5499801963839 | etot = -14.6424332454074 -515000 ekin = 0.17390874819978 | erot = 0.676495918872563 | epot = -15.4928379123882 | etot = -14.6424332453159 -516000 ekin = 0.158407108509004 | erot = 0.635773516025323 | epot = -15.4366138697724 | etot = -14.6424332452381 -517000 ekin = 0.1440133501839 | erot = 0.596033149118113 | epot = -15.3824797444781 | etot = -14.6424332451761 -518000 ekin = 0.131224514118008 | erot = 0.557712825688944 | epot = -15.3313705849373 | etot = -14.6424332451304 -519000 ekin = 0.120434042405821 | erot = 0.521106495597703 | epot = -15.283973783104 | etot = -14.6424332451005 -520000 ekin = 0.111924165176696 | erot = 0.48637644319974 | epot = -15.2407338534618 | etot = -14.6424332450854 -521000 ekin = 0.105864424815862 | erot = 0.453572806060421 | epot = -15.2018704759592 | etot = -14.6424332450829 -522000 ekin = 0.102315362067372 | erot = 0.422658367131508 | epot = -15.1674069742899 | etot = -14.642433245091 -523000 ekin = 0.101236366465152 | erot = 0.393536647097 | epot = -15.137206258669 | etot = -14.6424332451069 -524000 ekin = 0.102496717236721 | erot = 0.366081244308229 | epot = -15.1110112066728 | etot = -14.6424332451279 -525000 ekin = 0.105888887336008 | erot = 0.340164343214705 | epot = -15.088486475702 | etot = -14.6424332451513 -526000 ekin = 0.111143247850893 | erot = 0.315682368378702 | epot = -15.0692588614046 | etot = -14.642433245175 -527000 ekin = 0.117943398962381 | erot = 0.292576937807028 | epot = -15.0529535819665 | etot = -14.6424332451971 -528000 ekin = 0.125941474255768 | erot = 0.270849598243881 | epot = -15.0392243177156 | etot = -14.6424332452159 -529000 ekin = 0.134772916010344 | erot = 0.250569317239541 | epot = -15.0277754784805 | etot = -14.6424332452306 -530000 ekin = 0.144070383403707 | erot = 0.231872340652279 | epot = -15.0183759692969 | etot = -14.6424332452409 -531000 ekin = 0.153476601970632 | erot = 0.214954741435395 | epot = -15.010864588653 | etot = -14.642433245247 -532000 ekin = 0.1626560540789 | erot = 0.200058697649321 | epot = -15.0051479969777 | etot = -14.6424332452495 -533000 ekin = 0.171305419081489 | erot = 0.187454143184939 | epot = -15.0011928075153 | etot = -14.6424332452489 -534000 ekin = 0.179162595540411 | erot = 0.177417842695355 | epot = -14.9990136834822 | etot = -14.6424332452464 -535000 ekin = 0.186014006486684 | erot = 0.170212094444257 | epot = -14.9986593461736 | etot = -14.6424332452427 -536000 ekin = 0.191699759240443 | erot = 0.166065149228308 | epot = -15.0001981537074 | etot = -14.6424332452386 -537000 ekin = 0.196116169931545 | erot = 0.165155084981508 | epot = -15.0037045001479 | etot = -14.6424332452349 -538000 ekin = 0.199215220533704 | erot = 0.167598364573368 | epot = -15.0092468303392 | etot = -14.6424332452321 -539000 ekin = 0.201000709669604 | erot = 0.173443713619075 | epot = -15.0168776685195 | etot = -14.6424332452308 -540000 ekin = 0.201521164038046 | erot = 0.182671367033628 | epot = -15.026625776303 | etot = -14.6424332452313 -541000 ekin = 0.200859940141535 | erot = 0.195197211442984 | epot = -15.0384903968185 | etot = -14.642433245234 -542000 ekin = 0.199123298889063 | erot = 0.210880936223687 | epot = -15.0524374803519 | etot = -14.6424332452391 -543000 ekin = 0.196427519384046 | erot = 0.2295370177894 | epot = -15.0683977824198 | etot = -14.6424332452464 -544000 ekin = 0.192886294945241 | erot = 0.25094720200222 | epot = -15.0862667422039 | etot = -14.6424332452565 -545000 ekin = 0.188599710887441 | erot = 0.274873110235132 | epot = -15.1059060663912 | etot = -14.6424332452687 -546000 ekin = 0.183646045242704 | erot = 0.301067663118917 | epot = -15.1271469536446 | etot = -14.642433245283 -547000 ekin = 0.178077473818685 | erot = 0.329284179373518 | epot = -15.1497948984912 | etot = -14.642433245299 -548000 ekin = 0.171920510267331 | erot = 0.359282253783689 | epot = -15.1736360093672 | etot = -14.6424332453162 -549000 ekin = 0.165181670578021 | erot = 0.390829837831202 | epot = -15.1984447537431 | etot = -14.6424332453339 -550000 ekin = 0.157858408655527 | erot = 0.423701326917663 | epot = -15.2239929809248 | etot = -14.6424332453516 -551000 ekin = 0.149954809005965 | erot = 0.457671882716405 | epot = -15.2500599370908 | etot = -14.6424332453685 -552000 ekin = 0.141500835823196 | erot = 0.492508662660419 | epot = -15.2764427438674 | etot = -14.6424332453838 -553000 ekin = 0.132573145481942 | erot = 0.527960055124252 | epot = -15.3029664460031 | etot = -14.6424332453969 -554000 ekin = 0.123314645148993 | erot = 0.563744383269579 | epot = -15.329492273826 | etot = -14.6424332454074 -555000 ekin = 0.11394927090318 | erot = 0.599539792623581 | epot = -15.3559223089418 | etot = -14.642433245415 -556000 ekin = 0.104788088807789 | erot = 0.634977129563578 | epot = -15.3821984637916 | etot = -14.6424332454203 -557000 ekin = 0.0962230654780937 | erot = 0.669637513724418 | epot = -15.4082938246266 | etot = -14.6424332454241 -558000 ekin = 0.0887059614428439 | erot = 0.703055990480566 | epot = -15.4341951973516 | etot = -14.6424332454282 -559000 ekin = 0.0827118847741871 | erot = 0.734732129424035 | epot = -15.4598772596329 | etot = -14.6424332454346 -560000 ekin = 0.0786899547259807 | erot = 0.764147748398847 | epot = -15.4852709485702 | etot = -14.6424332454454 -561000 ekin = 0.0770067720633659 | erot = 0.790791153075989 | epot = -15.5102311706017 | etot = -14.6424332454624 -562000 ekin = 0.0778911706764631 | erot = 0.814186471629129 | epot = -15.534510887792 | etot = -14.6424332454864 -563000 ekin = 0.0813901113672907 | erot = 0.833925925483065 | epot = -15.5577492823675 | etot = -14.6424332455171 -564000 ekin = 0.0873448530219359 | erot = 0.849702302565726 | epot = -15.57948040114 | etot = -14.6424332455523 -565000 ekin = 0.0953935152543113 | erot = 0.861338569497175 | epot = -15.5991653303401 | etot = -14.6424332455886 -566000 ekin = 0.105001366119702 | erot = 0.868811531657282 | epot = -15.6162461433985 | etot = -14.6424332456215 -567000 ekin = 0.115514789210848 | erot = 0.872266750928135 | epot = -15.6302147857853 | etot = -14.6424332456464 -568000 ekin = 0.126230320990576 | erot = 0.872022546760986 | epot = -15.6406861134105 | etot = -14.6424332456589 -569000 ekin = 0.136467575205475 | erot = 0.868561781937934 | epot = -15.6474626027995 | etot = -14.6424332456561 -570000 ekin = 0.145634823229257 | erot = 0.862511177262809 | epot = -15.650579246129 | etot = -14.642433245637 -571000 ekin = 0.153278250260102 | erot = 0.854608991356203 | epot = -15.6503204872187 | etot = -14.6424332456024 -572000 ekin = 0.159109636953932 | erot = 0.845662918616737 | epot = -15.6472058011258 | etot = -14.6424332455552 -573000 ekin = 0.163011362017374 | erot = 0.836500892319944 | epot = -15.6419454998372 | etot = -14.6424332454999 -574000 ekin = 0.165021239080146 | erot = 0.82791805820528 | epot = -15.6353725427274 | etot = -14.642433245442 -575000 ekin = 0.165302195908609 | erot = 0.820623479704234 | epot = -15.628358921 | etot = -14.6424332453872 -576000 ekin = 0.164102988101204 | erot = 0.815190165399022 | epot = -15.6217263988411 | etot = -14.6424332453409 -577000 ekin = 0.16171615238716 | erot = 0.812011817944629 | epot = -15.6161612156398 | etot = -14.642433245308 -578000 ekin = 0.158438569371814 | erot = 0.811269345694708 | epot = -15.6121411603584 | etot = -14.6424332452919 -579000 ekin = 0.154538688869361 | erot = 0.812909695780807 | epot = -15.6098816299448 | etot = -14.6424332452946 -580000 ekin = 0.150232988454484 | erot = 0.816638977241892 | epot = -15.6093052110128 | etot = -14.6424332453164 -581000 ekin = 0.145672809814972 | erot = 0.821931135411058 | epot = -15.610037190582 | etot = -14.642433245356 -582000 ekin = 0.140941476791515 | erot = 0.828052590350937 | epot = -15.6114273125529 | etot = -14.6424332454104 -583000 ekin = 0.136060602599172 | erot = 0.834102246896438 | epot = -15.6125960949711 | etot = -14.6424332454755 -584000 ekin = 0.131003759896596 | erot = 0.839065139158377 | epot = -15.6125021446008 | etot = -14.6424332455458 -585000 ekin = 0.125715216483019 | erot = 0.841876757449112 | epot = -15.6100252195477 | etot = -14.6424332456156 -586000 ekin = 0.120131224768949 | erot = 0.841493945666844 | epot = -15.6040584161145 | etot = -14.6424332456787 -587000 ekin = 0.114201380572134 | erot = 0.836967317753832 | epot = -15.5936019440557 | etot = -14.6424332457297 -588000 ekin = 0.107907808226742 | erot = 0.827509595983301 | epot = -15.5778506499739 | etot = -14.6424332457638 -589000 ekin = 0.101280337909734 | erot = 0.81255426067366 | epot = -15.5562678443609 | etot = -14.6424332457776 -590000 ekin = 0.0944063548788447 | erot = 0.791799488420614 | epot = -15.5286390890685 | etot = -14.642433245769 -591000 ekin = 0.0874345511052151 | erot = 0.76523351922336 | epot = -15.4951013160666 | etot = -14.642433245738 -592000 ekin = 0.0805723392085189 | erot = 0.733139214285282 | epot = -15.45614479918 | etot = -14.6424332456862 -593000 ekin = 0.0740771594080953 | erot = 0.696077455348749 | epot = -15.4125878603736 | etot = -14.6424332456168 -594000 ekin = 0.0682423089599914 | erot = 0.654850963358167 | epot = -15.3655265178524 | etot = -14.6424332455342 -595000 ekin = 0.0633782539014622 | erot = 0.610451848323624 | epot = -15.316263347669 | etot = -14.6424332454439 -596000 ekin = 0.0597906540649622 | erot = 0.563997548401124 | epot = -15.266221447818 | etot = -14.6424332453519 -597000 ekin = 0.0577565493624107 | erot = 0.516660644084268 | epot = -15.2168504387109 | etot = -14.6424332452643 -598000 ekin = 0.0575003158536292 | erot = 0.46959829435364 | epot = -15.1695318553937 | etot = -14.6424332451864 -599000 ekin = 0.0591710965286411 | erot = 0.423886769451092 | epot = -15.125491111103 | etot = -14.6424332451233 -600000 ekin = 0.0628234356891151 | erot = 0.380465849281473 | epot = -15.085722530049 | etot = -14.6424332450784 -601000 ekin = 0.0684027903378462 | erot = 0.340096852289088 | epot = -15.0509328876808 | etot = -14.6424332450539 -602000 ekin = 0.0757374499128992 | erot = 0.303336891508859 | epot = -15.0215075864721 | etot = -14.6424332450503 -603000 ekin = 0.0845381560106908 | erot = 0.270530726252483 | epot = -14.9975021273299 | etot = -14.6424332450667 -604000 ekin = 0.0944063594078219 | erot = 0.241820347963514 | epot = -14.9786599524718 | etot = -14.6424332451004 -605000 ekin = 0.104851562460546 | erot = 0.217171224791095 | epot = -14.9644560323987 | etot = -14.6424332451471 -606000 ekin = 0.115317556389809 | erot = 0.196412930356164 | epot = -14.9541637319473 | etot = -14.6424332452013 -607000 ekin = 0.125216580353243 | erot = 0.179290709847465 | epot = -14.9469405354577 | etot = -14.6424332452569 -608000 ekin = 0.133969542490526 | erot = 0.165523445157702 | epot = -14.9419262329557 | etot = -14.6424332453075 -609000 ekin = 0.141049537028475 | erot = 0.154862582265136 | epot = -14.9383453646401 | etot = -14.6424332453465 -610000 ekin = 0.146025095175903 | erot = 0.147146040888474 | epot = -14.9356043814332 | etot = -14.6424332453689 -611000 ekin = 0.148599079335708 | erot = 0.142341118193759 | epot = -14.9333734429004 | etot = -14.6424332453709 -612000 ekin = 0.148639027542189 | erot = 0.140571068727531 | epot = -14.9316433416207 | etot = -14.6424332453509 -613000 ekin = 0.146195193893286 | erot = 0.142121441395761 | epot = -14.9307498805988 | etot = -14.6424332453097 -614000 ekin = 0.141503544705005 | erot = 0.147424293659447 | epot = -14.931361083615 | etot = -14.6424332452505 -615000 ekin = 0.134972482669537 | erot = 0.157020849768784 | epot = -14.9344265776169 | etot = -14.6424332451786 -616000 ekin = 0.127153892887427 | erot = 0.171505679772597 | epot = -14.941092817761 | etot = -14.642433245101 -617000 ekin = 0.11870096049717 | erot = 0.191457667915229 | epot = -14.9525918734383 | etot = -14.6424332450259 -618000 ekin = 0.110316794781908 | erot = 0.217364584491545 | epot = -14.9701146242349 | etot = -14.6424332449614 -619000 ekin = 0.102698942666063 | erot = 0.24954877623369 | epot = -14.9946809638151 | etot = -14.6424332449153 -620000 ekin = 0.0964852203315362 | erot = 0.288101317493775 | epot = -15.0270197827191 | etot = -14.6424332448938 -621000 ekin = 0.0922059091525968 | erot = 0.332831044367712 | epot = -15.0674701984216 | etot = -14.6424332449013 -622000 ekin = 0.0902463647100715 | erot = 0.38323345186412 | epot = -15.1159130615138 | etot = -14.6424332449397 -623000 ekin = 0.0908226920702821 | erot = 0.438482716267927 | epot = -15.1717386533468 | etot = -14.6424332450086 -624000 ekin = 0.0939716062521676 | erot = 0.497448307340542 | epot = -15.2338531586981 | etot = -14.6424332451054 -625000 ekin = 0.0995541611224928 | erot = 0.558735886785353 | epot = -15.3007232931327 | etot = -14.6424332452249 -626000 ekin = 0.10727185932578 | erot = 0.620750477457182 | epot = -15.3704555821433 | etot = -14.6424332453603 -627000 ekin = 0.11669282673767 | erot = 0.681778220901769 | epot = -15.440904293143 | etot = -14.6424332455036 -628000 ekin = 0.127285245273611 | erot = 0.740081431769978 | epot = -15.5097999226894 | etot = -14.6424332456458 -629000 ekin = 0.138455039153878 | erot = 0.794000196770909 | epot = -15.574888481703 | etot = -14.6424332457782 -630000 ekin = 0.149584842937125 | erot = 0.842052640240603 | epot = -15.6340707290701 | etot = -14.6424332458924 -631000 ekin = 0.16007149985305 | erot = 0.883025442878479 | epot = -15.6855301887134 | etot = -14.6424332459819 -632000 ekin = 0.169359720292797 | erot = 0.916046503426873 | epot = -15.7278394697614 | etot = -14.6424332460418 -633000 ekin = 0.17697005369257 | erot = 0.940632922941154 | epot = -15.7600362227032 | etot = -14.6424332460695 -634000 ekin = 0.182519961289978 | erot = 0.956709735134137 | epot = -15.781662942489 | etot = -14.6424332460649 -635000 ekin = 0.185737466035669 | erot = 0.964597760206484 | epot = -15.7927684722726 | etot = -14.6424332460304 -636000 ekin = 0.186467519303327 | erot = 0.964972204256472 | epot = -15.7938729695301 | etot = -14.6424332459703 -637000 ekin = 0.184671774604503 | erot = 0.958796660376594 | epot = -15.7859016808714 | etot = -14.6424332458903 -638000 ekin = 0.180422825778069 | erot = 0.947239527072976 | epot = -15.770095598648 | etot = -14.6424332457969 -639000 ekin = 0.173894119064868 | erot = 0.931581224196161 | epot = -15.7479085889582 | etot = -14.6424332456971 -640000 ekin = 0.165346701827808 | erot = 0.913120838753317 | epot = -15.7209007861785 | etot = -14.6424332455974 -641000 ekin = 0.155113786103713 | erot = 0.893090060089577 | epot = -15.6906370916966 | etot = -14.6424332455033 -642000 ekin = 0.143583869244232 | erot = 0.872580710306069 | epot = -15.6585978249697 | etot = -14.6424332454194 -643000 ekin = 0.131182953689577 | erot = 0.852490168054228 | epot = -15.6261063670927 | etot = -14.6424332453489 -644000 ekin = 0.11835630576118 | erot = 0.833486853990155 | epot = -15.5942764050452 | etot = -14.6424332452939 -645000 ekin = 0.105550209085084 | erot = 0.815995971212681 | epot = -15.5639794255528 | etot = -14.642433245255 -646000 ekin = 0.093194274419463 | erot = 0.800204061931152 | epot = -15.5358315815826 | etot = -14.642433245232 -647000 ekin = 0.0816850001800759 | erot = 0.786079744440879 | epot = -15.5101979898445 | etot = -14.6424332452235 -648000 ekin = 0.0713713598437969 | erot = 0.773407243193161 | epot = -15.4872118482646 | etot = -14.6424332452277 -649000 ekin = 0.0625431628717073 | erot = 0.761828976530834 | epot = -15.4668053846445 | etot = -14.642433245242 -650000 ekin = 0.0554227735503065 | erot = 0.750893453414394 | epot = -15.4487494722282 | etot = -14.6424332452635 -651000 ekin = 0.0501605027658154 | erot = 0.740104978449003 | epot = -15.4326987265042 | etot = -14.6424332452894 -652000 ekin = 0.0468336713663407 | erot = 0.728972100421355 | epot = -15.4182390171044 | etot = -14.6424332453167 -653000 ekin = 0.0454490492573823 | erot = 0.717052285945779 | epot = -15.4049345805458 | etot = -14.6424332453426 -654000 ekin = 0.0459481524943509 | erot = 0.70399086978471 | epot = -15.392372267644 | etot = -14.6424332453649 -655000 ekin = 0.0482147495286276 | erot = 0.689552835107397 | epot = -15.3802008300174 | etot = -14.6424332453814 -656000 ekin = 0.0520838761262644 | erot = 0.673646332749874 | epot = -15.3681634542669 | etot = -14.6424332453908 -657000 ekin = 0.0573516620848622 | erot = 0.656337023115527 | epot = -15.3561219305923 | etot = -14.6424332453919 -658000 ekin = 0.0637853134928166 | erot = 0.637852348219607 | epot = -15.344070907097 | etot = -14.6424332453846 -659000 ekin = 0.0711326702869886 | erot = 0.618574815847844 | epot = -15.3321407315043 | etot = -14.6424332453694 -660000 ekin = 0.0791308828101371 | erot = 0.599023454708784 | epot = -15.3205875828668 | etot = -14.6424332453479 -661000 ekin = 0.0875139366233974 | erot = 0.57982293974748 | epot = -15.309770121693 | etot = -14.6424332453222 -662000 ekin = 0.0960190004199823 | erot = 0.561660610347651 | epot = -15.3001128560629 | etot = -14.6424332452952 -663000 ekin = 0.104391848885353 | erot = 0.545232746054702 | epot = -15.2920578402108 | etot = -14.6424332452707 -664000 ekin = 0.112391863390337 | erot = 0.531182949318112 | epot = -15.2860080579609 | etot = -14.6424332452524 -665000 ekin = 0.119797262721372 | erot = 0.520037124796779 | epot = -15.2822676327621 | etot = -14.6424332452439 -666000 ekin = 0.126411190063575 | erot = 0.512141060960667 | epot = -15.2809854962725 | etot = -14.6424332452483 -667000 ekin = 0.132069035725156 | erot = 0.50760768172899 | epot = -15.2821099627212 | etot = -14.6424332452671 -668000 ekin = 0.136646914542223 | erot = 0.506281315754211 | epot = -15.2853614755972 | etot = -14.6424332453008 -669000 ekin = 0.140070616013037 | erot = 0.507725566171581 | epot = -15.2902294275325 | etot = -14.6424332453479 -670000 ekin = 0.142323740906691 | erot = 0.511239425098608 | epot = -15.2959964114102 | etot = -14.6424332454049 -671000 ekin = 0.143453306303075 | erot = 0.515903234044913 | epot = -15.3017897858151 | etot = -14.6424332454671 -672000 ekin = 0.143571012732429 | erot = 0.520652256718095 | epot = -15.3066565149792 | etot = -14.6424332455287 -673000 ekin = 0.142848733836965 | erot = 0.524371563356991 | epot = -15.3096535427773 | etot = -14.6424332455833 -674000 ekin = 0.141507613277731 | erot = 0.526002362930676 | epot = -15.3099432218337 | etot = -14.6424332456253 -675000 ekin = 0.139801302825604 | erot = 0.524647629024546 | epot = -15.3068821775003 | etot = -14.6424332456501 -676000 ekin = 0.137995095210655 | erot = 0.519664439041476 | epot = -15.3000927799068 | etot = -14.6424332456546 -677000 ekin = 0.136343677285201 | erot = 0.510732098517963 | epot = -15.2895090214411 | etot = -14.6424332456379 -678000 ekin = 0.135070664122621 | erot = 0.497888575256477 | epot = -15.2753924849801 | etot = -14.642433245601 -679000 ekin = 0.134352810444884 | erot = 0.481532294132544 | epot = -15.2583183501238 | etot = -14.6424332455464 -680000 ekin = 0.134310862655773 | erot = 0.462390968605323 | epot = -15.2391350767392 | etot = -14.6424332454781 -681000 ekin = 0.135007638923145 | erot = 0.441462941784857 | epot = -15.218903826109 | etot = -14.642433245401 -682000 ekin = 0.13645246152461 | erot = 0.419938865037855 | epot = -15.1988245718826 | etot = -14.6424332453201 -683000 ekin = 0.138609887397967 | erot = 0.399112293315506 | epot = -15.180155425954 | etot = -14.6424332452405 -684000 ekin = 0.141410065648281 | erot = 0.38028718176242 | epot = -15.164130492578 | etot = -14.6424332451673 -685000 ekin = 0.144758102722259 | erot = 0.364688846299456 | epot = -15.1518801941268 | etot = -14.6424332451051 -686000 ekin = 0.148540467119441 | erot = 0.353383275614529 | epot = -15.1443569877921 | etot = -14.6424332450581 -687000 ekin = 0.152627512098729 | erot = 0.347208212230897 | epot = -15.1422689693592 | etot = -14.6424332450296 -688000 ekin = 0.156872371008247 | erot = 0.346718408271177 | epot = -15.1460240243021 | etot = -14.6424332450226 -689000 ekin = 0.161107527974783 | erot = 0.35214694111545 | epot = -15.1556877141289 | etot = -14.6424332450387 -690000 ekin = 0.165141087380649 | erot = 0.36338430494212 | epot = -15.1709586374008 | etot = -14.6424332450781 -691000 ekin = 0.168755042649078 | erot = 0.379976931156632 | epot = -15.1911652189454 | etot = -14.6424332451396 -692000 ekin = 0.171707649703689 | erot = 0.401146558397852 | epot = -15.215287453322 | etot = -14.6424332452204 -693000 ekin = 0.173741393443089 | erot = 0.42583123278867 | epot = -15.2420058715475 | etot = -14.6424332453157 -694000 ekin = 0.174597110624771 | erot = 0.452747528140126 | epot = -15.2697778841841 | etot = -14.6424332454192 -695000 ekin = 0.174033757472238 | erot = 0.480471830922422 | epot = -15.2969388339178 | etot = -14.6424332455232 -696000 ekin = 0.171852263364757 | erot = 0.507536398158356 | epot = -15.3218219071425 | etot = -14.6424332456194 -697000 ekin = 0.167921065290933 | erot = 0.532533688693164 | epot = -15.3428879996837 | etot = -14.6424332456996 -698000 ekin = 0.162200409477029 | erot = 0.554220619925199 | epot = -15.3588542751586 | etot = -14.6424332457564 -699000 ekin = 0.154762415715643 | erot = 0.571613361028106 | epot = -15.3688090225278 | etot = -14.642433245784 -700000 ekin = 0.145804230008803 | erot = 0.584063387088072 | epot = -15.3723008628759 | etot = -14.6424332457791 -701000 ekin = 0.135652269558616 | erot = 0.591306922721422 | epot = -15.3693924380207 | etot = -14.6424332457407 -702000 ekin = 0.124756460207487 | erot = 0.593482464349051 | epot = -15.3606721702277 | etot = -14.6424332456711 -703000 ekin = 0.113674325951271 | erot = 0.591114401856995 | epot = -15.3472219733833 | etot = -14.642433245575 -704000 ekin = 0.1030456759456 | erot = 0.585064323196589 | epot = -15.3305432446015 | etot = -14.6424332454593 -705000 ekin = 0.0935593581963262 | erot = 0.576454826534689 | epot = -15.3124474300639 | etot = -14.6424332453329 -706000 ekin = 0.0859140824284925 | erot = 0.566573150256724 | epot = -15.2949204778902 | etot = -14.642433245205 -707000 ekin = 0.0807756759557919 | erot = 0.556763427609511 | epot = -15.279972348651 | etot = -14.6424332450857 -708000 ekin = 0.0787333622600079 | erot = 0.548316855291324 | epot = -15.2694834625352 | etot = -14.6424332449839 -709000 ekin = 0.0802577669151073 | erot = 0.542368667954005 | epot = -15.2650596797768 | etot = -14.6424332449077 -710000 ekin = 0.0856633545528672 | erot = 0.539809747049325 | epot = -15.2679063464655 | etot = -14.6424332448633 -711000 ekin = 0.095077851902745 | erot = 0.541219180891425 | epot = -15.278730277649 | etot = -14.6424332448548 -712000 ekin = 0.108420876622167 | erot = 0.546822307911541 | epot = -15.2976764294173 | etot = -14.6424332448836 -713000 ekin = 0.125393451694849 | erot = 0.556476834657793 | epot = -15.3243035313014 | etot = -14.6424332449487 -714000 ekin = 0.145479367621451 | erot = 0.56968760011942 | epot = -15.3576002127876 | etot = -14.6424332450467 -715000 ekin = 0.167958541116837 | erot = 0.585648522303156 | epot = -15.396040308592 | etot = -14.642433245172 -716000 ekin = 0.191931735851211 | erot = 0.603308292531433 | epot = -15.4376732736996 | etot = -14.6424332453169 -717000 ekin = 0.216355400176877 | erot = 0.621454592037058 | epot = -15.4802432376869 | etot = -14.6424332454729 -718000 ekin = 0.24008505651043 | erot = 0.638810139731555 | epot = -15.5213284418724 | etot = -14.6424332456304 -719000 ekin = 0.261925698575348 | erot = 0.654132895986132 | epot = -15.5584918403414 | etot = -14.6424332457799 -720000 ekin = 0.280687969311602 | erot = 0.6663123798671 | epot = -15.5894335950909 | etot = -14.6424332459122 -721000 ekin = 0.295249345589177 | erot = 0.674454385927726 | epot = -15.612136977536 | etot = -14.6424332460191 -722000 ekin = 0.304619886333769 | erot = 0.677947410255128 | epot = -15.6250005426823 | etot = -14.6424332460934 -723000 ekin = 0.308011983728025 | erot = 0.676505724570436 | epot = -15.6269509544278 | etot = -14.6424332461294 -724000 ekin = 0.304912667284422 | erot = 0.670186105899586 | epot = -15.617532019307 | etot = -14.642433246123 -725000 ekin = 0.295155116711621 | erot = 0.659377522489412 | epot = -15.596965885273 | etot = -14.642433246072 -726000 ekin = 0.278983134900163 | erot = 0.644765363158375 | epot = -15.5661817440352 | etot = -14.6424332459767 -727000 ekin = 0.257098790794435 | erot = 0.627273860362892 | epot = -15.5268058969976 | etot = -14.6424332458402 -728000 ekin = 0.230680158274999 | erot = 0.607992016180427 | epot = -15.4811054201245 | etot = -14.6424332456691 -729000 ekin = 0.201354496276734 | erot = 0.588089464034349 | epot = -15.4318772057847 | etot = -14.6424332454737 -730000 ekin = 0.171114103979347 | erot = 0.56872921471559 | epot = -15.3822765639634 | etot = -14.6424332452685 -731000 ekin = 0.142168923912302 | erot = 0.55098413507048 | epot = -15.335586304054 | etot = -14.6424332450712 -732000 ekin = 0.116742007100633 | erot = 0.535763349043665 | epot = -15.2949386010453 | etot = -14.642433244901 -733000 ekin = 0.09682930275761 | erot = 0.523753647321524 | epot = -15.2630161948552 | etot = -14.6424332447761 -734000 ekin = 0.0839596135620733 | erot = 0.515379592338451 | epot = -15.2417724506113 | etot = -14.6424332447107 -735000 ekin = 0.0789983701793142 | erot = 0.510784464195818 | epot = -15.2322160790872 | etot = -14.6424332447121 -736000 ekin = 0.0820355551944443 | erot = 0.509832642266179 | epot = -15.2343014422398 | etot = -14.6424332447791 -737000 ekin = 0.0923827123871823 | erot = 0.512132550855379 | epot = -15.2469485081446 | etot = -14.642433244902 -738000 ekin = 0.10868044851431 | erot = 0.517077971027559 | epot = -15.2681916646065 | etot = -14.6424332450646 -739000 ekin = 0.129093715683514 | erot = 0.523904364926965 | epot = -15.2954313258571 | etot = -14.6424332452466 -740000 ekin = 0.151555277793959 | erot = 0.531755895780137 | epot = -15.3257444190018 | etot = -14.6424332454277 -741000 ekin = 0.174012721806636 | erot = 0.539758083454087 | epot = -15.3562040508504 | etot = -14.6424332455896 -742000 ekin = 0.194640916831482 | erot = 0.54709054970013 | epot = -15.3841647122503 | etot = -14.6424332457187 -743000 ekin = 0.211995737398838 | erot = 0.553054125338314 | epot = -15.4074831085433 | etot = -14.6424332458062 -744000 ekin = 0.225100508723079 | erot = 0.557126762310524 | epot = -15.424660516882 | etot = -14.6424332458484 -745000 ekin = 0.233469424487108 | erot = 0.559003260239957 | epot = -15.4349059305735 | etot = -14.6424332458464 -746000 ekin = 0.237079913465558 | erot = 0.558614810500983 | epot = -15.4381279697713 | etot = -14.6424332458048 -747000 ekin = 0.236308652985589 | erot = 0.556125790084016 | epot = -15.4348676888005 | etot = -14.6424332457309 -748000 ekin = 0.231845097888752 | erot = 0.55190707933143 | epot = -15.4261854228542 | etot = -14.642433245634 -749000 ekin = 0.224593843485221 | erot = 0.546487360031015 | epot = -15.4135144490412 | etot = -14.6424332455249 -750000 ekin = 0.215574369393402 | erot = 0.540486233486425 | epot = -15.3984938482944 | etot = -14.6424332454146 -751000 ekin = 0.205824583428198 | erot = 0.534535356766148 | epot = -15.3827931855081 | etot = -14.6424332453138 -752000 ekin = 0.196313335743884 | erot = 0.52919581522017 | epot = -15.3679423961961 | etot = -14.642433245232 -753000 ekin = 0.187866475789629 | erot = 0.524881252733656 | epot = -15.3551809737001 | etot = -14.6424332451768 -754000 ekin = 0.181110613628486 | erot = 0.521796491099562 | epot = -15.3453403498807 | etot = -14.6424332451526 -755000 ekin = 0.176438042206913 | erot = 0.519900210808863 | epot = -15.3387714981765 | etot = -14.6424332451607 -756000 ekin = 0.173994962649932 | erot = 0.518897676286876 | epot = -15.3353258841353 | etot = -14.6424332451985 -757000 ekin = 0.173693190273803 | erot = 0.518265706184404 | epot = -15.3343921417187 | etot = -14.6424332452605 -758000 ekin = 0.175243155018275 | erot = 0.517307659823502 | epot = -15.3349840601801 | etot = -14.6424332453383 -759000 ekin = 0.178203703096672 | erot = 0.515231902166426 | epot = -15.3358688506853 | etot = -14.6424332454222 -760000 ekin = 0.182042463552542 | erot = 0.511243837950911 | epot = -15.3357195470056 | etot = -14.6424332455021 -761000 ekin = 0.186199747764937 | erot = 0.504639825549636 | epot = -15.3332728188833 | etot = -14.6424332455687 -762000 ekin = 0.190149235948647 | erot = 0.494891409035961 | epot = -15.3274738905993 | etot = -14.6424332456147 -763000 ekin = 0.193449921097656 | erot = 0.48171023828929 | epot = -15.3175934050219 | etot = -14.642433245635 -764000 ekin = 0.195785552428858 | erot = 0.465087294353624 | epot = -15.3033060924099 | etot = -14.6424332456274 -765000 ekin = 0.196989678186435 | erot = 0.445303873494018 | epot = -15.2847267972728 | etot = -14.6424332455924 -766000 ekin = 0.197055919183657 | erot = 0.422915440293833 | epot = -15.2624046050103 | etot = -14.6424332455328 -767000 ekin = 0.196134076493791 | erot = 0.398712320924463 | epot = -15.2372796428714 | etot = -14.6424332454532 -768000 ekin = 0.19451309665161 | erot = 0.373662938959324 | epot = -15.2106092809708 | etot = -14.6424332453598 -769000 ekin = 0.192592017625545 | erot = 0.348845887485747 | epot = -15.183871150371 | etot = -14.6424332452597 -770000 ekin = 0.190840163684042 | erot = 0.325376840212043 | epot = -15.1586502490567 | etot = -14.6424332451606 -771000 ekin = 0.189748397224706 | erot = 0.304335529899335 | epot = -15.1365171721945 | etot = -14.6424332450705 -772000 ekin = 0.189774341847512 | erot = 0.286697153920059 | epot = -15.1189047407643 | etot = -14.6424332449968 -773000 ekin = 0.191286034497103 | erot = 0.273271857835136 | epot = -15.1069911372781 | etot = -14.6424332449458 -774000 ekin = 0.194510000604928 | erot = 0.264655458968671 | epot = -15.1015987044965 | etot = -14.6424332449229 -775000 ekin = 0.1994906396753 | erot = 0.261194193154413 | epot = -15.1031180777602 | etot = -14.6424332449305 -776000 ekin = 0.20606747706162 | erot = 0.262965803934266 | epot = -15.1114665259645 | etot = -14.6424332449687 -777000 ekin = 0.213875019082075 | erot = 0.269778568411878 | epot = -15.1260868325288 | etot = -14.6424332450348 -778000 ekin = 0.222366868961501 | erot = 0.281188790675803 | epot = -15.1459889047609 | etot = -14.6424332451236 -779000 ekin = 0.23086210226578 | erot = 0.296535944176041 | epot = -15.1698312916694 | etot = -14.6424332452276 -780000 ekin = 0.238608567016832 | erot = 0.314993169091967 | epot = -15.1960349814467 | etot = -14.6424332453379 -781000 ekin = 0.244855557739749 | erot = 0.335629445236581 | epot = -15.2229182484218 | etot = -14.6424332454454 -782000 ekin = 0.24892761247725 | erot = 0.357478674286814 | epot = -15.2488395323052 | etot = -14.6424332455412 -783000 ekin = 0.250291897528933 | erot = 0.379610269028307 | epot = -15.2723354121746 | etot = -14.6424332456174 -784000 ekin = 0.248613283253142 | erot = 0.401195731122951 | epot = -15.2922422600441 | etot = -14.642433245668 -785000 ekin = 0.243793133451306 | erot = 0.421566090466591 | epot = -15.307792469607 | etot = -14.6424332456891 -786000 ekin = 0.235989501853544 | erot = 0.440255905206922 | epot = -15.3186786527391 | etot = -14.6424332456787 -787000 ekin = 0.225617610785755 | erot = 0.457030673432498 | epot = -15.3250815298558 | etot = -14.6424332456375 -788000 ekin = 0.213330260903068 | erot = 0.471895861696116 | epot = -15.3276593681681 | etot = -14.6424332455689 -789000 ekin = 0.199978499678474 | erot = 0.485087183883212 | epot = -15.3274989290401 | etot = -14.6424332454784 -790000 ekin = 0.186553834704413 | erot = 0.497043141243068 | epot = -15.3260302213206 | etot = -14.6424332453731 -791000 ekin = 0.174114766793401 | erot = 0.508362048570016 | epot = -15.3249100606255 | etot = -14.6424332452621 -792000 ekin = 0.163702420432354 | erot = 0.519746739181041 | epot = -15.3258824047684 | etot = -14.642433245155 -793000 ekin = 0.156252224966272 | erot = 0.531940822989567 | epot = -15.3306262930174 | etot = -14.6424332450615 -794000 ekin = 0.152510350034305 | erot = 0.545660777315136 | epot = -15.3406043723396 | etot = -14.6424332449902 -795000 ekin = 0.15296425115691 | erot = 0.561528326981077 | epot = -15.3569258230862 | etot = -14.6424332449482 -796000 ekin = 0.157795747355293 | erot = 0.58000757877803 | epot = -15.3802365710733 | etot = -14.64243324494 -797000 ekin = 0.166862457855209 | erot = 0.601351255569628 | epot = -15.4106469583921 | etot = -14.6424332449673 -798000 ekin = 0.179709603428639 | erot = 0.625560121845548 | epot = -15.4477029703033 | etot = -14.6424332450291 -799000 ekin = 0.195609966057174 | erot = 0.652359247176621 | epot = -15.4904024583554 | etot = -14.6424332451216 -800000 ekin = 0.213626158786275 | erot = 0.681194021873727 | epot = -15.5372534258987 | etot = -14.6424332452387 -801000 ekin = 0.23268704018842 | erot = 0.711247726386662 | epot = -15.5863680119477 | etot = -14.6424332453727 -802000 ekin = 0.251669429101161 | erot = 0.74148091983623 | epot = -15.6355835944521 | etot = -14.6424332455147 -803000 ekin = 0.269477067853805 | erot = 0.77069100842129 | epot = -15.6826013219308 | etot = -14.6424332456557 -804000 ekin = 0.285110541453744 | erot = 0.797588259158567 | epot = -15.7251320463987 | etot = -14.6424332457864 -805000 ekin = 0.297723982502972 | erot = 0.820882528799733 | epot = -15.7610397572013 | etot = -14.6424332458986 -806000 ekin = 0.306666387684833 | erot = 0.839373432913609 | epot = -15.7884730665839 | etot = -14.6424332459854 -807000 ekin = 0.31150697555439 | erot = 0.852035914445983 | epot = -15.805976136042 | etot = -14.6424332460416 -808000 ekin = 0.312045176252642 | erot = 0.858093398528306 | epot = -15.8125718208452 | etot = -14.6424332460642 -809000 ekin = 0.308306642387692 | erot = 0.857071970758726 | epot = -15.8078118591988 | etot = -14.6424332460524 -810000 ekin = 0.300527220561155 | erot = 0.848831113928873 | epot = -15.7917915804976 | etot = -14.6424332460076 -811000 ekin = 0.289127204421254 | erot = 0.833569138622274 | epot = -15.7651295889768 | etot = -14.6424332459333 -812000 ekin = 0.274678427602453 | erot = 0.81180411649313 | epot = -15.7289157899302 | etot = -14.6424332458346 -813000 ekin = 0.25786683558395 | erot = 0.784333459542784 | epot = -15.6846335408444 | etot = -14.6424332457177 -814000 ekin = 0.239453080594243 | erot = 0.752176980196514 | epot = -15.6340633063802 | etot = -14.6424332455895 -815000 ekin = 0.220233415151703 | erot = 0.716509170266734 | epot = -15.5791758308754 | etot = -14.642433245457 -816000 ekin = 0.201002751046678 | erot = 0.678586569748113 | epot = -15.5220225661216 | etot = -14.6424332453268 -817000 ekin = 0.182521261080269 | erot = 0.639675603864976 | epot = -15.4646301101501 | etot = -14.6424332452049 -818000 ekin = 0.16548540152786 | erot = 0.600985363831456 | epot = -15.4089040104558 | etot = -14.6424332450964 -819000 ekin = 0.15050378978042 | erot = 0.563608719249299 | epot = -15.3565457540354 | etot = -14.6424332450057 -820000 ekin = 0.138078032178478 | erot = 0.528474068972393 | epot = -15.3089853460865 | etot = -14.6424332449356 -821000 ekin = 0.128588386730135 | erot = 0.496309093117806 | epot = -15.2673307247362 | etot = -14.6424332448883 -822000 ekin = 0.122284066136812 | erot = 0.467617125515789 | epot = -15.2323344365172 | etot = -14.6424332448646 -823000 ekin = 0.119278020924339 | erot = 0.44266622847877 | epot = -15.2043774942677 | etot = -14.6424332448646 -824000 ekin = 0.119546158603677 | erot = 0.421490682738665 | epot = -15.1834700862295 | etot = -14.6424332448872 -825000 ekin = 0.122931110514549 | erot = 0.403904342223771 | epot = -15.1692686976685 | etot = -14.6424332449302 -826000 ekin = 0.129150803764327 | erot = 0.389525075000029 | epot = -15.161109123755 | etot = -14.6424332449907 -827000 ekin = 0.137812176399179 | erot = 0.377809252270532 | epot = -15.1580546737345 | etot = -14.6424332450648 -828000 ekin = 0.148430331608382 | erot = 0.368094906962796 | epot = -15.1589584837191 | etot = -14.6424332451479 -829000 ekin = 0.160453205761696 | erot = 0.359651737511967 | epot = -15.1625381885082 | etot = -14.6424332452346 -830000 ekin = 0.17329138289678 | erot = 0.351735589545236 | epot = -15.1674602177611 | etot = -14.6424332453191 -831000 ekin = 0.186352012962992 | erot = 0.343644456329796 | epot = -15.1724297146884 | etot = -14.6424332453957 -832000 ekin = 0.19907492460549 | erot = 0.334772487920949 | epot = -15.1762806579855 | etot = -14.642433245459 -833000 ekin = 0.21096808488054 | erot = 0.324658115188717 | epot = -15.1780594455737 | etot = -14.6424332455044 -834000 ekin = 0.22163875725698 | erot = 0.313022323442326 | epot = -15.1770943262282 | etot = -14.6424332455289 -835000 ekin = 0.230816330001966 | erot = 0.299793483326653 | epot = -15.1730430588596 | etot = -14.642433245531 -836000 ekin = 0.238363132174234 | erot = 0.28511603996084 | epot = -15.1659124176466 | etot = -14.6424332455115 -837000 ekin = 0.244270841530998 | erot = 0.269341751259632 | epot = -15.1560458382641 | etot = -14.6424332454734 -838000 ekin = 0.248642320235733 | erot = 0.25300390410384 | epot = -15.1440794697607 | etot = -14.6424332454212 -839000 ekin = 0.251661569327697 | erot = 0.23677675898714 | epot = -15.1308715736755 | etot = -14.6424332453607 -840000 ekin = 0.253557306828274 | erot = 0.221424057161473 | epot = -15.1174146092878 | etot = -14.642433245298 -841000 ekin = 0.254567562696821 | erot = 0.207741475743574 | epot = -15.104742283679 | etot = -14.6424332452386 -842000 ekin = 0.254912814683751 | erot = 0.196498262354278 | epot = -15.0938443222248 | etot = -14.6424332451868 -843000 ekin = 0.254783130765828 | erot = 0.188382921787058 | epot = -15.085599297698 | etot = -14.6424332451451 -844000 ekin = 0.254340789697888 | erot = 0.183956927272106 | epot = -15.0807309620847 | etot = -14.6424332451147 -845000 ekin = 0.253734932891713 | erot = 0.183619247980611 | epot = -15.0797874259676 | etot = -14.6424332450953 -846000 ekin = 0.253120504196155 | erot = 0.187583282239862 | epot = -15.0831370315226 | etot = -14.6424332450866 -847000 ekin = 0.252671650088266 | erot = 0.195866742639111 | epot = -15.0909716378154 | etot = -14.642433245088 -848000 ekin = 0.25258091531028 | erot = 0.20829422246314 | epot = -15.1033083828732 | etot = -14.6424332450998 -849000 ekin = 0.253039966848252 | erot = 0.224511555531826 | epot = -15.1199847675027 | etot = -14.6424332451227 -850000 ekin = 0.254204001798515 | erot = 0.244010590097797 | epot = -15.1406478370536 | etot = -14.6424332451573 -851000 ekin = 0.256148339026787 | erot = 0.26616256360263 | epot = -15.1647441478333 | etot = -14.6424332452039 -852000 ekin = 0.258829686440588 | erot = 0.290257858698213 | epot = -15.1915207904 | etot = -14.6424332452612 -853000 ekin = 0.262064657828587 | erot = 0.315549558167727 | epot = -15.2200474613225 | etot = -14.6424332453262 -854000 ekin = 0.265534116122648 | erot = 0.341297947736379 | epot = -15.2492653092531 | etot = -14.6424332453941 -855000 ekin = 0.26881517465358 | erot = 0.366813004430893 | epot = -15.2780614245436 | etot = -14.6424332454591 -856000 ekin = 0.271435486954603 | erot = 0.391492007901445 | epot = -15.305360740371 | etot = -14.642433245515 -857000 ekin = 0.272939108063008 | erot = 0.414849750473414 | epot = -15.3302221040928 | etot = -14.6424332455564 -858000 ekin = 0.272951155039785 | erot = 0.436539390688027 | epot = -15.3519237913071 | etot = -14.6424332455793 -859000 ekin = 0.271229880676472 | erot = 0.456362750059341 | epot = -15.3700258763176 | etot = -14.6424332455817 -860000 ekin = 0.267698633833911 | erot = 0.474269718460682 | epot = -15.3844015978589 | etot = -14.6424332455643 -861000 ekin = 0.262455001752904 | erot = 0.490347316007815 | epot = -15.3952355632896 | etot = -14.6424332455289 -862000 ekin = 0.255758797176706 | erot = 0.504799761298941 | epot = -15.402991803955 | etot = -14.6424332454794 -863000 ekin = 0.248003564341433 | erot = 0.517921532812514 | epot = -15.4083583425743 | etot = -14.6424332454204 -864000 ekin = 0.23967765558487 | erot = 0.5300658235034 | epot = -15.4121767244453 | etot = -14.642433245357 -865000 ekin = 0.23132088944539 | erot = 0.541610953534341 | epot = -15.4153650882739 | etot = -14.6424332452941 -866000 ekin = 0.223481813676297 | erot = 0.552927233331988 | epot = -15.4188422922445 | etot = -14.6424332452362 -867000 ekin = 0.216679174491969 | erot = 0.564346499432351 | epot = -15.4234589191111 | etot = -14.6424332451867 -868000 ekin = 0.211369750018244 | erot = 0.57613613893885 | epot = -15.4299391341058 | etot = -14.6424332451487 -869000 ekin = 0.207923502308331 | erot = 0.588478941151472 | epot = -15.4388356885839 | etot = -14.6424332451241 -870000 ekin = 0.206606153000455 | erot = 0.601459626890416 | epot = -15.4504990250046 | etot = -14.6424332451137 -871000 ekin = 0.207568796758621 | erot = 0.615058451105655 | epot = -15.4650604929822 | etot = -14.6424332451179 -872000 ekin = 0.210843969902065 | erot = 0.62915187575959 | epot = -15.4824290907976 | etot = -14.642433245136 -873000 ekin = 0.216347593119461 | erot = 0.643519970833663 | epot = -15.5023008091198 | etot = -14.6424332451666 -874000 ekin = 0.223886305143511 | erot = 0.65785990973072 | epot = -15.5241794600822 | etot = -14.6424332452079 -875000 ekin = 0.233169807553207 | erot = 0.67180466221101 | epot = -15.5474077150216 | etot = -14.6424332452574 -876000 ekin = 0.243827877963662 | erot = 0.684945735800061 | epot = -15.5712068590757 | etot = -14.642433245312 -877000 ekin = 0.255431632545988 | erot = 0.696858567354671 | epot = -15.5947234452691 | etot = -14.6424332453684 -878000 ekin = 0.267518408513276 | erot = 0.707128927388885 | epot = -15.6170805813255 | etot = -14.6424332454234 -879000 ekin = 0.279619300259048 | erot = 0.71537849572129 | epot = -15.6374310414537 | etot = -14.6424332454734 -880000 ekin = 0.291287955020511 | erot = 0.721287639199272 | epot = -15.6550088397353 | etot = -14.6424332455155 -881000 ekin = 0.30212877846463 | erot = 0.724613422810775 | epot = -15.6691754468226 | etot = -14.6424332455472 -882000 ekin = 0.311822304068824 | erot = 0.725201068176889 | epot = -15.6794566178125 | etot = -14.6424332455668 -883000 ekin = 0.320145243787706 | erot = 0.722987481104172 | epot = -15.6855659704655 | etot = -14.6424332455736 -884000 ekin = 0.326982762198909 | erot = 0.717996120159159 | epot = -15.6874121279265 | etot = -14.6424332455684 -885000 ekin = 0.332330882212481 | erot = 0.710323349672059 | epot = -15.6850874774374 | etot = -14.6424332455528 -886000 ekin = 0.33628767333099 | erot = 0.700117442976239 | epot = -15.678838361837 | etot = -14.6424332455298 -887000 ekin = 0.339032964151614 | erot = 0.687552454437006 | epot = -15.6690186640916 | etot = -14.642433245503 -888000 ekin = 0.340797654544347 | erot = 0.67280010094551 | epot = -15.6560310009666 | etot = -14.6424332454768 -889000 ekin = 0.341825106158976 | erot = 0.656003407102339 | epot = -15.6402617587166 | etot = -14.6424332454552 -890000 ekin = 0.342328347575176 | erot = 0.63725601316603 | epot = -15.6220176061831 | etot = -14.6424332454419 -891000 ekin = 0.342447730492056 | erot = 0.616590618570594 | epot = -15.601471594502 | etot = -14.6424332454393 -892000 ekin = 0.342214057411724 | erot = 0.593979026506924 | epot = -15.5786263293674 | etot = -14.6424332454488 -893000 ekin = 0.341522004910123 | erot = 0.569344767734232 | epot = -15.5533000181139 | etot = -14.6424332454695 -894000 ekin = 0.340117934117577 | erot = 0.542587519917294 | epot = -15.5251386995343 | etot = -14.6424332454994 -895000 ekin = 0.337605044782497 | erot = 0.51361677898196 | epot = -15.4936550692992 | etot = -14.6424332455348 -896000 ekin = 0.333467462872322 | erot = 0.482390775175684 | epot = -15.4582914836184 | etot = -14.6424332455704 -897000 ekin = 0.327113397522066 | erot = 0.448955709004578 | epot = -15.418502352127 | etot = -14.6424332456003 -898000 ekin = 0.317936017621476 | erot = 0.413480165460528 | epot = -15.3738494287003 | etot = -14.6424332456182 -899000 ekin = 0.305389123797598 | erot = 0.376280077470489 | epot = -15.3241024468861 | etot = -14.642433245618 -900000 ekin = 0.289072881398049 | erot = 0.337830752319602 | epot = -15.2693368793114 | etot = -14.6424332455938 -901000 ekin = 0.268822686263612 | erot = 0.298764046956934 | epot = -15.2100199787618 | etot = -14.6424332455413 -902000 ekin = 0.244791653973738 | erot = 0.259850521116738 | epot = -15.1470754205486 | etot = -14.6424332454581 -903000 ekin = 0.217514571467803 | erot = 0.221968047208507 | epot = -15.0819158640206 | etot = -14.6424332453443 -904000 ekin = 0.187939204416829 | erot = 0.186059692010109 | epot = -15.0164321416307 | etot = -14.6424332452037 -905000 ekin = 0.157410847736455 | erot = 0.153084564881008 | epot = -14.9529286576612 | etot = -14.6424332450437 -906000 ekin = 0.127599356275899 | erot = 0.123965703542346 | epot = -14.8939983046941 | etot = -14.6424332448759 -907000 ekin = 0.100365589134322 | erot = 0.0995389863868474 | epot = -14.8423378202363 | etot = -14.6424332447151 -908000 ekin = 0.077575985596966 | erot = 0.0805066337376087 | epot = -14.800515863912 | etot = -14.6424332445775 -909000 ekin = 0.0608876950043041 | erot = 0.0673982354547353 | epot = -14.7707191749375 | etot = -14.6424332444784 -910000 ekin = 0.0515382922982525 | erot = 0.0605415547693243 | epot = -14.7545130914978 | etot = -14.6424332444302 -911000 ekin = 0.0501789452889699 | erot = 0.0600446989615507 | epot = -14.7526568886895 | etot = -14.642433244439 -912000 ekin = 0.0567846925720978 | erot = 0.065790645022677 | epot = -14.7650085820984 | etot = -14.6424332445036 -913000 ekin = 0.0706603747930292 | erot = 0.0774445361871137 | epot = -14.7905381555968 | etot = -14.6424332446166 -914000 ekin = 0.0905398584091615 | erot = 0.0944735694308371 | epot = -14.8274466726047 | etot = -14.6424332447647 -915000 ekin = 0.114756144628398 | erot = 0.116178630208142 | epot = -14.8733680197681 | etot = -14.6424332449316 -916000 ekin = 0.141447043402251 | erot = 0.141736093139704 | epot = -14.9256163816432 | etot = -14.6424332451012 -917000 ekin = 0.168758535419812 | erot = 0.170247440489189 | epot = -14.9814392211683 | etot = -14.6424332452593 -918000 ekin = 0.195014913439607 | erot = 0.200793639368855 | epot = -15.0382417982036 | etot = -14.6424332453951 -919000 ekin = 0.218837422083647 | erot = 0.232490666336242 | epot = -15.0937613339215 | etot = -14.6424332455016 -920000 ekin = 0.239206641023718 | erot = 0.264542267092076 | epot = -15.1461821536915 | etot = -14.6424332455757 -921000 ekin = 0.255474577148654 | erot = 0.296286050802385 | epot = -15.1941938735684 | etot = -14.6424332456174 -922000 ekin = 0.267338631215765 | erot = 0.327229363205489 | epot = -15.2370012400499 | etot = -14.6424332456286 -923000 ekin = 0.274791412214202 | erot = 0.357072039937939 | epot = -15.2742966977655 | etot = -14.6424332456134 -924000 ekin = 0.278059017516371 | erot = 0.385714059433155 | epot = -15.3062063225259 | etot = -14.6424332455763 -925000 ekin = 0.277537405168372 | erot = 0.41324722009601 | epot = -15.3332178707874 | etot = -14.642433245523 -926000 ekin = 0.273733135238329 | erot = 0.439931173662005 | epot = -15.3560975543592 | etot = -14.6424332454589 -927000 ekin = 0.267211859641524 | erot = 0.466155363882809 | epot = -15.3758004689143 | etot = -14.6424332453899 -928000 ekin = 0.258555847536078 | erot = 0.492389553503158 | epot = -15.3933786463609 | etot = -14.6424332453217 -929000 ekin = 0.248330567891891 | erot = 0.519126582982283 | epot = -15.4098903961336 | etot = -14.6424332452594 -930000 ekin = 0.237059747166165 | erot = 0.546821711632301 | epot = -15.4263147040064 | etot = -14.6424332452079 -931000 ekin = 0.22520814480582 | erot = 0.575833282923993 | epot = -15.4434746729008 | etot = -14.6424332451709 -932000 ekin = 0.213171319365827 | erot = 0.606369490852174 | epot = -15.4619740553694 | etot = -14.6424332451514 -933000 ekin = 0.201271722995889 | erot = 0.63844569037927 | epot = -15.482150658526 | etot = -14.6424332451508 -934000 ekin = 0.189760460110152 | erot = 0.671856006699522 | epot = -15.5040497119791 | etot = -14.6424332451694 -935000 ekin = 0.178823941838377 | erot = 0.706161996587761 | epot = -15.527419183632 | etot = -14.6424332452058 -936000 ekin = 0.168594479114955 | erot = 0.740699865837585 | epot = -15.55172759021 | etot = -14.6424332452575 -937000 ekin = 0.159163635634861 | erot = 0.774606336206385 | epot = -15.5762032171619 | etot = -14.6424332453207 -938000 ekin = 0.150596971914849 | erot = 0.806861786796458 | epot = -15.5998920041019 | etot = -14.6424332453906 -939000 ekin = 0.142948711632359 | erot = 0.836347883526831 | epot = -15.6217298406214 | etot = -14.6424332454622 -940000 ekin = 0.136274889171099 | erot = 0.861915676028948 | epot = -15.64062381073 | etot = -14.6424332455299 -941000 ekin = 0.130643703198872 | erot = 0.882459199120565 | epot = -15.6555361479082 | etot = -14.6424332455888 -942000 ekin = 0.126142088160694 | erot = 0.896989065172162 | epot = -15.6655643989671 | etot = -14.6424332456342 -943000 ekin = 0.122877886110172 | erot = 0.904700444358873 | epot = -15.6700115761318 | etot = -14.6424332456628 -944000 ekin = 0.120977407412063 | erot = 0.905030230236876 | epot = -15.6684408833212 | etot = -14.6424332456723 -945000 ekin = 0.120578563690669 | erot = 0.897699054745604 | epot = -15.6607108640983 | etot = -14.642433245662 -946000 ekin = 0.12182010359348 | erot = 0.882735070928404 | epot = -15.6469884201544 | etot = -14.6424332456325 -947000 ekin = 0.124827761129084 | erot = 0.86047793559626 | epot = -15.6277389423113 | etot = -14.642433245586 -948000 ekin = 0.129698334168674 | erot = 0.831563037037796 | epot = -15.6036946167321 | etot = -14.6424332455257 -949000 ekin = 0.13648285755817 | erot = 0.796887554722047 | epot = -15.5758036577362 | etot = -14.6424332454559 -950000 ekin = 0.14517013893121 | erot = 0.757561255988166 | epot = -15.545164640301 | etot = -14.6424332453816 -951000 ekin = 0.155672002995183 | erot = 0.71484591609363 | epot = -15.5129511643966 | etot = -14.6424332453078 -952000 ekin = 0.167811650836291 | erot = 0.670087833250127 | epot = -15.480332729326 | etot = -14.6424332452396 -953000 ekin = 0.181316579471303 | erot = 0.624648095211848 | epot = -15.4483979198644 | etot = -14.6424332451812 -954000 ekin = 0.195817500701208 | erot = 0.579835080695611 | epot = -15.4180858265331 | etot = -14.6424332451363 -955000 ekin = 0.21085460687672 | erot = 0.536843219768569 | epot = -15.3901310717525 | etot = -14.6424332451072 -956000 ekin = 0.225892299837344 | erot = 0.496701376791255 | epot = -15.3650269217236 | etot = -14.642433245095 -957000 ekin = 0.240343066498587 | erot = 0.460233438093626 | epot = -15.3430097496914 | etot = -14.6424332450992 -958000 ekin = 0.253600493839353 | erot = 0.428032849893872 | epot = -15.324066588851 | etot = -14.6424332451178 -959000 ekin = 0.265080433748287 | erot = 0.400452005458765 | epot = -15.3079656843544 | etot = -14.6424332451473 -960000 ekin = 0.274268068130606 | erot = 0.377606549449485 | epot = -15.2943078627635 | etot = -14.6424332451834 -961000 ekin = 0.280767178003658 | erot = 0.359393861249483 | epot = -15.2825942844742 | etot = -14.642433245221 -962000 ekin = 0.284346484063545 | erot = 0.345524198816493 | epot = -15.2723039281349 | etot = -14.6424332452549 -963000 ekin = 0.28497681608998 | erot = 0.33556223232907 | epot = -15.2629722936994 | etot = -14.6424332452804 -964000 ekin = 0.282852494248157 | erot = 0.328975986496775 | epot = -15.2542617260389 | etot = -14.642433245294 -965000 ekin = 0.278391086615737 | erot = 0.325189577598745 | epot = -15.2460139095084 | etot = -14.6424332452939 -966000 ekin = 0.272207924679743 | erot = 0.323635640150781 | epot = -15.2382768101107 | etot = -14.6424332452802 -967000 ekin = 0.265065367870864 | erot = 0.323803079987444 | epot = -15.2313016931133 | etot = -14.642433245255 -968000 ekin = 0.25780129371415 | erot = 0.325275872290811 | epot = -15.2255104112269 | etot = -14.6424332452219 -969000 ekin = 0.251245661474385 | erot = 0.327759142576306 | epot = -15.2214380492365 | etot = -14.6424332451859 -970000 ekin = 0.246137008993216 | erot = 0.331089781181249 | epot = -15.2196600353262 | etot = -14.6424332451517 -971000 ekin = 0.243051319616145 | erot = 0.33523032566537 | epot = -15.2207148904055 | etot = -14.642433245124 -972000 ekin = 0.242353409638764 | erot = 0.340246678804933 | epot = -15.2250333335501 | etot = -14.6424332451064 -973000 ekin = 0.244176338162503 | erot = 0.346272190710957 | epot = -15.2328817739746 | etot = -14.6424332451011 -974000 ekin = 0.248428661658007 | erot = 0.353462430362089 | epot = -15.2443243371296 | etot = -14.6424332451095 -975000 ekin = 0.254824314802991 | erot = 0.361946299430811 | epot = -15.2592038593653 | etot = -14.6424332451315 -976000 ekin = 0.262926848820441 | erot = 0.371779749930123 | epot = -15.277139843917 | etot = -14.6424332451665 -977000 ekin = 0.272199235330791 | erot = 0.382908123264411 | epot = -15.2975406038079 | etot = -14.6424332452127 -978000 ekin = 0.282052066851645 | erot = 0.395142048097818 | epot = -15.3196273602177 | etot = -14.6424332452682 -979000 ekin = 0.291885751913936 | erot = 0.408150081471835 | epot = -15.3424690787158 | etot = -14.6424332453301 -980000 ekin = 0.301125083789936 | erot = 0.421469125223117 | epot = -15.365027454408 | etot = -14.642433245395 -981000 ekin = 0.309246535917406 | erot = 0.434531423656849 | epot = -15.3862112050333 | etot = -14.642433245459 -982000 ekin = 0.315799497490907 | erot = 0.446704965617073 | epot = -15.4049377086261 | etot = -14.6424332455181 -983000 ekin = 0.320422573221183 | erot = 0.457342632744156 | epot = -15.4201984515336 | etot = -14.6424332455683 -984000 ekin = 0.322855465258642 | erot = 0.465834622599602 | epot = -15.431123333464 | etot = -14.6424332456058 -985000 ekin = 0.322946302475343 | erot = 0.471658590974231 | epot = -15.4370381390774 | etot = -14.6424332456279 -986000 ekin = 0.320653917805922 | erot = 0.474422556590712 | epot = -15.4375097200295 | etot = -14.6424332456328 -987000 ekin = 0.316044627362369 | erot = 0.473896755515841 | epot = -15.4323746284984 | etot = -14.6424332456202 -988000 ekin = 0.309283477268975 | erot = 0.470032116945433 | epot = -15.421748839805 | etot = -14.6424332455906 -989000 ekin = 0.300620522169441 | erot = 0.462964620622199 | epot = -15.4060183883375 | etot = -14.6424332455459 -990000 ekin = 0.290373280691476 | erot = 0.45300626299518 | epot = -15.3858127891754 | etot = -14.6424332454887 -991000 ekin = 0.278906915705959 | erot = 0.440624526219509 | epot = -15.3619646873478 | etot = -14.6424332454224 -992000 ekin = 0.266613826415441 | erot = 0.426413006891514 | epot = -15.3354600786573 | etot = -14.6424332453503 -993000 ekin = 0.253894212446822 | erot = 0.411056197524864 | epot = -15.3073836552479 | etot = -14.6424332452762 -994000 ekin = 0.241138837000364 | erot = 0.395291372388786 | epot = -15.2788634545923 | etot = -14.6424332452032 -995000 ekin = 0.228714768907212 | erot = 0.379870207855612 | epot = -15.2510182218971 | etot = -14.6424332451343 -996000 ekin = 0.2169544174706 | erot = 0.365522282707863 | epot = -15.2249099452504 | etot = -14.642433245072 -997000 ekin = 0.206147766456188 | erot = 0.352922066139109 | epot = -15.2015030776136 | etot = -14.6424332450183 -998000 ekin = 0.196537413157987 | erot = 0.342660495991805 | epot = -15.1816311541246 | etot = -14.6424332449748 -999000 ekin = 0.188315843913178 | erot = 0.335221830006205 | epot = -15.1659709188618 | etot = -14.6424332449424 -1000000 ekin = 0.181624323067817 | erot = 0.330966139649826 | epot = -15.1550237076397 | etot = -14.642433244922 - 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -8.4815516e-05 -Loop time of 29.1595 on 4 procs for 1000000 steps with 10 atoms - -Performance: 29630.171 tau/day, 34294.179 timesteps/s -96.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.8549 | 9.7585 | 17.369 | 226.0 | 33.47 -Bond | 0.12382 | 0.38401 | 0.60938 | 32.9 | 1.32 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.9104 | 3.7862 | 4.6404 | 31.7 | 12.98 -Output | 2e-05 | 2.775e-05 | 3.1e-05 | 0.0 | 0.00 -Modify | 0.27411 | 1.1629 | 1.994 | 64.7 | 3.99 -Other | | 14.07 | | | 48.24 - -Nlocal: 2.5 ave 5 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10 max 5 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 17.5 ave 33 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 70 -Ave neighs/atom = 7 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:29 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 index d80e7bbc0ebd0b083f2880bec12599853f28e681..143e20c70ba322342d4f2d0141fc247ce96f956d 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 @@ -31,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525 # oxDNA pair interactions pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..be12914ad6fbb77930115a4ba62cd904e0053ae3 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.1 @@ -0,0 +1,1168 @@ +LAMMPS (7 Aug 2019) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.0001 secs + read_data CPU = 0.001436 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.956 + ghost atom cutoff = 1.956 + binsize = 0.978, bins = 41 41 41 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685) +Per MPI rank memory allocation (min/avg/max) = 2.838 | 2.838 | 2.838 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 +1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287 +2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165 +3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165 +4000 ekin = 2.04461800191989 | erot = 1.49015219763161 | epot = -24.2959428773347 | etot = -20.7611726777832 +5000 ekin = 1.76794859210155 | erot = 2.54289684465819 | epot = -24.2337587736863 | etot = -19.9229133369266 +6000 ekin = 3.1106424806079 | erot = 2.04409805200893 | epot = -24.1585729744133 | etot = -19.0038324417964 +7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107 +8000 ekin = 2.82489935901743 | erot = 2.66790555575695 | epot = -24.0194805097633 | etot = -18.526675594989 +9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972 +10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334 +11000 ekin = 2.33860420545645 | erot = 2.06778039137701 | epot = -23.6589739475584 | etot = -19.2525893507249 +12000 ekin = 2.71377849618258 | erot = 2.08757199120023 | epot = -23.5483571834756 | etot = -18.7470066960928 +13000 ekin = 2.62930153930326 | erot = 2.36926332727578 | epot = -23.4509629615768 | etot = -18.4523980949977 +14000 ekin = 3.08200416316113 | erot = 2.52340746291245 | epot = -23.3378147651053 | etot = -17.7324031390317 +15000 ekin = 2.98008664779269 | erot = 1.871644860882 | epot = -23.1940665570191 | etot = -18.3423350483444 +16000 ekin = 2.18422481774796 | erot = 2.13029325858585 | epot = -23.0709946755646 | etot = -18.7564765992308 +17000 ekin = 1.86029951221073 | erot = 2.30856215831156 | epot = -22.9148241979648 | etot = -18.7459625274425 +18000 ekin = 2.26757205264074 | erot = 1.23282183419698 | epot = -22.7667657090377 | etot = -19.2663718222 +19000 ekin = 2.39717301992408 | erot = 2.43814713185076 | epot = -22.6249045514987 | etot = -17.7895843997239 +20000 ekin = 2.4972090427325 | erot = 2.14695469209109 | epot = -22.4687873897505 | etot = -17.8246236549269 +21000 ekin = 2.97591775854817 | erot = 2.40996811711196 | epot = -22.580475447988 | etot = -17.1945895723278 +22000 ekin = 3.04727168578733 | erot = 1.83825256427931 | epot = -22.6695853833015 | etot = -17.7840611332348 +23000 ekin = 2.64835731773193 | erot = 2.22162785501705 | epot = -22.6565689169972 | etot = -17.7865837442483 +24000 ekin = 2.64866576787001 | erot = 2.80157082833923 | epot = -22.6222797420052 | etot = -17.172043145796 +25000 ekin = 2.29527970143855 | erot = 2.22049811939068 | epot = -22.6228421013006 | etot = -18.1070642804714 +26000 ekin = 1.6242512251805 | erot = 2.52390475262917 | epot = -22.6746055892862 | etot = -18.5264496114765 +27000 ekin = 1.74746467550781 | erot = 3.7138606202505 | epot = -22.7150312690974 | etot = -17.253705973339 +28000 ekin = 2.26500128280479 | erot = 2.34791343563182 | epot = -22.7926648585827 | etot = -18.1797501401461 +29000 ekin = 2.04774074424512 | erot = 1.86347261547111 | epot = -22.8081204933408 | etot = -18.8969071336246 +30000 ekin = 2.41140146125466 | erot = 1.8629691542147 | epot = -22.7764612164305 | etot = -18.5020906009611 +31000 ekin = 2.76447800297261 | erot = 2.73932534046809 | epot = -22.7808698156252 | etot = -17.2770664721845 +32000 ekin = 2.08103539953574 | erot = 2.81216171106145 | epot = -22.8081908465747 | etot = -17.9149937359775 +33000 ekin = 2.08672340074227 | erot = 3.65510023442519 | epot = -22.7575363468642 | etot = -17.0157127116967 +34000 ekin = 2.34180742039869 | erot = 3.10027175201876 | epot = -22.6657421559553 | etot = -17.2236629835378 +35000 ekin = 2.32430602395272 | erot = 2.01607522370048 | epot = -22.5813705492547 | etot = -18.2409893016015 +36000 ekin = 1.91917507775106 | erot = 1.97289747304336 | epot = -22.481118994336 | etot = -18.5890464435415 +37000 ekin = 1.57560528527468 | erot = 2.63029511887644 | epot = -22.4456699464305 | etot = -18.2397695422794 +38000 ekin = 2.20652731867584 | erot = 2.89671984141264 | epot = -22.3965902387972 | etot = -17.2933430787087 +39000 ekin = 2.54765822667969 | erot = 2.47352619735436 | epot = -22.3525131983352 | etot = -17.3313287743011 +40000 ekin = 2.24172560748699 | erot = 1.87314319107769 | epot = -22.3791956830638 | etot = -18.2643268844991 +41000 ekin = 2.45176361826215 | erot = 2.49992612251746 | epot = -22.4441192111886 | etot = -17.492429470409 +42000 ekin = 2.68254780786499 | erot = 2.0438213169699 | epot = -22.4352265851614 | etot = -17.7088574603265 +43000 ekin = 2.39383336858508 | erot = 1.66587291396323 | epot = -22.4337243898147 | etot = -18.3740181072664 +44000 ekin = 2.30758870966957 | erot = 2.39381816537747 | epot = -22.4636201484765 | etot = -17.7622132734295 +45000 ekin = 1.84308929771583 | erot = 2.25880380151545 | epot = -22.5697712917434 | etot = -18.4678781925121 +46000 ekin = 1.98608215049724 | erot = 3.02136983211364 | epot = -22.5606085774834 | etot = -17.5531565948725 +47000 ekin = 1.31457586857023 | erot = 1.99780932836914 | epot = -22.5522289127255 | etot = -19.2398437157861 +48000 ekin = 2.59855199680394 | erot = 1.90772345027383 | epot = -22.5972680906755 | etot = -18.0909926435977 +49000 ekin = 2.32140483916261 | erot = 2.72932938830521 | epot = -22.6070371995253 | etot = -17.5563029720575 +50000 ekin = 2.48248035385828 | erot = 3.42713570109106 | epot = -22.5294064222472 | etot = -16.6197903672978 +51000 ekin = 2.73677705777971 | erot = 1.43285265191039 | epot = -22.4272695862992 | etot = -18.2576398766091 +52000 ekin = 3.03746109762767 | erot = 1.97878223690382 | epot = -22.4105817052323 | etot = -17.3943383707008 +53000 ekin = 2.4689045601064 | erot = 4.26434186327669 | epot = -22.4059567857723 | etot = -15.6727103623892 +54000 ekin = 2.48025904071626 | erot = 2.36957879662633 | epot = -22.4049729842648 | etot = -17.5551351469222 +55000 ekin = 2.28269445417385 | erot = 1.92149293107792 | epot = -22.4643082993723 | etot = -18.2601209141205 +56000 ekin = 2.36225428889468 | erot = 2.21818002425494 | epot = -22.5516502452858 | etot = -17.9712159321362 +57000 ekin = 2.5222034650231 | erot = 2.87044520913644 | epot = -22.6517599833464 | etot = -17.2591113091869 +58000 ekin = 2.50677816066749 | erot = 2.80087142998997 | epot = -22.7046490897181 | etot = -17.3969994990606 +59000 ekin = 2.7442153349817 | erot = 2.17375311266844 | epot = -22.7630968852436 | etot = -17.8451284375935 +60000 ekin = 3.28881699963203 | erot = 1.98491245229836 | epot = -22.7493813857703 | etot = -17.47565193384 +61000 ekin = 2.42749732003947 | erot = 1.80500042748844 | epot = -22.6954080097403 | etot = -18.4629102622124 +62000 ekin = 2.82051548232979 | erot = 1.69220614985812 | epot = -22.5840860651656 | etot = -18.0713644329777 +63000 ekin = 3.66818847100114 | erot = 1.91510536540652 | epot = -22.4235299160084 | etot = -16.8402360796007 +64000 ekin = 3.60192162647095 | erot = 3.02302140162941 | epot = -22.4028966408393 | etot = -15.777953612739 +65000 ekin = 3.37797300912953 | erot = 3.90646944425566 | epot = -22.3508227873684 | etot = -15.0663803339832 +66000 ekin = 2.90796062513305 | erot = 2.46538835419996 | epot = -22.2656130116827 | etot = -16.8922640323497 +67000 ekin = 2.57641483706472 | erot = 2.10639257083139 | epot = -22.1586423836372 | etot = -17.4758349757411 +68000 ekin = 2.55169027274651 | erot = 2.46870040285814 | epot = -22.1454741588101 | etot = -17.1250834832055 +69000 ekin = 2.42897294997603 | erot = 2.86774435615082 | epot = -22.1788582092805 | etot = -16.8821409031537 +70000 ekin = 3.08406596014674 | erot = 2.51171720098585 | epot = -22.2680651617951 | etot = -16.6722820006625 +71000 ekin = 2.55052721315253 | erot = 2.49486492124422 | epot = -22.3940848075588 | etot = -17.3486926731621 +72000 ekin = 1.77666138705941 | erot = 2.52301579845698 | epot = -22.4956655989823 | etot = -18.195988413466 +73000 ekin = 1.86857924146303 | erot = 2.33110810852355 | epot = -22.5401005215028 | etot = -18.3404131715162 +74000 ekin = 3.14875320805145 | erot = 2.120028079616 | epot = -22.5354282257997 | etot = -17.2666469381323 +75000 ekin = 2.60566180511119 | erot = 2.16421143606062 | epot = -22.5109742574449 | etot = -17.7411010162731 +76000 ekin = 1.94500512300058 | erot = 1.94681992806367 | epot = -22.513456138446 | etot = -18.6216310873818 +77000 ekin = 2.09005510206219 | erot = 2.13354294429721 | epot = -22.5157248384152 | etot = -18.2921267920558 +78000 ekin = 2.48381695181472 | erot = 2.49598603867483 | epot = -22.449809286019 | etot = -17.4700062955294 +79000 ekin = 3.09582217320064 | erot = 2.46630074007713 | epot = -22.3464652405845 | etot = -16.7843423273067 +80000 ekin = 2.51380629427529 | erot = 1.89207626467031 | epot = -22.2775752521274 | etot = -17.8716926931818 +81000 ekin = 2.32322780911516 | erot = 2.24954513249786 | epot = -22.2655235360185 | etot = -17.6927505944055 +82000 ekin = 1.54779729878415 | erot = 2.01487148845306 | epot = -22.2126473128098 | etot = -18.6499785255726 +83000 ekin = 2.24267653112482 | erot = 3.34721522119021 | epot = -22.2063282117648 | etot = -16.6164364594498 +84000 ekin = 2.86948852339533 | erot = 2.11915315181828 | epot = -22.2055386975617 | etot = -17.2168970223481 +85000 ekin = 3.13802387827786 | erot = 2.93900498543376 | epot = -22.2240733080823 | etot = -16.1470444443707 +86000 ekin = 3.46160079449537 | erot = 2.80798287444336 | epot = -22.2732645073154 | etot = -16.0036808383767 +87000 ekin = 3.63139446909085 | erot = 2.3166794204513 | epot = -22.2567856660101 | etot = -16.3087117764679 +88000 ekin = 3.15348314879937 | erot = 2.27857637090329 | epot = -22.2154422326698 | etot = -16.7833827129672 +89000 ekin = 3.30271147105659 | erot = 1.80791256125565 | epot = -22.1564153597822 | etot = -17.04579132747 +90000 ekin = 2.42655906518195 | erot = 2.24507038389519 | epot = -21.9481188512568 | etot = -17.2764894021797 +91000 ekin = 1.89051217909395 | erot = 2.51049066719492 | epot = -21.7877769537305 | etot = -17.3867741074417 +92000 ekin = 2.0783366846668 | erot = 2.218324246302 | epot = -21.6997103074281 | etot = -17.4030493764594 +93000 ekin = 1.94321435585196 | erot = 2.99473985773913 | epot = -21.6748650469777 | etot = -16.7369108333866 +94000 ekin = 2.07878576812463 | erot = 3.37631892101902 | epot = -21.7659932416399 | etot = -16.3108885524962 +95000 ekin = 2.1051772140777 | erot = 2.08345895044788 | epot = -21.8951718799354 | etot = -17.7065357154098 +96000 ekin = 2.68821593238919 | erot = 1.86988637992411 | epot = -21.9622848400866 | etot = -17.4041825277733 +97000 ekin = 1.95061152706206 | erot = 2.81054215683074 | epot = -22.0229813258884 | etot = -17.2618276419956 +98000 ekin = 1.98463063611221 | erot = 2.05732763357978 | epot = -22.0930102039111 | etot = -18.0510519342191 +99000 ekin = 2.51292852217217 | erot = 3.54194472638844 | epot = -22.1990887572979 | etot = -16.1442155087373 +100000 ekin = 1.8757570387949 | erot = 2.36907855808758 | epot = -22.3484095874379 | etot = -18.1035739905555 +101000 ekin = 1.66160772204006 | erot = 3.59766032223856 | epot = -22.3604908173889 | etot = -17.1012227731103 +102000 ekin = 1.62075182718473 | erot = 3.34420068488168 | epot = -22.3063629504086 | etot = -17.3414104383422 +103000 ekin = 2.00871148652538 | erot = 2.33677124900284 | epot = -22.2755578526919 | etot = -17.9300751171637 +104000 ekin = 2.04513709976292 | erot = 2.74664593650968 | epot = -22.2818713634636 | etot = -17.490088327191 +105000 ekin = 1.87027868596139 | erot = 1.9892238921824 | epot = -22.2235039092989 | etot = -18.3640013311551 +106000 ekin = 1.71540784443942 | erot = 1.91779531106878 | epot = -22.2562839843324 | etot = -18.6230808288242 +107000 ekin = 2.61024905591622 | erot = 1.57446439985465 | epot = -22.3171357124015 | etot = -18.1324222566306 +108000 ekin = 2.13751756724178 | erot = 2.18822458113097 | epot = -22.2268794585968 | etot = -17.9011373102241 +109000 ekin = 2.24408198608307 | erot = 2.11438299352725 | epot = -22.076564108576 | etot = -17.7180991289656 +110000 ekin = 1.66706562020821 | erot = 2.50986066169371 | epot = -22.0833343008135 | etot = -17.9064080189116 +111000 ekin = 2.30463895640873 | erot = 2.2498256085699 | epot = -22.0940837732695 | etot = -17.5396192082909 +112000 ekin = 2.63019524472748 | erot = 2.43696110420533 | epot = -22.0953344558745 | etot = -17.0281781069417 +113000 ekin = 2.42282638113981 | erot = 3.06190927482914 | epot = -22.1061661458172 | etot = -16.6214304898483 +114000 ekin = 2.34214572325658 | erot = 2.31899235523686 | epot = -22.0941430549287 | etot = -17.4330049764353 +115000 ekin = 1.70336449422736 | erot = 3.10166879044198 | epot = -22.1252095896431 | etot = -17.3201763049738 +116000 ekin = 1.51705870113214 | erot = 2.21425252709697 | epot = -22.1823772627204 | etot = -18.4510660344913 +117000 ekin = 1.70129809180508 | erot = 2.34142425076373 | epot = -22.2067668262467 | etot = -18.1640444836778 +118000 ekin = 2.20482827236051 | erot = 2.31797148095037 | epot = -22.1855414590756 | etot = -17.6627417057647 +119000 ekin = 2.54272629601484 | erot = 2.46528921750297 | epot = -22.2113175246519 | etot = -17.2033020111341 +120000 ekin = 1.76640390552554 | erot = 2.16116304616033 | epot = -22.1536331723645 | etot = -18.2260662206786 +121000 ekin = 2.81281157959689 | erot = 2.31761005518346 | epot = -22.1492969323238 | etot = -17.0188752975435 +122000 ekin = 3.25156823587966 | erot = 3.31679050874321 | epot = -22.2050361016165 | etot = -15.6366773569937 +123000 ekin = 2.87462309654082 | erot = 3.25604816714397 | epot = -22.1785374359393 | etot = -16.0478661722545 +124000 ekin = 2.18213410260632 | erot = 2.77182209342783 | epot = -22.0161464482697 | etot = -17.0621902522356 +125000 ekin = 1.85317252616068 | erot = 1.36623599567638 | epot = -21.8721650279343 | etot = -18.6527565060973 +126000 ekin = 2.47747071965844 | erot = 3.09909384826332 | epot = -21.8840309142636 | etot = -16.3074663463419 +127000 ekin = 2.42177426273027 | erot = 2.35209644429657 | epot = -21.8861939604609 | etot = -17.112323253434 +128000 ekin = 2.76000040231248 | erot = 1.82316788372391 | epot = -21.8538456680959 | etot = -17.2706773820595 +129000 ekin = 2.78355536315488 | erot = 2.888519816215 | epot = -21.9251039267855 | etot = -16.2530287474156 +130000 ekin = 3.26834278926798 | erot = 2.56228354573333 | epot = -22.0546105678548 | etot = -16.2239842328535 +131000 ekin = 2.64714688907849 | erot = 2.51107513446137 | epot = -22.096116019268 | etot = -16.9378939957281 +132000 ekin = 2.61847248883525 | erot = 3.3889916433416 | epot = -22.1218916777657 | etot = -16.1144275455889 +133000 ekin = 2.03408861514006 | erot = 2.87401070790187 | epot = -22.0785989417619 | etot = -17.17049961872 +134000 ekin = 1.64140897264888 | erot = 1.66986416585675 | epot = -22.0323643102284 | etot = -18.7210911717227 +135000 ekin = 2.46650096367446 | erot = 2.11112061110699 | epot = -21.9976572593398 | etot = -17.4200356845584 +136000 ekin = 2.32880805911731 | erot = 3.05940125193233 | epot = -21.8983392007846 | etot = -16.510129889735 +137000 ekin = 2.7601019905106 | erot = 2.47443779429795 | epot = -21.7521252642038 | etot = -16.5175854793953 +138000 ekin = 3.30162084678948 | erot = 1.73084735415552 | epot = -21.7423849642074 | etot = -16.7099167632624 +139000 ekin = 2.76669064053124 | erot = 1.72642745910432 | epot = -21.8898577306653 | etot = -17.3967396310297 +140000 ekin = 2.73595287215366 | erot = 2.46891829250481 | epot = -21.9884857831832 | etot = -16.7836146185247 +141000 ekin = 2.79316289615843 | erot = 2.46753088695596 | epot = -22.0064855648442 | etot = -16.7457917817298 +142000 ekin = 3.51694745558128 | erot = 3.49862438784826 | epot = -21.962319333545 | etot = -14.9467474901155 +143000 ekin = 2.58689934548697 | erot = 2.04008576044028 | epot = -21.9563338194556 | etot = -17.3293487135283 +144000 ekin = 3.72611917000993 | erot = 3.04855733322794 | epot = -21.9536376487795 | etot = -15.1789611455416 +145000 ekin = 3.61191106831146 | erot = 2.71915407989906 | epot = -21.8705426653329 | etot = -15.5394775171224 +146000 ekin = 3.85060594912678 | erot = 2.47210219931339 | epot = -21.828585815392 | etot = -15.5058776669519 +147000 ekin = 3.26481933196161 | erot = 2.06864347299802 | epot = -21.6752809049182 | etot = -16.3418180999586 +148000 ekin = 2.47977997895053 | erot = 1.65169267241013 | epot = -21.4172781734275 | etot = -17.2858055220668 +149000 ekin = 2.70771685463074 | erot = 2.28028425953226 | epot = -21.2324293178538 | etot = -16.2444282036908 +150000 ekin = 2.60726181496431 | erot = 2.88955230103661 | epot = -21.1265494068529 | etot = -15.629735290852 +151000 ekin = 2.06865005733849 | erot = 2.13537039813292 | epot = -21.0304193709382 | etot = -16.8263989154668 +152000 ekin = 2.41210154812788 | erot = 2.60104053370076 | epot = -20.8967777045301 | etot = -15.8836356227015 +153000 ekin = 2.12406231442824 | erot = 2.25444655142795 | epot = -20.9199278716093 | etot = -16.5414190057531 +154000 ekin = 2.34622678455546 | erot = 2.58439374093404 | epot = -21.0040588663532 | etot = -16.0734383408637 +155000 ekin = 2.08240965570453 | erot = 3.02621505767145 | epot = -21.0204738431415 | etot = -15.9118491297655 +156000 ekin = 2.04576145796301 | erot = 3.17151405834468 | epot = -20.8558463949478 | etot = -15.6385708786401 +157000 ekin = 2.36459548410747 | erot = 1.89207417055427 | epot = -20.8025485082276 | etot = -16.5458788535658 +158000 ekin = 2.16996178916575 | erot = 2.46547727482115 | epot = -20.8673070433023 | etot = -16.2318679793154 +159000 ekin = 2.86272730849306 | erot = 2.27590841865057 | epot = -20.9710387207244 | etot = -15.8324029935808 +160000 ekin = 2.19288173853783 | erot = 2.36312829884112 | epot = -21.0403123366074 | etot = -16.4843022992285 +161000 ekin = 2.14059248149909 | erot = 2.42872837990481 | epot = -21.1333683100402 | etot = -16.5640474486363 +162000 ekin = 1.76077466564934 | erot = 2.66561836368342 | epot = -21.1782130850258 | etot = -16.751820055693 +163000 ekin = 2.23068698955416 | erot = 2.02664945757243 | epot = -21.3281780197228 | etot = -17.0708415725962 +164000 ekin = 2.75358320318999 | erot = 1.43717365990088 | epot = -21.4675480212853 | etot = -17.2767911581944 +165000 ekin = 2.65171600986478 | erot = 2.29632253260763 | epot = -21.493178025826 | etot = -16.5451394833535 +166000 ekin = 3.27298673277591 | erot = 2.41252396730594 | epot = -21.4477711984926 | etot = -15.7622604984108 +167000 ekin = 3.02574105268454 | erot = 2.02770436019795 | epot = -21.5236773217565 | etot = -16.470231908874 +168000 ekin = 3.14659813654157 | erot = 1.83746079413209 | epot = -21.5547269116735 | etot = -16.5706679809999 +169000 ekin = 2.22493755697303 | erot = 2.67175500860651 | epot = -21.466220607731 | etot = -16.5695280421515 +170000 ekin = 2.41921977325642 | erot = 2.49142716001799 | epot = -21.3123035293872 | etot = -16.4016565961128 +171000 ekin = 1.89798915040775 | erot = 2.39492100285877 | epot = -21.2153991969518 | etot = -16.9224890436852 +172000 ekin = 2.86894215563085 | erot = 3.22914449693157 | epot = -21.182735220644 | etot = -15.0846485680816 +173000 ekin = 2.74888252418688 | erot = 2.13556434483052 | epot = -21.2166792789417 | etot = -16.3322324099243 +174000 ekin = 2.45887587066864 | erot = 2.23682521338054 | epot = -21.263305665856 | etot = -16.5676045818068 +175000 ekin = 2.84703517745998 | erot = 2.3938125491638 | epot = -21.2430876358358 | etot = -16.002239909212 +176000 ekin = 2.14025231000119 | erot = 1.89894722702465 | epot = -21.3238321496633 | etot = -17.2846326126374 +177000 ekin = 2.5795061901144 | erot = 2.75365074391217 | epot = -21.3022195274207 | etot = -15.9690625933941 +178000 ekin = 1.83122028490792 | erot = 2.59468068841507 | epot = -21.2483113201278 | etot = -16.8224103468048 +179000 ekin = 2.50706581632049 | erot = 2.39180466236872 | epot = -21.3152464598323 | etot = -16.4163759811431 +180000 ekin = 1.88211034410738 | erot = 2.47063835849691 | epot = -21.4741119346399 | etot = -17.1213632320356 +181000 ekin = 1.74209654097779 | erot = 3.05723824722444 | epot = -21.4808621715441 | etot = -16.6815273833419 +182000 ekin = 1.55789914013104 | erot = 2.05767448814763 | epot = -21.423526482018 | etot = -17.8079528537393 +183000 ekin = 2.00937540548924 | erot = 2.80898978674436 | epot = -21.491360735728 | etot = -16.6729955434944 +184000 ekin = 2.69285960778353 | erot = 2.42969439668745 | epot = -21.6024209898207 | etot = -16.4798669853497 +185000 ekin = 3.01326925127938 | erot = 3.19083239326424 | epot = -21.673025896793 | etot = -15.4689242522494 +186000 ekin = 3.20830671536381 | erot = 2.428990168692 | epot = -21.7143665695974 | etot = -16.0770696855416 +187000 ekin = 2.67290610091901 | erot = 3.415604047156 | epot = -21.6726605039612 | etot = -15.5841503558862 +188000 ekin = 2.89349337388583 | erot = 3.06258669113778 | epot = -21.6216664732831 | etot = -15.6655864082595 +189000 ekin = 2.65435973176119 | erot = 1.82043381700643 | epot = -21.5604872976484 | etot = -17.0856937488808 +190000 ekin = 2.21855159698309 | erot = 1.84826944038784 | epot = -21.5263477340277 | etot = -17.4595266966568 +191000 ekin = 2.26980616064111 | erot = 2.05944589507645 | epot = -21.4543005141096 | etot = -17.1250484583921 +192000 ekin = 2.27219103053707 | erot = 3.11210788791053 | epot = -21.4899273087561 | etot = -16.1056283903085 +193000 ekin = 1.95008147026928 | erot = 1.8964892153402 | epot = -21.4843079374127 | etot = -17.6377372518032 +194000 ekin = 2.45477671526092 | erot = 2.02723042426762 | epot = -21.3709228769336 | etot = -16.8889157374051 +195000 ekin = 3.09567411006595 | erot = 2.10081767143638 | epot = -21.3012041149762 | etot = -16.1047123334738 +196000 ekin = 2.67423122149492 | erot = 2.5073818975552 | epot = -21.2164124023052 | etot = -16.0347992832551 +197000 ekin = 2.50338730962556 | erot = 2.07349764616723 | epot = -21.0418674869219 | etot = -16.4649825311292 +198000 ekin = 2.66945928982615 | erot = 1.79012921820211 | epot = -21.0169215356765 | etot = -16.5573330276482 +199000 ekin = 2.53947964790256 | erot = 2.33176467953654 | epot = -21.0171165577067 | etot = -16.1458722302676 +200000 ekin = 2.90451062704866 | erot = 1.42170066957003 | epot = -21.0113804229742 | etot = -16.6851691263555 +201000 ekin = 2.68927776239674 | erot = 1.56650335894555 | epot = -21.024591639958 | etot = -16.7688105186157 +202000 ekin = 2.2601329351618 | erot = 2.25401443373178 | epot = -20.9769308007641 | etot = -16.4627834318705 +203000 ekin = 2.12073487355488 | erot = 2.03553028991747 | epot = -20.9190359464919 | etot = -16.7627707830196 +204000 ekin = 2.11829086582789 | erot = 1.89731962488618 | epot = -20.9376264283537 | etot = -16.9220159376396 +205000 ekin = 1.30964171332167 | erot = 2.12770406224884 | epot = -20.9991335630718 | etot = -17.5617877875013 +206000 ekin = 1.39940057572523 | erot = 2.24496791209125 | epot = -20.9639192190619 | etot = -17.3195507312454 +207000 ekin = 1.8871608804017 | erot = 1.79849326266381 | epot = -21.0552898160204 | etot = -17.3696356729549 +208000 ekin = 1.81558541079754 | erot = 3.24210836817276 | epot = -21.3060144768833 | etot = -16.248320697913 +209000 ekin = 2.79588064252181 | erot = 2.34671491738324 | epot = -21.4301997554494 | etot = -16.2876041955444 +210000 ekin = 3.17544887511568 | erot = 3.12704516116656 | epot = -21.5100449360931 | etot = -15.2075508998109 +211000 ekin = 2.47442327377227 | erot = 2.0990867711376 | epot = -21.6455723047062 | etot = -17.0720622597963 +212000 ekin = 2.36672302145397 | erot = 1.93445871446417 | epot = -21.7283038297487 | etot = -17.4271220938306 +213000 ekin = 1.91045426241161 | erot = 2.52535628540463 | epot = -21.8158508544504 | etot = -17.3800403066341 +214000 ekin = 1.99794025866062 | erot = 2.49896939492129 | epot = -21.8606548137084 | etot = -17.3637451601265 +215000 ekin = 1.97741561009525 | erot = 3.17667494473256 | epot = -21.8701701582032 | etot = -16.7160796033754 +216000 ekin = 1.88829990821377 | erot = 1.87402623825167 | epot = -21.8343889393413 | etot = -18.0720627928758 +217000 ekin = 2.10000293878933 | erot = 1.95052404495888 | epot = -21.8965404786646 | etot = -17.8460134949164 +218000 ekin = 2.34753598782339 | erot = 1.696950195044 | epot = -21.8560027679963 | etot = -17.8115165851289 +219000 ekin = 2.497223564463 | erot = 2.20999914485703 | epot = -21.8797649478059 | etot = -17.1725422384859 +220000 ekin = 1.75274593087922 | erot = 3.03992746556403 | epot = -21.8491595252171 | etot = -17.0564861287739 +221000 ekin = 1.78874686645809 | erot = 2.79359542964648 | epot = -21.869798634642 | etot = -17.2874563385374 +222000 ekin = 2.63608430516661 | erot = 2.86817933637385 | epot = -21.8351218383832 | etot = -16.3308581968427 +223000 ekin = 3.02706758581511 | erot = 1.93888641555348 | epot = -21.8582453001765 | etot = -16.8922912988079 +224000 ekin = 2.71704451339112 | erot = 2.42079327531438 | epot = -21.8188420875657 | etot = -16.6810042988602 +225000 ekin = 2.04245190508396 | erot = 3.38216222891908 | epot = -21.8232190868647 | etot = -16.3986049528616 +226000 ekin = 2.37968015829255 | erot = 2.38384696857064 | epot = -21.8913549487127 | etot = -17.1278278218495 +227000 ekin = 2.73883397024414 | erot = 2.62491632372019 | epot = -21.9496900700866 | etot = -16.5859397761223 +228000 ekin = 2.06833362780412 | erot = 2.25049628751226 | epot = -21.9946760345141 | etot = -17.6758461191977 +229000 ekin = 1.78618617304217 | erot = 1.8050959150033 | epot = -22.0671964085329 | etot = -18.4759143204874 +230000 ekin = 2.76967283780387 | erot = 2.22492545317995 | epot = -22.0913590121729 | etot = -17.096760721189 +231000 ekin = 3.15653922952316 | erot = 2.77099247609324 | epot = -22.0635255129442 | etot = -16.1359938073278 +232000 ekin = 1.86633326635991 | erot = 1.70672288688982 | epot = -22.0959715052868 | etot = -18.5229153520371 +233000 ekin = 1.75856846080021 | erot = 1.55694263125625 | epot = -22.0729289884755 | etot = -18.757417896419 +234000 ekin = 2.32322575892498 | erot = 2.05793864740336 | epot = -21.9849429433607 | etot = -17.6037785370324 +235000 ekin = 1.95327191686568 | erot = 2.5251933888586 | epot = -21.9357201856671 | etot = -17.4572548799429 +236000 ekin = 2.25952484966859 | erot = 1.90005304846995 | epot = -21.942247136874 | etot = -17.7826692387355 +237000 ekin = 2.49082301609303 | erot = 2.65327564887437 | epot = -22.0049130762793 | etot = -16.8608144113119 +238000 ekin = 2.21076048871751 | erot = 2.74154862479022 | epot = -22.0553236426831 | etot = -17.1030145291753 +239000 ekin = 2.71464884454142 | erot = 2.48739530580561 | epot = -22.0661894571024 | etot = -16.8641453067553 +240000 ekin = 3.08961933821573 | erot = 2.17857064931928 | epot = -21.9596599475175 | etot = -16.6914699599825 +241000 ekin = 3.04172562407922 | erot = 2.64442433974962 | epot = -21.8729500648239 | etot = -16.186800100995 +242000 ekin = 2.21355627539455 | erot = 2.33429157450905 | epot = -21.7850463200937 | etot = -17.2371984701901 +243000 ekin = 1.52065138183895 | erot = 2.81375224845252 | epot = -21.7246720043569 | etot = -17.3902683740654 +244000 ekin = 1.9035257658383 | erot = 2.43821138840077 | epot = -21.6320468184553 | etot = -17.2903096642163 +245000 ekin = 1.96342069667741 | erot = 2.61760141174562 | epot = -21.5097899449579 | etot = -16.9287678365349 +246000 ekin = 2.05478829283867 | erot = 2.42643933263095 | epot = -21.4781109635141 | etot = -16.9968833380445 +247000 ekin = 1.54618395739204 | erot = 2.28537401295508 | epot = -21.4411828355571 | etot = -17.60962486521 +248000 ekin = 1.83924983769608 | erot = 2.55904554412921 | epot = -21.4587985205917 | etot = -17.0605031387664 +249000 ekin = 1.78703007063825 | erot = 2.0341134947543 | epot = -21.5166075601389 | etot = -17.6954639947463 +250000 ekin = 1.69317901626952 | erot = 3.38262002358101 | epot = -21.5380480709887 | etot = -16.4622490311382 +251000 ekin = 2.13799462687096 | erot = 3.25868442484789 | epot = -21.5254595658407 | etot = -16.1287805141218 +252000 ekin = 2.04357045453397 | erot = 2.53079336098229 | epot = -21.5456931883613 | etot = -16.9713293728451 +253000 ekin = 1.63287738205388 | erot = 3.20992823373495 | epot = -21.5622010587546 | etot = -16.7193954429658 +254000 ekin = 2.31269246359595 | erot = 3.10766702207072 | epot = -21.5505863172023 | etot = -16.1302268315356 +255000 ekin = 2.50767926641465 | erot = 2.76631276495167 | epot = -21.5288449153182 | etot = -16.2548528839519 +256000 ekin = 1.97163698305487 | erot = 2.61682132599932 | epot = -21.5273539828766 | etot = -16.9388956738224 +257000 ekin = 2.21091422886156 | erot = 3.2624387389365 | epot = -21.5385504601778 | etot = -16.0651974923797 +258000 ekin = 2.0351730783025 | erot = 1.8469346151236 | epot = -21.6544556001777 | etot = -17.7723479067517 +259000 ekin = 2.85718947138203 | erot = 2.78701165242274 | epot = -21.7587237542941 | etot = -16.1145226304893 +260000 ekin = 2.90387286634677 | erot = 2.18817434737476 | epot = -21.8080383126912 | etot = -16.7159910989697 +261000 ekin = 2.76190440948559 | erot = 2.33968169215534 | epot = -21.8592909726424 | etot = -16.7577048710014 +262000 ekin = 3.50919242681177 | erot = 1.76925994550144 | epot = -21.8779228441576 | etot = -16.5994704718444 +263000 ekin = 3.07696270254057 | erot = 2.41477320555762 | epot = -21.807856600428 | etot = -16.3161206923298 +264000 ekin = 2.26633389925754 | erot = 2.04161743361597 | epot = -21.837292812857 | etot = -17.5293414799835 +265000 ekin = 1.95747124461578 | erot = 2.50813008798838 | epot = -21.8490876266416 | etot = -17.3834862940374 +266000 ekin = 2.34517905801099 | erot = 3.31486209922485 | epot = -21.8287737874741 | etot = -16.1687326302383 +267000 ekin = 1.7403019336191 | erot = 2.23366459528058 | epot = -21.699850097441 | etot = -17.7258835685413 +268000 ekin = 2.04858677018809 | erot = 3.28744422098426 | epot = -21.6459408923622 | etot = -16.3099099011899 +269000 ekin = 1.93146929709292 | erot = 2.79280735598121 | epot = -21.5497738027119 | etot = -16.8254971496378 +270000 ekin = 2.19788894271021 | erot = 2.64563279687103 | epot = -21.4165389672397 | etot = -16.5730172276584 +271000 ekin = 2.21923220579694 | erot = 3.10768708967445 | epot = -21.2197121954352 | etot = -15.8927928999638 +272000 ekin = 2.54992061853164 | erot = 2.29721880581853 | epot = -21.0816515756818 | etot = -16.2345121513317 +273000 ekin = 1.91461840783801 | erot = 2.01420401968474 | epot = -21.0503637141725 | etot = -17.1215412866498 +274000 ekin = 1.89671513770877 | erot = 2.24334386161734 | epot = -21.09671034383 | etot = -16.9566513445039 +275000 ekin = 1.78930707116537 | erot = 3.0975468786599 | epot = -21.1385700371941 | etot = -16.2517160873688 +276000 ekin = 3.37110328153969 | erot = 2.4195732425753 | epot = -21.0908388312032 | etot = -15.3001623070883 +277000 ekin = 2.38921825148496 | erot = 1.50604988822735 | epot = -21.0346208839969 | etot = -17.1393527442846 +278000 ekin = 2.51997301930637 | erot = 2.14026171776895 | epot = -21.0117379332913 | etot = -16.351503196216 +279000 ekin = 1.88315206280857 | erot = 2.37342905263992 | epot = -20.9993757709145 | etot = -16.742794655466 +280000 ekin = 2.33534713190787 | erot = 3.5862646828722 | epot = -20.8573252930133 | etot = -14.9357134782333 +281000 ekin = 1.75252641954511 | erot = 1.7907930540809 | epot = -20.9036528826791 | etot = -17.3603334090531 +282000 ekin = 2.26373977259215 | erot = 3.04032073608634 | epot = -20.8497513702237 | etot = -15.5456908615452 +283000 ekin = 2.17833871394429 | erot = 2.20833158301337 | epot = -20.8002776734785 | etot = -16.4136073765208 +284000 ekin = 1.9148667268656 | erot = 2.21521993135969 | epot = -20.8277491648056 | etot = -16.6976625065803 +285000 ekin = 3.15634443167765 | erot = 1.8003323160485 | epot = -21.0046435881196 | etot = -16.0479668403934 +286000 ekin = 3.8487757495733 | erot = 1.82969969667575 | epot = -21.1628555811447 | etot = -15.4843801348956 +287000 ekin = 3.60615742824732 | erot = 2.91608688151216 | epot = -21.2126952882302 | etot = -14.6904509784707 +288000 ekin = 3.19613259393802 | erot = 1.67736393077136 | epot = -21.1713552834963 | etot = -16.297858758787 +289000 ekin = 2.45584885114799 | erot = 2.77781979747334 | epot = -21.1669115721543 | etot = -15.9332429235329 +290000 ekin = 2.74570408981358 | erot = 2.40443247852242 | epot = -21.1874427766533 | etot = -16.0373062083173 +291000 ekin = 2.10295274468233 | erot = 2.37092484671536 | epot = -21.2419107014543 | etot = -16.7680331100566 +292000 ekin = 2.36118713930733 | erot = 2.05558127949018 | epot = -21.3137361602548 | etot = -16.8969677414573 +293000 ekin = 2.27861963088251 | erot = 2.35874555054765 | epot = -21.4302415460532 | etot = -16.7928763646231 +294000 ekin = 2.9331598281302 | erot = 2.90313008187785 | epot = -21.5210917917479 | etot = -15.6848018817398 +295000 ekin = 2.66360761710435 | erot = 2.28100565751945 | epot = -21.6885021477336 | etot = -16.7438888731098 +296000 ekin = 2.1876782716447 | erot = 2.90589885547355 | epot = -21.7355037190159 | etot = -16.6419265918976 +297000 ekin = 2.15987738107364 | erot = 3.29819575592636 | epot = -21.7177655658755 | etot = -16.2596924288755 +298000 ekin = 2.92956976611296 | erot = 2.36377210613469 | epot = -21.6748271071565 | etot = -16.3814852349089 +299000 ekin = 3.19167138064488 | erot = 2.23480811780852 | epot = -21.8042612344918 | etot = -16.3777817360384 +300000 ekin = 3.31335728469821 | erot = 1.38932157247169 | epot = -21.8799906137234 | etot = -17.1773117565535 +301000 ekin = 2.39061971962409 | erot = 3.30110260608967 | epot = -21.8919200817915 | etot = -16.2001977560777 +302000 ekin = 2.95446070602901 | erot = 3.2304815881765 | epot = -21.8557645140423 | etot = -15.6708222198368 +303000 ekin = 2.44700205353934 | erot = 2.60676303242281 | epot = -21.8414046718167 | etot = -16.7876395858546 +304000 ekin = 2.23578509140698 | erot = 2.68770420047941 | epot = -21.7680601199659 | etot = -16.8445708280795 +305000 ekin = 2.35505207220215 | erot = 2.38230031155849 | epot = -21.7344089784493 | etot = -16.9970565946886 +306000 ekin = 1.91790567526689 | erot = 2.9010749400323 | epot = -21.717000482235 | etot = -16.8980198669359 +307000 ekin = 2.48241777758708 | erot = 2.0836708009946 | epot = -21.6510481218459 | etot = -17.0849595432642 +308000 ekin = 2.77531620706104 | erot = 2.63103510715158 | epot = -21.6349123878085 | etot = -16.2285610735959 +309000 ekin = 2.30440955942791 | erot = 2.1249829765834 | epot = -21.5927938975113 | etot = -17.1634013615 +310000 ekin = 2.50879527040005 | erot = 3.21338829421538 | epot = -21.6043932917724 | etot = -15.882209727157 +311000 ekin = 2.31939145866558 | erot = 3.03649241514155 | epot = -21.6247503351754 | etot = -16.2688664613682 +312000 ekin = 1.78383134659847 | erot = 3.26262247889992 | epot = -21.4948144284683 | etot = -16.4483606029699 +313000 ekin = 1.6465994694839 | erot = 2.08133087588837 | epot = -21.4920309735611 | etot = -17.7641006281888 +314000 ekin = 2.2552391830868 | erot = 2.55077633299238 | epot = -21.5103692936943 | etot = -16.7043537776152 +315000 ekin = 2.53527343915149 | erot = 2.13089997124612 | epot = -21.5923709217299 | etot = -16.9261975113323 +316000 ekin = 1.99944427781285 | erot = 1.80072924409704 | epot = -21.6039893771529 | etot = -17.803815855243 +317000 ekin = 2.11848744585804 | erot = 2.01459693810074 | epot = -21.5948976630665 | etot = -17.4618132791077 +318000 ekin = 2.29013024301854 | erot = 1.92405818620914 | epot = -21.564369594692 | etot = -17.3501811654644 +319000 ekin = 1.97314693278018 | erot = 1.67996578959134 | epot = -21.455480840084 | etot = -17.8023681177125 +320000 ekin = 2.45681719546632 | erot = 3.0783514449974 | epot = -21.39241255381 | etot = -15.8572439133463 +321000 ekin = 1.85729238455499 | erot = 2.67083565671244 | epot = -21.4338188292509 | etot = -16.9056907879835 +322000 ekin = 1.96132292396412 | erot = 3.36792274118282 | epot = -21.3663490830084 | etot = -16.0371034178615 +323000 ekin = 1.94437285233568 | erot = 2.09558156605688 | epot = -21.4151250968679 | etot = -17.3751706784753 +324000 ekin = 2.229181524904 | erot = 2.4674418745061 | epot = -21.5323859085629 | etot = -16.8357625091528 +325000 ekin = 2.74582842770392 | erot = 2.36717454305098 | epot = -21.6443544237971 | etot = -16.5313514530422 +326000 ekin = 1.91124551133375 | erot = 1.93084217743114 | epot = -21.7077957426601 | etot = -17.8657080538952 +327000 ekin = 3.05627483509655 | erot = 1.67325209460962 | epot = -21.7948818019127 | etot = -17.0653548722066 +328000 ekin = 2.73933273476856 | erot = 1.92380912803776 | epot = -21.8364014823585 | etot = -17.1732596195522 +329000 ekin = 2.95907896099514 | erot = 3.1565416835668 | epot = -21.898199971646 | etot = -15.782579327084 +330000 ekin = 2.90795110595274 | erot = 2.01765890034967 | epot = -21.9037795505257 | etot = -16.9781695442233 +331000 ekin = 2.27446048340228 | erot = 2.03754878634057 | epot = -21.8760842049291 | etot = -17.5640749351862 +332000 ekin = 2.43262938612094 | erot = 3.19219171897212 | epot = -21.9305186945661 | etot = -16.3056975894731 +333000 ekin = 2.47357651298171 | erot = 2.700610458147 | epot = -22.0416691323271 | etot = -16.8674821611983 +334000 ekin = 2.38171387374892 | erot = 3.00424927873367 | epot = -22.0746318522987 | etot = -16.6886686998161 +335000 ekin = 2.10465470910016 | erot = 3.57382014016835 | epot = -22.1175420615631 | etot = -16.4390672122946 +336000 ekin = 2.61374577374184 | erot = 2.133869272813 | epot = -22.0898825119599 | etot = -17.3422674654051 +337000 ekin = 2.72124526751511 | erot = 2.748004804814 | epot = -22.076853713162 | etot = -16.6076036408329 +338000 ekin = 1.83524121485422 | erot = 2.24338894827196 | epot = -22.1591955034455 | etot = -18.0805653403193 +339000 ekin = 1.54928432997333 | erot = 2.49812246084902 | epot = -22.2022398834669 | etot = -18.1548330926446 +340000 ekin = 1.44405714940631 | erot = 4.0451327092417 | epot = -22.1149458734012 | etot = -16.6257560147532 +341000 ekin = 1.67447392575554 | erot = 2.77749751745985 | epot = -22.0760831546714 | etot = -17.624111711456 +342000 ekin = 1.9825676117275 | erot = 2.71655566521085 | epot = -22.1563522566983 | etot = -17.4572289797599 +343000 ekin = 2.68213676683887 | erot = 3.16686462846914 | epot = -22.2498477633288 | etot = -16.4008463680208 +344000 ekin = 1.77905771753907 | erot = 2.19153667254072 | epot = -22.2907212723871 | etot = -18.3201268823073 +345000 ekin = 1.5460499615042 | erot = 1.85960255696713 | epot = -22.3447003428976 | etot = -18.9390478244263 +346000 ekin = 1.71554664484034 | erot = 1.79880968736712 | epot = -22.3117022609054 | etot = -18.7973459286979 +347000 ekin = 1.38672912049481 | erot = 2.61484473767932 | epot = -22.3325032395119 | etot = -18.3309293813378 +348000 ekin = 2.15015924850684 | erot = 2.86300326453563 | epot = -22.3337312775956 | etot = -17.3205687645531 +349000 ekin = 1.83066085453602 | erot = 1.98441326494869 | epot = -22.3967822584584 | etot = -18.5817081389737 +350000 ekin = 1.83318738252649 | erot = 2.56907029661255 | epot = -22.4577827539416 | etot = -18.0555250748025 +351000 ekin = 1.72790505260219 | erot = 2.87456274671835 | epot = -22.5159555107051 | etot = -17.9134877113846 +352000 ekin = 2.80786740016944 | erot = 2.0875044812577 | epot = -22.6549834386892 | etot = -17.759611557262 +353000 ekin = 3.5492801472091 | erot = 1.42584537334882 | epot = -22.6849212734238 | etot = -17.7097957528659 +354000 ekin = 3.49129244374804 | erot = 2.25156548638802 | epot = -22.6041826206929 | etot = -16.8613246905569 +355000 ekin = 2.06248783371663 | erot = 2.92733565233051 | epot = -22.5494488364626 | etot = -17.5596253504155 +356000 ekin = 2.13415426306311 | erot = 3.32668319049642 | epot = -22.6122425286522 | etot = -17.1514050750926 +357000 ekin = 2.75897049849731 | erot = 2.51843165594441 | epot = -22.6042888591884 | etot = -17.3268867047467 +358000 ekin = 2.51778220496547 | erot = 2.28374144764325 | epot = -22.5654155469983 | etot = -17.7638918943896 +359000 ekin = 3.2037278512604 | erot = 2.5552016027623 | epot = -22.6749569097325 | etot = -16.9160274557098 +360000 ekin = 2.52669169359922 | erot = 1.97563796824026 | epot = -22.7314557612253 | etot = -18.2291260993859 +361000 ekin = 2.60424632123629 | erot = 2.51068088850828 | epot = -22.771502374375 | etot = -17.6565751646305 +362000 ekin = 2.43350156723209 | erot = 3.84566788758402 | epot = -22.7352151098033 | etot = -16.4560456549872 +363000 ekin = 2.91069717970493 | erot = 1.99710098714123 | epot = -22.6302259934473 | etot = -17.7224278266012 +364000 ekin = 2.25538328683251 | erot = 1.87832387363457 | epot = -22.508362529619 | etot = -18.3746553691519 +365000 ekin = 2.04575884197224 | erot = 2.79774206841199 | epot = -22.3322627384259 | etot = -17.4887618280416 +366000 ekin = 2.26894187965217 | erot = 1.94379382552235 | epot = -22.2788727984905 | etot = -18.066137093316 +367000 ekin = 2.82509630766736 | erot = 2.50361468767087 | epot = -22.3209381619451 | etot = -16.9922271666069 +368000 ekin = 2.81542036602321 | erot = 2.1873362764449 | epot = -22.4297259451244 | etot = -17.4269693026563 +369000 ekin = 2.30426035796381 | erot = 2.85653411706989 | epot = -22.4923286665587 | etot = -17.331534191525 +370000 ekin = 2.67871033327546 | erot = 2.11464921695178 | epot = -22.5780698607969 | etot = -17.7847103105697 +371000 ekin = 2.19281044135006 | erot = 3.6016596066429 | epot = -22.6424730832336 | etot = -16.8480030352406 +372000 ekin = 1.77481259468411 | erot = 3.40654744438101 | epot = -22.7147683829007 | etot = -17.5334083438356 +373000 ekin = 2.15551547517191 | erot = 2.78778252361832 | epot = -22.755949721432 | etot = -17.8126517226417 +374000 ekin = 2.71938368055485 | erot = 3.58127823243844 | epot = -22.9084433694728 | etot = -16.6077814564795 +375000 ekin = 2.42759321485977 | erot = 2.97421271787163 | epot = -22.9740378563777 | etot = -17.5722319236463 +376000 ekin = 3.39126830110572 | erot = 3.24733797625005 | epot = -22.9874015798134 | etot = -16.3487953024577 +377000 ekin = 3.20966733323473 | erot = 2.6593406036448 | epot = -22.9452111216364 | etot = -17.0762031847569 +378000 ekin = 1.56095946168132 | erot = 2.6615903394499 | epot = -22.9575870308252 | etot = -18.735037229694 +379000 ekin = 1.94985687485381 | erot = 2.5408521625583 | epot = -22.9834751642938 | etot = -18.4927661268817 +380000 ekin = 2.65820438237073 | erot = 2.88045867212572 | epot = -22.9984703542082 | etot = -17.4598072997117 +381000 ekin = 2.97084599252829 | erot = 2.18892549461573 | epot = -23.0341895570111 | etot = -17.8744180698671 +382000 ekin = 2.61355176942653 | erot = 2.02938704043227 | epot = -23.0084119715099 | etot = -18.3654731616511 +383000 ekin = 2.03830671072154 | erot = 2.50516194855526 | epot = -23.0393965606452 | etot = -18.4959279013684 +384000 ekin = 2.1060608733416 | erot = 2.21840250458949 | epot = -23.0602182522592 | etot = -18.7357548743281 +385000 ekin = 1.89114918519107 | erot = 1.63701051320101 | epot = -23.0834434146805 | etot = -19.5552837162885 +386000 ekin = 1.55124380123707 | erot = 1.36147797265396 | epot = -23.1300518396948 | etot = -20.2173300658038 +387000 ekin = 2.19627825752355 | erot = 1.75751396098972 | epot = -23.1280875332419 | etot = -19.1742953147286 +388000 ekin = 1.96387084539616 | erot = 1.95852585326806 | epot = -23.0327752892414 | etot = -19.1103785905772 +389000 ekin = 2.50801560941705 | erot = 2.32519825784834 | epot = -23.0011464671234 | etot = -18.167932599858 +390000 ekin = 2.03596866068489 | erot = 1.88295618907178 | epot = -22.8810338311574 | etot = -18.9621089814008 +391000 ekin = 1.8098591016452 | erot = 2.39622167162876 | epot = -22.8195566463199 | etot = -18.613475873046 +392000 ekin = 2.17725370142732 | erot = 2.87094426544089 | epot = -22.7839731045438 | etot = -17.7357751376756 +393000 ekin = 2.14224634181996 | erot = 3.1724297430366 | epot = -22.8435025538356 | etot = -17.5288264689791 +394000 ekin = 1.97769550804366 | erot = 2.16375300420729 | epot = -22.8342667825711 | etot = -18.6928182703201 +395000 ekin = 2.03687268736298 | erot = 2.49567469731649 | epot = -22.8892034986303 | etot = -18.3566561139508 +396000 ekin = 2.16189109047463 | erot = 1.95308746486161 | epot = -22.9781386034885 | etot = -18.8631600481523 +397000 ekin = 2.41744222422408 | erot = 1.65310699287474 | epot = -23.0900453292844 | etot = -19.0194961121856 +398000 ekin = 3.58905654436294 | erot = 2.5193025650333 | epot = -23.2070733343384 | etot = -17.0987142249422 +399000 ekin = 2.65051654249497 | erot = 1.78138450529863 | epot = -23.3040478764214 | etot = -18.8721468286278 +400000 ekin = 2.49402752614129 | erot = 2.10290777432181 | epot = -23.3608759462318 | etot = -18.7639406457687 +401000 ekin = 2.04176177605463 | erot = 2.154995213856 | epot = -23.403960339401 | etot = -19.2072033494904 +402000 ekin = 2.4450587586146 | erot = 2.11318097973378 | epot = -23.3975262709887 | etot = -18.8392865326403 +403000 ekin = 2.54858079745147 | erot = 2.81138206601918 | epot = -23.4760646986769 | etot = -18.1161018352062 +404000 ekin = 2.21063952462117 | erot = 2.64710865829565 | epot = -23.574696037266 | etot = -18.7169478543492 +405000 ekin = 2.47328118101333 | erot = 2.40933750599425 | epot = -23.5927917139468 | etot = -18.7101730269392 +406000 ekin = 2.24891173527799 | erot = 2.23777884116048 | epot = -23.6086191890416 | etot = -19.1219286126031 +407000 ekin = 2.0107940045037 | erot = 2.78642832526901 | epot = -23.5246032469977 | etot = -18.727380917225 +408000 ekin = 2.59464051790823 | erot = 2.59123578102095 | epot = -23.4198302602655 | etot = -18.2339539613363 +409000 ekin = 2.37170880608735 | erot = 2.26136902851216 | epot = -23.3172581937239 | etot = -18.6841803591244 +410000 ekin = 1.99754661347186 | erot = 1.95523998485755 | epot = -23.2950402043272 | etot = -19.3422536059978 +411000 ekin = 1.8693657058423 | erot = 2.63899492681176 | epot = -23.249036763304 | etot = -18.7406761306499 +412000 ekin = 1.98214047746227 | erot = 2.68315820775203 | epot = -23.198735748328 | etot = -18.5334370631137 +413000 ekin = 2.39078873487372 | erot = 2.65589562872907 | epot = -23.1435198518626 | etot = -18.0968354882598 +414000 ekin = 2.40821090859774 | erot = 1.75574324408226 | epot = -23.0725048141376 | etot = -18.9085506614576 +415000 ekin = 2.74601981183014 | erot = 2.43675176686817 | epot = -23.1211711904485 | etot = -17.9383996117502 +416000 ekin = 2.08828454200993 | erot = 2.7678350652622 | epot = -23.1383119239964 | etot = -18.2821923167243 +417000 ekin = 2.01455344430628 | erot = 1.95306265456051 | epot = -23.1433633505286 | etot = -19.1757472516618 +418000 ekin = 2.42716528853986 | erot = 2.57642821145487 | epot = -23.1275317971309 | etot = -18.1239382971362 +419000 ekin = 3.04095103685797 | erot = 2.58427576972737 | epot = -23.0602279332616 | etot = -17.4350011266763 +420000 ekin = 2.6360746280152 | erot = 2.44478111019392 | epot = -22.9820923151719 | etot = -17.9012365769628 +421000 ekin = 2.53019765722915 | erot = 1.78389585255477 | epot = -22.9707435541328 | etot = -18.6566500443489 +422000 ekin = 2.72457425772367 | erot = 1.6776863488635 | epot = -22.9542997027494 | etot = -18.5520390961622 +423000 ekin = 2.11402997037893 | erot = 2.55034580375606 | epot = -22.8263851956496 | etot = -18.1620094215146 +424000 ekin = 1.8895880210325 | erot = 2.31332431343562 | epot = -22.7726668881719 | etot = -18.5697545537038 +425000 ekin = 2.3595116370971 | erot = 1.95762380637299 | epot = -22.7752082759345 | etot = -18.4580728324644 +426000 ekin = 2.23706657164627 | erot = 2.60016134755149 | epot = -22.7844114251539 | etot = -17.9471835059561 +427000 ekin = 1.88801598248841 | erot = 2.12415782350884 | epot = -22.9416586386638 | etot = -18.9294848326665 +428000 ekin = 1.92849031333042 | erot = 2.44097902588718 | epot = -23.0611368174398 | etot = -18.6916674782222 +429000 ekin = 1.70536802258415 | erot = 2.14916257389791 | epot = -23.0556586745392 | etot = -19.2011280780571 +430000 ekin = 2.30226095973205 | erot = 2.14689932813605 | epot = -23.0606502516207 | etot = -18.6114899637526 +431000 ekin = 2.45988288454318 | erot = 2.42278380298656 | epot = -23.072977722388 | etot = -18.1903110348583 +432000 ekin = 2.80869332724974 | erot = 2.19954129490929 | epot = -23.0939746542043 | etot = -18.0857400320453 +433000 ekin = 2.21130556188281 | erot = 1.62882156110629 | epot = -23.1534080352157 | etot = -19.3132809122266 +434000 ekin = 2.60574953870751 | erot = 2.36088790768805 | epot = -23.1901717047878 | etot = -18.2235342583922 +435000 ekin = 2.30377529593091 | erot = 2.53917715731258 | epot = -23.1716983948431 | etot = -18.3287459415996 +436000 ekin = 2.42707603554826 | erot = 2.75234181061923 | epot = -23.2197996577196 | etot = -18.0403818115521 +437000 ekin = 1.65090540276075 | erot = 3.25345231298367 | epot = -23.2216366145387 | etot = -18.3172788987943 +438000 ekin = 1.56145302974407 | erot = 2.60950810563797 | epot = -23.1303770792278 | etot = -18.9594159438457 +439000 ekin = 2.30955439722235 | erot = 1.94011743371101 | epot = -23.1353170794496 | etot = -18.8856452485163 +440000 ekin = 2.53037674867674 | erot = 3.06527042861028 | epot = -23.1968589452919 | etot = -17.6012117680049 +441000 ekin = 2.80107707952535 | erot = 2.53664155736543 | epot = -23.1712373428918 | etot = -17.833518706001 +442000 ekin = 2.92536323090713 | erot = 2.88384500930019 | epot = -23.1123001627208 | etot = -17.3030919225134 +443000 ekin = 1.96543935969483 | erot = 1.75344963155201 | epot = -23.0380529084377 | etot = -19.3191639171909 +444000 ekin = 2.00309477401364 | erot = 2.23897509587737 | epot = -22.9472103119533 | etot = -18.7051404420622 +445000 ekin = 2.20302071819723 | erot = 2.06928381371827 | epot = -22.7775434364172 | etot = -18.5052389045017 +446000 ekin = 2.43487889302299 | erot = 2.377515560078 | epot = -22.6838190597697 | etot = -17.8714246066687 +447000 ekin = 2.2620819636031 | erot = 2.41400188145195 | epot = -22.7082516636545 | etot = -18.0321678185995 +448000 ekin = 2.16184472791984 | erot = 1.93539407204276 | epot = -22.8144859493263 | etot = -18.7172471493637 +449000 ekin = 2.21107967973114 | erot = 2.3465968297874 | epot = -22.9059503054159 | etot = -18.3482737958973 +450000 ekin = 2.74677740004439 | erot = 1.97222921372039 | epot = -22.860755926716 | etot = -18.1417493129512 +451000 ekin = 2.2050889378155 | erot = 2.13042736119388 | epot = -22.8862608894795 | etot = -18.5507445904702 +452000 ekin = 2.52760608607095 | erot = 2.34006815636601 | epot = -22.9138111972132 | etot = -18.0461369547763 +453000 ekin = 2.23448825172916 | erot = 1.77834418215733 | epot = -22.887923830179 | etot = -18.8750913962925 +454000 ekin = 2.4343851915949 | erot = 2.59700848533281 | epot = -22.8184361849035 | etot = -17.7870425079758 +455000 ekin = 2.04195793930991 | erot = 2.79639043747678 | epot = -22.6032980500353 | etot = -17.7649496732486 +456000 ekin = 2.00799933710202 | erot = 2.53653815407518 | epot = -22.4355596266521 | etot = -17.8910221354749 +457000 ekin = 2.60426208759882 | erot = 2.4660961287619 | epot = -22.3409120082077 | etot = -17.270553791847 +458000 ekin = 2.01368468059036 | erot = 1.99613816245311 | epot = -22.2549400327204 | etot = -18.245117189677 +459000 ekin = 1.73688781588864 | erot = 2.48572034306896 | epot = -22.2282088298766 | etot = -18.005600670919 +460000 ekin = 1.91682575775988 | erot = 2.08308677023945 | epot = -22.2211874714415 | etot = -18.2212749434422 +461000 ekin = 1.54933673126937 | erot = 1.29454502815254 | epot = -22.1945151049366 | etot = -19.3506333455147 +462000 ekin = 2.44160489340629 | erot = 1.34721473707676 | epot = -22.2846713076969 | etot = -18.4958516772139 +463000 ekin = 2.63165365707666 | erot = 2.0814376012804 | epot = -22.4004513395624 | etot = -17.6873600812053 +464000 ekin = 2.67929276186416 | erot = 3.72563793061089 | epot = -22.5200042545287 | etot = -16.1150735620537 +465000 ekin = 1.94880111369478 | erot = 2.23148844819347 | epot = -22.6855542963289 | etot = -18.5052647344406 +466000 ekin = 2.1385304963889 | erot = 2.95056624305954 | epot = -22.7822881705531 | etot = -17.6931914311046 +467000 ekin = 2.46452767169614 | erot = 2.10778480770081 | epot = -22.9485753844865 | etot = -18.3762629050896 +468000 ekin = 1.98589158006998 | erot = 1.62816092182055 | epot = -23.0180008829523 | etot = -19.4039483810618 +469000 ekin = 2.498810820967 | erot = 2.63615462725918 | epot = -23.054783396884 | etot = -17.9198179486578 +470000 ekin = 2.91491361681312 | erot = 3.19115611298995 | epot = -23.0448741101698 | etot = -16.9388043803668 +471000 ekin = 2.37554627514204 | erot = 1.71739792236247 | epot = -22.9932329645512 | etot = -18.9002887670467 +472000 ekin = 2.18486807923518 | erot = 2.00687069908099 | epot = -22.9563182572701 | etot = -18.7645794789539 +473000 ekin = 2.36185345820898 | erot = 2.86259041401026 | epot = -22.9161024426124 | etot = -17.6916585703932 +474000 ekin = 2.17077693495272 | erot = 2.59376596740917 | epot = -22.7894018760352 | etot = -18.0248589736733 +475000 ekin = 2.37844153079293 | erot = 2.01112751381906 | epot = -22.6793191497968 | etot = -18.2897501051848 +476000 ekin = 2.08763676439641 | erot = 2.5964762445522 | epot = -22.6700039875051 | etot = -17.9858909785565 +477000 ekin = 2.52249432714936 | erot = 3.55251934739866 | epot = -22.6424099194916 | etot = -16.5673962449435 +478000 ekin = 2.40424947791157 | erot = 2.73239117258612 | epot = -22.5447763252279 | etot = -17.4081356747302 +479000 ekin = 1.27637524434413 | erot = 2.99749792697948 | epot = -22.4994949498981 | etot = -18.2256217785744 +480000 ekin = 1.81374950293816 | erot = 2.1438931713594 | epot = -22.4678405170784 | etot = -18.5101978427808 +481000 ekin = 2.39496774186199 | erot = 3.18299441824516 | epot = -22.4930736763177 | etot = -16.9151115162106 +482000 ekin = 3.21051763720184 | erot = 2.40962326270832 | epot = -22.4479376181303 | etot = -16.8277967182201 +483000 ekin = 3.06081116762376 | erot = 2.49856996934408 | epot = -22.4288948733282 | etot = -16.8695137363604 +484000 ekin = 2.7452293328759 | erot = 2.53012629993102 | epot = -22.483756332919 | etot = -17.2084007001121 +485000 ekin = 3.3310309518052 | erot = 2.42091818181916 | epot = -22.4922555047181 | etot = -16.7403063710937 +486000 ekin = 1.99323479363108 | erot = 1.76127718142274 | epot = -22.5432098594131 | etot = -18.7886978843592 +487000 ekin = 2.64825718911654 | erot = 2.50204426232018 | epot = -22.6407366935241 | etot = -17.4904352420874 +488000 ekin = 1.76385891719471 | erot = 2.64266555173499 | epot = -22.6990728058785 | etot = -18.2925483369488 +489000 ekin = 2.10357630534276 | erot = 2.95613916443126 | epot = -22.7877124402072 | etot = -17.7279969704332 +490000 ekin = 2.33515649128315 | erot = 2.32995416999058 | epot = -22.7920703811402 | etot = -18.1269597198665 +491000 ekin = 2.48752587426648 | erot = 2.58310949760556 | epot = -22.7834811495388 | etot = -17.7128457776667 +492000 ekin = 3.2982066520449 | erot = 2.18682924183924 | epot = -22.7674519489923 | etot = -17.2824160551081 +493000 ekin = 3.40238156707507 | erot = 2.35717041222451 | epot = -22.7149408840448 | etot = -16.9553889047452 +494000 ekin = 3.59348050162499 | erot = 2.23182460532056 | epot = -22.708168229549 | etot = -16.8828631226035 +495000 ekin = 2.52030309238563 | erot = 2.16229430067424 | epot = -22.6973031832711 | etot = -18.0147057902112 +496000 ekin = 1.96100991422337 | erot = 3.58581695215167 | epot = -22.7342002900882 | etot = -17.1873734237132 +497000 ekin = 2.22286479259681 | erot = 2.49495319949133 | epot = -22.752706201593 | etot = -18.0348882095048 +498000 ekin = 1.71033952564695 | erot = 2.41331591511583 | epot = -22.7131621100867 | etot = -18.5895066693239 +499000 ekin = 2.4191986430073 | erot = 2.8234951953182 | epot = -22.7304918052926 | etot = -17.4877979669671 +500000 ekin = 2.76271068346558 | erot = 2.22796445937143 | epot = -22.810945568044 | etot = -17.820270425207 +501000 ekin = 2.97642553987186 | erot = 1.97769778889399 | epot = -22.8306304048615 | etot = -17.8765070760957 +502000 ekin = 2.96175345860855 | erot = 1.80859086419486 | epot = -22.8525538190094 | etot = -18.082209496206 +503000 ekin = 2.51126831088416 | erot = 2.88572311841927 | epot = -22.8673362278445 | etot = -17.4703447985411 +504000 ekin = 2.84611165351303 | erot = 2.67626783872459 | epot = -22.784891957601 | etot = -17.2625124653634 +505000 ekin = 2.96124584448914 | erot = 2.59100575301931 | epot = -22.8251284225259 | etot = -17.2728768250174 +506000 ekin = 2.19858217910528 | erot = 1.97142936872076 | epot = -22.8530995461461 | etot = -18.6830879983201 +507000 ekin = 2.27398115142402 | erot = 2.68837996151519 | epot = -22.8141163798141 | etot = -17.8517552668749 +508000 ekin = 2.64439339973838 | erot = 2.0475646786945 | epot = -22.8146247157345 | etot = -18.1226666373017 +509000 ekin = 2.96023637315629 | erot = 2.90549934754533 | epot = -22.8719625385966 | etot = -17.006226817895 +510000 ekin = 2.26067558634545 | erot = 2.8086491851952 | epot = -22.9774448292235 | etot = -17.9081200576829 +511000 ekin = 2.88512738978599 | erot = 2.15263877534437 | epot = -23.0866728482479 | etot = -18.0489066831176 +512000 ekin = 2.17783748155516 | erot = 2.31389139764185 | epot = -23.1520181882638 | etot = -18.6602893090668 +513000 ekin = 1.69717952556151 | erot = 2.88265468656803 | epot = -23.1640284548406 | etot = -18.5841942427111 +514000 ekin = 1.72432024724117 | erot = 2.32742209152174 | epot = -23.1602225830814 | etot = -19.1084802443185 +515000 ekin = 2.00525337522086 | erot = 1.80102864435032 | epot = -23.1548763180746 | etot = -19.3485942985034 +516000 ekin = 3.04706172157038 | erot = 1.54171785431327 | epot = -23.1202751246552 | etot = -18.5314955487715 +517000 ekin = 2.47323892251936 | erot = 2.10799615007356 | epot = -23.0942246440307 | etot = -18.5129895714378 +518000 ekin = 2.03556879740597 | erot = 2.51531294708502 | epot = -23.01998934344 | etot = -18.469107598949 +519000 ekin = 1.59255614728459 | erot = 1.63520468579906 | epot = -22.9787913166931 | etot = -19.7510304836094 +520000 ekin = 2.17210761761844 | erot = 1.89753667353918 | epot = -22.9877149955356 | etot = -18.918070704378 +521000 ekin = 1.98466680078867 | erot = 2.09219045542652 | epot = -23.0348541858322 | etot = -18.957996929617 +522000 ekin = 2.72098469914433 | erot = 2.1956565861946 | epot = -23.1001210576501 | etot = -18.1834797723112 +523000 ekin = 2.26033454380754 | erot = 1.67112114369622 | epot = -23.1475509854344 | etot = -19.2160952979307 +524000 ekin = 2.34603831546138 | erot = 2.10546610119491 | epot = -23.1746761633772 | etot = -18.7231717467209 +525000 ekin = 2.13671314300235 | erot = 2.07172081705865 | epot = -23.241177743004 | etot = -19.032743782943 +526000 ekin = 2.50849953901566 | erot = 2.27662230434507 | epot = -23.3179050583979 | etot = -18.5327832150372 +527000 ekin = 3.04322527932213 | erot = 1.8128057083239 | epot = -23.3977373118239 | etot = -18.5417063241779 +528000 ekin = 2.57230318237901 | erot = 2.54386055260816 | epot = -23.4208428708382 | etot = -18.3046791358511 +529000 ekin = 2.39361269633634 | erot = 1.91637577362227 | epot = -23.3966015599491 | etot = -19.0866130899905 +530000 ekin = 3.35629379074241 | erot = 3.41683815876465 | epot = -23.2977853851851 | etot = -16.5246534356781 +531000 ekin = 2.52741741752382 | erot = 2.3407534240764 | epot = -23.1721175623278 | etot = -18.3039467207275 +532000 ekin = 2.78397051305127 | erot = 1.78575123294092 | epot = -23.2171711834401 | etot = -18.6474494374479 +533000 ekin = 2.27408274334042 | erot = 2.01427501035043 | epot = -23.2885684059726 | etot = -19.0002106522818 +534000 ekin = 2.54998010491124 | erot = 2.01645453645071 | epot = -23.340767920006 | etot = -18.7743332786441 +535000 ekin = 2.49595662250557 | erot = 2.09586427439367 | epot = -23.3878755759449 | etot = -18.7960546790457 +536000 ekin = 2.47717157546008 | erot = 1.92116873587366 | epot = -23.3847675210095 | etot = -18.9864272096758 +537000 ekin = 1.75235621440223 | erot = 2.11852052216088 | epot = -23.4590860280326 | etot = -19.5882092914695 +538000 ekin = 2.19317209186636 | erot = 2.75191518419655 | epot = -23.5517834707225 | etot = -18.6066961946596 +539000 ekin = 2.16135327665118 | erot = 2.25935011393787 | epot = -23.5718250119028 | etot = -19.1511216213138 +540000 ekin = 2.35701554620647 | erot = 1.64495290573329 | epot = -23.5490867129451 | etot = -19.5471182610053 +541000 ekin = 2.61451212811978 | erot = 2.52550284426681 | epot = -23.5334576350384 | etot = -18.3934426626519 +542000 ekin = 2.78909215024064 | erot = 2.09346850400964 | epot = -23.5754619290989 | etot = -18.6929012748486 +543000 ekin = 2.77024528778679 | erot = 1.84116991183092 | epot = -23.4849560716084 | etot = -18.8735408719907 +544000 ekin = 2.1580752918837 | erot = 1.50139575300258 | epot = -23.4530822422947 | etot = -19.7936111974084 +545000 ekin = 1.7286020488633 | erot = 2.56468335549414 | epot = -23.4524953434144 | etot = -19.159209939057 +546000 ekin = 2.38494138419347 | erot = 1.87772638427252 | epot = -23.4950389557033 | etot = -19.2323711872373 +547000 ekin = 2.44871634556834 | erot = 2.44464466893215 | epot = -23.544915775382 | etot = -18.6515547608815 +548000 ekin = 2.36962922994878 | erot = 2.40235228488721 | epot = -23.5548428056052 | etot = -18.7828612907692 +549000 ekin = 2.57958168249613 | erot = 2.04930779813672 | epot = -23.5565149978683 | etot = -18.9276255172355 +550000 ekin = 1.97931366474269 | erot = 1.85207468704395 | epot = -23.5614067919063 | etot = -19.7300184401196 +551000 ekin = 2.4121774327081 | erot = 2.03489368862991 | epot = -23.5115216908382 | etot = -19.0644505695002 +552000 ekin = 2.6621149390197 | erot = 1.41279265378133 | epot = -23.3450678435402 | etot = -19.2701602507391 +553000 ekin = 1.76359346131444 | erot = 2.63019210822712 | epot = -23.1435570943958 | etot = -18.7497715248542 +554000 ekin = 2.29840754300074 | erot = 2.34424452982823 | epot = -23.1114395278817 | etot = -18.4687874550527 +555000 ekin = 3.29672420152567 | erot = 1.64146930698358 | epot = -23.0891292168917 | etot = -18.1509357083825 +556000 ekin = 2.92076699655597 | erot = 2.59602967895814 | epot = -23.0268314200472 | etot = -17.5100347445331 +557000 ekin = 2.90322014804996 | erot = 3.1605266889492 | epot = -23.0146480567181 | etot = -16.950901219719 +558000 ekin = 2.78018761002223 | erot = 2.5982694700676 | epot = -22.7877399275349 | etot = -17.4092828474451 +559000 ekin = 2.48661596771862 | erot = 3.22596665511857 | epot = -22.8226574327834 | etot = -17.1100748099462 +560000 ekin = 2.34942852601697 | erot = 2.327731628774 | epot = -22.8255608134696 | etot = -18.1484006586786 +561000 ekin = 2.0520192544917 | erot = 2.90306975046936 | epot = -22.8488516051139 | etot = -17.8937626001529 +562000 ekin = 2.18821919117372 | erot = 3.66499439159822 | epot = -22.7618817506902 | etot = -16.9086681679183 +563000 ekin = 3.11505518852414 | erot = 2.28057725990563 | epot = -22.791430640287 | etot = -17.3957981918573 +564000 ekin = 2.45343120006931 | erot = 2.36321638506707 | epot = -22.75807077839 | etot = -17.9414231932536 +565000 ekin = 2.7783583550222 | erot = 2.07073547186411 | epot = -22.7486053888412 | etot = -17.8995115619549 +566000 ekin = 2.43655641927934 | erot = 2.19832280178868 | epot = -22.7227654505166 | etot = -18.0878862294486 +567000 ekin = 2.71233133108495 | erot = 2.01281091173406 | epot = -22.8839744455115 | etot = -18.1588322026925 +568000 ekin = 3.12450796157709 | erot = 1.93520150351062 | epot = -22.9625972279254 | etot = -17.9028877628377 +569000 ekin = 3.72714267701978 | erot = 2.06562452789051 | epot = -22.9814174117752 | etot = -17.1886502068649 +570000 ekin = 2.68808623045676 | erot = 2.36042122391806 | epot = -22.9989590266921 | etot = -17.9504515723172 +571000 ekin = 1.97223467321356 | erot = 2.85558181274648 | epot = -22.9369001315648 | etot = -18.1090836456047 +572000 ekin = 2.41820497321229 | erot = 2.40910077907643 | epot = -22.934930836907 | etot = -18.1076250846182 +573000 ekin = 1.76702714285011 | erot = 2.31739567602696 | epot = -22.9768902017483 | etot = -18.8924673828712 +574000 ekin = 2.0874025921411 | erot = 2.59288012722137 | epot = -23.0518321557917 | etot = -18.3715494364292 +575000 ekin = 2.34020490338785 | erot = 2.78500973557001 | epot = -23.106579446946 | etot = -17.9813648079881 +576000 ekin = 2.15506609467458 | erot = 3.30452875380292 | epot = -23.1521162771299 | etot = -17.6925214286524 +577000 ekin = 2.45698150895878 | erot = 2.31876672704205 | epot = -23.1781917242716 | etot = -18.4024434882707 +578000 ekin = 2.59353106592521 | erot = 2.33790294336519 | epot = -23.2101395643706 | etot = -18.2787055550802 +579000 ekin = 2.58102015460711 | erot = 1.71748063175117 | epot = -23.1865014452815 | etot = -18.8880006589232 +580000 ekin = 2.30361750578347 | erot = 2.8741056437962 | epot = -23.2045008793077 | etot = -18.026777729728 +581000 ekin = 2.45915247103345 | erot = 2.59640238490727 | epot = -23.1882783600354 | etot = -18.1327235040947 +582000 ekin = 2.33801590725495 | erot = 3.19256035650618 | epot = -23.2501410058056 | etot = -17.7195647420445 +583000 ekin = 1.95982078382854 | erot = 2.81944051586209 | epot = -23.4085593869414 | etot = -18.6292980872508 +584000 ekin = 2.00358327245437 | erot = 1.71267270263011 | epot = -23.4960310960901 | etot = -19.7797751210056 +585000 ekin = 2.28859150562676 | erot = 2.0630904691126 | epot = -23.5306230166998 | etot = -19.1789410419605 +586000 ekin = 2.21858454582015 | erot = 1.97776854350182 | epot = -23.4873397268816 | etot = -19.2909866375597 +587000 ekin = 3.70065233550663 | erot = 1.82187748311298 | epot = -23.4652388428898 | etot = -17.9427090242702 +588000 ekin = 3.49447328534893 | erot = 2.31981981591505 | epot = -23.3985567739262 | etot = -17.5842636726622 +589000 ekin = 2.66144502802388 | erot = 3.02756546370718 | epot = -23.2783756079917 | etot = -17.5893651162606 +590000 ekin = 1.52141257336427 | erot = 2.09874614600564 | epot = -23.1290158071881 | etot = -19.5088570878182 +591000 ekin = 1.82897193042274 | erot = 1.75592223095375 | epot = -23.0622736076073 | etot = -19.4773794462309 +592000 ekin = 2.49491276892189 | erot = 2.54829881978519 | epot = -23.054885494985 | etot = -18.0116739062779 +593000 ekin = 2.36845716276157 | erot = 1.78503341410574 | epot = -23.005264310194 | etot = -18.8517737333267 +594000 ekin = 2.07907010887473 | erot = 2.14563658430187 | epot = -22.9611396232755 | etot = -18.7364329300989 +595000 ekin = 2.62736231723873 | erot = 2.03975825744529 | epot = -22.9495489717352 | etot = -18.2824283970512 +596000 ekin = 2.58985967531624 | erot = 2.12449830164847 | epot = -22.9908505579802 | etot = -18.2764925810155 +597000 ekin = 3.02540042664856 | erot = 3.14256707367046 | epot = -22.9740991012936 | etot = -16.8061316009745 +598000 ekin = 3.44397104083287 | erot = 2.86057908398569 | epot = -23.0035411551227 | etot = -16.6989910303041 +599000 ekin = 2.13932500926498 | erot = 3.49187029024977 | epot = -22.9657391359987 | etot = -17.334543836484 +600000 ekin = 2.19758597945325 | erot = 2.49610822362373 | epot = -22.9452235009931 | etot = -18.2515292979161 +601000 ekin = 2.80918982916751 | erot = 2.81768433603374 | epot = -22.8970508934525 | etot = -17.2701767282512 +602000 ekin = 2.30031523379462 | erot = 2.40907304500536 | epot = -22.8523950981498 | etot = -18.1430068193498 +603000 ekin = 1.91335501396421 | erot = 1.99518053980753 | epot = -22.7884152302357 | etot = -18.879879676464 +604000 ekin = 2.5976715095492 | erot = 3.14351403383687 | epot = -22.7430641975848 | etot = -17.0018786541988 +605000 ekin = 2.63203298717973 | erot = 2.07906613894389 | epot = -22.7307949909782 | etot = -18.0196958648546 +606000 ekin = 2.9467839928978 | erot = 2.03982213630798 | epot = -22.6555302524726 | etot = -17.6689241232668 +607000 ekin = 2.85272606479019 | erot = 2.36693467257681 | epot = -22.6318548820143 | etot = -17.4121941446473 +608000 ekin = 3.6642968125636 | erot = 2.46706737589237 | epot = -22.5724662590777 | etot = -16.4411020706218 +609000 ekin = 2.69343886620625 | erot = 2.25873504143679 | epot = -22.6007364465804 | etot = -17.6485625389374 +610000 ekin = 2.99904616523659 | erot = 2.13621966615345 | epot = -22.5973658485054 | etot = -17.4621000171154 +611000 ekin = 3.86832985948945 | erot = 2.12096644577641 | epot = -22.5702925425382 | etot = -16.5809962372723 +612000 ekin = 2.88515301824619 | erot = 2.45910554524357 | epot = -22.4848584522585 | etot = -17.1405998887687 +613000 ekin = 2.9367425327116 | erot = 2.14436169371535 | epot = -22.465526703267 | etot = -17.38442247684 +614000 ekin = 2.791164628763 | erot = 2.02440953964802 | epot = -22.5207406301148 | etot = -17.7051664617038 +615000 ekin = 2.29338048298908 | erot = 2.3882887247098 | epot = -22.6082782403584 | etot = -17.9266090326595 +616000 ekin = 1.78195169789474 | erot = 2.45334803626969 | epot = -22.6887534547644 | etot = -18.4534537206 +617000 ekin = 2.57505808534158 | erot = 2.55345758187858 | epot = -22.7014638394959 | etot = -17.5729481722758 +618000 ekin = 2.29561379442387 | erot = 2.680432593555 | epot = -22.629958627306 | etot = -17.6539122393271 +619000 ekin = 1.94323313590202 | erot = 2.009649111577 | epot = -22.5681911047399 | etot = -18.6153088572609 +620000 ekin = 2.92263589097657 | erot = 2.15657756066215 | epot = -22.6264664894927 | etot = -17.547253037854 +621000 ekin = 2.90437881656455 | erot = 1.70649555848316 | epot = -22.6654194475729 | etot = -18.0545450725252 +622000 ekin = 2.03426149564846 | erot = 2.51826459248401 | epot = -22.6086250578043 | etot = -18.0560989696718 +623000 ekin = 1.98348786592096 | erot = 3.08484972830227 | epot = -22.6234743341759 | etot = -17.5551367399526 +624000 ekin = 2.08463083558977 | erot = 2.64004606903046 | epot = -22.6266529328942 | etot = -17.901976028274 +625000 ekin = 2.52963490334088 | erot = 2.37033264022621 | epot = -22.6750436783155 | etot = -17.7750761347484 +626000 ekin = 2.73147680333726 | erot = 2.07051651598001 | epot = -22.7272383647964 | etot = -17.9252450454791 +627000 ekin = 2.23447399123207 | erot = 2.35288557052268 | epot = -22.7136740507756 | etot = -18.1263144890208 +628000 ekin = 2.28933754695897 | erot = 2.29676268895052 | epot = -22.6176528573237 | etot = -18.0315526214142 +629000 ekin = 2.5355466362136 | erot = 1.92082543033527 | epot = -22.5693331526923 | etot = -18.1129610861434 +630000 ekin = 3.11700824717167 | erot = 2.51611049765935 | epot = -22.5144695759914 | etot = -16.8813508311604 +631000 ekin = 2.38844807455605 | erot = 3.31601650504459 | epot = -22.5190998334877 | etot = -16.8146352538871 +632000 ekin = 2.59939587493747 | erot = 2.51496212358956 | epot = -22.4711049664696 | etot = -17.3567469679426 +633000 ekin = 2.45338619933598 | erot = 1.89874016257144 | epot = -22.4394257686937 | etot = -18.0872994067863 +634000 ekin = 2.23819111967046 | erot = 1.98305652730464 | epot = -22.3433365860708 | etot = -18.1220889390957 +635000 ekin = 2.22438000857701 | erot = 1.95893208021227 | epot = -22.2877959440852 | etot = -18.1044838552959 +636000 ekin = 2.26938644192168 | erot = 2.77816773779857 | epot = -22.304696935737 | etot = -17.2571427560167 +637000 ekin = 1.97799147515645 | erot = 2.59610837639353 | epot = -22.3353238115757 | etot = -17.7612239600257 +638000 ekin = 2.54901279963356 | erot = 3.14232301833367 | epot = -22.3113570318406 | etot = -16.6200212138734 +639000 ekin = 2.38194254982011 | erot = 2.49468098011845 | epot = -22.2696251856513 | etot = -17.3930016557128 +640000 ekin = 2.07438054408915 | erot = 2.20336226777043 | epot = -22.1673693230787 | etot = -17.8896265112191 +641000 ekin = 2.49150296422893 | erot = 3.53882164550033 | epot = -22.0473233874349 | etot = -16.0169987777057 +642000 ekin = 3.37964058409635 | erot = 2.18458831029802 | epot = -21.9324522713975 | etot = -16.3682233770031 +643000 ekin = 2.80862431007863 | erot = 2.40815089193716 | epot = -21.8726014240441 | etot = -16.6558262220283 +644000 ekin = 2.952235016065 | erot = 1.92776262379328 | epot = -21.826057423183 | etot = -16.9460597833247 +645000 ekin = 4.10488984334312 | erot = 1.89062109330212 | epot = -21.7981661301139 | etot = -15.8026551934687 +646000 ekin = 2.50234872105284 | erot = 2.00205075040523 | epot = -21.7221642434957 | etot = -17.2177647720376 +647000 ekin = 2.52267281239588 | erot = 2.19481558810104 | epot = -21.7438885460027 | etot = -17.0264001455058 +648000 ekin = 2.99344241657583 | erot = 2.11139263207284 | epot = -21.7373240000025 | etot = -16.6324889513538 +649000 ekin = 2.55027365085816 | erot = 3.20350991793738 | epot = -21.7192481424448 | etot = -15.9654645736493 +650000 ekin = 3.75163896052813 | erot = 2.4418921228228 | epot = -21.6756681314987 | etot = -15.4821370481477 +651000 ekin = 3.29740056237165 | erot = 2.36780448747274 | epot = -21.5372361691658 | etot = -15.8720311193214 +652000 ekin = 2.54645886055824 | erot = 2.99097829596978 | epot = -21.4549655298412 | etot = -15.9175283733132 +653000 ekin = 2.88682688109756 | erot = 2.53633970608341 | epot = -21.4696471597398 | etot = -16.0464805725588 +654000 ekin = 2.28614085804932 | erot = 2.12026601708472 | epot = -21.5642684321318 | etot = -17.1578615569977 +655000 ekin = 2.20709609517087 | erot = 2.10729950549553 | epot = -21.5349466292622 | etot = -17.2205510285958 +656000 ekin = 2.40310876229413 | erot = 2.09663823500904 | epot = -21.5631924595209 | etot = -17.0634454622177 +657000 ekin = 2.7886551346751 | erot = 2.19608839827218 | epot = -21.794507747247 | etot = -16.8097642142997 +658000 ekin = 3.1025713807162 | erot = 2.59154293692775 | epot = -21.9667559942099 | etot = -16.272641676566 +659000 ekin = 2.88891106020276 | erot = 3.47010878893494 | epot = -22.0542552611187 | etot = -15.695235411981 +660000 ekin = 2.90074521854052 | erot = 1.62850743298555 | epot = -22.1003034196589 | etot = -17.5710507681328 +661000 ekin = 3.26666543815737 | erot = 1.86223225384177 | epot = -22.202664217118 | etot = -17.0737665251188 +662000 ekin = 3.1558491019044 | erot = 2.16868634291727 | epot = -22.3049478747804 | etot = -16.9804124299587 +663000 ekin = 1.94349853674084 | erot = 2.45687952722592 | epot = -22.3908978754177 | etot = -17.990519811451 +664000 ekin = 1.454458209604 | erot = 1.37641815749115 | epot = -22.5088813854797 | etot = -19.6780050183846 +665000 ekin = 1.57568561901953 | erot = 2.30379312359824 | epot = -22.5957949572926 | etot = -18.7163162146748 +666000 ekin = 2.46162449261636 | erot = 1.76978614573264 | epot = -22.7431602236663 | etot = -18.5117495853173 +667000 ekin = 2.82410423268351 | erot = 2.33836663659489 | epot = -22.9350563238977 | etot = -17.7725854546193 +668000 ekin = 2.7371768611619 | erot = 3.18779777915036 | epot = -23.0188768131826 | etot = -17.0939021728703 +669000 ekin = 3.41035672635338 | erot = 2.45479601777613 | epot = -23.0718232403885 | etot = -17.206670496259 +670000 ekin = 2.54649164859505 | erot = 1.99520979169172 | epot = -23.0246775830825 | etot = -18.4829761427958 +671000 ekin = 2.3802025684166 | erot = 3.0074273699854 | epot = -23.0023479116087 | etot = -17.6147179732067 +672000 ekin = 3.0126952152146 | erot = 2.55297219144564 | epot = -22.9947723733501 | etot = -17.4291049666899 +673000 ekin = 3.39486270740071 | erot = 2.38087002620332 | epot = -22.9033457919094 | etot = -17.1276130583054 +674000 ekin = 3.13698489626099 | erot = 2.10609113054063 | epot = -22.8089270617647 | etot = -17.5658510349631 +675000 ekin = 2.32294130821675 | erot = 1.5285851482073 | epot = -22.6840603385672 | etot = -18.8325338821431 +676000 ekin = 2.43564726401376 | erot = 2.26860623636407 | epot = -22.6133446272027 | etot = -17.9090911268249 +677000 ekin = 2.75162757613842 | erot = 1.94219014743456 | epot = -22.7039380847022 | etot = -18.0101203611292 +678000 ekin = 2.86321973687601 | erot = 1.66387788364135 | epot = -22.7223510604726 | etot = -18.1952534399552 +679000 ekin = 2.35079208772869 | erot = 2.70386328048643 | epot = -22.7977445343494 | etot = -17.7430891661343 +680000 ekin = 2.48449675729004 | erot = 2.90645575582477 | epot = -22.8559375688936 | etot = -17.4649850557788 +681000 ekin = 1.91581136662334 | erot = 2.58179603882022 | epot = -22.7891325966099 | etot = -18.2915251911663 +682000 ekin = 2.10466427353706 | erot = 2.69470735868806 | epot = -22.6959043279181 | etot = -17.896532695693 +683000 ekin = 2.34504535409022 | erot = 2.11592035700792 | epot = -22.5718670441909 | etot = -18.1109013330928 +684000 ekin = 2.87198876498959 | erot = 2.65732173958707 | epot = -22.4986977268024 | etot = -16.9693872222258 +685000 ekin = 3.03375238110976 | erot = 2.18190577381517 | epot = -22.4634189289575 | etot = -17.2477607740326 +686000 ekin = 2.46248931777657 | erot = 2.43025710170916 | epot = -22.4079029677659 | etot = -17.5151565482801 +687000 ekin = 2.74662486817896 | erot = 1.7960915256241 | epot = -22.3360381567114 | etot = -17.7933217629083 +688000 ekin = 1.81703718003043 | erot = 2.06511603415636 | epot = -22.3083758541198 | etot = -18.426222639933 +689000 ekin = 2.84202633430564 | erot = 1.92033962884778 | epot = -22.3752571185822 | etot = -17.6128911554288 +690000 ekin = 2.07525448405017 | erot = 2.46342632176819 | epot = -22.4633535431152 | etot = -17.9246727372969 +691000 ekin = 2.12558517800138 | erot = 2.52961097164003 | epot = -22.483426266766 | etot = -17.8282301171246 +692000 ekin = 2.86720433292881 | erot = 2.65102150657024 | epot = -22.4003374064863 | etot = -16.8821115669873 +693000 ekin = 2.30143055084864 | erot = 2.5229094638336 | epot = -22.2859681228792 | etot = -17.461628108197 +694000 ekin = 2.88400701080874 | erot = 2.34320802755438 | epot = -22.206318584282 | etot = -16.9791035459188 +695000 ekin = 2.93184722112895 | erot = 2.22933507376833 | epot = -22.2348177906806 | etot = -17.0736354957833 +696000 ekin = 2.63173546326796 | erot = 2.3427536957083 | epot = -22.274597219839 | etot = -17.3001080608628 +697000 ekin = 1.87084079501972 | erot = 1.78050094908735 | epot = -22.2730387150936 | etot = -18.6216969709865 +698000 ekin = 2.19791428580687 | erot = 2.8288358175635 | epot = -22.2819378523405 | etot = -17.2551877489701 +699000 ekin = 2.34279295545267 | erot = 2.07514436344562 | epot = -22.2061425261575 | etot = -17.7882052072592 +700000 ekin = 2.576803119019 | erot = 2.32167543064961 | epot = -22.1658685747825 | etot = -17.2673900251139 +701000 ekin = 2.9943865807539 | erot = 1.89982533986206 | epot = -22.2191193266439 | etot = -17.324907406028 +702000 ekin = 2.68548464757459 | erot = 2.65050744453208 | epot = -22.2547415922757 | etot = -16.918749500169 +703000 ekin = 2.01996957402024 | erot = 2.04032822241737 | epot = -22.3253693056515 | etot = -18.2650715092139 +704000 ekin = 1.58871069317829 | erot = 1.64014270467762 | epot = -22.3617232281452 | etot = -19.1328698302893 +705000 ekin = 2.30894157549819 | erot = 1.90252913035992 | epot = -22.4307958564623 | etot = -18.2193251506042 +706000 ekin = 2.61729186445574 | erot = 3.218798680391 | epot = -22.5603358780911 | etot = -16.7242453332444 +707000 ekin = 2.60797107906866 | erot = 2.31455039977395 | epot = -22.7102471053997 | etot = -17.7877256265571 +708000 ekin = 1.81633850341999 | erot = 2.34822575669415 | epot = -22.841408787855 | etot = -18.6768445277409 +709000 ekin = 1.83541322105378 | erot = 2.51792380003795 | epot = -23.0137235815795 | etot = -18.6603865604878 +710000 ekin = 2.2142058326246 | erot = 1.92378721690473 | epot = -23.1433453130909 | etot = -19.0053522635615 +711000 ekin = 2.06744054454475 | erot = 2.39811709353191 | epot = -23.1532717948857 | etot = -18.687714156809 +712000 ekin = 2.17279472706359 | erot = 1.75362175342097 | epot = -23.0479262273957 | etot = -19.1215097469111 +713000 ekin = 2.87118830138478 | erot = 1.54943993787552 | epot = -22.8430575230907 | etot = -18.4224292838304 +714000 ekin = 2.01079466743967 | erot = 1.87510988392748 | epot = -22.9212969433221 | etot = -19.035392391955 +715000 ekin = 2.49921829589267 | erot = 1.91934008289236 | epot = -22.9679126658062 | etot = -18.5493542870212 +716000 ekin = 2.94666510633352 | erot = 2.18714442405523 | epot = -23.0339970974289 | etot = -17.9001875670402 +717000 ekin = 3.07404079722086 | erot = 2.46628262765132 | epot = -23.1869721551174 | etot = -17.6466487302453 +718000 ekin = 3.4706007837111 | erot = 2.28206620506092 | epot = -23.2524492340769 | etot = -17.4997822453048 +719000 ekin = 4.08343792096554 | erot = 3.10429377075216 | epot = -23.2448292181926 | etot = -16.0570975264749 +720000 ekin = 2.52774819763972 | erot = 1.92867508904583 | epot = -23.1435084559682 | etot = -18.6870851692827 +721000 ekin = 2.58294244811584 | erot = 2.03830531780331 | epot = -23.0601633758883 | etot = -18.4389156099692 +722000 ekin = 1.94458885450861 | erot = 2.32008660802526 | epot = -22.9811929404573 | etot = -18.7165174779234 +723000 ekin = 2.41998340576259 | erot = 2.1236972897937 | epot = -23.0570939793877 | etot = -18.5134132838314 +724000 ekin = 1.90406371300861 | erot = 1.97533505769878 | epot = -23.1267629042384 | etot = -19.247364133531 +725000 ekin = 2.14287056473421 | erot = 2.79289687450021 | epot = -23.1695632046138 | etot = -18.2337957653794 +726000 ekin = 2.2642331709972 | erot = 2.55343019202652 | epot = -23.243290908371 | etot = -18.4256275453472 +727000 ekin = 1.69816397656715 | erot = 2.64011919415554 | epot = -23.298837689321 | etot = -18.9605545185983 +728000 ekin = 2.23000862561933 | erot = 3.58521470578671 | epot = -23.3528245832468 | etot = -17.5376012518407 +729000 ekin = 2.70076566380344 | erot = 1.73367306410749 | epot = -23.3971276122796 | etot = -18.9626888843687 +730000 ekin = 2.5481867380276 | erot = 2.77394958410254 | epot = -23.3988686964745 | etot = -18.0767323743443 +731000 ekin = 2.69782550956094 | erot = 2.04855826523076 | epot = -23.4310969813891 | etot = -18.6847132065974 +732000 ekin = 2.79613002753752 | erot = 1.87867430486715 | epot = -23.4885161441653 | etot = -18.8137118117607 +733000 ekin = 2.20346728125046 | erot = 2.64365594749975 | epot = -23.5261309431819 | etot = -18.6790077144317 +734000 ekin = 1.69780111261444 | erot = 2.3091790956079 | epot = -23.5188046470475 | etot = -19.5118244388251 +735000 ekin = 2.18402736165936 | erot = 2.7205162023087 | epot = -23.4712689506938 | etot = -18.5667253867257 +736000 ekin = 2.26138696009404 | erot = 1.17083930058802 | epot = -23.4348107178754 | etot = -20.0025844571934 +737000 ekin = 2.22219419044795 | erot = 3.14114682990361 | epot = -23.3869288757725 | etot = -18.023587855421 +738000 ekin = 1.75464981631084 | erot = 2.28485941478057 | epot = -23.2709893028053 | etot = -19.2314800717139 +739000 ekin = 1.41806378584361 | erot = 2.1671403411282 | epot = -23.2213775300889 | etot = -19.6361734031171 +740000 ekin = 1.90901017596351 | erot = 2.27102763422489 | epot = -23.1829198366047 | etot = -19.0028820264163 +741000 ekin = 1.9930994487751 | erot = 2.73523269523397 | epot = -23.1169670577824 | etot = -18.3886349137733 +742000 ekin = 1.99876411117686 | erot = 1.89882876917754 | epot = -23.0300825800851 | etot = -19.1324896997307 +743000 ekin = 1.96472814667687 | erot = 2.79504722629174 | epot = -22.8990488521609 | etot = -18.1392734791923 +744000 ekin = 2.02442646092311 | erot = 2.35044838626027 | epot = -22.8186526150799 | etot = -18.4437777678966 +745000 ekin = 1.65344231988822 | erot = 1.87919095141021 | epot = -22.7624827109091 | etot = -19.2298494396107 +746000 ekin = 2.1034668185472 | erot = 2.03078530569665 | epot = -22.743454277698 | etot = -18.6092021534542 +747000 ekin = 3.06690414848489 | erot = 1.67540297869492 | epot = -22.7625979159322 | etot = -18.0202907887524 +748000 ekin = 3.069654144834 | erot = 1.86014593098644 | epot = -22.8118567150739 | etot = -17.8820566392535 +749000 ekin = 2.53718696167217 | erot = 2.02710579059033 | epot = -22.8431046011969 | etot = -18.2788118489344 +750000 ekin = 2.75657354808099 | erot = 2.34953156046291 | epot = -22.9548205390759 | etot = -17.848715430532 +751000 ekin = 2.52290020835147 | erot = 2.3487376359998 | epot = -23.0238691402084 | etot = -18.1522312958571 +752000 ekin = 2.47222247869325 | erot = 1.68679846444686 | epot = -22.9958559112492 | etot = -18.836834968109 +753000 ekin = 2.48263277172424 | erot = 1.54669382815741 | epot = -23.0858212396418 | etot = -19.0564946397602 +754000 ekin = 2.54806257410879 | erot = 2.26636466676165 | epot = -23.1896472696843 | etot = -18.3752200288138 +755000 ekin = 1.53168409517921 | erot = 2.22665478278015 | epot = -23.2059118234918 | etot = -19.4475729455324 +756000 ekin = 2.10751715527953 | erot = 2.4052577432668 | epot = -23.114150245375 | etot = -18.6013753468287 +757000 ekin = 2.93395895491028 | erot = 2.05821177584909 | epot = -23.0783355599275 | etot = -18.0861648291681 +758000 ekin = 2.38307945406232 | erot = 2.50598165375058 | epot = -22.9691152621287 | etot = -18.0800541543158 +759000 ekin = 2.60292884338835 | erot = 2.36916677072546 | epot = -22.7987274767846 | etot = -17.8266318626708 +760000 ekin = 3.2284318196987 | erot = 2.73822716520638 | epot = -22.6756147646272 | etot = -16.7089557797221 +761000 ekin = 3.41868727786494 | erot = 1.68975765213406 | epot = -22.5638952547581 | etot = -17.4554503247591 +762000 ekin = 3.43033946346107 | erot = 2.5283975140253 | epot = -22.3549032489322 | etot = -16.3961662714458 +763000 ekin = 2.65773094814485 | erot = 1.83975133975561 | epot = -22.234833339183 | etot = -17.7373510512825 +764000 ekin = 2.3815484472129 | erot = 2.70684992442147 | epot = -22.0890752688231 | etot = -17.0006768971887 +765000 ekin = 2.23212803588897 | erot = 1.94868597739427 | epot = -21.9918715237933 | etot = -17.81105751051 +766000 ekin = 2.49097891886065 | erot = 1.96764603993156 | epot = -21.8443436680801 | etot = -17.3857187092879 +767000 ekin = 2.3457921497675 | erot = 2.64636009163513 | epot = -21.7634962034013 | etot = -16.7713439619986 +768000 ekin = 1.87671147825106 | erot = 2.05549869178485 | epot = -21.7324638416528 | etot = -17.8002536716169 +769000 ekin = 3.05058687860239 | erot = 2.66104171022372 | epot = -21.66792195987 | etot = -15.9562933710439 +770000 ekin = 2.44115683640633 | erot = 1.97554932479749 | epot = -21.644882066475 | etot = -17.2281759052712 +771000 ekin = 2.2368746400443 | erot = 2.55040970708786 | epot = -21.5811924169692 | etot = -16.793908069837 +772000 ekin = 2.76529680592008 | erot = 1.97873499811185 | epot = -21.6543448952384 | etot = -16.9103130912064 +773000 ekin = 2.14632888240093 | erot = 2.41330587525514 | epot = -21.7728828090227 | etot = -17.2132480513667 +774000 ekin = 2.19848545803079 | erot = 1.9765131024719 | epot = -21.8398858604883 | etot = -17.6648872999856 +775000 ekin = 2.52300137989083 | erot = 2.80935365273515 | epot = -22.0219985274259 | etot = -16.6896434947999 +776000 ekin = 3.15842485269273 | erot = 2.47066157093647 | epot = -22.183029096161 | etot = -16.5539426725318 +777000 ekin = 1.91784338934576 | erot = 1.76045300517084 | epot = -22.2259652888115 | etot = -18.5476688942949 +778000 ekin = 2.93738066043324 | erot = 2.2945784249029 | epot = -22.2339481852394 | etot = -17.0019890999032 +779000 ekin = 3.09847206114319 | erot = 2.04557717006051 | epot = -22.240438366259 | etot = -17.0963891350553 +780000 ekin = 2.86127568397807 | erot = 3.12055135138658 | epot = -22.1865692766137 | etot = -16.204742241249 +781000 ekin = 2.36069914420785 | erot = 3.53186431088486 | epot = -22.1210563364352 | etot = -16.2284928813425 +782000 ekin = 2.31592690319261 | erot = 2.85730598644038 | epot = -22.0302855151548 | etot = -16.8570526255218 +783000 ekin = 1.86647729944746 | erot = 3.03450246093098 | epot = -21.8860143679489 | etot = -16.9850346075704 +784000 ekin = 2.04055627573201 | erot = 2.26047908607292 | epot = -21.7534271639392 | etot = -17.4523918021343 +785000 ekin = 2.02248469828703 | erot = 2.13950421850547 | epot = -21.6318967501917 | etot = -17.4699078333992 +786000 ekin = 2.34211746551601 | erot = 2.34838133643265 | epot = -21.5890308210084 | etot = -16.8985320190597 +787000 ekin = 2.74971447554938 | erot = 2.24123553296042 | epot = -21.5192132515562 | etot = -16.5282632430464 +788000 ekin = 2.14142056672038 | erot = 2.27008574684965 | epot = -21.4982362621713 | etot = -17.0867299486013 +789000 ekin = 1.98580913341303 | erot = 2.00702444041792 | epot = -21.5235331659838 | etot = -17.5306995921528 +790000 ekin = 1.68578263083924 | erot = 1.43485602862151 | epot = -21.64400815936 | etot = -18.5233694998993 +791000 ekin = 2.13583938840528 | erot = 2.53730095458943 | epot = -21.7916440698418 | etot = -17.1185037268471 +792000 ekin = 1.71937483898028 | erot = 2.19563804216009 | epot = -21.8794946709408 | etot = -17.9644817898004 +793000 ekin = 3.15868943755339 | erot = 1.94575875708421 | epot = -22.0398145404618 | etot = -16.9353663458242 +794000 ekin = 2.45478602538954 | erot = 3.00825554959563 | epot = -22.0843165283013 | etot = -16.6212749533161 +795000 ekin = 2.87760320917195 | erot = 3.06920266633563 | epot = -22.1595628991904 | etot = -16.2127570236828 +796000 ekin = 2.29816690595059 | erot = 1.61510864654315 | epot = -22.1869705548184 | etot = -18.2736950023247 +797000 ekin = 2.19015256067211 | erot = 3.65734446008355 | epot = -22.1432608090644 | etot = -16.2957637883088 +798000 ekin = 2.12018787925579 | erot = 2.92822258455554 | epot = -22.1311312789224 | etot = -17.0827208151111 +799000 ekin = 2.49416140154829 | erot = 2.73328283280218 | epot = -22.0825726051882 | etot = -16.8551283708377 +800000 ekin = 2.18932007838552 | erot = 2.97640731559392 | epot = -21.979362152191 | etot = -16.8136347582115 +801000 ekin = 2.58827112124839 | erot = 2.74404424837261 | epot = -21.9108490336924 | etot = -16.5785336640714 +802000 ekin = 3.07870342348167 | erot = 2.87961505564287 | epot = -21.822560433681 | etot = -15.8642419545565 +803000 ekin = 2.23986243680641 | erot = 2.50525058807596 | epot = -21.7275940818101 | etot = -16.9824810569277 +804000 ekin = 2.91885860068427 | erot = 1.5788904045143 | epot = -21.6896376725624 | etot = -17.1918886673638 +805000 ekin = 2.68277363980194 | erot = 3.05527868915739 | epot = -21.6710764398127 | etot = -15.9330241108534 +806000 ekin = 2.77769607049014 | erot = 2.18887276909082 | epot = -21.6314833902337 | etot = -16.6649145506527 +807000 ekin = 2.12673239079667 | erot = 2.86003407600808 | epot = -21.7295924017744 | etot = -16.7428259349697 +808000 ekin = 1.89599614774678 | erot = 2.29237053227661 | epot = -21.7511361510417 | etot = -17.5627694710183 +809000 ekin = 1.96405066221971 | erot = 1.92110393348365 | epot = -21.7075506883706 | etot = -17.8223960926673 +810000 ekin = 2.01518137594274 | erot = 2.60119247286599 | epot = -21.678838587473 | etot = -17.0624647386642 +811000 ekin = 2.31084800889289 | erot = 1.75270367309064 | epot = -21.6837819033719 | etot = -17.6202302213883 +812000 ekin = 2.57701031002089 | erot = 2.34932304073588 | epot = -21.7246716033188 | etot = -16.7983382525621 +813000 ekin = 2.87706904926075 | erot = 2.35686610624155 | epot = -21.837592223605 | etot = -16.6036570681027 +814000 ekin = 2.89908405023865 | erot = 2.31423299883228 | epot = -21.8379261473902 | etot = -16.6246090983192 +815000 ekin = 2.54050064212256 | erot = 2.82732568868833 | epot = -21.6068952707049 | etot = -16.2390689398941 +816000 ekin = 2.17040404256386 | erot = 2.53711088209172 | epot = -21.5560322071983 | etot = -16.8485172825427 +817000 ekin = 1.7842696071831 | erot = 2.67810959410574 | epot = -21.8738878035325 | etot = -17.4115086022437 +818000 ekin = 2.29659398017838 | erot = 2.63718862373663 | epot = -22.164277271391 | etot = -17.230494667476 +819000 ekin = 2.15801167884062 | erot = 2.62095572928875 | epot = -22.1816109590115 | etot = -17.4026435508822 +820000 ekin = 1.94384548213955 | erot = 2.28597987799276 | epot = -22.0986187375022 | etot = -17.8687933773699 +821000 ekin = 2.10513194007576 | erot = 2.38698175569218 | epot = -22.1146754444785 | etot = -17.6225617487105 +822000 ekin = 2.24819716786441 | erot = 2.15258805680875 | epot = -22.0539472940486 | etot = -17.6531620693754 +823000 ekin = 2.26584952085582 | erot = 2.60619852526611 | epot = -22.0924201800579 | etot = -17.220372133936 +824000 ekin = 1.65187935478513 | erot = 1.4870311903723 | epot = -22.1682955997986 | etot = -19.0293850546411 +825000 ekin = 1.60213094818648 | erot = 1.98592524368395 | epot = -22.1687104063708 | etot = -18.5806542145004 +826000 ekin = 1.97430720107255 | erot = 2.19175014677162 | epot = -22.1061881978655 | etot = -17.9401308500213 +827000 ekin = 2.1793755983405 | erot = 2.44975419075934 | epot = -21.9704586607304 | etot = -17.3413288716306 +828000 ekin = 1.90399088418587 | erot = 2.72532994798818 | epot = -21.9585923270583 | etot = -17.3292714948842 +829000 ekin = 2.06478103068883 | erot = 2.96583035402588 | epot = -21.9849402038682 | etot = -16.9543288191535 +830000 ekin = 1.98920675238979 | erot = 2.15331250444996 | epot = -22.0339146439702 | etot = -17.8913953871305 +831000 ekin = 2.33567462674689 | erot = 2.36888807413496 | epot = -22.1271573756461 | etot = -17.4225946747643 +832000 ekin = 2.0119470999192 | erot = 1.94769143293625 | epot = -22.2038482709588 | etot = -18.2442097381034 +833000 ekin = 2.26025933495881 | erot = 2.16012558191463 | epot = -22.2882501045414 | etot = -17.867865187668 +834000 ekin = 2.11529426445865 | erot = 1.52405523315359 | epot = -22.3075608649826 | etot = -18.6682113673703 +835000 ekin = 2.89920750905511 | erot = 2.7380108175103 | epot = -22.3942491248321 | etot = -16.7570307982667 +836000 ekin = 3.33069528982658 | erot = 2.42771267807861 | epot = -22.4321737300744 | etot = -16.6737657621692 +837000 ekin = 2.74831774333782 | erot = 2.31991750378627 | epot = -22.4290234552873 | etot = -17.3607882081632 +838000 ekin = 3.13714871682187 | erot = 3.21601751721778 | epot = -22.4642383906451 | etot = -16.1110721566054 +839000 ekin = 2.73358272751807 | erot = 2.60144488190506 | epot = -22.4062682687368 | etot = -17.0712406593137 +840000 ekin = 2.96121930874636 | erot = 1.42725942278118 | epot = -22.3293755621294 | etot = -17.9408968306019 +841000 ekin = 2.95134811170867 | erot = 2.67666861874609 | epot = -22.2936348151224 | etot = -16.6656180846677 +842000 ekin = 2.15783928636402 | erot = 2.30287195796693 | epot = -22.2978011147172 | etot = -17.8370898703863 +843000 ekin = 2.84565152669617 | erot = 2.05108014775141 | epot = -22.3162908719779 | etot = -17.4195591975303 +844000 ekin = 2.99645803669157 | erot = 1.50433298006521 | epot = -22.3768320579304 | etot = -17.8760410411737 +845000 ekin = 3.20248025697125 | erot = 2.27246140825563 | epot = -22.3985708422076 | etot = -16.9236291769807 +846000 ekin = 3.35773945734322 | erot = 2.54074745551552 | epot = -22.4144833015876 | etot = -16.5159963887289 +847000 ekin = 2.17779203733109 | erot = 2.7381758118846 | epot = -22.3524825149514 | etot = -17.4365146657357 +848000 ekin = 2.51627348417144 | erot = 2.81170686694718 | epot = -22.2066307862469 | etot = -16.8786504351283 +849000 ekin = 1.99679455190556 | erot = 2.56855846773091 | epot = -22.0763062134929 | etot = -17.5109531938564 +850000 ekin = 2.05799123916876 | erot = 1.80888056240784 | epot = -22.0665032506706 | etot = -18.1996314490939 +851000 ekin = 2.08889793767921 | erot = 1.8617218179029 | epot = -22.0629711763889 | etot = -18.1123514208068 +852000 ekin = 1.68990805178902 | erot = 1.42763535981883 | epot = -22.002100112701 | etot = -18.8845567010931 +853000 ekin = 1.99310886654811 | erot = 3.05226969048295 | epot = -22.0306903552278 | etot = -16.9853117981967 +854000 ekin = 2.98378700534986 | erot = 2.23102745240541 | epot = -22.1115820238811 | etot = -16.8967675661258 +855000 ekin = 2.17087415585277 | erot = 2.83781472268789 | epot = -22.1115106395971 | etot = -17.1028217610564 +856000 ekin = 2.42228475387308 | erot = 1.53328604594478 | epot = -22.0841888628209 | etot = -18.128618063003 +857000 ekin = 2.50431566526893 | erot = 2.80498769176515 | epot = -21.9881235267534 | etot = -16.6788201697193 +858000 ekin = 2.17333686672378 | erot = 2.82591115507169 | epot = -21.9093201368614 | etot = -16.910072115066 +859000 ekin = 2.29930070497242 | erot = 2.3241736893906 | epot = -21.8849849636104 | etot = -17.2615105692473 +860000 ekin = 1.99153024057672 | erot = 1.9467463860015 | epot = -21.8998709373217 | etot = -17.9615943107435 +861000 ekin = 2.69177523559624 | erot = 2.23997750036372 | epot = -21.8915522194994 | etot = -16.9597994835394 +862000 ekin = 2.86117050047984 | erot = 2.41530060322762 | epot = -21.876687883023 | etot = -16.6002167793155 +863000 ekin = 2.59841547044275 | erot = 3.3501705008543 | epot = -21.8162649771436 | etot = -15.8676790058466 +864000 ekin = 2.92496272611018 | erot = 2.30350236144452 | epot = -21.7820358973268 | etot = -16.5535708097721 +865000 ekin = 1.94718216128952 | erot = 2.16572180916631 | epot = -21.7000823492195 | etot = -17.5871783787637 +866000 ekin = 1.99006127871689 | erot = 1.65011901234954 | epot = -21.6190182409268 | etot = -17.9788379498603 +867000 ekin = 1.76250718110787 | erot = 3.37958608370305 | epot = -21.5401486584561 | etot = -16.3980553936452 +868000 ekin = 1.845623450314 | erot = 2.78812196028612 | epot = -21.5771917352235 | etot = -16.9434463246233 +869000 ekin = 2.39300849969204 | erot = 2.38301618173174 | epot = -21.6710790825578 | etot = -16.8950544011341 +870000 ekin = 1.91899243212541 | erot = 3.2222244071739 | epot = -21.6734733803871 | etot = -16.5322565410878 +871000 ekin = 3.10255827845531 | erot = 2.95454268850896 | epot = -21.5913249106744 | etot = -15.5342239437101 +872000 ekin = 2.94582883077842 | erot = 1.38261935263093 | epot = -21.4597055547832 | etot = -17.1312573713739 +873000 ekin = 2.72830997927424 | erot = 2.23223699637274 | epot = -21.3657566950046 | etot = -16.4052097193576 +874000 ekin = 2.41464704842015 | erot = 2.10351476791495 | epot = -21.2635161734954 | etot = -16.7453543571603 +875000 ekin = 2.99468455803482 | erot = 2.72761242382526 | epot = -21.2488881289381 | etot = -15.526591147078 +876000 ekin = 2.13382009818493 | erot = 2.23152059294678 | epot = -21.2388603913311 | etot = -16.8735197001994 +877000 ekin = 1.839391763993 | erot = 1.60727997722601 | epot = -21.2015948102408 | etot = -17.7549230690218 +878000 ekin = 2.01267175782179 | erot = 2.73109796378377 | epot = -21.2125253160263 | etot = -16.4687555944207 +879000 ekin = 1.42911941081343 | erot = 2.17371661448624 | epot = -21.1345316334464 | etot = -17.5316956081467 +880000 ekin = 2.10605339224632 | erot = 2.58847517789128 | epot = -21.0787246891645 | etot = -16.3841961190269 +881000 ekin = 1.54924791070118 | erot = 2.0068513915418 | epot = -21.1356465207066 | etot = -17.5795472184636 +882000 ekin = 2.19964315713499 | erot = 2.65509097106008 | epot = -21.2389026935677 | etot = -16.3841685653726 +883000 ekin = 2.20850404171077 | erot = 2.22833605977578 | epot = -21.3067394383395 | etot = -16.8698993368529 +884000 ekin = 2.76978562647275 | erot = 2.10395845939756 | epot = -21.3429618615585 | etot = -16.4692177756882 +885000 ekin = 1.93339807672781 | erot = 1.77156241344967 | epot = -21.3858074096933 | etot = -17.6808469195158 +886000 ekin = 2.00408769971894 | erot = 3.10736267931441 | epot = -21.3935346347812 | etot = -16.2820842557478 +887000 ekin = 1.96987943750801 | erot = 2.82035886899743 | epot = -21.3967073105592 | etot = -16.6064690040538 +888000 ekin = 1.91464371566411 | erot = 2.33371232948867 | epot = -21.4767119016419 | etot = -17.2283558564891 +889000 ekin = 1.88227414130202 | erot = 2.45915914930409 | epot = -21.5790392436829 | etot = -17.2376059530768 +890000 ekin = 1.84515176532447 | erot = 2.24992378831494 | epot = -21.6747594004542 | etot = -17.5796838468148 +891000 ekin = 2.6016566869706 | erot = 2.34500453305754 | epot = -21.8016735536793 | etot = -16.8550123336512 +892000 ekin = 2.7128775188686 | erot = 2.69544224573133 | epot = -21.9063749565584 | etot = -16.4980551919585 +893000 ekin = 2.17862714611329 | erot = 2.98452123742224 | epot = -21.9155556335137 | etot = -16.7524072499782 +894000 ekin = 2.52079948361477 | erot = 2.46355933674926 | epot = -21.915110079455 | etot = -16.930751259091 +895000 ekin = 2.53566097944338 | erot = 2.45130454442941 | epot = -21.9477860878339 | etot = -16.9608205639611 +896000 ekin = 1.84455393639214 | erot = 2.77499090684944 | epot = -21.9167554809878 | etot = -17.2972106377462 +897000 ekin = 2.38519326880695 | erot = 2.01980287317302 | epot = -21.8644918203992 | etot = -17.4594956784193 +898000 ekin = 2.14354914407572 | erot = 1.89196669459414 | epot = -21.7953104274974 | etot = -17.7597945888275 +899000 ekin = 2.65485657727374 | erot = 2.32374560038192 | epot = -21.6964754705568 | etot = -16.7178732929012 +900000 ekin = 2.1437154528087 | erot = 2.28119066740276 | epot = -21.6934954112434 | etot = -17.268589291032 +901000 ekin = 1.93965814946881 | erot = 1.81495571440911 | epot = -21.7369092433376 | etot = -17.9822953794597 +902000 ekin = 2.60993957981555 | erot = 2.50321386623392 | epot = -21.6842517568354 | etot = -16.5710983107859 +903000 ekin = 1.87484955546756 | erot = 2.17008893987963 | epot = -21.6383913984978 | etot = -17.5934529031506 +904000 ekin = 1.87454064845764 | erot = 2.32484081519397 | epot = -21.5866637125315 | etot = -17.3872822488799 +905000 ekin = 2.31407473814843 | erot = 2.1509486854239 | epot = -21.5154415841816 | etot = -17.0504181606093 +906000 ekin = 2.49583383758853 | erot = 2.25091096848465 | epot = -21.5170853902294 | etot = -16.7703405841563 +907000 ekin = 4.19798796104344 | erot = 2.50305323228071 | epot = -21.5976736513859 | etot = -14.8966324580618 +908000 ekin = 3.26730891548756 | erot = 2.11222217905481 | epot = -21.7526644402476 | etot = -16.3731333457052 +909000 ekin = 2.64106561110374 | erot = 1.92197432194202 | epot = -21.8748043207924 | etot = -17.3117643877466 +910000 ekin = 2.61805562731904 | erot = 2.90737422678701 | epot = -21.9709470207745 | etot = -16.4455171666684 +911000 ekin = 2.62012718860141 | erot = 4.35318528241846 | epot = -22.0282478750366 | etot = -15.0549354040167 +912000 ekin = 3.07628909273118 | erot = 3.69371809788395 | epot = -22.0511180009901 | etot = -15.281110810375 +913000 ekin = 2.82956898268831 | erot = 2.17078429141199 | epot = -22.0149543706266 | etot = -17.0146010965263 +914000 ekin = 2.16386655780066 | erot = 1.22303673036133 | epot = -21.9243495493209 | etot = -18.5374462611589 +915000 ekin = 1.59447095066509 | erot = 2.95966391292002 | epot = -21.8264580452026 | etot = -17.2723231816175 +916000 ekin = 2.58365539107523 | erot = 3.75147270955031 | epot = -21.8922962938608 | etot = -15.5571681932352 +917000 ekin = 3.01643029206974 | erot = 2.88035639021002 | epot = -21.9150526568514 | etot = -16.0182659745717 +918000 ekin = 2.89929776900147 | erot = 2.64137394041292 | epot = -21.9078998623094 | etot = -16.367228152895 +919000 ekin = 3.20476671865013 | erot = 2.76036957969156 | epot = -21.8878055443404 | etot = -15.9226692459988 +920000 ekin = 2.28949350558684 | erot = 2.38558870046818 | epot = -21.8659406759968 | etot = -17.1908584699418 +921000 ekin = 2.39158312157105 | erot = 2.44959700788173 | epot = -21.8638974869224 | etot = -17.0227173574697 +922000 ekin = 2.30678787768012 | erot = 2.42145678067296 | epot = -21.8218369909645 | etot = -17.0935923326115 +923000 ekin = 2.49697778842282 | erot = 2.66565493744117 | epot = -21.8078634464733 | etot = -16.6452307206093 +924000 ekin = 1.55676047489502 | erot = 2.97115254541004 | epot = -21.7829722234117 | etot = -17.2550592031067 +925000 ekin = 1.86603413909289 | erot = 1.96274861601778 | epot = -21.7288604040749 | etot = -17.9000776489642 +926000 ekin = 1.36993364395821 | erot = 2.11749584641398 | epot = -21.7083442855148 | etot = -18.2209147951426 +927000 ekin = 2.55718977538496 | erot = 2.0810909504888 | epot = -21.7242353526193 | etot = -17.0859546267455 +928000 ekin = 2.0974272910786 | erot = 2.73922911267238 | epot = -21.7673808868819 | etot = -16.9307244831309 +929000 ekin = 1.85550591174834 | erot = 1.84990976935038 | epot = -21.8639426090857 | etot = -18.158526927987 +930000 ekin = 1.99594723517185 | erot = 2.09151231016389 | epot = -21.8461015073053 | etot = -17.7586419619695 +931000 ekin = 2.45331651079282 | erot = 1.86703658018613 | epot = -21.7382799817762 | etot = -17.4179268907972 +932000 ekin = 2.76909250526758 | erot = 2.34990175754268 | epot = -21.7639792890093 | etot = -16.6449850261991 +933000 ekin = 3.0474736633548 | erot = 2.52740756503519 | epot = -21.6783727845496 | etot = -16.1034915561596 +934000 ekin = 2.93463275640818 | erot = 2.48893095891024 | epot = -21.5784996926914 | etot = -16.154935977373 +935000 ekin = 2.77799347567548 | erot = 2.13929358412249 | epot = -21.5334239467005 | etot = -16.6161368869026 +936000 ekin = 2.96529953690397 | erot = 2.07095365726716 | epot = -21.5249249864244 | etot = -16.4886717922532 +937000 ekin = 3.04850537701749 | erot = 2.32432162998051 | epot = -21.4386642161072 | etot = -16.0658372091092 +938000 ekin = 2.99262628505359 | erot = 2.35224559307843 | epot = -21.3457080466207 | etot = -16.0008361684887 +939000 ekin = 2.61238181353702 | erot = 2.26780356837291 | epot = -21.3079422537804 | etot = -16.4277568718705 +940000 ekin = 2.65930112044941 | erot = 2.75497479722395 | epot = -21.2170493356503 | etot = -15.802773417977 +941000 ekin = 2.27574261339217 | erot = 2.61419196501688 | epot = -21.1297657597673 | etot = -16.2398311813582 +942000 ekin = 1.89172011891054 | erot = 2.82029488513786 | epot = -21.0410099256113 | etot = -16.3289949215629 +943000 ekin = 2.47643464476757 | erot = 2.34737109151876 | epot = -21.0466687727979 | etot = -16.2228630365116 +944000 ekin = 2.13883995897326 | erot = 1.92577316206138 | epot = -21.0114219746513 | etot = -16.9468088536167 +945000 ekin = 2.57768697869113 | erot = 2.2147013612407 | epot = -21.0634624131725 | etot = -16.2710740732407 +946000 ekin = 2.36420709243625 | erot = 2.89647330776423 | epot = -21.088814693033 | etot = -15.8281342928325 +947000 ekin = 2.07104171538468 | erot = 1.86575631327234 | epot = -21.1004860950452 | etot = -17.1636880663882 +948000 ekin = 1.85532958802996 | erot = 1.3695283408655 | epot = -21.1364231315616 | etot = -17.9115652026661 +949000 ekin = 1.76206591178366 | erot = 2.3173732855863 | epot = -21.1463744779337 | etot = -17.0669352805638 +950000 ekin = 1.72021033353108 | erot = 2.24191394295308 | epot = -21.1376324866856 | etot = -17.1755082102014 +951000 ekin = 1.96140007830504 | erot = 2.32248863487759 | epot = -21.1955927656813 | etot = -16.9117040524987 +952000 ekin = 2.93256201500608 | erot = 2.74550490827502 | epot = -21.2347810245411 | etot = -15.55671410126 +953000 ekin = 2.95031285986317 | erot = 2.39822873263993 | epot = -21.2526091831331 | etot = -15.90406759063 +954000 ekin = 3.09579074538114 | erot = 1.98159252445736 | epot = -21.1641538136742 | etot = -16.0867705438357 +955000 ekin = 3.59360323486037 | erot = 2.06789679071822 | epot = -21.0522880782498 | etot = -15.3907880526712 +956000 ekin = 2.97416074498496 | erot = 3.66953591785752 | epot = -20.9097603766373 | etot = -14.2660637137949 +957000 ekin = 3.03140562067951 | erot = 2.66078083760708 | epot = -20.7419058677841 | etot = -15.0497194094975 +958000 ekin = 2.68913434704071 | erot = 2.94057112873836 | epot = -20.5488384129042 | etot = -14.9191329371251 +959000 ekin = 1.93264217407773 | erot = 2.45198406257093 | epot = -20.468781161493 | etot = -16.0841549248444 +960000 ekin = 1.49632279167951 | erot = 3.13346348599985 | epot = -20.4844974178569 | etot = -15.8547111401775 +961000 ekin = 1.96353429663481 | erot = 2.07553358516995 | epot = -20.4805590123498 | etot = -16.441491130545 +962000 ekin = 2.02830196392006 | erot = 1.88908496389352 | epot = -20.5374211599972 | etot = -16.6200342321836 +963000 ekin = 1.80829526034561 | erot = 2.46258345726263 | epot = -20.5841835730968 | etot = -16.3133048554886 +964000 ekin = 2.79449124937197 | erot = 2.42527551362849 | epot = -20.6238805444481 | etot = -15.4041137814476 +965000 ekin = 2.53493670506136 | erot = 2.27804362684504 | epot = -20.6549300812152 | etot = -15.8419497493088 +966000 ekin = 2.0920817650402 | erot = 2.27478990703182 | epot = -20.7044739042411 | etot = -16.3376022321691 +967000 ekin = 1.55562260797661 | erot = 3.55543363172459 | epot = -20.739375276301 | etot = -15.6283190365998 +968000 ekin = 1.93439891222236 | erot = 2.37295903815892 | epot = -20.7189229543385 | etot = -16.4115650039573 +969000 ekin = 2.16199728898304 | erot = 2.46012052524939 | epot = -20.6747113173024 | etot = -16.05259350307 +970000 ekin = 1.84926216722517 | erot = 2.96951777569265 | epot = -20.6011599981509 | etot = -15.7823800552331 +971000 ekin = 1.93656411083027 | erot = 3.08724923997924 | epot = -20.5835250734812 | etot = -15.5597117226717 +972000 ekin = 1.90452783927712 | erot = 2.58230766783158 | epot = -20.578290598021 | etot = -16.0914550909123 +973000 ekin = 2.1922712122506 | erot = 2.92686386394502 | epot = -20.5868173702649 | etot = -15.4676822940693 +974000 ekin = 2.53094641465528 | erot = 2.69271305556796 | epot = -20.5382547781502 | etot = -15.314595307927 +975000 ekin = 3.41187201669924 | erot = 2.32917219553093 | epot = -20.5109803919918 | etot = -14.7699361797616 +976000 ekin = 2.88156114272554 | erot = 3.10474521611247 | epot = -20.5158119249461 | etot = -14.5295055661081 +977000 ekin = 2.73962881168093 | erot = 2.50884169958545 | epot = -20.4964590298 | etot = -15.2479885185336 +978000 ekin = 1.79682802545478 | erot = 2.06924041504343 | epot = -20.4730821934977 | etot = -16.6070137529995 +979000 ekin = 1.86521389998383 | erot = 2.22151626929009 | epot = -20.4069392895634 | etot = -16.3202091202895 +980000 ekin = 1.92383169177415 | erot = 1.56425965548878 | epot = -20.3533353734708 | etot = -16.8652440262079 +981000 ekin = 1.5511019928294 | erot = 2.05381225133935 | epot = -20.3970890782076 | etot = -16.7921748340389 +982000 ekin = 1.85559395816059 | erot = 1.96991369841494 | epot = -20.499354149896 | etot = -16.6738464933205 +983000 ekin = 2.75061857015335 | erot = 1.7944840218308 | epot = -20.5241519929378 | etot = -15.9790494009537 +984000 ekin = 3.65069712553538 | erot = 2.64237329124736 | epot = -20.6374699142712 | etot = -14.3443994974885 +985000 ekin = 2.95637321931061 | erot = 2.18846412126772 | epot = -20.8122975273334 | etot = -15.6674601867551 +986000 ekin = 2.87072902054599 | erot = 2.18810434250118 | epot = -20.9390290724606 | etot = -15.8801957094134 +987000 ekin = 3.37463328642758 | erot = 2.53713666674669 | epot = -21.0098323012659 | etot = -15.0980623480916 +988000 ekin = 3.45107854450337 | erot = 3.23625536313168 | epot = -21.0554260480417 | etot = -14.3680921404067 +989000 ekin = 2.83591404363755 | erot = 2.20564156324815 | epot = -21.19499265416 | etot = -16.1534370472743 +990000 ekin = 2.79864389348437 | erot = 1.8317842666354 | epot = -21.1880268304373 | etot = -16.5575986703175 +991000 ekin = 3.14781925181036 | erot = 3.20782471808911 | epot = -21.1115234865128 | etot = -14.7558795166133 +992000 ekin = 3.30033725309946 | erot = 2.62749912694386 | epot = -21.0030296251662 | etot = -15.0751932451229 +993000 ekin = 3.07374297249948 | erot = 2.22697230616356 | epot = -20.9385586572609 | etot = -15.6378433785979 +994000 ekin = 3.21461776403449 | erot = 2.80599707993707 | epot = -20.8790524582442 | etot = -14.8584376142726 +995000 ekin = 3.25071478747345 | erot = 1.73415439498321 | epot = -20.8037804714002 | etot = -15.8189112889435 +996000 ekin = 3.07999632962569 | erot = 3.18107550500823 | epot = -20.7805295335828 | etot = -14.5194576989488 +997000 ekin = 2.97118118001025 | erot = 3.14046656474894 | epot = -20.7334885248755 | etot = -14.6218407801163 +998000 ekin = 3.09169861594907 | erot = 1.99060706981745 | epot = -20.6553134096535 | etot = -15.573007723887 +999000 ekin = 2.07498130576584 | erot = 2.75045972766921 | epot = -20.616091526295 | etot = -15.7906504928599 +1000000 ekin = 2.07851119592057 | erot = 2.11869313853035 | epot = -20.4539417072875 | etot = -16.2567373728365 + 1000000 0.092378275 -1.3359709 0.057599499 -1.1484644 2.8477973e-05 +Loop time of 36.5086 on 1 procs for 1000000 steps with 16 atoms + +Performance: 23665.686 tau/day, 27390.840 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 26.481 | 26.481 | 26.481 | 0.0 | 72.53 +Bond | 0.7951 | 0.7951 | 0.7951 | 0.0 | 2.18 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.16717 | 0.16717 | 0.16717 | 0.0 | 0.46 +Output | 1.1e-05 | 1.1e-05 | 1.1e-05 | 0.0 | 0.00 +Modify | 8.7926 | 8.7926 | 8.7926 | 0.0 | 24.08 +Other | | 0.273 | | | 0.75 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 102 ave 102 max 102 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 102 +Ave neighs/atom = 6.375 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:36 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..730853a0da7d267ec17428c54861dde9ed60d1b4 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.07Aug19.duplex2.g++.4 @@ -0,0 +1,1168 @@ +LAMMPS (7 Aug 2019) +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000184 secs + read_data CPU = 0.003429 secs + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 1000000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.956 + ghost atom cutoff = 1.956 + binsize = 0.978, bins = 41 41 41 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685) +Per MPI rank memory allocation (min/avg/max) = 7.455 | 7.637 | 7.819 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 +1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 +2000 ekin = 2.15911766687235 | erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504 +3000 ekin = 3.26561948796015 | erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198 +4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505 +5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 +6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 +7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 +8000 ekin = 2.51333548501169 | erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614 +9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 +10000 ekin = 2.36632635249862 | erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463 +11000 ekin = 2.03296432220126 | erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202 +12000 ekin = 2.65352743446956 | erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194 +13000 ekin = 1.89067421214403 | erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949 +14000 ekin = 1.90680463918722 | erot = 2.12745987027399 | epot = -23.7545354032947 | etot = -19.7202708938335 +15000 ekin = 2.40428667481004 | erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361 +16000 ekin = 2.7510166356243 | erot = 1.18896277635344 | epot = -23.5745121257654 | etot = -19.6345327137876 +17000 ekin = 2.44090826892662 | erot = 2.38166706806441 | epot = -23.5888433865641 | etot = -18.766268049573 +18000 ekin = 2.16977970545217 | erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939 +19000 ekin = 2.19378610033861 | erot = 2.45183819484609 | epot = -23.5449084745393 | etot = -18.8992841793546 +20000 ekin = 2.07734013817241 | erot = 1.81448496219961 | epot = -23.5782673056893 | etot = -19.6864422053173 +21000 ekin = 2.27781532351243 | erot = 2.76369118136086 | epot = -23.5986545956161 | etot = -18.5571480907428 +22000 ekin = 2.69375785791379 | erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449207 +23000 ekin = 1.99952884103097 | erot = 2.28032953163857 | epot = -23.4448504933921 | etot = -19.1649921207226 +24000 ekin = 2.19993258930349 | erot = 2.97916455146848 | epot = -23.365299008021 | etot = -18.1862018672491 +25000 ekin = 2.28089469652686 | erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537 +26000 ekin = 1.99390998801617 | erot = 2.79250495479074 | epot = -23.1859723519608 | etot = -18.3995574091539 +27000 ekin = 2.00992865272585 | erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421 +28000 ekin = 2.00322172723407 | erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913 +29000 ekin = 2.52361436071784 | erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138 +30000 ekin = 1.94969919616482 | erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198 +31000 ekin = 1.81286761012387 | erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782 +32000 ekin = 1.88389491638451 | erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051 +33000 ekin = 1.78524470387102 | erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434 +34000 ekin = 2.28023843988047 | erot = 3.11357086039974 | epot = -23.0617618407572 | etot = -17.667952540477 +35000 ekin = 2.88795920533174 | erot = 1.81662227096289 | epot = -23.1342233361349 | etot = -18.4296418598403 +36000 ekin = 2.40018487148211 | erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096 +37000 ekin = 2.22699211630433 | erot = 1.73889017332475 | epot = -23.2291614908027 | etot = -19.2632792011737 +38000 ekin = 2.13593461964592 | erot = 3.07590136326315 | epot = -23.1607724763685 | etot = -17.9489364934594 +39000 ekin = 2.08839393640823 | erot = 2.80471150509566 | epot = -23.1352878747759 | etot = -18.242182433272 +40000 ekin = 2.94982054413846 | erot = 2.19484102372241 | epot = -23.1842229043853 | etot = -18.0395613365244 +41000 ekin = 2.47855373480179 | erot = 3.46795094832272 | epot = -23.1698888629099 | etot = -17.2233841797854 +42000 ekin = 2.57225931171306 | erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682 +43000 ekin = 2.16695829201326 | erot = 2.67063324875935 | epot = -22.9841690345739 | etot = -18.1465774938013 +44000 ekin = 2.3251045436594 | erot = 3.31069456451415 | epot = -22.9099977707014 | etot = -17.2741986625279 +45000 ekin = 1.8593572517472 | erot = 3.48256913429864 | epot = -22.7853293556222 | etot = -17.4434029695763 +46000 ekin = 2.59906260222481 | erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741 +47000 ekin = 1.90419350976819 | erot = 3.39352467596445 | epot = -22.5624536061979 | etot = -17.2647354204652 +48000 ekin = 2.46191536162942 | erot = 2.50024189038397 | epot = -22.5888330081063 | etot = -17.6266757560929 +49000 ekin = 3.18008619674969 | erot = 2.18329398142911 | epot = -22.6110647388652 | etot = -17.2476845606864 +50000 ekin = 2.92380640638812 | erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295054 +51000 ekin = 2.8672950322524 | erot = 2.67529217516736 | epot = -22.6748886664557 | etot = -17.132301459036 +52000 ekin = 2.30283827457733 | erot = 1.82645474029551 | epot = -22.6607030819086 | etot = -18.5314100670358 +53000 ekin = 3.18697616339314 | erot = 1.6721126504968 | epot = -22.7158951183044 | etot = -17.8568063044145 +54000 ekin = 2.63274995193147 | erot = 1.96664130685842 | epot = -22.7877787224364 | etot = -18.1883874636465 +55000 ekin = 3.18311630681889 | erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793 +56000 ekin = 2.55275960671528 | erot = 3.05720384772626 | epot = -22.8187750450683 | etot = -17.2088115906267 +57000 ekin = 2.43682051944964 | erot = 3.45782031837858 | epot = -22.7770565571277 | etot = -16.8824157192995 +58000 ekin = 1.93888380963701 | erot = 2.51321017005837 | epot = -22.7135987564736 | etot = -18.2615047767782 +59000 ekin = 2.5584899615086 | erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831 +60000 ekin = 2.80661395039301 | erot = 2.89055248290058 | epot = -22.5801959967487 | etot = -16.8830295634551 +61000 ekin = 2.68598657973729 | erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677 +62000 ekin = 2.74493324548126 | erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319 +63000 ekin = 2.65627195091607 | erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079 +64000 ekin = 2.12379240032878 | erot = 2.79203441675509 | epot = -22.3495990435982 | etot = -17.4337722265143 +65000 ekin = 1.86782238979936 | erot = 2.70277079938777 | epot = -22.3710220966341 | etot = -17.8004289074469 +66000 ekin = 2.74983103317414 | erot = 1.93532287297332 | epot = -22.3642892005434 | etot = -17.679135294396 +67000 ekin = 2.51092055125345 | erot = 2.46618624666166 | epot = -22.3997780561407 | etot = -17.4226712582256 +68000 ekin = 2.95469759114171 | erot = 1.97026833535318 | epot = -22.465077041847 | etot = -17.5401111153521 +69000 ekin = 2.60179538487172 | erot = 2.27022574694886 | epot = -22.4013876082185 | etot = -17.529366476398 +70000 ekin = 2.38624525335422 | erot = 2.82124637267727 | epot = -22.3329612644328 | etot = -17.1254696384013 +71000 ekin = 2.6264191985346 | erot = 2.8933242992384 | epot = -22.3324946257813 | etot = -16.8127511280083 +72000 ekin = 2.93199679301318 | erot = 2.83600213853039 | epot = -22.4418753486332 | etot = -16.6738764170896 +73000 ekin = 2.20521324648382 | erot = 3.05063841714452 | epot = -22.5078076718832 | etot = -17.2519560082549 +74000 ekin = 2.16594519672766 | erot = 2.82993872672919 | epot = -22.5187768617569 | etot = -17.5228929383001 +75000 ekin = 1.52753824412461 | erot = 1.91758574309004 | epot = -22.6434864113427 | etot = -19.198362424128 +76000 ekin = 1.89477517532867 | erot = 2.83145375092216 | epot = -22.7507099037207 | etot = -18.0244809774698 +77000 ekin = 2.84722966394523 | erot = 3.20523918524772 | epot = -22.8263123696514 | etot = -16.7738435204584 +78000 ekin = 2.44900478430451 | erot = 2.80964787966681 | epot = -22.811923730311 | etot = -17.5532710663397 +79000 ekin = 2.16549328835507 | erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255 +80000 ekin = 2.38929173610466 | erot = 2.5835599737549 | epot = -22.7453472674482 | etot = -17.7724955575887 +81000 ekin = 2.74182188149 | erot = 1.92580771183152 | epot = -22.6872721828912 | etot = -18.0196425895697 +82000 ekin = 1.90254633515813 | erot = 1.70958501101744 | epot = -22.5904815431895 | etot = -18.9783501970139 +83000 ekin = 1.63862423461032 | erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292 +84000 ekin = 1.65768128899531 | erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674 +85000 ekin = 2.40787065796921 | erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645 +86000 ekin = 2.51073542405177 | erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608 +87000 ekin = 2.13729284484532 | erot = 1.97886338867606 | epot = -22.4457225556766 | etot = -18.3295663221553 +88000 ekin = 1.7511616822056 | erot = 2.36434608342923 | epot = -22.4232555875235 | etot = -18.3077478218887 +89000 ekin = 1.85498863251071 | erot = 3.29466014836524 | epot = -22.4615925106509 | etot = -17.3119437297749 +90000 ekin = 2.22730928223451 | erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706 +91000 ekin = 2.40026068010467 | erot = 3.13124542611032 | epot = -22.5445138059197 | etot = -17.0130076997047 +92000 ekin = 2.69184894487886 | erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756694 +93000 ekin = 3.04452081584098 | erot = 3.02893158250343 | epot = -22.4857514998612 | etot = -16.4122991015168 +94000 ekin = 3.21054020599498 | erot = 1.87554208928456 | epot = -22.58235617796 | etot = -17.4962738826805 +95000 ekin = 3.49164555041805 | erot = 2.891072597541 | epot = -22.651746211573 | etot = -16.269028063614 +96000 ekin = 2.89611459837769 | erot = 2.3840369162805 | epot = -22.6376886129393 | etot = -17.3575370982811 +97000 ekin = 1.94001816357314 | erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036 +98000 ekin = 2.21812472183551 | erot = 3.66512951907027 | epot = -22.540020786367 | etot = -16.6567665454612 +99000 ekin = 1.96304801418099 | erot = 2.78092002528642 | epot = -22.4500077741119 | etot = -17.7060397346445 +100000 ekin = 1.78146596589238 | erot = 2.66087063973067 | epot = -22.380628502186 | etot = -17.9382918965629 +101000 ekin = 2.13576431486591 | erot = 2.39189697670581 | epot = -22.3671198416411 | etot = -17.8394585500694 +102000 ekin = 1.54265458925823 | erot = 2.31301627489862 | epot = -22.3596033820569 | etot = -18.5039325179 +103000 ekin = 1.6493299781162 | erot = 2.8270014677761 | epot = -22.4044472055819 | etot = -17.9281157596896 +104000 ekin = 1.88425130865015 | erot = 3.36695629589131 | epot = -22.4614117565727 | etot = -17.2102041520312 +105000 ekin = 2.0873628063424 | erot = 1.99902589912496 | epot = -22.4857870795246 | etot = -18.3993983740573 +106000 ekin = 2.85192200005482 | erot = 1.96124421177816 | epot = -22.4885148263279 | etot = -17.6753486144949 +107000 ekin = 2.27699301124082 | erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666 +108000 ekin = 2.43341212242249 | erot = 1.71014523953267 | epot = -22.4750159709764 | etot = -18.3314586090212 +109000 ekin = 2.3240302459673 | erot = 2.92730273400666 | epot = -22.454444740465 | etot = -17.203111760491 +110000 ekin = 2.75939007795593 | erot = 2.37261248457831 | epot = -22.4066316113364 | etot = -17.2746290488021 +111000 ekin = 2.30202775259985 | erot = 2.09098171366695 | epot = -22.340628179725 | etot = -17.9476187134582 +112000 ekin = 2.89672803093986 | erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143 +113000 ekin = 2.80286812020301 | erot = 1.68317583122193 | epot = -22.1739192926258 | etot = -17.6878753412008 +114000 ekin = 3.41134331362354 | erot = 2.66279011393035 | epot = -22.2993892060878 | etot = -16.225255778534 +115000 ekin = 3.04096848543599 | erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327 +116000 ekin = 3.18249263106367 | erot = 3.2187278057963 | epot = -22.376612031037 | etot = -15.975391594177 +117000 ekin = 3.04033644338919 | erot = 2.41632774149289 | epot = -22.3406101341932 | etot = -16.8839459493112 +118000 ekin = 3.22976632794611 | erot = 1.46870208555872 | epot = -22.262910646297 | etot = -17.5644422327922 +119000 ekin = 2.35815331598994 | erot = 3.0746467591689 | epot = -22.21629705762 | etot = -16.7834969824611 +120000 ekin = 1.93901604028919 | erot = 2.21087803685819 | epot = -22.1596747789505 | etot = -18.0097807018031 +121000 ekin = 1.9479198834689 | erot = 3.06697908719323 | epot = -22.1473490758083 | etot = -17.1324501051462 +122000 ekin = 1.69642311218451 | erot = 1.71065948591523 | epot = -22.235021693017 | etot = -18.8279390949172 +123000 ekin = 1.74537927001903 | erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348 +124000 ekin = 2.74229806685693 | erot = 1.94346011848798 | epot = -22.3376426377462 | etot = -17.6518844524013 +125000 ekin = 2.7762803161376 | erot = 1.95737420539166 | epot = -22.3561899601979 | etot = -17.6225354386687 +126000 ekin = 2.05898577806786 | erot = 1.47493157618748 | epot = -22.3918669376121 | etot = -18.8579495833568 +127000 ekin = 1.88620727578863 | erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304 +128000 ekin = 1.65027256647601 | erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694 +129000 ekin = 2.51771860981078 | erot = 2.38745668871878 | epot = -22.3622404512641 | etot = -17.4570651527345 +130000 ekin = 1.60778116741171 | erot = 2.81983062254804 | epot = -22.3043401463427 | etot = -17.8767283563829 +131000 ekin = 2.27966529707091 | erot = 2.29465997580787 | epot = -22.1860056729234 | etot = -17.6116804000446 +132000 ekin = 2.94605151024306 | erot = 2.34727265039698 | epot = -22.1004107829513 | etot = -16.8070866223112 +133000 ekin = 2.00184520718143 | erot = 2.13597622566091 | epot = -22.0860804435183 | etot = -17.948259010676 +134000 ekin = 1.54536260297594 | erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194 +135000 ekin = 1.7899169229158 | erot = 2.40585579784187 | epot = -22.0564792277569 | etot = -17.8607065069993 +136000 ekin = 1.63315069688348 | erot = 2.13968964990471 | epot = -22.0645410751456 | etot = -18.2917007283574 +137000 ekin = 2.36475220491125 | erot = 1.9307510547685 | epot = -22.101884847306 | etot = -17.8063815876263 +138000 ekin = 2.9554682114977 | erot = 1.58329215843879 | epot = -22.1589207193491 | etot = -17.6201603494126 +139000 ekin = 3.18559985564368 | erot = 2.24978247982886 | epot = -22.2766713145626 | etot = -16.84128897909 +140000 ekin = 2.25331500051846 | erot = 3.04264261269698 | epot = -22.4413209794808 | etot = -17.1453633662654 +141000 ekin = 1.8939664036255 | erot = 3.12730191483889 | epot = -22.6943708703896 | etot = -17.6731025519252 +142000 ekin = 2.48698722341786 | erot = 2.50204475841096 | epot = -22.8022645411413 | etot = -17.8132325593125 +143000 ekin = 2.39031114354902 | erot = 2.72027514737476 | epot = -22.7789363640122 | etot = -17.6683500730884 +144000 ekin = 1.93009742932804 | erot = 2.68112648713777 | epot = -22.6600942975093 | etot = -18.0488703810435 +145000 ekin = 1.81543048110687 | erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640414 +146000 ekin = 2.4125202126428 | erot = 2.08569022934172 | epot = -22.5607640770181 | etot = -18.0625536350336 +147000 ekin = 1.44642974398304 | erot = 1.86921415702346 | epot = -22.4437745695726 | etot = -19.1281306685661 +148000 ekin = 1.94224767107088 | erot = 2.57935525538891 | epot = -22.4110987100047 | etot = -17.8894957835449 +149000 ekin = 2.03195649040454 | erot = 3.31786202502785 | epot = -22.312227106758 | etot = -16.9624085913257 +150000 ekin = 2.47792894576432 | erot = 2.68612874200304 | epot = -22.1392843642773 | etot = -16.97522667651 +151000 ekin = 2.75692645092955 | erot = 1.8812256584813 | epot = -21.9329416416723 | etot = -17.2947895322614 +152000 ekin = 2.7753834344323 | erot = 1.78115734250796 | epot = -21.7450724909841 | etot = -17.1885317140438 +153000 ekin = 3.09316888168833 | erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934 +154000 ekin = 2.31433640945477 | erot = 2.19304386678895 | epot = -21.5946356595637 | etot = -17.08725538332 +155000 ekin = 1.94169881401553 | erot = 2.67959698479411 | epot = -21.6941053409437 | etot = -17.072809542134 +156000 ekin = 2.69151609119638 | erot = 2.25048211983204 | epot = -21.7610571974251 | etot = -16.8190589863967 +157000 ekin = 3.89507004263776 | erot = 2.74501587672577 | epot = -21.8157728797743 | etot = -15.1756869604107 +158000 ekin = 2.88173407476086 | erot = 2.69702262693025 | epot = -21.8854957137509 | etot = -16.3067390120598 +159000 ekin = 3.15173323195918 | erot = 2.6174347371013 | epot = -21.8245251626835 | etot = -16.055357193623 +160000 ekin = 2.54983562435716 | erot = 3.26037467643909 | epot = -21.8527884226329 | etot = -16.0425781218367 +161000 ekin = 2.47569624391789 | erot = 2.4441841652721 | epot = -21.7973550812187 | etot = -16.8774746720287 +162000 ekin = 2.94228722137381 | erot = 2.59784970938384 | epot = -21.7813251561029 | etot = -16.2411882253452 +163000 ekin = 3.25812805712344 | erot = 2.25239331007842 | epot = -21.8200893075211 | etot = -16.3095679403192 +164000 ekin = 3.52786799143084 | erot = 2.22392713421412 | epot = -21.7646946348872 | etot = -16.0128995092423 +165000 ekin = 2.47839548873418 | erot = 2.58744140761169 | epot = -21.6790952945041 | etot = -16.6132583981583 +166000 ekin = 2.14435847552792 | erot = 3.04732688845808 | epot = -21.6219995979977 | etot = -16.4303142340117 +167000 ekin = 2.77664659649902 | erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831 +168000 ekin = 1.74464407802389 | erot = 2.78052653338966 | epot = -21.4288999288375 | etot = -16.903729317424 +169000 ekin = 1.8068912909333 | erot = 2.46391033708928 | epot = -21.4128285618694 | etot = -17.1420269338468 +170000 ekin = 1.69498145941511 | erot = 2.88911238881156 | epot = -21.4319269866204 | etot = -16.8478331383937 +171000 ekin = 2.15326316196646 | erot = 1.6134654780187 | epot = -21.2861470779284 | etot = -17.5194184379432 +172000 ekin = 1.67904916339532 | erot = 2.36509147316374 | epot = -21.1250864759441 | etot = -17.080945839385 +173000 ekin = 2.05349972960735 | erot = 2.18864665107749 | epot = -21.0744450592631 | etot = -16.8322986785783 +174000 ekin = 2.49402795941962 | erot = 3.1039231700088 | epot = -20.9332609664625 | etot = -15.335309837034 +175000 ekin = 2.60611029063986 | erot = 2.90993176119179 | epot = -20.8533230180669 | etot = -15.3372809662352 +176000 ekin = 2.14535974511638 | erot = 2.6771051102154 | epot = -20.8508037764829 | etot = -16.0283389211512 +177000 ekin = 2.82654664242577 | erot = 2.8064781965732 | epot = -20.9303681620826 | etot = -15.2973433230837 +178000 ekin = 3.17006270723388 | erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933 +179000 ekin = 2.33834827123179 | erot = 2.84870047825868 | epot = -21.1082901606944 | etot = -15.9212414112039 +180000 ekin = 2.39362550925046 | erot = 2.94575326168225 | epot = -21.1089731290028 | etot = -15.7695943580701 +181000 ekin = 2.78703231260152 | erot = 3.29998898392533 | epot = -21.0761138110654 | etot = -14.9890925145385 +182000 ekin = 3.023383912392 | erot = 2.3253310746288 | epot = -21.0444377426861 | etot = -15.6957227556653 +183000 ekin = 2.44126401356994 | erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424 +184000 ekin = 2.56448211253962 | erot = 2.77267067014069 | epot = -20.6657911214549 | etot = -15.3286383387746 +185000 ekin = 2.16427057092672 | erot = 1.95880146934287 | epot = -20.5647658775173 | etot = -16.4416938372477 +186000 ekin = 2.06536030915311 | erot = 3.1459346313777 | epot = -20.4537584304771 | etot = -15.2424634899463 +187000 ekin = 2.43846121057803 | erot = 1.93593042270706 | epot = -20.4775765627296 | etot = -16.1031849294445 +188000 ekin = 2.28827356508696 | erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372 +189000 ekin = 1.67206333515897 | erot = 3.05807378739725 | epot = -20.6184572736204 | etot = -15.8883201510642 +190000 ekin = 1.96995062226967 | erot = 2.943019674394 | epot = -20.6150380630742 | etot = -15.7020677664105 +191000 ekin = 2.31558303301195 | erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708366 +192000 ekin = 3.58105122568799 | erot = 2.89866835149673 | epot = -20.5550364560059 | etot = -14.0753168788212 +193000 ekin = 2.69738971383614 | erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358 +194000 ekin = 2.65963556416735 | erot = 2.28486501061266 | epot = -20.4488832942326 | etot = -15.5043827194525 +195000 ekin = 1.85289053427901 | erot = 2.65318671222086 | epot = -20.3816844231207 | etot = -15.8756071766209 +196000 ekin = 2.28257181147918 | erot = 2.31175601065464 | epot = -20.4051132325268 | etot = -15.810785410393 +197000 ekin = 2.49770460330585 | erot = 2.55587879440512 | epot = -20.4716020539923 | etot = -15.4180186562813 +198000 ekin = 2.01700960777428 | erot = 1.51922008609382 | epot = -20.4907970823155 | etot = -16.9545673884474 +199000 ekin = 1.50027537520987 | erot = 2.19604462463445 | epot = -20.5138434458212 | etot = -16.8175234459769 +200000 ekin = 1.64850512926723 | erot = 2.45966335482571 | epot = -20.4934420686449 | etot = -16.385273584552 +201000 ekin = 2.62997533994907 | erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916 +202000 ekin = 2.30895175475241 | erot = 2.55653293887659 | epot = -20.6262537118088 | etot = -15.7607690181798 +203000 ekin = 1.64768887888552 | erot = 2.11556417528284 | epot = -20.6617888215465 | etot = -16.8985357673782 +204000 ekin = 2.01924097320136 | erot = 1.97748949636931 | epot = -20.7002685556681 | etot = -16.7035380860975 +205000 ekin = 2.97656554045711 | erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806697 +206000 ekin = 2.56613069661945 | erot = 2.2162424422446 | epot = -21.0621833598182 | etot = -16.2798102209542 +207000 ekin = 3.44850636848559 | erot = 2.48816050856267 | epot = -21.2038849430866 | etot = -15.2672180660384 +208000 ekin = 2.54208934028226 | erot = 2.22605232144503 | epot = -21.3476404533667 | etot = -16.5794987916394 +209000 ekin = 3.84151461096732 | erot = 2.16534559513904 | epot = -21.4932373455843 | etot = -15.486377139478 +210000 ekin = 3.06873591712904 | erot = 2.24760815652572 | epot = -21.6427793540355 | etot = -16.3264352803807 +211000 ekin = 1.64176280869923 | erot = 2.17721976802013 | epot = -21.8130439048271 | etot = -17.9940613281078 +212000 ekin = 2.5985934050661 | erot = 2.41520703335867 | epot = -21.9964648294562 | etot = -16.9826643910315 +213000 ekin = 2.51136104390039 | erot = 1.99503544560739 | epot = -22.161492842604 | etot = -17.6550963530962 +214000 ekin = 2.77089845962619 | erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179 +215000 ekin = 2.53408528186206 | erot = 1.84963848601796 | epot = -22.1148567901871 | etot = -17.7311330223071 +216000 ekin = 2.52671619876928 | erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469 +217000 ekin = 2.50171921508545 | erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455 +218000 ekin = 2.43936294263937 | erot = 2.41974828067302 | epot = -22.2447049583244 | etot = -17.385593735012 +219000 ekin = 2.30221269367205 | erot = 2.65120674162377 | epot = -22.2807164841742 | etot = -17.3272970488784 +220000 ekin = 1.70065256620687 | erot = 2.34758543213917 | epot = -22.2809933538228 | etot = -18.2327553554767 +221000 ekin = 2.09298237125575 | erot = 2.4788648159591 | epot = -22.267957001012 | etot = -17.6961098137972 +222000 ekin = 1.58469709510937 | erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659 +223000 ekin = 1.83926923346352 | erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791 +224000 ekin = 2.59583657132575 | erot = 2.93869915115498 | epot = -22.1425986650605 | etot = -16.6080629425798 +225000 ekin = 3.29351563254165 | erot = 2.84339535814139 | epot = -22.12757310355 | etot = -15.990662112867 +226000 ekin = 3.03135339447922 | erot = 2.08293143143603 | epot = -22.15283624886 | etot = -17.0385514229448 +227000 ekin = 2.50176282992082 | erot = 3.15084128846394 | epot = -22.2250438959745 | etot = -16.5724397775897 +228000 ekin = 2.32013498351673 | erot = 2.67554406359434 | epot = -22.3177515383564 | etot = -17.3220724912453 +229000 ekin = 2.89545450975318 | erot = 2.90735055857064 | epot = -22.4361496683347 | etot = -16.6333446000109 +230000 ekin = 2.28321229485933 | erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863 +231000 ekin = 2.0778632375453 | erot = 3.1067397369644 | epot = -22.5896609633152 | etot = -17.4050579888055 +232000 ekin = 2.1202374109541 | erot = 1.98747810033065 | epot = -22.5738924334392 | etot = -18.4661769221544 +233000 ekin = 2.33571877855589 | erot = 2.83585090202734 | epot = -22.5402065195541 | etot = -17.3686368389708 +234000 ekin = 2.10578223747154 | erot = 2.07381218733635 | epot = -22.5507693150832 | etot = -18.3711748902754 +235000 ekin = 2.44321041214394 | erot = 2.80846352304316 | epot = -22.5606929563186 | etot = -17.3090190211315 +236000 ekin = 2.93630791731799 | erot = 3.06315918531728 | epot = -22.4860653874721 | etot = -16.4865982848368 +237000 ekin = 3.21264879506079 | erot = 3.26866508478298 | epot = -22.3683553437861 | etot = -15.8870414639423 +238000 ekin = 2.46595539123277 | erot = 2.32502019506662 | epot = -22.3144456769666 | etot = -17.5234700906672 +239000 ekin = 2.10325864915823 | erot = 2.47631139904042 | epot = -22.301139292181 | etot = -17.7215692439824 +240000 ekin = 1.77270999777839 | erot = 2.60141429112663 | epot = -22.2344206081543 | etot = -17.8602963192493 +241000 ekin = 1.94952922244078 | erot = 1.39715216866763 | epot = -22.2207225048761 | etot = -18.8740411137677 +242000 ekin = 3.05687991591411 | erot = 2.00862394928705 | epot = -22.2213200390943 | etot = -17.1558161738932 +243000 ekin = 2.86735711945299 | erot = 1.7994811867468 | epot = -22.2697610280427 | etot = -17.6029227218429 +244000 ekin = 2.00525854269389 | erot = 2.36445341214556 | epot = -22.2726788994494 | etot = -17.90296694461 +245000 ekin = 2.28011102404838 | erot = 2.787005205328 | epot = -22.2995433574618 | etot = -17.2324271280854 +246000 ekin = 2.06819738789813 | erot = 2.24624952782284 | epot = -22.2551680110137 | etot = -17.9407210952928 +247000 ekin = 1.69964711256213 | erot = 3.22260619239826 | epot = -22.1916408256116 | etot = -17.2693875206512 +248000 ekin = 1.92997585194759 | erot = 3.61155944514366 | epot = -22.0096484177852 | etot = -16.468113120694 +249000 ekin = 2.16278530892653 | erot = 3.27771891456707 | epot = -21.8856058980726 | etot = -16.445101674579 +250000 ekin = 2.32204054211025 | erot = 2.46317574116849 | epot = -21.8028762710591 | etot = -17.0176599877804 +251000 ekin = 1.23768964067255 | erot = 2.241505337621 | epot = -21.7630657074039 | etot = -18.2838707291104 +252000 ekin = 1.79818833522214 | erot = 2.12556386664128 | epot = -21.7586349357284 | etot = -17.834882733865 +253000 ekin = 2.12809689846393 | erot = 2.59685639208403 | epot = -21.7226495687757 | etot = -16.9976962782278 +254000 ekin = 2.46813261968533 | erot = 2.00391812662871 | epot = -21.7113918037362 | etot = -17.2393410574221 +255000 ekin = 2.31566729087291 | erot = 2.03619058028117 | epot = -21.7265453183256 | etot = -17.3746874471715 +256000 ekin = 2.87223929491326 | erot = 2.61790933826622 | epot = -21.659332511914 | etot = -16.1691838787345 +257000 ekin = 2.85756762932926 | erot = 2.08174673916199 | epot = -21.6161821054731 | etot = -16.6768677369818 +258000 ekin = 2.06111021157734 | erot = 2.32748664972428 | epot = -21.5132485706726 | etot = -17.124651709371 +259000 ekin = 2.23305784057759 | erot = 2.88843859953736 | epot = -21.5040039667854 | etot = -16.3825075266705 +260000 ekin = 2.49862397932476 | erot = 2.3833688584839 | epot = -21.488210637319 | etot = -16.6062177995103 +261000 ekin = 2.09280296934734 | erot = 2.39632540029206 | epot = -21.4325331777953 | etot = -16.9434048081559 +262000 ekin = 2.33576913564289 | erot = 2.67273419354396 | epot = -21.3832241450035 | etot = -16.3747208158166 +263000 ekin = 2.20536189489354 | erot = 2.71530627040564 | epot = -21.4329409070981 | etot = -16.5122727417989 +264000 ekin = 2.2858247573423 | erot = 2.76839346219662 | epot = -21.3931084431599 | etot = -16.338890223621 +265000 ekin = 1.70928536820409 | erot = 1.79395423442895 | epot = -21.2682341921474 | etot = -17.7649945895143 +266000 ekin = 2.48721735474525 | erot = 2.08745460533225 | epot = -21.1746995817337 | etot = -16.6000276216562 +267000 ekin = 2.69283567987773 | erot = 2.10301910407212 | epot = -21.1705161290062 | etot = -16.3746613450563 +268000 ekin = 3.00000233743719 | erot = 2.80954585635721 | epot = -21.1647521126509 | etot = -15.3552039188565 +269000 ekin = 3.50713810468527 | erot = 2.35763817348002 | epot = -21.1537110688983 | etot = -15.288934790733 +270000 ekin = 3.50686942248863 | erot = 1.86462765875889 | epot = -21.1925508822801 | etot = -15.8210538010326 +271000 ekin = 3.57026082273992 | erot = 2.08172467795388 | epot = -21.277581718294 | etot = -15.6255962176003 +272000 ekin = 2.4484752533773 | erot = 3.08466485039763 | epot = -21.3619851902072 | etot = -15.8288450864322 +273000 ekin = 2.39748176307242 | erot = 3.1335505044672 | epot = -21.4386234252579 | etot = -15.9075911577183 +274000 ekin = 2.48208144431864 | erot = 2.00552494041966 | epot = -21.4476232953882 | etot = -16.9600169106499 +275000 ekin = 2.4872108114937 | erot = 3.05413598233607 | epot = -21.4713984309062 | etot = -15.9300516370765 +276000 ekin = 2.82709589676966 | erot = 2.88384306577857 | epot = -21.443459011816 | etot = -15.7325200492678 +277000 ekin = 2.23479555963312 | erot = 2.20310851955639 | epot = -21.3883073251199 | etot = -16.9504032459304 +278000 ekin = 2.81418916407429 | erot = 3.24537052192614 | epot = -21.3155364074003 | etot = -15.2559767213999 +279000 ekin = 2.57366525203698 | erot = 1.81705578305929 | epot = -21.2862101233851 | etot = -16.8954890882888 +280000 ekin = 2.41063464320149 | erot = 1.76282693004732 | epot = -21.254962528096 | etot = -17.0815009548472 +281000 ekin = 2.58126226070487 | erot = 2.29258221702168 | epot = -21.306394928225 | etot = -16.4325504504985 +282000 ekin = 3.02016903398222 | erot = 2.4309452389034 | epot = -21.4340900724633 | etot = -15.9829757995777 +283000 ekin = 2.5926914979033 | erot = 2.11330689541034 | epot = -21.6296517079942 | etot = -16.9236533146805 +284000 ekin = 2.51704243107537 | erot = 3.13156683036759 | epot = -21.7452694753527 | etot = -16.0966602139097 +285000 ekin = 2.4236537221525 | erot = 1.77228258125505 | epot = -21.8557019037769 | etot = -17.6597656003694 +286000 ekin = 1.94467195521662 | erot = 2.03660974116722 | epot = -21.901435736722 | etot = -17.9201540403382 +287000 ekin = 2.56319670376176 | erot = 2.60867050510154 | epot = -21.9067509934901 | etot = -16.7348837846268 +288000 ekin = 2.19574207425736 | erot = 1.69805542160022 | epot = -21.8143855675961 | etot = -17.9205880717385 +289000 ekin = 2.35326278833023 | erot = 1.65840109676148 | epot = -21.6976038565285 | etot = -17.6859399714368 +290000 ekin = 2.35194561775041 | erot = 1.99444238353745 | epot = -21.6551012116075 | etot = -17.3087132103196 +291000 ekin = 1.48585281531713 | erot = 2.66475825861556 | epot = -21.56036793472 | etot = -17.4097568607873 +292000 ekin = 2.1073994475645 | erot = 2.42809824662638 | epot = -21.4451596117638 | etot = -16.9096619175729 +293000 ekin = 2.11618090223715 | erot = 1.86694554151196 | epot = -21.3593625692768 | etot = -17.3762361255277 +294000 ekin = 2.06078090566327 | erot = 2.13941873359473 | epot = -21.232623310094 | etot = -17.032423670836 +295000 ekin = 2.11467178034796 | erot = 2.32673436675183 | epot = -21.1123588667461 | etot = -16.6709527196463 +296000 ekin = 1.53087058859334 | erot = 2.94008409149154 | epot = -21.2112197533848 | etot = -16.7402650732999 +297000 ekin = 2.52732986791201 | erot = 2.18380855337859 | epot = -21.1955190508786 | etot = -16.484380629588 +298000 ekin = 1.89033945823201 | erot = 2.02521913176003 | epot = -21.2593750718295 | etot = -17.3438164818375 +299000 ekin = 1.87142873048437 | erot = 1.6640456322155 | epot = -21.2919162310488 | etot = -17.7564418683489 +300000 ekin = 2.23872615546785 | erot = 1.50807257618898 | epot = -21.3339204593826 | etot = -17.5871217277257 +301000 ekin = 1.99965506724556 | erot = 2.00145094516845 | epot = -21.4707589194324 | etot = -17.4696529070184 +302000 ekin = 1.76370349732521 | erot = 2.2378770890149 | epot = -21.5675275978257 | etot = -17.5659470114856 +303000 ekin = 2.69610887251788 | erot = 1.69957221429742 | epot = -21.5563765448091 | etot = -17.1606954579938 +304000 ekin = 2.55447143501921 | erot = 2.02060813090351 | epot = -21.5692327321341 | etot = -16.9941531662114 +305000 ekin = 2.38230604232715 | erot = 2.31489374428117 | epot = -21.5335950166329 | etot = -16.8363952300246 +306000 ekin = 2.07785475765117 | erot = 2.45230660685968 | epot = -21.4550895345846 | etot = -16.9249281700738 +307000 ekin = 3.17130424567277 | erot = 3.29574614566804 | epot = -21.4151535289883 | etot = -14.9481031376475 +308000 ekin = 3.40959217051674 | erot = 2.68389483402971 | epot = -21.4778643688409 | etot = -15.3843773642944 +309000 ekin = 2.36068264180093 | erot = 2.91715332823343 | epot = -21.5794336507741 | etot = -16.3015976807397 +310000 ekin = 2.49952357229221 | erot = 2.3602895089614 | epot = -21.5982142524176 | etot = -16.738401171164 +311000 ekin = 2.53288726180907 | erot = 2.29596940545853 | epot = -21.6418553661547 | etot = -16.8129986988871 +312000 ekin = 2.05123272208704 | erot = 2.92023923411836 | epot = -21.7377547517075 | etot = -16.7662827955021 +313000 ekin = 1.80834719374889 | erot = 2.29357283142128 | epot = -21.7993116362532 | etot = -17.697391611083 +314000 ekin = 2.30684015099018 | erot = 2.20859462712275 | epot = -21.8029398081388 | etot = -17.2875050300258 +315000 ekin = 1.86413924486173 | erot = 2.14748794238473 | epot = -21.8550418960799 | etot = -17.8434147088335 +316000 ekin = 2.20558056533516 | erot = 3.03447287931581 | epot = -21.8868412075708 | etot = -16.6467877629199 +317000 ekin = 2.4782093112548 | erot = 3.56870099099487 | epot = -21.9902146748518 | etot = -15.9433043726022 +318000 ekin = 2.36582343801679 | erot = 3.01887804681551 | epot = -22.1178732891163 | etot = -16.7331718042839 +319000 ekin = 2.40464629760758 | erot = 3.15910789488741 | epot = -22.2289401281564 | etot = -16.6651859356615 +320000 ekin = 1.80206494109346 | erot = 2.83527990295433 | epot = -22.3120263401861 | etot = -17.6746814961383 +321000 ekin = 2.91146951948762 | erot = 2.25772268449837 | epot = -22.3029455835946 | etot = -17.1337533796087 +322000 ekin = 2.8226351296685 | erot = 2.67950826833979 | epot = -22.3041650189947 | etot = -16.8020216209864 +323000 ekin = 2.067323568424 | erot = 2.31975284775299 | epot = -22.3338840353559 | etot = -17.9468076191789 +324000 ekin = 2.6012747278288 | erot = 2.58351861537749 | epot = -22.3215168526943 | etot = -17.1367235094881 +325000 ekin = 3.45560055552842 | erot = 2.50162515355503 | epot = -22.1825527777624 | etot = -16.2253270686789 +326000 ekin = 3.51422890604519 | erot = 2.8442606101801 | epot = -22.0201095272524 | etot = -15.6616200110271 +327000 ekin = 2.63551490316294 | erot = 2.20570805472232 | epot = -21.9384479867006 | etot = -17.0972250288154 +328000 ekin = 1.8043914440792 | erot = 2.37599512200969 | epot = -21.8619803976419 | etot = -17.681593831553 +329000 ekin = 2.15766181563134 | erot = 2.45286496267961 | epot = -21.8518523862111 | etot = -17.2413256079002 +330000 ekin = 1.8483425992464 | erot = 2.03367429366602 | epot = -21.7684095252419 | etot = -17.8863926323295 +331000 ekin = 2.3531484336258 | erot = 1.80165819621477 | epot = -21.7197009414848 | etot = -17.5648943116442 +332000 ekin = 1.67855936307207 | erot = 2.53341219651311 | epot = -21.733643435588 | etot = -17.5216718760028 +333000 ekin = 1.60376334688456 | erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256 +334000 ekin = 2.2655199008178 | erot = 2.62486254825417 | epot = -21.879497107847 | etot = -16.989114658775 +335000 ekin = 2.91208137486082 | erot = 3.11052870452009 | epot = -21.9161692767171 | etot = -15.8935591973362 +336000 ekin = 2.73132973682385 | erot = 2.56213100489405 | epot = -21.8312488568505 | etot = -16.5377881151326 +337000 ekin = 3.15411918141902 | erot = 3.875128198312 | epot = -21.9061152574783 | etot = -14.8768678777473 +338000 ekin = 2.33141760424507 | erot = 2.13211945089679 | epot = -21.913746111238 | etot = -17.4502090560961 +339000 ekin = 1.71915361945718 | erot = 2.31270220754042 | epot = -21.9042074773719 | etot = -17.8723516503743 +340000 ekin = 1.62199393011805 | erot = 3.16990972384469 | epot = -21.8898233676231 | etot = -17.0979197136604 +341000 ekin = 1.71588704296646 | erot = 3.17642860992462 | epot = -21.8345558128149 | etot = -16.9422401599238 +342000 ekin = 1.82178091247658 | erot = 2.58875985611025 | epot = -21.7161502950572 | etot = -17.3056095264704 +343000 ekin = 3.08559255942693 | erot = 2.94813449265469 | epot = -21.7030445300996 | etot = -15.669317478018 +344000 ekin = 2.95985387154984 | erot = 3.11547515850352 | epot = -21.681548329552 | etot = -15.6062192994986 +345000 ekin = 2.33428072266864 | erot = 2.8804443128302 | epot = -21.6567075042343 | etot = -16.4419824687354 +346000 ekin = 2.02077664062698 | erot = 3.45936833964706 | epot = -21.5877268821218 | etot = -16.1075819018477 +347000 ekin = 2.34924784800441 | erot = 1.93056350805623 | epot = -21.4896151766054 | etot = -17.2098038205448 +348000 ekin = 2.79839267202794 | erot = 2.79408776517961 | epot = -21.4682057474677 | etot = -15.8757253102602 +349000 ekin = 2.33820470114615 | erot = 3.12966318670512 | epot = -21.5603039389198 | etot = -16.0924360510685 +350000 ekin = 2.22383234890832 | erot = 2.3888687038801 | epot = -21.5375784703117 | etot = -16.9248774175232 +351000 ekin = 2.33329735253339 | erot = 2.84447430695177 | epot = -21.5078106306152 | etot = -16.33003897113 +352000 ekin = 2.74923373919409 | erot = 2.76796181793622 | epot = -21.5537134920816 | etot = -16.0365179349513 +353000 ekin = 1.76111836153718 | erot = 2.12255592617517 | epot = -21.5037017999955 | etot = -17.6200275122832 +354000 ekin = 2.29967358188085 | erot = 2.37615363620183 | epot = -21.559257977819 | etot = -16.8834307597363 +355000 ekin = 2.32956787601564 | erot = 2.41406261152025 | epot = -21.5311925684016 | etot = -16.7875620808657 +356000 ekin = 2.99536507165416 | erot = 3.01337867890171 | epot = -21.461213826164 | etot = -15.4524700756081 +357000 ekin = 1.79487551861702 | erot = 2.1478177575683 | epot = -21.4425100027869 | etot = -17.4998167266015 +358000 ekin = 2.06856992699964 | erot = 1.91585051553708 | epot = -21.4597512525557 | etot = -17.475330810019 +359000 ekin = 2.03457633089973 | erot = 2.13725650388116 | epot = -21.4345843672419 | etot = -17.2627515324611 +360000 ekin = 2.64289898809605 | erot = 2.45722294398596 | epot = -21.3798303659972 | etot = -16.2797084339152 +361000 ekin = 2.44681633772951 | erot = 2.40323525392196 | epot = -21.4535746870957 | etot = -16.6035230954443 +362000 ekin = 2.27284400709389 | erot = 2.04866562998477 | epot = -21.4444048899961 | etot = -17.1228952529174 +363000 ekin = 3.23945885057604 | erot = 1.79247859381385 | epot = -21.4992698914106 | etot = -16.4673324470207 +364000 ekin = 3.01124200487832 | erot = 2.16495867321709 | epot = -21.5330648567406 | etot = -16.3568641786452 +365000 ekin = 2.51472285580871 | erot = 2.29864111879032 | epot = -21.6252096459668 | etot = -16.8118456713678 +366000 ekin = 2.59356655410024 | erot = 2.21031948632571 | epot = -21.6397726115723 | etot = -16.8358865711463 +367000 ekin = 2.23422490605625 | erot = 1.85375489374337 | epot = -21.7036464131406 | etot = -17.615666613341 +368000 ekin = 2.4774770785368 | erot = 2.36511710555107 | epot = -21.7442459693683 | etot = -16.9016517852804 +369000 ekin = 2.03854183495617 | erot = 2.80790943599038 | epot = -21.8295461127419 | etot = -16.9830948417954 +370000 ekin = 2.08495509326203 | erot = 2.15717784784086 | epot = -21.8579547558588 | etot = -17.6158218147559 +371000 ekin = 2.1649158804987 | erot = 2.10731342711639 | epot = -21.7507302872469 | etot = -17.4785009796318 +372000 ekin = 1.83416420958724 | erot = 1.90082367490456 | epot = -21.6784224725519 | etot = -17.9434345880601 +373000 ekin = 1.97176482573297 | erot = 1.7779600789095 | epot = -21.6393712386778 | etot = -17.8896463340353 +374000 ekin = 2.89940710658305 | erot = 1.91194262525378 | epot = -21.5337545453635 | etot = -16.7224048135267 +375000 ekin = 2.32339676163341 | erot = 1.92362318361284 | epot = -21.421709102519 | etot = -17.1746891572728 +376000 ekin = 2.59047552311153 | erot = 2.32394149083979 | epot = -21.4139727856534 | etot = -16.4995557717021 +377000 ekin = 2.24598863840517 | erot = 1.65770205797294 | epot = -21.3405339068232 | etot = -17.4368432104451 +378000 ekin = 2.38351514056703 | erot = 2.54156262207208 | epot = -21.3122380587448 | etot = -16.3871602961057 +379000 ekin = 2.08457212928957 | erot = 2.11819645676891 | epot = -21.2663127721437 | etot = -17.0635441860852 +380000 ekin = 2.62168026009058 | erot = 2.36576073073355 | epot = -21.2469701231191 | etot = -16.259529132295 +381000 ekin = 2.42554871977307 | erot = 2.21588725182519 | epot = -21.2594018196931 | etot = -16.6179658480948 +382000 ekin = 2.04454090532122 | erot = 3.35199327879854 | epot = -21.3507561156203 | etot = -15.9542219315006 +383000 ekin = 2.5775676978984 | erot = 1.58356833947096 | epot = -21.4206473136967 | etot = -17.2595112763273 +384000 ekin = 2.32411392435712 | erot = 2.07034159075991 | epot = -21.4254017003271 | etot = -17.0309461852101 +385000 ekin = 1.93815279071873 | erot = 3.2997037447625 | epot = -21.4993838182002 | etot = -16.2615272827189 +386000 ekin = 2.10645704249442 | erot = 2.94380940917573 | epot = -21.5050572923383 | etot = -16.4547908406681 +387000 ekin = 2.28625118399722 | erot = 2.40488022694899 | epot = -21.4350466670762 | etot = -16.74391525613 +388000 ekin = 2.84183807689895 | erot = 2.72440789072404 | epot = -21.448767296848 | etot = -15.882521329225 +389000 ekin = 3.39750799106376 | erot = 3.08194517695383 | epot = -21.6559630447603 | etot = -15.1765098767427 +390000 ekin = 2.82211920760118 | erot = 2.04880343622588 | epot = -21.7229608878358 | etot = -16.8520382440088 +391000 ekin = 2.25113345866118 | erot = 2.45876014532077 | epot = -21.7793475672487 | etot = -17.0694539632668 +392000 ekin = 2.6777973992177 | erot = 2.7527860471579 | epot = -21.9200377033298 | etot = -16.4894542569542 +393000 ekin = 2.07336639249412 | erot = 1.66102921524042 | epot = -22.0500496423093 | etot = -18.3156540345748 +394000 ekin = 2.1138614951422 | erot = 2.4065490584156 | epot = -22.0647062581752 | etot = -17.5442957046174 +395000 ekin = 2.46967791557608 | erot = 2.46187607744979 | epot = -22.0113006362931 | etot = -17.0797466432672 +396000 ekin = 3.17858061422169 | erot = 1.60030928107608 | epot = -21.9570022338792 | etot = -17.1781123385814 +397000 ekin = 2.37483507726777 | erot = 2.17387816921976 | epot = -21.8769234701934 | etot = -17.3282102237059 +398000 ekin = 2.29815779154461 | erot = 2.20148627030488 | epot = -21.8293641014529 | etot = -17.3297200396034 +399000 ekin = 2.66620669497936 | erot = 2.78316441348841 | epot = -21.7420307764657 | etot = -16.2926596679979 +400000 ekin = 1.8196142363994 | erot = 2.77573291920481 | epot = -21.7225828560707 | etot = -17.1272357004665 +401000 ekin = 2.39347596566752 | erot = 3.11237720134103 | epot = -21.763219812775 | etot = -16.2573666457665 +402000 ekin = 4.0137909252526 | erot = 3.58756310879366 | epot = -21.6952307126455 | etot = -14.0938766785993 +403000 ekin = 3.6423872335827 | erot = 3.44210139074532 | epot = -21.6932224157202 | etot = -14.6087337913922 +404000 ekin = 2.52116102522202 | erot = 2.99286839639892 | epot = -21.7395466120138 | etot = -16.2255171903929 +405000 ekin = 2.80514548558626 | erot = 3.09807228440151 | epot = -21.809681120553 | etot = -15.9064633505652 +406000 ekin = 2.32696376764902 | erot = 2.03572639782902 | epot = -21.9111381639248 | etot = -17.5484479984467 +407000 ekin = 2.33504128016394 | erot = 1.91320949168965 | epot = -21.9359478399847 | etot = -17.6876970681311 +408000 ekin = 1.90942025822264 | erot = 2.20375631379572 | epot = -21.9849314014527 | etot = -17.8717548294343 +409000 ekin = 1.98818542800297 | erot = 1.95540808206522 | epot = -22.03783497597 | etot = -18.0942414659018 +410000 ekin = 1.59823476401333 | erot = 1.9127296785249 | epot = -22.0830507565095 | etot = -18.5720863139713 +411000 ekin = 1.87320182179615 | erot = 2.46575148951074 | epot = -22.1911106440467 | etot = -17.8521573327398 +412000 ekin = 2.51909186028136 | erot = 2.65534868642726 | epot = -22.281680067606 | etot = -17.1072395208973 +413000 ekin = 2.80929435327118 | erot = 3.19888285052217 | epot = -22.190767996874 | etot = -16.1825907930807 +414000 ekin = 2.79014519733558 | erot = 2.72515195410933 | epot = -22.1448630242429 | etot = -16.629565872798 +415000 ekin = 2.4678901908732 | erot = 2.24891720770208 | epot = -22.1977268949424 | etot = -17.4809194963671 +416000 ekin = 3.30766536008867 | erot = 1.55878918639504 | epot = -22.1694878213559 | etot = -17.3030332748721 +417000 ekin = 3.95074944679109 | erot = 2.44780201516574 | epot = -22.1018895242094 | etot = -15.7033380622526 +418000 ekin = 2.77340936693416 | erot = 2.68993840817536 | epot = -21.977327562767 | etot = -16.5139797876575 +419000 ekin = 2.38275203991917 | erot = 2.97769109273479 | epot = -21.9010102007428 | etot = -16.5405670680889 +420000 ekin = 1.80397709765343 | erot = 1.82715488758969 | epot = -21.8849019003165 | etot = -18.2537699150733 +421000 ekin = 1.35294173647286 | erot = 1.7746327595132 | epot = -21.8324727162454 | etot = -18.7048982202594 +422000 ekin = 1.39101035408782 | erot = 2.74626781088315 | epot = -21.892204423852 | etot = -17.7549262588811 +423000 ekin = 1.58313118355037 | erot = 3.07988587276088 | epot = -21.9303489156375 | etot = -17.2673318593263 +424000 ekin = 2.38308976422853 | erot = 2.02905632834229 | epot = -22.0003513420111 | etot = -17.5882052494403 +425000 ekin = 2.32292982636641 | erot = 2.54472792699358 | epot = -22.0461884305752 | etot = -17.1785306772153 +426000 ekin = 2.07274921207621 | erot = 3.12068562025983 | epot = -21.9899604929779 | etot = -16.7965256606418 +427000 ekin = 2.16499158921496 | erot = 2.43609860560844 | epot = -21.8837565028179 | etot = -17.2826663079945 +428000 ekin = 1.81001230881453 | erot = 1.65184910311941 | epot = -21.8651168729133 | etot = -18.4032554609794 +429000 ekin = 1.67080799563552 | erot = 2.55829004033941 | epot = -21.823203822061 | etot = -17.5941057860861 +430000 ekin = 2.68658781224627 | erot = 2.85919253371561 | epot = -21.8545360487503 | etot = -16.3087557027884 +431000 ekin = 2.77334901985549 | erot = 1.57746917070685 | epot = -21.8360353910943 | etot = -17.485217200532 +432000 ekin = 2.50244674166437 | erot = 1.60779258881598 | epot = -21.7381087453319 | etot = -17.6278694148515 +433000 ekin = 1.85649371322474 | erot = 2.4917335891794 | epot = -21.7919912827364 | etot = -17.4437639803322 +434000 ekin = 2.89302367450635 | erot = 2.79890045602688 | epot = -21.923157505168 | etot = -16.2312333746347 +435000 ekin = 3.67647442700572 | erot = 1.38588132381275 | epot = -22.1019777057281 | etot = -17.0396219549096 +436000 ekin = 3.05510329104703 | erot = 2.00142902882896 | epot = -22.1034257027065 | etot = -17.0468933828305 +437000 ekin = 3.23341172893811 | erot = 1.78346855436478 | epot = -22.113702088725 | etot = -17.0968218054221 +438000 ekin = 2.86378458795303 | erot = 1.84588842157477 | epot = -22.072414124752 | etot = -17.3627411152242 +439000 ekin = 2.41407153953135 | erot = 2.70066632790347 | epot = -22.0535011599235 | etot = -16.9387632924887 +440000 ekin = 2.22110309163133 | erot = 3.01674685818988 | epot = -22.0773629228071 | etot = -16.8395129729859 +441000 ekin = 2.89520033479411 | erot = 2.87911130379517 | epot = -22.209849236351 | etot = -16.4355375977617 +442000 ekin = 2.05598301233623 | erot = 1.73562369066664 | epot = -22.2689079268811 | etot = -18.4773012238783 +443000 ekin = 1.86650631344268 | erot = 2.00816178040311 | epot = -22.3072964279924 | etot = -18.4326283341466 +444000 ekin = 2.06088560705619 | erot = 2.15265011198711 | epot = -22.3186686701218 | etot = -18.1051329510785 +445000 ekin = 2.10029110633058 | erot = 2.2800331405132 | epot = -22.3739249314238 | etot = -17.99360068458 +446000 ekin = 2.42121462246176 | erot = 2.8536509710476 | epot = -22.4030820729313 | etot = -17.128216479422 +447000 ekin = 2.19905370994783 | erot = 2.98216231903378 | epot = -22.4760062523441 | etot = -17.2947902233625 +448000 ekin = 2.35344530580996 | erot = 2.94496431571717 | epot = -22.4927466941726 | etot = -17.1943370726455 +449000 ekin = 2.39032460069844 | erot = 2.92889137252357 | epot = -22.5027878081879 | etot = -17.1835718349658 +450000 ekin = 1.87543018481826 | erot = 1.69603328668915 | epot = -22.4562462785527 | etot = -18.8847828070453 +451000 ekin = 2.01850498861611 | erot = 1.92812989993404 | epot = -22.4817672986218 | etot = -18.5351324100716 +452000 ekin = 1.36652609658347 | erot = 1.87105620810406 | epot = -22.4501755877893 | etot = -19.2125932831017 +453000 ekin = 2.0599225820261 | erot = 2.56027964608567 | epot = -22.2765869721545 | etot = -17.6563847440427 +454000 ekin = 1.47421749728914 | erot = 2.19120144206329 | epot = -22.1381671023588 | etot = -18.4727481630063 +455000 ekin = 1.65550022307771 | erot = 2.72165814308167 | epot = -21.9904394751434 | etot = -17.613281108984 +456000 ekin = 2.34827062603187 | erot = 2.00722438151078 | epot = -21.9105114729144 | etot = -17.5550164653718 +457000 ekin = 2.01338249991754 | erot = 2.37170378033693 | epot = -21.8819790372449 | etot = -17.4968927569904 +458000 ekin = 1.72815421955305 | erot = 2.26329746701055 | epot = -21.911604405066 | etot = -17.9201527185024 +459000 ekin = 2.48347398227002 | erot = 2.3237619692994 | epot = -21.9949404038568 | etot = -17.1877044522873 +460000 ekin = 2.18770854699574 | erot = 2.00081662918321 | epot = -21.9585322440375 | etot = -17.7700070678585 +461000 ekin = 2.27716435663743 | erot = 2.90195656269068 | epot = -21.8877682177659 | etot = -16.7086472984378 +462000 ekin = 2.61244889701714 | erot = 1.79757533309512 | epot = -21.9143949779912 | etot = -17.5043707478789 +463000 ekin = 2.55684814656523 | erot = 3.31200610027655 | epot = -21.8497749242033 | etot = -15.9809206773615 +464000 ekin = 2.15312235839157 | erot = 2.38947690136822 | epot = -21.7825241097983 | etot = -17.2399248500385 +465000 ekin = 2.5257577253008 | erot = 3.61331808321474 | epot = -21.7072705251899 | etot = -15.5681947166744 +466000 ekin = 1.97943618964771 | erot = 2.8868852833762 | epot = -21.7222514097774 | etot = -16.8559299367534 +467000 ekin = 1.62882257493983 | erot = 2.60892282315519 | epot = -21.8080861041927 | etot = -17.5703407060977 +468000 ekin = 1.09823854644375 | erot = 3.35073251937298 | epot = -21.8523811012329 | etot = -17.4034100354162 +469000 ekin = 1.70229597385131 | erot = 2.75889840726388 | epot = -21.8665756757502 | etot = -17.405381294635 +470000 ekin = 1.85844768422772 | erot = 2.8706546217625 | epot = -21.9036130079376 | etot = -17.1745107019474 +471000 ekin = 2.74399539924327 | erot = 2.34943354955081 | epot = -21.9543989717239 | etot = -16.8609700229298 +472000 ekin = 2.7182617922689 | erot = 2.13581917182001 | epot = -22.0449294707038 | etot = -17.1908485066148 +473000 ekin = 2.29380642077304 | erot = 2.07595163501546 | epot = -22.0706135180041 | etot = -17.7008554622156 +474000 ekin = 2.22690782122655 | erot = 2.16470599013948 | epot = -22.0704871162386 | etot = -17.6788733048726 +475000 ekin = 2.4978679533329 | erot = 2.09510196885224 | epot = -22.0509742163569 | etot = -17.4580042941717 +476000 ekin = 2.20264299239668 | erot = 1.76757923556402 | epot = -21.9427521555982 | etot = -17.9725299276375 +477000 ekin = 2.45872237399503 | erot = 2.38426997478537 | epot = -21.9051474088982 | etot = -17.0621550601178 +478000 ekin = 1.8990596403089 | erot = 2.04864356713722 | epot = -21.9114508304737 | etot = -17.9637476230276 +479000 ekin = 2.2713390213749 | erot = 3.08755197682257 | epot = -21.8872829373265 | etot = -16.5283919391291 +480000 ekin = 1.67015605151468 | erot = 2.76560365045838 | epot = -21.8968158425889 | etot = -17.4610561406158 +481000 ekin = 1.81882995680353 | erot = 2.94136105971067 | epot = -21.8571304925408 | etot = -17.0969394760266 +482000 ekin = 2.15305069632652 | erot = 2.07327897823918 | epot = -21.8152992914385 | etot = -17.5889696168728 +483000 ekin = 1.50004535981758 | erot = 1.99364343935403 | epot = -21.7843644990947 | etot = -18.2906756999231 +484000 ekin = 1.85234844255529 | erot = 2.3400023120278 | epot = -21.8614293841666 | etot = -17.6690786295835 +485000 ekin = 1.64682178328831 | erot = 2.50437862576678 | epot = -21.8969405008956 | etot = -17.7457400918405 +486000 ekin = 1.86104257115938 | erot = 2.15995925522771 | epot = -21.8879397421696 | etot = -17.8669379157825 +487000 ekin = 2.34639026339217 | erot = 3.11622773972824 | epot = -21.9707194220382 | etot = -16.5081014189178 +488000 ekin = 2.27484994031488 | erot = 3.28147617368228 | epot = -21.9426475486812 | etot = -16.3863214346841 +489000 ekin = 2.38811933287365 | erot = 2.56070014238266 | epot = -21.8600861168089 | etot = -16.9112666415526 +490000 ekin = 2.12976254880773 | erot = 3.54525746010286 | epot = -21.7617637919249 | etot = -16.0867437830143 +491000 ekin = 2.20850764560418 | erot = 2.48919239454319 | epot = -21.6468680069132 | etot = -16.9491679667658 +492000 ekin = 2.43957739853024 | erot = 2.7632318669038 | epot = -21.6230951653168 | etot = -16.4202858998828 +493000 ekin = 1.79391622496105 | erot = 2.2905251847004 | epot = -21.6945975278841 | etot = -17.6101561182226 +494000 ekin = 2.11542949642227 | erot = 3.01313865872483 | epot = -21.7637004472039 | etot = -16.6351322920568 +495000 ekin = 2.1568591957283 | erot = 2.49005677705245 | epot = -21.8783556810053 | etot = -17.2314397082246 +496000 ekin = 2.0603755282602 | erot = 2.606986291047 | epot = -21.9276220332962 | etot = -17.260260213989 +497000 ekin = 2.52228141248763 | erot = 1.71013019276801 | epot = -21.8769629373864 | etot = -17.6445513321307 +498000 ekin = 2.1539450080541 | erot = 1.78777085700022 | epot = -21.8243748366057 | etot = -17.8826589715514 +499000 ekin = 3.01296343053108 | erot = 1.73934813146709 | epot = -21.839263268044 | etot = -17.0869517060458 +500000 ekin = 2.7664211971855 | erot = 2.50182215373005 | epot = -21.830671988603 | etot = -16.5624286376875 +501000 ekin = 2.69367571720338 | erot = 2.99042817784737 | epot = -21.7039103667138 | etot = -16.0198064716631 +502000 ekin = 1.91666556639459 | erot = 3.89815239299715 | epot = -21.5845300715443 | etot = -15.7697121121525 +503000 ekin = 1.80513448090424 | erot = 2.94463129244922 | epot = -21.408846856306 | etot = -16.6590810829525 +504000 ekin = 1.70082883689618 | erot = 3.04312463877849 | epot = -21.3315058298563 | etot = -16.5875523541817 +505000 ekin = 2.75953000022913 | erot = 2.14635942194521 | epot = -21.3525103549444 | etot = -16.4466209327701 +506000 ekin = 2.29728093923375 | erot = 2.04403144683578 | epot = -21.3794572010067 | etot = -17.0381448149372 +507000 ekin = 3.17636857959624 | erot = 2.42164349794529 | epot = -21.4731108320935 | etot = -15.8750987545519 +508000 ekin = 2.53590109429522 | erot = 2.52790695399208 | epot = -21.6300410847596 | etot = -16.5662330364723 +509000 ekin = 2.12748393236721 | erot = 2.83071060777934 | epot = -21.7781347526393 | etot = -16.8199402124928 +510000 ekin = 2.16138023827908 | erot = 1.44739524871433 | epot = -21.8661383228762 | etot = -18.2573628358828 +511000 ekin = 2.5432337386743 | erot = 2.7710867437818 | epot = -21.9670096484362 | etot = -16.65268916598 +512000 ekin = 2.32820226144234 | erot = 2.80424931634042 | epot = -22.0177071813426 | etot = -16.8852556035598 +513000 ekin = 2.47700215188742 | erot = 2.17127792631492 | epot = -22.0110285387343 | etot = -17.362748460532 +514000 ekin = 2.76651136580706 | erot = 2.55680467976049 | epot = -22.0909970005814 | etot = -16.7676809550139 +515000 ekin = 2.5202331965388 | erot = 1.82499891391154 | epot = -22.1712715169566 | etot = -17.8260394065062 +516000 ekin = 2.81741012640848 | erot = 2.22255273815335 | epot = -22.2621950124766 | etot = -17.2222321479148 +517000 ekin = 2.03287831599843 | erot = 2.04932227860397 | epot = -22.2794486174447 | etot = -18.1972480228423 +518000 ekin = 2.18753527424292 | erot = 2.76011341951324 | epot = -22.2667176836094 | etot = -17.3190689898532 +519000 ekin = 2.23127004412532 | erot = 2.23036422155453 | epot = -22.3641437250361 | etot = -17.9025094593563 +520000 ekin = 1.88835704965194 | erot = 2.20137678015023 | epot = -22.4547788180202 | etot = -18.365044988218 +521000 ekin = 2.57911594310158 | erot = 1.87216207270883 | epot = -22.6071563154982 | etot = -18.1558782996878 +522000 ekin = 3.47551915105824 | erot = 1.7762374523623 | epot = -22.6852629490162 | etot = -17.4335063455957 +523000 ekin = 2.84545293485785 | erot = 2.47507537559666 | epot = -22.727728352182 | etot = -17.4072000417275 +524000 ekin = 2.40278895519472 | erot = 2.37529684497553 | epot = -22.6643160930411 | etot = -17.8862302928709 +525000 ekin = 1.5950703357501 | erot = 2.61508341973266 | epot = -22.5633164974796 | etot = -18.3531627419968 +526000 ekin = 1.67007684014044 | erot = 1.59545284095806 | epot = -22.511319978416 | etot = -19.2457902973175 +527000 ekin = 2.19667533945247 | erot = 1.9333023124675 | epot = -22.4181345854017 | etot = -18.2881569334817 +528000 ekin = 2.6386695788743 | erot = 2.84200507572112 | epot = -22.4271496272375 | etot = -16.9464749726421 +529000 ekin = 2.71685924097597 | erot = 3.01195511036351 | epot = -22.4607209136928 | etot = -16.7319065623533 +530000 ekin = 2.59646038482582 | erot = 2.1317692819235 | epot = -22.3209630404852 | etot = -17.5927333737359 +531000 ekin = 2.96818211550215 | erot = 2.35836906019033 | epot = -22.2240561584028 | etot = -16.8975049827104 +532000 ekin = 2.54400448114086 | erot = 2.32266423688291 | epot = -22.2383323718679 | etot = -17.3716636538441 +533000 ekin = 2.47235456553947 | erot = 2.96337386592411 | epot = -22.2434312615742 | etot = -16.8077028301106 +534000 ekin = 2.104894788263 | erot = 2.03894640697442 | epot = -22.2624131617689 | etot = -18.1185719665315 +535000 ekin = 3.76811893478762 | erot = 2.64694643296526 | epot = -22.2342741399369 | etot = -15.819208772184 +536000 ekin = 2.78932048770647 | erot = 1.95046774407586 | epot = -22.1710588414062 | etot = -17.4312706096239 +537000 ekin = 2.84547413963847 | erot = 2.62354406512568 | epot = -22.0792539675812 | etot = -16.610235762817 +538000 ekin = 2.67615418297318 | erot = 2.08962546790894 | epot = -21.9560559397441 | etot = -17.190276288862 +539000 ekin = 2.73041224389435 | erot = 2.35761678189142 | epot = -22.0360310245606 | etot = -16.9480019987748 +540000 ekin = 2.45513520817504 | erot = 2.49807124796169 | epot = -22.1997448500024 | etot = -17.2465383938656 +541000 ekin = 3.48268229748521 | erot = 2.77797330372247 | epot = -22.2939060084684 | etot = -16.0332504072607 +542000 ekin = 2.48960436886327 | erot = 2.8733247922981 | epot = -22.3004887690915 | etot = -16.9375596079301 +543000 ekin = 2.34699181381529 | erot = 2.86167842257192 | epot = -22.3027783678197 | etot = -17.0941081314325 +544000 ekin = 2.22918134297116 | erot = 1.46827924617159 | epot = -22.2757921511234 | etot = -18.5783315619807 +545000 ekin = 2.45393652663684 | erot = 2.14178562937395 | epot = -22.2696521197313 | etot = -17.6739299637206 +546000 ekin = 1.98434977645849 | erot = 2.24144093113159 | epot = -22.232171992891 | etot = -18.0063812853009 +547000 ekin = 2.56230350196472 | erot = 1.89574625912019 | epot = -22.2013923967025 | etot = -17.7433426356176 +548000 ekin = 1.72907614338158 | erot = 1.64127030305736 | epot = -22.1897325934373 | etot = -18.8193861469984 +549000 ekin = 1.95696682165777 | erot = 2.64539988943053 | epot = -22.3281210018679 | etot = -17.7257542907796 +550000 ekin = 1.80672944936439 | erot = 1.58554489058936 | epot = -22.4379557312283 | etot = -19.0456813912745 +551000 ekin = 2.19785864069661 | erot = 2.26344341600384 | epot = -22.4944444264338 | etot = -18.0331423697333 +552000 ekin = 2.074442528674 | erot = 2.49246441473271 | epot = -22.5313734934249 | etot = -17.9644665500182 +553000 ekin = 2.94841939583913 | erot = 2.12309786300742 | epot = -22.5870982488507 | etot = -17.5155809900042 +554000 ekin = 2.86687820100223 | erot = 1.94287298381726 | epot = -22.755332978123 | etot = -17.9455817933035 +555000 ekin = 2.43102414091851 | erot = 2.28708167460999 | epot = -22.8409516497234 | etot = -18.1228458341949 +556000 ekin = 2.31020008885682 | erot = 2.55815314755914 | epot = -22.8777743355339 | etot = -18.0094210991179 +557000 ekin = 2.81359485404959 | erot = 1.42586137655668 | epot = -22.93912738 | etot = -18.6996711493938 +558000 ekin = 2.79709708533547 | erot = 1.99545051650402 | epot = -22.9823826800612 | etot = -18.1898350782217 +559000 ekin = 3.34842854089641 | erot = 2.30939572175805 | epot = -23.0558646505447 | etot = -17.3980403878902 +560000 ekin = 3.12583165184862 | erot = 2.33613566970364 | epot = -23.0537007225862 | etot = -17.591733401034 +561000 ekin = 2.91276096736789 | erot = 2.07459481236915 | epot = -22.9822607654341 | etot = -17.994904985697 +562000 ekin = 3.33017095598494 | erot = 2.52215992853225 | epot = -22.8889363116258 | etot = -17.0366054271086 +563000 ekin = 2.70200701416855 | erot = 1.647701133792 | epot = -22.8712722594835 | etot = -18.521564111523 +564000 ekin = 2.82953631474814 | erot = 2.52900560163797 | epot = -22.8387855460795 | etot = -17.4802436296934 +565000 ekin = 2.67999888917709 | erot = 2.05091800967451 | epot = -22.7937507048715 | etot = -18.0628338060199 +566000 ekin = 2.32986557500305 | erot = 2.16379904557212 | epot = -22.8028233873669 | etot = -18.3091587667917 +567000 ekin = 1.92319601586312 | erot = 2.83258522428555 | epot = -22.7588270107033 | etot = -18.0030457705546 +568000 ekin = 2.1767237164987 | erot = 2.23391201707387 | epot = -22.7857243432792 | etot = -18.3750886097066 +569000 ekin = 2.44197408396629 | erot = 2.65159536305571 | epot = -22.7197314796374 | etot = -17.6261620326154 +570000 ekin = 2.4317740620905 | erot = 1.89764945519459 | epot = -22.6963472615905 | etot = -18.3669237443054 +571000 ekin = 2.86160521289846 | erot = 2.96804382024776 | epot = -22.6961835038032 | etot = -16.8665344706569 +572000 ekin = 1.92662919536387 | erot = 3.79135909534693 | epot = -22.6587081618988 | etot = -16.940719871188 +573000 ekin = 2.40137439242945 | erot = 2.2998261335634 | epot = -22.6365074046859 | etot = -17.935306878693 +574000 ekin = 1.68882589350908 | erot = 2.3209740449249 | epot = -22.6783832960445 | etot = -18.6685833576106 +575000 ekin = 1.85490665091732 | erot = 1.85640808911422 | epot = -22.7444448136904 | etot = -19.0331300736588 +576000 ekin = 3.24775679594035 | erot = 2.9556926821431 | epot = -22.6991990620438 | etot = -16.4957495839603 +577000 ekin = 2.89423151645282 | erot = 2.87486712706734 | epot = -22.6284365608021 | etot = -16.8593379172819 +578000 ekin = 2.40460916677569 | erot = 2.78216711024701 | epot = -22.4348874817265 | etot = -17.2481112047038 +579000 ekin = 2.40580528046575 | erot = 1.99557814482532 | epot = -22.2889136736671 | etot = -17.887530248376 +580000 ekin = 2.69817090358906 | erot = 1.94741864170503 | epot = -22.1754486864787 | etot = -17.5298591411846 +581000 ekin = 2.06309668646281 | erot = 2.97621367011722 | epot = -22.0670098600828 | etot = -17.0276995035027 +582000 ekin = 2.33869527454826 | erot = 3.07898324506956 | epot = -21.9478320300714 | etot = -16.5301535104536 +583000 ekin = 2.23428959741494 | erot = 2.68476693088862 | epot = -21.837983720672 | etot = -16.9189271923684 +584000 ekin = 2.94321016295283 | erot = 2.59995039730548 | epot = -21.7517635625831 | etot = -16.2086030023248 +585000 ekin = 2.36063475490837 | erot = 2.49112677628939 | epot = -21.7173359488816 | etot = -16.8655744176838 +586000 ekin = 3.56583702163526 | erot = 2.02487858259688 | epot = -21.7707868137138 | etot = -16.1800712094817 +587000 ekin = 3.53727585853245 | erot = 1.97258932652022 | epot = -21.7665121756112 | etot = -16.2566469905585 +588000 ekin = 2.82339556293758 | erot = 1.59340504807044 | epot = -21.7545319340973 | etot = -17.3377313230892 +589000 ekin = 2.31627310139818 | erot = 2.20582604523298 | epot = -21.8199173705564 | etot = -17.2978182239252 +590000 ekin = 2.57616671531331 | erot = 1.72768273328208 | epot = -21.8427138199642 | etot = -17.5388643713688 +591000 ekin = 1.91473306171853 | erot = 3.80604384238377 | epot = -21.9351393124188 | etot = -16.2143624083165 +592000 ekin = 2.11222958764659 | erot = 2.84208333850203 | epot = -21.9639458839076 | etot = -17.0096329577589 +593000 ekin = 1.66462149590471 | erot = 2.46217253451012 | epot = -21.9921445323971 | etot = -17.8653505019823 +594000 ekin = 1.86314045588477 | erot = 2.37275936142268 | epot = -22.1149191228505 | etot = -17.879019305543 +595000 ekin = 1.6397125755004 | erot = 2.14970246798561 | epot = -22.2960530768755 | etot = -18.5066380333895 +596000 ekin = 1.86247376576132 | erot = 1.56938095427869 | epot = -22.4014957466218 | etot = -18.9696410265818 +597000 ekin = 2.21073901406701 | erot = 2.3087175693751 | epot = -22.4599242604732 | etot = -17.9404676770311 +598000 ekin = 1.8660134932493 | erot = 3.02311727399813 | epot = -22.5165298316334 | etot = -17.6273990643859 +599000 ekin = 2.86271635930755 | erot = 2.19928854437227 | epot = -22.536599708025 | etot = -17.4745948043452 +600000 ekin = 2.65062163067179 | erot = 2.14533898812782 | epot = -22.4620537969304 | etot = -17.6660931781308 +601000 ekin = 2.97018864875202 | erot = 3.19824090103878 | epot = -22.3271949752462 | etot = -16.1587654254554 +602000 ekin = 2.93416893709001 | erot = 2.68627449040958 | epot = -22.2245183728174 | etot = -16.6040749453178 +603000 ekin = 2.5987545006459 | erot = 2.71301833029978 | epot = -22.1705323477201 | etot = -16.8587595167745 +604000 ekin = 1.79059859762797 | erot = 2.11515305424794 | epot = -22.1931056020217 | etot = -18.2873539501458 +605000 ekin = 1.82914051863722 | erot = 2.27656979248766 | epot = -22.2183915784731 | etot = -18.1126812673482 +606000 ekin = 2.33864125390345 | erot = 2.204164937778 | epot = -22.1617656383863 | etot = -17.6189594467048 +607000 ekin = 2.72666217259876 | erot = 2.97710334336218 | epot = -22.1572786906588 | etot = -16.4535131746978 +608000 ekin = 2.45226937954678 | erot = 2.41232790919961 | epot = -22.1263051367364 | etot = -17.2617078479901 +609000 ekin = 1.91032127854288 | erot = 2.62712516529566 | epot = -22.0127581830193 | etot = -17.4753117391807 +610000 ekin = 3.01319055031108 | erot = 2.17098104720964 | epot = -21.930499629869 | etot = -16.7463280323483 +611000 ekin = 2.44410994437292 | erot = 2.75159061185421 | epot = -21.9258193850468 | etot = -16.7301188288197 +612000 ekin = 2.50271115837173 | erot = 2.16817640692168 | epot = -21.9676183236645 | etot = -17.2967307583711 +613000 ekin = 3.01842230632867 | erot = 2.12784419676567 | epot = -22.0277467117808 | etot = -16.8814802086864 +614000 ekin = 2.25331711369829 | erot = 2.99334048390157 | epot = -22.0701464667307 | etot = -16.8234888691309 +615000 ekin = 1.66376443031995 | erot = 2.63613776051569 | epot = -21.9985978951916 | etot = -17.698695704356 +616000 ekin = 1.89454248699046 | erot = 2.87318355169532 | epot = -22.0041678369047 | etot = -17.2364417982189 +617000 ekin = 2.14789714287838 | erot = 2.51249074123956 | epot = -22.0251474680604 | etot = -17.3647595839425 +618000 ekin = 3.11174934178843 | erot = 2.74374306269141 | epot = -21.980284295602 | etot = -16.1247918911221 +619000 ekin = 3.4103621396818 | erot = 2.10616794159728 | epot = -21.9557959924961 | etot = -16.4392659112171 +620000 ekin = 4.28430989238205 | erot = 2.19572475327593 | epot = -21.9033881020935 | etot = -15.4233534564355 +621000 ekin = 3.095687767491 | erot = 2.55794040804605 | epot = -21.8286763731363 | etot = -16.1750481975993 +622000 ekin = 2.76030419206697 | erot = 2.60754397958254 | epot = -21.7459002641757 | etot = -16.3780520925262 +623000 ekin = 2.87269212022169 | erot = 2.90401311950188 | epot = -21.5853226709314 | etot = -15.8086174312079 +624000 ekin = 2.01889500087931 | erot = 3.41825755609794 | epot = -21.4095311686242 | etot = -15.972378611647 +625000 ekin = 2.87966631754696 | erot = 2.69115421564282 | epot = -21.2859406043045 | etot = -15.7151200711147 +626000 ekin = 2.56087279949319 | erot = 2.15801254335178 | epot = -21.2329175358055 | etot = -16.5140321929605 +627000 ekin = 2.30197939613517 | erot = 2.40176668957968 | epot = -21.2932794652838 | etot = -16.589533379569 +628000 ekin = 2.23988628353727 | erot = 2.75332535542196 | epot = -21.4558642198861 | etot = -16.4626525809268 +629000 ekin = 2.20891060851904 | erot = 1.97036896055008 | epot = -21.6109313731644 | etot = -17.4316518040953 +630000 ekin = 2.48711004105954 | erot = 2.14055508379569 | epot = -21.6286281269544 | etot = -17.0009630020992 +631000 ekin = 2.05035510102044 | erot = 1.78519131042562 | epot = -21.633635046353 | etot = -17.7980886349069 +632000 ekin = 1.65439924450982 | erot = 3.28310987077494 | epot = -21.6999899301469 | etot = -16.7624808148621 +633000 ekin = 2.34657988531209 | erot = 2.34109631044866 | epot = -21.8317647703271 | etot = -17.1440885745664 +634000 ekin = 2.31570267703931 | erot = 2.471293173825 | epot = -21.8814211467029 | etot = -17.0944252958386 +635000 ekin = 1.99068848818426 | erot = 3.35493927676211 | epot = -21.9111632351734 | etot = -16.565535470227 +636000 ekin = 2.50156763858621 | erot = 2.48847742334418 | epot = -21.8752689055209 | etot = -16.8852238435905 +637000 ekin = 2.76558055064046 | erot = 2.80410341825293 | epot = -21.7874464522771 | etot = -16.2177624833837 +638000 ekin = 2.45488734924466 | erot = 2.8151636333562 | epot = -21.8973623385979 | etot = -16.627311355997 +639000 ekin = 1.89221088715375 | erot = 2.13319565970052 | epot = -21.932098303477 | etot = -17.9066917566227 +640000 ekin = 2.12173400886946 | erot = 3.32302167857403 | epot = -21.8808288554835 | etot = -16.43607316804 +641000 ekin = 2.09554541112561 | erot = 2.23098450754965 | epot = -21.9203390995501 | etot = -17.5938091808749 +642000 ekin = 2.28696138506763 | erot = 2.67378976619351 | epot = -21.9723604262127 | etot = -17.0116092749516 +643000 ekin = 2.74450005384908 | erot = 2.20403941809547 | epot = -21.9235240791533 | etot = -16.9749846072087 +644000 ekin = 2.87909523138453 | erot = 3.40688779630215 | epot = -21.9417833997401 | etot = -15.6558003720534 +645000 ekin = 2.38284095628022 | erot = 2.10846397463902 | epot = -21.8306349073152 | etot = -17.3393299763959 +646000 ekin = 2.68568471833193 | erot = 1.80852105367058 | epot = -21.6853054888873 | etot = -17.1910997168848 +647000 ekin = 2.44462012552757 | erot = 2.00446720103468 | epot = -21.4974635292911 | etot = -17.0483762027288 +648000 ekin = 2.22150753159448 | erot = 1.69679185313771 | epot = -21.5947311257684 | etot = -17.6764317410362 +649000 ekin = 2.55943952639506 | erot = 1.77203724563614 | epot = -22.016770390185 | etot = -17.6852936181538 +650000 ekin = 2.72347255721059 | erot = 2.20418229003755 | epot = -22.1594214535889 | etot = -17.2317666063407 +651000 ekin = 2.25383373914402 | erot = 3.26326768595795 | epot = -22.2274805933885 | etot = -16.7103791682865 +652000 ekin = 2.35810253390822 | erot = 2.29591208392312 | epot = -22.2332195197311 | etot = -17.5792049018997 +653000 ekin = 2.06421004499471 | erot = 2.14171845474571 | epot = -22.2265612208312 | etot = -18.0206327210908 +654000 ekin = 2.30460304373657 | erot = 1.85567946278894 | epot = -22.2521914868227 | etot = -18.0919089802972 +655000 ekin = 2.1118882401511 | erot = 1.79072614414008 | epot = -22.2262193909715 | etot = -18.3236050066803 +656000 ekin = 2.44561836830366 | erot = 2.32567811025774 | epot = -22.187237628634 | etot = -17.4159411500726 +657000 ekin = 2.45751083141108 | erot = 2.86439216413737 | epot = -22.1805503246548 | etot = -16.8586473291064 +658000 ekin = 2.49955432693124 | erot = 2.85472680235229 | epot = -22.1390040132353 | etot = -16.7847228839518 +659000 ekin = 3.37980090980362 | erot = 2.77552992994233 | epot = -21.9898923341708 | etot = -15.8345614944248 +660000 ekin = 2.6941462621918 | erot = 1.99094454704572 | epot = -21.839770569098 | etot = -17.1546797598605 +661000 ekin = 2.21049176877593 | erot = 2.52393650500611 | epot = -21.6857326790217 | etot = -16.9513044052396 +662000 ekin = 2.06962867519899 | erot = 2.53976085175022 | epot = -21.6239147287108 | etot = -17.0145252017615 +663000 ekin = 2.27770295544224 | erot = 2.30124717941155 | epot = -21.5870186127932 | etot = -17.0080684779394 +664000 ekin = 2.39061717453214 | erot = 1.87616423363736 | epot = -21.4930500427881 | etot = -17.2262686346186 +665000 ekin = 2.6692440512318 | erot = 2.29240983153227 | epot = -21.4402310096657 | etot = -16.4785771269017 +666000 ekin = 1.66318176263893 | erot = 2.30827907651666 | epot = -21.3477804932103 | etot = -17.3763196540547 +667000 ekin = 1.65573830146343 | erot = 2.8261361193353 | epot = -21.2651811028886 | etot = -16.7833066820899 +668000 ekin = 2.50126196238916 | erot = 3.29062396521941 | epot = -21.1310768281354 | etot = -15.3391909005268 +669000 ekin = 1.61008562219097 | erot = 2.65727107854378 | epot = -21.0513800034041 | etot = -16.7840233026694 +670000 ekin = 2.21851826153844 | erot = 2.60770568109396 | epot = -20.9727942140714 | etot = -16.146570271439 +671000 ekin = 2.25905318343359 | erot = 2.1596549557503 | epot = -20.920836534986 | etot = -16.5021283958021 +672000 ekin = 1.93426342346647 | erot = 1.65365047668441 | epot = -20.8333028169839 | etot = -17.245388916833 +673000 ekin = 1.880896686753 | erot = 2.07483128120029 | epot = -20.79952620348 | etot = -16.8437982355267 +674000 ekin = 2.067834680573 | erot = 2.16234064938725 | epot = -20.8176950919606 | etot = -16.5875197620003 +675000 ekin = 2.03952283590142 | erot = 2.48129689359269 | epot = -20.8297865902612 | etot = -16.3089668607671 +676000 ekin = 2.44687523374789 | erot = 2.77932995735253 | epot = -20.8513819036484 | etot = -15.625176712548 +677000 ekin = 2.18851088067448 | erot = 2.61928925664188 | epot = -20.8589021998565 | etot = -16.0511020625401 +678000 ekin = 2.13451298865477 | erot = 2.78742961560771 | epot = -20.7380850837789 | etot = -15.8161424795164 +679000 ekin = 2.15556981522704 | erot = 2.17593910434841 | epot = -20.629255081746 | etot = -16.2977461621705 +680000 ekin = 2.07717451414439 | erot = 2.68436897198808 | epot = -20.6512705044544 | etot = -15.889727018322 +681000 ekin = 2.16836766753576 | erot = 1.8266629484308 | epot = -20.7392652191905 | etot = -16.744234603224 +682000 ekin = 3.01810965188601 | erot = 2.39774897550359 | epot = -20.7185667085479 | etot = -15.3027080811583 +683000 ekin = 2.84169666492797 | erot = 2.09885122074905 | epot = -20.7261705834807 | etot = -15.7856226978037 +684000 ekin = 1.96250352869369 | erot = 2.99543980855395 | epot = -20.769704567373 | etot = -15.8117612301254 +685000 ekin = 1.50086016290166 | erot = 2.04478648729578 | epot = -20.778895252848 | etot = -17.2332486026506 +686000 ekin = 2.30092983530379 | erot = 2.55442118756322 | epot = -20.7673358731011 | etot = -15.9119848502341 +687000 ekin = 1.86053862979304 | erot = 2.84846934037477 | epot = -20.7009117540898 | etot = -15.9919037839219 +688000 ekin = 2.56859020075851 | erot = 2.23263295871679 | epot = -20.6563366249256 | etot = -15.8551134654503 +689000 ekin = 2.74930141700632 | erot = 2.68327386026121 | epot = -20.8092642099637 | etot = -15.3766889326962 +690000 ekin = 2.67477310841299 | erot = 2.52397256899157 | epot = -21.0730303416649 | etot = -15.8742846642604 +691000 ekin = 2.28465281003007 | erot = 2.52273866559284 | epot = -21.2401157605126 | etot = -16.4327242848897 +692000 ekin = 2.42087744380445 | erot = 3.24812320332686 | epot = -21.2665776826931 | etot = -15.5975770355618 +693000 ekin = 2.37642605279042 | erot = 2.99546830568892 | epot = -21.3330277418611 | etot = -15.9611333833818 +694000 ekin = 2.69750178365984 | erot = 2.53085866970816 | epot = -21.521485598392 | etot = -16.293125145024 +695000 ekin = 2.49230316198816 | erot = 1.18105864485318 | epot = -21.6959912399269 | etot = -18.0226294330856 +696000 ekin = 1.86075498586631 | erot = 1.46501529683133 | epot = -21.6808441671222 | etot = -18.3550738844245 +697000 ekin = 2.40460770445908 | erot = 2.10461647488795 | epot = -21.7143559347048 | etot = -17.2051317553578 +698000 ekin = 2.32098148261586 | erot = 1.91506962097517 | epot = -21.7787361369849 | etot = -17.5426850333939 +699000 ekin = 2.44943497732062 | erot = 2.56143482106644 | epot = -21.7638026578475 | etot = -16.7529328594605 +700000 ekin = 2.13119890669415 | erot = 2.28802336161955 | epot = -21.6714710604343 | etot = -17.2522487921206 +701000 ekin = 2.1501316931424 | erot = 2.18565847708908 | epot = -21.5488216255628 | etot = -17.2130314553313 +702000 ekin = 1.57482438035703 | erot = 1.99931097090509 | epot = -21.5047640382371 | etot = -17.930628686975 +703000 ekin = 2.08829522236785 | erot = 2.17557396869524 | epot = -21.5242713758433 | etot = -17.2604021847802 +704000 ekin = 2.82144699483839 | erot = 1.94479401958833 | epot = -21.5462466947694 | etot = -16.7800056803427 +705000 ekin = 2.81019786745821 | erot = 2.16662483548889 | epot = -21.497690476826 | etot = -16.5208677738789 +706000 ekin = 1.97639068263159 | erot = 2.31468002405233 | epot = -21.494117475981 | etot = -17.2030467692971 +707000 ekin = 1.90740387464487 | erot = 2.04436544372038 | epot = -21.5505486138141 | etot = -17.5987792954489 +708000 ekin = 2.4927128838246 | erot = 2.15829540621564 | epot = -21.5728746117359 | etot = -16.9218663216957 +709000 ekin = 2.89296518644075 | erot = 2.58120965850486 | epot = -21.6152997801578 | etot = -16.1411249352122 +710000 ekin = 2.18515172086139 | erot = 2.27924743097099 | epot = -21.5865916502444 | etot = -17.122192498412 +711000 ekin = 2.31589231212299 | erot = 1.401439259779 | epot = -21.6089597508522 | etot = -17.8916281789502 +712000 ekin = 2.55835611026778 | erot = 2.27281573655803 | epot = -21.7227687229585 | etot = -16.8915968761327 +713000 ekin = 1.95615391137192 | erot = 2.31806852238961 | epot = -21.8059432402922 | etot = -17.5317208065307 +714000 ekin = 2.56238583099812 | erot = 2.10850361056243 | epot = -21.8681675013086 | etot = -17.1972780597481 +715000 ekin = 2.4232111465345 | erot = 3.74023135295618 | epot = -21.8498336266088 | etot = -15.6863911271181 +716000 ekin = 2.83316600532177 | erot = 2.84850242081139 | epot = -21.7640231598546 | etot = -16.0823547337214 +717000 ekin = 3.45113934412559 | erot = 3.205984621772 | epot = -21.667790662391 | etot = -15.0106666964934 +718000 ekin = 3.10736232683018 | erot = 3.94031338601798 | epot = -21.5629179727886 | etot = -14.5152422599405 +719000 ekin = 2.38564322644681 | erot = 2.9508981175584 | epot = -21.5481188237003 | etot = -16.211577479695 +720000 ekin = 2.22543420991222 | erot = 3.14305432696275 | epot = -21.5381615962024 | etot = -16.1696730593274 +721000 ekin = 1.71709109813907 | erot = 2.2393943036399 | epot = -21.4645851946691 | etot = -17.5080997928901 +722000 ekin = 1.93213958129582 | erot = 2.81573218276728 | epot = -21.4896847080113 | etot = -16.7418129439482 +723000 ekin = 2.3814534534689 | erot = 2.55666957995949 | epot = -21.4374887927968 | etot = -16.4993657593684 +724000 ekin = 1.74740284448188 | erot = 2.45556175689041 | epot = -21.4125175551609 | etot = -17.2095529537886 +725000 ekin = 2.29233638352032 | erot = 2.9526701477774 | epot = -21.4751392844086 | etot = -16.2301327531109 +726000 ekin = 1.63503646092183 | erot = 2.30649262262118 | epot = -21.5156851039583 | etot = -17.5741560204153 +727000 ekin = 2.46705454176008 | erot = 3.19802987014479 | epot = -21.5382715508197 | etot = -15.8731871389148 +728000 ekin = 2.21709576272191 | erot = 2.16616227421247 | epot = -21.5244744557248 | etot = -17.1412164187904 +729000 ekin = 1.89396537247993 | erot = 1.66596987620968 | epot = -21.5644109232526 | etot = -18.004475674563 +730000 ekin = 1.78155182892059 | erot = 2.15399661961712 | epot = -21.5594738957829 | etot = -17.6239254472452 +731000 ekin = 2.16713092512296 | erot = 2.96875570154115 | epot = -21.4952326145865 | etot = -16.3593459879224 +732000 ekin = 2.40927355189018 | erot = 2.27189990077001 | epot = -21.3831563581627 | etot = -16.7019829055025 +733000 ekin = 3.04824198143783 | erot = 2.57289903054808 | epot = -21.429005165309 | etot = -15.8078641533231 +734000 ekin = 2.36703883022854 | erot = 2.04468815017472 | epot = -21.4926214065432 | etot = -17.0808944261399 +735000 ekin = 2.13292788677937 | erot = 1.55097035487249 | epot = -21.5455592190822 | etot = -17.8616609774303 +736000 ekin = 2.13562110082196 | erot = 3.45795834862289 | epot = -21.6515763333194 | etot = -16.0579968838746 +737000 ekin = 1.73550703692746 | erot = 3.58781244645386 | epot = -21.6785680654269 | etot = -16.3552485820456 +738000 ekin = 2.0113668076702 | erot = 2.50533140705365 | epot = -21.7068415263434 | etot = -17.1901433116196 +739000 ekin = 1.85122466968334 | erot = 2.19323904324284 | epot = -21.7211705032463 | etot = -17.6767067903201 +740000 ekin = 2.84677298867338 | erot = 2.79086338446698 | epot = -21.7460997683893 | etot = -16.108463395249 +741000 ekin = 2.47281769013275 | erot = 2.90867674862121 | epot = -21.8038806031312 | etot = -16.4223861643773 +742000 ekin = 2.74212748781964 | erot = 3.26601844940294 | epot = -21.9417105639309 | etot = -15.9335646267083 +743000 ekin = 2.23337436613032 | erot = 3.2075209993525 | epot = -22.0769938861091 | etot = -16.6360985206263 +744000 ekin = 2.0100758296396 | erot = 3.7920839882707 | epot = -22.1581491314472 | etot = -16.3559893135369 +745000 ekin = 3.14168435406401 | erot = 2.32756039064278 | epot = -22.155279170971 | etot = -16.6860344262642 +746000 ekin = 2.96147960587595 | erot = 2.6491977864153 | epot = -22.131657657659 | etot = -16.5209802653678 +747000 ekin = 2.31713973406909 | erot = 2.05388385027237 | epot = -22.1362115743712 | etot = -17.7651879900298 +748000 ekin = 2.36228107661837 | erot = 2.41530550223612 | epot = -22.1703943251347 | etot = -17.3928077462802 +749000 ekin = 2.07006713072585 | erot = 2.7743291960411 | epot = -22.1708421357978 | etot = -17.3264458090308 +750000 ekin = 1.65834656870048 | erot = 2.38415657369843 | epot = -22.2465520170919 | etot = -18.204048874693 +751000 ekin = 1.79302728344389 | erot = 2.82710216006102 | epot = -22.3488339479635 | etot = -17.7287045044586 +752000 ekin = 1.35555517803007 | erot = 1.4601978358921 | epot = -22.4342877547318 | etot = -19.6185347408097 +753000 ekin = 1.88586262445723 | erot = 2.44014879801272 | epot = -22.3837690917336 | etot = -18.0577576692637 +754000 ekin = 1.74745498380874 | erot = 2.73612011854202 | epot = -22.2852965474799 | etot = -17.8017214451291 +755000 ekin = 2.39590781949903 | erot = 2.41019902787153 | epot = -22.2066358684386 | etot = -17.400529021068 +756000 ekin = 1.83745653598817 | erot = 2.79024351605602 | epot = -22.133592240187 | etot = -17.5058921881428 +757000 ekin = 1.97281200687049 | erot = 2.57792722235947 | epot = -22.0604464398181 | etot = -17.5097072105881 +758000 ekin = 1.18945619136922 | erot = 2.72372183682493 | epot = -21.9899494795137 | etot = -18.0767714513196 +759000 ekin = 2.16230453116658 | erot = 1.39722896511083 | epot = -22.0003304659983 | etot = -18.4407969697209 +760000 ekin = 2.57253050230033 | erot = 2.33269711137816 | epot = -22.0357457302398 | etot = -17.1305181165613 +761000 ekin = 2.08545216810508 | erot = 2.24940559703297 | epot = -22.1132097744114 | etot = -17.7783520092733 +762000 ekin = 2.13509249172208 | erot = 1.66078369856518 | epot = -22.1380840935026 | etot = -18.3422079032154 +763000 ekin = 2.42851727622126 | erot = 3.36016749294485 | epot = -22.2079173436288 | etot = -16.4192325744626 +764000 ekin = 2.84703530894743 | erot = 2.79172375883346 | epot = -22.2143624032421 | etot = -16.5756033354612 +765000 ekin = 1.81325658345262 | erot = 2.77448180912351 | epot = -22.1194010453623 | etot = -17.5316626527862 +766000 ekin = 2.64831101430988 | erot = 2.31381649708591 | epot = -21.9919179324216 | etot = -17.0297904210258 +767000 ekin = 2.58949745571041 | erot = 2.86718473216887 | epot = -21.9087370669524 | etot = -16.4520548790732 +768000 ekin = 1.86313167956692 | erot = 2.78552244417216 | epot = -21.9381577980074 | etot = -17.2895036742683 +769000 ekin = 2.40162376419982 | erot = 2.31402374045874 | epot = -22.0373843590673 | etot = -17.3217368544087 +770000 ekin = 2.49146487205159 | erot = 3.23101926076329 | epot = -22.1439576198693 | etot = -16.4214734870544 +771000 ekin = 2.3322633774286 | erot = 2.27787220200643 | epot = -22.1812213688414 | etot = -17.5710857894063 +772000 ekin = 2.28990016215835 | erot = 2.99389364569334 | epot = -22.2765115340955 | etot = -16.9927177262438 +773000 ekin = 2.23002457595115 | erot = 1.82240115552767 | epot = -22.3379686916384 | etot = -18.2855429601596 +774000 ekin = 2.82350297312971 | erot = 2.21054815770296 | epot = -22.331524297742 | etot = -17.2974731669094 +775000 ekin = 1.82305982105504 | erot = 1.8710033654222 | epot = -22.2729891281483 | etot = -18.5789259416711 +776000 ekin = 1.39169167990076 | erot = 3.16027505319294 | epot = -22.2459295451277 | etot = -17.6939628120339 +777000 ekin = 1.6265637770548 | erot = 2.80881827044758 | epot = -22.1611617112313 | etot = -17.7257796637289 +778000 ekin = 1.49436478903863 | erot = 2.24161236856228 | epot = -22.1732646444852 | etot = -18.4372874868843 +779000 ekin = 1.88107404119766 | erot = 1.90732846459751 | epot = -22.2125828989309 | etot = -18.4241803931357 +780000 ekin = 1.70209634464212 | erot = 2.30515299210351 | epot = -22.2800747799125 | etot = -18.2728254431668 +781000 ekin = 2.12615575710868 | erot = 2.56065358398065 | epot = -22.3657963731658 | etot = -17.6789870320765 +782000 ekin = 2.60319344794517 | erot = 1.95716880667361 | epot = -22.278889588664 | etot = -17.7185273340452 +783000 ekin = 2.19489638548848 | erot = 2.9003350616753 | epot = -22.2004563501245 | etot = -17.1052249029607 +784000 ekin = 2.84914111009349 | erot = 2.24051018422877 | epot = -22.2093010900996 | etot = -17.1196497957773 +785000 ekin = 3.14240765153577 | erot = 2.92860772919915 | epot = -22.2500274240077 | etot = -16.1790120432728 +786000 ekin = 2.83372300736036 | erot = 3.44593690351847 | epot = -22.2923595270368 | etot = -16.0126996161579 +787000 ekin = 2.41074903520556 | erot = 3.01381650302091 | epot = -22.2329745868673 | etot = -16.8084090486409 +788000 ekin = 1.99557665602945 | erot = 2.01600225895996 | epot = -22.1996915458458 | etot = -18.1881126308564 +789000 ekin = 2.46258971641134 | erot = 2.27406771625315 | epot = -22.1314921413931 | etot = -17.3948347087286 +790000 ekin = 3.5794195002921 | erot = 2.82440864812442 | epot = -22.0691321886934 | etot = -15.6653040402769 +791000 ekin = 3.1240271028451 | erot = 2.42401718962738 | epot = -22.0808685046086 | etot = -16.5328242121361 +792000 ekin = 3.95429056548242 | erot = 1.97241939137156 | epot = -22.0156932891881 | etot = -16.0889833323341 +793000 ekin = 2.26828416500901 | erot = 2.58677202552917 | epot = -21.9219598803777 | etot = -17.0669036898395 +794000 ekin = 2.16106559150924 | erot = 2.4431093127412 | epot = -21.7619518452423 | etot = -17.1577769409919 +795000 ekin = 1.62519700428841 | erot = 2.41826691867446 | epot = -21.6012749849542 | etot = -17.5578110619913 +796000 ekin = 2.18377144801669 | erot = 2.13093440679002 | epot = -21.4820337714693 | etot = -17.1673279166626 +797000 ekin = 1.81427862345352 | erot = 1.99534051513422 | epot = -21.473919591557 | etot = -17.6643004529692 +798000 ekin = 2.22012195132989 | erot = 2.51363796316556 | epot = -21.5008270155092 | etot = -16.7670671010137 +799000 ekin = 1.88984581553594 | erot = 2.87047971528298 | epot = -21.4708608053325 | etot = -16.7105352745136 +800000 ekin = 2.14235800297793 | erot = 2.35196377273804 | epot = -21.3792596865245 | etot = -16.8849379108086 +801000 ekin = 1.84302686949433 | erot = 1.65480855802627 | epot = -21.2211741734437 | etot = -17.7233387459231 +802000 ekin = 2.20305615004887 | erot = 2.22355768328246 | epot = -21.1073599995259 | etot = -16.6807461661946 +803000 ekin = 2.64836814873033 | erot = 1.90761871804861 | epot = -21.0752041885471 | etot = -16.5192173217681 +804000 ekin = 2.34495845479317 | erot = 2.89112045330492 | epot = -21.0176734836814 | etot = -15.7815945755833 +805000 ekin = 1.79915640284781 | erot = 2.71685844764874 | epot = -20.8858433761952 | etot = -16.3698285256987 +806000 ekin = 1.74992507845556 | erot = 2.08517047523252 | epot = -20.8503301901419 | etot = -17.0152346364538 +807000 ekin = 1.57172452594495 | erot = 1.70422569898767 | epot = -20.9092333967052 | etot = -17.6332831717726 +808000 ekin = 2.08106901002531 | erot = 2.40367065218829 | epot = -20.9858691795981 | etot = -16.5011295173845 +809000 ekin = 2.61736488835992 | erot = 1.51251405170843 | epot = -20.9790910298502 | etot = -16.8492120897818 +810000 ekin = 3.07344763503492 | erot = 2.65428122600393 | epot = -20.896297890317 | etot = -15.1685690292781 +811000 ekin = 3.02889983101699 | erot = 3.61686315729188 | epot = -20.939661602879 | etot = -14.2938986145701 +812000 ekin = 2.13832655324419 | erot = 2.7919099294265 | epot = -21.0260005012597 | etot = -16.095764018589 +813000 ekin = 2.19077235410927 | erot = 3.16158040032407 | epot = -21.2169108164964 | etot = -15.864558062063 +814000 ekin = 1.70775111413747 | erot = 2.98436840501864 | epot = -21.308951189013 | etot = -16.6168316698569 +815000 ekin = 2.14630779714624 | erot = 2.27335416843265 | epot = -21.3099230783926 | etot = -16.8902611128137 +816000 ekin = 2.70331501775258 | erot = 1.53093796189123 | epot = -21.3384418834226 | etot = -17.1041889037787 +817000 ekin = 2.55738086811903 | erot = 2.58558173150041 | epot = -21.4691891608916 | etot = -16.3262265612721 +818000 ekin = 2.27829786328906 | erot = 2.260897256821 | epot = -21.5162183667694 | etot = -16.9770232466593 +819000 ekin = 2.10478260130361 | erot = 3.02380855832958 | epot = -21.5292309310153 | etot = -16.4006397713821 +820000 ekin = 2.50608188233135 | erot = 2.71783485224717 | epot = -21.5036816055507 | etot = -16.2797648709722 +821000 ekin = 2.62609848062628 | erot = 2.55164634943843 | epot = -21.4787661851639 | etot = -16.3010213550992 +822000 ekin = 3.63941681915299 | erot = 2.2024689491713 | epot = -21.4688230156577 | etot = -15.6269372473334 +823000 ekin = 3.58953515450024 | erot = 2.73556206545622 | epot = -21.4650227341942 | etot = -15.1399255142377 +824000 ekin = 4.11304720722591 | erot = 3.29174595135478 | epot = -21.4062011377905 | etot = -14.0014079792098 +825000 ekin = 2.90620097853795 | erot = 3.46409084826251 | epot = -21.2436944546109 | etot = -14.8734026278104 +826000 ekin = 1.7218843819517 | erot = 1.97028277378147 | epot = -21.0473904580338 | etot = -17.3552233023006 +827000 ekin = 1.9124069409458 | erot = 2.55760488338654 | epot = -20.9206700763424 | etot = -16.45065825201 +828000 ekin = 2.38145056979363 | erot = 2.55544957149179 | epot = -20.8204865756542 | etot = -15.8835864343688 +829000 ekin = 2.24733826946605 | erot = 1.78474837345225 | epot = -20.7084449579387 | etot = -16.6763583150204 +830000 ekin = 2.52795893691036 | erot = 2.3414672428271 | epot = -20.5883731027638 | etot = -15.7189469230263 +831000 ekin = 2.68310001004753 | erot = 2.07407005901147 | epot = -20.4364451382899 | etot = -15.6792750692309 +832000 ekin = 2.67323424264011 | erot = 2.02167788192501 | epot = -20.3691783993746 | etot = -15.6742662748095 +833000 ekin = 2.55071664949192 | erot = 2.59972899624768 | epot = -20.3036213925319 | etot = -15.1531757467923 +834000 ekin = 2.87089088359563 | erot = 2.32463192225235 | epot = -20.2984653371648 | etot = -15.1029425313168 +835000 ekin = 2.77558903596269 | erot = 2.73757154391998 | epot = -20.4022293845422 | etot = -14.8890688046595 +836000 ekin = 2.57713146919654 | erot = 2.85322310545494 | epot = -20.5403137141641 | etot = -15.1099591395126 +837000 ekin = 1.78075406754283 | erot = 1.97503243561096 | epot = -20.5889142070484 | etot = -16.8331277038946 +838000 ekin = 1.98032617531701 | erot = 2.79829467073938 | epot = -20.6049667376349 | etot = -15.8263458915785 +839000 ekin = 2.0003179521848 | erot = 2.70198331564816 | epot = -20.5921495833285 | etot = -15.8898483154956 +840000 ekin = 1.70031236242703 | erot = 2.95685689490569 | epot = -20.6678372916037 | etot = -16.010668034271 +841000 ekin = 2.77705100359314 | erot = 2.84742847205068 | epot = -20.7929304121764 | etot = -15.1684509365326 +842000 ekin = 2.54393458307436 | erot = 2.87172695192628 | epot = -20.8173418291016 | etot = -15.401680294101 +843000 ekin = 2.00273625390939 | erot = 2.63437491598434 | epot = -20.8053999188197 | etot = -16.168288748926 +844000 ekin = 1.52900749569349 | erot = 1.92882434140972 | epot = -20.8427655387949 | etot = -17.3849337016917 +845000 ekin = 2.27176799938834 | erot = 2.308436365406 | epot = -20.9384881501646 | etot = -16.3582837853702 +846000 ekin = 2.06718804989496 | erot = 2.33108662324979 | epot = -21.0085032159671 | etot = -16.6102285428223 +847000 ekin = 2.457310325364 | erot = 2.64112097293887 | epot = -20.9624761048838 | etot = -15.8640448065809 +848000 ekin = 2.13894899278459 | erot = 1.46487099434192 | epot = -20.9909626022984 | etot = -17.3871426151719 +849000 ekin = 2.0007946308419 | erot = 2.48568109050423 | epot = -20.9995492646628 | etot = -16.5130735433167 +850000 ekin = 2.54186297995285 | erot = 2.66929613872207 | epot = -20.9906717645298 | etot = -15.7795126458549 +851000 ekin = 2.16443404123472 | erot = 2.92830981454153 | epot = -20.9932718794597 | etot = -15.9005280236835 +852000 ekin = 2.48255398040851 | erot = 2.46238001266594 | epot = -21.018749118108 | etot = -16.0738151250335 +853000 ekin = 2.4154146701692 | erot = 2.97520224443384 | epot = -20.9598722543997 | etot = -15.5692553397967 +854000 ekin = 2.35150751079562 | erot = 2.85453387569364 | epot = -20.8693696367608 | etot = -15.6633282502715 +855000 ekin = 2.36749640703667 | erot = 2.06753408358231 | epot = -20.8980197782033 | etot = -16.4629892875844 +856000 ekin = 2.52164598863741 | erot = 2.75265020302048 | epot = -20.800830948998 | etot = -15.5265347573401 +857000 ekin = 2.55862872070476 | erot = 3.03030828592915 | epot = -20.6910887919773 | etot = -15.1021517853434 +858000 ekin = 3.12628251408762 | erot = 2.14554604261068 | epot = -20.6394579492303 | etot = -15.367629392532 +859000 ekin = 2.91259413572112 | erot = 2.23773675238282 | epot = -20.6611486479508 | etot = -15.5108177598468 +860000 ekin = 2.88318377110752 | erot = 1.51972062646443 | epot = -20.6828066069552 | etot = -16.2799022093832 +861000 ekin = 2.33529167415754 | erot = 2.8511661779126 | epot = -20.6796212139896 | etot = -15.4931633619195 +862000 ekin = 3.06091745354043 | erot = 1.86960550588563 | epot = -20.7257485328209 | etot = -15.7952255733948 +863000 ekin = 2.88295223464283 | erot = 1.77743902656173 | epot = -20.8340328987095 | etot = -16.1736416375049 +864000 ekin = 2.95602292127632 | erot = 2.65056410715308 | epot = -21.0162954561449 | etot = -15.4097084277155 +865000 ekin = 3.3172549369506 | erot = 2.24347319046513 | epot = -21.1441095096618 | etot = -15.583381382246 +866000 ekin = 2.8446879555804 | erot = 3.16802464112884 | epot = -21.2275167371631 | etot = -15.2148041404539 +867000 ekin = 2.74149808612436 | erot = 3.09628634794253 | epot = -21.2140642048228 | etot = -15.3762797707559 +868000 ekin = 2.1914148486481 | erot = 2.23765996064103 | epot = -21.1661691183493 | etot = -16.7370943090602 +869000 ekin = 2.92726848075923 | erot = 2.49663936074754 | epot = -21.1109612585255 | etot = -15.6870534170188 +870000 ekin = 2.47986538741064 | erot = 2.11907230969516 | epot = -21.0900293946684 | etot = -16.4910916975626 +871000 ekin = 2.18342640526418 | erot = 2.37474045896627 | epot = -20.9804914418025 | etot = -16.422324577572 +872000 ekin = 1.52873571215978 | erot = 2.08908078804673 | epot = -20.9343176993391 | etot = -17.3165011991326 +873000 ekin = 1.39281578471524 | erot = 2.29034780878958 | epot = -21.0007866828842 | etot = -17.3176230893794 +874000 ekin = 1.40786554880768 | erot = 2.7700797003235 | epot = -21.1600842742429 | etot = -16.9821390251117 +875000 ekin = 1.18320018517441 | erot = 2.73058842883511 | epot = -21.2959059488291 | etot = -17.3821173348196 +876000 ekin = 1.8300189393038 | erot = 2.99586941144886 | epot = -21.3298635968752 | etot = -16.5039752461226 +877000 ekin = 2.38032906471076 | erot = 2.03722695211226 | epot = -21.415279075283 | etot = -16.99772305846 +878000 ekin = 2.12938516841269 | erot = 1.75666654131942 | epot = -21.412657760354 | etot = -17.5266060506219 +879000 ekin = 2.23837299177367 | erot = 2.71307243504656 | epot = -21.4006541150457 | etot = -16.4492086882254 +880000 ekin = 2.68032631557358 | erot = 2.78439945590096 | epot = -21.4462782448912 | etot = -15.9815524734167 +881000 ekin = 2.86810525851389 | erot = 2.35959915589953 | epot = -21.4314549447334 | etot = -16.20375053032 +882000 ekin = 2.33172283615115 | erot = 2.17176020371465 | epot = -21.369535469283 | etot = -16.8660524294172 +883000 ekin = 2.36331150998289 | erot = 1.97634374053965 | epot = -21.1748990104138 | etot = -16.8352437598913 +884000 ekin = 2.53782271833829 | erot = 2.25243670168426 | epot = -21.0795767771653 | etot = -16.2893173571427 +885000 ekin = 2.86057103069744 | erot = 2.27462544190307 | epot = -21.0782171958266 | etot = -15.9430207232261 +886000 ekin = 3.17034195996096 | erot = 1.74832646729411 | epot = -21.1280719510453 | etot = -16.2094035237903 +887000 ekin = 2.66023408534638 | erot = 2.49426802108018 | epot = -21.1909579488462 | etot = -16.0364558424197 +888000 ekin = 2.14156056158803 | erot = 2.83065920295554 | epot = -21.2749898508176 | etot = -16.302770086274 +889000 ekin = 2.13776380125426 | erot = 2.19994227158627 | epot = -21.1902576201104 | etot = -16.8525515472698 +890000 ekin = 1.76446650263826 | erot = 2.97354753014624 | epot = -21.2518724314555 | etot = -16.513858398671 +891000 ekin = 1.64433607192947 | erot = 2.28044235221046 | epot = -21.375947191058 | etot = -17.4511687669181 +892000 ekin = 1.97381907006142 | erot = 2.35969977765342 | epot = -21.5200869372681 | etot = -17.1865680895533 +893000 ekin = 1.77998159671209 | erot = 1.83959134574388 | epot = -21.5960425863495 | etot = -17.9764696438935 +894000 ekin = 2.8098996128374 | erot = 2.80337844303784 | epot = -21.6896955865519 | etot = -16.0764175306767 +895000 ekin = 2.03570642281182 | erot = 2.73641442629083 | epot = -21.77632807541 | etot = -17.0042072263074 +896000 ekin = 1.6670401968188 | erot = 2.55842313387756 | epot = -21.9079691828366 | etot = -17.6825058521402 +897000 ekin = 1.79364820755772 | erot = 2.35937074837062 | epot = -22.0466195733302 | etot = -17.8936006174018 +898000 ekin = 1.8410334890959 | erot = 2.41596980112091 | epot = -22.0792153246985 | etot = -17.8222120344817 +899000 ekin = 1.6644807831865 | erot = 3.06295573986189 | epot = -22.0050930291629 | etot = -17.2776565061145 +900000 ekin = 2.15301263014261 | erot = 2.62503812958041 | epot = -21.9769631774149 | etot = -17.1989124176919 +901000 ekin = 2.4332352507602 | erot = 2.69661561775584 | epot = -22.0455467285607 | etot = -16.9156958600446 +902000 ekin = 2.57983518470479 | erot = 2.40634661051273 | epot = -22.0504126836938 | etot = -17.0642308884763 +903000 ekin = 2.38804084084237 | erot = 2.40369143268286 | epot = -22.0548572254259 | etot = -17.2631249519006 +904000 ekin = 1.9975679938241 | erot = 3.15736733739655 | epot = -22.0783783499621 | etot = -16.9234430187414 +905000 ekin = 2.28042135995783 | erot = 2.20746001153526 | epot = -22.092475444409 | etot = -17.6045940729159 +906000 ekin = 2.49914497220397 | erot = 1.67106173041058 | epot = -22.064929274197 | etot = -17.8947225715825 +907000 ekin = 2.34170753461351 | erot = 2.16830189815579 | epot = -21.9182395193391 | etot = -17.4082300865698 +908000 ekin = 2.83101675354561 | erot = 2.39226452568029 | epot = -21.9393923471478 | etot = -16.7161110679219 +909000 ekin = 3.13519044247879 | erot = 2.07053636961477 | epot = -22.044039894957 | etot = -16.8383130828635 +910000 ekin = 2.91492350277448 | erot = 3.54269221448406 | epot = -22.1774209001616 | etot = -15.7198051829031 +911000 ekin = 1.86299522014884 | erot = 2.75425299355676 | epot = -22.2318842654016 | etot = -17.614636051696 +912000 ekin = 2.64270620869814 | erot = 1.86916034984856 | epot = -22.2816929482531 | etot = -17.7698263897064 +913000 ekin = 2.45835259040075 | erot = 2.03343540339216 | epot = -22.4051980318983 | etot = -17.9134100381054 +914000 ekin = 2.01630257583654 | erot = 3.01931541129968 | epot = -22.505580829989 | etot = -17.4699628428528 +915000 ekin = 2.73550820750709 | erot = 2.14051989379167 | epot = -22.5067223019054 | etot = -17.6306942006067 +916000 ekin = 2.38833694849903 | erot = 3.26236542376324 | epot = -22.5299732656691 | etot = -16.8792708934068 +917000 ekin = 2.21211072529668 | erot = 2.24425221182157 | epot = -22.5175498112378 | etot = -18.0611868741195 +918000 ekin = 2.11721632678553 | erot = 2.05681940825278 | epot = -22.4485798442658 | etot = -18.2745441092275 +919000 ekin = 2.6606540164524 | erot = 2.41853759346261 | epot = -22.4819256778216 | etot = -17.4027340679066 +920000 ekin = 3.26471044916532 | erot = 2.75531911342507 | epot = -22.5858600689149 | etot = -16.5658305063245 +921000 ekin = 2.72028388628926 | erot = 1.96960596371279 | epot = -22.639440275186 | etot = -17.949550425184 +922000 ekin = 1.43428549123066 | erot = 1.52428475569853 | epot = -22.6914991306332 | etot = -19.732928883704 +923000 ekin = 1.67603986848274 | erot = 1.86522020655461 | epot = -22.7510571233686 | etot = -19.2097970483312 +924000 ekin = 2.15000311118185 | erot = 1.53327070095754 | epot = -22.722341324193 | etot = -19.0390675120536 +925000 ekin = 2.27769316315993 | erot = 1.35582914777291 | epot = -22.6317669747038 | etot = -18.9982446637709 +926000 ekin = 2.00370753803371 | erot = 2.07123237010035 | epot = -22.5811533157097 | etot = -18.5062134075756 +927000 ekin = 2.51631428248841 | erot = 1.98711239136866 | epot = -22.6957752134474 | etot = -18.1923485395903 +928000 ekin = 2.57502157703452 | erot = 2.51449316644154 | epot = -22.8486668477058 | etot = -17.7591521042298 +929000 ekin = 2.66015175923782 | erot = 1.82991995656989 | epot = -22.8894816710891 | etot = -18.3994099552814 +930000 ekin = 2.41758548277495 | erot = 2.00977019739401 | epot = -22.9023129289068 | etot = -18.4749572487379 +931000 ekin = 3.01936517399357 | erot = 2.11115283295648 | epot = -22.8598478032752 | etot = -17.7293297963251 +932000 ekin = 2.34904883629147 | erot = 1.8713492953404 | epot = -22.900230384769 | etot = -18.6798322531371 +933000 ekin = 2.16775611540091 | erot = 2.8379626481367 | epot = -22.9075292968864 | etot = -17.9018105333488 +934000 ekin = 2.17428610858913 | erot = 2.118912762995 | epot = -22.9275911153101 | etot = -18.634392243726 +935000 ekin = 2.35380058127246 | erot = 2.22719757040087 | epot = -22.9178791070039 | etot = -18.3368809553305 +936000 ekin = 2.29398857252167 | erot = 2.52122883801966 | epot = -23.0254587453495 | etot = -18.2102413348082 +937000 ekin = 2.32405492839276 | erot = 2.82571975062451 | epot = -23.1134869099966 | etot = -17.9637122309793 +938000 ekin = 2.46190818228192 | erot = 1.99586541720566 | epot = -23.1690855883853 | etot = -18.7113119888977 +939000 ekin = 2.99494633358445 | erot = 2.11200579979089 | epot = -23.1621265982256 | etot = -18.0551744648502 +940000 ekin = 3.76773061527755 | erot = 2.67954167018355 | epot = -23.1020260319689 | etot = -16.6547537465078 +941000 ekin = 3.15108874053801 | erot = 2.26610050109567 | epot = -23.0042404655516 | etot = -17.587051223918 +942000 ekin = 3.50311245643908 | erot = 1.88373602143018 | epot = -22.9671180112669 | etot = -17.5802695333976 +943000 ekin = 3.82043792465856 | erot = 2.71285823250349 | epot = -22.9404059827705 | etot = -16.4071098256084 +944000 ekin = 2.68278476017665 | erot = 2.75585489458162 | epot = -22.919058077481 | etot = -17.4804184227228 +945000 ekin = 2.55880828345199 | erot = 2.02741981318915 | epot = -22.8232630911494 | etot = -18.2370349945083 +946000 ekin = 2.47548691870273 | erot = 1.66864059361738 | epot = -22.6586979544826 | etot = -18.5145704421625 +947000 ekin = 2.41867478100658 | erot = 1.99274780926995 | epot = -22.5542133657 | etot = -18.1427907754235 +948000 ekin = 3.54970439277898 | erot = 2.57756240201335 | epot = -22.4104376157296 | etot = -16.2831708209373 +949000 ekin = 2.9858997616607 | erot = 2.44208964275301 | epot = -22.197141123001 | etot = -16.7691517185873 +950000 ekin = 1.82147308870195 | erot = 3.0508389937934 | epot = -22.0435130221227 | etot = -17.1712009396273 +951000 ekin = 2.20031505253436 | erot = 2.38004890424645 | epot = -22.0174402075992 | etot = -17.4370762508184 +952000 ekin = 2.14165422682636 | erot = 1.67045420750587 | epot = -21.9875031647927 | etot = -18.1753947304605 +953000 ekin = 2.29833469428311 | erot = 1.97349532600851 | epot = -21.9532851584681 | etot = -17.6814551381765 +954000 ekin = 1.48835290094507 | erot = 3.35692451991829 | epot = -21.8812774176255 | etot = -17.0359999967621 +955000 ekin = 1.87513794155826 | erot = 2.65898918540887 | epot = -21.7919528937349 | etot = -17.2578257667677 +956000 ekin = 1.6947359470094 | erot = 2.15427252360414 | epot = -21.7268035908356 | etot = -17.8777951202221 +957000 ekin = 1.75579814865835 | erot = 1.63901039608815 | epot = -21.7007270322021 | etot = -18.3059184874556 +958000 ekin = 1.59869777656518 | erot = 2.20104985114388 | epot = -21.7023937250484 | etot = -17.9026460973393 +959000 ekin = 2.58438881562724 | erot = 2.4897790743314 | epot = -21.7153511733982 | etot = -16.6411832834396 +960000 ekin = 2.53916903929276 | erot = 2.05995138561216 | epot = -21.7134163297425 | etot = -17.1142959048376 +961000 ekin = 2.28282707786747 | erot = 2.18347157951505 | epot = -21.7152390799839 | etot = -17.2489404226014 +962000 ekin = 1.65520100959905 | erot = 3.51416445242779 | epot = -21.7329558565077 | etot = -16.5635903944808 +963000 ekin = 1.99568689924178 | erot = 1.50126173817714 | epot = -21.6847527677603 | etot = -18.1878041303414 +964000 ekin = 2.18616111169191 | erot = 2.27601428306194 | epot = -21.6212716735791 | etot = -17.1590962788252 +965000 ekin = 2.12688674785305 | erot = 2.31141713690626 | epot = -21.6018715374843 | etot = -17.163567652725 +966000 ekin = 3.18043989665769 | erot = 3.42455452205087 | epot = -21.638305203769 | etot = -15.0333107850605 +967000 ekin = 3.07300409154253 | erot = 2.17511749698305 | epot = -21.5951488445701 | etot = -16.3470272560445 +968000 ekin = 2.0866315065553 | erot = 2.13997027735021 | epot = -21.5232721871232 | etot = -17.2966704032177 +969000 ekin = 2.26951411936363 | erot = 2.21822796004343 | epot = -21.4611553284776 | etot = -16.9734132490706 +970000 ekin = 2.49167396599781 | erot = 2.62083774678041 | epot = -21.4077353682587 | etot = -16.2952236554805 +971000 ekin = 2.497450596106 | erot = 2.64553775005008 | epot = -21.3712924820093 | etot = -16.2283041358532 +972000 ekin = 3.2069302084461 | erot = 2.47011294488449 | epot = -21.3144344371103 | etot = -15.6373912837797 +973000 ekin = 3.3593544808794 | erot = 2.62917582888826 | epot = -21.2433830591838 | etot = -15.2548527494161 +974000 ekin = 2.71069552226069 | erot = 2.13944446989065 | epot = -21.140426885518 | etot = -16.2902868933666 +975000 ekin = 1.81165819781674 | erot = 2.10218924092724 | epot = -21.0499905566304 | etot = -17.1361431178865 +976000 ekin = 2.36984742020937 | erot = 1.38488988265326 | epot = -20.9803229653516 | etot = -17.225585662489 +977000 ekin = 2.83728662155799 | erot = 3.02976542728587 | epot = -21.086860961914 | etot = -15.2198089130702 +978000 ekin = 3.14169266917129 | erot = 3.02799812032624 | epot = -21.1408187166748 | etot = -14.9711279271773 +979000 ekin = 3.63725915757345 | erot = 2.47075910077981 | epot = -21.0348329782418 | etot = -14.9268147198886 +980000 ekin = 3.42622785415584 | erot = 3.24164435781271 | epot = -20.9604411583363 | etot = -14.2925689463678 +981000 ekin = 2.9282364939793 | erot = 2.44516658563951 | epot = -20.9993890158381 | etot = -15.6259859362193 +982000 ekin = 2.04558911070081 | erot = 2.21302288881361 | epot = -21.0172581853275 | etot = -16.7586461858131 +983000 ekin = 2.56053983213182 | erot = 1.98406283304106 | epot = -21.0054554868711 | etot = -16.4608528216982 +984000 ekin = 2.31455025377678 | erot = 2.58584391470351 | epot = -21.05287489473 | etot = -16.1524807262497 +985000 ekin = 2.31703817263369 | erot = 2.99965025262552 | epot = -21.1270579315131 | etot = -15.8103695062539 +986000 ekin = 2.05103854432386 | erot = 2.1535155091137 | epot = -21.2182405597612 | etot = -17.0136865063237 +987000 ekin = 2.41899263793244 | erot = 1.58416150281502 | epot = -21.1906087726859 | etot = -17.1874546319385 +988000 ekin = 2.75135283132847 | erot = 2.70498731016256 | epot = -21.0902697836801 | etot = -15.633929642189 +989000 ekin = 2.29408577956131 | erot = 2.85656205344492 | epot = -21.0178170251466 | etot = -15.8671691921404 +990000 ekin = 2.23414139649767 | erot = 2.58987928207188 | epot = -20.9412338597722 | etot = -16.1172131812026 +991000 ekin = 2.20140095465642 | erot = 2.53421928109186 | epot = -20.8284298905317 | etot = -16.0928096547835 +992000 ekin = 1.73516341340694 | erot = 2.49726908126816 | epot = -20.8981414535471 | etot = -16.665708958872 +993000 ekin = 1.38883779880923 | erot = 1.96818984395136 | epot = -20.9939445972527 | etot = -17.6369169544921 +994000 ekin = 1.48978908674571 | erot = 2.95636513336702 | epot = -21.0608370227912 | etot = -16.6146828026784 +995000 ekin = 2.31404204513712 | erot = 1.67482961392506 | epot = -21.1264761824826 | etot = -17.1376045234204 +996000 ekin = 2.8977650484701 | erot = 2.85063328331353 | epot = -21.0879631716189 | etot = -15.3395648398353 +997000 ekin = 3.12980664910276 | erot = 2.14994147346884 | epot = -21.0789162715404 | etot = -15.7991681489688 +998000 ekin = 2.21592279552962 | erot = 3.03017611615785 | epot = -20.9989402817529 | etot = -15.7528413700655 +999000 ekin = 2.60947995309596 | erot = 1.73829419308786 | epot = -20.9136108602424 | etot = -16.5658367140585 +1000000 ekin = 2.32269547490306 | erot = 2.87794942105205 | epot = -20.9071852604882 | etot = -15.7065403645331 + 1000000 0.10323091 -1.356822 0.050122912 -1.1615306 0.00013791576 +Loop time of 36.2166 on 4 procs for 1000000 steps with 16 atoms + +Performance: 23856.477 tau/day, 27611.663 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.54933 | 13.254 | 25.208 | 308.0 | 36.60 +Bond | 0.08723 | 0.416 | 0.70003 | 44.1 | 1.15 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.659 | 2.7239 | 2.7669 | 2.4 | 7.52 +Output | 1.4e-05 | 2.25e-05 | 2.6e-05 | 0.0 | 0.00 +Modify | 0.22084 | 2.7927 | 5.3062 | 134.0 | 7.71 +Other | | 17.03 | | | 47.02 + +Nlocal: 4 ave 8 max 0 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 10 ave 12 max 8 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 39.75 ave 77 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 159 +Ave neighs/atom = 9.9375 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:36 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 deleted file mode 100644 index 29eaec2dab72c68f9224d2d17f1bfb69ea038e37..0000000000000000000000000000000000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.1 +++ /dev/null @@ -1,1167 +0,0 @@ -LAMMPS (18 Jun 2019) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000135 secs - read_data CPU = 0.002118 secs - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 -1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287 -2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165 -3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165 -4000 ekin = 2.04461800191989 | erot = 1.49015219763161 | epot = -24.2959428773347 | etot = -20.7611726777832 -5000 ekin = 1.76794859210155 | erot = 2.54289684465819 | epot = -24.2337587736863 | etot = -19.9229133369266 -6000 ekin = 3.1106424806079 | erot = 2.04409805200893 | epot = -24.1585729744133 | etot = -19.0038324417964 -7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107 -8000 ekin = 2.82489935901743 | erot = 2.66790555575695 | epot = -24.0194805097633 | etot = -18.526675594989 -9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972 -10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334 -11000 ekin = 2.33860420545645 | erot = 2.067780391377 | epot = -23.6589739475584 | etot = -19.2525893507249 -12000 ekin = 2.71377849618258 | erot = 2.08757199120023 | epot = -23.5483571834756 | etot = -18.7470066960928 -13000 ekin = 2.62930153930326 | erot = 2.36926332727578 | epot = -23.4509629615768 | etot = -18.4523980949977 -14000 ekin = 3.08200416316113 | erot = 2.52340746291244 | epot = -23.3378147651053 | etot = -17.7324031390317 -15000 ekin = 2.98008664779269 | erot = 1.871644860882 | epot = -23.1940665570191 | etot = -18.3423350483444 -16000 ekin = 2.18422481774796 | erot = 2.13029325858584 | epot = -23.0709946755646 | etot = -18.7564765992308 -17000 ekin = 1.86029951221073 | erot = 2.30856215831156 | epot = -22.9148241979648 | etot = -18.7459625274425 -18000 ekin = 2.26757205264074 | erot = 1.23282183419698 | epot = -22.7667657090377 | etot = -19.2663718222 -19000 ekin = 2.39717301992408 | erot = 2.43814713185077 | epot = -22.6249045514987 | etot = -17.7895843997239 -20000 ekin = 2.4972090427325 | erot = 2.14695469209109 | epot = -22.4687873897505 | etot = -17.824623654927 -21000 ekin = 2.97591775854817 | erot = 2.40996811711195 | epot = -22.580475447988 | etot = -17.1945895723278 -22000 ekin = 3.04727168578733 | erot = 1.83825256427932 | epot = -22.6695853833015 | etot = -17.7840611332348 -23000 ekin = 2.64835731773193 | erot = 2.22162785501705 | epot = -22.6565689169972 | etot = -17.7865837442483 -24000 ekin = 2.64866576787001 | erot = 2.80157082833922 | epot = -22.6222797420052 | etot = -17.172043145796 -25000 ekin = 2.29527970143855 | erot = 2.22049811939069 | epot = -22.6228421013006 | etot = -18.1070642804714 -26000 ekin = 1.6242512251805 | erot = 2.52390475262917 | epot = -22.6746055892862 | etot = -18.5264496114765 -27000 ekin = 1.74746467550781 | erot = 3.7138606202505 | epot = -22.7150312690973 | etot = -17.253705973339 -28000 ekin = 2.26500128280479 | erot = 2.34791343563183 | epot = -22.7926648585827 | etot = -18.179750140146 -29000 ekin = 2.04774074424512 | erot = 1.86347261547111 | epot = -22.8081204933408 | etot = -18.8969071336246 -30000 ekin = 2.41140146125466 | erot = 1.86296915421469 | epot = -22.7764612164305 | etot = -18.5020906009612 -31000 ekin = 2.76447800297261 | erot = 2.7393253404681 | epot = -22.7808698156252 | etot = -17.2770664721845 -32000 ekin = 2.08103539953574 | erot = 2.81216171106146 | epot = -22.8081908465747 | etot = -17.9149937359775 -33000 ekin = 2.08672340074227 | erot = 3.65510023442519 | epot = -22.7575363468642 | etot = -17.0157127116967 -34000 ekin = 2.34180742039869 | erot = 3.10027175201874 | epot = -22.6657421559553 | etot = -17.2236629835378 -35000 ekin = 2.32430602395272 | erot = 2.01607522370048 | epot = -22.5813705492547 | etot = -18.2409893016015 -36000 ekin = 1.91917507775106 | erot = 1.97289747304336 | epot = -22.481118994336 | etot = -18.5890464435416 -37000 ekin = 1.57560528527468 | erot = 2.63029511887642 | epot = -22.4456699464305 | etot = -18.2397695422794 -38000 ekin = 2.20652731867584 | erot = 2.89671984141264 | epot = -22.3965902387972 | etot = -17.2933430787087 -39000 ekin = 2.54765822667968 | erot = 2.47352619735437 | epot = -22.3525131983352 | etot = -17.3313287743012 -40000 ekin = 2.24172560748699 | erot = 1.87314319107769 | epot = -22.3791956830638 | etot = -18.2643268844991 -41000 ekin = 2.45176361826215 | erot = 2.49992612251747 | epot = -22.4441192111887 | etot = -17.492429470409 -42000 ekin = 2.68254780786499 | erot = 2.04382131696989 | epot = -22.4352265851614 | etot = -17.7088574603266 -43000 ekin = 2.39383336858508 | erot = 1.66587291396325 | epot = -22.4337243898148 | etot = -18.3740181072664 -44000 ekin = 2.30758870966958 | erot = 2.39381816537748 | epot = -22.4636201484766 | etot = -17.7622132734295 -45000 ekin = 1.84308929771583 | erot = 2.25880380151546 | epot = -22.5697712917435 | etot = -18.4678781925122 -46000 ekin = 1.98608215049724 | erot = 3.02136983211363 | epot = -22.5606085774834 | etot = -17.5531565948725 -47000 ekin = 1.31457586857024 | erot = 1.99780932836913 | epot = -22.5522289127255 | etot = -19.2398437157862 -48000 ekin = 2.59855199680394 | erot = 1.90772345027383 | epot = -22.5972680906756 | etot = -18.0909926435978 -49000 ekin = 2.32140483916261 | erot = 2.72932938830521 | epot = -22.6070371995253 | etot = -17.5563029720575 -50000 ekin = 2.48248035385828 | erot = 3.42713570109107 | epot = -22.5294064222472 | etot = -16.6197903672979 -51000 ekin = 2.73677705777971 | erot = 1.43285265191038 | epot = -22.4272695862992 | etot = -18.2576398766091 -52000 ekin = 3.03746109762767 | erot = 1.97878223690383 | epot = -22.4105817052324 | etot = -17.3943383707009 -53000 ekin = 2.4689045601064 | erot = 4.26434186327668 | epot = -22.4059567857723 | etot = -15.6727103623892 -54000 ekin = 2.48025904071626 | erot = 2.36957879662632 | epot = -22.4049729842648 | etot = -17.5551351469222 -55000 ekin = 2.28269445417385 | erot = 1.92149293107792 | epot = -22.4643082993723 | etot = -18.2601209141205 -56000 ekin = 2.36225428889468 | erot = 2.21818002425493 | epot = -22.5516502452859 | etot = -17.9712159321363 -57000 ekin = 2.5222034650231 | erot = 2.87044520913643 | epot = -22.6517599833465 | etot = -17.259111309187 -58000 ekin = 2.50677816066749 | erot = 2.80087142998998 | epot = -22.7046490897181 | etot = -17.3969994990606 -59000 ekin = 2.7442153349817 | erot = 2.17375311266844 | epot = -22.7630968852437 | etot = -17.8451284375935 -60000 ekin = 3.28881699963202 | erot = 1.98491245229834 | epot = -22.7493813857704 | etot = -17.47565193384 -61000 ekin = 2.42749732003947 | erot = 1.80500042748845 | epot = -22.6954080097403 | etot = -18.4629102622124 -62000 ekin = 2.82051548232979 | erot = 1.69220614985812 | epot = -22.5840860651657 | etot = -18.0713644329778 -63000 ekin = 3.66818847100113 | erot = 1.91510536540651 | epot = -22.4235299160084 | etot = -16.8402360796008 -64000 ekin = 3.60192162647095 | erot = 3.02302140162941 | epot = -22.4028966408394 | etot = -15.777953612739 -65000 ekin = 3.37797300912952 | erot = 3.90646944425564 | epot = -22.3508227873685 | etot = -15.0663803339833 -66000 ekin = 2.90796062513305 | erot = 2.46538835419998 | epot = -22.2656130116827 | etot = -16.8922640323497 -67000 ekin = 2.57641483706472 | erot = 2.1063925708314 | epot = -22.1586423836372 | etot = -17.4758349757411 -68000 ekin = 2.5516902727465 | erot = 2.46870040285813 | epot = -22.1454741588102 | etot = -17.1250834832056 -69000 ekin = 2.42897294997603 | erot = 2.86774435615082 | epot = -22.1788582092806 | etot = -16.8821409031537 -70000 ekin = 3.08406596014674 | erot = 2.51171720098584 | epot = -22.2680651617951 | etot = -16.6722820006626 -71000 ekin = 2.55052721315253 | erot = 2.49486492124423 | epot = -22.3940848075589 | etot = -17.3486926731621 -72000 ekin = 1.77666138705941 | erot = 2.52301579845699 | epot = -22.4956655989824 | etot = -18.195988413466 -73000 ekin = 1.86857924146303 | erot = 2.33110810852355 | epot = -22.5401005215029 | etot = -18.3404131715163 -74000 ekin = 3.14875320805144 | erot = 2.12002807961601 | epot = -22.5354282257998 | etot = -17.2666469381323 -75000 ekin = 2.60566180511119 | erot = 2.16421143606062 | epot = -22.5109742574449 | etot = -17.7411010162731 -76000 ekin = 1.94500512300058 | erot = 1.94681992806367 | epot = -22.5134561384461 | etot = -18.6216310873819 -77000 ekin = 2.09005510206219 | erot = 2.13354294429721 | epot = -22.5157248384152 | etot = -18.2921267920558 -78000 ekin = 2.48381695181472 | erot = 2.49598603867482 | epot = -22.449809286019 | etot = -17.4700062955295 -79000 ekin = 3.09582217320064 | erot = 2.46630074007712 | epot = -22.3464652405845 | etot = -16.7843423273068 -80000 ekin = 2.51380629427529 | erot = 1.89207626467031 | epot = -22.2775752521275 | etot = -17.8716926931819 -81000 ekin = 2.32322780911516 | erot = 2.24954513249787 | epot = -22.2655235360186 | etot = -17.6927505944055 -82000 ekin = 1.54779729878415 | erot = 2.01487148845307 | epot = -22.2126473128098 | etot = -18.6499785255726 -83000 ekin = 2.24267653112482 | erot = 3.34721522119025 | epot = -22.2063282117648 | etot = -16.6164364594498 -84000 ekin = 2.86948852339533 | erot = 2.11915315181827 | epot = -22.2055386975617 | etot = -17.2168970223481 -85000 ekin = 3.13802387827786 | erot = 2.93900498543376 | epot = -22.2240733080824 | etot = -16.1470444443708 -86000 ekin = 3.46160079449538 | erot = 2.80798287444336 | epot = -22.2732645073155 | etot = -16.0036808383767 -87000 ekin = 3.63139446909085 | erot = 2.3166794204513 | epot = -22.2567856660101 | etot = -16.308711776468 -88000 ekin = 3.15348314879937 | erot = 2.2785763709033 | epot = -22.2154422326699 | etot = -16.7833827129672 -89000 ekin = 3.30271147105659 | erot = 1.80791256125564 | epot = -22.1564153597823 | etot = -17.04579132747 -90000 ekin = 2.42655906518194 | erot = 2.24507038389518 | epot = -21.9481188512569 | etot = -17.2764894021798 -91000 ekin = 1.89051217909395 | erot = 2.51049066719493 | epot = -21.7877769537306 | etot = -17.3867741074417 -92000 ekin = 2.07833668466679 | erot = 2.218324246302 | epot = -21.6997103074282 | etot = -17.4030493764594 -93000 ekin = 1.94321435585196 | erot = 2.99473985773914 | epot = -21.6748650469777 | etot = -16.7369108333866 -94000 ekin = 2.07878576812463 | erot = 3.37631892101902 | epot = -21.7659932416399 | etot = -16.3108885524963 -95000 ekin = 2.10517721407769 | erot = 2.08345895044788 | epot = -21.8951718799354 | etot = -17.7065357154098 -96000 ekin = 2.68821593238919 | erot = 1.86988637992409 | epot = -21.9622848400866 | etot = -17.4041825277733 -97000 ekin = 1.95061152706206 | erot = 2.81054215683073 | epot = -22.0229813258884 | etot = -17.2618276419957 -98000 ekin = 1.98463063611221 | erot = 2.05732763357977 | epot = -22.0930102039112 | etot = -18.0510519342192 -99000 ekin = 2.51292852217217 | erot = 3.54194472638845 | epot = -22.199088757298 | etot = -16.1442155087374 -100000 ekin = 1.8757570387949 | erot = 2.3690785580876 | epot = -22.348409587438 | etot = -18.1035739905555 -101000 ekin = 1.66160772204006 | erot = 3.59766032223856 | epot = -22.3604908173889 | etot = -17.1012227731103 -102000 ekin = 1.62075182718474 | erot = 3.3442006848817 | epot = -22.3063629504087 | etot = -17.3414104383422 -103000 ekin = 2.00871148652538 | erot = 2.33677124900284 | epot = -22.275557852692 | etot = -17.9300751171637 -104000 ekin = 2.04513709976292 | erot = 2.74664593650967 | epot = -22.2818713634637 | etot = -17.4900883271911 -105000 ekin = 1.87027868596139 | erot = 1.98922389218239 | epot = -22.223503909299 | etot = -18.3640013311552 -106000 ekin = 1.71540784443942 | erot = 1.9177953110688 | epot = -22.2562839843324 | etot = -18.6230808288242 -107000 ekin = 2.61024905591622 | erot = 1.57446439985464 | epot = -22.3171357124015 | etot = -18.1324222566306 -108000 ekin = 2.13751756724178 | erot = 2.18822458113098 | epot = -22.2268794585969 | etot = -17.9011373102241 -109000 ekin = 2.24408198608307 | erot = 2.11438299352724 | epot = -22.076564108576 | etot = -17.7180991289657 -110000 ekin = 1.66706562020821 | erot = 2.50986066169373 | epot = -22.0833343008135 | etot = -17.9064080189116 -111000 ekin = 2.30463895640872 | erot = 2.24982560856989 | epot = -22.0940837732696 | etot = -17.539619208291 -112000 ekin = 2.63019524472749 | erot = 2.43696110420532 | epot = -22.0953344558745 | etot = -17.0281781069417 -113000 ekin = 2.42282638113981 | erot = 3.06190927482913 | epot = -22.1061661458173 | etot = -16.6214304898484 -114000 ekin = 2.34214572325658 | erot = 2.31899235523686 | epot = -22.0941430549288 | etot = -17.4330049764353 -115000 ekin = 1.70336449422736 | erot = 3.10166879044198 | epot = -22.1252095896431 | etot = -17.3201763049738 -116000 ekin = 1.51705870113214 | erot = 2.21425252709695 | epot = -22.1823772627204 | etot = -18.4510660344913 -117000 ekin = 1.70129809180508 | erot = 2.34142425076372 | epot = -22.2067668262467 | etot = -18.1640444836779 -118000 ekin = 2.20482827236051 | erot = 2.3179714809504 | epot = -22.1855414590757 | etot = -17.6627417057647 -119000 ekin = 2.54272629601484 | erot = 2.46528921750297 | epot = -22.2113175246519 | etot = -17.2033020111341 -120000 ekin = 1.76640390552554 | erot = 2.16116304616032 | epot = -22.1536331723646 | etot = -18.2260662206787 -121000 ekin = 2.81281157959688 | erot = 2.31761005518346 | epot = -22.1492969323239 | etot = -17.0188752975435 -122000 ekin = 3.25156823587966 | erot = 3.31679050874322 | epot = -22.2050361016166 | etot = -15.6366773569938 -123000 ekin = 2.87462309654081 | erot = 3.25604816714397 | epot = -22.1785374359393 | etot = -16.0478661722546 -124000 ekin = 2.18213410260632 | erot = 2.77182209342785 | epot = -22.0161464482698 | etot = -17.0621902522356 -125000 ekin = 1.85317252616068 | erot = 1.36623599567638 | epot = -21.8721650279344 | etot = -18.6527565060973 -126000 ekin = 2.47747071965844 | erot = 3.09909384826334 | epot = -21.8840309142636 | etot = -16.3074663463419 -127000 ekin = 2.42177426273027 | erot = 2.35209644429656 | epot = -21.8861939604609 | etot = -17.1123232534341 -128000 ekin = 2.76000040231245 | erot = 1.8231678837239 | epot = -21.8538456680958 | etot = -17.2706773820595 -129000 ekin = 2.78355536315491 | erot = 2.88851981621501 | epot = -21.9251039267855 | etot = -16.2530287474156 -130000 ekin = 3.26834278926799 | erot = 2.56228354573336 | epot = -22.0546105678549 | etot = -16.2239842328536 -131000 ekin = 2.64714688907849 | erot = 2.51107513446137 | epot = -22.0961160192681 | etot = -16.9378939957282 -132000 ekin = 2.61847248883524 | erot = 3.38899164334156 | epot = -22.1218916777659 | etot = -16.1144275455891 -133000 ekin = 2.03408861514006 | erot = 2.87401070790187 | epot = -22.0785989417621 | etot = -17.1704996187202 -134000 ekin = 1.64140897264888 | erot = 1.66986416585675 | epot = -22.0323643102285 | etot = -18.7210911717228 -135000 ekin = 2.46650096367446 | erot = 2.111120611107 | epot = -21.9976572593399 | etot = -17.4200356845585 -136000 ekin = 2.32880805911731 | erot = 3.05940125193231 | epot = -21.8983392007847 | etot = -16.5101298897351 -137000 ekin = 2.7601019905106 | erot = 2.47443779429795 | epot = -21.752125264204 | etot = -16.5175854793954 -138000 ekin = 3.30162084678948 | erot = 1.73084735415554 | epot = -21.7423849642075 | etot = -16.7099167632625 -139000 ekin = 2.76669064053124 | erot = 1.72642745910431 | epot = -21.8898577306654 | etot = -17.3967396310298 -140000 ekin = 2.73595287215366 | erot = 2.46891829250481 | epot = -21.9884857831833 | etot = -16.7836146185249 -141000 ekin = 2.79316289615844 | erot = 2.46753088695597 | epot = -22.0064855648443 | etot = -16.7457917817299 -142000 ekin = 3.51694745558129 | erot = 3.49862438784827 | epot = -21.9623193335451 | etot = -14.9467474901156 -143000 ekin = 2.58689934548697 | erot = 2.04008576044027 | epot = -21.9563338194557 | etot = -17.3293487135285 -144000 ekin = 3.72611917000993 | erot = 3.04855733322793 | epot = -21.9536376487796 | etot = -15.1789611455417 -145000 ekin = 3.61191106831147 | erot = 2.71915407989904 | epot = -21.870542665333 | etot = -15.5394775171225 -146000 ekin = 3.85060594912677 | erot = 2.47210219931339 | epot = -21.8285858153921 | etot = -15.505877666952 -147000 ekin = 3.26481933196161 | erot = 2.06864347299802 | epot = -21.6752809049183 | etot = -16.3418180999587 -148000 ekin = 2.47977997895053 | erot = 1.65169267241014 | epot = -21.4172781734276 | etot = -17.2858055220669 -149000 ekin = 2.70771685463074 | erot = 2.28028425953227 | epot = -21.2324293178539 | etot = -16.2444282036909 -150000 ekin = 2.60726181496431 | erot = 2.88955230103659 | epot = -21.126549406853 | etot = -15.6297352908521 -151000 ekin = 2.06865005733849 | erot = 2.13537039813292 | epot = -21.0304193709383 | etot = -16.8263989154669 -152000 ekin = 2.41210154812787 | erot = 2.60104053370075 | epot = -20.8967777045302 | etot = -15.8836356227016 -153000 ekin = 2.12406231442824 | erot = 2.25444655142795 | epot = -20.9199278716094 | etot = -16.5414190057532 -154000 ekin = 2.34622678455546 | erot = 2.58439374093403 | epot = -21.0040588663533 | etot = -16.0734383408638 -155000 ekin = 2.08240965570452 | erot = 3.02621505767145 | epot = -21.0204738431416 | etot = -15.9118491297656 -156000 ekin = 2.04576145796301 | erot = 3.17151405834467 | epot = -20.8558463949479 | etot = -15.6385708786402 -157000 ekin = 2.36459548410747 | erot = 1.89207417055424 | epot = -20.8025485082277 | etot = -16.545878853566 -158000 ekin = 2.16996178916575 | erot = 2.46547727482113 | epot = -20.8673070433024 | etot = -16.2318679793155 -159000 ekin = 2.86272730849306 | erot = 2.27590841865057 | epot = -20.9710387207245 | etot = -15.8324029935809 -160000 ekin = 2.19288173853782 | erot = 2.36312829884111 | epot = -21.0403123366075 | etot = -16.4843022992286 -161000 ekin = 2.14059248149909 | erot = 2.4287283799048 | epot = -21.1333683100403 | etot = -16.5640474486365 -162000 ekin = 1.76077466564934 | erot = 2.66561836368342 | epot = -21.1782130850259 | etot = -16.7518200556931 -163000 ekin = 2.23068698955417 | erot = 2.02664945757243 | epot = -21.3281780197228 | etot = -17.0708415725963 -164000 ekin = 2.75358320318999 | erot = 1.43717365990088 | epot = -21.4675480212853 | etot = -17.2767911581945 -165000 ekin = 2.65171600986478 | erot = 2.29632253260765 | epot = -21.493178025826 | etot = -16.5451394833536 -166000 ekin = 3.27298673277591 | erot = 2.41252396730596 | epot = -21.4477711984927 | etot = -15.7622604984108 -167000 ekin = 3.02574105268454 | erot = 2.02770436019795 | epot = -21.5236773217566 | etot = -16.4702319088741 -168000 ekin = 3.14659813654158 | erot = 1.8374607941321 | epot = -21.5547269116736 | etot = -16.5706679809999 -169000 ekin = 2.22493755697302 | erot = 2.67175500860652 | epot = -21.4662206077311 | etot = -16.5695280421515 -170000 ekin = 2.41921977325643 | erot = 2.49142716001801 | epot = -21.3123035293873 | etot = -16.4016565961128 -171000 ekin = 1.89798915040775 | erot = 2.39492100285877 | epot = -21.2153991969519 | etot = -16.9224890436853 -172000 ekin = 2.86894215563086 | erot = 3.22914449693158 | epot = -21.1827352206441 | etot = -15.0846485680816 -173000 ekin = 2.74888252418688 | erot = 2.13556434483052 | epot = -21.2166792789418 | etot = -16.3322324099244 -174000 ekin = 2.45887587066864 | erot = 2.23682521338056 | epot = -21.2633056658561 | etot = -16.5676045818069 -175000 ekin = 2.84703517745999 | erot = 2.39381254916381 | epot = -21.2430876358358 | etot = -16.002239909212 -176000 ekin = 2.14025231000119 | erot = 1.89894722702466 | epot = -21.3238321496633 | etot = -17.2846326126375 -177000 ekin = 2.5795061901144 | erot = 2.75365074391219 | epot = -21.3022195274207 | etot = -15.9690625933941 -178000 ekin = 1.83122028490793 | erot = 2.59468068841507 | epot = -21.2483113201278 | etot = -16.8224103468048 -179000 ekin = 2.50706581632049 | erot = 2.3918046623687 | epot = -21.3152464598324 | etot = -16.4163759811432 -180000 ekin = 1.88211034410738 | erot = 2.47063835849692 | epot = -21.4741119346399 | etot = -17.1213632320356 -181000 ekin = 1.74209654097779 | erot = 3.05723824722444 | epot = -21.4808621715442 | etot = -16.681527383342 -182000 ekin = 1.55789914013104 | erot = 2.05767448814763 | epot = -21.423526482018 | etot = -17.8079528537394 -183000 ekin = 2.00937540548925 | erot = 2.80898978674436 | epot = -21.491360735728 | etot = -16.6729955434944 -184000 ekin = 2.69285960778353 | erot = 2.42969439668747 | epot = -21.6024209898208 | etot = -16.4798669853498 -185000 ekin = 3.01326925127938 | erot = 3.19083239326424 | epot = -21.6730258967931 | etot = -15.4689242522495 -186000 ekin = 3.2083067153638 | erot = 2.42899016869201 | epot = -21.7143665695974 | etot = -16.0770696855416 -187000 ekin = 2.672906100919 | erot = 3.41560404715603 | epot = -21.6726605039613 | etot = -15.5841503558862 -188000 ekin = 2.89349337388582 | erot = 3.06258669113775 | epot = -21.6216664732832 | etot = -15.6655864082597 -189000 ekin = 2.65435973176118 | erot = 1.82043381700644 | epot = -21.5604872976485 | etot = -17.0856937488809 -190000 ekin = 2.21855159698309 | erot = 1.84826944038784 | epot = -21.5263477340278 | etot = -17.4595266966569 -191000 ekin = 2.26980616064111 | erot = 2.05944589507645 | epot = -21.4543005141097 | etot = -17.1250484583921 -192000 ekin = 2.27219103053707 | erot = 3.11210788791052 | epot = -21.4899273087562 | etot = -16.1056283903086 -193000 ekin = 1.95008147026928 | erot = 1.89648921534019 | epot = -21.4843079374128 | etot = -17.6377372518033 -194000 ekin = 2.45477671526091 | erot = 2.0272304242676 | epot = -21.3709228769337 | etot = -16.8889157374052 -195000 ekin = 3.09567411006595 | erot = 2.10081767143638 | epot = -21.3012041149762 | etot = -16.1047123334739 -196000 ekin = 2.67423122149492 | erot = 2.50738189755519 | epot = -21.2164124023053 | etot = -16.0347992832552 -197000 ekin = 2.50338730962556 | erot = 2.07349764616723 | epot = -21.041867486922 | etot = -16.4649825311292 -198000 ekin = 2.66945928982616 | erot = 1.79012921820209 | epot = -21.0169215356766 | etot = -16.5573330276483 -199000 ekin = 2.53947964790256 | erot = 2.33176467953655 | epot = -21.0171165577067 | etot = -16.1458722302676 -200000 ekin = 2.90451062704866 | erot = 1.42170066957004 | epot = -21.0113804229743 | etot = -16.6851691263556 -201000 ekin = 2.68927776239674 | erot = 1.56650335894554 | epot = -21.0245916399581 | etot = -16.7688105186158 -202000 ekin = 2.2601329351618 | erot = 2.25401443373177 | epot = -20.9769308007641 | etot = -16.4627834318706 -203000 ekin = 2.12073487355488 | erot = 2.03553028991747 | epot = -20.919035946492 | etot = -16.7627707830197 -204000 ekin = 2.11829086582788 | erot = 1.89731962488617 | epot = -20.9376264283538 | etot = -16.9220159376397 -205000 ekin = 1.30964171332167 | erot = 2.12770406224885 | epot = -20.9991335630718 | etot = -17.5617877875013 -206000 ekin = 1.39940057572522 | erot = 2.24496791209126 | epot = -20.963919219062 | etot = -17.3195507312455 -207000 ekin = 1.8871608804017 | erot = 1.79849326266382 | epot = -21.0552898160204 | etot = -17.3696356729549 -208000 ekin = 1.81558541079753 | erot = 3.24210836817276 | epot = -21.3060144768834 | etot = -16.2483206979131 -209000 ekin = 2.79588064252181 | erot = 2.3467149173832 | epot = -21.4301997554495 | etot = -16.2876041955445 -210000 ekin = 3.17544887511567 | erot = 3.12704516116654 | epot = -21.5100449360932 | etot = -15.2075508998109 -211000 ekin = 2.47442327377226 | erot = 2.0990867711376 | epot = -21.6455723047062 | etot = -17.0720622597963 -212000 ekin = 2.36672302145397 | erot = 1.93445871446419 | epot = -21.7283038297487 | etot = -17.4271220938306 -213000 ekin = 1.91045426241161 | erot = 2.52535628540462 | epot = -21.8158508544504 | etot = -17.3800403066341 -214000 ekin = 1.99794025866061 | erot = 2.49896939492127 | epot = -21.8606548137084 | etot = -17.3637451601266 -215000 ekin = 1.97741561009525 | erot = 3.17667494473254 | epot = -21.8701701582032 | etot = -16.7160796033754 -216000 ekin = 1.88829990821377 | erot = 1.87402623825167 | epot = -21.8343889393413 | etot = -18.0720627928759 -217000 ekin = 2.10000293878932 | erot = 1.95052404495887 | epot = -21.8965404786646 | etot = -17.8460134949164 -218000 ekin = 2.34753598782339 | erot = 1.69695019504401 | epot = -21.8560027679962 | etot = -17.8115165851288 -219000 ekin = 2.497223564463 | erot = 2.20999914485705 | epot = -21.8797649478059 | etot = -17.1725422384859 -220000 ekin = 1.75274593087921 | erot = 3.03992746556406 | epot = -21.8491595252171 | etot = -17.0564861287739 -221000 ekin = 1.78874686645809 | erot = 2.79359542964647 | epot = -21.869798634642 | etot = -17.2874563385375 -222000 ekin = 2.63608430516661 | erot = 2.86817933637385 | epot = -21.8351218383832 | etot = -16.3308581968427 -223000 ekin = 3.02706758581511 | erot = 1.93888641555348 | epot = -21.8582453001765 | etot = -16.8922912988079 -224000 ekin = 2.71704451339112 | erot = 2.42079327531441 | epot = -21.8188420875657 | etot = -16.6810042988601 -225000 ekin = 2.04245190508395 | erot = 3.38216222891907 | epot = -21.8232190868647 | etot = -16.3986049528616 -226000 ekin = 2.37968015829255 | erot = 2.38384696857065 | epot = -21.8913549487127 | etot = -17.1278278218495 -227000 ekin = 2.73883397024414 | erot = 2.62491632372019 | epot = -21.9496900700867 | etot = -16.5859397761223 -228000 ekin = 2.06833362780412 | erot = 2.25049628751225 | epot = -21.9946760345141 | etot = -17.6758461191977 -229000 ekin = 1.78618617304217 | erot = 1.80509591500329 | epot = -22.0671964085329 | etot = -18.4759143204874 -230000 ekin = 2.76967283780387 | erot = 2.22492545317995 | epot = -22.0913590121729 | etot = -17.0967607211891 -231000 ekin = 3.15653922952316 | erot = 2.77099247609325 | epot = -22.0635255129442 | etot = -16.1359938073278 -232000 ekin = 1.86633326635991 | erot = 1.70672288688982 | epot = -22.0959715052869 | etot = -18.5229153520371 -233000 ekin = 1.75856846080021 | erot = 1.55694263125625 | epot = -22.0729289884755 | etot = -18.7574178964191 -234000 ekin = 2.32322575892498 | erot = 2.05793864740336 | epot = -21.9849429433607 | etot = -17.6037785370324 -235000 ekin = 1.95327191686568 | erot = 2.52519338885861 | epot = -21.9357201856672 | etot = -17.4572548799429 -236000 ekin = 2.25952484966859 | erot = 1.90005304846995 | epot = -21.9422471368741 | etot = -17.7826692387355 -237000 ekin = 2.49082301609303 | erot = 2.65327564887437 | epot = -22.0049130762794 | etot = -16.860814411312 -238000 ekin = 2.21076048871751 | erot = 2.74154862479023 | epot = -22.0553236426831 | etot = -17.1030145291754 -239000 ekin = 2.71464884454142 | erot = 2.48739530580561 | epot = -22.0661894571024 | etot = -16.8641453067554 -240000 ekin = 3.08961933821573 | erot = 2.17857064931927 | epot = -21.9596599475175 | etot = -16.6914699599825 -241000 ekin = 3.04172562407922 | erot = 2.64442433974962 | epot = -21.872950064824 | etot = -16.1868001009951 -242000 ekin = 2.21355627539455 | erot = 2.33429157450905 | epot = -21.7850463200938 | etot = -17.2371984701902 -243000 ekin = 1.52065138183895 | erot = 2.81375224845254 | epot = -21.724672004357 | etot = -17.3902683740655 -244000 ekin = 1.90352576583831 | erot = 2.43821138840079 | epot = -21.6320468184555 | etot = -17.2903096642164 -245000 ekin = 1.96342069667742 | erot = 2.61760141174562 | epot = -21.509789944958 | etot = -16.928767836535 -246000 ekin = 2.05478829283868 | erot = 2.42643933263093 | epot = -21.4781109635143 | etot = -16.9968833380447 -247000 ekin = 1.54618395739204 | erot = 2.28537401295509 | epot = -21.4411828355572 | etot = -17.6096248652101 -248000 ekin = 1.83924983769609 | erot = 2.55904554412921 | epot = -21.4587985205918 | etot = -17.0605031387665 -249000 ekin = 1.78703007063825 | erot = 2.03411349475431 | epot = -21.516607560139 | etot = -17.6954639947464 -250000 ekin = 1.69317901626952 | erot = 3.382620023581 | epot = -21.5380480709889 | etot = -16.4622490311384 -251000 ekin = 2.13799462687096 | erot = 3.25868442484789 | epot = -21.5254595658408 | etot = -16.1287805141219 -252000 ekin = 2.04357045453396 | erot = 2.53079336098227 | epot = -21.5456931883614 | etot = -16.9713293728452 -253000 ekin = 1.63287738205387 | erot = 3.20992823373492 | epot = -21.5622010587548 | etot = -16.719395442966 -254000 ekin = 2.31269246359595 | erot = 3.10766702207071 | epot = -21.5505863172024 | etot = -16.1302268315358 -255000 ekin = 2.50767926641465 | erot = 2.76631276495167 | epot = -21.5288449153183 | etot = -16.254852883952 -256000 ekin = 1.97163698305487 | erot = 2.61682132599931 | epot = -21.5273539828767 | etot = -16.9388956738225 -257000 ekin = 2.21091422886157 | erot = 3.2624387389365 | epot = -21.5385504601779 | etot = -16.0651974923798 -258000 ekin = 2.0351730783025 | erot = 1.84693461512361 | epot = -21.6544556001779 | etot = -17.7723479067518 -259000 ekin = 2.85718947138204 | erot = 2.78701165242275 | epot = -21.7587237542941 | etot = -16.1145226304893 -260000 ekin = 2.90387286634678 | erot = 2.18817434737477 | epot = -21.8080383126913 | etot = -16.7159910989698 -261000 ekin = 2.76190440948559 | erot = 2.33968169215532 | epot = -21.8592909726424 | etot = -16.7577048710015 -262000 ekin = 3.50919242681178 | erot = 1.76925994550144 | epot = -21.8779228441577 | etot = -16.5994704718445 -263000 ekin = 3.07696270254058 | erot = 2.41477320555763 | epot = -21.8078566004281 | etot = -16.3161206923299 -264000 ekin = 2.26633389925754 | erot = 2.04161743361595 | epot = -21.8372928128571 | etot = -17.5293414799836 -265000 ekin = 1.95747124461577 | erot = 2.5081300879884 | epot = -21.8490876266416 | etot = -17.3834862940375 -266000 ekin = 2.34517905801099 | erot = 3.31486209922478 | epot = -21.8287737874741 | etot = -16.1687326302383 -267000 ekin = 1.74030193361906 | erot = 2.23366459528059 | epot = -21.699850097441 | etot = -17.7258835685413 -268000 ekin = 2.04858677018814 | erot = 3.28744422098426 | epot = -21.6459408923623 | etot = -16.3099099011899 -269000 ekin = 1.93146929709294 | erot = 2.79280735598121 | epot = -21.549773802712 | etot = -16.8254971496378 -270000 ekin = 2.19788894271016 | erot = 2.64563279687103 | epot = -21.4165389672397 | etot = -16.5730172276585 -271000 ekin = 2.21923220579694 | erot = 3.10768708967444 | epot = -21.2197121954353 | etot = -15.8927928999639 -272000 ekin = 2.54992061853163 | erot = 2.29721880581853 | epot = -21.0816515756819 | etot = -16.2345121513317 -273000 ekin = 1.914618407838 | erot = 2.01420401968473 | epot = -21.0503637141725 | etot = -17.1215412866498 -274000 ekin = 1.89671513770876 | erot = 2.24334386161735 | epot = -21.0967103438301 | etot = -16.9566513445039 -275000 ekin = 1.78930707116537 | erot = 3.09754687865994 | epot = -21.1385700371941 | etot = -16.2517160873688 -276000 ekin = 3.37110328153971 | erot = 2.41957324257529 | epot = -21.0908388312033 | etot = -15.3001623070883 -277000 ekin = 2.38921825148496 | erot = 1.50604988822737 | epot = -21.034620883997 | etot = -17.1393527442847 -278000 ekin = 2.51997301930638 | erot = 2.14026171776896 | epot = -21.0117379332914 | etot = -16.351503196216 -279000 ekin = 1.88315206280857 | erot = 2.37342905263994 | epot = -20.9993757709145 | etot = -16.742794655466 -280000 ekin = 2.33534713190787 | erot = 3.58626468287222 | epot = -20.8573252930133 | etot = -14.9357134782332 -281000 ekin = 1.75252641954511 | erot = 1.7907930540809 | epot = -20.9036528826792 | etot = -17.3603334090531 -282000 ekin = 2.26373977259215 | erot = 3.04032073608633 | epot = -20.8497513702237 | etot = -15.5456908615452 -283000 ekin = 2.1783387139443 | erot = 2.20833158301333 | epot = -20.8002776734785 | etot = -16.4136073765209 -284000 ekin = 1.9148667268656 | erot = 2.21521993135969 | epot = -20.8277491648056 | etot = -16.6976625065804 -285000 ekin = 3.15634443167765 | erot = 1.80033231604849 | epot = -21.0046435881196 | etot = -16.0479668403934 -286000 ekin = 3.84877574957331 | erot = 1.82969969667577 | epot = -21.1628555811447 | etot = -15.4843801348956 -287000 ekin = 3.60615742824732 | erot = 2.91608688151215 | epot = -21.2126952882302 | etot = -14.6904509784708 -288000 ekin = 3.19613259393802 | erot = 1.67736393077137 | epot = -21.1713552834963 | etot = -16.297858758787 -289000 ekin = 2.45584885114799 | erot = 2.77781979747336 | epot = -21.1669115721543 | etot = -15.9332429235329 -290000 ekin = 2.74570408981357 | erot = 2.40443247852242 | epot = -21.1874427766533 | etot = -16.0373062083173 -291000 ekin = 2.10295274468233 | erot = 2.37092484671539 | epot = -21.2419107014544 | etot = -16.7680331100567 -292000 ekin = 2.36118713930732 | erot = 2.05558127949017 | epot = -21.3137361602548 | etot = -16.8969677414573 -293000 ekin = 2.2786196308825 | erot = 2.35874555054765 | epot = -21.4302415460533 | etot = -16.7928763646231 -294000 ekin = 2.93315982813019 | erot = 2.90313008187785 | epot = -21.5210917917479 | etot = -15.6848018817399 -295000 ekin = 2.66360761710434 | erot = 2.28100565751945 | epot = -21.6885021477336 | etot = -16.7438888731098 -296000 ekin = 2.18767827164471 | erot = 2.90589885547353 | epot = -21.7355037190159 | etot = -16.6419265918977 -297000 ekin = 2.15987738107365 | erot = 3.29819575592636 | epot = -21.7177655658756 | etot = -16.2596924288756 -298000 ekin = 2.92956976611296 | erot = 2.36377210613469 | epot = -21.6748271071566 | etot = -16.3814852349089 -299000 ekin = 3.19167138064488 | erot = 2.23480811780853 | epot = -21.8042612344918 | etot = -16.3777817360384 -300000 ekin = 3.3133572846982 | erot = 1.38932157247169 | epot = -21.8799906137235 | etot = -17.1773117565536 -301000 ekin = 2.39061971962408 | erot = 3.30110260608963 | epot = -21.8919200817915 | etot = -16.2001977560778 -302000 ekin = 2.954460706029 | erot = 3.2304815881765 | epot = -21.8557645140423 | etot = -15.6708222198368 -303000 ekin = 2.44700205353933 | erot = 2.60676303242282 | epot = -21.8414046718167 | etot = -16.7876395858546 -304000 ekin = 2.23578509140697 | erot = 2.68770420047938 | epot = -21.7680601199659 | etot = -16.8445708280796 -305000 ekin = 2.35505207220215 | erot = 2.3823003115585 | epot = -21.7344089784493 | etot = -16.9970565946887 -306000 ekin = 1.91790567526689 | erot = 2.90107494003232 | epot = -21.7170004822351 | etot = -16.8980198669359 -307000 ekin = 2.48241777758708 | erot = 2.0836708009946 | epot = -21.6510481218459 | etot = -17.0849595432642 -308000 ekin = 2.77531620706104 | erot = 2.63103510715158 | epot = -21.6349123878086 | etot = -16.2285610735959 -309000 ekin = 2.30440955942791 | erot = 2.1249829765834 | epot = -21.5927938975113 | etot = -17.1634013615 -310000 ekin = 2.50879527040005 | erot = 3.21338829421535 | epot = -21.6043932917725 | etot = -15.8822097271571 -311000 ekin = 2.31939145866558 | erot = 3.03649241514151 | epot = -21.6247503351754 | etot = -16.2688664613683 -312000 ekin = 1.78383134659847 | erot = 3.26262247889992 | epot = -21.4948144284683 | etot = -16.4483606029699 -313000 ekin = 1.6465994694839 | erot = 2.08133087588833 | epot = -21.4920309735611 | etot = -17.7641006281889 -314000 ekin = 2.2552391830868 | erot = 2.55077633299239 | epot = -21.5103692936944 | etot = -16.7043537776152 -315000 ekin = 2.5352734391515 | erot = 2.13089997124613 | epot = -21.5923709217299 | etot = -16.9261975113323 -316000 ekin = 1.99944427781285 | erot = 1.80072924409704 | epot = -21.6039893771529 | etot = -17.803815855243 -317000 ekin = 2.11848744585804 | erot = 2.01459693810075 | epot = -21.5948976630665 | etot = -17.4618132791077 -318000 ekin = 2.29013024301854 | erot = 1.92405818620914 | epot = -21.5643695946921 | etot = -17.3501811654644 -319000 ekin = 1.97314693278018 | erot = 1.67996578959134 | epot = -21.4554808400841 | etot = -17.8023681177126 -320000 ekin = 2.45681719546631 | erot = 3.07835144499744 | epot = -21.3924125538101 | etot = -15.8572439133463 -321000 ekin = 1.85729238455498 | erot = 2.67083565671245 | epot = -21.433818829251 | etot = -16.9056907879836 -322000 ekin = 1.96132292396412 | erot = 3.36792274118279 | epot = -21.3663490830085 | etot = -16.0371034178616 -323000 ekin = 1.94437285233567 | erot = 2.09558156605687 | epot = -21.4151250968679 | etot = -17.3751706784754 -324000 ekin = 2.229181524904 | erot = 2.4674418745061 | epot = -21.532385908563 | etot = -16.8357625091529 -325000 ekin = 2.74582842770392 | erot = 2.36717454305098 | epot = -21.6443544237971 | etot = -16.5313514530422 -326000 ekin = 1.91124551133375 | erot = 1.93084217743114 | epot = -21.7077957426602 | etot = -17.8657080538953 -327000 ekin = 3.05627483509655 | erot = 1.67325209460963 | epot = -21.7948818019128 | etot = -17.0653548722066 -328000 ekin = 2.73933273476856 | erot = 1.92380912803777 | epot = -21.8364014823586 | etot = -17.1732596195523 -329000 ekin = 2.95907896099514 | erot = 3.15654168356681 | epot = -21.898199971646 | etot = -15.7825793270841 -330000 ekin = 2.90795110595274 | erot = 2.01765890034968 | epot = -21.9037795505258 | etot = -16.9781695442234 -331000 ekin = 2.27446048340228 | erot = 2.03754878634056 | epot = -21.8760842049291 | etot = -17.5640749351863 -332000 ekin = 2.43262938612094 | erot = 3.19219171897213 | epot = -21.9305186945662 | etot = -16.3056975894732 -333000 ekin = 2.47357651298171 | erot = 2.70061045814697 | epot = -22.0416691323271 | etot = -16.8674821611985 -334000 ekin = 2.38171387374892 | erot = 3.00424927873366 | epot = -22.0746318522988 | etot = -16.6886686998162 -335000 ekin = 2.10465470910016 | erot = 3.57382014016833 | epot = -22.1175420615632 | etot = -16.4390672122947 -336000 ekin = 2.61374577374183 | erot = 2.13386927281299 | epot = -22.08988251196 | etot = -17.3422674654052 -337000 ekin = 2.72124526751511 | erot = 2.74800480481403 | epot = -22.0768537131621 | etot = -16.607603640833 -338000 ekin = 1.83524121485421 | erot = 2.24338894827196 | epot = -22.1591955034455 | etot = -18.0805653403194 -339000 ekin = 1.54928432997334 | erot = 2.49812246084905 | epot = -22.202239883467 | etot = -18.1548330926446 -340000 ekin = 1.44405714940632 | erot = 4.0451327092417 | epot = -22.1149458734013 | etot = -16.6257560147533 -341000 ekin = 1.67447392575555 | erot = 2.77749751745982 | epot = -22.0760831546714 | etot = -17.624111711456 -342000 ekin = 1.9825676117275 | erot = 2.71655566521084 | epot = -22.1563522566984 | etot = -17.45722897976 -343000 ekin = 2.68213676683887 | erot = 3.16686462846914 | epot = -22.2498477633288 | etot = -16.4008463680208 -344000 ekin = 1.77905771753907 | erot = 2.19153667254074 | epot = -22.2907212723871 | etot = -18.3201268823073 -345000 ekin = 1.5460499615042 | erot = 1.85960255696712 | epot = -22.3447003428977 | etot = -18.9390478244264 -346000 ekin = 1.71554664484034 | erot = 1.79880968736714 | epot = -22.3117022609055 | etot = -18.797345928698 -347000 ekin = 1.38672912049481 | erot = 2.61484473767931 | epot = -22.332503239512 | etot = -18.3309293813379 -348000 ekin = 2.15015924850684 | erot = 2.86300326453563 | epot = -22.3337312775957 | etot = -17.3205687645532 -349000 ekin = 1.83066085453602 | erot = 1.9844132649487 | epot = -22.3967822584585 | etot = -18.5817081389738 -350000 ekin = 1.83318738252649 | erot = 2.56907029661254 | epot = -22.4577827539416 | etot = -18.0555250748026 -351000 ekin = 1.72790505260219 | erot = 2.87456274671834 | epot = -22.5159555107051 | etot = -17.9134877113846 -352000 ekin = 2.80786740016944 | erot = 2.08750448125769 | epot = -22.6549834386892 | etot = -17.7596115572621 -353000 ekin = 3.5492801472091 | erot = 1.42584537334883 | epot = -22.6849212734238 | etot = -17.7097957528659 -354000 ekin = 3.49129244374804 | erot = 2.25156548638802 | epot = -22.604182620693 | etot = -16.861324690557 -355000 ekin = 2.06248783371663 | erot = 2.92733565233054 | epot = -22.5494488364627 | etot = -17.5596253504155 -356000 ekin = 2.13415426306312 | erot = 3.32668319049641 | epot = -22.6122425286523 | etot = -17.1514050750927 -357000 ekin = 2.75897049849731 | erot = 2.51843165594436 | epot = -22.6042888591885 | etot = -17.3268867047468 -358000 ekin = 2.51778220496547 | erot = 2.28374144764325 | epot = -22.5654155469984 | etot = -17.7638918943897 -359000 ekin = 3.2037278512604 | erot = 2.5552016027623 | epot = -22.6749569097326 | etot = -16.91602745571 -360000 ekin = 2.52669169359923 | erot = 1.97563796824025 | epot = -22.7314557612254 | etot = -18.229126099386 -361000 ekin = 2.60424632123629 | erot = 2.51068088850826 | epot = -22.7715023743751 | etot = -17.6565751646306 -362000 ekin = 2.43350156723209 | erot = 3.84566788758402 | epot = -22.7352151098034 | etot = -16.4560456549873 -363000 ekin = 2.91069717970492 | erot = 1.99710098714122 | epot = -22.6302259934474 | etot = -17.7224278266013 -364000 ekin = 2.2553832868325 | erot = 1.87832387363455 | epot = -22.5083625296191 | etot = -18.374655369152 -365000 ekin = 2.04575884197224 | erot = 2.797742068412 | epot = -22.332262738426 | etot = -17.4887618280417 -366000 ekin = 2.26894187965217 | erot = 1.94379382552235 | epot = -22.2788727984906 | etot = -18.0661370933161 -367000 ekin = 2.82509630766737 | erot = 2.50361468767084 | epot = -22.3209381619452 | etot = -16.992227166607 -368000 ekin = 2.81542036602322 | erot = 2.18733627644489 | epot = -22.4297259451244 | etot = -17.4269693026563 -369000 ekin = 2.30426035796382 | erot = 2.85653411706989 | epot = -22.4923286665588 | etot = -17.3315341915251 -370000 ekin = 2.67871033327547 | erot = 2.11464921695177 | epot = -22.578069860797 | etot = -17.7847103105697 -371000 ekin = 2.19281044135007 | erot = 3.60165960664287 | epot = -22.6424730832337 | etot = -16.8480030352407 -372000 ekin = 1.77481259468411 | erot = 3.406547444381 | epot = -22.7147683829008 | etot = -17.5334083438357 -373000 ekin = 2.15551547517191 | erot = 2.7877825236183 | epot = -22.7559497214321 | etot = -17.8126517226419 -374000 ekin = 2.71938368055486 | erot = 3.58127823243842 | epot = -22.9084433694729 | etot = -16.6077814564796 -375000 ekin = 2.42759321485976 | erot = 2.9742127178716 | epot = -22.9740378563778 | etot = -17.5722319236464 -376000 ekin = 3.39126830110572 | erot = 3.24733797625004 | epot = -22.9874015798135 | etot = -16.3487953024578 -377000 ekin = 3.20966733323472 | erot = 2.65934060364476 | epot = -22.9452111216365 | etot = -17.076203184757 -378000 ekin = 1.56095946168131 | erot = 2.66159033944991 | epot = -22.9575870308253 | etot = -18.7350372296941 -379000 ekin = 1.9498568748538 | erot = 2.54085216255828 | epot = -22.9834751642939 | etot = -18.4927661268818 -380000 ekin = 2.65820438237073 | erot = 2.88045867212573 | epot = -22.9984703542083 | etot = -17.4598072997118 -381000 ekin = 2.97084599252829 | erot = 2.18892549461574 | epot = -23.0341895570111 | etot = -17.8744180698671 -382000 ekin = 2.61355176942653 | erot = 2.02938704043227 | epot = -23.00841197151 | etot = -18.3654731616512 -383000 ekin = 2.03830671072154 | erot = 2.50516194855525 | epot = -23.0393965606452 | etot = -18.4959279013684 -384000 ekin = 2.1060608733416 | erot = 2.2184025045895 | epot = -23.0602182522593 | etot = -18.7357548743282 -385000 ekin = 1.89114918519107 | erot = 1.63701051320103 | epot = -23.0834434146806 | etot = -19.5552837162885 -386000 ekin = 1.55124380123707 | erot = 1.36147797265396 | epot = -23.1300518396949 | etot = -20.2173300658039 -387000 ekin = 2.19627825752355 | erot = 1.75751396098972 | epot = -23.1280875332419 | etot = -19.1742953147287 -388000 ekin = 1.96387084539616 | erot = 1.95852585326804 | epot = -23.0327752892415 | etot = -19.1103785905773 -389000 ekin = 2.50801560941705 | erot = 2.32519825784836 | epot = -23.0011464671235 | etot = -18.1679325998581 -390000 ekin = 2.03596866068489 | erot = 1.88295618907177 | epot = -22.8810338311575 | etot = -18.9621089814009 -391000 ekin = 1.8098591016452 | erot = 2.39622167162874 | epot = -22.81955664632 | etot = -18.613475873046 -392000 ekin = 2.17725370142733 | erot = 2.87094426544089 | epot = -22.7839731045438 | etot = -17.7357751376756 -393000 ekin = 2.14224634181997 | erot = 3.17242974303658 | epot = -22.8435025538357 | etot = -17.5288264689792 -394000 ekin = 1.97769550804367 | erot = 2.16375300420729 | epot = -22.8342667825711 | etot = -18.6928182703201 -395000 ekin = 2.03687268736298 | erot = 2.49567469731651 | epot = -22.8892034986303 | etot = -18.3566561139508 -396000 ekin = 2.16189109047463 | erot = 1.95308746486161 | epot = -22.9781386034885 | etot = -18.8631600481523 -397000 ekin = 2.41744222422408 | erot = 1.65310699287476 | epot = -23.0900453292844 | etot = -19.0194961121856 -398000 ekin = 3.58905654436294 | erot = 2.51930256503331 | epot = -23.2070733343384 | etot = -17.0987142249422 -399000 ekin = 2.65051654249497 | erot = 1.78138450529865 | epot = -23.3040478764215 | etot = -18.8721468286279 -400000 ekin = 2.49402752614129 | erot = 2.10290777432183 | epot = -23.3608759462318 | etot = -18.7639406457687 -401000 ekin = 2.04176177605462 | erot = 2.154995213856 | epot = -23.4039603394011 | etot = -19.2072033494905 -402000 ekin = 2.44505875861459 | erot = 2.11318097973378 | epot = -23.3975262709888 | etot = -18.8392865326404 -403000 ekin = 2.54858079745147 | erot = 2.81138206601919 | epot = -23.476064698677 | etot = -18.1161018352063 -404000 ekin = 2.21063952462117 | erot = 2.64710865829565 | epot = -23.574696037266 | etot = -18.7169478543492 -405000 ekin = 2.47328118101332 | erot = 2.40933750599425 | epot = -23.5927917139469 | etot = -18.7101730269393 -406000 ekin = 2.24891173527799 | erot = 2.23777884116047 | epot = -23.6086191890417 | etot = -19.1219286126032 -407000 ekin = 2.0107940045037 | erot = 2.78642832526904 | epot = -23.5246032469978 | etot = -18.727380917225 -408000 ekin = 2.59464051790823 | erot = 2.59123578102097 | epot = -23.4198302602656 | etot = -18.2339539613364 -409000 ekin = 2.37170880608734 | erot = 2.26136902851213 | epot = -23.317258193724 | etot = -18.6841803591245 -410000 ekin = 1.99754661347185 | erot = 1.95523998485755 | epot = -23.2950402043273 | etot = -19.3422536059979 -411000 ekin = 1.8693657058423 | erot = 2.63899492681176 | epot = -23.2490367633041 | etot = -18.74067613065 -412000 ekin = 1.98214047746227 | erot = 2.68315820775202 | epot = -23.1987357483281 | etot = -18.5334370631139 -413000 ekin = 2.39078873487373 | erot = 2.65589562872907 | epot = -23.1435198518627 | etot = -18.0968354882599 -414000 ekin = 2.40821090859775 | erot = 1.75574324408225 | epot = -23.0725048141377 | etot = -18.9085506614577 -415000 ekin = 2.74601981183015 | erot = 2.43675176686816 | epot = -23.1211711904486 | etot = -17.9383996117503 -416000 ekin = 2.08828454200993 | erot = 2.76783506526218 | epot = -23.1383119239965 | etot = -18.2821923167244 -417000 ekin = 2.01455344430628 | erot = 1.95306265456051 | epot = -23.1433633505287 | etot = -19.1757472516619 -418000 ekin = 2.42716528853985 | erot = 2.57642821145486 | epot = -23.127531797131 | etot = -18.1239382971363 -419000 ekin = 3.04095103685797 | erot = 2.58427576972734 | epot = -23.0602279332617 | etot = -17.4350011266764 -420000 ekin = 2.6360746280152 | erot = 2.44478111019393 | epot = -22.982092315172 | etot = -17.9012365769629 -421000 ekin = 2.53019765722915 | erot = 1.78389585255477 | epot = -22.9707435541329 | etot = -18.6566500443489 -422000 ekin = 2.72457425772367 | erot = 1.67768634886349 | epot = -22.9542997027495 | etot = -18.5520390961623 -423000 ekin = 2.11402997037893 | erot = 2.55034580375608 | epot = -22.8263851956497 | etot = -18.1620094215147 -424000 ekin = 1.8895880210325 | erot = 2.31332431343561 | epot = -22.772666888172 | etot = -18.5697545537039 -425000 ekin = 2.3595116370971 | erot = 1.95762380637298 | epot = -22.7752082759346 | etot = -18.4580728324645 -426000 ekin = 2.23706657164627 | erot = 2.60016134755148 | epot = -22.7844114251539 | etot = -17.9471835059562 -427000 ekin = 1.88801598248841 | erot = 2.12415782350886 | epot = -22.9416586386639 | etot = -18.9294848326666 -428000 ekin = 1.92849031333042 | erot = 2.44097902588716 | epot = -23.0611368174399 | etot = -18.6916674782223 -429000 ekin = 1.70536802258415 | erot = 2.14916257389792 | epot = -23.0556586745393 | etot = -19.2011280780572 -430000 ekin = 2.30226095973205 | erot = 2.14689932813604 | epot = -23.0606502516208 | etot = -18.6114899637527 -431000 ekin = 2.45988288454318 | erot = 2.42278380298657 | epot = -23.0729777223881 | etot = -18.1903110348583 -432000 ekin = 2.80869332724974 | erot = 2.19954129490925 | epot = -23.0939746542044 | etot = -18.0857400320454 -433000 ekin = 2.21130556188282 | erot = 1.62882156110628 | epot = -23.1534080352157 | etot = -19.3132809122266 -434000 ekin = 2.60574953870752 | erot = 2.36088790768803 | epot = -23.1901717047879 | etot = -18.2235342583923 -435000 ekin = 2.30377529593091 | erot = 2.53917715731259 | epot = -23.1716983948432 | etot = -18.3287459415997 -436000 ekin = 2.42707603554825 | erot = 2.75234181061924 | epot = -23.2197996577197 | etot = -18.0403818115522 -437000 ekin = 1.65090540276074 | erot = 3.25345231298367 | epot = -23.2216366145388 | etot = -18.3172788987944 -438000 ekin = 1.56145302974407 | erot = 2.60950810563796 | epot = -23.1303770792278 | etot = -18.9594159438458 -439000 ekin = 2.30955439722234 | erot = 1.94011743371103 | epot = -23.1353170794497 | etot = -18.8856452485163 -440000 ekin = 2.53037674867674 | erot = 3.0652704286103 | epot = -23.196858945292 | etot = -17.601211768005 -441000 ekin = 2.80107707952534 | erot = 2.53664155736544 | epot = -23.1712373428919 | etot = -17.8335187060011 -442000 ekin = 2.92536323090713 | erot = 2.88384500930017 | epot = -23.1123001627208 | etot = -17.3030919225135 -443000 ekin = 1.96543935969482 | erot = 1.753449631552 | epot = -23.0380529084377 | etot = -19.3191639171909 -444000 ekin = 2.00309477401363 | erot = 2.23897509587739 | epot = -22.9472103119533 | etot = -18.7051404420623 -445000 ekin = 2.20302071819722 | erot = 2.06928381371828 | epot = -22.7775434364172 | etot = -18.5052389045017 -446000 ekin = 2.43487889302299 | erot = 2.37751556007798 | epot = -22.6838190597697 | etot = -17.8714246066687 -447000 ekin = 2.2620819636031 | erot = 2.41400188145197 | epot = -22.7082516636546 | etot = -18.0321678185995 -448000 ekin = 2.16184472791984 | erot = 1.93539407204278 | epot = -22.8144859493263 | etot = -18.7172471493637 -449000 ekin = 2.21107967973114 | erot = 2.34659682978741 | epot = -22.9059503054159 | etot = -18.3482737958974 -450000 ekin = 2.74677740004439 | erot = 1.97222921372039 | epot = -22.860755926716 | etot = -18.1417493129513 -451000 ekin = 2.2050889378155 | erot = 2.13042736119389 | epot = -22.8862608894796 | etot = -18.5507445904702 -452000 ekin = 2.52760608607095 | erot = 2.34006815636601 | epot = -22.9138111972133 | etot = -18.0461369547763 -453000 ekin = 2.23448825172916 | erot = 1.77834418215733 | epot = -22.8879238301791 | etot = -18.8750913962926 -454000 ekin = 2.4343851915949 | erot = 2.59700848533281 | epot = -22.8184361849036 | etot = -17.7870425079759 -455000 ekin = 2.04195793930991 | erot = 2.79639043747681 | epot = -22.6032980500354 | etot = -17.7649496732487 -456000 ekin = 2.00799933710202 | erot = 2.53653815407518 | epot = -22.4355596266522 | etot = -17.891022135475 -457000 ekin = 2.60426208759883 | erot = 2.46609612876191 | epot = -22.3409120082078 | etot = -17.270553791847 -458000 ekin = 2.01368468059037 | erot = 1.9961381624531 | epot = -22.2549400327205 | etot = -18.2451171896771 -459000 ekin = 1.73688781588865 | erot = 2.48572034306896 | epot = -22.2282088298767 | etot = -18.0056006709191 -460000 ekin = 1.91682575775988 | erot = 2.08308677023944 | epot = -22.2211874714416 | etot = -18.2212749434423 -461000 ekin = 1.54933673126938 | erot = 1.29454502815255 | epot = -22.1945151049368 | etot = -19.3506333455148 -462000 ekin = 2.44160489340629 | erot = 1.34721473707676 | epot = -22.284671307697 | etot = -18.495851677214 -463000 ekin = 2.63165365707667 | erot = 2.08143760128039 | epot = -22.4004513395625 | etot = -17.6873600812055 -464000 ekin = 2.67929276186416 | erot = 3.72563793061087 | epot = -22.5200042545289 | etot = -16.1150735620538 -465000 ekin = 1.94880111369479 | erot = 2.23148844819348 | epot = -22.685554296329 | etot = -18.5052647344407 -466000 ekin = 2.13853049638891 | erot = 2.95056624305957 | epot = -22.7822881705531 | etot = -17.6931914311046 -467000 ekin = 2.46452767169615 | erot = 2.1077848077008 | epot = -22.9485753844866 | etot = -18.3762629050896 -468000 ekin = 1.98589158006998 | erot = 1.62816092182055 | epot = -23.0180008829524 | etot = -19.4039483810618 -469000 ekin = 2.498810820967 | erot = 2.6361546272592 | epot = -23.0547833968841 | etot = -17.9198179486579 -470000 ekin = 2.91491361681313 | erot = 3.19115611298998 | epot = -23.0448741101699 | etot = -16.9388043803668 -471000 ekin = 2.37554627514204 | erot = 1.71739792236247 | epot = -22.9932329645513 | etot = -18.9002887670468 -472000 ekin = 2.18486807923518 | erot = 2.00687069908099 | epot = -22.9563182572702 | etot = -18.764579478954 -473000 ekin = 2.36185345820899 | erot = 2.86259041401023 | epot = -22.9161024426125 | etot = -17.6916585703933 -474000 ekin = 2.17077693495272 | erot = 2.59376596740919 | epot = -22.7894018760352 | etot = -18.0248589736733 -475000 ekin = 2.37844153079293 | erot = 2.01112751381907 | epot = -22.6793191497969 | etot = -18.2897501051849 -476000 ekin = 2.0876367643964 | erot = 2.59647624455221 | epot = -22.6700039875052 | etot = -17.9858909785566 -477000 ekin = 2.52249432714936 | erot = 3.55251934739867 | epot = -22.6424099194916 | etot = -16.5673962449436 -478000 ekin = 2.40424947791157 | erot = 2.7323911725861 | epot = -22.544776325228 | etot = -17.4081356747303 -479000 ekin = 1.27637524434413 | erot = 2.99749792697945 | epot = -22.4994949498981 | etot = -18.2256217785745 -480000 ekin = 1.81374950293817 | erot = 2.14389317135939 | epot = -22.4678405170784 | etot = -18.5101978427809 -481000 ekin = 2.39496774186199 | erot = 3.18299441824521 | epot = -22.4930736763177 | etot = -16.9151115162105 -482000 ekin = 3.21051763720184 | erot = 2.40962326270833 | epot = -22.4479376181304 | etot = -16.8277967182202 -483000 ekin = 3.06081116762377 | erot = 2.49856996934407 | epot = -22.4288948733283 | etot = -16.8695137363604 -484000 ekin = 2.7452293328759 | erot = 2.53012629993099 | epot = -22.483756332919 | etot = -17.2084007001121 -485000 ekin = 3.33103095180521 | erot = 2.42091818181918 | epot = -22.4922555047182 | etot = -16.7403063710938 -486000 ekin = 1.99323479363108 | erot = 1.76127718142275 | epot = -22.5432098594131 | etot = -18.7886978843593 -487000 ekin = 2.64825718911654 | erot = 2.50204426232017 | epot = -22.6407366935241 | etot = -17.4904352420874 -488000 ekin = 1.76385891719471 | erot = 2.64266555173498 | epot = -22.6990728058786 | etot = -18.2925483369489 -489000 ekin = 2.10357630534276 | erot = 2.95613916443127 | epot = -22.7877124402073 | etot = -17.7279969704332 -490000 ekin = 2.33515649128314 | erot = 2.32995416999058 | epot = -22.7920703811403 | etot = -18.1269597198666 -491000 ekin = 2.48752587426647 | erot = 2.58310949760555 | epot = -22.7834811495388 | etot = -17.7128457776668 -492000 ekin = 3.29820665204489 | erot = 2.18682924183924 | epot = -22.7674519489923 | etot = -17.2824160551082 -493000 ekin = 3.40238156707506 | erot = 2.35717041222451 | epot = -22.7149408840448 | etot = -16.9553889047452 -494000 ekin = 3.59348050162499 | erot = 2.23182460532058 | epot = -22.7081682295491 | etot = -16.8828631226035 -495000 ekin = 2.52030309238562 | erot = 2.16229430067423 | epot = -22.6973031832711 | etot = -18.0147057902113 -496000 ekin = 1.96100991422337 | erot = 3.58581695215166 | epot = -22.7342002900882 | etot = -17.1873734237132 -497000 ekin = 2.2228647925968 | erot = 2.49495319949133 | epot = -22.752706201593 | etot = -18.0348882095048 -498000 ekin = 1.71033952564695 | erot = 2.41331591511584 | epot = -22.7131621100867 | etot = -18.589506669324 -499000 ekin = 2.41919864300729 | erot = 2.82349519531821 | epot = -22.7304918052927 | etot = -17.4877979669672 -500000 ekin = 2.76271068346558 | erot = 2.22796445937143 | epot = -22.810945568044 | etot = -17.820270425207 -501000 ekin = 2.97642553987186 | erot = 1.97769778889399 | epot = -22.8306304048616 | etot = -17.8765070760957 -502000 ekin = 2.96175345860856 | erot = 1.80859086419487 | epot = -22.8525538190094 | etot = -18.082209496206 -503000 ekin = 2.51126831088417 | erot = 2.88572311841927 | epot = -22.8673362278446 | etot = -17.4703447985412 -504000 ekin = 2.84611165351303 | erot = 2.67626783872459 | epot = -22.784891957601 | etot = -17.2625124653634 -505000 ekin = 2.96124584448914 | erot = 2.59100575301934 | epot = -22.8251284225258 | etot = -17.2728768250174 -506000 ekin = 2.19858217910528 | erot = 1.97142936872076 | epot = -22.8530995461462 | etot = -18.6830879983201 -507000 ekin = 2.27398115142402 | erot = 2.68837996151517 | epot = -22.8141163798141 | etot = -17.8517552668749 -508000 ekin = 2.64439339973837 | erot = 2.04756467869449 | epot = -22.8146247157345 | etot = -18.1226666373017 -509000 ekin = 2.96023637315629 | erot = 2.90549934754532 | epot = -22.8719625385967 | etot = -17.0062268178951 -510000 ekin = 2.26067558634546 | erot = 2.80864918519521 | epot = -22.9774448292236 | etot = -17.9081200576829 -511000 ekin = 2.88512738978599 | erot = 2.15263877534437 | epot = -23.086672848248 | etot = -18.0489066831176 -512000 ekin = 2.17783748155516 | erot = 2.31389139764186 | epot = -23.1520181882638 | etot = -18.6602893090668 -513000 ekin = 1.69717952556151 | erot = 2.88265468656805 | epot = -23.1640284548407 | etot = -18.5841942427111 -514000 ekin = 1.72432024724117 | erot = 2.32742209152174 | epot = -23.1602225830814 | etot = -19.1084802443185 -515000 ekin = 2.00525337522086 | erot = 1.80102864435032 | epot = -23.1548763180746 | etot = -19.3485942985034 -516000 ekin = 3.04706172157038 | erot = 1.54171785431326 | epot = -23.1202751246552 | etot = -18.5314955487716 -517000 ekin = 2.47323892251936 | erot = 2.10799615007355 | epot = -23.0942246440307 | etot = -18.5129895714378 -518000 ekin = 2.03556879740597 | erot = 2.51531294708502 | epot = -23.01998934344 | etot = -18.4691075989491 -519000 ekin = 1.59255614728459 | erot = 1.63520468579907 | epot = -22.9787913166931 | etot = -19.7510304836094 -520000 ekin = 2.17210761761845 | erot = 1.8975366735392 | epot = -22.9877149955356 | etot = -18.918070704378 -521000 ekin = 1.98466680078867 | erot = 2.09219045542651 | epot = -23.0348541858322 | etot = -18.9579969296171 -522000 ekin = 2.72098469914434 | erot = 2.19565658619456 | epot = -23.1001210576502 | etot = -18.1834797723113 -523000 ekin = 2.26033454380754 | erot = 1.67112114369622 | epot = -23.1475509854345 | etot = -19.2160952979307 -524000 ekin = 2.34603831546138 | erot = 2.1054661011949 | epot = -23.1746761633773 | etot = -18.723171746721 -525000 ekin = 2.13671314300235 | erot = 2.07172081705863 | epot = -23.241177743004 | etot = -19.032743782943 -526000 ekin = 2.50849953901566 | erot = 2.27662230434506 | epot = -23.3179050583979 | etot = -18.5327832150372 -527000 ekin = 3.04322527932213 | erot = 1.8128057083239 | epot = -23.3977373118239 | etot = -18.5417063241779 -528000 ekin = 2.572303182379 | erot = 2.54386055260816 | epot = -23.4208428708383 | etot = -18.3046791358511 -529000 ekin = 2.39361269633634 | erot = 1.91637577362227 | epot = -23.3966015599491 | etot = -19.0866130899905 -530000 ekin = 3.3562937907424 | erot = 3.41683815876463 | epot = -23.2977853851852 | etot = -16.5246534356781 -531000 ekin = 2.52741741752381 | erot = 2.34075342407645 | epot = -23.1721175623278 | etot = -18.3039467207275 -532000 ekin = 2.78397051305127 | erot = 1.78575123294094 | epot = -23.2171711834401 | etot = -18.6474494374479 -533000 ekin = 2.27408274334042 | erot = 2.01427501035043 | epot = -23.2885684059727 | etot = -19.0002106522818 -534000 ekin = 2.54998010491125 | erot = 2.0164545364507 | epot = -23.340767920006 | etot = -18.7743332786441 -535000 ekin = 2.49595662250557 | erot = 2.09586427439366 | epot = -23.3878755759449 | etot = -18.7960546790457 -536000 ekin = 2.47717157546008 | erot = 1.92116873587364 | epot = -23.3847675210095 | etot = -18.9864272096758 -537000 ekin = 1.75235621440219 | erot = 2.11852052216092 | epot = -23.4590860280326 | etot = -19.5882092914695 -538000 ekin = 2.19317209186629 | erot = 2.75191518419657 | epot = -23.5517834707225 | etot = -18.6066961946597 -539000 ekin = 2.16135327665114 | erot = 2.25935011393788 | epot = -23.5718250119029 | etot = -19.1511216213139 -540000 ekin = 2.35701554620647 | erot = 1.6449529057333 | epot = -23.5490867129451 | etot = -19.5471182610054 -541000 ekin = 2.61451212811978 | erot = 2.52550284426682 | epot = -23.5334576350385 | etot = -18.3934426626519 -542000 ekin = 2.78909215024063 | erot = 2.09346850400965 | epot = -23.5754619290989 | etot = -18.6929012748486 -543000 ekin = 2.77024528778678 | erot = 1.84116991183092 | epot = -23.4849560716084 | etot = -18.8735408719907 -544000 ekin = 2.15807529188369 | erot = 1.50139575300257 | epot = -23.4530822422947 | etot = -19.7936111974084 -545000 ekin = 1.72860204886329 | erot = 2.56468335549414 | epot = -23.4524953434144 | etot = -19.159209939057 -546000 ekin = 2.38494138419348 | erot = 1.87772638427254 | epot = -23.4950389557033 | etot = -19.2323711872372 -547000 ekin = 2.44871634556835 | erot = 2.44464466893214 | epot = -23.544915775382 | etot = -18.6515547608815 -548000 ekin = 2.36962922994878 | erot = 2.40235228488721 | epot = -23.5548428056052 | etot = -18.7828612907692 -549000 ekin = 2.57958168249614 | erot = 2.04930779813674 | epot = -23.5565149978683 | etot = -18.9276255172355 -550000 ekin = 1.9793136647427 | erot = 1.85207468704394 | epot = -23.5614067919063 | etot = -19.7300184401196 -551000 ekin = 2.4121774327081 | erot = 2.0348936886299 | epot = -23.5115216908382 | etot = -19.0644505695002 -552000 ekin = 2.6621149390197 | erot = 1.41279265378133 | epot = -23.3450678435402 | etot = -19.2701602507391 -553000 ekin = 1.76359346131444 | erot = 2.63019210822711 | epot = -23.1435570943958 | etot = -18.7497715248542 -554000 ekin = 2.29840754300073 | erot = 2.34424452982823 | epot = -23.1114395278817 | etot = -18.4687874550527 -555000 ekin = 3.29672420152566 | erot = 1.64146930698359 | epot = -23.0891292168918 | etot = -18.1509357083825 -556000 ekin = 2.92076699655596 | erot = 2.59602967895818 | epot = -23.0268314200472 | etot = -17.5100347445331 -557000 ekin = 2.90322014804994 | erot = 3.16052668894921 | epot = -23.0146480567181 | etot = -16.950901219719 -558000 ekin = 2.78018761002222 | erot = 2.59826947006759 | epot = -22.7877399275349 | etot = -17.4092828474451 -559000 ekin = 2.48661596771862 | erot = 3.22596665511856 | epot = -22.8226574327834 | etot = -17.1100748099462 -560000 ekin = 2.34942852601698 | erot = 2.32773162877396 | epot = -22.8255608134696 | etot = -18.1484006586786 -561000 ekin = 2.0520192544917 | erot = 2.90306975046936 | epot = -22.8488516051139 | etot = -17.8937626001529 -562000 ekin = 2.18821919117372 | erot = 3.66499439159819 | epot = -22.7618817506902 | etot = -16.9086681679183 -563000 ekin = 3.11505518852414 | erot = 2.28057725990564 | epot = -22.791430640287 | etot = -17.3957981918572 -564000 ekin = 2.45343120006931 | erot = 2.36321638506708 | epot = -22.75807077839 | etot = -17.9414231932536 -565000 ekin = 2.77835835502221 | erot = 2.07073547186409 | epot = -22.7486053888412 | etot = -17.8995115619549 -566000 ekin = 2.43655641927934 | erot = 2.19832280178868 | epot = -22.7227654505166 | etot = -18.0878862294486 -567000 ekin = 2.71233133108494 | erot = 2.01281091173405 | epot = -22.8839744455115 | etot = -18.1588322026925 -568000 ekin = 3.12450796157708 | erot = 1.93520150351061 | epot = -22.9625972279254 | etot = -17.9028877628377 -569000 ekin = 3.72714267701977 | erot = 2.06562452789051 | epot = -22.9814174117752 | etot = -17.1886502068649 -570000 ekin = 2.68808623045676 | erot = 2.36042122391805 | epot = -22.998959026692 | etot = -17.9504515723172 -571000 ekin = 1.97223467321356 | erot = 2.85558181274648 | epot = -22.9369001315648 | etot = -18.1090836456047 -572000 ekin = 2.4182049732123 | erot = 2.40910077907643 | epot = -22.934930836907 | etot = -18.1076250846182 -573000 ekin = 1.76702714285012 | erot = 2.31739567602694 | epot = -22.9768902017483 | etot = -18.8924673828712 -574000 ekin = 2.08740259214111 | erot = 2.59288012722136 | epot = -23.0518321557917 | etot = -18.3715494364293 -575000 ekin = 2.34020490338786 | erot = 2.78500973557001 | epot = -23.106579446946 | etot = -17.9813648079881 -576000 ekin = 2.15506609467459 | erot = 3.3045287538029 | epot = -23.1521162771299 | etot = -17.6925214286524 -577000 ekin = 2.45698150895878 | erot = 2.31876672704204 | epot = -23.1781917242715 | etot = -18.4024434882707 -578000 ekin = 2.59353106592521 | erot = 2.33790294336519 | epot = -23.2101395643707 | etot = -18.2787055550803 -579000 ekin = 2.58102015460712 | erot = 1.71748063175117 | epot = -23.1865014452815 | etot = -18.8880006589232 -580000 ekin = 2.30361750578347 | erot = 2.87410564379621 | epot = -23.2045008793077 | etot = -18.026777729728 -581000 ekin = 2.45915247103344 | erot = 2.59640238490727 | epot = -23.1882783600354 | etot = -18.1327235040947 -582000 ekin = 2.33801590725494 | erot = 3.19256035650617 | epot = -23.2501410058056 | etot = -17.7195647420445 -583000 ekin = 1.95982078382855 | erot = 2.81944051586213 | epot = -23.4085593869414 | etot = -18.6292980872508 -584000 ekin = 2.00358327245437 | erot = 1.7126727026301 | epot = -23.4960310960901 | etot = -19.7797751210056 -585000 ekin = 2.28859150562676 | erot = 2.06309046911262 | epot = -23.5306230166998 | etot = -19.1789410419604 -586000 ekin = 2.21858454582016 | erot = 1.97776854350186 | epot = -23.4873397268816 | etot = -19.2909866375596 -587000 ekin = 3.70065233550663 | erot = 1.82187748311298 | epot = -23.4652388428899 | etot = -17.9427090242702 -588000 ekin = 3.49447328534893 | erot = 2.31981981591506 | epot = -23.3985567739262 | etot = -17.5842636726622 -589000 ekin = 2.66144502802388 | erot = 3.02756546370717 | epot = -23.2783756079917 | etot = -17.5893651162607 -590000 ekin = 1.52141257336428 | erot = 2.09874614600563 | epot = -23.1290158071881 | etot = -19.5088570878182 -591000 ekin = 1.82897193042274 | erot = 1.75592223095374 | epot = -23.0622736076073 | etot = -19.4773794462309 -592000 ekin = 2.49491276892191 | erot = 2.5482988197852 | epot = -23.054885494985 | etot = -18.0116739062779 -593000 ekin = 2.36845716276159 | erot = 1.78503341410575 | epot = -23.005264310194 | etot = -18.8517737333267 -594000 ekin = 2.07907010887474 | erot = 2.14563658430187 | epot = -22.9611396232755 | etot = -18.7364329300989 -595000 ekin = 2.62736231723874 | erot = 2.0397582574453 | epot = -22.9495489717352 | etot = -18.2824283970512 -596000 ekin = 2.58985967531625 | erot = 2.12449830164849 | epot = -22.9908505579803 | etot = -18.2764925810155 -597000 ekin = 3.02540042664856 | erot = 3.14256707367048 | epot = -22.9740991012936 | etot = -16.8061316009746 -598000 ekin = 3.44397104083287 | erot = 2.8605790839857 | epot = -23.0035411551228 | etot = -16.6989910303042 -599000 ekin = 2.13932500926498 | erot = 3.49187029024979 | epot = -22.9657391359988 | etot = -17.334543836484 -600000 ekin = 2.19758597945326 | erot = 2.49610822362376 | epot = -22.9452235009931 | etot = -18.2515292979161 -601000 ekin = 2.80918982916752 | erot = 2.81768433603376 | epot = -22.8970508934525 | etot = -17.2701767282513 -602000 ekin = 2.30031523379463 | erot = 2.40907304500534 | epot = -22.8523950981499 | etot = -18.1430068193499 -603000 ekin = 1.91335501396421 | erot = 1.99518053980753 | epot = -22.7884152302358 | etot = -18.879879676464 -604000 ekin = 2.5976715095492 | erot = 3.14351403383687 | epot = -22.7430641975849 | etot = -17.0018786541988 -605000 ekin = 2.63203298717972 | erot = 2.07906613894389 | epot = -22.7307949909783 | etot = -18.0196958648547 -606000 ekin = 2.94678399289781 | erot = 2.03982213630799 | epot = -22.6555302524726 | etot = -17.6689241232668 -607000 ekin = 2.85272606479019 | erot = 2.36693467257681 | epot = -22.6318548820144 | etot = -17.4121941446474 -608000 ekin = 3.6642968125636 | erot = 2.46706737589234 | epot = -22.5724662590778 | etot = -16.4411020706219 -609000 ekin = 2.69343886620625 | erot = 2.25873504143679 | epot = -22.6007364465805 | etot = -17.6485625389374 -610000 ekin = 2.99904616523658 | erot = 2.13621966615343 | epot = -22.5973658485054 | etot = -17.4621000171154 -611000 ekin = 3.86832985948944 | erot = 2.12096644577641 | epot = -22.5702925425382 | etot = -16.5809962372724 -612000 ekin = 2.88515301824618 | erot = 2.45910554524357 | epot = -22.4848584522585 | etot = -17.1405998887688 -613000 ekin = 2.9367425327116 | erot = 2.14436169371533 | epot = -22.465526703267 | etot = -17.3844224768401 -614000 ekin = 2.79116462876301 | erot = 2.024409539648 | epot = -22.5207406301148 | etot = -17.7051664617038 -615000 ekin = 2.29338048298908 | erot = 2.38828872470982 | epot = -22.6082782403584 | etot = -17.9266090326595 -616000 ekin = 1.78195169789474 | erot = 2.45334803626968 | epot = -22.6887534547644 | etot = -18.4534537206 -617000 ekin = 2.57505808534158 | erot = 2.55345758187858 | epot = -22.701463839496 | etot = -17.5729481722758 -618000 ekin = 2.29561379442387 | erot = 2.68043259355499 | epot = -22.629958627306 | etot = -17.6539122393272 -619000 ekin = 1.94323313590202 | erot = 2.00964911157699 | epot = -22.56819110474 | etot = -18.6153088572609 -620000 ekin = 2.92263589097657 | erot = 2.15657756066215 | epot = -22.6264664894927 | etot = -17.547253037854 -621000 ekin = 2.90437881656455 | erot = 1.70649555848315 | epot = -22.665419447573 | etot = -18.0545450725253 -622000 ekin = 2.03426149564846 | erot = 2.51826459248401 | epot = -22.6086250578043 | etot = -18.0560989696718 -623000 ekin = 1.98348786592096 | erot = 3.08484972830227 | epot = -22.6234743341759 | etot = -17.5551367399527 -624000 ekin = 2.08463083558977 | erot = 2.64004606903047 | epot = -22.6266529328942 | etot = -17.901976028274 -625000 ekin = 2.52963490334089 | erot = 2.37033264022622 | epot = -22.6750436783156 | etot = -17.7750761347485 -626000 ekin = 2.73147680333726 | erot = 2.07051651598004 | epot = -22.7272383647964 | etot = -17.9252450454791 -627000 ekin = 2.23447399123207 | erot = 2.35288557052269 | epot = -22.7136740507756 | etot = -18.1263144890208 -628000 ekin = 2.28933754695897 | erot = 2.29676268895054 | epot = -22.6176528573237 | etot = -18.0315526214142 -629000 ekin = 2.5355466362136 | erot = 1.92082543033528 | epot = -22.5693331526924 | etot = -18.1129610861435 -630000 ekin = 3.11700824717166 | erot = 2.51611049765935 | epot = -22.5144695759915 | etot = -16.8813508311605 -631000 ekin = 2.38844807455604 | erot = 3.31601650504458 | epot = -22.5190998334878 | etot = -16.8146352538871 -632000 ekin = 2.59939587493746 | erot = 2.51496212358955 | epot = -22.4711049664696 | etot = -17.3567469679426 -633000 ekin = 2.45338619933597 | erot = 1.89874016257143 | epot = -22.4394257686937 | etot = -18.0872994067863 -634000 ekin = 2.23819111967047 | erot = 1.98305652730466 | epot = -22.3433365860708 | etot = -18.1220889390957 -635000 ekin = 2.22438000857702 | erot = 1.95893208021227 | epot = -22.2877959440852 | etot = -18.1044838552959 -636000 ekin = 2.26938644192167 | erot = 2.77816773779856 | epot = -22.304696935737 | etot = -17.2571427560168 -637000 ekin = 1.97799147515645 | erot = 2.59610837639352 | epot = -22.3353238115758 | etot = -17.7612239600258 -638000 ekin = 2.54901279963355 | erot = 3.14232301833368 | epot = -22.3113570318407 | etot = -16.6200212138734 -639000 ekin = 2.38194254982011 | erot = 2.49468098011844 | epot = -22.2696251856514 | etot = -17.3930016557128 -640000 ekin = 2.07438054408915 | erot = 2.20336226777045 | epot = -22.1673693230788 | etot = -17.8896265112192 -641000 ekin = 2.49150296422893 | erot = 3.53882164550033 | epot = -22.047323387435 | etot = -16.0169987777057 -642000 ekin = 3.37964058409635 | erot = 2.18458831029801 | epot = -21.9324522713976 | etot = -16.3682233770032 -643000 ekin = 2.80862431007863 | erot = 2.40815089193716 | epot = -21.8726014240441 | etot = -16.6558262220283 -644000 ekin = 2.952235016065 | erot = 1.92776262379328 | epot = -21.826057423183 | etot = -16.9460597833247 -645000 ekin = 4.10488984334312 | erot = 1.89062109330214 | epot = -21.7981661301139 | etot = -15.8026551934687 -646000 ekin = 2.50234872105284 | erot = 2.00205075040523 | epot = -21.7221642434957 | etot = -17.2177647720377 -647000 ekin = 2.52267281239589 | erot = 2.19481558810105 | epot = -21.7438885460027 | etot = -17.0264001455058 -648000 ekin = 2.99344241657584 | erot = 2.11139263207284 | epot = -21.7373240000025 | etot = -16.6324889513538 -649000 ekin = 2.55027365085816 | erot = 3.20350991793738 | epot = -21.7192481424448 | etot = -15.9654645736493 -650000 ekin = 3.75163896052813 | erot = 2.44189212282279 | epot = -21.6756681314987 | etot = -15.4821370481478 -651000 ekin = 3.29740056237165 | erot = 2.36780448747275 | epot = -21.5372361691658 | etot = -15.8720311193214 -652000 ekin = 2.54645886055823 | erot = 2.99097829596978 | epot = -21.4549655298412 | etot = -15.9175283733132 -653000 ekin = 2.88682688109756 | erot = 2.53633970608342 | epot = -21.4696471597398 | etot = -16.0464805725588 -654000 ekin = 2.28614085804932 | erot = 2.12026601708473 | epot = -21.5642684321318 | etot = -17.1578615569978 -655000 ekin = 2.20709609517087 | erot = 2.10729950549551 | epot = -21.5349466292622 | etot = -17.2205510285959 -656000 ekin = 2.40310876229413 | erot = 2.09663823500903 | epot = -21.5631924595209 | etot = -17.0634454622178 -657000 ekin = 2.7886551346751 | erot = 2.19608839827219 | epot = -21.794507747247 | etot = -16.8097642142998 -658000 ekin = 3.1025713807162 | erot = 2.59154293692773 | epot = -21.96675599421 | etot = -16.2726416765661 -659000 ekin = 2.88891106020275 | erot = 3.47010878893494 | epot = -22.0542552611187 | etot = -15.695235411981 -660000 ekin = 2.90074521854052 | erot = 1.62850743298554 | epot = -22.1003034196589 | etot = -17.5710507681328 -661000 ekin = 3.26666543815737 | erot = 1.86223225384175 | epot = -22.202664217118 | etot = -17.0737665251189 -662000 ekin = 3.1558491019044 | erot = 2.16868634291728 | epot = -22.3049478747805 | etot = -16.9804124299588 -663000 ekin = 1.94349853674083 | erot = 2.45687952722591 | epot = -22.3908978754178 | etot = -17.990519811451 -664000 ekin = 1.45445820960401 | erot = 1.37641815749115 | epot = -22.5088813854798 | etot = -19.6780050183846 -665000 ekin = 1.57568561901953 | erot = 2.30379312359823 | epot = -22.5957949572927 | etot = -18.7163162146749 -666000 ekin = 2.46162449261636 | erot = 1.76978614573263 | epot = -22.7431602236664 | etot = -18.5117495853174 -667000 ekin = 2.82410423268351 | erot = 2.3383666365949 | epot = -22.9350563238978 | etot = -17.7725854546194 -668000 ekin = 2.73717686116191 | erot = 3.18779777915035 | epot = -23.0188768131827 | etot = -17.0939021728704 -669000 ekin = 3.41035672635339 | erot = 2.45479601777612 | epot = -23.0718232403886 | etot = -17.2066704962591 -670000 ekin = 2.54649164859505 | erot = 1.99520979169172 | epot = -23.0246775830826 | etot = -18.4829761427959 -671000 ekin = 2.3802025684166 | erot = 3.00742736998541 | epot = -23.0023479116088 | etot = -17.6147179732068 -672000 ekin = 3.0126952152146 | erot = 2.55297219144565 | epot = -22.9947723733502 | etot = -17.4291049666899 -673000 ekin = 3.39486270740071 | erot = 2.3808700262033 | epot = -22.9033457919095 | etot = -17.1276130583054 -674000 ekin = 3.13698489626099 | erot = 2.10609113054063 | epot = -22.8089270617647 | etot = -17.5658510349631 -675000 ekin = 2.32294130821675 | erot = 1.5285851482073 | epot = -22.6840603385672 | etot = -18.8325338821432 -676000 ekin = 2.43564726401376 | erot = 2.26860623636408 | epot = -22.6133446272028 | etot = -17.909091126825 -677000 ekin = 2.75162757613842 | erot = 1.94219014743457 | epot = -22.7039380847023 | etot = -18.0101203611293 -678000 ekin = 2.86321973687601 | erot = 1.66387788364136 | epot = -22.7223510604726 | etot = -18.1952534399553 -679000 ekin = 2.35079208772869 | erot = 2.70386328048641 | epot = -22.7977445343495 | etot = -17.7430891661344 -680000 ekin = 2.48449675729004 | erot = 2.90645575582477 | epot = -22.8559375688936 | etot = -17.4649850557788 -681000 ekin = 1.91581136662333 | erot = 2.58179603882022 | epot = -22.7891325966099 | etot = -18.2915251911664 -682000 ekin = 2.10466427353705 | erot = 2.69470735868807 | epot = -22.6959043279182 | etot = -17.896532695693 -683000 ekin = 2.34504535409021 | erot = 2.11592035700791 | epot = -22.5718670441909 | etot = -18.1109013330928 -684000 ekin = 2.87198876498958 | erot = 2.65732173958706 | epot = -22.4986977268025 | etot = -16.9693872222258 -685000 ekin = 3.03375238110975 | erot = 2.18190577381518 | epot = -22.4634189289575 | etot = -17.2477607740326 -686000 ekin = 2.46248931777656 | erot = 2.43025710170918 | epot = -22.4079029677658 | etot = -17.5151565482801 -687000 ekin = 2.74662486817896 | erot = 1.79609152562411 | epot = -22.3360381567114 | etot = -17.7933217629083 -688000 ekin = 1.81703718003042 | erot = 2.06511603415635 | epot = -22.3083758541198 | etot = -18.426222639933 -689000 ekin = 2.84202633430564 | erot = 1.92033962884777 | epot = -22.3752571185822 | etot = -17.6128911554288 -690000 ekin = 2.07525448405017 | erot = 2.46342632176817 | epot = -22.4633535431152 | etot = -17.9246727372969 -691000 ekin = 2.12558517800138 | erot = 2.52961097164 | epot = -22.483426266766 | etot = -17.8282301171246 -692000 ekin = 2.86720433292881 | erot = 2.65102150657025 | epot = -22.4003374064863 | etot = -16.8821115669873 -693000 ekin = 2.30143055084864 | erot = 2.52290946383361 | epot = -22.2859681228792 | etot = -17.4616281081969 -694000 ekin = 2.88400701080875 | erot = 2.34320802755437 | epot = -22.206318584282 | etot = -16.9791035459189 -695000 ekin = 2.93184722112895 | erot = 2.22933507376834 | epot = -22.2348177906806 | etot = -17.0736354957833 -696000 ekin = 2.63173546326796 | erot = 2.34275369570833 | epot = -22.274597219839 | etot = -17.3001080608627 -697000 ekin = 1.87084079501972 | erot = 1.78050094908734 | epot = -22.2730387150935 | etot = -18.6216969709865 -698000 ekin = 2.19791428580687 | erot = 2.82883581756349 | epot = -22.2819378523405 | etot = -17.2551877489701 -699000 ekin = 2.34279295545267 | erot = 2.07514436344563 | epot = -22.2061425261575 | etot = -17.7882052072592 -700000 ekin = 2.576803119019 | erot = 2.32167543064962 | epot = -22.1658685747825 | etot = -17.2673900251139 -701000 ekin = 2.9943865807539 | erot = 1.89982533986206 | epot = -22.2191193266439 | etot = -17.324907406028 -702000 ekin = 2.68548464757459 | erot = 2.65050744453208 | epot = -22.2547415922757 | etot = -16.918749500169 -703000 ekin = 2.01996957402024 | erot = 2.04032822241737 | epot = -22.3253693056515 | etot = -18.2650715092139 -704000 ekin = 1.58871069317829 | erot = 1.64014270467762 | epot = -22.3617232281452 | etot = -19.1328698302893 -705000 ekin = 2.3089415754982 | erot = 1.90252913035993 | epot = -22.4307958564623 | etot = -18.2193251506042 -706000 ekin = 2.61729186445574 | erot = 3.21879868039103 | epot = -22.5603358780911 | etot = -16.7242453332443 -707000 ekin = 2.60797107906866 | erot = 2.31455039977396 | epot = -22.7102471053997 | etot = -17.7877256265571 -708000 ekin = 1.81633850341999 | erot = 2.3482257566942 | epot = -22.841408787855 | etot = -18.6768445277408 -709000 ekin = 1.83541322105378 | erot = 2.51792380003796 | epot = -23.0137235815795 | etot = -18.6603865604878 -710000 ekin = 2.2142058326246 | erot = 1.92378721690473 | epot = -23.1433453130909 | etot = -19.0053522635615 -711000 ekin = 2.06744054454467 | erot = 2.3981170935319 | epot = -23.1532717948855 | etot = -18.687714156809 -712000 ekin = 2.1727947270635 | erot = 1.75362175342097 | epot = -23.0479262273955 | etot = -19.121509746911 -713000 ekin = 2.87118830138474 | erot = 1.54943993787555 | epot = -22.8430575230906 | etot = -18.4224292838303 -714000 ekin = 2.0107946674397 | erot = 1.87510988392751 | epot = -22.9212969433221 | etot = -19.0353923919549 -715000 ekin = 2.4992182958927 | erot = 1.91934008289236 | epot = -22.9679126658062 | etot = -18.5493542870211 -716000 ekin = 2.94666510633353 | erot = 2.18714442405523 | epot = -23.033997097429 | etot = -17.9001875670402 -717000 ekin = 3.07404079722085 | erot = 2.46628262765133 | epot = -23.1869721551174 | etot = -17.6466487302452 -718000 ekin = 3.47060078371109 | erot = 2.28206620506093 | epot = -23.2524492340768 | etot = -17.4997822453048 -719000 ekin = 4.08343792096552 | erot = 3.10429377075217 | epot = -23.2448292181926 | etot = -16.0570975264749 -720000 ekin = 2.52774819763971 | erot = 1.92867508904585 | epot = -23.1435084559682 | etot = -18.6870851692826 -721000 ekin = 2.58294244811584 | erot = 2.0383053178033 | epot = -23.0601633758883 | etot = -18.4389156099691 -722000 ekin = 1.9445888545086 | erot = 2.32008660802523 | epot = -22.9811929404572 | etot = -18.7165174779234 -723000 ekin = 2.41998340576259 | erot = 2.12369728979369 | epot = -23.0570939793876 | etot = -18.5134132838314 -724000 ekin = 1.90406371300861 | erot = 1.97533505769876 | epot = -23.1267629042383 | etot = -19.247364133531 -725000 ekin = 2.14287056473422 | erot = 2.79289687450022 | epot = -23.1695632046138 | etot = -18.2337957653794 -726000 ekin = 2.26423317099721 | erot = 2.55343019202652 | epot = -23.2432909083709 | etot = -18.4256275453472 -727000 ekin = 1.69816397656716 | erot = 2.64011919415556 | epot = -23.298837689321 | etot = -18.9605545185982 -728000 ekin = 2.23000862561934 | erot = 3.58521470578671 | epot = -23.3528245832467 | etot = -17.5376012518407 -729000 ekin = 2.70076566380343 | erot = 1.73367306410751 | epot = -23.3971276122796 | etot = -18.9626888843686 -730000 ekin = 2.54818673802759 | erot = 2.77394958410256 | epot = -23.3988686964744 | etot = -18.0767323743443 -731000 ekin = 2.69782550956093 | erot = 2.04855826523075 | epot = -23.4310969813891 | etot = -18.6847132065974 -732000 ekin = 2.79613002753752 | erot = 1.87867430486715 | epot = -23.4885161441653 | etot = -18.8137118117607 -733000 ekin = 2.20346728125046 | erot = 2.64365594749975 | epot = -23.5261309431819 | etot = -18.6790077144317 -734000 ekin = 1.69780111261443 | erot = 2.30917909560787 | epot = -23.5188046470475 | etot = -19.5118244388252 -735000 ekin = 2.18402736165936 | erot = 2.72051620230871 | epot = -23.4712689506938 | etot = -18.5667253867257 -736000 ekin = 2.26138696009404 | erot = 1.17083930058803 | epot = -23.4348107178754 | etot = -20.0025844571934 -737000 ekin = 2.22219419044796 | erot = 3.14114682990362 | epot = -23.3869288757725 | etot = -18.0235878554209 -738000 ekin = 1.75464981631084 | erot = 2.28485941478058 | epot = -23.2709893028052 | etot = -19.2314800717138 -739000 ekin = 1.41806378584362 | erot = 2.16714034112821 | epot = -23.2213775300889 | etot = -19.636173403117 -740000 ekin = 1.90901017596351 | erot = 2.27102763422491 | epot = -23.1829198366046 | etot = -19.0028820264162 -741000 ekin = 1.9930994487751 | erot = 2.73523269523399 | epot = -23.1169670577824 | etot = -18.3886349137733 -742000 ekin = 1.99876411117685 | erot = 1.89882876917754 | epot = -23.0300825800851 | etot = -19.1324896997307 -743000 ekin = 1.96472814667687 | erot = 2.79504722629174 | epot = -22.8990488521609 | etot = -18.1392734791923 -744000 ekin = 2.02442646092311 | erot = 2.35044838626024 | epot = -22.8186526150799 | etot = -18.4437777678966 -745000 ekin = 1.65344231988822 | erot = 1.87919095141018 | epot = -22.7624827109091 | etot = -19.2298494396107 -746000 ekin = 2.1034668185472 | erot = 2.03078530569663 | epot = -22.743454277698 | etot = -18.6092021534542 -747000 ekin = 3.06690414848489 | erot = 1.6754029786949 | epot = -22.7625979159322 | etot = -18.0202907887524 -748000 ekin = 3.06965414483401 | erot = 1.86014593098643 | epot = -22.8118567150739 | etot = -17.8820566392535 -749000 ekin = 2.53718696167217 | erot = 2.02710579059033 | epot = -22.8431046011969 | etot = -18.2788118489344 -750000 ekin = 2.75657354808099 | erot = 2.34953156046291 | epot = -22.9548205390759 | etot = -17.848715430532 -751000 ekin = 2.52290020835147 | erot = 2.34873763599977 | epot = -23.0238691402084 | etot = -18.1522312958572 -752000 ekin = 2.47222247869325 | erot = 1.68679846444683 | epot = -22.9958559112491 | etot = -18.8368349681091 -753000 ekin = 2.48263277172423 | erot = 1.54669382815742 | epot = -23.0858212396418 | etot = -19.0564946397602 -754000 ekin = 2.54806257410878 | erot = 2.26636466676163 | epot = -23.1896472696842 | etot = -18.3752200288138 -755000 ekin = 1.53168409517921 | erot = 2.22665478278013 | epot = -23.2059118234918 | etot = -19.4475729455324 -756000 ekin = 2.10751715527953 | erot = 2.40525774326678 | epot = -23.114150245375 | etot = -18.6013753468287 -757000 ekin = 2.93395895491028 | erot = 2.05821177584909 | epot = -23.0783355599275 | etot = -18.0861648291682 -758000 ekin = 2.38307945406232 | erot = 2.50598165375058 | epot = -22.9691152621287 | etot = -18.0800541543158 -759000 ekin = 2.60292884338835 | erot = 2.36916677072548 | epot = -22.7987274767845 | etot = -17.8266318626707 -760000 ekin = 3.2284318196987 | erot = 2.73822716520638 | epot = -22.6756147646272 | etot = -16.7089557797221 -761000 ekin = 3.41868727786494 | erot = 1.68975765213408 | epot = -22.5638952547581 | etot = -17.4554503247591 -762000 ekin = 3.43033946346107 | erot = 2.5283975140253 | epot = -22.3549032489322 | etot = -16.3961662714458 -763000 ekin = 2.65773094814485 | erot = 1.83975133975562 | epot = -22.234833339183 | etot = -17.7373510512825 -764000 ekin = 2.3815484472129 | erot = 2.70684992442147 | epot = -22.0890752688231 | etot = -17.0006768971887 -765000 ekin = 2.23212803588897 | erot = 1.94868597739427 | epot = -21.9918715237933 | etot = -17.81105751051 -766000 ekin = 2.49097891886066 | erot = 1.96764603993156 | epot = -21.8443436680801 | etot = -17.3857187092879 -767000 ekin = 2.3457921497675 | erot = 2.64636009163513 | epot = -21.7634962034012 | etot = -16.7713439619986 -768000 ekin = 1.87671147825106 | erot = 2.05549869178485 | epot = -21.7324638416528 | etot = -17.8002536716169 -769000 ekin = 3.05058687860239 | erot = 2.66104171022372 | epot = -21.66792195987 | etot = -15.9562933710439 -770000 ekin = 2.44115683640633 | erot = 1.97554932479751 | epot = -21.6448820664751 | etot = -17.2281759052712 -771000 ekin = 2.23687464004429 | erot = 2.55040970708789 | epot = -21.5811924169692 | etot = -16.793908069837 -772000 ekin = 2.76529680592008 | erot = 1.97873499811185 | epot = -21.6543448952384 | etot = -16.9103130912064 -773000 ekin = 2.14632888240094 | erot = 2.41330587525514 | epot = -21.7728828090228 | etot = -17.2132480513667 -774000 ekin = 2.19848545803079 | erot = 1.9765131024719 | epot = -21.8398858604883 | etot = -17.6648872999856 -775000 ekin = 2.52300137989083 | erot = 2.80935365273515 | epot = -22.0219985274259 | etot = -16.6896434947999 -776000 ekin = 3.15842485269274 | erot = 2.47066157093645 | epot = -22.183029096161 | etot = -16.5539426725319 -777000 ekin = 1.91784338934576 | erot = 1.76045300517081 | epot = -22.2259652888115 | etot = -18.547668894295 -778000 ekin = 2.93738066043324 | erot = 2.29457842490289 | epot = -22.2339481852394 | etot = -17.0019890999032 -779000 ekin = 3.09847206114319 | erot = 2.0455771700605 | epot = -22.240438366259 | etot = -17.0963891350553 -780000 ekin = 2.86127568397807 | erot = 3.12055135138658 | epot = -22.1865692766137 | etot = -16.204742241249 -781000 ekin = 2.36069914420785 | erot = 3.53186431088487 | epot = -22.1210563364352 | etot = -16.2284928813425 -782000 ekin = 2.31592690319261 | erot = 2.85730598644035 | epot = -22.0302855151548 | etot = -16.8570526255218 -783000 ekin = 1.86647729944746 | erot = 3.03450246093099 | epot = -21.886014367949 | etot = -16.9850346075705 -784000 ekin = 2.04055627573201 | erot = 2.26047908607293 | epot = -21.7534271639393 | etot = -17.4523918021343 -785000 ekin = 2.02248469828703 | erot = 2.13950421850547 | epot = -21.6318967501918 | etot = -17.4699078333993 -786000 ekin = 2.34211746551602 | erot = 2.34838133643265 | epot = -21.5890308210084 | etot = -16.8985320190598 -787000 ekin = 2.74971447554938 | erot = 2.24123553296042 | epot = -21.5192132515563 | etot = -16.5282632430465 -788000 ekin = 2.14142056672039 | erot = 2.27008574684965 | epot = -21.4982362621714 | etot = -17.0867299486013 -789000 ekin = 1.98580913341303 | erot = 2.00702444041791 | epot = -21.5235331659838 | etot = -17.5306995921529 -790000 ekin = 1.68578263083924 | erot = 1.43485602862151 | epot = -21.6440081593601 | etot = -18.5233694998993 -791000 ekin = 2.13583938840528 | erot = 2.5373009545894 | epot = -21.7916440698418 | etot = -17.1185037268471 -792000 ekin = 1.71937483898028 | erot = 2.19563804216011 | epot = -21.8794946709408 | etot = -17.9644817898004 -793000 ekin = 3.15868943755338 | erot = 1.94575875708421 | epot = -22.0398145404617 | etot = -16.9353663458242 -794000 ekin = 2.45478602538954 | erot = 3.00825554959563 | epot = -22.0843165283013 | etot = -16.6212749533161 -795000 ekin = 2.87760320917193 | erot = 3.06920266633565 | epot = -22.1595628991904 | etot = -16.2127570236829 -796000 ekin = 2.29816690595058 | erot = 1.61510864654315 | epot = -22.1869705548184 | etot = -18.2736950023247 -797000 ekin = 2.1901525606721 | erot = 3.65734446008353 | epot = -22.1432608090644 | etot = -16.2957637883088 -798000 ekin = 2.12018787925578 | erot = 2.92822258455555 | epot = -22.1311312789224 | etot = -17.0827208151111 -799000 ekin = 2.49416140154829 | erot = 2.73328283280216 | epot = -22.0825726051882 | etot = -16.8551283708378 -800000 ekin = 2.18932007838552 | erot = 2.97640731559393 | epot = -21.979362152191 | etot = -16.8136347582115 -801000 ekin = 2.58827112124838 | erot = 2.7440442483726 | epot = -21.9108490336924 | etot = -16.5785336640714 -802000 ekin = 3.07870342348167 | erot = 2.87961505564287 | epot = -21.822560433681 | etot = -15.8642419545565 -803000 ekin = 2.2398624368064 | erot = 2.50525058807596 | epot = -21.72759408181 | etot = -16.9824810569277 -804000 ekin = 2.91885860068426 | erot = 1.57889040451428 | epot = -21.6896376725624 | etot = -17.1918886673638 -805000 ekin = 2.68277363980193 | erot = 3.05527868915738 | epot = -21.6710764398127 | etot = -15.9330241108534 -806000 ekin = 2.77769607049014 | erot = 2.1888727690908 | epot = -21.6314833902337 | etot = -16.6649145506527 -807000 ekin = 2.12673239079668 | erot = 2.86003407600806 | epot = -21.7295924017744 | etot = -16.7428259349697 -808000 ekin = 1.89599614774678 | erot = 2.29237053227662 | epot = -21.7511361510417 | etot = -17.5627694710183 -809000 ekin = 1.96405066221971 | erot = 1.92110393348368 | epot = -21.7075506883706 | etot = -17.8223960926672 -810000 ekin = 2.01518137594275 | erot = 2.60119247286596 | epot = -21.6788385874729 | etot = -17.0624647386642 -811000 ekin = 2.31084800889289 | erot = 1.75270367309064 | epot = -21.6837819033719 | etot = -17.6202302213883 -812000 ekin = 2.5770103100209 | erot = 2.34932304073588 | epot = -21.7246716033188 | etot = -16.798338252562 -813000 ekin = 2.87706904926076 | erot = 2.35686610624154 | epot = -21.8375922236049 | etot = -16.6036570681026 -814000 ekin = 2.89908405023866 | erot = 2.31423299883226 | epot = -21.8379261473901 | etot = -16.6246090983192 -815000 ekin = 2.54050064212256 | erot = 2.82732568868829 | epot = -21.6068952707049 | etot = -16.2390689398941 -816000 ekin = 2.17040404256387 | erot = 2.53711088209172 | epot = -21.5560322071983 | etot = -16.8485172825427 -817000 ekin = 1.7842696071831 | erot = 2.67810959410576 | epot = -21.8738878035325 | etot = -17.4115086022437 -818000 ekin = 2.29659398017838 | erot = 2.63718862373664 | epot = -22.164277271391 | etot = -17.230494667476 -819000 ekin = 2.15801167884062 | erot = 2.62095572928877 | epot = -22.1816109590116 | etot = -17.4026435508822 -820000 ekin = 1.94384548213955 | erot = 2.28597987799275 | epot = -22.0986187375022 | etot = -17.8687933773699 -821000 ekin = 2.10513194007576 | erot = 2.38698175569219 | epot = -22.1146754444785 | etot = -17.6225617487105 -822000 ekin = 2.24819716786441 | erot = 2.15258805680875 | epot = -22.0539472940486 | etot = -17.6531620693754 -823000 ekin = 2.26584952085583 | erot = 2.60619852526611 | epot = -22.0924201800579 | etot = -17.220372133936 -824000 ekin = 1.65187935478514 | erot = 1.48703119037228 | epot = -22.1682955997986 | etot = -19.0293850546412 -825000 ekin = 1.60213094818648 | erot = 1.98592524368393 | epot = -22.1687104063708 | etot = -18.5806542145004 -826000 ekin = 1.97430720107255 | erot = 2.19175014677159 | epot = -22.1061881978655 | etot = -17.9401308500213 -827000 ekin = 2.1793755983405 | erot = 2.44975419075935 | epot = -21.9704586607304 | etot = -17.3413288716305 -828000 ekin = 1.90399088418588 | erot = 2.72532994798816 | epot = -21.9585923270583 | etot = -17.3292714948842 -829000 ekin = 2.06478103068884 | erot = 2.9658303540259 | epot = -21.9849402038682 | etot = -16.9543288191534 -830000 ekin = 1.98920675238979 | erot = 2.15331250444996 | epot = -22.0339146439702 | etot = -17.8913953871305 -831000 ekin = 2.33567462674689 | erot = 2.36888807413497 | epot = -22.1271573756461 | etot = -17.4225946747643 -832000 ekin = 2.0119470999192 | erot = 1.94769143293625 | epot = -22.2038482709588 | etot = -18.2442097381034 -833000 ekin = 2.26025933495881 | erot = 2.16012558191462 | epot = -22.2882501045414 | etot = -17.867865187668 -834000 ekin = 2.11529426445865 | erot = 1.52405523315358 | epot = -22.3075608649826 | etot = -18.6682113673703 -835000 ekin = 2.8992075090551 | erot = 2.73801081751029 | epot = -22.3942491248321 | etot = -16.7570307982667 -836000 ekin = 3.33069528982658 | erot = 2.4277126780786 | epot = -22.4321737300744 | etot = -16.6737657621692 -837000 ekin = 2.74831774333782 | erot = 2.31991750378628 | epot = -22.4290234552872 | etot = -17.3607882081631 -838000 ekin = 3.13714871682188 | erot = 3.21601751721777 | epot = -22.4642383906451 | etot = -16.1110721566054 -839000 ekin = 2.73358272751807 | erot = 2.60144488190506 | epot = -22.4062682687368 | etot = -17.0712406593137 -840000 ekin = 2.96121930874637 | erot = 1.42725942278118 | epot = -22.3293755621294 | etot = -17.9408968306018 -841000 ekin = 2.95134811170866 | erot = 2.67666861874608 | epot = -22.2936348151224 | etot = -16.6656180846677 -842000 ekin = 2.15783928636401 | erot = 2.30287195796693 | epot = -22.2978011147172 | etot = -17.8370898703863 -843000 ekin = 2.84565152669617 | erot = 2.0510801477514 | epot = -22.3162908719779 | etot = -17.4195591975303 -844000 ekin = 2.99645803669157 | erot = 1.50433298006521 | epot = -22.3768320579304 | etot = -17.8760410411736 -845000 ekin = 3.20248025697125 | erot = 2.27246140825564 | epot = -22.3985708422076 | etot = -16.9236291769807 -846000 ekin = 3.35773945734322 | erot = 2.54074745551552 | epot = -22.4144833015876 | etot = -16.5159963887289 -847000 ekin = 2.17779203733109 | erot = 2.73817581188461 | epot = -22.3524825149514 | etot = -17.4365146657357 -848000 ekin = 2.51627348417144 | erot = 2.81170686694717 | epot = -22.2066307862469 | etot = -16.8786504351283 -849000 ekin = 1.99679455190557 | erot = 2.56855846773092 | epot = -22.0763062134929 | etot = -17.5109531938564 -850000 ekin = 2.05799123916876 | erot = 1.80888056240785 | epot = -22.0665032506706 | etot = -18.1996314490939 -851000 ekin = 2.0888979376792 | erot = 1.86172181790289 | epot = -22.0629711763889 | etot = -18.1123514208068 -852000 ekin = 1.68990805178902 | erot = 1.42763535981882 | epot = -22.002100112701 | etot = -18.8845567010931 -853000 ekin = 1.99310886654811 | erot = 3.05226969048292 | epot = -22.0306903552278 | etot = -16.9853117981968 -854000 ekin = 2.98378700534986 | erot = 2.2310274524054 | epot = -22.1115820238811 | etot = -16.8967675661258 -855000 ekin = 2.17087415585277 | erot = 2.8378147226879 | epot = -22.1115106395971 | etot = -17.1028217610564 -856000 ekin = 2.42228475387308 | erot = 1.53328604594478 | epot = -22.0841888628209 | etot = -18.128618063003 -857000 ekin = 2.50431566526894 | erot = 2.80498769176516 | epot = -21.9881235267534 | etot = -16.6788201697193 -858000 ekin = 2.17333686672378 | erot = 2.8259111550717 | epot = -21.9093201368614 | etot = -16.9100721150659 -859000 ekin = 2.29930070497243 | erot = 2.32417368939061 | epot = -21.8849849636104 | etot = -17.2615105692473 -860000 ekin = 1.99153024057672 | erot = 1.94674638600151 | epot = -21.8998709373217 | etot = -17.9615943107434 -861000 ekin = 2.69177523559624 | erot = 2.23997750036373 | epot = -21.8915522194994 | etot = -16.9597994835394 -862000 ekin = 2.86117050047984 | erot = 2.41530060322761 | epot = -21.876687883023 | etot = -16.6002167793156 -863000 ekin = 2.59841547044276 | erot = 3.3501705008543 | epot = -21.8162649771437 | etot = -15.8676790058467 -864000 ekin = 2.92496272611018 | erot = 2.30350236144453 | epot = -21.7820358973268 | etot = -16.5535708097721 -865000 ekin = 1.94718216128952 | erot = 2.16572180916633 | epot = -21.7000823492195 | etot = -17.5871783787636 -866000 ekin = 1.99006127871689 | erot = 1.65011901234952 | epot = -21.6190182409268 | etot = -17.9788379498604 -867000 ekin = 1.76250718110787 | erot = 3.37958608370307 | epot = -21.5401486584561 | etot = -16.3980553936452 -868000 ekin = 1.845623450314 | erot = 2.78812196028616 | epot = -21.5771917352235 | etot = -16.9434463246234 -869000 ekin = 2.39300849969205 | erot = 2.38301618173176 | epot = -21.6710790825578 | etot = -16.895054401134 -870000 ekin = 1.91899243212541 | erot = 3.22222440717393 | epot = -21.6734733803871 | etot = -16.5322565410878 -871000 ekin = 3.10255827845531 | erot = 2.95454268850896 | epot = -21.5913249106744 | etot = -15.5342239437101 -872000 ekin = 2.94582883077842 | erot = 1.38261935263093 | epot = -21.4597055547833 | etot = -17.1312573713739 -873000 ekin = 2.72830997927423 | erot = 2.23223699637274 | epot = -21.3657566950046 | etot = -16.4052097193577 -874000 ekin = 2.41464704842015 | erot = 2.10351476791496 | epot = -21.2635161734954 | etot = -16.7453543571603 -875000 ekin = 2.99468455803482 | erot = 2.72761242382524 | epot = -21.2488881289381 | etot = -15.526591147078 -876000 ekin = 2.13382009818493 | erot = 2.23152059294678 | epot = -21.2388603913311 | etot = -16.8735197001994 -877000 ekin = 1.839391763993 | erot = 1.607279977226 | epot = -21.2015948102408 | etot = -17.7549230690218 -878000 ekin = 2.01267175782178 | erot = 2.73109796378376 | epot = -21.2125253160263 | etot = -16.4687555944208 -879000 ekin = 1.42911941081343 | erot = 2.17371661448622 | epot = -21.1345316334464 | etot = -17.5316956081468 -880000 ekin = 2.10605339224633 | erot = 2.5884751778913 | epot = -21.0787246891645 | etot = -16.3841961190269 -881000 ekin = 1.54924791070118 | erot = 2.0068513915418 | epot = -21.1356465207066 | etot = -17.5795472184637 -882000 ekin = 2.199643157135 | erot = 2.65509097106007 | epot = -21.2389026935677 | etot = -16.3841685653726 -883000 ekin = 2.20850404171077 | erot = 2.22833605977577 | epot = -21.3067394383395 | etot = -16.869899336853 -884000 ekin = 2.76978562647275 | erot = 2.10395845939756 | epot = -21.3429618615585 | etot = -16.4692177756882 -885000 ekin = 1.93339807672781 | erot = 1.77156241344967 | epot = -21.3858074096933 | etot = -17.6808469195158 -886000 ekin = 2.00408769971894 | erot = 3.10736267931439 | epot = -21.3935346347812 | etot = -16.2820842557479 -887000 ekin = 1.96987943750801 | erot = 2.82035886899744 | epot = -21.3967073105593 | etot = -16.6064690040538 -888000 ekin = 1.91464371566411 | erot = 2.33371232948867 | epot = -21.4767119016419 | etot = -17.2283558564891 -889000 ekin = 1.88227414130201 | erot = 2.45915914930408 | epot = -21.5790392436829 | etot = -17.2376059530768 -890000 ekin = 1.84515176532447 | erot = 2.24992378831499 | epot = -21.6747594004542 | etot = -17.5796838468148 -891000 ekin = 2.6016566869706 | erot = 2.34500453305753 | epot = -21.8016735536793 | etot = -16.8550123336512 -892000 ekin = 2.71287751886859 | erot = 2.69544224573131 | epot = -21.9063749565585 | etot = -16.4980551919586 -893000 ekin = 2.17862714611329 | erot = 2.98452123742221 | epot = -21.9155556335137 | etot = -16.7524072499782 -894000 ekin = 2.52079948361477 | erot = 2.46355933674925 | epot = -21.915110079455 | etot = -16.930751259091 -895000 ekin = 2.53566097944338 | erot = 2.4513045444294 | epot = -21.947786087834 | etot = -16.9608205639612 -896000 ekin = 1.84455393639213 | erot = 2.77499090684945 | epot = -21.9167554809878 | etot = -17.2972106377463 -897000 ekin = 2.38519326880694 | erot = 2.019802873173 | epot = -21.8644918203993 | etot = -17.4594956784193 -898000 ekin = 2.14354914407572 | erot = 1.89196669459414 | epot = -21.7953104274974 | etot = -17.7597945888276 -899000 ekin = 2.65485657727374 | erot = 2.3237456003819 | epot = -21.6964754705568 | etot = -16.7178732929012 -900000 ekin = 2.1437154528087 | erot = 2.28119066740275 | epot = -21.6934954112434 | etot = -17.2685892910319 -901000 ekin = 1.93965814946881 | erot = 1.81495571440908 | epot = -21.7369092433376 | etot = -17.9822953794597 -902000 ekin = 2.60993957981555 | erot = 2.50321386623391 | epot = -21.6842517568354 | etot = -16.571098310786 -903000 ekin = 1.87484955546757 | erot = 2.17008893987962 | epot = -21.6383913984978 | etot = -17.5934529031506 -904000 ekin = 1.87454064845764 | erot = 2.32484081519398 | epot = -21.5866637125315 | etot = -17.3872822488799 -905000 ekin = 2.31407473814844 | erot = 2.15094868542391 | epot = -21.5154415841816 | etot = -17.0504181606093 -906000 ekin = 2.49583383758853 | erot = 2.25091096848461 | epot = -21.5170853902294 | etot = -16.7703405841563 -907000 ekin = 4.19798796104344 | erot = 2.5030532322807 | epot = -21.5976736513859 | etot = -14.8966324580618 -908000 ekin = 3.26730891548756 | erot = 2.11222217905481 | epot = -21.7526644402476 | etot = -16.3731333457052 -909000 ekin = 2.64106561110374 | erot = 1.92197432194202 | epot = -21.8748043207924 | etot = -17.3117643877467 -910000 ekin = 2.61805562731904 | erot = 2.90737422678703 | epot = -21.9709470207745 | etot = -16.4455171666685 -911000 ekin = 2.62012718860141 | erot = 4.35318528241844 | epot = -22.0282478750366 | etot = -15.0549354040167 -912000 ekin = 3.07628909273118 | erot = 3.69371809788395 | epot = -22.0511180009901 | etot = -15.281110810375 -913000 ekin = 2.82956898268831 | erot = 2.17078429141201 | epot = -22.0149543706266 | etot = -17.0146010965263 -914000 ekin = 2.16386655780066 | erot = 1.22303673036133 | epot = -21.9243495493208 | etot = -18.5374462611589 -915000 ekin = 1.59447095066509 | erot = 2.95966391292002 | epot = -21.8264580452026 | etot = -17.2723231816175 -916000 ekin = 2.58365539107523 | erot = 3.75147270955029 | epot = -21.8922962938608 | etot = -15.5571681932352 -917000 ekin = 3.01643029206973 | erot = 2.88035639021004 | epot = -21.9150526568514 | etot = -16.0182659745717 -918000 ekin = 2.89929776900147 | erot = 2.64137394041291 | epot = -21.9078998623094 | etot = -16.367228152895 -919000 ekin = 3.20476671865012 | erot = 2.76036957969153 | epot = -21.8878055443404 | etot = -15.9226692459988 -920000 ekin = 2.28949350558683 | erot = 2.38558870046816 | epot = -21.8659406759967 | etot = -17.1908584699418 -921000 ekin = 2.39158312157105 | erot = 2.44959700788167 | epot = -21.8638974869225 | etot = -17.0227173574697 -922000 ekin = 2.30678787768012 | erot = 2.42145678067298 | epot = -21.8218369909645 | etot = -17.0935923326114 -923000 ekin = 2.49697778842282 | erot = 2.66565493744118 | epot = -21.8078634464733 | etot = -16.6452307206093 -924000 ekin = 1.55676047489501 | erot = 2.97115254541007 | epot = -21.7829722234117 | etot = -17.2550592031067 -925000 ekin = 1.86603413909288 | erot = 1.96274861601779 | epot = -21.7288604040749 | etot = -17.9000776489642 -926000 ekin = 1.36993364395821 | erot = 2.11749584641399 | epot = -21.7083442855147 | etot = -18.2209147951426 -927000 ekin = 2.55718977538496 | erot = 2.08109095048881 | epot = -21.7242353526192 | etot = -17.0859546267455 -928000 ekin = 2.0974272910786 | erot = 2.73922911267236 | epot = -21.7673808868819 | etot = -16.9307244831309 -929000 ekin = 1.85550591174834 | erot = 1.84990976935039 | epot = -21.8639426090857 | etot = -18.158526927987 -930000 ekin = 1.99594723517184 | erot = 2.09151231016387 | epot = -21.8461015073053 | etot = -17.7586419619696 -931000 ekin = 2.45331651079283 | erot = 1.86703658018613 | epot = -21.7382799817762 | etot = -17.4179268907972 -932000 ekin = 2.76909250526759 | erot = 2.34990175754269 | epot = -21.7639792890094 | etot = -16.6449850261991 -933000 ekin = 3.04747366335481 | erot = 2.52740756503515 | epot = -21.6783727845496 | etot = -16.1034915561597 -934000 ekin = 2.93463275640818 | erot = 2.48893095891026 | epot = -21.5784996926914 | etot = -16.1549359773729 -935000 ekin = 2.77799347567549 | erot = 2.1392935841225 | epot = -21.5334239467005 | etot = -16.6161368869025 -936000 ekin = 2.96529953690398 | erot = 2.07095365726714 | epot = -21.5249249864244 | etot = -16.4886717922533 -937000 ekin = 3.0485053770175 | erot = 2.32432162998051 | epot = -21.4386642161072 | etot = -16.0658372091092 -938000 ekin = 2.9926262850536 | erot = 2.35224559307843 | epot = -21.3457080466208 | etot = -16.0008361684887 -939000 ekin = 2.61238181353703 | erot = 2.26780356837292 | epot = -21.3079422537804 | etot = -16.4277568718705 -940000 ekin = 2.65930112044942 | erot = 2.75497479722395 | epot = -21.2170493356504 | etot = -15.802773417977 -941000 ekin = 2.27574261339217 | erot = 2.61419196501686 | epot = -21.1297657597673 | etot = -16.2398311813583 -942000 ekin = 1.89172011891055 | erot = 2.82029488513784 | epot = -21.0410099256114 | etot = -16.328994921563 -943000 ekin = 2.47643464476757 | erot = 2.34737109151876 | epot = -21.046668772798 | etot = -16.2228630365117 -944000 ekin = 2.13883995897326 | erot = 1.92577316206138 | epot = -21.0114219746514 | etot = -16.9468088536167 -945000 ekin = 2.57768697869113 | erot = 2.21470136124069 | epot = -21.0634624131725 | etot = -16.2710740732407 -946000 ekin = 2.36420709243625 | erot = 2.89647330776424 | epot = -21.088814693033 | etot = -15.8281342928325 -947000 ekin = 2.07104171538467 | erot = 1.86575631327232 | epot = -21.1004860950452 | etot = -17.1636880663882 -948000 ekin = 1.85532958802997 | erot = 1.36952834086551 | epot = -21.1364231315616 | etot = -17.9115652026661 -949000 ekin = 1.76206591178366 | erot = 2.31737328558629 | epot = -21.1463744779337 | etot = -17.0669352805638 -950000 ekin = 1.72021033353108 | erot = 2.24191394295309 | epot = -21.1376324866856 | etot = -17.1755082102014 -951000 ekin = 1.96140007830504 | erot = 2.32248863487758 | epot = -21.1955927656813 | etot = -16.9117040524987 -952000 ekin = 2.93256201500608 | erot = 2.74550490827503 | epot = -21.234781024541 | etot = -15.5567141012599 -953000 ekin = 2.95031285986317 | erot = 2.39822873263993 | epot = -21.252609183133 | etot = -15.9040675906299 -954000 ekin = 3.09579074538114 | erot = 1.98159252445734 | epot = -21.1641538136742 | etot = -16.0867705438357 -955000 ekin = 3.59360323486038 | erot = 2.06789679071821 | epot = -21.0522880782498 | etot = -15.3907880526712 -956000 ekin = 2.97416074498497 | erot = 3.66953591785751 | epot = -20.9097603766373 | etot = -14.2660637137948 -957000 ekin = 3.03140562067951 | erot = 2.66078083760708 | epot = -20.741905867784 | etot = -15.0497194094974 -958000 ekin = 2.68913434704072 | erot = 2.94057112873834 | epot = -20.5488384129041 | etot = -14.9191329371251 -959000 ekin = 1.93264217407773 | erot = 2.45198406257092 | epot = -20.468781161493 | etot = -16.0841549248444 -960000 ekin = 1.49632279167952 | erot = 3.13346348599987 | epot = -20.4844974178568 | etot = -15.8547111401774 -961000 ekin = 1.96353429663481 | erot = 2.07553358516994 | epot = -20.4805590123497 | etot = -16.441491130545 -962000 ekin = 2.02830196392007 | erot = 1.88908496389356 | epot = -20.5374211599971 | etot = -16.6200342321835 -963000 ekin = 1.80829526034561 | erot = 2.46258345726267 | epot = -20.5841835730967 | etot = -16.3133048554884 -964000 ekin = 2.79449124937198 | erot = 2.42527551362846 | epot = -20.623880544448 | etot = -15.4041137814476 -965000 ekin = 2.53493670506137 | erot = 2.27804362684503 | epot = -20.6549300812151 | etot = -15.8419497493087 -966000 ekin = 2.0920817650402 | erot = 2.27478990703181 | epot = -20.704473904241 | etot = -16.337602232169 -967000 ekin = 1.55562260797661 | erot = 3.55543363172458 | epot = -20.739375276301 | etot = -15.6283190365998 -968000 ekin = 1.93439891222236 | erot = 2.37295903815892 | epot = -20.7189229543385 | etot = -16.4115650039572 -969000 ekin = 2.16199728898303 | erot = 2.4601205252494 | epot = -20.6747113173023 | etot = -16.0525935030699 -970000 ekin = 1.84926216722517 | erot = 2.96951777569267 | epot = -20.6011599981509 | etot = -15.7823800552331 -971000 ekin = 1.93656411083027 | erot = 3.08724923997924 | epot = -20.5835250734812 | etot = -15.5597117226717 -972000 ekin = 1.90452783927713 | erot = 2.5823076678316 | epot = -20.5782905980209 | etot = -16.0914550909122 -973000 ekin = 2.1922712122506 | erot = 2.92686386394502 | epot = -20.5868173702649 | etot = -15.4676822940693 -974000 ekin = 2.53094641465528 | erot = 2.69271305556795 | epot = -20.5382547781502 | etot = -15.314595307927 -975000 ekin = 3.41187201669925 | erot = 2.32917219553093 | epot = -20.5109803919917 | etot = -14.7699361797616 -976000 ekin = 2.88156114272554 | erot = 3.10474521611246 | epot = -20.5158119249461 | etot = -14.5295055661081 -977000 ekin = 2.73962881168093 | erot = 2.50884169958543 | epot = -20.4964590297999 | etot = -15.2479885185336 -978000 ekin = 1.79682802545478 | erot = 2.06924041504343 | epot = -20.4730821934977 | etot = -16.6070137529995 -979000 ekin = 1.86521389998383 | erot = 2.22151626929011 | epot = -20.4069392895634 | etot = -16.3202091202894 -980000 ekin = 1.92383169177414 | erot = 1.56425965548877 | epot = -20.3533353734708 | etot = -16.8652440262079 -981000 ekin = 1.55110199282939 | erot = 2.05381225133935 | epot = -20.3970890782076 | etot = -16.7921748340389 -982000 ekin = 1.85559395816058 | erot = 1.96991369841493 | epot = -20.499354149896 | etot = -16.6738464933205 -983000 ekin = 2.75061857015333 | erot = 1.7944840218308 | epot = -20.5241519929378 | etot = -15.9790494009537 -984000 ekin = 3.65069712553537 | erot = 2.64237329124733 | epot = -20.6374699142712 | etot = -14.3443994974885 -985000 ekin = 2.9563732193106 | erot = 2.18846412126773 | epot = -20.8122975273334 | etot = -15.6674601867551 -986000 ekin = 2.87072902054599 | erot = 2.18810434250119 | epot = -20.9390290724605 | etot = -15.8801957094134 -987000 ekin = 3.37463328642758 | erot = 2.5371366667467 | epot = -21.0098323012658 | etot = -15.0980623480916 -988000 ekin = 3.45107854450338 | erot = 3.23625536313169 | epot = -21.0554260480417 | etot = -14.3680921404067 -989000 ekin = 2.83591404363756 | erot = 2.20564156324817 | epot = -21.19499265416 | etot = -16.1534370472743 -990000 ekin = 2.79864389348437 | erot = 1.83178426663539 | epot = -21.1880268304373 | etot = -16.5575986703175 -991000 ekin = 3.14781925181036 | erot = 3.2078247180891 | epot = -21.1115234865128 | etot = -14.7558795166133 -992000 ekin = 3.30033725309946 | erot = 2.62749912694387 | epot = -21.0030296251662 | etot = -15.0751932451229 -993000 ekin = 3.07374297249949 | erot = 2.22697230616356 | epot = -20.9385586572609 | etot = -15.6378433785979 -994000 ekin = 3.21461776403449 | erot = 2.80599707993708 | epot = -20.8790524582442 | etot = -14.8584376142727 -995000 ekin = 3.25071478747345 | erot = 1.73415439498321 | epot = -20.8037804714002 | etot = -15.8189112889436 -996000 ekin = 3.07999632962569 | erot = 3.18107550500824 | epot = -20.7805295335828 | etot = -14.5194576989488 -997000 ekin = 2.97118118001025 | erot = 3.14046656474894 | epot = -20.7334885248756 | etot = -14.6218407801164 -998000 ekin = 3.09169861594907 | erot = 1.99060706981745 | epot = -20.6553134096535 | etot = -15.573007723887 -999000 ekin = 2.07498130576584 | erot = 2.75045972766921 | epot = -20.616091526295 | etot = -15.79065049286 -1000000 ekin = 2.07851119592057 | erot = 2.11869313853035 | epot = -20.4539417072875 | etot = -16.2567373728366 - 1000000 0.092378275 -1.3359709 0.057599499 -1.1484644 2.8477973e-05 -Loop time of 38.201 on 1 procs for 1000000 steps with 16 atoms - -Performance: 22617.237 tau/day, 26177.358 timesteps/s -98.6% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 27.344 | 27.344 | 27.344 | 0.0 | 71.58 -Bond | 0.88043 | 0.88043 | 0.88043 | 0.0 | 2.30 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.2073 | 0.2073 | 0.2073 | 0.0 | 0.54 -Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 -Modify | 9.4379 | 9.4379 | 9.4379 | 0.0 | 24.71 -Other | | 0.331 | | | 0.87 - -Nlocal: 16 ave 16 max 16 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 88 ave 88 max 88 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 88 -Ave neighs/atom = 5.5 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:38 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 deleted file mode 100644 index 30105703791c8d6aadf2a5d3c37d2a5e58185029..0000000000000000000000000000000000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.18Jun19.duplex2.g++.4 +++ /dev/null @@ -1,1167 +0,0 @@ -LAMMPS (18 Jun 2019) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 -variable T equal 0.1 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000189 secs - read_data CPU = 0.003505 secs - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/stk seqav 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 ${T} 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 6.0760034e-06 -1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 -2000 ekin = 2.15911766687235 | erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504 -3000 ekin = 3.26561948796015 | erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198 -4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505 -5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 -6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 -7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 -8000 ekin = 2.51333548501169 | erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614 -9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 -10000 ekin = 2.36632635249862 | erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463 -11000 ekin = 2.03296432220126 | erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202 -12000 ekin = 2.65352743446956 | erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194 -13000 ekin = 1.89067421214403 | erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949 -14000 ekin = 1.90680463918722 | erot = 2.127459870274 | epot = -23.7545354032947 | etot = -19.7202708938335 -15000 ekin = 2.40428667481004 | erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361 -16000 ekin = 2.7510166356243 | erot = 1.18896277635345 | epot = -23.5745121257654 | etot = -19.6345327137876 -17000 ekin = 2.44090826892662 | erot = 2.38166706806442 | epot = -23.5888433865641 | etot = -18.766268049573 -18000 ekin = 2.16977970545217 | erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939 -19000 ekin = 2.19378610033861 | erot = 2.45183819484608 | epot = -23.5449084745393 | etot = -18.8992841793546 -20000 ekin = 2.07734013817241 | erot = 1.81448496219961 | epot = -23.5782673056894 | etot = -19.6864422053173 -21000 ekin = 2.27781532351243 | erot = 2.76369118136087 | epot = -23.5986545956161 | etot = -18.5571480907428 -22000 ekin = 2.69375785791379 | erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449208 -23000 ekin = 1.99952884103097 | erot = 2.28032953163858 | epot = -23.4448504933921 | etot = -19.1649921207226 -24000 ekin = 2.19993258930349 | erot = 2.97916455146846 | epot = -23.365299008021 | etot = -18.1862018672491 -25000 ekin = 2.28089469652686 | erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537 -26000 ekin = 1.99390998801618 | erot = 2.79250495479073 | epot = -23.1859723519608 | etot = -18.3995574091539 -27000 ekin = 2.00992865272585 | erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421 -28000 ekin = 2.00322172723407 | erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913 -29000 ekin = 2.52361436071784 | erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138 -30000 ekin = 1.94969919616482 | erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198 -31000 ekin = 1.81286761012387 | erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782 -32000 ekin = 1.88389491638451 | erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051 -33000 ekin = 1.78524470387102 | erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434 -34000 ekin = 2.28023843988047 | erot = 3.11357086039976 | epot = -23.0617618407572 | etot = -17.6679525404769 -35000 ekin = 2.88795920533174 | erot = 1.81662227096288 | epot = -23.1342233361349 | etot = -18.4296418598403 -36000 ekin = 2.40018487148211 | erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096 -37000 ekin = 2.22699211630433 | erot = 1.73889017332476 | epot = -23.2291614908027 | etot = -19.2632792011736 -38000 ekin = 2.13593461964592 | erot = 3.07590136326317 | epot = -23.1607724763685 | etot = -17.9489364934594 -39000 ekin = 2.08839393640823 | erot = 2.80471150509565 | epot = -23.1352878747759 | etot = -18.242182433272 -40000 ekin = 2.94982054413846 | erot = 2.19484102372242 | epot = -23.1842229043853 | etot = -18.0395613365244 -41000 ekin = 2.47855373480178 | erot = 3.46795094832273 | epot = -23.1698888629099 | etot = -17.2233841797854 -42000 ekin = 2.57225931171306 | erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682 -43000 ekin = 2.16695829201326 | erot = 2.67063324875933 | epot = -22.9841690345739 | etot = -18.1465774938013 -44000 ekin = 2.3251045436594 | erot = 3.31069456451417 | epot = -22.9099977707014 | etot = -17.2741986625278 -45000 ekin = 1.8593572517472 | erot = 3.48256913429863 | epot = -22.7853293556222 | etot = -17.4434029695763 -46000 ekin = 2.59906260222482 | erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741 -47000 ekin = 1.9041935097682 | erot = 3.39352467596442 | epot = -22.5624536061979 | etot = -17.2647354204653 -48000 ekin = 2.46191536162938 | erot = 2.50024189038396 | epot = -22.5888330081063 | etot = -17.626675756093 -49000 ekin = 3.18008619674965 | erot = 2.18329398142911 | epot = -22.6110647388653 | etot = -17.2476845606865 -50000 ekin = 2.92380640638808 | erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295055 -51000 ekin = 2.86729503225236 | erot = 2.67529217516738 | epot = -22.6748886664557 | etot = -17.132301459036 -52000 ekin = 2.30283827457731 | erot = 1.82645474029553 | epot = -22.6607030819086 | etot = -18.5314100670358 -53000 ekin = 3.18697616339313 | erot = 1.67211265049679 | epot = -22.7158951183044 | etot = -17.8568063044145 -54000 ekin = 2.63274995193146 | erot = 1.96664130685844 | epot = -22.7877787224364 | etot = -18.1883874636465 -55000 ekin = 3.18311630681888 | erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793 -56000 ekin = 2.55275960671527 | erot = 3.05720384772627 | epot = -22.8187750450683 | etot = -17.2088115906267 -57000 ekin = 2.43682051944963 | erot = 3.45782031837861 | epot = -22.7770565571277 | etot = -16.8824157192995 -58000 ekin = 1.93888380963701 | erot = 2.51321017005842 | epot = -22.7135987564736 | etot = -18.2615047767781 -59000 ekin = 2.5584899615086 | erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831 -60000 ekin = 2.80661395039301 | erot = 2.89055248290059 | epot = -22.5801959967487 | etot = -16.8830295634551 -61000 ekin = 2.68598657973729 | erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677 -62000 ekin = 2.74493324548126 | erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319 -63000 ekin = 2.65627195091608 | erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079 -64000 ekin = 2.12379240032878 | erot = 2.79203441675508 | epot = -22.3495990435982 | etot = -17.4337722265143 -65000 ekin = 1.86782238979936 | erot = 2.70277079938775 | epot = -22.3710220966341 | etot = -17.800428907447 -66000 ekin = 2.74983103317414 | erot = 1.93532287297328 | epot = -22.3642892005435 | etot = -17.6791352943961 -67000 ekin = 2.51092055125345 | erot = 2.46618624666164 | epot = -22.3997780561407 | etot = -17.4226712582257 -68000 ekin = 2.95469759114172 | erot = 1.97026833535316 | epot = -22.465077041847 | etot = -17.5401111153521 -69000 ekin = 2.60179538487173 | erot = 2.27022574694886 | epot = -22.4013876082186 | etot = -17.529366476398 -70000 ekin = 2.38624525335423 | erot = 2.82124637267728 | epot = -22.3329612644329 | etot = -17.1254696384013 -71000 ekin = 2.62641919853461 | erot = 2.89332429923839 | epot = -22.3324946257813 | etot = -16.8127511280083 -72000 ekin = 2.93199679301318 | erot = 2.83600213853038 | epot = -22.4418753486332 | etot = -16.6738764170897 -73000 ekin = 2.20521324648382 | erot = 3.0506384171445 | epot = -22.5078076718832 | etot = -17.2519560082549 -74000 ekin = 2.16594519672766 | erot = 2.82993872672918 | epot = -22.5187768617569 | etot = -17.5228929383001 -75000 ekin = 1.52753824412461 | erot = 1.91758574309003 | epot = -22.6434864113427 | etot = -19.198362424128 -76000 ekin = 1.89477517532868 | erot = 2.83145375092217 | epot = -22.7507099037207 | etot = -18.0244809774699 -77000 ekin = 2.84722966394523 | erot = 3.20523918524771 | epot = -22.8263123696514 | etot = -16.7738435204585 -78000 ekin = 2.44900478430451 | erot = 2.80964787966682 | epot = -22.8119237303111 | etot = -17.5532710663397 -79000 ekin = 2.16549328835506 | erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255 -80000 ekin = 2.38929173610466 | erot = 2.58355997375491 | epot = -22.7453472674483 | etot = -17.7724955575887 -81000 ekin = 2.74182188148999 | erot = 1.92580771183151 | epot = -22.6872721828913 | etot = -18.0196425895698 -82000 ekin = 1.90254633515813 | erot = 1.70958501101745 | epot = -22.5904815431895 | etot = -18.9783501970139 -83000 ekin = 1.63862423461032 | erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292 -84000 ekin = 1.65768128899531 | erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674 -85000 ekin = 2.40787065796921 | erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645 -86000 ekin = 2.51073542405177 | erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608 -87000 ekin = 2.13729284484532 | erot = 1.97886338867606 | epot = -22.4457225556767 | etot = -18.3295663221553 -88000 ekin = 1.7511616822056 | erot = 2.36434608342924 | epot = -22.4232555875236 | etot = -18.3077478218887 -89000 ekin = 1.85498863251071 | erot = 3.29466014836527 | epot = -22.4615925106509 | etot = -17.3119437297749 -90000 ekin = 2.22730928223451 | erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706 -91000 ekin = 2.40026068010467 | erot = 3.1312454261103 | epot = -22.5445138059197 | etot = -17.0130076997047 -92000 ekin = 2.69184894487886 | erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756693 -93000 ekin = 3.04452081584098 | erot = 3.0289315825034 | epot = -22.4857514998612 | etot = -16.4122991015169 -94000 ekin = 3.21054020599498 | erot = 1.87554208928457 | epot = -22.58235617796 | etot = -17.4962738826805 -95000 ekin = 3.49164555041805 | erot = 2.89107259754101 | epot = -22.651746211573 | etot = -16.2690280636139 -96000 ekin = 2.8961145983777 | erot = 2.38403691628048 | epot = -22.6376886129393 | etot = -17.3575370982811 -97000 ekin = 1.94001816357315 | erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036 -98000 ekin = 2.21812472183551 | erot = 3.66512951907029 | epot = -22.5400207863669 | etot = -16.6567665454611 -99000 ekin = 1.96304801418099 | erot = 2.78092002528644 | epot = -22.4500077741119 | etot = -17.7060397346444 -100000 ekin = 1.78146596589238 | erot = 2.66087063973067 | epot = -22.3806285021859 | etot = -17.9382918965629 -101000 ekin = 2.13576431486591 | erot = 2.39189697670582 | epot = -22.3671198416411 | etot = -17.8394585500694 -102000 ekin = 1.54265458925823 | erot = 2.31301627489861 | epot = -22.3596033820568 | etot = -18.5039325179 -103000 ekin = 1.6493299781162 | erot = 2.82700146777614 | epot = -22.4044472055819 | etot = -17.9281157596895 -104000 ekin = 1.88425130865015 | erot = 3.36695629589132 | epot = -22.4614117565727 | etot = -17.2102041520312 -105000 ekin = 2.0873628063424 | erot = 1.99902589912497 | epot = -22.4857870795246 | etot = -18.3993983740572 -106000 ekin = 2.85192200005481 | erot = 1.96124421177818 | epot = -22.4885148263279 | etot = -17.6753486144949 -107000 ekin = 2.27699301124082 | erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666 -108000 ekin = 2.43341212242248 | erot = 1.7101452395327 | epot = -22.4750159709763 | etot = -18.3314586090212 -109000 ekin = 2.3240302459673 | erot = 2.92730273400661 | epot = -22.4544447404649 | etot = -17.203111760491 -110000 ekin = 2.75939007795593 | erot = 2.3726124845783 | epot = -22.4066316113363 | etot = -17.2746290488021 -111000 ekin = 2.30202775259985 | erot = 2.09098171366697 | epot = -22.340628179725 | etot = -17.9476187134581 -112000 ekin = 2.89672803093986 | erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143 -113000 ekin = 2.802868120203 | erot = 1.68317583122193 | epot = -22.1739192926257 | etot = -17.6878753412008 -114000 ekin = 3.41134331362353 | erot = 2.66279011393036 | epot = -22.2993892060878 | etot = -16.2252557785339 -115000 ekin = 3.04096848543598 | erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327 -116000 ekin = 3.18249263106367 | erot = 3.21872780579631 | epot = -22.3766120310369 | etot = -15.975391594177 -117000 ekin = 3.04033644338918 | erot = 2.4163277414929 | epot = -22.3406101341932 | etot = -16.8839459493111 -118000 ekin = 3.2297663279461 | erot = 1.46870208555873 | epot = -22.262910646297 | etot = -17.5644422327922 -119000 ekin = 2.35815331598994 | erot = 3.07464675916892 | epot = -22.21629705762 | etot = -16.7834969824611 -120000 ekin = 1.93901604028919 | erot = 2.21087803685818 | epot = -22.1596747789505 | etot = -18.0097807018031 -121000 ekin = 1.94791988346889 | erot = 3.06697908719322 | epot = -22.1473490758084 | etot = -17.1324501051462 -122000 ekin = 1.69642311218451 | erot = 1.71065948591522 | epot = -22.235021693017 | etot = -18.8279390949172 -123000 ekin = 1.74537927001903 | erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348 -124000 ekin = 2.74229806685692 | erot = 1.94346011848795 | epot = -22.3376426377462 | etot = -17.6518844524013 -125000 ekin = 2.77628031613761 | erot = 1.95737420539167 | epot = -22.3561899601979 | etot = -17.6225354386686 -126000 ekin = 2.05898577806786 | erot = 1.47493157618749 | epot = -22.3918669376121 | etot = -18.8579495833568 -127000 ekin = 1.88620727578863 | erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304 -128000 ekin = 1.65027256647601 | erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694 -129000 ekin = 2.51771860981078 | erot = 2.38745668871875 | epot = -22.3622404512641 | etot = -17.4570651527346 -130000 ekin = 1.60778116741171 | erot = 2.81983062254802 | epot = -22.3043401463426 | etot = -17.8767283563829 -131000 ekin = 2.27966529707091 | erot = 2.29465997580789 | epot = -22.1860056729234 | etot = -17.6116804000446 -132000 ekin = 2.94605151024306 | erot = 2.34727265039698 | epot = -22.1004107829512 | etot = -16.8070866223112 -133000 ekin = 2.00184520718143 | erot = 2.13597622566089 | epot = -22.0860804435183 | etot = -17.948259010676 -134000 ekin = 1.54536260297594 | erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194 -135000 ekin = 1.7899169229158 | erot = 2.40585579784188 | epot = -22.0564792277569 | etot = -17.8607065069992 -136000 ekin = 1.63315069688348 | erot = 2.13968964990471 | epot = -22.0645410751455 | etot = -18.2917007283573 -137000 ekin = 2.36475220491125 | erot = 1.93075105476848 | epot = -22.101884847306 | etot = -17.8063815876262 -138000 ekin = 2.9554682114977 | erot = 1.58329215843879 | epot = -22.158920719349 | etot = -17.6201603494125 -139000 ekin = 3.18559985564368 | erot = 2.24978247982886 | epot = -22.2766713145625 | etot = -16.84128897909 -140000 ekin = 2.25331500051846 | erot = 3.04264261269698 | epot = -22.4413209794807 | etot = -17.1453633662653 -141000 ekin = 1.8939664036255 | erot = 3.12730191483887 | epot = -22.6943708703895 | etot = -17.6731025519251 -142000 ekin = 2.48698722341786 | erot = 2.50204475841097 | epot = -22.8022645411412 | etot = -17.8132325593124 -143000 ekin = 2.39031114354901 | erot = 2.72027514737474 | epot = -22.7789363640121 | etot = -17.6683500730884 -144000 ekin = 1.93009742932803 | erot = 2.68112648713777 | epot = -22.6600942975092 | etot = -18.0488703810434 -145000 ekin = 1.81543048110687 | erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640413 -146000 ekin = 2.4125202126428 | erot = 2.0856902293417 | epot = -22.560764077018 | etot = -18.0625536350335 -147000 ekin = 1.44642974398304 | erot = 1.86921415702345 | epot = -22.4437745695725 | etot = -19.128130668566 -148000 ekin = 1.94224767107089 | erot = 2.57935525538892 | epot = -22.4110987100046 | etot = -17.8894957835448 -149000 ekin = 2.03195649040454 | erot = 3.31786202502786 | epot = -22.312227106758 | etot = -16.9624085913256 -150000 ekin = 2.47792894576431 | erot = 2.68612874200302 | epot = -22.1392843642772 | etot = -16.9752266765099 -151000 ekin = 2.75692645092955 | erot = 1.88122565848133 | epot = -21.9329416416722 | etot = -17.2947895322613 -152000 ekin = 2.7753834344323 | erot = 1.78115734250796 | epot = -21.745072490984 | etot = -17.1885317140438 -153000 ekin = 3.09316888168833 | erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934 -154000 ekin = 2.31433640945477 | erot = 2.19304386678896 | epot = -21.5946356595636 | etot = -17.0872553833199 -155000 ekin = 1.94169881401553 | erot = 2.67959698479411 | epot = -21.6941053409436 | etot = -17.0728095421339 -156000 ekin = 2.69151609119638 | erot = 2.25048211983205 | epot = -21.7610571974251 | etot = -16.8190589863966 -157000 ekin = 3.89507004263776 | erot = 2.74501587672577 | epot = -21.8157728797742 | etot = -15.1756869604107 -158000 ekin = 2.88173407476086 | erot = 2.69702262693026 | epot = -21.8854957137509 | etot = -16.3067390120597 -159000 ekin = 3.15173323195919 | erot = 2.61743473710129 | epot = -21.8245251626835 | etot = -16.055357193623 -160000 ekin = 2.54983562435716 | erot = 3.26037467643908 | epot = -21.8527884226329 | etot = -16.0425781218366 -161000 ekin = 2.47569624391789 | erot = 2.44418416527208 | epot = -21.7973550812186 | etot = -16.8774746720287 -162000 ekin = 2.9422872213738 | erot = 2.59784970938383 | epot = -21.7813251561028 | etot = -16.2411882253452 -163000 ekin = 3.25812805712343 | erot = 2.2523933100784 | epot = -21.820089307521 | etot = -16.3095679403192 -164000 ekin = 3.52786799143084 | erot = 2.22392713421413 | epot = -21.7646946348872 | etot = -16.0128995092422 -165000 ekin = 2.47839548873417 | erot = 2.58744140761171 | epot = -21.679095294504 | etot = -16.6132583981582 -166000 ekin = 2.14435847552791 | erot = 3.04732688845808 | epot = -21.6219995979976 | etot = -16.4303142340116 -167000 ekin = 2.77664659649902 | erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831 -168000 ekin = 1.74464407802389 | erot = 2.78052653338967 | epot = -21.4288999288374 | etot = -16.9037293174239 -169000 ekin = 1.80689129093329 | erot = 2.46391033708927 | epot = -21.4128285618694 | etot = -17.1420269338468 -170000 ekin = 1.6949814594151 | erot = 2.88911238881154 | epot = -21.4319269866203 | etot = -16.8478331383937 -171000 ekin = 2.15326316196645 | erot = 1.61346547801869 | epot = -21.2861470779283 | etot = -17.5194184379432 -172000 ekin = 1.67904916339532 | erot = 2.36509147316375 | epot = -21.1250864759441 | etot = -17.080945839385 -173000 ekin = 2.05349972960735 | erot = 2.1886466510775 | epot = -21.0744450592631 | etot = -16.8322986785782 -174000 ekin = 2.49402795941962 | erot = 3.10392317000879 | epot = -20.9332609664624 | etot = -15.335309837034 -175000 ekin = 2.60611029063986 | erot = 2.90993176119182 | epot = -20.8533230180668 | etot = -15.3372809662352 -176000 ekin = 2.14535974511637 | erot = 2.67710511021539 | epot = -20.8508037764829 | etot = -16.0283389211511 -177000 ekin = 2.82654664242577 | erot = 2.80647819657321 | epot = -20.9303681620826 | etot = -15.2973433230836 -178000 ekin = 3.17006270723388 | erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933 -179000 ekin = 2.33834827123178 | erot = 2.84870047825869 | epot = -21.1082901606943 | etot = -15.9212414112039 -180000 ekin = 2.39362550925045 | erot = 2.94575326168227 | epot = -21.1089731290028 | etot = -15.7695943580701 -181000 ekin = 2.78703231260152 | erot = 3.29998898392537 | epot = -21.0761138110654 | etot = -14.9890925145385 -182000 ekin = 3.02338391239199 | erot = 2.32533107462881 | epot = -21.0444377426861 | etot = -15.6957227556653 -183000 ekin = 2.44126401356994 | erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424 -184000 ekin = 2.56448211253962 | erot = 2.77267067014066 | epot = -20.6657911214549 | etot = -15.3286383387746 -185000 ekin = 2.16427057092672 | erot = 1.95880146934286 | epot = -20.5647658775173 | etot = -16.4416938372477 -186000 ekin = 2.06536030915311 | erot = 3.14593463137772 | epot = -20.4537584304771 | etot = -15.2424634899463 -187000 ekin = 2.43846121057803 | erot = 1.93593042270703 | epot = -20.4775765627296 | etot = -16.1031849294445 -188000 ekin = 2.28827356508696 | erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372 -189000 ekin = 1.67206333515898 | erot = 3.05807378739729 | epot = -20.6184572736204 | etot = -15.8883201510642 -190000 ekin = 1.96995062226968 | erot = 2.94301967439401 | epot = -20.6150380630742 | etot = -15.7020677664105 -191000 ekin = 2.31558303301195 | erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708367 -192000 ekin = 3.58105122568799 | erot = 2.89866835149675 | epot = -20.555036456006 | etot = -14.0753168788213 -193000 ekin = 2.69738971383614 | erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358 -194000 ekin = 2.65963556416735 | erot = 2.28486501061268 | epot = -20.4488832942326 | etot = -15.5043827194526 -195000 ekin = 1.85289053427901 | erot = 2.65318671222087 | epot = -20.3816844231208 | etot = -15.8756071766209 -196000 ekin = 2.28257181147918 | erot = 2.31175601065462 | epot = -20.4051132325268 | etot = -15.810785410393 -197000 ekin = 2.49770460330585 | erot = 2.55587879440511 | epot = -20.4716020539923 | etot = -15.4180186562814 -198000 ekin = 2.01700960777427 | erot = 1.51922008609382 | epot = -20.4907970823156 | etot = -16.9545673884475 -199000 ekin = 1.50027537520987 | erot = 2.19604462463446 | epot = -20.5138434458212 | etot = -16.8175234459769 -200000 ekin = 1.64850512926723 | erot = 2.4596633548257 | epot = -20.4934420686449 | etot = -16.385273584552 -201000 ekin = 2.62997533994907 | erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916 -202000 ekin = 2.3089517547524 | erot = 2.5565329388766 | epot = -20.6262537118088 | etot = -15.7607690181798 -203000 ekin = 1.64768887888551 | erot = 2.11556417528285 | epot = -20.6617888215465 | etot = -16.8985357673782 -204000 ekin = 2.01924097320136 | erot = 1.97748949636931 | epot = -20.7002685556682 | etot = -16.7035380860975 -205000 ekin = 2.97656554045711 | erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806698 -206000 ekin = 2.56613069661945 | erot = 2.21624244224461 | epot = -21.0621833598182 | etot = -16.2798102209542 -207000 ekin = 3.44850636848559 | erot = 2.48816050856267 | epot = -21.2038849430867 | etot = -15.2672180660384 -208000 ekin = 2.54208934028226 | erot = 2.22605232144502 | epot = -21.3476404533667 | etot = -16.5794987916394 -209000 ekin = 3.84151461096732 | erot = 2.16534559513903 | epot = -21.4932373455843 | etot = -15.486377139478 -210000 ekin = 3.06873591712904 | erot = 2.24760815652574 | epot = -21.6427793540355 | etot = -16.3264352803807 -211000 ekin = 1.64176280869923 | erot = 2.17721976802011 | epot = -21.8130439048272 | etot = -17.9940613281078 -212000 ekin = 2.5985934050661 | erot = 2.41520703335869 | epot = -21.9964648294563 | etot = -16.9826643910315 -213000 ekin = 2.51136104390039 | erot = 1.99503544560738 | epot = -22.161492842604 | etot = -17.6550963530962 -214000 ekin = 2.77089845962619 | erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179 -215000 ekin = 2.53408528186206 | erot = 1.84963848601798 | epot = -22.1148567901871 | etot = -17.7311330223071 -216000 ekin = 2.52671619876928 | erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469 -217000 ekin = 2.50171921508545 | erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455 -218000 ekin = 2.43936294263937 | erot = 2.41974828067303 | epot = -22.2447049583244 | etot = -17.385593735012 -219000 ekin = 2.30221269367205 | erot = 2.65120674162376 | epot = -22.2807164841742 | etot = -17.3272970488784 -220000 ekin = 1.70065256620687 | erot = 2.34758543213915 | epot = -22.2809933538228 | etot = -18.2327553554768 -221000 ekin = 2.09298237125575 | erot = 2.47886481595909 | epot = -22.267957001012 | etot = -17.6961098137972 -222000 ekin = 1.58469709510937 | erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659 -223000 ekin = 1.83926923346352 | erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791 -224000 ekin = 2.59583657132575 | erot = 2.93869915115497 | epot = -22.1425986650605 | etot = -16.6080629425798 -225000 ekin = 3.29351563254165 | erot = 2.8433953581414 | epot = -22.12757310355 | etot = -15.9906621128669 -226000 ekin = 3.03135339447922 | erot = 2.08293143143602 | epot = -22.15283624886 | etot = -17.0385514229448 -227000 ekin = 2.50176282992082 | erot = 3.15084128846394 | epot = -22.2250438959744 | etot = -16.5724397775897 -228000 ekin = 2.32013498351673 | erot = 2.67554406359439 | epot = -22.3177515383563 | etot = -17.3220724912452 -229000 ekin = 2.89545450975319 | erot = 2.90735055857068 | epot = -22.4361496683348 | etot = -16.6333446000109 -230000 ekin = 2.28321229485933 | erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863 -231000 ekin = 2.0778632375453 | erot = 3.10673973696436 | epot = -22.5896609633152 | etot = -17.4050579888055 -232000 ekin = 2.1202374109541 | erot = 1.98747810033065 | epot = -22.5738924334392 | etot = -18.4661769221544 -233000 ekin = 2.33571877855589 | erot = 2.83585090202738 | epot = -22.5402065195541 | etot = -17.3686368389708 -234000 ekin = 2.10578223747154 | erot = 2.07381218733635 | epot = -22.5507693150833 | etot = -18.3711748902754 -235000 ekin = 2.44321041214394 | erot = 2.80846352304318 | epot = -22.5606929563186 | etot = -17.3090190211315 -236000 ekin = 2.93630791731799 | erot = 3.0631591853173 | epot = -22.4860653874722 | etot = -16.4865982848369 -237000 ekin = 3.21264879506079 | erot = 3.26866508478298 | epot = -22.3683553437862 | etot = -15.8870414639424 -238000 ekin = 2.46595539123277 | erot = 2.32502019506664 | epot = -22.3144456769666 | etot = -17.5234700906672 -239000 ekin = 2.10325864915823 | erot = 2.47631139904042 | epot = -22.3011392921811 | etot = -17.7215692439825 -240000 ekin = 1.77270999777839 | erot = 2.60141429112664 | epot = -22.2344206081543 | etot = -17.8602963192493 -241000 ekin = 1.94952922244078 | erot = 1.39715216866764 | epot = -22.2207225048761 | etot = -18.8740411137677 -242000 ekin = 3.05687991591411 | erot = 2.00862394928705 | epot = -22.2213200390944 | etot = -17.1558161738932 -243000 ekin = 2.86735711945299 | erot = 1.79948118674678 | epot = -22.2697610280427 | etot = -17.6029227218429 -244000 ekin = 2.00525854269389 | erot = 2.36445341214555 | epot = -22.2726788994494 | etot = -17.90296694461 -245000 ekin = 2.28011102404838 | erot = 2.787005205328 | epot = -22.2995433574618 | etot = -17.2324271280854 -246000 ekin = 2.06819738789813 | erot = 2.24624952782285 | epot = -22.2551680110138 | etot = -17.9407210952928 -247000 ekin = 1.69964711256213 | erot = 3.22260619239827 | epot = -22.1916408256116 | etot = -17.2693875206512 -248000 ekin = 1.92997585194759 | erot = 3.61155944514373 | epot = -22.0096484177853 | etot = -16.4681131206939 -249000 ekin = 2.16278530892653 | erot = 3.27771891456709 | epot = -21.8856058980727 | etot = -16.4451016745791 -250000 ekin = 2.32204054211024 | erot = 2.46317574116847 | epot = -21.8028762710592 | etot = -17.0176599877804 -251000 ekin = 1.23768964067254 | erot = 2.24150533762101 | epot = -21.763065707404 | etot = -18.2838707291104 -252000 ekin = 1.79818833522214 | erot = 2.12556386664128 | epot = -21.7586349357285 | etot = -17.8348827338651 -253000 ekin = 2.12809689846393 | erot = 2.59685639208402 | epot = -21.7226495687758 | etot = -16.9976962782278 -254000 ekin = 2.46813261968532 | erot = 2.00391812662869 | epot = -21.7113918037362 | etot = -17.2393410574222 -255000 ekin = 2.3156672908729 | erot = 2.03619058028117 | epot = -21.7265453183257 | etot = -17.3746874471716 -256000 ekin = 2.87223929491326 | erot = 2.61790933826624 | epot = -21.659332511914 | etot = -16.1691838787345 -257000 ekin = 2.85756762932927 | erot = 2.081746739162 | epot = -21.6161821054731 | etot = -16.6768677369819 -258000 ekin = 2.06111021157734 | erot = 2.32748664972428 | epot = -21.5132485706727 | etot = -17.124651709371 -259000 ekin = 2.23305784057759 | erot = 2.88843859953735 | epot = -21.5040039667855 | etot = -16.3825075266705 -260000 ekin = 2.49862397932476 | erot = 2.38336885848389 | epot = -21.488210637319 | etot = -16.6062177995103 -261000 ekin = 2.09280296934734 | erot = 2.39632540029205 | epot = -21.4325331777953 | etot = -16.9434048081559 -262000 ekin = 2.33576913564289 | erot = 2.67273419354397 | epot = -21.3832241450035 | etot = -16.3747208158166 -263000 ekin = 2.20536189489354 | erot = 2.71530627040565 | epot = -21.4329409070981 | etot = -16.5122727417989 -264000 ekin = 2.2858247573423 | erot = 2.76839346219664 | epot = -21.39310844316 | etot = -16.338890223621 -265000 ekin = 1.70928536820409 | erot = 1.79395423442894 | epot = -21.2682341921474 | etot = -17.7649945895144 -266000 ekin = 2.48721735474525 | erot = 2.08745460533224 | epot = -21.1746995817337 | etot = -16.6000276216562 -267000 ekin = 2.69283567987773 | erot = 2.10301910407211 | epot = -21.1705161290062 | etot = -16.3746613450564 -268000 ekin = 3.00000233743719 | erot = 2.80954585635721 | epot = -21.164752112651 | etot = -15.3552039188566 -269000 ekin = 3.50713810468527 | erot = 2.35763817348003 | epot = -21.1537110688984 | etot = -15.2889347907331 -270000 ekin = 3.50686942248863 | erot = 1.86462765875888 | epot = -21.1925508822801 | etot = -15.8210538010326 -271000 ekin = 3.57026082273992 | erot = 2.08172467795384 | epot = -21.2775817182941 | etot = -15.6255962176003 -272000 ekin = 2.4484752533773 | erot = 3.08466485039761 | epot = -21.3619851902072 | etot = -15.8288450864322 -273000 ekin = 2.39748176307241 | erot = 3.13355050446718 | epot = -21.4386234252579 | etot = -15.9075911577183 -274000 ekin = 2.48208144431863 | erot = 2.00552494041967 | epot = -21.4476232953882 | etot = -16.9600169106499 -275000 ekin = 2.48721081149369 | erot = 3.05413598233603 | epot = -21.4713984309062 | etot = -15.9300516370765 -276000 ekin = 2.82709589676966 | erot = 2.88384306577856 | epot = -21.4434590118161 | etot = -15.7325200492679 -277000 ekin = 2.23479555963313 | erot = 2.20310851955638 | epot = -21.3883073251199 | etot = -16.9504032459304 -278000 ekin = 2.81418916407429 | erot = 3.24537052192613 | epot = -21.3155364074003 | etot = -15.2559767213999 -279000 ekin = 2.57366525203699 | erot = 1.81705578305929 | epot = -21.2862101233851 | etot = -16.8954890882888 -280000 ekin = 2.41063464320149 | erot = 1.76282693004731 | epot = -21.2549625280961 | etot = -17.0815009548473 -281000 ekin = 2.58126226070487 | erot = 2.29258221702166 | epot = -21.306394928225 | etot = -16.4325504504985 -282000 ekin = 3.02016903398222 | erot = 2.43094523890341 | epot = -21.4340900724633 | etot = -15.9829757995777 -283000 ekin = 2.59269149790331 | erot = 2.11330689541033 | epot = -21.6296517079942 | etot = -16.9236533146806 -284000 ekin = 2.51704243107537 | erot = 3.13156683036761 | epot = -21.7452694753527 | etot = -16.0966602139097 -285000 ekin = 2.4236537221525 | erot = 1.77228258125507 | epot = -21.8557019037769 | etot = -17.6597656003693 -286000 ekin = 1.9446719552166 | erot = 2.0366097411672 | epot = -21.901435736722 | etot = -17.9201540403382 -287000 ekin = 2.56319670376172 | erot = 2.60867050510166 | epot = -21.90675099349 | etot = -16.7348837846266 -288000 ekin = 2.19574207425738 | erot = 1.69805542160023 | epot = -21.8143855675961 | etot = -17.9205880717385 -289000 ekin = 2.35326278833027 | erot = 1.65840109676146 | epot = -21.6976038565284 | etot = -17.6859399714367 -290000 ekin = 2.3519456177505 | erot = 1.99444238353744 | epot = -21.6551012116075 | etot = -17.3087132103195 -291000 ekin = 1.48585281531715 | erot = 2.66475825861554 | epot = -21.56036793472 | etot = -17.4097568607873 -292000 ekin = 2.10739944756451 | erot = 2.42809824662638 | epot = -21.4451596117638 | etot = -16.9096619175729 -293000 ekin = 2.11618090223716 | erot = 1.86694554151198 | epot = -21.3593625692767 | etot = -17.3762361255276 -294000 ekin = 2.06078090566332 | erot = 2.13941873359476 | epot = -21.2326233100941 | etot = -17.032423670836 -295000 ekin = 2.11467178034793 | erot = 2.3267343667518 | epot = -21.1123588667461 | etot = -16.6709527196464 -296000 ekin = 1.53087058859331 | erot = 2.94008409149153 | epot = -21.2112197533848 | etot = -16.7402650732999 -297000 ekin = 2.52732986791196 | erot = 2.18380855337858 | epot = -21.1955190508786 | etot = -16.4843806295881 -298000 ekin = 1.89033945823196 | erot = 2.02521913176001 | epot = -21.2593750718296 | etot = -17.3438164818376 -299000 ekin = 1.87142873048436 | erot = 1.66404563221549 | epot = -21.2919162310488 | etot = -17.7564418683489 -300000 ekin = 2.23872615546788 | erot = 1.50807257618897 | epot = -21.3339204593826 | etot = -17.5871217277258 -301000 ekin = 1.99965506724558 | erot = 2.00145094516844 | epot = -21.4707589194325 | etot = -17.4696529070184 -302000 ekin = 1.76370349732521 | erot = 2.23787708901487 | epot = -21.5675275978257 | etot = -17.5659470114856 -303000 ekin = 2.69610887251788 | erot = 1.6995722142974 | epot = -21.5563765448092 | etot = -17.1606954579939 -304000 ekin = 2.55447143501921 | erot = 2.02060813090349 | epot = -21.5692327321341 | etot = -16.9941531662114 -305000 ekin = 2.38230604232717 | erot = 2.31489374428114 | epot = -21.5335950166329 | etot = -16.8363952300246 -306000 ekin = 2.07785475765118 | erot = 2.4523066068597 | epot = -21.4550895345847 | etot = -16.9249281700738 -307000 ekin = 3.17130424567278 | erot = 3.29574614566806 | epot = -21.4151535289883 | etot = -14.9481031376474 -308000 ekin = 3.40959217051674 | erot = 2.68389483402973 | epot = -21.4778643688409 | etot = -15.3843773642944 -309000 ekin = 2.36068264180093 | erot = 2.91715332823342 | epot = -21.5794336507741 | etot = -16.3015976807398 -310000 ekin = 2.4995235722922 | erot = 2.36028950896138 | epot = -21.5982142524176 | etot = -16.738401171164 -311000 ekin = 2.53288726180906 | erot = 2.29596940545851 | epot = -21.6418553661547 | etot = -16.8129986988871 -312000 ekin = 2.05123272208704 | erot = 2.92023923411834 | epot = -21.7377547517075 | etot = -16.7662827955022 -313000 ekin = 1.80834719374888 | erot = 2.29357283142125 | epot = -21.7993116362532 | etot = -17.6973916110831 -314000 ekin = 2.30684015099018 | erot = 2.20859462712272 | epot = -21.8029398081388 | etot = -17.2875050300259 -315000 ekin = 1.86413924486173 | erot = 2.14748794238475 | epot = -21.8550418960799 | etot = -17.8434147088335 -316000 ekin = 2.20558056533516 | erot = 3.03447287931582 | epot = -21.8868412075709 | etot = -16.6467877629199 -317000 ekin = 2.47820931125479 | erot = 3.56870099099487 | epot = -21.9902146748519 | etot = -15.9433043726022 -318000 ekin = 2.36582343801679 | erot = 3.01887804681552 | epot = -22.1178732891163 | etot = -16.733171804284 -319000 ekin = 2.40464629760758 | erot = 3.15910789488741 | epot = -22.2289401281565 | etot = -16.6651859356615 -320000 ekin = 1.80206494109346 | erot = 2.83527990295434 | epot = -22.3120263401861 | etot = -17.6746814961383 -321000 ekin = 2.91146951948762 | erot = 2.25772268449837 | epot = -22.3029455835947 | etot = -17.1337533796087 -322000 ekin = 2.8226351296685 | erot = 2.67950826833977 | epot = -22.3041650189947 | etot = -16.8020216209865 -323000 ekin = 2.067323568424 | erot = 2.319752847753 | epot = -22.3338840353559 | etot = -17.9468076191789 -324000 ekin = 2.6012747278288 | erot = 2.58351861537749 | epot = -22.3215168526944 | etot = -17.1367235094881 -325000 ekin = 3.45560055552843 | erot = 2.50162515355505 | epot = -22.1825527777624 | etot = -16.2253270686789 -326000 ekin = 3.51422890604519 | erot = 2.84426061018012 | epot = -22.0201095272525 | etot = -15.6616200110272 -327000 ekin = 2.63551490316295 | erot = 2.20570805472231 | epot = -21.9384479867007 | etot = -17.0972250288154 -328000 ekin = 1.8043914440792 | erot = 2.37599512200968 | epot = -21.861980397642 | etot = -17.6815938315531 -329000 ekin = 2.15766181563134 | erot = 2.45286496267961 | epot = -21.8518523862112 | etot = -17.2413256079002 -330000 ekin = 1.8483425992464 | erot = 2.03367429366601 | epot = -21.768409525242 | etot = -17.8863926323296 -331000 ekin = 2.3531484336258 | erot = 1.80165819621476 | epot = -21.7197009414848 | etot = -17.5648943116443 -332000 ekin = 1.67855936307207 | erot = 2.5334121965131 | epot = -21.7336434355881 | etot = -17.5216718760029 -333000 ekin = 1.60376334688456 | erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256 -334000 ekin = 2.26551990081779 | erot = 2.62486254825415 | epot = -21.8794971078471 | etot = -16.9891146587751 -335000 ekin = 2.91208137486081 | erot = 3.11052870452009 | epot = -21.9161692767172 | etot = -15.8935591973363 -336000 ekin = 2.73132973682385 | erot = 2.56213100489412 | epot = -21.8312488568505 | etot = -16.5377881151325 -337000 ekin = 3.15411918141902 | erot = 3.87512819831194 | epot = -21.9061152574783 | etot = -14.8768678777473 -338000 ekin = 2.33141760424507 | erot = 2.13211945089677 | epot = -21.913746111238 | etot = -17.4502090560962 -339000 ekin = 1.71915361945719 | erot = 2.31270220754042 | epot = -21.904207477372 | etot = -17.8723516503744 -340000 ekin = 1.62199393011804 | erot = 3.16990972384471 | epot = -21.8898233676232 | etot = -17.0979197136604 -341000 ekin = 1.71588704296646 | erot = 3.17642860992459 | epot = -21.8345558128149 | etot = -16.9422401599239 -342000 ekin = 1.82178091247658 | erot = 2.58875985611024 | epot = -21.7161502950573 | etot = -17.3056095264705 -343000 ekin = 3.08559255942693 | erot = 2.94813449265471 | epot = -21.7030445300997 | etot = -15.669317478018 -344000 ekin = 2.95985387154984 | erot = 3.1154751585035 | epot = -21.6815483295521 | etot = -15.6062192994987 -345000 ekin = 2.33428072266864 | erot = 2.88044431283017 | epot = -21.6567075042343 | etot = -16.4419824687355 -346000 ekin = 2.02077664062698 | erot = 3.45936833964707 | epot = -21.5877268821218 | etot = -16.1075819018478 -347000 ekin = 2.34924784800441 | erot = 1.93056350805623 | epot = -21.4896151766055 | etot = -17.2098038205448 -348000 ekin = 2.79839267202794 | erot = 2.79408776517963 | epot = -21.4682057474678 | etot = -15.8757253102602 -349000 ekin = 2.33820470114614 | erot = 3.12966318670513 | epot = -21.5603039389198 | etot = -16.0924360510685 -350000 ekin = 2.22383234890832 | erot = 2.38886870388011 | epot = -21.5375784703117 | etot = -16.9248774175233 -351000 ekin = 2.33329735253339 | erot = 2.84447430695179 | epot = -21.5078106306152 | etot = -16.33003897113 -352000 ekin = 2.74923373919408 | erot = 2.76796181793625 | epot = -21.5537134920816 | etot = -16.0365179349512 -353000 ekin = 1.76111836153717 | erot = 2.12255592617518 | epot = -21.5037017999955 | etot = -17.6200275122832 -354000 ekin = 2.29967358188085 | erot = 2.37615363620183 | epot = -21.559257977819 | etot = -16.8834307597364 -355000 ekin = 2.32956787601564 | erot = 2.41406261152025 | epot = -21.5311925684016 | etot = -16.7875620808657 -356000 ekin = 2.99536507165417 | erot = 3.0133786789017 | epot = -21.461213826164 | etot = -15.4524700756081 -357000 ekin = 1.79487551861702 | erot = 2.14781775756832 | epot = -21.4425100027869 | etot = -17.4998167266016 -358000 ekin = 2.06856992699964 | erot = 1.9158505155371 | epot = -21.4597512525557 | etot = -17.475330810019 -359000 ekin = 2.03457633089973 | erot = 2.13725650388114 | epot = -21.434584367242 | etot = -17.2627515324611 -360000 ekin = 2.64289898809605 | erot = 2.45722294398598 | epot = -21.3798303659973 | etot = -16.2797084339152 -361000 ekin = 2.44681633772951 | erot = 2.40323525392197 | epot = -21.4535746870958 | etot = -16.6035230954443 -362000 ekin = 2.27284400709389 | erot = 2.04866562998477 | epot = -21.4444048899961 | etot = -17.1228952529175 -363000 ekin = 3.23945885057604 | erot = 1.79247859381387 | epot = -21.4992698914106 | etot = -16.4673324470207 -364000 ekin = 3.01124200487831 | erot = 2.16495867321708 | epot = -21.5330648567406 | etot = -16.3568641786452 -365000 ekin = 2.51472285580867 | erot = 2.29864111879035 | epot = -21.6252096459669 | etot = -16.8118456713679 -366000 ekin = 2.59356655410022 | erot = 2.21031948632573 | epot = -21.6397726115723 | etot = -16.8358865711464 -367000 ekin = 2.23422490605626 | erot = 1.85375489374336 | epot = -21.7036464131406 | etot = -17.615666613341 -368000 ekin = 2.47747707853682 | erot = 2.36511710555106 | epot = -21.7442459693683 | etot = -16.9016517852804 -369000 ekin = 2.03854183495619 | erot = 2.80790943599038 | epot = -21.829546112742 | etot = -16.9830948417954 -370000 ekin = 2.08495509326204 | erot = 2.15717784784087 | epot = -21.8579547558588 | etot = -17.6158218147559 -371000 ekin = 2.1649158804987 | erot = 2.10731342711637 | epot = -21.750730287247 | etot = -17.4785009796319 -372000 ekin = 1.83416420958724 | erot = 1.90082367490453 | epot = -21.6784224725519 | etot = -17.9434345880602 -373000 ekin = 1.97176482573297 | erot = 1.77796007890949 | epot = -21.6393712386778 | etot = -17.8896463340354 -374000 ekin = 2.89940710658305 | erot = 1.91194262525378 | epot = -21.5337545453636 | etot = -16.7224048135267 -375000 ekin = 2.32339676163341 | erot = 1.92362318361284 | epot = -21.4217091025191 | etot = -17.1746891572728 -376000 ekin = 2.59047552311153 | erot = 2.32394149083979 | epot = -21.4139727856534 | etot = -16.4995557717021 -377000 ekin = 2.24598863840517 | erot = 1.65770205797294 | epot = -21.3405339068232 | etot = -17.4368432104451 -378000 ekin = 2.38351514056703 | erot = 2.54156262207207 | epot = -21.3122380587448 | etot = -16.3871602961057 -379000 ekin = 2.08457212928958 | erot = 2.11819645676889 | epot = -21.2663127721437 | etot = -17.0635441860853 -380000 ekin = 2.62168026009058 | erot = 2.36576073073357 | epot = -21.2469701231192 | etot = -16.259529132295 -381000 ekin = 2.42554871977308 | erot = 2.21588725182519 | epot = -21.2594018196931 | etot = -16.6179658480948 -382000 ekin = 2.04454090532126 | erot = 3.35199327879852 | epot = -21.3507561156204 | etot = -15.9542219315006 -383000 ekin = 2.57756769789846 | erot = 1.58356833947095 | epot = -21.4206473136967 | etot = -17.2595112763272 -384000 ekin = 2.32411392435712 | erot = 2.07034159075996 | epot = -21.425401700327 | etot = -17.03094618521 -385000 ekin = 1.93815279071873 | erot = 3.29970374476252 | epot = -21.4993838182002 | etot = -16.2615272827189 -386000 ekin = 2.10645704249442 | erot = 2.94380940917572 | epot = -21.5050572923383 | etot = -16.4547908406681 -387000 ekin = 2.28625118399721 | erot = 2.404880226949 | epot = -21.4350466670762 | etot = -16.74391525613 -388000 ekin = 2.84183807689895 | erot = 2.72440789072405 | epot = -21.448767296848 | etot = -15.882521329225 -389000 ekin = 3.39750799106372 | erot = 3.08194517695386 | epot = -21.6559630447603 | etot = -15.1765098767427 -390000 ekin = 2.82211920760115 | erot = 2.04880343622589 | epot = -21.7229608878358 | etot = -16.8520382440088 -391000 ekin = 2.25113345866117 | erot = 2.45876014532077 | epot = -21.7793475672488 | etot = -17.0694539632668 -392000 ekin = 2.6777973992177 | erot = 2.75278604715789 | epot = -21.9200377033298 | etot = -16.4894542569542 -393000 ekin = 2.07336639249413 | erot = 1.66102921524042 | epot = -22.0500496423094 | etot = -18.3156540345748 -394000 ekin = 2.1138614951422 | erot = 2.4065490584156 | epot = -22.0647062581752 | etot = -17.5442957046174 -395000 ekin = 2.46967791557607 | erot = 2.46187607744978 | epot = -22.0113006362931 | etot = -17.0797466432672 -396000 ekin = 3.17858061422168 | erot = 1.60030928107608 | epot = -21.9570022338792 | etot = -17.1781123385814 -397000 ekin = 2.37483507726776 | erot = 2.17387816921976 | epot = -21.8769234701935 | etot = -17.3282102237059 -398000 ekin = 2.29815779154461 | erot = 2.2014862703049 | epot = -21.8293641014529 | etot = -17.3297200396034 -399000 ekin = 2.66620669497936 | erot = 2.78316441348845 | epot = -21.7420307764657 | etot = -16.2926596679979 -400000 ekin = 1.8196142363994 | erot = 2.77573291920477 | epot = -21.7225828560707 | etot = -17.1272357004666 -401000 ekin = 2.39347596566753 | erot = 3.11237720134102 | epot = -21.7632198127751 | etot = -16.2573666457665 -402000 ekin = 4.01379092525261 | erot = 3.58756310879361 | epot = -21.6952307126456 | etot = -14.0938766785994 -403000 ekin = 3.64238723358271 | erot = 3.44210139074533 | epot = -21.6932224157202 | etot = -14.6087337913922 -404000 ekin = 2.52116102522202 | erot = 2.99286839639893 | epot = -21.7395466120138 | etot = -16.2255171903929 -405000 ekin = 2.80514548558626 | erot = 3.09807228440149 | epot = -21.809681120553 | etot = -15.9064633505653 -406000 ekin = 2.32696376764902 | erot = 2.03572639782902 | epot = -21.9111381639248 | etot = -17.5484479984468 -407000 ekin = 2.33504128016395 | erot = 1.91320949168965 | epot = -21.9359478399848 | etot = -17.6876970681312 -408000 ekin = 1.90942025822265 | erot = 2.20375631379574 | epot = -21.9849314014528 | etot = -17.8717548294344 -409000 ekin = 1.98818542800297 | erot = 1.95540808206523 | epot = -22.0378349759701 | etot = -18.0942414659019 -410000 ekin = 1.59823476401333 | erot = 1.91272967852491 | epot = -22.0830507565096 | etot = -18.5720863139714 -411000 ekin = 1.87320182179615 | erot = 2.46575148951076 | epot = -22.1911106440468 | etot = -17.8521573327399 -412000 ekin = 2.51909186028136 | erot = 2.65534868642724 | epot = -22.281680067606 | etot = -17.1072395208974 -413000 ekin = 2.80929435327118 | erot = 3.19888285052217 | epot = -22.1907679968741 | etot = -16.1825907930808 -414000 ekin = 2.79014519733558 | erot = 2.7251519541093 | epot = -22.144863024243 | etot = -16.6295658727981 -415000 ekin = 2.46789019087319 | erot = 2.24891720770208 | epot = -22.1977268949425 | etot = -17.4809194963672 -416000 ekin = 3.30766536008866 | erot = 1.55878918639505 | epot = -22.1694878213559 | etot = -17.3030332748722 -417000 ekin = 3.95074944679108 | erot = 2.44780201516577 | epot = -22.1018895242095 | etot = -15.7033380622526 -418000 ekin = 2.77340936693415 | erot = 2.68993840817536 | epot = -21.977327562767 | etot = -16.5139797876575 -419000 ekin = 2.38275203991917 | erot = 2.97769109273478 | epot = -21.9010102007429 | etot = -16.5405670680889 -420000 ekin = 1.80397709765343 | erot = 1.82715488758969 | epot = -21.8849019003165 | etot = -18.2537699150734 -421000 ekin = 1.35294173647286 | erot = 1.7746327595132 | epot = -21.8324727162455 | etot = -18.7048982202595 -422000 ekin = 1.39101035408781 | erot = 2.74626781088313 | epot = -21.8922044238521 | etot = -17.7549262588811 -423000 ekin = 1.58313118355036 | erot = 3.0798858727609 | epot = -21.9303489156376 | etot = -17.2673318593263 -424000 ekin = 2.38308976422853 | erot = 2.0290563283423 | epot = -22.0003513420112 | etot = -17.5882052494403 -425000 ekin = 2.32292982636642 | erot = 2.54472792699355 | epot = -22.0461884305753 | etot = -17.1785306772154 -426000 ekin = 2.07274921207622 | erot = 3.12068562025985 | epot = -21.9899604929779 | etot = -16.7965256606419 -427000 ekin = 2.16499158921497 | erot = 2.43609860560844 | epot = -21.883756502818 | etot = -17.2826663079946 -428000 ekin = 1.81001230881454 | erot = 1.6518491031194 | epot = -21.8651168729134 | etot = -18.4032554609795 -429000 ekin = 1.67080799563552 | erot = 2.55829004033943 | epot = -21.823203822061 | etot = -17.5941057860861 -430000 ekin = 2.68658781224627 | erot = 2.8591925337156 | epot = -21.8545360487503 | etot = -16.3087557027885 -431000 ekin = 2.77334901985549 | erot = 1.57746917070686 | epot = -21.8360353910944 | etot = -17.485217200532 -432000 ekin = 2.50244674166436 | erot = 1.60779258881598 | epot = -21.7381087453319 | etot = -17.6278694148516 -433000 ekin = 1.85649371322473 | erot = 2.4917335891794 | epot = -21.7919912827364 | etot = -17.4437639803323 -434000 ekin = 2.89302367450635 | erot = 2.7989004560269 | epot = -21.923157505168 | etot = -16.2312333746348 -435000 ekin = 3.67647442700572 | erot = 1.38588132381276 | epot = -22.1019777057281 | etot = -17.0396219549097 -436000 ekin = 3.05510329104703 | erot = 2.00142902882896 | epot = -22.1034257027066 | etot = -17.0468933828306 -437000 ekin = 3.2334117289381 | erot = 1.78346855436481 | epot = -22.1137020887251 | etot = -17.0968218054222 -438000 ekin = 2.86378458795303 | erot = 1.84588842157479 | epot = -22.072414124752 | etot = -17.3627411152242 -439000 ekin = 2.41407153953135 | erot = 2.70066632790346 | epot = -22.0535011599236 | etot = -16.9387632924888 -440000 ekin = 2.22110309163132 | erot = 3.0167468581899 | epot = -22.0773629228072 | etot = -16.839512972986 -441000 ekin = 2.8952003347941 | erot = 2.87911130379518 | epot = -22.2098492363511 | etot = -16.4355375977618 -442000 ekin = 2.05598301233622 | erot = 1.73562369066667 | epot = -22.2689079268812 | etot = -18.4773012238783 -443000 ekin = 1.86650631344267 | erot = 2.00816178040311 | epot = -22.3072964279925 | etot = -18.4326283341467 -444000 ekin = 2.06088560705618 | erot = 2.15265011198712 | epot = -22.3186686701219 | etot = -18.1051329510786 -445000 ekin = 2.10029110633057 | erot = 2.2800331405132 | epot = -22.3739249314238 | etot = -17.9936006845801 -446000 ekin = 2.42121462246176 | erot = 2.85365097104764 | epot = -22.4030820729314 | etot = -17.128216479422 -447000 ekin = 2.19905370994782 | erot = 2.98216231903379 | epot = -22.4760062523442 | etot = -17.2947902233625 -448000 ekin = 2.35344530580996 | erot = 2.94496431571713 | epot = -22.4927466941727 | etot = -17.1943370726456 -449000 ekin = 2.39032460069844 | erot = 2.92889137252356 | epot = -22.5027878081879 | etot = -17.1835718349659 -450000 ekin = 1.87543018481826 | erot = 1.69603328668916 | epot = -22.4562462785528 | etot = -18.8847828070454 -451000 ekin = 2.01850498861611 | erot = 1.92812989993404 | epot = -22.4817672986218 | etot = -18.5351324100716 -452000 ekin = 1.36652609658347 | erot = 1.87105620810406 | epot = -22.4501755877893 | etot = -19.2125932831018 -453000 ekin = 2.0599225820261 | erot = 2.56027964608567 | epot = -22.2765869721545 | etot = -17.6563847440428 -454000 ekin = 1.47421749728914 | erot = 2.19120144206327 | epot = -22.1381671023588 | etot = -18.4727481630064 -455000 ekin = 1.65550022307771 | erot = 2.72165814308168 | epot = -21.9904394751434 | etot = -17.613281108984 -456000 ekin = 2.34827062603187 | erot = 2.00722438151074 | epot = -21.9105114729144 | etot = -17.5550164653718 -457000 ekin = 2.01338249991754 | erot = 2.37170378033695 | epot = -21.8819790372449 | etot = -17.4968927569904 -458000 ekin = 1.72815421955305 | erot = 2.26329746701056 | epot = -21.9116044050661 | etot = -17.9201527185024 -459000 ekin = 2.48347398227002 | erot = 2.32376196929941 | epot = -21.9949404038568 | etot = -17.1877044522874 -460000 ekin = 2.18770854699575 | erot = 2.00081662918322 | epot = -21.9585322440375 | etot = -17.7700070678586 -461000 ekin = 2.27716435663744 | erot = 2.9019565626907 | epot = -21.8877682177659 | etot = -16.7086472984378 -462000 ekin = 2.61244889701715 | erot = 1.79757533309513 | epot = -21.9143949779912 | etot = -17.5043707478789 -463000 ekin = 2.55684814656524 | erot = 3.31200610027657 | epot = -21.8497749242034 | etot = -15.9809206773616 -464000 ekin = 2.15312235839157 | erot = 2.38947690136822 | epot = -21.7825241097983 | etot = -17.2399248500385 -465000 ekin = 2.5257577253008 | erot = 3.61331808321477 | epot = -21.70727052519 | etot = -15.5681947166744 -466000 ekin = 1.97943618964772 | erot = 2.88688528337621 | epot = -21.7222514097774 | etot = -16.8559299367535 -467000 ekin = 1.62882257493983 | erot = 2.60892282315519 | epot = -21.8080861041928 | etot = -17.5703407060978 -468000 ekin = 1.09823854644375 | erot = 3.35073251937299 | epot = -21.8523811012329 | etot = -17.4034100354162 -469000 ekin = 1.70229597385131 | erot = 2.7588984072639 | epot = -21.8665756757502 | etot = -17.405381294635 -470000 ekin = 1.85844768422772 | erot = 2.8706546217625 | epot = -21.9036130079376 | etot = -17.1745107019474 -471000 ekin = 2.74399539924327 | erot = 2.34943354955083 | epot = -21.9543989717239 | etot = -16.8609700229298 -472000 ekin = 2.7182617922689 | erot = 2.13581917182001 | epot = -22.0449294707038 | etot = -17.1908485066149 -473000 ekin = 2.29380642077304 | erot = 2.07595163501546 | epot = -22.0706135180041 | etot = -17.7008554622156 -474000 ekin = 2.22690782122656 | erot = 2.1647059901395 | epot = -22.0704871162386 | etot = -17.6788733048726 -475000 ekin = 2.4978679533329 | erot = 2.09510196885223 | epot = -22.0509742163569 | etot = -17.4580042941718 -476000 ekin = 2.20264299239668 | erot = 1.76757923556403 | epot = -21.9427521555982 | etot = -17.9725299276375 -477000 ekin = 2.45872237399503 | erot = 2.38426997478539 | epot = -21.9051474088983 | etot = -17.0621550601178 -478000 ekin = 1.89905964030889 | erot = 2.04864356713722 | epot = -21.9114508304737 | etot = -17.9637476230276 -479000 ekin = 2.27133902137491 | erot = 3.08755197682257 | epot = -21.8872829373266 | etot = -16.5283919391291 -480000 ekin = 1.67015605151468 | erot = 2.76560365045837 | epot = -21.8968158425889 | etot = -17.4610561406158 -481000 ekin = 1.81882995680354 | erot = 2.94136105971067 | epot = -21.8571304925407 | etot = -17.0969394760265 -482000 ekin = 2.15305069632653 | erot = 2.07327897823918 | epot = -21.8152992914385 | etot = -17.5889696168728 -483000 ekin = 1.50004535981758 | erot = 1.99364343935404 | epot = -21.7843644990947 | etot = -18.2906756999231 -484000 ekin = 1.85234844255529 | erot = 2.34000231202781 | epot = -21.8614293841666 | etot = -17.6690786295835 -485000 ekin = 1.64682178328831 | erot = 2.50437862576679 | epot = -21.8969405008956 | etot = -17.7457400918405 -486000 ekin = 1.86104257115938 | erot = 2.15995925522771 | epot = -21.8879397421696 | etot = -17.8669379157825 -487000 ekin = 2.34639026339217 | erot = 3.11622773972825 | epot = -21.9707194220382 | etot = -16.5081014189178 -488000 ekin = 2.27484994031488 | erot = 3.28147617368226 | epot = -21.9426475486812 | etot = -16.3863214346841 -489000 ekin = 2.38811933287365 | erot = 2.56070014238266 | epot = -21.8600861168089 | etot = -16.9112666415526 -490000 ekin = 2.12976254880773 | erot = 3.54525746010289 | epot = -21.7617637919249 | etot = -16.0867437830143 -491000 ekin = 2.20850764560417 | erot = 2.48919239454317 | epot = -21.6468680069132 | etot = -16.9491679667658 -492000 ekin = 2.43957739853024 | erot = 2.76323186690378 | epot = -21.6230951653168 | etot = -16.4202858998828 -493000 ekin = 1.79391622496105 | erot = 2.29052518470042 | epot = -21.6945975278841 | etot = -17.6101561182226 -494000 ekin = 2.11542949642227 | erot = 3.01313865872481 | epot = -21.7637004472039 | etot = -16.6351322920568 -495000 ekin = 2.1568591957283 | erot = 2.49005677705245 | epot = -21.8783556810053 | etot = -17.2314397082246 -496000 ekin = 2.06037552826019 | erot = 2.60698629104699 | epot = -21.9276220332962 | etot = -17.260260213989 -497000 ekin = 2.52228141248763 | erot = 1.710130192768 | epot = -21.8769629373864 | etot = -17.6445513321307 -498000 ekin = 2.15394500805411 | erot = 1.78777085700022 | epot = -21.8243748366056 | etot = -17.8826589715513 -499000 ekin = 3.01296343053108 | erot = 1.73934813146708 | epot = -21.8392632680439 | etot = -17.0869517060458 -500000 ekin = 2.76642119718551 | erot = 2.50182215373002 | epot = -21.830671988603 | etot = -16.5624286376875 -501000 ekin = 2.69367571720338 | erot = 2.99042817784739 | epot = -21.7039103667138 | etot = -16.0198064716631 -502000 ekin = 1.91666556639459 | erot = 3.89815239299714 | epot = -21.5845300715443 | etot = -15.7697121121525 -503000 ekin = 1.80513448090424 | erot = 2.94463129244922 | epot = -21.408846856306 | etot = -16.6590810829525 -504000 ekin = 1.70082883689617 | erot = 3.04312463877848 | epot = -21.3315058298563 | etot = -16.5875523541817 -505000 ekin = 2.75953000022913 | erot = 2.14635942194519 | epot = -21.3525103549444 | etot = -16.4466209327701 -506000 ekin = 2.29728093923375 | erot = 2.04403144683579 | epot = -21.3794572010067 | etot = -17.0381448149372 -507000 ekin = 3.17636857959624 | erot = 2.42164349794529 | epot = -21.4731108320934 | etot = -15.8750987545519 -508000 ekin = 2.53590109429522 | erot = 2.52790695399208 | epot = -21.6300410847596 | etot = -16.5662330364723 -509000 ekin = 2.12748393236722 | erot = 2.83071060777933 | epot = -21.7781347526393 | etot = -16.8199402124927 -510000 ekin = 2.16138023827908 | erot = 1.44739524871434 | epot = -21.8661383228762 | etot = -18.2573628358828 -511000 ekin = 2.5432337386743 | erot = 2.77108674378182 | epot = -21.9670096484361 | etot = -16.65268916598 -512000 ekin = 2.32820226144235 | erot = 2.8042493163404 | epot = -22.0177071813425 | etot = -16.8852556035598 -513000 ekin = 2.47700215188743 | erot = 2.17127792631492 | epot = -22.0110285387343 | etot = -17.3627484605319 -514000 ekin = 2.76651136580707 | erot = 2.55680467976047 | epot = -22.0909970005814 | etot = -16.7676809550138 -515000 ekin = 2.5202331965388 | erot = 1.82499891391154 | epot = -22.1712715169565 | etot = -17.8260394065062 -516000 ekin = 2.81741012640848 | erot = 2.22255273815334 | epot = -22.2621950124766 | etot = -17.2222321479148 -517000 ekin = 2.03287831599844 | erot = 2.04932227860395 | epot = -22.2794486174447 | etot = -18.1972480228423 -518000 ekin = 2.18753527424292 | erot = 2.76011341951323 | epot = -22.2667176836093 | etot = -17.3190689898532 -519000 ekin = 2.23127004412533 | erot = 2.23036422155453 | epot = -22.3641437250361 | etot = -17.9025094593562 -520000 ekin = 1.88835704965194 | erot = 2.20137678015021 | epot = -22.4547788180201 | etot = -18.365044988218 -521000 ekin = 2.57911594310157 | erot = 1.87216207270883 | epot = -22.6071563154982 | etot = -18.1558782996878 -522000 ekin = 3.47551915105823 | erot = 1.7762374523623 | epot = -22.6852629490162 | etot = -17.4335063455956 -523000 ekin = 2.84545293485784 | erot = 2.47507537559667 | epot = -22.727728352182 | etot = -17.4072000417275 -524000 ekin = 2.40278895519472 | erot = 2.37529684497552 | epot = -22.6643160930411 | etot = -17.8862302928709 -525000 ekin = 1.59507033575009 | erot = 2.61508341973268 | epot = -22.5633164974795 | etot = -18.3531627419968 -526000 ekin = 1.67007684014044 | erot = 1.59545284095808 | epot = -22.511319978416 | etot = -19.2457902973175 -527000 ekin = 2.19667533945247 | erot = 1.93330231246752 | epot = -22.4181345854017 | etot = -18.2881569334817 -528000 ekin = 2.6386695788743 | erot = 2.84200507572115 | epot = -22.4271496272375 | etot = -16.946474972642 -529000 ekin = 2.71685924097597 | erot = 3.01195511036354 | epot = -22.4607209136928 | etot = -16.7319065623533 -530000 ekin = 2.59646038482582 | erot = 2.1317692819235 | epot = -22.3209630404852 | etot = -17.5927333737358 -531000 ekin = 2.96818211550215 | erot = 2.35836906019033 | epot = -22.2240561584028 | etot = -16.8975049827103 -532000 ekin = 2.54400448114086 | erot = 2.32266423688292 | epot = -22.2383323718678 | etot = -17.3716636538441 -533000 ekin = 2.47235456553948 | erot = 2.96337386592411 | epot = -22.2434312615742 | etot = -16.8077028301106 -534000 ekin = 2.104894788263 | erot = 2.03894640697441 | epot = -22.2624131617689 | etot = -18.1185719665315 -535000 ekin = 3.76811893478762 | erot = 2.64694643296526 | epot = -22.2342741399369 | etot = -15.819208772184 -536000 ekin = 2.78932048770646 | erot = 1.95046774407585 | epot = -22.1710588414062 | etot = -17.4312706096239 -537000 ekin = 2.84547413963846 | erot = 2.6235440651257 | epot = -22.0792539675812 | etot = -16.610235762817 -538000 ekin = 2.67615418297317 | erot = 2.08962546790895 | epot = -21.9560559397441 | etot = -17.190276288862 -539000 ekin = 2.73041224389434 | erot = 2.35761678189143 | epot = -22.0360310245606 | etot = -16.9480019987748 -540000 ekin = 2.45513520817505 | erot = 2.4980712479617 | epot = -22.1997448500024 | etot = -17.2465383938656 -541000 ekin = 3.48268229748523 | erot = 2.77797330372245 | epot = -22.2939060084685 | etot = -16.0332504072608 -542000 ekin = 2.48960436886327 | erot = 2.87332479229809 | epot = -22.3004887690915 | etot = -16.9375596079301 -543000 ekin = 2.34699181381528 | erot = 2.86167842257193 | epot = -22.3027783678197 | etot = -17.0941081314325 -544000 ekin = 2.22918134297116 | erot = 1.4682792461716 | epot = -22.2757921511235 | etot = -18.5783315619807 -545000 ekin = 2.45393652663684 | erot = 2.14178562937392 | epot = -22.2696521197313 | etot = -17.6739299637206 -546000 ekin = 1.98434977645849 | erot = 2.24144093113159 | epot = -22.232171992891 | etot = -18.0063812853009 -547000 ekin = 2.56230350196472 | erot = 1.8957462591202 | epot = -22.2013923967025 | etot = -17.7433426356176 -548000 ekin = 1.72907614338158 | erot = 1.64127030305735 | epot = -22.1897325934373 | etot = -18.8193861469984 -549000 ekin = 1.95696682165776 | erot = 2.64539988943055 | epot = -22.3281210018679 | etot = -17.7257542907796 -550000 ekin = 1.80672944936439 | erot = 1.58554489058937 | epot = -22.4379557312283 | etot = -19.0456813912745 -551000 ekin = 2.19785864069661 | erot = 2.26344341600386 | epot = -22.4944444264338 | etot = -18.0331423697333 -552000 ekin = 2.074442528674 | erot = 2.49246441473273 | epot = -22.5313734934249 | etot = -17.9644665500182 -553000 ekin = 2.94841939583913 | erot = 2.1230978630074 | epot = -22.5870982488507 | etot = -17.5155809900042 -554000 ekin = 2.86687820100223 | erot = 1.9428729838172 | epot = -22.755332978123 | etot = -17.9455817933036 -555000 ekin = 2.43102414091851 | erot = 2.28708167460996 | epot = -22.8409516497233 | etot = -18.1228458341949 -556000 ekin = 2.31020008885682 | erot = 2.55815314755913 | epot = -22.8777743355338 | etot = -18.0094210991179 -557000 ekin = 2.81359485404958 | erot = 1.42586137655665 | epot = -22.93912738 | etot = -18.6996711493938 -558000 ekin = 2.7970970853355 | erot = 1.99545051650404 | epot = -22.9823826800611 | etot = -18.1898350782216 -559000 ekin = 3.34842854089643 | erot = 2.30939572175805 | epot = -23.0558646505447 | etot = -17.3980403878902 -560000 ekin = 3.12583165184862 | erot = 2.33613566970363 | epot = -23.0537007225862 | etot = -17.591733401034 -561000 ekin = 2.9127609673679 | erot = 2.07459481236913 | epot = -22.982260765434 | etot = -17.994904985697 -562000 ekin = 3.33017095598494 | erot = 2.52215992853225 | epot = -22.8889363116257 | etot = -17.0366054271086 -563000 ekin = 2.70200701416854 | erot = 1.64770113379199 | epot = -22.8712722594835 | etot = -18.521564111523 -564000 ekin = 2.82953631474813 | erot = 2.52900560163798 | epot = -22.8387855460795 | etot = -17.4802436296934 -565000 ekin = 2.67999888917708 | erot = 2.05091800967453 | epot = -22.7937507048715 | etot = -18.0628338060199 -566000 ekin = 2.32986557500305 | erot = 2.16379904557213 | epot = -22.8028233873669 | etot = -18.3091587667917 -567000 ekin = 1.92319601586312 | erot = 2.83258522428556 | epot = -22.7588270107033 | etot = -18.0030457705546 -568000 ekin = 2.1767237164987 | erot = 2.23391201707386 | epot = -22.7857243432792 | etot = -18.3750886097066 -569000 ekin = 2.44197408396629 | erot = 2.6515953630557 | epot = -22.7197314796374 | etot = -17.6261620326154 -570000 ekin = 2.43177406209051 | erot = 1.89764945519458 | epot = -22.6963472615904 | etot = -18.3669237443054 -571000 ekin = 2.86160521289847 | erot = 2.96804382024775 | epot = -22.6961835038031 | etot = -16.8665344706569 -572000 ekin = 1.92662919536387 | erot = 3.79135909534691 | epot = -22.6587081618987 | etot = -16.940719871188 -573000 ekin = 2.40137439242946 | erot = 2.29982613356341 | epot = -22.6365074046858 | etot = -17.935306878693 -574000 ekin = 1.68882589350908 | erot = 2.3209740449249 | epot = -22.6783832960445 | etot = -18.6685833576105 -575000 ekin = 1.85490665091732 | erot = 1.8564080891142 | epot = -22.7444448136904 | etot = -19.0331300736588 -576000 ekin = 3.24775679594035 | erot = 2.9556926821431 | epot = -22.6991990620437 | etot = -16.4957495839603 -577000 ekin = 2.89423151645282 | erot = 2.87486712706735 | epot = -22.628436560802 | etot = -16.8593379172818 -578000 ekin = 2.4046091667757 | erot = 2.78216711024699 | epot = -22.4348874817265 | etot = -17.2481112047039 -579000 ekin = 2.40580528046576 | erot = 1.9955781448253 | epot = -22.288913673667 | etot = -17.887530248376 -580000 ekin = 2.69817090358906 | erot = 1.94741864170502 | epot = -22.1754486864787 | etot = -17.5298591411846 -581000 ekin = 2.06309668646281 | erot = 2.97621367011722 | epot = -22.0670098600828 | etot = -17.0276995035027 -582000 ekin = 2.33869527454826 | erot = 3.07898324506955 | epot = -21.9478320300713 | etot = -16.5301535104535 -583000 ekin = 2.23428959741495 | erot = 2.68476693088864 | epot = -21.837983720672 | etot = -16.9189271923684 -584000 ekin = 2.94321016295282 | erot = 2.59995039730549 | epot = -21.7517635625832 | etot = -16.2086030023248 -585000 ekin = 2.36063475490835 | erot = 2.49112677628938 | epot = -21.7173359488816 | etot = -16.8655744176839 -586000 ekin = 3.56583702163525 | erot = 2.02487858259688 | epot = -21.7707868137138 | etot = -16.1800712094817 -587000 ekin = 3.53727585853243 | erot = 1.9725893265202 | epot = -21.7665121756112 | etot = -16.2566469905585 -588000 ekin = 2.82339556293757 | erot = 1.59340504807046 | epot = -21.7545319340972 | etot = -17.3377313230892 -589000 ekin = 2.31627310139818 | erot = 2.20582604523299 | epot = -21.8199173705563 | etot = -17.2978182239252 -590000 ekin = 2.57616671531331 | erot = 1.72768273328208 | epot = -21.8427138199642 | etot = -17.5388643713688 -591000 ekin = 1.91473306171853 | erot = 3.80604384238379 | epot = -21.9351393124187 | etot = -16.2143624083164 -592000 ekin = 2.11222958764659 | erot = 2.84208333850205 | epot = -21.9639458839076 | etot = -17.0096329577589 -593000 ekin = 1.66462149590471 | erot = 2.46217253451014 | epot = -21.9921445323971 | etot = -17.8653505019822 -594000 ekin = 1.86314045588476 | erot = 2.37275936142268 | epot = -22.1149191228505 | etot = -17.879019305543 -595000 ekin = 1.6397125755004 | erot = 2.1497024679856 | epot = -22.2960530768755 | etot = -18.5066380333895 -596000 ekin = 1.86247376576131 | erot = 1.5693809542787 | epot = -22.4014957466218 | etot = -18.9696410265818 -597000 ekin = 2.210739014067 | erot = 2.3087175693751 | epot = -22.4599242604733 | etot = -17.9404676770312 -598000 ekin = 1.8660134932493 | erot = 3.02311727399809 | epot = -22.5165298316334 | etot = -17.627399064386 -599000 ekin = 2.86271635930755 | erot = 2.19928854437227 | epot = -22.536599708025 | etot = -17.4745948043452 -600000 ekin = 2.65062163067179 | erot = 2.14533898812782 | epot = -22.4620537969303 | etot = -17.6660931781307 -601000 ekin = 2.97018864875202 | erot = 3.19824090103877 | epot = -22.3271949752462 | etot = -16.1587654254554 -602000 ekin = 2.93416893709001 | erot = 2.68627449040958 | epot = -22.2245183728173 | etot = -16.6040749453177 -603000 ekin = 2.5987545006459 | erot = 2.71301833029982 | epot = -22.1705323477201 | etot = -16.8587595167744 -604000 ekin = 1.79059859762797 | erot = 2.11515305424796 | epot = -22.1931056020217 | etot = -18.2873539501458 -605000 ekin = 1.82914051863723 | erot = 2.27656979248766 | epot = -22.2183915784731 | etot = -18.1126812673482 -606000 ekin = 2.33864125390345 | erot = 2.204164937778 | epot = -22.1617656383863 | etot = -17.6189594467048 -607000 ekin = 2.72666217259876 | erot = 2.97710334336218 | epot = -22.1572786906588 | etot = -16.4535131746978 -608000 ekin = 2.45226937954678 | erot = 2.41232790919959 | epot = -22.1263051367364 | etot = -17.2617078479901 -609000 ekin = 1.91032127854288 | erot = 2.62712516529567 | epot = -22.0127581830193 | etot = -17.4753117391807 -610000 ekin = 3.01319055031108 | erot = 2.17098104720965 | epot = -21.930499629869 | etot = -16.7463280323483 -611000 ekin = 2.44410994437293 | erot = 2.75159061185424 | epot = -21.9258193850468 | etot = -16.7301188288197 -612000 ekin = 2.50271115837174 | erot = 2.16817640692169 | epot = -21.9676183236645 | etot = -17.2967307583711 -613000 ekin = 3.01842230632868 | erot = 2.12784419676567 | epot = -22.0277467117807 | etot = -16.8814802086864 -614000 ekin = 2.25331711369829 | erot = 2.99334048390158 | epot = -22.0701464667307 | etot = -16.8234888691309 -615000 ekin = 1.66376443031995 | erot = 2.63613776051569 | epot = -21.9985978951916 | etot = -17.698695704356 -616000 ekin = 1.89454248699046 | erot = 2.87318355169532 | epot = -22.0041678369046 | etot = -17.2364417982189 -617000 ekin = 2.14789714287838 | erot = 2.51249074123957 | epot = -22.0251474680604 | etot = -17.3647595839425 -618000 ekin = 3.11174934178844 | erot = 2.74374306269141 | epot = -21.980284295602 | etot = -16.1247918911221 -619000 ekin = 3.41036213968179 | erot = 2.10616794159728 | epot = -21.9557959924962 | etot = -16.4392659112171 -620000 ekin = 4.28430989238205 | erot = 2.19572475327593 | epot = -21.9033881020935 | etot = -15.4233534564355 -621000 ekin = 3.095687767491 | erot = 2.55794040804605 | epot = -21.8286763731363 | etot = -16.1750481975993 -622000 ekin = 2.76030419206697 | erot = 2.60754397958254 | epot = -21.7459002641757 | etot = -16.3780520925262 -623000 ekin = 2.87269212022169 | erot = 2.90401311950186 | epot = -21.5853226709315 | etot = -15.8086174312079 -624000 ekin = 2.01889500087932 | erot = 3.41825755609791 | epot = -21.4095311686242 | etot = -15.972378611647 -625000 ekin = 2.87966631754697 | erot = 2.69115421564283 | epot = -21.2859406043045 | etot = -15.7151200711147 -626000 ekin = 2.56087279949319 | erot = 2.15801254335177 | epot = -21.2329175358055 | etot = -16.5140321929606 -627000 ekin = 2.30197939613517 | erot = 2.40176668957967 | epot = -21.2932794652839 | etot = -16.589533379569 -628000 ekin = 2.23988628353727 | erot = 2.75332535542195 | epot = -21.4558642198861 | etot = -16.4626525809268 -629000 ekin = 2.20891060851904 | erot = 1.97036896055006 | epot = -21.6109313731644 | etot = -17.4316518040953 -630000 ekin = 2.48711004105954 | erot = 2.14055508379566 | epot = -21.6286281269545 | etot = -17.0009630020993 -631000 ekin = 2.05035510102044 | erot = 1.78519131042561 | epot = -21.633635046353 | etot = -17.798088634907 -632000 ekin = 1.65439924450982 | erot = 3.28310987077496 | epot = -21.6999899301469 | etot = -16.7624808148621 -633000 ekin = 2.34657988531209 | erot = 2.34109631044869 | epot = -21.8317647703271 | etot = -17.1440885745664 -634000 ekin = 2.31570267703931 | erot = 2.471293173825 | epot = -21.8814211467029 | etot = -17.0944252958386 -635000 ekin = 1.99068848818427 | erot = 3.35493927676214 | epot = -21.9111632351734 | etot = -16.565535470227 -636000 ekin = 2.5015676385862 | erot = 2.48847742334419 | epot = -21.8752689055209 | etot = -16.8852238435905 -637000 ekin = 2.76558055064046 | erot = 2.80410341825293 | epot = -21.7874464522772 | etot = -16.2177624833838 -638000 ekin = 2.45488734924466 | erot = 2.81516363335622 | epot = -21.897362338598 | etot = -16.6273113559971 -639000 ekin = 1.89221088715375 | erot = 2.13319565970052 | epot = -21.932098303477 | etot = -17.9066917566227 -640000 ekin = 2.12173400886946 | erot = 3.32302167857403 | epot = -21.8808288554836 | etot = -16.4360731680401 -641000 ekin = 2.09554541112562 | erot = 2.23098450754968 | epot = -21.9203390995502 | etot = -17.5938091808749 -642000 ekin = 2.28696138506763 | erot = 2.67378976619349 | epot = -21.9723604262128 | etot = -17.0116092749517 -643000 ekin = 2.74450005384908 | erot = 2.20403941809548 | epot = -21.9235240791533 | etot = -16.9749846072088 -644000 ekin = 2.87909523138453 | erot = 3.40688779630214 | epot = -21.9417833997402 | etot = -15.6558003720535 -645000 ekin = 2.38284095628021 | erot = 2.10846397463902 | epot = -21.8306349073152 | etot = -17.339329976396 -646000 ekin = 2.68568471833193 | erot = 1.8085210536706 | epot = -21.6853054888873 | etot = -17.1910997168848 -647000 ekin = 2.44462012552757 | erot = 2.00446720103467 | epot = -21.4974635292911 | etot = -17.0483762027288 -648000 ekin = 2.22150753159449 | erot = 1.69679185313772 | epot = -21.5947311257684 | etot = -17.6764317410362 -649000 ekin = 2.55943952639507 | erot = 1.77203724563615 | epot = -22.016770390185 | etot = -17.6852936181538 -650000 ekin = 2.7234725572106 | erot = 2.20418229003755 | epot = -22.1594214535889 | etot = -17.2317666063407 -651000 ekin = 2.25383373914402 | erot = 3.26326768595798 | epot = -22.2274805933885 | etot = -16.7103791682865 -652000 ekin = 2.35810253390822 | erot = 2.29591208392313 | epot = -22.2332195197311 | etot = -17.5792049018997 -653000 ekin = 2.06421004499471 | erot = 2.1417184547457 | epot = -22.2265612208312 | etot = -18.0206327210908 -654000 ekin = 2.30460304373657 | erot = 1.85567946278894 | epot = -22.2521914868228 | etot = -18.0919089802973 -655000 ekin = 2.11188824015111 | erot = 1.79072614414006 | epot = -22.2262193909715 | etot = -18.3236050066803 -656000 ekin = 2.44561836830367 | erot = 2.32567811025775 | epot = -22.1872376286341 | etot = -17.4159411500727 -657000 ekin = 2.45751083141108 | erot = 2.86439216413734 | epot = -22.1805503246548 | etot = -16.8586473291064 -658000 ekin = 2.49955432693124 | erot = 2.85472680235227 | epot = -22.1390040132353 | etot = -16.7847228839518 -659000 ekin = 3.37980090980363 | erot = 2.77552992994233 | epot = -21.9898923341708 | etot = -15.8345614944249 -660000 ekin = 2.6941462621918 | erot = 1.99094454704574 | epot = -21.839770569098 | etot = -17.1546797598605 -661000 ekin = 2.21049176877594 | erot = 2.52393650500608 | epot = -21.6857326790217 | etot = -16.9513044052397 -662000 ekin = 2.06962867519899 | erot = 2.53976085175021 | epot = -21.6239147287108 | etot = -17.0145252017616 -663000 ekin = 2.27770295544224 | erot = 2.30124717941155 | epot = -21.5870186127932 | etot = -17.0080684779394 -664000 ekin = 2.39061717453214 | erot = 1.87616423363735 | epot = -21.4930500427881 | etot = -17.2262686346187 -665000 ekin = 2.66924405123179 | erot = 2.29240983153227 | epot = -21.4402310096658 | etot = -16.4785771269017 -666000 ekin = 1.66318176263893 | erot = 2.30827907651666 | epot = -21.3477804932103 | etot = -17.3763196540548 -667000 ekin = 1.65573830146343 | erot = 2.8261361193353 | epot = -21.2651811028886 | etot = -16.7833066820899 -668000 ekin = 2.50126196238916 | erot = 3.29062396521939 | epot = -21.1310768281354 | etot = -15.3391909005269 -669000 ekin = 1.61008562219097 | erot = 2.65727107854378 | epot = -21.0513800034042 | etot = -16.7840233026694 -670000 ekin = 2.21851826153844 | erot = 2.60770568109394 | epot = -20.9727942140714 | etot = -16.146570271439 -671000 ekin = 2.25905318343359 | erot = 2.15965495575029 | epot = -20.920836534986 | etot = -16.5021283958021 -672000 ekin = 1.93426342346647 | erot = 1.65365047668441 | epot = -20.8333028169839 | etot = -17.245388916833 -673000 ekin = 1.880896686753 | erot = 2.07483128120029 | epot = -20.79952620348 | etot = -16.8437982355267 -674000 ekin = 2.06783468057301 | erot = 2.16234064938726 | epot = -20.8176950919606 | etot = -16.5875197620003 -675000 ekin = 2.03952283590142 | erot = 2.48129689359269 | epot = -20.8297865902612 | etot = -16.3089668607671 -676000 ekin = 2.44687523374789 | erot = 2.77932995735251 | epot = -20.8513819036485 | etot = -15.6251767125481 -677000 ekin = 2.18851088067448 | erot = 2.6192892566419 | epot = -20.8589021998565 | etot = -16.0511020625401 -678000 ekin = 2.13451298865477 | erot = 2.78742961560772 | epot = -20.7380850837789 | etot = -15.8161424795164 -679000 ekin = 2.15556981522704 | erot = 2.17593910434841 | epot = -20.629255081746 | etot = -16.2977461621706 -680000 ekin = 2.0771745141444 | erot = 2.68436897198806 | epot = -20.6512705044545 | etot = -15.889727018322 -681000 ekin = 2.16836766753576 | erot = 1.82666294843077 | epot = -20.7392652191906 | etot = -16.744234603224 -682000 ekin = 3.01810965188601 | erot = 2.39774897550361 | epot = -20.7185667085479 | etot = -15.3027080811583 -683000 ekin = 2.84169666492797 | erot = 2.09885122074905 | epot = -20.7261705834808 | etot = -15.7856226978037 -684000 ekin = 1.9625035286937 | erot = 2.99543980855394 | epot = -20.7697045673731 | etot = -15.8117612301254 -685000 ekin = 1.50086016290167 | erot = 2.04478648729578 | epot = -20.7788952528481 | etot = -17.2332486026506 -686000 ekin = 2.3009298353038 | erot = 2.55442118756325 | epot = -20.7673358731011 | etot = -15.9119848502341 -687000 ekin = 1.86053862979306 | erot = 2.84846934037481 | epot = -20.7009117540898 | etot = -15.9919037839219 -688000 ekin = 2.56859020075852 | erot = 2.23263295871676 | epot = -20.6563366249257 | etot = -15.8551134654504 -689000 ekin = 2.7493014170063 | erot = 2.68327386026116 | epot = -20.8092642099637 | etot = -15.3766889326963 -690000 ekin = 2.67477310841297 | erot = 2.52397256899153 | epot = -21.0730303416649 | etot = -15.8742846642604 -691000 ekin = 2.28465281003006 | erot = 2.52273866559282 | epot = -21.2401157605126 | etot = -16.4327242848897 -692000 ekin = 2.42087744380444 | erot = 3.24812320332686 | epot = -21.2665776826931 | etot = -15.5975770355618 -693000 ekin = 2.37642605279041 | erot = 2.99546830568891 | epot = -21.3330277418611 | etot = -15.9611333833818 -694000 ekin = 2.69750178365984 | erot = 2.53085866970816 | epot = -21.521485598392 | etot = -16.293125145024 -695000 ekin = 2.49230316198816 | erot = 1.18105864485318 | epot = -21.6959912399269 | etot = -18.0226294330856 -696000 ekin = 1.86075498586631 | erot = 1.46501529683133 | epot = -21.6808441671222 | etot = -18.3550738844245 -697000 ekin = 2.40460770445908 | erot = 2.10461647488794 | epot = -21.7143559347048 | etot = -17.2051317553578 -698000 ekin = 2.32098148261586 | erot = 1.91506962097515 | epot = -21.7787361369849 | etot = -17.5426850333939 -699000 ekin = 2.44943497732062 | erot = 2.56143482106644 | epot = -21.7638026578475 | etot = -16.7529328594605 -700000 ekin = 2.13119890669415 | erot = 2.28802336161954 | epot = -21.6714710604343 | etot = -17.2522487921206 -701000 ekin = 2.15013169314239 | erot = 2.18565847708907 | epot = -21.5488216255628 | etot = -17.2130314553313 -702000 ekin = 1.57482438035702 | erot = 1.99931097090508 | epot = -21.5047640382371 | etot = -17.930628686975 -703000 ekin = 2.08829522236785 | erot = 2.17557396869524 | epot = -21.5242713758434 | etot = -17.2604021847803 -704000 ekin = 2.82144699483839 | erot = 1.94479401958833 | epot = -21.5462466947694 | etot = -16.7800056803427 -705000 ekin = 2.81019786745821 | erot = 2.16662483548889 | epot = -21.497690476826 | etot = -16.5208677738789 -706000 ekin = 1.97639068263159 | erot = 2.31468002405233 | epot = -21.494117475981 | etot = -17.2030467692971 -707000 ekin = 1.90740387464487 | erot = 2.04436544372037 | epot = -21.5505486138142 | etot = -17.5987792954489 -708000 ekin = 2.4927128838246 | erot = 2.15829540621563 | epot = -21.5728746117359 | etot = -16.9218663216957 -709000 ekin = 2.89296518644075 | erot = 2.58120965850485 | epot = -21.6152997801578 | etot = -16.1411249352122 -710000 ekin = 2.18515172086139 | erot = 2.27924743097097 | epot = -21.5865916502444 | etot = -17.122192498412 -711000 ekin = 2.31589231212299 | erot = 1.40143925977899 | epot = -21.6089597508522 | etot = -17.8916281789502 -712000 ekin = 2.55835611026778 | erot = 2.27281573655802 | epot = -21.7227687229586 | etot = -16.8915968761328 -713000 ekin = 1.95615391137192 | erot = 2.3180685223896 | epot = -21.8059432402922 | etot = -17.5317208065307 -714000 ekin = 2.56238583099812 | erot = 2.10850361056242 | epot = -21.8681675013087 | etot = -17.1972780597481 -715000 ekin = 2.42321114653449 | erot = 3.74023135295615 | epot = -21.8498336266088 | etot = -15.6863911271181 -716000 ekin = 2.83316600532177 | erot = 2.84850242081136 | epot = -21.7640231598546 | etot = -16.0823547337214 -717000 ekin = 3.45113934412558 | erot = 3.20598462177201 | epot = -21.667790662391 | etot = -15.0106666964934 -718000 ekin = 3.10736232683018 | erot = 3.94031338601797 | epot = -21.5629179727886 | etot = -14.5152422599405 -719000 ekin = 2.38564322644681 | erot = 2.95089811755838 | epot = -21.5481188237003 | etot = -16.2115774796951 -720000 ekin = 2.22543420991222 | erot = 3.14305432696276 | epot = -21.5381615962024 | etot = -16.1696730593274 -721000 ekin = 1.71709109813907 | erot = 2.23939430363989 | epot = -21.4645851946691 | etot = -17.5080997928902 -722000 ekin = 1.93213958129581 | erot = 2.81573218276728 | epot = -21.4896847080113 | etot = -16.7418129439482 -723000 ekin = 2.3814534534689 | erot = 2.55666957995948 | epot = -21.4374887927968 | etot = -16.4993657593684 -724000 ekin = 1.74740284448188 | erot = 2.4555617568904 | epot = -21.4125175551609 | etot = -17.2095529537886 -725000 ekin = 2.29233638352032 | erot = 2.9526701477774 | epot = -21.4751392844086 | etot = -16.2301327531109 -726000 ekin = 1.63503646092182 | erot = 2.30649262262117 | epot = -21.5156851039584 | etot = -17.5741560204154 -727000 ekin = 2.46705454176008 | erot = 3.19802987014479 | epot = -21.5382715508196 | etot = -15.8731871389148 -728000 ekin = 2.21709576272191 | erot = 2.16616227421244 | epot = -21.5244744557248 | etot = -17.1412164187904 -729000 ekin = 1.89396537247993 | erot = 1.66596987620967 | epot = -21.5644109232526 | etot = -18.004475674563 -730000 ekin = 1.78155182892059 | erot = 2.15399661961713 | epot = -21.5594738957829 | etot = -17.6239254472452 -731000 ekin = 2.16713092512296 | erot = 2.96875570154118 | epot = -21.4952326145865 | etot = -16.3593459879223 -732000 ekin = 2.40927355189018 | erot = 2.27189990077002 | epot = -21.3831563581627 | etot = -16.7019829055024 -733000 ekin = 3.04824198143784 | erot = 2.57289903054807 | epot = -21.429005165309 | etot = -15.8078641533231 -734000 ekin = 2.36703883022855 | erot = 2.04468815017469 | epot = -21.4926214065432 | etot = -17.0808944261399 -735000 ekin = 2.13292788677937 | erot = 1.55097035487251 | epot = -21.5455592190822 | etot = -17.8616609774303 -736000 ekin = 2.13562110082196 | erot = 3.45795834862287 | epot = -21.6515763333194 | etot = -16.0579968838746 -737000 ekin = 1.73550703692746 | erot = 3.58781244645382 | epot = -21.6785680654269 | etot = -16.3552485820456 -738000 ekin = 2.01136680767019 | erot = 2.50533140705366 | epot = -21.7068415263434 | etot = -17.1901433116196 -739000 ekin = 1.85122466968333 | erot = 2.19323904324285 | epot = -21.7211705032462 | etot = -17.6767067903201 -740000 ekin = 2.84677298867337 | erot = 2.79086338446698 | epot = -21.7460997683893 | etot = -16.108463395249 -741000 ekin = 2.47281769013274 | erot = 2.90867674862121 | epot = -21.8038806031312 | etot = -16.4223861643772 -742000 ekin = 2.74212748781964 | erot = 3.26601844940295 | epot = -21.9417105639309 | etot = -15.9335646267083 -743000 ekin = 2.23337436613032 | erot = 3.20752099935254 | epot = -22.0769938861091 | etot = -16.6360985206262 -744000 ekin = 2.01007582963959 | erot = 3.79208398827071 | epot = -22.1581491314472 | etot = -16.3559893135369 -745000 ekin = 3.14168435406402 | erot = 2.32756039064277 | epot = -22.1552791709709 | etot = -16.6860344262642 -746000 ekin = 2.96147960587595 | erot = 2.64919778641529 | epot = -22.131657657659 | etot = -16.5209802653678 -747000 ekin = 2.31713973406909 | erot = 2.0538838502724 | epot = -22.1362115743712 | etot = -17.7651879900297 -748000 ekin = 2.36228107661837 | erot = 2.41530550223615 | epot = -22.1703943251347 | etot = -17.3928077462802 -749000 ekin = 2.07006713072585 | erot = 2.7743291960411 | epot = -22.1708421357978 | etot = -17.3264458090308 -750000 ekin = 1.65834656870048 | erot = 2.38415657369843 | epot = -22.2465520170919 | etot = -18.204048874693 -751000 ekin = 1.79302728344389 | erot = 2.827102160061 | epot = -22.3488339479635 | etot = -17.7287045044586 -752000 ekin = 1.35555517803007 | erot = 1.46019783589209 | epot = -22.4342877547318 | etot = -19.6185347408096 -753000 ekin = 1.88586262445723 | erot = 2.44014879801272 | epot = -22.3837690917336 | etot = -18.0577576692636 -754000 ekin = 1.74745498380874 | erot = 2.73612011854199 | epot = -22.2852965474798 | etot = -17.8017214451291 -755000 ekin = 2.39590781949902 | erot = 2.41019902787154 | epot = -22.2066358684386 | etot = -17.400529021068 -756000 ekin = 1.83745653598818 | erot = 2.79024351605605 | epot = -22.133592240187 | etot = -17.5058921881428 -757000 ekin = 1.97281200687049 | erot = 2.57792722235948 | epot = -22.0604464398181 | etot = -17.5097072105881 -758000 ekin = 1.18945619136922 | erot = 2.72372183682492 | epot = -21.9899494795137 | etot = -18.0767714513196 -759000 ekin = 2.16230453116658 | erot = 1.39722896511084 | epot = -22.0003304659983 | etot = -18.4407969697208 -760000 ekin = 2.57253050230035 | erot = 2.33269711137819 | epot = -22.0357457302398 | etot = -17.1305181165612 -761000 ekin = 2.08545216810511 | erot = 2.24940559703297 | epot = -22.1132097744113 | etot = -17.7783520092733 -762000 ekin = 2.13509249172209 | erot = 1.66078369856518 | epot = -22.1380840935026 | etot = -18.3422079032154 -763000 ekin = 2.42851727622128 | erot = 3.36016749294484 | epot = -22.2079173436287 | etot = -16.4192325744626 -764000 ekin = 2.84703530894743 | erot = 2.79172375883345 | epot = -22.2143624032421 | etot = -16.5756033354612 -765000 ekin = 1.81325658345262 | erot = 2.77448180912351 | epot = -22.1194010453623 | etot = -17.5316626527862 -766000 ekin = 2.64831101430988 | erot = 2.3138164970859 | epot = -21.9919179324216 | etot = -17.0297904210258 -767000 ekin = 2.58949745571041 | erot = 2.86718473216884 | epot = -21.9087370669524 | etot = -16.4520548790732 -768000 ekin = 1.86313167956692 | erot = 2.78552244417217 | epot = -21.9381577980074 | etot = -17.2895036742683 -769000 ekin = 2.40162376419982 | erot = 2.31402374045875 | epot = -22.0373843590672 | etot = -17.3217368544087 -770000 ekin = 2.49146487205159 | erot = 3.23101926076328 | epot = -22.1439576198693 | etot = -16.4214734870544 -771000 ekin = 2.33226337742861 | erot = 2.27787220200643 | epot = -22.1812213688414 | etot = -17.5710857894063 -772000 ekin = 2.28990016215835 | erot = 2.99389364569332 | epot = -22.2765115340955 | etot = -16.9927177262439 -773000 ekin = 2.23002457595115 | erot = 1.82240115552767 | epot = -22.3379686916384 | etot = -18.2855429601596 -774000 ekin = 2.82350297312971 | erot = 2.21054815770298 | epot = -22.331524297742 | etot = -17.2974731669093 -775000 ekin = 1.82305982105504 | erot = 1.87100336542221 | epot = -22.2729891281483 | etot = -18.578925941671 -776000 ekin = 1.39169167990077 | erot = 3.16027505319296 | epot = -22.2459295451276 | etot = -17.6939628120339 -777000 ekin = 1.6265637770548 | erot = 2.80881827044756 | epot = -22.1611617112313 | etot = -17.7257796637289 -778000 ekin = 1.49436478903862 | erot = 2.24161236856226 | epot = -22.1732646444852 | etot = -18.4372874868843 -779000 ekin = 1.88107404119766 | erot = 1.90732846459751 | epot = -22.2125828989308 | etot = -18.4241803931357 -780000 ekin = 1.70209634464211 | erot = 2.30515299210351 | epot = -22.2800747799124 | etot = -18.2728254431668 -781000 ekin = 2.12615575710868 | erot = 2.5606535839807 | epot = -22.3657963731658 | etot = -17.6789870320765 -782000 ekin = 2.60319344794517 | erot = 1.9571688066736 | epot = -22.278889588664 | etot = -17.7185273340452 -783000 ekin = 2.19489638548848 | erot = 2.9003350616753 | epot = -22.2004563501245 | etot = -17.1052249029607 -784000 ekin = 2.84914111009349 | erot = 2.24051018422878 | epot = -22.2093010900996 | etot = -17.1196497957773 -785000 ekin = 3.14240765153577 | erot = 2.92860772919915 | epot = -22.2500274240077 | etot = -16.1790120432728 -786000 ekin = 2.83372300736036 | erot = 3.44593690351849 | epot = -22.2923595270367 | etot = -16.0126996161579 -787000 ekin = 2.41074903520556 | erot = 3.01381650302092 | epot = -22.2329745868673 | etot = -16.8084090486408 -788000 ekin = 1.99557665602945 | erot = 2.01600225895996 | epot = -22.1996915458458 | etot = -18.1881126308564 -789000 ekin = 2.46258971641133 | erot = 2.27406771625316 | epot = -22.1314921413931 | etot = -17.3948347087286 -790000 ekin = 3.5794195002921 | erot = 2.82440864812442 | epot = -22.0691321886934 | etot = -15.6653040402769 -791000 ekin = 3.1240271028451 | erot = 2.42401718962737 | epot = -22.0808685046086 | etot = -16.5328242121361 -792000 ekin = 3.95429056548242 | erot = 1.97241939137157 | epot = -22.0156932891881 | etot = -16.0889833323341 -793000 ekin = 2.26828416500901 | erot = 2.58677202552917 | epot = -21.9219598803777 | etot = -17.0669036898395 -794000 ekin = 2.16106559150924 | erot = 2.44310931274122 | epot = -21.7619518452423 | etot = -17.1577769409919 -795000 ekin = 1.62519700428841 | erot = 2.41826691867446 | epot = -21.6012749849542 | etot = -17.5578110619913 -796000 ekin = 2.18377144801669 | erot = 2.13093440679001 | epot = -21.4820337714693 | etot = -17.1673279166626 -797000 ekin = 1.81427862345353 | erot = 1.99534051513419 | epot = -21.4739195915569 | etot = -17.6643004529692 -798000 ekin = 2.2201219513299 | erot = 2.51363796316553 | epot = -21.5008270155092 | etot = -16.7670671010138 -799000 ekin = 1.88984581553595 | erot = 2.87047971528298 | epot = -21.4708608053325 | etot = -16.7105352745136 -800000 ekin = 2.14235800297794 | erot = 2.35196377273805 | epot = -21.3792596865246 | etot = -16.8849379108086 -801000 ekin = 1.84302686949433 | erot = 1.65480855802629 | epot = -21.2211741734437 | etot = -17.7233387459231 -802000 ekin = 2.20305615004888 | erot = 2.22355768328245 | epot = -21.1073599995259 | etot = -16.6807461661946 -803000 ekin = 2.64836814873033 | erot = 1.90761871804858 | epot = -21.0752041885471 | etot = -16.5192173217682 -804000 ekin = 2.34495845479317 | erot = 2.89112045330492 | epot = -21.0176734836814 | etot = -15.7815945755833 -805000 ekin = 1.79915640284781 | erot = 2.71685844764875 | epot = -20.8858433761952 | etot = -16.3698285256987 -806000 ekin = 1.74992507845556 | erot = 2.08517047523252 | epot = -20.8503301901419 | etot = -17.0152346364538 -807000 ekin = 1.57172452594494 | erot = 1.70422569898767 | epot = -20.9092333967053 | etot = -17.6332831717727 -808000 ekin = 2.08106901002531 | erot = 2.4036706521883 | epot = -20.9858691795981 | etot = -16.5011295173845 -809000 ekin = 2.61736488835992 | erot = 1.51251405170843 | epot = -20.9790910298502 | etot = -16.8492120897819 -810000 ekin = 3.07344763503492 | erot = 2.65428122600395 | epot = -20.896297890317 | etot = -15.1685690292781 -811000 ekin = 3.028899831017 | erot = 3.61686315729187 | epot = -20.939661602879 | etot = -14.2938986145701 -812000 ekin = 2.13832655324419 | erot = 2.7919099294265 | epot = -21.0260005012597 | etot = -16.095764018589 -813000 ekin = 2.19077235410927 | erot = 3.16158040032406 | epot = -21.2169108164964 | etot = -15.8645580620631 -814000 ekin = 1.70775111413747 | erot = 2.98436840501864 | epot = -21.3089511890131 | etot = -16.6168316698569 -815000 ekin = 2.14630779714624 | erot = 2.27335416843263 | epot = -21.3099230783927 | etot = -16.8902611128138 -816000 ekin = 2.70331501775258 | erot = 1.53093796189124 | epot = -21.3384418834226 | etot = -17.1041889037788 -817000 ekin = 2.55738086811903 | erot = 2.58558173150041 | epot = -21.4691891608916 | etot = -16.3262265612722 -818000 ekin = 2.27829786328906 | erot = 2.26089725682103 | epot = -21.5162183667694 | etot = -16.9770232466593 -819000 ekin = 2.10478260130361 | erot = 3.02380855832961 | epot = -21.5292309310153 | etot = -16.4006397713821 -820000 ekin = 2.50608188233135 | erot = 2.71783485224719 | epot = -21.5036816055507 | etot = -16.2797648709722 -821000 ekin = 2.62609848062629 | erot = 2.55164634943844 | epot = -21.478766185164 | etot = -16.3010213550993 -822000 ekin = 3.63941681915299 | erot = 2.20246894917129 | epot = -21.4688230156577 | etot = -15.6269372473334 -823000 ekin = 3.58953515450024 | erot = 2.73556206545619 | epot = -21.4650227341943 | etot = -15.1399255142378 -824000 ekin = 4.11304720722591 | erot = 3.2917459513548 | epot = -21.4062011377905 | etot = -14.0014079792098 -825000 ekin = 2.90620097853796 | erot = 3.46409084826251 | epot = -21.2436944546109 | etot = -14.8734026278105 -826000 ekin = 1.72188438195169 | erot = 1.97028277378148 | epot = -21.0473904580338 | etot = -17.3552233023007 -827000 ekin = 1.9124069409458 | erot = 2.55760488338657 | epot = -20.9206700763425 | etot = -16.4506582520101 -828000 ekin = 2.38145056979363 | erot = 2.55544957149182 | epot = -20.8204865756543 | etot = -15.8835864343689 -829000 ekin = 2.24733826946605 | erot = 1.78474837345228 | epot = -20.7084449579388 | etot = -16.6763583150204 -830000 ekin = 2.52795893691035 | erot = 2.34146724282711 | epot = -20.5883731027638 | etot = -15.7189469230264 -831000 ekin = 2.68310001004752 | erot = 2.07407005901145 | epot = -20.4364451382899 | etot = -15.679275069231 -832000 ekin = 2.6732342426401 | erot = 2.02167788192499 | epot = -20.3691783993746 | etot = -15.6742662748095 -833000 ekin = 2.55071664949192 | erot = 2.59972899624767 | epot = -20.3036213925319 | etot = -15.1531757467923 -834000 ekin = 2.87089088359563 | erot = 2.32463192225235 | epot = -20.2984653371648 | etot = -15.1029425313168 -835000 ekin = 2.77558903596269 | erot = 2.73757154391999 | epot = -20.4022293845421 | etot = -14.8890688046595 -836000 ekin = 2.57713146919653 | erot = 2.85322310545496 | epot = -20.5403137141641 | etot = -15.1099591395126 -837000 ekin = 1.78075406754283 | erot = 1.97503243561096 | epot = -20.5889142070484 | etot = -16.8331277038946 -838000 ekin = 1.98032617531701 | erot = 2.7982946707394 | epot = -20.6049667376349 | etot = -15.8263458915785 -839000 ekin = 2.0003179521848 | erot = 2.70198331564815 | epot = -20.5921495833285 | etot = -15.8898483154955 -840000 ekin = 1.70031236242703 | erot = 2.95685689490568 | epot = -20.6678372916037 | etot = -16.010668034271 -841000 ekin = 2.77705100359315 | erot = 2.84742847205069 | epot = -20.7929304121763 | etot = -15.1684509365325 -842000 ekin = 2.54393458307436 | erot = 2.87172695192627 | epot = -20.8173418291016 | etot = -15.401680294101 -843000 ekin = 2.00273625390939 | erot = 2.63437491598434 | epot = -20.8053999188197 | etot = -16.1682887489259 -844000 ekin = 1.52900749569349 | erot = 1.92882434140971 | epot = -20.8427655387949 | etot = -17.3849337016917 -845000 ekin = 2.27176799938834 | erot = 2.308436365406 | epot = -20.9384881501645 | etot = -16.3582837853702 -846000 ekin = 2.06718804989496 | erot = 2.33108662324981 | epot = -21.008503215967 | etot = -16.6102285428222 -847000 ekin = 2.457310325364 | erot = 2.64112097293887 | epot = -20.9624761048838 | etot = -15.8640448065809 -848000 ekin = 2.13894899278459 | erot = 1.46487099434192 | epot = -20.9909626022984 | etot = -17.3871426151719 -849000 ekin = 2.0007946308419 | erot = 2.48568109050424 | epot = -20.9995492646628 | etot = -16.5130735433167 -850000 ekin = 2.54186297995285 | erot = 2.66929613872204 | epot = -20.9906717645298 | etot = -15.7795126458549 -851000 ekin = 2.16443404123472 | erot = 2.92830981454153 | epot = -20.9932718794597 | etot = -15.9005280236835 -852000 ekin = 2.48255398040851 | erot = 2.46238001266592 | epot = -21.018749118108 | etot = -16.0738151250336 -853000 ekin = 2.41541467016921 | erot = 2.97520224443385 | epot = -20.9598722543997 | etot = -15.5692553397966 -854000 ekin = 2.35150751079563 | erot = 2.85453387569363 | epot = -20.8693696367608 | etot = -15.6633282502715 -855000 ekin = 2.36749640703667 | erot = 2.0675340835823 | epot = -20.8980197782034 | etot = -16.4629892875844 -856000 ekin = 2.52164598863741 | erot = 2.75265020302047 | epot = -20.800830948998 | etot = -15.5265347573401 -857000 ekin = 2.55862872070476 | erot = 3.03030828592914 | epot = -20.6910887919773 | etot = -15.1021517853434 -858000 ekin = 3.12628251408762 | erot = 2.1455460426107 | epot = -20.6394579492303 | etot = -15.367629392532 -859000 ekin = 2.91259413572113 | erot = 2.23773675238284 | epot = -20.6611486479508 | etot = -15.5108177598468 -860000 ekin = 2.88318377110752 | erot = 1.51972062646443 | epot = -20.6828066069552 | etot = -16.2799022093833 -861000 ekin = 2.33529167415754 | erot = 2.85116617791259 | epot = -20.6796212139896 | etot = -15.4931633619195 -862000 ekin = 3.06091745354043 | erot = 1.86960550588563 | epot = -20.7257485328209 | etot = -15.7952255733949 -863000 ekin = 2.88295223464283 | erot = 1.77743902656171 | epot = -20.8340328987095 | etot = -16.173641637505 -864000 ekin = 2.95602292127633 | erot = 2.6505641071531 | epot = -21.016295456145 | etot = -15.4097084277156 -865000 ekin = 3.3172549369506 | erot = 2.24347319046513 | epot = -21.1441095096619 | etot = -15.5833813822461 -866000 ekin = 2.8446879555804 | erot = 3.16802464112883 | epot = -21.2275167371632 | etot = -15.214804140454 -867000 ekin = 2.74149808612435 | erot = 3.09628634794253 | epot = -21.2140642048229 | etot = -15.376279770756 -868000 ekin = 2.19141484864809 | erot = 2.23765996064101 | epot = -21.1661691183494 | etot = -16.7370943090603 -869000 ekin = 2.92726848075923 | erot = 2.49663936074752 | epot = -21.1109612585256 | etot = -15.6870534170189 -870000 ekin = 2.47986538741064 | erot = 2.11907230969515 | epot = -21.0900293946685 | etot = -16.4910916975627 -871000 ekin = 2.18342640526418 | erot = 2.37474045896628 | epot = -20.9804914418025 | etot = -16.422324577572 -872000 ekin = 1.52873571215978 | erot = 2.08908078804674 | epot = -20.9343176993392 | etot = -17.3165011991327 -873000 ekin = 1.39281578471524 | erot = 2.29034780878957 | epot = -21.0007866828842 | etot = -17.3176230893794 -874000 ekin = 1.40786554880768 | erot = 2.77007970032348 | epot = -21.160084274243 | etot = -16.9821390251118 -875000 ekin = 1.18320018517441 | erot = 2.7305884288351 | epot = -21.2959059488291 | etot = -17.3821173348196 -876000 ekin = 1.8300189393038 | erot = 2.99586941144887 | epot = -21.3298635968753 | etot = -16.5039752461226 -877000 ekin = 2.38032906471076 | erot = 2.03722695211227 | epot = -21.4152790752831 | etot = -16.99772305846 -878000 ekin = 2.1293851684127 | erot = 1.75666654131943 | epot = -21.412657760354 | etot = -17.5266060506219 -879000 ekin = 2.23837299177368 | erot = 2.71307243504657 | epot = -21.4006541150457 | etot = -16.4492086882254 -880000 ekin = 2.68032631557358 | erot = 2.78439945590096 | epot = -21.4462782448912 | etot = -15.9815524734167 -881000 ekin = 2.86810525851389 | erot = 2.35959915589952 | epot = -21.4314549447334 | etot = -16.20375053032 -882000 ekin = 2.33172283615115 | erot = 2.17176020371467 | epot = -21.369535469283 | etot = -16.8660524294172 -883000 ekin = 2.36331150998289 | erot = 1.97634374053966 | epot = -21.1748990104138 | etot = -16.8352437598913 -884000 ekin = 2.53782271833829 | erot = 2.25243670168427 | epot = -21.0795767771653 | etot = -16.2893173571427 -885000 ekin = 2.86057103069745 | erot = 2.27462544190307 | epot = -21.0782171958267 | etot = -15.9430207232262 -886000 ekin = 3.17034195996096 | erot = 1.74832646729409 | epot = -21.1280719510453 | etot = -16.2094035237903 -887000 ekin = 2.66023408534638 | erot = 2.49426802108016 | epot = -21.1909579488462 | etot = -16.0364558424197 -888000 ekin = 2.14156056158802 | erot = 2.83065920295552 | epot = -21.2749898508176 | etot = -16.302770086274 -889000 ekin = 2.13776380125426 | erot = 2.19994227158624 | epot = -21.1902576201104 | etot = -16.8525515472699 -890000 ekin = 1.76446650263826 | erot = 2.97354753014624 | epot = -21.2518724314555 | etot = -16.513858398671 -891000 ekin = 1.64433607192947 | erot = 2.28044235221045 | epot = -21.3759471910581 | etot = -17.4511687669181 -892000 ekin = 1.97381907006142 | erot = 2.35969977765342 | epot = -21.5200869372681 | etot = -17.1865680895533 -893000 ekin = 1.77998159671209 | erot = 1.83959134574388 | epot = -21.5960425863495 | etot = -17.9764696438935 -894000 ekin = 2.8098996128374 | erot = 2.80337844303785 | epot = -21.6896955865519 | etot = -16.0764175306767 -895000 ekin = 2.03570642281182 | erot = 2.73641442629084 | epot = -21.77632807541 | etot = -17.0042072263074 -896000 ekin = 1.6670401968188 | erot = 2.55842313387756 | epot = -21.9079691828366 | etot = -17.6825058521403 -897000 ekin = 1.79364820755772 | erot = 2.35937074837063 | epot = -22.0466195733302 | etot = -17.8936006174018 -898000 ekin = 1.84103348909591 | erot = 2.4159698011209 | epot = -22.0792153246985 | etot = -17.8222120344817 -899000 ekin = 1.6644807831865 | erot = 3.06295573986192 | epot = -22.0050930291629 | etot = -17.2776565061145 -900000 ekin = 2.15301263014261 | erot = 2.62503812958044 | epot = -21.9769631774149 | etot = -17.1989124176918 -901000 ekin = 2.43323525076021 | erot = 2.69661561775585 | epot = -22.0455467285607 | etot = -16.9156958600446 -902000 ekin = 2.57983518470479 | erot = 2.40634661051271 | epot = -22.0504126836938 | etot = -17.0642308884763 -903000 ekin = 2.38804084084236 | erot = 2.40369143268286 | epot = -22.0548572254258 | etot = -17.2631249519006 -904000 ekin = 1.9975679938241 | erot = 3.15736733739655 | epot = -22.0783783499621 | etot = -16.9234430187414 -905000 ekin = 2.28042135995781 | erot = 2.20746001153526 | epot = -22.092475444409 | etot = -17.604594072916 -906000 ekin = 2.49914497220395 | erot = 1.67106173041057 | epot = -22.0649292741971 | etot = -17.8947225715826 -907000 ekin = 2.34170753461351 | erot = 2.16830189815579 | epot = -21.9182395193391 | etot = -17.4082300865698 -908000 ekin = 2.83101675354561 | erot = 2.39226452568031 | epot = -21.9393923471479 | etot = -16.7161110679219 -909000 ekin = 3.13519044247878 | erot = 2.07053636961478 | epot = -22.044039894957 | etot = -16.8383130828634 -910000 ekin = 2.91492350277448 | erot = 3.54269221448408 | epot = -22.1774209001616 | etot = -15.719805182903 -911000 ekin = 1.86299522014884 | erot = 2.75425299355676 | epot = -22.2318842654016 | etot = -17.614636051696 -912000 ekin = 2.64270620869814 | erot = 1.86916034984858 | epot = -22.2816929482531 | etot = -17.7698263897064 -913000 ekin = 2.45835259040075 | erot = 2.03343540339216 | epot = -22.4051980318983 | etot = -17.9134100381054 -914000 ekin = 2.01630257583653 | erot = 3.01931541129968 | epot = -22.505580829989 | etot = -17.4699628428528 -915000 ekin = 2.73550820750709 | erot = 2.14051989379169 | epot = -22.5067223019054 | etot = -17.6306942006067 -916000 ekin = 2.38833694849903 | erot = 3.26236542376325 | epot = -22.5299732656691 | etot = -16.8792708934068 -917000 ekin = 2.21211072529667 | erot = 2.24425221182159 | epot = -22.5175498112378 | etot = -18.0611868741195 -918000 ekin = 2.11721632678553 | erot = 2.05681940825278 | epot = -22.4485798442659 | etot = -18.2745441092275 -919000 ekin = 2.6606540164524 | erot = 2.41853759346262 | epot = -22.4819256778217 | etot = -17.4027340679066 -920000 ekin = 3.26471044916532 | erot = 2.75531911342505 | epot = -22.5858600689149 | etot = -16.5658305063245 -921000 ekin = 2.72028388628927 | erot = 1.9696059637128 | epot = -22.639440275186 | etot = -17.949550425184 -922000 ekin = 1.43428549123066 | erot = 1.52428475569853 | epot = -22.6914991306332 | etot = -19.732928883704 -923000 ekin = 1.67603986848274 | erot = 1.86522020655464 | epot = -22.7510571233686 | etot = -19.2097970483313 -924000 ekin = 2.15000311118185 | erot = 1.53327070095755 | epot = -22.722341324193 | etot = -19.0390675120536 -925000 ekin = 2.27769316315993 | erot = 1.3558291477729 | epot = -22.6317669747038 | etot = -18.9982446637709 -926000 ekin = 2.0037075380337 | erot = 2.07123237010034 | epot = -22.5811533157097 | etot = -18.5062134075756 -927000 ekin = 2.5163142824884 | erot = 1.98711239136866 | epot = -22.6957752134474 | etot = -18.1923485395904 -928000 ekin = 2.57502157703452 | erot = 2.51449316644151 | epot = -22.8486668477058 | etot = -17.7591521042298 -929000 ekin = 2.66015175923782 | erot = 1.82991995656989 | epot = -22.8894816710891 | etot = -18.3994099552814 -930000 ekin = 2.41758548277495 | erot = 2.00977019739402 | epot = -22.9023129289068 | etot = -18.4749572487378 -931000 ekin = 3.01936517399357 | erot = 2.11115283295647 | epot = -22.8598478032752 | etot = -17.7293297963252 -932000 ekin = 2.34904883629147 | erot = 1.87134929534042 | epot = -22.900230384769 | etot = -18.6798322531371 -933000 ekin = 2.16775611540091 | erot = 2.83796264813669 | epot = -22.9075292968864 | etot = -17.9018105333488 -934000 ekin = 2.17428610858913 | erot = 2.11891276299501 | epot = -22.9275911153101 | etot = -18.634392243726 -935000 ekin = 2.35380058127247 | erot = 2.22719757040085 | epot = -22.9178791070039 | etot = -18.3368809553306 -936000 ekin = 2.29398857252167 | erot = 2.52122883801967 | epot = -23.0254587453496 | etot = -18.2102413348082 -937000 ekin = 2.32405492839276 | erot = 2.82571975062453 | epot = -23.1134869099967 | etot = -17.9637122309794 -938000 ekin = 2.46190818228192 | erot = 1.99586541720566 | epot = -23.1690855883853 | etot = -18.7113119888978 -939000 ekin = 2.99494633358444 | erot = 2.1120057997909 | epot = -23.1621265982256 | etot = -18.0551744648503 -940000 ekin = 3.76773061527755 | erot = 2.67954167018356 | epot = -23.1020260319689 | etot = -16.6547537465078 -941000 ekin = 3.15108874053801 | erot = 2.26610050109568 | epot = -23.0042404655517 | etot = -17.587051223918 -942000 ekin = 3.50311245643907 | erot = 1.88373602143018 | epot = -22.9671180112669 | etot = -17.5802695333976 -943000 ekin = 3.82043792465856 | erot = 2.71285823250348 | epot = -22.9404059827705 | etot = -16.4071098256085 -944000 ekin = 2.68278476017665 | erot = 2.75585489458161 | epot = -22.919058077481 | etot = -17.4804184227228 -945000 ekin = 2.55880828345198 | erot = 2.02741981318914 | epot = -22.8232630911495 | etot = -18.2370349945083 -946000 ekin = 2.47548691870273 | erot = 1.66864059361738 | epot = -22.6586979544826 | etot = -18.5145704421625 -947000 ekin = 2.41867478100658 | erot = 1.99274780926995 | epot = -22.5542133657 | etot = -18.1427907754235 -948000 ekin = 3.54970439277899 | erot = 2.57756240201333 | epot = -22.4104376157296 | etot = -16.2831708209373 -949000 ekin = 2.98589976166071 | erot = 2.44208964275302 | epot = -22.1971411230011 | etot = -16.7691517185873 -950000 ekin = 1.82147308870195 | erot = 3.05083899379338 | epot = -22.0435130221227 | etot = -17.1712009396274 -951000 ekin = 2.20031505253436 | erot = 2.38004890424644 | epot = -22.0174402075992 | etot = -17.4370762508184 -952000 ekin = 2.14165422682636 | erot = 1.67045420750585 | epot = -21.9875031647927 | etot = -18.1753947304605 -953000 ekin = 2.2983346942831 | erot = 1.97349532600851 | epot = -21.9532851584681 | etot = -17.6814551381765 -954000 ekin = 1.48835290094507 | erot = 3.35692451991831 | epot = -21.8812774176255 | etot = -17.0359999967621 -955000 ekin = 1.87513794155827 | erot = 2.65898918540887 | epot = -21.7919528937348 | etot = -17.2578257667677 -956000 ekin = 1.6947359470094 | erot = 2.15427252360414 | epot = -21.7268035908356 | etot = -17.877795120222 -957000 ekin = 1.75579814865835 | erot = 1.63901039608816 | epot = -21.700727032202 | etot = -18.3059184874555 -958000 ekin = 1.59869777656518 | erot = 2.20104985114387 | epot = -21.7023937250484 | etot = -17.9026460973393 -959000 ekin = 2.58438881562724 | erot = 2.4897790743314 | epot = -21.7153511733982 | etot = -16.6411832834396 -960000 ekin = 2.53916903929276 | erot = 2.05995138561213 | epot = -21.7134163297425 | etot = -17.1142959048376 -961000 ekin = 2.28282707786747 | erot = 2.18347157951504 | epot = -21.7152390799838 | etot = -17.2489404226013 -962000 ekin = 1.65520100959905 | erot = 3.51416445242775 | epot = -21.7329558565076 | etot = -16.5635903944808 -963000 ekin = 1.99568689924178 | erot = 1.50126173817713 | epot = -21.6847527677603 | etot = -18.1878041303413 -964000 ekin = 2.18616111169191 | erot = 2.27601428306196 | epot = -21.621271673579 | etot = -17.1590962788252 -965000 ekin = 2.12688674785305 | erot = 2.31141713690626 | epot = -21.6018715374842 | etot = -17.1635676527249 -966000 ekin = 3.18043989665769 | erot = 3.42455452205085 | epot = -21.638305203769 | etot = -15.0333107850605 -967000 ekin = 3.07300409154252 | erot = 2.17511749698304 | epot = -21.5951488445701 | etot = -16.3470272560445 -968000 ekin = 2.08663150655529 | erot = 2.13997027735021 | epot = -21.5232721871232 | etot = -17.2966704032177 -969000 ekin = 2.26951411936363 | erot = 2.21822796004341 | epot = -21.4611553284775 | etot = -16.9734132490705 -970000 ekin = 2.49167396599781 | erot = 2.62083774678039 | epot = -21.4077353682587 | etot = -16.2952236554805 -971000 ekin = 2.497450596106 | erot = 2.64553775005007 | epot = -21.3712924820092 | etot = -16.2283041358532 -972000 ekin = 3.2069302084461 | erot = 2.4701129448845 | epot = -21.3144344371103 | etot = -15.6373912837797 -973000 ekin = 3.35935448087941 | erot = 2.62917582888825 | epot = -21.2433830591837 | etot = -15.254852749416 -974000 ekin = 2.71069552226069 | erot = 2.13944446989067 | epot = -21.1404268855179 | etot = -16.2902868933666 -975000 ekin = 1.81165819781674 | erot = 2.10218924092727 | epot = -21.0499905566304 | etot = -17.1361431178864 -976000 ekin = 2.36984742020937 | erot = 1.38488988265325 | epot = -20.9803229653515 | etot = -17.2255856624889 -977000 ekin = 2.83728662155799 | erot = 3.02976542728586 | epot = -21.086860961914 | etot = -15.2198089130701 -978000 ekin = 3.14169266917128 | erot = 3.0279981203262 | epot = -21.1408187166748 | etot = -14.9711279271773 -979000 ekin = 3.63725915757345 | erot = 2.47075910077982 | epot = -21.0348329782418 | etot = -14.9268147198885 -980000 ekin = 3.42622785415583 | erot = 3.24164435781272 | epot = -20.9604411583362 | etot = -14.2925689463677 -981000 ekin = 2.9282364939793 | erot = 2.44516658563954 | epot = -20.999389015838 | etot = -15.6259859362192 -982000 ekin = 2.0455891107008 | erot = 2.21302288881361 | epot = -21.0172581853275 | etot = -16.7586461858131 -983000 ekin = 2.56053983213181 | erot = 1.98406283304104 | epot = -21.0054554868711 | etot = -16.4608528216982 -984000 ekin = 2.31455025377678 | erot = 2.58584391470351 | epot = -21.0528748947299 | etot = -16.1524807262496 -985000 ekin = 2.31703817263368 | erot = 2.99965025262552 | epot = -21.1270579315131 | etot = -15.8103695062539 -986000 ekin = 2.05103854432386 | erot = 2.1535155091137 | epot = -21.2182405597612 | etot = -17.0136865063236 -987000 ekin = 2.41899263793244 | erot = 1.58416150281503 | epot = -21.1906087726859 | etot = -17.1874546319384 -988000 ekin = 2.75135283132848 | erot = 2.70498731016258 | epot = -21.09026978368 | etot = -15.633929642189 -989000 ekin = 2.29408577956131 | erot = 2.85656205344493 | epot = -21.0178170251465 | etot = -15.8671691921403 -990000 ekin = 2.23414139649767 | erot = 2.58987928207187 | epot = -20.9412338597721 | etot = -16.1172131812026 -991000 ekin = 2.20140095465642 | erot = 2.53421928109187 | epot = -20.8284298905317 | etot = -16.0928096547834 -992000 ekin = 1.73516341340694 | erot = 2.49726908126814 | epot = -20.8981414535471 | etot = -16.665708958872 -993000 ekin = 1.38883779880922 | erot = 1.96818984395137 | epot = -20.9939445972527 | etot = -17.6369169544921 -994000 ekin = 1.48978908674571 | erot = 2.95636513336706 | epot = -21.0608370227912 | etot = -16.6146828026784 -995000 ekin = 2.31404204513712 | erot = 1.67482961392509 | epot = -21.1264761824825 | etot = -17.1376045234203 -996000 ekin = 2.89776504847011 | erot = 2.85063328331353 | epot = -21.0879631716189 | etot = -15.3395648398353 -997000 ekin = 3.12980664910277 | erot = 2.14994147346883 | epot = -21.0789162715404 | etot = -15.7991681489688 -998000 ekin = 2.21592279552962 | erot = 3.03017611615784 | epot = -20.9989402817529 | etot = -15.7528413700654 -999000 ekin = 2.60947995309596 | erot = 1.73829419308785 | epot = -20.9136108602423 | etot = -16.5658367140585 -1000000 ekin = 2.32269547490306 | erot = 2.87794942105203 | epot = -20.9071852604882 | etot = -15.7065403645331 - 1000000 0.10323091 -1.356822 0.050122912 -1.1615306 0.00013791576 -Loop time of 52.0267 on 4 procs for 1000000 steps with 16 atoms - -Performance: 16606.850 tau/day, 19220.892 timesteps/s -96.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.92946 | 16.932 | 31.787 | 338.2 | 32.55 -Bond | 0.12904 | 0.54878 | 0.89134 | 46.8 | 1.05 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 4.2008 | 5.1678 | 6.1197 | 36.6 | 9.93 -Output | 2.1e-05 | 3.15e-05 | 3.6e-05 | 0.0 | 0.00 -Modify | 0.32128 | 3.4221 | 6.4024 | 143.6 | 6.58 -Other | | 25.96 | | | 49.89 - -Nlocal: 4 ave 8 max 0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 9 ave 10 max 8 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 34.5 ave 67 max 0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 138 -Ave neighs/atom = 8.625 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:52 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 index 9ff9d3c4db6def81c3f8daf553d700422a691913..0f7fd1c0dbcf066ff45541cbfcac699235716f1f 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 @@ -24,14 +24,14 @@ set atom * mass 3.1575 group all type 1 4 -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 rename to examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1 index a699d8726df932394793623adf2d896d0a515c7c..5a8d156ec4f6422a59d5e9d353cd25cc58743d58 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (18 Jun 2019) +LAMMPS (7 Aug 2019) variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 @@ -35,8 +35,8 @@ read_data data.duplex1 2 = max # of 1-3 neighbors 2 = max # of 1-4 neighbors 4 = max # of special neighbors - special bonds CPU = 0.000102 secs - read_data CPU = 0.002436 secs + special bonds CPU = 0.000116 secs + read_data CPU = 0.002026 secs set atom * mass 3.1575 10 settings made for mass @@ -44,15 +44,15 @@ set atom * mass 3.1575 group all type 1 4 10 atoms in group all -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -135,7 +135,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06 1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342 @@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press 999000 ekin = 0.190992053959174 | erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562 1000000 ekin = 0.179708146665509 | erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05 -Loop time of 20.4903 on 1 procs for 1000000 steps with 10 atoms +Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms -Performance: 42166.322 tau/day, 48803.614 timesteps/s -98.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 46907.305 tau/day, 54290.862 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 16.542 | 16.542 | 16.542 | 0.0 | 80.73 -Bond | 0.62224 | 0.62224 | 0.62224 | 0.0 | 3.04 +Pair | 14.935 | 14.935 | 14.935 | 0.0 | 81.08 +Bond | 0.55556 | 0.55556 | 0.55556 | 0.0 | 3.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.21974 | 0.21974 | 0.21974 | 0.0 | 1.07 +Comm | 0.16028 | 0.16028 | 0.16028 | 0.0 | 0.87 Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 -Modify | 2.7798 | 2.7798 | 2.7798 | 0.0 | 13.57 -Other | | 0.3269 | | | 1.60 +Modify | 2.5402 | 2.5402 | 2.5402 | 0.0 | 13.79 +Other | | 0.2285 | | | 1.24 Nlocal: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1169,4 +1169,4 @@ Neighbor list builds = 0 Dangerous builds = 0 #write_restart config.${number}.* -Total wall time: 0:00:20 +Total wall time: 0:00:18 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 rename to examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4 index 9856a9c95bc39b054e663c59f62b199adec27997..329e720074385ec80180d9a43b213aa87c63899d 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.18Jun19.duplex1.g++.4 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.07Aug19.duplex1.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (18 Jun 2019) +LAMMPS (7 Aug 2019) variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 @@ -35,8 +35,8 @@ read_data data.duplex1 2 = max # of 1-3 neighbors 2 = max # of 1-4 neighbors 4 = max # of special neighbors - special bonds CPU = 0.000196 secs - read_data CPU = 0.003266 secs + special bonds CPU = 0.000198 secs + read_data CPU = 0.004522 secs set atom * mass 3.1575 10 settings made for mass @@ -44,15 +44,15 @@ set atom * mass 3.1575 group all type 1 4 10 atoms in group all -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -135,7 +135,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1.4712768 0.009525411 -1.4617514 4.663076e-06 1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342 @@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press 999000 ekin = 0.190992053959209 | erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563 1000000 ekin = 0.179708146665587 | erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -3.7544839e-05 -Loop time of 28.9854 on 4 procs for 1000000 steps with 10 atoms +Loop time of 20.7945 on 4 procs for 1000000 steps with 10 atoms -Performance: 29808.075 tau/day, 34500.086 timesteps/s -96.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 41549.361 tau/day, 48089.538 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.85571 | 9.8341 | 18.111 | 228.8 | 33.93 -Bond | 0.12393 | 0.38078 | 0.62324 | 32.7 | 1.31 +Pair | 0.66725 | 7.9254 | 14.304 | 209.9 | 38.11 +Bond | 0.095496 | 0.30973 | 0.49863 | 30.5 | 1.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.795 | 3.6269 | 4.4228 | 30.4 | 12.51 -Output | 1.8e-05 | 2.575e-05 | 2.9e-05 | 0.0 | 0.00 -Modify | 0.24721 | 1.1083 | 1.9206 | 64.1 | 3.82 -Other | | 14.04 | | | 48.42 +Comm | 1.8943 | 2.1825 | 2.4604 | 15.6 | 10.50 +Output | 2e-05 | 2.9e-05 | 3.2e-05 | 0.0 | 0.00 +Modify | 0.18231 | 0.95644 | 1.673 | 62.4 | 4.60 +Other | | 9.421 | | | 45.30 Nlocal: 2.5 ave 5 max 0 min Histogram: 1 0 1 0 0 0 0 0 1 1 @@ -1169,4 +1169,4 @@ Neighbor list builds = 0 Dangerous builds = 0 #write_restart config.${number}.* -Total wall time: 0:00:28 +Total wall time: 0:00:20 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 index 3850dfcedf18aa2bb7fbae4b189d092cc9d6b1dc..5f2fde4b125fcf0fb771a444bb7a5c0eb0ac69fe 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 @@ -2,6 +2,7 @@ variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 + units lj dimension 3 @@ -23,14 +24,14 @@ set atom * mass 3.1575 group all type 1 4 -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 rename to examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1 index e4478a89420f1e46ce79711508a403c2f60d856c..c934279c1a0a17f0a7ef08da568af8d36277c3ab 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.1 @@ -1,8 +1,9 @@ -LAMMPS (18 Jun 2019) +LAMMPS (7 Aug 2019) variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 + units lj dimension 3 @@ -34,8 +35,8 @@ read_data data.duplex2 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors - special bonds CPU = 0.000103 secs - read_data CPU = 0.00215 secs + special bonds CPU = 0.000127 secs + read_data CPU = 0.001506 secs set atom * mass 3.1575 16 settings made for mass @@ -43,15 +44,15 @@ set atom * mass 3.1575 group all type 1 4 16 atoms in group all -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -136,7 +137,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.026 | 3.026 | 3.026 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05 1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817 @@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press 999000 ekin = 2.08919327368179 | erot = 2.76364485800616 | epot = -20.9705413117635 | etot = -16.1177031800756 1000000 ekin = 2.11761701334905 | erot = 2.1409630347026 | epot = -20.9096627221725 | etot = -16.6510826741208 1000000 0.094116312 -1.3659956 0.059141691 -1.1745029 -3.0654283e-05 -Loop time of 43.6978 on 1 procs for 1000000 steps with 16 atoms +Loop time of 39.73 on 1 procs for 1000000 steps with 16 atoms -Performance: 19772.150 tau/day, 22884.433 timesteps/s -98.6% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 21746.777 tau/day, 25169.881 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 32.769 | 32.769 | 32.769 | 0.0 | 74.99 -Bond | 0.93071 | 0.93071 | 0.93071 | 0.0 | 2.13 +Pair | 29.698 | 29.698 | 29.698 | 0.0 | 74.75 +Bond | 0.84677 | 0.84677 | 0.84677 | 0.0 | 2.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.19584 | 0.19584 | 0.19584 | 0.0 | 0.45 -Output | 1e-05 | 1e-05 | 1e-05 | 0.0 | 0.00 -Modify | 9.4507 | 9.4507 | 9.4507 | 0.0 | 21.63 -Other | | 0.3515 | | | 0.80 +Comm | 0.15576 | 0.15576 | 0.15576 | 0.0 | 0.39 +Output | 7e-06 | 7e-06 | 7e-06 | 0.0 | 0.00 +Modify | 8.7714 | 8.7714 | 8.7714 | 0.0 | 22.08 +Other | | 0.2585 | | | 0.65 Nlocal: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1170,4 +1171,4 @@ Neighbor list builds = 0 Dangerous builds = 0 #write_restart config.${number}.* -Total wall time: 0:00:43 +Total wall time: 0:00:39 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 rename to examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4 index 8989bce5efb0ddf39bf95854a36bc2cd50dd58ac..ba8fd4a657c1fbee9a2f6d95c655e9a086a429b2 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.18Jun19.duplex2.g++.4 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.07Aug19.duplex2.g++.4 @@ -1,8 +1,9 @@ -LAMMPS (18 Jun 2019) +LAMMPS (7 Aug 2019) variable number equal 2 variable ofreq equal 1000 variable efreq equal 1000 variable T equal 0.1 + units lj dimension 3 @@ -34,8 +35,8 @@ read_data data.duplex2 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors - special bonds CPU = 0.000162 secs - read_data CPU = 0.002971 secs + special bonds CPU = 0.000188 secs + read_data CPU = 0.002335 secs set atom * mass 3.1575 16 settings made for mass @@ -43,15 +44,15 @@ set atom * mass 3.1575 group all type 1 4 16 atoms in group all -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -136,7 +137,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.778 | 7.96 | 8.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1.5358787 0.0096742456 -1.5262045 1.0127369e-05 1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698 @@ -1140,21 +1141,21 @@ Step Temp E_pair E_mol TotEng Press 999000 ekin = 2.61553981530106 | erot = 1.7387289184571 | epot = -21.0217257279766 | etot = -16.6674569942185 1000000 ekin = 2.34012577497833 | erot = 2.86436388995813 | epot = -21.0201566044041 | etot = -15.8156669394676 1000000 0.10400559 -1.3746133 0.060853481 -1.1675019 0.00013752759 -Loop time of 59.4195 on 4 procs for 1000000 steps with 16 atoms +Loop time of 44.9291 on 4 procs for 1000000 steps with 16 atoms -Performance: 14540.686 tau/day, 16829.497 timesteps/s -96.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 19230.287 tau/day, 22257.276 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.0304 | 20.212 | 37.839 | 369.5 | 34.02 -Bond | 0.12844 | 0.57006 | 0.95643 | 49.6 | 0.96 +Pair | 0.75183 | 16.839 | 31.47 | 339.4 | 37.48 +Bond | 0.10416 | 0.48181 | 0.82289 | 46.2 | 1.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 4.3935 | 5.5635 | 6.7052 | 44.2 | 9.36 -Output | 2.3e-05 | 3.575e-05 | 4.1e-05 | 0.0 | 0.00 -Modify | 0.3513 | 3.4695 | 6.4366 | 144.3 | 5.84 -Other | | 29.6 | | | 49.82 +Comm | 3.0032 | 3.0414 | 3.0759 | 1.7 | 6.77 +Output | 1.6e-05 | 2.2e-05 | 2.4e-05 | 0.0 | 0.00 +Modify | 0.25426 | 2.929 | 5.4956 | 134.9 | 6.52 +Other | | 21.64 | | | 48.16 Nlocal: 4 ave 8 max 0 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -1170,4 +1171,4 @@ Neighbor list builds = 0 Dangerous builds = 0 #write_restart config.${number}.* -Total wall time: 0:00:59 +Total wall time: 0:00:44 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 index 51d6334f557dd8c4c42c0277cdb1d5598e11b3f9..fd75a6fc3f44662b69209705fd304088d725f294 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3 @@ -24,14 +24,14 @@ set atom * mass 1.0 group all type 1 4 -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 rename to examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 index 6b8b7161d50bee01da9225c0dfc8b96ac218af2b..8f70e9ec965e5d8c833df8000188d013c4a85aff 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (18 Jun 2019) +LAMMPS (7 Aug 2019) variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 @@ -35,8 +35,8 @@ read_data data.duplex3 2 = max # of 1-3 neighbors 2 = max # of 1-4 neighbors 4 = max # of special neighbors - special bonds CPU = 0.000113 secs - read_data CPU = 0.00275 secs + special bonds CPU = 0.000145 secs + read_data CPU = 0.001965 secs set atom * mass 1.0 10 settings made for mass @@ -44,15 +44,15 @@ set atom * mass 1.0 group all type 1 4 10 atoms in group all -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -135,7 +135,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06 1000 ekin = 0.00366431201929618 | erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679 @@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press 999000 ekin = 0.330110494517114 | erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385 1000000 ekin = 0.345190458650495 | erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498 1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06 -Loop time of 20.5464 on 1 procs for 1000000 steps with 10 atoms +Loop time of 25.9663 on 1 procs for 1000000 steps with 10 atoms -Performance: 42051.215 tau/day, 48670.388 timesteps/s -98.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 33273.840 tau/day, 38511.388 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 16.716 | 16.716 | 16.716 | 0.0 | 81.36 -Bond | 0.6285 | 0.6285 | 0.6285 | 0.0 | 3.06 +Pair | 21.428 | 21.428 | 21.428 | 0.0 | 82.52 +Bond | 0.76981 | 0.76981 | 0.76981 | 0.0 | 2.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.187 | 0.187 | 0.187 | 0.0 | 0.91 -Output | 6e-06 | 6e-06 | 6e-06 | 0.0 | 0.00 -Modify | 2.7186 | 2.7186 | 2.7186 | 0.0 | 13.23 -Other | | 0.2965 | | | 1.44 +Comm | 0.25709 | 0.25709 | 0.25709 | 0.0 | 0.99 +Output | 9e-06 | 9e-06 | 9e-06 | 0.0 | 0.00 +Modify | 3.1584 | 3.1584 | 3.1584 | 0.0 | 12.16 +Other | | 0.3534 | | | 1.36 Nlocal: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1169,4 +1169,4 @@ Neighbor list builds = 0 Dangerous builds = 0 #write_restart config.${number}.* -Total wall time: 0:00:20 +Total wall time: 0:00:25 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 rename to examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 index 60722d106361b5389e9ddff31c97956721c44e72..f110e20906587a7975f29ca1f60c27e1833e6a48 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex3/log.07Aug19.duplex3.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (18 Jun 2019) +LAMMPS (7 Aug 2019) variable number equal 1 variable ofreq equal 1000 variable efreq equal 1000 @@ -35,8 +35,8 @@ read_data data.duplex3 2 = max # of 1-3 neighbors 2 = max # of 1-4 neighbors 4 = max # of special neighbors - special bonds CPU = 0.000189 secs - read_data CPU = 0.003302 secs + special bonds CPU = 0.000188 secs + read_data CPU = 0.002791 secs set atom * mass 1.0 10 settings made for mass @@ -44,15 +44,15 @@ set atom * mass 1.0 group all type 1 4 10 atoms in group all -# oxDNA bond interactions - FENE backbone +# oxDNA2 bond interactions - FENE backbone bond_style oxdna2/fene bond_coeff * 2.0 0.25 0.7564 -# oxDNA pair interactions +# oxDNA2 pair interactions pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 @@ -135,7 +135,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1.4720158 0.009525411 -1.4624904 3.1370518e-06 1000 ekin = 0.00366431201929595 | erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679 @@ -1139,21 +1139,21 @@ Step Temp E_pair E_mol TotEng Press 999000 ekin = 0.330110494517446 | erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851 1000000 ekin = 0.345190458651126 | erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498 1000000 0.025569664 -1.5839232 0.020799898 -1.5286042 -3.5789082e-06 -Loop time of 30.1999 on 4 procs for 1000000 steps with 10 atoms +Loop time of 20.0167 on 4 procs for 1000000 steps with 10 atoms -Performance: 28609.339 tau/day, 33112.661 timesteps/s -96.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 43164.007 tau/day, 49958.342 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.90762 | 10.291 | 18.476 | 234.3 | 34.08 -Bond | 0.11783 | 0.39332 | 0.61914 | 34.0 | 1.30 +Pair | 0.59089 | 7.5652 | 13.908 | 205.5 | 37.79 +Bond | 0.090803 | 0.29363 | 0.47758 | 29.6 | 1.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.8711 | 3.8042 | 4.7159 | 34.0 | 12.60 -Output | 2e-05 | 3.15e-05 | 3.6e-05 | 0.0 | 0.00 -Modify | 0.27052 | 1.1583 | 1.9428 | 63.9 | 3.84 -Other | | 14.55 | | | 48.19 +Comm | 1.7298 | 2.0312 | 2.2983 | 16.6 | 10.15 +Output | 1.4e-05 | 2.075e-05 | 2.3e-05 | 0.0 | 0.00 +Modify | 0.17638 | 0.90613 | 1.5893 | 60.1 | 4.53 +Other | | 9.22 | | | 46.06 Nlocal: 2.5 ave 5 max 0 min Histogram: 1 0 1 0 0 0 0 0 1 1 @@ -1169,4 +1169,4 @@ Neighbor list builds = 0 Dangerous builds = 0 #write_restart config.${number}.* -Total wall time: 0:00:30 +Total wall time: 0:00:20 diff --git a/examples/USER/drude/toluene/data.toluene b/examples/USER/drude/toluene/data.toluene index 48d44016d782c207004557b4a03eaed0a7835ee5..d67af7c311129bdd15133d569d8fb30247cca710 100644 --- a/examples/USER/drude/toluene/data.toluene +++ b/examples/USER/drude/toluene/data.toluene @@ -79,10 +79,10 @@ Dihedral Coeffs Improper Coeffs - 1 0.0000 2.1999 0.0000 0.0000 # CAO-CAO-CAT-CTT - 2 0.0000 2.1999 0.0000 0.0000 # CAT-CAM-CAO-HAT - 3 0.0000 2.1999 0.0000 0.0000 # CAO-CAP-CAM-HAT - 4 0.0000 2.1999 0.0000 0.0000 # CAM-CAM-CAP-HAT + 1 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAO-CAT-CTT + 2 2.1999 0.0000 0.0000 -1.0000 0 # CAT-CAM-CAO-HAT + 3 2.1999 0.0000 0.0000 -1.0000 0 # CAO-CAP-CAM-HAT + 4 2.1999 0.0000 0.0000 -1.0000 0 # CAM-CAM-CAP-HAT Atoms diff --git a/examples/USER/drude/toluene/in.toluene.lang b/examples/USER/drude/toluene/in.toluene.lang index 8f00c24a4b2739f9418cefed4d438c005091f433..ba40a3bcde321d41592f5287452995f0a1fcd971 100644 --- a/examples/USER/drude/toluene/in.toluene.lang +++ b/examples/USER/drude/toluene/in.toluene.lang @@ -7,7 +7,7 @@ atom_style full bond_style harmonic angle_style harmonic dihedral_style opls -improper_style opls +improper_style fourier special_bonds lj/coul 0.0 0.0 0.5 pair_style lj/cut/thole/long 2.600 8.0 8.0 @@ -109,7 +109,7 @@ fix fNPH all nve compute cTEMP all temp/drude -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] thermo 50 timestep 0.5 diff --git a/examples/USER/drude/toluene/in.toluene.nh b/examples/USER/drude/toluene/in.toluene.nh index 05b35ca91936b4573d9fc8f49af13bce78e5f99c..7a5aecc57969c1f2e6741080db21ff10d52e8452 100644 --- a/examples/USER/drude/toluene/in.toluene.nh +++ b/examples/USER/drude/toluene/in.toluene.nh @@ -7,7 +7,7 @@ atom_style full bond_style harmonic angle_style harmonic dihedral_style opls -improper_style opls +improper_style fourier special_bonds lj/coul 0.0 0.0 0.5 pair_style lj/cut/thole/long 2.600 8.0 8.0 @@ -115,7 +115,7 @@ fix fINVERSE all drude/transform/inverse fix fMOMENTUM all momentum 100 linear 1 1 1 -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] thermo 50 timestep 0.5 diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 deleted file mode 100644 index 08cc2f0f5c429c083cac7b3ff864c8bef3086674..0000000000000000000000000000000000000000 --- a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -ERROR: Unknown improper style opls (src/force.cpp:634) -Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 deleted file mode 100644 index 08cc2f0f5c429c083cac7b3ff864c8bef3086674..0000000000000000000000000000000000000000 --- a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -ERROR: Unknown improper style opls (src/force.cpp:634) -Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 deleted file mode 100644 index a6807f8ee1dffa955e5566453a2d0a3cab82cab1..0000000000000000000000000000000000000000 --- a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -ERROR: Unknown improper style opls (src/force.cpp:634) -Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 deleted file mode 100644 index a6807f8ee1dffa955e5566453a2d0a3cab82cab1..0000000000000000000000000000000000000000 --- a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -ERROR: Unknown improper style opls (src/force.cpp:634) -Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1 b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..71ffdb0c8caf095e243335feeb7fe8b85fd92a49 --- /dev/null +++ b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1 @@ -0,0 +1,254 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style fourier +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/thole/long 2.600 8.0 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.toluene extra/special/per/atom 1 + orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5500 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 8 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... + 5500 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6000 dihedrals + reading impropers ... + 1500 impropers + 5 = max # of 1-2 neighbors + 10 = max # of 1-3 neighbors + 16 = max # of 1-4 neighbors + 20 = max # of special neighbors + special bonds CPU = 0.00199628 secs + read_data CPU = 0.0169649 secs + +comm_modify vel yes + +group gTOLUENE molecule 1:250 +5500 atoms in group gTOLUENE +group gCORES type 1 2 3 4 5 6 7 +3750 atoms in group gCORES +group gDRUDES type 8 9 10 11 12 +1750 atoms in group gDRUDES + +pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT +pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO +pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM +pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP +pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT +pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT +pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT +pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO +pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM +pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP +pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT +pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT +pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT +pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM +pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP +pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT +pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT +pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT +pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP +pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT +pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT +pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT +pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT +pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT +pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT +pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT +pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT +pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT +pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT +pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO +pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM +pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP +pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT +pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT +pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO +pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM +pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP +pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT +pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT +pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO +pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM +pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP +pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT +pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT +pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO +pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM +pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP +pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT +pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT +pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO +pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM +pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP +pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT +pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT +pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO +pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM +pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP +pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT +pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO +pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM +pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP +pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT +pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM +pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP +pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT +pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP +pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT +pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C C C C N N D D D D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 + 1250 = # of size 2 clusters + 0 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.000807762 secs + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nve + +compute cTEMP all temp/drude + +thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:323) + G vector (1/distance) = 0.382011 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0325934 + estimated relative force accuracy = 9.8154e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 103823 64000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 19 +New max number of 1-2 to 1-4 neighbors: 20 (+1) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/thole/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes +Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 + 50 4782.1702 4728.7435 328.28767 53.426722 1812.2203 685.37824 683.70917 -3277.1645 797.34329 1305983.2 -1306631.2 16874.358 48631.318 448.52419 116.25477 + 100 2906.0879 3699.8031 256.85465 -793.7152 978.15364 778.36908 862.30899 -3270.1722 468.44888 1306096.8 -1306707.6 15631.384 48631.318 382.26408 35.748403 + 150 2089.0918 3593.0499 249.44342 -1503.9581 751.32283 803.47802 668.4757 -3277.5983 128.17444 1306138.5 -1306716.3 15193.04 48631.318 384.75632 10.892446 + 200 1547.3302 3248.639 225.53309 -1701.3089 699.65977 814.31164 692.83227 -3276.3957 -66.671816 1306160.9 -1306725.9 13787.676 48631.318 351.28242 3.8458668 + 250 1177.9323 3095.949 214.93276 -1918.0167 688.87262 842.44531 615.89218 -3278.4465 -210.06178 1306154.3 -1306731 8808.5835 48631.318 335.8115 1.8330994 + 300 895.90313 2870.3451 199.27046 -1974.442 734.95873 858.58147 624.00862 -3278.6022 -342.01951 1306163.6 -1306735 3388.4841 48631.318 311.56815 1.2987715 + 350 669.25785 2764.9587 191.95413 -2095.7009 662.44028 860.79714 602.69567 -3278.776 -376.37081 1306172.3 -1306738.8 8494.9184 48631.318 300.19414 1.1358594 + 400 531.21609 2722.6775 189.01881 -2191.4614 684.34049 868.77818 576.86096 -3280.1649 -459.66591 1306160 -1306741.6 6726.3087 48631.318 295.59622 1.1315427 + 450 427.05425 2611.7588 181.3184 -2184.7046 719.2042 891.88178 591.2282 -3279.339 -534.65069 1306172.2 -1306745.2 2398.5394 48631.318 283.56126 1.0726045 + 500 310.44891 2556.0967 177.45412 -2245.6477 720.86526 841.50195 586.3417 -3279.3029 -539.81715 1306169.5 -1306744.8 3028.595 48631.318 277.52314 1.0406334 + 550 207.83114 2531.3051 175.73299 -2323.4739 674.71188 855.2132 555.53227 -3280.0378 -553.93222 1306171.9 -1306746.9 4609.4408 48631.318 274.80629 1.0748601 + 600 88.81557 2459.9059 170.77619 -2371.0903 692.4485 834.47484 550.85905 -3280.9086 -595.31802 1306171.4 -1306744 2107.9995 48631.318 267.06312 1.0301965 + 650 75.616307 2416.9747 167.79573 -2341.3584 703.57186 869.98959 564.81201 -3280.7522 -619.8016 1306168 -1306747.2 1236.4829 48631.318 262.3542 1.0968447 + 700 49.832719 2415.7344 167.70963 -2365.9017 683.61663 882.67915 555.23571 -3280.7778 -615.06862 1306159.9 -1306751.4 2985.7048 48631.318 262.23095 1.0762424 + 750 41.513638 2427.218 168.50687 -2385.7044 698.87619 863.2938 564.58197 -3280.0156 -637.29964 1306160.1 -1306755.3 1653.117 48631.318 263.49803 1.0451977 + 800 109.53032 2481.9041 172.30339 -2372.3738 697.22709 897.36555 561.28745 -3280.6784 -651.29564 1306155 -1306751.3 1219.8761 48631.318 269.43698 1.0647792 + 850 98.142203 2502.3132 173.72026 -2404.171 696.5382 878.83293 566.44302 -3280.2837 -663.94587 1306155.6 -1306757.4 1122.7487 48631.318 271.67716 1.030267 + 900 62.992675 2409.7324 167.29295 -2346.7397 722.00541 896.64662 560.66083 -3279.4915 -644.05458 1306153.6 -1306756.1 1604.295 48631.318 261.58656 1.0609836 + 950 5.6677468 2403.5067 166.86073 -2397.839 725.07222 891.00249 556.81977 -3279.7848 -672.66389 1306141 -1306759.2 1019.1694 48631.318 260.91187 1.0562387 + 1000 38.526968 2444.97 169.73928 -2406.4431 704.72993 920.68493 534.59035 -3281.2673 -667.78091 1306141.1 -1306758.5 486.79846 48631.318 265.39928 1.098473 + 1050 21.698026 2388.6306 165.82798 -2366.9326 712.15539 934.39244 546.92027 -3281.1469 -654.7449 1306137.4 -1306761.9 1556.1256 48631.318 259.28203 1.0760765 + 1100 -26.971225 2433.8428 168.96678 -2460.814 710.11081 881.19212 524.51547 -3281.7925 -667.53202 1306137.1 -1306764.4 1203.8971 48631.318 264.20441 1.0706085 + 1150 -49.171269 2375.9688 164.94895 -2425.14 729.78127 918.79575 518.21967 -3281.6542 -675.7239 1306130.4 -1306765 229.44016 48631.318 257.89845 1.086519 + 1200 -53.421342 2422.0091 168.14524 -2475.4304 710.67274 884.2589 523.32524 -3282.2275 -674.49333 1306130.9 -1306767.9 -131.09655 48631.318 262.91124 1.0804821 + 1250 -58.534776 2394.4031 166.22873 -2452.9378 680.27486 909.58096 532.81959 -3281.5551 -653.13731 1306127 -1306767.9 546.96357 48631.318 259.92916 1.0424914 + 1300 -24.151217 2431.9902 168.83817 -2456.1414 681.27127 919.39245 536.41899 -3281.3717 -661.90875 1306121.6 -1306771.5 1455.7512 48631.318 264.00712 1.0630558 + 1350 -38.973062 2438.6194 169.2984 -2477.5925 707.96118 912.62518 519.44533 -3281.6739 -687.67183 1306126.1 -1306774.4 -1470.4442 48631.318 264.70225 1.1091537 + 1400 11.896539 2384.5407 165.54404 -2372.6442 719.03374 950.93261 550.5639 -3280.4581 -663.4921 1306122 -1306771.3 465.12854 48631.318 258.83564 1.0785364 + 1450 -13.118691 2436.6246 169.15991 -2449.7433 661.04397 933.07103 561.29537 -3280.6997 -672.68495 1306123.9 -1306775.7 -108.46564 48631.318 264.50636 1.0718787 + 1500 -38.151755 2417.4849 167.83116 -2455.6367 688.81484 892.35701 565.29013 -3279.6716 -662.1817 1306116.9 -1306777.2 517.89634 48631.318 262.44549 1.0338083 + 1550 -71.663334 2405.7016 167.01311 -2477.3649 681.78925 876.31247 559.003 -3280.451 -649.16641 1306112.8 -1306777.7 925.49349 48631.318 261.148 1.0609731 + 1600 -13.900431 2419.481 167.96973 -2433.3814 718.46559 909.67964 559.06779 -3280.8163 -667.6092 1306108 -1306780.2 13.95808 48631.318 262.63632 1.080229 + 1650 -16.403222 2431.075 168.77464 -2447.4783 710.99509 907.65662 551.60307 -3279.8852 -661.52624 1306104.5 -1306780.8 726.89923 48631.318 263.91553 1.0489963 + 1700 -18.555086 2438.2062 169.26971 -2456.7613 665.90475 943.02217 542.86579 -3280.9017 -657.99229 1306108 -1306777.7 801.41078 48631.318 264.67663 1.0750708 + 1750 -6.9249446 2443.9707 169.6699 -2450.8956 733.23573 890.06857 560.83229 -3280.362 -670.93883 1306098.3 -1306782.1 47.037748 48631.318 265.30892 1.0661143 + 1800 -21.686222 2434.3375 169.00113 -2456.0237 729.35297 899.9733 561.59516 -3280.4727 -680.98901 1306096.5 -1306782 495.63617 48631.318 264.25723 1.0723683 + 1850 -72.916947 2408.8254 167.22998 -2481.7423 683.24984 904.13282 549.97726 -3279.6699 -652.63212 1306099.2 -1306786 -120.61674 48631.318 261.48504 1.0659808 + 1900 -55.4099 2415.455 167.69023 -2470.8649 700.4473 904.72264 565.5266 -3280.4533 -673.23082 1306099.6 -1306787.4 202.15936 48631.318 262.20353 1.0709756 + 1950 -79.877997 2409.2307 167.25812 -2489.1087 695.9536 894.4541 564.7034 -3279.3581 -680.33472 1306100.8 -1306785.3 213.72828 48631.318 261.52921 1.0658433 + 2000 -102.20457 2399.4263 166.57746 -2501.6309 689.67819 894.58596 565.53233 -3280.7595 -680.39032 1306096.4 -1306786.6 1113.7499 48631.318 260.46311 1.0647045 +Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms + +Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 48.825 | 48.825 | 48.825 | 0.0 | 71.36 +Bond | 2.8852 | 2.8852 | 2.8852 | 0.0 | 4.22 +Kspace | 13.795 | 13.795 | 13.795 | 0.0 | 20.16 +Neigh | 1.0731 | 1.0731 | 1.0731 | 0.0 | 1.57 +Comm | 0.27067 | 0.27067 | 0.27067 | 0.0 | 0.40 +Output | 0.0031168 | 0.0031168 | 0.0031168 | 0.0 | 0.00 +Modify | 1.5207 | 1.5207 | 1.5207 | 0.0 | 2.22 +Other | | 0.04541 | | | 0.07 + +Nlocal: 5500 ave 5500 max 5500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 13157 ave 13157 max 13157 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1338215 +Ave neighs/atom = 243.312 +Ave special neighs/atom = 15.6364 +Neighbor list builds = 32 +Dangerous builds = 0 +Total wall time: 0:01:08 diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4 b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..df7d58ac88ab37b3c608bccde0fb14ed5e05ca11 --- /dev/null +++ b/examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4 @@ -0,0 +1,254 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style fourier +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/thole/long 2.600 8.0 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.toluene extra/special/per/atom 1 + orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 5500 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 8 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... + 5500 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6000 dihedrals + reading impropers ... + 1500 impropers + 5 = max # of 1-2 neighbors + 10 = max # of 1-3 neighbors + 16 = max # of 1-4 neighbors + 20 = max # of special neighbors + special bonds CPU = 0.000747919 secs + read_data CPU = 0.0168228 secs + +comm_modify vel yes + +group gTOLUENE molecule 1:250 +5500 atoms in group gTOLUENE +group gCORES type 1 2 3 4 5 6 7 +3750 atoms in group gCORES +group gDRUDES type 8 9 10 11 12 +1750 atoms in group gDRUDES + +pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT +pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO +pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM +pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP +pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT +pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT +pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT +pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO +pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM +pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP +pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT +pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT +pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT +pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM +pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP +pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT +pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT +pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT +pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP +pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT +pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT +pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT +pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT +pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT +pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT +pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT +pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT +pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT +pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT +pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO +pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM +pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP +pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT +pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT +pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO +pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM +pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP +pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT +pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT +pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO +pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM +pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP +pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT +pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT +pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO +pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM +pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP +pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT +pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT +pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO +pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM +pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP +pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT +pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT +pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO +pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM +pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP +pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT +pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO +pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM +pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP +pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT +pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM +pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP +pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT +pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP +pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT +pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C C C C N N D D D D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 + 1250 = # of size 2 clusters + 0 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.000355244 secs + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nve + +compute cTEMP all temp/drude + +thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:323) + G vector (1/distance) = 0.382011 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0325934 + estimated relative force accuracy = 9.8154e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 34263 16000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 19 +New max number of 1-2 to 1-4 neighbors: 20 (+1) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/thole/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes +Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 + 50 4712.9507 4669.1606 324.15119 43.790082 1798.561 670.61319 690.16967 -3276.9493 811.643 1305983.2 -1306633.5 17164.771 48631.318 442.24313 116.13094 + 100 2865.9139 3726.4166 258.70226 -860.50272 968.87546 749.70761 860.70151 -3270.7784 427.14745 1306104.7 -1306700.9 15017.273 48631.318 385.10628 35.845353 + 150 1982.6673 3535.974 245.481 -1553.3068 764.86116 768.15837 658.70182 -3278.7906 108.49859 1306136.5 -1306711.2 16495.352 48631.318 378.64023 10.723986 + 200 1440.0277 3240.5932 224.97452 -1800.5656 687.71813 791.29356 643.82915 -3276.9293 -99.549986 1306172.9 -1306719.8 13234.476 48631.318 350.46321 3.7468464 + 250 1103.2915 3018.496 209.55567 -1915.2045 677.97905 825.32748 642.78891 -3278.0801 -226.1853 1306168.5 -1306725.5 8774.9103 48631.318 327.36313 1.8722119 + 300 789.07159 2827.1716 196.27319 -2038.1 735.96101 852.72545 589.14167 -3280.0357 -374.66018 1306169 -1306730.2 2259.1028 48631.318 306.85585 1.3262598 + 350 599.10023 2732.3739 189.69197 -2133.2737 677.67006 863.22888 565.41674 -3280.5231 -403.28794 1306177.4 -1306733.2 7989.222 48631.318 296.64126 1.1534418 + 400 428.26436 2591.2884 179.89727 -2163.0241 676.18745 849.24505 612.34065 -3277.4703 -457.85799 1306173.6 -1306739.1 7282.1438 48631.318 281.34719 1.0502762 + 450 307.26859 2534.2468 175.93722 -2226.9782 712.17636 853.98862 578.01327 -3279.7731 -533.87422 1306179.7 -1306737.2 1897.9643 48631.318 275.11317 1.0980929 + 500 234.60959 2495.1082 173.22007 -2260.4987 707.43541 878.25753 547.08402 -3281.2756 -549.04991 1306176.5 -1306739.5 2683.0639 48631.318 270.85452 1.0984718 + 550 203.34751 2445.6535 169.78673 -2242.306 669.03724 892.85034 599.20664 -3279.0757 -559.81157 1306175.9 -1306740.4 4512.9992 48631.318 265.49465 1.0628812 + 600 205.63573 2526.5892 175.4056 -2320.9535 685.64073 887.97693 557.42296 -3280.0332 -597.34755 1306167.8 -1306742.5 2999.5823 48631.318 274.29935 1.064682 + 650 176.23031 2526.3124 175.38638 -2350.0821 714.15285 895.42115 540.39191 -3280.8567 -636.27783 1306165.7 -1306748.6 871.68316 48631.318 274.2807 1.0442089 + 700 106.97524 2441.1059 169.47101 -2334.1306 697.16018 905.51407 564.71847 -3279.6208 -631.62324 1306159.4 -1306749.6 1953.8241 48631.318 264.98935 1.0771037 + 750 76.695104 2435.6635 169.09318 -2358.9684 672.01039 934.63351 545.64024 -3281.1075 -629.89722 1306152.4 -1306752.6 3044.0155 48631.318 264.39002 1.0932471 + 800 57.614075 2456.928 170.56945 -2399.3139 720.76364 898.68013 534.10051 -3281.5897 -659.64354 1306145.5 -1306757.1 1691.9503 48631.318 266.72089 1.0622697 + 850 -44.931126 2390.0608 165.92727 -2434.9919 708.70192 888.26851 537.13087 -3281.355 -665.17283 1306137.8 -1306760.3 123.07165 48631.318 259.45151 1.0516426 + 900 -96.878205 2358.862 163.76133 -2455.7403 672.98976 868.41571 546.69492 -3280.6939 -636.80102 1306134.5 -1306760.9 1955.7005 48631.318 256.05598 1.05337 + 950 -80.012575 2374.4497 164.84349 -2454.4623 679.59722 880.35157 548.35372 -3280.6061 -643.44517 1306125.8 -1306764.5 1510.9809 48631.318 257.72442 1.1017392 + 1000 -21.440874 2440.6729 169.44096 -2462.1138 718.56593 868.65109 555.54643 -3279.8516 -686.71673 1306126.6 -1306765 -1148.6212 48631.318 264.92977 1.1019339 + 1050 16.46903 2382.6961 165.41598 -2366.2271 712.51245 913.35848 579.81678 -3280.0559 -657.12122 1306129.3 -1306764 1004.5778 48631.318 258.64076 1.0684155 + 1100 35.847247 2483.1985 172.39325 -2447.3513 685.05704 889.42278 553.73166 -3280.0177 -663.67201 1306134.3 -1306766.2 699.1824 48631.318 269.56773 1.0838094 + 1150 -4.9817843 2431.4725 168.80223 -2436.4543 720.51056 868.17547 569.09902 -3280.5829 -677.99865 1306133.1 -1306768.7 435.19118 48631.318 263.96966 1.0303202 + 1200 -23.907197 2443.6035 169.64441 -2467.5107 684.96437 887.58483 549.43666 -3280.3144 -679.46182 1306137.2 -1306766.9 367.11148 48631.318 265.28645 1.0344036 + 1250 -16.904671 2389.9447 165.91921 -2406.8494 722.06959 902.90076 568.35616 -3280.6829 -683.32029 1306132.9 -1306769.1 76.759445 48631.318 259.41697 1.0908431 + 1300 -1.7822102 2410.2768 167.33074 -2412.0591 706.98675 904.31941 551.23506 -3280.7552 -651.51211 1306127.3 -1306769.6 1659.1113 48631.318 261.64093 1.0701648 + 1350 -3.569473 2446.3901 169.83786 -2449.9595 686.13971 894.85839 558.36242 -3279.9941 -664.59508 1306129 -1306773.7 783.32881 48631.318 265.5696 1.0709072 + 1400 -33.385576 2400.262 166.63547 -2433.6476 709.5808 890.68408 571.13105 -3280.1428 -674.51247 1306123.4 -1306773.8 -751.38571 48631.318 260.54522 1.080234 + 1450 -11.215152 2405.5409 167.00196 -2416.756 703.72038 913.21131 552.64196 -3280.9831 -649.19774 1306120.3 -1306776.4 1817.2174 48631.318 261.14741 1.031193 + 1500 -25.974102 2435.8375 169.10527 -2461.8116 689.93174 900.70619 552.63711 -3280.1497 -671.17989 1306124 -1306777.8 -98.941796 48631.318 264.45069 1.0190784 + 1550 -76.496407 2394.8126 166.25716 -2471.309 706.96953 886.06919 549.9101 -3280.8434 -659.57745 1306105.9 -1306779.7 -7.0989994 48631.318 259.95403 1.0772144 + 1600 -79.549932 2395.1114 166.2779 -2474.6614 684.11692 888.93332 562.94522 -3280.1665 -665.21744 1306114.4 -1306779.6 320.58515 48631.318 260.00641 1.0425978 + 1650 -99.702003 2360.5652 163.87957 -2460.2672 706.21244 900.9253 540.36599 -3280.2308 -655.96077 1306109.7 -1306781.3 307.35487 48631.318 256.23383 1.0666637 + 1700 -69.422658 2372.1727 164.68541 -2441.5954 676.79347 913.90473 581.60658 -3279.997 -670.33218 1306115.7 -1306779.3 -204.22848 48631.318 257.50963 1.0434075 + 1750 -80.889897 2425.3592 168.37782 -2506.2491 672.88937 911.52373 523.74733 -3280.4796 -673.90027 1306122 -1306782 965.12568 48631.318 263.26491 1.1001595 + 1800 -82.419368 2361.798 163.96515 -2444.2173 716.51571 882.9729 577.92505 -3278.9279 -671.67438 1306111.6 -1306782.6 -44.954517 48631.318 256.36957 1.0636692 + 1850 -93.715705 2373.3359 164.76616 -2467.0516 713.02466 907.03621 563.38626 -3280.2576 -693.30963 1306104.6 -1306781.5 -979.95945 48631.318 257.62543 1.0628288 + 1900 -73.60945 2449.5873 170.05983 -2523.1967 683.65116 893.94251 539.90847 -3281.4318 -680.16358 1306108 -1306787.1 598.18213 48631.318 265.91405 1.0766352 + 1950 -66.068291 2437.3691 169.21159 -2503.4374 672.5168 877.42934 573.56499 -3279.885 -668.54185 1306109.2 -1306787.7 733.05074 48631.318 264.61409 1.0224258 + 2000 -91.043979 2374.4077 164.84057 -2465.4516 692.13299 909.46192 574.60109 -3279.837 -672.33599 1306102.4 -1306791.8 -665.61581 48631.318 257.76275 1.0263294 +Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms + +Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s +94.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.918 | 13.096 | 14.137 | 27.0 | 55.10 +Bond | 0.74012 | 0.76511 | 0.79225 | 2.9 | 3.22 +Kspace | 6.7821 | 7.8285 | 9.0172 | 35.4 | 32.94 +Neigh | 0.37249 | 0.37262 | 0.37278 | 0.0 | 1.57 +Comm | 0.70503 | 0.7188 | 0.72807 | 1.1 | 3.02 +Output | 0.0018752 | 0.0047592 | 0.013386 | 7.2 | 0.02 +Modify | 0.91164 | 0.91644 | 0.92123 | 0.5 | 3.86 +Other | | 0.06335 | | | 0.27 + +Nlocal: 1375 ave 1381 max 1368 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 7803.75 ave 7856 max 7755 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 334465 ave 349504 max 315867 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 1337859 +Ave neighs/atom = 243.247 +Ave special neighs/atom = 15.6364 +Neighbor list builds = 32 +Dangerous builds = 0 +Total wall time: 0:00:23 diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1 b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..be5d856d1ed1f3b0990fdf221c6e16ebb0073a07 --- /dev/null +++ b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1 @@ -0,0 +1,262 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style fourier +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/thole/long 2.600 8.0 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.toluene extra/special/per/atom 1 + orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5500 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 8 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... + 5500 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6000 dihedrals + reading impropers ... + 1500 impropers + 5 = max # of 1-2 neighbors + 10 = max # of 1-3 neighbors + 16 = max # of 1-4 neighbors + 20 = max # of special neighbors + special bonds CPU = 0.0019815 secs + read_data CPU = 0.0168803 secs + +comm_modify vel yes + +group gTOLUENE molecule 1:250 +5500 atoms in group gTOLUENE +group gCORES type 1 2 3 4 5 6 7 +3750 atoms in group gCORES +group gDRUDES type 8 9 10 11 12 +1750 atoms in group gDRUDES + +pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT +pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO +pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM +pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP +pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT +pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT +pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT +pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO +pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM +pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP +pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT +pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT +pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT +pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM +pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP +pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT +pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT +pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT +pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP +pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT +pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT +pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT +pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT +pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT +pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT +pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT +pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT +pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT +pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT +pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO +pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM +pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP +pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT +pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT +pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO +pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM +pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP +pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT +pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT +pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO +pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM +pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP +pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT +pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT +pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO +pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM +pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP +pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT +pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT +pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO +pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM +pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP +pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT +pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT +pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO +pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM +pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP +pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT +pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO +pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM +pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP +pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT +pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM +pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP +pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT +pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP +pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT +pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT + + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C C C C N N D D D D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 + 1250 = # of size 2 clusters + 0 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.000715256 secs + +compute cTEMP_CORE gCORES temp/com +compute cTEMP all temp/drude + +fix fDIRECT all drude/transform/direct +fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 260 100.0 +fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 1 20.0 +fix fINVERSE all drude/transform/inverse + +fix fMOMENTUM all momentum 100 linear 1 1 1 + +thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:323) + G vector (1/distance) = 0.382011 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0325934 + estimated relative force accuracy = 9.8154e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 103823 64000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 19 +New max number of 1-2 to 1-4 neighbors: 20 (+1) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/thole/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes +Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 + 50 3563.3755 4630.6343 321.47655 -1067.2588 735.72049 604.78665 689.14827 -3277.411 815.58183 1306088.7 -1306723.8 17813.424 48631.318 503.827 0.0087118192 + 100 3327.4724 4395.1107 305.12559 -1067.6382 597.93176 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.337 48631.318 478.20171 0.0075985539 + 150 3036.9065 4740.2304 329.08513 -1703.3239 558.64983 619.91284 658.80687 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215188 + 200 2697.958 4559.3445 316.52733 -1861.3864 522.09334 593.89129 754.61446 -3273.49 87.660461 1306183.9 -1306730 17888.936 48631.318 496.07143 0.0068706164 + 250 2348.7568 4410.585 306.19988 -2061.8283 506.05007 575.35171 715.55054 -3276.3261 -18.364473 1306177.3 -1306741.4 11592.05 48631.318 479.88562 0.0071741032 + 300 2019.8258 4040.1415 280.48226 -2020.3157 604.3077 641.66689 693.93801 -3278.5312 -115.73641 1306183.2 -1306749.1 3631.3628 48631.318 439.57995 0.0069886387 + 350 1699.5166 3944.9851 273.87613 -2245.4685 452.07416 638.0653 658.79117 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22694 0.0062868111 + 400 1399.2929 3726.098 258.68014 -2326.8051 457.91943 621.44726 639.39903 -3279.2395 -188.85914 1306185.4 -1306762.8 10792.274 48631.318 405.41134 0.0059340078 + 450 1120.5249 3518.345 244.25712 -2397.8201 519.48856 584.65789 646.36689 -3278.6685 -289.59913 1306184.1 -1306764.2 2755.5598 48631.318 382.80716 0.0055707485 + 500 868.0166 3359.8794 233.25583 -2491.8628 460.7393 581.49563 581.01731 -3281.5544 -252.20169 1306184.3 -1306765.7 6120.3639 48631.318 365.56528 0.0058756154 + 550 637.01567 3214.9521 223.19441 -2577.9364 431.81483 578.87411 540.94047 -3281.5337 -266.36075 1306182.8 -1306764.5 8622.4334 48631.318 349.79661 0.0058589653 + 600 418.04086 3113.4064 216.14472 -2695.3655 430.45935 538.68157 522.24598 -3283.456 -311.87901 1306174.3 -1306765.8 7068.9273 48631.318 338.74797 0.0059567598 + 650 218.5966 2930.8439 203.47052 -2712.2473 514.47294 514.28379 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.553736 48631.318 318.88482 0.0052667842 + 700 45.22721 2830.1443 196.47956 -2784.917 451.11156 498.26423 541.18835 -3282.1427 -375.95313 1306157.1 -1306774.4 3947.6276 48631.318 307.92741 0.0068019029 + 750 -114.28621 2798.3153 194.26988 -2912.6016 412.753 503.2878 481.32173 -3284.3411 -393.53984 1306147 -1306779.1 7143.3414 48631.318 304.46466 0.0061596717 + 800 -263.63817 2694.8084 187.08403 -2958.4466 455.67914 487.49754 476.8659 -3284.3133 -451.9578 1306145 -1306787.2 1185.9502 48631.318 293.20288 0.0058203332 + 850 -397.71592 2559.1921 177.66902 -2956.9081 458.83317 481.2262 478.31241 -3284.068 -437.26503 1306138.6 -1306792.6 346.80209 48631.318 278.44745 0.0054921692 + 900 -515.1823 2544.8753 176.67509 -3060.0576 395.00163 457.58988 446.68352 -3285.485 -423.56221 1306145 -1306795.3 3712.8598 48631.318 276.88864 0.0074054008 + 950 -617.28259 2451.1723 170.16987 -3068.4549 383.64277 446.59877 434.4624 -3285.1348 -391.59344 1306142.3 -1306798.7 5429.2488 48631.318 266.69431 0.0057487316 + 1000 -703.15534 2334.837 162.09342 -3037.9923 424.34948 462.21112 451.80809 -3284.3803 -426.53369 1306133.9 -1306799.3 1137.6145 48631.318 254.03675 0.0053914731 + 1050 -771.1763 2303.837 159.94128 -3075.0133 426.21409 436.50718 435.09987 -3285.1939 -411.14054 1306125.6 -1306802.1 1636.9383 48631.318 250.66295 0.0069342505 + 1100 -822.72236 2283.4196 158.52382 -3106.142 376.67684 447.77729 418.45768 -3286.5919 -377.48204 1306118.9 -1306803.8 4760.5163 48631.318 248.44119 0.0074025012 + 1150 -857.06075 2259.0717 156.8335 -3116.1324 400.31523 431.65981 457.68066 -3285.1977 -430.47723 1306115.8 -1306805.9 3194.5161 48631.318 245.79223 0.007063589 + 1200 -875.50848 2238.2637 155.38893 -3113.7722 445.38524 460.97125 432.10511 -3285.4238 -472.46606 1306114.7 -1306809 -653.49784 48631.318 243.52819 0.0071448738 + 1250 -880.37572 2294.6889 159.30618 -3175.0646 411.35427 444.73793 420.06468 -3286.0366 -458.05371 1306104.4 -1306811.5 945.80793 48631.318 249.66481 0.011853487 + 1300 -871.31064 2284.2298 158.58007 -3155.5405 404.97412 441.75285 426.34477 -3285.4859 -424.79609 1306094.9 -1306813.2 4406.6196 48631.318 248.48563 0.084424118 + 1350 -816.70005 2325.9264 161.47481 -3142.6265 696.80296 442.50053 431.19923 -3285.7859 -450.2699 1305836.2 -1306813.3 593.8098 48631.318 251.40749 2.9297319 + 1400 -794.25335 2263.5101 157.14163 -3057.7635 645.65165 466.22086 446.22268 -3285.1821 -420.65317 1305903.7 -1306813.8 1386.3633 48631.318 245.20554 1.8916154 + 1450 -776.10866 2287.6575 158.81803 -3063.7661 427.03477 479.10627 439.67495 -3285.9537 -395.13186 1306087.6 -1306816.1 2936.7806 48631.318 248.87167 0.061343245 + 1500 -725.48181 2371.413 164.63266 -3096.8948 390.03204 464.30903 446.91959 -3284.7809 -393.16613 1306095.4 -1306815.6 3544.25 48631.318 258.01286 0.011586563 + 1550 -671.4904 2315.9297 160.7808 -2987.4201 457.04935 500.25282 464.76203 -3284.9311 -400.98103 1306091.7 -1306815.3 2052.6339 48631.318 251.97726 0.0094517862 + 1600 -618.83633 2449.0918 170.02543 -3067.9281 425.47487 474.65876 471.99171 -3284.3677 -430.32107 1306091.3 -1306816.6 441.15682 48631.318 266.46311 0.014260935 + 1650 -567.82245 2425.2238 168.36842 -2993.0462 421.01953 511.27133 463.22065 -3285.038 -377.24066 1306088.4 -1306814.7 5198.8565 48631.318 263.83185 0.074738268 + 1700 -502.4486 2441.8554 169.52305 -2944.304 642.39962 512.90234 490.38297 -3283.9751 -417.39288 1305929.1 -1306817.7 1141.4411 48631.318 264.52393 2.043674 + 1750 -459.52196 2499.0746 173.49543 -2958.5966 679.38259 505.31787 484.77659 -3284.6272 -384.27736 1305861.6 -1306820.8 1527.2046 48631.318 270.10074 3.1869342 + 1800 -471.14403 2476.2266 171.90923 -2947.3706 442.47741 530.45656 474.03057 -3284.0954 -371.95117 1306084.3 -1306822.6 3392.2533 48631.318 269.36446 0.10416401 + 1850 -462.80763 2536.7112 176.10831 -2999.5188 437.08241 525.07462 474.0838 -3283.7906 -422.23719 1306091.6 -1306821.3 1629.8629 48631.318 275.99502 0.016806806 + 1900 -469.89289 2468.9765 171.4059 -2938.8694 446.77624 531.61059 496.01046 -3284.2338 -395.15325 1306085.7 -1306819.6 3119.5402 48631.318 268.62645 0.014601992 + 1950 -491.08007 2445.5966 169.78278 -2936.6767 457.80452 527.23373 470.18125 -3283.9608 -391.86377 1306101.9 -1306818 1122.5275 48631.318 266.08018 0.018911601 + 2000 -518.40811 2418.7208 167.91696 -2937.1289 415.93135 536.5973 480.44651 -3283.7881 -363.72783 1306096.2 -1306818.7 4475.7317 48631.318 263.09007 0.13504326 +Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms + +Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s +97.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 48.367 | 48.367 | 48.367 | 0.0 | 68.42 +Bond | 2.9191 | 2.9191 | 2.9191 | 0.0 | 4.13 +Kspace | 14.266 | 14.266 | 14.266 | 0.0 | 20.18 +Neigh | 1.5262 | 1.5262 | 1.5262 | 0.0 | 2.16 +Comm | 0.27841 | 0.27841 | 0.27841 | 0.0 | 0.39 +Output | 0.0035572 | 0.0035572 | 0.0035572 | 0.0 | 0.01 +Modify | 3.2856 | 3.2856 | 3.2856 | 0.0 | 4.65 +Other | | 0.05018 | | | 0.07 + +Nlocal: 5500 ave 5500 max 5500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 15317 ave 15317 max 15317 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1302849 +Ave neighs/atom = 236.882 +Ave special neighs/atom = 15.6364 +Neighbor list builds = 44 +Dangerous builds = 0 +Total wall time: 0:01:10 diff --git a/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4 b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..8d58260754d304b83ba4438d1a8c08e76f013277 --- /dev/null +++ b/examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4 @@ -0,0 +1,262 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style fourier +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/thole/long 2.600 8.0 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.toluene extra/special/per/atom 1 + orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 5500 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 8 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... + 5500 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6000 dihedrals + reading impropers ... + 1500 impropers + 5 = max # of 1-2 neighbors + 10 = max # of 1-3 neighbors + 16 = max # of 1-4 neighbors + 20 = max # of special neighbors + special bonds CPU = 0.000718355 secs + read_data CPU = 0.0167146 secs + +comm_modify vel yes + +group gTOLUENE molecule 1:250 +5500 atoms in group gTOLUENE +group gCORES type 1 2 3 4 5 6 7 +3750 atoms in group gCORES +group gDRUDES type 8 9 10 11 12 +1750 atoms in group gDRUDES + +pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT +pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO +pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM +pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP +pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT +pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT +pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT +pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO +pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM +pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP +pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT +pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT +pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT +pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM +pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP +pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT +pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT +pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT +pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP +pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT +pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT +pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT +pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT +pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT +pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT +pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT +pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT +pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT +pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT +pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO +pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM +pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP +pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT +pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT +pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO +pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM +pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP +pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT +pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT +pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO +pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM +pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP +pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT +pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT +pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO +pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM +pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP +pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT +pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT +pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO +pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM +pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP +pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT +pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT +pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO +pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM +pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP +pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT +pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO +pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM +pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP +pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT +pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM +pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP +pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT +pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP +pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT +pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT + + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C C C C N N D D D D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 + 1250 = # of size 2 clusters + 0 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + find clusters CPU = 0.000344038 secs + +compute cTEMP_CORE gCORES temp/com +compute cTEMP all temp/drude + +fix fDIRECT all drude/transform/direct +fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 260 100.0 +fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 1 20.0 +fix fINVERSE all drude/transform/inverse + +fix fMOMENTUM all momentum 100 linear 1 1 1 + +thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:323) + G vector (1/distance) = 0.382011 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0325934 + estimated relative force accuracy = 9.8154e-05 + using double precision FFTW3 + 3d grid and FFT values/proc = 34263 16000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 19 +New max number of 1-2 to 1-4 neighbors: 20 (+1) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/thole/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes +Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 11086.347 2910.7282 202.07402 8175.6191 6565.4851 20.333365 1.0706727e-06 -3299.85 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 + 50 3563.376 4630.6343 321.47655 -1067.2583 735.72048 604.78665 689.14826 -3277.411 815.58183 1306088.7 -1306723.8 17813.425 48631.318 503.827 0.0087118179 + 100 3327.4722 4395.1107 305.12559 -1067.6385 597.93175 651.62645 945.4151 -3267.2851 584.58833 1306135.9 -1306715.8 17407.335 48631.318 478.2017 0.0075985638 + 150 3036.9065 4740.2304 329.08513 -1703.3238 558.64983 619.91284 658.80686 -3278.7837 285.12462 1306173 -1306720 18448.248 48631.318 515.75286 0.0063215227 + 200 2697.9581 4559.3445 316.52734 -1861.3864 522.09335 593.8913 754.61446 -3273.49 87.660464 1306183.9 -1306730 17888.937 48631.318 496.07143 0.006870622 + 250 2348.7563 4410.585 306.19988 -2061.8288 506.05006 575.35172 715.55055 -3276.3261 -18.364482 1306177.3 -1306741.4 11592.049 48631.318 479.88562 0.0071741023 + 300 2019.8256 4040.1415 280.48225 -2020.3159 604.30771 641.66688 693.93802 -3278.5312 -115.73639 1306183.2 -1306749.1 3631.3625 48631.318 439.57995 0.0069886424 + 350 1699.5169 3944.9851 273.87613 -2245.4682 452.07416 638.06529 658.79116 -3279.6053 -157.07584 1306196.9 -1306754.6 13544.368 48631.318 429.22695 0.0062868216 + 400 1399.2927 3726.098 258.68014 -2326.8053 457.91943 621.44727 639.39905 -3279.2395 -188.85912 1306185.4 -1306762.8 10792.273 48631.318 405.41133 0.0059340084 + 450 1120.5246 3518.345 244.25712 -2397.8204 519.48859 584.6579 646.36688 -3278.6685 -289.59912 1306184.1 -1306764.2 2755.5597 48631.318 382.80717 0.005570751 + 500 868.01643 3359.8794 233.25583 -2491.863 460.73928 581.49568 581.01732 -3281.5544 -252.20168 1306184.3 -1306765.7 6120.364 48631.318 365.56528 0.0058756204 + 550 637.01646 3214.9521 223.19441 -2577.9356 431.81484 578.87415 540.94046 -3281.5337 -266.36074 1306182.8 -1306764.5 8622.4353 48631.318 349.79661 0.0058589476 + 600 418.04028 3113.4063 216.14471 -2695.3661 430.45936 538.68158 522.24597 -3283.456 -311.87897 1306174.3 -1306765.8 7068.9275 48631.318 338.74796 0.0059567639 + 650 218.59562 2930.8439 203.47052 -2712.2482 514.47296 514.2838 551.52551 -3282.0904 -405.37401 1306164.5 -1306769.5 -13.554086 48631.318 318.88481 0.0052667849 + 700 45.227739 2830.1443 196.47957 -2784.9165 451.11157 498.26426 541.18833 -3282.1427 -375.95321 1306157.1 -1306774.4 3947.6268 48631.318 307.92741 0.0068018884 + 750 -114.28676 2798.3154 194.26988 -2912.6022 412.75298 503.28782 481.32167 -3284.3411 -393.53987 1306147 -1306779.1 7143.3424 48631.318 304.46466 0.0061596613 + 800 -263.63827 2694.8085 187.08403 -2958.4468 455.67916 487.49754 476.86576 -3284.3133 -451.95784 1306145 -1306787.2 1185.9474 48631.318 293.20289 0.0058203323 + 850 -397.71592 2559.1922 177.66903 -2956.9082 458.83313 481.22619 478.31233 -3284.068 -437.26509 1306138.6 -1306792.6 346.80221 48631.318 278.44747 0.0054921238 + 900 -515.18134 2544.8753 176.67509 -3060.0567 395.0016 457.5898 446.68361 -3285.485 -423.56234 1306145.1 -1306795.3 3712.8594 48631.318 276.88864 0.0074054726 + 950 -617.28607 2451.1721 170.16985 -3068.4582 383.6428 446.59872 434.46241 -3285.1348 -391.59326 1306142.3 -1306798.7 5429.2191 48631.318 266.69429 0.0057487961 + 1000 -703.15541 2334.8366 162.09339 -3037.992 424.34957 462.21115 451.80811 -3284.3803 -426.53346 1306133.9 -1306799.3 1137.6144 48631.318 254.03671 0.0053915025 + 1050 -771.17572 2303.8364 159.94123 -3075.0121 426.21406 436.50744 435.10013 -3285.1938 -411.13999 1306125.6 -1306802.1 1636.9467 48631.318 250.66288 0.0069341736 + 1100 -822.72317 2283.421 158.52392 -3106.1442 376.67703 447.77728 418.45763 -3286.5919 -377.48075 1306118.9 -1306803.8 4760.4718 48631.318 248.44134 0.0074024122 + 1150 -857.06061 2259.0725 156.83355 -3116.1331 400.31517 431.65949 457.68078 -3285.1977 -430.47775 1306115.8 -1306805.9 3194.5159 48631.318 245.79231 0.007063706 + 1200 -875.50971 2238.2632 155.38889 -3113.7729 445.38534 460.97161 432.10511 -3285.4238 -472.46582 1306114.7 -1306809 -653.49627 48631.318 243.52813 0.0071446561 + 1250 -880.37609 2294.689 159.30619 -3175.0651 411.35498 444.73774 420.06429 -3286.0366 -458.05353 1306104.4 -1306811.5 945.79687 48631.318 249.66483 0.011854196 + 1300 -871.31122 2284.2295 158.58005 -3155.5407 404.97869 441.75305 426.34479 -3285.4859 -424.79602 1306094.8 -1306813.2 4406.6128 48631.318 248.4856 0.084411062 + 1350 -816.69657 2325.9211 161.47444 -3142.6176 696.85542 442.50059 431.19981 -3285.7859 -450.27129 1305836.1 -1306813.3 593.86622 48631.318 251.40736 2.9289249 + 1400 -794.25213 2263.5122 157.14177 -3057.7643 645.6531 466.2204 446.22253 -3285.1821 -420.65316 1305903.7 -1306813.8 1386.3481 48631.318 245.20568 1.8917548 + 1450 -776.1076 2287.6591 158.81814 -3063.7667 427.0331 479.10417 439.67675 -3285.9536 -395.13308 1306087.6 -1306816.1 2936.7117 48631.318 248.87185 0.061341392 + 1500 -725.48032 2371.4108 164.63251 -3096.8911 390.03135 464.30817 446.91941 -3284.7808 -393.16302 1306095.4 -1306815.6 3544.3635 48631.318 258.01262 0.011585228 + 1550 -671.48696 2315.9233 160.78035 -2987.4102 457.04771 500.26018 464.7623 -3284.931 -400.98142 1306091.7 -1306815.3 2052.6204 48631.318 251.97656 0.0094518433 + 1600 -618.82679 2449.0893 170.02525 -3067.9161 425.47171 474.66369 471.99137 -3284.3677 -430.3224 1306091.3 -1306816.6 441.31257 48631.318 266.46283 0.014263201 + 1650 -567.82233 2425.2281 168.36872 -2993.0504 421.02008 511.26686 463.22202 -3285.0378 -377.24205 1306088.4 -1306814.7 5198.6214 48631.318 263.83232 0.074728934 + 1700 -502.46013 2441.8437 169.52224 -2944.3039 642.39863 512.90005 490.39655 -3283.975 -417.39351 1305929.1 -1306817.7 1141.2401 48631.318 264.52268 2.0436397 + 1750 -459.52135 2499.0847 173.49613 -2958.606 679.34078 505.30943 484.78276 -3284.6269 -384.28217 1305861.7 -1306820.8 1527.0852 48631.318 270.10144 3.1876179 + 1800 -471.14322 2476.2445 171.91047 -2947.3877 442.48278 530.4566 474.0343 -3284.0957 -371.97492 1306084.3 -1306822.6 3392.0306 48631.318 269.36641 0.1041603 + 1850 -462.80151 2536.7173 176.10873 -2999.5188 437.07855 525.05914 474.07725 -3283.7908 -422.22641 1306091.6 -1306821.3 1630.1204 48631.318 275.99568 0.016808725 + 1900 -469.8785 2468.9596 171.40473 -2938.8381 446.7879 531.6128 496.02681 -3284.2335 -395.17163 1306085.7 -1306819.6 3119.2384 48631.318 268.62462 0.014603394 + 1950 -491.07182 2445.6794 169.78853 -2936.7512 457.80204 527.21208 470.1608 -3283.9622 -391.90163 1306101.9 -1306818 1122.0978 48631.318 266.08919 0.018903661 + 2000 -518.41243 2418.604 167.90885 -2937.0165 415.92605 536.62844 480.48912 -3283.7876 -363.72641 1306096.2 -1306818.7 4474.8778 48631.318 263.07743 0.13492637 +Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms + +Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.452 | 12.249 | 12.556 | 13.2 | 54.88 +Bond | 0.71352 | 0.72923 | 0.74557 | 1.3 | 3.27 +Kspace | 5.7189 | 6.0293 | 6.8195 | 18.6 | 27.01 +Neigh | 0.44028 | 0.44044 | 0.44065 | 0.0 | 1.97 +Comm | 0.39667 | 0.40817 | 0.41558 | 1.1 | 1.83 +Output | 0.0019479 | 0.0032187 | 0.0068657 | 3.7 | 0.01 +Modify | 2.413 | 2.4256 | 2.4347 | 0.5 | 10.87 +Other | | 0.0349 | | | 0.16 + +Nlocal: 1375 ave 1407 max 1349 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 8082.5 ave 8114 max 8047 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 325715 ave 343636 max 314954 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 1302860 +Ave neighs/atom = 236.884 +Ave special neighs/atom = 15.6364 +Neighbor list builds = 44 +Dangerous builds = 0 +Total wall time: 0:00:22 diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.data b/examples/USER/misc/local_density/benzene_water/benzene_water.data new file mode 100644 index 0000000000000000000000000000000000000000..96a969670e748cd8bfd7ed5402ffe708ecf26abe --- /dev/null +++ b/examples/USER/misc/local_density/benzene_water/benzene_water.data @@ -0,0 +1,1406 @@ +LAMMPS data file for 380 CG benzene, 1000 CG water particles + + 1380 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 2 atom types + 0 bond types + 0 angle types + 0 dihedral types + 0 improper types + +-1.2865e+01 1.2865e+01 xlo xhi +-1.2865e+01 1.2865e+01 ylo yhi +-6.4829e+01 6.4829e+01 zlo zhi + +Masses + + 1 78.1100 + 2 18.0100 + +Atoms + + 1 1 1 1.13167e+01 1.36833e+00 3.59100e+01 + 2 2 1 -2.54005e+00 -6.77848e+00 6.31800e+01 + 3 3 1 3.45833e+00 2.99833e+00 1.77200e+01 + 4 4 1 -5.29338e+00 -3.98015e+00 1.79183e+01 + 5 5 1 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-1.14501e+01 1.47000e+00 -6.54785e+00 + 1377 1377 2 6.75000e+00 -5.59015e+00 -4.47678e+01 + 1378 1378 2 -5.04005e+00 -1.10502e+01 -2.49178e+01 + 1379 1379 2 -1.02401e+01 -9.00150e-01 -2.25278e+01 + 1380 1380 2 4.23000e+00 -7.94015e+00 -2.07378e+01 + diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.in b/examples/USER/misc/local_density/benzene_water/benzene_water.in new file mode 100644 index 0000000000000000000000000000000000000000..01fb3f27e5d1477d9ad4bdf2fb339a53b4599a1e --- /dev/null +++ b/examples/USER/misc/local_density/benzene_water/benzene_water.in @@ -0,0 +1,62 @@ +# LAMMPS input file for 26.5% benzene mole fraction solution +# with 380 benzene and 1000 water molecules, +# using all possible local density potentials +# between benzene and water +# +# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara +# +# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693 + + + +# Initialize simulation box +dimension 3 +boundary p p p +units real +atom_style molecular + +# Set potential styles +pair_style hybrid/overlay table spline 500 local/density + +# Read molecule data and set initial velocities +read_data benzene_water.data +velocity all create 3.0000e+02 16611 rot yes dist gaussian + +# Assign potentials +pair_coeff 1 1 table benzene_water.pair.table PairBB +pair_coeff 1 2 table benzene_water.pair.table PairWW +pair_coeff 2 2 table benzene_water.pair.table PairBW +pair_coeff * * local/density benzene_water.localdensity.table + +# Recentering during minimization and equilibration +fix recentering all recenter 0.0 0.0 0.0 units box + +# Thermostat & time integration +timestep 2.0 +thermo 100 +thermo_style custom temp ke pe etotal ebond eangle edihed evdwl + +# Minimization +minimize 1.e-4 0.0 10000 10000 + +# Set up integration parameters +fix timeintegration all nve +fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890 + +# Equilibration (for realistic results, run for 5000000 steps) +reset_timestep 0 +run 5000 + +# Turn off recentering during production phase +unfix recentering + +# Setup trajectory output +dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element +dump_modify myDump element B W +dump_modify myDump sort id + +# Production (for realistic results, run for 10000000 steps) +reset_timestep 0 +run 1000 + + diff --git a/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table b/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table new file mode 100644 index 0000000000000000000000000000000000000000..b0d63dbbbf7e88ffaf8dc6c72806cf7bf3532954 --- /dev/null +++ b/examples/USER/misc/local_density/benzene_water/benzene_water.localdensity.table @@ -0,0 +1,2024 @@ +# local density potentials: (B,B), (W,W), (B,W), (W,B) + +4 500 + + 6.5000000e+00 7.5000000e+00 +1 +1 + 0.0000000e+00 2.0000000e+01 4.0080160e-02 + 1.5200000e+00 + 1.5200000e+00 + 1.5200000e+00 + 1.5200000e+00 + 1.5200000e+00 + 1.5200000e+00 + 1.5200000e+00 + 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b/examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..928906edbda6c8cf6f05ff8ac47472e2d7bb46d5 --- /dev/null +++ b/examples/USER/misc/local_density/benzene_water/log.04Sep19.g++.1 @@ -0,0 +1,267 @@ +LAMMPS (7 Aug 2019) +# LAMMPS input file for 26.5% benzene mole fraction solution +# with 380 benzene and 1000 water molecules, +# using all possible local density potentials +# between benzene and water +# +# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara +# +# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693 + + + +# Initialize simulation box +dimension 3 +boundary p p p +units real +atom_style molecular + +# Set potential styles +pair_style hybrid/overlay table spline 500 local/density + +# Read molecule data and set initial velocities +read_data benzene_water.data + orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829) + 1 by 1 by 8 MPI processor grid + reading atoms ... + 1380 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000566959 secs + read_data CPU = 0.00661397 secs +velocity all create 3.0000e+02 16611 rot yes dist gaussian + +# Assign potentials +pair_coeff 1 1 table benzene_water.pair.table PairBB +WARNING: 33 of 500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:483) +WARNING: 150 of 500 distance values in table with relative error + over 1e-06 to re-computed values (../pair_table.cpp:492) +pair_coeff 1 2 table benzene_water.pair.table PairWW +WARNING: 61 of 500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:483) +WARNING: 90 of 500 distance values in table with relative error + over 1e-06 to re-computed values (../pair_table.cpp:492) +pair_coeff 2 2 table benzene_water.pair.table PairBW +WARNING: 108 of 500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:483) +WARNING: 135 of 500 distance values in table with relative error + over 1e-06 to re-computed values (../pair_table.cpp:492) +pair_coeff * * local/density benzene_water.localdensity.table + +# Recentering during minimization and equilibration +fix recentering all recenter 0.0 0.0 0.0 units box + +# Thermostat & time integration +timestep 2.0 +thermo 100 +thermo_style custom temp ke pe etotal ebond eangle edihed evdwl + +# Minimization +minimize 1.e-4 0.0 10000 10000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.25 + ghost atom cutoff = 15.25 + binsize = 7.625, bins = 4 4 18 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair local/density, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes +Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl + 300 1233.1611 4162.3053 5395.4665 0 0 0 4162.3053 + 300 1233.1611 2275.526 3508.6871 0 0 0 2275.526 +Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms + +71.3% CPU use with 8 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + 4162.30533361 2208.86525108 2275.52597861 + Force two-norm initial, final = 259.364 69.3915 + Force max component initial, final = 22.2077 8.31436 + Final line search alpha, max atom move = 2.90022e-12 2.41135e-11 + Iterations, force evaluations = 40 110 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.053192 | 0.23903 | 0.32779 | 17.2 | 67.75 +Bond | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 | 0.0 | 0.00 +Neigh | 0.00044513 | 0.0023614 | 0.0063851 | 5.1 | 0.67 +Comm | 0.015469 | 0.090432 | 0.20295 | 20.0 | 25.63 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.02098 | | | 5.95 + +Nlocal: 172.5 ave 348 max 72 min +Histogram: 5 0 0 0 0 0 0 0 1 2 +Nghost: 2193.62 ave 4352 max 932 min +Histogram: 3 0 0 2 0 0 2 0 0 1 +Neighs: 9700.5 ave 20535 max 3685 min +Histogram: 5 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 77604 +Ave neighs/atom = 56.2348 +Ave special neighs/atom = 0 +Neighbor list builds = 2 +Dangerous builds = 0 + +# Set up integration parameters +fix timeintegration all nve +fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 81890 + +# Equilibration (for realistic results, run for 5000000 steps) +reset_timestep 0 +run 5000 +WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131) +Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes +Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl + 300 1233.1611 2866.9109 4100.0721 0 0 0 2866.9109 + 273.33541 1123.5553 3983.2007 5106.756 0 0 0 3983.2007 + 293.68078 1207.1857 3319.6601 4526.8458 0 0 0 3319.6601 + 314.21462 1291.5908 3389.2178 4680.8086 0 0 0 3389.2178 + 323.77563 1330.8917 3332.9828 4663.8745 0 0 0 3332.9828 + 302.5902 1243.8082 3461.7692 4705.5774 0 0 0 3461.7692 + 295.39324 1214.2249 3411.5727 4625.7976 0 0 0 3411.5727 + 320.52341 1317.5234 3453.1931 4770.7164 0 0 0 3453.1931 + 312.00777 1282.5195 3403.3443 4685.8638 0 0 0 3403.3443 + 307.96774 1265.9128 3429.7809 4695.6937 0 0 0 3429.7809 + 294.75922 1211.6187 3388.8404 4600.4591 0 0 0 3388.8404 + 311.24567 1279.3869 3514.9603 4794.3472 0 0 0 3514.9603 + 306.6152 1260.3531 3447.2011 4707.5542 0 0 0 3447.2011 + 305.23306 1254.6718 3375.5092 4630.181 0 0 0 3375.5092 + 321.62889 1322.0675 3460.2581 4782.3256 0 0 0 3460.2581 + 316.37725 1300.4804 3437.0312 4737.5116 0 0 0 3437.0312 + 322.90522 1327.3139 3389.1262 4716.44 0 0 0 3389.1262 + 307.57893 1264.3146 3359.8491 4624.1637 0 0 0 3359.8491 + 302.22607 1242.3115 3406.1711 4648.4826 0 0 0 3406.1711 + 302.73997 1244.4239 3220.2582 4464.6821 0 0 0 3220.2582 + 303.66194 1248.2137 3318.4629 4566.6765 0 0 0 3318.4629 + 308.73862 1269.0815 3369.5894 4638.671 0 0 0 3369.5894 + 315.60294 1297.2976 3411.2405 4708.5381 0 0 0 3411.2405 + 310.0113 1274.3129 3360.1054 4634.4183 0 0 0 3360.1054 + 302.36229 1242.8714 3326.9845 4569.8559 0 0 0 3326.9845 + 317.78659 1306.2735 3355.4976 4661.7711 0 0 0 3355.4976 + 302.50479 1243.4571 3317.6846 4561.1417 0 0 0 3317.6846 + 304.29249 1250.8056 3423.5068 4674.3124 0 0 0 3423.5068 + 305.99948 1257.8222 3432.9395 4690.7617 0 0 0 3432.9395 + 309.93363 1273.9937 3393.657 4667.6506 0 0 0 3393.657 + 316.14884 1299.5415 3463.0636 4762.6051 0 0 0 3463.0636 + 300.38817 1234.7567 3309.2495 4544.0062 0 0 0 3309.2495 + 311.05735 1278.6128 3304.4418 4583.0546 0 0 0 3304.4418 + 311.11872 1278.865 3291.1891 4570.0542 0 0 0 3291.1891 + 315.74338 1297.8749 3341.3063 4639.1812 0 0 0 3341.3063 + 297.5658 1223.1552 3316.3862 4539.5414 0 0 0 3316.3862 + 311.79033 1281.6257 3357.4556 4639.0813 0 0 0 3357.4556 + 310.93666 1278.1167 3414.7694 4692.8861 0 0 0 3414.7694 + 307.37298 1263.468 3337.3889 4600.8569 0 0 0 3337.3889 + 298.84185 1228.4005 3329.6173 4558.0178 0 0 0 3329.6173 + 310.54684 1276.5143 3351.0852 4627.5995 0 0 0 3351.0852 + 300.0871 1233.5191 3302.2315 4535.7506 0 0 0 3302.2315 + 304.69078 1252.4427 3324.2508 4576.6935 0 0 0 3324.2508 + 313.50714 1288.6827 3330.4088 4619.0915 0 0 0 3330.4088 + 329.80018 1355.6559 3301.86 4657.5159 0 0 0 3301.86 + 304.57609 1251.9713 3365.2938 4617.2652 0 0 0 3365.2938 + 308.73584 1269.0701 3344.4155 4613.4856 0 0 0 3344.4155 + 306.90951 1261.5629 3304.4698 4566.0327 0 0 0 3304.4698 + 308.85761 1269.5707 3392.1511 4661.7218 0 0 0 3392.1511 + 302.78788 1244.6208 3317.0849 4561.7057 0 0 0 3317.0849 + 321.68092 1322.2813 3321.5755 4643.8568 0 0 0 3321.5755 +Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms + +Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s +69.6% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.1872 | 10.542 | 14.607 | 116.7 | 64.65 +Bond | 0.00044084 | 0.00069669 | 0.00095081 | 0.0 | 0.00 +Neigh | 0.026948 | 0.15225 | 0.44344 | 42.0 | 0.93 +Comm | 0.63452 | 4.2953 | 9.49 | 133.9 | 26.34 +Output | 0.0016391 | 0.012378 | 0.050919 | 13.9 | 0.08 +Modify | 0.45894 | 1.2107 | 4.4629 | 116.4 | 7.42 +Other | | 0.09292 | | | 0.57 + +Nlocal: 172.5 ave 380 max 70 min +Histogram: 5 0 0 0 0 0 0 1 1 1 +Nghost: 2213 ave 4440 max 903 min +Histogram: 3 0 0 2 0 0 2 0 0 1 +Neighs: 10042.5 ave 24051 max 3500 min +Histogram: 5 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 80340 +Ave neighs/atom = 58.2174 +Ave special neighs/atom = 0 +Neighbor list builds = 123 +Dangerous builds = 1 + +# Turn off recentering during production phase +unfix recentering + +# Setup trajectory output +dump myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element +dump_modify myDump element B W +dump_modify myDump sort id + +# Production (for realistic results, run for 10000000 steps) +reset_timestep 0 +run 1000 +Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes +Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl + 321.68092 1322.2813 3784.0834 5106.3647 0 0 0 3784.0834 + 310.59763 1276.7231 3318.3283 4595.0513 0 0 0 3318.3283 + 303.39445 1247.1141 3324.1191 4571.2332 0 0 0 3324.1191 + 311.37275 1279.9092 3305.0901 4584.9993 0 0 0 3305.0901 + 311.29071 1279.572 3248.216 4527.788 0 0 0 3248.216 + 314.53456 1292.906 3283.4563 4576.3623 0 0 0 3283.4563 + 316.52595 1301.0916 3258.9171 4560.0087 0 0 0 3258.9171 + 318.92447 1310.9509 3235.6256 4546.5765 0 0 0 3235.6256 + 311.79212 1281.6331 3308.099 4589.7321 0 0 0 3308.099 + 305.52477 1255.8709 3267.6907 4523.5616 0 0 0 3267.6907 + 301.07457 1237.5782 3206.3997 4443.9779 0 0 0 3206.3997 +Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms + +Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s +60.8% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.656 | 2.5078 | 3.5775 | 57.7 | 56.46 +Bond | 0.00013375 | 0.0001854 | 0.0002377 | 0.0 | 0.00 +Neigh | 0.0048757 | 0.029188 | 0.090432 | 18.9 | 0.66 +Comm | 0.51836 | 1.4427 | 2.6285 | 56.9 | 32.48 +Output | 0.083084 | 0.089199 | 0.10333 | 2.3 | 2.01 +Modify | 0.0087376 | 0.019705 | 0.038437 | 8.4 | 0.44 +Other | | 0.3526 | | | 7.94 + +Nlocal: 172.5 ave 388 max 69 min +Histogram: 5 0 0 0 0 0 0 2 0 1 +Nghost: 2207.88 ave 4429 max 896 min +Histogram: 3 0 0 2 0 0 2 0 0 1 +Neighs: 10094.1 ave 24847 max 3403 min +Histogram: 5 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 80753 +Ave neighs/atom = 58.5167 +Ave special neighs/atom = 0 +Neighbor list builds = 23 +Dangerous builds = 0 + + +Total wall time: 0:00:21 diff --git a/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1 b/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..618e9949469be29e8d3ecadc5c32273f6e9e4356 --- /dev/null +++ b/examples/USER/misc/local_density/methanol_implicit_water/log.04Sep19.g++.1 @@ -0,0 +1,226 @@ +LAMMPS (7 Aug 2019) +# LAMMPS input file for 50.0% methanol mole fraction solution +# with 2500 methanol molecules in implicit water. +# +# +# Author: David Rosenberger, van der Vegt Group, TU Darmstadt +# +# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019) + + +# Initialize simulation box +dimension 3 +boundary p p p +units real +atom_style molecular + +# Set potential styles +pair_style hybrid/overlay table spline 500 local/density + +# Read molecule data and set initial velocities +read_data methanol_implicit_water.data + orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 2500 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.00063014 secs + read_data CPU = 0.00599909 secs +velocity all create 3.0000e+02 12142 rot yes dist gaussian + +# Assign potentials +pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM +WARNING: 93 of 500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:483) +WARNING: 254 of 500 distance values in table with relative error + over 1e-06 to re-computed values (../pair_table.cpp:492) +pair_coeff * * local/density methanol_implicit_water.localdensity.table + + + + +#Recentering during minimization and equilibration +fix recentering all recenter 0.0 0.0 0.0 units box + +#Thermostat & time integration +timestep 1.0 +thermo 100 +thermo_style custom etotal ke pe temp evdwl + +#minimization +minimize 1.e-4 0.0 1000 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair local/density, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes +TotEng KinEng PotEng Temp E_vdwl + 1470.3564 2234.7133 -764.35689 300 -764.35689 + 46.496766 2234.7133 -2188.2165 300 -2188.2165 + 7.9030246 2234.7133 -2226.8103 300 -2226.8103 +Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms + +91.4% CPU use with 8 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -764.356892369 -2227.85589084 -2226.81026984 + Force two-norm initial, final = 134.911 3.83896 + Force max component initial, final = 14.1117 1.07422 + Final line search alpha, max atom move = 5.06747e-10 5.44356e-10 + Iterations, force evaluations = 121 154 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41442 | 0.41976 | 0.42434 | 0.5 | 90.47 +Bond | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 | 0.0 | 0.00 +Neigh | 0.0084722 | 0.0090862 | 0.010038 | 0.5 | 1.96 +Comm | 0.022712 | 0.028157 | 0.034072 | 1.9 | 6.07 +Output | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 | 0.0 | 0.01 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.006937 | | | 1.50 + +Nlocal: 312.5 ave 333 max 299 min +Histogram: 2 2 0 0 1 0 2 0 0 1 +Nghost: 2546 ave 2580 max 2517 min +Histogram: 1 1 0 3 0 1 0 0 0 2 +Neighs: 33215.4 ave 37251 max 29183 min +Histogram: 1 0 0 1 2 2 0 1 0 1 + +Total # of neighbors = 265723 +Ave neighs/atom = 106.289 +Ave special neighs/atom = 0 +Neighbor list builds = 6 +Dangerous builds = 0 + +#set up integration parameters +fix timeintegration all nve +fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915 + +#Equilibration (for realistic results, run for 2000000 steps) +reset_timestep 0 +thermo 200 +thermo_style custom etotal ke pe temp evdwl + +#run equilibration +run 2000 +WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131) +Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes +TotEng KinEng PotEng Temp E_vdwl + 177.26822 2234.7133 -2057.4451 300 -2057.4451 + 736.24287 2151.2608 -1415.0179 288.79688 -1415.0179 + 963.07617 2090.6433 -1127.5671 280.65926 -1127.5671 + 1148.9049 2173.1327 -1024.2279 291.73309 -1024.2279 + 1303.6409 2279.8586 -976.21767 306.06055 -976.21767 + 1355.42 2281.0383 -925.61826 306.21892 -925.61826 + 1394.5206 2276.2093 -881.68863 305.57064 -881.68863 + 1346.9764 2215.2973 -868.32091 297.3935 -868.32091 + 1381.3654 2248.8061 -867.44063 301.89189 -867.44063 + 1315.8059 2189.3193 -873.51332 293.90606 -873.51332 + 1314.4456 2209.7431 -895.29752 296.64787 -895.29752 +Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms + +Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s +80.5% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2693 | 5.3572 | 5.457 | 2.1 | 83.84 +Bond | 0.00028825 | 0.00033835 | 0.00039148 | 0.0 | 0.01 +Neigh | 0.0296 | 0.032337 | 0.035071 | 0.9 | 0.51 +Comm | 0.64679 | 0.73397 | 0.80847 | 5.2 | 11.49 +Output | 0.00033498 | 0.00051582 | 0.0015228 | 0.0 | 0.01 +Modify | 0.16395 | 0.18919 | 0.21056 | 3.9 | 2.96 +Other | | 0.07636 | | | 1.19 + +Nlocal: 312.5 ave 337 max 295 min +Histogram: 2 2 0 1 0 0 0 1 1 1 +Nghost: 2551.62 ave 2582 max 2525 min +Histogram: 2 1 0 0 1 1 1 0 1 1 +Neighs: 33241.8 ave 37659 max 29705 min +Histogram: 2 0 0 2 2 0 0 0 1 1 + +Total # of neighbors = 265934 +Ave neighs/atom = 106.374 +Ave special neighs/atom = 0 +Neighbor list builds = 21 +Dangerous builds = 0 + +#turn off recentering during production run +unfix recentering + + +#setup trajectory output +dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element +dump_modify myDump element M +dump_modify myDump sort id + +#run production (for realistic results, run for 10000000 steps) +reset_timestep 0 +thermo 1000 +thermo_style custom etotal ke pe temp evdwl +run 10000 +Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes +TotEng KinEng PotEng Temp E_vdwl + 1442.5428 2209.7431 -767.20027 296.64787 -767.20027 + 1391.8624 2262.6889 -870.82656 303.7556 -870.82656 + 1375.914 2244.6176 -868.7036 301.3296 -868.7036 + 1345.9064 2227.2324 -881.32599 298.99573 -881.32599 + 1379.2334 2278.1156 -898.88222 305.82657 -898.88222 + 1389.7928 2255.8062 -866.01341 302.83163 -866.01341 + 1380.4549 2258.2108 -877.75582 303.15443 -877.75582 + 1380.8489 2256.9432 -876.09428 302.98426 -876.09428 + 1326.5151 2225.7408 -899.22577 298.79549 -899.22577 + 1376.6025 2253.0128 -876.41028 302.45662 -876.41028 + 1331.0008 2218.1033 -887.10258 297.77019 -887.10258 +Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms + +Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s +89.3% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 21.635 | 21.916 | 22.237 | 3.9 | 86.08 +Bond | 0.0011308 | 0.0013149 | 0.0016932 | 0.5 | 0.01 +Neigh | 0.14593 | 0.15675 | 0.16667 | 1.9 | 0.62 +Comm | 1.3789 | 1.7502 | 1.9558 | 13.7 | 6.87 +Output | 0.34664 | 0.82927 | 1.2013 | 32.8 | 3.26 +Modify | 0.24904 | 0.25842 | 0.26907 | 1.2 | 1.02 +Other | | 0.5475 | | | 2.15 + +Nlocal: 312.5 ave 327 max 298 min +Histogram: 2 0 0 1 1 0 1 1 1 1 +Nghost: 2575 ave 2601 max 2559 min +Histogram: 2 0 3 1 0 0 0 0 1 1 +Neighs: 33223.2 ave 35920 max 30303 min +Histogram: 1 1 1 1 0 1 0 0 0 3 + +Total # of neighbors = 265786 +Ave neighs/atom = 106.314 +Ave special neighs/atom = 0 +Neighbor list builds = 103 +Dangerous builds = 0 + + +Total wall time: 0:00:32 diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data new file mode 100644 index 0000000000000000000000000000000000000000..1dd9eccc7c61616e493a6650673bbe8e592ac75d --- /dev/null +++ b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.data @@ -0,0 +1,2525 @@ +LAMMPS Description + + 2500 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 1 atom types + 0 bond types + 0 angle types + 0 dihedral types + 0 improper types + +-3.1123e+01 3.1123e+01 xlo xhi +-3.1123e+01 3.1123e+01 ylo yhi +-3.1123e+01 3.1123e+01 zlo zhi + +Masses + + 1 32.0000 + +Atoms + + 1 1 1 -1.20055e+01 1.00800e+01 5.26000e+00 + 2 2 1 -5.60545e+00 2.34700e+01 3.10400e+01 + 3 3 1 1.33900e+01 1.50700e+01 -1.56654e+01 + 4 4 1 -3.57545e+00 -1.71754e+01 -7.17545e+00 + 5 5 1 1.09000e+01 1.67100e+01 -2.57554e+01 + 6 6 1 1.96400e+01 -6.07545e+00 -2.72454e+01 + 7 7 1 -7.56545e+00 -1.92354e+01 -2.37154e+01 + 8 8 1 -5.72545e+00 -2.45654e+01 -2.34154e+01 + 9 9 1 -1.71655e+01 2.46700e+01 1.76300e+01 + 10 10 1 8.06000e+00 4.73000e+00 -7.34545e+00 + 11 11 1 2.32300e+01 -2.01054e+01 1.78600e+01 + 12 12 1 -2.05955e+01 1.44500e+01 -6.35545e+00 + 13 13 1 1.80700e+01 2.19800e+01 -4.22545e+00 + 14 14 1 -1.26355e+01 -2.92545e+00 -2.09154e+01 + 15 15 1 -2.05255e+01 -2.12254e+01 -2.21454e+01 + 16 16 1 6.69000e+00 2.60700e+01 1.22700e+01 + 17 17 1 1.08600e+01 -2.00054e+01 -2.82854e+01 + 18 18 1 -1.89255e+01 3.30000e-01 1.15200e+01 + 19 19 1 1.85400e+01 1.31900e+01 -7.98545e+00 + 20 20 1 -1.49055e+01 1.45900e+01 -2.19354e+01 + 21 21 1 1.91400e+01 -2.43054e+01 -2.54454e+01 + 22 22 1 1.04200e+01 -2.94954e+01 -2.95654e+01 + 23 23 1 -7.37545e+00 2.08500e+01 2.58700e+01 + 24 24 1 1.25600e+01 2.80000e-01 -1.38054e+01 + 25 25 1 -2.11055e+01 1.01500e+01 3.10000e+01 + 26 26 1 2.78800e+01 -1.10254e+01 1.86300e+01 + 27 27 1 2.17000e+00 -3.01454e+01 1.67700e+01 + 28 28 1 2.76700e+01 1.44600e+01 -1.37954e+01 + 29 29 1 2.15200e+01 -3.45545e+00 4.45000e+00 + 30 30 1 -8.15545e+00 1.89500e+01 -2.73954e+01 + 31 31 1 -5.89545e+00 -1.45954e+01 2.62100e+01 + 32 32 1 2.29600e+01 -1.23154e+01 2.91800e+01 + 33 33 1 4.87000e+00 -2.65754e+01 8.54000e+00 + 34 34 1 1.93000e+00 -1.43554e+01 1.85200e+01 + 35 35 1 -2.78355e+01 -2.84754e+01 -2.38454e+01 + 36 36 1 3.08000e+00 -2.54354e+01 1.99500e+01 + 37 37 1 2.12700e+01 -6.71545e+00 1.28000e+00 + 38 38 1 -3.45545e+00 -2.41754e+01 1.49600e+01 + 39 39 1 2.54700e+01 1.63000e+01 6.99000e+00 + 40 40 1 -1.80855e+01 2.44800e+01 4.97000e+00 + 41 41 1 1.28400e+01 -1.15446e-01 -2.87954e+01 + 42 42 1 -7.86545e+00 2.17000e+00 1.67100e+01 + 43 43 1 2.42300e+01 -8.29545e+00 2.04200e+01 + 44 44 1 -4.35545e+00 4.68000e+00 2.66200e+01 + 45 45 1 -1.53655e+01 -1.15154e+01 1.35000e+00 + 46 46 1 -2.67255e+01 -2.33054e+01 -3.01254e+01 + 47 47 1 1.13800e+01 -3.05554e+01 -2.18054e+01 + 48 48 1 2.05100e+01 1.55100e+01 -6.31545e+00 + 49 49 1 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b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.in @@ -0,0 +1,68 @@ +# LAMMPS input file for 50.0% methanol mole fraction solution +# with 2500 methanol molecules in implicit water. +# +# +# Author: David Rosenberger, van der Vegt Group, TU Darmstadt +# +# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019) + + +# Initialize simulation box +dimension 3 +boundary p p p +units real +atom_style molecular + +# Set potential styles +pair_style hybrid/overlay table spline 500 local/density + +# Read molecule data and set initial velocities +read_data methanol_implicit_water.data +velocity all create 3.0000e+02 12142 rot yes dist gaussian + +# Assign potentials +pair_coeff 1 1 table methanol_implicit_water.pair.table PairMM +pair_coeff * * local/density methanol_implicit_water.localdensity.table + + + + +#Recentering during minimization and equilibration +fix recentering all recenter 0.0 0.0 0.0 units box + +#Thermostat & time integration +timestep 1.0 +thermo 100 +thermo_style custom etotal ke pe temp evdwl + +#minimization +minimize 1.e-4 0.0 1000 1000 + +#set up integration parameters +fix timeintegration all nve +fix thermostat all langevin 3.0000e+02 3.0000e+02 1.0000e+02 59915 + +#Equilibration (for realistic results, run for 2000000 steps) +reset_timestep 0 +thermo 200 +thermo_style custom etotal ke pe temp evdwl + +#run equilibration +run 2000 + +#turn off recentering during production run +unfix recentering + + +#setup trajectory output +dump myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element +dump_modify myDump element M +dump_modify myDump sort id + +#run production (for realistic results, run for 10000000 steps) +reset_timestep 0 +thermo 1000 +thermo_style custom etotal ke pe temp evdwl +run 10000 + + diff --git a/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table new file mode 100644 index 0000000000000000000000000000000000000000..b9b4a082bc5766686ba0df7802f3f6772d0a9173 --- /dev/null +++ b/examples/USER/misc/local_density/methanol_implicit_water/methanol_implicit_water.localdensity.table @@ -0,0 +1,509 @@ +#LOCAL DENSITY POTENTIALS + +1 500 + + 5.3000000e+00 6.3000000e+00 +1 +1 + 0.0000000e+00 2.6000000e+01 5.2104208e-02 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 1.4810000e-01 + 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0.0000e+00 +486 9.7194e+00 0.0000e+00 0.0000e+00 +487 9.7395e+00 0.0000e+00 0.0000e+00 +488 9.7595e+00 0.0000e+00 0.0000e+00 +489 9.7796e+00 0.0000e+00 0.0000e+00 +490 9.7996e+00 0.0000e+00 0.0000e+00 +491 9.8196e+00 0.0000e+00 0.0000e+00 +492 9.8397e+00 0.0000e+00 0.0000e+00 +493 9.8597e+00 0.0000e+00 0.0000e+00 +494 9.8798e+00 0.0000e+00 0.0000e+00 +495 9.8998e+00 0.0000e+00 0.0000e+00 +496 9.9198e+00 0.0000e+00 0.0000e+00 +497 9.9399e+00 0.0000e+00 0.0000e+00 +498 9.9599e+00 0.0000e+00 0.0000e+00 +499 9.9800e+00 0.0000e+00 0.0000e+00 +500 1.0000e+01 0.0000e+00 0.0000e+00 + + diff --git a/examples/USER/phonon/dynamical_matrix_command/python/README.md b/examples/USER/phonon/dynamical_matrix_command/python/README.md new file mode 100755 index 0000000000000000000000000000000000000000..5b3c11febd067a8e5e002bdaa65c4dff5b377db7 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/python/README.md @@ -0,0 +1,12 @@ +# LAMMPS LATTICE DYNAMICS COMMANDS + +## DYNAMICAL MATRIX CALCULATOR + +This directory contains the ingredients to calculate a dynamical matrix with python. + +Example: +``` +python dynmat.py +``` + +## Requires: MANYBODY and MOLECULE packages and the Python Library Interface diff --git a/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py b/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py new file mode 100644 index 0000000000000000000000000000000000000000..2a3a0b5a2f839fa8a4cf3625f109a46e810559f2 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/python/dynmat.py @@ -0,0 +1,42 @@ +"""Made by Charlie Sievers Ph.D. Candidate, UC Davis, Donadio Lab 2019""" +# from mpi4py import MPI +from lammps import lammps +import numpy as np + +# comm = MPI.COMM_WORLD +# rank = comm.Get_rank() + +""" LAMMPS VARIABLES """ + +# data files +infile = "silicon_input_file.lmp" +ff_file = "ff-silicon.lmp" + +# full output useful for testing +lmp = lammps() + +# reduced output useful reducing IO for production runs +# lmp = lammps(cmdargs=["-screen", "none", "-log", "none"]) + +# lammps commands +lmp.command("atom_style full") +lmp.command("units metal") +lmp.command("processors * * *") +lmp.command("neighbor 1 bin") +lmp.command("boundary p p p") + +# read data and force field file +lmp.command("read_data {}".format(infile)) +lmp.file("{}".format(ff_file)) + +lmp.command("dynamical_matrix all eskm 0.000001 file dynmat.dat") + +dynmat = np.loadtxt("dynmat.dat") +dynlen = int(3*np.sqrt(len(dynmat)/3)) +dynmat = dynmat.reshape((dynlen, dynlen)) + +eigvals, eigvecs = np.linalg.eig(dynmat) + +# frequencies in THz +omegas = np.sqrt(np.abs(eigvals)) +print(omegas) diff --git a/examples/gcmc/CO2.txt b/examples/gcmc/CO2.txt index 72e593e3f2b1d9da040ba3e7bc9424e759f24fb7..c9fb8616c223a33df7cfa10870a783190dc684b3 100644 --- a/examples/gcmc/CO2.txt +++ b/examples/gcmc/CO2.txt @@ -12,15 +12,15 @@ Coords Types -1 1 -2 2 -3 2 +1 1 +2 2 +3 2 -Charges +Charges -1 0.7 -2 -0.35 -3 -0.35 +1 0.7 +2 -0.35 +3 -0.35 Bonds diff --git a/examples/gcmc/H2O.txt b/examples/gcmc/H2O.txt index b56f869693ea2be0da413b2260de353e512c80e7..e5a5e4fe9312d985ea46162b384ec96f6b0ebc25 100644 --- a/examples/gcmc/H2O.txt +++ b/examples/gcmc/H2O.txt @@ -1,4 +1,4 @@ -# CO2 molecule file. TraPPE model. +# Water molecule. SPC/E model. 3 atoms 2 bonds @@ -12,15 +12,15 @@ Coords Types -1 1 -2 2 -3 2 +1 1 +2 2 +3 2 -Charges +Charges 1 -0.8472 -2 0.4236 -3 0.4236 +2 0.4236 +3 0.4236 Bonds diff --git a/examples/gjf/README.md b/examples/gjf/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e6886cb2dd03be5aa3f28a506a3ee7e91aca1a1e --- /dev/null +++ b/examples/gjf/README.md @@ -0,0 +1,13 @@ +# LAMMPS GJF-2GJ THERMOSTAT EXAMPLE + +## GJF-2GJ THERMOSTAT + +This directory contains the ingredients to run an NVT simulation using the GJF-2GJ thermostat. + +Example: +``` +NP=4 #number of processors +mpirun -np $NP lmp_mpi -in.gjf.vhalf +``` + +## Required LAMMPS packages: MOLECULE package diff --git a/examples/gjf/argon.lmp b/examples/gjf/argon.lmp new file mode 100644 index 0000000000000000000000000000000000000000..00214b4c5472f461dc4648dd187d214e95b1b933 --- /dev/null +++ b/examples/gjf/argon.lmp @@ -0,0 +1,886 @@ +LAMMPS description + + 864 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 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index 0000000000000000000000000000000000000000..b6f7bc931a5cbfe17b426cfcb3ad99cee6902b50 --- /dev/null +++ b/examples/gjf/ff-argon.lmp @@ -0,0 +1,20 @@ +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Ar equal 1 + +############# +#Atom Masses# +############# + +mass ${Ar} 39.903 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style lj/cubic +pair_coeff * * 0.0102701 3.42 + diff --git a/examples/gjf/in.gjf.vfull b/examples/gjf/in.gjf.vfull new file mode 100644 index 0000000000000000000000000000000000000000..40512ac37abfe67281a0a5d854fab627b2c73609 --- /dev/null +++ b/examples/gjf/in.gjf.vfull @@ -0,0 +1,23 @@ +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + +include ff-argon.lmp + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix lang all langevin 10 10 1 26488 gjf vfull +fix nve all nve + +thermo 200 +run 5000 + + diff --git a/examples/gjf/in.gjf.vhalf b/examples/gjf/in.gjf.vhalf new file mode 100644 index 0000000000000000000000000000000000000000..63fb8bd46790c880530856ef52ae237e990c9feb --- /dev/null +++ b/examples/gjf/in.gjf.vhalf @@ -0,0 +1,23 @@ +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + +include ff-argon.lmp + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix lang all langevin 10 10 1 26488 gjf vhalf +fix nve all nve + +thermo 200 +run 5000 + + diff --git a/examples/gjf/log.15Oct19.gjf.vfull.g++.1 b/examples/gjf/log.15Oct19.gjf.vfull.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..e3e9cce1248698e09773314b49eda76a9a397c27 --- /dev/null +++ b/examples/gjf/log.15Oct19.gjf.vfull.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (19 Sep 2019) + using 1 OpenMP thread(s) per MPI task +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + orthogonal box = (0 0 0) to (32.146 32.146 32.146) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 864 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000150019 secs + read_data CPU = 0.001946 secs + +include ff-argon.lmp +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Ar equal 1 + +############# +#Atom Masses# +############# + +mass ${Ar} 39.903 +mass 1 39.903 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style lj/cubic +pair_coeff * * 0.0102701 3.42 + + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix lang all langevin 10 10 1 26488 gjf vfull +fix nve all nve + +thermo 200 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.94072 + ghost atom cutoff = 6.94072 + binsize = 3.47036, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.875 | 6.875 | 6.875 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 11.080223 -56.207655 0 -54.97164 37.215524 + 200 8.2588471 -55.073602 0 -54.152316 339.80416 + 400 8.1427292 -55.072244 0 -54.16391 338.91883 + 600 8.7595618 -55.066739 0 -54.089596 344.25426 + 800 8.550633 -55.148315 0 -54.194479 318.9385 + 1000 8.5394337 -55.125709 0 -54.173122 326.59471 + 1200 8.565973 -55.114892 0 -54.159345 328.5193 + 1400 8.2092914 -55.109233 0 -54.193475 329.56161 + 1600 8.209495 -55.138161 0 -54.22238 321.39971 + 1800 8.4039924 -55.13355 0 -54.196072 322.64214 + 2000 8.4548937 -55.062994 0 -54.119838 343.29888 + 2200 8.3775139 -55.13364 0 -54.199116 323.63744 + 2400 8.537332 -55.163702 0 -54.21135 315.62864 + 2600 8.672488 -55.112054 0 -54.144625 330.1106 + 2800 8.3000218 -55.147275 0 -54.221396 318.73112 + 3000 8.3552421 -55.135164 0 -54.203124 323.53075 + 3200 8.4126798 -55.135753 0 -54.197306 321.48817 + 3400 8.4986413 -55.135408 0 -54.187372 323.42951 + 3600 8.38431 -55.103932 0 -54.16865 330.68929 + 3800 8.8262454 -55.103648 0 -54.119067 332.97779 + 4000 7.9658136 -55.120402 0 -54.231803 324.9595 + 4200 8.2265544 -55.129011 0 -54.211327 323.87069 + 4400 8.1253738 -55.153089 0 -54.246691 316.304 + 4600 8.2010823 -55.124053 0 -54.20921 325.98402 + 4800 8.5512149 -55.075877 0 -54.121976 338.30137 + 5000 8.4737659 -55.158604 0 -54.213343 316.22418 +Loop time of 2.73236 on 1 procs for 5000 steps with 864 atoms + +Performance: 15810.507 ns/day, 0.002 hours/ns, 1829.920 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4262 | 1.4262 | 1.4262 | 0.0 | 52.20 +Bond | 0.00042836 | 0.00042836 | 0.00042836 | 0.0 | 0.02 +Neigh | 0.12819 | 0.12819 | 0.12819 | 0.0 | 4.69 +Comm | 0.058611 | 0.058611 | 0.058611 | 0.0 | 2.15 +Output | 0.00047283 | 0.00047283 | 0.00047283 | 0.0 | 0.02 +Modify | 1.0924 | 1.0924 | 1.0924 | 0.0 | 39.98 +Other | | 0.02605 | | | 0.95 + +Nlocal: 864 ave 864 max 864 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1593 ave 1593 max 1593 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18143 ave 18143 max 18143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18143 +Ave neighs/atom = 20.9988 +Ave special neighs/atom = 0 +Neighbor list builds = 158 +Dangerous builds = 5 + + +Total wall time: 0:00:02 diff --git a/examples/gjf/log.15Oct19.gjf.vfull.g++.4 b/examples/gjf/log.15Oct19.gjf.vfull.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..95caed5dc923f95ebbb0cb3669df59b9107bf0cb --- /dev/null +++ b/examples/gjf/log.15Oct19.gjf.vfull.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (19 Sep 2019) + using 1 OpenMP thread(s) per MPI task +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + orthogonal box = (0 0 0) to (32.146 32.146 32.146) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 864 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000556268 secs + read_data CPU = 0.003817 secs + +include ff-argon.lmp +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Ar equal 1 + +############# +#Atom Masses# +############# + +mass ${Ar} 39.903 +mass 1 39.903 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style lj/cubic +pair_coeff * * 0.0102701 3.42 + + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix lang all langevin 10 10 1 26488 gjf vfull +fix nve all nve + +thermo 200 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.94072 + ghost atom cutoff = 6.94072 + binsize = 3.47036, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.808 | 6.808 | 6.808 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 11.080228 -56.207655 0 -54.971639 37.215541 + 200 8.4818184 -55.127334 0 -54.181174 324.96159 + 400 8.5960916 -55.09236 0 -54.133453 334.83136 + 600 8.1607556 -55.073136 0 -54.162791 339.035 + 800 8.8350489 -55.133382 0 -54.147819 324.48149 + 1000 8.5692704 -55.118463 0 -54.162548 327.26328 + 1200 8.4174147 -55.126297 0 -54.187322 324.4248 + 1400 8.6362603 -55.123075 0 -54.159688 326.7798 + 1600 8.222512 -55.153799 0 -54.236565 317.8147 + 1800 8.324523 -55.116698 0 -54.188085 327.35373 + 2000 7.9615959 -55.155825 0 -54.267697 315.37215 + 2200 8.495968 -55.083943 0 -54.136205 336.67775 + 2400 7.7926986 -55.044816 0 -54.175529 344.87758 + 2600 8.1551351 -55.069404 0 -54.159687 339.60901 + 2800 8.2593599 -55.084151 0 -54.162807 336.54935 + 3000 8.2860869 -55.110296 0 -54.185971 328.99074 + 3200 8.4074534 -55.123576 0 -54.185712 326.06823 + 3400 8.6694364 -55.128925 0 -54.161836 324.67512 + 3600 8.5718984 -55.129861 0 -54.173653 325.20586 + 3800 8.508102 -55.099093 0 -54.150001 333.91437 + 4000 8.2966658 -55.117782 0 -54.192276 327.13516 + 4200 8.7641728 -55.135792 0 -54.158136 324.00844 + 4400 8.8827909 -55.096369 0 -54.10548 335.08467 + 4600 8.7666577 -55.127213 0 -54.149279 326.15539 + 4800 8.6670762 -55.163395 0 -54.19657 316.48383 + 5000 8.1893094 -55.073756 0 -54.160226 337.95271 +Loop time of 0.870594 on 4 procs for 5000 steps with 864 atoms + +Performance: 49621.267 ns/day, 0.000 hours/ns, 5743.202 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.33582 | 0.35125 | 0.3724 | 2.3 | 40.35 +Bond | 0.00030267 | 0.00031316 | 0.00033538 | 0.0 | 0.04 +Neigh | 0.034246 | 0.03479 | 0.035904 | 0.4 | 4.00 +Comm | 0.15068 | 0.17419 | 0.19191 | 3.6 | 20.01 +Output | 0.00044776 | 0.00054703 | 0.00083177 | 0.0 | 0.06 +Modify | 0.27679 | 0.28079 | 0.28849 | 0.9 | 32.25 +Other | | 0.02871 | | | 3.30 + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 888.75 ave 899 max 876 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 4536 ave 4737 max 4335 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 18144 +Ave neighs/atom = 21 +Ave special neighs/atom = 0 +Neighbor list builds = 178 +Dangerous builds = 11 + + +Total wall time: 0:00:00 diff --git a/examples/gjf/log.15Oct19.gjf.vhalf.g++.1 b/examples/gjf/log.15Oct19.gjf.vhalf.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..a87b20a88779346f43c2c3b72343543396aff19a --- /dev/null +++ b/examples/gjf/log.15Oct19.gjf.vhalf.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (19 Sep 2019) + using 1 OpenMP thread(s) per MPI task +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + orthogonal box = (0 0 0) to (32.146 32.146 32.146) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 864 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000147804 secs + read_data CPU = 0.00194898 secs + +include ff-argon.lmp +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Ar equal 1 + +############# +#Atom Masses# +############# + +mass ${Ar} 39.903 +mass 1 39.903 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style lj/cubic +pair_coeff * * 0.0102701 3.42 + + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix lang all langevin 10 10 1 26488 gjf vhalf +fix nve all nve + +thermo 200 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.94072 + ghost atom cutoff = 6.94072 + binsize = 3.47036, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.5 | 6.5 | 6.5 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 11.080223 -56.207655 0 -54.97164 37.215524 + 200 9.8808568 -55.073602 0 -53.971378 345.62207 + 400 9.8712816 -55.072244 0 -53.971088 345.11889 + 600 10.528988 -55.066739 0 -53.892214 350.60093 + 800 10.167171 -55.148315 0 -54.014152 324.73679 + 1000 10.029026 -55.125709 0 -54.006956 331.93766 + 1200 10.194424 -55.114892 0 -53.977688 334.36032 + 1400 9.3473846 -55.109233 0 -54.066518 333.64378 + 1600 9.7774071 -55.138161 0 -54.047477 327.02358 + 1800 9.9814275 -55.13355 0 -54.020107 328.30017 + 2000 10.2515 -55.062994 0 -53.919424 349.74304 + 2200 9.8126922 -55.13364 0 -54.039019 328.78521 + 2400 10.044314 -55.163702 0 -54.043244 321.03397 + 2600 10.543316 -55.112054 0 -53.935932 336.82099 + 2800 9.7874375 -55.147275 0 -54.055472 324.06626 + 3000 9.7703821 -55.135164 0 -54.045263 328.60665 + 3200 10.141958 -55.135753 0 -54.004402 327.69084 + 3400 10.160576 -55.135408 0 -54.00198 329.39063 + 3600 10.044652 -55.103932 0 -53.983436 336.64469 + 3800 10.662403 -55.103648 0 -53.914241 339.56382 + 4000 9.2921047 -55.120402 0 -54.083853 329.71671 + 4200 9.8744553 -55.129011 0 -54.027501 329.78147 + 4400 9.4085964 -55.153089 0 -54.103546 320.90673 + 4600 9.5463801 -55.124053 0 -54.05914 330.80941 + 4800 10.223884 -55.075877 0 -53.935387 344.30099 + 5000 9.6243338 -55.158604 0 -54.084996 320.3511 +Loop time of 2.29551 on 1 procs for 5000 steps with 864 atoms + +Performance: 18819.358 ns/day, 0.001 hours/ns, 2178.166 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4393 | 1.4393 | 1.4393 | 0.0 | 62.70 +Bond | 0.0004441 | 0.0004441 | 0.0004441 | 0.0 | 0.02 +Neigh | 0.12136 | 0.12136 | 0.12136 | 0.0 | 5.29 +Comm | 0.059342 | 0.059342 | 0.059342 | 0.0 | 2.59 +Output | 0.00046968 | 0.00046968 | 0.00046968 | 0.0 | 0.02 +Modify | 0.64937 | 0.64937 | 0.64937 | 0.0 | 28.29 +Other | | 0.02522 | | | 1.10 + +Nlocal: 864 ave 864 max 864 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1593 ave 1593 max 1593 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18143 ave 18143 max 18143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18143 +Ave neighs/atom = 20.9988 +Ave special neighs/atom = 0 +Neighbor list builds = 158 +Dangerous builds = 5 + + +Total wall time: 0:00:02 diff --git a/examples/gjf/log.15Oct19.gjf.vhalf.g++.4 b/examples/gjf/log.15Oct19.gjf.vhalf.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..a70a67a89c1edcb55247ca01cea9d4d0ff1fe944 --- /dev/null +++ b/examples/gjf/log.15Oct19.gjf.vhalf.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (19 Sep 2019) + using 1 OpenMP thread(s) per MPI task +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + orthogonal box = (0 0 0) to (32.146 32.146 32.146) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 864 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000315903 secs + read_data CPU = 0.0653752 secs + +include ff-argon.lmp +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Ar equal 1 + +############# +#Atom Masses# +############# + +mass ${Ar} 39.903 +mass 1 39.903 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style lj/cubic +pair_coeff * * 0.0102701 3.42 + + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix lang all langevin 10 10 1 26488 gjf vhalf +fix nve all nve + +thermo 200 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.94072 + ghost atom cutoff = 6.94072 + binsize = 3.47036, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.433 | 6.433 | 6.433 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 11.080228 -56.207655 0 -54.971639 37.215541 + 200 9.8046716 -55.127334 0 -54.033608 329.70647 + 400 10.174622 -55.09236 0 -53.957366 340.49331 + 600 9.9812299 -55.073136 0 -53.959714 345.56477 + 800 10.512874 -55.133382 0 -53.960655 330.4996 + 1000 9.9587885 -55.118463 0 -54.007545 332.24728 + 1200 10.236607 -55.126297 0 -53.984388 330.94998 + 1400 10.134679 -55.123075 0 -53.992537 332.15441 + 1600 9.8934078 -55.153799 0 -54.050174 323.80795 + 1800 10.064966 -55.116698 0 -53.993936 333.59644 + 2000 9.6736107 -55.155825 0 -54.076719 321.5129 + 2200 10.264537 -55.083943 0 -53.938918 343.02135 + 2400 9.5640032 -55.044816 0 -53.977937 351.23099 + 2600 9.6581077 -55.069404 0 -53.992028 344.99996 + 2800 9.9622575 -55.084151 0 -53.972846 342.6574 + 3000 9.8724909 -55.110296 0 -54.009005 334.68094 + 3200 10.032027 -55.123576 0 -54.004488 331.89534 + 3400 10.221132 -55.128925 0 -53.988742 330.24082 + 3600 10.085802 -55.129861 0 -54.004774 330.63601 + 3800 10.098545 -55.099093 0 -53.972585 339.61905 + 4000 10.000257 -55.117782 0 -54.002238 333.24569 + 4200 10.20477 -55.135792 0 -53.997435 329.17565 + 4400 10.545132 -55.096369 0 -53.920044 341.04725 + 4600 10.376108 -55.127213 0 -53.969743 331.92825 + 4800 10.247392 -55.163395 0 -54.020283 322.15219 + 5000 9.7753102 -55.073756 0 -53.983305 343.64146 +Loop time of 1.19785 on 4 procs for 5000 steps with 864 atoms + +Performance: 36064.674 ns/day, 0.001 hours/ns, 4174.152 timesteps/s +88.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.36387 | 0.38652 | 0.44086 | 5.1 | 32.27 +Bond | 0.00028847 | 0.00030833 | 0.000338 | 0.0 | 0.03 +Neigh | 0.033934 | 0.034959 | 0.036917 | 0.6 | 2.92 +Comm | 0.39292 | 0.47821 | 0.52198 | 7.3 | 39.92 +Output | 0.00050343 | 0.0012343 | 0.0023338 | 1.9 | 0.10 +Modify | 0.1605 | 0.17963 | 0.19457 | 2.9 | 15.00 +Other | | 0.117 | | | 9.77 + +Nlocal: 216 ave 216 max 216 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 888.75 ave 899 max 876 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 4536 ave 4737 max 4335 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 18144 +Ave neighs/atom = 21 +Ave special neighs/atom = 0 +Neighbor list builds = 178 +Dangerous builds = 11 + + +Total wall time: 0:00:01 diff --git a/examples/snap/WBe_Wood_PRB2019.snap b/examples/snap/WBe_Wood_PRB2019.snap new file mode 120000 index 0000000000000000000000000000000000000000..35454e3eb8fdb90affca0d46667ce92cfe88e471 --- /dev/null +++ b/examples/snap/WBe_Wood_PRB2019.snap @@ -0,0 +1 @@ +../../potentials/WBe_Wood_PRB2019.snap \ No newline at end of file diff --git a/examples/snap/WBe_Wood_PRB2019.snapcoeff b/examples/snap/WBe_Wood_PRB2019.snapcoeff new file mode 120000 index 0000000000000000000000000000000000000000..b734e526101b9855de8ffa7e071cdf71817087da --- /dev/null +++ b/examples/snap/WBe_Wood_PRB2019.snapcoeff @@ -0,0 +1 @@ +../../potentials/WBe_Wood_PRB2019.snapcoeff \ No newline at end of file diff --git a/examples/snap/WBe_Wood_PRB2019.snapparam b/examples/snap/WBe_Wood_PRB2019.snapparam new file mode 120000 index 0000000000000000000000000000000000000000..8f3530ffd639ae8c43585157a2978cb56dccbb17 --- /dev/null +++ b/examples/snap/WBe_Wood_PRB2019.snapparam @@ -0,0 +1 @@ +../../potentials/WBe_Wood_PRB2019.snapparam \ No newline at end of file diff --git a/examples/snap/in.snap.Mo_Chen b/examples/snap/in.snap.Mo_Chen index 007bce2462c31bd4af51b8b84d71b9df09a8ede2..bb9fb0900ddbae22842cbcaa42baa08faf12f6b0 100644 --- a/examples/snap/in.snap.Mo_Chen +++ b/examples/snap/in.snap.Mo_Chen @@ -1,11 +1,11 @@ -# Demonstrate SNAP Ta potential +# Demonstrate SNAP Mo potential # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 3.160 -units metal +units metal # generate the box and atom positions using a BCC lattice @@ -13,12 +13,12 @@ variable nx equal ${nrep} variable ny equal ${nrep} variable nz equal ${nrep} -boundary p p p +boundary p p p lattice bcc $a -region box block 0 ${nx} 0 ${ny} 0 ${nz} -create_box 1 box -create_atoms 1 box +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box mass 1 183.84 @@ -28,7 +28,7 @@ include Mo_Chen_PRM2017.snap # Setup output -thermo 10 +thermo 10 thermo_modify norm yes # Set up NVE run diff --git a/examples/snap/in.snap.Ta06A b/examples/snap/in.snap.Ta06A index 38a24b8c0644cc404dd285e739da8ba14e29ab5f..0ca5275e9710e85924f20040c94991f3077bf61c 100644 --- a/examples/snap/in.snap.Ta06A +++ b/examples/snap/in.snap.Ta06A @@ -5,7 +5,7 @@ variable nsteps index 100 variable nrep equal 4 variable a equal 3.316 -units metal +units metal # generate the box and atom positions using a BCC lattice @@ -13,12 +13,12 @@ variable nx equal ${nrep} variable ny equal ${nrep} variable nz equal ${nrep} -boundary p p p +boundary p p p lattice bcc $a -region box block 0 ${nx} 0 ${ny} 0 ${nz} -create_box 1 box -create_atoms 1 box +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box mass 1 180.88 @@ -28,7 +28,7 @@ include Ta06A.snap # Setup output -thermo 10 +thermo 10 thermo_modify norm yes # Set up NVE run diff --git a/examples/snap/in.snap.W.2940 b/examples/snap/in.snap.W.2940 index e1abf861e6f0b4a981de55f510acb33a5caca07b..7e59b5198e384466c3f607c4a44576671e972dd5 100644 --- a/examples/snap/in.snap.W.2940 +++ b/examples/snap/in.snap.W.2940 @@ -1,11 +1,11 @@ -# Demonstrate SNAP Ta potential +# Demonstrate SNAP W potential # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 3.1803 -units metal +units metal # generate the box and atom positions using a BCC lattice @@ -13,12 +13,12 @@ variable nx equal ${nrep} variable ny equal ${nrep} variable nz equal ${nrep} -boundary p p p +boundary p p p lattice bcc $a -region box block 0 ${nx} 0 ${ny} 0 ${nz} -create_box 1 box -create_atoms 1 box +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 1 box +create_atoms 1 box mass 1 183.84 @@ -28,7 +28,7 @@ include W_2940_2017_2.snap # Setup output -thermo 10 +thermo 10 thermo_modify norm yes # Set up NVE run diff --git a/examples/snap/in.snap.WBe.PRB2019 b/examples/snap/in.snap.WBe.PRB2019 new file mode 100644 index 0000000000000000000000000000000000000000..6b342ea56fafbba2919c47ca45d247b1477484bc --- /dev/null +++ b/examples/snap/in.snap.WBe.PRB2019 @@ -0,0 +1,48 @@ +# Demonstrate SNAP W-Be potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.1803 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable ny equal ${nrep} +variable nz equal ${nrep} + +boundary p p p + +lattice bcc $a +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 2 box +create_atoms 1 box +mass 1 183.84 +mass 2 9.012182 + +set group all type/fraction 2 0.05 3590153 # Change 5% of W to He +group tungsten type 1 +group beryllium type 2 +# choose potential + +include WBe_Wood_PRB2019.snap + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} + diff --git a/examples/snap/in.snap.hybrid.WSNAP.HePair b/examples/snap/in.snap.hybrid.WSNAP.HePair index 1f16fa64a28902f97b32b25d9500b9c78fca1cd0..1092c281198d98dd79609569c4e71c0fc18897b5 100644 --- a/examples/snap/in.snap.hybrid.WSNAP.HePair +++ b/examples/snap/in.snap.hybrid.WSNAP.HePair @@ -1,11 +1,11 @@ -# Demonstrate SNAP Ta potential +# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 3.1803 -units metal +units metal # generate the box and atom positions using a BCC lattice @@ -13,25 +13,25 @@ variable nx equal ${nrep} variable ny equal ${nrep} variable nz equal ${nrep} -boundary p p p +boundary p p p lattice bcc $a -region box block 0 ${nx} 0 ${ny} 0 ${nz} -create_box 2 box -create_atoms 1 box +region box block 0 ${nx} 0 ${ny} 0 ${nz} +create_box 2 box +create_atoms 1 box mass 1 183.84 mass 2 4.0026 -set group all type/fraction 2 0.05 3590153 # Change 5% of W to He -group tungsten type 1 -group helium type 2 +set group all type/fraction 2 0.05 3590153 # Change 5% of W to He +group tungsten type 1 +group helium type 2 # choose potential include W_2940_2017_2_He_JW2013.snap # Setup output -thermo 10 +thermo 10 thermo_modify norm yes # Set up NVE run diff --git a/examples/snap/log.18Sep19.snap.WBeSNAP.g++.1 b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..2b889e036b976b4b719a0ff2a7950ab660556981 --- /dev/null +++ b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.1 @@ -0,0 +1,154 @@ +LAMMPS (7 Aug 2019) +# Demonstrate SNAP W-Be potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.1803 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.1803 +Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000234842 secs +mass 1 183.84 +mass 2 9.012182 + +set group all type/fraction 2 0.05 3590153 # Change 5% of W to He + 5 settings made for type/fraction +group tungsten type 1 +123 atoms in group tungsten +group beryllium type 2 +5 atoms in group beryllium +# choose potential + +include WBe_Wood_PRB2019.snap +# Definition of SNAP+ZBL potential. +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz1 equal 74 +variable zblz2 equal 4 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 74 ${zblz1} +pair_coeff 1 1 zbl 74 74 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 74 ${zblz2} +pair_coeff 1 2 zbl 74 4 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 4 ${zblz2} +pair_coeff 2 2 zbl 4 4 +pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be +SNAP Element = W, Radius 0.5, Weight 1 +SNAP Element = Be, Radius 0.417932, Weight 0.959049 +SNAP keyword rcutfac 4.8123 +SNAP keyword twojmax 8 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 1 +SNAP keyword quadraticflag 0 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8123 + ghost atom cutoff = 5.8123 + binsize = 2.90615, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -8.5980876 0 -8.5596125 -35284.855 + 10 299.29029 -8.5979965 0 -8.5596125 -35299.259 + 20 288.99334 -8.5966759 0 -8.5596124 -35004.093 + 30 269.91027 -8.5942284 0 -8.5596123 -34447.077 + 40 243.57361 -8.5908505 0 -8.5596121 -33687.105 + 50 212.21385 -8.5868284 0 -8.5596119 -32821.864 + 60 178.77144 -8.5825391 0 -8.5596116 -31971.17 + 70 146.71854 -8.578428 0 -8.5596113 -31245.51 + 80 119.50956 -8.5749383 0 -8.5596111 -30724.137 + 90 99.872785 -8.5724197 0 -8.559611 -30440.244 + 100 89.604584 -8.5711027 0 -8.5596109 -30392.805 +Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms + +Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s +199.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.1672 | 3.1672 | 3.1672 | 0.0 | 99.97 +Neigh | 0.00030208 | 0.00030208 | 0.00030208 | 0.0 | 0.01 +Comm | 0.00029612 | 0.00029612 | 0.00029612 | 0.0 | 0.01 +Output | 0.00019813 | 0.00019813 | 0.00019813 | 0.0 | 0.01 +Modify | 0.00014448 | 0.00014448 | 0.00014448 | 0.0 | 0.00 +Other | | 0.0001433 | | | 0.00 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3710 ave 3710 max 3710 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7420 ave 7420 max 7420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7420 +Ave neighs/atom = 57.9688 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/snap/log.18Sep19.snap.WBeSNAP.g++.4 b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..d8cdae6810d12d125859305cd6cd4a232f46380b --- /dev/null +++ b/examples/snap/log.18Sep19.snap.WBeSNAP.g++.4 @@ -0,0 +1,154 @@ +LAMMPS (7 Aug 2019) +# Demonstrate SNAP W-Be potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.1803 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.1803 +Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + create_atoms CPU = 0.000317097 secs +mass 1 183.84 +mass 2 9.012182 + +set group all type/fraction 2 0.05 3590153 # Change 5% of W to He + 5 settings made for type/fraction +group tungsten type 1 +123 atoms in group tungsten +group beryllium type 2 +5 atoms in group beryllium +# choose potential + +include WBe_Wood_PRB2019.snap +# Definition of SNAP+ZBL potential. +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz1 equal 74 +variable zblz2 equal 4 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 1 zbl 74 ${zblz1} +pair_coeff 1 1 zbl 74 74 +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 1 2 zbl 74 ${zblz2} +pair_coeff 1 2 zbl 74 4 +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff 2 2 zbl 4 ${zblz2} +pair_coeff 2 2 zbl 4 4 +pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be +SNAP Element = W, Radius 0.5, Weight 1 +SNAP Element = Be, Radius 0.417932, Weight 0.959049 +SNAP keyword rcutfac 4.8123 +SNAP keyword twojmax 8 +SNAP keyword rfac0 0.99363 +SNAP keyword rmin0 0 +SNAP keyword bzeroflag 1 +SNAP keyword quadraticflag 0 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.8123 + ghost atom cutoff = 5.8123 + binsize = 2.90615, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -8.5980876 0 -8.5596125 -35284.855 + 10 296.24946 -8.5976065 0 -8.5596124 -35140.29 + 20 282.27904 -8.5958147 0 -8.5596123 -34710.3 + 30 259.54978 -8.5928995 0 -8.5596121 -34060.43 + 40 230.41412 -8.5891626 0 -8.5596119 -33258.275 + 50 197.85135 -8.5849861 0 -8.5596116 -32389.527 + 60 165.21732 -8.5808005 0 -8.5596113 -31550.426 + 70 135.94024 -8.5770455 0 -8.5596111 -30839.006 + 80 113.06617 -8.5741117 0 -8.5596109 -30339.177 + 90 98.542347 -8.572249 0 -8.5596109 -30094.29 + 100 92.524343 -8.5714774 0 -8.5596111 -30091.988 +Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms + +Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.79079 | 0.79788 | 0.80888 | 0.8 | 98.06 +Neigh | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 | 0.0 | 0.01 +Comm | 0.0041246 | 0.01515 | 0.022235 | 5.5 | 1.86 +Output | 0.000144 | 0.00017095 | 0.00024796 | 0.0 | 0.02 +Modify | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 | 0.0 | 0.01 +Other | | 0.000338 | | | 0.04 + +Nlocal: 32 ave 37 max 28 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 431 ave 435 max 426 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 927 ave 1071 max 821 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +FullNghs: 1854 ave 2144 max 1624 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 7416 +Ave neighs/atom = 57.9375 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/steinhardt/in.bcc b/examples/steinhardt/in.bcc new file mode 100644 index 0000000000000000000000000000000000000000..a0348fdcd95769dfa0d4817fd6a2dfe28de5bb56 --- /dev/null +++ b/examples/steinhardt/in.bcc @@ -0,0 +1,91 @@ +# Steinhardt-Nelson bond orientational order parameters for BCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice bcc 1.0 +region box block 0 3 0 3 0 3 +create_box 1 box +create_atoms 1 box + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_coeff * * 1.0 1.0 ${rcut} + +# 14 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] +compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 + +# check Q_l values + +print " " +print "*******************************************************************" +print " " +print "Comparison with reference values of Q_l " +print " [Table I in W. Mickel, S. C. Kapfer," +print " G. E. Schroeder-Turkand, K. Mecke, " +print " J. Chem. Phys. 138, 044501 (2013).]" +print " " + +variable q2ref equal 0.0 +variable q4ref equal 0.036 +variable q6ref equal 0.511 +variable q8ref equal 0.429 +variable q10ref equal 0.195 +variable q12ref equal 0.405 + +variable q2 equal c_avql[1] +variable q4 equal c_avql[2] +variable q6 equal c_avql[3] +variable q8 equal c_avql[4] +variable q10 equal c_avql[5] +variable q12 equal c_avql[6] + +print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" + +# check W_l_hat values + +print " " +print "Comparison with reference values of W_l_hat" +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " +print " Phys. Rev. B 28, 784 (1983).]" +print " " + +variable w4hatref equal 0.159317 +variable w6hatref equal 0.013161 +variable w8hatref equal -0.058455 +variable w10hatref equal -0.090130 + +variable w4hat equal c_avwlhat[2] +variable w6hat equal c_avwlhat[3] +variable w8hat equal c_avwlhat[4] +variable w10hat equal c_avwlhat[5] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +print " " +print "*******************************************************************" +print " " diff --git a/examples/steinhardt/in.fcc b/examples/steinhardt/in.fcc new file mode 100644 index 0000000000000000000000000000000000000000..6d2775d0bb55dd8a011ddff177a921f8af9943f3 --- /dev/null +++ b/examples/steinhardt/in.fcc @@ -0,0 +1,88 @@ +# Steinhardt-Nelson bond orientational order parameters for FCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice fcc 1.0 +region box block 0 3 0 3 0 3 +create_box 1 box +create_atoms 1 box + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_coeff * * 1.0 1.0 ${rcut} + +# 12 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 + +# check Q_l values + +print " " +print "*******************************************************************" +print " " +print "Comparison with reference values of Q_l " +print " [Table I in W. Mickel, S. C. Kapfer," +print " G. E. Schroeder-Turkand, K. Mecke, " +print " J. Chem. Phys. 138, 044501 (2013).]" +print " " + +variable q4ref equal 0.190 +variable q6ref equal 0.575 +variable q8ref equal 0.404 +variable q10ref equal 0.013 +variable q12ref equal 0.600 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" + +# check W_l_hat values + +print " " +print "Comparison with reference values of W_l_hat" +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " +print " Phys. Rev. B 28, 784 (1983).]" +print " " + +variable w4hatref equal -0.159316 +variable w6hatref equal -0.013161 +variable w8hatref equal 0.058454 +variable w10hatref equal -0.090128 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +print " " +print "*******************************************************************" +print " " diff --git a/examples/steinhardt/in.icos b/examples/steinhardt/in.icos new file mode 100644 index 0000000000000000000000000000000000000000..d0d61a902db44ca43876cdc762de42bb7c2a1ab3 --- /dev/null +++ b/examples/steinhardt/in.icos @@ -0,0 +1,106 @@ +# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster +# W_6_hat is sensitive to icosohedral order + +variable rcut equal 1.2 # a bit bigger than LJ Rmin +variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2) + +# create a perfect fcc crystallite + +atom_style atomic +boundary s s s +lattice fcc 1.0 # neighbors at LJ Rmin +region box block 0 2 0 2 0 2 +create_box 1 box +create_atoms 1 box +mass 1 1.0 + +region centralatom sphere 1 1 1 0.0 side in +group centralatom region centralatom + +region mysphere sphere 1 1 1 ${rcutred} side out +delete_atoms region mysphere + +# LJ potential + +pair_style lj/cut 100.0 +pair_coeff * * 1.0 1.0 100.0 + +# define output for central atom + +compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL +compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] +variable q6 equal c_avql[2] +variable w6hat equal c_avwlhat[2] + +compute mype all pe/atom +compute centralatompe centralatom reduce ave c_mype + +# gently equilibrate the crystallite + +velocity all create 0.001 482748 +fix 1 all nve +neighbor 0.3 bin +neigh_modify every 1 check no delay 0 +timestep 0.003 +thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat +thermo 10 + +run 10 + +# quench to icosehedral cluster + +minimize 1.0e-10 1.0e-6 100 1000 + +# check Q_l values + +print " " +print "*******************************************************************" +print " " +print "Comparison with reference values of Q_l " +print " [Table I in W. Mickel, S. C. Kapfer," +print " G. E. Schroeder-Turkand, K. Mecke, " +print " J. Chem. Phys. 138, 044501 (2013).]" +print " " + +variable q4ref equal 0.0 +variable q6ref equal 0.663 +variable q8ref equal 0.0 +variable q10ref equal 0.363 +variable q12ref equal 0.585 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" + +# check W_l_hat values + +print " " +print "Comparison with reference values of W_l_hat" +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " +print " Phys. Rev. B 28, 784 (1983).]" +print " " + +variable w6hatref equal -0.169754 +variable w10hatref equal -0.093967 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] +variable w12hat equal c_avwlhat[5] + +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +print " " +print "*******************************************************************" +print " " + diff --git a/examples/steinhardt/log.13Sept18.bcc.g++.1 b/examples/steinhardt/log.13Sept18.bcc.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..b0a82fca90479010b9fe9d9e6d912d62d29d447e --- /dev/null +++ b/examples/steinhardt/log.13Sept18.bcc.g++.1 @@ -0,0 +1,176 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# Steinhardt-Nelson bond orientational order parameters for BCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice bcc 1.0 +Lattice spacing in x,y,z = 1.25992 1.25992 1.25992 +region box block 0 3 0 3 0 3 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 54 atoms + create_atoms CPU = 0.000282049 secs + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_style lj/cut 3 +pair_coeff * * 1.0 1.0 ${rcut} +pair_coeff * * 1.0 1.0 3 + +# 14 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] +compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute orientorder/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.746 | 3.746 | 3.746 Mbytes +Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avql[6] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] c_avwlhat[6] + 0 0 -7.8104466 -7.8104466 8.6570408e-17 0.036369648 0.51068823 0.42932247 0.19519122 0.40479919 0 0.15931737 0.013160601 0.058454791 -0.090130212 -0.049573639 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 54 atoms + +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1187 ave 1187 max 1187 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4536 ave 4536 max 4536 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 9072 ave 9072 max 9072 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9072 +Ave neighs/atom = 168 +Neighbor list builds = 0 +Dangerous builds = 0 + +# check Q_l values + +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +print "Comparison with reference values of Q_l " +Comparison with reference values of Q_l +print " [Table I in W. Mickel, S. C. Kapfer," + [Table I in W. Mickel, S. C. Kapfer, +print " G. E. Schroeder-Turkand, K. Mecke, " + G. E. Schroeder-Turkand, K. Mecke, +print " J. Chem. Phys. 138, 044501 (2013).]" + J. Chem. Phys. 138, 044501 (2013).] +print " " + + +variable q2ref equal 0.0 +variable q4ref equal 0.036 +variable q6ref equal 0.511 +variable q8ref equal 0.429 +variable q10ref equal 0.195 +variable q12ref equal 0.405 + +variable q2 equal c_avql[1] +variable q4 equal c_avql[2] +variable q6 equal c_avql[3] +variable q8 equal c_avql[4] +variable q10 equal c_avql[5] +variable q12 equal c_avql[6] + +print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" +q2 = 0.000000 delta = 0.0000 +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +q4 = 0.036370 delta = 0.0004 +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +q6 = 0.510688 delta = -0.0003 +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +q8 = 0.429322 delta = 0.0003 +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +q10 = 0.195191 delta = 0.0002 +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" +q12 = 0.404799 delta = -0.0002 + +# check W_l_hat values + +print " " + +print "Comparison with reference values of W_l_hat" +Comparison with reference values of W_l_hat +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " + [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, +print " Phys. Rev. B 28, 784 (1983).]" + Phys. Rev. B 28, 784 (1983).] +print " " + + +variable w4hatref equal 0.159317 +variable w6hatref equal 0.013161 +variable w8hatref equal -0.058455 +variable w10hatref equal -0.090130 + +variable w4hat equal c_avwlhat[2] +variable w6hat equal c_avwlhat[3] +variable w8hat equal c_avwlhat[4] +variable w10hat equal c_avwlhat[5] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +w4hat = 0.159317 delta = 0.000000 +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +w6hat = 0.013161 delta = -0.000000 +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +w8hat = 0.058455 delta = 0.116910 +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +w10hat = -0.090130 delta = -0.000000 +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +Total wall time: 0:00:00 diff --git a/examples/steinhardt/log.13Sept18.bcc.g++.4 b/examples/steinhardt/log.13Sept18.bcc.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..ee1f0c69c1e7389ffc328a5f96799439861f2ddd --- /dev/null +++ b/examples/steinhardt/log.13Sept18.bcc.g++.4 @@ -0,0 +1,176 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# Steinhardt-Nelson bond orientational order parameters for BCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice bcc 1.0 +Lattice spacing in x,y,z = 1.25992 1.25992 1.25992 +region box block 0 3 0 3 0 3 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.77976 3.77976 3.77976) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 54 atoms + create_atoms CPU = 0.000533104 secs + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_style lj/cut 3 +pair_coeff * * 1.0 1.0 ${rcut} +pair_coeff * * 1.0 1.0 3 + +# 14 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom degrees 6 2 4 6 8 10 12 nnn 14 wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] c_qlwlhat[6] +compute avwlhat all reduce ave c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] c_qlwlhat[11] c_qlwlhat[12] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute orientorder/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.722 | 3.722 | 3.722 Mbytes +Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avql[6] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] c_avwlhat[6] + 0 0 -7.8104466 -7.8104466 8.6382997e-17 0.036369648 0.51068823 0.42932247 0.19519122 0.40479919 0 0.15931737 0.013160601 0.058454791 -0.090130212 -0.049573639 +Loop time of 3.99351e-06 on 4 procs for 0 steps with 54 atoms + +87.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.994e-06 | | |100.00 + +Nlocal: 13.5 ave 15 max 12 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 819.5 ave 821 max 818 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 1134 ave 1260 max 1008 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 2268 ave 2520 max 2016 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 9072 +Ave neighs/atom = 168 +Neighbor list builds = 0 +Dangerous builds = 0 + +# check Q_l values + +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +print "Comparison with reference values of Q_l " +Comparison with reference values of Q_l +print " [Table I in W. Mickel, S. C. Kapfer," + [Table I in W. Mickel, S. C. Kapfer, +print " G. E. Schroeder-Turkand, K. Mecke, " + G. E. Schroeder-Turkand, K. Mecke, +print " J. Chem. Phys. 138, 044501 (2013).]" + J. Chem. Phys. 138, 044501 (2013).] +print " " + + +variable q2ref equal 0.0 +variable q4ref equal 0.036 +variable q6ref equal 0.511 +variable q8ref equal 0.429 +variable q10ref equal 0.195 +variable q12ref equal 0.405 + +variable q2 equal c_avql[1] +variable q4 equal c_avql[2] +variable q6 equal c_avql[3] +variable q8 equal c_avql[4] +variable q10 equal c_avql[5] +variable q12 equal c_avql[6] + +print "q2 = $(v_q2:%10.6f) delta = $(v_q2-v_q2ref:%10.4f)" +q2 = 0.000000 delta = 0.0000 +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +q4 = 0.036370 delta = 0.0004 +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +q6 = 0.510688 delta = -0.0003 +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +q8 = 0.429322 delta = 0.0003 +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +q10 = 0.195191 delta = 0.0002 +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" +q12 = 0.404799 delta = -0.0002 + +# check W_l_hat values + +print " " + +print "Comparison with reference values of W_l_hat" +Comparison with reference values of W_l_hat +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " + [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, +print " Phys. Rev. B 28, 784 (1983).]" + Phys. Rev. B 28, 784 (1983).] +print " " + + +variable w4hatref equal 0.159317 +variable w6hatref equal 0.013161 +variable w8hatref equal -0.058455 +variable w10hatref equal -0.090130 + +variable w4hat equal c_avwlhat[2] +variable w6hat equal c_avwlhat[3] +variable w8hat equal c_avwlhat[4] +variable w10hat equal c_avwlhat[5] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +w4hat = 0.159317 delta = 0.000000 +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +w6hat = 0.013161 delta = -0.000000 +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +w8hat = 0.058455 delta = 0.116910 +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +w10hat = -0.090130 delta = -0.000000 +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +Total wall time: 0:00:00 diff --git a/examples/steinhardt/log.13Sept18.fcc.g++.1 b/examples/steinhardt/log.13Sept18.fcc.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..a34a33d7b1419f9916fe83958f33703c3a7cc779 --- /dev/null +++ b/examples/steinhardt/log.13Sept18.fcc.g++.1 @@ -0,0 +1,172 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# Steinhardt-Nelson bond orientational order parameters for FCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0 3 0 3 0 3 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.7622 4.7622 4.7622) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 108 atoms + create_atoms CPU = 0.000289917 secs + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_style lj/cut 3 +pair_coeff * * 1.0 1.0 ${rcut} +pair_coeff * * 1.0 1.0 3 + +# 12 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute orientorder/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.767 | 3.767 | 3.767 Mbytes +Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] + 0 0 -8.1295091 -8.1295091 0.19094065 0.57452426 0.40391456 0.012857043 0.60008302 -0.15931737 -0.013160601 0.058454791 -0.090130212 0.087390889 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 108 atoms + +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1580 ave 1580 max 1580 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7560 ave 7560 max 7560 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15120 ave 15120 max 15120 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15120 +Ave neighs/atom = 140 +Neighbor list builds = 0 +Dangerous builds = 0 + +# check Q_l values + +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +print "Comparison with reference values of Q_l " +Comparison with reference values of Q_l +print " [Table I in W. Mickel, S. C. Kapfer," + [Table I in W. Mickel, S. C. Kapfer, +print " G. E. Schroeder-Turkand, K. Mecke, " + G. E. Schroeder-Turkand, K. Mecke, +print " J. Chem. Phys. 138, 044501 (2013).]" + J. Chem. Phys. 138, 044501 (2013).] +print " " + + +variable q4ref equal 0.190 +variable q6ref equal 0.575 +variable q8ref equal 0.404 +variable q10ref equal 0.013 +variable q12ref equal 0.600 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +q4 = 0.190941 delta = 0.0009 +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +q6 = 0.574524 delta = -0.0005 +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +q8 = 0.403915 delta = -0.0001 +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +q10 = 0.012857 delta = -0.0001 +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" +q12 = 0.600083 delta = 0.0001 + +# check W_l_hat values + +print " " + +print "Comparison with reference values of W_l_hat" +Comparison with reference values of W_l_hat +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " + [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, +print " Phys. Rev. B 28, 784 (1983).]" + Phys. Rev. B 28, 784 (1983).] +print " " + + +variable w4hatref equal -0.159316 +variable w6hatref equal -0.013161 +variable w8hatref equal 0.058454 +variable w10hatref equal -0.090128 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +w4hat = -0.159317 delta = -0.000001 +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +w6hat = -0.013161 delta = 0.000000 +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +w8hat = 0.058455 delta = 0.000001 +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +w10hat = -0.090130 delta = -0.000002 +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +Total wall time: 0:00:00 diff --git a/examples/steinhardt/log.13Sept18.fcc.g++.4 b/examples/steinhardt/log.13Sept18.fcc.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..8573488be62467ca3f799c142d474ed7ac05572e --- /dev/null +++ b/examples/steinhardt/log.13Sept18.fcc.g++.4 @@ -0,0 +1,172 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# Steinhardt-Nelson bond orientational order parameters for FCC + +variable rcut equal 3.0 + +boundary p p p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice fcc 1.0 +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0 3 0 3 0 3 +create_box 1 box +Created orthogonal box = (0 0 0) to (4.7622 4.7622 4.7622) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 108 atoms + create_atoms CPU = 0.000549078 secs + +mass 1 1.0 + +# LJ potentials + +pair_style lj/cut ${rcut} +pair_style lj/cut 3 +pair_coeff * * 1.0 1.0 ${rcut} +pair_coeff * * 1.0 1.0 3 + +# 12 neighbors, perfect crystal + +compute qlwlhat all orientorder/atom wl/hat yes +compute avql all reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat all reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] + +thermo_style custom step temp epair etotal c_avql[*] c_avwlhat[*] + +run 0 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:52) +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute orientorder/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.737 | 3.737 | 3.737 Mbytes +Step Temp E_pair TotEng c_avql[1] c_avql[2] c_avql[3] c_avql[4] c_avql[5] c_avwlhat[1] c_avwlhat[2] c_avwlhat[3] c_avwlhat[4] c_avwlhat[5] + 0 0 -8.1295091 -8.1295091 0.19094065 0.57452426 0.40391456 0.012857043 0.60008302 -0.15931737 -0.013160601 0.058454791 -0.090130212 0.087390889 +Loop time of 3.09944e-06 on 4 procs for 0 steps with 108 atoms + +88.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 3.099e-06 | | |100.00 + +Nlocal: 27 ave 27 max 27 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1053 ave 1053 max 1053 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 1890 ave 1890 max 1890 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 3780 ave 3780 max 3780 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15120 +Ave neighs/atom = 140 +Neighbor list builds = 0 +Dangerous builds = 0 + +# check Q_l values + +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +print "Comparison with reference values of Q_l " +Comparison with reference values of Q_l +print " [Table I in W. Mickel, S. C. Kapfer," + [Table I in W. Mickel, S. C. Kapfer, +print " G. E. Schroeder-Turkand, K. Mecke, " + G. E. Schroeder-Turkand, K. Mecke, +print " J. Chem. Phys. 138, 044501 (2013).]" + J. Chem. Phys. 138, 044501 (2013).] +print " " + + +variable q4ref equal 0.190 +variable q6ref equal 0.575 +variable q8ref equal 0.404 +variable q10ref equal 0.013 +variable q12ref equal 0.600 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +q4 = 0.190941 delta = 0.0009 +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +q6 = 0.574524 delta = -0.0005 +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +q8 = 0.403915 delta = -0.0001 +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +q10 = 0.012857 delta = -0.0001 +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" +q12 = 0.600083 delta = 0.0001 + +# check W_l_hat values + +print " " + +print "Comparison with reference values of W_l_hat" +Comparison with reference values of W_l_hat +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " + [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, +print " Phys. Rev. B 28, 784 (1983).]" + Phys. Rev. B 28, 784 (1983).] +print " " + + +variable w4hatref equal -0.159316 +variable w6hatref equal -0.013161 +variable w8hatref equal 0.058454 +variable w10hatref equal -0.090128 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] + +print "w4hat = $(v_w4hat:%10.6f) delta = $(v_w4hat-v_w4hatref:%10.6f)" +w4hat = -0.159317 delta = -0.000001 +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +w6hat = -0.013161 delta = 0.000000 +print "w8hat = $(v_w8hat:%10.6f) delta = $(v_w8hat-v_w8hatref:%10.6f)" +w8hat = 0.058455 delta = 0.000001 +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +w10hat = -0.090130 delta = -0.000002 +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +Total wall time: 0:00:00 diff --git a/examples/steinhardt/log.13Sept18.icos.g++.1 b/examples/steinhardt/log.13Sept18.icos.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..f42fd346db45e270cfe14aaa5ec032c72a5e058f --- /dev/null +++ b/examples/steinhardt/log.13Sept18.icos.g++.1 @@ -0,0 +1,235 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster +# W_6_hat is sensitive to icosohedral order + +variable rcut equal 1.2 # a bit bigger than LJ Rmin +variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2) + +# create a perfect fcc crystallite + +atom_style atomic +boundary s s s +lattice fcc 1.0 # neighbors at LJ Rmin +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0 2 0 2 0 2 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.1748 3.1748 3.1748) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 63 atoms + create_atoms CPU = 0.000341177 secs +mass 1 1.0 + +region centralatom sphere 1 1 1 0.0 side in +group centralatom region centralatom +1 atoms in group centralatom + +region mysphere sphere 1 1 1 ${rcutred} side out +region mysphere sphere 1 1 1 0.75 side out +delete_atoms region mysphere +Deleted 50 atoms, new total = 13 + +# LJ potential + +pair_style lj/cut 100.0 +pair_coeff * * 1.0 1.0 100.0 + +# define output for central atom + +compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL +compute qlwlhat all orientorder/atom wl/hat yes cutoff 1.2 nnn NULL +compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] +variable q6 equal c_avql[2] +variable w6hat equal c_avwlhat[2] + +compute mype all pe/atom +compute centralatompe centralatom reduce ave c_mype + +# gently equilibrate the crystallite + +velocity all create 0.001 482748 +fix 1 all nve +neighbor 0.3 bin +neigh_modify every 1 check no delay 0 +timestep 0.003 +thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat +thermo 10 + +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 100.3 + ghost atom cutoff = 100.3 + binsize = 50.15, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute orientorder/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 60.87 | 60.87 | 60.87 Mbytes +Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat + 0 0.001 -3.134107 -3.1327224 -6 0.57452426 -0.013160601 + 10 0.0021974351 -3.1357656 -3.132723 -5.9995795 0.57450739 -0.013160482 +Loop time of 0.210631 on 1 procs for 10 steps with 13 atoms + +Performance: 12305.887 tau/day, 47.476 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.01 +Neigh | 0.13335 | 0.13335 | 0.13335 | 0.0 | 63.31 +Comm | 1.4782e-05 | 1.4782e-05 | 1.4782e-05 | 0.0 | 0.01 +Output | 0.033121 | 0.033121 | 0.033121 | 0.0 | 15.72 +Modify | 2.8849e-05 | 2.8849e-05 | 2.8849e-05 | 0.0 | 0.01 +Other | | 0.0441 | | | 20.94 + +Nlocal: 13 ave 13 max 13 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 78 ave 78 max 78 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 156 ave 156 max 156 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 156 +Ave neighs/atom = 12 +Neighbor list builds = 10 +Dangerous builds not checked + +# quench to icosehedral cluster + +minimize 1.0e-10 1.0e-6 100 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes +Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat + 10 0.0021974351 -3.1357656 -3.132723 -5.9995795 0.57450739 -0.013160482 + 20 0.0021974351 -3.1449631 -3.1419205 -5.9766502 0.57452794 -0.01317299 + 30 0.0021974351 -3.377441 -3.3743984 -5.6930377 0.65479437 -0.16922776 + 40 0.0021974351 -3.4096335 -3.4065909 -5.6325443 0.66328926 -0.16975382 + 49 0.0021974351 -3.409754 -3.4067114 -5.6323333 0.66332496 -0.16975389 +Loop time of 0.0821278 on 1 procs for 39 steps with 13 atoms + +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -3.13576562743 -3.40975395481 -3.40975395503 + Force two-norm initial, final = 6.44841 0.000945077 + Force max component initial, final = 1.43234 0.000348946 + Final line search alpha, max atom move = 1 0.000348946 + Iterations, force evaluations = 39 94 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00020051 | 0.00020051 | 0.00020051 | 0.0 | 0.24 +Neigh | 0.024762 | 0.024762 | 0.024762 | 0.0 | 30.15 +Comm | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.02 +Output | 0.048263 | 0.048263 | 0.048263 | 0.0 | 58.77 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.00889 | | | 10.82 + +Nlocal: 13 ave 13 max 13 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 78 ave 78 max 78 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 156 ave 156 max 156 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 156 +Ave neighs/atom = 12 +Neighbor list builds = 3 +Dangerous builds not checked + +# check Q_l values + +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +print "Comparison with reference values of Q_l " +Comparison with reference values of Q_l +print " [Table I in W. Mickel, S. C. Kapfer," + [Table I in W. Mickel, S. C. Kapfer, +print " G. E. Schroeder-Turkand, K. Mecke, " + G. E. Schroeder-Turkand, K. Mecke, +print " J. Chem. Phys. 138, 044501 (2013).]" + J. Chem. Phys. 138, 044501 (2013).] +print " " + + +variable q4ref equal 0.0 +variable q6ref equal 0.663 +variable q8ref equal 0.0 +variable q10ref equal 0.363 +variable q12ref equal 0.585 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +q4 = 0.000002 delta = 0.0000 +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +q6 = 0.663325 delta = 0.0003 +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +q8 = 0.000003 delta = 0.0000 +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +q10 = 0.362951 delta = -0.0000 +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" +q12 = 0.585423 delta = 0.0004 + +# check W_l_hat values + +print " " + +print "Comparison with reference values of W_l_hat" +Comparison with reference values of W_l_hat +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " + [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, +print " Phys. Rev. B 28, 784 (1983).]" + Phys. Rev. B 28, 784 (1983).] +print " " + + +variable w6hatref equal -0.169754 +variable w10hatref equal -0.093967 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] +variable w12hat equal c_avwlhat[5] + +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +w6hat = -0.169754 delta = 0.000000 +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +w10hat = -0.093968 delta = -0.000001 +print " " + +print "*******************************************************************" +******************************************************************* +print " " + + +Total wall time: 0:00:00 diff --git a/examples/steinhardt/log.13Sept18.icos.g++.4 b/examples/steinhardt/log.13Sept18.icos.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..d64e179c8f5c066301321265cd2b6568d7b29773 --- /dev/null +++ b/examples/steinhardt/log.13Sept18.icos.g++.4 @@ -0,0 +1,235 @@ +LAMMPS (7 Aug 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93) + using 1 OpenMP thread(s) per MPI task +# Steinhardt-Nelson bond orientational order parameters for icosahedral cluster +# W_6_hat is sensitive to icosohedral order + +variable rcut equal 1.2 # a bit bigger than LJ Rmin +variable rcutred equal 0.75 # a bit bigger than 1/sqrt(2) + +# create a perfect fcc crystallite + +atom_style atomic +boundary s s s +lattice fcc 1.0 # neighbors at LJ Rmin +Lattice spacing in x,y,z = 1.5874 1.5874 1.5874 +region box block 0 2 0 2 0 2 +create_box 1 box +Created orthogonal box = (0 0 0) to (3.1748 3.1748 3.1748) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 63 atoms + create_atoms CPU = 0.000592947 secs +mass 1 1.0 + +region centralatom sphere 1 1 1 0.0 side in +group centralatom region centralatom +1 atoms in group centralatom + +region mysphere sphere 1 1 1 ${rcutred} side out +region mysphere sphere 1 1 1 0.75 side out +delete_atoms region mysphere +Deleted 50 atoms, new total = 13 + +# LJ potential + +pair_style lj/cut 100.0 +pair_coeff * * 1.0 1.0 100.0 + +# define output for central atom + +compute qlwlhat all orientorder/atom wl/hat yes cutoff ${rcut} nnn NULL +compute qlwlhat all orientorder/atom wl/hat yes cutoff 1.2 nnn NULL +compute avql centralatom reduce ave c_qlwlhat[1] c_qlwlhat[2] c_qlwlhat[3] c_qlwlhat[4] c_qlwlhat[5] +compute avwlhat centralatom reduce ave c_qlwlhat[6] c_qlwlhat[7] c_qlwlhat[8] c_qlwlhat[9] c_qlwlhat[10] +variable q6 equal c_avql[2] +variable w6hat equal c_avwlhat[2] + +compute mype all pe/atom +compute centralatompe centralatom reduce ave c_mype + +# gently equilibrate the crystallite + +velocity all create 0.001 482748 +fix 1 all nve +neighbor 0.3 bin +neigh_modify every 1 check no delay 0 +timestep 0.003 +thermo_style custom step temp epair etotal c_centralatompe v_q6 v_w6hat +thermo 10 + +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 100.3 + ghost atom cutoff = 100.3 + binsize = 50.15, bins = 1 1 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute orientorder/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 60.76 | 60.76 | 60.76 Mbytes +Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat + 0 0.001 -3.134107 -3.1327224 -6 0.57452426 -0.013160601 + 10 0.0021821015 -3.1357444 -3.132723 -5.9994885 0.57450756 -0.013160431 +Loop time of 0.15387 on 4 procs for 10 steps with 13 atoms + +Performance: 16845.410 tau/day, 64.990 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.7752e-06 | 1.7285e-05 | 2.9087e-05 | 0.0 | 0.01 +Neigh | 0.055218 | 0.065482 | 0.073829 | 2.9 | 42.56 +Comm | 0.0061202 | 0.018279 | 0.028283 | 6.3 | 11.88 +Output | 0.020282 | 0.020287 | 0.020298 | 0.0 | 13.18 +Modify | 2.7895e-05 | 2.8968e-05 | 2.9802e-05 | 0.0 | 0.02 +Other | | 0.04978 | | | 32.35 + +Nlocal: 3.25 ave 4 max 2 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 9.75 ave 11 max 9 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 19.5 ave 35 max 7 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +FullNghs: 39 ave 48 max 24 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 156 +Ave neighs/atom = 12 +Neighbor list builds = 10 +Dangerous builds not checked + +# quench to icosehedral cluster + +minimize 1.0e-10 1.0e-6 100 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 112.9 | 112.9 | 112.9 Mbytes +Step Temp E_pair TotEng c_centralatompe v_q6 v_w6hat + 10 0.0021821015 -3.1357444 -3.132723 -5.9994885 0.57450756 -0.013160431 + 20 0.0021821015 -3.1449613 -3.1419399 -5.9764731 0.57452454 -0.01316152 + 30 0.0021821015 -3.3366586 -3.3336372 -5.7717004 0.63679987 -0.16411081 + 40 0.0021821015 -3.4097262 -3.4067048 -5.6321229 0.66331761 -0.16975374 + 49 0.0021821015 -3.409754 -3.4067326 -5.6323347 0.66332496 -0.16975389 +Loop time of 0.0932837 on 4 procs for 39 steps with 13 atoms + +97.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -3.13574438249 -3.40975395519 -3.40975395529 + Force two-norm initial, final = 6.46606 0.000429142 + Force max component initial, final = 1.45519 0.000196446 + Final line search alpha, max atom move = 1 0.000196446 + Iterations, force evaluations = 39 98 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.4121e-05 | 9.0897e-05 | 0.00014281 | 0.0 | 0.10 +Neigh | 0.019662 | 0.02379 | 0.03176 | 3.0 | 25.50 +Comm | 0.0072601 | 0.014304 | 0.019575 | 3.8 | 15.33 +Output | 0.033646 | 0.033654 | 0.03368 | 0.0 | 36.08 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.02144 | | | 22.99 + +Nlocal: 3.25 ave 6 max 1 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Nghost: 9.75 ave 12 max 7 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 19.5 ave 49 max 1 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +FullNghs: 39 ave 72 max 12 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 156 +Ave neighs/atom = 12 +Neighbor list builds = 5 +Dangerous builds not checked + +# check Q_l values + +print " " + +print "*******************************************************************" +******************************************************************* +print " " + +print "Comparison with reference values of Q_l " +Comparison with reference values of Q_l +print " [Table I in W. Mickel, S. C. Kapfer," + [Table I in W. Mickel, S. C. Kapfer, +print " G. E. Schroeder-Turkand, K. Mecke, " + G. E. Schroeder-Turkand, K. Mecke, +print " J. Chem. Phys. 138, 044501 (2013).]" + J. Chem. Phys. 138, 044501 (2013).] +print " " + + +variable q4ref equal 0.0 +variable q6ref equal 0.663 +variable q8ref equal 0.0 +variable q10ref equal 0.363 +variable q12ref equal 0.585 + +variable q4 equal c_avql[1] +variable q6 equal c_avql[2] +variable q8 equal c_avql[3] +variable q10 equal c_avql[4] +variable q12 equal c_avql[5] + +print "q4 = $(v_q4:%10.6f) delta = $(v_q4-v_q4ref:%10.4f)" +q4 = 0.000001 delta = 0.0000 +print "q6 = $(v_q6:%10.6f) delta = $(v_q6-v_q6ref:%10.4f)" +q6 = 0.663325 delta = 0.0003 +print "q8 = $(v_q8:%10.6f) delta = $(v_q8-v_q8ref:%10.4f)" +q8 = 0.000002 delta = 0.0000 +print "q10 = $(v_q10:%10.6f) delta = $(v_q10-v_q10ref:%10.4f)" +q10 = 0.362951 delta = -0.0000 +print "q12 = $(v_q12:%10.6f) delta = $(v_q12-v_q12ref:%10.4f)" +q12 = 0.585423 delta = 0.0004 + +# check W_l_hat values + +print " " + +print "Comparison with reference values of W_l_hat" +Comparison with reference values of W_l_hat +print " [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, " + [Table I in P. Steinhardt, D. Nelson, and M. Ronchetti, +print " Phys. Rev. B 28, 784 (1983).]" + Phys. Rev. B 28, 784 (1983).] +print " " + + +variable w6hatref equal -0.169754 +variable w10hatref equal -0.093967 + +variable w4hat equal c_avwlhat[1] +variable w6hat equal c_avwlhat[2] +variable w8hat equal c_avwlhat[3] +variable w10hat equal c_avwlhat[4] +variable w12hat equal c_avwlhat[5] + +print "w6hat = $(v_w6hat:%10.6f) delta = $(v_w6hat-v_w6hatref:%10.6f)" +w6hat = -0.169754 delta = 0.000000 +print "w10hat = $(v_w10hat:%10.6f) delta = $(v_w10hat-v_w10hatref:%10.6f)" +w10hat = -0.093968 delta = -0.000001 +print " " + +print "*******************************************************************" +******************************************************************* +print " " + + +Total wall time: 0:00:00 diff --git a/lib/atc/ATC_Coupling.cpp b/lib/atc/ATC_Coupling.cpp index b021584186ba68e68763aaccddcaeab4b617c2d0..9468064f8d92fd2fe48f87e1d73f9e55c58fc126 100644 --- a/lib/atc/ATC_Coupling.cpp +++ b/lib/atc/ATC_Coupling.cpp @@ -1693,7 +1693,7 @@ namespace ATC { extrinsicModelManager_.construct_transfers(); } //-------------------------------------------------- - void ATC_Coupling::delete_mass_mat_time_filter(FieldName thisField) + void ATC_Coupling::delete_mass_mat_time_filter(FieldName /* thisField */) { } //-------------------------------------------------- diff --git a/lib/atc/ATC_Coupling.h b/lib/atc/ATC_Coupling.h index 002041b536c97c1ca756aa82b3ade4f8c68d6d55..3816a8279886cc3c7bba5af7bfcd3ca94f778a32 100644 --- a/lib/atc/ATC_Coupling.h +++ b/lib/atc/ATC_Coupling.h @@ -131,7 +131,7 @@ namespace ATC { virtual void initialize_mesh_data(void); // public for FieldIntegrator - bool source_atomic_quadrature(FieldName field) + bool source_atomic_quadrature(FieldName /* field */) { return (sourceIntegration_ == FULL_DOMAIN_ATOMIC_QUADRATURE_SOURCE); } ATC::IntegrationDomainType source_integration() { return sourceIntegration_; } diff --git a/lib/atc/ATC_CouplingMomentumEnergy.cpp b/lib/atc/ATC_CouplingMomentumEnergy.cpp index c4f7829c60095abc26ff80f10b44961d24ca3a23..bf0edc71fb8ade68a9a16786c4a47d89a7e5f09d 100644 --- a/lib/atc/ATC_CouplingMomentumEnergy.cpp +++ b/lib/atc/ATC_CouplingMomentumEnergy.cpp @@ -319,7 +319,7 @@ namespace ATC { // modify // parses inputs and modifies state of the filter //-------------------------------------------------------- - bool ATC_CouplingMomentumEnergy::modify(int narg, char **arg) + bool ATC_CouplingMomentumEnergy::modify(int /* narg */, char ** /* arg */) { return false; } diff --git a/lib/atc/ATC_Method.h b/lib/atc/ATC_Method.h index aa8f2387216237e5267eedc3651fb8025553f684..e356243e03b4d07506ab835e83f12e297491f391 100644 --- a/lib/atc/ATC_Method.h +++ b/lib/atc/ATC_Method.h @@ -140,9 +140,9 @@ namespace ATC { /** compute scalar for output */ virtual double compute_scalar() {return 0.;} /** compute vector for output */ - virtual double compute_vector(int n) {return 0.;} + virtual double compute_vector(int /* n */) {return 0.;} /** compute vector for output */ - virtual double compute_array(int irow, int icol) {return 0.;}; + virtual double compute_array(int /* irow */, int /* icol */) {return 0.;}; int scalar_flag() const {return scalarFlag_;} int vector_flag() const {return vectorFlag_;} int size_vector() const {return sizeVector_;} @@ -398,8 +398,8 @@ namespace ATC { // /** determine weighting method for atomic integration */ // void compute_consistent_md_mass_matrix(const SPAR_MAT & shapeFunctionMatrix, // SPAR_MAT & mdMassMatrix); - virtual void compute_md_mass_matrix(FieldName thisField, - DIAG_MAT & massMat) {}; + virtual void compute_md_mass_matrix(FieldName /* thisField */, + DIAG_MAT & /* massMat */) {}; /** access to md mass matrices */ DIAG_MAN &mass_mat_md_inv(FieldName thisField) diff --git a/lib/atc/ATC_Transfer.cpp b/lib/atc/ATC_Transfer.cpp index 968dcbbea71ae3c610d0ff486e424617a8482a12..c876f466341f84bfde5d912218afd125cfc4e15d 100644 --- a/lib/atc/ATC_Transfer.cpp +++ b/lib/atc/ATC_Transfer.cpp @@ -1658,7 +1658,7 @@ namespace ATC { } //-------------------------------------------------------------------- void ATC_Transfer::compute_vacancy_concentration(DENS_MAT & Cv, - const DENS_MAT & H, const DENS_MAT & rhoN) + const DENS_MAT & H, const DENS_MAT & /* rhoN */) { int * type = lammpsInterface_->atom_type(); DENS_MAT new_rho(nNodes_,1); diff --git a/lib/atc/ATC_TransferPartitionOfUnity.cpp b/lib/atc/ATC_TransferPartitionOfUnity.cpp index a847a8ee3b56fb8d3f2b1ef5b86021f66010687d..5d83fd8fd77156c842e717c9129deb2e3f64fe78 100644 --- a/lib/atc/ATC_TransferPartitionOfUnity.cpp +++ b/lib/atc/ATC_TransferPartitionOfUnity.cpp @@ -54,7 +54,7 @@ namespace ATC { //------------------------------------------------------------------- void ATC_TransferPartitionOfUnity::compute_projection( - const DENS_MAT & atomData, DENS_MAT & nodeData) + const DENS_MAT & /* atomData */, DENS_MAT & /* nodeData */) { throw ATC_Error("unimplemented function"); } diff --git a/lib/atc/AtomicRegulator.cpp b/lib/atc/AtomicRegulator.cpp index 9d329852af676022984f1f8a23ce119557e97496..9c7e7588162610e30bf3ab7842ac8ee5c7801288 100644 --- a/lib/atc/AtomicRegulator.cpp +++ b/lib/atc/AtomicRegulator.cpp @@ -158,7 +158,7 @@ namespace ATC { // parses and adjusts controller state based on // user input, in the style of LAMMPS user input //-------------------------------------------------------- - bool AtomicRegulator::modify(int narg, char **arg) + bool AtomicRegulator::modify(int /* narg */, char **arg) { bool foundMatch = false; diff --git a/lib/atc/AtomicRegulator.h b/lib/atc/AtomicRegulator.h index 454f54989daa54b5a2083a7c378dc81ac47e1b92..8fb7de10060e0441012f9de648184d235ced411c 100644 --- a/lib/atc/AtomicRegulator.h +++ b/lib/atc/AtomicRegulator.h @@ -90,7 +90,7 @@ namespace ATC { /** add output information */ virtual void output(OUTPUT_LIST & outputData) const; - virtual double compute_vector(int n) const {return 0;} + virtual double compute_vector(int /* n */) const {return 0;} /** final work at the end of a run */ virtual void finish(); @@ -123,14 +123,15 @@ namespace ATC { virtual void pack_fields(RESTART_LIST & data); /** thermo output */ - virtual int size_vector(int s) const {return 0;}; + virtual int size_vector(int /* s */) const {return 0;}; // coupling to FE state /** FE state variable regulator is applied to */ virtual RegulatorTargetType regulator_target() const {return regulatorTarget_;}; /** type of boundary coupling */ //TEMP_JAT field variable should be removed - virtual RegulatorCouplingType coupling_mode(const FieldName field=NUM_TOTAL_FIELDS) const {return couplingMode_;}; + virtual RegulatorCouplingType coupling_mode(const FieldName /* field */) const {return couplingMode_;}; + virtual RegulatorCouplingType coupling_mode() const {return couplingMode_;}; /** compute the thermal boundary flux, must be consistent with regulator */ virtual void compute_boundary_flux(FIELDS & fields); /** add contributions (if any) to the finite element right-hand side */ @@ -140,7 +141,7 @@ namespace ATC { /** returns a pointer to the DENS_MAN associated with the tag, creates a new data member if necessary */ DENS_MAN * regulator_data(const std::string tag, int nCols); /** can externally set regulator dynamic contributions */ - virtual void reset_lambda_contribution(const DENS_MAT & target, const FieldName field) {}; + virtual void reset_lambda_contribution(const DENS_MAT & /* target */, const FieldName /* field */) {}; virtual void reset_lambda_contribution(const DENS_MAT & target) { reset_lambda_contribution(target,NUM_TOTAL_FIELDS); } /** returns a const pointer to the DENS_MAN associated with the tag, or NULL */ const DENS_MAN * regulator_data(const std::string tag) const; @@ -291,29 +292,29 @@ namespace ATC { virtual void reset_nlocal(){}; /** set up atom to material identification */ - virtual void reset_atom_materials(const Array & elementToMaterialMap, - const MatrixDependencyManager * atomElement){}; + virtual void reset_atom_materials(const Array & /* elementToMaterialMap */, + const MatrixDependencyManager * /* atomElement */){}; /** applies regulator to atoms in the pre-predictor phase */ - virtual void apply_pre_predictor(double dt){}; + virtual void apply_pre_predictor(double /* dt */){}; /** applies regulator to atoms in the mid-predictor phase */ - virtual void apply_mid_predictor(double dt){}; + virtual void apply_mid_predictor(double /* dt */){}; /** applies regulator to atoms in the post-predictor phase */ - virtual void apply_post_predictor(double dt){}; + virtual void apply_post_predictor(double /* dt */){}; /** applies regulator to atoms in the pre-corrector phase */ - virtual void apply_pre_corrector(double dt){}; + virtual void apply_pre_corrector(double /* dt */){}; /** applies regulator to atoms in the post-corrector phase */ - virtual void apply_post_corrector(double dt){}; + virtual void apply_post_corrector(double /* dt */){}; /** applies regulator to atoms in the pre-corrector phase */ - virtual void apply_pre_force(double dt){}; + virtual void apply_pre_force(double /* dt */){}; /** applies regulator to atoms in the post-corrector phase */ - virtual void apply_post_force(double dt){}; + virtual void apply_post_force(double /* dt */){}; /** applies regulator in pre-force phase */ virtual void pre_force(){}; @@ -328,17 +329,17 @@ namespace ATC { virtual void compute_boundary_flux(FIELDS & fields); /** add contributions (if any) to the finite element right-hand side */ - virtual void add_to_rhs(FIELDS & rhs){}; + virtual void add_to_rhs(FIELDS & /* rhs */){}; /** get data for output */ - virtual void output(OUTPUT_LIST & outputData){}; - virtual double compute_vector(int n) const {return 0;} + virtual void output(OUTPUT_LIST & /* outputData */){}; + virtual double compute_vector(int /* n */) const {return 0;} /** final work at the end of a run */ virtual void finish(){}; /** pack fields for restart */ - virtual void pack_fields(RESTART_LIST & data){}; + virtual void pack_fields(RESTART_LIST & /* data */){}; protected: diff --git a/lib/atc/BodyForce.h b/lib/atc/BodyForce.h index eef5df03bece9d6831739919a81f072565e06899..10d7cf66c11b9785e283d1d89ffffe289df1d238 100644 --- a/lib/atc/BodyForce.h +++ b/lib/atc/BodyForce.h @@ -18,8 +18,8 @@ namespace ATC { public: BodyForce() {}; virtual ~BodyForce() {}; - virtual bool body_force(const FIELD_MATS &fields, - DENS_MAT &flux) const { return false; }; + virtual bool body_force(const FIELD_MATS & /* fields */, + DENS_MAT & /* flux */) const { return false; }; }; /** @@ -49,7 +49,7 @@ namespace ATC { class BodyForceElectricField : public BodyForce { public: - BodyForceElectricField(std::fstream &matfile,std::map & parameters) + BodyForceElectricField(std::fstream & /* matfile */,std::map & /* parameters */) { throw ATC_Error("unimplemented due to issues with accessing electric field"); } virtual ~BodyForceElectricField() {}; virtual bool body_force(const FIELD_MATS &fields, diff --git a/lib/atc/CbPotential.h b/lib/atc/CbPotential.h index 44b9b7c1de7d3e8fc0b7502611366f949a4eae06..e218ae2254a8a095581026f9dd783f22ced406ad 100644 --- a/lib/atc/CbPotential.h +++ b/lib/atc/CbPotential.h @@ -40,7 +40,7 @@ namespace ATC //! @name Pairwise interaction term and derivatives. //@{ - virtual double phi (const double &r) const { return 0.0; } + virtual double phi (const double & /* r */) const { return 0.0; } virtual double phi_r (const double &r) const; virtual double phi_rr (const double &r) const; virtual double phi_rrr(const double &r) const; @@ -48,11 +48,11 @@ namespace ATC //! @name Embedding terms. Electron cloud density and embedding functions //@{ - virtual double rho (const double &r) const { return 0.0; } + virtual double rho (const double & /* r */) const { return 0.0; } virtual double rho_r (const double &r) const; virtual double rho_rr(const double &r) const; virtual double rho_rrr(const double &r) const; - virtual double F (const double &p) const { return 0.0; } + virtual double F (const double & /* p */) const { return 0.0; } virtual double F_p (const double &p) const; virtual double F_pp(const double &p) const; virtual double F_ppp(const double &p) const; @@ -60,7 +60,7 @@ namespace ATC //! @name Three-body terms and derivatives //@{ - virtual double phi3 (const double &q) const {return 0.0; } + virtual double phi3 (const double & /* q */) const {return 0.0; } virtual double phi3_q (const double &q) const; virtual double phi3_qq(const double &q) const; //@} diff --git a/lib/atc/ChargeRegulator.cpp b/lib/atc/ChargeRegulator.cpp index 2e899fcc8e830a4309ab4fadaabf9c32c4de6dc6..cbfda69480eb49dc3636e0cc7c09c84f24ecbede 100644 --- a/lib/atc/ChargeRegulator.cpp +++ b/lib/atc/ChargeRegulator.cpp @@ -53,7 +53,7 @@ namespace ATC { // parses and adjusts charge regulator state based on // user input, in the style of LAMMPS user input //-------------------------------------------------------- - bool ChargeRegulator::modify(int narg, char **arg) + bool ChargeRegulator::modify(int /* narg */, char ** /* arg */) { bool foundMatch = false; return foundMatch; @@ -241,7 +241,7 @@ namespace ATC { //-------------------------------------------------------- // output //-------------------------------------------------------- - void ChargeRegulatorMethod::output(OUTPUT_LIST & outputData) + void ChargeRegulatorMethod::output(OUTPUT_LIST & /* outputData */) { //vector localSum(sum_.size()); //lammpsInteface_->allsum(localSum.pointer,sum_.pointer,sum_.size()); @@ -383,7 +383,7 @@ namespace ATC { //-------------------------------------------------------- // change potential/charge pre-force calculation //-------------------------------------------------------- - void ChargeRegulatorMethodFeedback::apply_pre_force(double dt) + void ChargeRegulatorMethodFeedback::apply_pre_force(double /* dt */) { sum_ = 0; @@ -455,7 +455,7 @@ namespace ATC { //-------------------------------------------------------- // change potential/charge post-force calculation //-------------------------------------------------------- - void ChargeRegulatorMethodImageCharge::apply_post_force(double dt) + void ChargeRegulatorMethodImageCharge::apply_post_force(double /* dt */) { sum_ = 0; apply_local_forces(); @@ -644,7 +644,7 @@ namespace ATC { //-------------------------------------------------------- // add effective forces post LAMMPS force call //-------------------------------------------------------- - void ChargeRegulatorMethodEffectiveCharge::apply_post_force(double dt) + void ChargeRegulatorMethodEffectiveCharge::apply_post_force(double /* dt */) { apply_local_forces(); } diff --git a/lib/atc/ChargeRegulator.h b/lib/atc/ChargeRegulator.h index b51707b9cd0fb6ffc04a6467836e9b6eadc48064..f250a955e8cc8418537c38f685434846082900dc 100644 --- a/lib/atc/ChargeRegulator.h +++ b/lib/atc/ChargeRegulator.h @@ -65,7 +65,7 @@ namespace ATC { virtual void apply_pre_force(double dt); virtual void apply_post_force(double dt); virtual void output(OUTPUT_LIST & outputData) const; - virtual double compute_vector(int n) const {return 0;} // TODO + virtual double compute_vector(int /* n */) const {return 0;} // TODO void assign_poisson_solver(PoissonSolver * solver) { poissonSolver_ = solver;} PoissonSolver * poisson_solver(void) { return poissonSolver_;} @@ -97,8 +97,8 @@ namespace ATC { ~ChargeRegulatorMethod(){}; virtual void initialize(void); void set_greens_functions(); - virtual void apply_pre_force(double dt){}; - virtual void apply_post_force(double dt){}; + virtual void apply_pre_force(double /* dt */){}; + virtual void apply_post_force(double /* dt */){}; virtual void set_weights() {}; const DENS_VEC & total_influence() const { return sum_;} virtual void output(OUTPUT_LIST & outputData); diff --git a/lib/atc/CloneVector.h b/lib/atc/CloneVector.h index 0c3bef8c5931840f67cb80e29404137ab9bb91c8..02db700f279b0e08c099d0d350c87ce027aec84a 100644 --- a/lib/atc/CloneVector.h +++ b/lib/atc/CloneVector.h @@ -72,7 +72,7 @@ CloneVector::CloneVector(const Matrix &c, int dim, INDEX idx) // Construct from a DiagonalMatrix //----------------------------------------------------------------------------- template -CloneVector::CloneVector(const DiagonalMatrix &c, INDEX idx) +CloneVector::CloneVector(const DiagonalMatrix &c, INDEX /* idx */) : Vector(), _baseV(NULL), _baseM(const_cast*>(&c)) , _clone_type(CLONE_DIAG), _idx(0) {} @@ -80,7 +80,7 @@ CloneVector::CloneVector(const DiagonalMatrix &c, INDEX idx) // value (const) indexing operator //----------------------------------------------------------------------------- template -T CloneVector::operator()(INDEX i, INDEX j) const + T CloneVector::operator()(INDEX i, INDEX /* j */) const { return (*this)[i]; } @@ -88,7 +88,7 @@ T CloneVector::operator()(INDEX i, INDEX j) const // reference index operator //----------------------------------------------------------------------------- template -T& CloneVector::operator()(INDEX i, INDEX j) +T& CloneVector::operator()(INDEX i, INDEX /* j */) { return (*this)[i]; } diff --git a/lib/atc/ConcentrationRegulator.cpp b/lib/atc/ConcentrationRegulator.cpp index c734a5d98db3b49aea427223d398fc54708e6579..8055433f5da68ae181d2e7cadeec5862bc769a3b 100644 --- a/lib/atc/ConcentrationRegulator.cpp +++ b/lib/atc/ConcentrationRegulator.cpp @@ -47,7 +47,7 @@ const double kMinScale_ = 10000.; // parses and adjusts charge regulator state based on // user input, in the style of LAMMPS user input //-------------------------------------------------------- - bool ConcentrationRegulator::modify(int narg, char **arg) + bool ConcentrationRegulator::modify(int /* narg */, char ** /* arg */) { bool foundMatch = false; return foundMatch; @@ -166,7 +166,7 @@ const double kMinScale_ = 10000.; //-------------------------------------------------------- // size vector //-------------------------------------------------------- - int ConcentrationRegulator::size_vector(int i) const + int ConcentrationRegulator::size_vector(int /* i */) const { int n = (regulators_.size())*5; if (n==0) n = 20; @@ -319,7 +319,7 @@ const double kMinScale_ = 10000.; //-------------------------------------------------------- // accept //-------------------------------------------------------- - bool ConcentrationRegulatorMethodTransition::accept(double energy, double T) const + bool ConcentrationRegulatorMethodTransition::accept(double energy, double /* T */) const { #ifdef ATC_VERBOSE2 if (energy < maxEnergy_) lammpsInterface_->print_msg(" energy "+to_string(energy)+" "+to_string(rngCounter_)); @@ -423,7 +423,7 @@ const double kMinScale_ = 10000.; int * tag = lammpsInterface_->atom_tag(); for (itr = list.begin(); itr != list.end(); itr++) { int atag = tag[itr->second]; - double d = abs(atag-r); + double d = fabs(atag-r); if (d < min) { min = d; idx = i; diff --git a/lib/atc/ConcentrationRegulator.h b/lib/atc/ConcentrationRegulator.h index 3645880cc51d9b541f2ae29bb97d58ea2e388a53..952cf883394da9cfafa0ca5ba1188b19f6d5febd 100644 --- a/lib/atc/ConcentrationRegulator.h +++ b/lib/atc/ConcentrationRegulator.h @@ -60,19 +60,19 @@ namespace ATC { //WIP_JAT need a nicer way to consistently handle sets of regulators, not sure how yet // application steps /** apply the regulator in the pre-predictor phase */ - virtual void apply_pre_predictor(double dt, int timeStep){}; + virtual void apply_pre_predictor(double /* dt */, int /* timeStep */){}; /** apply the regulator in the mid-predictor phase */ - virtual void apply_mid_predictor(double dt, int timeStep){}; + virtual void apply_mid_predictor(double /* dt */, int /* timeStep */){}; /** apply the regulator in the post-predictor phase */ - virtual void apply_post_predictor(double dt, int timeStep){}; + virtual void apply_post_predictor(double /* dt */, int /* timeStep */){}; /** apply the regulator in the pre-correction phase */ - virtual void apply_pre_corrector(double dt, int timeStep){}; + virtual void apply_pre_corrector(double /* dt */, int /* timeStep */){}; /** apply the regulator in the post-correction phase */ - virtual void apply_post_corrector(double dt, int timeStep){}; + virtual void apply_post_corrector(double /* dt */, int /* timeStep */){}; /** compute the thermal boundary flux, must be consistent with regulator */ - virtual void compute_boundary_flux(FIELDS & fields){}; + virtual void compute_boundary_flux(FIELDS & /* fields */){}; /** add contributions (if any) to the finite element right-hand side */ - virtual void add_to_rhs(FIELDS & rhs){}; + virtual void add_to_rhs(FIELDS & /* rhs */){}; /** prior to exchanges */ virtual void pre_force(); @@ -113,8 +113,8 @@ namespace ATC { virtual void pre_exchange() {}; virtual void finish() {}; virtual void set_weights() {}; - virtual double compute_vector(int n) const { return 0;} - virtual void output(OUTPUT_LIST & outputData){}; + virtual double compute_vector(int /* n */) const { return 0;} + virtual void output(OUTPUT_LIST & /* outputData */){}; private: ConcentrationRegulatorMethod(); // DO NOT define this }; @@ -144,7 +144,7 @@ namespace ATC { virtual double compute_vector(int n) const; protected: /** set transition state: epsilon and charge */ - int mask(int type, int groupbit) {return 0;} + int mask(int /* type */, int /* groupbit */) {return 0;} int count(void) const; int excess(void) const; double energy(int id) const; diff --git a/lib/atc/DenseVector.h b/lib/atc/DenseVector.h index 70e223d988ea0a7d066c0bbf9557018e5db29aae..38ed68f937d048191afa159ba1f4242f9f5b0851 100644 --- a/lib/atc/DenseVector.h +++ b/lib/atc/DenseVector.h @@ -31,8 +31,10 @@ public: // overloaded inline virtual functions T operator[](INDEX i) const { VICK(i) return _data[i]; } T& operator[](INDEX i) { VICK(i) return _data[i]; } - T operator()(INDEX i, INDEX j=0) const { VICK(i) return _data[i]; } - T& operator()(INDEX i, INDEX j=0) { VICK(i) return _data[i]; } + T operator()(INDEX i, INDEX /* j */) const { VICK(i) return _data[i]; } + T& operator()(INDEX i, INDEX /* j */) { VICK(i) return _data[i]; } + T operator()(INDEX i) const { VICK(i) return _data[i]; } + T& operator()(INDEX i) { VICK(i) return _data[i]; } void set_all_elements_to(const T &v) { int sz = this->size(); for (INDEX i = 0; i < sz; i++) _data[i] = v; @@ -62,7 +64,7 @@ private: // resizes the matrix and optionally copies over what still fits, ignores cols //----------------------------------------------------------------------------- template -void DenseVector::resize(INDEX rows, INDEX cols, bool copy) + void DenseVector::resize(INDEX rows, INDEX /* cols */, bool copy) { if (_size==rows) return; // if is correct size, done if (!copy) diff --git a/lib/atc/DiagonalMatrix.h b/lib/atc/DiagonalMatrix.h index 516fb478785b0c3aabcdc1bd19b7539864a9a3c5..6c2fe23144665544da4a6f093006340f43ef1741 100644 --- a/lib/atc/DiagonalMatrix.h +++ b/lib/atc/DiagonalMatrix.h @@ -49,7 +49,8 @@ class DiagonalMatrix : public Matrix void write_restart(FILE *f) const; // Dump matrix contents to screen (not defined for all datatypes) - std::string to_string(int p=myPrecision) const { return _data->to_string(); } + std::string to_string(int /* p */) const { return _data->to_string(); } + std::string to_string() const { return _data->to_string(); } using Matrix::matlab; void matlab(std::ostream &o, const std::string &s="D") const; @@ -78,8 +79,8 @@ class DiagonalMatrix : public Matrix protected: void _set_equal(const Matrix &r); - DiagonalMatrix& operator=(const Vector &c) {} - DiagonalMatrix& operator=(const Matrix &c) {} + DiagonalMatrix& operator=(const Vector & /* c */) {} + DiagonalMatrix& operator=(const Matrix & /* c */) {} private: void _delete(); @@ -246,7 +247,7 @@ void DiagonalMatrix::_delete() // resizes the matrix, ignores nCols, optionally zeros //----------------------------------------------------------------------------- template -void DiagonalMatrix::reset(INDEX rows, INDEX cols, bool zero) +void DiagonalMatrix::reset(INDEX rows, INDEX /* cols */, bool zero) { _delete(); _data = new DenseVector(rows, zero); @@ -255,7 +256,7 @@ void DiagonalMatrix::reset(INDEX rows, INDEX cols, bool zero) // resizes the matrix, ignores nCols, optionally copies what fits //----------------------------------------------------------------------------- template -void DiagonalMatrix::resize(INDEX rows, INDEX cols, bool copy) +void DiagonalMatrix::resize(INDEX rows, INDEX /* cols */, bool copy) { _data->resize(rows, copy); } @@ -327,7 +328,7 @@ void DiagonalMatrix::shallowreset(const DenseMatrix &c) // reference indexing operator - must throw an error if i!=j //----------------------------------------------------------------------------- template -T& DiagonalMatrix::operator()(INDEX i, INDEX j) +T& DiagonalMatrix::operator()(INDEX i, INDEX /* j */) { GCK(*this,*this,i!=j,"DiagonalMatrix: tried to index off diagonal"); return (*this)[i]; diff --git a/lib/atc/ElasticTimeIntegrator.cpp b/lib/atc/ElasticTimeIntegrator.cpp index c2a592d46c73af0907ac531f82417cf1e21da32a..9793f6a58ed1bb9c29631fcad5957a78b977e7ee 100644 --- a/lib/atc/ElasticTimeIntegrator.cpp +++ b/lib/atc/ElasticTimeIntegrator.cpp @@ -27,7 +27,7 @@ namespace ATC { // modify // parses inputs and modifies state of the integrator //-------------------------------------------------------- - bool MomentumTimeIntegrator::modify(int narg, char **arg) + bool MomentumTimeIntegrator::modify(int /* narg */, char **arg) { bool foundMatch = false; int argIndex = 0; @@ -611,7 +611,7 @@ namespace ATC { // compute_velocity_delta //-------------------------------------------------------- void ElasticTimeIntegratorFractionalStep::compute_velocity_delta(const DENS_MAT & atomicMomentumDelta, - double dt) + double /* dt */) { DENS_MAT & myAtomicVelocityDelta(atomicVelocityDelta_.set_quantity()); myAtomicVelocityDelta = nodalAtomicMomentumOld_ + atomicMomentumDelta; @@ -832,7 +832,7 @@ namespace ATC { // compute_velocity_delta //-------------------------------------------------------- void FluidsTimeIntegratorGear::compute_velocity_delta(const DENS_MAT & atomicMomentumDelta, - double dt) + double /* dt */) { DENS_MAT & myAtomicVelocityDelta(atomicVelocityDelta_.set_quantity()); myAtomicVelocityDelta = nodalAtomicMomentumOld_ + atomicMomentumDelta; diff --git a/lib/atc/ElectronChargeDensity.cpp b/lib/atc/ElectronChargeDensity.cpp index 69127a9335ce6e4c43a52677510d4922e3507328..14c764e46e7416e784a61d6cc4cb3a72d2db7daa 100644 --- a/lib/atc/ElectronChargeDensity.cpp +++ b/lib/atc/ElectronChargeDensity.cpp @@ -14,7 +14,7 @@ using std::vector; namespace ATC { ElectronChargeDensityInterpolation::ElectronChargeDensityInterpolation( - fstream &fileId, map & parameters) + fstream &fileId, map & /* parameters */) : ElectronChargeDensity(), n_() { if (!fileId.is_open()) throw ATC_Error("cannot open material file"); diff --git a/lib/atc/ElectronChargeDensity.h b/lib/atc/ElectronChargeDensity.h index a5288c0b19086ec0f630e0a9093eb9456f63ec05..ac6052a9ef48d9c7eb359fd8f81f9837c3f3c761 100644 --- a/lib/atc/ElectronChargeDensity.h +++ b/lib/atc/ElectronChargeDensity.h @@ -21,17 +21,17 @@ namespace ATC { public: ElectronChargeDensity() {}; virtual ~ElectronChargeDensity() {}; - virtual bool electron_charge_density(const FIELD_MATS &fields, - DENS_MAT &flux) const { return false; }; + virtual bool electron_charge_density(const FIELD_MATS & /* fields */, + DENS_MAT & /* flux */) const { return false; }; - virtual void D_electron_charge_density(const FieldName fieldName, - const FIELD_MATS &fields, - DENS_MAT &flux) const + virtual void D_electron_charge_density(const FieldName /* fieldName */, + const FIELD_MATS & /* fields */, + DENS_MAT & /* flux */) const { throw ATC_Error("Charge density D_electron_charge_density unimplemented function");} - virtual void band_edge_potential(const FIELD_MATS &fields, - DENS_MAT &density) const + virtual void band_edge_potential(const FIELD_MATS & /* fields */, + DENS_MAT & /* density */) const { throw ATC_Error("Charge density band_edge_potential unimplemented function");} }; //----------------------------------------------------------------------- @@ -58,7 +58,7 @@ namespace ATC { flux *= -1.; return true; }; - virtual void D_electron_charge_density(const FieldName field, + virtual void D_electron_charge_density(const FieldName /* field */, const FIELD_MATS &fields, DENS_MAT &coef) const { @@ -94,7 +94,7 @@ namespace ATC { flux *= -C_; return true; }; - virtual void D_electron_charge_density(const FieldName field, + virtual void D_electron_charge_density(const FieldName /* field */, const FIELD_MATS &fields, DENS_MAT &coef) const { @@ -150,7 +150,7 @@ namespace ATC { density *= -1.; return true; }; - virtual void D_electron_charge_density(const FieldName field, + virtual void D_electron_charge_density(const FieldName /* field */, const FIELD_MATS &fields, DENS_MAT &coef) const { @@ -235,7 +235,7 @@ namespace ATC { } return true; }; - virtual void D_electron_charge_density(const FieldName fieldName, + virtual void D_electron_charge_density(const FieldName /* fieldName */, const FIELD_MATS &fields, DENS_MAT &coef) const { diff --git a/lib/atc/ElectronDragPower.cpp b/lib/atc/ElectronDragPower.cpp index aff6be610622555fa5ec458d7ac48d8d520aec8f..7fe31f0120a7b9b520d6da13e2df83535dc61c36 100644 --- a/lib/atc/ElectronDragPower.cpp +++ b/lib/atc/ElectronDragPower.cpp @@ -39,7 +39,7 @@ ElectronDragPowerLinear::ElectronDragPowerLinear(fstream &fileId, } bool ElectronDragPowerLinear::electron_drag_power(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, DENS_MAT & flux) { diff --git a/lib/atc/ElectronDragPower.h b/lib/atc/ElectronDragPower.h index 92103fe3e8993faf980bdbb826a6d4bcce8b6cd3..12c1472e37e37839af27388fa32ac62efffc99e4 100644 --- a/lib/atc/ElectronDragPower.h +++ b/lib/atc/ElectronDragPower.h @@ -21,9 +21,9 @@ namespace ATC { ElectronDragPower() {}; virtual ~ElectronDragPower() {}; /** computes drag power */ - virtual bool electron_drag_power(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, - DENS_MAT & flux) + virtual bool electron_drag_power(const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* gradFields */, + DENS_MAT & /* flux */) { return false; }; diff --git a/lib/atc/ElectronFlux.cpp b/lib/atc/ElectronFlux.cpp index 8ae8503a311b53ab28b08f0580f40ecc24ae4e75..4894a32daea8e92863dc8cc2d2501e27820f2799 100644 --- a/lib/atc/ElectronFlux.cpp +++ b/lib/atc/ElectronFlux.cpp @@ -79,7 +79,7 @@ ElectronFluxThermopower::ElectronFluxThermopower( } ElectronFluxConvection::ElectronFluxConvection( - fstream &fileId, map & parameters) + fstream &fileId, map & /* parameters */) : ElectronFlux() { if (!fileId.is_open()) throw ATC_Error("cannot open material file"); diff --git a/lib/atc/ElectronFlux.h b/lib/atc/ElectronFlux.h index 013f9aac4250e29efd5fc3dea7fec1ce44c7fa41..b9cfd2305cf7154e70e0aa34ba751236c4835134 100644 --- a/lib/atc/ElectronFlux.h +++ b/lib/atc/ElectronFlux.h @@ -19,7 +19,7 @@ namespace ATC { virtual ~ElectronFlux() {}; /** computes flux */ virtual void electron_flux(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, DENS_MAT_VEC &flux) { @@ -211,7 +211,7 @@ namespace ATC { ElectronFluxConvection(std::fstream &matfile,std::map & parameters); virtual ~ElectronFluxConvection() {}; virtual void electron_flux(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, DENS_MAT_VEC &flux) { // flux = n v diff --git a/lib/atc/ElectronHeatCapacity.h b/lib/atc/ElectronHeatCapacity.h index aefc3d681ce746a7f4282f198b6f752e3230ad3d..f27d8193a024cb8b27acb28f9c6ed846f6f47097 100644 --- a/lib/atc/ElectronHeatCapacity.h +++ b/lib/atc/ElectronHeatCapacity.h @@ -51,7 +51,7 @@ namespace ATC { capacity = electronHeatCapacity_; }; virtual void D_electron_heat_capacity(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, DENS_MAT_VEC & Dcapacity) { FIELD_MATS::const_iterator etField = fields.find(ELECTRON_TEMPERATURE); @@ -91,7 +91,7 @@ namespace ATC { const DENS_MAT & T = etField->second; capacity = electronHeatCapacity_*T; }; - virtual void D_electron_heat_capacity(const FIELD_MATS &fields, + virtual void D_electron_heat_capacity(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &Dcapacity) { diff --git a/lib/atc/ElectronHeatFlux.h b/lib/atc/ElectronHeatFlux.h index 12a68fed7090be6c976a1008bda0cde97ddc96d7..41c89d6c6d681af2f44a86b44717081c23dfe1ad 100644 --- a/lib/atc/ElectronHeatFlux.h +++ b/lib/atc/ElectronHeatFlux.h @@ -21,7 +21,7 @@ namespace ATC { virtual ~ElectronHeatFlux() {}; /** computes heat flux */ virtual void electron_heat_flux(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, DENS_MAT_VEC &flux) { @@ -70,7 +70,7 @@ namespace ATC { ElectronHeatFluxLinear(std::fstream &matfile,std::map & parameters, /*const*/ ElectronHeatCapacity * electronHeatCapacity = NULL); virtual ~ElectronHeatFluxLinear() {}; - virtual void electron_heat_flux(const FIELD_MATS &fields, + virtual void electron_heat_flux(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &flux) { diff --git a/lib/atc/ElectronPhononExchange.h b/lib/atc/ElectronPhononExchange.h index 59cc61b4d278366f8eea702a85757e04c8d89ad9..303745151340c58d75cb746f0864b339226d3f2c 100644 --- a/lib/atc/ElectronPhononExchange.h +++ b/lib/atc/ElectronPhononExchange.h @@ -21,8 +21,8 @@ namespace ATC { ElectronPhononExchange() {}; virtual ~ElectronPhononExchange() {}; /** computes heat capacity */ - virtual bool electron_phonon_exchange(const FIELD_MATS &fields, - DENS_MAT &flux) { return false; } + virtual bool electron_phonon_exchange(const FIELD_MATS & /* fields */, + DENS_MAT & /* flux */) { return false; } }; //------------------------------------------------------------------- diff --git a/lib/atc/ExtrinsicModel.cpp b/lib/atc/ExtrinsicModel.cpp index cdf556f4c1a1f5b7f98bf859efbf4ad5bad39285..b20b2a26d17ffa72d6e77064780d3c13df2a4fff 100644 --- a/lib/atc/ExtrinsicModel.cpp +++ b/lib/atc/ExtrinsicModel.cpp @@ -114,7 +114,7 @@ namespace ATC { ATC::LammpsInterface::instance()->print_msg_once(ss.str()); myModel = new ExtrinsicModelElectrostatic (this,modelType,matFileName); - } + } else myModel = NULL; extrinsicModels_.push_back(myModel); // add new fields to fields data @@ -339,7 +339,7 @@ namespace ATC { //-------------------------------------------------------- ExtrinsicModel::ExtrinsicModel(ExtrinsicModelManager * modelManager, ExtrinsicModelType modelType, - string matFileName) : + string /* matFileName */) : atc_(modelManager->atc()), modelManager_(modelManager), modelType_(modelType), diff --git a/lib/atc/ExtrinsicModel.h b/lib/atc/ExtrinsicModel.h index 99acf59ef263ffeb4130ad45d92d7e6671d4f658..66282fb505e0903829a2eabfe538b39d7a6abb3a 100644 --- a/lib/atc/ExtrinsicModel.h +++ b/lib/atc/ExtrinsicModel.h @@ -221,7 +221,7 @@ namespace ATC { virtual ~ExtrinsicModel(); /** parser/modifier */ - virtual bool modify(int narg, char **arg) {return false;}; + virtual bool modify(int /* narg */, char ** /* arg */) {return false;}; /** construct transfers needed by the model */ virtual void construct_transfers(){}; @@ -230,11 +230,11 @@ namespace ATC { virtual void initialize(); /** set up LAMMPS display variables */ - virtual int size_vector(int externalSize) {return 0;}; + virtual int size_vector(int /* externalSize */) {return 0;}; /** get LAMMPS display variables */ virtual double compute_scalar(void) { return 0.0; } - virtual bool compute_vector(int n, double & value) {return false;}; + virtual bool compute_vector(int /* n */, double & /* value */) {return false;}; /** post integration run */ // is this called at end of run or simulation @@ -259,10 +259,10 @@ namespace ATC { virtual void post_final_integrate(){}; /** Set sources to AtC equation */ - virtual void set_sources(FIELDS & fields, FIELDS & sources){}; + virtual void set_sources(FIELDS & /* fields */, FIELDS & /* sources */){}; /** Add model-specific output data */ - virtual void output(OUTPUT_LIST & outputData){}; + virtual void output(OUTPUT_LIST & /* outputData */){}; /** get the fields and their sizes */ void num_fields(std::map & fieldSizes); diff --git a/lib/atc/ExtrinsicModelElectrostatic.cpp b/lib/atc/ExtrinsicModelElectrostatic.cpp index 03766920e3588e50fd0152534b40a44386136ff8..b10e77a3069bacbc8e78c07d618a23c311e5127b 100644 --- a/lib/atc/ExtrinsicModelElectrostatic.cpp +++ b/lib/atc/ExtrinsicModelElectrostatic.cpp @@ -827,7 +827,7 @@ namespace ATC { // apply_charged_surfaces //-------------------------------------------------------- void ExtrinsicModelElectrostatic::apply_charged_surfaces - (MATRIX & potential) + (MATRIX & /* potential */) { //double qE2f = LammpsInterface::instance()->qe2f(); double qV2e = LammpsInterface::instance()->qv2e(); diff --git a/lib/atc/FE_Engine.cpp b/lib/atc/FE_Engine.cpp index efcde66d782fa9ce27bd596ad3418645c6b30b2f..bef135a5f24fd68be94e01a868a1e4c755f34cc3 100644 --- a/lib/atc/FE_Engine.cpp +++ b/lib/atc/FE_Engine.cpp @@ -721,7 +721,7 @@ namespace ATC{ const SPAR_MAT &N, const SPAR_MAT_VEC &dN, SPAR_MAT &tangent, - const DenseMatrix *elementMask ) const + const DenseMatrix * /* elementMask */ ) const { int nn = nNodesUnique_; FieldName rowField = row_col.first; @@ -1298,7 +1298,7 @@ namespace ATC{ const PhysicsModel * physicsModel, const Array & elementMaterials, FIELDS &rhs, - bool freeOnly, + bool /* freeOnly */, const DenseMatrix *elementMask) const { vector usedFields; @@ -2503,7 +2503,7 @@ namespace ATC{ // previously computed nodal sources //----------------------------------------------------------------- void FE_Engine::add_sources(const Array &fieldMask, - const double time, + const double /* time */, const FIELDS &sources, FIELDS &nodalSources) const { diff --git a/lib/atc/FE_Engine.h b/lib/atc/FE_Engine.h index bc3fb0e4a56a36b3b67d4c82c4cedda99411db35..18dae0e6b4737160e9744d84b80db2106798df2b 100644 --- a/lib/atc/FE_Engine.h +++ b/lib/atc/FE_Engine.h @@ -345,7 +345,7 @@ namespace ATC { /** integrate a nodal field over an face set */ - DENS_VEC integrate(const DENS_MAT &field, const FSET & fset) const + DENS_VEC integrate(const DENS_MAT & /* field */, const FSET & /* fset */) const { throw ATC_Error(FILELINE,"unimplemented function"); } /*@}*/ @@ -496,7 +496,8 @@ namespace ATC { /** set kernel */ void set_kernel(KernelFunction* ptr); - KernelFunction *kernel(int i=0) { return kernelFunction_; } + KernelFunction *kernel(int /* i */) { return kernelFunction_; } + KernelFunction *kernel() { return kernelFunction_; } private: //---------------------------------------------------------------- diff --git a/lib/atc/FE_Mesh.cpp b/lib/atc/FE_Mesh.cpp index b090bf2881bdbb9855c7098ccc7b5f2a6d4a4f7a..4ea10a681af5cc62a843ad98307705637506d993 100644 --- a/lib/atc/FE_Mesh.cpp +++ b/lib/atc/FE_Mesh.cpp @@ -797,7 +797,7 @@ namespace ATC { { int node = element_connectivity_unique(ielem, inode); nodeSet.insert(node); - inode++; + inode++; // XXX: is this correct? } } } @@ -832,7 +832,7 @@ namespace ATC { { int node = element_connectivity_unique(ielem, inode); nodeSet.erase(node); - inode++; + inode++; // XXX: is this correct? } } } @@ -1788,7 +1788,7 @@ namespace ATC { // ------------------------------------------------------------- // setup_periodicity // ------------------------------------------------------------- - void FE_3DMesh::setup_periodicity(double tol) + void FE_3DMesh::setup_periodicity(double /* tol */) { // unique <-> global id maps globalToUniqueMap_.reset(nNodes_); @@ -2119,10 +2119,9 @@ namespace ATC { // divide between all processors, we get the next-highest // power of 2. vector > procEltLists = tree_->getElemIDs(depth); - int numEltLists = procEltLists.size(); // Make sure the KD tree is behaving as expected. - assert(numEltLists >= nProcs); + assert(procEltLists.size() >= nProcs); // If the KD-tree was not able to return enough divisions, // duplicate the largest list. diff --git a/lib/atc/FE_Mesh.h b/lib/atc/FE_Mesh.h index be40d7cb28e21265646d5320a2ecce105eddb98c..0b2df7b65600d0a63ecfc809215761ebc1721130 100644 --- a/lib/atc/FE_Mesh.h +++ b/lib/atc/FE_Mesh.h @@ -691,7 +691,7 @@ namespace ATC { void departition_mesh(void); - virtual void element_size(const int ielem, + virtual void element_size(const int /* ielem */, double &hx, double &hy, double &hz) { hx = L_[0]/n_[0]; hy = L_[1]/n_[1]; hz = L_[2]/n_[2]; } diff --git a/lib/atc/FieldEulerIntegrator.cpp b/lib/atc/FieldEulerIntegrator.cpp index eeea0cd4eb8aa3a17d787ddc1c14cb4701412285..0abc71cbaba6dd1dd2200e86cce99855b3b37a4f 100644 --- a/lib/atc/FieldEulerIntegrator.cpp +++ b/lib/atc/FieldEulerIntegrator.cpp @@ -46,7 +46,7 @@ FieldExplicitEulerIntegrator::FieldExplicitEulerIntegrator( // -------------------------------------------------------------------- // update // -------------------------------------------------------------------- -void FieldExplicitEulerIntegrator::update(const double dt, double time, + void FieldExplicitEulerIntegrator::update(const double dt, double /* time */, FIELDS & fields, FIELDS & rhs) { // write and add update mass matrix to handled time variation @@ -81,7 +81,7 @@ FieldImplicitEulerIntegrator::FieldImplicitEulerIntegrator( // update // -------------------------------------------------------------------- void FieldImplicitEulerIntegrator::update(const double dt, double time, - FIELDS & fields, FIELDS & rhs) + FIELDS & fields, FIELDS & /* rhs */) { // solver handles bcs FieldImplicitSolveOperator solver(atc_, fields, fieldName_, rhsMask_, physicsModel_, @@ -127,8 +127,8 @@ FieldImplicitDirectEulerIntegrator::~FieldImplicitDirectEulerIntegrator() // -------------------------------------------------------------------- // initialize // -------------------------------------------------------------------- -void FieldImplicitDirectEulerIntegrator::initialize(const double dt, double time, - FIELDS & fields) + void FieldImplicitDirectEulerIntegrator::initialize(const double dt, double /* time */, + FIELDS & /* fields */) { std::pair p(fieldName_,fieldName_); Array2D rmask = atc_->rhs_mask(); @@ -140,7 +140,7 @@ void FieldImplicitDirectEulerIntegrator::initialize(const double dt, double time // -------------------------------------------------------------------- // update // -------------------------------------------------------------------- -void FieldImplicitDirectEulerIntegrator::update(const double dt, double time, + void FieldImplicitDirectEulerIntegrator::update(const double /* dt */, double /* time */, FIELDS & fields, FIELDS & rhs) { atc_->compute_rhs_vector(rhsMask_, fields, rhs, diff --git a/lib/atc/FieldEulerIntegrator.h b/lib/atc/FieldEulerIntegrator.h index f349ada5d47b2e5a47b3f1f564770c42627e1ae3..c7b79f85d97b0a4d44cea75a96db7f6332544c77 100644 --- a/lib/atc/FieldEulerIntegrator.h +++ b/lib/atc/FieldEulerIntegrator.h @@ -41,8 +41,8 @@ class FieldEulerIntegrator { virtual ~FieldEulerIntegrator() {}; /** initialize */ - virtual void initialize(const double dt, const double time, - FIELDS & fields) {}; + virtual void initialize(const double /* dt */, const double /* time */, + FIELDS & /* fields */) {}; /** update */ virtual void update(const double dt, const double time, diff --git a/lib/atc/FieldManager.cpp b/lib/atc/FieldManager.cpp index ce9f859533fccb528fefe96a237a0dd41e4fec09..338f06acad81395cef3188acf8d1893e6fcefe67 100644 --- a/lib/atc/FieldManager.cpp +++ b/lib/atc/FieldManager.cpp @@ -298,7 +298,7 @@ typedef PerAtomQuantity PAQ; //----------------------------------------------------------------------------- //* REFERENCE_POTENTIAL_ENERGY //----------------------------------------------------------------------------- - DENS_MAN * FieldManager::reference_potential_energy(string name) + DENS_MAN * FieldManager::reference_potential_energy(string /* name */) { DENS_MAN * rpe = interscaleManager_.dense_matrix(field_to_string(REFERENCE_POTENTIAL_ENERGY)); if (! rpe ) { diff --git a/lib/atc/FieldManager.h b/lib/atc/FieldManager.h index d3db3f268a65da6546c417245bd0fd500e40f610..9a9867641752c1678ac79129a50383570baedcc2 100644 --- a/lib/atc/FieldManager.h +++ b/lib/atc/FieldManager.h @@ -123,7 +123,7 @@ namespace ATC { DENS_MAN * projected_atom_quantity(FieldName field,std::string name, PAQ * atomic, DIAG_MAN * normalization = NULL); DENS_MAN * scaled_projected_atom_quantity(FieldName field,std::string name, PAQ * atomic, double scale, DIAG_MAN * normalization = NULL); DENS_MAN * referenced_projected_atom_quantity(FieldName field, std::string name, PAQ * atomic, DENS_MAN * reference, DIAG_MAN * normalization = NULL); - DENS_MAN * inferred_atom_quantity(FieldName field, std::string name, PAQ * atomic){return NULL;}; + DENS_MAN * inferred_atom_quantity(FieldName /* field */, std::string /* name */, PAQ * /* atomic */){return NULL;}; PAQ * prolonged_field(FieldName field); private: FieldManager(void); diff --git a/lib/atc/Function.cpp b/lib/atc/Function.cpp index 12396937bd75a149285d92ae3435964dcc399738..70f8bbfa41b5e8ade3ac80c0f01b5cad93626bb3 100644 --- a/lib/atc/Function.cpp +++ b/lib/atc/Function.cpp @@ -16,7 +16,7 @@ namespace ATC { //==================================================================== // UXT_Function //=================================================================== - UXT_Function::UXT_Function(int narg, double* args) { } + UXT_Function::UXT_Function(int /* narg */, double* /* args */) { } //==================================================================== // UXT_Function_Mgr //==================================================================== @@ -312,7 +312,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL; } ATC::LammpsInterface::instance()->print_msg_once(ss.str()); } - double PiecewiseLinearFunction::f(double * x, double t) + double PiecewiseLinearFunction::f(double * x, double /* t */) { double s = mask[0]*(x[0]-x0[0])+mask[1]*(x[1]-x0[1])+mask[2]*(x[2]-x0[2]); @@ -355,7 +355,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL; return slope[0]*(x[0]-x0[0])+slope[1]*(x[1]-x0[1])+slope[2]*(x[2]-x0[2]) + C0; } - double LinearTemporalRamp::dfdt(double* x, double t) { + double LinearTemporalRamp::dfdt(double* x, double /* t */) { return mask_slope[0]*(x[0]-x0[0])+mask_slope[1]*(x[1]-x0[1])+mask_slope[2]*(x[2]-x0[2]) + C0_slope; } @@ -499,7 +499,7 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL; if (i == 0) { dx = xs_(1)-xs_(0); } else if (i+1 == npts_) { dx = xs_(npts_-1)-xs_(npts_-2); } else { dx= 0.5*(xs_(i+1)-xs_(i-1)); } - if (abs(dx-dx0) > 1.e-8) throw ATC_Error("InterpolationFunction::initialize non-uniform data spacing not handled currently"); + if (fabs(dx-dx0) > 1.e-8) throw ATC_Error("InterpolationFunction::initialize non-uniform data spacing not handled currently"); fps_(i) *= dx; } // options: calculate / adjust tangents for monotonicity diff --git a/lib/atc/Function.h b/lib/atc/Function.h index 4572009f92a39729fb4b5342aaeb691b8099a76d..0c654fa47ca7c90430d86491977d91ecd0c028db 100644 --- a/lib/atc/Function.h +++ b/lib/atc/Function.h @@ -29,8 +29,8 @@ namespace ATC { virtual inline ARG_NAMES args(void) {ARG_NAMES names; return names;}; /** (1st) derivative of function wrt to a field */ - virtual inline double dfd(FieldName field, ARGS& args ) {return 0.0;}; - virtual inline void dfd(FieldName field, ARGS& args, DENS_MAT vals ) {}; + virtual inline double dfd(FieldName /* field */, ARGS& /* args */) {return 0.0;}; + virtual inline void dfd(FieldName /* field */, ARGS& /* args */, DENS_MAT /* vals */ ) {}; // addl: d2fd2(field1, field2, args), linearization(), grad_args @@ -70,8 +70,8 @@ namespace ATC { LinearFieldFunction(int nargs, char** args); virtual ~LinearFieldFunction(void) {}; - inline double f(double* u, double* x, double t) {return c1_*u[0]-c0_;} - inline double dfd(FieldName field, ARGS& args) {return c1_;} + inline double f(double* u, double* /* x */, double /* t */) {return c1_*u[0]-c0_;} + inline double dfd(FieldName /* field */, ARGS& /* args */) {return c1_;} private : double c0_,c1_; @@ -90,9 +90,9 @@ namespace ATC { const std::string & tag() { return tag_;} /** function value */ - virtual inline double f(double * u, double* x, double t) {return 0.0;}; + virtual inline double f(double * /* u */, double* /* x */, double /* t */) {return 0.0;}; /** derivative of function wrt to field */ - virtual inline double dfdu(double * u, double* x, double t) {return 0.0;}; + virtual inline double dfdu(double * /* u */, double* /* x */, double /* t */) {return 0.0;}; protected: /** tag : name of function */ @@ -136,8 +136,8 @@ namespace ATC { //inline double f(double* u, double* x, double t) {return c1_*(u[0]-c0_);} - inline double f(double* u, double* x, double t) {return c1_*u[0]+c0_;} - inline double dfdu(double* u, double* x, double t) {return c1_;} + inline double f(double* u, double* /* x */, double /* t */) {return c1_*u[0]+c0_;} + inline double dfdu(double* /* u */, double* /* x */, double /* t */) {return c1_;} private : double c0_,c1_; @@ -156,13 +156,13 @@ namespace ATC { const std::string & tag() { return tag_;} /** function value */ - virtual inline double f(double* x, double t) {return 0.0;}; + virtual inline double f(double* /* x */, double /* t */) {return 0.0;}; /** time derivative of function */ - virtual inline double dfdt(double* x, double t) {return 0.0;}; + virtual inline double dfdt(double* /* x */, double /* t */) {return 0.0;}; /** 2nd time derivative of function */ - virtual inline double ddfdt(double* x, double t) {return 0.0;}; + virtual inline double ddfdt(double* /* x */, double /* t */) {return 0.0;}; /** 3rd time derivative of function */ - virtual inline double dddfdt(double* x, double t) {return 0.0;}; + virtual inline double dddfdt(double* /* x */, double /* t */) {return 0.0;}; protected: /** mask : masks x,y,z dependence, x0 : origin */ @@ -210,7 +210,7 @@ namespace ATC { ConstantFunction(double arg); virtual ~ConstantFunction(void) {}; - inline double f(double* x, double t) + inline double f(double* /* x */, double /* t */) {return C0;}; private : @@ -227,7 +227,7 @@ namespace ATC { LinearFunction(int nargs, double* args); virtual ~LinearFunction(void) {}; - double f(double* x, double t) + double f(double* x, double /* t */) {return mask[0]*(x[0]-x0[0])+mask[1]*(x[1]-x0[1])+mask[2]*(x[2]-x0[2]) + C0;}; private : @@ -280,7 +280,7 @@ namespace ATC { QuadraticFunction(int nargs, double* args); virtual ~QuadraticFunction(void) {}; - inline double f(double* x, double t) + inline double f(double* x, double /* t */) {return C2[0]*(x[0]-x0[0])*(x[0]-x0[0])+ C2[1]*(x[1]-x0[1])*(x[1]-x0[1])+ @@ -324,7 +324,7 @@ namespace ATC { virtual ~GaussianFunction(void){}; // 1/(2 pi \sigma)^(n/2) exp(-1/2 x.x/\sigma^2 ) for n = dimension - inline double f(double* x, double t) + inline double f(double* x, double /* t */) {return C*exp(-(mask[0]*(x[0]-x0[0])*(x[0]-x0[0]) +mask[1]*(x[1]-x0[1])*(x[1]-x0[1]) +mask[2]*(x[2]-x0[2])*(x[2]-x0[2]))/tau/tau) + C0;}; @@ -362,10 +362,10 @@ namespace ATC { TemporalRamp(int nargs, double* args); virtual ~TemporalRamp(void) {}; - inline double f(double* x, double t) + inline double f(double* /* x */, double t) {return f_initial + slope*t;}; - inline double dfdt(double* x, double t) + inline double dfdt(double* /* x */, double /* t */) {return slope;}; private : @@ -382,7 +382,7 @@ namespace ATC { RadialPower(int nargs, double* args); virtual ~RadialPower(void) {}; - inline double f(double* x, double t) + inline double f(double* x, double /* t */) { double dx = x[0]-x0[0]; double dy = x[1]-x0[1]; double dz = x[2]-x0[2]; double r = mask[0]*dx*dx+mask[1]*dy*dy+mask[2]*dz*dz; r = sqrt(r); diff --git a/lib/atc/FundamentalAtomicQuantity.h b/lib/atc/FundamentalAtomicQuantity.h index 63c474755265ade0572ac6f9c3a8e847ab94d3c3..6561b8112d320dc8741a234220d95916a17711b7 100644 --- a/lib/atc/FundamentalAtomicQuantity.h +++ b/lib/atc/FundamentalAtomicQuantity.h @@ -82,43 +82,43 @@ namespace ATC { virtual ~AtomMass() {}; /** sets the quantity to a given value */ - virtual void operator=(const DENS_MAT & target) + virtual void operator=(const DENS_MAT & /* target */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** sets the quantity to a given constant value */ - virtual void operator=(const double & target) + virtual void operator=(const double & /* target */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DENS_MAT & addition) + virtual void operator+=(const DENS_MAT & /* addition */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(double addition) + virtual void operator+=(double /* addition */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DENS_MAT & subtraction) + virtual void operator-=(const DENS_MAT & /* subtraction */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(double subtracts) + virtual void operator-=(double /* subtracts */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DENS_MAT & multiplier) + virtual void operator*=(const DENS_MAT & /* multiplier */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(double multiplier) + virtual void operator*=(double /* multiplier */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DENS_MAT & divisor) + virtual void operator/=(const DENS_MAT & /* divisor */) {throw ATC_Error("Cannot modify type-based atom mass");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(double divisor) + virtual void operator/=(double /* divisor */) {throw ATC_Error("Cannot modify type-based atom mass");}; protected: @@ -182,39 +182,39 @@ namespace ATC { {throw ATC_Error("ComputedAtomQuantity::set_quantity - Cannot modify computed per atom quantities"); return quantity_;}; /** sets the quantity to a given constant value */ - virtual void operator=(const DENS_MAT & target) + virtual void operator=(const DENS_MAT & /* target */) {throw ATC_Error("ComputedAtomQuantity::operator= - Cannot modify computed per atom quantities");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DENS_MAT & addition) + virtual void operator+=(const DENS_MAT & /* addition */) {throw ATC_Error("ComputedAtomQuantity::operator+= - Cannot modify computed per atom quantities");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(double addition) + virtual void operator+=(double /* addition */) {throw ATC_Error("ComputedAtomQuantity::operator+= - Cannot modify computed per atom quantities");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DENS_MAT & subtraction) + virtual void operator-=(const DENS_MAT & /* subtraction */) {throw ATC_Error("ComputedAtomQuantity::operator-= - Cannot modify computed per atom quantities");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(double subtraction) + virtual void operator-=(double /* subtraction */) {throw ATC_Error("ComputedAtomQuantity::operator-= - Cannot modify computed per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DENS_MAT & multiplier) + virtual void operator*=(const DENS_MAT & /* multiplier */) {throw ATC_Error("ComputedAtomQuantity::operator*= - Cannot modify computed per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(double multiplier) + virtual void operator*=(double /* multiplier */) {throw ATC_Error("ComputedAtomQuantity::operator*= - Cannot modify computed per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DENS_MAT & divisor) + virtual void operator/=(const DENS_MAT & /* divisor */) {throw ATC_Error("ComputedAtomQuantity::operator/= - Cannot modify computed per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(double divisor) + virtual void operator/=(double /* divisor */) {throw ATC_Error("ComputedAtomQuantity::operator/= - Cannot modify computed per atom quantities");}; protected: diff --git a/lib/atc/KernelFunction.cpp b/lib/atc/KernelFunction.cpp index 80e41a15509bd1c4efd77f42e5d55e30e0a6f910..70a1616e0162ff1284ebf3f23c5b540c77400a96 100644 --- a/lib/atc/KernelFunction.cpp +++ b/lib/atc/KernelFunction.cpp @@ -123,7 +123,7 @@ namespace ATC { // KernelFunction //------------------------------------------------------------------------ // constructor - KernelFunction::KernelFunction(int nparameters, double* parameters): + KernelFunction::KernelFunction(int /* nparameters */, double* parameters): Rc_(0),invRc_(0),nsd_(3), lammpsInterface_(LammpsInterface::instance()) { @@ -286,7 +286,7 @@ namespace ATC { } // function derivative value - void KernelFunctionStep::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionStep::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -378,7 +378,7 @@ namespace ATC { } // function derivative value - void KernelFunctionCell::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionCell::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -518,7 +518,7 @@ namespace ATC { } // function derivative value - void KernelFunctionCubicSphere::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionCubicSphere::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -548,7 +548,7 @@ namespace ATC { } // function derivative value - void KernelFunctionQuarticSphere::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionQuarticSphere::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -581,7 +581,7 @@ namespace ATC { } // function derivative value - void KernelFunctionCubicCyl::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionCubicCyl::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -614,7 +614,7 @@ namespace ATC { } // function derivative value - void KernelFunctionQuarticCyl::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionQuarticCyl::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -646,7 +646,7 @@ namespace ATC { } // function derivative value - void KernelFunctionCubicBar::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionCubicBar::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } @@ -719,7 +719,7 @@ namespace ATC { } // function derivative value - void KernelFunctionQuarticBar::derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const + void KernelFunctionQuarticBar::derivative(const DENS_VEC& /* x_atom */, DENS_VEC& deriv) const { deriv.reset(nsd_); } diff --git a/lib/atc/KernelFunction.h b/lib/atc/KernelFunction.h index 99668525374b7e5e1f4c4460667a130ef0cad684..6922ed9a7b5579dc8b657b5eaca8ddda4e26a434 100644 --- a/lib/atc/KernelFunction.h +++ b/lib/atc/KernelFunction.h @@ -83,7 +83,7 @@ namespace ATC { // function derivative virtual void derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const; // bond function value - virtual double bond(DENS_VEC& xa, DENS_VEC&xb, double lam1, double lam2) const + virtual double bond(DENS_VEC& /* xa */, DENS_VEC& /* xb */, double lam1, double lam2) const { return lam2-lam1; } }; @@ -105,7 +105,7 @@ namespace ATC { // function derivative virtual void derivative(const DENS_VEC& x_atom, DENS_VEC& deriv) const; // bond function value - virtual double bond(DENS_VEC& xa, DENS_VEC&xb, double lam1, double lam2) const + virtual double bond(DENS_VEC& /* xa */, DENS_VEC& /* xb */, double lam1, double lam2) const {return lam2 -lam1;} // bond intercept values : origin is the node position void bond_intercepts(DENS_VEC& xa, DENS_VEC& xb, diff --git a/lib/atc/KinetoThermostat.cpp b/lib/atc/KinetoThermostat.cpp index bdc11238ad37128f40d203dd0befbf90762bc9f1..c10f7eb4581c06e4857e2d3af3d1e597cc7fa007 100644 --- a/lib/atc/KinetoThermostat.cpp +++ b/lib/atc/KinetoThermostat.cpp @@ -32,7 +32,7 @@ namespace ATC { // parses and adjusts thermostat state based on // user input, in the style of LAMMPS user input //-------------------------------------------------------- - bool KinetoThermostat::modify(int narg, char **arg) + bool KinetoThermostat::modify(int /* narg */, char ** /* arg */) { bool foundMatch = false; return foundMatch; @@ -171,7 +171,7 @@ namespace ATC { // sets up the right-hand side of the // kinetostat equations //-------------------------------------------------------- - void VelocityRescaleCombined::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void VelocityRescaleCombined::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { rhs = ((atc_->mass_mat_md(VELOCITY)).quantity())*(velocity_.quantity()); rhs -= thermostatCorrection_->quantity(); @@ -682,8 +682,8 @@ namespace ATC { // sets up and solves linear system for lambda, if the // bool is true it iterators to a non-linear solution //-------------------------------------------------------- - void KinetoThermostatGlcFs::compute_lambda(double dt, - bool iterateSolution) + void KinetoThermostatGlcFs::compute_lambda(double /* dt */, + bool /* iterateSolution */) { // ITERATIVE SOLUTION } @@ -692,7 +692,7 @@ namespace ATC { // output: // adds all relevant output to outputData //-------------------------------------------------------- - void KinetoThermostatGlcFs::output(OUTPUT_LIST & outputData) + void KinetoThermostatGlcFs::output(OUTPUT_LIST & /* outputData */) { // DO NOT CALL INDIVIDUAL REGULATORS // OUTPUT TOTAL FORCE AND TOTAL POWER diff --git a/lib/atc/KinetoThermostat.h b/lib/atc/KinetoThermostat.h index 465da6b49a051566e8ef2413a088d024406d4f20..6f7d11373455f8f19410c32bd5ffe5a8536bbb35 100644 --- a/lib/atc/KinetoThermostat.h +++ b/lib/atc/KinetoThermostat.h @@ -75,8 +75,11 @@ namespace ATC { KinetoThermostatShapeFunction(AtomicRegulator * kinetoThermostat, int couplingMaxIterations, - const std::string & regulatorPrefix = "") : RegulatorMethod(kinetoThermostat), + const std::string & /* regulatorPrefix */) : RegulatorMethod(kinetoThermostat), couplingMaxIterations_(couplingMaxIterations) {}; + KinetoThermostatShapeFunction(AtomicRegulator * kinetoThermostat, + int couplingMaxIterations) + : RegulatorMethod(kinetoThermostat), couplingMaxIterations_(couplingMaxIterations) {}; virtual ~KinetoThermostatShapeFunction() {}; @@ -120,9 +123,9 @@ namespace ATC { virtual void initialize(); /** applies kinetostat to atoms */ - virtual void apply_mid_predictor(double dt){}; + virtual void apply_mid_predictor(double /* dt */){}; /** applies kinetostat to atoms */ - virtual void apply_post_corrector(double dt){}; + virtual void apply_post_corrector(double /* dt */){}; /** local shape function matrices are incompatible with this mode */ virtual bool use_local_shape_functions() const {return false;}; @@ -142,15 +145,17 @@ namespace ATC { // disable un-needed functionality /** does initial filtering operations before main computation */ - virtual void apply_pre_filtering(double dt){}; + virtual void apply_pre_filtering(double /* dt */){}; /** applies kinetostat correction to atoms */ - virtual void apply_kinetostat(double dt) {}; + virtual void apply_kinetostat(double /* dt */) {}; /** computes the nodal FE force applied by the kinetostat */ - virtual void compute_nodal_lambda_force(double dt){}; + virtual void compute_nodal_lambda_force(double /* dt */){}; /** apply any required corrections for localized kinetostats */ - virtual void apply_localization_correction(const DENS_MAT & source, - DENS_MAT & nodalField, - double weight = 1.){}; + virtual void apply_localization_correction(const DENS_MAT & /* source */, + DENS_MAT & /* nodalField */, + double /* weight */){}; + virtual void apply_localization_correction(const DENS_MAT & /* source */, + DENS_MAT & /* nodalField */){}; private: @@ -177,7 +182,7 @@ namespace ATC { // deactivate un-needed methods /** applies thermostat to atoms in the post-corrector phase */ - virtual void apply_post_corrector(double dt){}; + virtual void apply_post_corrector(double /* dt */){}; protected: @@ -187,7 +192,7 @@ namespace ATC { // deactivate un-needed methods /** apply solution to atomic quantities */ - virtual void apply_to_atoms(PerAtomQuantity * atomVelocities){}; + virtual void apply_to_atoms(PerAtomQuantity * /* atomVelocities */){}; /** construct the RHS vector */ virtual void set_rhs(DENS_MAT & rhs); @@ -223,7 +228,7 @@ namespace ATC { virtual void apply_post_corrector(double dt); /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */ - virtual void compute_boundary_flux(FIELDS & fields) + virtual void compute_boundary_flux(FIELDS & /* fields */) {boundaryFlux_[TEMPERATURE] = 0.; boundaryFlux_[VELOCITY] = 0.;}; /** get data for output */ @@ -291,7 +296,7 @@ namespace ATC { // deactivate un-needed methods /** applies thermostat to atoms in the post-corrector phase */ - virtual void apply_post_corrector(double dt){}; + virtual void apply_post_corrector(double /* dt */){}; protected: @@ -301,7 +306,7 @@ namespace ATC { // deactivate un-needed methods /** apply solution to atomic quantities */ - virtual void apply_to_atoms(PerAtomQuantity * atomVelocities){}; + virtual void apply_to_atoms(PerAtomQuantity * /* atomVelocities */){}; /** construct the RHS vector */ virtual void set_rhs(DENS_MAT & rhs); diff --git a/lib/atc/Kinetostat.cpp b/lib/atc/Kinetostat.cpp index 17c5b6caf7030e090aff1d1f3cad0739d00f13e5..8093d5925a2011bb1a9f96a067087f338cf71314 100644 --- a/lib/atc/Kinetostat.cpp +++ b/lib/atc/Kinetostat.cpp @@ -445,7 +445,7 @@ namespace ATC { //-------------------------------------------------------- void GlcKinetostat::apply_to_atoms(PerAtomQuantity * quantity, const DENS_MAT & lambdaAtom, - double dt) + double /* dt */) { *quantity -= lambdaAtom; } @@ -576,7 +576,7 @@ namespace ATC { // sets up the right-hand side of the // kinetostat equations //-------------------------------------------------------- - void DisplacementGlc::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void DisplacementGlc::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { // form rhs : sum_a (hatN_Ia * x_ai) - (Upsilon)_Ii rhs = nodalAtomicMassWeightedDisplacement_->quantity(); @@ -922,7 +922,7 @@ namespace ATC { // sets up the right-hand side of the // kinetostat equations //-------------------------------------------------------- - void VelocityGlc::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void VelocityGlc::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { // form rhs : sum_a (hatN_Ia * x_ai) - (\dot{Upsilon})_Ii rhs = nodalAtomicMomentum_->quantity(); @@ -1252,7 +1252,7 @@ namespace ATC { // sets up the RHS of the kinetostat equations // for the coupling parameter lambda //-------------------------------------------------------- - void StressFlux::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void StressFlux::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { // (a) for flux based : // form rhs : \int N_I r dV - \sum_g N_Ig^* f_g @@ -1381,7 +1381,7 @@ namespace ATC { // computes the boundary flux to be consistent with // the controller //-------------------------------------------------------- - void StressFluxGhost::compute_boundary_flux(FIELDS & fields) + void StressFluxGhost::compute_boundary_flux(FIELDS & /* fields */) { // This is only used in computation of atomic sources boundaryFlux_[VELOCITY] = 0.; @@ -1407,7 +1407,7 @@ namespace ATC { // sets up the RHS of the kinetostat equations // for the coupling parameter lambda //-------------------------------------------------------- - void StressFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void StressFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { // (a) for flux based : // form rhs : \int N_I r dV - \sum_g N_Ig^* f_g @@ -1985,7 +1985,7 @@ namespace ATC { // sets up the RHS of the kinetostat equations // for the coupling parameter lambda //-------------------------------------------------------- - void KinetostatFlux::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void KinetostatFlux::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { // (a) for flux based : // form rhs : \int N_I r dV - \sum_g N_Ig^* f_g @@ -2056,7 +2056,7 @@ namespace ATC { // computes the boundary flux to be consistent with // the controller //-------------------------------------------------------- - void KinetostatFluxGhost::compute_boundary_flux(FIELDS & fields) + void KinetostatFluxGhost::compute_boundary_flux(FIELDS & /* fields */) { // This is only used in computation of atomic sources boundaryFlux_[VELOCITY] = 0.; @@ -2086,7 +2086,7 @@ namespace ATC { // sets up the RHS of the kinetostat equations // for the coupling parameter lambda //-------------------------------------------------------- - void KinetostatFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double dt) + void KinetostatFluxGhost::set_kinetostat_rhs(DENS_MAT & rhs, double /* dt */) { // (a) for flux based : // form rhs : \int N_I r dV - \sum_g N_Ig^* f_g @@ -2348,7 +2348,7 @@ namespace ATC { //-------------------------------------------------------- void KinetostatFixed::add_to_momentum(const DENS_MAT & nodalLambdaForce, DENS_MAT & deltaMomentum, - double dt) + double /* dt */) { deltaMomentum.resize(nNodes_,nsd_); const set & regulatedNodes(regulatedNodes_->quantity()); diff --git a/lib/atc/Kinetostat.h b/lib/atc/Kinetostat.h index 3d9b8cd5d21980160392ff4771eb05a4f84e28bb..691b929e9f5bea061bff4cbc6aa96554c7e9cc37 100644 --- a/lib/atc/Kinetostat.h +++ b/lib/atc/Kinetostat.h @@ -129,9 +129,11 @@ namespace ATC { double dt=0.); /** apply any required corrections for localized kinetostats */ - virtual void apply_localization_correction(const DENS_MAT & source, - DENS_MAT & nodalField, - double weight = 1.){}; + virtual void apply_localization_correction(const DENS_MAT & /* source */, + DENS_MAT & /* nodalField */, + double /* weight */){}; + virtual void apply_localization_correction(const DENS_MAT & /* source */, + DENS_MAT & /* nodalField */){}; // member data /** nodeset corresponding to Hoover coupling */ @@ -761,7 +763,7 @@ namespace ATC { virtual void apply_post_corrector(double dt); /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */ - virtual void compute_boundary_flux(FIELDS & fields) + virtual void compute_boundary_flux(FIELDS & /* fields */) {boundaryFlux_[VELOCITY] = 0.;}; /** determine if local shape function matrices are needed */ diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index 2238d930f4d4fb3f5eb25fac636168743e35d0f3..9c2223f5552c6ddffe33f45cf800dc9ded9bfc6b 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -902,7 +902,7 @@ int LammpsInterface::reset_ghosts(int deln) const //* energy for interactions within the shortrange cutoff double LammpsInterface::shortrange_energy(double *coord, - int itype, int id, double max) const + int itype, int id, double /* max */) const { LAMMPS_NS::Atom * atom = lammps_->atom; double **x = atom->x; @@ -1293,7 +1293,7 @@ int LammpsInterface::nsteps() const { return lammps_->update->nsteps; } int LammpsInterface::sbmask(int j) const {return j >> SBBITS & 3; } -void LammpsInterface::set_list(int id, LAMMPS_NS::NeighList *ptr) { list_ = ptr; } +void LammpsInterface::set_list(int /* id */, LAMMPS_NS::NeighList *ptr) { list_ = ptr; } int LammpsInterface::neighbor_list_inum() const { return list_->inum; } diff --git a/lib/atc/Material.cpp b/lib/atc/Material.cpp index 22273de2efed31015eaf826efd93592a86d950e0..676a87524f0d2bd5d5140745f2b58d766adde8d8 100644 --- a/lib/atc/Material.cpp +++ b/lib/atc/Material.cpp @@ -816,7 +816,7 @@ void Material::inv_effective_mass( }; //--------------------------------------------------------------------- void Material::heat_flux( - const FIELD_MATS & fields, + const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS & gradFields, DENS_MAT_VEC & flux) const { @@ -865,7 +865,7 @@ bool Material::electron_drag_power( //--------------------------------------------------------------------- bool Material::electron_recombination( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, DENS_MAT & recombination) const { // 1/tau (n - n0) @@ -937,7 +937,7 @@ void Material::electron_flux( } //--------------------------------------------------------------------- void Material::electric_field( - const FIELD_MATS &fields, + const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &flux) const { @@ -950,7 +950,7 @@ void Material::electric_field( } //--------------------------------------------------------------------- void Material::electric_displacement( - const FIELD_MATS &fields, + const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &flux) const { diff --git a/lib/atc/Matrix.h b/lib/atc/Matrix.h index e806ebd0168c1bbc924a42a8d3ee8d229d4d90a9..6745ea96db6d905a1d69505c5c2d4c15e71d81ba 100644 --- a/lib/atc/Matrix.h +++ b/lib/atc/Matrix.h @@ -248,7 +248,7 @@ DenseMatrix operator-(const Matrix &A, const Matrix &B) //* performs a matrix-matrix multiply with general type implementation template void MultAB(const Matrix &A, const Matrix &B, DenseMatrix &C, - const bool At, const bool Bt, T a, T b) + const bool At, const bool Bt, T /* a */, T b) { const INDEX sA[2] = {A.nRows(), A.nCols()}; // m is sA[At] k is sA[!At] const INDEX sB[2] = {B.nRows(), B.nCols()}; // k is sB[Bt] n is sB[!Bt] diff --git a/lib/atc/MeshReader.cpp b/lib/atc/MeshReader.cpp index 14101f1297ae9a6f7b14e5f5ed30bd050bb66dd0..c4896ec7270cf741710c46b8c6f4bcae8a7207d7 100644 --- a/lib/atc/MeshReader.cpp +++ b/lib/atc/MeshReader.cpp @@ -20,7 +20,7 @@ namespace ATC { /** constructor, takes a filename */ MeshReader::MeshReader(string filename, Array periodicity, - double tol) + double /* tol */) : meshfile_(filename), periodicity_(periodicity), nNodes_(0), diff --git a/lib/atc/MoleculeSet.cpp b/lib/atc/MoleculeSet.cpp index 618261f18639e076410d43e750b64a8c53554134..e3b1ed30d4ba70c5844b857474b7e3c708a18eba 100644 --- a/lib/atc/MoleculeSet.cpp +++ b/lib/atc/MoleculeSet.cpp @@ -165,7 +165,7 @@ namespace ATC { // Constructor //-------------------------------------------------------- SmallMoleculeSet::SmallMoleculeSet(ATC_Method * atc, int groupBit, - PerAtomQuantity * bondList, PerAtomQuantity * numBond) : + PerAtomQuantity * bondList, PerAtomQuantity * /* numBond */) : MoleculeSet(atc,groupBit), bondList_(bondList) { diff --git a/lib/atc/NonLinearSolver.h b/lib/atc/NonLinearSolver.h index d3d906a39a8857f1ef337f4545e06d5404c11b99..010e3ee72e80924861511050dfd238807ed5a037 100644 --- a/lib/atc/NonLinearSolver.h +++ b/lib/atc/NonLinearSolver.h @@ -20,7 +20,7 @@ class TangentOperator { public: TangentOperator(){}; virtual ~TangentOperator(){}; - virtual void function(const VECTOR & x, DENS_VEC & f) {}; // =0; + virtual void function(const VECTOR & /* x */, DENS_VEC & /* f */) {}; // =0; virtual void tangent(const VECTOR & x, DENS_VEC & f, MATRIX & dfdx) =0; //virtual void function(const VECTOR & x, VECTOR & f) {}; // =0; //virtual void tangent(const VECTOR & x, VECTOR & f, MATRIX & dfdx) {}; // =0; diff --git a/lib/atc/OutputManager.cpp b/lib/atc/OutputManager.cpp index 4340c8b8b0a3ca3c308be3838385a2b36a7b3c9a..066c240cabddaf7a0e36e0471f2993b8477259d3 100644 --- a/lib/atc/OutputManager.cpp +++ b/lib/atc/OutputManager.cpp @@ -161,8 +161,8 @@ void OutputManager::read_restart_file(string fileName, RESTART_LIST *data) for (int i = 0; i < field_data->nRows(); ++i) { for (int j = 0; j < field_data->nCols(); ++j) { double myVal; - fread(&myVal,sizeof(double),1,fp); - (*field_data)(i,j) = myVal; + if (fread(&myVal,sizeof(double),1,fp) == 1) + (*field_data)(i,j) = myVal; } } @@ -792,7 +792,7 @@ void OutputManager::write_data_vtk(OUTPUT_LIST *data) } /** write (ensight gold : ASCII "C" format) dictionary */ -void OutputManager::write_dictionary(double time, OUTPUT_LIST *data) +void OutputManager::write_dictionary(double /* time */, OUTPUT_LIST *data) { // file names string dict_file_name = outputPrefix_ + ".case"; diff --git a/lib/atc/POEMSChain.h b/lib/atc/POEMSChain.h deleted file mode 100644 index 7dc143a9d9a1f56a2286726f196f48efad50000d..0000000000000000000000000000000000000000 --- a/lib/atc/POEMSChain.h +++ /dev/null @@ -1,73 +0,0 @@ -/* - *_________________________________________________________________________* - * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * - * DESCRIPTION: SEE READ-ME * - * FILE NAME: PoemsChain.h * - * AUTHORS: See Author List * - * GRANTS: See Grants List * - * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * - * LICENSE: Please see License Agreement * - * DOWNLOAD: Free at www.rpi.edu/~anderk5 * - * ADMINISTRATOR: Prof. Kurt Anderson * - * Computational Dynamics Lab * - * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * - * CONTACT: anderk5@rpi.edu * - *_________________________________________________________________________*/ - -#ifndef POEMSCHAIN_H_ -#define POEMSCHAIN_H_ - -#include "poemslist.h" - -struct ChildRingData { - List * childRing; - int entranceNodeId; -}; - -struct POEMSChain{ - ~POEMSChain(){ - for(int i = 0; i < childChains.GetNumElements(); i++) - { - delete childChains(i); - } - } - //void printTreeStructure(int tabs); - //void getTreeAsList(List * temp); - List listOfNodes; - List childChains; - POEMSChain * parentChain; - List childRings; - - - void printTreeStructure(int tabs){ - for(int i = 0; i < tabs; i++) - { - cout << "\t"; - } - cout << "Chain: "; - for(int i = 0; i < listOfNodes.GetNumElements(); i++) - { - cout << *(listOfNodes(i)) << " "; - } - cout << endl; - for(int i = 0; i < childChains.GetNumElements(); i++) - { - childChains(i)->printTreeStructure(tabs + 1); - } - } - void getTreeAsList(List * temp) - { - for(int i = 0; i < listOfNodes.GetNumElements(); i++) - { - int * integer = new int; - *integer = *(listOfNodes(i)); - temp->Append(integer); - } - for(int i = 0; i < childChains.GetNumElements(); i++) - { - childChains(i)->getTreeAsList(temp); - } - } -}; -#endif diff --git a/lib/atc/PerAtomQuantity-inl.h b/lib/atc/PerAtomQuantity-inl.h index 037c3adedad96cf18ca279bb2945500e01f256a3..f95e5d306d19c8f5a91bd569809bb4c786107064 100644 --- a/lib/atc/PerAtomQuantity-inl.h +++ b/lib/atc/PerAtomQuantity-inl.h @@ -177,7 +177,7 @@ namespace ATC { //----------------------------------------------------------------- template int PerAtomQuantity::pack_comm(int index, double *buf, - int pbc_flag, int *pbc) + int /* pbc_flag */, int * /* pbc */) { if (this->need_reset()) this->reset(); DenseMatrix & myQuantity(this->quantity_); @@ -256,7 +256,7 @@ namespace ATC { //----------------------------------------------------------------- template int LammpsAtomQuantity::pack_comm(int index, double *buf, - int pbc_flag, int *pbc) + int /* pbc_flag */, int * /* pbc */) { if (this->need_reset()) this->reset(); int bufIdx = 0; @@ -550,7 +550,7 @@ namespace ATC { //----------------------------------------------------------------- template int PerAtomDiagonalMatrix::pack_comm(int index, double *buf, - int pbc_flag, int *pbc) + int /* pbc_flag */, int * /* pbc */) { if (this->need_reset()) this->reset(); DiagonalMatrix & myQuantity(this->quantity_); @@ -756,8 +756,8 @@ namespace ATC { // pack values in local atom-based arrays for passing to ghosts on another proc //----------------------------------------------------------------- template - int PerAtomSparseMatrix::pack_comm(int index, double *buf, - int pbc_flag, int *pbc) + int PerAtomSparseMatrix::pack_comm(int /* index */, double * /* buf */, + int /* pbc_flag */, int */* pbc */) { return 0; } @@ -766,7 +766,7 @@ namespace ATC { // unpack values in local atom-based arrays for passing to ghosts on another proc //----------------------------------------------------------------- template - int PerAtomSparseMatrix::unpack_comm(int index, double *buf) + int PerAtomSparseMatrix::unpack_comm(int /* index */, double * /* buf */) { return 0; } diff --git a/lib/atc/PerAtomQuantity.h b/lib/atc/PerAtomQuantity.h index 548918c9ccceea76a9e98fa4b68c91ee404ceae8..e6cb19981a7e1f34149f83bcf39180700bd588e7 100644 --- a/lib/atc/PerAtomQuantity.h +++ b/lib/atc/PerAtomQuantity.h @@ -274,26 +274,26 @@ namespace ATC { virtual int memory_usage() const {return 0;}; /** packs up data for parallel transfer when atoms change processors */ - virtual int pack_exchange(int i, double *buffer) {return 0;}; + virtual int pack_exchange(int /* i */, double */* buffer */) {return 0;}; /** unpacks data after parallel transfer when atoms change processors */ - virtual int unpack_exchange(int i, double *buffer) {return 0;}; + virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** packs up data for parallel transfer to ghost atoms on other processors */ - virtual int pack_comm(int index, double *buf, - int pbc_flag, int *pbc) {return 0;}; + virtual int pack_comm(int /* index */, double * /* buf */, + int /* pbc_flag */, int * /* pbc */) {return 0;}; /** unpacks data after parallel transfer to ghost atoms on other processors */ - virtual int unpack_comm(int index, double *buf) {return 0;}; + virtual int unpack_comm(int /* index */, double * /* buf */) {return 0;}; /** returns size of per-atom communication */ virtual int size_comm() const {return 0;}; /** changes size of temperary lammps storage data if transfer is being used */ - virtual void grow_lammps_array(int nmax, const std::string & tag) {}; + virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {}; /** rearrange memory of temporary lammps storage data, called from copy_array */ - virtual void copy_lammps_array(int i, int j) {}; + virtual void copy_lammps_array(int /* i */, int /* j */) {}; protected: @@ -396,43 +396,43 @@ namespace ATC { {throw ATC_Error("ProtectedClonedAtomQuantity::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;}; /** sets the quantity to a given value */ - virtual void operator=(const DenseMatrix & target) + virtual void operator=(const DenseMatrix & /* target */) {throw ATC_Error("ProtectedClonedAtomQuantity::set_quantity - Cannot modify protected per atom quantities");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator= - Cannot modify protected per atom quantities");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DenseMatrix & addition) + virtual void operator+=(const DenseMatrix & /* addition */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator+= - Cannot modify protected per atom quantities");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator+= - Cannot modify protected per atom quantities");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DenseMatrix & subtraction) + virtual void operator-=(const DenseMatrix & /* subtraction */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator-= - Cannot modify protected per atom quantities");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator-= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DenseMatrix & multiplier) + virtual void operator*=(const DenseMatrix & /* multiplier */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DenseMatrix & divisor) + virtual void operator/=(const DenseMatrix & /* divisor */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator/= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("ProtectedClonedAtomQuantity::operator/= - Cannot modify protected per atom quantities");}; protected: @@ -517,43 +517,43 @@ namespace ATC { {throw ATC_Error("ProtectedAtomQuantity::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;}; /** sets the quantity to a given value */ - virtual void operator=(const DenseMatrix & target) + virtual void operator=(const DenseMatrix & /* target */) {throw ATC_Error("ProtectedAtomQuantity::set_quantity - Cannot modify protected per atom quantities");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("ProtectedAtomQuantity::operator= - Cannot modify protected per atom quantities");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DenseMatrix & addition) + virtual void operator+=(const DenseMatrix & /* addition */) {throw ATC_Error("ProtectedAtomQuantity::operator+= - Cannot modify protected per atom quantities");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("ProtectedAtomQuantity::operator+= - Cannot modify protected per atom quantities");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DenseMatrix & subtraction) + virtual void operator-=(const DenseMatrix & /* subtraction */) {throw ATC_Error("ProtectedAtomQuantity::operator-= - Cannot modify protected per atom quantities");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("ProtectedAtomQuantity::operator-= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DenseMatrix & multiplier) + virtual void operator*=(const DenseMatrix & /* multiplier */) {throw ATC_Error("ProtectedAtomQuantity::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("ProtectedAtomQuantity::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DenseMatrix & divisor) + virtual void operator/=(const DenseMatrix & /* divisor */) {throw ATC_Error("ProtectedAtomQuantity::operator/= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("ProtectedAtomQuantity::operator/= - Cannot modify protected per atom quantities");}; protected: @@ -646,43 +646,43 @@ namespace ATC { {throw ATC_Error("ProtectedLammpsAtomQuantity::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;}; /** sets the quantity to a given value */ - virtual void operator=(const DenseMatrix & target) + virtual void operator=(const DenseMatrix & /* target */) {throw ATC_Error("ProtectedLammpsAtomQuantity::set_quantity - Cannot modify protected per atom quantities");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator= - Cannot modify protected per atom quantities");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DenseMatrix & addition) + virtual void operator+=(const DenseMatrix & /* addition */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator+= - Cannot modify protected per atom quantities");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator+= - Cannot modify protected per atom quantities");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DenseMatrix & subtraction) + virtual void operator-=(const DenseMatrix & /* subtraction */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator-= - Cannot modify protected per atom quantities");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator-= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DenseMatrix & multiplier) + virtual void operator*=(const DenseMatrix & /* multiplier */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DenseMatrix & divisor) + virtual void operator/=(const DenseMatrix & /* divisor */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator/= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("ProtectedLammpsAtomQuantity::operator/= - Cannot modify protected per atom quantities");}; protected: @@ -734,16 +734,16 @@ namespace ATC { virtual int memory_usage() const {return 0;}; /** packs up data for parallel transfer */ - virtual int pack_exchange(int i, double *buffer) {return 0;}; + virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** unpacks data after parallel transfer */ - virtual int unpack_exchange(int i, double *buffer) {return 0;}; + virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** changes size of temperary lammps storage data if transfer is being used */ - virtual void grow_lammps_array(int nmax, const std::string & tag) {}; + virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {}; /** rearrange memory of temporary lammps storage data, called from copy_array */ - virtual void copy_lammps_array(int i, int j) {}; + virtual void copy_lammps_array(int /* i */, int /* j */) {}; protected: @@ -791,16 +791,16 @@ namespace ATC { virtual int memory_usage() const {return 0;}; /** packs up data for parallel transfer */ - virtual int pack_exchange(int i, double *buffer) {return 0;}; + virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** unpacks data after parallel transfer */ - virtual int unpack_exchange(int i, double *buffer) {return 0;}; + virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** changes size of temperary lammps storage data if transfer is being used */ - virtual void grow_lammps_array(int nmax, const std::string & tag) {}; + virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {}; /** rearrange memory of temporary lammps storage data, called from copy_array */ - virtual void copy_lammps_array(int i, int j) {}; + virtual void copy_lammps_array(int /* i */, int /* j */) {}; protected: @@ -1066,43 +1066,43 @@ namespace ATC { {throw ATC_Error("ProtectedAtomDiagonalMatrix::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;}; /** sets the quantity to a given value */ - virtual void operator=(const DiagonalMatrix & target) + virtual void operator=(const DiagonalMatrix & /* target */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::set_quantity - Cannot modify protected per atom quantities");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator= - Cannot modify protected per atom quantities");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DiagonalMatrix & addition) + virtual void operator+=(const DiagonalMatrix & /* addition */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator+= - Cannot modify protected per atom quantities");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator+= - Cannot modify protected per atom quantities");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DiagonalMatrix & subtraction) + virtual void operator-=(const DiagonalMatrix & /* subtraction */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator-= - Cannot modify protected per atom quantities");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator-= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DiagonalMatrix & multiplier) + virtual void operator*=(const DiagonalMatrix & /* multiplier */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DiagonalMatrix & divisor) + virtual void operator/=(const DiagonalMatrix & /* divisor */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator/= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("ProtectedAtomDiagonalMatrix::operator/= - Cannot modify protected per atom quantities");}; protected: @@ -1331,43 +1331,43 @@ namespace ATC { {throw ATC_Error("ProtectedAtomSparseMatrix::set_quantity - Cannot modify protected per atom quantities"); return this->quantity_;}; /** sets the quantity to a given value */ - virtual void operator=(const SparseMatrix & target) + virtual void operator=(const SparseMatrix & /* target */) {throw ATC_Error("ProtectedAtomSparseMatrix::set_quantity - Cannot modify protected per atom quantities");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator= - Cannot modify protected per atom quantities");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const SparseMatrix & addition) + virtual void operator+=(const SparseMatrix & /* addition */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator+= - Cannot modify protected per atom quantities");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator+= - Cannot modify protected per atom quantities");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const SparseMatrix & subtraction) + virtual void operator-=(const SparseMatrix & /* subtraction */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator-= - Cannot modify protected per atom quantities");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator-= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const SparseMatrix & multiplier) + virtual void operator*=(const SparseMatrix & /* multiplier */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator*= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const SparseMatrix & divisor) + virtual void operator/=(const SparseMatrix & /* divisor */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator/= - Cannot modify protected per atom quantities");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("ProtectedAtomSparseMatrix::operator/= - Cannot modify protected per atom quantities");}; protected: @@ -1420,27 +1420,27 @@ namespace ATC { virtual int memory_usage() const {return 0;}; /** packs up data for parallel transfer when atoms change processors */ - virtual int pack_exchange(int i, double *buffer) {return 0;}; + virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** unpacks data after parallel transfer when atoms change processors */ - virtual int unpack_exchange(int i, double *buffer) {return 0;}; + virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;}; // pack/unpack_comm only valid if the quantity is over all real and processor ghost atoms /** packs up data for parallel transfer to ghost atoms on other processors */ - virtual int pack_comm(int index, double *buf, - int pbc_flag, int *pbc) {return 0;}; + virtual int pack_comm(int /* index */, double * /* buf */, + int /* pbc_flag */, int * /* pbc */) {return 0;}; /** unpacks data after parallel transfer to ghost atoms on other processors */ - virtual int unpack_comm(int index, double *buf) {return 0;}; + virtual int unpack_comm(int /* index */, double * /* buf */) {return 0;}; /** returns per-atom size of communicated data */ virtual int size_comm() const {return 0;}; /** changes size of temperary lammps storage data if transfer is being used */ - virtual void grow_lammps_array(int nmax, const std::string & tag) {}; + virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {}; /** rearrange memory of temporary lammps storage data, called from copy_array */ - virtual void copy_lammps_array(int i, int j) {}; + virtual void copy_lammps_array(int /* i */, int /* j */) {}; protected: diff --git a/lib/atc/PerAtomQuantityLibrary.cpp b/lib/atc/PerAtomQuantityLibrary.cpp index 36f92524515dcbe3f6ada9716a9b499c0f49ae5a..7f8a9b879a6552b9420abba18ba654d67eb93309 100644 --- a/lib/atc/PerAtomQuantityLibrary.cpp +++ b/lib/atc/PerAtomQuantityLibrary.cpp @@ -1129,7 +1129,7 @@ namespace ATC { FluctuatingKineticTensor::FluctuatingKineticTensor(ATC_Method * atc, PerAtomQuantity * atomVelocities, PerAtomQuantity * atomMasses, - PerAtomQuantity * atomMeanVelocities, + PerAtomQuantity * /* atomMeanVelocities */, AtomType atomType) : ProtectedAtomQuantity(atc,6,atomType), atomVelocities_(atomVelocities), diff --git a/lib/atc/PerAtomQuantityLibrary.h b/lib/atc/PerAtomQuantityLibrary.h index b3db140f8233850baf77f1c00171faa66ba1fa26..0089df7855a178010ed3b52a2ba824dc54b5feeb 100644 --- a/lib/atc/PerAtomQuantityLibrary.h +++ b/lib/atc/PerAtomQuantityLibrary.h @@ -1045,26 +1045,26 @@ namespace ATC { virtual int memory_usage() const {return 0;}; /** packs up data for parallel transfer when atoms change processors */ - virtual int pack_exchange(int i, double *buffer) {return 0;}; + virtual int pack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** unpacks data after parallel transfer when atoms change processors */ - virtual int unpack_exchange(int i, double *buffer) {return 0;}; + virtual int unpack_exchange(int /* i */, double * /* buffer */) {return 0;}; /** packs up data for parallel transfer to ghost atoms on other processors */ - virtual int pack_comm(int index, double *buf, - int pbc_flag, int *pbc) {return 0;}; + virtual int pack_comm(int /* index */, double * /* buf */, + int /* pbc_flag */, int * /* pbc */) {return 0;}; /** unpacks data after parallel transfer to ghost atoms on other processors */ - virtual int unpack_comm(int index, double *buf) {return 0;}; + virtual int unpack_comm(int /* index */, double * /* buf */) {return 0;}; /** returns size of per-atom communication */ virtual int size_comm() const {return 0;}; /** changes size of temperary lammps storage data if transfer is being used */ - virtual void grow_lammps_array(int nmax, const std::string & tag) {}; + virtual void grow_lammps_array(int /* nmax */, const std::string & /* tag */) {}; /** rearrange memory of temporary lammps storage data, called from copy_array */ - virtual void copy_lammps_array(int i, int j) {}; + virtual void copy_lammps_array(int /* i */, int /* j */) {}; protected: diff --git a/lib/atc/PerPairQuantity.cpp b/lib/atc/PerPairQuantity.cpp index 86ad331eca2301f488e2548eb592d24dbb7a04cd..3632a87aa93c3d043fab5e86888f930e1f21fe2a 100644 --- a/lib/atc/PerPairQuantity.cpp +++ b/lib/atc/PerPairQuantity.cpp @@ -281,7 +281,6 @@ void BondMatrixKernel::reset(void) const int nNodes = feMesh_->num_nodes_unique(); quantity_.reset(nNodes,nPairs); double lam1,lam2; - std::pair< int,int > pair_jk; int heartbeatFreq = (nNodes <= 10 ? 1 : (int) nNodes / 10); HeartBeat beat("computing bond matrix ",heartbeatFreq); beat.start(); @@ -337,7 +336,6 @@ void BondMatrixPartitionOfUnity::reset(void) const int nodes_per_element = feMesh_->num_nodes_per_element(); Array node_list(nodes_per_element); DENS_VEC shp(nodes_per_element); - std::pair< int,int > pair_jk; int heartbeatFreq = (int) nPairs / 10; HeartBeat beat("computing bond matrix ",heartbeatFreq); beat.start(); diff --git a/lib/atc/PhysicsModel.h b/lib/atc/PhysicsModel.h index ce25174d90a51f2825bb261ef6a7f53e9624f633..50b327ce0b64b18bfe9adcca27402c8861500bdf 100644 --- a/lib/atc/PhysicsModel.h +++ b/lib/atc/PhysicsModel.h @@ -47,7 +47,7 @@ namespace ATC void initialize(void); // set timescale parameters based on a given lengthscale - virtual void set_timescales(const double lengthscale) {}; + virtual void set_timescales(const double /* lengthscale */) {}; /** access number of materials */ int nMaterials(void) const { return materials_.size(); } diff --git a/lib/atc/PoissonSolver.cpp b/lib/atc/PoissonSolver.cpp index b3c077b5930bceb5186c21050b026e17a88c65fe..86670ae218ed507e5a6ec5d4281e2cbca9699925 100644 --- a/lib/atc/PoissonSolver.cpp +++ b/lib/atc/PoissonSolver.cpp @@ -71,7 +71,7 @@ PoissonSolver::~PoissonSolver() // Parser // -------------------------------------------------------------------- -bool PoissonSolver::modify(int narg, char **arg) + bool PoissonSolver::modify(int /* narg */, char **arg) { bool match = false; /*! \page man_poisson_solver fix_modify AtC poisson_solver diff --git a/lib/atc/PolynomialSolver.cpp b/lib/atc/PolynomialSolver.cpp index 9088a7eaf363f1a8bf15a3f7b14de003a0b0ed88..b498b3b5bbc9d7ddd35e043c567e0da5bfcc4e6d 100644 --- a/lib/atc/PolynomialSolver.cpp +++ b/lib/atc/PolynomialSolver.cpp @@ -104,7 +104,7 @@ namespace ATC { // solve ode with polynomial source : y'n + a_n-1 y'n-1 + ... = b_n x^n +... void integrate_ode(double x, - int na, double * a, double * y0, double * y, int nb, double *b ) + int na, double * a, double * y0, double * y, int nb, double * /* b */ ) { if (na == 2) { // particular diff --git a/lib/atc/SchrodingerSolver.cpp b/lib/atc/SchrodingerSolver.cpp index 92eb1a7a625c876dfb3f466111f7d64c7b3bb16c..d79fa85595427a39a536a96b14995f057a0f7920 100644 --- a/lib/atc/SchrodingerSolver.cpp +++ b/lib/atc/SchrodingerSolver.cpp @@ -66,7 +66,7 @@ double fermi_dirac(const double E, const double T) M_ = sparseM.dense_copy(); } //----------------------------------------------------- - bool SchrodingerSolver::solve(FIELDS & fields) + bool SchrodingerSolver::solve(FIELDS & /* fields */) { // typedef struct{float real, imag;} COMPLEX; @@ -132,7 +132,7 @@ double fermi_dirac(const double E, const double T) //-------------------------------------------------------- // compute charge density per slice //-------------------------------------------------------- - bool SliceSchrodingerSolver::solve(FIELDS & fields) + bool SliceSchrodingerSolver::solve(FIELDS & /* fields */) { // fields DENS_MAT & psi = (atc_->field(ELECTRON_WAVEFUNCTION)).set_quantity(); @@ -250,7 +250,7 @@ double fermi_dirac(const double E, const double T) { } //---------------------------------------------------------- - bool SchrodingerPoissonManager::modify(int narg, char **arg) + bool SchrodingerPoissonManager::modify(int /* narg */, char **arg) { bool match = false; int argIndx = 0; @@ -350,7 +350,7 @@ double fermi_dirac(const double E, const double T) } //---------------------------------------------------------------------- - void SchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & fluxes) + void SchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & /* fluxes */) { if ((atc_->prescribed_data_manager()->all_fixed(ELECTRON_WAVEFUNCTION)) && (atc_->prescribed_data_manager()->all_fixed(ELECTRIC_POTENTIAL))) { @@ -739,7 +739,7 @@ double fermi_dirac(const double E, const double T) if (solver_) delete solver_; } //-------------------------------------------------------------------------- - void GlobalSliceSchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & fluxes) + void GlobalSliceSchrodingerPoissonSolver::solve(FIELDS & rhs, GRAD_FIELD_MATS & /* fluxes */) { const DENS_MAT & phi = (atc_->fields_[ELECTRIC_POTENTIAL]).quantity(); const DENS_MAT & n = (atc_->fields_[ELECTRON_DENSITY] ).quantity(); diff --git a/lib/atc/SchrodingerSolver.h b/lib/atc/SchrodingerSolver.h index 9b8616b4589525ad66a1e8eac8c360f986ed6823..e2addc48a36928ba11013078c9cc47d6d0ca12db 100644 --- a/lib/atc/SchrodingerSolver.h +++ b/lib/atc/SchrodingerSolver.h @@ -41,7 +41,7 @@ class SchrodingerSolver { virtual ~SchrodingerSolver(){}; /** parser */ - bool modify(int narg, char **arg){ return false;} + bool modify(int /* narg */, char ** /* arg */){ return false;} /** initialize */ void initialize(void); @@ -103,7 +103,7 @@ class SliceSchrodingerSolver : public SchrodingerSolver { virtual ~SliceSchrodingerSolver(){}; /** parser */ - bool modify(int narg, char **arg){return false;} + bool modify(int /* narg */, char ** /* arg */){return false;} /** initialize */ void initialize(void); diff --git a/lib/atc/SparseMatrix-inl.h b/lib/atc/SparseMatrix-inl.h index f70dd0361d3cf52e519fef06abc07f0518c86b21..36867ad8dee572c846d5c36ead8477dbc18ee283 100644 --- a/lib/atc/SparseMatrix-inl.h +++ b/lib/atc/SparseMatrix-inl.h @@ -498,7 +498,7 @@ TRIPLET SparseMatrix::triplet(INDEX i) const // full reset - completely wipes out all SparseMatrix data, zero is ignored //----------------------------------------------------------------------------- template -void SparseMatrix::reset(INDEX rows, INDEX cols, bool zero) +void SparseMatrix::reset(INDEX rows, INDEX cols, bool /* zero */) { _delete(); _nRows = rows; @@ -545,7 +545,7 @@ void SparseMatrix::reset(const DenseMatrix& D, double TOL) // copy - dangerous: ignores rows & columns //----------------------------------------------------------------------------- template -void SparseMatrix::copy(const T * ptr, INDEX rows, INDEX cols) +void SparseMatrix::copy(const T * /* ptr */, INDEX /* rows */, INDEX /* cols */) { std::cout << "SparseMatrix::copy() has no effect.\n"; throw; diff --git a/lib/atc/SparseVector-inl.h b/lib/atc/SparseVector-inl.h index 204c412d6da3374ce72c82bef05393ae90464b84..760eb66f5856aac502986bf33c514f792543f421 100644 --- a/lib/atc/SparseVector-inl.h +++ b/lib/atc/SparseVector-inl.h @@ -106,7 +106,7 @@ std::string SparseVector::to_string() const // Indexes the ith component of the vector or returns zero if not found. template -T SparseVector::operator()(INDEX i, INDEX j) const +T SparseVector::operator()(INDEX i, INDEX /* j */) const { STORE::const_iterator it = data_.find(i); if (it == data_.end()) return 0.0; @@ -115,7 +115,7 @@ T SparseVector::operator()(INDEX i, INDEX j) const // Indexes the ith component of the vector or returns zero if not found. template -T& SparseVector::operator()(INDEX i, INDEX j) +T& SparseVector::operator()(INDEX i, INDEX /* j */) { return data_[i]; } @@ -129,7 +129,7 @@ template T SparseVector::operator[](INDEX i) const // Indexes the ith component of the vector or returns zero if not found. template T& SparseVector::operator[](INDEX i) { - return (*this)[i]; + return (*this)(i); } // Returns a pair (index, value) for a nonzero in the vector. @@ -177,7 +177,7 @@ SparseVector& SparseVector::operator=(const SparseVector &c) // Changes the size of the SparseVector template -void SparseVector::resize(INDEX nRows, INDEX nCols, bool copy) +void SparseVector::resize(INDEX nRows, INDEX /* nCols */, bool copy) { length_ = nRows; STORE::iterator it; @@ -202,16 +202,14 @@ void SparseVector::zero() template -void SparseVector::copy(const T* ptr, INDEX nRows, INDEX nCols) +void SparseVector::copy(const T* /* ptr */, INDEX /* nRows */, INDEX /* nCols */) { - } template -void SparseVector::write_restart(FILE *F) const +void SparseVector::write_restart(FILE */* F */) const { - } // writes a stream to a matlab script to recreate this variable diff --git a/lib/atc/SpeciesTimeIntegrator.cpp b/lib/atc/SpeciesTimeIntegrator.cpp index bf9f1a8888516dc1105306f4cca17815f2368245..3a196e745af207b4de1cade45e16a803154c9f6f 100644 --- a/lib/atc/SpeciesTimeIntegrator.cpp +++ b/lib/atc/SpeciesTimeIntegrator.cpp @@ -37,7 +37,7 @@ namespace ATC { // modify // parses inputs and modifies state of the filter //-------------------------------------------------------- - bool SpeciesTimeIntegrator::modify(int narg, char **arg) + bool SpeciesTimeIntegrator::modify(int /* narg */, char ** /* arg */) { bool match = false; @@ -185,7 +185,7 @@ namespace ATC { // first time integration computations // before FractionalStep step 2 //-------------------------------------------------------- - void SpeciesTimeIntegratorFractionalStep::pre_final_integrate1(double dt) + void SpeciesTimeIntegratorFractionalStep::pre_final_integrate1(double /* dt */) { // Compute MD contribution to FEM equation @@ -244,7 +244,7 @@ namespace ATC { //-------------------------------------------------------- // pre_initial_integrate1 //-------------------------------------------------------- - void SpeciesTimeIntegratorFractionalStepFiltered::pre_final_integrate1(double dt) + void SpeciesTimeIntegratorFractionalStepFiltered::pre_final_integrate1(double /* dt */) { } diff --git a/lib/atc/Stress.cpp b/lib/atc/Stress.cpp index df329f9faf3b0600e1ef07d34747413bb955469b..906b15986e5ab2dfd23a721d222df0075c243fa4 100644 --- a/lib/atc/Stress.cpp +++ b/lib/atc/Stress.cpp @@ -62,7 +62,7 @@ void deformation_gradient(const DENS_MAT_VEC &du, INDEX q, MATRIX &F) // E = 1/2 stress*strain for linear elastic models //============================================================================= -void Stress::elastic_energy(const FIELD_MATS &fields, + void Stress::elastic_energy(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT &energy) const { @@ -103,7 +103,7 @@ StressLinearElastic::StressLinearElastic(fstream &fileId) // compute the stress at N integration points from the displacement gradient // T_{ij} = 1/2*C_{ijkl}* (u_{k,l} + u_{l,k}) //============================================================================= -void StressLinearElastic::stress(const FIELD_MATS &fields, + void StressLinearElastic::stress(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &sigma) { @@ -159,7 +159,7 @@ StressCubicElastic::StressCubicElastic(fstream &fileId) // compute the stress at N integration points from the displacement gradient // T_{ij} = 1/2*C_{ijkl}*(u_{k,l} + u_{l,k}) //--------------------------------------------------------------------------- -void StressCubicElastic::stress(const FIELD_MATS &fields, + void StressCubicElastic::stress(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &sigma) { @@ -200,7 +200,7 @@ void StressCubicElastic::stress(const FIELD_MATS &fields, // = 1/2 (4 c44 (u12^2 + u13^2 + u23^2) + 2 c12 (u11 u22 + u11 u33 + u22 u33) // + c11 (u11^2 + u22^2 + u33^2)) //--------------------------------------------------------------------------- -void StressCubicElastic::elastic_energy(const FIELD_MATS &fields, + void StressCubicElastic::elastic_energy(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT &energy) const { diff --git a/lib/atc/Stress.h b/lib/atc/Stress.h index bf406551928827f5d76d7f9156c1cb8c8d2bf39c..513cdb2d973ceaf0b629f83742bcdda170b0529d 100644 --- a/lib/atc/Stress.h +++ b/lib/atc/Stress.h @@ -24,7 +24,7 @@ namespace ATC { virtual ~Stress() {}; virtual void initialize(void){}; //* Returns parameter values, (Nothing uses this). - virtual void parameters(std::map ¶meters) {} + virtual void parameters(std::map & /* parameters */) {} //* Computes stress given a displacement gradient. //* Units: mvv/L^3 (i.e. for units Real: g/(mol ps^2 A^2) ) virtual void stress(const FIELD_MATS &fields, @@ -36,7 +36,7 @@ namespace ATC { const GRAD_FIELD_MATS &gradFields, DENS_MAT &energy) const; //* Returns the material tangent at a given deformation gradient. - virtual void tangent(const MATRIX &F, MATRIX &C) const + virtual void tangent(const MATRIX & /* F */, MATRIX & /* C */) const {throw ATC_Error("Stress::tangent: unimplemented function");} }; @@ -59,7 +59,7 @@ namespace ATC { virtual void elastic_energy(const FIELD_MATS &fields, const GRAD_FIELD_MATS &gradFields, DENS_MAT &energy) const; - virtual void tangent(const MATRIX &F, MATRIX &C) const {C=C_;} + virtual void tangent(const MATRIX & /* F */, MATRIX &C) const {C=C_;} protected: double c11_, c12_, c44_; DENS_MAT C_; diff --git a/lib/atc/SystemProcessor.h b/lib/atc/SystemProcessor.h deleted file mode 100644 index 9ef511f997eec6caceff76db05fa60a635e413cc..0000000000000000000000000000000000000000 --- a/lib/atc/SystemProcessor.h +++ /dev/null @@ -1,283 +0,0 @@ -/* - *_________________________________________________________________________* - * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE * - * DESCRIPTION: SEE READ-ME * - * FILE NAME: SystemProcessor.h * - * AUTHORS: See Author List * - * GRANTS: See Grants List * - * COPYRIGHT: (C) 2005 by Authors as listed in Author's List * - * LICENSE: Please see License Agreement * - * DOWNLOAD: Free at www.rpi.edu/~anderk5 * - * ADMINISTRATOR: Prof. Kurt Anderson * - * Computational Dynamics Lab * - * Rensselaer Polytechnic Institute * - * 110 8th St. Troy NY 12180 * - * CONTACT: anderk5@rpi.edu * - *_________________________________________________________________________*/ - -#ifndef _SYS_PROCESSOR_H_ -#define _SYS_PROCESSOR_H_ -#include "poemslist.h" -#include "poemstree.h" -#include "POEMSChain.h" - - -struct POEMSNode { - List links; - List taken; - int idNumber; - bool visited; - - ~POEMSNode(){ - for(int i = 0; i < taken.GetNumElements(); i++) - { - delete taken(i); - } - }; -}; - - -class SystemProcessor{ -private: - Tree nodes; -// List forDeletion; - List headsOfSystems; - List > ringsInSystem; - POEMSNode * findSingleLink(TreeNode * aNode); - POEMSChain * AddNewChain(POEMSNode * currentNode); - bool setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode); -public: - SystemProcessor(void); - - ~SystemProcessor(void) { - headsOfSystems.DeleteValues(); - for(int i = 0; i < ringsInSystem.GetNumElements(); i++) - { - for(int k = 0; k < ringsInSystem(i)->GetNumElements(); i++) - { - delete (*ringsInSystem(i))(k); - } - } - }; - void processArray(int** links, int numLinks); - List * getSystemData(); - int getNumberOfHeadChains(); -}; - -SystemProcessor::SystemProcessor(void){ -} - -void SystemProcessor::processArray(int** links, int numLinks) -{ - bool * false_var; //holds the value false; needed because a constant cannot be put into a list; the list requires a - //reference. - for(int i = 0; i < numLinks; i++) //go through all the links in the input array - { - if(!nodes.Find(links[i][0])) //if the first node in the pair is not found in the storage tree - { - POEMSNode * newNode = new POEMSNode; //make a new node -// forDeletion.Append(newNode); - newNode->idNumber = links[i][0]; //set its ID to the value - newNode->visited = false; //set it to be unvisited - nodes.Insert(links[i][0], links[i][0], (void *) newNode); //and add it to the tree storage structure - } - if(!nodes.Find(links[i][1])) //repeat process for the other half of each link - { - POEMSNode * newNode = new POEMSNode; -// forDeletion.Append(newNode); - newNode->idNumber = links[i][1]; - newNode->visited = false; - nodes.Insert(links[i][1], links[i][1], (void *) newNode); - } - POEMSNode * firstNode = (POEMSNode *)nodes.Find(links[i][0]); //now that we are sure both nodes exist, - POEMSNode * secondNode = (POEMSNode *)nodes.Find(links[i][1]); //we can get both of them out of the tree - firstNode->links.Append(secondNode); //and add the link from the first to the second... - false_var = new bool; - *false_var = false; //make a new false boolean to note that the link between these two - firstNode->taken.Append(false_var); //has not already been taken, and append it to the taken list - secondNode->links.Append(firstNode); //repeat process for link from second node to first - false_var = new bool; - *false_var = false; - secondNode->taken.Append(false_var); - } - - TreeNode * temp = nodes.GetRoot(); //get the root node of the node storage tree - POEMSNode * currentNode; - do - { - currentNode = findSingleLink(temp); //find the start of the next available chain - if(currentNode != NULL) - { - headsOfSystems.Append(AddNewChain(currentNode)); //and add it to the headsOfSystems list of chains - } - } - while(currentNode != NULL); //repeat this until all chains have been added -} - -POEMSChain * SystemProcessor::AddNewChain(POEMSNode * currentNode){ - if(currentNode == NULL) //Termination condition; if the currentNode is null, then return null - { - return NULL; - } - int * tmp; - POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occuring before being assigned as the current node. - POEMSChain * newChain = new POEMSChain; //make a new POEMSChain object. This will be the object returned - - if(currentNode->links.GetNumElements() == 0) //if we have no links from this node, then the whole chain is only one node. Add this node to the chain and return it; mark node as visited for future reference - { - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); - return newChain; - } - while(currentNode->links.GetNumElements() <= 2) //we go until we get to a node that branches, or both branches have already been taken both branches can already be taken if a loop with no spurs is found in the input data - { - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); //append the current node to the chain & mark as visited - //cout << "Appending node " << currentNode->idNumber << " to chain" << endl; - nextNode = currentNode->links.GetHeadElement()->value; //the next node is the first or second value stored in the links array - //of the current node. We get the first value... - if(!setLinkVisited(currentNode, nextNode)) //...and see if it points back to where we came from. If it does... - { //either way, we set this link as visited - if(currentNode->links.GetNumElements() == 1) //if it does, then if that is the only link to this node, we're done with the chain, so append the chain to the list and return the newly created chain - { -// headsOfSystems.Append(newChain); - return newChain; - } - nextNode = currentNode->links.GetHeadElement()->next->value;//follow the other link if there is one, so we go down the chain - if(!setLinkVisited(currentNode, nextNode)) //mark link as followed, so we know not to backtrack - { - // headsOfSystems.Append(newChain); - return newChain; //This condition, where no branches have occurred but both links have already - //been taken can only occur in a loop with no spurs; add this loop to the - //system (currently added as a chain for consistency), and return. - } - } - currentNode = nextNode; //set the current node to be the next node in the chain - } - currentNode->visited = true; - tmp = new int; - *tmp = currentNode->idNumber; - newChain->listOfNodes.Append(tmp); //append the last node before branch (node shared jointly with branch chains) - //re-mark as visited, just to make sure - ListElement * tempNode = currentNode->links.GetHeadElement(); //go through all of the links, one at a time that branch - POEMSChain * tempChain = NULL; //temporary variable to hold data - while(tempNode != NULL) //when we have followed all links, stop - { - if(setLinkVisited(tempNode->value, currentNode)) //dont backtrack, or create closed loops - { - tempChain = AddNewChain(tempNode->value); //Add a new chain created out of the next node down that link - tempChain->parentChain = newChain; //set the parent to be this chain - newChain->childChains.Append(tempChain); //append the chain to this chain's list of child chains - } - tempNode = tempNode->next; //go to process the next chain - } - //headsOfSystems.Append(newChain); //append this chain to the system list - return newChain; -} - -POEMSNode * SystemProcessor::findSingleLink(TreeNode * aNode) -//This function takes the root of a search tree containing POEMSNodes and returns a POEMSNode corresponding to the start of a chain in the -//system. It finds a node that has not been visited before, and only has one link; this node will be used as the head of the chain. -{ - if(aNode == NULL) - { - return NULL; - } - POEMSNode * returnVal = (POEMSNode *)aNode->GetAuxData(); //get the poemsnode data out of the treenode - POEMSNode * detectLoneLoops = NULL; //is used to handle a loop that has no protruding chains - if(returnVal->visited == false) - { - detectLoneLoops = returnVal; //if we find any node that has not been visited yet, save it - } - if(returnVal->links.GetNumElements() == 1 && returnVal->visited == false) //see if it has one element and hasnt been visited already - { - return returnVal; //return the node is it meets this criteria - } - returnVal = findSingleLink(aNode->Left()); //otherwise, check the left subtree - if(returnVal == NULL) //and if we find nothing... - { - returnVal = findSingleLink(aNode->Right()); //check the right subtree - } - if(returnVal == NULL) //if we could not find any chains - { - returnVal = detectLoneLoops; //see if we found any nodes at all that havent been processed - } - return returnVal; //return what we find (will be NULL if no new chains are - //found) -} - -bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNode) -//setLinkVisited sets the links between these two nodes as visited. If they are already visited, it returns false. Otherwise, it sets -//them as visited and returns true. This function is used to see whether a certain path has been taken already in the graph structure. -//If it has been, then we need to know so we dont follow it again; this prevents infinite recursion when there is a loop, and prevents -//backtracking up a chain that has already been made. The list of booleans denoting if a link has been visited is called 'taken' and is -//part of the POEMSNode struct. The list is the same size as the list of pointers to other nodes, and stores the boolean visited/unvisited -//value for that particular link. Because each link is represented twice, (once at each node in the link), both of the boolean values need -//to be set in the event that the link has to be set as visited. -{ - //cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... "; - ListElement * tmp = firstNode->links.GetHeadElement(); //get the head element of the list of pointers for node 1 - ListElement * tmp2 = firstNode->taken.GetHeadElement(); //get the head element of the list of bool isVisited flags for node 1 - while(tmp->value != NULL || tmp2->value != NULL) //go through untill we reach the end of the lists - { - if(tmp->value == secondNode) //if we find the link to the other node - { - if(*(tmp2->value) == true) //if the link has already been visited - { - //cout << "visited already" << endl; - return false; //return false to indicate that the link has been visited before this attempt - } - else //otherwise, visit it - { - *tmp2->value = true; - } - break; - } - tmp = tmp->next; //go check next link - tmp2 = tmp2->next; - } - - tmp = secondNode->links.GetHeadElement(); //now, if the link was unvisited, we need to go set the other node's list such that - //it also knows this link is being visited - tmp2 = secondNode->taken.GetHeadElement(); - while(tmp->value != NULL || tmp2->value != NULL) //go through the list - { - if(tmp->value == firstNode) //if we find the link - { - if(*(tmp2->value) == true) //and it has already been visited, then signal an error; this shouldnt ever happen - { - cout << "Error in parsing structure! Should never reach this condition! \n" << - "Record of visited links out of synch between two adjacent nodes.\n"; - return false; - } - else - { - *tmp2->value = true; //set the appropriate value to true to indicate this link has been visited - } - break; - } - tmp = tmp->next; - tmp2 = tmp2->next; - } - //cout << "not visited" << endl; - return true; //return true to indicate that this is the first time the link has been visited -} - -List * SystemProcessor::getSystemData(void) //Gets the list of POEMSChains that comprise the system. Might eventually only - //return chains linked to the reference plane, but currently returns every chain - //in the system. -{ - return &headsOfSystems; -} - -int SystemProcessor::getNumberOfHeadChains(void) //This function isnt implemented yet, and might be taken out entirely; this was a holdover - //from when I intended to return an array of chain pointers, rather than a list of chains - //It will probably be deleted once I finish figuring out exactly what needs to be returned -{ - return 0; -} -#endif diff --git a/lib/atc/ThermalTimeIntegrator.cpp b/lib/atc/ThermalTimeIntegrator.cpp index 8186437bfaab0feeb259ba8f195bf8bb11ba0788..f68f46b01f63500e4576248a11f730b61bc0cca7 100644 --- a/lib/atc/ThermalTimeIntegrator.cpp +++ b/lib/atc/ThermalTimeIntegrator.cpp @@ -28,7 +28,7 @@ namespace ATC { // modify // parses inputs and modifies state of the integrator //-------------------------------------------------------- - bool ThermalTimeIntegrator::modify(int narg, char **arg) + bool ThermalTimeIntegrator::modify(int /* narg */, char **arg) { bool foundMatch = false; int argIndex = 0; @@ -570,7 +570,7 @@ namespace ATC { // compute_temperature_delta //-------------------------------------------------------- void ThermalTimeIntegratorFractionalStep::compute_temperature_delta(const DENS_MAT & atomicEnergyDelta, - double dt) + double /* dt */) { DENS_MAT & myAtomicTemperatureDelta(atomicTemperatureDelta_.set_quantity()); myAtomicTemperatureDelta = nodalAtomicEnergyOld_.quantity() + atomicEnergyDelta; diff --git a/lib/atc/Thermostat.cpp b/lib/atc/Thermostat.cpp index 41312bd851543870d00e9b3e4865b8ca6c42d49e..0ede724371ba845d01f69b46907357dff8b3ab28 100644 --- a/lib/atc/Thermostat.cpp +++ b/lib/atc/Thermostat.cpp @@ -483,7 +483,7 @@ namespace ATC { // manages the solution of the // thermostat equations and variables //-------------------------------------------------------- - void ThermostatRescale::compute_thermostat(double dt) + void ThermostatRescale::compute_thermostat(double /* dt */) { // compute right-hand side this->set_rhs(_rhs_); @@ -738,7 +738,7 @@ namespace ATC { // Constructor //-------------------------------------------------------- ThermostatGlcFs::ThermostatGlcFs(AtomicRegulator * thermostat, - int lambdaMaxIterations, + int /* lambdaMaxIterations */, const string & regulatorPrefix) : RegulatorMethod(thermostat,regulatorPrefix), lambdaSolver_(NULL), @@ -1225,7 +1225,7 @@ namespace ATC { // fixed (uncoupled) nodes //-------------------------------------------------------- void ThermostatIntegratorFlux::set_thermostat_rhs(DENS_MAT & rhs, - double dt) + double /* dt */) { // only tested with flux != 0 + ess bc = 0 @@ -1586,7 +1586,7 @@ namespace ATC { //-------------------------------------------------------- void ThermostatIntegratorFixed::add_to_energy(const DENS_MAT & nodalLambdaPower, DENS_MAT & deltaEnergy, - double dt) + double /* dt */) { deltaEnergy.resize(nNodes_,1); @@ -2387,7 +2387,7 @@ namespace ATC { // determines the power exerted by the Hoover // thermostat at each FE node //-------------------------------------------------------- - void ThermostatHooverVerlet::add_to_lambda_power(const DENS_MAT & myLambdaForce, + void ThermostatHooverVerlet::add_to_lambda_power(const DENS_MAT & /* myLambdaForce */, double dt) { _myNodalLambdaPower_ = nodalAtomicHooverLambdaPower_->quantity(); @@ -2593,7 +2593,7 @@ namespace ATC { // determines the power exerted by the Hoover // thermostat at each FE node //-------------------------------------------------------- - void ThermostatHooverVerletFiltered::add_to_lambda_power(const DENS_MAT & myLambdaForce, + void ThermostatHooverVerletFiltered::add_to_lambda_power(const DENS_MAT & /* myLambdaForce */, double dt) { _myNodalLambdaPower_ = nodalAtomicHooverLambdaPower_->quantity(); diff --git a/lib/atc/Thermostat.h b/lib/atc/Thermostat.h index 65dbba7e1541c5642756d55dde2d7a1626b71007..95d2d1162d9d1c1b35ed5214335d8bd31add115f 100644 --- a/lib/atc/Thermostat.h +++ b/lib/atc/Thermostat.h @@ -128,7 +128,7 @@ namespace ATC { virtual void apply_post_corrector(double dt); /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */ - virtual void compute_boundary_flux(FIELDS & fields) + virtual void compute_boundary_flux(FIELDS & /* fields */) {boundaryFlux_[TEMPERATURE] = 0.;}; /** get data for output */ @@ -540,7 +540,7 @@ namespace ATC { virtual void apply_post_corrector(double dt); /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */ - virtual void compute_boundary_flux(FIELDS & fields) + virtual void compute_boundary_flux(FIELDS & /* fields */) {boundaryFlux_[TEMPERATURE] = 0.;}; /** determine if local shape function matrices are needed */ @@ -917,7 +917,7 @@ namespace ATC { virtual void finish() {}; /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */ - virtual void compute_boundary_flux(FIELDS & fields) + virtual void compute_boundary_flux(FIELDS & /* fields */) {boundaryFlux_[TEMPERATURE] = 0.;}; protected: @@ -1022,7 +1022,7 @@ namespace ATC { virtual void finish() {}; /** compute boundary flux, requires thermostat input since it is part of the coupling scheme */ - virtual void compute_boundary_flux(FIELDS & fields) + virtual void compute_boundary_flux(FIELDS & /* fields */) {boundaryFlux_[TEMPERATURE] = 0.;}; protected: diff --git a/lib/atc/TimeFilter.cpp b/lib/atc/TimeFilter.cpp index cb6aff9bebb1762ca83db340dd422034b7f60243..08cb64c8fe9310ed9ab9e7d1c9664ad9c2332910 100644 --- a/lib/atc/TimeFilter.cpp +++ b/lib/atc/TimeFilter.cpp @@ -40,7 +40,7 @@ namespace ATC { // modify // parses input commands //-------------------------------------------------------- - bool TimeFilterManager::modify(int narg, char ** arg) + bool TimeFilterManager::modify(int /* narg */, char ** arg) { bool foundMatch = false; @@ -210,7 +210,7 @@ namespace ATC { } else if (filterType_ == STEP_FILTER) { newTimeFilter = new TimeFilterStep(*this); - } + } else newTimeFilter = NULL; } else { // default to return base class newTimeFilter = new TimeFilter(*this); diff --git a/lib/atc/TimeFilter.h b/lib/atc/TimeFilter.h index 6f7d65f36611193e75e57231b991249e4ebfd8e7..321d9bb8e6a1be36d3a33cc43c670e2526be562f 100644 --- a/lib/atc/TimeFilter.h +++ b/lib/atc/TimeFilter.h @@ -143,62 +143,62 @@ namespace ATC { virtual void initialize(){}; /** pre time integration with a target for an initial condition */ - virtual void initialize(const MATRIX & target){initialize();}; + virtual void initialize(const MATRIX & /* target */){initialize();}; /** Step 1: apply first step in a time filter update in the pre integration phase */ - virtual void apply_pre_step1(MATRIX & filteredQuantity, + virtual void apply_pre_step1(MATRIX & /* filteredQuantity */, const MATRIX & unFilteredQuantity, - double dt) + double /* dt */) { TimeFilter::unFilteredQuantityOld_ = unFilteredQuantity;} /** Step 2: apply second step in a time filter update in pre integration phase */ - virtual void apply_pre_step2(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_pre_step2(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** Step 3: apply first step in a time filter update in post integration phase */ virtual void apply_post_step1(MATRIX & filteredQuantity, const MATRIX & unFilteredQuantity, - double dt) + double /* dt */) { filteredQuantity = unFilteredQuantity;}; /** Step 4: apply second step in a time filter update in post integration phase */ virtual void apply_post_step2(MATRIX & filteredQuantity, const MATRIX & unFilteredQuantity, - double dt) + double /* dt */) { filteredQuantity = unFilteredQuantity;} /** coefficient multipling unfiltered terms in apply_pre_step1 method */ - virtual double unfiltered_coefficient_pre_s1(double dt){return 0.;}; + virtual double unfiltered_coefficient_pre_s1(double /* dt */){return 0.;}; /** coefficient multipling old filtered terms in apply_pre_step1 method */ - virtual double filtered_coefficient_pre_s1(double dt){return 0.;}; + virtual double filtered_coefficient_pre_s1(double /* dt */){return 0.;}; /** coefficient multipling unfiltered terms in apply_post_step1 method */ - virtual double unfiltered_coefficient_post_s1(double dt){return 0.;}; + virtual double unfiltered_coefficient_post_s1(double /* dt */){return 0.;}; /** coefficient multipling old filtered terms in apply_post_step1 method */ - virtual double filtered_coefficient_post_s1(double dt){return 0.;}; + virtual double filtered_coefficient_post_s1(double /* dt */){return 0.;}; /** coefficient multipling unfiltered terms in apply_pre_step2 method */ - virtual double unfiltered_coefficient_pre_s2(double dt){return 0.;}; + virtual double unfiltered_coefficient_pre_s2(double /* dt */){return 0.;}; /** coefficient multipling old filtered terms in apply_pre_step2 method */ - virtual double filtered_coefficient_pre_s2(double dt){return 0.;}; + virtual double filtered_coefficient_pre_s2(double /* dt */){return 0.;}; /** coefficient multipling unfiltered terms in apply_post_step2 method */ - virtual double unfiltered_coefficient_post_s2(double dt){return 0.;}; + virtual double unfiltered_coefficient_post_s2(double /* dt */){return 0.;}; /** coefficient multipling old filtered terms in apply_post_step2 method */ - virtual double filtered_coefficient_post_s2(double dt){return 0.;}; + virtual double filtered_coefficient_post_s2(double /* dt */){return 0.;}; /** rate of filtered quantity to be called in post integration phase */ virtual void rate(MATRIX & rate, - const MATRIX & filteredQuantity, + const MATRIX & /* filteredQuantity */, const MATRIX & unFilteredQuantity, double dt = 0.0) { rate = 1/dt*(unFilteredQuantity - TimeFilter::unFilteredQuantityOld_);}; @@ -243,30 +243,36 @@ namespace ATC { // destructor virtual ~TimeFilterExponential(){}; /** apply first step in a time filter update in the pre integration phase */ - virtual void apply_pre_step1(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_pre_step1(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** apply second step in a time filter update in pre integration phase */ - virtual void apply_pre_step2(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_pre_step2(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** apply first step in a time filter update in post integration phase */ - virtual void apply_post_step1(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_post_step1(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** apply second step in a time filter update in post integration phase */ - virtual void apply_post_step2(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_post_step2(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** time rate of filtered quantity */ virtual void rate(MATRIX & rate, - const MATRIX & filteredQuantity, - const MATRIX & unfilteredQuantity, - double dt = 0) + const MATRIX & filteredQuantity, + const MATRIX & unfilteredQuantity, + double /* dt */) + { double tau = TimeFilter::filterScale_; + rate = 1/tau*(unfilteredQuantity - filteredQuantity); }; + + virtual void rate(MATRIX & rate, + const MATRIX & filteredQuantity, + const MATRIX & unfilteredQuantity) { double tau = TimeFilter::filterScale_; rate = 1/tau*(unfilteredQuantity - filteredQuantity); }; @@ -702,19 +708,19 @@ namespace ATC { virtual void initialize(const MATRIX & target); /** apply first step in a time filter update in the pre integration phase */ - virtual void apply_pre_step1(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_pre_step1(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** apply second step in a time filter update in pre integration phase */ - virtual void apply_pre_step2(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_pre_step2(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** apply first step in a time filter update in post integration phase */ - virtual void apply_post_step1(MATRIX & filteredQuantity, - const MATRIX & unFilteredQuantity, - double dt) {}; + virtual void apply_post_step1(MATRIX & /* filteredQuantity */, + const MATRIX & /* unFilteredQuantity */, + double /* dt */) {}; /** apply second step in a time filter update in post integration phase */ virtual void apply_post_step2(MATRIX & filteredQuantity, @@ -726,9 +732,14 @@ namespace ATC { /** time rate of filtered quantity */ virtual void rate(MATRIX & rate, - const MATRIX & filteredQuantity, - const MATRIX & unfilteredQuantity, - double dt = 0) + const MATRIX & filteredQuantity, + const MATRIX & unfilteredQuantity, + double /* dt */) + { rate = 1/elapsedTime_*(unfilteredQuantity - filteredQuantity); } + + virtual void rate(MATRIX & rate, + const MATRIX & filteredQuantity, + const MATRIX & unfilteredQuantity) { rate = 1/elapsedTime_*(unfilteredQuantity - filteredQuantity); } protected: diff --git a/lib/atc/TimeIntegrator.h b/lib/atc/TimeIntegrator.h index 2753386d06270e935896b30718d072630f8a0360..ceeb7610fbdcfeb008b2110afac14162cd97b680 100644 --- a/lib/atc/TimeIntegrator.h +++ b/lib/atc/TimeIntegrator.h @@ -31,13 +31,13 @@ namespace ATC { virtual void construct_transfers(){}; /** Predictor phase, Verlet first step for velocity */ - virtual void init_integrate_velocity(double dt){}; + virtual void init_integrate_velocity(double /* dt */){}; /** Predictor phase, Verlet first step for position */ - virtual void init_integrate_position(double dt){}; + virtual void init_integrate_position(double /* dt */){}; /** Corrector phase, Verlet second step for velocity */ - virtual void final_integrate(double dt){}; + virtual void final_integrate(double /* dt */){}; }; @@ -128,7 +128,7 @@ namespace ATC { virtual ~TimeIntegrator(); /** parser/modifier */ - virtual bool modify(int narg, char **arg){return false;}; + virtual bool modify(int /* narg */, char ** /* arg */){return false;}; /** create objects to implement requested numerical method */ virtual void construct_methods() = 0; @@ -251,26 +251,26 @@ namespace ATC { // time step methods, corresponding to ATC_Coupling and TimeIntegrator /** first part of pre_initial_integrate */ - virtual void pre_initial_integrate1(double dt){}; + virtual void pre_initial_integrate1(double /* dt */){}; /** second part of pre_initial_integrate */ - virtual void pre_initial_integrate2(double dt){}; + virtual void pre_initial_integrate2(double /* dt */){}; /** first part of post_initial_integrate */ - virtual void post_initial_integrate1(double dt){}; + virtual void post_initial_integrate1(double /* dt */){}; /** second part of post_initial_integrate */ - virtual void post_initial_integrate2(double dt){}; + virtual void post_initial_integrate2(double /* dt */){}; /** first part of pre_final_integrate */ - virtual void pre_final_integrate1(double dt){}; + virtual void pre_final_integrate1(double /* dt */){}; /** second part of pre_final_integrate */ - virtual void pre_final_integrate2(double dt){}; + virtual void pre_final_integrate2(double /* dt */){}; /** first part of post_final_integrate */ - virtual void post_final_integrate1(double dt){}; + virtual void post_final_integrate1(double /* dt */){}; /** second part of post_final_integrate */ - virtual void post_final_integrate2(double dt){}; + virtual void post_final_integrate2(double /* dt */){}; /** third part of post_final_integrate */ - virtual void post_final_integrate3(double dt){}; + virtual void post_final_integrate3(double /* dt */){}; /** checks to see if first RHS computation is needed */ virtual bool has_final_predictor() {return false;}; @@ -282,9 +282,9 @@ namespace ATC { /** post processing step */ virtual void post_process(){}; /** add output data */ - virtual void output(OUTPUT_LIST & outputData){}; + virtual void output(OUTPUT_LIST & /* outputData */){}; /** pack persistent fields */ - virtual void pack_fields(RESTART_LIST & data){}; + virtual void pack_fields(RESTART_LIST & /* data */){}; /** finalize any states */ virtual void finish(){}; diff --git a/lib/atc/TransferLibrary.cpp b/lib/atc/TransferLibrary.cpp index a6bba5ca2360df45b7f9946bc3ad60b9793832ec..d0db0076d77b4581521dcc3f9463450f8e34cdb1 100644 --- a/lib/atc/TransferLibrary.cpp +++ b/lib/atc/TransferLibrary.cpp @@ -705,7 +705,7 @@ namespace ATC { //-------------------------------------------------------- // Constructor //-------------------------------------------------------- - ReducedSparseMatrix::ReducedSparseMatrix(ATC_Method * atc, + ReducedSparseMatrix::ReducedSparseMatrix(ATC_Method * /* atc */, SPAR_MAN * source, LargeToSmallAtomMap * map) : SparseMatrixTransfer(), @@ -782,7 +782,7 @@ namespace ATC { //-------------------------------------------------------- // Constructor //-------------------------------------------------------- - RowMappedSparseMatrixVector::RowMappedSparseMatrixVector(ATC_Method * atc, + RowMappedSparseMatrixVector::RowMappedSparseMatrixVector(ATC_Method * /* atc */, VectorDependencyManager * source, LargeToSmallAtomMap * map) : VectorTransfer(), @@ -846,7 +846,7 @@ namespace ATC { //-------------------------------------------------------- // Constructor //-------------------------------------------------------- - MappedDiagonalMatrix::MappedDiagonalMatrix(ATC_Method * atc, + MappedDiagonalMatrix::MappedDiagonalMatrix(ATC_Method * /* atc */, DIAG_MAN * source, LargeToSmallAtomMap * map) : DiagonalMatrixTransfer(), @@ -892,7 +892,7 @@ namespace ATC { //-------------------------------------------------------- // Constructor //-------------------------------------------------------- - MappedQuantity::MappedQuantity(ATC_Method * atc, + MappedQuantity::MappedQuantity(ATC_Method * /* atc */, DENS_MAN * source, LargeToSmallMap * map) : DenseMatrixTransfer(), diff --git a/lib/atc/TransferOperator.cpp b/lib/atc/TransferOperator.cpp index efa4bc1da2e3d01d3344314c9c17d010e97c86a1..ab91141c6af7ed2585b218954d351c82f714a1f4 100644 --- a/lib/atc/TransferOperator.cpp +++ b/lib/atc/TransferOperator.cpp @@ -868,7 +868,7 @@ namespace ATC { //-------------------------------------------------------- // Constructor //-------------------------------------------------------- - MatToGradBySparse::MatToGradBySparse(ATC_Method * atc, + MatToGradBySparse::MatToGradBySparse(ATC_Method * /* atc */, DENS_MAN * source, VectorDependencyManager * gradientMatrices) : MatToMatTransfer(source), diff --git a/lib/atc/TransferOperator.h b/lib/atc/TransferOperator.h index 333e8d2a698b774b3d16d30c76970f7edf22d388..0ab92805bedf196e8863c7e447e794830b6fb47f 100644 --- a/lib/atc/TransferOperator.h +++ b/lib/atc/TransferOperator.h @@ -42,43 +42,43 @@ namespace ATC { /** sets the quantity to a given value */ - virtual void operator=(const DenseMatrix & target) + virtual void operator=(const DenseMatrix & /* target */) {throw ATC_Error("DenseMatrixTransfer::set_quantity - Cannot modify transfer-based matrices");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("DenseMatrixTransfer::operator= - Cannot modify transfer-based matrices");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DenseMatrix & addition) + virtual void operator+=(const DenseMatrix & /* addition */) {throw ATC_Error("DenseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("DenseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DenseMatrix & subtraction) + virtual void operator-=(const DenseMatrix & /* subtraction */) {throw ATC_Error("DenseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("DenseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DenseMatrix & multiplier) + virtual void operator*=(const DenseMatrix & /* multiplier */) {throw ATC_Error("DenseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("DenseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DenseMatrix & divisor) + virtual void operator/=(const DenseMatrix & /* divisor */) {throw ATC_Error("DenseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("DenseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");}; protected: @@ -113,43 +113,43 @@ namespace ATC { /** sets the quantity to a given value */ - virtual void operator=(const SparseMatrix & target) + virtual void operator=(const SparseMatrix & /* target */) {throw ATC_Error("SparseMatrixTransfer::set_quantity - Cannot modify transfer-based matrices");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("SparseMatrixTransfer::operator= - Cannot modify transfer-based matrices");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const SparseMatrix & addition) + virtual void operator+=(const SparseMatrix & /* addition */) {throw ATC_Error("SparseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("SparseMatrixTransfer::operator+= - Cannot modify transfer-based matrices");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const SparseMatrix & subtraction) + virtual void operator-=(const SparseMatrix & /* subtraction */) {throw ATC_Error("SparseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("SparseMatrixTransfer::operator-= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const SparseMatrix & multiplier) + virtual void operator*=(const SparseMatrix & /* multiplier */) {throw ATC_Error("SparseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("SparseMatrixTransfer::operator*= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const SparseMatrix & divisor) + virtual void operator/=(const SparseMatrix & /* divisor */) {throw ATC_Error("SparseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("SparseMatrixTransfer::operator/= - Cannot modify transfer-based matrices");}; protected: @@ -184,43 +184,43 @@ namespace ATC { /** sets the quantity to a given value */ - virtual void operator=(const DiagonalMatrix & target) + virtual void operator=(const DiagonalMatrix & /* target */) {throw ATC_Error("DiagonalMatrixTransfer::set_quantity - Cannot modify transfer-based matrices");}; /** sets the quantity to a given constant value */ - virtual void operator=(const T & target) + virtual void operator=(const T & /* target */) {throw ATC_Error("DiagonalMatrixTransfer::operator= - Cannot modify transfer-based matrices");}; /** adds the given data to the Lammps quantity */ - virtual void operator+=(const DiagonalMatrix & addition) + virtual void operator+=(const DiagonalMatrix & /* addition */) {throw ATC_Error("DiagonalMatrixTransfer::operator+= - Cannot modify transfer-based matrices");}; /** adds the scalar data to the Lammps quantity for AtC atoms */ - virtual void operator+=(T addition) + virtual void operator+=(T /* addition */) {throw ATC_Error("DiagonalMatrixTransfer::operator+= - Cannot modify transfer-based matrices");}; /** subtracts the given data from the Lammps quantity */ - virtual void operator-=(const DiagonalMatrix & subtraction) + virtual void operator-=(const DiagonalMatrix & /* subtraction */) {throw ATC_Error("DiagonalMatrixTransfer::operator-= - Cannot modify transfer-based matrices");}; /** subtracts the scalar data from the Lammps quantity for AtC atoms */ - virtual void operator-=(T subtraction) + virtual void operator-=(T /* subtraction */) {throw ATC_Error("DiagonalMatrixTransfer::operator-= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(const DiagonalMatrix & multiplier) + virtual void operator*=(const DiagonalMatrix & /* multiplier */) {throw ATC_Error("DiagonalMatrixTransfer::operator*= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator*=(T multiplier) + virtual void operator*=(T /* multiplier */) {throw ATC_Error("DiagonalMatrixTransfer::operator*= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(const DiagonalMatrix & divisor) + virtual void operator/=(const DiagonalMatrix & /* divisor */) {throw ATC_Error("DiagonalMatrixTransfer::operator/= - Cannot modify transfer-based matrices");}; /** multiples the Lammps quantity by the given data, input is indexed in AtC atom counts */ - virtual void operator/=(T divisor) + virtual void operator/=(T /* divisor */) {throw ATC_Error("DiagonalMatrixTransfer::operator/= - Cannot modify transfer-based matrices");}; protected: diff --git a/lib/atc/Utility.h b/lib/atc/Utility.h index d975d4804ae87ac5ee9043ae206bedbf1e815782..2c0ea7270f78d4b30e2e4eefa4f7bc51bc58a626 100644 --- a/lib/atc/Utility.h +++ b/lib/atc/Utility.h @@ -59,10 +59,10 @@ namespace ATC_Utility return ( (dblL > dblR) || ((dblL <= (dblR + \ std::numeric_limits::epsilon() * \ - tolMult * std::max(abs(dblL), abs(dblR)))) && + tolMult * std::max(fabs(dblL), fabs(dblR)))) && (dblR <= (dblL + \ std::numeric_limits::epsilon() * \ - tolMult * std::max(abs(dblL), abs(dblR)))))); + tolMult * std::max(fabs(dblL), fabs(dblR)))))); } inline double tolerance(double x, double tol = parsetol_) { diff --git a/lib/atc/Vector.h b/lib/atc/Vector.h index ff04b0720de7bc4bcc96c50b75cb769cc1315298..884a080d7d46ccd0d73d8393136a3b21dcf832f9 100644 --- a/lib/atc/Vector.h +++ b/lib/atc/Vector.h @@ -61,7 +61,7 @@ public: //* performs a matrix-vector multiply with default naive implementation template void MultMv(const Matrix &A, const Vector &v, DenseVector &c, - const bool At, T a, T b) + const bool At, T /* a */, T b) { const INDEX sA[2] = {A.nRows(), A.nCols()}; // m is sA[At] k is sA[!At] const INDEX M=sA[At], K=sA[!At]; diff --git a/lib/atc/ViscousStress.cpp b/lib/atc/ViscousStress.cpp index 4053cf6cb703d5ef88a38c2413bc6dbf8554bd6b..305769af68d2c9b379cb90e79e6980ed6acb0c2e 100644 --- a/lib/atc/ViscousStress.cpp +++ b/lib/atc/ViscousStress.cpp @@ -34,7 +34,7 @@ ViscousStressConstant::ViscousStressConstant(fstream &fileId) // compute the stress at N integration points from the velocity gradients // T_{ij} = viscosity * du_i/dx_j //============================================================================= -void ViscousStressConstant::viscous_stress(const FIELD_MATS &fields, + void ViscousStressConstant::viscous_stress(const FIELD_MATS & /* fields */, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &sigma) { diff --git a/lib/atc/ViscousStress.h b/lib/atc/ViscousStress.h index d9da270452ce1bb94ff7ef71fbeb4acee5f35e07..1636aa5bc3f70c5475703dbc3aeac88f19c8fa00 100644 --- a/lib/atc/ViscousStress.h +++ b/lib/atc/ViscousStress.h @@ -22,17 +22,17 @@ namespace ATC { virtual ~ViscousStress() {}; virtual void initialize(void){}; //* Returns parameter values, (Nothing uses this). - virtual void parameters(std::map ¶meters) {} + virtual void parameters(std::map & /* parameters */) {} //* Computes viscous stress given a strain rate tensor. //* Units: mvv/L^3 (i.e. for units Real: g/(mol ps^2 A^2) ) virtual void viscous_stress(const FIELD_MATS &fields, const GRAD_FIELD_MATS &gradFields, DENS_MAT_VEC &stress)=0; - virtual void viscosity(const FIELD_MATS & fields, - DENS_MAT & coefs) const + virtual void viscosity(const FIELD_MATS & /* fields */, + DENS_MAT & /* coefs */) const {throw ATC_Error("ViscousStress::viscosity: unimplemented function");} //* Returns the derivative of the stress tensor for a given strain-rate tensor. - virtual void tangent(const MATRIX &F, MATRIX &C) const + virtual void tangent(const MATRIX & /* F */, MATRIX & /* C */) const {throw ATC_Error("ViscousStress::tangent: unimplemented function");} }; diff --git a/lib/atc/WeakEquation.h b/lib/atc/WeakEquation.h index 84f2b5bb4853233982faeedcf37311b5ce22e2ce..bf349a2a53e00e2aaec13b8e8d20e7ebf2a8a1a2 100644 --- a/lib/atc/WeakEquation.h +++ b/lib/atc/WeakEquation.h @@ -32,52 +32,52 @@ class WeakEquation { /** integrand that used to form the energy */ virtual bool has_E_integrand(void) const {return false;} - virtual void E_integrand(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, - DENS_MAT &energy ) const {}; + virtual void E_integrand(const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, + DENS_MAT & /* energy */ ) const {}; /** density that used to form the mass matrix */ virtual bool has_M_integrand(void) const {return false;} - virtual void M_integrand(const FIELD_MATS &fields, - const Material * material, - DENS_MAT &density ) const {}; + virtual void M_integrand(const FIELD_MATS & /* fields */, + const Material * /* material */, + DENS_MAT & /* density */ ) const {}; /** flux that is integrated with B = Grad N as its weight */ virtual bool has_B_integrand(void) const {return false;} - virtual void B_integrand(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, - DENS_MAT_VEC &flux) const {}; + virtual void B_integrand(const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, + DENS_MAT_VEC & /* flux */) const {}; /** flux that is integrated with N as its weight */ virtual bool has_N_integrand(void) const {return false;} // N_integrand bool is for masking in FE_Engine - virtual bool N_integrand(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, - DENS_MAT &flux) const {return false;}; + virtual bool N_integrand(const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, + DENS_MAT & /* flux */) const {return false;}; /** stiffness matrix */ // linear - virtual void BB_tangent_coefficients(const FieldName field, - const Material * material, - DENS_MAT &coefs) const {}; - virtual void NN_tangent_coefficients(const FieldName field, - const Material * material, - DENS_MAT &coefs) const {}; + virtual void BB_tangent_coefficients(const FieldName /* field */, + const Material * /* material */, + DENS_MAT & /* coefs */) const {}; + virtual void NN_tangent_coefficients(const FieldName /* field */, + const Material * /* material */, + DENS_MAT & /* coefs */) const {}; // non-linear virtual bool has_BB_tangent_coefficients(void) const {return false;} - virtual void BB_tangent_coefficients(const FieldName field, - const FIELD_MATS &fields, - const Material * material, - DENS_MAT &coefs) const {}; + virtual void BB_tangent_coefficients(const FieldName /* field */, + const FIELD_MATS & /* fields */, + const Material * /* material */, + DENS_MAT & /* coefs */) const {}; virtual bool has_NN_tangent_coefficients(void) const {return false;} - virtual void NN_tangent_coefficients(const FieldName field, - const FIELD_MATS &fields, - const Material * material, - DENS_MAT &coefs) const {}; + virtual void NN_tangent_coefficients(const FieldName /* field */, + const FIELD_MATS & /* fields */, + const Material * /* material */, + DENS_MAT & /* coefs */) const {}; /** type of equation */ PDE_Type type(void) const {return type_;} diff --git a/lib/atc/WeakEquationChargeDiffusion.cpp b/lib/atc/WeakEquationChargeDiffusion.cpp index 05152579fc665d63f37ec3724ac3515d3ce191be..6593e90622bd06430ae67e45dc9e803b859d5205 100644 --- a/lib/atc/WeakEquationChargeDiffusion.cpp +++ b/lib/atc/WeakEquationChargeDiffusion.cpp @@ -26,7 +26,7 @@ WeakEquationChargeDiffusion::~WeakEquationChargeDiffusion(void) //--------------------------------------------------------------------- void WeakEquationChargeDiffusion::M_integrand( const FIELD_MATS &fields, - const Material * material, + const Material * /* material */, DENS_MAT & capacity ) const { FIELD_MATS::const_iterator rhoField = fields.find(CHARGE_DENSITY); diff --git a/lib/atc/WeakEquationDiffusion.cpp b/lib/atc/WeakEquationDiffusion.cpp index 1af7d2f7f3ad01440d7bd75b18efeace01e8a4d4..5470d30b1b9364515bc0287156a54bd6213e93bb 100644 --- a/lib/atc/WeakEquationDiffusion.cpp +++ b/lib/atc/WeakEquationDiffusion.cpp @@ -26,7 +26,7 @@ WeakEquationDiffusion::~WeakEquationDiffusion(void) //--------------------------------------------------------------------- void WeakEquationDiffusion::M_integrand( const FIELD_MATS &fields, - const Material * material, + const Material * /* material */, DENS_MAT & capacity ) const { FIELD_MATS::const_iterator rhoField = fields.find(SPECIES_CONCENTRATION); @@ -38,10 +38,10 @@ void WeakEquationDiffusion::M_integrand( // compute flux //-------------------------------------------------------------- void WeakEquationDiffusion::B_integrand( - const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, - DENS_MAT_VEC &flux) const + const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, + DENS_MAT_VEC & /* flux */) const { // material->diffusion_flux(fields, grad_fields, flux[SPECIES_CONCENTRATION]); } diff --git a/lib/atc/WeakEquationElectronContinuity.cpp b/lib/atc/WeakEquationElectronContinuity.cpp index 3b2a18b0f26877b4e5c830ed900884849fe49dd3..193da6e2c713858aef6a5128840bd3c227f1533a 100644 --- a/lib/atc/WeakEquationElectronContinuity.cpp +++ b/lib/atc/WeakEquationElectronContinuity.cpp @@ -24,7 +24,7 @@ WeakEquationElectronContinuity::~WeakEquationElectronContinuity(void) //--------------------------------------------------------------------- void WeakEquationElectronContinuity::M_integrand( const FIELD_MATS &fields, - const Material * material, + const Material * /* material */, DENS_MAT & density ) const { FIELD_MATS::const_iterator nField = fields.find(ELECTRON_DENSITY); @@ -72,7 +72,7 @@ WeakEquationElectronEquilibrium::~WeakEquationElectronEquilibrium(void) //--------------------------------------------------------------------- void WeakEquationElectronEquilibrium::M_integrand( const FIELD_MATS &fields, - const Material * material, + const Material * /* material */, DENS_MAT & density ) const { FIELD_MATS::const_iterator nField = fields.find(ELECTRON_DENSITY); @@ -85,7 +85,7 @@ void WeakEquationElectronEquilibrium::M_integrand( bool WeakEquationElectronEquilibrium::N_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT &flux) const { diff --git a/lib/atc/WeakEquationElectronMomentum.cpp b/lib/atc/WeakEquationElectronMomentum.cpp index 37484f61d563991f99d826b1bffc593f508f62f7..c4728c7bd51413ffa5f06d251cc2b501fd6755d7 100644 --- a/lib/atc/WeakEquationElectronMomentum.cpp +++ b/lib/atc/WeakEquationElectronMomentum.cpp @@ -79,7 +79,7 @@ void WeakEquationElectronMomentum::M_integrand( //-------------------------------------------------------------- void WeakEquationElectronMomentum::B_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT_VEC &flux) const { diff --git a/lib/atc/WeakEquationElectronMomentum.h b/lib/atc/WeakEquationElectronMomentum.h index a3bc62bef71a323428cc6c64077816825cafa874..0010b012cd5762db8731af777b43e277fd3cebad 100644 --- a/lib/atc/WeakEquationElectronMomentum.h +++ b/lib/atc/WeakEquationElectronMomentum.h @@ -78,10 +78,10 @@ namespace ATC{ /** flux that is integrated with grad N as its weight */ virtual bool has_B_integrand(void) const {return false;} - virtual void B_integrand(const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, - DENS_MAT_VEC &flux) const {}; + virtual void B_integrand(const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, + DENS_MAT_VEC &/* flux */) const {}; /** flux that is integrated with N as its weight */ virtual bool has_N_integrand(void) const {return true;} diff --git a/lib/atc/WeakEquationElectronTemperature.cpp b/lib/atc/WeakEquationElectronTemperature.cpp index 97a21628d8bfc285197676d99ec5a0eba78898fb..72315dd1e658501bff863154b314e27ed9ed434e 100644 --- a/lib/atc/WeakEquationElectronTemperature.cpp +++ b/lib/atc/WeakEquationElectronTemperature.cpp @@ -26,7 +26,7 @@ WeakEquationElectronTemperature::~WeakEquationElectronTemperature(void) //--------------------------------------------------------------------- void WeakEquationElectronTemperature::E_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT & energy ) const { @@ -61,7 +61,7 @@ void WeakEquationElectronTemperature::B_integrand( //--------------------------------------------------------------------- bool WeakEquationElectronTemperature::N_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT &flux) const { diff --git a/lib/atc/WeakEquationMassDiffusion.cpp b/lib/atc/WeakEquationMassDiffusion.cpp index 5e4445442b8aacf266b60a90f8d5486c2b4edbf5..47ca01bbe45ad9f6d73e0697ba4202f7b63de462 100644 --- a/lib/atc/WeakEquationMassDiffusion.cpp +++ b/lib/atc/WeakEquationMassDiffusion.cpp @@ -26,7 +26,7 @@ WeakEquationMassDiffusion::~WeakEquationMassDiffusion(void) //--------------------------------------------------------------------- void WeakEquationMassDiffusion::M_integrand( const FIELD_MATS &fields, - const Material * material, + const Material * /* material */, DENS_MAT & capacity ) const { FIELD_MATS::const_iterator dField = fields.find(MASS_DENSITY); @@ -38,10 +38,10 @@ void WeakEquationMassDiffusion::M_integrand( // compute flux //-------------------------------------------------------------- void WeakEquationMassDiffusion::B_integrand( - const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, - DENS_MAT_VEC &flux) const + const FIELD_MATS & /* fields */, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, + DENS_MAT_VEC & /* flux */) const { // material->mass_flux(fields, grad_fields, flux[MASS_DENSITY]); } diff --git a/lib/atc/WeakEquationMomentum.cpp b/lib/atc/WeakEquationMomentum.cpp index 04e52b6c9cdf9318ca53016f059db6607d266e88..39400d3167b5692bddfde8e2886635d378688ba2 100644 --- a/lib/atc/WeakEquationMomentum.cpp +++ b/lib/atc/WeakEquationMomentum.cpp @@ -45,7 +45,7 @@ void WeakEquationMomentum::B_integrand( //-------------------------------------------------------------- bool WeakEquationMomentum::N_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT &flux) const { @@ -137,7 +137,7 @@ void WeakEquationMomentumDiffusion::B_integrand( //--------------------------------------------------------------------- void WeakEquationMomentumDiffusion::BB_tangent_coefficients( - const FieldName field, + const FieldName /* field */, const FIELD_MATS &fields, const Material* material, DENS_MAT &coefs) const @@ -148,7 +148,7 @@ void WeakEquationMomentumDiffusion::BB_tangent_coefficients( //-------------------------------------------------------------- bool WeakEquationMomentumDiffusion::N_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT &flux) const { diff --git a/lib/atc/WeakEquationPhononTemperature.cpp b/lib/atc/WeakEquationPhononTemperature.cpp index aef1cd4c539c388ed1c05b1bbf2cf6324bc548e3..fe1ac894bdbf394dec0346de466532d188400d0b 100644 --- a/lib/atc/WeakEquationPhononTemperature.cpp +++ b/lib/atc/WeakEquationPhononTemperature.cpp @@ -26,7 +26,7 @@ WeakEquationPhononTemperature::~WeakEquationPhononTemperature(void) //--------------------------------------------------------------------- void WeakEquationPhononTemperature::E_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &gradFields, + const GRAD_FIELD_MATS & /* gradFields */, const Material * material, DENS_MAT &energy) const { diff --git a/lib/atc/WeakEquationPoisson.cpp b/lib/atc/WeakEquationPoisson.cpp index 02e8655dc0e6161a697be41883bee6c4d39d5048..4440c02bd37c17b9f599fb95eb0981428b171696 100644 --- a/lib/atc/WeakEquationPoisson.cpp +++ b/lib/atc/WeakEquationPoisson.cpp @@ -36,7 +36,7 @@ void WeakEquationPoisson::B_integrand( //--------------------------------------------------------------------- void WeakEquationPoisson::BB_tangent_coefficients( - const FieldName field, + const FieldName /* field */, const FIELD_MATS &fields, const Material* material, DENS_MAT &coefs) const @@ -47,7 +47,7 @@ void WeakEquationPoisson::BB_tangent_coefficients( //--------------------------------------------------------------------- bool WeakEquationPoisson::N_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, + const GRAD_FIELD_MATS & /* grad_fields */, const Material * material, DENS_MAT &flux) const { @@ -56,7 +56,7 @@ bool WeakEquationPoisson::N_integrand( //--------------------------------------------------------------------- void WeakEquationPoisson::NN_tangent_coefficients( - const FieldName field, + const FieldName /* field */, const FIELD_MATS &fields, const Material* material, DENS_MAT &coefs) const @@ -78,8 +78,8 @@ WeakEquationPoissonConstantRHS::WeakEquationPoissonConstantRHS() //--------------------------------------------------------------------- bool WeakEquationPoissonConstantRHS::N_integrand( const FIELD_MATS &fields, - const GRAD_FIELD_MATS &grad_fields, - const Material * material, + const GRAD_FIELD_MATS & /* grad_fields */, + const Material * /* material */, DENS_MAT &flux) const { diff --git a/lib/atc/WeakEquationPoisson.h b/lib/atc/WeakEquationPoisson.h index 667034525d17381a59e9de200f2452cc64b99157..b004b350ceabf490866c1cccfcacf31168313b55 100644 --- a/lib/atc/WeakEquationPoisson.h +++ b/lib/atc/WeakEquationPoisson.h @@ -98,10 +98,10 @@ class WeakEquationPoissonConstantRHS : public WeakEquationPoisson { /** rhs is constant */ virtual bool has_NN_tangent_coefficients(void) const {return false;} - virtual void NN_tangent_coefficients(const FieldName field, - const FIELD_MATS &fields, - const Material * material, - DENS_MAT &coefs) const {}; + virtual void NN_tangent_coefficients(const FieldName /* field */, + const FIELD_MATS & /* fields */, + const Material * /* material */, + DENS_MAT & /* coefs */) const {}; virtual std::set needs_material_functions(void) const { diff --git a/lib/atc/WeakEquationSchrodinger.cpp b/lib/atc/WeakEquationSchrodinger.cpp index 3663b8c80642333b3027a63cdfc256de9a7c36c0..07497b1fd5a0a0d45837a0706508596e88b6a014 100644 --- a/lib/atc/WeakEquationSchrodinger.cpp +++ b/lib/atc/WeakEquationSchrodinger.cpp @@ -23,7 +23,7 @@ WeakEquationSchrodinger::~WeakEquationSchrodinger(void) //--------------------------------------------------------------------- void WeakEquationSchrodinger::BB_tangent_coefficients( - const FieldName field, + const FieldName /* field */, const FIELD_MATS & fields, const Material* material, DENS_MAT &coefs) const @@ -33,7 +33,7 @@ void WeakEquationSchrodinger::BB_tangent_coefficients( //--------------------------------------------------------------------- void WeakEquationSchrodinger::NN_tangent_coefficients( - const FieldName field, + const FieldName /* field */, const FIELD_MATS & fields, const Material* material, DENS_MAT & V) const diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h index 400b3fb7d2e970e1773ade440ff25ce1b295139f..4c8364671a602bed5932df5a773d6482fb3e01c6 100644 --- a/lib/awpmd/ivutils/include/logexc.h +++ b/lib/awpmd/ivutils/include/logexc.h @@ -43,12 +43,12 @@ enum vbLEVELS{ template struct log_exception_traits{ /// exeption level according to the vbLEVELS - static int level(const exc_t &signal){ return vblFATAL; } + static int level(const exc_t & /* signal */){ return vblFATAL; } /// the string name of exception category - static string name(const exc_t &signal){ return typeid(exc_t).name();} + static string name(const exc_t & /* signal */){ return typeid(exc_t).name();} /// adds some more explanations to the description /// default behaviour: nothing done - static exc_t add_words(const exc_t &orig, const char *words){ + static exc_t add_words(const exc_t &orig, const char * /* words */){ return orig; } }; @@ -80,7 +80,7 @@ struct log_exception_traits{ return "integer exception";*/ } /// default behaviour: nothing done - static int add_words(const int &orig, const char *words){ + static int add_words(const int &orig, const char * /* words */){ return orig; } }; @@ -90,14 +90,11 @@ template<> struct log_exception_traits{ static int level(const enum vbLEVELS &signal){ return log_exception_traits::level(signal); } static string name(const enum vbLEVELS &signal){ return log_exception_traits::name(signal); } - static enum vbLEVELS add_words(const enum vbLEVELS &orig, const char *words){ + static enum vbLEVELS add_words(const enum vbLEVELS &orig, const char * /* words */){ return orig; } }; - - - /// Logger class to control (computational) function behaviour when something requiring user attention has happened. /// message(signal,errcode, text) is used to either throw an exception or return errorcode /// At first, the the level of error is determined via log_exception_traits<>::level(signal) @@ -205,7 +202,7 @@ public: return errcode; } - virtual void log_text(int level, const char *messtype, const char *messtext){ + virtual void log_text(int /* level */, const char *messtype, const char *messtext){ if(descriptor!="") // descriptor is used as header printf("%s:\n",descriptor.c_str()); if(string(messtype)!=string("")) diff --git a/lib/awpmd/ivutils/include/pairhash.h b/lib/awpmd/ivutils/include/pairhash.h index a4eed54385822f0f4ab0780de9852e736fe5ac1e..1fbc1b8b648bfc38de4ee690588488f8bf4c77ed 100644 --- a/lib/awpmd/ivutils/include/pairhash.h +++ b/lib/awpmd/ivutils/include/pairhash.h @@ -324,7 +324,7 @@ public: } //e initializes by unmanaged pointer - sqmatrix(size_t n, T *ptr):size(n){ + sqmatrix(size_t n, T * /* ptr */):size(n){ init(n); } diff --git a/lib/awpmd/ivutils/include/wavepacket.h b/lib/awpmd/ivutils/include/wavepacket.h index e24ac4e23744b741cc82ae30b9320705c0fe7d0d..c4f383702281d154bb6489c9901c87123c951916 100644 --- a/lib/awpmd/ivutils/include/wavepacket.h +++ b/lib/awpmd/ivutils/include/wavepacket.h @@ -24,7 +24,7 @@ class WavePacket; ///\en Template for v=der operation in \ref Wavepacket::int2phys_der() template struct eq_second : public binary_function { - Type operator()(const Type& _Left, const Type& _Right) const{ + Type operator()(const Type& /* _Left */, const Type& _Right) const{ return _Right; } }; @@ -32,7 +32,7 @@ struct eq_second : public binary_function { ///\en Template for v=-der operation in \ref Wavepacket::int2phys_der() template struct eq_minus_second : public binary_function { - Type operator()(const Type& _Left, const Type& _Right) const{ + Type operator()(const Type& /* _Left */, const Type& _Right) const{ return -_Right; } }; diff --git a/lib/awpmd/systems/interact/TCP/wpmd.h b/lib/awpmd/systems/interact/TCP/wpmd.h index c0132bd6e3fcfd72a3c19961490f4493398e9913..bcb99e2092bb83461dc84f7df6a09d5e70d6385d 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd.h +++ b/lib/awpmd/systems/interact/TCP/wpmd.h @@ -425,7 +425,7 @@ public: /// calculated only once based on particle tags) /// If force multiplier is zero, then the term may be omitted (energy will also be zero). /// NOW ASSIGNS BASED ON THE FIRST PAIR ONLY - pair check_part1(int s1,int icj1,int ick2, int s2=-1,int icj3=-1,int ick4=-1){ + pair check_part1(int s1,int icj1,int ick2){ int res=check_ee(s1,icj1,ick2); if(res==1){ // my term //printf(" *\n"); diff --git a/lib/awpmd/systems/interact/TCP/wpmd_split.cpp b/lib/awpmd/systems/interact/TCP/wpmd_split.cpp index 361fae1f34a5c09746c6f64486158c2dc620a0c4..691dbac91b90a50c7627db8c9ef5bd862b7a051d 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd_split.cpp +++ b/lib/awpmd/systems/interact/TCP/wpmd_split.cpp @@ -331,7 +331,7 @@ void AWPMD_split::get_el_forces(int flag, Vector_3P fe_x, fe_pw[ic1+k1]+=E_der[s1][indw1+8*k1+1]/(2*w*h_plank); for(int i=0;i<3;i++){ fe_x[ic1+k1][i]+= -2*real(wk.a)*E_der[s1][indw1+8*k1+2+2*i]-2*imag(wk.a)*E_der[s1][indw1+8*k1+2+2*i+1]; - fe_p[ic1+k1][i]+= (-E_der[s1][indw1+8*k1+2+2*i+1])*(m_electron/h_plank); //*(h_plank/m_electron); + fe_p[ic1+k1][i]+= (-E_der[s1][indw1+8*k1+2+2*i+1])*(m_electron/h_plank); // *(h_plank/m_electron); fe_pw[ic1+k1]+=(r[i]*E_der[s1][indw1+8*k1+2+2*i+1]/w)/h_plank; fe_w[ic1+k1]+=2*r[i]*(t*E_der[s1][indw1+8*k1+2+2*i]+imag(wk.a)*E_der[s1][indw1+8*k1+2+2*i+1]/w); }*/ @@ -368,7 +368,6 @@ int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, for(int c1=0;c1 $@ @for src in $^ ; do \ obj=`basename $$src .cpp`.o ; \ - $(CXX) -MM $(COLVARS_INCFLAGS) -Ilepton/include -DLEPTON \ + $(CXX) -MM $(COLVARS_INCFLAGS) $(LEPTON_INCFLAGS) \ -MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \ done diff --git a/lib/colvars/Makefile.g++ b/lib/colvars/Makefile.g++ index 556e39d070d78b0de98e5775a4e0179d7fdb9db2..6fa5131d6f917c3a9267a15b64abb6cc27f7f5ee 100644 --- a/lib/colvars/Makefile.g++ +++ b/lib/colvars/Makefile.g++ @@ -6,7 +6,7 @@ COLVARS_LIB = libcolvars.a COLVARS_OBJ_DIR = CXX = g++ -CXXFLAGS = -O2 -g -Wall -fPIC -funroll-loops +CXXFLAGS = -std=c++0x -O2 -g -Wall -fPIC -funroll-loops AR = ar ARFLAGS = -rscv SHELL = /bin/sh diff --git a/lib/colvars/Makefile.g++-debug b/lib/colvars/Makefile.g++-debug index a6ca2f81249d09704b284998ea107ead2414b66f..89c650a0fee893ecd25453e883477b5d6c553f3d 100644 --- a/lib/colvars/Makefile.g++-debug +++ b/lib/colvars/Makefile.g++-debug @@ -1,5 +1,5 @@ # -*- makefile -*- to build Colvars module with GNU compiler -COLVARS_DEBUG = "YES" +COLVARS_DEBUG = yes include Makefile.g++ diff --git a/lib/colvars/Makefile.g++-no-lepton b/lib/colvars/Makefile.g++-no-lepton new file mode 100644 index 0000000000000000000000000000000000000000..19497272aa7ee370b5fc29b251d6da9f7565e47b --- /dev/null +++ b/lib/colvars/Makefile.g++-no-lepton @@ -0,0 +1,5 @@ +# -*- makefile -*- to build Colvars module with GNU compiler + +COLVARS_LEPTON = no + +include Makefile.g++ diff --git a/lib/colvars/README b/lib/colvars/README index 087528748b6b2e80b6d76adcd1bb95b21b42c020..6be1b8dd58638c1877e5fd7336a87252d0d294d0 100644 --- a/lib/colvars/README +++ b/lib/colvars/README @@ -8,79 +8,83 @@ The module itself implements a variety of functions and algorithms, including free-energy estimators based on thermodynamic forces, non-equilibrium work and probability distributions. -For a brief description see: - http://colvars.github.io/ - https://github.com/colvars/colvars/ - -## How to build +## Documentation -This directory has source files to build a library that LAMMPS -links against when using the USER-COLVARS package. +For a brief description see: + https://colvars.github.io/ + https://github.com/Colvars/colvars/ -This library must be built with a C++ compiler, *before* LAMMPS is built and -*after* packages are configured, so that LAMMPS can link against it. -You can use the provided Makefile.* files or create your own, specific to your -compiler and system. For example: +For the reference manual see: + http://colvars.github.io/colvars-refman-lammps - cd src - make yes-user-colvars - cd ../lib/colvars - make -f Makefile.g++ +A PDF copy is also at: + doc/PDF/colvars-refman-lammps.pdf -where Makefile.g++ uses the GNU C++ compiler and is a good template to start. +Also available is a Doxygen-based developer documentation: + http://colvars.github.io/doxygen/html/ -**Optional**: if you use the Install.py script provided in this folder, you -can give the machine name as the '-m' argument. This can be the suffix of one -of the files from either this folder, or from src/MAKE/MACHINES. -*This is only supported by the Install.py within the lib/colvars folder*. +The reference article is: + G. Fiorin, M. L. Klein, and J. Hénin, + Molecular Physics 111, 3345 (2013). + http://dx.doi.org/10.1080/00268976.2013.813594 -When you are done building this library, two files should -exist in this directory: -libcolvars.a the library LAMMPS will link against -Makefile.lammps settings the LAMMPS Makefile will import +## Requirements -IMPORTANT: You must examine the final Makefile.lammps to insure it is -correct for your system, else the LAMMPS build will likely fail. +The Colvars library can be built for the most part with all major versions of +the C++ language. -If you want to set a debug flag recognized by the library, the -settings in Makefile.common should work. +A few of the most recent features require C++11 support. In particular, the +library is optionally built together with the +"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also +included in the LAMMPS distribution. Lepton implements the +"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction +feature, and requires C++11 support. -Note: some Colvars functions use the Lepton mathematical expression parser, -which is here included (no additional steps required). For more details, see: - https://simtk.org/projects/lepton +See "here"_https://colvars.github.io/README-c++11.html for a detailed list of +C++11-only features. -## Documentation +## How to build (CMake) -For the reference manual see: - http://colvars.github.io/colvars-refman-lammps +This is the recommended build recipe: no additional settings are normally +needed besides "-D PKG_USER-COLVARS=yes". -A copy of the reference manual is also in: - doc/PDF/colvars-refman-lammps.pdf +Building and linking of Lepton (or other C++11-only features) is enabled +automatically when compilation is carried out with C++11 support, and disabled +otherwise. Optionally, Lepton build may be manually controlled with the flag +"-D COLVARS_LEPTON=yes|no". -Also available is a Doxygen-based developer documentation: - http://colvars.github.io/doxygen/html/ -The reference article is: - G. Fiorin, M. L. Klein, and J. Henin, - Molecular Physics 111, 3345 (2013). - http://dx.doi.org/10.1080/00268976.2013.813594 +## How to build (traditional make) +Before building LAMMPS, one must build the Colvars library in lib/colvars. -## Updating to the latest version +This can be done manually in the same folder by using or adapting one of the +provided Makefiles: for example, Makefile.g++ for the GNU compiler. -To recompile LAMMPS with the most recent version of this module, the `master` -branch of this repository from GitHub, or clone it via git: +In general, it is safer to use build setting consistent with the rest of +LAMMPS. This is best carried out from the LAMMPS src directory using a +command like these, which simply invoke the lib/colvars/Install.py script with +the specified args: - git clone https://github.com/colvars/colvars.git +make lib-colvars # print help message +make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") +make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") +make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre -and run the provided `update-colvars-code.sh` script against the unpacked -LAMMPS source tree: +The "machine" argument of the "-m" flag is used to find a Makefile.machine to +use as build recipe. If it does not already exist in lib/colvars, it will be +auto-generated by using compiler flags consistent with those parsed from the +core LAMMPS makefiles. - ./update-colvars-code.sh /path/to/lammps/folder +Optional flags may be specified as environment variables: -Please report bugs and request new features at: -https://github.com/colvars/colvars/issues +COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) +COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) +The build should produce two files: the library lib/colvars/libcolvars.a +(which also includes Lepton objects if enabled) and the specification file +lib/colvars/Makefile.lammps. The latter is auto-generated, and normally does +not need to be edited. diff --git a/lib/colvars/lepton/include/lepton/CompiledExpression.h b/lib/colvars/lepton/include/lepton/CompiledExpression.h index 67442e0cf5140a1cbcfd03945304c39ae0fff815..c7e393e93ba22009ea5197293f316e051b4c98db 100644 --- a/lib/colvars/lepton/include/lepton/CompiledExpression.h +++ b/lib/colvars/lepton/include/lepton/CompiledExpression.h @@ -9,7 +9,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2013-2016 Stanford University and the Authors. * + * Portions copyright (c) 2013-2019 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -52,9 +52,9 @@ class ParsedExpression; * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate * it many times as quickly as possible. You should treat it as an opaque object; none of the internal representation * is visible. - * + * * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression. - * + * * WARNING: CompiledExpression is NOT thread safe. You should never access a CompiledExpression from two threads at * the same time. */ @@ -99,10 +99,11 @@ private: mutable std::vector workspace; mutable std::vector argValues; std::map dummyVariables; - void* jitCode; + double (*jitCode)(); #ifdef LEPTON_USE_JIT void generateJitCode(); - void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86XmmVar& dest, asmjit::X86XmmVar& arg, double (*function)(double)); + void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg, double (*function)(double)); + void generateTwoArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg1, asmjit::X86Xmm& arg2, double (*function)(double, double)); std::vector constants; asmjit::JitRuntime runtime; #endif diff --git a/lib/colvars/lepton/include/lepton/CustomFunction.h b/lib/colvars/lepton/include/lepton/CustomFunction.h index 5c5586105f7f20d5ca218b6d5f12b2ad34d19629..fbb0ddd52a6b6fa8c166172a7e34704e1ca58db3 100644 --- a/lib/colvars/lepton/include/lepton/CustomFunction.h +++ b/lib/colvars/lepton/include/lepton/CustomFunction.h @@ -72,6 +72,38 @@ public: virtual CustomFunction* clone() const = 0; }; +/** + * This class is an implementation of CustomFunction that does no computation. It just returns + * 0 for the value and derivatives. This is useful when using the parser to analyze expressions + * rather than to evaluate them. You can just create PlaceholderFunctions to represent any custom + * functions that may appear in expressions. + */ + +class LEPTON_EXPORT PlaceholderFunction : public CustomFunction { +public: + /** + * Create a Placeholder function. + * + * @param numArgs the number of arguments the function expects + */ + PlaceholderFunction(int numArgs) : numArgs(numArgs) { + } + int getNumArguments() const { + return numArgs; + } + double evaluate(const double* arguments) const { + return 0.0; + } + double evaluateDerivative(const double* arguments, const int* derivOrder) const { + return 0.0; + } + CustomFunction* clone() const { + return new PlaceholderFunction(numArgs); + }; +private: + int numArgs; +}; + } // namespace Lepton #endif /*LEPTON_CUSTOM_FUNCTION_H_*/ diff --git a/lib/colvars/lepton/include/lepton/ExpressionProgram.h b/lib/colvars/lepton/include/lepton/ExpressionProgram.h index 94d37f471d08bb7b2041aa3c42aafc6a3bc5bac0..a49a9094d0c823e369c4e148b4d1fadec03e78a1 100644 --- a/lib/colvars/lepton/include/lepton/ExpressionProgram.h +++ b/lib/colvars/lepton/include/lepton/ExpressionProgram.h @@ -9,7 +9,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009 Stanford University and the Authors. * + * Portions copyright (c) 2009-2018 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -65,6 +65,14 @@ public: * Get an Operation in this program. */ const Operation& getOperation(int index) const; + /** + * Change an Operation in this program. + * + * The Operation must have been allocated on the heap with the "new" operator. + * The ExpressionProgram assumes ownership of it and will delete it when it + * is no longer needed. + */ + void setOperation(int index, Operation* operation); /** * Get the size of the stack needed to execute this program. This is the largest number of elements present * on the stack at any point during evaluation. diff --git a/lib/colvars/lepton/include/lepton/Operation.h b/lib/colvars/lepton/include/lepton/Operation.h index f7a8b78163403eea136b92c48a35d7b69e97a419..1ddde0b8c0e3af86542c486accc8d44f7df1d43f 100644 --- a/lib/colvars/lepton/include/lepton/Operation.h +++ b/lib/colvars/lepton/include/lepton/Operation.h @@ -9,7 +9,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009-2015 Stanford University and the Authors. * + * Portions copyright (c) 2009-2019 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -63,7 +63,7 @@ public: * can be used when processing or analyzing parsed expressions. */ enum Id {CONSTANT, VARIABLE, CUSTOM, ADD, SUBTRACT, MULTIPLY, DIVIDE, POWER, NEGATE, SQRT, EXP, LOG, - SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, SQUARE, CUBE, RECIPROCAL, + SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, ATAN2, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, SQUARE, CUBE, RECIPROCAL, ADD_CONSTANT, MULTIPLY_CONSTANT, POWER_CONSTANT, MIN, MAX, ABS, FLOOR, CEIL, SELECT}; /** * Get the name of this Operation. @@ -137,6 +137,7 @@ public: class Asin; class Acos; class Atan; + class Atan2; class Sinh; class Cosh; class Tanh; @@ -226,6 +227,11 @@ class LEPTON_EXPORT Operation::Custom : public Operation { public: Custom(const std::string& name, CustomFunction* function) : name(name), function(function), isDerivative(false), derivOrder(function->getNumArguments(), 0) { } + Custom(const std::string& name, CustomFunction* function, const std::vector& derivOrder) : name(name), function(function), isDerivative(false), derivOrder(derivOrder) { + for (int order : derivOrder) + if (order != 0) + isDerivative = true; + } Custom(const Custom& base, int derivIndex) : name(base.name), function(base.function->clone()), isDerivative(true), derivOrder(base.derivOrder) { derivOrder[derivIndex]++; } @@ -684,6 +690,28 @@ public: ExpressionTreeNode differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const; }; +class LEPTON_EXPORT Operation::Atan2 : public Operation { +public: + Atan2() { + } + std::string getName() const { + return "atan2"; + } + Id getId() const { + return ATAN2; + } + int getNumArguments() const { + return 2; + } + Operation* clone() const { + return new Atan2(); + } + double evaluate(double* args, const std::map& variables) const { + return std::atan2(args[0], args[1]); + } + ExpressionTreeNode differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const; +}; + class LEPTON_EXPORT Operation::Sinh : public Operation { public: Sinh() { @@ -989,7 +1017,7 @@ public: double evaluate(double* args, const std::map& variables) const { if (isIntPower) { // Integer powers can be computed much more quickly by repeated multiplication. - + int exponent = intValue; double base = args[0]; if (exponent < 0) { diff --git a/lib/colvars/lepton/src/CompiledExpression.cpp b/lib/colvars/lepton/src/CompiledExpression.cpp index 302f294ee2380e58326833d526b77b1904755ee6..1ad348b47d922e9571ccf99aad70f350889111e4 100644 --- a/lib/colvars/lepton/src/CompiledExpression.cpp +++ b/lib/colvars/lepton/src/CompiledExpression.cpp @@ -6,7 +6,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2013-2016 Stanford University and the Authors. * + * Portions copyright (c) 2013-2019 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -84,17 +84,17 @@ CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expr void CompiledExpression::compileExpression(const ExpressionTreeNode& node, vector >& temps) { if (findTempIndex(node, temps) != -1) return; // We have already processed a node identical to this one. - + // Process the child nodes. - + vector args; for (int i = 0; i < node.getChildren().size(); i++) { compileExpression(node.getChildren()[i], temps); args.push_back(findTempIndex(node.getChildren()[i], temps)); } - + // Process this node. - + if (node.getOperation().getId() == Operation::VARIABLE) { variableIndices[node.getOperation().getName()] = (int) workspace.size(); variableNames.insert(node.getOperation().getName()); @@ -108,7 +108,7 @@ void CompiledExpression::compileExpression(const ExpressionTreeNode& node, vecto arguments[stepIndex].push_back(0); // The value won't actually be used. We just need something there. else { // If the arguments are sequential, we can just pass a pointer to the first one. - + bool sequential = true; for (int i = 1; i < args.size(); i++) if (args[i] != args[i-1]+1) @@ -148,12 +148,12 @@ void CompiledExpression::setVariableLocations(map& variableLoca variablePointers = variableLocations; #ifdef LEPTON_USE_JIT // Rebuild the JIT code. - + if (workspace.size() > 0) generateJitCode(); #else // Make a list of all variables we will need to copy before evaluating the expression. - + variablesToCopy.clear(); for (map::const_iterator iter = variableIndices.begin(); iter != variableIndices.end(); ++iter) { map::iterator pointer = variablePointers.find(iter->first); @@ -165,13 +165,13 @@ void CompiledExpression::setVariableLocations(map& variableLoca double CompiledExpression::evaluate() const { #ifdef LEPTON_USE_JIT - return ((double (*)()) jitCode)(); + return jitCode(); #else for (int i = 0; i < variablesToCopy.size(); i++) *variablesToCopy[i].first = *variablesToCopy[i].second; // Loop over the operations and evaluate each one. - + for (int step = 0; step < operation.size(); step++) { const vector& args = arguments[step]; if (args.size() == 1) @@ -188,34 +188,36 @@ double CompiledExpression::evaluate() const { #ifdef LEPTON_USE_JIT static double evaluateOperation(Operation* op, double* args) { - map* dummyVariables = NULL; - return op->evaluate(args, *dummyVariables); + static map dummyVariables; + return op->evaluate(args, dummyVariables); } void CompiledExpression::generateJitCode() { - X86Compiler c(&runtime); - c.addFunc(kFuncConvHost, FuncBuilder0()); - vector workspaceVar(workspace.size()); + CodeHolder code; + code.init(runtime.getCodeInfo()); + X86Compiler c(&code); + c.addFunc(FuncSignature0()); + vector workspaceVar(workspace.size()); for (int i = 0; i < (int) workspaceVar.size(); i++) - workspaceVar[i] = c.newXmmVar(kX86VarTypeXmmSd); - X86GpVar argsPointer(c); + workspaceVar[i] = c.newXmmSd(); + X86Gp argsPointer = c.newIntPtr(); c.mov(argsPointer, imm_ptr(&argValues[0])); - + // Load the arguments into variables. - + for (set::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) { map::iterator index = variableIndices.find(*iter); - X86GpVar variablePointer(c); + X86Gp variablePointer = c.newIntPtr(); c.mov(variablePointer, imm_ptr(&getVariableReference(index->first))); c.movsd(workspaceVar[index->second], x86::ptr(variablePointer, 0, 0)); } // Make a list of all constants that will be needed for evaluation. - + vector operationConstantIndex(operation.size(), -1); for (int step = 0; step < (int) operation.size(); step++) { // Find the constant value (if any) used by this operation. - + Operation& op = *operation[step]; double value; if (op.getId() == Operation::CONSTANT) @@ -232,9 +234,9 @@ void CompiledExpression::generateJitCode() { value = 1.0; else continue; - + // See if we already have a variable for this constant. - + for (int i = 0; i < (int) constants.size(); i++) if (value == constants[i]) { operationConstantIndex[step] = i; @@ -245,33 +247,33 @@ void CompiledExpression::generateJitCode() { constants.push_back(value); } } - + // Load constants into variables. - - vector constantVar(constants.size()); + + vector constantVar(constants.size()); if (constants.size() > 0) { - X86GpVar constantsPointer(c); + X86Gp constantsPointer = c.newIntPtr(); c.mov(constantsPointer, imm_ptr(&constants[0])); for (int i = 0; i < (int) constants.size(); i++) { - constantVar[i] = c.newXmmVar(kX86VarTypeXmmSd); + constantVar[i] = c.newXmmSd(); c.movsd(constantVar[i], x86::ptr(constantsPointer, 8*i, 0)); } } - + // Evaluate the operations. - + for (int step = 0; step < (int) operation.size(); step++) { Operation& op = *operation[step]; vector args = arguments[step]; if (args.size() == 1) { // One or more sequential arguments. Fill out the list. - + for (int i = 1; i < op.getNumArguments(); i++) args.push_back(args[0]+i); } - + // Generate instructions to execute this operation. - + switch (op.getId()) { case Operation::CONSTANT: c.movsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]); @@ -292,6 +294,9 @@ void CompiledExpression::generateJitCode() { c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]); c.divsd(workspaceVar[target[step]], workspaceVar[args[1]]); break; + case Operation::POWER: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], pow); + break; case Operation::NEGATE: c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]); c.subsd(workspaceVar[target[step]], workspaceVar[args[0]]); @@ -323,6 +328,9 @@ void CompiledExpression::generateJitCode() { case Operation::ATAN: generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atan); break; + case Operation::ATAN2: + generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2); + break; case Operation::SINH: generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinh); break; @@ -374,12 +382,12 @@ void CompiledExpression::generateJitCode() { break; default: // Just invoke evaluateOperation(). - + for (int i = 0; i < (int) args.size(); i++) c.movsd(x86::ptr(argsPointer, 8*i, 0), workspaceVar[args[i]]); - X86GpVar fn(c, kVarTypeIntPtr); + X86Gp fn = c.newIntPtr(); c.mov(fn, imm_ptr((void*) evaluateOperation)); - X86CallNode* call = c.call(fn, kFuncConvHost, FuncBuilder2()); + CCFuncCall* call = c.call(fn, FuncSignature2()); call->setArg(0, imm_ptr(&op)); call->setArg(1, imm_ptr(&argValues[0])); call->setRet(0, workspaceVar[target[step]]); @@ -387,14 +395,24 @@ void CompiledExpression::generateJitCode() { } c.ret(workspaceVar[workspace.size()-1]); c.endFunc(); - jitCode = c.make(); + c.finalize(); + runtime.add(&jitCode, &code); } -void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86XmmVar& dest, X86XmmVar& arg, double (*function)(double)) { - X86GpVar fn(c, kVarTypeIntPtr); +void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg, double (*function)(double)) { + X86Gp fn = c.newIntPtr(); c.mov(fn, imm_ptr((void*) function)); - X86CallNode* call = c.call(fn, kFuncConvHost, FuncBuilder1()); + CCFuncCall* call = c.call(fn, FuncSignature1()); call->setArg(0, arg); call->setRet(0, dest); } + +void CompiledExpression::generateTwoArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg1, X86Xmm& arg2, double (*function)(double, double)) { + X86Gp fn = c.newIntPtr(); + c.mov(fn, imm_ptr((void*) function)); + CCFuncCall* call = c.call(fn, FuncSignature2()); + call->setArg(0, arg1); + call->setArg(1, arg2); + call->setRet(0, dest); +} #endif diff --git a/lib/colvars/lepton/src/ExpressionProgram.cpp b/lib/colvars/lepton/src/ExpressionProgram.cpp index 65d3f0c79a6fac0a33a6fd6be49c8ab3f7678fee..bbbae8533f32b5a8dff9bde77a3ad811bf5affb3 100644 --- a/lib/colvars/lepton/src/ExpressionProgram.cpp +++ b/lib/colvars/lepton/src/ExpressionProgram.cpp @@ -6,7 +6,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009-2013 Stanford University and the Authors. * + * Portions copyright (c) 2009-2018 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -84,6 +84,11 @@ const Operation& ExpressionProgram::getOperation(int index) const { return *operations[index]; } +void ExpressionProgram::setOperation(int index, Operation* operation) { + delete operations[index]; + operations[index] = operation; +} + int ExpressionProgram::getStackSize() const { return stackSize; } diff --git a/lib/colvars/lepton/src/MSVC_erfc.h b/lib/colvars/lepton/src/MSVC_erfc.h index eadb20fdf89322f3836c058be530e10d53a629d6..c30a8ce542157a22db338c81b261678e3258cd8f 100644 --- a/lib/colvars/lepton/src/MSVC_erfc.h +++ b/lib/colvars/lepton/src/MSVC_erfc.h @@ -3,15 +3,15 @@ /* * Up to version 11 (VC++ 2012), Microsoft does not support the - * standard C99 erf() and erfc() functions so we have to fake them here. + * standard C99 erf() and erfc() functions so we have to fake them here. * These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800 * (VC11 has _MSC_VER=1700). */ -#if defined(_MSC_VER) +#if defined(_MSC_VER) #define M_PI 3.14159265358979323846264338327950288 -#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 +#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 /*************************** * erf.cpp * author: Steve Strand diff --git a/lib/colvars/lepton/src/Operation.cpp b/lib/colvars/lepton/src/Operation.cpp index 693dea2edec60db68740b715a8d589d32131bead..78741c481439513e5823e44019459fa99babdf70 100644 --- a/lib/colvars/lepton/src/Operation.cpp +++ b/lib/colvars/lepton/src/Operation.cpp @@ -7,7 +7,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009-2015 Stanford University and the Authors. * + * Portions copyright (c) 2009-2019 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -202,6 +202,16 @@ ExpressionTreeNode Operation::Atan::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { + return ExpressionTreeNode(new Operation::Divide(), + ExpressionTreeNode(new Operation::Subtract(), + ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]), + ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])), + ExpressionTreeNode(new Operation::Add(), + ExpressionTreeNode(new Operation::Square(), children[0]), + ExpressionTreeNode(new Operation::Square(), children[1]))); +} + ExpressionTreeNode Operation::Sinh::differentiate(const std::vector& children, const std::vector& childDerivs, const std::string& variable) const { return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Cosh(), diff --git a/lib/colvars/lepton/src/ParsedExpression.cpp b/lib/colvars/lepton/src/ParsedExpression.cpp index 6effd060072f7a9e10261c49d8812da15e850f8b..fd3b091d3cbe48b3d27457b4a9067a005fdbfa29 100644 --- a/lib/colvars/lepton/src/ParsedExpression.cpp +++ b/lib/colvars/lepton/src/ParsedExpression.cpp @@ -271,6 +271,16 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast(&node.getOperation())->getValue()), children[0].getChildren()[0]); break; } + case Operation::SQRT: + { + if (children[0].getOperation().getId() == Operation::SQUARE) // sqrt(square(x)) = abs(x) + return ExpressionTreeNode(new Operation::Abs(), children[0].getChildren()[0]); + } + case Operation::SQUARE: + { + if (children[0].getOperation().getId() == Operation::SQRT) // square(sqrt(x)) = x + return children[0].getChildren()[0]; + } default: { // If operation ID is not one of the above, diff --git a/lib/colvars/lepton/src/Parser.cpp b/lib/colvars/lepton/src/Parser.cpp index 6b19d7370de6baa44217e04cc48a7ad1ede72df7..e284add25819ebdc31cddf8df9152d024c6f7e4b 100644 --- a/lib/colvars/lepton/src/Parser.cpp +++ b/lib/colvars/lepton/src/Parser.cpp @@ -6,7 +6,7 @@ * Biological Structures at Stanford, funded under the NIH Roadmap for * * Medical Research, grant U54 GM072970. See https://simtk.org. * * * - * Portions copyright (c) 2009-2015 Stanford University and the Authors. * + * Portions copyright (c) 2009-2019 Stanford University and the Authors. * * Authors: Peter Eastman * * Contributors: * * * @@ -66,7 +66,7 @@ private: string Parser::trim(const string& expression) { // Remove leading and trailing spaces. - + int start, end; for (start = 0; start < (int) expression.size() && isspace(expression[start]); start++) ; @@ -313,6 +313,7 @@ Operation* Parser::getFunctionOperation(const std::string& name, const map(); nbor=new Neighbor(); + pair_program=NULL; } template BaseAtomicT::~BaseAtomic() { delete ans; delete nbor; + if (pair_program) delete pair_program; + k_pair_fast.clear(); + k_pair.clear(); } template @@ -109,19 +113,11 @@ void BaseAtomicT::clear_atomic() { device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes, _gpu_overhead,_driver_overhead,_threads_per_atom,screen); - if (_compiled) { - k_pair_fast.clear(); - k_pair.clear(); - delete pair_program; - _compiled=false; - } - time_pair.clear(); hd_balancer.clear(); nbor->clear(); ans->clear(); - device->clear(); } // --------------------------------------------------------------------------- @@ -276,6 +272,7 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str, return; std::string s_fast=std::string(kname)+"_fast"; + if (pair_program) delete pair_program; pair_program=new UCL_Program(dev); pair_program->load_string(pair_str,device->compile_string().c_str()); k_pair_fast.set_function(*pair_program,s_fast.c_str()); diff --git a/lib/gpu/lal_base_charge.cpp b/lib/gpu/lal_base_charge.cpp index 760e759201b1d22f9630eb7a07278c803f2ac3e7..17f30a704728a04b4990e05f71a6a0240b989d80 100644 --- a/lib/gpu/lal_base_charge.cpp +++ b/lib/gpu/lal_base_charge.cpp @@ -25,12 +25,16 @@ BaseChargeT::BaseCharge() : _compiled(false), _max_bytes(0) { device=&global_device; ans=new Answer(); nbor=new Neighbor(); + pair_program=NULL; } template BaseChargeT::~BaseCharge() { delete ans; delete nbor; + if (pair_program) delete pair_program; + k_pair_fast.clear(); + k_pair.clear(); } template @@ -111,19 +115,11 @@ void BaseChargeT::clear_atomic() { device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes, _gpu_overhead,_driver_overhead,_threads_per_atom,screen); - if (_compiled) { - k_pair_fast.clear(); - k_pair.clear(); - delete pair_program; - _compiled=false; - } - time_pair.clear(); hd_balancer.clear(); nbor->clear(); ans->clear(); - device->clear(); } // --------------------------------------------------------------------------- @@ -291,6 +287,7 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str, return; std::string s_fast=std::string(kname)+"_fast"; + if (pair_program) delete pair_program; pair_program=new UCL_Program(dev); pair_program->load_string(pair_str,device->compile_string().c_str()); k_pair_fast.set_function(*pair_program,s_fast.c_str()); diff --git a/lib/gpu/lal_base_dipole.cpp b/lib/gpu/lal_base_dipole.cpp index 56dcaf8e1248ca9665447a6ab7ceb9102b25a7f5..a4b0bf3c37a34f0cf332107a214e39025ba70a7b 100644 --- a/lib/gpu/lal_base_dipole.cpp +++ b/lib/gpu/lal_base_dipole.cpp @@ -25,12 +25,16 @@ BaseDipoleT::BaseDipole() : _compiled(false), _max_bytes(0) { device=&global_device; ans=new Answer(); nbor=new Neighbor(); + pair_program=NULL; } template BaseDipoleT::~BaseDipole() { delete ans; delete nbor; + if (pair_program) delete pair_program; + k_pair_fast.clear(); + k_pair.clear(); } template @@ -113,19 +117,11 @@ void BaseDipoleT::clear_atomic() { device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes, _gpu_overhead,_driver_overhead,_threads_per_atom,screen); - if (_compiled) { - k_pair_fast.clear(); - k_pair.clear(); - delete pair_program; - _compiled=false; - } - time_pair.clear(); hd_balancer.clear(); nbor->clear(); ans->clear(); - device->clear(); } // --------------------------------------------------------------------------- @@ -299,6 +295,7 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str, return; std::string s_fast=std::string(kname)+"_fast"; + if (pair_program) delete pair_program; pair_program=new UCL_Program(dev); pair_program->load_string(pair_str,device->compile_string().c_str()); k_pair_fast.set_function(*pair_program,s_fast.c_str()); diff --git a/lib/gpu/lal_base_dpd.cpp b/lib/gpu/lal_base_dpd.cpp index 66c8cf09e9214e5d3e8e4b366e2f148c21165fff..bf4533ad1ae09db39d2ab22c9caa3e7cfa1a3be6 100644 --- a/lib/gpu/lal_base_dpd.cpp +++ b/lib/gpu/lal_base_dpd.cpp @@ -25,12 +25,16 @@ BaseDPDT::BaseDPD() : _compiled(false), _max_bytes(0) { device=&global_device; ans=new Answer(); nbor=new Neighbor(); + pair_program=NULL; } template BaseDPDT::~BaseDPD() { delete ans; delete nbor; + if (pair_program) delete pair_program; + k_pair_fast.clear(); + k_pair.clear(); } template @@ -112,19 +116,11 @@ void BaseDPDT::clear_atomic() { device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes, _gpu_overhead,_driver_overhead,_threads_per_atom,screen); - if (_compiled) { - k_pair_fast.clear(); - k_pair.clear(); - delete pair_program; - _compiled=false; - } - time_pair.clear(); hd_balancer.clear(); nbor->clear(); ans->clear(); - device->clear(); } // --------------------------------------------------------------------------- @@ -297,6 +293,7 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str, return; std::string s_fast=std::string(kname)+"_fast"; + if (pair_program) delete pair_program; pair_program=new UCL_Program(dev); pair_program->load_string(pair_str,device->compile_string().c_str()); k_pair_fast.set_function(*pair_program,s_fast.c_str()); diff --git a/lib/gpu/lal_base_ellipsoid.cpp b/lib/gpu/lal_base_ellipsoid.cpp index b8d0b7a66666f08b17e531d20c25036ec630c790..dc323832642b23d8d0bef17020e22bdf1fcc87a8 100644 --- a/lib/gpu/lal_base_ellipsoid.cpp +++ b/lib/gpu/lal_base_ellipsoid.cpp @@ -33,12 +33,25 @@ BaseEllipsoidT::BaseEllipsoid() : _compiled(false), _max_bytes(0) { device=&global_device; ans=new Answer(); nbor=new Neighbor(); + nbor_program=NULL; + ellipsoid_program=NULL; + lj_program=NULL; } template BaseEllipsoidT::~BaseEllipsoid() { delete ans; delete nbor; + k_nbor_fast.clear(); + k_nbor.clear(); + k_ellipsoid.clear(); + k_ellipsoid_sphere.clear(); + k_sphere_ellipsoid.clear(); + k_lj_fast.clear(); + k_lj.clear(); + if (nbor_program) delete nbor_program; + if (ellipsoid_program) delete ellipsoid_program; + if (lj_program) delete lj_program; } template @@ -146,20 +159,6 @@ void BaseEllipsoidT::clear_base() { output_times(); host_olist.clear(); - if (_compiled) { - k_nbor_fast.clear(); - k_nbor.clear(); - k_ellipsoid.clear(); - k_ellipsoid_sphere.clear(); - k_sphere_ellipsoid.clear(); - k_lj_fast.clear(); - k_lj.clear(); - delete nbor_program; - delete ellipsoid_program; - delete lj_program; - _compiled=false; - } - time_nbor1.clear(); time_ellipsoid.clear(); time_nbor2.clear(); @@ -171,7 +170,6 @@ void BaseEllipsoidT::clear_base() { nbor->clear(); ans->clear(); - device->clear(); } template @@ -437,6 +435,7 @@ int** BaseEllipsoidT::compute(const int ago, const int inum_full, const int nall ans->copy_answers(eflag,vflag,eatom,vatom); device->add_ans_object(ans); hd_balancer.stop_timer(); + return nbor->host_jlist.begin()-host_start; } @@ -462,18 +461,21 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev, std::string flags=device->compile_string(); + if (nbor_program) delete nbor_program; nbor_program=new UCL_Program(dev); nbor_program->load_string(ellipsoid_nbor,flags.c_str()); k_nbor_fast.set_function(*nbor_program,"kernel_nbor_fast"); k_nbor.set_function(*nbor_program,"kernel_nbor"); neigh_tex.get_texture(*nbor_program,"pos_tex"); + if (ellipsoid_program) delete ellipsoid_program; ellipsoid_program=new UCL_Program(dev); ellipsoid_program->load_string(ellipsoid_string,flags.c_str()); k_ellipsoid.set_function(*ellipsoid_program,kname); pos_tex.get_texture(*ellipsoid_program,"pos_tex"); quat_tex.get_texture(*ellipsoid_program,"quat_tex"); + if (lj_program) delete lj_program; lj_program=new UCL_Program(dev); lj_program->load_string(lj_string,flags.c_str()); k_sphere_ellipsoid.set_function(*lj_program,s_sphere_ellipsoid.c_str()); diff --git a/lib/gpu/lal_base_three.cpp b/lib/gpu/lal_base_three.cpp index dc5678dd2429d7e4d423b5ef26d95bb5d8fffb1c..1715fc307489101d6268565f54a3679f5b505276 100644 --- a/lib/gpu/lal_base_three.cpp +++ b/lib/gpu/lal_base_three.cpp @@ -27,6 +27,7 @@ BaseThreeT::BaseThree() : _compiled(false), _max_bytes(0) { #ifdef THREE_CONCURRENT ans2=new Answer(); #endif + pair_program=NULL; } template @@ -36,6 +37,12 @@ BaseThreeT::~BaseThree() { #ifdef THREE_CONCURRENT delete ans2; #endif + if (pair_program) delete pair_program; + k_three_center.clear(); + k_three_end.clear(); + k_three_end_vatom.clear(); + k_pair.clear(); + k_short_nbor.clear(); } template @@ -139,16 +146,6 @@ void BaseThreeT::clear_atomic() { device->output_times(time_pair,*ans,*nbor,avg_split,_max_bytes+_max_an_bytes, _gpu_overhead,_driver_overhead,_threads_per_atom,screen); - if (_compiled) { - k_three_center.clear(); - k_three_end.clear(); - k_three_end_vatom.clear(); - k_pair.clear(); - k_short_nbor.clear(); - delete pair_program; - _compiled=false; - } - time_pair.clear(); hd_balancer.clear(); @@ -161,7 +158,6 @@ void BaseThreeT::clear_atomic() { // ucl_device will clean up the command queue in its destructor // ucl_device->pop_command_queue(); #endif - device->clear(); } // --------------------------------------------------------------------------- @@ -378,7 +374,7 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str, return; std::string vatom_name=std::string(three_end)+"_vatom"; - + if (pair_program) delete pair_program; pair_program=new UCL_Program(dev); pair_program->load_string(pair_str,device->compile_string().c_str()); k_three_center.set_function(*pair_program,three_center); diff --git a/lib/gpu/lal_gayberne.cu b/lib/gpu/lal_gayberne.cu index dc6e00ec82bb25150012596b0114dc0806e586a1..cd1ee59fc66c25d4a08e974007dbabf966f757b2 100644 --- a/lib/gpu/lal_gayberne.cu +++ b/lib/gpu/lal_gayberne.cu @@ -316,10 +316,9 @@ __kernel void k_gayberne(const __global numtyp4 *restrict x_, numtyp tempv[3]; gpu_row_times3(iota,b1,tempv); gpu_cross3(tempv,iota,tchi); - temp1 = (numtyp)-4.0*ir*ir; - tchi[0] *= temp1; - tchi[1] *= temp1; - tchi[2] *= temp1; + tchi[0] *= temp2; + tchi[1] *= temp2; + tchi[2] *= temp2; } numtyp temp2 = factor_lj*eta*chi; diff --git a/lib/gpu/lal_pppm.cpp b/lib/gpu/lal_pppm.cpp index 8b5012f31219628ea39737bfa287ecc83f39ceb6..84d6c16e1430ae8919d2bad52b90464bd3eae5bf 100644 --- a/lib/gpu/lal_pppm.cpp +++ b/lib/gpu/lal_pppm.cpp @@ -35,12 +35,17 @@ PPPMT::PPPM() : _allocated(false), _compiled(false), _max_bytes(0) { device=&global_device; ans=new Answer(); + pppm_program=NULL; } template PPPMT::~PPPM() { clear(0.0); delete ans; + k_particle_map.clear(); + k_make_rho.clear(); + k_interp.clear(); + if (pppm_program) delete pppm_program; } template @@ -192,14 +197,6 @@ void PPPMT::clear(const double cpu_time) { *ans,_max_bytes+_max_an_bytes,cpu_time, _cpu_idle_time,screen); - if (_compiled) { - k_particle_map.clear(); - k_make_rho.clear(); - k_interp.clear(); - delete pppm_program; - _compiled=false; - } - time_in.clear(); time_out.clear(); time_map.clear(); @@ -207,7 +204,6 @@ void PPPMT::clear(const double cpu_time) { time_interp.clear(); ans->clear(); - device->clear(); } // --------------------------------------------------------------------------- @@ -380,6 +376,7 @@ void PPPMT::compile_kernels(UCL_Device &dev) { ucl_template_name()+"4"; #endif + if (pppm_program) delete pppm_program; pppm_program=new UCL_Program(dev); #ifdef USE_OPENCL diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp index 336ba87588dbdd567673b22e93e1fdc9f110a12a..7c75a399290e1727c562f3bdc18cfbe1d6e80a4c 100644 --- a/lib/message/cslib/src/cslib.cpp +++ b/lib/message/cslib/src/cslib.cpp @@ -641,6 +641,7 @@ void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround) else if (ftype == 3) bigbytes = biglen * sizeof(float); else if (ftype == 4) bigbytes = biglen * sizeof(double); else if (ftype == 5) bigbytes = biglen * sizeof(char); + else bigbytes = 0; bigbytesround = roundup(bigbytes,8); if (nbuf + bigbytesround > INT_MAX) diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h index b4da9680268729c9ca75e29ebe73eac1c5b0522c..f2bf006881fe7828fc2608914485f0e87bce1bca 100644 --- a/lib/message/cslib/src/cslib.h +++ b/lib/message/cslib/src/cslib.h @@ -17,6 +17,10 @@ #include +#if defined(LAMMPS_BIGBIG) +#error CSlib is not compatible with -DLAMMPS_BIGBIG +#endif + namespace CSLIB_NS { class CSlib { diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index d56b68b8771c6be0a09534424eaa85fa5dba9ffa..668e681b3cb3050d3640a8d2d785fdbc9ec2df5c 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py', # settings -version = "2.5.2" +version = "2.5.3" mode = "static" # help message @@ -45,6 +45,7 @@ checksums = { \ '2.5.0' : '6224cd089493661e19ceacccd35cf911', \ '2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \ '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \ + '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \ } # parse and process arguments diff --git a/potentials/WBe_Wood_PRB2019.snap b/potentials/WBe_Wood_PRB2019.snap new file mode 100644 index 0000000000000000000000000000000000000000..6c32256a19a9bab8893c1d3865ab915ee39375ae --- /dev/null +++ b/potentials/WBe_Wood_PRB2019.snap @@ -0,0 +1,15 @@ +# DATE: 2019-09-18 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019) +# Definition of SNAP+ZBL potential. +variable zblcutinner equal 4 +variable zblcutouter equal 4.8 +variable zblz1 equal 74 +variable zblz2 equal 4 + +# Specify hybrid with SNAP and ZBL + +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_coeff 1 1 zbl ${zblz1} ${zblz1} +pair_coeff 1 2 zbl ${zblz1} ${zblz2} +pair_coeff 2 2 zbl ${zblz2} ${zblz2} +pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be + diff --git a/potentials/WBe_Wood_PRB2019.snapcoeff b/potentials/WBe_Wood_PRB2019.snapcoeff new file mode 100644 index 0000000000000000000000000000000000000000..c72baabd74b4a9ce8a4854a0fbaafd4bb861a40f --- /dev/null +++ b/potentials/WBe_Wood_PRB2019.snapcoeff @@ -0,0 +1,117 @@ +# LAMMPS SNAP coefficients for WBe + +2 56 +W 0.5 1 + -0.000000000000 # B[0] + -0.001487061994 # B[1, 0, 0, 0] + 0.075808306870 # B[2, 1, 0, 1] + 0.538735683870 # B[3, 1, 1, 2] + -0.074148039366 # B[4, 2, 0, 2] + 0.602629813770 # B[5, 2, 1, 3] + -0.147022424344 # B[6, 2, 2, 2] + 0.117756828488 # B[7, 2, 2, 4] + -0.026490439049 # B[8, 3, 0, 3] + -0.035162708767 # B[9, 3, 1, 4] + 0.064315385091 # B[10, 3, 2, 3] + -0.131936948089 # B[11, 3, 2, 5] + -0.021272860272 # B[12, 3, 3, 4] + -0.091171134054 # B[13, 3, 3, 6] + -0.024396224398 # B[14, 4, 0, 4] + -0.059813132803 # B[15, 4, 1, 5] + 0.069585393203 # B[16, 4, 2, 4] + -0.085344044181 # B[17, 4, 2, 6] + -0.155425254597 # B[18, 4, 3, 5] + -0.117031758367 # B[19, 4, 3, 7] + -0.040956258020 # B[20, 4, 4, 4] + -0.084465000389 # B[21, 4, 4, 6] + -0.020367513630 # B[22, 4, 4, 8] + -0.010730484318 # B[23, 5, 0, 5] + -0.054777575658 # B[24, 5, 1, 6] + 0.050742893747 # B[25, 5, 2, 5] + -0.004686334611 # B[26, 5, 2, 7] + -0.116372907121 # B[27, 5, 3, 6] + 0.005542497708 # B[28, 5, 3, 8] + -0.126526795635 # B[29, 5, 4, 5] + -0.080163926221 # B[30, 5, 4, 7] + -0.082426250179 # B[31, 5, 5, 6] + -0.010558777281 # B[32, 5, 5, 8] + -0.001939058038 # B[33, 6, 0, 6] + -0.027907949962 # B[34, 6, 1, 7] + 0.049483908476 # B[35, 6, 2, 6] + 0.005103754385 # B[36, 6, 2, 8] + -0.054751505141 # B[37, 6, 3, 7] + -0.055556071011 # B[38, 6, 4, 6] + -0.006026917619 # B[39, 6, 4, 8] + -0.060889030109 # B[40, 6, 5, 7] + -0.029977673973 # B[41, 6, 6, 6] + -0.014987527280 # B[42, 6, 6, 8] + -0.006697686658 # B[43, 7, 0, 7] + 0.017369624409 # B[44, 7, 1, 8] + 0.047864358817 # B[45, 7, 2, 7] + -0.001989812679 # B[46, 7, 3, 8] + 0.000153530925 # B[47, 7, 4, 7] + -0.003862356345 # B[48, 7, 5, 8] + -0.009754314198 # B[49, 7, 6, 7] + 0.000777958970 # B[50, 7, 7, 8] + -0.003031424287 # B[51, 8, 0, 8] + 0.015612715209 # B[52, 8, 2, 8] + 0.003210129646 # B[53, 8, 4, 8] + -0.013088799947 # B[54, 8, 6, 8] + 0.001465970755 # B[55, 8, 8, 8] +Be 0.417932 0.959049 + 0.000000000000 # B[0] + -0.000112143918 # B[1, 0, 0, 0] + 0.002449805180 # B[2, 1, 0, 1] + 0.189705916830 # B[3, 1, 1, 2] + -0.019967429692 # B[4, 2, 0, 2] + 0.286015704682 # B[5, 2, 1, 3] + 0.072864063124 # B[6, 2, 2, 2] + 0.108748154196 # B[7, 2, 2, 4] + -0.005203284351 # B[8, 3, 0, 3] + 0.043948598532 # B[9, 3, 1, 4] + 0.105425889093 # B[10, 3, 2, 3] + 0.060460134045 # B[11, 3, 2, 5] + -0.003406205141 # B[12, 3, 3, 4] + 0.002306765306 # B[13, 3, 3, 6] + -0.003845115174 # B[14, 4, 0, 4] + 0.029471162073 # B[15, 4, 1, 5] + 0.054901130330 # B[16, 4, 2, 4] + 0.010910192753 # B[17, 4, 2, 6] + 0.033885210622 # B[18, 4, 3, 5] + 0.008053439551 # B[19, 4, 3, 7] + -0.001432298168 # B[20, 4, 4, 4] + 0.017478027729 # B[21, 4, 4, 6] + -0.003402034990 # B[22, 4, 4, 8] + -0.002655339820 # B[23, 5, 0, 5] + 0.012668749892 # B[24, 5, 1, 6] + 0.037521561888 # B[25, 5, 2, 5] + -0.000682693314 # B[26, 5, 2, 7] + 0.008525913627 # B[27, 5, 3, 6] + 0.008977936348 # B[28, 5, 3, 8] + 0.006922732235 # B[29, 5, 4, 5] + 0.003031883044 # B[30, 5, 4, 7] + -0.000345577975 # B[31, 5, 5, 6] + -0.001041600679 # B[32, 5, 5, 8] + -0.001407625493 # B[33, 6, 0, 6] + 0.004211558640 # B[34, 6, 1, 7] + 0.014450875461 # B[35, 6, 2, 6] + -0.007033326252 # B[36, 6, 2, 8] + 0.004998742185 # B[37, 6, 3, 7] + -0.002824617682 # B[38, 6, 4, 6] + 0.003831871934 # B[39, 6, 4, 8] + -0.005700892700 # B[40, 6, 5, 7] + 0.000184422409 # B[41, 6, 6, 6] + 0.001592696824 # B[42, 6, 6, 8] + -0.000804927645 # B[43, 7, 0, 7] + 0.008465358642 # B[44, 7, 1, 8] + 0.005460531160 # B[45, 7, 2, 7] + -0.000639605094 # B[46, 7, 3, 8] + -0.002403948393 # B[47, 7, 4, 7] + -0.001267042453 # B[48, 7, 5, 8] + 0.003836940623 # B[49, 7, 6, 7] + 0.002333141437 # B[50, 7, 7, 8] + -0.000665360637 # B[51, 8, 0, 8] + -0.003460637865 # B[52, 8, 2, 8] + -0.001598726043 # B[53, 8, 4, 8] + 0.001478744304 # B[54, 8, 6, 8] + 0.000806643203 # B[55, 8, 8, 8] diff --git a/potentials/WBe_Wood_PRB2019.snapparam b/potentials/WBe_Wood_PRB2019.snapparam new file mode 100644 index 0000000000000000000000000000000000000000..e4fc4b44596a710f21df13de4d7dd9e31615d8eb --- /dev/null +++ b/potentials/WBe_Wood_PRB2019.snapparam @@ -0,0 +1,11 @@ +# required +rcutfac 4.8123 +twojmax 8 + +# optional + +rfac0 0.99363 +rmin0 0 +bzeroflag 1 +quadraticflag 0 + diff --git a/python/lammps.py b/python/lammps.py index 36cf2d2fddcc216eb0095b07e4fd2e3e6c0f3799..9a73688f658b0ab2123f9a8cb12492e2d440bea8 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -390,23 +390,23 @@ class lammps(object): def extract_compute(self,id,style,type): if id: id = id.encode() if type == 0: - if style > 0: return None - self.lib.lammps_extract_compute.restype = POINTER(c_double) - ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) - return ptr[0] + if style == 0: + self.lib.lammps_extract_compute.restype = POINTER(c_double) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) + return ptr[0] + elif style == 1: + return None + elif style == 2: + self.lib.lammps_extract_compute.restype = POINTER(c_int) + return ptr[0] if type == 1: self.lib.lammps_extract_compute.restype = POINTER(c_double) ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) return ptr if type == 2: - if style == 0: - self.lib.lammps_extract_compute.restype = POINTER(c_int) - ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) - return ptr[0] - else: - self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double)) - ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) - return ptr + self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double)) + ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type) + return ptr return None # extract fix info diff --git a/src/.gitignore b/src/.gitignore index 2d79018b28100ee0f047cd18572092400b9ad0ba..5848874d941bd3a53beae3984a6ef8a6cb369f67 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -161,6 +161,10 @@ /fix_setforce_spin.h /min_spin.cpp /min_spin.h +/min_spin_cg.cpp +/min_spin_cg.h +/min_spin_lbfgs.cpp +/min_spin_lbfgs.h /neb_spin.cpp /neb_spin.h /pair_spin.cpp diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 93b164c5038f7210b92c688f71db3bb0a9b0a2a7..51896aab8537090f072d2baeb181bc483336e493 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -28,6 +28,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -460,20 +461,20 @@ void PairGayBerne::read_restart(FILE *fp) int i,j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { - if (me == 0) fread(&setwell[i],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setwell[i],1,MPI_INT,0,world); if (setwell[i]) { - if (me == 0) fread(&well[i][0],sizeof(double),3,fp); + if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error); MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world); } for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -505,12 +506,12 @@ void PairGayBerne::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&gamma,sizeof(double),1,fp); - fread(&upsilon,sizeof(double),1,fp); - fread(&mu,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&gamma,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&upsilon,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&gamma,1,MPI_DOUBLE,0,world); MPI_Bcast(&upsilon,1,MPI_DOUBLE,0,world); @@ -643,10 +644,10 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3], dchi[2] = temp2*(iota[2]-temp1*r12hat[2]); temp1 = -eta*u_r; - temp2 = eta*chi; - fforce[0] = temp1*dchi[0]-temp2*dUr[0]; - fforce[1] = temp1*dchi[1]-temp2*dUr[1]; - fforce[2] = temp1*dchi[2]-temp2*dUr[2]; + temp3 = eta*chi; + fforce[0] = temp1*dchi[0]-temp3*dUr[0]; + fforce[1] = temp1*dchi[1]-temp3*dUr[1]; + fforce[2] = temp1*dchi[2]-temp3*dUr[2]; // torque for particle 1 and 2 // compute dUr @@ -667,18 +668,17 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3], MathExtra::vecmat(iota,b1,tempv); MathExtra::cross3(tempv,iota,dchi); - temp1 = -4.0/rsq; - dchi[0] *= temp1; - dchi[1] *= temp1; - dchi[2] *= temp1; + dchi[0] *= temp2; + dchi[1] *= temp2; + dchi[2] *= temp2; double dchi2[3]; if (newton_pair || j < nlocal) { MathExtra::vecmat(iota,b2,tempv); MathExtra::cross3(tempv,iota,dchi2); - dchi2[0] *= temp1; - dchi2[1] *= temp1; - dchi2[2] *= temp1; + dchi2[0] *= temp2; + dchi2[1] *= temp2; + dchi2[2] *= temp2; } // compute d_eta diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index f139564320cc283fef61b969ed54eca0763c4d10..dd4b11935e56b3ebc0525dbca5a341243db6d9b9 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -27,6 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -438,20 +439,20 @@ void PairRESquared::read_restart(FILE *fp) int i,j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { - if (me == 0) fread(&setwell[i],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setwell[i],1,MPI_INT,0,world); if (setwell[i]) { - if (me == 0) fread(&well[i][0],sizeof(double),3,fp); + if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,NULL,error); MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world); } for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -479,8 +480,8 @@ void PairRESquared::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index f5e18e9d89696903215c62b38dc5b6cf69241876..8e51f3ac5f8ad255c5c2b27defba9554a6d525d3 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -105,7 +105,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) int ni,nj,npi,npj,ifirst,jfirst; int nei,nej,iefirst,jefirst; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl; - double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij; + double rsq,r,radi,radj,k_nij,k_naij; double facc[3]; int *ilist,*jlist,*numneigh,**firstneigh; @@ -170,8 +170,6 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) ifirst = dfirst[i]; nei = ednum[i]; iefirst = edfirst[i]; - eradi = enclosing_radius[i]; - rradi = rounded_radius[i]; } for (jj = 0; jj < jnum; jj++) { @@ -197,8 +195,6 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) jfirst = dfirst[j]; nej = ednum[j]; jefirst = edfirst[j]; - eradj = enclosing_radius[j]; - rradj = rounded_radius[j]; k_nij = k_n[itype][jtype]; k_naij = k_na[itype][jtype]; @@ -207,7 +203,6 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) r = sqrt(rsq); if (r > radi + radj + cut_inner) continue; - rsqinv = 1.0 / rsq; if (npi == 1 && npj == 1) { sphere_against_sphere(i, j, delx, dely, delz, rsq, @@ -598,16 +593,13 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j, double k_n, double k_na, double** /*x*/, double** v, double** f, int evflag) { - double eradi,eradj,rradi,rradj; + double rradi,rradj; double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; - double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy; + double rij,rsqinv,R,fx,fy,fz,fpair,shift,energy; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; - eradi = enclosing_radius[i]; rradi = rounded_radius[i]; - - eradj = enclosing_radius[j]; rradj = rounded_radius[j]; rsqinv = 1.0/rsq; @@ -649,19 +641,6 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j, vt1 = vr1 - vn1; vt2 = vr2 - vn2; vt3 = vr3 - vn3; - - // normal friction term at contact - - fn[0] = -c_n * vn1; - fn[1] = -c_n * vn2; - fn[2] = -c_n * vn3; - - // tangential friction term at contact - // excluding the tangential deformation term - - ft[0] = -c_t * vt1; - ft[1] = -c_t * vt2; - ft[2] = -c_t * vt3; } f[i][0] += fx; @@ -703,20 +682,16 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j, int &num_contacts, double &evdwl, double* facc) { - int ni, npi, ifirst, nei, iefirst; - int nj, npj, jfirst, nej, jefirst; - double xpi[3], xpj[3], dist, eradi, eradj, rradi, rradj; + int ni, npi, ifirst; + int nj, jfirst, nej, jefirst; + double xpi[3], xpj[3], dist, eradj, rradi, rradj; double fx, fy, fz, energy; int interact; npi = dnum[i]; ifirst = dfirst[i]; - nei = ednum[i]; - iefirst = edfirst[i]; - eradi = enclosing_radius[i]; rradi = rounded_radius[i]; - npj = dnum[j]; jfirst = dfirst[j]; nej = ednum[j]; jefirst = edfirst[j]; diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 2df58d45cd102b7da87a4212606f2721335dff73..ff7e7fc25e5caafb49fbcbe97227e0582123da1d 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -271,7 +271,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) continue; } - int interact, num_contacts; + int num_contacts; Contact contact_list[MAX_CONTACTS]; num_contacts = 0; @@ -280,22 +280,22 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) #ifdef _POLYHEDRON_DEBUG printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j); #endif - interact = edge_against_face(i, j, itype, jtype, x, contact_list, - num_contacts, evdwl, facc); + edge_against_face(i, j, itype, jtype, x, contact_list, + num_contacts, evdwl, facc); // check interaction between j's edges and i' faces #ifdef _POLYHEDRON_DEBUG printf("\nINTERACTION between edges of %d vs. faces of %d:\n", j, i); #endif - interact = edge_against_face(j, i, jtype, itype, x, contact_list, - num_contacts, evdwl, facc); + edge_against_face(j, i, jtype, itype, x, contact_list, + num_contacts, evdwl, facc); // check interaction between i's edges and j' edges #ifdef _POLYHEDRON_DEBUG printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j); #endif - interact = edge_against_edge(i, j, itype, jtype, x, contact_list, - num_contacts, evdwl, facc); + edge_against_edge(i, j, itype, jtype, x, contact_list, + num_contacts, evdwl, facc); // estimate the contact area // also consider point contacts and line contacts @@ -2341,13 +2341,11 @@ void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list, void PairBodyRoundedPolyhedron::sanity_check() { - double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b; + double x1[3],x2[3],h_a[3],h_b[3],d_a,d_b; double a[3],b[3],t_a,t_b; x1[0] = 0; x1[1] = 3; x1[2] = 0; x2[0] = 3; x2[1] = 0; x2[2] = 0; - x3[0] = 4; x3[1] = 3; x3[2] = 0; - x4[0] = 5; x4[1] = 3; x4[2] = 0; a[0] = 0; a[1] = 0; a[2] = 0; b[0] = 4; b[1] = 0; b[2] = 0; diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 99e1b39c9d186b23eb005f983016ae10dc22e209..fe567ead344fe99740311c517db1146f2064db5f 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -372,19 +373,19 @@ void AngleClass2::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); - fread(&k2[1],sizeof(double),atom->nangletypes,fp); - fread(&k3[1],sizeof(double),atom->nangletypes,fp); - fread(&k4[1],sizeof(double),atom->nangletypes,fp); - - fread(&bb_k[1],sizeof(double),atom->nangletypes,fp); - fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp); - fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp); - - fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp); - fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp); - fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp); - fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error); + + utils::sfread(FLERR,&bb_k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&bb_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&bb_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + + utils::sfread(FLERR,&ba_k1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ba_k2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ba_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ba_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index cfc1a93bdee8aea5eb4426c6c56a1adf7c3a1931..0651db75fb035687fad1e43e9b794efc4c592129 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -182,10 +183,10 @@ void BondClass2::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); - fread(&k2[1],sizeof(double),atom->nbondtypes,fp); - fread(&k3[1],sizeof(double),atom->nbondtypes,fp); - fread(&k4[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&k3[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&k4[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 725228666eea6a5d59868e00c3680ad9a190342b..11faefee8fae718f08e8543405a294b1b45d79ed 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -835,45 +836,45 @@ void DihedralClass2::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&phi1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&phi2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&phi3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&aat_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + + utils::sfread(FLERR,&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index ca7ac95239035d3db6100f7c405b0150a55fb66d..a3b8b4b672372b8054673708c9285562dcabc266 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -604,15 +605,15 @@ void ImproperClass2::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k0[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi0[1],sizeof(double),atom->nimpropertypes,fp); - - fread(&aa_k1[1],sizeof(double),atom->nimpropertypes,fp); - fread(&aa_k2[1],sizeof(double),atom->nimpropertypes,fp); - fread(&aa_k3[1],sizeof(double),atom->nimpropertypes,fp); - fread(&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp); - fread(&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp); - fread(&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + + utils::sfread(FLERR,&aa_k1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&aa_k2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&aa_k3[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k0[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi0[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index a0088e52b7eedec7cf8b04d92a088ed0bd5aae71..641ca67226161e9670330539affc7ef5889fdfab 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -24,6 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -610,13 +611,13 @@ void PairLJClass2::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -645,10 +646,10 @@ void PairLJClass2::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index e999a3682e44d74ffca1c8f1abe7b5d20dae511d..89a0d74b5aeab90af007f46124a2b8cf6fa6680e 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -23,6 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -362,14 +363,14 @@ void PairLJClass2CoulCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -399,11 +400,11 @@ void PairLJClass2CoulCut::write_restart_settings(FILE *fp) void PairLJClass2CoulCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index b56c0769965db82d3a18a6c6ed805f0447f34713..5487878f2713f3866c3b752b9f4520263cab0359 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -805,13 +806,13 @@ void PairLJClass2CoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -842,13 +843,13 @@ void PairLJClass2CoulLong::write_restart_settings(FILE *fp) void PairLJClass2CoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index 71a5f8c0567d4617a0d5c9893d48846ad3bfea6c..d73789d8901126bf3364d59e8e7390060fcab327 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -36,6 +36,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -602,12 +603,12 @@ void PairBrownian::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -642,17 +643,17 @@ void PairBrownian::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&mu,sizeof(double),1,fp); - fread(&flaglog,sizeof(int),1,fp); - fread(&flagfld,sizeof(int),1,fp); - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&t_target, sizeof(double),1,fp); - fread(&seed, sizeof(int),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&flagHI,sizeof(int),1,fp); - fread(&flagVF,sizeof(int),1,fp); + utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagfld,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&t_target, sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed, sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&mu,1,MPI_DOUBLE,0,world); MPI_Bcast(&flaglog,1,MPI_INT,0,world); diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index ad25184181731f943aac1078b5eb2c1089bcab26..d1c6e4594fb74ad4713cca9cff2a8b00693344d7 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -25,6 +25,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathSpecial; @@ -394,15 +395,15 @@ void PairColloid::read_restart(FILE *fp) for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (comm->me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (comm->me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (comm->me == 0) { - fread(&a12[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&d1[i][j],sizeof(double),1,fp); - fread(&d2[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a12[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&d1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&d2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -432,9 +433,9 @@ void PairColloid::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4492de3cbb58902033ff70e5960312cfa2c83544..a72eaef679bc23878b2cc805778dc4f3bb369054 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -35,13 +35,14 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; // same as fix_wall.cpp -enum{EDGE,CONSTANT,VARIABLE}; +enum{NONE=0,EDGE,CONSTANT,VARIABLE}; /* ---------------------------------------------------------------------- */ @@ -682,12 +683,12 @@ void PairLubricate::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -720,15 +721,15 @@ void PairLubricate::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&mu,sizeof(double),1,fp); - fread(&flaglog,sizeof(int),1,fp); - fread(&flagfld,sizeof(int),1,fp); - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&flagHI,sizeof(int),1,fp); - fread(&flagVF,sizeof(int),1,fp); + utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagfld,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&mu,1,MPI_DOUBLE,0,world); MPI_Bcast(&flaglog,1,MPI_INT,0,world); diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 4f7e3917e86d84e92c6716ed58b1665d412da994..e8715cec365fa95f82cdf1e45a5c00e0ab51580a 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -34,6 +34,7 @@ #include "variable.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -1908,12 +1909,12 @@ void PairLubricateU::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -1945,14 +1946,14 @@ void PairLubricateU::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&mu,sizeof(double),1,fp); - fread(&flaglog,sizeof(int),1,fp); - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&flagHI,sizeof(int),1,fp); - fread(&flagVF,sizeof(int),1,fp); + utils::sfread(FLERR,&mu,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&flaglog,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagHI,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&flagVF,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&mu,1,MPI_DOUBLE,0,world); MPI_Bcast(&flaglog,1,MPI_INT,0,world); diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index ef7e6583be5e28d1af258aa636fa6c509816bc47..9be8d17b06552a0246296d37a846b88f33180b7e 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -108,27 +108,28 @@ void DumpAtomGZ::openfile() void DumpAtomGZ::write_header(bigint ndump) { if ((multiproc) || (!multiproc && me == 0)) { + if (unit_flag && !unit_count) { + ++unit_count; + gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); + + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); if (domain->triclinic == 0) { - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi); gzprintf(gzFp,"%g %g\n",boxylo,boxyhi); gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi); - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } else { - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy); gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz); gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz); - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } + gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } } diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 9c30f4742f92de2dcf92c2c4c2e22f28b9c1ca02..58ce98ad060ee6404490a7684de4246e1dff3aff 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -108,27 +108,28 @@ void DumpCustomGZ::openfile() void DumpCustomGZ::write_header(bigint ndump) { if ((multiproc) || (!multiproc && me == 0)) { + if (unit_flag && !unit_count) { + ++unit_count; + gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); + + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); if (domain->triclinic == 0) { - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi); gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi); gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi); - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } else { - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy); gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz); gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz); - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } + gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); } } diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp new file mode 100644 index 0000000000000000000000000000000000000000..c27c795f75a309fe218405df9bc5c13262394d16 --- /dev/null +++ b/src/COMPRESS/dump_local_gz.cpp @@ -0,0 +1,173 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "dump_local_gz.h" +#include "domain.h" +#include "error.h" +#include "update.h" + +#include + +using namespace LAMMPS_NS; + +DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : + DumpLocal(lmp, narg, arg) +{ + gzFp = NULL; + + if (!compressed) + error->all(FLERR,"Dump local/gz only writes compressed files"); +} + + +/* ---------------------------------------------------------------------- */ + +DumpLocalGZ::~DumpLocalGZ() +{ + if (gzFp) gzclose(gzFp); + gzFp = NULL; + fp = NULL; +} + + +/* ---------------------------------------------------------------------- + generic opening of a dump file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void DumpLocalGZ::openfile() +{ + // single file, already opened, so just return + + if (singlefile_opened) return; + if (multifile == 0) singlefile_opened = 1; + + // if one file per timestep, replace '*' with current timestep + + char *filecurrent = filename; + if (multiproc) filecurrent = multiname; + + if (multifile) { + char *filestar = filecurrent; + filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar,'*'); + *ptr = '\0'; + if (padflag == 0) + sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", + filestar,update->ntimestep,ptr+1); + else { + char bif[8],pad[16]; + strcpy(bif,BIGINT_FORMAT); + sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]); + sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1); + } + *ptr = '*'; + if (maxfiles > 0) { + if (numfiles < maxfiles) { + nameslist[numfiles] = new char[strlen(filecurrent)+1]; + strcpy(nameslist[numfiles],filecurrent); + ++numfiles; + } else { + remove(nameslist[fileidx]); + delete[] nameslist[fileidx]; + nameslist[fileidx] = new char[strlen(filecurrent)+1]; + strcpy(nameslist[fileidx],filecurrent); + fileidx = (fileidx + 1) % maxfiles; + } + } + } + + // each proc with filewriter = 1 opens a file + + if (filewriter) { + if (append_flag) { + gzFp = gzopen(filecurrent,"ab9"); + } else { + gzFp = gzopen(filecurrent,"wb9"); + } + + if (gzFp == NULL) error->one(FLERR,"Cannot open dump file"); + } else gzFp = NULL; + + // delete string with timestep replaced + + if (multifile) delete [] filecurrent; +} + +void DumpLocalGZ::write_header(bigint ndump) +{ + if ((multiproc) || (!multiproc && me == 0)) { + if (unit_flag && !unit_count) { + ++unit_count; + gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); + + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); + if (domain->triclinic == 0) { + gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); + gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi); + gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi); + gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi); + } else { + gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); + gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy); + gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz); + gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz); + } + gzprintf(gzFp,"ITEM: %s %s\n",label,columns); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpLocalGZ::write_data(int n, double *mybuf) +{ + if (buffer_flag == 1) { + gzwrite(gzFp,mybuf,sizeof(char)*n); + + } else { + int i,j; + int m = 0; + for (i = 0; i < n; i++) { + for (j = 0; j < size_one; j++) { + if (vtype[j] == INT) + gzprintf(gzFp,vformat[j],static_cast (mybuf[m])); + else gzprintf(gzFp,vformat[j],mybuf[m]); + m++; + } + gzprintf(gzFp,"\n"); + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpLocalGZ::write() +{ + DumpLocal::write(); + if (filewriter) { + if (multifile) { + gzclose(gzFp); + gzFp = NULL; + } else { + if (flush_flag) + gzflush(gzFp,Z_SYNC_FLUSH); + } + } +} + diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h new file mode 100644 index 0000000000000000000000000000000000000000..cc788863def9984b5305d3fbf94b960087185948 --- /dev/null +++ b/src/COMPRESS/dump_local_gz.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DUMP_CLASS + +DumpStyle(local/gz,DumpLocalGZ) + +#else + +#ifndef LMP_DUMP_LOCAL_GZ_H +#define LMP_DUMP_LOCAL_GZ_H + +#include "dump_local.h" +#include + +namespace LAMMPS_NS { + +class DumpLocalGZ : public DumpLocal { + public: + DumpLocalGZ(class LAMMPS *, int, char **); + virtual ~DumpLocalGZ(); + + protected: + gzFile gzFp; // file pointer for the compressed output stream + + virtual void openfile(); + virtual void write_header(bigint); + virtual void write_data(int, double *); + virtual void write(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Dump local/gz only writes compressed files + +The dump local/gz output file name must have a .gz suffix. + +E: Cannot open dump file + +Self-explanatory. + +*/ diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 14c511c1000354f0c68b0eb29d610a7ba8322b19..9f9e8973576cc432a277e1698d4ea5f2e17154c6 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -23,6 +23,7 @@ #include "memory.h" #include "error.h" #include "update.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -437,14 +438,14 @@ void PairLJCutDipoleCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -473,10 +474,10 @@ void PairLJCutDipoleCut::write_restart_settings(FILE *fp) void PairLJCutDipoleCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index fe020ed2e6bc937458c47357206197f0146c5391..7fc03005b58efde98383bbf41b18c8bebcb9df1a 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "update.h" - +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -490,13 +490,13 @@ void PairLJCutDipoleLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -524,10 +524,10 @@ void PairLJCutDipoleLong::write_restart_settings(FILE *fp) void PairLJCutDipoleLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 5e7819c2f43b688bd8d4169dab7e677ded3f3f07..481191534f8220aaddd5d04368334f055a98bb26 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -30,6 +30,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -63,10 +64,10 @@ void PairLJLongDipoleLong::options(char **arg, int order) if (!*arg) error->all(FLERR,"Illegal pair_style lj/long/dipole/long command"); for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i); switch (i) { - default: error->all(FLERR,"Illegal pair_style lj/long/dipole/long command"); case 0: ewald_order |= 1<all(FLERR,"Illegal pair_style lj/long/dipole/long command"); } } @@ -344,13 +345,13 @@ void PairLJLongDipoleLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon_read[i][j],sizeof(double),1,fp); - fread(&sigma_read[i][j],sizeof(double),1,fp); - fread(&cut_lj_read[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_read[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world); @@ -379,11 +380,11 @@ void PairLJLongDipoleLong::write_restart_settings(FILE *fp) void PairLJLongDipoleLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ewald_order,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h index 111d13c563a2fc129c1d6e816f38dd7479c8c97a..115e1f05747f30e9aa29020d8ca0719c2eacbcc6 100644 --- a/src/GPU/gpu_extra.h +++ b/src/GPU/gpu_extra.h @@ -133,4 +133,9 @@ E: Unknown error in GPU library Self-explanatory. +W: Increasing communication cutoff for GPU style + +The pair style has increased the communication cutoff to be consistent with +the communication cutoff requirements for this pair style when run on the GPU. + */ diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 8999cb6c47c59447810da14a057f2d7c5ac854c1..906f8a7e8383b5a7b17819eb77d929de3f86fa35 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -206,8 +206,11 @@ void PairSWGPU::init_style() neighbor->requests[irequest]->ghost = 1; } - if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) ) + if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) { comm->cutghostuser=2.0*cutmax + neighbor->skin; + if (comm->me == 0) + error->warning(FLERR,"Increasing communication cutoff for GPU style"); + } } /* ---------------------------------------------------------------------- diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index e0dc021b5742ff3f97bd0865ce7f9093955b239f..15fc5c95daf7b7ca16303d5cfe1584756a3729b0 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -240,8 +240,11 @@ void PairTersoffGPU::init_style() neighbor->requests[irequest]->ghost = 1; } - if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) ) + if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) { comm->cutghostuser = 2.0*cutmax + neighbor->skin; + if (comm->me == 0) + error->warning(FLERR,"Increasing communication cutoff for GPU style"); + } } /* ---------------------------------------------------------------------- diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index a17efb55e84a713744821444198e6007218037e1..2ff09c3248f74c43a8295187e4b7f0dad5e2565c 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -232,8 +232,11 @@ void PairTersoffMODGPU::init_style() neighbor->requests[irequest]->ghost = 1; } - if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) ) + if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) { comm->cutghostuser = 2.0*cutmax + neighbor->skin; + if (comm->me == 0) + error->warning(FLERR,"Increasing communication cutoff for GPU style"); + } } /* ---------------------------------------------------------------------- diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index 765d25f8e627c4df8a05df3469bbac60295cef81..b8d02f09abd6eba7465a2599a72896d30967601c 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -254,8 +254,11 @@ void PairTersoffZBLGPU::init_style() neighbor->requests[irequest]->ghost = 1; } - if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) ) + if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) { comm->cutghostuser = 2.0*cutmax + neighbor->skin; + if (comm->me == 0) + error->warning(FLERR,"Increasing communication cutoff for GPU style"); + } } /* ---------------------------------------------------------------------- diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index 3b74e5685eee23b8c3446c673ec08c12ac32546e..56199f7e548f9ead917767b8367b14c7131a0013 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -234,9 +234,11 @@ void PairVashishtaGPU::init_style() neighbor->requests[irequest]->ghost = 1; } - if (comm->cutghostuser < (2.0*cutmax + neighbor->skin) ) + if (comm->cutghostuser < (2.0*cutmax + neighbor->skin)) { comm->cutghostuser=2.0*cutmax + neighbor->skin; - + if (comm->me == 0) + error->warning(FLERR,"Increasing communication cutoff for GPU style"); + } } /* ---------------------------------------------------------------------- diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index b62b630be50354b1528db72c2ddda855b48d876a..41bc3c93d5096e74dcca83dcae9ca9cffbac2c62 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -167,8 +167,11 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : if (idnext) find_maxid(); // random number generator, same for all procs + // warm up the generator 30x to avoid correlations in first-particle + // positions if runs are repeated with consecutive seeds random = new RanPark(lmp,seed); + for (int ii=0; ii < 30; ii++) random->uniform(); // allgather arrays @@ -180,11 +183,8 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : // grav = gravity in distance/time^2 units // assume grav = -magnitude at this point, enforce in init() - int ifix; - for (ifix = 0; ifix < modify->nfix; ifix++) - if (utils::strmatch(modify->fix[ifix]->style,"^gravity")) break; - - if (ifix == modify->nfix) + int ifix = modify->find_fix_by_style("^gravity"); + if (ifix == -1) error->all(FLERR,"No fix gravity defined for fix pour"); grav = - ((FixGravity *) modify->fix[ifix])->magnitude * force->ftm2v; @@ -309,17 +309,12 @@ void FixPour::init() if (domain->triclinic) error->all(FLERR,"Cannot use fix pour with triclinic box"); - // insure gravity fix exists + // insure gravity fix (still) exists // for 3d must point in -z, for 2d must point in -y // else insertion cannot work - int ifix; - for (ifix = 0; ifix < modify->nfix; ifix++) { - if (strcmp(modify->fix[ifix]->style,"gravity") == 0) break; - if (strcmp(modify->fix[ifix]->style,"gravity/omp") == 0) break; - if (strstr(modify->fix[ifix]->style,"gravity/kk") != NULL) break; - } - if (ifix == modify->nfix) + int ifix = modify->find_fix_by_style("^gravity"); + if (ifix == -1) error->all(FLERR,"No fix gravity defined for fix pour"); double xgrav = ((FixGravity *) modify->fix[ifix])->xgrav; @@ -790,25 +785,27 @@ int FixPour::overlap(int i) return 1 if value is outside, 0 if inside ------------------------------------------------------------------------- */ -int FixPour::outside(int dim, double value, double lo, double hi) +bool FixPour::outside(int dim, double value, double lo, double hi) { double boxlo = domain->boxlo[dim]; double boxhi = domain->boxhi[dim]; + bool outside_pbc_range = true; + bool outside_regular_range = (value < lo || value > hi); if (domain->periodicity[dim]) { - if (lo < boxlo && hi > boxhi) { - return 0; + if ((lo < boxlo && hi > boxhi) || (hi - lo) > domain->prd[dim]) { + // value is always inside + outside_pbc_range = false; } else if (lo < boxlo) { - if (value > hi && value < lo + domain->prd[dim]) return 1; + // lower boundary crosses periodic boundary + outside_pbc_range = (value > hi && value < lo + domain->prd[dim]); } else if (hi > boxhi) { - if (value > hi - domain->prd[dim] && value < lo) return 1; - } else { - if (value < lo || value > hi) return 1; + // upper boundary crosses periodic boundary + outside_pbc_range = (value < lo && value > hi - domain->prd[dim]); } } - if (value < lo || value > hi) return 1; - return 0; + return (outside_pbc_range && outside_regular_range); } /* ---------------------------------------------------------------------- */ diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h index 63d0d39152964677d199312a748a3669cc1e7867..933ce8e6b77df188b337a94251a9ccfdd0227481 100644 --- a/src/GRANULAR/fix_pour.h +++ b/src/GRANULAR/fix_pour.h @@ -70,7 +70,7 @@ class FixPour : public Fix { void find_maxid(); int overlap(int); - int outside(int, double, double, double); + bool outside(int, double, double, double); void xyz_random(double, double *); double radius_sample(); void options(int, char **); diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index a6e67e06fff3759faa1396725439003dbefb262f..c8eec53a1deae4fab25d38cfd24aed73ee39e292 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -1143,8 +1143,7 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, a2 = a*a; knfac = normal_coeffs[0]*a; Fne = knfac*a2/Reff - TWOPI*a2*sqrt(4*coh*E/(M_PI*a)); - } - else{ + } else { knfac = E; //Hooke a = sqrt(dR); Fne = knfac*delta; @@ -1158,16 +1157,13 @@ void FixWallGran::granular(double rsq, double dx, double dy, double dz, if (damping_model == VELOCITY) { damp_normal = 1; - } - else if (damping_model == MASS_VELOCITY) { + } else if (damping_model == MASS_VELOCITY) { damp_normal = meff; - } - else if (damping_model == VISCOELASTIC) { + } else if (damping_model == VISCOELASTIC) { damp_normal = a*meff; - } - else if (damping_model == TSUJI) { + } else if (damping_model == TSUJI) { damp_normal = sqrt(meff*knfac); - } + } else damp_normal = 0.0; damp_normal_prefactor = normal_coeffs[1]*damp_normal; Fdamp = -damp_normal_prefactor*vnnr; diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 771a5566df40d3bf362aad8f1cd255e17db101da..de205dce913e92d5357bf395d1d305f8c9fc74cb 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -31,6 +31,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -540,7 +541,7 @@ void PairGranHookeHistory::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); } } @@ -566,12 +567,12 @@ void PairGranHookeHistory::write_restart_settings(FILE *fp) void PairGranHookeHistory::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&kn,sizeof(double),1,fp); - fread(&kt,sizeof(double),1,fp); - fread(&gamman,sizeof(double),1,fp); - fread(&gammat,sizeof(double),1,fp); - fread(&xmu,sizeof(double),1,fp); - fread(&dampflag,sizeof(int),1,fp); + utils::sfread(FLERR,&kn,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&kt,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamman,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gammat,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&xmu,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dampflag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&kn,1,MPI_DOUBLE,0,world); MPI_Bcast(&kt,1,MPI_DOUBLE,0,world); diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index b87e64a456c6aa703e94da9c09c37905cb72a6f5..85eab1fb9efe51cc923fddcb2422cdb96fc74ba1 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -34,6 +34,7 @@ See the README file in the top-level LAMMPS directory. #include "error.h" #include "math_const.h" #include "math_special.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -139,7 +140,7 @@ void PairGranular::compute(int eflag, int vflag) double wr1,wr2,wr3; double vtr1,vtr2,vtr3,vrel; - double knfac, damp_normal, damp_normal_prefactor; + double knfac, damp_normal=0.0, damp_normal_prefactor; double k_tangential, damp_tangential; double Fne, Ft, Fdamp, Fntot, Fncrit, Fscrit, Frcrit; double fs, fs1, fs2, fs3, tor1, tor2, tor3; @@ -305,6 +306,7 @@ void PairGranular::compute(int eflag, int vflag) delta = radsum - r; dR = delta*Reff; + if (normal_model[itype][jtype] == JKR) { touch[jj] = 1; R2=Reff*Reff; @@ -391,6 +393,7 @@ void PairGranular::compute(int eflag, int vflag) } else { Fncrit = fabs(Fntot); } + Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; //------------------------------ // tangential forces @@ -446,7 +449,6 @@ void PairGranular::compute(int eflag, int vflag) fs3 = -k_tangential*history[2] - damp_tangential*vtr3; // rescale frictional displacements and forces if needed - Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); if (fs > Fscrit) { shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + @@ -464,20 +466,20 @@ void PairGranular::compute(int eflag, int vflag) } else fs1 = fs2 = fs3 = 0.0; } } else { // classic pair gran/hooke (no history) - fs = meff*damp_tangential*vrel; - if (vrel != 0.0) Ft = MIN(Fne,fs) / vrel; + fs = damp_tangential*vrel; + if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; else Ft = 0.0; fs1 = -Ft*vtr1; fs2 = -Ft*vtr2; fs3 = -Ft*vtr3; } - if (roll_model[itype][jtype] != ROLL_NONE || - twist_model[itype][jtype] != TWIST_NONE){ + if (roll_model[itype][jtype] != ROLL_NONE || + twist_model[itype][jtype] != TWIST_NONE){ relrot1 = omega[i][0] - omega[j][0]; relrot2 = omega[i][1] - omega[j][1]; relrot3 = omega[i][2] - omega[j][2]; - // rolling velocity, + // rolling velocity, // see eq. 31 of Wang et al, Particuology v 23, p 49 (2015) // this is different from the Marshall papers, // which use the Bagi/Kuhn formulation @@ -485,7 +487,7 @@ void PairGranular::compute(int eflag, int vflag) // - 0.5*((radj-radi)/radsum)*vtr1; // - 0.5*((radj-radi)/radsum)*vtr2; // - 0.5*((radj-radi)/radsum)*vtr3; - } + } //**************************************** // rolling resistance //**************************************** @@ -635,7 +637,7 @@ void PairGranular::compute(int eflag, int vflag) torque[j][2] -= torroll3; } } - if (evflag) ev_tally_xyz(i,j,nlocal,0, + if (evflag) ev_tally_xyz(i,j,nlocal,force->newton_pair, 0.0,0.0,fx,fy,fz,delx,dely,delz); } } @@ -1114,7 +1116,7 @@ void PairGranular::init_style() double PairGranular::init_one(int i, int j) { - double cutoff; + double cutoff=0.0; if (setflag[i][j] == 0) { if ((normal_model[i][i] != normal_model[j][j]) || @@ -1250,20 +1252,20 @@ void PairGranular::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&normal_model[i][j],sizeof(int),1,fp); - fread(&damping_model[i][j],sizeof(int),1,fp); - fread(&tangential_model[i][j],sizeof(int),1,fp); - fread(&roll_model[i][j],sizeof(int),1,fp); - fread(&twist_model[i][j],sizeof(int),1,fp); - fread(normal_coeffs[i][j],sizeof(double),4,fp); - fread(tangential_coeffs[i][j],sizeof(double),3,fp); - fread(roll_coeffs[i][j],sizeof(double),3,fp); - fread(twist_coeffs[i][j],sizeof(double),3,fp); - fread(&cutoff_type[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&normal_model[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&damping_model[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tangential_model[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&roll_model[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&twist_model[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,normal_coeffs[i][j],sizeof(double),4,fp,NULL,error); + utils::sfread(FLERR,tangential_coeffs[i][j],sizeof(double),3,fp,NULL,error); + utils::sfread(FLERR,roll_coeffs[i][j],sizeof(double),3,fp,NULL,error); + utils::sfread(FLERR,twist_coeffs[i][j],sizeof(double),3,fp,NULL,error); + utils::sfread(FLERR,&cutoff_type[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&normal_model[i][j],1,MPI_INT,0,world); MPI_Bcast(&damping_model[i][j],1,MPI_INT,0,world); @@ -1374,22 +1376,6 @@ double PairGranular::single(int i, int j, int itype, int jtype, vn2 = ny*vnnr; vn3 = nz*vnnr; - double *rmass = atom->rmass; - int *mask = atom->mask; - mi = rmass[i]; - mj = rmass[j]; - if (fix_rigid) { - if (mass_rigid[i] > 0.0) mi = mass_rigid[i]; - if (mass_rigid[j] > 0.0) mj = mass_rigid[j]; - } - - meff = mi*mj / (mi+mj); - if (mask[i] & freeze_group_bit) meff = mj; - if (mask[j] & freeze_group_bit) meff = mi; - - delta = radsum - r; - dR = delta*Reff; - // tangential component vt1 = vr1 - vn1; @@ -1407,6 +1393,9 @@ double PairGranular::single(int i, int j, int itype, int jtype, // if I or J part of rigid body, use body mass // if I or J is frozen, meff is other particle + double *rmass = atom->rmass; + int *mask = atom->mask; + mi = rmass[i]; mj = rmass[j]; if (fix_rigid) { @@ -1451,11 +1440,13 @@ double PairGranular::single(int i, int j, int itype, int jtype, } if (damping_model[itype][jtype] == VELOCITY) { - damp_normal = normal_coeffs[itype][jtype][1]; + damp_normal = 1; + } else if (damping_model[itype][jtype] == MASS_VELOCITY) { + damp_normal = meff; } else if (damping_model[itype][jtype] == VISCOELASTIC) { - damp_normal = normal_coeffs[itype][jtype][1]*a*meff; + damp_normal = a*meff; } else if (damping_model[itype][jtype] == TSUJI) { - damp_normal = normal_coeffs[itype][jtype][1]*sqrt(meff*knfac); + damp_normal = sqrt(meff*knfac); } damp_normal_prefactor = normal_coeffs[itype][jtype][1]*damp_normal; @@ -1506,6 +1497,7 @@ double PairGranular::single(int i, int j, int itype, int jtype, } else { Fncrit = fabs(Fntot); } + Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; //------------------------------ // tangential forces @@ -1518,13 +1510,6 @@ double PairGranular::single(int i, int j, int itype, int jtype, k_tangential *= a; } else if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_RESCALE) { k_tangential *= a; - // on unloading, rescale the shear displacements - if (a < history[3]) { - double factor = a/history[3]; - history[0] *= factor; - history[1] *= factor; - history[2] *= factor; - } } shrmag = sqrt(history[0]*history[0] + history[1]*history[1] + @@ -1535,35 +1520,34 @@ double PairGranular::single(int i, int j, int itype, int jtype, fs2 = -k_tangential*history[1] - damp_tangential*vtr2; fs3 = -k_tangential*history[2] - damp_tangential*vtr3; - // rescale frictional displacements and forces if needed - Fscrit = tangential_coeffs[itype][jtype][2] * Fncrit; + // rescale frictional forces if needed fs = sqrt(fs1*fs1 + fs2*fs2 + fs3*fs3); if (fs > Fscrit) { if (shrmag != 0.0) { - history[0] = -1.0/k_tangential*(Fscrit*fs1/fs + damp_tangential*vtr1); - history[1] = -1.0/k_tangential*(Fscrit*fs2/fs + damp_tangential*vtr2); - history[2] = -1.0/k_tangential*(Fscrit*fs3/fs + damp_tangential*vtr3); fs1 *= Fscrit/fs; fs2 *= Fscrit/fs; fs3 *= Fscrit/fs; - } else fs1 = fs2 = fs3 = 0.0; + fs *= Fscrit/fs; + } else fs1 = fs2 = fs3 = fs = 0.0; } // classic pair gran/hooke (no history) } else { - fs = meff*damp_tangential*vrel; - if (vrel != 0.0) Ft = MIN(Fne,fs) / vrel; + fs = damp_tangential*vrel; + if (vrel != 0.0) Ft = MIN(Fscrit,fs) / vrel; else Ft = 0.0; fs1 = -Ft*vtr1; fs2 = -Ft*vtr2; fs3 = -Ft*vtr3; + fs = Ft*vrel; } //**************************************** // rolling resistance //**************************************** - if (roll_model[itype][jtype] != ROLL_NONE) { + if ((roll_model[itype][jtype] != ROLL_NONE) + || (twist_model[itype][jtype] != TWIST_NONE)) { relrot1 = omega[i][0] - omega[j][0]; relrot2 = omega[i][1] - omega[j][1]; relrot3 = omega[i][2] - omega[j][2]; @@ -1601,10 +1585,10 @@ double PairGranular::single(int i, int j, int itype, int jtype, fr1 *= Frcrit/fr; fr2 *= Frcrit/fr; fr3 *= Frcrit/fr; - } else fr1 = fr2 = fr3 = 0.0; + fr *= Frcrit/fr; + } else fr1 = fr2 = fr3 = fr = 0.0; } - - } + } else fr1 = fr2 = fr3 = fr = 0.0; //**************************************** // twisting torque, including history effects @@ -1628,8 +1612,12 @@ double PairGranular::single(int i, int j, int itype, int jtype, Mtcrit = mu_twist*Fncrit; // critical torque (eq 44) if (fabs(magtortwist) > Mtcrit) { magtortwist = -Mtcrit * signtwist; // eq 34 - } - } + } else magtortwist = 0.0; + } else magtortwist = 0.0; + + // set force and return no energy + + fforce = Fntot*rinv; // set single_extra quantities diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index d935d994bd71413a78773c119d687c8f99ada2d3..43b444418a1af150ccaeebeaea2dd4e4ea50cdea 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -740,19 +740,14 @@ void PairKIM::kim_init() kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles, &lmps_local_tot_num_atoms); - if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, - KIM_SUPPORT_STATUS_notSupported)) - kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs, - KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, - &(eng_vdwl)); + if (kimerror) error->all(FLERR,"Unable to set KIM argument pointer"); kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs, KIM_COMPUTE_CALLBACK_NAME_GetNeighborList, KIM_LANGUAGE_NAME_cpp, reinterpret_cast(get_neigh), reinterpret_cast(this)); - - if (kimerror) error->all(FLERR,"Unable to register KIM pointers"); + if (kimerror) error->all(FLERR,"Unable to set KIM call back pointer"); } /* ---------------------------------------------------------------------- */ @@ -763,6 +758,26 @@ void PairKIM::set_argument_pointers() kimerror = KIM_ComputeArguments_SetArgumentPointerDouble( pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0])); + // Set KIM pointer appropriately for Energy + if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, + KIM_SUPPORT_STATUS_notSupported)) + { + if (KIM_SupportStatus_Equal(kim_model_support_for_energy, + KIM_SUPPORT_STATUS_required) + || (eflag_global == 1)) + { + kimerror = kimerror || + KIM_ComputeArguments_SetArgumentPointerDouble( + pargs,KIM_COMPUTE_ARGUMENT_NAME_partialEnergy,&(eng_vdwl)); + } + else + { + kimerror = kimerror || + KIM_ComputeArguments_SetArgumentPointerDouble( + pargs,KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, + reinterpret_cast(NULL)); + } + } // Set KIM pointer appropriately for particalEnergy if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, KIM_SUPPORT_STATUS_required) diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 7c465128d830422ed9094a258671d990244c555e..8f3744bbf41eaa8b318f1f091d50d872b746c741 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -91,6 +91,8 @@ action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp action dihedral_charmm_kokkos.h dihedral_charmm.h action dihedral_class2_kokkos.cpp dihedral_class2.cpp action dihedral_class2_kokkos.h dihedral_class2.h +action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp +action dihedral_harmonic_kokkos.h dihedral_harmonic.h action dihedral_opls_kokkos.cpp dihedral_opls.cpp action dihedral_opls_kokkos.h dihedral_opls.h action domain_kokkos.cpp @@ -107,6 +109,8 @@ action fix_gravity_kokkos.cpp action fix_gravity_kokkos.h action fix_langevin_kokkos.cpp action fix_langevin_kokkos.h +action fix_minimize_kokkos.cpp +action fix_minimize_kokkos.h action fix_neigh_history_kokkos.cpp action fix_neigh_history_kokkos.h action fix_nh_kokkos.cpp @@ -179,6 +183,12 @@ action nbin_ssa_kokkos.cpp nbin_ssa.cpp action nbin_ssa_kokkos.h nbin_ssa.h action math_special_kokkos.cpp action math_special_kokkos.h +action min_cg_kokkos.cpp +action min_cg_kokkos.h +action min_kokkos.cpp +action min_kokkos.h +action min_linesearch_kokkos.cpp +action min_linesearch_kokkos.h action pair_buck_coul_cut_kokkos.cpp action pair_buck_coul_cut_kokkos.h action pair_buck_coul_long_kokkos.cpp pair_buck_coul_long.cpp diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp new file mode 100644 index 0000000000000000000000000000000000000000..dd77bc605ba347073e20b90c1721e48f43524b96 --- /dev/null +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -0,0 +1,537 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Stan Moore (SNL) +------------------------------------------------------------------------- */ + +#include "dihedral_harmonic_kokkos.h" +#include +#include +#include "atom_kokkos.h" +#include "comm.h" +#include "neighbor_kokkos.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "memory_kokkos.h" +#include "error.h" +#include "atom_masks.h" + +using namespace LAMMPS_NS; + +#define TOLERANCE 0.05 +#define SMALL 0.001 +#define SMALLER 0.00001 + +/* ---------------------------------------------------------------------- */ + +template +DihedralHarmonicKokkos::DihedralHarmonicKokkos(LAMMPS *lmp) : DihedralHarmonic(lmp) +{ + atomKK = (AtomKokkos *) atom; + neighborKK = (NeighborKokkos *) neighbor; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; + + k_warning_flag = DAT::tdual_int_scalar("Dihedral:warning_flag"); + d_warning_flag = k_warning_flag.view(); + h_warning_flag = k_warning_flag.h_view; +} + +/* ---------------------------------------------------------------------- */ + +template +DihedralHarmonicKokkos::~DihedralHarmonicKokkos() +{ + if (!copymode) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void DihedralHarmonicKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + ev_init(eflag,vflag,0); + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom"); + d_eatom = k_eatom.view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"dihedral:vatom"); + d_vatom = k_vatom.view(); + } + + k_k.template sync(); + k_cos_shift.template sync(); + k_sin_shift.template sync(); + k_sign.template sync(); + k_multiplicity.template sync(); + + x = atomKK->k_x.view(); + f = atomKK->k_f.view(); + neighborKK->k_dihedrallist.template sync(); + dihedrallist = neighborKK->k_dihedrallist.view(); + int ndihedrallist = neighborKK->ndihedrallist; + nlocal = atom->nlocal; + newton_bond = force->newton_bond; + + h_warning_flag() = 0; + k_warning_flag.template modify(); + k_warning_flag.template sync(); + + copymode = 1; + + // loop over neighbors of my atoms + + EV_FLOAT ev; + + if (evflag) { + if (newton_bond) { + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,ndihedrallist),*this,ev); + } + } else { + if (newton_bond) { + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy >(0,ndihedrallist),*this); + } + } + + // error check + + k_warning_flag.template modify(); + k_warning_flag.template sync(); + if (h_warning_flag()) + error->warning(FLERR,"Dihedral problem",0); + + if (eflag_global) energy += ev.evdwl; + if (vflag_global) { + virial[0] += ev.v[0]; + virial[1] += ev.v[1]; + virial[2] += ev.v[2]; + virial[3] += ev.v[3]; + virial[4] += ev.v[4]; + virial[5] += ev.v[5]; + } + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + copymode = 0; +} + +template +template +KOKKOS_INLINE_FUNCTION +void DihedralHarmonicKokkos::operator()(TagDihedralHarmonicCompute, const int &n, EV_FLOAT& ev) const { + + // The f array is atomic + Kokkos::View > a_f = f; + + const int i1 = dihedrallist(n,0); + const int i2 = dihedrallist(n,1); + const int i3 = dihedrallist(n,2); + const int i4 = dihedrallist(n,3); + const int type = dihedrallist(n,4); + + // 1st bond + + const F_FLOAT vb1x = x(i1,0) - x(i2,0); + const F_FLOAT vb1y = x(i1,1) - x(i2,1); + const F_FLOAT vb1z = x(i1,2) - x(i2,2); + + // 2nd bond + + const F_FLOAT vb2x = x(i3,0) - x(i2,0); + const F_FLOAT vb2y = x(i3,1) - x(i2,1); + const F_FLOAT vb2z = x(i3,2) - x(i2,2); + + const F_FLOAT vb2xm = -vb2x; + const F_FLOAT vb2ym = -vb2y; + const F_FLOAT vb2zm = -vb2z; + + // 3rd bond + + const F_FLOAT vb3x = x(i4,0) - x(i3,0); + const F_FLOAT vb3y = x(i4,1) - x(i3,1); + const F_FLOAT vb3z = x(i4,2) - x(i3,2); + + // c,s calculation + + const F_FLOAT ax = vb1y*vb2zm - vb1z*vb2ym; + const F_FLOAT ay = vb1z*vb2xm - vb1x*vb2zm; + const F_FLOAT az = vb1x*vb2ym - vb1y*vb2xm; + const F_FLOAT bx = vb3y*vb2zm - vb3z*vb2ym; + const F_FLOAT by = vb3z*vb2xm - vb3x*vb2zm; + const F_FLOAT bz = vb3x*vb2ym - vb3y*vb2xm; + + const F_FLOAT rasq = ax*ax + ay*ay + az*az; + const F_FLOAT rbsq = bx*bx + by*by + bz*bz; + const F_FLOAT rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm; + const F_FLOAT rg = sqrt(rgsq); + + F_FLOAT rginv,ra2inv,rb2inv; + rginv = ra2inv = rb2inv = 0.0; + if (rg > 0) rginv = 1.0/rg; + if (rasq > 0) ra2inv = 1.0/rasq; + if (rbsq > 0) rb2inv = 1.0/rbsq; + const F_FLOAT rabinv = sqrt(ra2inv*rb2inv); + + F_FLOAT c = (ax*bx + ay*by + az*bz)*rabinv; + const F_FLOAT s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); + + // error check + + if ((c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) && !d_warning_flag()) + Kokkos::atomic_fetch_add(&d_warning_flag(),1); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + const int m = d_multiplicity[type]; + F_FLOAT p = 1.0; + F_FLOAT ddf1,df1; + ddf1 = df1 = 0.0; + + for (int i = 0; i < m; i++) { + ddf1 = p*c - df1*s; + df1 = p*s + df1*c; + p = ddf1; + } + + p = p*d_cos_shift[type] + df1*d_sin_shift[type]; + df1 = df1*d_cos_shift[type] - ddf1*d_sin_shift[type]; + df1 *= -m; + p += 1.0; + + if (m == 0) { + p = 1.0 + d_cos_shift[type]; + df1 = 0.0; + } + + E_FLOAT edihedral = 0.0; + if (eflag) edihedral = d_k[type] * p; + + const F_FLOAT fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm; + const F_FLOAT hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm; + const F_FLOAT fga = fg*ra2inv*rginv; + const F_FLOAT hgb = hg*rb2inv*rginv; + const F_FLOAT gaa = -ra2inv*rg; + const F_FLOAT gbb = rb2inv*rg; + + const F_FLOAT dtfx = gaa*ax; + const F_FLOAT dtfy = gaa*ay; + const F_FLOAT dtfz = gaa*az; + const F_FLOAT dtgx = fga*ax - hgb*bx; + const F_FLOAT dtgy = fga*ay - hgb*by; + const F_FLOAT dtgz = fga*az - hgb*bz; + const F_FLOAT dthx = gbb*bx; + const F_FLOAT dthy = gbb*by; + const F_FLOAT dthz = gbb*bz; + + const F_FLOAT df = -d_k[type] * df1; + + const F_FLOAT sx2 = df*dtgx;; + const F_FLOAT sy2 = df*dtgy;; + const F_FLOAT sz2 = df*dtgz;; + + F_FLOAT f1[3],f2[3],f3[3],f4[3]; + f1[0] = df*dtfx; + f1[1] = df*dtfy; + f1[2] = df*dtfz; + + f2[0] = sx2 - f1[0]; + f2[1] = sy2 - f1[1]; + f2[2] = sz2 - f1[2]; + + f4[0] = df*dthx; + f4[1] = df*dthy; + f4[2] = df*dthz; + + f3[0] = -sx2 - f4[0]; + f3[1] = -sy2 - f4[1]; + f3[2] = -sz2 - f4[2]; + + // apply force to each of 4 atoms + + if (NEWTON_BOND || i1 < nlocal) { + a_f(i1,0) += f1[0]; + a_f(i1,1) += f1[1]; + a_f(i1,2) += f1[2]; + } + + if (NEWTON_BOND || i2 < nlocal) { + a_f(i2,0) += f2[0]; + a_f(i2,1) += f2[1]; + a_f(i2,2) += f2[2]; + } + + if (NEWTON_BOND || i3 < nlocal) { + a_f(i3,0) += f3[0]; + a_f(i3,1) += f3[1]; + a_f(i3,2) += f3[2]; + } + + if (NEWTON_BOND || i4 < nlocal) { + a_f(i4,0) += f4[0]; + a_f(i4,1) += f4[1]; + a_f(i4,2) += f4[2]; + } + + if (EVFLAG) + ev_tally(ev,i1,i2,i3,i4,edihedral,f1,f3,f4, + vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); +} + +template +template +KOKKOS_INLINE_FUNCTION +void DihedralHarmonicKokkos::operator()(TagDihedralHarmonicCompute, const int &n) const { + EV_FLOAT ev; + this->template operator()(TagDihedralHarmonicCompute(), n, ev); +} + +/* ---------------------------------------------------------------------- */ + +template +void DihedralHarmonicKokkos::allocate() +{ + DihedralHarmonic::allocate(); + + int n = atom->ndihedraltypes; + k_k = DAT::tdual_ffloat_1d("DihedralHarmonic::k",n+1); + k_cos_shift = DAT::tdual_ffloat_1d("DihedralHarmonic::cos_shift",n+1); + k_sin_shift = DAT::tdual_ffloat_1d("DihedralHarmonic::sin_shift",n+1); + k_sign = DAT::tdual_int_1d("DihedralHarmonic::sign",n+1); + k_multiplicity = DAT::tdual_int_1d("DihedralHarmonic::multiplicity",n+1); + + d_k = k_k.template view(); + d_cos_shift = k_cos_shift.template view(); + d_sin_shift = k_sin_shift.template view(); + d_sign = k_sign.template view(); + d_multiplicity = k_multiplicity.template view(); +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +template +void DihedralHarmonicKokkos::coeff(int narg, char **arg) +{ + DihedralHarmonic::coeff(narg, arg); + + int n = atom->ndihedraltypes; + for (int i = 1; i <= n; i++) { + k_k.h_view[i] = k[i]; + k_cos_shift.h_view[i] = cos_shift[i]; + k_sin_shift.h_view[i] = sin_shift[i]; + k_sign.h_view[i] = sign[i]; + k_multiplicity.h_view[i] = multiplicity[i]; + } + + k_k.template modify(); + k_cos_shift.template modify(); + k_sin_shift.template modify(); + k_sign.template modify(); + k_multiplicity.template modify(); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +template +void DihedralHarmonicKokkos::read_restart(FILE *fp) +{ + DihedralHarmonic::read_restart(fp); + + int n = atom->ndihedraltypes; + for (int i = 1; i <= n; i++) { + k_k.h_view[i] = k[i]; + k_cos_shift.h_view[i] = cos_shift[i]; + k_sin_shift.h_view[i] = sin_shift[i]; + k_sign.h_view[i] = sign[i]; + k_multiplicity.h_view[i] = multiplicity[i]; + } + + k_k.template modify(); + k_cos_shift.template modify(); + k_sin_shift.template modify(); + k_sign.template modify(); + k_multiplicity.template modify(); +} + +/* ---------------------------------------------------------------------- + tally energy and virial into global and per-atom accumulators + virial = r1F1 + r2F2 + r3F3 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4 + = (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4 + = vb1*f1 + vb2*f3 + (vb3+vb2)*f4 +------------------------------------------------------------------------- */ + +template +//template +KOKKOS_INLINE_FUNCTION +void DihedralHarmonicKokkos::ev_tally(EV_FLOAT &ev, const int i1, const int i2, const int i3, const int i4, + F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4, + const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z, + const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z, + const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const +{ + E_FLOAT edihedralquarter; + F_FLOAT v[6]; + + // The eatom and vatom arrays are atomic + Kokkos::View > v_eatom = k_eatom.view(); + Kokkos::View > v_vatom = k_vatom.view(); + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) ev.evdwl += edihedral; + else { + edihedralquarter = 0.25*edihedral; + if (i1 < nlocal) ev.evdwl += edihedralquarter; + if (i2 < nlocal) ev.evdwl += edihedralquarter; + if (i3 < nlocal) ev.evdwl += edihedralquarter; + if (i4 < nlocal) ev.evdwl += edihedralquarter; + } + } + if (eflag_atom) { + edihedralquarter = 0.25*edihedral; + if (newton_bond || i1 < nlocal) v_eatom[i1] += edihedralquarter; + if (newton_bond || i2 < nlocal) v_eatom[i2] += edihedralquarter; + if (newton_bond || i3 < nlocal) v_eatom[i3] += edihedralquarter; + if (newton_bond || i4 < nlocal) v_eatom[i4] += edihedralquarter; + } + } + + if (vflag_either) { + v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0]; + v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1]; + v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2]; + v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1]; + v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2]; + v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2]; + + if (vflag_global) { + if (newton_bond) { + ev.v[0] += v[0]; + ev.v[1] += v[1]; + ev.v[2] += v[2]; + ev.v[3] += v[3]; + ev.v[4] += v[4]; + ev.v[5] += v[5]; + } else { + if (i1 < nlocal) { + ev.v[0] += 0.25*v[0]; + ev.v[1] += 0.25*v[1]; + ev.v[2] += 0.25*v[2]; + ev.v[3] += 0.25*v[3]; + ev.v[4] += 0.25*v[4]; + ev.v[5] += 0.25*v[5]; + } + if (i2 < nlocal) { + ev.v[0] += 0.25*v[0]; + ev.v[1] += 0.25*v[1]; + ev.v[2] += 0.25*v[2]; + ev.v[3] += 0.25*v[3]; + ev.v[4] += 0.25*v[4]; + ev.v[5] += 0.25*v[5]; + } + if (i3 < nlocal) { + ev.v[0] += 0.25*v[0]; + ev.v[1] += 0.25*v[1]; + ev.v[2] += 0.25*v[2]; + ev.v[3] += 0.25*v[3]; + ev.v[4] += 0.25*v[4]; + ev.v[5] += 0.25*v[5]; + } + if (i4 < nlocal) { + ev.v[0] += 0.25*v[0]; + ev.v[1] += 0.25*v[1]; + ev.v[2] += 0.25*v[2]; + ev.v[3] += 0.25*v[3]; + ev.v[4] += 0.25*v[4]; + ev.v[5] += 0.25*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i1 < nlocal) { + v_vatom(i1,0) += 0.25*v[0]; + v_vatom(i1,1) += 0.25*v[1]; + v_vatom(i1,2) += 0.25*v[2]; + v_vatom(i1,3) += 0.25*v[3]; + v_vatom(i1,4) += 0.25*v[4]; + v_vatom(i1,5) += 0.25*v[5]; + } + if (newton_bond || i2 < nlocal) { + v_vatom(i2,0) += 0.25*v[0]; + v_vatom(i2,1) += 0.25*v[1]; + v_vatom(i2,2) += 0.25*v[2]; + v_vatom(i2,3) += 0.25*v[3]; + v_vatom(i2,4) += 0.25*v[4]; + v_vatom(i2,5) += 0.25*v[5]; + } + if (newton_bond || i3 < nlocal) { + v_vatom(i3,0) += 0.25*v[0]; + v_vatom(i3,1) += 0.25*v[1]; + v_vatom(i3,2) += 0.25*v[2]; + v_vatom(i3,3) += 0.25*v[3]; + v_vatom(i3,4) += 0.25*v[4]; + v_vatom(i3,5) += 0.25*v[5]; + } + if (newton_bond || i4 < nlocal) { + v_vatom(i4,0) += 0.25*v[0]; + v_vatom(i4,1) += 0.25*v[1]; + v_vatom(i4,2) += 0.25*v[2]; + v_vatom(i4,3) += 0.25*v[3]; + v_vatom(i4,4) += 0.25*v[4]; + v_vatom(i4,5) += 0.25*v[5]; + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class DihedralHarmonicKokkos; +#ifdef KOKKOS_ENABLE_CUDA +template class DihedralHarmonicKokkos; +#endif +} + diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.h b/src/KOKKOS/dihedral_harmonic_kokkos.h new file mode 100644 index 0000000000000000000000000000000000000000..f90e8944a4fb3646013f61300e7697146ab68a8f --- /dev/null +++ b/src/KOKKOS/dihedral_harmonic_kokkos.h @@ -0,0 +1,104 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DIHEDRAL_CLASS + +DihedralStyle(harmonic/kk,DihedralHarmonicKokkos) +DihedralStyle(harmonic/kk/device,DihedralHarmonicKokkos) +DihedralStyle(harmonic/kk/host,DihedralHarmonicKokkos) + +#else + +#ifndef LMP_DIHEDRAL_HARMONIC_KOKKOS_H +#define LMP_DIHEDRAL_HARMONIC_KOKKOS_H + +#include "dihedral_harmonic.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +struct TagDihedralHarmonicCompute{}; + +template +class DihedralHarmonicKokkos : public DihedralHarmonic { + public: + typedef DeviceType device_type; + typedef EV_FLOAT value_type; + typedef ArrayTypes AT; + + DihedralHarmonicKokkos(class LAMMPS *); + virtual ~DihedralHarmonicKokkos(); + void compute(int, int); + void coeff(int, char **); + void read_restart(FILE *); + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagDihedralHarmonicCompute, const int&, EV_FLOAT&) const; + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagDihedralHarmonicCompute, const int&) const; + + //template + KOKKOS_INLINE_FUNCTION + void ev_tally(EV_FLOAT &ev, const int i1, const int i2, const int i3, const int i4, + F_FLOAT &edihedral, F_FLOAT *f1, F_FLOAT *f3, F_FLOAT *f4, + const F_FLOAT &vb1x, const F_FLOAT &vb1y, const F_FLOAT &vb1z, + const F_FLOAT &vb2x, const F_FLOAT &vb2y, const F_FLOAT &vb2z, + const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const; + + protected: + + class NeighborKokkos *neighborKK; + + typename AT::t_x_array_randomread x; + typename AT::t_f_array f; + typename AT::t_int_2d dihedrallist; + + DAT::tdual_efloat_1d k_eatom; + DAT::tdual_virial_array k_vatom; + typename ArrayTypes::t_efloat_1d d_eatom; + typename ArrayTypes::t_virial_array d_vatom; + + int nlocal,newton_bond; + int eflag,vflag; + + DAT::tdual_int_scalar k_warning_flag; + typename AT::t_int_scalar d_warning_flag; + HAT::t_int_scalar h_warning_flag; + + DAT::tdual_ffloat_1d k_k; + DAT::tdual_ffloat_1d k_cos_shift; + DAT::tdual_ffloat_1d k_sin_shift; + DAT::tdual_int_1d k_sign; + DAT::tdual_int_1d k_multiplicity; + + typename AT::t_ffloat_1d d_k; + typename AT::t_ffloat_1d d_cos_shift; + typename AT::t_ffloat_1d d_sin_shift; + typename AT::t_int_1d d_sign; + typename AT::t_int_1d d_multiplicity; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 651f790a25ae1f4e895380434cf881e684abb19f..8818d60a11ac1cd001ef3bd8cd21df45f0c3d37e 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -61,7 +61,6 @@ FixLangevinKokkos::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a k_ratio.template modify(); if(gjfflag){ - nvalues = 3; grow_arrays(atomKK->nmax); atom->add_callback(0); // initialize franprev to zero @@ -69,8 +68,12 @@ FixLangevinKokkos::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a franprev[i][0] = 0.0; franprev[i][1] = 0.0; franprev[i][2] = 0.0; + lv[i][0] = 0.0; + lv[i][1] = 0.0; + lv[i][2] = 0.0; } k_franprev.template modify(); + k_lv.template modify(); } if(zeroflag){ k_fsumall = tdual_double_1d_3n("langevin:fsumall"); @@ -94,6 +97,7 @@ FixLangevinKokkos::~FixLangevinKokkos() memoryKK->destroy_kokkos(k_ratio,ratio); memoryKK->destroy_kokkos(k_flangevin,flangevin); if(gjfflag) memoryKK->destroy_kokkos(k_franprev,franprev); + if(gjfflag) memoryKK->destroy_kokkos(k_lv,lv); memoryKK->destroy_kokkos(k_tforce,tforce); } @@ -107,6 +111,10 @@ void FixLangevinKokkos::init() error->all(FLERR,"Fix langevin omega is not yet implemented with kokkos"); if(ascale) error->all(FLERR,"Fix langevin angmom is not yet implemented with kokkos"); + if(gjfflag && tbiasflag) + error->all(FLERR,"Fix langevin gjf + tbias is not yet implemented with kokkos"); + if(gjfflag && tbiasflag) + error->warning(FLERR,"Fix langevin gjf + kokkos is not implemented with random gaussians"); // prefactors are modified in the init k_gfactor1.template modify(); @@ -121,6 +129,40 @@ void FixLangevinKokkos::grow_arrays(int nmax) memoryKK->grow_kokkos(k_franprev,franprev,nmax,3,"langevin:franprev"); d_franprev = k_franprev.template view(); h_franprev = k_franprev.template view(); + memoryKK->grow_kokkos(k_lv,lv,nmax,3,"langevin:lv"); + d_lv = k_lv.template view(); + h_lv = k_lv.template view(); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixLangevinKokkos::initial_integrate(int vflag) +{ + atomKK->sync(execution_space,datamask_read); + atomKK->modified(execution_space,datamask_modify); + + v = atomKK->k_v.view(); + f = atomKK->k_f.view(); + int nlocal = atomKK->nlocal; + if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; + + FixLangevinKokkosInitialIntegrateFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); +} + +template +KOKKOS_INLINE_FUNCTION +void FixLangevinKokkos::initial_integrate_item(int i) const +{ + if (mask[i] & groupbit) { + f(i,0) /= gjfa; + f(i,1) /= gjfa; + f(i,2) /= gjfa; + v(i,0) = d_lv(i,0); + v(i,1) = d_lv(i,1); + v(i,2) = d_lv(i,2); + } } /* ---------------------------------------------------------------------- */ @@ -140,6 +182,7 @@ void FixLangevinKokkos::post_force(int vflag) k_gfactor2.template sync(); k_ratio.template sync(); if(gjfflag) k_franprev.template sync(); + if(gjfflag) k_lv.template sync(); boltz = force->boltz; dt = update->dt; @@ -162,7 +205,7 @@ void FixLangevinKokkos::post_force(int vflag) } // reallocate flangevin if necessary - if (tallyflag) { + if (tallyflag || osflag) { if (nlocal > maxatom1) { memoryKK->destroy_kokkos(k_flangevin,flangevin); maxatom1 = atomKK->nmax; @@ -177,7 +220,7 @@ void FixLangevinKokkos::post_force(int vflag) atomKK->sync(temperature->execution_space,temperature->datamask_read); temperature->compute_scalar(); temperature->remove_bias_all(); // modifies velocities - // if temeprature compute is kokkosized host-devcie comm won't be needed + // if temeprature compute is kokkosized host-device comm won't be needed atomKK->modified(temperature->execution_space,temperature->datamask_modify); atomKK->sync(execution_space,temperature->datamask_modify); } @@ -186,7 +229,7 @@ void FixLangevinKokkos::post_force(int vflag) FSUM s_fsum; if (tstyle == ATOM) if (gjfflag) - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass.data()) if (zeroflag) { @@ -257,7 +300,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass.data()) if (zeroflag) { @@ -329,7 +372,7 @@ void FixLangevinKokkos::post_force(int vflag) } else if (gjfflag) - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass.data()) if (zeroflag) { @@ -400,7 +443,7 @@ void FixLangevinKokkos::post_force(int vflag) Kokkos::parallel_for(nlocal,post_functor); } else - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass.data()) if (zeroflag) { @@ -481,7 +524,8 @@ void FixLangevinKokkos::post_force(int vflag) // set modify flags for the views modified in post_force functor if (gjfflag) k_franprev.template modify(); - if (tallyflag) k_flangevin.template modify(); + if (gjfflag) k_lv.template modify(); + if (tallyflag || osflag) k_flangevin.template modify(); // set total force to zero if (zeroflag) { @@ -550,6 +594,10 @@ FSUM FixLangevinKokkos::post_force_item(int i) const } if (Tp_GJF) { + d_lv(i,0) = gjfsib*v(i,0); + d_lv(i,1) = gjfsib*v(i,1); + d_lv(i,2) = gjfsib*v(i,2); + fswap = 0.5*(fran[0]+d_franprev(i,0)); d_franprev(i,0) = fran[0]; fran[0] = fswap; @@ -560,15 +608,15 @@ FSUM FixLangevinKokkos::post_force_item(int i) const d_franprev(i,2) = fran[2]; fran[2] = fswap; - fdrag[0] *= gjffac; - fdrag[1] *= gjffac; - fdrag[2] *= gjffac; - fran[0] *= gjffac; - fran[1] *= gjffac; - fran[2] *= gjffac; - f(i,0) *= gjffac; - f(i,1) *= gjffac; - f(i,2) *= gjffac; + fdrag[0] *= gjfa; + fdrag[1] *= gjfa; + fdrag[2] *= gjfa; + fran[0] *= gjfa; + fran[1] *= gjfa; + fran[2] *= gjfa; + f(i,0) *= gjfa; + f(i,1) *= gjfa; + f(i,2) *= gjfa; } f(i,0) += fdrag[0] + fran[0]; @@ -576,6 +624,17 @@ FSUM FixLangevinKokkos::post_force_item(int i) const f(i,2) += fdrag[2] + fran[2]; if (Tp_TALLY) { + if (Tp_GJF){ + fdrag[0] = gamma1*d_lv(i,0)/gjfsib/gjfsib; + fdrag[1] = gamma1*d_lv(i,1)/gjfsib/gjfsib; + fdrag[2] = gamma1*d_lv(i,2)/gjfsib/gjfsib; + fswap = (2*fran[0]/gjfa - d_franprev(i,0))/gjfsib; + fran[0] = fswap; + fswap = (2*fran[1]/gjfa - d_franprev(i,1))/gjfsib; + fran[1] = fswap; + fswap = (2*fran[2]/gjfa - d_franprev(i,2))/gjfsib; + fran[2] = fswap; + } d_flangevin(i,0) = fdrag[0] + fran[0]; d_flangevin(i,1) = fdrag[1] + fran[1]; d_flangevin(i,2) = fdrag[2] + fran[2]; @@ -719,9 +778,10 @@ double FixLangevinKokkos::compute_energy_item(int i) const template void FixLangevinKokkos::end_of_step() { - if (!tallyflag) return; + if (!tallyflag && !gjfflag) return; v = atomKK->k_v.template view(); + f = atomKK->k_f.template view(); mask = atomKK->k_mask.template view(); atomKK->sync(execution_space,V_MASK | MASK_MASK); @@ -733,9 +793,81 @@ void FixLangevinKokkos::end_of_step() FixLangevinKokkosTallyEnergyFunctor tally_functor(this); Kokkos::parallel_reduce(nlocal,tally_functor,energy_onestep); + if (gjfflag){ + if (rmass.data()) { + FixLangevinKokkosEndOfStepFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + } else { + mass = atomKK->k_mass.view(); + FixLangevinKokkosEndOfStepFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + } + } + energy += energy_onestep*update->dt; } +template +KOKKOS_INLINE_FUNCTION +void FixLangevinKokkos::end_of_step_item(int i) const { + double tmp[3]; + if (mask[i] & groupbit) { + const double dtfm = force->ftm2v * 0.5 * dt / mass[type[i]]; + tmp[0] = v(i,0); + tmp[1] = v(i,1); + tmp[2] = v(i,2); + if (!osflag){ + v(i,0) = d_lv(i,0); + v(i,1) = d_lv(i,1); + v(i,2) = d_lv(i,2); + } else { + v(i,0) = 0.5 * gjfsib * gjfsib * (v(i,0) + dtfm * f(i,0) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,0)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,0); + v(i,1) = 0.5 * gjfsib * gjfsib * (v(i,1) + dtfm * f(i,1) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,1)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,1); + v(i,2) = 0.5 * gjfsib * gjfsib * (v(i,2) + dtfm * f(i,2) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,2)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,2); + } + d_lv(i,0) = tmp[0]; + d_lv(i,1) = tmp[1]; + d_lv(i,2) = tmp[2]; + } +} + +template +KOKKOS_INLINE_FUNCTION +void FixLangevinKokkos::end_of_step_rmass_item(int i) const +{ + double tmp[3]; + if (mask[i] & groupbit) { + const double dtfm = force->ftm2v * 0.5 * dt / rmass[i]; + tmp[0] = v(i,0); + tmp[1] = v(i,1); + tmp[2] = v(i,2); + if (!osflag){ + v(i,0) = d_lv(i,0); + v(i,1) = d_lv(i,1); + v(i,2) = d_lv(i,2); + } else { + v(i,0) = 0.5 * gjfsib * gjfsib * (v(i,0) + dtfm * f(i,0) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,0)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,0); + v(i,1) = 0.5 * gjfsib * gjfsib * (v(i,1) + dtfm * f(i,1) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,1) - d_franprev(i,1)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,1); + v(i,2) = 0.5 * gjfsib * gjfsib * (v(i,2) + dtfm * f(i,2) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,2) - d_franprev(i,2)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,2); + } + d_lv(i,0) = tmp[0]; + d_lv(i,1) = tmp[1]; + d_lv(i,2) = tmp[2]; + } +} + /* ---------------------------------------------------------------------- copy values within local atom-based array ------------------------------------------------------------------------- */ @@ -743,10 +875,15 @@ void FixLangevinKokkos::end_of_step() template void FixLangevinKokkos::copy_arrays(int i, int j, int delflag) { - for (int m = 0; m < nvalues; m++) - h_franprev(j,m) = h_franprev(i,m); + h_franprev(j,0) = h_franprev(i,0); + h_franprev(j,1) = h_franprev(i,1); + h_franprev(j,2) = h_franprev(i,2); + h_lv(j,0) = h_lv(i,0); + h_lv(j,1) = h_lv(i,1); + h_lv(j,2) = h_lv(i,2); k_franprev.template modify(); + k_lv.template modify(); } @@ -765,6 +902,7 @@ void FixLangevinKokkos::cleanup_copy() tforce = NULL; gjfflag = 0; franprev = NULL; + lv = NULL; id = style = NULL; vatom = NULL; } diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h index 140fea81d69456c4d1b21d40a1b27c24c257e3fd..a6d467dfd77aa668ba10ca4cde20def98af8adfc 100644 --- a/src/KOKKOS/fix_langevin_kokkos.h +++ b/src/KOKKOS/fix_langevin_kokkos.h @@ -56,6 +56,9 @@ namespace LAMMPS_NS { template class FixLangevinKokkos; + template + class FixLangevinKokkosInitialIntegrateFunctor; + template class FixLangevinKokkosPostForceFunctor; @@ -72,6 +75,7 @@ namespace LAMMPS_NS { void cleanup_copy(); void init(); + void initial_integrate(int); void post_force(int); void reset_dt(); void grow_arrays(int); @@ -79,6 +83,12 @@ namespace LAMMPS_NS { double compute_scalar(); void end_of_step(); + KOKKOS_INLINE_FUNCTION + void initial_integrate_item(int) const; + + KOKKOS_INLINE_FUNCTION + void initial_integrate_rmass_item(int) const; + template KOKKOS_INLINE_FUNCTION @@ -90,14 +100,25 @@ namespace LAMMPS_NS { KOKKOS_INLINE_FUNCTION double compute_energy_item(int) const; + KOKKOS_INLINE_FUNCTION + void end_of_step_item(int) const; + + KOKKOS_INLINE_FUNCTION + void end_of_step_rmass_item(int) const; + private: class CommKokkos *commKK; typename ArrayTypes::t_float_1d rmass; + typename ArrayTypes::t_float_1d mass; typename ArrayTypes::tdual_double_2d k_franprev; typename ArrayTypes::t_double_2d d_franprev; HAT::t_double_2d h_franprev; + typename ArrayTypes::tdual_double_2d k_lv; + typename ArrayTypes::t_double_2d d_lv; + HAT::t_double_2d h_lv; + typename ArrayTypes::tdual_double_2d k_flangevin; typename ArrayTypes::t_double_2d d_flangevin; HAT::t_double_2d h_flangevin; @@ -130,6 +151,21 @@ namespace LAMMPS_NS { }; + template + struct FixLangevinKokkosInitialIntegrateFunctor { + typedef DeviceType device_type ; + FixLangevinKokkos c; + + FixLangevinKokkosInitialIntegrateFunctor(FixLangevinKokkos* c_ptr): + c(*c_ptr) {c.cleanup_copy();}; + + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + c.initial_integrate_item(i); + } + }; + + template struct FixLangevinKokkosPostForceFunctor { @@ -207,6 +243,21 @@ namespace LAMMPS_NS { update += source; } }; + + template + struct FixLangevinKokkosEndOfStepFunctor { + typedef DeviceType device_type ; + FixLangevinKokkos c; + + FixLangevinKokkosEndOfStepFunctor(FixLangevinKokkos* c_ptr): + c(*c_ptr) {c.cleanup_copy();} + + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + if (RMass) c.end_of_step_rmass_item(i); + else c.end_of_step_item(i); + } + }; } #endif @@ -231,4 +282,12 @@ E: Fix langevin variable returned negative temperature Self-explanatory. +E: Fix langevin gjf with tbias is not yet implemented with kokkos + +This option is not yet available. + +W: Fix langevin gjf using random gaussians is not implemented with kokkos + +This will most likely cause errors in kinetic fluctuations. + */ diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e7b10dbb8eae2c90a0593fd590fbaf028eb73fe9 --- /dev/null +++ b/src/KOKKOS/fix_minimize_kokkos.cpp @@ -0,0 +1,257 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "fix_minimize_kokkos.h" +#include "atom_kokkos.h" +#include "domain.h" +#include "memory_kokkos.h" +#include "atom_masks.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixMinimizeKokkos::FixMinimizeKokkos(LAMMPS *lmp, int narg, char **arg) : + FixMinimize(lmp, narg, arg) +{ + atomKK = (AtomKokkos *) atom; +} + +/* ---------------------------------------------------------------------- */ + +FixMinimizeKokkos::~FixMinimizeKokkos() +{ + memoryKK->destroy_kokkos(k_vectors,vectors); + vectors = NULL; +} + +/* ---------------------------------------------------------------------- + allocate/initialize memory for a new vector with 3 elements per atom +------------------------------------------------------------------------- */ + +void FixMinimizeKokkos::add_vector_kokkos() +{ + int n = 3; + + memory->grow(peratom,nvector+1,"minimize:peratom"); + peratom[nvector] = n; + + // d_vectors needs to be LayoutRight for subviews + + k_vectors.sync(); + + memoryKK->grow_kokkos(k_vectors,vectors,nvector+1,atom->nmax*n, + "minimize:vectors"); + d_vectors = k_vectors.d_view; + h_vectors = k_vectors.h_view; + + k_vectors.modify(); + + nvector++; +} + +/* ---------------------------------------------------------------------- + return a pointer to the Mth vector +------------------------------------------------------------------------- */ + +DAT::t_ffloat_1d FixMinimizeKokkos::request_vector_kokkos(int m) +{ + k_vectors.sync(); + + return Kokkos::subview(d_vectors,m,Kokkos::ALL); +} + +/* ---------------------------------------------------------------------- + reset x0 for atoms that moved across PBC via reneighboring in line search + x0 = 1st vector + must do minimum_image using original box stored at beginning of line search + swap & set_global_box() change to original box, then restore current box +------------------------------------------------------------------------- */ + +void FixMinimizeKokkos::reset_coords() +{ + box_swap(); + domain->set_global_box(); + + int nlocal = atom->nlocal; + + atomKK->sync(Device,X_MASK); + k_vectors.sync(); + + { + // local variables for lambda capture + + auto triclinic = domain->triclinic; + auto xperiodic = domain->xperiodic; + auto xprd_half = domain->xprd_half; + auto xprd = domain->xprd; + auto yperiodic = domain->yperiodic; + auto yprd_half = domain->yprd_half; + auto yprd = domain->yprd; + auto zperiodic = domain->zperiodic; + auto zprd_half = domain->zprd_half; + auto zprd = domain->zprd; + auto xy = domain->xy; + auto xz = domain->xz; + auto yz = domain->yz; + auto l_x = atomKK->k_x.d_view; + auto l_x0 = Kokkos::subview(d_vectors,0,Kokkos::ALL); + + Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(const int& i) { + const int n = i*3; + double dx0 = l_x(i,0) - l_x0[n]; + double dy0 = l_x(i,1) - l_x0[n+1]; + double dz0 = l_x(i,2) - l_x0[n+2]; + double dx = dx0; + double dy = dy0; + double dz = dz0; + // domain->minimum_image(dx,dy,dz); + { + if (triclinic == 0) { + if (xperiodic) { + if (fabs(dx) > xprd_half) { + if (dx < 0.0) dx += xprd; + else dx -= xprd; + } + } + if (yperiodic) { + if (fabs(dy) > yprd_half) { + if (dy < 0.0) dy += yprd; + else dy -= yprd; + } + } + if (zperiodic) { + if (fabs(dz) > zprd_half) { + if (dz < 0.0) dz += zprd; + else dz -= zprd; + } + } + + } else { + if (zperiodic) { + if (fabs(dz) > zprd_half) { + if (dz < 0.0) { + dz += zprd; + dy += yz; + dx += xz; + } else { + dz -= zprd; + dy -= yz; + dx -= xz; + } + } + } + if (yperiodic) { + if (fabs(dy) > yprd_half) { + if (dy < 0.0) { + dy += yprd; + dx += xy; + } else { + dy -= yprd; + dx -= xy; + } + } + } + if (xperiodic) { + if (fabs(dx) > xprd_half) { + if (dx < 0.0) dx += xprd; + else dx -= xprd; + } + } + } + } // end domain->minimum_image(dx,dy,dz); + if (dx != dx0) l_x0[n] = l_x(i,0) - dx; + if (dy != dy0) l_x0[n+1] = l_x(i,1) - dy; + if (dz != dz0) l_x0[n+2] = l_x(i,2) - dz; + }); + } + k_vectors.modify(); + + box_swap(); + domain->set_global_box(); +} + +/* ---------------------------------------------------------------------- + allocate local atom-based arrays +------------------------------------------------------------------------- */ + +void FixMinimizeKokkos::grow_arrays(int nmax) +{ + k_vectors.sync(); + memoryKK->grow_kokkos(k_vectors,vectors,nvector,3*nmax,"minimize:vector"); + d_vectors = k_vectors.d_view; + h_vectors = k_vectors.h_view; + k_vectors.modify(); +} + +/* ---------------------------------------------------------------------- + copy values within local atom-based arrays +------------------------------------------------------------------------- */ + +void FixMinimizeKokkos::copy_arrays(int i, int j, int /*delflag*/) +{ + int m,iper,nper,ni,nj; + + k_vectors.sync(); + + for (m = 0; m < nvector; m++) { + nper = 3; + ni = nper*i; + nj = nper*j; + for (iper = 0; iper < nper; iper++) h_vectors(m,nj++) = h_vectors(m,ni++); + } + + k_vectors.modify(); +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based arrays for exchange with another proc +------------------------------------------------------------------------- */ + +int FixMinimizeKokkos::pack_exchange(int i, double *buf) +{ + int m,iper,nper,ni; + + k_vectors.sync(); + + int n = 0; + for (m = 0; m < nvector; m++) { + nper = peratom[m]; + ni = nper*i; + for (iper = 0; iper < nper; iper++) buf[n++] = h_vectors(m,ni++); + } + return n; +} + +/* ---------------------------------------------------------------------- + unpack values in local atom-based arrays from exchange with another proc +------------------------------------------------------------------------- */ + +int FixMinimizeKokkos::unpack_exchange(int nlocal, double *buf) +{ + int m,iper,nper,ni; + + k_vectors.sync(); + + int n = 0; + for (m = 0; m < nvector; m++) { + nper = peratom[m]; + ni = nper*nlocal; + for (iper = 0; iper < nper; iper++) h_vectors(m,ni++) = buf[n++]; + } + + k_vectors.modify(); + + return n; +} diff --git a/src/KOKKOS/fix_minimize_kokkos.h b/src/KOKKOS/fix_minimize_kokkos.h new file mode 100644 index 0000000000000000000000000000000000000000..921cb2fc5da4a03c9424da0ff8d2ea7d4082cfd4 --- /dev/null +++ b/src/KOKKOS/fix_minimize_kokkos.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(MINIMIZE/kk,FixMinimizeKokkos) +FixStyle(MINIMIZE/kk/device,FixMinimizeKokkos) +FixStyle(MINIMIZE/kk/host,FixMinimizeKokkos) + +#else + +#ifndef LMP_FIX_MINIMIZE_KOKKOS_H +#define LMP_FIX_MINIMIZE_KOKKOS_H + +#include "fix_minimize.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +class FixMinimizeKokkos : public FixMinimize { + friend class MinLineSearchKokkos; + + public: + FixMinimizeKokkos(class LAMMPS *, int, char **); + virtual ~FixMinimizeKokkos(); + void init() {} + + void grow_arrays(int); + void copy_arrays(int, int, int); + int pack_exchange(int, double *); + int unpack_exchange(int, double *); + + void add_vector_kokkos(); + DAT::t_float_1d request_vector_kokkos(int); + void reset_coords(); + + DAT::tdual_float_2d k_vectors; + DAT::t_float_2d d_vectors; + HAT::t_float_2d h_vectors; +}; + +} + +#endif +#endif +/* ERROR/WARNING messages: + +*/ diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 32550e82852a3ea8881049c549c8c7c479959219..18dff991b2d7424cf1ec56b054e9768d4166192d 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -113,23 +113,37 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } iarg += 2; + int set_flag = 0; char *str; if ((str = getenv("SLURM_LOCALID"))) { int local_rank = atoi(str); device = local_rank % ngpus; if (device >= skip_gpu) device++; + set_flag = 1; + } + if ((str = getenv("MPT_LRANK"))) { + int local_rank = atoi(str); + device = local_rank % ngpus; + if (device >= skip_gpu) device++; + set_flag = 1; } if ((str = getenv("MV2_COMM_WORLD_LOCAL_RANK"))) { int local_rank = atoi(str); device = local_rank % ngpus; if (device >= skip_gpu) device++; + set_flag = 1; } if ((str = getenv("OMPI_COMM_WORLD_LOCAL_RANK"))) { int local_rank = atoi(str); device = local_rank % ngpus; if (device >= skip_gpu) device++; + set_flag = 1; } + if (ngpus > 1 && !set_flag) + error->all(FLERR,"Could not determine local MPI rank for multiple " + "GPUs with Kokkos CUDA because MPI library not recognized"); + } else if (strcmp(arg[iarg],"t") == 0 || strcmp(arg[iarg],"threads") == 0) { nthreads = atoi(arg[iarg+1]); diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index b9f1e66c68dea50513821ad1c50db267e51b08c7..7b605bee1e9fd513cda9f64e3d57000b448480ea 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -74,6 +74,11 @@ E: Invalid Kokkos command-line args Self-explanatory. See Section 2.7 of the manual for details. +E: Could not determine local MPI rank for multiple GPUs with Kokkos CUDA +because MPI library not recognized + +The local MPI rank was not found in one of four supported environment variables. + E: GPUs are requested but Kokkos has not been compiled for CUDA Recompile Kokkos with CUDA support to use GPUs. diff --git a/src/KOKKOS/min_cg_kokkos.cpp b/src/KOKKOS/min_cg_kokkos.cpp new file mode 100644 index 0000000000000000000000000000000000000000..47a4513bc0d7f32de4b62e7b2374c46dc1601b2c --- /dev/null +++ b/src/KOKKOS/min_cg_kokkos.cpp @@ -0,0 +1,178 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "min_cg_kokkos.h" +#include +#include +#include "update.h" +#include "output.h" +#include "timer.h" +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "fix_minimize_kokkos.h" + +using namespace LAMMPS_NS; + +// EPS_ENERGY = minimum normalization for energy tolerance + +#define EPS_ENERGY 1.0e-8 + +/* ---------------------------------------------------------------------- */ + +MinCGKokkos::MinCGKokkos(LAMMPS *lmp) : MinLineSearchKokkos(lmp) +{ + atomKK = (AtomKokkos *) atom; + kokkosable = 1; +} + +/* ---------------------------------------------------------------------- + minimization via conjugate gradient iterations +------------------------------------------------------------------------- */ + +int MinCGKokkos::iterate(int maxiter) +{ + int fail,ntimestep; + double beta,gg,dot[2],dotall[2]; + + fix_minimize_kk->k_vectors.sync(); + fix_minimize_kk->k_vectors.modify(); + + // nlimit = max # of CG iterations before restarting + // set to ndoftotal unless too big + + int nlimit = static_cast (MIN(MAXSMALLINT,ndoftotal)); + + // initialize working vectors + + { + // local variables for lambda capture + + auto l_h = h; + auto l_g = g; + auto l_fvec = fvec; + + Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) { + l_h[i] = l_fvec[i]; + l_g[i] = l_fvec[i]; + }); + } + + gg = fnorm_sqr(); + + for (int iter = 0; iter < maxiter; iter++) { + + if (timer->check_timeout(niter)) + return TIMEOUT; + + ntimestep = ++update->ntimestep; + niter++; + + // line minimization along direction h from current atom->x + + eprevious = ecurrent; + fail = (this->*linemin)(ecurrent,alpha_final); + if (fail) return fail; + + // function evaluation criterion + + if (neval >= update->max_eval) return MAXEVAL; + + // energy tolerance criterion + + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + return ETOL; + + // force tolerance criterion + + s_double2 sdot; + { + // local variables for lambda capture + + auto l_g = g; + auto l_fvec = fvec; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, s_double2& sdot) { + sdot.d0 += l_fvec[i]*l_fvec[i]; + sdot.d1 += l_fvec[i]*l_g[i]; + },sdot); + } + dot[0] = sdot.d0; + dot[1] = sdot.d1; + MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world); + + if (dotall[0] < update->ftol*update->ftol) return FTOL; + + // update new search direction h from new f = -Grad(x) and old g + // this is Polak-Ribieri formulation + // beta = dotall[0]/gg would be Fletcher-Reeves + // reinitialize CG every ndof iterations by setting beta = 0.0 + + beta = MAX(0.0,(dotall[0] - dotall[1])/gg); + if ((niter+1) % nlimit == 0) beta = 0.0; + gg = dotall[0]; + + { + // local variables for lambda capture + + auto l_h = h; + auto l_g = g; + auto l_fvec = fvec; + + Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) { + l_g[i] = l_fvec[i]; + l_h[i] = l_g[i] + beta*l_h[i]; + }); + } + + // reinitialize CG if new search direction h is not downhill + + double dot_0 = 0.0; + + { + // local variables for lambda capture + + auto l_h = h; + auto l_g = g; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, double& dot_0) { + dot_0 += l_g[i]*l_h[i]; + },dot_0); + } + dot[0] = dot_0; + MPI_Allreduce(dot,dotall,1,MPI_DOUBLE,MPI_SUM,world); + + if (dotall[0] <= 0.0) { + // local variables for lambda capture + + auto l_h = h; + auto l_g = g; + + Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) { + l_h[i] = l_g[i]; + }); + } + + // output for thermo, dump, restart files + + if (output->next == ntimestep) { + atomKK->sync(Host,ALL_MASK); + + timer->stamp(); + output->write(ntimestep); + timer->stamp(Timer::OUTPUT); + } + } + + return MAXITER; +} diff --git a/src/KOKKOS/min_cg_kokkos.h b/src/KOKKOS/min_cg_kokkos.h new file mode 100644 index 0000000000000000000000000000000000000000..745bf702c7205305bd1d91158b1cb08fdd0ecca4 --- /dev/null +++ b/src/KOKKOS/min_cg_kokkos.h @@ -0,0 +1,38 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef MINIMIZE_CLASS + +MinimizeStyle(cg/kk,MinCGKokkos) +MinimizeStyle(cg/kk/device,MinCGKokkos) +MinimizeStyle(cg/kk/host,MinCGKokkos) + +#else + +#ifndef LMP_MIN_CG_KOKKOS_H +#define LMP_MIN_CG_KOKKOS_H + +#include "min_linesearch_kokkos.h" + +namespace LAMMPS_NS { + +class MinCGKokkos : public MinLineSearchKokkos { + public: + MinCGKokkos(class LAMMPS *); + int iterate(int); +}; + +} + +#endif +#endif diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp new file mode 100644 index 0000000000000000000000000000000000000000..79ddbbab84d9728fb203fed0f5e3eace064b6b87 --- /dev/null +++ b/src/KOKKOS/min_kokkos.cpp @@ -0,0 +1,631 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Stan Moore (SNL) +------------------------------------------------------------------------- */ + +#include "min_kokkos.h" +#include +#include +#include +#include "atom_kokkos.h" +#include "atom_vec.h" +#include "domain.h" +#include "comm.h" +#include "update.h" +#include "modify.h" +#include "fix_minimize_kokkos.h" +#include "compute.h" +#include "neighbor.h" +#include "force.h" +#include "pair.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "output.h" +#include "thermo.h" +#include "timer.h" +#include "memory.h" +#include "error.h" +#include "kokkos.h" +#include "atom_masks.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +MinKokkos::MinKokkos(LAMMPS *lmp) : Min(lmp) +{ + atomKK = (AtomKokkos *) atom; + fix_minimize_kk = NULL; +} + +/* ---------------------------------------------------------------------- */ + +MinKokkos::~MinKokkos() +{ + +} + +/* ---------------------------------------------------------------------- */ + +void MinKokkos::init() +{ + Min::init(); + + fix_minimize_kk = (FixMinimizeKokkos*) fix_minimize; +} + +/* ---------------------------------------------------------------------- + setup before run +------------------------------------------------------------------------- */ + +void MinKokkos::setup(int flag) +{ + if (comm->me == 0 && screen) { + fprintf(screen,"Setting up %s style minimization ...\n", + update->minimize_style); + if (flag) { + fprintf(screen," Unit style : %s\n", update->unit_style); + fprintf(screen," Current step : " BIGINT_FORMAT "\n", + update->ntimestep); + timer->print_timeout(screen); + } + } + update->setupflag = 1; + + // setup extra global dof due to fixes + // cannot be done in init() b/c update init() is before modify init() + + nextra_global = modify->min_dof(); + if (nextra_global) { + fextra = new double[nextra_global]; + if (comm->me == 0 && screen) + fprintf(screen,"WARNING: Energy due to %d extra global DOFs will" + " be included in minimizer energies\n",nextra_global); + } + + // compute for potential energy + + int id = modify->find_compute("thermo_pe"); + if (id < 0) error->all(FLERR,"Minimization could not find thermo_pe compute"); + pe_compute = modify->compute[id]; + + // style-specific setup does two tasks + // setup extra global dof vectors + // setup extra per-atom dof vectors due to requests from Pair classes + // cannot be done in init() b/c update init() is before modify/pair init() + + setup_style(); + + // ndoftotal = total dof for entire minimization problem + // dof for atoms, extra per-atom, extra global + + bigint ndofme = 3 * static_cast(atom->nlocal); + for (int m = 0; m < nextra_atom; m++) + ndofme += extra_peratom[m]*atom->nlocal; + MPI_Allreduce(&ndofme,&ndoftotal,1,MPI_LMP_BIGINT,MPI_SUM,world); + ndoftotal += nextra_global; + + // setup domain, communication and neighboring + // acquire ghosts + // build neighbor lists + + atom->setup(); + modify->setup_pre_exchange(); + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + domain->reset_box(); + comm->setup(); + if (neighbor->style) neighbor->setup_bins(); + comm->exchange(); + if (atom->sortfreq > 0) atom->sort(); + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + domain->image_check(); + domain->box_too_small_check(); + modify->setup_pre_neighbor(); + neighbor->build(1); + modify->setup_post_neighbor(); + neighbor->ncalls = 0; + + // remove these restriction eventually + + if (searchflag == 0) { + if (nextra_global) + error->all(FLERR, + "Cannot use a damped dynamics min style with fix box/relax"); + if (nextra_atom) + error->all(FLERR, + "Cannot use a damped dynamics min style with per-atom DOF"); + } + + if (strcmp(update->minimize_style,"hftn") == 0) { + if (nextra_global) + error->all(FLERR, "Cannot use hftn min style with fix box/relax"); + if (nextra_atom) + error->all(FLERR, "Cannot use hftn min style with per-atom DOF"); + } + + // atoms may have migrated in comm->exchange() + + reset_vectors(); + + // compute all forces + + force->setup(); + ev_set(update->ntimestep); + force_clear(); + modify->setup_pre_force(vflag); + + if (pair_compute_flag) { + atomKK->sync(force->pair->execution_space,force->pair->datamask_read); + force->pair->compute(eflag,vflag); + atomKK->modified(force->pair->execution_space,force->pair->datamask_modify); + timer->stamp(Timer::PAIR); + } + else if (force->pair) force->pair->compute_dummy(eflag,vflag); + + if (atomKK->molecular) { + if (force->bond) { + atomKK->sync(force->bond->execution_space,force->bond->datamask_read); + force->bond->compute(eflag,vflag); + atomKK->modified(force->bond->execution_space,force->bond->datamask_modify); + } + if (force->angle) { + atomKK->sync(force->angle->execution_space,force->angle->datamask_read); + force->angle->compute(eflag,vflag); + atomKK->modified(force->angle->execution_space,force->angle->datamask_modify); + } + if (force->dihedral) { + atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read); + force->dihedral->compute(eflag,vflag); + atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify); + } + if (force->improper) { + atomKK->sync(force->improper->execution_space,force->improper->datamask_read); + force->improper->compute(eflag,vflag); + atomKK->modified(force->improper->execution_space,force->improper->datamask_modify); + } + timer->stamp(Timer::BOND); + } + + if(force->kspace) { + force->kspace->setup(); + if (kspace_compute_flag) { + atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read); + force->kspace->compute(eflag,vflag); + atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify); + timer->stamp(Timer::KSPACE); + } else force->kspace->compute_dummy(eflag,vflag); + } + + modify->setup_pre_reverse(eflag,vflag); + if (force->newton) comm->reverse_comm(); + + // update per-atom minimization variables stored by pair styles + + if (nextra_atom) + for (int m = 0; m < nextra_atom; m++) + requestor[m]->min_xf_get(m); + + lmp->kokkos->auto_sync = 0; + modify->setup(vflag); + output->setup(flag); + lmp->kokkos->auto_sync = 1; + update->setupflag = 0; + + // stats for initial thermo output + + ecurrent = pe_compute->compute_scalar(); + if (nextra_global) ecurrent += modify->min_energy(fextra); + if (output->thermo->normflag) ecurrent /= atom->natoms; + + einitial = ecurrent; + fnorm2_init = sqrt(fnorm_sqr()); + fnorminf_init = fnorm_inf(); +} + +/* ---------------------------------------------------------------------- + setup without output or one-time post-init setup + flag = 0 = just force calculation + flag = 1 = reneighbor and force calculation +------------------------------------------------------------------------- */ + +void MinKokkos::setup_minimal(int flag) +{ + update->setupflag = 1; + + // setup domain, communication and neighboring + // acquire ghosts + // build neighbor lists + + if (flag) { + modify->setup_pre_exchange(); + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + domain->reset_box(); + comm->setup(); + if (neighbor->style) neighbor->setup_bins(); + comm->exchange(); + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + domain->image_check(); + domain->box_too_small_check(); + modify->setup_pre_neighbor(); + neighbor->build(1); + modify->setup_post_neighbor(); + neighbor->ncalls = 0; + } + + // atoms may have migrated in comm->exchange() + + reset_vectors(); + + // compute all forces + + ev_set(update->ntimestep); + force_clear(); + modify->setup_pre_force(vflag); + + if (pair_compute_flag) { + atomKK->sync(force->pair->execution_space,force->pair->datamask_read); + force->pair->compute(eflag,vflag); + atomKK->modified(force->pair->execution_space,force->pair->datamask_modify); + timer->stamp(Timer::PAIR); + } + else if (force->pair) force->pair->compute_dummy(eflag,vflag); + + if (atomKK->molecular) { + if (force->bond) { + atomKK->sync(force->bond->execution_space,force->bond->datamask_read); + force->bond->compute(eflag,vflag); + atomKK->modified(force->bond->execution_space,force->bond->datamask_modify); + } + if (force->angle) { + atomKK->sync(force->angle->execution_space,force->angle->datamask_read); + force->angle->compute(eflag,vflag); + atomKK->modified(force->angle->execution_space,force->angle->datamask_modify); + } + if (force->dihedral) { + atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read); + force->dihedral->compute(eflag,vflag); + atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify); + } + if (force->improper) { + atomKK->sync(force->improper->execution_space,force->improper->datamask_read); + force->improper->compute(eflag,vflag); + atomKK->modified(force->improper->execution_space,force->improper->datamask_modify); + } + timer->stamp(Timer::BOND); + } + + if(force->kspace) { + force->kspace->setup(); + if (kspace_compute_flag) { + atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read); + force->kspace->compute(eflag,vflag); + atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify); + timer->stamp(Timer::KSPACE); + } else force->kspace->compute_dummy(eflag,vflag); + } + + modify->setup_pre_reverse(eflag,vflag); + if (force->newton) comm->reverse_comm(); + + // update per-atom minimization variables stored by pair styles + + if (nextra_atom) + for (int m = 0; m < nextra_atom; m++) + requestor[m]->min_xf_get(m); + + lmp->kokkos->auto_sync = 0; + modify->setup(vflag); + lmp->kokkos->auto_sync = 1; + update->setupflag = 0; + + // stats for Finish to print + + ecurrent = pe_compute->compute_scalar(); + if (nextra_global) ecurrent += modify->min_energy(fextra); + if (output->thermo->normflag) ecurrent /= atom->natoms; + + einitial = ecurrent; + fnorm2_init = sqrt(fnorm_sqr()); + fnorminf_init = fnorm_inf(); +} + +/* ---------------------------------------------------------------------- + perform minimization, calling iterate() for N steps +------------------------------------------------------------------------- */ + +void MinKokkos::run(int n) +{ + if (nextra_global) + error->all(FLERR,"Cannot yet use extra global DOFs (e.g. fix box/relax) " + "with Kokkos minimize"); + + if (nextra_global || nextra_atom) + error->all(FLERR,"Cannot yet use extra atom DOFs (e.g. USER-AWPMD and USER-EFF packages) " + "with Kokkos minimize"); + + // minimizer iterations + + lmp->kokkos->auto_sync = 0; + atomKK->sync(Device,ALL_MASK); + + stop_condition = iterate(n); + stopstr = stopstrings(stop_condition); + + // if early exit from iterate loop: + // set update->nsteps to niter for Finish stats to print + // set output->next values to this timestep + // call energy_force() to insure vflag is set when forces computed + // output->write does final output for thermo, dump, restart files + // add ntimestep to all computes that store invocation times + // since are hardwiring call to thermo/dumps and computes may not be ready + + if (stop_condition != MAXITER) { + update->nsteps = niter; + + if (update->restrict_output == 0) { + for (int idump = 0; idump < output->ndump; idump++) + output->next_dump[idump] = update->ntimestep; + output->next_dump_any = update->ntimestep; + if (output->restart_flag) { + output->next_restart = update->ntimestep; + if (output->restart_every_single) + output->next_restart_single = update->ntimestep; + if (output->restart_every_double) + output->next_restart_double = update->ntimestep; + } + } + output->next_thermo = update->ntimestep; + + modify->addstep_compute_all(update->ntimestep); + ecurrent = energy_force(0); + + atomKK->sync(Host,ALL_MASK); + output->write(update->ntimestep); + } + + atomKK->sync(Host,ALL_MASK); + lmp->kokkos->auto_sync = 1; +} + +/* ---------------------------------------------------------------------- + evaluate potential energy and forces + may migrate atoms due to reneighboring + return new energy, which should include nextra_global dof + return negative gradient stored in atom->f + return negative gradient for nextra_global dof in fextra +------------------------------------------------------------------------- */ + +double MinKokkos::energy_force(int resetflag) +{ + // check for reneighboring + // always communicate since minimizer moved atoms + + int nflag = neighbor->decide(); + + if (nflag == 0) { + timer->stamp(); + comm->forward_comm(); + timer->stamp(Timer::COMM); + } else { + if (modify->n_min_pre_exchange) { + timer->stamp(); + modify->min_pre_exchange(); + timer->stamp(Timer::MODIFY); + } + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + if (domain->box_change) { + domain->reset_box(); + comm->setup(); + if (neighbor->style) neighbor->setup_bins(); + } + timer->stamp(); + comm->exchange(); + if (atom->sortfreq > 0 && + update->ntimestep >= atom->nextsort) atom->sort(); + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + timer->stamp(Timer::COMM); + if (modify->n_min_pre_neighbor) { + modify->min_pre_neighbor(); + timer->stamp(Timer::MODIFY); + } + neighbor->build(1); + timer->stamp(Timer::NEIGH); + if (modify->n_min_post_neighbor) { + modify->min_post_neighbor(); + timer->stamp(Timer::MODIFY); + } + } + + ev_set(update->ntimestep); + force_clear(); + + timer->stamp(); + + if (modify->n_min_pre_force) { + modify->min_pre_force(vflag); + timer->stamp(Timer::MODIFY); + } + + if (pair_compute_flag) { + atomKK->sync(force->pair->execution_space,force->pair->datamask_read); + force->pair->compute(eflag,vflag); + atomKK->modified(force->pair->execution_space,force->pair->datamask_modify); + timer->stamp(Timer::PAIR); + } + + if (atom->molecular) { + if (force->bond) { + atomKK->sync(force->bond->execution_space,force->bond->datamask_read); + force->bond->compute(eflag,vflag); + atomKK->modified(force->bond->execution_space,force->bond->datamask_modify); + } + if (force->angle) { + atomKK->sync(force->angle->execution_space,force->angle->datamask_read); + force->angle->compute(eflag,vflag); + atomKK->modified(force->angle->execution_space,force->angle->datamask_modify); + } + if (force->dihedral) { + atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read); + force->dihedral->compute(eflag,vflag); + atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify); + } + if (force->improper) { + atomKK->sync(force->improper->execution_space,force->improper->datamask_read); + force->improper->compute(eflag,vflag); + atomKK->modified(force->improper->execution_space,force->improper->datamask_modify); + } + timer->stamp(Timer::BOND); + } + + if (kspace_compute_flag) { + atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read); + force->kspace->compute(eflag,vflag); + atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify); + timer->stamp(Timer::KSPACE); + } + + if (modify->n_min_pre_reverse) { + modify->min_pre_reverse(eflag,vflag); + timer->stamp(Timer::MODIFY); + } + + if (force->newton) { + comm->reverse_comm(); + timer->stamp(Timer::COMM); + } + + // fixes that affect minimization + + if (modify->n_min_post_force) { + timer->stamp(); + modify->min_post_force(vflag); + timer->stamp(Timer::MODIFY); + } + + // compute potential energy of system + // normalize if thermo PE does + + atomKK->sync(pe_compute->execution_space,pe_compute->datamask_read); + double energy = pe_compute->compute_scalar(); + atomKK->modified(pe_compute->execution_space,pe_compute->datamask_modify); + if (nextra_global) energy += modify->min_energy(fextra); + if (output->thermo->normflag) energy /= atom->natoms; + + // if reneighbored, atoms migrated + // if resetflag = 1, update x0 of atoms crossing PBC + // reset vectors used by lo-level minimizer + + if (nflag) { + if (resetflag) fix_minimize_kk->reset_coords(); + reset_vectors(); + } + return energy; +} + +/* ---------------------------------------------------------------------- + clear force on own & ghost atoms + clear other arrays as needed +------------------------------------------------------------------------- */ + +void MinKokkos::force_clear() +{ + if (external_force_clear) return; + + // clear global force array + // if either newton flag is set, also include ghosts + + atomKK->k_f.clear_sync_state(); // ignore host forces/torques since device views + atomKK->k_torque.clear_sync_state(); // will be cleared below + + int nzero = atom->nlocal; + if (force->newton) nzero += atom->nghost; + + if (nzero) { + // local variables for lambda capture + + auto l_f = atomKK->k_f.d_view; + auto l_torque = atomKK->k_torque.d_view; + auto l_torqueflag = torqueflag; + + Kokkos::parallel_for(nzero, LAMMPS_LAMBDA(int i) { + l_f(i,0) = 0.0; + l_f(i,1) = 0.0; + l_f(i,2) = 0.0; + if (l_torqueflag) { + l_torque(i,0) = 0.0; + l_torque(i,1) = 0.0; + l_torque(i,2) = 0.0; + } + }); + } + atomKK->modified(Device,F_MASK); +} + +/* ---------------------------------------------------------------------- + compute and return ||force||_2^2 +------------------------------------------------------------------------- */ + +double MinKokkos::fnorm_sqr() +{ + + double local_norm2_sqr = 0.0; + { + // local variables for lambda capture + + auto l_fvec = fvec; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(int i, double& local_norm2_sqr) { + local_norm2_sqr += l_fvec[i]*l_fvec[i]; + },local_norm2_sqr); + } + + double norm2_sqr = 0.0; + MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world); + + return norm2_sqr; +} + +/* ---------------------------------------------------------------------- + compute and return ||force||_inf +------------------------------------------------------------------------- */ + +double MinKokkos::fnorm_inf() +{ + + double local_norm_inf = 0.0; + { + // local variables for lambda capture + + auto l_fvec = fvec; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(int i, double& local_norm_inf) { + local_norm_inf = MAX(fabs(l_fvec[i]),local_norm_inf); + },Kokkos::Max(local_norm_inf)); + } + + double norm_inf = 0.0; + MPI_Allreduce(&local_norm_inf,&norm_inf,1,MPI_DOUBLE,MPI_MAX,world); + + return norm_inf; +} diff --git a/src/KOKKOS/min_kokkos.h b/src/KOKKOS/min_kokkos.h new file mode 100644 index 0000000000000000000000000000000000000000..49cd1d18492385800e330693bd64d2ded47139f4 --- /dev/null +++ b/src/KOKKOS/min_kokkos.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_MIN_KOKKOS_H +#define LMP_MIN_KOKKOS_H + +#include "min.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +class MinKokkos : public Min { + public: + MinKokkos(class LAMMPS *); + virtual ~MinKokkos(); + void init(); + void setup(int flag=1); + void setup_minimal(int); + void run(int); + double fnorm_sqr(); + double fnorm_inf(); + + virtual void init_style() {} + virtual void setup_style() = 0; + virtual void reset_vectors() = 0; + virtual int iterate(int) = 0; + + // possible return values of iterate() method + enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE, + ZEROQUAD,TRSMALL,INTERROR,TIMEOUT}; + + //protected: // won't compile with CUDA + class FixMinimizeKokkos *fix_minimize_kk; // fix that stores auxiliary data + + DAT::t_ffloat_1d xvec; // variables for atomic dof, as 1d vector + DAT::t_ffloat_1d fvec; // force vector for atomic dof, as 1d vector + + double energy_force(int); + void force_clear(); +}; + +} + +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp new file mode 100644 index 0000000000000000000000000000000000000000..cb07c7db86e805241a75e455b84ff349977ed717 --- /dev/null +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -0,0 +1,401 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Stan Moore (SNL) +------------------------------------------------------------------------- */ + +#include "min_linesearch_kokkos.h" +#include +#include +#include "atom_kokkos.h" +#include "modify.h" +#include "fix_minimize_kokkos.h" +#include "pair.h" +#include "output.h" +#include "thermo.h" +#include "error.h" +#include "atom_masks.h" + +using namespace LAMMPS_NS; + +// ALPHA_MAX = max alpha allowed to avoid long backtracks +// ALPHA_REDUCE = reduction ratio, should be in range [0.5,1) +// BACKTRACK_SLOPE, should be in range (0,0.5] +// QUADRATIC_TOL = tolerance on alpha0, should be in range [0.1,1) +// EMACH = machine accuracy limit of energy changes (1.0e-8) +// EPS_QUAD = tolerance for quadratic projection + +#define ALPHA_MAX 1.0 +#define ALPHA_REDUCE 0.5 +#define BACKTRACK_SLOPE 0.4 +#define QUADRATIC_TOL 0.1 +//#define EMACH 1.0e-8 +#define EMACH 1.0e-8 +#define EPS_QUAD 1.0e-28 + +/* ---------------------------------------------------------------------- */ + +MinLineSearchKokkos::MinLineSearchKokkos(LAMMPS *lmp) : MinKokkos(lmp) +{ + searchflag = 1; + atomKK = (AtomKokkos *) atom; +} + +/* ---------------------------------------------------------------------- */ + +MinLineSearchKokkos::~MinLineSearchKokkos() +{ + +} + +/* ---------------------------------------------------------------------- */ + +void MinLineSearchKokkos::init() +{ + MinKokkos::init(); + + if (linestyle == 1) linemin = &MinLineSearchKokkos::linemin_quadratic; + else error->all(FLERR,"Kokkos minimize only supports the 'min_modify line " + "quadratic' option"); +} + +/* ---------------------------------------------------------------------- */ + +void MinLineSearchKokkos::setup_style() +{ + // memory for x0,g,h for atomic dof + + fix_minimize_kk->add_vector_kokkos(); + fix_minimize_kk->add_vector_kokkos(); + fix_minimize_kk->add_vector_kokkos(); +} + +/* ---------------------------------------------------------------------- + set current vector lengths and pointers + called after atoms have migrated +------------------------------------------------------------------------- */ + +void MinLineSearchKokkos::reset_vectors() +{ + // atomic dof + + nvec = 3 * atom->nlocal; + atomKK->sync(Device,F_MASK|X_MASK); + auto d_x = atomKK->k_x.d_view; + auto d_f = atomKK->k_f.d_view; + + if (nvec) xvec = DAT::t_ffloat_1d(d_x.data(),d_x.size()); + if (nvec) fvec = DAT::t_ffloat_1d(d_f.data(),d_f.size()); + x0 = fix_minimize_kk->request_vector_kokkos(0); + g = fix_minimize_kk->request_vector_kokkos(1); + h = fix_minimize_kk->request_vector_kokkos(2); + + auto h_fvec = Kokkos::create_mirror_view(fvec); + Kokkos::deep_copy(h_fvec,fvec); +} + +/* ---------------------------------------------------------------------- + line minimization methods + find minimum-energy starting at x along h direction + input args: eoriginal = energy at initial x + input extra: n,x,x0,f,h for atomic, extra global, extra per-atom dof + output args: return 0 if successful move, non-zero alpha + return non-zero if failed + alpha = distance moved along h for x at min eng config + update neval counter of eng/force function evaluations + output extra: if fail, energy_force() of original x + if succeed, energy_force() at x + alpha*h + atom->x = coords at new configuration + atom->f = force at new configuration + ecurrent = energy of new configuration +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + // linemin: quadratic line search (adapted from Dennis and Schnabel) + // The objective function is approximated by a quadratic + // function in alpha, for sufficiently small alpha. + // This idea is the same as that used in the well-known secant + // method. However, since the change in the objective function + // (difference of two finite numbers) is not known as accurately + // as the gradient (which is close to zero), all the expressions + // are written in terms of gradients. In this way, we can converge + // the LAMMPS forces much closer to zero. + // + // We know E,Eprev,fh,fhprev. The Taylor series about alpha_prev + // truncated at the quadratic term is: + // + // E = Eprev - del_alpha*fhprev + (1/2)del_alpha^2*Hprev + // + // and + // + // fh = fhprev - del_alpha*Hprev + // + // where del_alpha = alpha-alpha_prev + // + // We solve these two equations for Hprev and E=Esolve, giving: + // + // Esolve = Eprev - del_alpha*(f+fprev)/2 + // + // We define relerr to be: + // + // relerr = |(Esolve-E)/Eprev| + // = |1.0 - (0.5*del_alpha*(f+fprev)+E)/Eprev| + // + // If this is accurate to within a reasonable tolerance, then + // we go ahead and use a secant step to fh = 0: + // + // alpha0 = alpha - (alpha-alphaprev)*fh/delfh; + // +------------------------------------------------------------------------- */ + +int MinLineSearchKokkos::linemin_quadratic(double eoriginal, double &alpha) +{ + double fdothall,fdothme,hme,hmaxall; + double de_ideal,de; + double delfh,engprev,relerr,alphaprev,fhprev,ff,fh,alpha0; + double dot[2],dotall[2]; + double alphamax; + + fix_minimize_kk->k_vectors.sync(); + fix_minimize_kk->k_vectors.modify(); + + // fdothall = projection of search dir along downhill gradient + // if search direction is not downhill, exit with error + + fdothme = 0.0; + { + // local variables for lambda capture + + auto l_fvec = fvec; + auto l_h = h; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, double& fdothme) { + fdothme += l_fvec[i]*l_h[i]; + },fdothme); + } + MPI_Allreduce(&fdothme,&fdothall,1,MPI_DOUBLE,MPI_SUM,world); + if (output->thermo->normflag) fdothall /= atom->natoms; + + if (fdothall <= 0.0) return DOWNHILL; + + // set alphamax so no dof is changed by more than max allowed amount + // for atom coords, max amount = dmax + // for extra per-atom dof, max amount = extra_max[] + // for extra global dof, max amount is set by fix + // also insure alphamax <= ALPHA_MAX + // else will have to backtrack from huge value when forces are tiny + // if all search dir components are already 0.0, exit with error + + + hme = 0.0; + { + // local variables for lambda capture + + auto l_h = h; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, double& hme) { + hme = MAX(hme,fabs(l_h[i])); + },Kokkos::Max(hme)); + } + MPI_Allreduce(&hme,&hmaxall,1,MPI_DOUBLE,MPI_MAX,world); + alphamax = MIN(ALPHA_MAX,dmax/hmaxall); + + if (hmaxall == 0.0) return ZEROFORCE; + + // store box and values of all dof at start of linesearch + + { + // local variables for lambda capture + + auto l_xvec = xvec; + auto l_x0 = x0; + + fix_minimize_kk->store_box(); + Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) { + l_x0[i] = l_xvec[i]; + }); + } + + // backtrack with alpha until energy decrease is sufficient + // or until get to small energy change, then perform quadratic projection + + alpha = alphamax; + fhprev = fdothall; + engprev = eoriginal; + alphaprev = 0.0; + + // // important diagnostic: test the gradient against energy + // double etmp; + // double alphatmp = alphamax*1.0e-4; + // etmp = alpha_step(alphatmp,1); + // printf("alpha = %g dele = %g dele_force = %g err = %g\n", + // alphatmp,etmp-eoriginal,-alphatmp*fdothall, + // etmp-eoriginal+alphatmp*fdothall); + // alpha_step(0.0,1); + + while (1) { + ecurrent = alpha_step(alpha,1); + + // compute new fh, alpha, delfh + + s_double2 sdot; + { + // local variables for lambda capture + + auto l_fvec = fvec; + auto l_h = h; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, s_double2& sdot) { + sdot.d0 += l_fvec[i]*l_fvec[i]; + sdot.d1 += l_fvec[i]*l_h[i]; + },sdot); + } + dot[0] = sdot.d0; + dot[1] = sdot.d1; + + MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world); + ff = dotall[0]; + fh = dotall[1]; + if (output->thermo->normflag) { + ff /= atom->natoms; + fh /= atom->natoms; + } + + delfh = fh - fhprev; + + // if fh or delfh is epsilon, reset to starting point, exit with error + + if (fabs(fh) < EPS_QUAD || fabs(delfh) < EPS_QUAD) { + ecurrent = alpha_step(0.0,0); + return ZEROQUAD; + } + + // Check if ready for quadratic projection, equivalent to secant method + // alpha0 = projected alpha + + relerr = fabs(1.0-(0.5*(alpha-alphaprev)*(fh+fhprev)+ecurrent)/engprev); + alpha0 = alpha - (alpha-alphaprev)*fh/delfh; + + if (relerr <= QUADRATIC_TOL && alpha0 > 0.0 && alpha0 < alphamax) { + ecurrent = alpha_step(alpha0,1); + if (ecurrent - eoriginal < EMACH) { + return 0; + } + } + + // if backtracking energy change is better than ideal, exit with success + + de_ideal = -BACKTRACK_SLOPE*alpha*fdothall; + de = ecurrent - eoriginal; + + if (de <= de_ideal) + return 0; + + // save previous state + + fhprev = fh; + engprev = ecurrent; + alphaprev = alpha; + + // reduce alpha + + alpha *= ALPHA_REDUCE; + + // backtracked all the way to 0.0 + // reset to starting point, exit with error + + if (alpha <= 0.0 || de_ideal >= -EMACH) { + ecurrent = alpha_step(0.0,0); + return ZEROALPHA; + } + } +} + +/* ---------------------------------------------------------------------- */ + +double MinLineSearchKokkos::alpha_step(double alpha, int resetflag) +{ + // reset to starting point + + atomKK->k_x.clear_sync_state(); // ignore if host positions since device + // positions will be reset below + { + // local variables for lambda capture + + auto l_xvec = xvec; + auto l_x0 = x0; + + Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) { + l_xvec[i] = l_x0[i]; + }); + } + + // step forward along h + + if (alpha > 0.0) { + // local variables for lambda capture + + auto l_xvec = xvec; + auto l_h = h; + + Kokkos::parallel_for(nvec, LAMMPS_LAMBDA(const int& i) { + l_xvec[i] += alpha*l_h[i]; + }); + } + + atomKK->modified(Device,X_MASK); + + // compute and return new energy + + neval++; + return energy_force(resetflag); +} + +/* ---------------------------------------------------------------------- */ + +// compute projection of force on: itself and the search direction + +double MinLineSearchKokkos::compute_dir_deriv(double &ff) +{ + double dot[2],dotall[2]; + double fh; + + // compute new fh, alpha, delfh + + s_double2 sdot; + { + // local variables for lambda capture + + auto l_fvec = fvec; + auto l_h = h; + + Kokkos::parallel_reduce(nvec, LAMMPS_LAMBDA(const int& i, s_double2& sdot) { + sdot.d0 += l_fvec[i]*l_fvec[i]; + sdot.d1 += l_fvec[i]*l_h[i]; + },sdot); + } + dot[0] = sdot.d0; + dot[1] = sdot.d1; + + MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world); + + ff = dotall[0]; + fh = dotall[1]; + if (output->thermo->normflag) { + ff /= atom->natoms; + fh /= atom->natoms; + } + + return fh; +} diff --git a/src/KOKKOS/min_linesearch_kokkos.h b/src/KOKKOS/min_linesearch_kokkos.h new file mode 100644 index 0000000000000000000000000000000000000000..70df13d1e7a8b3d75dfc098f4bf842368023c4ce --- /dev/null +++ b/src/KOKKOS/min_linesearch_kokkos.h @@ -0,0 +1,69 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_MIN_LSRCH_KOKKOS_H +#define LMP_MIN_LSRCH_KOKKOS_H + +#include "min_kokkos.h" + +namespace LAMMPS_NS { + + struct s_double2 { + double d0, d1; + KOKKOS_INLINE_FUNCTION + s_double2() { + d0 = d1 = 0.0; + } + KOKKOS_INLINE_FUNCTION + s_double2& operator+=(const s_double2 &rhs){ + d0 += rhs.d0; + d1 += rhs.d1; + return *this; + } + + KOKKOS_INLINE_FUNCTION + void operator+=(const volatile s_double2 &rhs) volatile { + d0 += rhs.d0; + d1 += rhs.d1; + } + }; + //typedef s_double2 double2; + +class MinLineSearchKokkos : public MinKokkos { + public: + MinLineSearchKokkos(class LAMMPS *); + ~MinLineSearchKokkos(); + void init(); + void setup_style(); + void reset_vectors(); + + //protected: // won't compile with CUDA + // vectors needed by linesearch minimizers + // allocated and stored by fix_minimize + // x,f are stored by parent or Atom class or Pair class + + DAT::t_ffloat_1d x0; // coords at start of linesearch + DAT::t_ffloat_1d g; // old gradient vector + DAT::t_ffloat_1d h; // search direction vector + + typedef int (MinLineSearchKokkos::*FnPtr)(double, double &); + FnPtr linemin; + int linemin_quadratic(double, double &); + + double alpha_step(double, int); + double compute_dir_deriv(double &); +}; + +} + +#endif diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index 2a3994f584992d5248a17c666166751b8bca6894..7650bf33507309aa97ef3bf64485141489a1f3d0 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -443,7 +443,7 @@ struct NPairKokkosBuildFunctorSize { const size_t sharedsize; NPairKokkosBuildFunctorSize(const NeighborKokkosExecute &_c, - const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {}; + const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {}; KOKKOS_INLINE_FUNCTION void operator() (const int & i) const { @@ -467,7 +467,7 @@ struct NPairKokkosBuildFunctorSize { const size_t sharedsize; NPairKokkosBuildFunctorSize(const NeighborKokkosExecute &_c, - const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {}; + const size_t _sharedsize): c(_c), sharedsize(_sharedsize) {}; KOKKOS_INLINE_FUNCTION void operator() (const int & i) const { diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index 8d1778e09189a167f54e5126a470d25e27a6d07e..e40353d970f8948fae3d061c430a349f9802703a 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -61,13 +61,13 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { template KOKKOS_INLINE_FUNCTION void ev_tally_xyz(EV_FLOAT &ev, int i, int j, - F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, - X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; template KOKKOS_INLINE_FUNCTION void ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j, - F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, - X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; + F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, + X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; protected: typename AT::t_x_array_randomread x; diff --git a/src/KOKKOS/pair_snap_kokkos.h b/src/KOKKOS/pair_snap_kokkos.h index 2193e9ff245ab4206907d88e144e8e20c6a8ca33..8586c4bdab37359eb91c2b3a0ecf75c116321187 100644 --- a/src/KOKKOS/pair_snap_kokkos.h +++ b/src/KOKKOS/pair_snap_kokkos.h @@ -39,6 +39,7 @@ struct TagPairSNAPPreUi{}; struct TagPairSNAPComputeUi{}; struct TagPairSNAPComputeZi{}; struct TagPairSNAPComputeBi{}; +struct TagPairSNAPZeroYi{}; struct TagPairSNAPComputeYi{}; struct TagPairSNAPComputeDuidrj{}; struct TagPairSNAPComputeDeidrj{}; @@ -73,19 +74,22 @@ public: void operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const; + void operator() (TagPairSNAPPreUi,const int& ii) const; KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy::member_type& team) const; + void operator() (TagPairSNAPComputeZi,const int& ii) const; KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy::member_type& team) const; KOKKOS_INLINE_FUNCTION - void operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy::member_type& team) const; + void operator() (TagPairSNAPZeroYi,const int& ii) const; + + KOKKOS_INLINE_FUNCTION + void operator() (TagPairSNAPComputeYi,const int& ii) const; KOKKOS_INLINE_FUNCTION void operator() (TagPairSNAPComputeDuidrj,const typename Kokkos::TeamPolicy::member_type& team) const; diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 95afcc5ec7333948eed06141f6a1d4be7caf4fe2..02c8554fa567f2dc47aebe72a1e3b1849a020204 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -184,22 +184,12 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_reduce("PairSNAPKokkos::find_max_neighs",inum, FindMaxNumNeighs(k_list), Kokkos::Experimental::Max(max_neighs)); int vector_length = 1; - int ui_vector_length = 1; int team_size = 1; - int yi_team_size = 1; int team_size_max = Kokkos::TeamPolicy::team_size_max(*this); #ifdef KOKKOS_ENABLE_CUDA team_size = 32;//max_neighs; if (team_size*vector_length > team_size_max) team_size = team_size_max/vector_length; - - yi_team_size = 256; - if (yi_team_size*vector_length > team_size_max) - yi_team_size = team_size_max/vector_length; - - ui_vector_length = 8; - if (team_size*ui_vector_length > team_size_max) - team_size = team_size_max/ui_vector_length; #endif if (beta_max < inum) { @@ -227,17 +217,21 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for("ComputeNeigh",policy_neigh,*this); //PreUi - typename Kokkos::TeamPolicy policy_preui(chunk_size,team_size,vector_length); + typename Kokkos::RangePolicy policy_preui(0,chunk_size); Kokkos::parallel_for("PreUi",policy_preui,*this); //ComputeUi - typename Kokkos::TeamPolicy policy_ui(((inum+team_size-1)/team_size)*max_neighs,team_size,ui_vector_length); + typename Kokkos::TeamPolicy policy_ui(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length); Kokkos::parallel_for("ComputeUi",policy_ui,*this); + //Ulisttot transpose + snaKK.transpose_ulisttot(); + //Compute bispectrum if (quadraticflag || eflag) { //ComputeZi - typename Kokkos::TeamPolicy policy_zi(chunk_size,team_size,vector_length); + int idxz_max = snaKK.idxz_max; + typename Kokkos::RangePolicy policy_zi(0,chunk_size*idxz_max); Kokkos::parallel_for("ComputeZi",policy_zi,*this); //ComputeBi @@ -250,7 +244,12 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) Kokkos::parallel_for("ComputeBeta",policy_beta,*this); //ComputeYi - typename Kokkos::TeamPolicy policy_yi(chunk_size,yi_team_size,vector_length); + typename Kokkos::RangePolicy policy_zero_yi(0,chunk_size); + Kokkos::parallel_for("ZeroYi",policy_zero_yi,*this); + + //ComputeYi + int idxz_max = snaKK.idxz_max; + typename Kokkos::RangePolicy policy_yi(0,chunk_size*idxz_max); Kokkos::parallel_for("ComputeYi",policy_yi,*this); //ComputeDuidrj @@ -504,10 +503,9 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeNeigh,const typen template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy::member_type& team) const { - int ii = team.league_rank(); +void PairSNAPKokkos::operator() (TagPairSNAPPreUi,const int& ii) const { SNAKokkos my_sna = snaKK; - my_sna.pre_ui(team,ii); + my_sna.pre_ui(ii); } template @@ -529,18 +527,23 @@ void PairSNAPKokkos::operator() (TagPairSNAPComputeUi,const typename template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPComputeYi,const typename Kokkos::TeamPolicy::member_type& team) const { - int ii = team.league_rank(); +void PairSNAPKokkos::operator() (TagPairSNAPZeroYi,const int& ii) const { SNAKokkos my_sna = snaKK; - my_sna.compute_yi(team,ii,d_beta); + my_sna.zero_yi(ii); } template KOKKOS_INLINE_FUNCTION -void PairSNAPKokkos::operator() (TagPairSNAPComputeZi,const typename Kokkos::TeamPolicy::member_type& team) const { - int ii = team.league_rank(); +void PairSNAPKokkos::operator() (TagPairSNAPComputeYi,const int& ii) const { + SNAKokkos my_sna = snaKK; + my_sna.compute_yi(ii,d_beta); +} + +template +KOKKOS_INLINE_FUNCTION +void PairSNAPKokkos::operator() (TagPairSNAPComputeZi,const int& ii) const { SNAKokkos my_sna = snaKK; - my_sna.compute_zi(team,ii); + my_sna.compute_zi(ii); } template diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 2dbfdcb47c5f7bb2b4f2ff72f9ed69d65b455507..7aa154c3d5137a1b117b82fc74605aad4784e293 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -26,16 +26,29 @@ namespace LAMMPS_NS { typedef double SNAreal; -typedef struct { SNAreal re, im; } SNAcomplex; -struct SNAKK_ZINDICES { - int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju; -}; +//typedef struct { SNAreal re, im; } SNAcomplex; +struct alignas(2*sizeof(SNAreal)) SNAcomplex{ + SNAreal re, im; + + KOKKOS_INLINE_FUNCTION + SNAcomplex() : re(0),im(0) + {} -struct SNAKK_BINDICES { - int j1, j2, j; + KOKKOS_INLINE_FUNCTION + SNAcomplex(SNAreal real_in, SNAreal imag_in) + :re(real_in),im(imag_in) + {} }; +//struct SNAKK_ZINDICES { +// int j1, j2, j, ma1min, ma2max, mb1min, mb2max, na, nb, jju; +//}; +// +//struct SNAKK_BINDICES { +// int j1, j2, j; +//}; + template class SNAKokkos { @@ -53,12 +66,32 @@ public: typedef Kokkos::View t_sna_1c; typedef Kokkos::View > t_sna_1c_atomic; typedef Kokkos::View t_sna_2c; - typedef Kokkos::View t_sna_2c_cpu; + typedef Kokkos::View t_sna_2c_lr; typedef Kokkos::View t_sna_3c; typedef Kokkos::View t_sna_4c; typedef Kokkos::View t_sna_3c3; typedef Kokkos::View t_sna_5c; +// Helper class to get ulisttot_r + +template +class UlisttotHelper { +public: + inline + static void transpose(T1 &ulisttot_lr, const T2 &ulisttot) { + Kokkos::deep_copy(ulisttot_lr,ulisttot); + } +}; + +template +class UlisttotHelper { +public: + inline + static void transpose(T1 &ulisttot_lr, const T2 &ulisttot) { + ulisttot_lr = ulisttot; + } +}; + inline SNAKokkos() {}; KOKKOS_INLINE_FUNCTION @@ -80,17 +113,22 @@ inline int ncoeff; +inline + void transpose_ulisttot(); + // functions for bispectrum coefficients KOKKOS_INLINE_FUNCTION - void pre_ui(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP + void pre_ui(const int&); // ForceSNAP KOKKOS_INLINE_FUNCTION void compute_ui(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION void compute_ui_orig(const typename Kokkos::TeamPolicy::member_type& team, int, int); // ForceSNAP KOKKOS_INLINE_FUNCTION - void compute_zi(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP + void compute_zi(const int&); // ForceSNAP + KOKKOS_INLINE_FUNCTION + void zero_yi(const int&); KOKKOS_INLINE_FUNCTION - void compute_yi(const typename Kokkos::TeamPolicy::member_type& team, int, + void compute_yi(int, const Kokkos::View &beta); // ForceSNAP KOKKOS_INLINE_FUNCTION void compute_bi(const typename Kokkos::TeamPolicy::member_type& team, int); // ForceSNAP @@ -129,23 +167,25 @@ inline int twojmax, diagonalstyle; t_sna_2d blist; - t_sna_2c_cpu ulisttot; + t_sna_2c ulisttot; + t_sna_2c_lr ulisttot_lr; t_sna_2c zlist; t_sna_3c ulist; - t_sna_2c ylist; + t_sna_2c_lr ylist; // derivatives of data t_sna_4c dulist; + int idxcg_max, idxu_max, idxz_max, idxb_max; + private: double rmin0, rfac0; //use indexlist instead of loops, constructor generates these // Same across all SNAKokkos - Kokkos::View idxz; - Kokkos::View idxb; - int idxcg_max, idxu_max, idxz_max, idxb_max; + Kokkos::View idxz; + Kokkos::View idxb; Kokkos::View idxcg_block; Kokkos::View idxu_block; Kokkos::View idxz_block; @@ -173,9 +213,9 @@ inline inline void init_rootpqarray(); // init() KOKKOS_INLINE_FUNCTION - void zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int); // compute_ui + void zero_uarraytot(const int&); // compute_ui KOKKOS_INLINE_FUNCTION - void addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, double); // compute_ui + void addself_uarraytot(const int&, const double&); // compute_ui KOKKOS_INLINE_FUNCTION void add_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int, int, double, double, double); // compute_ui diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 36765e9cd60964451584e61c22ce2b9f3ffc0f16..3e4ebc2e42cd0166e54500a73de2c06e77274b9f 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -117,7 +117,7 @@ void SNAKokkos::build_indexlist() if (j >= j1) idxb_count++; idxb_max = idxb_count; - idxb = Kokkos::View("SNAKokkos::idxb",idxb_max); + idxb = Kokkos::View("SNAKokkos::idxb",idxb_max); auto h_idxb = Kokkos::create_mirror_view(idxb); idxb_count = 0; @@ -125,9 +125,9 @@ void SNAKokkos::build_indexlist() for(int j2 = 0; j2 <= j1; j2++) for(int j = j1 - j2; j <= MIN(twojmax, j1 + j2); j += 2) if (j >= j1) { - h_idxb[idxb_count].j1 = j1; - h_idxb[idxb_count].j2 = j2; - h_idxb[idxb_count].j = j; + h_idxb(idxb_count,0) = j1; + h_idxb(idxb_count,1) = j2; + h_idxb(idxb_count,2) = j; idxb_count++; } Kokkos::deep_copy(idxb,h_idxb); @@ -160,7 +160,7 @@ void SNAKokkos::build_indexlist() idxz_count++; idxz_max = idxz_count; - idxz = Kokkos::View("SNAKokkos::idxz",idxz_max); + idxz = Kokkos::View("SNAKokkos::idxz",idxz_max); auto h_idxz = Kokkos::create_mirror_view(idxz); idxz_block = Kokkos::View("SNAKokkos::idxz_block", jdim,jdim,jdim); @@ -178,20 +178,20 @@ void SNAKokkos::build_indexlist() for (int mb = 0; 2*mb <= j; mb++) for (int ma = 0; ma <= j; ma++) { - h_idxz[idxz_count].j1 = j1; - h_idxz[idxz_count].j2 = j2; - h_idxz[idxz_count].j = j; - h_idxz[idxz_count].ma1min = MAX(0, (2 * ma - j - j2 + j1) / 2); - h_idxz[idxz_count].ma2max = (2 * ma - j - (2 * h_idxz[idxz_count].ma1min - j1) + j2) / 2; - h_idxz[idxz_count].na = MIN(j1, (2 * ma - j + j2 + j1) / 2) - h_idxz[idxz_count].ma1min + 1; - h_idxz[idxz_count].mb1min = MAX(0, (2 * mb - j - j2 + j1) / 2); - h_idxz[idxz_count].mb2max = (2 * mb - j - (2 * h_idxz[idxz_count].mb1min - j1) + j2) / 2; - h_idxz[idxz_count].nb = MIN(j1, (2 * mb - j + j2 + j1) / 2) - h_idxz[idxz_count].mb1min + 1; + h_idxz(idxz_count,0) = j1; + h_idxz(idxz_count,1) = j2; + h_idxz(idxz_count,2) = j; + h_idxz(idxz_count,3) = MAX(0, (2 * ma - j - j2 + j1) / 2); + h_idxz(idxz_count,4) = (2 * ma - j - (2 * h_idxz(idxz_count,3) - j1) + j2) / 2; + h_idxz(idxz_count,5) = MAX(0, (2 * mb - j - j2 + j1) / 2); + h_idxz(idxz_count,6) = (2 * mb - j - (2 * h_idxz(idxz_count,5) - j1) + j2) / 2; + h_idxz(idxz_count,7) = MIN(j1, (2 * ma - j + j2 + j1) / 2) - h_idxz(idxz_count,3) + 1; + h_idxz(idxz_count,8) = MIN(j1, (2 * mb - j + j2 + j1) / 2) - h_idxz(idxz_count,5) + 1; // apply to z(j1,j2,j,ma,mb) to unique element of y(j) const int jju = h_idxu_block[j] + (j+1)*mb + ma; - h_idxz[idxz_count].jju = jju; + h_idxz(idxz_count,9) = jju; idxz_count++; } @@ -225,11 +225,13 @@ void SNAKokkos::grow_rij(int newnatom, int newnmax) dedr = t_sna_3d("sna:dedr",natom,nmax,3); blist = t_sna_2d("sna:blist",natom,idxb_max); - ulisttot = t_sna_2c_cpu("sna:ulisttot",natom,idxu_max); + ulisttot = t_sna_2c("sna:ulisttot",natom,idxu_max); + if (!Kokkos::Impl::is_same::value) + ulisttot_lr = t_sna_2c_lr("sna:ulisttot_lr",natom,idxu_max); zlist = t_sna_2c("sna:zlist",natom,idxz_max); ulist = t_sna_3c("sna:ulist",natom,nmax,idxu_max); - ylist = t_sna_2c("sna:ylist",natom,idxu_max); + ylist = t_sna_2c_lr("sna:ylist",natom,idxu_max); dulist = t_sna_4c("sna:dulist",natom,nmax,idxu_max); } @@ -240,15 +242,15 @@ void SNAKokkos::grow_rij(int newnatom, int newnmax) template KOKKOS_INLINE_FUNCTION -void SNAKokkos::pre_ui(const typename Kokkos::TeamPolicy::member_type& team, int iatom) +void SNAKokkos::pre_ui(const int& iatom) { - if(team.team_rank() == 0) { - zero_uarraytot(team,iatom); + //if(team.team_rank() == 0) { + zero_uarraytot(iatom); //Kokkos::single(Kokkos::PerThread(team), [&] (){ - addself_uarraytot(team,iatom,wself); + addself_uarraytot(iatom,wself); //}); - } - team.team_barrier(); + //} + //team.team_barrier(); } /* ---------------------------------------------------------------------- @@ -278,106 +280,73 @@ void SNAKokkos::compute_ui(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_ui_orig(const typename Kokkos::TeamPolicy::member_type& team, int iatom, int jnum) +void SNAKokkos::compute_zi(const int& iter) { - double rsq, r, x, y, z, z0, theta0; - - // utot(j,ma,mb) = 0 for all j,ma,ma - // utot(j,ma,ma) = 1 for all j,ma - // for j in neighbors of i: - // compute r0 = (x,y,z,z0) - // utot(j,ma,mb) += u(r0;j,ma,mb) for all j,ma,mb - - if(team.team_rank() == 0) { - zero_uarraytot(team,iatom); - //Kokkos::single(Kokkos::PerThread(team), [&] (){ - addself_uarraytot(team,iatom,wself); - //}); - } - team.team_barrier(); - - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,jnum), - [&] (const int& j) { - //for(int j = 0; j < jnum; j++) { - x = rij(iatom,j,0); - y = rij(iatom,j,1); - z = rij(iatom,j,2); - rsq = x * x + y * y + z * z; - r = sqrt(rsq); - - theta0 = (r - rmin0) * rfac0 * MY_PI / (rcutij(iatom,j) - rmin0); - // theta0 = (r - rmin0) * rscale0; - z0 = r / tan(theta0); - - compute_uarray(team, iatom, j, x, y, z, z0, r); - //Kokkos::single(Kokkos::PerThread(team), [&] (){ - add_uarraytot(team, iatom, j, r, wj(iatom,j), rcutij(iatom,j)); - //}); - }); - + const int iatom = iter / idxz_max; + const int jjz = iter % idxz_max; + + const int j1 = idxz(jjz,0); + const int j2 = idxz(jjz,1); + const int j = idxz(jjz,2); + const int ma1min = idxz(jjz,3); + const int ma2max = idxz(jjz,4); + const int mb1min = idxz(jjz,5); + const int mb2max = idxz(jjz,6); + const int na = idxz(jjz,7); + const int nb = idxz(jjz,8); + + const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); + + zlist(iatom,jjz).re = 0.0; + zlist(iatom,jjz).im = 0.0; + + int jju1 = idxu_block[j1] + (j1+1)*mb1min; + int jju2 = idxu_block[j2] + (j2+1)*mb2max; + int icgb = mb1min*(j2+1) + mb2max; + for(int ib = 0; ib < nb; ib++) { + + double suma1_r = 0.0; + double suma1_i = 0.0; + + int ma1 = ma1min; + int ma2 = ma2max; + int icga = ma1min*(j2+1) + ma2max; + for(int ia = 0; ia < na; ia++) { + suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im); + suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re); + ma1++; + ma2--; + icga += j2; + } // end loop over ia + + zlist(iatom,jjz).re += cgblock[icgb] * suma1_r; + zlist(iatom,jjz).im += cgblock[icgb] * suma1_i; + + jju1 += j1+1; + jju2 -= j2+1; + icgb += j2; + } // end loop over ib } /* ---------------------------------------------------------------------- - compute Zi by summing over products of Ui + compute Yi from Ui without storing Zi, looping over zlist indices ------------------------------------------------------------------------- */ template KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy::member_type& team, int iatom) +void SNAKokkos::zero_yi(const int& iatom) { - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max), - [&] (const int& jjz) { - //for(int jjz = 0; jjz < idxz_max; jjz++) { - const int j1 = idxz[jjz].j1; - const int j2 = idxz[jjz].j2; - const int j = idxz[jjz].j; - const int ma1min = idxz[jjz].ma1min; - const int ma2max = idxz[jjz].ma2max; - const int na = idxz[jjz].na; - const int mb1min = idxz[jjz].mb1min; - const int mb2max = idxz[jjz].mb2max; - const int nb = idxz[jjz].nb; - - const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); - - zlist(iatom,jjz).re = 0.0; - zlist(iatom,jjz).im = 0.0; - - int jju1 = idxu_block[j1] + (j1+1)*mb1min; - int jju2 = idxu_block[j2] + (j2+1)*mb2max; - int icgb = mb1min*(j2+1) + mb2max; - for(int ib = 0; ib < nb; ib++) { - - double suma1_r = 0.0; - double suma1_i = 0.0; - - int ma1 = ma1min; - int ma2 = ma2max; - int icga = ma1min*(j2+1) + ma2max; - for(int ia = 0; ia < na; ia++) { - suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im); - suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re); - ma1++; - ma2--; - icga += j2; - } // end loop over ia - - zlist(iatom,jjz).re += cgblock[icgb] * suma1_r; - zlist(iatom,jjz).im += cgblock[icgb] * suma1_i; - - jju1 += j1+1; - jju2 -= j2+1; - icgb += j2; - } // end loop over ib - - }); // end loop over jjz + for (int j = 0; j < idxu_max; j++) + ylist(iatom,j) = {0.0,0.0}; } /* ---------------------------------------------------------------------- @@ -386,102 +355,82 @@ void SNAKokkos::compute_zi(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::compute_yi(const typename Kokkos::TeamPolicy::member_type& team, int iatom, +void SNAKokkos::compute_yi(int iter, const Kokkos::View &beta) { double betaj; - const int ii = iatom; - - { - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,ylist.extent(1)), - [&] (const int& i) { - ylist(iatom,i).re = 0.0; - ylist(iatom,i).im = 0.0; - }); - } - - //int flopsum = 0; - - Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxz_max), - [&] (const int& jjz) { - //for(int jjz = 0; jjz < idxz_max; jjz++) { - const int j1 = idxz[jjz].j1; - const int j2 = idxz[jjz].j2; - const int j = idxz[jjz].j; - const int ma1min = idxz[jjz].ma1min; - const int ma2max = idxz[jjz].ma2max; - const int na = idxz[jjz].na; - const int mb1min = idxz[jjz].mb1min; - const int mb2max = idxz[jjz].mb2max; - const int nb = idxz[jjz].nb; - - const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); - //int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2; - //int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2; - - double ztmp_r = 0.0; - double ztmp_i = 0.0; - - int jju1 = idxu_block[j1] + (j1+1)*mb1min; - int jju2 = idxu_block[j2] + (j2+1)*mb2max; - int icgb = mb1min*(j2+1) + mb2max; - for(int ib = 0; ib < nb; ib++) { - - double suma1_r = 0.0; - double suma1_i = 0.0; - - int ma1 = ma1min; - int ma2 = ma2max; - int icga = ma1min*(j2+1) + ma2max; - - for(int ia = 0; ia < na; ia++) { - suma1_r += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).re - ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).im); - suma1_i += cgblock[icga] * (ulisttot(iatom,jju1+ma1).re * ulisttot(iatom,jju2+ma2).im + ulisttot(iatom,jju1+ma1).im * ulisttot(iatom,jju2+ma2).re); - //flopsum += 10; - ma1++; - ma2--; - icga += j2; - } // end loop over ia - - ztmp_r += cgblock[icgb] * suma1_r; - ztmp_i += cgblock[icgb] * suma1_i; - jju1 += j1+1; - jju2 -= j2+1; - icgb += j2; - } // end loop over ib - - // apply to z(j1,j2,j,ma,mb) to unique element of y(j) - // find right y_list[jju] and beta(ii,jjb) entries - // multiply and divide by j+1 factors - // account for multiplicity of 1, 2, or 3 - - const int jju = idxz[jjz].jju; + const int iatom = iter / idxz_max; + const int jjz = iter % idxz_max; + + const int j1 = idxz(jjz,0); + const int j2 = idxz(jjz,1); + const int j = idxz(jjz,2); + const int ma1min = idxz(jjz,3); + const int ma2max = idxz(jjz,4); + const int mb1min = idxz(jjz,5); + const int mb2max = idxz(jjz,6); + const int na = idxz(jjz,7); + const int nb = idxz(jjz,8); + const int jju = idxz(jjz,9); + + const double* cgblock = cglist.data() + idxcg_block(j1,j2,j); + //int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2; + //int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2; + + double ztmp_r = 0.0; + double ztmp_i = 0.0; + + int jju1 = idxu_block[j1] + (j1+1)*mb1min; + int jju2 = idxu_block[j2] + (j2+1)*mb2max; + int icgb = mb1min*(j2+1) + mb2max; + for(int ib = 0; ib < nb; ib++) { + + double suma1_r = 0.0; + double suma1_i = 0.0; + + int ma1 = ma1min; + int ma2 = ma2max; + int icga = ma1min*(j2+1) + ma2max; + + for(int ia = 0; ia < na; ia++) { + suma1_r += cgblock[icga] * (ulisttot_lr(iatom,jju1+ma1).re * ulisttot_lr(iatom,jju2+ma2).re - ulisttot_lr(iatom,jju1+ma1).im * ulisttot_lr(iatom,jju2+ma2).im); + suma1_i += cgblock[icga] * (ulisttot_lr(iatom,jju1+ma1).re * ulisttot_lr(iatom,jju2+ma2).im + ulisttot_lr(iatom,jju1+ma1).im * ulisttot_lr(iatom,jju2+ma2).re); + ma1++; + ma2--; + icga += j2; + } // end loop over ia + + ztmp_r += cgblock[icgb] * suma1_r; + ztmp_i += cgblock[icgb] * suma1_i; + jju1 += j1+1; + jju2 -= j2+1; + icgb += j2; + } // end loop over ib + + // apply to z(j1,j2,j,ma,mb) to unique element of y(j) + // find right y_list[jju] and beta(iatom,jjb) entries + // multiply and divide by j+1 factors + // account for multiplicity of 1, 2, or 3 // pick out right beta value - if (j >= j1) { - const int jjb = idxb_block(j1,j2,j); - if (j1 == j) { - if (j2 == j) betaj = 3*beta(ii,jjb); - else betaj = 2*beta(ii,jjb); - } else betaj = beta(ii,jjb); - } else if (j >= j2) { - const int jjb = idxb_block(j,j2,j1); - if (j2 == j) betaj = 2*beta(ii,jjb)*(j1+1)/(j+1.0); - else betaj = beta(ii,jjb)*(j1+1)/(j+1.0); - } else { - const int jjb = idxb_block(j2,j,j1); - betaj = beta(ii,jjb)*(j1+1)/(j+1.0); - } - - Kokkos::single(Kokkos::PerThread(team), [&] () { - Kokkos::atomic_add(&(ylist(iatom,jju).re), betaj*ztmp_r); - Kokkos::atomic_add(&(ylist(iatom,jju).im), betaj*ztmp_i); - }); - - }); // end loop over jjz + if (j >= j1) { + const int jjb = idxb_block(j1,j2,j); + if (j1 == j) { + if (j2 == j) betaj = 3*beta(iatom,jjb); + else betaj = 2*beta(iatom,jjb); + } else betaj = beta(iatom,jjb); + } else if (j >= j2) { + const int jjb = idxb_block(j,j2,j1); + if (j2 == j) betaj = 2*beta(iatom,jjb)*(j1+1)/(j+1.0); + else betaj = beta(iatom,jjb)*(j1+1)/(j+1.0); + } else { + const int jjb = idxb_block(j2,j,j1); + betaj = beta(iatom,jjb)*(j1+1)/(j+1.0); + } - //printf("sum %i\n",flopsum); + Kokkos::atomic_add(&(ylist(iatom,jju).re), betaj*ztmp_r); + Kokkos::atomic_add(&(ylist(iatom,jju).im), betaj*ztmp_i); } /* ---------------------------------------------------------------------- @@ -556,9 +505,9 @@ void SNAKokkos::compute_bi(const typename Kokkos::TeamPolicy::compute_duidrj(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::zero_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int iatom) +void SNAKokkos::zero_uarraytot(const int& iatom) { { - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)), - [&] (const int& i) { + //Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,ulisttot.extent(1)), + // [&] (const int& i) { + for (int i = 0; i < ulisttot.extent(1); i++) { ulisttot(iatom,i).re = 0.0; ulisttot(iatom,i).im = 0.0; - }); + } + //}); } } @@ -663,18 +614,18 @@ void SNAKokkos::zero_uarraytot(const typename Kokkos::TeamPolicy KOKKOS_INLINE_FUNCTION -void SNAKokkos::addself_uarraytot(const typename Kokkos::TeamPolicy::member_type& team, int iatom, double wself_in) +void SNAKokkos::addself_uarraytot(const int& iatom, const double& wself_in) { - Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), - [&] (const int& j) { - //for (int j = 0; j <= twojmax; j++) + //Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,twojmax+1), + // [&] (const int& j) { + for (int j = 0; j <= twojmax; j++) { int jju = idxu_block[j]; for (int ma = 0; ma <= j; ma++) { ulisttot(iatom,jju).re = wself_in; ulisttot(iatom,jju).im = 0.0; jju += j+2; } - }); + }//}); } /* ---------------------------------------------------------------------- @@ -786,6 +737,12 @@ void SNAKokkos::compute_uarray(const typename Kokkos::TeamPolicy +void SNAKokkos::transpose_ulisttot() +{ + UlisttotHelper::transpose(ulisttot_lr,ulisttot); +} + /* ---------------------------------------------------------------------- compute derivatives of Wigner U-functions for one neighbor see comments in compute_uarray() @@ -1318,6 +1275,8 @@ double SNAKokkos::memory_usage() bytes += natom * idxu_max * sizeof(double) * 2; // ulist bytes += natom * idxu_max * sizeof(double) * 2; // ulisttot + if (!Kokkos::Impl::is_same::value) + bytes += natom * idxu_max * sizeof(double) * 2; // ulisttot_lr bytes += natom * idxu_max * 3 * sizeof(double) * 2; // dulist bytes += natom * idxz_max * sizeof(double) * 2; // zlist @@ -1329,8 +1288,8 @@ double SNAKokkos::memory_usage() bytes += jdim * jdim * jdim * sizeof(int); // idxz_block bytes += jdim * jdim * jdim * sizeof(int); // idxb_block - bytes += idxz_max * sizeof(SNAKK_ZINDICES); // idxz - bytes += idxb_max * sizeof(SNAKK_BINDICES); // idxb + bytes += idxz_max * 10 * sizeof(int); // idxz + bytes += idxb_max * 3 * sizeof(int); // idxb bytes += jdim * sizeof(double); // bzero diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 2d2f0a9815e2154a6ac53dc34b41f4f8ae875a5a..23952b71d8ccaa44babe39b111a7f1d12b6333d0 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -143,7 +143,6 @@ void VerletKokkos::setup(int flag) } else if (force->pair) force->pair->compute_dummy(eflag,vflag); - if (atomKK->molecular) { if (force->bond) { atomKK->sync(force->bond->execution_space,force->bond->datamask_read); @@ -248,7 +247,6 @@ void VerletKokkos::setup_minimal(int flag) } else if (force->pair) force->pair->compute_dummy(eflag,vflag); - if (atomKK->molecular) { if (force->bond) { atomKK->sync(force->bond->execution_space,force->bond->datamask_read); @@ -285,7 +283,9 @@ void VerletKokkos::setup_minimal(int flag) if (force->newton) comm->reverse_comm(); + lmp->kokkos->auto_sync = 0; modify->setup(vflag); + lmp->kokkos->auto_sync = 1; update->setupflag = 0; } diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index c3442beef51cd5b07e20042673fcf9e2a653ea8e..a003ce91fd585213aabeccc5d37a9f3a4c34e97e 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -69,7 +69,7 @@ void EwaldDipole::init() } // error check - + dipoleflag = atom->mu?1:0; qsum_qsq(0); // q[i] might not be declared ? @@ -77,13 +77,13 @@ void EwaldDipole::init() error->all(FLERR,"Cannot (yet) use charges with Kspace style EwaldDipole"); triclinic_check(); - + // no triclinic ewald dipole (yet) - + triclinic = domain->triclinic; if (triclinic) error->all(FLERR,"Cannot (yet) use EwaldDipole with triclinic box"); - + if (domain->dimension == 2) error->all(FLERR,"Cannot use EwaldDipole with 2d simulation"); @@ -91,7 +91,7 @@ void EwaldDipole::init() if (dipoleflag && strcmp(update->unit_style,"electron") == 0) error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles"); - + if (slabflag == 0 && domain->nonperiodic > 0) error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldDipole"); if (slabflag) { @@ -154,13 +154,13 @@ void EwaldDipole::init() if (!gewaldflag) { if (accuracy <= 0.0) error->all(FLERR,"KSpace accuracy must be > 0"); - + // initial guess with old method - + g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*mu2); if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff; else g_ewald = sqrt(-log(g_ewald)) / cutoff; - + // try Newton solver double g_ewald_new = @@ -246,7 +246,7 @@ void EwaldDipole::setup() double err; kxmax = 1; kymax = 1; - kzmax = 1; + kzmax = 1; // set kmax in 3 directions to respect accuracy @@ -340,7 +340,7 @@ double EwaldDipole::rms_dipole(int km, double prd, bigint natoms) if (natoms == 0) natoms = 1; // avoid division by zero // error from eq.(46), Wang et al., JCP 115, 6351 (2001) - + double value = 8*MY_PI*mu2*g_ewald/volume * sqrt(2*MY_PI*km*km*km/(15.0*natoms)) * exp(-MY_PI*MY_PI*km*km/(g_ewald*g_ewald*prd*prd)); @@ -410,7 +410,7 @@ void EwaldDipole::compute(int eflag, int vflag) int kx,ky,kz; double cypz,sypz,exprl,expim; - double partial,partial2,partial_peratom; + double partial,partial_peratom; double vcik[6]; double mudotk; @@ -428,7 +428,7 @@ void EwaldDipole::compute(int eflag, int vflag) for (i = 0; i < nlocal; i++) { for (j = 0; j<6; j++) vcik[j] = 0.0; - + // re-evaluating mu dot k mudotk = mu[i][0]*kx*unitk[0] + mu[i][1]*ky*unitk[1] + mu[i][2]*kz*unitk[2]; @@ -461,7 +461,7 @@ void EwaldDipole::compute(int eflag, int vflag) vc[k][3] += vcik[3] = -(partial_peratom * mu[i][0] * eg[k][1]); vc[k][4] += vcik[4] = -(partial_peratom * mu[i][0] * eg[k][2]); vc[k][5] += vcik[5] = -(partial_peratom * mu[i][1] * eg[k][2]); - + // taking re-part of struct_fact x exp(i*k*ri) // (for per-atom energy and virial calc.) @@ -469,7 +469,7 @@ void EwaldDipole::compute(int eflag, int vflag) if (eflag_atom) eatom[i] += mudotk*ug[k]*partial_peratom; if (vflag_atom) for (j = 0; j < 6; j++) - vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]); + vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]); } } } @@ -503,7 +503,7 @@ void EwaldDipole::compute(int eflag, int vflag) // global virial if (vflag_global) { - double uk, vk; + double uk; for (k = 0; k < kcount; k++) { uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]); for (j = 0; j < 6; j++) virial[j] += uk*vg[k][j] - vc[k][j]; @@ -518,7 +518,7 @@ void EwaldDipole::compute(int eflag, int vflag) if (eflag_atom) { for (i = 0; i < nlocal; i++) { eatom[i] -= (mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2]) - *2.0*g3/3.0/MY_PIS; + *2.0*g3/3.0/MY_PIS; eatom[i] *= muscale; } } @@ -556,7 +556,7 @@ void EwaldDipole::eik_dot_r() // loop on n kpoints and nlocal atoms // (k,0,0), (0,l,0), (0,0,m) - + // loop 1: k=1, l=1, m=1 // define first val. of cos and sin @@ -596,7 +596,7 @@ void EwaldDipole::eik_dot_r() cs[m-1][ic][i]*sn[1][ic][i]; cs[-m][ic][i] = cs[m][ic][i]; sn[-m][ic][i] = -sn[m][ic][i]; - mudotk = (mu[i][ic]*m*unitk[ic]); + mudotk = (mu[i][ic]*m*unitk[ic]); cstr1 += mudotk*cs[m][ic][i]; sstr1 += mudotk*sn[m][ic][i]; } @@ -617,19 +617,19 @@ void EwaldDipole::eik_dot_r() cstr2 = 0.0; sstr2 = 0.0; for (i = 0; i < nlocal; i++) { - mux = mu[i][0]; - muy = mu[i][1]; + mux = mu[i][0]; + muy = mu[i][1]; - // dir 1: (k,l,0) - mudotk = (mux*k*unitk[0] + muy*l*unitk[1]); + // dir 1: (k,l,0) + mudotk = (mux*k*unitk[0] + muy*l*unitk[1]); cstr1 += mudotk*(cs[k][0][i]*cs[l][1][i]-sn[k][0][i]*sn[l][1][i]); sstr1 += mudotk*(sn[k][0][i]*cs[l][1][i]+cs[k][0][i]*sn[l][1][i]); - - // dir 2: (k,-l,0) - mudotk = (mux*k*unitk[0] - muy*l*unitk[1]); + + // dir 2: (k,-l,0) + mudotk = (mux*k*unitk[0] - muy*l*unitk[1]); cstr2 += mudotk*(cs[k][0][i]*cs[l][1][i]+sn[k][0][i]*sn[l][1][i]); sstr2 += mudotk*(sn[k][0][i]*cs[l][1][i]-cs[k][0][i]*sn[l][1][i]); - } + } sfacrl[n] = cstr1; sfacim[n++] = sstr1; sfacrl[n] = cstr2; @@ -649,16 +649,16 @@ void EwaldDipole::eik_dot_r() cstr2 = 0.0; sstr2 = 0.0; for (i = 0; i < nlocal; i++) { - muy = mu[i][1]; - muz = mu[i][2]; + muy = mu[i][1]; + muz = mu[i][2]; - // dir 1: (0,l,m) - mudotk = (muy*l*unitk[1] + muz*m*unitk[2]); + // dir 1: (0,l,m) + mudotk = (muy*l*unitk[1] + muz*m*unitk[2]); cstr1 += mudotk*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]); sstr1 += mudotk*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]); - - // dir 2: (0,l,-m) - mudotk = (muy*l*unitk[1] - muz*m*unitk[2]); + + // dir 2: (0,l,-m) + mudotk = (muy*l*unitk[1] - muz*m*unitk[2]); cstr2 += mudotk*(cs[l][1][i]*cs[m][2][i]+sn[l][1][i]*sn[m][2][i]); sstr2 += mudotk*(sn[l][1][i]*cs[m][2][i]-cs[l][1][i]*sn[m][2][i]); } @@ -681,16 +681,16 @@ void EwaldDipole::eik_dot_r() cstr2 = 0.0; sstr2 = 0.0; for (i = 0; i < nlocal; i++) { - mux = mu[i][0]; - muz = mu[i][2]; + mux = mu[i][0]; + muz = mu[i][2]; - // dir 1: (k,0,m) - mudotk = (mux*k*unitk[0] + muz*m*unitk[2]); + // dir 1: (k,0,m) + mudotk = (mux*k*unitk[0] + muz*m*unitk[2]); cstr1 += mudotk*(cs[k][0][i]*cs[m][2][i]-sn[k][0][i]*sn[m][2][i]); sstr1 += mudotk*(sn[k][0][i]*cs[m][2][i]+cs[k][0][i]*sn[m][2][i]); - - // dir 2: (k,0,-m) - mudotk = (mux*k*unitk[0] - muz*m*unitk[2]); + + // dir 2: (k,0,-m) + mudotk = (mux*k*unitk[0] - muz*m*unitk[2]); cstr2 += mudotk*(cs[k][0][i]*cs[m][2][i]+sn[k][0][i]*sn[m][2][i]); sstr2 += mudotk*(sn[k][0][i]*cs[m][2][i]-cs[k][0][i]*sn[m][2][i]); } @@ -719,33 +719,33 @@ void EwaldDipole::eik_dot_r() cstr4 = 0.0; sstr4 = 0.0; for (i = 0; i < nlocal; i++) { - mux = mu[i][0]; - muy = mu[i][1]; - muz = mu[i][2]; + mux = mu[i][0]; + muy = mu[i][1]; + muz = mu[i][2]; - // dir 1: (k,l,m) - mudotk = (mux*k*unitk[0] + muy*l*unitk[1] + muz*m*unitk[2]); + // dir 1: (k,l,m) + mudotk = (mux*k*unitk[0] + muy*l*unitk[1] + muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr1 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr1 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); - // dir 2: (k,-l,m) - mudotk = (mux*k*unitk[0] - muy*l*unitk[1] + muz*m*unitk[2]); + // dir 2: (k,-l,m) + mudotk = (mux*k*unitk[0] - muy*l*unitk[1] + muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr2 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr2 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); - // dir 3: (k,l,-m) - mudotk = (mux*k*unitk[0] + muy*l*unitk[1] - muz*m*unitk[2]); + // dir 3: (k,l,-m) + mudotk = (mux*k*unitk[0] + muy*l*unitk[1] - muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr3 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr3 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); - // dir 4: (k,-l,-m) - mudotk = (mux*k*unitk[0] - muy*l*unitk[1] - muz*m*unitk[2]); + // dir 4: (k,-l,-m) + mudotk = (mux*k*unitk[0] - muy*l*unitk[1] - muz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr4 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); @@ -777,12 +777,10 @@ void EwaldDipole::slabcorr() { // compute local contribution to global dipole moment - double **x = atom->x; - double zprd = domain->zprd; - int nlocal = atom->nlocal; - double dipole = 0.0; double **mu = atom->mu; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) dipole += mu[i][2]; // sum local contributions to get global dipole moment diff --git a/src/KSPACE/ewald_dipole.h b/src/KSPACE/ewald_dipole.h index 741756487b812d093251730efe3fcf36f29fcb65..c8dd18565ce9429ebc6af0ec6af1ba440cd3ea71 100644 --- a/src/KSPACE/ewald_dipole.h +++ b/src/KSPACE/ewald_dipole.h @@ -34,10 +34,10 @@ class EwaldDipole : public Ewald { protected: double musum,musqsum,mu2; - double **tk; // field for torque - double **vc; // virial per k + double **tk; // field for torque + double **vc; // virial per k - void musum_musq(); + void musum_musq(); double rms_dipole(int, double, bigint); virtual void eik_dot_r(); void slabcorr(); diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index e7d67680a14fc903fc05912d7db1d68d9ecb50a3..531f4cdec5f39a72e0eb1f8d192f0b589e90d1fe 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -41,12 +41,12 @@ EwaldDipoleSpin::EwaldDipoleSpin(LAMMPS *lmp) : { dipoleflag = 0; spinflag = 1; - - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) - mub = 9.274e-4; // in A.Ang^2 - mu_0 = 785.15; // in eV/Ang/A^2 - mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz + + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + mub = 9.274e-4; // in A.Ang^2 + mu_0 = 785.15; // in eV/Ang/A^2 + mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 + mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } /* ---------------------------------------------------------------------- @@ -67,17 +67,17 @@ void EwaldDipoleSpin::init() } // error check - + spinflag = atom->sp?1:0; triclinic_check(); - + // no triclinic ewald spin (yet) - + triclinic = domain->triclinic; if (triclinic) error->all(FLERR,"Cannot (yet) use EwaldDipoleSpin with triclinic box"); - + if (domain->dimension == 2) error->all(FLERR,"Cannot use EwaldDipoleSpin with 2d simulation"); @@ -85,7 +85,7 @@ void EwaldDipoleSpin::init() if ((spinflag && strcmp(update->unit_style,"metal")) != 0) error->all(FLERR,"'metal' units have to be used with spins"); - + if (slabflag == 0 && domain->nonperiodic > 0) error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldDipoleSpin"); if (slabflag) { @@ -144,13 +144,13 @@ void EwaldDipoleSpin::init() if (!gewaldflag) { if (accuracy <= 0.0) error->all(FLERR,"KSpace accuracy must be > 0"); - + // initial guess with old method - + g_ewald = accuracy*sqrt(natoms*cutoff*xprd*yprd*zprd) / (2.0*mu2); if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/cutoff; else g_ewald = sqrt(-log(g_ewald)) / cutoff; - + // try Newton solver double g_ewald_new = @@ -236,7 +236,7 @@ void EwaldDipoleSpin::setup() double err; kxmax = 1; kymax = 1; - kzmax = 1; + kzmax = 1; // set kmax in 3 directions to respect accuracy @@ -384,7 +384,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) int kx,ky,kz; double cypz,sypz,exprl,expim; - double partial,partial2,partial_peratom; + double partial,partial_peratom; double vcik[6]; double mudotk; @@ -404,7 +404,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) for (j = 0; j<6; j++) vcik[j] = 0.0; // re-evaluating sp dot k - + spx = sp[i][0]*sp[i][3]; spy = sp[i][1]*sp[i][3]; spz = sp[i][2]*sp[i][3]; @@ -427,19 +427,19 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) // compute field for torque calculation partial_peratom = exprl*sfacrl_all[k] + expim*sfacim_all[k]; - tk[i][0] += partial2*eg[k][0]; - tk[i][1] += partial2*eg[k][1]; - tk[i][2] += partial2*eg[k][2]; + tk[i][0] += partial_peratom*eg[k][0]; + tk[i][1] += partial_peratom*eg[k][1]; + tk[i][2] += partial_peratom*eg[k][2]; // total and per-atom virial correction - + vc[k][0] += vcik[0] = -(partial_peratom * spx * eg[k][0]); vc[k][1] += vcik[1] = -(partial_peratom * spy * eg[k][1]); vc[k][2] += vcik[2] = -(partial_peratom * spz * eg[k][2]); vc[k][3] += vcik[3] = -(partial_peratom * spx * eg[k][1]); vc[k][4] += vcik[4] = -(partial_peratom * spx * eg[k][2]); vc[k][5] += vcik[5] = -(partial_peratom * spy * eg[k][2]); - + // taking re-part of struct_fact x exp(i*k*ri) // (for per-atom energy and virial calc.) @@ -447,13 +447,13 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) if (eflag_atom) eatom[i] += mudotk*ug[k]*partial_peratom; if (vflag_atom) for (j = 0; j < 6; j++) - vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]); + vatom[i][j] += (ug[k]*mudotk*vg[k][j]*partial_peratom - vcik[j]); } } } // force and mag. precession vectors calculation - + const double spscale = mub2mu0 * scale; const double spscale2 = mub2mu0hbinv * scale; @@ -465,7 +465,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) fm_long[i][1] += spscale2 * tk[i][1]; if (slabflag != 2) fm_long[i][2] += spscale2 * tk[i][3]; } - + // sum global energy across Kspace vevs and add in volume-dependent term // taking the re-part of struct_fact_i x struct_fact_j // substracting self energy and scaling @@ -482,7 +482,7 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) // global virial if (vflag_global) { - double uk, vk; + double uk; for (k = 0; k < kcount; k++) { uk = ug[k] * (sfacrl_all[k]*sfacrl_all[k] + sfacim_all[k]*sfacim_all[k]); for (j = 0; j < 6; j++) virial[j] += uk*vg[k][j] - vc[k][j]; @@ -496,11 +496,11 @@ void EwaldDipoleSpin::compute(int eflag, int vflag) if (evflag_atom) { if (eflag_atom) { for (i = 0; i < nlocal; i++) { - spx = sp[i][0]*sp[i][3]; - spy = sp[i][1]*sp[i][3]; - spz = sp[i][2]*sp[i][3]; + spx = sp[i][0]*sp[i][3]; + spy = sp[i][1]*sp[i][3]; + spz = sp[i][2]*sp[i][3]; eatom[i] -= (spx*spx + spy*spy + spz*spz) - *2.0*g3/3.0/MY_PIS; + *2.0*g3/3.0/MY_PIS; eatom[i] *= spscale; } } @@ -540,7 +540,7 @@ void EwaldDipoleSpin::eik_dot_r() // store n values of sum_j[ (mu_j dot k) exp(-k dot r_j) ] // (k,0,0), (0,l,0), (0,0,m) - + // loop 1: k=1, l=1, m=1 // define first val. of cos and sin @@ -556,7 +556,7 @@ void EwaldDipoleSpin::eik_dot_r() sn[1][ic][i] = sin(unitk[ic]*x[i][ic]); cs[-1][ic][i] = cs[1][ic][i]; sn[-1][ic][i] = -sn[1][ic][i]; - spi = sp[i][ic]*sp[i][3]; + spi = sp[i][ic]*sp[i][3]; mudotk = (spi*unitk[ic]); cstr1 += mudotk*cs[1][ic][i]; sstr1 += mudotk*sn[1][ic][i]; @@ -581,8 +581,8 @@ void EwaldDipoleSpin::eik_dot_r() cs[m-1][ic][i]*sn[1][ic][i]; cs[-m][ic][i] = cs[m][ic][i]; sn[-m][ic][i] = -sn[m][ic][i]; - spi = sp[i][ic]*sp[i][3]; - mudotk = (spi*m*unitk[ic]); + spi = sp[i][ic]*sp[i][3]; + mudotk = (spi*m*unitk[ic]); cstr1 += mudotk*cs[m][ic][i]; sstr1 += mudotk*sn[m][ic][i]; } @@ -603,19 +603,19 @@ void EwaldDipoleSpin::eik_dot_r() cstr2 = 0.0; sstr2 = 0.0; for (i = 0; i < nlocal; i++) { - spx = sp[i][0]*sp[i][3]; - spy = sp[i][1]*sp[i][3]; + spx = sp[i][0]*sp[i][3]; + spy = sp[i][1]*sp[i][3]; - // dir 1: (k,l,0) - mudotk = (spx*k*unitk[0] + spy*l*unitk[1]); + // dir 1: (k,l,0) + mudotk = (spx*k*unitk[0] + spy*l*unitk[1]); cstr1 += mudotk*(cs[k][0][i]*cs[l][1][i]-sn[k][0][i]*sn[l][1][i]); sstr1 += mudotk*(sn[k][0][i]*cs[l][1][i]+cs[k][0][i]*sn[l][1][i]); - - // dir 2: (k,-l,0) - mudotk = (spx*k*unitk[0] - spy*l*unitk[1]); + + // dir 2: (k,-l,0) + mudotk = (spx*k*unitk[0] - spy*l*unitk[1]); cstr2 += mudotk*(cs[k][0][i]*cs[l][1][i]+sn[k][0][i]*sn[l][1][i]); sstr2 += mudotk*(sn[k][0][i]*cs[l][1][i]-cs[k][0][i]*sn[l][1][i]); - } + } sfacrl[n] = cstr1; sfacim[n++] = sstr1; sfacrl[n] = cstr2; @@ -635,16 +635,16 @@ void EwaldDipoleSpin::eik_dot_r() cstr2 = 0.0; sstr2 = 0.0; for (i = 0; i < nlocal; i++) { - spy = sp[i][1]*sp[i][3]; - spz = sp[i][2]*sp[i][3]; + spy = sp[i][1]*sp[i][3]; + spz = sp[i][2]*sp[i][3]; - // dir 1: (0,l,m) - mudotk = (spy*l*unitk[1] + spz*m*unitk[2]); + // dir 1: (0,l,m) + mudotk = (spy*l*unitk[1] + spz*m*unitk[2]); cstr1 += mudotk*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]); sstr1 += mudotk*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]); - - // dir 2: (0,l,-m) - mudotk = (spy*l*unitk[1] - spz*m*unitk[2]); + + // dir 2: (0,l,-m) + mudotk = (spy*l*unitk[1] - spz*m*unitk[2]); cstr2 += mudotk*(cs[l][1][i]*cs[m][2][i]+sn[l][1][i]*sn[m][2][i]); sstr2 += mudotk*(sn[l][1][i]*cs[m][2][i]-cs[l][1][i]*sn[m][2][i]); } @@ -667,16 +667,16 @@ void EwaldDipoleSpin::eik_dot_r() cstr2 = 0.0; sstr2 = 0.0; for (i = 0; i < nlocal; i++) { - spx = sp[i][0]*sp[i][3]; - spz = sp[i][2]*sp[i][3]; + spx = sp[i][0]*sp[i][3]; + spz = sp[i][2]*sp[i][3]; - // dir 1: (k,0,m) - mudotk = (spx*k*unitk[0] + spz*m*unitk[2]); + // dir 1: (k,0,m) + mudotk = (spx*k*unitk[0] + spz*m*unitk[2]); cstr1 += mudotk*(cs[k][0][i]*cs[m][2][i]-sn[k][0][i]*sn[m][2][i]); sstr1 += mudotk*(sn[k][0][i]*cs[m][2][i]+cs[k][0][i]*sn[m][2][i]); - - // dir 2: (k,0,-m) - mudotk = (spx*k*unitk[0] - spz*m*unitk[2]); + + // dir 2: (k,0,-m) + mudotk = (spx*k*unitk[0] - spz*m*unitk[2]); cstr2 += mudotk*(cs[k][0][i]*cs[m][2][i]+sn[k][0][i]*sn[m][2][i]); sstr2 += mudotk*(sn[k][0][i]*cs[m][2][i]-cs[k][0][i]*sn[m][2][i]); } @@ -705,33 +705,33 @@ void EwaldDipoleSpin::eik_dot_r() cstr4 = 0.0; sstr4 = 0.0; for (i = 0; i < nlocal; i++) { - spx = sp[i][0]*sp[i][3]; - spy = sp[i][1]*sp[i][3]; - spz = sp[i][2]*sp[i][3]; + spx = sp[i][0]*sp[i][3]; + spy = sp[i][1]*sp[i][3]; + spz = sp[i][2]*sp[i][3]; - // dir 1: (k,l,m) - mudotk = (spx*k*unitk[0] + spy*l*unitk[1] + spz*m*unitk[2]); + // dir 1: (k,l,m) + mudotk = (spx*k*unitk[0] + spy*l*unitk[1] + spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr1 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr1 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); - // dir 2: (k,-l,m) - mudotk = (spx*k*unitk[0] - spy*l*unitk[1] + spz*m*unitk[2]); + // dir 2: (k,-l,m) + mudotk = (spx*k*unitk[0] - spy*l*unitk[1] + spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]; cstr2 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr2 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); - // dir 3: (k,l,-m) - mudotk = (spx*k*unitk[0] + spy*l*unitk[1] - spz*m*unitk[2]); + // dir 3: (k,l,-m) + mudotk = (spx*k*unitk[0] + spy*l*unitk[1] - spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]; slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr3 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); sstr3 += mudotk*(sn[k][0][i]*clpm + cs[k][0][i]*slpm); - // dir 4: (k,-l,-m) - mudotk = (spx*k*unitk[0] - spy*l*unitk[1] - spz*m*unitk[2]); + // dir 4: (k,-l,-m) + mudotk = (spx*k*unitk[0] - spy*l*unitk[1] - spz*m*unitk[2]); clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]; slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]; cstr4 += mudotk*(cs[k][0][i]*clpm - sn[k][0][i]*slpm); @@ -763,13 +763,11 @@ void EwaldDipoleSpin::slabcorr() { // compute local contribution to global dipole/spin moment - double **x = atom->x; - double zprd = domain->zprd; - int nlocal = atom->nlocal; - double spin = 0.0; double **sp = atom->sp; - double spx,spy,spz; + double spz; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { spz = sp[i][2]*sp[i][3]; spin += spz; diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index a7ac66fdd3fe68f8847ef7629130dbe8d3a223b2..a24ee4203c8e62c8fe5d43b6a6b61b09774e7382 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -131,6 +131,7 @@ void EwaldDisp::init() else if (ewald_mix==Pair::ARITHMETIC) { k = 2; break; } error->all(FLERR, "Unsupported mixing rule in kspace_style ewald/disp"); + break; default: error->all(FLERR,"Unsupported order in kspace_style ewald/disp"); } diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index cfd88609b3a14cf3008c7e8e16aff67e9afcadb3..a3a495621401a040f9432eac2673147537824e67 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -29,6 +29,7 @@ #include "neighbor.h" #include "modify.h" #include "compute.h" + #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) #define GOLD 1.618034 diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index e248a24ef73370de57e7638f334118d69789848e..b5b3eda64ff6000ef14f3f7ec2dc5ceeed51ad69 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -421,16 +422,16 @@ void PairBornCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&d[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -464,13 +465,13 @@ void PairBornCoulLong::write_restart_settings(FILE *fp) void PairBornCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index c97856fa3cfd7fad2bbd9220927d0b39179f0958..a46424baf7fa1c10322a4cc91f277fbbc9b062bb 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -24,6 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -399,14 +400,14 @@ void PairBuckCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -438,13 +439,13 @@ void PairBuckCoulLong::write_restart_settings(FILE *fp) void PairBuckCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 8127cbc1271645865dcd34671f37c976eba452d3..7f369045c37312754598ebf87b3fb1b13c54e7d9 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -31,6 +31,7 @@ #include "respa.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -65,10 +66,10 @@ void PairBuckLongCoulLong::options(char **arg, int order) if (!*arg) error->all(FLERR,"Illegal pair_style buck/long/coul/long command"); for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i); switch (i) { - default: error->all(FLERR,"Illegal pair_style buck/long/coul/long command"); case 0: ewald_order |= 1<all(FLERR,"Illegal pair_style buck/long/coul/long command"); } } @@ -355,14 +356,14 @@ void PairBuckLongCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&buck_a_read[i][j],sizeof(double),1,fp); - fread(&buck_rho_read[i][j],sizeof(double),1,fp); - fread(&buck_c_read[i][j],sizeof(double),1,fp); - fread(&cut_buck_read[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&buck_a_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck_rho_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck_c_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_buck_read[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&buck_a_read[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&buck_rho_read[i][j],1,MPI_DOUBLE,0,world); @@ -394,13 +395,13 @@ void PairBuckLongCoulLong::write_restart_settings(FILE *fp) void PairBuckLongCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_buck_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); - fread(&ewald_order,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_buck_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_buck_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 7cedf3d003a34a465e71c743662f7bb085a34d91..004835007d2eb9500a4522dabeb1f2df27c0c8cc 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -27,6 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -289,10 +290,10 @@ void PairCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) fread(&scale[i][j],sizeof(double),1,fp); + if (me == 0) utils::sfread(FLERR,&scale[i][j],sizeof(double),1,fp,NULL,error); MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world); } } @@ -318,11 +319,11 @@ void PairCoulLong::write_restart_settings(FILE *fp) void PairCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index 751ee77388965c1183cd9388634615cffaa0d43c..22ed923b491cb3dc2ede0d868485d4a5250f52f2 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -29,6 +29,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -822,14 +823,14 @@ void PairLJCharmmCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&eps14[i][j],sizeof(double),1,fp); - fread(&sigma14[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -861,13 +862,13 @@ void PairLJCharmmCoulLong::write_restart_settings(FILE *fp) void PairLJCharmmCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_inner,sizeof(double),1,fp); - fread(&cut_lj,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 494a3497686572dbafe2bd50cdb93a6704713963..ce7fda5f188d29c87c7dff49afeaad4f7d56bced 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -33,6 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -889,14 +890,14 @@ void PairLJCharmmfswCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&eps14[i][j],sizeof(double),1,fp); - fread(&sigma14[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -928,13 +929,13 @@ void PairLJCharmmfswCoulLong::write_restart_settings(FILE *fp) void PairLJCharmmfswCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_inner,sizeof(double),1,fp); - fread(&cut_lj,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index fb79451b375a3c9ab5ad407321667c1cf24a9a27..23e182435d6131afa303b02422247e3a23c2f800 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -31,6 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -793,13 +794,13 @@ void PairLJCutCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -830,13 +831,13 @@ void PairLJCutCoulLong::write_restart_settings(FILE *fp) void PairLJCutCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index c98092f19b455d9cd9907c5ca3d48ac277c4638e..a4f115568fedec88f7581ad2337a6447cc8a350f 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -30,6 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -528,19 +529,19 @@ void PairLJCutTIP4PLong::write_restart_settings(FILE *fp) void PairLJCutTIP4PLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 610fc4e89b5d6c29e6f32dbaeea6e17b58466ca3..4af3cdeecd2381903c009f6dff633bd2a769ab47 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -33,6 +33,7 @@ #include "respa.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -68,10 +69,10 @@ void PairLJLongCoulLong::options(char **arg, int order) if (!*arg) error->all(FLERR,"Illegal pair_style lj/long/coul/long command"); for (i=0; option[i]&&strcmp(arg[0], option[i]); ++i); switch (i) { - default: error->all(FLERR,"Illegal pair_style lj/long/coul/long command"); case 0: ewald_order |= 1<all(FLERR,"Illegal pair_style lj/long/coul/long command"); } } @@ -355,13 +356,13 @@ void PairLJLongCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon_read[i][j],sizeof(double),1,fp); - fread(&sigma_read[i][j],sizeof(double),1,fp); - fread(&cut_lj_read[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma_read[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_read[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon_read[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma_read[i][j],1,MPI_DOUBLE,0,world); @@ -392,13 +393,13 @@ void PairLJLongCoulLong::write_restart_settings(FILE *fp) void PairLJLongCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); - fread(&ewald_order,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&ewald_order,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index 08409dce72b038abe92a95ac5c932e4efe3ecb68..b46fb6489817410b14c4ff43ca1d4a6c2d028176 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -30,6 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -1539,18 +1540,18 @@ void PairLJLongTIP4PLong::write_restart_settings(FILE *fp) void PairLJLongTIP4PLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index 2c47f42beb2e440483cd4523c58f4589a9657e2a..c3ec44b7eb0169aded889fbef138abf3df542b4f 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -30,6 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -467,11 +468,11 @@ void PairTIP4PLong::read_restart_settings(FILE *fp) PairCoulLong::read_restart_settings(fp); if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 0eb761d9bef3e3142239c04e5b6feddb86f9be37..5d69ca27b6112d28a39d8420910fe8d3263a7585 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -59,11 +59,11 @@ enum{FORWARD_MU,FORWARD_MU_PERATOM}; PPPMDipole::PPPMDipole(LAMMPS *lmp) : PPPM(lmp), densityx_brick_dipole(NULL), densityy_brick_dipole(NULL), - densityz_brick_dipole(NULL), ux_brick_dipole(NULL), - uy_brick_dipole(NULL), uz_brick_dipole(NULL), vdxx_brick_dipole(NULL), - vdxy_brick_dipole(NULL), vdyy_brick_dipole(NULL), - vdxz_brick_dipole(NULL), vdyz_brick_dipole(NULL), - vdzz_brick_dipole(NULL), v0x_brick_dipole(NULL), v1x_brick_dipole(NULL), + densityz_brick_dipole(NULL), + vdxx_brick_dipole(NULL), vdyy_brick_dipole(NULL), vdzz_brick_dipole(NULL), + vdxy_brick_dipole(NULL), vdxz_brick_dipole(NULL), vdyz_brick_dipole(NULL), + ux_brick_dipole(NULL), uy_brick_dipole(NULL), uz_brick_dipole(NULL), + v0x_brick_dipole(NULL), v1x_brick_dipole(NULL), v2x_brick_dipole(NULL), v3x_brick_dipole(NULL), v4x_brick_dipole(NULL), v5x_brick_dipole(NULL), v0y_brick_dipole(NULL), v1y_brick_dipole(NULL), v2y_brick_dipole(NULL), v3y_brick_dipole(NULL), v4y_brick_dipole(NULL), @@ -534,10 +534,8 @@ void PPPMDipole::compute(int eflag, int vflag) // energy includes self-energy correction if (evflag_atom) { - double *q = atom->q; double **mu = atom->mu; int nlocal = atom->nlocal; - int ntotal = nlocal; if (eflag_atom) { for (i = 0; i < nlocal; i++) { @@ -836,7 +834,7 @@ void PPPMDipole::set_grid_global() while (1) { // set grid dimension - + nx_pppm = static_cast (xprd/h_x); ny_pppm = static_cast (yprd/h_y); nz_pppm = static_cast (zprd_slab/h_z); @@ -846,7 +844,7 @@ void PPPMDipole::set_grid_global() if (nz_pppm <= 1) nz_pppm = 2; // set local grid dimension - + int npey_fft,npez_fft; if (nz_pppm >= nprocs) { npey_fft = 1; @@ -926,11 +924,10 @@ double PPPMDipole::compute_qopt_dipole() const double unitkz = (MY_2PI/zprd_slab); double snx,sny,snz; - double cnx,cny,cnz; double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz; double sum1,sum2,dot1,dot2; - double numerator,denominator; - double u1,u2,u3,sqk; + double denominator; + double u1,sqk; int k,l,m,nx,ny,nz,kper,lper,mper; @@ -943,22 +940,18 @@ double PPPMDipole::compute_qopt_dipole() for (m = nzlo_fft; m <= nzhi_fft; m++) { mper = m - nz_pppm*(2*m/nz_pppm); snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm)); - cnz = cos(0.5*unitkz*mper*zprd_slab/nz_pppm); for (l = nylo_fft; l <= nyhi_fft; l++) { lper = l - ny_pppm*(2*l/ny_pppm); sny = square(sin(0.5*unitky*lper*yprd/ny_pppm)); - cny = cos(0.5*unitky*lper*yprd/ny_pppm); for (k = nxlo_fft; k <= nxhi_fft; k++) { kper = k - nx_pppm*(2*k/nx_pppm); snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm)); - cnx = cos(0.5*unitkx*kper*xprd/nx_pppm); sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper); if (sqk != 0.0) { - numerator = MY_4PI/sqk; denominator = gf_denom(snx,sny,snz); sum1 = 0.0; sum2 = 0.0; @@ -1021,10 +1014,9 @@ void PPPMDipole::compute_gf_dipole() const double unitkz = (MY_2PI/zprd_slab); double snx,sny,snz; - double cnx,cny,cnz; double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz; double sum1,dot1,dot2; - double numerator,denominator; + double denominator; double sqk; int k,l,m,n,nx,ny,nz,kper,lper,mper; @@ -1044,22 +1036,18 @@ void PPPMDipole::compute_gf_dipole() for (m = nzlo_fft; m <= nzhi_fft; m++) { mper = m - nz_pppm*(2*m/nz_pppm); snz = square(sin(0.5*unitkz*mper*zprd_slab/nz_pppm)); - cnz = cos(0.5*unitkz*mper*zprd_slab/nz_pppm); for (l = nylo_fft; l <= nyhi_fft; l++) { lper = l - ny_pppm*(2*l/ny_pppm); sny = square(sin(0.5*unitky*lper*yprd/ny_pppm)); - cny = cos(0.5*unitky*lper*yprd/ny_pppm); for (k = nxlo_fft; k <= nxhi_fft; k++) { kper = k - nx_pppm*(2*k/nx_pppm); snx = square(sin(0.5*unitkx*kper*xprd/nx_pppm)); - cnx = cos(0.5*unitkx*kper*xprd/nx_pppm); sqk = square(unitkx*kper) + square(unitky*lper) + square(unitkz*mper); if (sqk != 0.0) { - numerator = MY_4PI/sqk; denominator = gf_denom(snx,sny,snz); sum1 = 0.0; @@ -2389,12 +2377,10 @@ void PPPMDipole::slabcorr() { // compute local contribution to global dipole moment - double **x = atom->x; - double zprd = domain->zprd; - int nlocal = atom->nlocal; - double dipole = 0.0; double **mu = atom->mu; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) dipole += mu[i][2]; // sum local contributions to get global dipole moment @@ -2519,7 +2505,7 @@ double PPPMDipole::memory_usage() int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) * (nzhi_out-nzlo_out+1); bytes += 6 * nfft_both * sizeof(double); // vg - bytes += nfft_both * sizeof(double); // greensfn + bytes += nfft_both * sizeof(double); // greensfn bytes += nfft_both*5 * sizeof(FFT_SCALAR); // work*2*2 bytes += 9 * nbrick * sizeof(FFT_SCALAR); // ubrick*3 + vdbrick*6 bytes += nfft_both*7 * sizeof(FFT_SCALAR); // density_ffx*3 + work*2*2 diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 9e9f07322c2cde472a50dc82bb48ab14826f64d7..38757ced217cacff9d884a14196d9593e477e689 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -57,12 +57,12 @@ PPPMDipoleSpin::PPPMDipoleSpin(LAMMPS *lmp) : { dipoleflag = 0; spinflag = 1; - - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) - mub = 9.274e-4; // in A.Ang^2 - mu_0 = 785.15; // in eV/Ang/A^2 - mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz + + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + mub = 9.274e-4; // in A.Ang^2 + mu_0 = 785.15; // in eV/Ang/A^2 + mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 + mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } /* ---------------------------------------------------------------------- @@ -95,7 +95,7 @@ void PPPMDipoleSpin::init() // error check spinflag = atom->sp?1:0; - + triclinic_check(); if (triclinic != domain->triclinic) @@ -146,7 +146,7 @@ void PPPMDipoleSpin::init() // kspace TIP4P not yet supported // qdist = offset only for TIP4P fictitious charge - + qdist = 0.0; if (tip4pflag) error->all(FLERR,"Cannot yet use TIP4P with PPPMDipoleSpin"); @@ -177,7 +177,7 @@ void PPPMDipoleSpin::init() GridComm *cgtmp = NULL; int iteration = 0; - + while (order >= minorder) { if (iteration && me == 0) error->warning(FLERR,"Reducing PPPMDipoleSpin order b/c stencil extends " @@ -390,9 +390,9 @@ void PPPMDipoleSpin::compute(int eflag, int vflag) if (eflag_atom) { for (i = 0; i < nlocal; i++) { - spx = sp[i][0]*sp[i][3]; - spy = sp[i][1]*sp[i][3]; - spz = sp[i][2]*sp[i][3]; + spx = sp[i][0]*sp[i][3]; + spy = sp[i][1]*sp[i][3]; + spz = sp[i][2]*sp[i][3]; eatom[i] *= 0.5; eatom[i] -= (spx*spx + spy*spy + spz*spz)*2.0*g3/3.0/MY_PIS; eatom[i] *= spscale; @@ -552,7 +552,7 @@ void PPPMDipoleSpin::fieldforce_ik_spin() f[i][2] += spfactor*(vxz*spx + vyz*spy + vzz*spz); // store long-range mag. precessions - + const double spfactorh = mub2mu0hbinv * scale; fm_long[i][0] += spfactorh*ex; fm_long[i][1] += spfactorh*ey; @@ -663,13 +663,11 @@ void PPPMDipoleSpin::slabcorr() { // compute local contribution to global spin moment - double **x = atom->x; - double zprd = domain->zprd; - int nlocal = atom->nlocal; - double spin = 0.0; double **sp = atom->sp; - double spx,spy,spz; + double spz; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { spz = sp[i][2]*sp[i][3]; spin += spz; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index c30d55dd68aadffac42cd219faad6790690ed99a..abc33b90fa6448dae1c74a48af655c156725a18c 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -320,6 +320,8 @@ void PPPMDisp::init() mixflag == 1) && mixflag!= 2) { k = 1; break; } else if (ewald_mix==Pair::ARITHMETIC && mixflag!=2) { k = 2; break; } else if (mixflag == 2) { k = 3; break; } + else error->all(FLERR,"Unsupported mixing rule in kspace_style pppm/disp"); + break; default: sprintf(str, "Unsupported order in kspace_style " "pppm/disp, pair_style %s", force->pair_style); diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index f664a0dca3b0d2c45a30c8bac943389784b18612..5a0ced3674b1b81367d84f13bebee6f4a7cd5db0 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -500,11 +500,18 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM) // since local atoms are in lambda coordinates, but ghosts are not. int *sametag = atom->sametag; - double xo[3],xh1[3],xh2[3]; + double xo[3],xh1[3],xh2[3],xm[3]; + const int nlocal = atom->nlocal; - domain->lamda2x(x[i],xo); - domain->lamda2x(x[iH1],xh1); - domain->lamda2x(x[iH2],xh2); + for (int ii = 0; ii < 3; ++ii) { + xo[ii] = x[i][ii]; + xh1[ii] = x[iH1][ii]; + xh2[ii] = x[iH2][ii]; + } + + if (i < nlocal) domain->lamda2x(x[i],xo); + if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1); + if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2); double delx = xo[0] - xh1[0]; double dely = xo[1] - xh1[1]; @@ -513,6 +520,8 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM) double rsq; int closest = iH1; + // no need to run lamda2x() here -> ghost atoms + while (sametag[iH1] >= 0) { iH1 = sametag[iH1]; delx = xo[0] - x[iH1][0]; @@ -561,13 +570,13 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM) double dely2 = xh2[1] - xo[1]; double delz2 = xh2[2] - xo[2]; - xM[0] = xo[0] + alpha * 0.5 * (delx1 + delx2); - xM[1] = xo[1] + alpha * 0.5 * (dely1 + dely2); - xM[2] = xo[2] + alpha * 0.5 * (delz1 + delz2); + xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2); + xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2); + xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2); // ... and convert M to lamda space for PPPM - domain->x2lamda(xM,xM); + domain->x2lamda(xm,xM); } else { diff --git a/src/MAKE/MACHINES/Makefile.astra_arm b/src/MAKE/MACHINES/Makefile.astra_arm new file mode 100644 index 0000000000000000000000000000000000000000..3734208936fcdb6777896257015305506385dbc7 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.astra_arm @@ -0,0 +1,119 @@ +# astra_arm - ThunderX2 ARM/OpenMPI Based, use Arm-PL for FFTW + +# need to load the following modules: +# 1) arm-based developer pack + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = mpicxx +CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99 +DEPFLAGS = -M +LINK = mpicxx +LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99 +LIB = -lstdc++ +ARCHIVE = ar +ARFLAGS = -rcsv +SIZE = size + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW2 -armpl +FFT_PATH = +FFT_LIB = + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.astra_gcc b/src/MAKE/MACHINES/Makefile.astra_gcc new file mode 100644 index 0000000000000000000000000000000000000000..3ee43800fcec8213cecc4d7fd3388511494f539c --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.astra_gcc @@ -0,0 +1,119 @@ +# astra-gcc - ThunderX2 GCC/OpenMPI Based, FFTW + +# need to load the following modules: +# 1) arm-based developer pack + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = mpicxx +CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99 +DEPFLAGS = -M +LINK = mpicxx +LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99 +LIB = -lstdc++ +ARCHIVE = ar +ARFLAGS = -rcsv +SIZE = size + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW2 -I${FFTW_INC} +FFT_PATH = -I${FFTW_INC} +FFT_LIB = -L${FFTW_LIB} -lfftw3 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.theta b/src/MAKE/MACHINES/Makefile.theta index cad5a03b420274d6f99eed1f2a730ee671638eb9..663f2120204b3c2144c1ffac32e68d9bbdaa1e29 100644 --- a/src/MAKE/MACHINES/Makefile.theta +++ b/src/MAKE/MACHINES/Makefile.theta @@ -1,7 +1,5 @@ -# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT -# module load perftools-base perftools +# theta = Flags for Knights Landing Xeon Phi Processor, Intel Compiler, Cray MPI, MKL FFT # make theta -j 8 -# pat_build -g mpi -u ./lmp_theta SHELL = /bin/sh @@ -10,24 +8,16 @@ SHELL = /bin/sh # specify flags and libraries needed for your compiler CC = CC -mkl -#OPTFLAGS = -O0 -OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits +OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \ -fno-alias -ansi-alias -restrict $(OPTFLAGS) -#CCFLAGS += -DLMP_INTEL_NO_TBB -#CCFLAGS += -DLAMMPS_BIGBIG -#CCFLAGS += -D_USE_PAPI -#CCFLAGS += -D_USE_CRAYPAT_API +CCFLAGS += -std=c++11 SHFLAGS = -fPIC DEPFLAGS = -M LINK = $(CC) -LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LINKFLAGS += -dynamic -LIB = -#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc -LIB += -ltbbmalloc -#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs +LINKFLAGS = -g -qopenmp $(OPTFLAGS) -dynamic +LIB = -ltbbmalloc SIZE = size ARCHIVE = ar @@ -99,35 +89,35 @@ vpath %.h .. # Link target $(EXE): $(OBJ) - $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) - $(SIZE) $(EXE) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) # Library targets lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) shlib: $(OBJ) - $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ - $(OBJ) $(EXTRA_LIB) $(LIB) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) # Compilation rules %.o:%.cpp - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp - $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ %.o:%.cu - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< # Individual dependencies depend : fastdep.exe $(SRC) - @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 fastdep.exe: ../DEPEND/fastdep.c - icc -O -o $@ $< + icc -O -o $@ $< sinclude .depend diff --git a/src/MAKE/Makefile.mpi b/src/MAKE/Makefile.mpi index f30220da3da303f77eb81578bcf34d65683bb35a..3be2e20f95516efde10794c82628ad637517f5f6 100644 --- a/src/MAKE/Makefile.mpi +++ b/src/MAKE/Makefile.mpi @@ -26,12 +26,12 @@ SHLIBFLAGS = -shared # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings -# see possible settings in Section 2.2 (step 4) of manual +# see possible settings in Section 3.5 of the manual -LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 +LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 # -DLAMMPS_CXX98 # MPI library -# see discussion in Section 2.2 (step 5) of manual +# see discussion in Section 3.4 of the manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts diff --git a/src/MAKE/Makefile.serial b/src/MAKE/Makefile.serial index 5954d97761333e7978d9732f7020fa4f34a53bdf..86ddd0505399443f110bd39632a0cc4f260d091b 100644 --- a/src/MAKE/Makefile.serial +++ b/src/MAKE/Makefile.serial @@ -26,12 +26,12 @@ SHLIBFLAGS = -shared # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings -# see possible settings in Section 2.2 (step 4) of manual +# see possible settings in Section 3.5 of the manual -LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 +LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 # -DLAMMPS_CXX98 # MPI library -# see discussion in Section 2.2 (step 5) of manual +# see discussion in Section 3.4 of the manual # MPI wrapper compiler/linker can provide this info # can point to dummy MPI library in src/STUBS as in Makefile.serial # use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts diff --git a/src/MAKE/OPTIONS/Makefile.intel_coprocessor b/src/MAKE/OPTIONS/Makefile.intel_coprocessor index 75e4d89170c5f2d2431dfe1151bd1b23b3a3bd14..44f5c99f709a2bf83ce2704012f0dd6ca66ef18f 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_coprocessor +++ b/src/MAKE/OPTIONS/Makefile.intel_coprocessor @@ -6,7 +6,7 @@ SHELL = /bin/sh # compiler/linker settings # specify flags and libraries needed for your compiler -CC = mpiicpc +CC = mpiicpc -std=c++11 MIC_OPT = -qoffload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" CCFLAGS = -g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \ -xHost -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT \ @@ -14,7 +14,7 @@ CCFLAGS = -g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \ SHFLAGS = -fPIC DEPFLAGS = -M -LINK = mpiicpc +LINK = mpiicpc -std=c++11 LINKFLAGS = -g -O3 -xHost -qopenmp -qoffload LIB = -ltbbmalloc SIZE = size diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu b/src/MAKE/OPTIONS/Makefile.intel_cpu index 831b16d85413aab7c01cbd398c27c278cbaaa858..f52b4f30292e7350f309e5a0ae11bd7ac624bdb7 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu @@ -6,15 +6,16 @@ SHELL = /bin/sh # compiler/linker settings # specify flags and libraries needed for your compiler -CC = mpiicpc +CC = mpiicpc -std=c++11 OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ -qopt-zmm-usage=high -CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \ - -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) +CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ + -I$(MKLROOT)/include SHFLAGS = -fPIC DEPFLAGS = -M -LINK = mpiicpc +LINK = mpiicpc -std=c++11 LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi index 926518f35452be99017aadd323c1da4ce0856381..07d720a5920e2e130ed22978e019b22c6692f7c7 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi @@ -6,15 +6,16 @@ SHELL = /bin/sh # compiler/linker settings # specify flags and libraries needed for your compiler -CC = mpiicpc +CC = mpiicpc -std=c++11 OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ -qopt-zmm-usage=high -CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \ - -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) +CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ + -I$(MKLROOT)/include SHFLAGS = -fPIC DEPFLAGS = -M -LINK = mpiicpc +LINK = mpiicpc -std=c++11 LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich index 61934b69b4dc9db1caa2c01a6a91e2395be53a50..51cf975e5c31de822544e0e8a2ae7a5a7d3da8ea 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_mpich @@ -6,15 +6,16 @@ SHELL = /bin/sh # compiler/linker settings # specify flags and libraries needed for your compiler -CC = mpicxx -cxx=icc +CC = mpicxx -cxx=icc -std=c++11 OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ -qopt-zmm-usage=high -CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \ - -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) +CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ + -I$(MKLROOT)/include SHFLAGS = -fPIC DEPFLAGS = -M -LINK = mpicxx -cxx=icc +LINK = mpicxx -cxx=icc -std=c++11 LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size diff --git a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi index ee26443f7da617d79995af1a61a08f09b1ef316e..342637a460f37ec650c6075a7adc8e1f1a08f6cf 100644 --- a/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi +++ b/src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi @@ -7,15 +7,16 @@ SHELL = /bin/sh # specify flags and libraries needed for your compiler export OMPI_CXX = icc -CC = mpicxx +CC = mpicxx -std=c++11 OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ -qopt-zmm-usage=high -CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \ - -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) +CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ + -I$(MKLROOT)/include SHFLAGS = -fPIC DEPFLAGS = -M -LINK = mpicxx +LINK = mpicxx -std=c++11 LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size diff --git a/src/MAKE/OPTIONS/Makefile.knl b/src/MAKE/OPTIONS/Makefile.knl index 8e266a4fce859e58e661080e6bd446489a7dec1d..ab1b756a676124b3e720caed28b3570f1f3ce081 100644 --- a/src/MAKE/OPTIONS/Makefile.knl +++ b/src/MAKE/OPTIONS/Makefile.knl @@ -6,16 +6,17 @@ SHELL = /bin/sh # compiler/linker settings # specify flags and libraries needed for your compiler -CC = mpiicpc +CC = mpiicpc -std=c++11 OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -CCFLAGS = -qopenmp -qno-offload -fno-alias -ansi-alias -restrict \ - -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) +CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ + -I$(MKLROOT)/include SHFLAGS = -fPIC DEPFLAGS = -M -LINK = mpiicpc -LINKFLAGS = -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc +LINK = mpiicpc -std=c++11 +LINKFLAGS = -qopenmp $(OPTFLAGS) -L$(MKLROOT)/lib/intel64/ +LIB = -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core SIZE = size ARCHIVE = ar @@ -54,8 +55,7 @@ MPI_LIB = FFT_INC = -DFFT_MKL -DFFT_SINGLE FFT_PATH = -FFT_LIB = -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \ - -lmkl_sequential -lmkl_core +FFT_LIB = # JPEG and/or PNG library # see discussion in Section 2.2 (step 7) of manual diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index fcc3a3efd24a0b607a898543f9e8bcbd30839695..7cdffa7ea9d6dd78fe21edd8b318d222d8b097a4 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -3391,8 +3391,8 @@ void PairAIREBO::read_file(char *filename) // skip initial comment line and check for potential file style identifier comment - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (((variant == AIREBO) && (strncmp(s,"# AIREBO ",9) != 0)) || ((variant == REBO_2) && (strncmp(s,"# REBO2 ",8) != 0)) diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index e604f44003c6d8ff0747d39d4325fe8758eaa9ab..e943b6bfddbc318e0ae21723cad4be6af76404f6 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -27,6 +27,7 @@ #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -310,10 +311,10 @@ void PairATM::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) { - if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp); + if (me == 0) utils::sfread(FLERR,&nu[i][j][k],sizeof(double),1,fp,NULL,error); MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world); } } @@ -338,8 +339,8 @@ void PairATM::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&cut_triple,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_triple,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_triple,1,MPI_DOUBLE,0,world); diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 6b7468558e6dd7c73d326570944f05b2733ffa7f..1b08e4b88dd67ec6b6b879c83615e5616e81ab5e 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -45,6 +45,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -61,6 +62,10 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp) manybody_flag = 1; ghostneigh = 1; + BOP_index = NULL; + BOP_index3 = NULL; + BOP_total = NULL; + BOP_total3 = NULL; map = NULL; pi_a = NULL; pro_delta = NULL; @@ -102,6 +107,8 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp) rij = NULL; neigh_index = NULL; neigh_index3 = NULL; + neigh_flag = NULL; + neigh_flag3 = NULL; cosAng = NULL; betaS = NULL; dBetaS = NULL; @@ -4976,13 +4983,13 @@ void PairBOP::read_table(char *filename) snprintf(str,128,"Cannot open BOP potential file %s",filename); error->one(FLERR,str); } - fgets(s,MAXLINE,fp); // skip first comment line - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%d",&bop_types); elements = new char*[bop_types]; for(i=0;ione(FLERR,str); } - fgets(s,MAXLINE,fp); // skip first comment line + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // skip first comment line for(i=0;icutmax) cutmax=rcut[i]; - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lf%lf%lf%lf",&sigma_c[i],&sigma_a[i],&pi_c[i],&pi_a[i]); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]); } if(nws==3) { @@ -5109,56 +5116,56 @@ void PairBOP::read_table(char *filename) for(k=j;kdestroy(neigh_flag3); memory->destroy(neigh_index); memory->destroy(neigh_index3); + itypeSigBk = NULL; + itypePiBk = NULL; + neigh_flag = NULL; + neigh_flag3 = NULL; + neigh_index = NULL; + neigh_index3 = NULL; if(otfly==0) { memory->destroy(cosAng); memory->destroy(dcAng); diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 6f1732dbb74cf8038fada15c09679355c909604f..bf66ea550a0f7b6c1dbae04837632c68cb70e0b9 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -33,6 +33,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -319,12 +320,13 @@ void PairComb3::read_lib() // open libraray file on proc 0 if (comm->me == 0) { - FILE *fp = force->open_potential("lib.comb3"); + const char filename[] = "lib.comb3"; + FILE *fp = force->open_potential(filename); if (fp == NULL) error->one(FLERR,"Cannot open COMB3 lib.comb3 file"); // read and store at the same time - fgets(s,MAXLIB,fp); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -335,7 +337,7 @@ void PairComb3::read_lib() ccutoff[4] = atof(words[4]); ccutoff[5] = atof(words[5]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -347,7 +349,7 @@ void PairComb3::read_lib() ch_a[5] = atof(words[5]); ch_a[6] = atof(words[6]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -355,7 +357,7 @@ void PairComb3::read_lib() nsplrad = atoi(words[1]); nspltor = atoi(words[2]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -363,7 +365,7 @@ void PairComb3::read_lib() maxy = atoi(words[1]); maxz = atoi(words[2]); - fgets(s,MAXLIB,fp); + utils::sfgets(FLERR,s,MAXLIB,fp,filename,error); nwords = 0; words[nwords++] = strtok(s," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue; @@ -372,7 +374,7 @@ void PairComb3::read_lib() maxconj = atoi(words[2]); for (l=0; lmass); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); nwords = sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -784,7 +785,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list) int i = 0; while (i < n) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error); ptr = strtok(line," \t\n\r\f"); list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr); diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 5b7f9877d7067e1b0747be7e16f01dfde5a6fcb3..a9622f9e075de0eacd0c3e3f5555a30911dbe727 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -23,6 +23,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMAlloy::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMAlloy::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); nwords = sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -188,7 +189,7 @@ void PairEAMAlloy::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index 7e007839227b7a59e77266e445738843fac19800..c91e7b5298b9bba1dc76632390b053b173ef06bb 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -23,6 +23,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMFS::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMFS::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); nwords = sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -190,7 +191,7 @@ void PairEAMFS::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index dd65d92cddc07bbb96170083ef1f02ba4bbbc7f6..dc1c7fa01993d3332a48c6647edefc690c15decc 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -966,11 +967,11 @@ int PairEIM::grabpair(FILE *fptr, int i, int j) sscanf(data,"%lg %lg %lg %lg %lg", &setfl->rcutphiA[ij],&setfl->rcutphiR[ij], &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error); sscanf(line,"%lg %lg %lg %lg %lg", &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij], &setfl->rq[ij],&setfl->rcutsigma[ij]); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error); sscanf(line,"%lg %lg %lg %d", &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij], &setfl->tp[ij]); diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 873a675cd90ec6fd51c1f0b55375c8479a160167..cc97fd9e9b56c82e8b601adf69b76bbfdb4eb680 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -29,6 +29,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -978,43 +979,43 @@ void PairLCBOP::read_file(char *filename) // skip initial comment lines while (1) { - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; } // read parameters - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&gamma_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&A); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&B_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&B_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&alpha); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&beta_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&beta_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&d); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_4); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&C_6); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&L); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&kappa); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&R_0); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&R_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_0); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_1_LR); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&r_2_LR); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&v_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&v_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&lambda_1); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&lambda_2); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&eps); - fgets(s,MAXLINE,fp); sscanf(s,"%lg",&delta); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&gamma_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&A); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&B_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&B_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&alpha); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&beta_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&beta_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&d); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_4); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&C_6); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&L); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&kappa); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&R_0); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&R_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_0); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_1_LR); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&r_2_LR); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&v_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&v_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&lambda_1); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&lambda_2); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&eps); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg",&delta); while (1) { - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; } @@ -1023,27 +1024,27 @@ void PairLCBOP::read_file(char *filename) for (k = 0; k < 2; k++) { // 2 values of N_ij_conj for (l = 0; l < 3; l++) { // 3 types of data: f, dfdx, dfdy for (i = 0; i < 4; i++) { // 4x4 matrix - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf(s,"%lg %lg %lg %lg", &F_conj_data[i][0][k][l], &F_conj_data[i][1][k][l], &F_conj_data[i][2][k][l], &F_conj_data[i][3][k][l]); } - while (1) { fgets(s,MAXLINE,fp); if (s[0] != '#') break; } + while (1) { utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; } } } // G spline // x coordinates of mesh points - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf( s,"%lg %lg %lg %lg %lg %lg", &gX[0], &gX[1], &gX[2], &gX[3], &gX[4], &gX[5] ); for (i = 0; i < 6; i++) { // for each power in polynomial - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); sscanf( s,"%lg %lg %lg %lg %lg", &gC[i][0], &gC[i][1], &gC[i][2], &gC[i][3], &gC[i][4] ); diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index d3964b292c79a7003e370ed985dc03f1f0754c86..8db4d63d4cf684dc5a6bd0a4947595d7f56b13da 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -29,6 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -573,8 +574,8 @@ void PairPolymorphic::read_file(char *file) error->one(FLERR,str); } // move past comments to first data line - fgets(line,MAXLINE,fp); - while (line == strchr(line,'#')) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + while (line == strchr(line,'#')) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -590,7 +591,7 @@ void PairPolymorphic::read_file(char *file) // map the elements in the potential file to LAMMPS atom types for (int i = 0; i < nelements; i++) { if (comm->me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -608,7 +609,7 @@ void PairPolymorphic::read_file(char *file) } // sizes if (comm->me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } @@ -644,7 +645,7 @@ void PairPolymorphic::read_file(char *file) for (int i = 0; i < npair; i++) { PairParameters & p = pairParameters[i]; if (comm->me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -875,7 +876,7 @@ void PairPolymorphic::grab(FILE *fp, int n, double *list) int i = 0; while (i < n) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); ptr = strtok(line," \t\n\r\f"); list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 43bffa7e8d467008e7b058c354416bd1124f1be1..dbb68b56f722e7cabe817337d1406c70fa3c61bb 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -27,6 +27,7 @@ #include "domain.h" #include "update.h" #include "random_mars.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -345,12 +346,12 @@ void PairDSMC::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -378,11 +379,11 @@ void PairDSMC::write_restart_settings(FILE *fp) void PairDSMC::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&max_cell_size,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&max_cell_size,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index f8fc3497466c6e817f657db5d709bfa481259bdb..214025be6340eb78af0bce980983741818a66cfe 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -28,7 +28,7 @@ void Message::command(int narg, char **arg) { if (narg < 3) error->all(FLERR,"Illegal message command"); - int clientserver; + int clientserver=0; if (strcmp(arg[0],"client") == 0) clientserver = 1; else if (strcmp(arg[0],"server") == 0) clientserver = 2; else error->all(FLERR,"Illegal message command"); diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index c9d4958594fb07eafdc53f4a8f4dd087ad30ce98..b33d58aab1d42f98c2f985dedb95ab8b385e9e76 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -184,8 +184,11 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) : if (idnext) find_maxid(); // random number generator, same for all procs + // warm up the generator 30x to avoid correlations in first-particle + // positions if runs are repeated with consecutive seeds random = new RanPark(lmp,seed); + for (int ii=0; ii < 30; ii++) random->uniform(); // set up reneighboring diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index d868254c50992f71ab6f4279d0e0cf11335ffb5f..c7e7af90577e91dcd7fff95ca5b439db66892ba7 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -56,8 +56,11 @@ FixEvaporate::FixEvaporate(LAMMPS *lmp, int narg, char **arg) : if (seed <= 0) error->all(FLERR,"Illegal fix evaporate command"); // random number generator, same for all procs + // warm up the generator 30x to avoid correlations in first-particle + // positions if runs are repeated with consecutive seeds random = new RanPark(lmp,seed); + for (int ii=0; ii < 30; ii++) random->uniform(); // optional args diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index a084491a78990be8cec35d3606b721d79837a790..07731fe93be45ce3de4358320a4d87b0f0b04fd3 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -318,15 +319,15 @@ void PairNMCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&e0[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&nn[i][j],sizeof(double),1,fp); - fread(&mm[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); @@ -356,10 +357,10 @@ void PairNMCut::write_restart_settings(FILE *fp) void PairNMCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index df8a34062ad234d6eb76f74676739d8ac741f252..270f4080ee3e2c4ff015c1d5a3e93ac9fb0186e4 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -369,16 +370,16 @@ void PairNMCutCoulCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&e0[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&nn[i][j],sizeof(double),1,fp); - fread(&mm[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); @@ -410,11 +411,11 @@ void PairNMCutCoulCut::write_restart_settings(FILE *fp) void PairNMCutCoulCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 4109fb0d9e23f63d919671c419bb3c403c580b7b..b63ede2b635624cf64f166e8cc0a357cf2716fe6 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -28,6 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -413,15 +414,15 @@ void PairNMCutCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&e0[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&nn[i][j],sizeof(double),1,fp); - fread(&mm[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&e0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&nn[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mm[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); @@ -454,13 +455,13 @@ void PairNMCutCoulLong::write_restart_settings(FILE *fp) void PairNMCutCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 8a45f293681790410256182380594d743c5e9680..161ad90ea383529c9ec8dca84062406e25fbaa51 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -245,10 +246,10 @@ void AngleCharmm::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); - fread(&k_ub[1],sizeof(double),atom->nangletypes,fp); - fread(&r_ub[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k_ub[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&r_ub[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 645cf66ff28ab49f498b8ceeb3405abadd94a68c..59593d24484a9cb1c7bbb16c0c9696e7aab19226 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -193,7 +194,7 @@ void AngleCosine::read_restart(FILE *fp) { allocate(); - if (comm->me == 0) fread(&k[1],sizeof(double),atom->nangletypes,fp); + if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 22c2f7ce8b957d1eb7f1882441b0231171f396cf..95f299683eb6b91d9e995e757a1f90a2b5dee037 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -27,6 +27,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -246,9 +247,9 @@ void AngleCosinePeriodic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&b[1],sizeof(int),atom->nangletypes,fp); - fread(&multiplicity[1],sizeof(int),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&b[1],sizeof(int),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index 56b3ee58cf45e46ee07cd3d361001651c9bb3bcd..9056600c3f89f6c5e8aba0de8c8fbf19a1fb60b5 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -215,8 +216,8 @@ void AngleCosineSquared::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 2e96884c9da82e134b62da8fc28af6a093607366..baeb9a8ed83c57c6e7965c94240103c1613a9651 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -215,8 +216,8 @@ void AngleHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 54046c2ba8acad6c9ef3d48c8c53ae5577ca25b2..b6439084a60cd18509931170dc67d5ca0241bb01 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -29,6 +29,7 @@ #include "memory.h" #include "error.h" #include "utils.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -309,8 +310,8 @@ void AngleTable::write_restart_settings(FILE *fp) void AngleTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 776291701b8d72f394f5057c71eea5784c2286ba..b8e197a3444b33ab79689c686c76d624084d3f68 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -215,10 +216,10 @@ void BondFENE::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); - fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp); - fread(&sigma[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index d03dfd912549e441fafbb6c2dc656332dfed6177..9cdc2639a58512f6280c45f2e35e5cf4c53c6867 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -224,11 +225,11 @@ void BondFENEExpand::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); - fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp); - fread(&sigma[1],sizeof(double),atom->nbondtypes,fp); - fread(&shift[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&sigma[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&shift[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 284c9202fd08612914e67a0cebdf9f141b13e2be..6732cc4457f53966a02cbc2ffdd4433385a88152 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -166,8 +167,8 @@ void BondGromos::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 7b19034629827cae20edec4ab5b03cac64165caa..569c92f99dfe9b00c4663815b940de2e9214da7d 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -167,8 +168,8 @@ void BondHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 6e16070cae322dc23195a460e6a4e67d2154e0a5..249f92928f384ec34df3640e8b21ad002a0338ac 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -171,9 +172,9 @@ void BondMorse::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&d0[1],sizeof(double),atom->nbondtypes,fp); - fread(&alpha[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&d0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&alpha[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index e06b1b9aac1b46b3b0eec342540158a37e601156..ee943ad28f0495702f54b99f0261aee038798c97 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -20,6 +20,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -166,9 +167,9 @@ void BondNonlinear::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); - fread(&lamda[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&epsilon[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&lamda[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index 352b642bbec3d5880163232fbe22e40259315b24..813e322473fe5d6ff458bc8ab062e3581af32bb6 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -25,6 +25,7 @@ #include "pair.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -275,11 +276,11 @@ void BondQuartic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&b1[1],sizeof(double),atom->nbondtypes,fp); - fread(&b2[1],sizeof(double),atom->nbondtypes,fp); - fread(&rc[1],sizeof(double),atom->nbondtypes,fp); - fread(&u0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&b1[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&b2[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&rc[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&u0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&b1[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index ce41303a7d4ec605cb3f8b7fd03622616b5dd1fb..20e4e311c8aaac8d1ae568a38f4968593a7e84a7 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -252,8 +252,8 @@ void BondTable::write_restart_settings(FILE *fp) void BondTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 8cc071302466cda461449431d8374e81140fdb98..e66165efd7908121faf6392a0f917e7ba080c1dc 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -29,6 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -423,11 +424,11 @@ void DihedralCharmm::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp); - fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp); - fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&weightflag,sizeof(int),1,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world); diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index f384c4cd3650005afe34ff875c3fc82b2359f42f..efff35d9c5cdd29e66b18d7cb5a00f4f06664391 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -32,6 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -466,11 +467,11 @@ void DihedralCharmmfsw::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp); - fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp); - fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&weightflag,sizeof(int),1,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&shift[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&weight[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&weightflag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world); diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index f1e5811a8499f0e0d5ad68a5ad6274b43b2d0f00..48adf0790338ce96faea4a82d573da6307d21b6d 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -25,6 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -42,7 +43,7 @@ DihedralHarmonic::DihedralHarmonic(LAMMPS *lmp) : Dihedral(lmp) DihedralHarmonic::~DihedralHarmonic() { - if (allocated) { + if (allocated && !copymode) { memory->destroy(setflag); memory->destroy(k); memory->destroy(sign); @@ -327,9 +328,9 @@ void DihedralHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&sign[1],sizeof(int),atom->ndihedraltypes,fp); - fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&sign[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world); diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h index 938e59918bd5256dee97de73c93b05025df432ee..6792d16a203776f93d53ae3a88d0b909ca065dd8 100644 --- a/src/MOLECULE/dihedral_harmonic.h +++ b/src/MOLECULE/dihedral_harmonic.h @@ -29,16 +29,16 @@ class DihedralHarmonic : public Dihedral { DihedralHarmonic(class LAMMPS *); virtual ~DihedralHarmonic(); virtual void compute(int, int); - void coeff(int, char **); + virtual void coeff(int, char **); void write_restart(FILE *); - void read_restart(FILE *); + virtual void read_restart(FILE *); void write_data(FILE *); protected: double *k,*cos_shift,*sin_shift; int *sign,*multiplicity; - void allocate(); + virtual void allocate(); }; } diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index 56f7a3b5e8b79a05fcaaf9b4806c33401b0cf330..26461883c6493a3b49af44bf32775cbc0c4e9a81 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -322,9 +323,9 @@ void DihedralHelix::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&aphi[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&bphi[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&cphi[1],sizeof(double),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&aphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&bphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&cphi[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&aphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&bphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index eda7cede3e63b83a0fcabccad5ddbc09713f1ad0..b5db6852478ab5be87a145e19584d63c40d4b8f1 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -25,6 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -318,11 +319,11 @@ void DihedralMultiHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&a1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&a2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&a3[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&a4[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&a5[1],sizeof(double),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&a1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&a2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&a3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&a4[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&a5[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&a1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&a2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 556efd850a7d5eee0489bf9a2853d0cb46bce7ae..5dd268b39fd1de0207cd96588fe134ac9b1b4073 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -25,6 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -330,10 +331,10 @@ void DihedralOPLS::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k4[1],sizeof(double),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&k1[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&k3[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&k4[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index abd2d4e11e98967de6c1c18808d35023eacde9bb..0ffb3f3c316ad00feeb8d85ce7656f4846248568 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -21,6 +21,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -333,9 +334,9 @@ void ImproperCvff::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&sign[1],sizeof(int),atom->nimpropertypes,fp); - fread(&multiplicity[1],sizeof(int),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&sign[1],sizeof(int),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&sign[1],atom->nimpropertypes,MPI_INT,0,world); diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 778fe646e16932327d8fc9e30b0b37b44ffbb9e1..e90bc04c90610d2a2ec4db8df0fc62883e6f0136 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -274,8 +275,8 @@ void ImproperHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index d3adf199935746039992fe55a8934ec7e4b444ec..5259b6baf4135ed6b6fc3ffa9b3dc269acff85cc 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -315,9 +316,9 @@ void ImproperUmbrella::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&kw[1],sizeof(double),atom->nimpropertypes,fp); - fread(&w0[1],sizeof(double),atom->nimpropertypes,fp); - fread(&C[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&kw[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&w0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&C[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&kw[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&w0[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index 5ebfe0a11082b4952260140df926776a2956dba7..0712f6be737c920e1dd704ff2bc29f5e15dfc3fb 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -374,14 +375,14 @@ void PairLJCharmmCoulCharmm::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&eps14[i][j],sizeof(double),1,fp); - fread(&sigma14[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -435,12 +436,12 @@ void PairLJCharmmCoulCharmm::write_restart_settings(FILE *fp) void PairLJCharmmCoulCharmm::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_inner,sizeof(double),1,fp); - fread(&cut_lj,sizeof(double),1,fp); - fread(&cut_coul_inner,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 4fb7cc522902b016c26b3cef6053d4747bb44346..026b96c00cc1075a255072dbbcef2fa4b37e7fd9 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -432,14 +433,14 @@ void PairLJCharmmfswCoulCharmmfsh::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&eps14[i][j],sizeof(double),1,fp); - fread(&sigma14[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -469,11 +470,11 @@ void PairLJCharmmfswCoulCharmmfsh::write_restart_settings(FILE *fp) void PairLJCharmmfswCoulCharmmfsh::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_inner,sizeof(double),1,fp); - fread(&cut_lj,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index e5f25a511b4805a1e105459589830315789156c4..673fb83066e891abc282d9eeec1ddef81ce053bd 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -30,6 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -617,13 +618,13 @@ void PairLJCutTIP4PCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -659,17 +660,17 @@ void PairLJCutTIP4PCut::write_restart_settings(FILE *fp) void PairLJCutTIP4PCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 3a6702c9b26eefed68d0c927b0886d99901574ee..334dbf89c8bc4ead54e6e343cbcb733a326dc37a 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -28,6 +28,7 @@ #include "comm.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -474,7 +475,7 @@ void PairTIP4PCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); } } @@ -501,13 +502,13 @@ void PairTIP4PCut::write_restart_settings(FILE *fp) void PairTIP4PCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); - fread(&cut_coul,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp index 230b766725f92b57eb2ebfd5417c6cdf540f088f..8bea52f1cff68ad696df267c36781b7da985042f 100644 --- a/src/PERI/compute_damage_atom.cpp +++ b/src/PERI/compute_damage_atom.cpp @@ -59,11 +59,9 @@ void ComputeDamageAtom::init() // find associated PERI_NEIGH fix that must exist - ifix_peri = -1; - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; + ifix_peri = modify->find_fix_by_style("PERI_NEIGH"); if (ifix_peri == -1) - error->all(FLERR,"Compute damage/atom requires peridynamic potential"); + error->all(FLERR,"Compute damage/atom requires a peridynamic potential"); } /* ---------------------------------------------------------------------- */ diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp index 095f61983888055385fc2a1c42c27ec69bf9b936..65a25cda03174fd2a0d20fbdc39e96ed42efc181 100644 --- a/src/PERI/compute_dilatation_atom.cpp +++ b/src/PERI/compute_dilatation_atom.cpp @@ -66,10 +66,10 @@ void ComputeDilatationAtom::init() // check PD pair style isPMB = isLPS = isVES = isEPS = 0; - if (force->pair_match("peri/pmb",1)) isPMB = 1; - if (force->pair_match("peri/lps",1)) isLPS = 1; - if (force->pair_match("peri/ves",1)) isVES = 1; - if (force->pair_match("peri/eps",1)) isEPS = 1; + if (force->pair_match("^peri/pmb",0)) isPMB = 1; + if (force->pair_match("^peri/lps",0)) isLPS = 1; + if (force->pair_match("^peri/ves",0)) isVES = 1; + if (force->pair_match("^peri/eps",0)) isEPS = 1; if (isPMB) error->all(FLERR,"Compute dilatation/atom cannot be used " @@ -77,10 +77,7 @@ void ComputeDilatationAtom::init() // find associated PERI_NEIGH fix that must exist - int ifix_peri = -1; - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; - if (ifix_peri == -1) + if (modify->find_fix_by_style("^PERI_NEIGH") == -1) error->all(FLERR,"Compute dilatation/atom requires Peridynamic pair style"); } diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp index e312630b6225c3ada14aa217d513af9b3cbb675e..d90e2115069ee4fd0ba07025fe4fd6807e7086e6 100644 --- a/src/PERI/compute_plasticity_atom.cpp +++ b/src/PERI/compute_plasticity_atom.cpp @@ -66,11 +66,9 @@ void ComputePlasticityAtom::init() // find associated PERI_NEIGH fix that must exist - ifix_peri = -1; - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; + ifix_peri = modify->find_fix_by_style("^PERI_NEIGH"); if (ifix_peri == -1) - error->all(FLERR,"Compute plasticity/atom requires Peridynamic pair style"); + error->all(FLERR,"Compute plasticity/atom requires a Peridynamics pair style"); } /* ---------------------------------------------------------------------- */ diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 2579a9b75a56f09f3420837d56a6b532d15d45c8..cd2ab3a2d0f41c6f8b85310d4c7500e349885b9e 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -524,9 +525,9 @@ void PairPeriEPS::init_style() // find associated PERI_NEIGH fix that must exist // could have changed locations in fix list since created - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; - if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist"); + ifix_peri = modify->find_fix_by_style("^PERI_NEIGH"); + if (ifix_peri == -1) + error->all(FLERR,"Fix peri neigh does not exist"); neighbor->request(this,instance_me); } @@ -564,16 +565,16 @@ void PairPeriEPS::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&bulkmodulus[i][j],sizeof(double),1,fp); - fread(&shearmodulus[i][j],sizeof(double),1,fp); - fread(&s00[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - fread(&m_yieldstress[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&m_yieldstress[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world); diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index f32ce5fb1c1299224c0b842c17678a4e6250e503..0ad6a7b0d2c7dc8d2028f3fb6cc549cc52b52743 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "math_const.h" using namespace LAMMPS_NS; @@ -450,9 +451,9 @@ void PairPeriLPS::init_style() // find associated PERI_NEIGH fix that must exist // could have changed locations in fix list since created - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; - if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist"); + ifix_peri = modify->find_fix_by_style("^PERI_NEIGH"); + if (ifix_peri == -1) + error->all(FLERR,"Fix peri neigh does not exist"); neighbor->request(this,instance_me); } @@ -489,15 +490,15 @@ void PairPeriLPS::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&bulkmodulus[i][j],sizeof(double),1,fp); - fread(&shearmodulus[i][j],sizeof(double),1,fp); - fread(&s00[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world); diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index ceab40d88d582bc61eedbc373ca3f6ca411d5fc2..88aca99efb002a1ab872605de568fd8c1f94a584 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -32,6 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -380,9 +381,9 @@ void PairPeriPMB::init_style() // find associated PERI_NEIGH fix that must exist // could have changed locations in fix list since created - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; - if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist"); + ifix_peri = modify->find_fix_by_style("^PERI_NEIGH"); + if (ifix_peri == -1) + error->all(FLERR,"Fix peri neigh does not exist"); neighbor->request(this,instance_me); } @@ -418,14 +419,14 @@ void PairPeriPMB::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&kspring[i][j],sizeof(double),1,fp); - fread(&s00[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&kspring[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&kspring[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world); diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index bd1eaa5fd25e236e7f5a0a573a073c032580c94b..1cef9635a996d793e5e216ed304d698a3f39a4a0 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "update.h" using namespace LAMMPS_NS; @@ -506,9 +507,9 @@ void PairPeriVES::init_style() // find associated PERI_NEIGH fix that must exist // could have changed locations in fix list since created - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i; - if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist"); + ifix_peri = modify->find_fix_by_style("^PERI_NEIGH"); + if (ifix_peri == -1) + error->all(FLERR,"Fix peri neigh does not exist"); neighbor->request(this,instance_me); } @@ -547,17 +548,17 @@ void PairPeriVES::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&bulkmodulus[i][j],sizeof(double),1,fp); - fread(&shearmodulus[i][j],sizeof(double),1,fp); - fread(&s00[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - fread(&m_lambdai[i][j],sizeof(double),1,fp); - fread(&m_taubi[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&bulkmodulus[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shearmodulus[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&s00[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&m_lambdai[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&m_taubi[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world); diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 7768c01a41d45b8f43ec90f3800a22813341ef9f..84ba33e28acfb9ebfacb15b6a7c14425439b39a2 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -476,6 +476,7 @@ int FixQEq::pack_forward_comm(int n, int *list, double *buf, for(m = 0; m < n; m++) buf[m] = t[list[m]]; else if( pack_flag == 4 ) for(m = 0; m < n; m++) buf[m] = atom->q[list[m]]; + else m = 0; return m; } diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 8a51f6d00e692c19e9b32d7e98453866446388e5..b2fbb740719798bd3ba497db4ec1b89d55b4e3bf 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -197,7 +197,7 @@ void TAD::command(int narg, char **arg) args = new char*[narg2]; args[0] = min_style; - update->create_minimize(narg2,args); + update->create_minimize(narg2,args,1); delete [] args; @@ -711,7 +711,7 @@ void TAD::perform_neb(int ievent) args = new char*[narg2]; args[0] = min_style_neb; - update->create_minimize(narg2,args); + update->create_minimize(narg2,args,1); delete [] args; @@ -777,7 +777,7 @@ void TAD::perform_neb(int ievent) args = new char*[narg2]; args[0] = min_style; - update->create_minimize(narg2,args); + update->create_minimize(narg2,args,1); update->etol = etol; update->ftol = ftol; diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 912f5294036a5535dde7246140fab15dd5ab4dcd..3e6130ac7cf39aa38d50c66b34bd2c0e5e1e0486 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -34,25 +34,12 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "rigid_const.h" using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; - -enum{SINGLE,MOLECULE,GROUP}; -enum{NONE,XYZ,XY,YZ,XZ}; -enum{ISO,ANISO,TRICLINIC}; - -#define MAXLINE 1024 -#define CHUNK 1024 -#define ATTRIBUTE_PERBODY 20 - -#define TOLERANCE 1.0e-6 -#define EPSILON 1.0e-7 - -#define SINERTIA 0.4 // moment of inertia prefactor for sphere -#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid -#define LINERTIA (1.0/12.0) // moment of inertia prefactor for line segment +using namespace RigidConst; /* ---------------------------------------------------------------------- */ @@ -605,21 +592,6 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : for (ibody = 0; ibody < nbody; ibody++) if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body"); - // bitmasks for properties of extended particles - - POINT = 1; - SPHERE = 2; - ELLIPSOID = 4; - LINE = 8; - TRIANGLE = 16; - DIPOLE = 32; - OMEGA = 64; - ANGMOM = 128; - TORQUE = 256; - - MINUSPI = -MY_PI; - TWOPI = 2.0*MY_PI; - // wait to setup bodies until first init() using current atom properties setupflag = 0; @@ -1472,8 +1444,8 @@ void FixRigid::set_xv() if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]); else theta_body = -2.0*acos(quat[ibody][0]); theta = orient[i][0] + theta_body; - while (theta <= MINUSPI) theta += TWOPI; - while (theta > MY_PI) theta -= TWOPI; + while (theta <= -MY_PI) theta += MY_2PI; + while (theta > MY_PI) theta -= MY_2PI; lbonus[line[i]].theta = theta; omega_one[i][0] = omega[ibody][0]; omega_one[i][1] = omega[ibody][1]; @@ -2018,8 +1990,8 @@ void FixRigid::setup_bodies_static() if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]); else theta_body = -2.0*acos(quat[ibody][0]); orient[i][0] = lbonus[line[i]].theta - theta_body; - while (orient[i][0] <= MINUSPI) orient[i][0] += TWOPI; - while (orient[i][0] > MY_PI) orient[i][0] -= TWOPI; + while (orient[i][0] <= -MY_PI) orient[i][0] += MY_2PI; + while (orient[i][0] > MY_PI) orient[i][0] -= MY_2PI; if (orientflag == 4) orient[i][1] = orient[i][2] = orient[i][3] = 0.0; } else if (eflags[i] & TRIANGLE) { quatatom = tbonus[tri[i]].quat; diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h index d9d7b07ce8e84443e0fb5c13485d0bec518f834c..8c4ab9ed49760303882447f7f45a1624d63980c6 100644 --- a/src/RIGID/fix_rigid.h +++ b/src/RIGID/fix_rigid.h @@ -65,7 +65,6 @@ class FixRigid : public Fix { double dtv,dtf,dtq; double *step_respa; int triclinic; - double MINUSPI,TWOPI; char *inpfile; // file to read rigid body attributes from int rstyle; // SINGLE,MOLECULE,GROUP @@ -137,9 +136,6 @@ class FixRigid : public Fix { class AtomVecLine *avec_line; class AtomVecTri *avec_tri; - int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags - int OMEGA,ANGMOM,TORQUE; - void image_shift(); void set_xv(); void set_v(); diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp index 4738e253f6374cc65009fdde01d02c868c5b74bd..6ffb997ffa7dbb5a56b4c96bd401cb7fca5d41f3 100644 --- a/src/RIGID/fix_rigid_nh.cpp +++ b/src/RIGID/fix_rigid_nh.cpp @@ -33,14 +33,11 @@ #include "kspace.h" #include "memory.h" #include "error.h" +#include "rigid_const.h" using namespace LAMMPS_NS; using namespace FixConst; - -enum{NONE,XYZ,XY,YZ,XZ}; // same as in FixRigid -enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid - -#define EPSILON 1.0e-7 +using namespace RigidConst; /* ---------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 1545e913c033e139d7c7edf2f2fb4c363559c50b..136796ce1802f3c9a2695e1e2d2f69fe2aa308d4 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -34,17 +34,12 @@ #include "kspace.h" #include "memory.h" #include "error.h" +#include "rigid_const.h" using namespace LAMMPS_NS; using namespace FixConst; using namespace MathExtra; - -enum{NONE,XYZ,XY,YZ,XZ}; // same as in FixRigid -enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid - -#define EPSILON 1.0e-7 - -enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF}; +using namespace RigidConst; /* ---------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 14e230ab9cc42c3912aed6dfa71a5d1406a43580..ba570d58403c62792663121d9fb8902b2e1c1883 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -38,34 +38,17 @@ #include "hashlittle.h" #include "memory.h" #include "error.h" +#include "rigid_const.h" #include using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; +using namespace RigidConst; #define RVOUS 1 // 0 for irregular, 1 for all2all -#define MAXLINE 1024 -#define CHUNK 1024 -#define ATTRIBUTE_PERBODY 20 - -#define TOLERANCE 1.0e-6 -#define EPSILON 1.0e-7 -#define BIG 1.0e20 - -#define SINERTIA 0.4 // moment of inertia prefactor for sphere -#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid -#define LINERTIA (1.0/12.0) // moment of inertia prefactor for line segment - -#define DELTA_BODY 10000 - -enum{NONE,XYZ,XY,YZ,XZ}; // same as in FixRigid -enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid - -enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF}; - /* ---------------------------------------------------------------------- */ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : @@ -455,21 +438,6 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : comm_forward = 1 + bodysize; comm_reverse = 6; - // bitmasks for properties of extended particles - - POINT = 1; - SPHERE = 2; - ELLIPSOID = 4; - LINE = 8; - TRIANGLE = 16; - DIPOLE = 32; - OMEGA = 64; - ANGMOM = 128; - TORQUE = 256; - - MINUSPI = -MY_PI; - TWOPI = 2.0*MY_PI; - // atom style pointers to particles that store extra info avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); @@ -1384,8 +1352,8 @@ void FixRigidSmall::set_xv() if (b->quat[3] >= 0.0) theta_body = 2.0*acos(b->quat[0]); else theta_body = -2.0*acos(b->quat[0]); theta = orient[i][0] + theta_body; - while (theta <= MINUSPI) theta += TWOPI; - while (theta > MY_PI) theta -= TWOPI; + while (theta <= -MY_PI) theta += MY_2PI; + while (theta > MY_PI) theta -= MY_2PI; lbonus[line[i]].theta = theta; omega[i][0] = b->omega[0]; omega[i][1] = b->omega[1]; @@ -2155,8 +2123,8 @@ void FixRigidSmall::setup_bodies_static() if (b->quat[3] >= 0.0) theta_body = 2.0*acos(b->quat[0]); else theta_body = -2.0*acos(b->quat[0]); orient[i][0] = lbonus[line[i]].theta - theta_body; - while (orient[i][0] <= MINUSPI) orient[i][0] += TWOPI; - while (orient[i][0] > MY_PI) orient[i][0] -= TWOPI; + while (orient[i][0] <= -MY_PI) orient[i][0] += MY_2PI; + while (orient[i][0] > MY_PI) orient[i][0] -= MY_2PI; if (orientflag == 4) orient[i][1] = orient[i][2] = orient[i][3] = 0.0; } else if (eflags[i] & TRIANGLE) { quatatom = tbonus[tri[i]].quat; diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index 6dae443d1ca6bdf9a7c3d90f39160bfe8a376dac..0d1cdb59634700da4159a90e046539c41b06ac0e 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -72,7 +72,6 @@ class FixRigidSmall : public Fix { double dtv,dtf,dtq; double *step_respa; int triclinic; - double MINUSPI,TWOPI; char *inpfile; // file to read rigid body attributes from int setupflag; // 1 if body properties are setup, else 0 @@ -129,9 +128,6 @@ class FixRigidSmall : public Fix { int dorientflag; // 1 if particles store dipole orientation int reinitflag; // 1 if re-initialize rigid bodies between runs - int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags - int OMEGA,ANGMOM,TORQUE; - class AtomVecEllipsoid *avec_ellipsoid; class AtomVecLine *avec_line; class AtomVecTri *avec_tri; diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 48a08118c5f73648157ca9d317e6620dedf11e71..054985ba72e8d04437f5de7dba518ed01ef94d27 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -32,6 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -360,9 +361,8 @@ void FixShake::init() // could have changed locations in fix list since created // set ptrs to rRESPA variables - if (strstr(update->integrate_style,"respa")) { - for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"RESPA") == 0) ifix_respa = i; + if (utils::strmatch(update->integrate_style,"^respa")) { + ifix_respa = modify->find_fix_by_style("^RESPA"); nlevels_respa = ((Respa *) update->integrate)->nlevels; loop_respa = ((Respa *) update->integrate)->loop; step_respa = ((Respa *) update->integrate)->step; diff --git a/src/RIGID/rigid_const.h b/src/RIGID/rigid_const.h new file mode 100644 index 0000000000000000000000000000000000000000..14db517fcd68316431c9d394837535be0fbfb256 --- /dev/null +++ b/src/RIGID/rigid_const.h @@ -0,0 +1,54 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_RIGID_CONST_H +#define LMP_RIGID_CONST_H + +namespace LAMMPS_NS { + namespace RigidConst { + + enum{SINGLE,MOLECULE,GROUP}; + enum{NONE,XYZ,XY,YZ,XZ}; + enum{ISO,ANISO,TRICLINIC}; + enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF}; + + enum {POINT = 1<<0, + SPHERE = 1<<1, + ELLIPSOID = 1<<2, + LINE = 1<<3, + TRIANGLE = 1<<4, + DIPOLE = 1<<5, + OMEGA = 1<<6, + ANGMOM = 1<<7, + TORQUE = 1<<8 + }; + + static const double TOLERANCE = 1.0e-6; + static const double EPSILON = 1.0e-7; + static const double BIG = 1.0e20; + + // moment of inertia prefactor for sphere + static const double SINERTIA = 0.4; + // moment of inertia prefactor for ellipsoid + static const double EINERTIA = 0.2; + // moment of inertia prefactor for line segment + static const double LINERTIA = 1.0/12.0; + + static const int MAXLINE = 1024; + static const int CHUNK = 1024; + static const int DELTA_BODY = 10000; + static const int ATTRIBUTE_PERBODY = 20; + } +} + +#endif diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 59b333fa31737f917313bf33b9c60685433ff9ad..133f0e414bfff9faa640837109b9b28fc3656664 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -273,7 +273,7 @@ void PairSNAP::compute_bispectrum() { int i,j,jnum,ninside; double delx,dely,delz,rsq; - int *jlist,*numneigh,**firstneigh; + int *jlist; double **x = atom->x; int *type = atom->type; @@ -350,9 +350,9 @@ void PairSNAP::allocate() global settings ------------------------------------------------------------------------- */ -void PairSNAP::settings(int narg, char **arg) +void PairSNAP::settings(int narg, char ** /* arg */) { - for (int i=0; i < narg; i++) + if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp index 01d2d12b8f5085678c59f35d7c367a50801a9205..9e8768c47752ef05ab3f949357c21a5579ea92b3 100644 --- a/src/SNAP/sna.cpp +++ b/src/SNAP/sna.cpp @@ -20,6 +20,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "comm.h" using namespace std; using namespace LAMMPS_NS; @@ -283,6 +284,7 @@ void SNA::build_indexlist() void SNA::init() { init_clebsch_gordan(); + // print_clebsch_gordan(); init_rootpqarray(); } @@ -348,7 +350,6 @@ void SNA::compute_ui(int jnum) void SNA::compute_zi() { - int ma2, mb2; for(int jjz = 0; jjz < idxz_max; jjz++) { const int j1 = idxz[jjz].j1; const int j2 = idxz[jjz].j2; @@ -405,8 +406,6 @@ void SNA::compute_zi() void SNA::compute_yi(const double* beta) { - int j; - int jjz; int jju; double betaj; @@ -420,7 +419,6 @@ void SNA::compute_yi(const double* beta) } // end loop over ma, mb } // end loop over j - int ma2, mb2; for(int jjz = 0; jjz < idxz_max; jjz++) { const int j1 = idxz[jjz].j1; const int j2 = idxz[jjz].j2; @@ -433,8 +431,6 @@ void SNA::compute_yi(const double* beta) const int nb = idxz[jjz].nb; const double* cgblock = cglist + idxcg_block[j1][j2][j]; - int mb = (2 * (mb1min+mb2max) - j1 - j2 + j) / 2; - int ma = (2 * (ma1min+ma2max) - j1 - j2 + j) / 2; double ztmp_r = 0.0; double ztmp_i = 0.0; @@ -547,7 +543,6 @@ void SNA::compute_deidrj(double* dedr) jju++; } - int ma = mb; double* dudr_r = dulist_r[jju]; double* dudr_i = dulist_i[jju]; double jjjmambyarray_r = ylist_r[jju]; @@ -656,10 +651,6 @@ void SNA::compute_dbidrj() double* dbdr; double* dudr_r, *dudr_i; double sumzdu_r[3]; - double** jjjzarray_r; - double** jjjzarray_i; - double jjjmambzarray_r; - double jjjmambzarray_i; int jjz, jju; for(int jjb = 0; jjb < idxb_max; jjb++) { @@ -706,7 +697,6 @@ void SNA::compute_dbidrj() jjz++; jju++; } - int ma = mb; dudr_r = dulist_r[jju]; dudr_i = dulist_i[jju]; for(int k = 0; k < 3; k++) @@ -756,7 +746,6 @@ void SNA::compute_dbidrj() jjz++; jju++; } - int ma = mb; dudr_r = dulist_r[jju]; dudr_i = dulist_i[jju]; for(int k = 0; k < 3; k++) @@ -806,7 +795,6 @@ void SNA::compute_dbidrj() jjz++; jju++; } - int ma = mb; dudr_r = dulist_r[jju]; dudr_i = dulist_i[jju]; for(int k = 0; k < 3; k++) @@ -1515,6 +1503,40 @@ void SNA::init_clebsch_gordan() } } +/* ---------------------------------------------------------------------- + print out values of Clebsch-Gordan coefficients + format and notation follows VMK Table 8.11 +------------------------------------------------------------------------- */ + +void SNA::print_clebsch_gordan() +{ + if (comm->me) return; + + int aa2, bb2, cc2; + for (int j = 0; j <= twojmax; j += 1) { + printf("c = %g\n",j/2.0); + printf("a alpha b beta C_{a alpha b beta}^{c alpha+beta}\n"); + for (int j1 = 0; j1 <= twojmax; j1++) + for (int j2 = 0; j2 <= j1; j2++) + if (j1-j2 <= j && j1+j2 >= j && (j1+j2+j)%2 == 0) { + int idxcg_count = idxcg_block[j1][j2][j]; + for (int m1 = 0; m1 <= j1; m1++) { + aa2 = 2*m1-j1; + for (int m2 = 0; m2 <= j2; m2++) { + bb2 = 2*m2-j2; + double cgtmp = cglist[idxcg_count]; + cc2 = aa2+bb2; + if (cc2 >= -j && cc2 <= j) + if (j1 != j2 || (aa2 > bb2 && aa2 >= -bb2) || (aa2 == bb2 && aa2 >= 0)) + printf("%4g %4g %4g %4g %10.6g\n", + j1/2.0,aa2/2.0,j2/2.0,bb2/2.0,cgtmp); + idxcg_count++; + } + } + } + } +} + /* ---------------------------------------------------------------------- pre-compute table of sqrt[p/m2], p, q = 1,twojmax the p = 0, q = 0 entries are allocated and skipped for convenience. diff --git a/src/SNAP/sna.h b/src/SNAP/sna.h index e6bf4e3f9efc228afea568d54b5e42b9cf40d3da..5ea65fd84b266e86b28db83a603e5e0807be5689 100644 --- a/src/SNAP/sna.h +++ b/src/SNAP/sna.h @@ -103,6 +103,7 @@ private: void create_twojmax_arrays(); void destroy_twojmax_arrays(); void init_clebsch_gordan(); + void print_clebsch_gordan(); void init_rootpqarray(); void zero_uarraytot(); void addself_uarraytot(double); diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index b1b466b5a47dcd9a539c862093bce109636627eb..9b4f1916ae010041ca9ec1c8114710b0b955b131 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -91,12 +91,17 @@ FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : // defining lattice_flag + // changing the lattice option, from (yes,no) -> (moving,frozen) + // for now, (yes,no) still works (to avoid user's confusions). + int iarg = 3; while (iarg < narg) { if (strcmp(arg[iarg],"lattice") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix/NVE/spin command"); if (strcmp(arg[iarg+1],"no") == 0) lattice_flag = 0; + else if (strcmp(arg[iarg+1],"frozen") == 0) lattice_flag = 0; else if (strcmp(arg[iarg+1],"yes") == 0) lattice_flag = 1; + else if (strcmp(arg[iarg+1],"moving") == 0) lattice_flag = 1; else error->all(FLERR,"Illegal fix/NVE/spin command"); iarg += 2; } else error->all(FLERR,"Illegal fix/NVE/spin command"); diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h index 1e3b87c1fb82b79cd1302077ed0ec1bcb20be595..5871f721be0b3a32df4bd9edf4bf411563ad3a84 100644 --- a/src/SPIN/fix_nve_spin.h +++ b/src/SPIN/fix_nve_spin.h @@ -52,7 +52,7 @@ friend class PairSpin; double dtv, dtf, dts; // velocity, force, and spin timesteps - int nlocal_max; // max value of nlocal (for lists size) + int nlocal_max; // max value of nlocal (for size of lists) int pair_spin_flag; // magnetic pair flags int long_spin_flag; // magnetic long-range flag diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index 553526ea8e9460da515e411dd67adcc2cce949cf..7315aca0567fe8951e9dbb0b83b8115ae9a68b59 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -41,15 +41,15 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -MinSpin::MinSpin(LAMMPS *lmp) : Min(lmp) {} +MinSpin::MinSpin(LAMMPS *lmp) : Min(lmp) { + alpha_damp = 1.0; + discrete_factor = 10.0; +} /* ---------------------------------------------------------------------- */ void MinSpin::init() { - alpha_damp = 1.0; - discrete_factor = 10.0; - Min::init(); dts = dt = update->dt; @@ -77,12 +77,12 @@ void MinSpin::setup_style() int MinSpin::modify_param(int narg, char **arg) { if (strcmp(arg[0],"alpha_damp") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (narg < 2) error->all(FLERR,"Illegal min_modify command"); alpha_damp = force->numeric(FLERR,arg[1]); return 2; } if (strcmp(arg[0],"discrete_factor") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + if (narg < 2) error->all(FLERR,"Illegal min_modify command"); discrete_factor = force->numeric(FLERR,arg[1]); return 2; } @@ -116,7 +116,7 @@ void MinSpin::reset_vectors() int MinSpin::iterate(int maxiter) { bigint ntimestep; - double fmdotfm; + double fmdotfm,fmsq; int flag,flagall; for (int iter = 0; iter < maxiter; iter++) { @@ -130,7 +130,7 @@ int MinSpin::iterate(int maxiter) // optimize timestep accross processes / replicas // need a force calculation for timestep optimization - energy_force(0); + if (iter == 0) energy_force(0); dts = evaluate_dt(); // apply damped precessional dynamics to the spins @@ -163,8 +163,13 @@ int MinSpin::iterate(int maxiter) // magnetic torque tolerance criterion // sync across replicas if running multi-replica minimization + fmdotfm = fmsq = 0.0; if (update->ftol > 0.0) { - fmdotfm = fmnorm_sqr(); + if (normstyle == MAX) fmsq = max_torque(); // max torque norm + else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm + else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm + else error->all(FLERR,"Illegal min_modify command"); + fmdotfm = fmsq*fmsq; if (update->multireplica == 0) { if (fmdotfm < update->ftol*update->ftol) return FTOL; } else { @@ -242,7 +247,7 @@ void MinSpin::advance_spins(double dts) double **sp = atom->sp; double **fm = atom->fm; double tdampx,tdampy,tdampz; - double msq,scale,fm2,energy,dts2; + double fm2,energy,dts2; double cp[3],g[3]; dts2 = dts*dts; @@ -288,37 +293,3 @@ void MinSpin::advance_spins(double dts) // because no need for simplecticity } } - -/* ---------------------------------------------------------------------- - compute and return ||mag. torque||_2^2 -------------------------------------------------------------------------- */ - -double MinSpin::fmnorm_sqr() -{ - int nlocal = atom->nlocal; - double tx,ty,tz; - double **sp = atom->sp; - double **fm = atom->fm; - - // calc. magnetic torques - - double local_norm2_sqr = 0.0; - for (int i = 0; i < nlocal; i++) { - tx = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]); - ty = (fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]); - tz = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]); - - local_norm2_sqr += tx*tx + ty*ty + tz*tz; - } - - // no extra atom calc. for spins - - if (nextra_atom) - error->all(FLERR,"extra atom option not available yet"); - - double norm2_sqr = 0.0; - MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world); - - return norm2_sqr; -} - diff --git a/src/SPIN/min_spin.h b/src/SPIN/min_spin.h index fbc624a9ccf82b8030b6811af08406e54ff47fd1..f2df81e58cf303a3056e721e0995a6ba5f86fc56 100644 --- a/src/SPIN/min_spin.h +++ b/src/SPIN/min_spin.h @@ -35,7 +35,6 @@ class MinSpin : public Min { int iterate(int); double evaluate_dt(); void advance_spins(double); - double fmnorm_sqr(); private: diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp new file mode 100644 index 0000000000000000000000000000000000000000..95bbcf437b1a70bef31dc6a707933fb8285a4cce --- /dev/null +++ b/src/SPIN/min_spin_cg.cpp @@ -0,0 +1,649 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Aleksei Ivanov (University of Iceland) + Julien Tranchida (SNL) + + Please cite the related publication: + Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust + Algorithm for the Minimisation of the Energy of Spin Systems. arXiv + preprint arXiv:1904.02669. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "min_spin_cg.h" +#include "universe.h" +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "force.h" +#include "update.h" +#include "output.h" +#include "timer.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "math_special.h" +#include "math_const.h" +#include "universe.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +static const char cite_minstyle_spin_cg[] = + "min_style spin/cg command:\n\n" + "@article{ivanov2019fast,\n" + "title={Fast and Robust Algorithm for the Minimisation of the Energy of " + "Spin Systems},\n" + "author={Ivanov, A. V and Uzdin, V. M. and J{\'o}nsson, H.},\n" + "journal={arXiv preprint arXiv:1904.02669},\n" + "year={2019}\n" + "}\n\n"; + +// EPS_ENERGY = minimum normalization for energy tolerance + +#define EPS_ENERGY 1.0e-8 + +#define DELAYSTEP 5 + +/* ---------------------------------------------------------------------- */ + +MinSpinCG::MinSpinCG(LAMMPS *lmp) : + Min(lmp), g_old(NULL), g_cur(NULL), p_s(NULL), sp_copy(NULL) +{ + if (lmp->citeme) lmp->citeme->add(cite_minstyle_spin_cg); + nlocal_max = 0; + + // nreplica = number of partitions + // ireplica = which world I am in universe + + nreplica = universe->nworlds; + ireplica = universe->iworld; + use_line_search = 0; // no line search as default option for CG + + discrete_factor = 10.0; +} + +/* ---------------------------------------------------------------------- */ + +MinSpinCG::~MinSpinCG() +{ + memory->destroy(g_old); + memory->destroy(g_cur); + memory->destroy(p_s); + if (use_line_search) + memory->destroy(sp_copy); +} + +/* ---------------------------------------------------------------------- */ + +void MinSpinCG::init() +{ + local_iter = 0; + der_e_cur = 0.0; + der_e_pr = 0.0; + + Min::init(); + + // warning if line_search combined to gneb + + if ((nreplica >= 1) && (linestyle != 4) && (comm->me == 0)) + error->warning(FLERR,"Line search incompatible gneb"); + + // set back use_line_search to 0 if more than one replica + + if (linestyle == 3 && nreplica == 1){ + use_line_search = 1; + } + else{ + use_line_search = 0; + } + + dts = dt = update->dt; + last_negative = update->ntimestep; + + // allocate tables + + nlocal_max = atom->nlocal; + memory->grow(g_old,3*nlocal_max,"min/spin/cg:g_old"); + memory->grow(g_cur,3*nlocal_max,"min/spin/cg:g_cur"); + memory->grow(p_s,3*nlocal_max,"min/spin/cg:p_s"); + if (use_line_search) + memory->grow(sp_copy,nlocal_max,3,"min/spin/cg:sp_copy"); +} + +/* ---------------------------------------------------------------------- */ + +void MinSpinCG::setup_style() +{ + double **v = atom->v; + int nlocal = atom->nlocal; + + // check if the atom/spin style is defined + + if (!atom->sp_flag) + error->all(FLERR,"min spin/cg requires atom/spin style"); + + for (int i = 0; i < nlocal; i++) + v[i][0] = v[i][1] = v[i][2] = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +int MinSpinCG::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"discrete_factor") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + discrete_factor = force->numeric(FLERR,arg[1]); + return 2; + } + return 0; +} + +/* ---------------------------------------------------------------------- + set current vector lengths and pointers + called after atoms have migrated +------------------------------------------------------------------------- */ + +void MinSpinCG::reset_vectors() +{ + // atomic dof + + // size sp is 4N vector + nvec = 4 * atom->nlocal; + if (nvec) spvec = atom->sp[0]; + + nvec = 3 * atom->nlocal; + if (nvec) fmvec = atom->fm[0]; + + if (nvec) xvec = atom->x[0]; + if (nvec) fvec = atom->f[0]; +} + +/* ---------------------------------------------------------------------- + minimization via orthogonal spin optimisation +------------------------------------------------------------------------- */ + +int MinSpinCG::iterate(int maxiter) +{ + int nlocal = atom->nlocal; + bigint ntimestep; + double fmdotfm,fmsq; + int flag, flagall; + double **sp = atom->sp; + double der_e_cur_tmp = 0.0; + + if (nlocal_max < nlocal) { + local_iter = 0; + nlocal_max = nlocal; + memory->grow(g_old,3*nlocal_max,"min/spin/cg:g_old"); + memory->grow(g_cur,3*nlocal_max,"min/spin/cg:g_cur"); + memory->grow(p_s,3*nlocal_max,"min/spin/cg:p_s"); + if (use_line_search) + memory->grow(sp_copy,nlocal_max,3,"min/spin/cg:sp_copy"); + } + + for (int iter = 0; iter < maxiter; iter++) { + + if (timer->check_timeout(niter)) + return TIMEOUT; + + ntimestep = ++update->ntimestep; + niter++; + + // optimize timestep accross processes / replicas + // need a force calculation for timestep optimization + + if (use_line_search) { + + // here we need to do line search + if (local_iter == 0){ + calc_gradient(); + } + + calc_search_direction(); + der_e_cur = 0.0; + for (int i = 0; i < 3 * nlocal; i++) + der_e_cur += g_cur[i] * p_s[i]; + MPI_Allreduce(&der_e_cur,&der_e_cur_tmp,1,MPI_DOUBLE,MPI_SUM,world); + der_e_cur = der_e_cur_tmp; + if (update->multireplica == 1) { + MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + for (int i = 0; i < nlocal; i++) + for (int j = 0; j < 3; j++) + sp_copy[i][j] = sp[i][j]; + + eprevious = ecurrent; + der_e_pr = der_e_cur; + calc_and_make_step(0.0, 1.0, 0); + } + else{ + + // here we don't do line search + // if gneb calc., nreplica > 1 + // then calculate gradients and advance spins + // of intermediate replicas only + calc_gradient(); + calc_search_direction(); + advance_spins(); + neval++; + eprevious = ecurrent; + ecurrent = energy_force(0); + } + + // energy tolerance criterion + // only check after DELAYSTEP elapsed since velocties reset to 0 + // sync across replicas if running multi-replica minimization + + if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { + if (update->multireplica == 0) { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + return ETOL; + } else { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return ETOL; + } + } + + // magnetic torque tolerance criterion + // sync across replicas if running multi-replica minimization + + fmdotfm = fmsq = 0.0; + if (update->ftol > 0.0) { + if (normstyle == MAX) fmsq = max_torque(); // max torque norm + else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm + else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm + else error->all(FLERR,"Illegal min_modify command"); + fmdotfm = fmsq*fmsq; + if (update->multireplica == 0) { + if (fmdotfm < update->ftol*update->ftol) return FTOL; + } else { + if (fmdotfm < update->ftol*update->ftol) flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return FTOL; + } + } + + // output for thermo, dump, restart files + + if (output->next == ntimestep) { + timer->stamp(); + output->write(ntimestep); + timer->stamp(Timer::OUTPUT); + } + } + + return MAXITER; +} + +/* ---------------------------------------------------------------------- + calculate gradients +---------------------------------------------------------------------- */ + +void MinSpinCG::calc_gradient() +{ + int nlocal = atom->nlocal; + double **sp = atom->sp; + double **fm = atom->fm; + double hbar = force->hplanck/MY_2PI; + double factor; + + if (use_line_search) + factor = hbar; + else factor = evaluate_dt(); + + // loop on all spins on proc. + + for (int i = 0; i < nlocal; i++) { + g_cur[3 * i + 0] = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]) * factor; + g_cur[3 * i + 1] = -(fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]) * factor; + g_cur[3 * i + 2] = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]) * factor; + } +} + +/* ---------------------------------------------------------------------- + search direction: + The Fletcher-Reeves conj. grad. method + See Jorge Nocedal and Stephen J. Wright 'Numerical + Optimization' Second Edition, 2006 (p. 121) +---------------------------------------------------------------------- */ + +void MinSpinCG::calc_search_direction() +{ + int nlocal = atom->nlocal; + double g2old = 0.0; + double g2 = 0.0; + double beta = 0.0; + + double g2_global = 0.0; + double g2old_global = 0.0; + + double factor = 1.0; + + // for multiple replica do not move end points + if (nreplica > 1) + if (ireplica == 0 || ireplica == nreplica - 1) + factor = 0.0; + + + if (local_iter == 0 || local_iter % 5 == 0){ // steepest descent direction + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = -g_cur[i] * factor; + g_old[i] = g_cur[i] * factor; + } + } else { // conjugate direction + for (int i = 0; i < 3 * nlocal; i++) { + g2old += g_old[i] * g_old[i]; + g2 += g_cur[i] * g_cur[i]; + } + + // now we need to collect/broadcast beta on this replica + // need to check what is beta for GNEB + + MPI_Allreduce(&g2,&g2_global,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&g2old,&g2old_global,1,MPI_DOUBLE,MPI_SUM,world); + + // Sum over all replicas. Good for GNEB. + + if (nreplica > 1) { + g2 = g2_global * factor; + g2old = g2old_global * factor; + MPI_Allreduce(&g2,&g2_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + MPI_Allreduce(&g2old,&g2old_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + if (fabs(g2_global) < 1.0e-60) beta = 0.0; + else beta = g2_global / g2old_global; + + // calculate conjugate direction + + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = (beta * p_s[i] - g_cur[i]) * factor; + g_old[i] = g_cur[i] * factor; + } + } + + local_iter++; +} + +/* ---------------------------------------------------------------------- + rotation of spins along the search direction +---------------------------------------------------------------------- */ + +void MinSpinCG::advance_spins() +{ + int nlocal = atom->nlocal; + double **sp = atom->sp; + double rot_mat[9]; // exponential of matrix made of search direction + double s_new[3]; + + // loop on all spins on proc. + + for (int i = 0; i < nlocal; i++) { + rodrigues_rotation(p_s + 3 * i, rot_mat); + + // rotate spins + + vm3(rot_mat, sp[i], s_new); + for (int j = 0; j < 3; j++) sp[i][j] = s_new[j]; + } +} + +/* ---------------------------------------------------------------------- + calculate 3x3 matrix exponential using Rodrigues' formula + (R. Murray, Z. Li, and S. Shankar Sastry, + A Mathematical Introduction to + Robotic Manipulation (1994), p. 28 and 30). + + upp_tr - vector x, y, z so that one calculate + U = exp(A) with A= [[0, x, y], + [-x, 0, z], + [-y, -z, 0]] +------------------------------------------------------------------------- */ + +void MinSpinCG::rodrigues_rotation(const double *upp_tr, double *out) +{ + double theta,A,B,D,x,y,z; + double s1,s2,s3,a1,a2,a3; + + if (fabs(upp_tr[0]) < 1.0e-40 && + fabs(upp_tr[1]) < 1.0e-40 && + fabs(upp_tr[2]) < 1.0e-40){ + + // if upp_tr is zero, return unity matrix + + for(int k = 0; k < 3; k++){ + for(int m = 0; m < 3; m++){ + if (m == k) out[3 * k + m] = 1.0; + else out[3 * k + m] = 0.0; + } + } + return; + } + + theta = sqrt(upp_tr[0] * upp_tr[0] + + upp_tr[1] * upp_tr[1] + + upp_tr[2] * upp_tr[2]); + + A = cos(theta); + B = sin(theta); + D = 1.0 - A; + x = upp_tr[0]/theta; + y = upp_tr[1]/theta; + z = upp_tr[2]/theta; + + // diagonal elements of U + + out[0] = A + z * z * D; + out[4] = A + y * y * D; + out[8] = A + x * x * D; + + // off diagonal of U + + s1 = -y * z *D; + s2 = x * z * D; + s3 = -x * y * D; + + a1 = x * B; + a2 = y * B; + a3 = z * B; + + out[1] = s1 + a1; + out[3] = s1 - a1; + out[2] = s2 + a2; + out[6] = s2 - a2; + out[5] = s3 + a3; + out[7] = s3 - a3; + +} + +/* ---------------------------------------------------------------------- + out = vector^T x m, + m -- 3x3 matrix , v -- 3-d vector +------------------------------------------------------------------------- */ + +void MinSpinCG::vm3(const double *m, const double *v, double *out) +{ + for(int i = 0; i < 3; i++){ + out[i] = 0.0; + for(int j = 0; j < 3; j++) out[i] += *(m + 3 * j + i) * v[j]; + } +} + +/* ---------------------------------------------------------------------- + advance spins +------------------------------------------------------------------------- */ + +void MinSpinCG::make_step(double c, double *energy_and_der) +{ + double p_scaled[3]; + int nlocal = atom->nlocal; + double rot_mat[9]; // exponential of matrix made of search direction + double s_new[3]; + double **sp = atom->sp; + double der_e_cur_tmp = 0.0; + + for (int i = 0; i < nlocal; i++) { + + // scale the search direction + + for (int j = 0; j < 3; j++) p_scaled[j] = c * p_s[3 * i + j]; + + // calculate rotation matrix + + rodrigues_rotation(p_scaled, rot_mat); + + // rotate spins + + vm3(rot_mat, sp[i], s_new); + for (int j = 0; j < 3; j++) sp[i][j] = s_new[j]; + } + + ecurrent = energy_force(0); + calc_gradient(); + neval++; + der_e_cur = 0.0; + for (int i = 0; i < 3 * nlocal; i++) { + der_e_cur += g_cur[i] * p_s[i]; + } + MPI_Allreduce(&der_e_cur,&der_e_cur_tmp,1,MPI_DOUBLE,MPI_SUM,world); + der_e_cur = der_e_cur_tmp; + if (update->multireplica == 1) { + MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + energy_and_der[0] = ecurrent; + energy_and_der[1] = der_e_cur; +} + +/* ---------------------------------------------------------------------- + Calculate step length which satisfies approximate Wolfe conditions + using the cubic interpolation +------------------------------------------------------------------------- */ + +int MinSpinCG::calc_and_make_step(double a, double b, int index) +{ + double e_and_d[2] = {0.0,0.0}; + double alpha,c1,c2,c3; + double **sp = atom->sp; + int nlocal = atom->nlocal; + + make_step(b,e_and_d); + ecurrent = e_and_d[0]; + der_e_cur = e_and_d[1]; + index++; + + if (adescent(eprevious,e_and_d[0]) || index == 5){ + MPI_Bcast(&b,1,MPI_DOUBLE,0,world); + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = b * p_s[i]; + } + return 1; + } + else { + double r,f0,f1,df0,df1; + r = b - a; + f0 = eprevious; + f1 = ecurrent; + df0 = der_e_pr; + df1 = der_e_cur; + + c1 = -2.0*(f1-f0)/(r*r*r)+(df1+df0)/(r*r); + c2 = 3.0*(f1-f0)/(r*r)-(df1+2.0*df0)/(r); + c3 = df0; + + // f(x) = c1 x^3 + c2 x^2 + c3 x^1 + c4 + // has minimum at alpha below. We do not check boundaries. + + alpha = (-c2 + sqrt(c2*c2 - 3.0*c1*c3))/(3.0*c1); + MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world); + + if (alpha < 0.0) alpha = r/2.0; + + for (int i = 0; i < nlocal; i++) { + for (int j = 0; j < 3; j++) sp[i][j] = sp_copy[i][j]; + } + calc_and_make_step(0.0, alpha, index); + } + + return 0; +} + +/* ---------------------------------------------------------------------- + Approximate descent +------------------------------------------------------------------------- */ + +int MinSpinCG::adescent(double phi_0, double phi_j){ + + double eps = 1.0e-6; + + if (phi_j<=phi_0+eps*fabs(phi_0)) + return 1; + else + return 0; +} + +/* ---------------------------------------------------------------------- + evaluate max timestep +---------------------------------------------------------------------- */ + +double MinSpinCG::evaluate_dt() +{ + double dtmax; + double fmsq; + double fmaxsqone,fmaxsqloc,fmaxsqall; + int nlocal = atom->nlocal; + double **fm = atom->fm; + + // finding max fm on this proc. + + fmsq = fmaxsqone = fmaxsqloc = fmaxsqall = 0.0; + for (int i = 0; i < nlocal; i++) { + fmsq = fm[i][0]*fm[i][0]+fm[i][1]*fm[i][1]+fm[i][2]*fm[i][2]; + fmaxsqone = MAX(fmaxsqone,fmsq); + } + + // finding max fm on this replica + + fmaxsqloc = fmaxsqone; + MPI_Allreduce(&fmaxsqone,&fmaxsqloc,1,MPI_DOUBLE,MPI_MAX,world); + + // finding max fm over all replicas, if necessary + // this communicator would be invalid for multiprocess replicas + + fmaxsqall = fmaxsqloc; + if (update->multireplica == 1) { + fmaxsqall = fmaxsqloc; + MPI_Allreduce(&fmaxsqloc,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,universe->uworld); + } + + if (fmaxsqall == 0.0) + error->all(FLERR,"Incorrect fmaxsqall calculation"); + + // define max timestep by dividing by the + // inverse of max frequency by discrete_factor + + dtmax = MY_2PI/(discrete_factor*sqrt(fmaxsqall)); + + return dtmax; +} diff --git a/src/SPIN/min_spin_cg.h b/src/SPIN/min_spin_cg.h new file mode 100644 index 0000000000000000000000000000000000000000..0eed7a61e6b45c70cbacb8ac6f7ac60fba861ed7 --- /dev/null +++ b/src/SPIN/min_spin_cg.h @@ -0,0 +1,71 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef MINIMIZE_CLASS + +MinimizeStyle(spin/cg, MinSpinCG) + +#else + +#ifndef LMP_MIN_SPIN_CG_H +#define LMP_MIN_SPIN_CG_H + +#include "min.h" + +namespace LAMMPS_NS { + +class MinSpinCG: public Min { + public: + MinSpinCG(class LAMMPS *); + virtual ~MinSpinCG(); + void init(); + void setup_style(); + void reset_vectors(); + int modify_param(int, char **); + int iterate(int); + + private: + int local_iter; // for neb + int nlocal_max; // max value of nlocal (for size of lists) + int use_line_search; // use line search or not. + int ireplica,nreplica; // for neb + double dt; // global timestep + double dts; // spin timestep + double discrete_factor; // factor for spin timestep evaluation + double der_e_cur; // current derivative along search dir. + double der_e_pr; // previous derivative along search dir. + double *spvec; // variables for atomic dof, as 1d vector + double *fmvec; // variables for atomic dof, as 1d vector + double *g_old; // gradient vector at previous step + double *g_cur; // current gradient vector + double *p_s; // search direction vector + double **sp_copy; // copy of the spins + + void advance_spins(); + void calc_gradient(); + void calc_search_direction(); + void vm3(const double *, const double *, double *); + void rodrigues_rotation(const double *, double *); + void make_step(double, double *); + int calc_and_make_step(double, double, int); + int adescent(double, double); + double evaluate_dt(); + double maximum_rotation(double *); + + bigint last_negative; +}; + +} + +#endif +#endif diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..f86bdd5d48d1ad269b34e9ba36e6c035ff14fcdf --- /dev/null +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -0,0 +1,754 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Aleksei Ivanov (University of Iceland) + Julien Tranchida (SNL) + + Please cite the related publication: + Ivanov, A. V., Uzdin, V. M., & Jónsson, H. (2019). Fast and Robust + Algorithm for the Minimisation of the Energy of Spin Systems. arXiv + preprint arXiv:1904.02669. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "min_spin_lbfgs.h" +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "force.h" +#include "update.h" +#include "output.h" +#include "timer.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "math_special.h" +#include "math_const.h" +#include "universe.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +static const char cite_minstyle_spin_lbfgs[] = + "min_style spin/lbfgs command:\n\n" + "@article{ivanov2019fast,\n" + "title={Fast and Robust Algorithm for the Minimisation of the Energy of " + "Spin Systems},\n" + "author={Ivanov, A. V and Uzdin, V. M. and J{\'o}nsson, H.},\n" + "journal={arXiv preprint arXiv:1904.02669},\n" + "year={2019}\n" + "}\n\n"; + +// EPS_ENERGY = minimum normalization for energy tolerance + +#define EPS_ENERGY 1.0e-8 + +#define DELAYSTEP 5 + +/* ---------------------------------------------------------------------- */ + +MinSpinLBFGS::MinSpinLBFGS(LAMMPS *lmp) : + Min(lmp), g_old(NULL), g_cur(NULL), p_s(NULL), rho(NULL), ds(NULL), dy(NULL), sp_copy(NULL) +{ + if (lmp->citeme) lmp->citeme->add(cite_minstyle_spin_lbfgs); + nlocal_max = 0; + + // nreplica = number of partitions + // ireplica = which world I am in universe + + nreplica = universe->nworlds; + ireplica = universe->iworld; + use_line_search = 0; // no line search as default option for LBFGS + + maxepsrot = MY_2PI / (100.0); + +} + +/* ---------------------------------------------------------------------- */ + +MinSpinLBFGS::~MinSpinLBFGS() +{ + memory->destroy(g_old); + memory->destroy(g_cur); + memory->destroy(p_s); + memory->destroy(ds); + memory->destroy(dy); + memory->destroy(rho); + if (use_line_search) + memory->destroy(sp_copy); +} + +/* ---------------------------------------------------------------------- */ + +void MinSpinLBFGS::init() +{ + num_mem = 3; + local_iter = 0; + der_e_cur = 0.0; + der_e_pr = 0.0; + + Min::init(); + + // warning if line_search combined to gneb + + if ((nreplica >= 1) && (linestyle != 4) && (comm->me == 0)) + error->warning(FLERR,"Line search incompatible gneb"); + + // set back use_line_search to 0 if more than one replica + + if (linestyle == 3 && nreplica == 1){ + use_line_search = 1; + } + else{ + use_line_search = 0; + } + + last_negative = update->ntimestep; + + // allocate tables + + nlocal_max = atom->nlocal; + memory->grow(g_old,3*nlocal_max,"min/spin/lbfgs:g_old"); + memory->grow(g_cur,3*nlocal_max,"min/spin/lbfgs:g_cur"); + memory->grow(p_s,3*nlocal_max,"min/spin/lbfgs:p_s"); + memory->grow(rho,num_mem,"min/spin/lbfgs:rho"); + memory->grow(ds,num_mem,3*nlocal_max,"min/spin/lbfgs:ds"); + memory->grow(dy,num_mem,3*nlocal_max,"min/spin/lbfgs:dy"); + if (use_line_search) + memory->grow(sp_copy,nlocal_max,3,"min/spin/lbfgs:sp_copy"); + +} + +/* ---------------------------------------------------------------------- */ + +void MinSpinLBFGS::setup_style() +{ + double **v = atom->v; + int nlocal = atom->nlocal; + + // check if the atom/spin style is defined + + if (!atom->sp_flag) + error->all(FLERR,"min spin/lbfgs requires atom/spin style"); + + for (int i = 0; i < nlocal; i++) + v[i][0] = v[i][1] = v[i][2] = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +int MinSpinLBFGS::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"discrete_factor") == 0) { + if (narg < 2) error->all(FLERR,"Illegal min_modify command"); + double discrete_factor; + discrete_factor = force->numeric(FLERR,arg[1]); + maxepsrot = MY_2PI / (10 * discrete_factor); + return 2; + } + return 0; +} + +/* ---------------------------------------------------------------------- + set current vector lengths and pointers + called after atoms have migrated +------------------------------------------------------------------------- */ + +void MinSpinLBFGS::reset_vectors() +{ + // atomic dof + + // size sp is 4N vector + nvec = 4 * atom->nlocal; + if (nvec) spvec = atom->sp[0]; + + nvec = 3 * atom->nlocal; + if (nvec) fmvec = atom->fm[0]; + + if (nvec) xvec = atom->x[0]; + if (nvec) fvec = atom->f[0]; +} + +/* ---------------------------------------------------------------------- + minimization via damped spin dynamics +------------------------------------------------------------------------- */ + +int MinSpinLBFGS::iterate(int maxiter) +{ + int nlocal = atom->nlocal; + bigint ntimestep; + double fmdotfm,fmsq; + int flag, flagall; + double **sp = atom->sp; + double der_e_cur_tmp = 0.0; + + if (nlocal_max < nlocal) { + nlocal_max = nlocal; + local_iter = 0; + memory->grow(g_old,3*nlocal_max,"min/spin/lbfgs:g_old"); + memory->grow(g_cur,3*nlocal_max,"min/spin/lbfgs:g_cur"); + memory->grow(p_s,3*nlocal_max,"min/spin/lbfgs:p_s"); + memory->grow(rho,num_mem,"min/spin/lbfgs:rho"); + memory->grow(ds,num_mem,3*nlocal_max,"min/spin/lbfgs:ds"); + memory->grow(dy,num_mem,3*nlocal_max,"min/spin/lbfgs:dy"); + if (use_line_search) + memory->grow(sp_copy,nlocal_max,3,"min/spin/lbfgs:sp_copy"); + } + + for (int iter = 0; iter < maxiter; iter++) { + + if (timer->check_timeout(niter)) + return TIMEOUT; + + ntimestep = ++update->ntimestep; + niter++; + + // optimize timestep accross processes / replicas + // need a force calculation for timestep optimization + + if (use_line_search) { + + // here we need to do line search + if (local_iter == 0){ + eprevious = ecurrent; + ecurrent = energy_force(0); + calc_gradient(); + } + + calc_search_direction(); + der_e_cur = 0.0; + for (int i = 0; i < 3 * nlocal; i++) + der_e_cur += g_cur[i] * p_s[i]; + MPI_Allreduce(&der_e_cur,&der_e_cur_tmp,1,MPI_DOUBLE,MPI_SUM,world); + der_e_cur = der_e_cur_tmp; + if (update->multireplica == 1) { + MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + for (int i = 0; i < nlocal; i++) + for (int j = 0; j < 3; j++) + sp_copy[i][j] = sp[i][j]; + + eprevious = ecurrent; + der_e_pr = der_e_cur; + calc_and_make_step(0.0, 1.0, 0); + } + else{ + + // here we don't do line search + // but use cutoff rotation angle + // if gneb calc., nreplica > 1 + // then calculate gradients and advance spins + // of intermediate replicas only + eprevious = ecurrent; + ecurrent = energy_force(0); + calc_gradient(); + calc_search_direction(); + advance_spins(); + neval++; + } + + // energy tolerance criterion + // only check after DELAYSTEP elapsed since velocties reset to 0 + // sync across replicas if running multi-replica minimization + + if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { + if (update->multireplica == 0) { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + return ETOL; + } else { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return ETOL; + } + } + + // magnetic torque tolerance criterion + // sync across replicas if running multi-replica minimization + + fmdotfm = fmsq = 0.0; + if (update->ftol > 0.0) { + if (normstyle == MAX) fmsq = max_torque(); // max torque norm + else if (normstyle == INF) fmsq = inf_torque(); // inf torque norm + else if (normstyle == TWO) fmsq = total_torque(); // Euclidean torque 2-norm + else error->all(FLERR,"Illegal min_modify command"); + fmdotfm = fmsq*fmsq; + if (update->multireplica == 0) { + if (fmdotfm < update->ftol*update->ftol) return FTOL; + } else { + if (fmdotfm < update->ftol*update->ftol) flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return FTOL; + } + } + + // output for thermo, dump, restart files + + if (output->next == ntimestep) { + timer->stamp(); + output->write(ntimestep); + timer->stamp(Timer::OUTPUT); + } + } + + return MAXITER; +} + +/* ---------------------------------------------------------------------- + calculate gradients +---------------------------------------------------------------------- */ + +void MinSpinLBFGS::calc_gradient() +{ + int nlocal = atom->nlocal; + double **sp = atom->sp; + double **fm = atom->fm; + double hbar = force->hplanck/MY_2PI; + + // loop on all spins on proc. + + for (int i = 0; i < nlocal; i++) { + g_cur[3 * i + 0] = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]) * hbar; + g_cur[3 * i + 1] = -(fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]) * hbar; + g_cur[3 * i + 2] = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]) * hbar; + } +} + +/* ---------------------------------------------------------------------- + search direction: + Limited-memory BFGS. + See Jorge Nocedal and Stephen J. Wright 'Numerical + Optimization' Second Edition, 2006 (p. 177) +---------------------------------------------------------------------- */ + +void MinSpinLBFGS::calc_search_direction() +{ + int nlocal = atom->nlocal; + + double dyds = 0.0; + double sq = 0.0; + double yy = 0.0; + double yr = 0.0; + double beta = 0.0; + + double dyds_global = 0.0; + double sq_global = 0.0; + double yy_global = 0.0; + double yr_global = 0.0; + + int m_index = local_iter % num_mem; // memory index + int c_ind = 0; + double *q; + double *alpha; + + double factor; + double scaling = 1.0; + + // for multiple replica do not move end points + if (nreplica > 1) { + if (ireplica == 0 || ireplica == nreplica - 1) { + factor = 0.0; + } + else factor = 1.0; + }else{ + factor = 1.0; + } + + if (local_iter == 0){ // steepest descent direction + + //if no line search then calculate maximum rotation + if (use_line_search == 0) + scaling = maximum_rotation(g_cur); + + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = -g_cur[i] * factor * scaling;; + g_old[i] = g_cur[i] * factor; + for (int k = 0; k < num_mem; k++){ + ds[k][i] = 0.0; + dy[k][i] = 0.0; + } + } + for (int k = 0; k < num_mem; k++) + rho[k] = 0.0; + + } else { + dyds = 0.0; + for (int i = 0; i < 3 * nlocal; i++) { + ds[m_index][i] = p_s[i]; + dy[m_index][i] = g_cur[i] - g_old[i]; + dyds += ds[m_index][i] * dy[m_index][i]; + } + MPI_Allreduce(&dyds, &dyds_global, 1, MPI_DOUBLE, MPI_SUM, world); + + if (nreplica > 1) { + dyds_global *= factor; + dyds = dyds_global; + MPI_Allreduce(&dyds, &dyds_global, 1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + if (fabs(dyds_global) > 1.0e-60) rho[m_index] = 1.0 / dyds_global; + else rho[m_index] = 1.0e60; + + if (rho[m_index] < 0.0){ + local_iter = 0; + return calc_search_direction(); + } + q = (double *) calloc(3*nlocal, sizeof(double)); + alpha = (double *) calloc(num_mem, sizeof(double)); + // set the q vector + + for (int i = 0; i < 3 * nlocal; i++) { + q[i] = g_cur[i]; + } + + // loop over last m indecies + for(int k = num_mem - 1; k > -1; k--) { + // this loop should run from the newest memory to the oldest one. + + c_ind = (k + m_index + 1) % num_mem; + + // dot product between dg and q + + sq = 0.0; + for (int i = 0; i < 3 * nlocal; i++) { + sq += ds[c_ind][i] * q[i]; + } + MPI_Allreduce(&sq,&sq_global,1,MPI_DOUBLE,MPI_SUM,world); + if (nreplica > 1) { + sq_global *= factor; + sq = sq_global; + MPI_Allreduce(&sq,&sq_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + // update alpha + + alpha[c_ind] = rho[c_ind] * sq_global; + + // update q + + for (int i = 0; i < 3 * nlocal; i++) { + q[i] -= alpha[c_ind] * dy[c_ind][i]; + } + } + + // dot product between dg with itself + yy = 0.0; + for (int i = 0; i < 3 * nlocal; i++) { + yy += dy[m_index][i] * dy[m_index][i]; + } + MPI_Allreduce(&yy,&yy_global,1,MPI_DOUBLE,MPI_SUM,world); + if (nreplica > 1) { + yy_global *= factor; + yy = yy_global; + MPI_Allreduce(&yy,&yy_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + // calculate now search direction + + double devis = rho[m_index] * yy_global; + + if (fabs(devis) > 1.0e-60) { + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = factor * q[i] / devis; + } + }else{ + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = factor * q[i] * 1.0e60; + } + } + + for (int k = 0; k < num_mem; k++){ + // this loop should run from the oldest memory to the newest one. + + if (local_iter < num_mem) c_ind = k; + else c_ind = (k + m_index + 1) % num_mem; + + // dot product between p and da + yr = 0.0; + for (int i = 0; i < 3 * nlocal; i++) { + yr += dy[c_ind][i] * p_s[i]; + } + + MPI_Allreduce(&yr,&yr_global,1,MPI_DOUBLE,MPI_SUM,world); + if (nreplica > 1) { + yr_global *= factor; + yr = yr_global; + MPI_Allreduce(&yr,&yr_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + beta = rho[c_ind] * yr_global; + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] += ds[c_ind][i] * (alpha[c_ind] - beta); + } + } + if (use_line_search == 0) + scaling = maximum_rotation(p_s); + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = - factor * p_s[i] * scaling; + g_old[i] = g_cur[i] * factor; + } + free(q); + free(alpha); + } + local_iter++; +} + +/* ---------------------------------------------------------------------- + rotation of spins along the search direction +---------------------------------------------------------------------- */ + +void MinSpinLBFGS::advance_spins() +{ + int nlocal = atom->nlocal; + double **sp = atom->sp; + double rot_mat[9]; // exponential of matrix made of search direction + double s_new[3]; + + // loop on all spins on proc. + + for (int i = 0; i < nlocal; i++) { + rodrigues_rotation(p_s + 3 * i, rot_mat); + + // rotate spins + + vm3(rot_mat, sp[i], s_new); + for (int j = 0; j < 3; j++) sp[i][j] = s_new[j]; + } +} + +/* ---------------------------------------------------------------------- + calculate 3x3 matrix exponential using Rodrigues' formula + (R. Murray, Z. Li, and S. Shankar Sastry, + A Mathematical Introduction to + Robotic Manipulation (1994), p. 28 and 30). + + upp_tr - vector x, y, z so that one calculate + U = exp(A) with A= [[0, x, y], + [-x, 0, z], + [-y, -z, 0]] +------------------------------------------------------------------------- */ + +void MinSpinLBFGS::rodrigues_rotation(const double *upp_tr, double *out) +{ + double theta,A,B,D,x,y,z; + double s1,s2,s3,a1,a2,a3; + + if (fabs(upp_tr[0]) < 1.0e-40 && + fabs(upp_tr[1]) < 1.0e-40 && + fabs(upp_tr[2]) < 1.0e-40){ + + // if upp_tr is zero, return unity matrix + for(int k = 0; k < 3; k++){ + for(int m = 0; m < 3; m++){ + if (m == k) out[3 * k + m] = 1.0; + else out[3 * k + m] = 0.0; + } + } + return; + } + + theta = sqrt(upp_tr[0] * upp_tr[0] + + upp_tr[1] * upp_tr[1] + + upp_tr[2] * upp_tr[2]); + + A = cos(theta); + B = sin(theta); + D = 1 - A; + x = upp_tr[0]/theta; + y = upp_tr[1]/theta; + z = upp_tr[2]/theta; + + // diagonal elements of U + + out[0] = A + z * z * D; + out[4] = A + y * y * D; + out[8] = A + x * x * D; + + // off diagonal of U + + s1 = -y * z *D; + s2 = x * z * D; + s3 = -x * y * D; + + a1 = x * B; + a2 = y * B; + a3 = z * B; + + out[1] = s1 + a1; + out[3] = s1 - a1; + out[2] = s2 + a2; + out[6] = s2 - a2; + out[5] = s3 + a3; + out[7] = s3 - a3; + +} + +/* ---------------------------------------------------------------------- + out = vector^T x m, + m -- 3x3 matrix , v -- 3-d vector +------------------------------------------------------------------------- */ + +void MinSpinLBFGS::vm3(const double *m, const double *v, double *out) +{ + for(int i = 0; i < 3; i++){ + out[i] = 0.0; + for(int j = 0; j < 3; j++) + out[i] += *(m + 3 * j + i) * v[j]; + } +} + + +void MinSpinLBFGS::make_step(double c, double *energy_and_der) +{ + double p_scaled[3]; + int nlocal = atom->nlocal; + double rot_mat[9]; // exponential of matrix made of search direction + double s_new[3]; + double **sp = atom->sp; + double der_e_cur_tmp = 0.0; + + for (int i = 0; i < nlocal; i++) { + + // scale the search direction + + for (int j = 0; j < 3; j++) p_scaled[j] = c * p_s[3 * i + j]; + + // calculate rotation matrix + + rodrigues_rotation(p_scaled, rot_mat); + + // rotate spins + + vm3(rot_mat, sp[i], s_new); + for (int j = 0; j < 3; j++) sp[i][j] = s_new[j]; + } + + ecurrent = energy_force(0); + calc_gradient(); + neval++; + der_e_cur = 0.0; + for (int i = 0; i < 3 * nlocal; i++) { + der_e_cur += g_cur[i] * p_s[i]; + } + MPI_Allreduce(&der_e_cur,&der_e_cur_tmp, 1, MPI_DOUBLE, MPI_SUM, world); + der_e_cur = der_e_cur_tmp; + if (update->multireplica == 1) { + MPI_Allreduce(&der_e_cur_tmp,&der_e_cur,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + + energy_and_der[0] = ecurrent; + energy_and_der[1] = der_e_cur; +} + +/* ---------------------------------------------------------------------- + Calculate step length which satisfies approximate Wolfe conditions + using the cubic interpolation +------------------------------------------------------------------------- */ + +int MinSpinLBFGS::calc_and_make_step(double a, double b, int index) +{ + double e_and_d[2] = {0.0,0.0}; + double alpha,c1,c2,c3; + double **sp = atom->sp; + int nlocal = atom->nlocal; + + make_step(b,e_and_d); + ecurrent = e_and_d[0]; + der_e_cur = e_and_d[1]; + index++; + + if (adescent(eprevious,e_and_d[0]) || index == 5){ + MPI_Bcast(&b,1,MPI_DOUBLE,0,world); + for (int i = 0; i < 3 * nlocal; i++) { + p_s[i] = b * p_s[i]; + } + return 1; + } + else{ + double r,f0,f1,df0,df1; + r = b - a; + f0 = eprevious; + f1 = ecurrent; + df0 = der_e_pr; + df1 = der_e_cur; + + c1 = -2.0*(f1-f0)/(r*r*r)+(df1+df0)/(r*r); + c2 = 3.0*(f1-f0)/(r*r)-(df1+2.0*df0)/(r); + c3 = df0; + + // f(x) = c1 x^3 + c2 x^2 + c3 x^1 + c4 + // has minimum at alpha below. We do not check boundaries. + + alpha = (-c2 + sqrt(c2*c2 - 3.0*c1*c3))/(3.0*c1); + MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world); + + if (alpha < 0.0) alpha = r/2.0; + + for (int i = 0; i < nlocal; i++) { + for (int j = 0; j < 3; j++) sp[i][j] = sp_copy[i][j]; + } + calc_and_make_step(0.0, alpha, index); + } + + return 0; +} + +/* ---------------------------------------------------------------------- + Approximate descent +------------------------------------------------------------------------- */ + +int MinSpinLBFGS::adescent(double phi_0, double phi_j){ + + double eps = 1.0e-6; + + if (phi_j<=phi_0+eps*fabs(phi_0)) + return 1; + else + return 0; +} + +double MinSpinLBFGS::maximum_rotation(double *p) +{ + double norm2,norm2_global,scaling,alpha; + int nlocal = atom->nlocal; + int ntotal = 0; + + norm2 = 0.0; + for (int i = 0; i < 3 * nlocal; i++) norm2 += p[i] * p[i]; + + MPI_Allreduce(&norm2,&norm2_global,1,MPI_DOUBLE,MPI_SUM,world); + if (nreplica > 1) { + norm2 = norm2_global; + MPI_Allreduce(&norm2,&norm2_global,1,MPI_DOUBLE,MPI_SUM,universe->uworld); + } + MPI_Allreduce(&nlocal,&ntotal,1,MPI_INT,MPI_SUM,world); + if (nreplica > 1) { + nlocal = ntotal; + MPI_Allreduce(&nlocal,&ntotal,1,MPI_INT,MPI_SUM,universe->uworld); + } + + scaling = (maxepsrot * sqrt((double) ntotal / norm2_global)); + + if (scaling < 1.0) alpha = scaling; + else alpha = 1.0; + + return alpha; +} diff --git a/src/SPIN/min_spin_lbfgs.h b/src/SPIN/min_spin_lbfgs.h new file mode 100644 index 0000000000000000000000000000000000000000..cead605b3279044e6d7c325b2aafb63c1fe84d88 --- /dev/null +++ b/src/SPIN/min_spin_lbfgs.h @@ -0,0 +1,72 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef MINIMIZE_CLASS + +MinimizeStyle(spin/lbfgs, MinSpinLBFGS) + +#else + +#ifndef LMP_MIN_SPIN_LBFGS_H +#define LMP_MIN_SPIN_LBFGS_H + +#include "min.h" + +namespace LAMMPS_NS { + +class MinSpinLBFGS: public Min { + public: + MinSpinLBFGS(class LAMMPS *); + virtual ~MinSpinLBFGS(); + void init(); + void setup_style(); + int modify_param(int, char **); + void reset_vectors(); + int iterate(int); + + private: + int local_iter; // for neb + int use_line_search; // use line search or not. + int nlocal_max; // max value of nlocal (for size of lists) + int ireplica,nreplica; // for neb + double der_e_cur; // current derivative along search dir. + double der_e_pr; // previous derivative along search dir. + double maxepsrot; + double *spvec; // variables for atomic dof, as 1d vector + double *fmvec; // variables for atomic dof, as 1d vector + double *g_old; // gradient vector at previous step + double *g_cur; // current gradient vector + double *p_s; // search direction vector + + void advance_spins(); + void calc_gradient(); + void calc_search_direction(); + void vm3(const double *, const double *, double *); + void rodrigues_rotation(const double *, double *); + void make_step(double, double *); + int calc_and_make_step(double, double, int); + int adescent(double, double); + double maximum_rotation(double *); + + double *rho; // estimation of curvature + double **ds; // change in rotation matrix between two iterations, da + double **dy; // change in gradients between two iterations, dg + double **sp_copy; // copy of the spins + int num_mem; // number of stored steps + bigint last_negative; +}; + +} + +#endif +#endif diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 2bcfe6573af1b62b1b7d81a7f10381d73b2e8f52..559fd1cb49ccb168232d86e1a176e5bd0ce54874 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -43,6 +43,8 @@ #include "timer.h" #include "memory.h" #include "error.h" +#include "math_const.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -186,8 +188,8 @@ void NEBSpin::run() if (update->minimize->searchflag) error->all(FLERR,"NEBSpin requires damped dynamics minimizer"); - if (strcmp(update->minimize_style,"spin") != 0) - error->all(FLERR,"NEBSpin requires spin minimizer"); + if (!utils::strmatch(update->minimize_style,"^spin")) + error->all(FLERR,"NEBSpin requires a spin minimizer"); // setup regular NEBSpin minimization @@ -243,6 +245,8 @@ void NEBSpin::run() timer->init(); timer->barrier_start(); + // if(ireplica != 0 && ireplica != nreplica -1) + while (update->minimize->niter < n1steps) { update->minimize->run(nevery); print_status(); @@ -639,7 +643,7 @@ int NEBSpin::initial_rotation(double *spi, double *sploc, double fraction) kcrossy = kz*spix - kx*spiz; kcrossz = kx*spiy - ky*spix; - kdots = kx*spix + ky*spiz + kz*spiz; + kdots = kx*spix + ky*spiy + kz*spiz; omega = acos(sidotsf); omega *= fraction; diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index fef247c09b973077d4fa1cc46879c879801b6b9b..d956729e602651045b2e4ae7f66385c568d9e932 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -24,13 +24,17 @@ #include "pair_spin.h" #include #include "atom.h" +#include "comm.h" #include "error.h" #include "fix.h" #include "force.h" #include "math_const.h" #include "modify.h" +#include "neighbor.h" +#include "neigh_request.h" #include "pair.h" #include "update.h" +#include "fix_nve_spin.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -41,7 +45,9 @@ PairSpin::PairSpin(LAMMPS *lmp) : Pair(lmp) { hbar = force->hplanck/MY_2PI; single_enable = 0; + respa_enable = 0; no_virial_fdotr_compute = 1; + lattice_flag = 0; } /* ---------------------------------------------------------------------- */ @@ -57,11 +63,10 @@ void PairSpin::settings(int narg, char **/*arg*/) if (narg < 1 || narg > 2) error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); - // pair/spin need the metal unit style + // pair spin/* need the metal unit style if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"pair/spin style requires metal units"); - + error->all(FLERR,"Spin pair styles require metal units"); } /* ---------------------------------------------------------------------- @@ -73,13 +78,24 @@ void PairSpin::init_style() if (!atom->sp_flag) error->all(FLERR,"Pair spin requires atom/spin style"); - // checking if nve/spin is a listed fix + // checking if nve/spin or neb/spin is a listed fix + + bool have_fix = ((modify->find_fix_by_style("^nve/spin") != -1) + || (modify->find_fix_by_style("^neb/spin") != -1)); + + if (!have_fix && (comm->me == 0)) + error->warning(FLERR,"Using spin pair style without nve/spin or neb/spin"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // get the lattice_flag from nve/spin + + int ifix = modify->find_fix_by_style("^nve/spin"); + if (ifix >=0) + lattice_flag = ((FixNVESpin *) modify->fix[ifix])->lattice_flag; - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - ifix++; - } - if (ifix == modify->nfix) - error->all(FLERR,"pair/spin style requires nve/spin"); } diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h index 3a909e1d1305bc4bed4ad8b92d28cd3384509fc1..0111814c72ec39ceb34768d9dde2a30832ca2e20 100644 --- a/src/SPIN/pair_spin.h +++ b/src/SPIN/pair_spin.h @@ -34,6 +34,7 @@ friend class FixNVESpin; protected: double hbar; // Planck constant (eV.ps.rad-1) + int lattice_flag; // flag for mech force computation virtual void allocate() {} }; diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index fb0ec8bb20bbbe91fec92918694674cc0f26685e..4ff90323f26f46b005e4e78fca0f5f4a9f7801a8 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -27,40 +27,31 @@ #include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" #include "math_const.h" #include "memory.h" #include "modify.h" #include "error.h" #include "update.h" - +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; /* ---------------------------------------------------------------------- */ -PairSpinDipoleCut::PairSpinDipoleCut(LAMMPS *lmp) : PairSpin(lmp), -lockfixnvespin(NULL) +PairSpinDipoleCut::PairSpinDipoleCut(LAMMPS *lmp) : PairSpin(lmp) { - single_enable = 0; spinflag = 1; - respa_enable = 0; - no_virial_fdotr_compute = 1; - lattice_flag = 0; - - hbar = force->hplanck/MY_2PI; // eV/(rad.THz) - mub = 9.274e-4; // in A.Ang^2 - mu_0 = 785.15; // in eV/Ang/A^2 - mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 - //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV - mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz + hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + mub = 9.274e-4; // in A.Ang^2 + mu_0 = 785.15; // in eV/Ang/A^2 + mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV.Ang^3 + //mub2mu0 = mub * mub * mu_0 / (4.0*MY_PI); // in eV + mub2mu0hbinv = mub2mu0 / hbar; // in rad.THz } /* ---------------------------------------------------------------------- @@ -82,14 +73,7 @@ PairSpinDipoleCut::~PairSpinDipoleCut() void PairSpinDipoleCut::settings(int narg, char **arg) { - if (narg < 1 || narg > 2) - error->all(FLERR,"Incorrect args in pair_style command"); - - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin simulations require metal unit style"); - - if (!atom->sp) - error->all(FLERR,"Pair/spin style requires atom attribute sp"); + PairSpin::settings(narg,arg); cut_spin_long_global = force->numeric(FLERR,arg[0]); @@ -137,43 +121,6 @@ void PairSpinDipoleCut::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairSpinDipoleCut::init_style() -{ - if (!atom->sp_flag) - error->all(FLERR,"Pair spin requires atom/spin style"); - - // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // checking if nve/spin or neb/spin are a listed fix - - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; - ifix++; - } - if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); - - // get the lattice_flag from nve/spin - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { - lockfixnvespin = (FixNVESpin *) modify->fix[i]; - lattice_flag = lockfixnvespin->lattice_flag; - } - } - -} - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ @@ -323,7 +270,7 @@ void PairSpinDipoleCut::compute(int eflag, int vflag) void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) { int j,jnum,itype,jtype,ntypes; - int *ilist,*jlist,*numneigh,**firstneigh; + int *jlist,*numneigh,**firstneigh; double rsq,rinv,r2inv,r3inv,local_cut2; double xi[3],rij[3],eij[3],spi[4],spj[4]; @@ -410,7 +357,7 @@ void PairSpinDipoleCut::compute_single_pair(int ii, double fmi[3]) compute dipolar interaction between spins i and j ------------------------------------------------------------------------- */ -void PairSpinDipoleCut::compute_dipolar(int i, int j, double eij[3], +void PairSpinDipoleCut::compute_dipolar(int /* i */, int /* j */, double eij[3], double fmi[3], double spi[4], double spj[4], double r3inv) { double sjdotr; @@ -430,7 +377,7 @@ void PairSpinDipoleCut::compute_dipolar(int i, int j, double eij[3], atom i and atom j ------------------------------------------------------------------------- */ -void PairSpinDipoleCut::compute_dipolar_mech(int i, int j, double eij[3], +void PairSpinDipoleCut::compute_dipolar_mech(int /* i */, int /* j */, double eij[3], double fi[3], double spi[3], double spj[3], double r2inv) { double sisj,sieij,sjeij; @@ -500,11 +447,11 @@ void PairSpinDipoleCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut_spin_long[i][j],sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); } @@ -529,8 +476,8 @@ void PairSpinDipoleCut::write_restart_settings(FILE *fp) void PairSpinDipoleCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_spin_long_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_long_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_long_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/SPIN/pair_spin_dipole_cut.h b/src/SPIN/pair_spin_dipole_cut.h index 77e452b179e1c2b33bbc14041186492d9bb4a875..f9159a629fbc34e10969665683e922b67a03c444 100644 --- a/src/SPIN/pair_spin_dipole_cut.h +++ b/src/SPIN/pair_spin_dipole_cut.h @@ -29,12 +29,11 @@ class PairSpinDipoleCut : public PairSpin { double cut_coul; double **sigma; - PairSpinDipoleCut(class LAMMPS *); - ~PairSpinDipoleCut(); + PairSpinDipoleCut(LAMMPS *); + virtual ~PairSpinDipoleCut(); void settings(int, char **); void coeff(int, char **); double init_one(int, int); - void init_style(); void *extract(const char *, int &); void compute(int, int); @@ -53,7 +52,7 @@ class PairSpinDipoleCut : public PairSpin { double cut_spin_long_global; // global long cutoff distance protected: - double hbar; // reduced Planck's constant + double hbar; // reduced Planck's constant double mub; // Bohr's magneton double mu_0; // vacuum permeability double mub2mu0; // prefactor for mech force @@ -64,9 +63,6 @@ class PairSpinDipoleCut : public PairSpin { double g_ewald; int ewald_order; - int lattice_flag; // flag for mech force computation - class FixNVESpin *lockfixnvespin; // ptr for setups - void allocate(); }; diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 670fccfce28c0a698bb162d18d973e69583470da..3805eb3291c946ebc5708447253d70288780b73d 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -22,11 +22,8 @@ #include #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" #include "kspace.h" #include "math_const.h" @@ -34,7 +31,7 @@ #include "modify.h" #include "error.h" #include "update.h" - +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -49,14 +46,9 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -PairSpinDipoleLong::PairSpinDipoleLong(LAMMPS *lmp) : PairSpin(lmp), -lockfixnvespin(NULL) +PairSpinDipoleLong::PairSpinDipoleLong(LAMMPS *lmp) : PairSpin(lmp) { - single_enable = 0; ewaldflag = pppmflag = spinflag = 1; - respa_enable = 0; - no_virial_fdotr_compute = 1; - lattice_flag = 0; hbar = force->hplanck/MY_2PI; // eV/(rad.THz) mub = 9.274e-4; // in A.Ang^2 @@ -86,11 +78,7 @@ PairSpinDipoleLong::~PairSpinDipoleLong() void PairSpinDipoleLong::settings(int narg, char **arg) { - if (narg < 1 || narg > 2) - error->all(FLERR,"Incorrect args in pair_style command"); - - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin simulations require metal unit style"); + PairSpin::settings(narg,arg); cut_spin_long_global = force->numeric(FLERR,arg[0]); @@ -106,7 +94,6 @@ void PairSpinDipoleLong::settings(int narg, char **arg) } } } - } /* ---------------------------------------------------------------------- @@ -144,34 +131,7 @@ void PairSpinDipoleLong::coeff(int narg, char **arg) void PairSpinDipoleLong::init_style() { - if (!atom->sp_flag) - error->all(FLERR,"Pair spin requires atom/spin style"); - - // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // checking if nve/spin or neb/spin are a listed fix - - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; - ifix++; - } - if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); - - // get the lattice_flag from nve/spin - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { - lockfixnvespin = (FixNVESpin *) modify->fix[i]; - lattice_flag = lockfixnvespin->lattice_flag; - } - } + PairSpin::init_style(); // insure use of KSpace long-range solver, set g_ewald @@ -354,10 +314,9 @@ void PairSpinDipoleLong::compute(int eflag, int vflag) void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) { - //int i,j,jj,jnum,itype,jtype; int j,jj,jnum,itype,jtype,ntypes; int k,locflag; - int *ilist,*jlist,*numneigh,**firstneigh; + int *jlist,*numneigh,**firstneigh; double r,rinv,r2inv,rsq,grij,expm2,t,erfc; double local_cut2,pre1,pre2,pre3; double bij[4],xi[3],rij[3],eij[3],spi[4],spj[4]; @@ -367,7 +326,6 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) double **sp = atom->sp; double **fm_long = atom->fm_long; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; @@ -405,7 +363,6 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) // computation of the exchange interaction // loop over neighbors of atom i - //i = ilist[ii]; xi[0] = x[ii][0]; xi[1] = x[ii][1]; xi[2] = x[ii][2]; @@ -471,7 +428,7 @@ void PairSpinDipoleLong::compute_single_pair(int ii, double fmi[3]) compute dipolar interaction between spins i and j ------------------------------------------------------------------------- */ -void PairSpinDipoleLong::compute_long(int i, int j, double eij[3], +void PairSpinDipoleLong::compute_long(int /* i */, int /* j */, double eij[3], double bij[4], double fmi[3], double spi[4], double spj[4]) { double sjeij,pre; @@ -494,7 +451,7 @@ void PairSpinDipoleLong::compute_long(int i, int j, double eij[3], atom i and atom j ------------------------------------------------------------------------- */ -void PairSpinDipoleLong::compute_long_mech(int i, int j, double eij[3], +void PairSpinDipoleLong::compute_long_mech(int /* i */, int /* j */, double eij[3], double bij[4], double fi[3], double spi[3], double spj[3]) { double sisj,sieij,sjeij,b2,b3; @@ -569,11 +526,11 @@ void PairSpinDipoleLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut_spin_long[i][j],sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_long[i][j],sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_long[i][j],1,MPI_INT,0,world); } @@ -598,8 +555,8 @@ void PairSpinDipoleLong::write_restart_settings(FILE *fp) void PairSpinDipoleLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_spin_long_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_long_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_long_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/SPIN/pair_spin_dipole_long.h b/src/SPIN/pair_spin_dipole_long.h index 6a05f560322a4031801a2f38c4bd10e40d6ee30d..1997cbbc55fd06722dcf0abb76c3b9bdbfc77062 100644 --- a/src/SPIN/pair_spin_dipole_long.h +++ b/src/SPIN/pair_spin_dipole_long.h @@ -29,12 +29,12 @@ class PairSpinDipoleLong : public PairSpin { double cut_coul; double **sigma; - PairSpinDipoleLong(class LAMMPS *); - ~PairSpinDipoleLong(); + PairSpinDipoleLong(LAMMPS *); + virtual ~PairSpinDipoleLong(); void settings(int, char **); void coeff(int, char **); - double init_one(int, int); void init_style(); + double init_one(int, int); void *extract(const char *, int &); void compute(int, int); @@ -64,9 +64,6 @@ class PairSpinDipoleLong : public PairSpin { double g_ewald; int ewald_order; - int lattice_flag; // flag for mech force computation - class FixNVESpin *lockfixnvespin; // ptr for setups - void allocate(); }; diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index afd2deaa6a30d3677765a60050048cdc37b700c4..af68c0d256a22ffa579de67198712c05dbff7ad4 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -30,28 +30,16 @@ #include "error.h" #include "force.h" #include "fix.h" -#include "fix_nve_spin.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "modify.h" #include "update.h" +#include "utils.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairSpinDmi::PairSpinDmi(LAMMPS *lmp) : PairSpin(lmp), -lockfixnvespin(NULL) -{ - single_enable = 0; - no_virial_fdotr_compute = 1; - lattice_flag = 0; -} - -/* ---------------------------------------------------------------------- */ - PairSpinDmi::~PairSpinDmi() { if (allocated) { @@ -74,11 +62,7 @@ PairSpinDmi::~PairSpinDmi() void PairSpinDmi::settings(int narg, char **arg) { - if (narg < 1 || narg > 2) - error->all(FLERR,"Incorrect number of args in pair/spin/dmi command"); - - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin simulations require metal unit style"); + PairSpin::settings(narg,arg); cut_spin_dmi_global = force->numeric(FLERR,arg[0]); @@ -144,44 +128,6 @@ void PairSpinDmi::coeff(int narg, char **arg) } if (count == 0) error->all(FLERR,"Incorrect args in pair_style command"); - -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairSpinDmi::init_style() -{ - if (!atom->sp_flag) - error->all(FLERR,"Pair spin requires atom/spin style"); - - // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // checking if nve/spin is a listed fix - - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; - ifix++; - } - if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); - - // get the lattice_flag from nve/spin - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { - lockfixnvespin = (FixNVESpin *) modify->fix[i]; - lattice_flag = lockfixnvespin->lattice_flag; - } - } - } /* ---------------------------------------------------------------------- @@ -313,7 +259,7 @@ void PairSpinDmi::compute(int eflag, int vflag) if (eflag) { evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); - evdwl *= hbar; + evdwl *= 0.5*hbar; } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, @@ -427,9 +373,9 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype]; dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype]; - fmi[0] -= (dmiy*spj[2] - dmiz*spj[1]); - fmi[1] -= (dmiz*spj[0] - dmix*spj[2]); - fmi[2] -= (dmix*spj[1] - dmiy*spj[0]); + fmi[0] -= 2.0*(dmiy*spj[2] - dmiz*spj[1]); + fmi[1] -= 2.0*(dmiz*spj[0] - dmix*spj[2]); + fmi[2] -= 2.0*(dmix*spj[1] - dmiy*spj[0]); } /* ---------------------------------------------------------------------- @@ -532,18 +478,18 @@ void PairSpinDmi::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&DM[i][j],sizeof(double),1,fp); - fread(&v_dmx[i][j],sizeof(double),1,fp); - fread(&v_dmy[i][j],sizeof(double),1,fp); - fread(&v_dmz[i][j],sizeof(double),1,fp); - fread(&vmech_dmx[i][j],sizeof(double),1,fp); - fread(&vmech_dmy[i][j],sizeof(double),1,fp); - fread(&vmech_dmz[i][j],sizeof(double),1,fp); - fread(&cut_spin_dmi[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&DM[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&v_dmx[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&v_dmy[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&v_dmz[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&vmech_dmx[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&vmech_dmy[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&vmech_dmz[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_spin_dmi[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&DM[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&v_dmx[i][j],1,MPI_DOUBLE,0,world); @@ -577,9 +523,9 @@ void PairSpinDmi::write_restart_settings(FILE *fp) void PairSpinDmi::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_spin_dmi_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_dmi_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_dmi_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h index 68e42e879dfe15577d6bf73fe8f80a5593530dfd..ac2aa387b3bb309981588ab5d5dfe0400f57ef9a 100644 --- a/src/SPIN/pair_spin_dmi.h +++ b/src/SPIN/pair_spin_dmi.h @@ -26,11 +26,10 @@ namespace LAMMPS_NS { class PairSpinDmi : public PairSpin { public: - PairSpinDmi(class LAMMPS *); + PairSpinDmi(LAMMPS *lmp) : PairSpin(lmp) {} virtual ~PairSpinDmi(); void settings(int, char **); void coeff(int, char **); - void init_style(); double init_one(int, int); void *extract(const char *, int &); @@ -53,9 +52,6 @@ class PairSpinDmi : public PairSpin { double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction double **cut_spin_dmi; // cutoff distance dmi - int lattice_flag; // flag for mech force computation - class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups - void allocate(); }; diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index cc28018ad0ea145f13ae9f9266fece49c867aaf5..ce5cf325c6586ca7db38b3f1a0dd9c9f0b872ee4 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -29,29 +29,17 @@ #include "comm.h" #include "error.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "modify.h" #include "update.h" +#include "utils.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairSpinExchange::PairSpinExchange(LAMMPS *lmp) : PairSpin(lmp), -lockfixnvespin(NULL) -{ - single_enable = 0; - no_virial_fdotr_compute = 1; - lattice_flag = 0; -} - -/* ---------------------------------------------------------------------- */ - PairSpinExchange::~PairSpinExchange() { if (allocated) { @@ -71,11 +59,7 @@ PairSpinExchange::~PairSpinExchange() void PairSpinExchange::settings(int narg, char **arg) { - if (narg < 1 || narg > 7) - error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); - - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin simulations require metal unit style"); + PairSpin::settings(narg,arg); cut_spin_exchange_global = force->numeric(FLERR,arg[0]); @@ -89,7 +73,6 @@ void PairSpinExchange::settings(int narg, char **arg) cut_spin_exchange[i][j] = cut_spin_exchange_global; } } - } /* ---------------------------------------------------------------------- @@ -134,43 +117,6 @@ void PairSpinExchange::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args in pair_style command"); } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairSpinExchange::init_style() -{ - if (!atom->sp_flag) - error->all(FLERR,"Pair spin requires atom/spin style"); - - // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // checking if nve/spin or neb/spin are a listed fix - - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; - ifix++; - } - if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); - - // get the lattice_flag from nve/spin - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { - lockfixnvespin = (FixNVESpin *) modify->fix[i]; - lattice_flag = lockfixnvespin->lattice_flag; - } - } - -} - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ @@ -296,7 +242,7 @@ void PairSpinExchange::compute(int eflag, int vflag) if (eflag) { evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); - evdwl *= hbar; + evdwl *= 0.5*hbar; } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, @@ -405,9 +351,9 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3], Jex *= (1.0-J2[itype][jtype]*ra); Jex *= exp(-ra); - fmi[0] += Jex*spj[0]; - fmi[1] += Jex*spj[1]; - fmi[2] += Jex*spj[2]; + fmi[0] += 2.0*Jex*spj[0]; + fmi[1] += 2.0*Jex*spj[1]; + fmi[2] += 2.0*Jex*spj[2]; } /* ---------------------------------------------------------------------- @@ -497,15 +443,15 @@ void PairSpinExchange::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&J1_mag[i][j],sizeof(double),1,fp); - fread(&J1_mech[i][j],sizeof(double),1,fp); - fread(&J2[i][j],sizeof(double),1,fp); - fread(&J2[i][j],sizeof(double),1,fp); - fread(&cut_spin_exchange[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&J1_mag[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&J1_mech[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&J2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&J3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_spin_exchange[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&J1_mag[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&J1_mech[i][j],1,MPI_DOUBLE,0,world); @@ -536,9 +482,9 @@ void PairSpinExchange::write_restart_settings(FILE *fp) void PairSpinExchange::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_spin_exchange_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_exchange_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_exchange_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h index b524a513eb3229e755a94fbbcdcfb485dc92cf00..5feb99210fbed0a25637670ded91ad61ca2d851d 100644 --- a/src/SPIN/pair_spin_exchange.h +++ b/src/SPIN/pair_spin_exchange.h @@ -26,11 +26,10 @@ namespace LAMMPS_NS { class PairSpinExchange : public PairSpin { public: - PairSpinExchange(class LAMMPS *); + PairSpinExchange(LAMMPS *lmp) : PairSpin(lmp) {} virtual ~PairSpinExchange(); void settings(int, char **); void coeff(int, char **); - void init_style(); double init_one(int, int); void *extract(const char *, int &); @@ -53,9 +52,6 @@ class PairSpinExchange : public PairSpin { double **J2, **J3; // J1 in eV, J2 adim, J3 in Ang double **cut_spin_exchange; // cutoff distance exchange - int lattice_flag; // flag for mech force computation - class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups - void allocate(); }; diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 6756ebc3ccddf2c2c3a298a0f284dbea75e85962..664f8df56c18b540e14d679830912141ebac3fcf 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -29,29 +29,17 @@ #include "comm.h" #include "error.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "modify.h" #include "update.h" +#include "utils.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairSpinMagelec::PairSpinMagelec(LAMMPS *lmp) : PairSpin(lmp), -lockfixnvespin(NULL) -{ - single_enable = 0; - no_virial_fdotr_compute = 1; - lattice_flag = 0; -} - -/* ---------------------------------------------------------------------- */ - PairSpinMagelec::~PairSpinMagelec() { if (allocated) { @@ -72,11 +60,8 @@ PairSpinMagelec::~PairSpinMagelec() void PairSpinMagelec::settings(int narg, char **arg) { - if (narg < 1 || narg > 2) - error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin simulations require metal unit style"); + PairSpin::settings(narg,arg); cut_spin_magelec_global = force->numeric(FLERR,arg[0]); @@ -140,43 +125,6 @@ void PairSpinMagelec::coeff(int narg, char **arg) error->all(FLERR,"Incorrect args in pair_style command"); } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairSpinMagelec::init_style() -{ - if (!atom->sp_flag) - error->all(FLERR,"Pair spin requires atom/spin style"); - - // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // checking if nve/spin is a listed fix - - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; - ifix++; - } - if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); - - // get the lattice_flag from nve/spin - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { - lockfixnvespin = (FixNVESpin *) modify->fix[i]; - lattice_flag = lockfixnvespin->lattice_flag; - } - } - -} - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ @@ -516,15 +464,15 @@ void PairSpinMagelec::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&ME[i][j],sizeof(double),1,fp); - fread(&v_mex[i][j],sizeof(double),1,fp); - fread(&v_mey[i][j],sizeof(double),1,fp); - fread(&v_mez[i][j],sizeof(double),1,fp); - fread(&cut_spin_magelec[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&ME[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&v_mex[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&v_mey[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&v_mez[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_spin_magelec[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&ME[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&v_mex[i][j],1,MPI_DOUBLE,0,world); @@ -554,9 +502,9 @@ void PairSpinMagelec::write_restart_settings(FILE *fp) void PairSpinMagelec::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_spin_magelec_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_magelec_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_magelec_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h index 5e72a4c35e47d74bcf04e13a8495582239b11383..b9e820b1d1379b73e46c54929e00969ba4c3aa5a 100644 --- a/src/SPIN/pair_spin_magelec.h +++ b/src/SPIN/pair_spin_magelec.h @@ -26,11 +26,10 @@ namespace LAMMPS_NS { class PairSpinMagelec : public PairSpin { public: - PairSpinMagelec(class LAMMPS *); + PairSpinMagelec(LAMMPS *lmp) : PairSpin(lmp) {} virtual ~PairSpinMagelec(); void settings(int, char **); void coeff(int, char **); - void init_style(); double init_one(int, int); void *extract(const char *, int &); @@ -52,9 +51,6 @@ class PairSpinMagelec : public PairSpin { double **v_mex, **v_mey, **v_mez; // magelec direction double **cut_spin_magelec; // magelec cutoff distance - int lattice_flag; // flag for mech force computation - class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups - void allocate(); }; diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 355ba20f398405726fde38d9fc23c348909a5507..a3114497a6b5b7e9d9cc6984f8705d663de3f7ee 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -29,29 +29,17 @@ #include "comm.h" #include "error.h" #include "fix.h" -#include "fix_nve_spin.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" #include "modify.h" #include "update.h" +#include "utils.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairSpinNeel::PairSpinNeel(LAMMPS *lmp) : PairSpin(lmp), -lockfixnvespin(NULL) -{ - single_enable = 0; - no_virial_fdotr_compute = 1; - lattice_flag = 0; -} - -/* ---------------------------------------------------------------------- */ - PairSpinNeel::~PairSpinNeel() { if (allocated) { @@ -75,11 +63,7 @@ PairSpinNeel::~PairSpinNeel() void PairSpinNeel::settings(int narg, char **arg) { - if (narg < 1 || narg > 2) - error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); - - if (strcmp(update->unit_style,"metal") != 0) - error->all(FLERR,"Spin simulations require metal unit style"); + PairSpin::settings(narg,arg); cut_spin_neel_global = force->numeric(FLERR,arg[0]); @@ -146,43 +130,6 @@ void PairSpinNeel::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairSpinNeel::init_style() -{ - if (!atom->sp_flag) - error->all(FLERR,"Pair spin requires atom/spin style"); - - // need a full neighbor list - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - - // checking if nve/spin is a listed fix - - int ifix = 0; - while (ifix < modify->nfix) { - if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; - if (strcmp(modify->fix[ifix]->style,"neb/spin") == 0) break; - ifix++; - } - if ((ifix == modify->nfix) && (comm->me == 0)) - error->warning(FLERR,"Using pair/spin style without nve/spin or neb/spin"); - - // get the lattice_flag from nve/spin - - for (int i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { - lockfixnvespin = (FixNVESpin *) modify->fix[i]; - lattice_flag = lockfixnvespin->lattice_flag; - } - } - -} - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ @@ -643,10 +590,8 @@ void PairSpinNeel::allocate() memory->create(q3,n+1,n+1,"pair/spin/soc/neel:q3"); memory->create(cutsq,n+1,n+1,"pair/spin/soc/neel:cutsq"); - } - /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ @@ -687,19 +632,19 @@ void PairSpinNeel::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&g1[i][j],sizeof(double),1,fp); - fread(&g1_mech[i][j],sizeof(double),1,fp); - fread(&g2[i][j],sizeof(double),1,fp); - fread(&g2[i][j],sizeof(double),1,fp); - fread(&q1[i][j],sizeof(double),1,fp); - fread(&q1_mech[i][j],sizeof(double),1,fp); - fread(&q2[i][j],sizeof(double),1,fp); - fread(&q2[i][j],sizeof(double),1,fp); - fread(&cut_spin_neel[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&g1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&g1_mech[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&g2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&g3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&q1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&q1_mech[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&q2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&q3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_spin_neel[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&g1[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&g1_mech[i][j],1,MPI_DOUBLE,0,world); @@ -733,9 +678,9 @@ void PairSpinNeel::write_restart_settings(FILE *fp) void PairSpinNeel::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_spin_neel_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_spin_neel_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_spin_neel_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h index f60d7d2dca0e6ac72ea3c0111698f79d60ea2f37..796d8b53f0277c5b03193bce78bb3341b6cd670f 100644 --- a/src/SPIN/pair_spin_neel.h +++ b/src/SPIN/pair_spin_neel.h @@ -26,11 +26,10 @@ namespace LAMMPS_NS { class PairSpinNeel : public PairSpin { public: - PairSpinNeel(class LAMMPS *); + PairSpinNeel(LAMMPS *lmp) : PairSpin(lmp) {} virtual ~PairSpinNeel(); void settings(int, char **); void coeff(int, char **); - void init_style(); double init_one(int, int); void *extract(const char *, int &); @@ -57,10 +56,6 @@ class PairSpinNeel : public PairSpin { double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang double **cut_spin_neel; // cutoff distance exchange - int lattice_flag; // flag for mech force computation - class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups - - void allocate(); }; diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index f56d3616c856efedb62de7eead1f2657511c1c22..a5a00f86a5aac41b7e74151c658115ea9cd7728a 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -12,14 +12,13 @@ ------------------------------------------------------------------------ */ /* Single-processor "stub" versions of MPI routines */ -/* -I. in Makefile insures dummy mpi.h in this dir is included */ #include #include #include #include #include -#include +#include "mpi.h" #include "../version.h" /* data structure for double/int */ diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index e2a1768f55c9b356f78f0272d301bc64fabb4196..0e9cd02ad6c6d886d5aa13231f3b693f91ed0e57 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -581,7 +581,7 @@ void FixATC::min_setup(int vflag) setup(vflag); } -void FixATC::setup(int vflag) +void FixATC::setup(int /* vflag */) { comm->forward_comm_fix(this); @@ -642,7 +642,7 @@ void FixATC::grow_arrays(int nmax) atc_->grow_arrays(nmax); } -void FixATC::copy_arrays(int i, int j, int delflag) +void FixATC::copy_arrays(int i, int j, int /* delflag */) { atc_->copy_arrays(i,j); } @@ -675,7 +675,7 @@ void FixATC::unpack_forward_comm(int n, int first, double *buf) pack values in local atom-based arrays for restart file ------------------------------------------------------------------------- */ -int FixATC::pack_restart(int i, double *buf){ +int FixATC::pack_restart(int /* i */, double * /* buf */){ return 0; } @@ -683,7 +683,7 @@ int FixATC::pack_restart(int i, double *buf){ unpack values from atom->extra array to restart the fix ------------------------------------------------------------------------- */ -void FixATC::unpack_restart(int nlocal, int nth){ +void FixATC::unpack_restart(int /* nlocal */, int /* nth */){ } /* ---------------------------------------------------------------------- @@ -698,7 +698,7 @@ int FixATC::maxsize_restart(){ size of atom nlocal's restart data ------------------------------------------------------------------------- */ -int FixATC::size_restart(int nlocal){ +int FixATC::size_restart(int /* nlocal */){ return 0; } @@ -706,7 +706,7 @@ int FixATC::size_restart(int nlocal){ pack entire state of Fix into one write ------------------------------------------------------------------------- */ -void FixATC::write_restart(FILE *fp){ +void FixATC::write_restart(FILE * /* fp */){ char ** args = new char*[2]; args[0] = new char[50]; @@ -728,7 +728,7 @@ void FixATC::write_restart(FILE *fp){ use state info from restart file to restart the Fix ------------------------------------------------------------------------- */ -void FixATC::restart(char *buf){ +void FixATC::restart(char * /* buf */){ char ** args = new char*[2]; args[0] = new char[50]; @@ -750,7 +750,7 @@ void FixATC::restart(char *buf){ allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixATC::initial_integrate(int vflag) +void FixATC::initial_integrate(int /* vflag */) { try { atc_->pre_init_integrate(); @@ -836,7 +836,7 @@ void FixATC::pre_neighbor() } } /* ---------------------------------------------------------------------- */ -void FixATC::pre_force(int vflag) +void FixATC::pre_force(int /* vflag */) { try { @@ -848,7 +848,7 @@ void FixATC::pre_force(int vflag) } } /* ---------------------------------------------------------------------- */ -void FixATC::post_force(int vflag) +void FixATC::post_force(int /* vflag */) { try { @@ -884,7 +884,7 @@ void FixATC::setup_pre_neighbor() } } /* ---------------------------------------------------------------------- */ -void FixATC::min_pre_force(int vflag) +void FixATC::min_pre_force(int /* vflag */) { try { atc_->min_pre_force(); @@ -896,7 +896,7 @@ void FixATC::min_pre_force(int vflag) } /* ---------------------------------------------------------------------- */ -void FixATC::min_post_force(int vflag) +void FixATC::min_post_force(int /* vflag */) { try { atc_->min_post_force(); diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index a147a11081f18e37b94461e0a0e6f402ffc3da6c..b4a1cbf72a715077de53727737fdb145d3887f01 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -72,7 +72,7 @@ void FixNVEAwpmd::init() allow for only per-type mass ------------------------------------------------------------------------- */ -void FixNVEAwpmd::initial_integrate(int vflag) +void FixNVEAwpmd::initial_integrate(int /* vflag */) { @@ -117,7 +117,7 @@ void FixNVEAwpmd::final_integrate(){} /* ---------------------------------------------------------------------- */ -void FixNVEAwpmd::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixNVEAwpmd::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -131,7 +131,7 @@ void FixNVEAwpmd::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixNVEAwpmd::final_integrate_respa(int ilevel, int iloop) +void FixNVEAwpmd::final_integrate_respa(int ilevel, int /* iloop */) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 75ebb0e2515653fff5f0768f6373041fd54b49b7..092327c367bfa07830110fa291c17255a891fffa 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -32,6 +32,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "logexc.h" #include "vector_3.h" @@ -600,10 +601,10 @@ void PairAWPMDCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) fread(&cut[i][j],sizeof(double),1,fp); + if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } } @@ -627,9 +628,9 @@ void PairAWPMDCut::write_restart_settings(FILE *fp) void PairAWPMDCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); @@ -642,7 +643,7 @@ void PairAWPMDCut::read_restart_settings(FILE *fp) these arrays are stored locally by pair style ------------------------------------------------------------------------- */ -void PairAWPMDCut::min_xf_pointers(int ignore, double **xextra, double **fextra) +void PairAWPMDCut::min_xf_pointers(int /* ignore */, double **xextra, double **fextra) { // grow arrays if necessary // need to be atom->nmax in length @@ -665,7 +666,7 @@ void PairAWPMDCut::min_xf_pointers(int ignore, double **xextra, double **fextra) calculate and store in min_eradius and min_erforce ------------------------------------------------------------------------- */ -void PairAWPMDCut::min_xf_get(int ignore) +void PairAWPMDCut::min_xf_get(int /* ignore */) { double *eradius = atom->eradius; double *erforce = atom->erforce; @@ -704,7 +705,7 @@ void PairAWPMDCut::min_xf_get(int ignore) propagate the minimizer values to the atom values ------------------------------------------------------------------------- */ -void PairAWPMDCut::min_x_set(int ignore) +void PairAWPMDCut::min_x_set(int /* ignore */) { double *eradius = atom->eradius; double **v=atom->v; diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index f549fc423d34ced167a98ee0e93b97355dc6aa55..1cb332df8fd970d739356ecf07440e19746efb23 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" @@ -379,9 +380,9 @@ void BondOxdnaFene::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&Delta[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&Delta[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&Delta[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 609b63e27f35919daaa1a7a6868fc2d95025a0e0..51ff26cc6e60363e8c90c765d8d7411e5172dca8 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" @@ -676,20 +677,6 @@ void PairOxdna2Coaxstk::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdna2Coaxstk::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); - -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -829,47 +816,47 @@ void PairOxdna2Coaxstk::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&k_cxst[i][j],sizeof(double),1,fp); - fread(&cut_cxst_0[i][j],sizeof(double),1,fp); - fread(&cut_cxst_c[i][j],sizeof(double),1,fp); - fread(&cut_cxst_lo[i][j],sizeof(double),1,fp); - fread(&cut_cxst_hi[i][j],sizeof(double),1,fp); - fread(&cut_cxst_lc[i][j],sizeof(double),1,fp); - fread(&cut_cxst_hc[i][j],sizeof(double),1,fp); - fread(&b_cxst_lo[i][j],sizeof(double),1,fp); - fread(&b_cxst_hi[i][j],sizeof(double),1,fp); - - fread(&a_cxst1[i][j],sizeof(double),1,fp); - fread(&theta_cxst1_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst1[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst1_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst4[i][j],sizeof(double),1,fp); - fread(&theta_cxst4_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst4[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst4_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst5[i][j],sizeof(double),1,fp); - fread(&theta_cxst5_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst5_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst5[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst5_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst6[i][j],sizeof(double),1,fp); - fread(&theta_cxst6_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst6_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst6[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst6_c[i][j],sizeof(double),1,fp); - - fread(&AA_cxst1[i][j],sizeof(double),1,fp); - fread(&BB_cxst1[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&k_cxst[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst_hi[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst1_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst1_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst4_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst4_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst4_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst5_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst5_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst5_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst6_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst6_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst6_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&AA_cxst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&BB_cxst1[i][j],sizeof(double),1,fp,NULL,error); } @@ -933,9 +920,9 @@ void PairOxdna2Coaxstk::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/USER-CGDNA/pair_oxdna2_coaxstk.h index be8d6d6b3752474e6d32936c0c20e0c27496908f..e20d1b3fdcb47aeb280c7f0b7e333413272981d6 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.h +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.h @@ -31,7 +31,6 @@ class PairOxdna2Coaxstk : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 630dd7a55920efaf364614e3e11093ef5729b4b9..44413ee7f139d91771e72b30ea65cc11276f719a 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -25,6 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" @@ -358,19 +359,6 @@ void PairOxdna2Dh::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/dh"); } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdna2Dh::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -450,16 +438,16 @@ void PairOxdna2Dh::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&kappa_dh[i][j],sizeof(double),1,fp); - fread(&qeff_dh_pf[i][j],sizeof(double),1,fp); - fread(&b_dh[i][j],sizeof(double),1,fp); - fread(&cut_dh_ast[i][j],sizeof(double),1,fp); - fread(&cut_dh_c[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&kappa_dh[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&qeff_dh_pf[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_dh[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_dh_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_dh_c[i][j],sizeof(double),1,fp,NULL,error); } @@ -492,9 +480,9 @@ void PairOxdna2Dh::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/USER-CGDNA/pair_oxdna2_dh.h index b40346e1cf130e935ffe7497096dae72dc73c030..7c907168e37b461fbd63ad4d4aeb757bd6dd4269 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.h +++ b/src/USER-CGDNA/pair_oxdna2_dh.h @@ -32,7 +32,6 @@ class PairOxdna2Dh : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index d71acc2029f34f0d0e56aca88a60db54897b6f08..f0777fcdbdcee473474645a3121a8c7192e9b390 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" @@ -822,20 +823,6 @@ void PairOxdnaCoaxstk::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdnaCoaxstk::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); - -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -988,53 +975,53 @@ void PairOxdnaCoaxstk::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&k_cxst[i][j],sizeof(double),1,fp); - fread(&cut_cxst_0[i][j],sizeof(double),1,fp); - fread(&cut_cxst_c[i][j],sizeof(double),1,fp); - fread(&cut_cxst_lo[i][j],sizeof(double),1,fp); - fread(&cut_cxst_hi[i][j],sizeof(double),1,fp); - fread(&cut_cxst_lc[i][j],sizeof(double),1,fp); - fread(&cut_cxst_hc[i][j],sizeof(double),1,fp); - fread(&b_cxst_lo[i][j],sizeof(double),1,fp); - fread(&b_cxst_hi[i][j],sizeof(double),1,fp); - - fread(&a_cxst1[i][j],sizeof(double),1,fp); - fread(&theta_cxst1_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst1_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst1[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst1_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst4[i][j],sizeof(double),1,fp); - fread(&theta_cxst4_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst4_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst4[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst4_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst5[i][j],sizeof(double),1,fp); - fread(&theta_cxst5_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst5_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst5[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst5_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst6[i][j],sizeof(double),1,fp); - fread(&theta_cxst6_0[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst6_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst6[i][j],sizeof(double),1,fp); - fread(&dtheta_cxst6_c[i][j],sizeof(double),1,fp); - - fread(&a_cxst3p[i][j],sizeof(double),1,fp); - fread(&cosphi_cxst3p_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst3p[i][j],sizeof(double),1,fp); - fread(&cosphi_cxst3p_c[i][j],sizeof(double),1,fp); - fread(&a_cxst4p[i][j],sizeof(double),1,fp); - fread(&cosphi_cxst4p_ast[i][j],sizeof(double),1,fp); - fread(&b_cxst4p[i][j],sizeof(double),1,fp); - fread(&cosphi_cxst4p_c[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&k_cxst[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_cxst_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst_hi[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst1_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst1_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst4_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst4_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst4_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst5_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst5_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst5_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_cxst6_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst6_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_cxst6_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_cxst3p[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_cxst3p_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst3p[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_cxst3p_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&a_cxst4p[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_cxst4p_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_cxst4p[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_cxst4p_c[i][j],sizeof(double),1,fp,NULL,error); } @@ -1104,9 +1091,9 @@ void PairOxdnaCoaxstk::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/USER-CGDNA/pair_oxdna_coaxstk.h index f9228c94a213b78d11c5e9d14c20c16f38bcde54..e89e9bdbaa51a77e3ae097be43736485764ce0b9 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.h +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.h @@ -31,7 +31,6 @@ class PairOxdnaCoaxstk : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index f187fc7403af849370e817c1712ff2037f537ef9..8506f5e3d1a640b2e426794c6e03c091654bfe08 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" @@ -562,20 +563,6 @@ void PairOxdnaExcv::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdnaExcv::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); - -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -710,26 +697,26 @@ void PairOxdnaExcv::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon_ss[i][j],sizeof(double),1,fp); - fread(&sigma_ss[i][j],sizeof(double),1,fp); - fread(&cut_ss_ast[i][j],sizeof(double),1,fp); - fread(&b_ss[i][j],sizeof(double),1,fp); - fread(&cut_ss_c[i][j],sizeof(double),1,fp); - fread(&epsilon_sb[i][j],sizeof(double),1,fp); - fread(&sigma_sb[i][j],sizeof(double),1,fp); - fread(&cut_sb_ast[i][j],sizeof(double),1,fp); - fread(&b_sb[i][j],sizeof(double),1,fp); - fread(&cut_sb_c[i][j],sizeof(double),1,fp); - fread(&epsilon_bb[i][j],sizeof(double),1,fp); - fread(&sigma_bb[i][j],sizeof(double),1,fp); - fread(&cut_bb_ast[i][j],sizeof(double),1,fp); - fread(&b_bb[i][j],sizeof(double),1,fp); - fread(&cut_bb_c[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon_ss[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma_ss[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_ss_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_ss[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_ss_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&epsilon_sb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma_sb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_sb_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_sb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_sb_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&epsilon_bb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma_bb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_bb_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_bb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_bb_c[i][j],sizeof(double),1,fp,NULL,error); } @@ -772,9 +759,9 @@ void PairOxdnaExcv::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/USER-CGDNA/pair_oxdna_excv.h index c80a112feca66025cf773df9eed5cb7a2c3ea8b4..34fd323ec12e8038505f5dae39f4eec91b2b86cf 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.h +++ b/src/USER-CGDNA/pair_oxdna_excv.h @@ -33,7 +33,6 @@ class PairOxdnaExcv : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index e9852d0e3880cd11215f545056b8d0f08c4cac97..9e4bb1c273dc3f2b09a3cdb7bdce09474c5b463a 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -26,26 +26,43 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; using namespace MFOxdna; -// sequence-specific base-pairing strength -// A:0 C:1 G:2 T:3, 5'- (i,j) -3' -static const double alpha_hb[4][4] = -{{1.00000,1.00000,1.00000,0.82915}, - {1.00000,1.00000,1.15413,1.00000}, - {1.00000,1.15413,1.00000,1.00000}, - {0.82915,1.00000,1.00000,1.00000}}; - /* ---------------------------------------------------------------------- */ PairOxdnaHbond::PairOxdnaHbond(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + + // sequence-specific base-pairing strength + // A:0 C:1 G:2 T:3, 5'- [i][j] -3' + + alpha_hb[0][0] = 1.00000; + alpha_hb[0][1] = 1.00000; + alpha_hb[0][2] = 1.00000; + alpha_hb[0][3] = 0.82915; + + alpha_hb[1][0] = 1.00000; + alpha_hb[1][1] = 1.00000; + alpha_hb[1][2] = 1.15413; + alpha_hb[1][3] = 1.00000; + + alpha_hb[2][0] = 1.00000; + alpha_hb[2][1] = 1.15413; + alpha_hb[2][2] = 1.00000; + alpha_hb[2][3] = 1.00000; + + alpha_hb[3][0] = 0.82915; + alpha_hb[3][1] = 1.00000; + alpha_hb[3][2] = 1.00000; + alpha_hb[3][3] = 1.00000; + } /* ---------------------------------------------------------------------- */ @@ -616,7 +633,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) if (narg != 27) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/hbond"); if (!allocated) allocate(); - int ilo,ihi,jlo,jhi; + int ilo,ihi,jlo,jhi,imod4,jmod4; force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); @@ -729,8 +746,13 @@ void PairOxdnaHbond::coeff(int narg, char **arg) for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { + imod4 = i%4; + if (imod4 == 0) imod4 = 4; + jmod4 = j%4; + if (jmod4 == 0) jmod4 = 4; + epsilon_hb[i][j] = epsilon_hb_one; - if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[i-1][j-1]; + if (seqdepflag) epsilon_hb[i][j] *= alpha_hb[imod4-1][jmod4-1]; a_hb[i][j] = a_hb_one; cut_hb_0[i][j] = cut_hb_0_one; cut_hb_c[i][j] = cut_hb_c_one; @@ -741,7 +763,7 @@ void PairOxdnaHbond::coeff(int narg, char **arg) b_hb_lo[i][j] = b_hb_lo_one; b_hb_hi[i][j] = b_hb_hi_one; shift_hb[i][j] = shift_hb_one; - if (seqdepflag) shift_hb[i][j] *= alpha_hb[i-1][j-1]; + if (seqdepflag) shift_hb[i][j] *= alpha_hb[imod4-1][jmod4-1]; a_hb1[i][j] = a_hb1_one; theta_hb1_0[i][j] = theta_hb1_0_one; @@ -788,20 +810,6 @@ void PairOxdnaHbond::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdnaHbond::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); - -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -820,6 +828,7 @@ void PairOxdnaHbond::init_list(int id, NeighList *ptr) double PairOxdnaHbond::init_one(int i, int j) { + int imod4,jmod4; if (setflag[i][j] == 0) { error->all(FLERR,"Coefficient mixing not defined in oxDNA"); @@ -828,8 +837,13 @@ double PairOxdnaHbond::init_one(int i, int j) error->all(FLERR,"Offset not supported in oxDNA"); } + imod4 = i%4; + if (imod4 == 0) imod4 = 4; + jmod4 = j%4; + if (jmod4 == 0) jmod4 = 4; + if (seqdepflag) { - epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1]; + epsilon_hb[j][i] = epsilon_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1]; } else { epsilon_hb[j][i] = epsilon_hb[i][j]; @@ -844,7 +858,7 @@ double PairOxdnaHbond::init_one(int i, int j) cut_hb_lc[j][i] = cut_hb_lc[i][j]; cut_hb_hc[j][i] = cut_hb_hc[i][j]; if (seqdepflag) { - shift_hb[j][i] = shift_hb[i][j] / alpha_hb[i-1][j-1] * alpha_hb[j-1][i-1]; + shift_hb[j][i] = shift_hb[i][j] / alpha_hb[imod4-1][jmod4-1] * alpha_hb[jmod4-1][imod4-1]; } else { shift_hb[j][i] = shift_hb[i][j]; @@ -973,58 +987,58 @@ void PairOxdnaHbond::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon_hb[i][j],sizeof(double),1,fp); - fread(&a_hb[i][j],sizeof(double),1,fp); - fread(&cut_hb_0[i][j],sizeof(double),1,fp); - fread(&cut_hb_c[i][j],sizeof(double),1,fp); - fread(&cut_hb_lo[i][j],sizeof(double),1,fp); - fread(&cut_hb_hi[i][j],sizeof(double),1,fp); - fread(&cut_hb_lc[i][j],sizeof(double),1,fp); - fread(&cut_hb_hc[i][j],sizeof(double),1,fp); - fread(&b_hb_lo[i][j],sizeof(double),1,fp); - fread(&b_hb_hi[i][j],sizeof(double),1,fp); - fread(&shift_hb[i][j],sizeof(double),1,fp); - - fread(&a_hb1[i][j],sizeof(double),1,fp); - fread(&theta_hb1_0[i][j],sizeof(double),1,fp); - fread(&dtheta_hb1_ast[i][j],sizeof(double),1,fp); - fread(&b_hb1[i][j],sizeof(double),1,fp); - fread(&dtheta_hb1_c[i][j],sizeof(double),1,fp); - - fread(&a_hb2[i][j],sizeof(double),1,fp); - fread(&theta_hb2_0[i][j],sizeof(double),1,fp); - fread(&dtheta_hb2_ast[i][j],sizeof(double),1,fp); - fread(&b_hb2[i][j],sizeof(double),1,fp); - fread(&dtheta_hb2_c[i][j],sizeof(double),1,fp); - - fread(&a_hb3[i][j],sizeof(double),1,fp); - fread(&theta_hb3_0[i][j],sizeof(double),1,fp); - fread(&dtheta_hb3_ast[i][j],sizeof(double),1,fp); - fread(&b_hb3[i][j],sizeof(double),1,fp); - fread(&dtheta_hb3_c[i][j],sizeof(double),1,fp); - - fread(&a_hb4[i][j],sizeof(double),1,fp); - fread(&theta_hb4_0[i][j],sizeof(double),1,fp); - fread(&dtheta_hb4_ast[i][j],sizeof(double),1,fp); - fread(&b_hb4[i][j],sizeof(double),1,fp); - fread(&dtheta_hb4_c[i][j],sizeof(double),1,fp); - - fread(&a_hb7[i][j],sizeof(double),1,fp); - fread(&theta_hb7_0[i][j],sizeof(double),1,fp); - fread(&dtheta_hb7_ast[i][j],sizeof(double),1,fp); - fread(&b_hb7[i][j],sizeof(double),1,fp); - fread(&dtheta_hb7_c[i][j],sizeof(double),1,fp); - - fread(&a_hb8[i][j],sizeof(double),1,fp); - fread(&theta_hb8_0[i][j],sizeof(double),1,fp); - fread(&dtheta_hb8_ast[i][j],sizeof(double),1,fp); - fread(&b_hb8[i][j],sizeof(double),1,fp); - fread(&dtheta_hb8_c[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon_hb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&a_hb[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_hb_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_hb_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_hb_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_hb_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_hb_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_hb_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shift_hb[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_hb1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_hb1_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb1_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_hb2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_hb2_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb2_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb2_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_hb3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_hb3_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb3_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb3_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_hb4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_hb4_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb4_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb4_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_hb7[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_hb7_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb7_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb7[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb7_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_hb8[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_hb8_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb8_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_hb8[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_hb8_c[i][j],sizeof(double),1,fp,NULL,error); } @@ -1099,9 +1113,9 @@ void PairOxdnaHbond::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/USER-CGDNA/pair_oxdna_hbond.h index 028853a0872fdbca9990b3a73aa4ff72e1813782..fe451480a8d1800d27d48d8303eafc0ce295d2ae 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.h +++ b/src/USER-CGDNA/pair_oxdna_hbond.h @@ -32,7 +32,6 @@ class PairOxdnaHbond : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); @@ -45,6 +44,7 @@ class PairOxdnaHbond : public Pair { protected: // h-bonding interaction + double alpha_hb[4][4]; double **epsilon_hb, **a_hb, **cut_hb_0, **cut_hb_c, **cut_hb_lo, **cut_hb_hi; double **cut_hb_lc, **cut_hb_hc, **b_hb_lo, **b_hb_hi, **shift_hb; double **cutsq_hb_hc; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index 3d0c4e9136bf31485c38a08fe51b441876d94123..9db554366b8cbba6626f785a628843d98e6d12f8 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -26,26 +26,43 @@ #include "neighbor.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" using namespace LAMMPS_NS; using namespace MFOxdna; -// sequence-specific stacking strength -// A:0 C:1 G:2 T:3, 5'- (i,j) -3' -static const double eta_st[4][4] = -{{1.11960,1.00852,0.96950,0.99632}, - {1.01889,0.97804,1.02681,0.96950}, - {0.98169,1.05913,0.97804,1.00852}, - {0.94694,0.98169,1.01889,0.96383}}; - /* ---------------------------------------------------------------------- */ PairOxdnaStk::PairOxdnaStk(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; writedata = 1; + + // sequence-specific stacking strength + // A:0 C:1 G:2 T:3, 5'- [i][j] -3' + + eta_st[0][0] = 1.11960; + eta_st[0][1] = 1.00852; + eta_st[0][2] = 0.96950; + eta_st[0][3] = 0.99632; + + eta_st[1][0] = 1.01889; + eta_st[1][1] = 0.97804; + eta_st[1][2] = 1.02681; + eta_st[1][3] = 0.96950; + + eta_st[2][0] = 0.98169; + eta_st[2][1] = 1.05913; + eta_st[2][2] = 0.97804; + eta_st[2][3] = 1.00852; + + eta_st[3][0] = 0.94694; + eta_st[3][1] = 0.98169; + eta_st[3][2] = 1.01889; + eta_st[3][3] = 0.96383; + } /* ---------------------------------------------------------------------- */ @@ -761,7 +778,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk"); if (!allocated) allocate(); - int ilo,ihi,jlo,jhi; + int ilo,ihi,jlo,jhi,imod4,jmod4; force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); @@ -852,16 +869,21 @@ void PairOxdnaStk::coeff(int narg, char **arg) dtheta_st6_c_one = 1/(a_st6_one*dtheta_st6_ast_one); b_st1_one = a_st1_one*a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one/(1-a_st1_one*cosphi_st1_ast_one*cosphi_st1_ast_one); - cosphi_st1_c_one=1/(a_st1_one*cosphi_st1_ast_one); + cosphi_st1_c_one = 1/(a_st1_one*cosphi_st1_ast_one); b_st2_one = a_st2_one*a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one/(1-a_st2_one*cosphi_st2_ast_one*cosphi_st2_ast_one); - cosphi_st2_c_one=1/(a_st2_one*cosphi_st2_ast_one); + cosphi_st2_c_one = 1/(a_st2_one*cosphi_st2_ast_one); for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { + imod4 = i%4; + if (imod4 == 0) imod4 = 4; + jmod4 = j%4; + if (jmod4 == 0) jmod4 = 4; + epsilon_st[i][j] = epsilon_st_one; - if (seqdepflag) epsilon_st[i][j] *= eta_st[i-1][j-1]; + if (seqdepflag) epsilon_st[i][j] *= eta_st[imod4-1][jmod4-1]; a_st[i][j] = a_st_one; cut_st_0[i][j] = cut_st_0_one; cut_st_c[i][j] = cut_st_c_one; @@ -872,7 +894,7 @@ void PairOxdnaStk::coeff(int narg, char **arg) b_st_lo[i][j] = b_st_lo_one; b_st_hi[i][j] = b_st_hi_one; shift_st[i][j] = shift_st_one; - if (seqdepflag) shift_st[i][j] *= eta_st[i-1][j-1]; + if (seqdepflag) shift_st[i][j] *= eta_st[imod4-1][jmod4-1]; a_st4[i][j] = a_st4_one; theta_st4_0[i][j] = theta_st4_0_one; @@ -911,20 +933,6 @@ void PairOxdnaStk::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdnaStk::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); - -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -944,6 +952,8 @@ void PairOxdnaStk::init_list(int id, NeighList *ptr) double PairOxdnaStk::init_one(int i, int j) { + int imod4,jmod4; + if (setflag[i][j] == 0) { error->all(FLERR,"Coefficient mixing not defined in oxDNA"); } @@ -951,8 +961,13 @@ double PairOxdnaStk::init_one(int i, int j) error->all(FLERR,"Offset not supported in oxDNA"); } + imod4 = i%4; + if (imod4 == 0) imod4 = 4; + jmod4 = j%4; + if (jmod4 == 0) jmod4 = 4; + if (seqdepflag) { - epsilon_st[j][i] = epsilon_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; + epsilon_st[j][i] = epsilon_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1]; } else { epsilon_st[j][i] = epsilon_st[i][j]; @@ -967,7 +982,7 @@ double PairOxdnaStk::init_one(int i, int j) cut_st_lc[j][i] = cut_st_lc[i][j]; cut_st_hc[j][i] = cut_st_hc[i][j]; if (seqdepflag) { - shift_st[j][i] = shift_st[i][j] / eta_st[i-1][j-1] * eta_st[j-1][i-1]; + shift_st[j][i] = shift_st[i][j] / eta_st[imod4-1][jmod4-1] * eta_st[jmod4-1][imod4-1]; } else { shift_st[j][i] = shift_st[i][j]; @@ -1079,49 +1094,49 @@ void PairOxdnaStk::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon_st[i][j],sizeof(double),1,fp); - fread(&a_st[i][j],sizeof(double),1,fp); - fread(&cut_st_0[i][j],sizeof(double),1,fp); - fread(&cut_st_c[i][j],sizeof(double),1,fp); - fread(&cut_st_lo[i][j],sizeof(double),1,fp); - fread(&cut_st_hi[i][j],sizeof(double),1,fp); - fread(&cut_st_lc[i][j],sizeof(double),1,fp); - fread(&cut_st_hc[i][j],sizeof(double),1,fp); - fread(&b_st_lo[i][j],sizeof(double),1,fp); - fread(&b_st_hi[i][j],sizeof(double),1,fp); - fread(&shift_st[i][j],sizeof(double),1,fp); - - fread(&a_st4[i][j],sizeof(double),1,fp); - fread(&theta_st4_0[i][j],sizeof(double),1,fp); - fread(&dtheta_st4_ast[i][j],sizeof(double),1,fp); - fread(&b_st4[i][j],sizeof(double),1,fp); - fread(&dtheta_st4_c[i][j],sizeof(double),1,fp); - - fread(&a_st5[i][j],sizeof(double),1,fp); - fread(&theta_st5_0[i][j],sizeof(double),1,fp); - fread(&dtheta_st5_ast[i][j],sizeof(double),1,fp); - fread(&b_st5[i][j],sizeof(double),1,fp); - fread(&dtheta_st5_c[i][j],sizeof(double),1,fp); - - fread(&a_st6[i][j],sizeof(double),1,fp); - fread(&theta_st6_0[i][j],sizeof(double),1,fp); - fread(&dtheta_st6_ast[i][j],sizeof(double),1,fp); - fread(&b_st6[i][j],sizeof(double),1,fp); - fread(&dtheta_st6_c[i][j],sizeof(double),1,fp); - - fread(&a_st1[i][j],sizeof(double),1,fp); - fread(&cosphi_st1_ast[i][j],sizeof(double),1,fp); - fread(&b_st1[i][j],sizeof(double),1,fp); - fread(&cosphi_st1_c[i][j],sizeof(double),1,fp); - fread(&a_st2[i][j],sizeof(double),1,fp); - fread(&cosphi_st2_ast[i][j],sizeof(double),1,fp); - fread(&b_st2[i][j],sizeof(double),1,fp); - fread(&cosphi_st2_c[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon_st[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&a_st[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_st_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shift_st[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st4_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st4_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st4_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st5_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st5_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st5[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st5_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_st6_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st6_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st6[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_st6_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_st1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st1_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&a_st2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st2_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_st2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cosphi_st2_c[i][j],sizeof(double),1,fp,NULL,error); } @@ -1187,9 +1202,9 @@ void PairOxdnaStk::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/USER-CGDNA/pair_oxdna_stk.h index 581e87f4b22ed810af8f4d6ee69923c6bf5e4898..29ed168ca347270ff95e84e1c4343901791f551d 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.h +++ b/src/USER-CGDNA/pair_oxdna_stk.h @@ -32,7 +32,6 @@ class PairOxdnaStk : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); @@ -45,6 +44,7 @@ class PairOxdnaStk : public Pair { protected: // stacking interaction + double eta_st[4][4]; double stacking_strength(double, double, double); double **epsilon_st, **a_st, **cut_st_0, **cut_st_c; double **cut_st_lo, **cut_st_hi; diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 95f569481836f225c185a0f96990d61db91e9b9f..a1fc86bd4d8e18862869c29a916c46cb6e9e381f 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "atom_vec_ellipsoid.h" #include "math_extra.h" @@ -776,20 +777,6 @@ void PairOxdnaXstk::coeff(int narg, char **arg) } -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairOxdnaXstk::init_style() -{ - int irequest; - - // request regular neighbor lists - - irequest = neighbor->request(this,instance_me); - -} - /* ---------------------------------------------------------------------- neighbor callback to inform pair style of neighbor list to use regular ------------------------------------------------------------------------- */ @@ -947,56 +934,56 @@ void PairOxdnaXstk::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&k_xst[i][j],sizeof(double),1,fp); - fread(&cut_xst_0[i][j],sizeof(double),1,fp); - fread(&cut_xst_c[i][j],sizeof(double),1,fp); - fread(&cut_xst_lo[i][j],sizeof(double),1,fp); - fread(&cut_xst_hi[i][j],sizeof(double),1,fp); - fread(&cut_xst_lc[i][j],sizeof(double),1,fp); - fread(&cut_xst_hc[i][j],sizeof(double),1,fp); - fread(&b_xst_lo[i][j],sizeof(double),1,fp); - fread(&b_xst_hi[i][j],sizeof(double),1,fp); - - fread(&a_xst1[i][j],sizeof(double),1,fp); - fread(&theta_xst1_0[i][j],sizeof(double),1,fp); - fread(&dtheta_xst1_ast[i][j],sizeof(double),1,fp); - fread(&b_xst1[i][j],sizeof(double),1,fp); - fread(&dtheta_xst1_c[i][j],sizeof(double),1,fp); - - fread(&a_xst2[i][j],sizeof(double),1,fp); - fread(&theta_xst2_0[i][j],sizeof(double),1,fp); - fread(&dtheta_xst2_ast[i][j],sizeof(double),1,fp); - fread(&b_xst2[i][j],sizeof(double),1,fp); - fread(&dtheta_xst2_c[i][j],sizeof(double),1,fp); - - fread(&a_xst3[i][j],sizeof(double),1,fp); - fread(&theta_xst3_0[i][j],sizeof(double),1,fp); - fread(&dtheta_xst3_ast[i][j],sizeof(double),1,fp); - fread(&b_xst3[i][j],sizeof(double),1,fp); - fread(&dtheta_xst3_c[i][j],sizeof(double),1,fp); - - fread(&a_xst4[i][j],sizeof(double),1,fp); - fread(&theta_xst4_0[i][j],sizeof(double),1,fp); - fread(&dtheta_xst4_ast[i][j],sizeof(double),1,fp); - fread(&b_xst4[i][j],sizeof(double),1,fp); - fread(&dtheta_xst4_c[i][j],sizeof(double),1,fp); - - fread(&a_xst7[i][j],sizeof(double),1,fp); - fread(&theta_xst7_0[i][j],sizeof(double),1,fp); - fread(&dtheta_xst7_ast[i][j],sizeof(double),1,fp); - fread(&b_xst7[i][j],sizeof(double),1,fp); - fread(&dtheta_xst7_c[i][j],sizeof(double),1,fp); - - fread(&a_xst8[i][j],sizeof(double),1,fp); - fread(&theta_xst8_0[i][j],sizeof(double),1,fp); - fread(&dtheta_xst8_ast[i][j],sizeof(double),1,fp); - fread(&b_xst8[i][j],sizeof(double),1,fp); - fread(&dtheta_xst8_c[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&k_xst[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_hi[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_lc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_xst_hc[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst_lo[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst_hi[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst1_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst1_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst1_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst2_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst2_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst2_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst3_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst3_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst3_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst4_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst4_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst4_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst7[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst7_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst7_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst7[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst7_c[i][j],sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&a_xst8[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&theta_xst8_0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst8_ast[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b_xst8[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dtheta_xst8_c[i][j],sizeof(double),1,fp,NULL,error); } @@ -1069,9 +1056,9 @@ void PairOxdnaXstk::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/USER-CGDNA/pair_oxdna_xstk.h index 5c443a4dac28459528b33cc0b1828892742b4e2b..d2fc7fde89440ea5c026e855fc35e19d6c059b08 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.h +++ b/src/USER-CGDNA/pair_oxdna_xstk.h @@ -32,7 +32,6 @@ class PairOxdnaXstk : public Pair { virtual void compute(int, int); void settings(int, char **); void coeff(int, char **); - void init_style(); void init_list(int, class NeighList *); double init_one(int, int); void write_restart(FILE *); diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index 862c165bbd06511a23685112d8cd4b5d718c3d0b..11b3a8308c99abb3f3a30cf5a2f1a87ea2b93bb6 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -30,6 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "lj_sdk_common.h" @@ -332,9 +333,9 @@ void AngleSDK::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); - fread(&repscale[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&repscale[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 1301dc41551fa79921ef9cbfd2dd951e80852bfd..3e4f8deee8842fc6f633f71b47b8b19e45332100 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" @@ -373,14 +374,14 @@ void PairLJSDK::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&lj_type[i][j],sizeof(int),1,fp); - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&lj_type[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world); MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); @@ -410,10 +411,10 @@ void PairLJSDK::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index 62acf00d279893259ef6563ad05d68202c93b7bd..5721e72d083dff247d20a4128e8fba55da22626e 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -28,6 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" @@ -465,14 +466,14 @@ void PairLJSDKCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&lj_type[i][j],sizeof(int),1,fp); - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&lj_type[i][j],sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world); MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); @@ -504,13 +505,13 @@ void PairLJSDKCoulLong::write_restart_settings(FILE *fp) void PairLJSDKCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index a1369df2fb3f90dd117b276dde349b4ecd00093f..3756208212cfca6012988970cbdb06c07a1d6ff8 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -126,7 +126,7 @@ void Ndx2Group::command(int narg, char **arg) } name = find_section(fp,NULL); if (name != NULL) { - len=strlen(name); + len=strlen(name)+1; // skip over group "all", which is called "System" in gromacs if (strcmp(name,"System") == 0) continue; @@ -152,8 +152,8 @@ void Ndx2Group::command(int narg, char **arg) MPI_Bcast(&len,1,MPI_INT,0,world); if (len > 0) { delete[] name; - name = new char[len+1]; - MPI_Bcast(name,len+1,MPI_CHAR,0,world); + name = new char[len]; + MPI_Bcast(name,len,MPI_CHAR,0,world); MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1)); @@ -174,7 +174,7 @@ void Ndx2Group::command(int narg, char **arg) if (name != NULL) delete[] name; rewind(fp); name = find_section(fp,arg[idx]); - if (name != NULL) len=strlen(name); + if (name != NULL) len=strlen(name)+1; if (screen) fprintf(screen," %s group '%s'\n", @@ -185,7 +185,7 @@ void Ndx2Group::command(int narg, char **arg) MPI_Bcast(&len,1,MPI_INT,0,world); if (len > 0) { - MPI_Bcast(name,len+1,MPI_CHAR,0,world); + MPI_Bcast(name,len,MPI_CHAR,0,world); // read tags for atoms in group and broadcast num = 0; tags = read_section(fp,num); @@ -199,8 +199,8 @@ void Ndx2Group::command(int narg, char **arg) MPI_Bcast(&len,1,MPI_INT,0,world); if (len > 0) { delete[] name; - name = new char[len+1]; - MPI_Bcast(name,len+1,MPI_CHAR,0,world); + name = new char[len]; + MPI_Bcast(name,len,MPI_CHAR,0,world); MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world); tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1)); diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 971d9bd380b6a7bebcf3149616222402ab294b0c..3ae25f223cd1a5024f864d0979f35098b5625294 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -510,7 +510,7 @@ void ComputeSAED::compute_vector() if (me == 0 && echo) { if (screen) - fprintf(screen," 100%% \nTime ellapsed during compute_saed = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0); + fprintf(screen," 100%% \nTime elapsed during compute_saed = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0); } delete [] xlocal; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index f48951f1ff7cfeb00066df13b8b28dc9a3ded1f7..7f69449282b04cadd7181bb2c393ed43edc6fc91 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -513,7 +513,7 @@ void ComputeXRD::compute_array() if (me == 0 && echo) { if (screen) - fprintf(screen," 100%% \nTime ellapsed during compute_xrd = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0); + fprintf(screen," 100%% \nTime elapsed during compute_xrd = %0.2f sec using %0.2f Mbytes/processor\n-----\n", t2-t0, bytes/1024.0/1024.0); } delete [] scratch; diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index ff9a186c47a4e8ebd61d28e530a713b42cf1cc14..dc6310ae42097fa7aa8c8d3ad96e0e4d394b172a 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -23,6 +23,7 @@ #include "error.h" #include "force.h" #include "memory.h" +#include "utils.h" #define MAXLINE 1024 @@ -214,16 +215,16 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,tb2,line); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,tb2,line); memory->create(tb->rfile,tb->ninput,"eos:rfile"); memory->create(tb->efile,tb->ninput,"eos:efile"); @@ -233,9 +234,9 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword) // read r,e table values from file int itmp; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]); sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]); } diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index 9f1bd6a3bbcaaca743fa8c39ae5490ea2f438ede..152b58dbb743260b69ec57c89ffdaa41921cd2b8 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -26,6 +26,7 @@ #include "memory.h" #include "comm.h" #include "modify.h" +#include "utils.h" #define MAXLINE 1024 @@ -433,16 +434,16 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); tb2->ninput = tb->ninput; memory->create(tb->rfile,tb->ninput,"eos:rfile"); @@ -470,9 +471,9 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword) int ispecies; int ninputs = tb->ninput; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < ninputs; i++) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); nwords = atom->count_words(line); if(nwords != nspecies+2){ diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 1cb9d68d063b0c9d275e90927979b0a3824fdbe4..5b62972d1bf14d927021dc7be6c507439f28e0be 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -30,6 +30,7 @@ #include "memory.h" #include "modify.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -313,7 +314,7 @@ void PairDPDfdt::init_style() error->all(FLERR,"Pair dpd/fdt requires ghost atoms store velocity"); splitFDT_flag = false; - int irequest = neighbor->request(this,instance_me); + neighbor->request(this,instance_me); for (int i = 0; i < modify->nfix; i++) if (strncmp(modify->fix[i]->style,"shardlow", 8) == 0){ splitFDT_flag = true; @@ -375,13 +376,13 @@ void PairDPDfdt::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a0[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -410,10 +411,10 @@ void PairDPDfdt::write_restart_settings(FILE *fp) void PairDPDfdt::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&temperature,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 22741a055d5124a0fd3924f1f19f069dc76c6356..5ea8d2e9e1e00b6a3a442cbd48b9be913b89413f 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -30,6 +30,7 @@ #include "memory.h" #include "modify.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -406,7 +407,7 @@ void PairDPDfdtEnergy::init_style() error->all(FLERR,"Pair dpd/fdt/energy requires ghost atoms store velocity"); splitFDT_flag = false; - int irequest = neighbor->request(this,instance_me); + neighbor->request(this,instance_me); for (int i = 0; i < modify->nfix; i++) if (strncmp(modify->fix[i]->style,"shardlow", 8) == 0){ splitFDT_flag = true; @@ -476,14 +477,14 @@ void PairDPDfdtEnergy::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a0[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&kappa[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&kappa[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -513,9 +514,9 @@ void PairDPDfdtEnergy::write_restart_settings(FILE *fp) void PairDPDfdtEnergy::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&seed,1,MPI_INT,0,world); diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 5cf2859ae3914dd852968ebcfe2492bcb6d71118..5e23113feb0d24d05be5031aea4ec235a81cff81 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -24,6 +24,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "modify.h" #include "fix.h" @@ -968,11 +969,11 @@ void PairExp6rx::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } @@ -998,10 +999,10 @@ void PairExp6rx::write_restart_settings(FILE *fp) void PairExp6rx::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index ffc1562f88e7a599e601ec3d24d16d818cf3b540..1cbb29a93c13f63a3c21260d4e8e1aad81175d0f 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -33,7 +33,9 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "citeme.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -362,16 +364,16 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); } // read args on 2nd line of section - // allocate table arrays for file values + // allocate table arrays for file valuesutils::s - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); @@ -384,9 +386,9 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword) int itmp; double rtmp; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); if (tb->rflag == RLINEAR) @@ -705,8 +707,8 @@ void PairMultiLucy::write_restart_settings(FILE *fp) void PairMultiLucy::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 801e8ff0396620de85ad3f06ee18cbd5845bfe75..36ca7e0321e517196b46cde024c4ec1372758985 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -33,9 +33,11 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "citeme.h" #include "modify.h" #include "fix.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -507,16 +509,16 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); @@ -529,9 +531,9 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) int itmp; double rtmp; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]); if (tb->rflag == RLINEAR) @@ -850,8 +852,8 @@ void PairMultiLucyRX::write_restart_settings(FILE *fp) void PairMultiLucyRX::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 851effd89c8fc5229ca1684d8e3e5df0bf6ef65c..98c2ff196a1f64620dfa550c090fc4d06ec051dd 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -29,6 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "modify.h" #include "domain.h" @@ -357,7 +358,7 @@ void PairLJCutTholeLong::init_style() error->all(FLERR, "Pair style lj/cut/thole/long requires fix drude"); fix_drude = (FixDrude *) modify->fix[ifix]; - int irequest = neighbor->request(this,instance_me); + neighbor->request(this,instance_me); cut_coulsq = cut_coul * cut_coul; @@ -488,16 +489,16 @@ void PairLJCutTholeLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&polar[i][j],sizeof(double),1,fp); - fread(&thole[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&polar[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&thole[i][j],sizeof(double),1,fp,NULL,error); ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -533,15 +534,15 @@ void PairLJCutTholeLong::write_restart_settings(FILE *fp) void PairLJCutTholeLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&thole_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&thole_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 1f81263e95b72e3838d60238e08ea669602d3956..6eadfa8bf6795dc71050ba9c3e0a93d1120b95ab 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -22,6 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "fix.h" #include "fix_drude.h" #include "domain.h" @@ -311,13 +312,13 @@ void PairThole::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&polar[i][j],sizeof(double),1,fp); - fread(&thole[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&polar[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&thole[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.); } MPI_Bcast(&polar[i][j],1,MPI_DOUBLE,0,world); @@ -347,10 +348,10 @@ void PairThole::write_restart_settings(FILE *fp) void PairThole::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&thole_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&thole_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&thole_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index a4c0557620588fa45ea4b42cb7bd2176a6abd810..e7aed14030acfc4a44a8a33a76213efbf487d30a 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -965,10 +966,10 @@ void PairEffCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) fread(&cut[i][j],sizeof(double),1,fp); + if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } } @@ -992,9 +993,9 @@ void PairEffCut::write_restart_settings(FILE *fp) void PairEffCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index a4ff3ca846cc79fc492ca7b614cea4e727fb62a1..5a87a2f7403dfde0b45b6c157ba1f4559ba00a43 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -272,12 +273,12 @@ void PairCoulCutSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -306,12 +307,12 @@ void PairCoulCutSoft::write_restart_settings(FILE *fp) void PairCoulCutSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index c0030f89358d53e04619356e3932a5f80e37826c..a631dca1b7e9d4d939f9c2da8f0850809e1ab066 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -28,6 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -294,11 +295,11 @@ void PairCoulLongSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) - fread(&lambda[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); } } @@ -325,12 +326,12 @@ void PairCoulLongSoft::write_restart_settings(FILE *fp) void PairCoulLongSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index 4c3be6addbefa64152cd45e5587ec913ac2ea892..f20d351d1c671d4c81f0b92063bf5d3744c93784 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -31,6 +31,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -836,15 +837,15 @@ void PairLJCharmmCoulLongSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&eps14[i][j],sizeof(double),1,fp); - fread(&sigma14[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&eps14[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma14[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -879,15 +880,15 @@ void PairLJCharmmCoulLongSoft::write_restart_settings(FILE *fp) void PairLJCharmmCoulLongSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_inner,sizeof(double),1,fp); - fread(&cut_lj,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index bbe67e4ff3e50eaaf5b9b83c4cbb35c5c6a993c4..4913cf1271f9029c9b71f52b99d24ab9b4775a84 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -23,6 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -380,15 +381,15 @@ void PairLJClass2CoulCutSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -423,15 +424,15 @@ void PairLJClass2CoulCutSoft::write_restart_settings(FILE *fp) void PairLJClass2CoulCutSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index a3e0f732a22cef32aa79d3f1271635d1a4b6f2a4..dda10ed9e098d810a23855f2f31463cef5d83a9f 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -24,6 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -396,14 +397,14 @@ void PairLJClass2CoulLongSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -437,15 +438,15 @@ void PairLJClass2CoulLongSoft::write_restart_settings(FILE *fp) void PairLJClass2CoulLongSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index d98a5db5f397252ce32ff04cd98dab80dee18c00..eccc07f7c1e5aa1abeeab8e1cb0b2ed4daa878e6 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -319,14 +320,14 @@ void PairLJClass2Soft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -358,12 +359,12 @@ void PairLJClass2Soft::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 38fcb6fc07446cb9aa262ef091c0be081128aa06..6e5e746879a2899ebd16aa1118a78c897acc2295 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -376,15 +377,15 @@ void PairLJCutCoulCutSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -419,15 +420,15 @@ void PairLJCutCoulCutSoft::write_restart_settings(FILE *fp) void PairLJCutCoulCutSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 740daabf627489f73b953bafcbb6b6198cee1b62..cf80a3e40540ab15f0b58d9c4639b74d8654670b 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -32,6 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -792,14 +793,14 @@ void PairLJCutCoulLongSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -833,15 +834,15 @@ void PairLJCutCoulLongSoft::write_restart_settings(FILE *fp) void PairLJCutCoulLongSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphac,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 5e9a77877e85f9456bc4f87903be81b369baeb77..62b7e769777a59844ccade2c09d539173d65f1b2 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -31,6 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -653,14 +654,14 @@ void PairLJCutSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -693,13 +694,13 @@ void PairLJCutSoft::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); + utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,NULL,error); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index d4f6dcb91093ccb2e1dc3a8f13b33d8f1b045ff1..0601a641ac8e49ea8f4b9f78202260cd06968b22 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -516,17 +517,17 @@ void PairLJCutTIP4PLongSoft::read_restart_settings(FILE *fp) PairLJCutCoulLongSoft::read_restart_settings(fp); if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); + + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 2803e7df49e69e5f86e598c000f4af854d8572dc..54123bf3cdd61155f870b78b100bc3a21c230e5b 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -22,6 +22,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathSpecial; @@ -312,15 +313,15 @@ void PairMorseSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&d0[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 9cea5b54c5d129c8a4dd631c34f8f19658589aec..d5e1ae116cf782e0382c062e75ddd161ef6b0d57 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -31,6 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -453,11 +454,11 @@ void PairTIP4PLongSoft::read_restart_settings(FILE *fp) PairCoulLongSoft::read_restart_settings(fp); if (comm->me == 0) { - fread(&typeO,sizeof(int),1,fp); - fread(&typeH,sizeof(int),1,fp); - fread(&typeB,sizeof(int),1,fp); - fread(&typeA,sizeof(int),1,fp); - fread(&qdist,sizeof(double),1,fp); + utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&typeO,1,MPI_INT,0,world); MPI_Bcast(&typeH,1,MPI_INT,0,world); diff --git a/src/USER-INTEL/TEST/run_benchmarks.sh b/src/USER-INTEL/TEST/run_benchmarks.sh index 10bd79e0d1fd6bd0197c41b555266e7a70fa2815..e26c633b681729faaa90f13b80e757409039f97e 100755 --- a/src/USER-INTEL/TEST/run_benchmarks.sh +++ b/src/USER-INTEL/TEST/run_benchmarks.sh @@ -40,7 +40,7 @@ export LMP_THREAD_LIST="2" # -- For 2 threads per core w/ HT enabled # End settings for your system ######################################################################### -export WORKLOADS="lj rhodo rhodo_lrt lc sw water eam" +export WORKLOADS="lj rhodo lc sw water eam airebo dpd tersoff" export LMP_ARGS="-pk intel 0 -sf intel -screen none -v d 1" export RLMP_ARGS="-pk intel 0 lrt yes -sf intel -screen none -v d 1" @@ -51,7 +51,7 @@ export LOG_DIR=$LOG_DIR_HOST"_"$LOG_DIR_HEADER"_"$DATE_STRING mkdir $LOG_DIR export I_MPI_PIN_DOMAIN=core -export I_MPI_FABRICS=shm +#export I_MPI_FABRICS=shm export KMP_BLOCKTIME=0 echo -n "Creating restart file...." @@ -59,13 +59,12 @@ $MPI -np $LMP_CORES $LMP_BIN -in in.lc_generate_restart -log none $LMP_ARGS echo "Done." for threads in $LMP_THREAD_LIST do - export OMP_NUM_THREADS=$threads for workload in $WORKLOADS do export LOGFILE=$LOG_DIR/$workload.$LMP_CORES"c"$threads"t".log echo "Running $LOGFILE" cmd="$MPI -np $LMP_CORES $LMP_BIN -in in.intel.$workload -log $LOGFILE $LMP_ARGS"; - rthreads=$threads + export OMP_NUM_THREADS=$threads unset KMP_AFFINITY $cmd diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index e1e09fd3da4b3ee0bab35ef0953d385c8b1264eb..00b032d49513d512b8bc67dbcebfefb53e7fa2f3 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -150,8 +150,8 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const int nlocal = atom->nlocal; #ifndef _LMP_INTEL_OFFLOAD - int * const mask = atom->mask; - tagint * const molecule = atom->molecule; + int * _noalias const mask = atom->mask; + tagint * _noalias const molecule = atom->molecule; #endif int moltemplate; @@ -162,7 +162,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, "Can't use moltemplate with npair style full/bin/ghost/intel."); int tnum; - int *overflow; + int * _noalias overflow; #ifdef _LMP_INTEL_OFFLOAD double *timer_compute; if (offload) { @@ -200,7 +200,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const int mbinx = this->mbinx; const int mbiny = this->mbiny; const int mbinz = this->mbinz; - const int * const stencilxyz = &this->stencilxyz[0][0]; + const int * _noalias const stencilxyz = &this->stencilxyz[0][0]; int sb = 1; if (special_flag[1] == 0) { @@ -295,7 +295,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int pack_offset = maxnbors; int ct = (ifrom + tid * 2) * maxnbors; - int *neighptr = intel_list + ct; + int * _noalias neighptr = intel_list + ct; const int obound = pack_offset + maxnbors * 2; const int toffs = tid * ncache_stride; @@ -370,7 +370,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int n = maxnbors; int n2 = n * 2; - int *neighptr2 = neighptr; + int * _noalias neighptr2 = neighptr; const flt_t * _noalias cutsq; if (i < nlocal) cutsq = cutneighsq; else cutsq = cutneighghostsq; diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index ad9ec6e7d3a048506a1746f6630ce459d9955cda..a82d3f29e59af7e7c3cc11ecf7e95870480c3640 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -154,12 +154,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, const int nlocal = atom->nlocal; #ifndef _LMP_INTEL_OFFLOAD - int * const mask = atom->mask; - tagint * const molecule = atom->molecule; + int * _noalias const mask = atom->mask; + tagint * _noalias const molecule = atom->molecule; #endif int tnum; - int *overflow; + int * _noalias overflow; #ifdef _LMP_INTEL_OFFLOAD double *timer_compute; if (offload) { @@ -298,8 +298,8 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, const int obound = maxnbors * 3; #endif int ct = (ifrom + tid * 2) * maxnbors; - int *neighptr = intel_list + ct; - int *neighptr2; + int * _noalias neighptr = intel_list + ct; + int * _noalias neighptr2; if (THREE) neighptr2 = neighptr; const int toffs = tid * ncache_stride; diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index 4ebdce9a962d4ce225450c4bde708e684bea1345..690496d5469b5919021edb340ea27597dbd6936e 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -283,7 +283,7 @@ void PairDPDIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ sv0, sv1, sv2, sv3, sv4, sv5) #endif diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 32d7e74cbca6d99672c5fa5c5602e5b8ce28a9c6..984823f07ec9393dc2e91dbe31a74e4b81753af4 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -305,7 +305,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, acc_t rhoi = (acc_t)0.0; int ej = 0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma ivdep #endif for (int jj = 0; jj < jnum; jj++) { @@ -324,7 +324,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma simd reduction(+:rhoi) #endif for (int jj = 0; jj < ej; jj++) { @@ -411,7 +411,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, if (EFLAG) tevdwl = (acc_t)0.0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma simd reduction(+:tevdwl) #endif for (int ii = iifrom; ii < iito; ++ii) { @@ -485,7 +485,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, int ej = 0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma ivdep #endif for (int jj = 0; jj < jnum; jj++) { @@ -507,7 +507,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, } #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ sv0, sv1, sv2, sv3, sv4, sv5) #endif diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp index 862dee22874bfd1c63324a60865e4f746daacf17..30e61f67b9596bc27021f2d0a875675ce9646b45 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/USER-INTEL/pair_gayberne_intel.cpp @@ -555,10 +555,10 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, dchi_2 = temp2 * (iota_2 - temp1 * r12hat_2); temp1 = -eta * u_r; - temp2 = eta * chi; - fforce_0 = temp1 * dchi_0 - temp2 * dUr_0; - fforce_1 = temp1 * dchi_1 - temp2 * dUr_1; - fforce_2 = temp1 * dchi_2 - temp2 * dUr_2; + temp3 = eta * chi; + fforce_0 = temp1 * dchi_0 - temp3 * dUr_0; + fforce_1 = temp1 * dchi_1 - temp3 * dUr_1; + fforce_2 = temp1 * dchi_2 - temp3 * dUr_2; // torque for particle 1 and 2 // compute dUr @@ -579,18 +579,17 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, ME_vecmat(iota, b1, tempv); ME_cross3(tempv, iota, dchi); - temp1 = (flt_t)-4.0 / rsq_form[jj]; - dchi_0 *= temp1; - dchi_1 *= temp1; - dchi_2 *= temp1; + dchi_0 *= temp2; + dchi_1 *= temp2; + dchi_2 *= temp2; flt_t dchi2_0, dchi2_1, dchi2_2; if (NEWTON_PAIR) { ME_vecmat(iota, b2, tempv); ME_cross3(tempv, iota, dchi2); - dchi2_0 *= temp1; - dchi2_1 *= temp1; - dchi2_2 *= temp1; + dchi2_0 *= temp2; + dchi2_1 *= temp2; + dchi2_2 *= temp2; } // compute d_eta diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index 39db9c7333799b9aaa3a0086d07cd714f97d2ab9..f6f83b752ae5bff4b396a9cb1752ca784c0d4819 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -236,7 +236,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag, if (vflag==1) sv0 = sv1 = sv2 = sv3 = sv4 = sv5 = (acc_t)0; #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned + #pragma vector aligned nog2s #pragma simd reduction(+:fxtmp, fytmp, fztmp, fwtmp, sevdwl, \ sv0, sv1, sv2, sv3, sv4, sv5) #endif diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index f72b6d6b93243a81e7be514f922953e94208b687..c32477513d0b4172815a31681e0509ae8a9ace36 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -31,6 +31,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -452,24 +453,24 @@ void PairEDPD::read_restart(FILE *fp) int me = comm->me; for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a0[i][j],sizeof(double),1,fp); - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&power[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - fread(&kappa[i][j],sizeof(double),1,fp); - fread(&powerT[i][j],sizeof(double),1,fp); - fread(&cutT[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&power[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&kappa[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&powerT[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cutT[i][j],sizeof(double),1,fp,NULL,error); if(power_flag) for (int k = 0; k < 4; k++) - fread(&sc[i][j][k],sizeof(double),1,fp); + utils::sfread(FLERR,&sc[i][j][k],sizeof(double),1,fp,NULL,error); if(kappa_flag) for (int k = 0; k < 4; k++) - fread(&kc[i][j][k],sizeof(double),1,fp); + utils::sfread(FLERR,&kc[i][j][k],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); @@ -507,9 +508,9 @@ void PairEDPD::write_restart_settings(FILE *fp) void PairEDPD::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&seed,1,MPI_INT,0,world); diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index 56adad26ce86719f817639d0551c7ab1e5190fbb..7f98e6da794e8b8dbc31d86a29564bd5fdcd0723 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -30,6 +30,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -347,15 +348,15 @@ void PairMDPD::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&A_att[i][j],sizeof(double),1,fp); - fread(&B_rep[i][j],sizeof(double),1,fp); - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - fread(&cut_r[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&A_att[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&B_rep[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_r[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&A_att[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&B_rep[i][j],1,MPI_DOUBLE,0,world); @@ -385,10 +386,10 @@ void PairMDPD::write_restart_settings(FILE *fp) void PairMDPD::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&temperature,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 346401b1ba576e7444809e8e5c45ac0993860cb3..f5350de53dd63f345a4b0c784114f855d41140ac 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -29,6 +29,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -394,19 +395,19 @@ void PairTDPD::read_restart(FILE *fp) int me = comm->me; for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a0[i][j],sizeof(double),1,fp); - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&power[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - fread(&cutcc[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&power[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cutcc[i][j],sizeof(double),1,fp,NULL,error); for(int k=0; kme == 0) { - fread(&temperature,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 442feedf87735cb37c082e2f549612b105da6def..3b96f3685d8079af2182ea8cbe52c8cf181ed37c 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -84,6 +84,7 @@ pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), s pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 +pair_style local/density, Tanmoy Sanyal (tanmoy dot 7989 at gmail.com) and M. Scott Shell (UCSB), and David Rosenberger (TU Darmstadt), 9 Sept 19 pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17 pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12 diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index b18ddc79d3d3bae4303f65a82a4d72d2375ed80c..d403b61c426d0a6bb40fe052117d1c6ffa36d404 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -224,10 +225,10 @@ void AngleCosineShift::read_restart(FILE *fp) if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&kcost[1],sizeof(double),atom->nangletypes,fp); - fread(&ksint[1],sizeof(double),atom->nangletypes,fp); - fread(&theta[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&kcost[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ksint[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&kcost[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index 79cb0fea7ca71c8facff410ec53b36b9e689561e..ef5a2824b90c22a09f1b59f4dc7f5dceff12fff4 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -256,11 +257,11 @@ void AngleCosineShiftExp::read_restart(FILE *fp) if (comm->me == 0) { - fread(&umin[1],sizeof(double),atom->nangletypes,fp); - fread(&a[1],sizeof(double),atom->nangletypes,fp); - fread(&cost[1],sizeof(double),atom->nangletypes,fp); - fread(&sint[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&umin[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&a[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&cost[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&sint[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&umin[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&a[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 0956ba3b8f31fcdbb266d7f2399d3c7f9b203ba7..e2fd7e618f7d8478470e9f7c42d50e317cb4d533 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -205,8 +206,8 @@ void AngleDipole::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&gamma0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&gamma0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&gamma0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index dcf5080431cb383374abc902542d5ebddf83b834..f83c9c4f8822ae5214c25e1613a73e62ee83bf07 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -231,10 +232,10 @@ void AngleFourier::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&C0[1],sizeof(double),atom->nangletypes,fp); - fread(&C1[1],sizeof(double),atom->nangletypes,fp); - fread(&C2[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&C0[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&C1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&C2[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&C0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index bbe3f8520b45c064edec0f0a5ef615e83d970366..baf4953760ba8da9189e623bdf715a4c8cdc4fca 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -237,9 +238,9 @@ void AngleFourierSimple::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&C[1],sizeof(double),atom->nangletypes,fp); - fread(&N[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&C[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&N[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&C[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 5c5f3411e423bcce0c458c418299a8561cbc297d..097e774f17393b947ca0c988d3073a34e240aaac 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -232,10 +233,10 @@ void AngleQuartic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k2[1],sizeof(double),atom->nangletypes,fp); - fread(&k3[1],sizeof(double),atom->nangletypes,fp); - fread(&k4[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world); MPI_Bcast(&k3[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index fdd31117831fed94b6d98c042503061e5987cae1..79e401eddb94ff3518b250902f02b19a5a0725b3 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -176,9 +177,9 @@ void BondHarmonicShift::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); - fread(&r1[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r1[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 0688cb428a75b63357e8d29c86bda7469107513e..aa051f4bece831d418de891810f94f0529bed090 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -178,9 +179,9 @@ void BondHarmonicShiftCut::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); - fread(&r1[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r1[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp index a0ee6089b70d90acfd928ce5440b15fbc15cca21..8c660cfb9ec3e7241499611b794e823f6362f321 100644 --- a/src/USER-MISC/compute_gyration_shape.cpp +++ b/src/USER-MISC/compute_gyration_shape.cpp @@ -112,19 +112,15 @@ void ComputeGyrationShape::compute_vector() } // compute the shape parameters of the gyration tensor - double sq_eigen_x = MathSpecial::square(evalues[0]); - double sq_eigen_y = MathSpecial::square(evalues[1]); - double sq_eigen_z = MathSpecial::square(evalues[2]); - - double nominator = MathSpecial::square(sq_eigen_x) - + MathSpecial::square(sq_eigen_y) - + MathSpecial::square(sq_eigen_z); - double denominator = MathSpecial::square(sq_eigen_x+sq_eigen_y+sq_eigen_z); + double nominator = MathSpecial::square(evalues[0]) + + MathSpecial::square(evalues[1]) + + MathSpecial::square(evalues[2]); + double denominator = MathSpecial::square(evalues[0]+evalues[1]+evalues[2]); vector[0] = evalues[0]; vector[1] = evalues[1]; vector[2] = evalues[2]; - vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y); - vector[4] = sq_eigen_y - sq_eigen_x; - vector[5] = 0.5*(3*nominator/denominator - 1.0); + vector[3] = evalues[0] - 0.5*(evalues[1] + evalues[2]); + vector[4] = evalues[1] - evalues[2]; + vector[5] = 1.5*nominator/denominator - 0.5; } diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index a14084b9ca65da710b2a3e7110867beb72262653..f1c2e9ba3a82f891fee1547d4c26af4c03f961b2 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -214,7 +214,7 @@ void ComputeHMA::init() { neighbor->requests[irequest]->occasional = 1; } -void ComputeHMA::init_list(int id, NeighList *ptr) +void ComputeHMA::init_list(int /* id */, NeighList *ptr) { list = ptr; } @@ -318,11 +318,9 @@ void ComputeHMA::compute_vector() double phiSum = 0.0; if (computeCv>-1) { comm->forward_comm_compute(this); - int *type = atom->type; double** cutsq = force->pair->cutsq; if (force->pair) { double **x = atom->x; - double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_lj = force->special_lj; @@ -459,16 +457,8 @@ double ComputeHMA::virial_compute(int n) /* ---------------------------------------------------------------------- */ int ComputeHMA::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) + int /* pbc_flag */, int * /* pbc */) { - double **xoriginal = fix->astore; - imageint *image = atom->image; - double **x = atom->x; - double *h = domain->h; - double xprd = domain->xprd; - double yprd = domain->yprd; - double zprd = domain->zprd; - int m = 0; for (int ii = 0; ii < n; ii++) { int i = list[ii]; @@ -483,7 +473,6 @@ int ComputeHMA::pack_forward_comm(int n, int *list, double *buf, void ComputeHMA::unpack_forward_comm(int n, int first, double *buf) { - double **xoriginal = fix->astore; int i,m,last; m = 0; diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 820dfabdeb6dc48ab97e97698778d3b5ac9c0555..0537e555a272fadfe5c77b4cf234c4d380f07036 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -26,6 +26,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -321,11 +322,11 @@ void DihedralCosineShiftExp::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&umin[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&a[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&cost[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&sint[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&theta[1],sizeof(double),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&umin[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&a[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&cost[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&sint[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&theta[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&umin[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&a[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index 7cc250b1a882f80daf94b85f72e22ee7fbfe8e3d..f30a5e1eabf717682560133c98f79c15f373e8dc 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -364,7 +365,7 @@ void DihedralFourier::read_restart(FILE *fp) allocate(); if (comm->me == 0) - fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world); @@ -379,9 +380,9 @@ void DihedralFourier::read_restart(FILE *fp) if (comm->me == 0) { for (int i=1; i<=atom->ndihedraltypes; i++) { - fread(k[i],sizeof(double),nterms[i],fp); - fread(multiplicity[i],sizeof(int),nterms[i],fp); - fread(shift[i],sizeof(double),nterms[i],fp); + utils::sfread(FLERR,k[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,multiplicity[i],sizeof(int),nterms[i],fp,NULL,error); + utils::sfread(FLERR,shift[i],sizeof(double),nterms[i],fp,NULL,error); } } diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index f1e0018689cf3fa85134049dea750fd95ed254c7..56254a5c03251c54dfcc22cd12568b37682be369 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -26,6 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -318,7 +319,7 @@ void DihedralNHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) - fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world); @@ -328,7 +329,7 @@ void DihedralNHarmonic::read_restart(FILE *fp) if (comm->me == 0) { for(int i = 1; i <= atom->ndihedraltypes; i++) - fread(a[i],sizeof(double),nterms[i],fp); + utils::sfread(FLERR,a[i],sizeof(double),nterms[i],fp,NULL,error); } for (int i = 1; i <= atom->ndihedraltypes; i++ ) diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 02effc2f4fd5425eaf4c767fc47563823531a592..28efad65b7b088d8dedc682253825c4f9e583628 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -325,8 +326,8 @@ void DihedralQuadratic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi0[1],sizeof(double),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); + utils::sfread(FLERR,&phi0[1],sizeof(double),atom->ndihedraltypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&phi0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 78d45f923d12683deb4dec3d9e748d0a20810b4a..c72570c4942ae36eb15e6701ee4a1a81cf7e99b3 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -30,6 +30,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace std; using namespace LAMMPS_NS; @@ -755,7 +756,7 @@ void DihedralSpherical::read_restart(FILE *fp) allocate(); if (comm->me == 0) - fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp); + utils::sfread(FLERR,&nterms[1],sizeof(int),atom->ndihedraltypes,fp,NULL,error); MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world); @@ -775,16 +776,16 @@ void DihedralSpherical::read_restart(FILE *fp) if (comm->me == 0) { for (int i=1; i<=atom->ndihedraltypes; i++) { - fread(Ccoeff[i],sizeof(double),nterms[i],fp); - fread(phi_mult[i],sizeof(double),nterms[i],fp); - fread(phi_shift[i],sizeof(double),nterms[i],fp); - fread(phi_offset[i],sizeof(double),nterms[i],fp); - fread(theta1_mult[i],sizeof(double),nterms[i],fp); - fread(theta1_shift[i],sizeof(double),nterms[i],fp); - fread(theta1_offset[i],sizeof(double),nterms[i],fp); - fread(theta2_mult[i],sizeof(double),nterms[i],fp); - fread(theta2_shift[i],sizeof(double),nterms[i],fp); - fread(theta2_offset[i],sizeof(double),nterms[i],fp); + utils::sfread(FLERR,Ccoeff[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,phi_mult[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,phi_shift[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,phi_offset[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,theta1_mult[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,theta1_shift[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,theta1_offset[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,theta2_mult[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,theta2_shift[i],sizeof(double),nterms[i],fp,NULL,error); + utils::sfread(FLERR,theta2_offset[i],sizeof(double),nterms[i],fp,NULL,error); } } diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index 59a16f376fa8a7d6a02c6be64c6647214ca7c6f1..a14c3d9d79d6930a1bb9124068bc817d3ca9fbb1 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -33,6 +33,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "dihedral_table.h" #include "utils.h" @@ -1042,8 +1043,8 @@ void DihedralTable::write_restart_settings(FILE *fp) void DihedralTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 87f0c9bf665d2878632ab1bbcaa8ece598d93680..8d530253c25c14bee1d5870d9099f61bb1cb77f3 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -1029,8 +1029,8 @@ void DihedralTableCut::write_restart_settings(FILE *fp) void DihedralTableCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index b1bcc07fa781cf2b266b80911705df959a9e9571..3a28e47cda0077797f1a38c886cbcae4b955dc5c 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -504,7 +504,8 @@ void FixAveCorrelateLong::end_of_step() fflush(fp); if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index 05dc54c57e3ec71f6a8b8681f6f5c9e87bb433f7..bfa93e178c23a00355bb4259360bf28fec41ac42 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -35,6 +35,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) #include "molecule.h" #include "group.h" #include "citeme.h" +#include "math_const.h" #include "memory.h" #include "error.h" @@ -42,6 +43,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) using namespace LAMMPS_NS; using namespace FixConst; +using namespace MathConst; static const char cite_fix_bond_react[] = "fix bond/react:\n\n" @@ -56,9 +58,8 @@ static const char cite_fix_bond_react[] = #define BIG 1.0e20 #define DELTA 16 -#define MAXLINE 256 #define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm -#define MAXCONARGS 5 // max # of arguments for any type of constraint +#define MAXCONARGS 7 // max # of arguments for any type of constraint + rxnID // various statuses of superimpose algorithm: // ACCEPT: site successfully matched to pre-reacted template @@ -69,6 +70,9 @@ static const char cite_fix_bond_react[] = // RESTORE: restore mode, load most recent restore point enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE}; +// types of available reaction constraints +enum{DISTANCE,ANGLE,ARRHENIUS}; + /* ---------------------------------------------------------------------- */ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : @@ -87,6 +91,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : MPI_Comm_size(world,&nprocs); newton_bond = force->newton_bond; + restart_global = 1; attempted_rxn = 0; force_reneighbor = 1; next_reneighbor = -1; @@ -94,6 +99,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : global_freq = 1; extvector = 0; rxnID = 0; + nconstraints = 0; + narrhenius = 0; status = PROCEED; nxspecial = NULL; @@ -107,7 +114,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : master_group = (char *) "bond_react_MASTER_group"; // by using fixed group names, only one instance of fix bond/react is allowed. - if (modify->find_fix_by_style("bond/react") != -1) + if (modify->find_fix_by_style("^bond/react") != -1) error->all(FLERR,"Only one instance of fix bond/react allowed at a time"); // let's find number of reactions specified @@ -169,8 +176,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(limit_duration,nreacts,"bond/react:limit_duration"); memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag"); - memory->create(nconstraints,nreacts,"bond/react:nconstraints"); - memory->create(constraints,nreacts,MAXCONARGS,"bond/react:constraints"); + memory->create(constraints,1,MAXCONARGS,"bond/react:constraints"); memory->create(iatomtype,nreacts,"bond/react:iatomtype"); memory->create(jatomtype,nreacts,"bond/react:jatomtype"); memory->create(ibonding,nreacts,"bond/react:ibonding"); @@ -188,7 +194,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : max_rxn[i] = INT_MAX; stabilize_steps_flag[i] = 0; update_edges_flag[i] = 0; - nconstraints[i] = 0; // set default limit duration to 60 timesteps limit_duration[i] = 60; reaction_count[i] = 0; @@ -207,7 +212,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : iarg++; - rxn_name[rxn] = arg[iarg++]; + int n = strlen(arg[iarg]) + 1; + if (n > MAXLINE) error->all(FLERR,"Reaction name (react-ID) is too long (limit: 256 characters)"); + strncpy(rxn_name[rxn],arg[iarg++],n); int igroup = group->find(arg[iarg++]); if (igroup == -1) error->all(FLERR,"Could not find fix group ID"); @@ -316,6 +323,16 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : find_landlocked_atoms(i); } + // initialize Marsaglia RNG with processor-unique seed (Arrhenius prob) + + rrhandom = new class RanMars*[narrhenius]; + int tmp = 0; + for (int i = 0; i < nconstraints; i++) { + if (constraints[i][1] == ARRHENIUS) { + rrhandom[tmp++] = new RanMars(lmp,(int) constraints[i][6] + me); + } + } + for (int i = 0; i < nreacts; i++) { delete [] files[i]; } @@ -342,7 +359,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } } - // initialize Marsaglia RNG with processor-unique seed + // initialize Marsaglia RNG with processor-unique seed ('prob' keyword) random = new class RanMars*[nreacts]; for (int i = 0; i < nreacts; i++) { @@ -386,6 +403,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : id_fix3 = NULL; statted_id = NULL; custom_exclude_flag = 0; + + // used to store restart info + set = new Set[nreacts]; + memset(set,0,nreacts*sizeof(Set)); } /* ---------------------------------------------------------------------- */ @@ -469,6 +490,7 @@ FixBondReact::~FixBondReact() delete [] statted_id; delete [] guess_branch; delete [] pioneer_count; + delete [] set; if (group) { char **newarg; @@ -1131,6 +1153,22 @@ void FixBondReact::superimpose_algorithm() glove[myjbonding-1][1] = created[lcl_inst][1][rxnID]; glove_counter++; + // special case, only two atoms in reaction templates + // then: bonding onemol_nxspecials guaranteed to be equal, and either 0 or 1 + if (glove_counter == onemol->natoms) { + tagint local_atom1 = atom->map(glove[myibonding-1][1]); + tagint local_atom2 = atom->map(glove[myjbonding-1][1]); + if ( (nxspecial[local_atom1][0] == onemol_nxspecial[myibonding-1][0] && + nxspecial[local_atom2][0] == nxspecial[local_atom1][0]) && + (nxspecial[local_atom1][0] == 0 || + xspecial[local_atom1][0] == atom->tag[local_atom2]) && + check_constraints() ) { + status = ACCEPT; + glove_ghostcheck(); + } else + status = REJECT; + } + avail_guesses = 0; for (int i = 0; i < max_natoms; i++) @@ -1209,7 +1247,7 @@ void FixBondReact::superimpose_algorithm() rxn_by_proc[j] = -1; // corresponds to ghostly int itemp = 0; for (int j = 0; j < nprocs; j++) - for (int k = 0; k < local_rxn_count[j]; k++) + for (int k = 0; k < local_rxncounts[j]; k++) rxn_by_proc[itemp++] = j; std::random_shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn]); for (int j = 0; j < nprocs; j++) @@ -1610,26 +1648,97 @@ evaluate constraints: return 0 if any aren't satisfied int FixBondReact::check_constraints() { - tagint atom1,atom2; + tagint atom1,atom2,atom3; double delx,dely,delz,rsq; + double delx1,dely1,delz1,delx2,dely2,delz2; + double rsq1,rsq2,r1,r2,c,t,prrhob; double **x = atom->x; - for (int i = 0; i < nconstraints[rxnID]; i++) { - if (constraints[rxnID][0] == 0) { // 'distance' type - atom1 = atom->map(glove[(int) constraints[rxnID][1]-1][1]); - atom2 = atom->map(glove[(int) constraints[rxnID][2]-1][1]); - delx = x[atom1][0] - x[atom2][0]; - dely = x[atom1][1] - x[atom2][1]; - delz = x[atom1][2] - x[atom2][2]; - domain->minimum_image(delx,dely,delz); // ghost location fix - rsq = delx*delx + dely*dely + delz*delz; - if (rsq < constraints[rxnID][3] || rsq > constraints[rxnID][4]) return 0; + for (int i = 0; i < nconstraints; i++) { + if (constraints[i][0] == rxnID) { + if (constraints[i][1] == DISTANCE) { + atom1 = atom->map(glove[(int) constraints[i][2]-1][1]); + atom2 = atom->map(glove[(int) constraints[i][3]-1][1]); + delx = x[atom1][0] - x[atom2][0]; + dely = x[atom1][1] - x[atom2][1]; + delz = x[atom1][2] - x[atom2][2]; + domain->minimum_image(delx,dely,delz); // ghost location fix + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < constraints[i][4] || rsq > constraints[i][5]) return 0; + } else if (constraints[i][1] == ANGLE) { + atom1 = atom->map(glove[(int) constraints[i][2]-1][1]); + atom2 = atom->map(glove[(int) constraints[i][3]-1][1]); + atom3 = atom->map(glove[(int) constraints[i][4]-1][1]); + + // 1st bond + delx1 = x[atom1][0] - x[atom2][0]; + dely1 = x[atom1][1] - x[atom2][1]; + delz1 = x[atom1][2] - x[atom2][2]; + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + // 2nd bond + delx2 = x[atom3][0] - x[atom2][0]; + dely2 = x[atom3][1] - x[atom2][1]; + delz2 = x[atom3][2] - x[atom2][2]; + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); + + // angle (cos and sin) + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + if (acos(c) < constraints[i][5] || acos(c) > constraints[i][6]) return 0; + } else if (constraints[i][1] == ARRHENIUS) { + t = get_temperature(); + prrhob = constraints[i][3]*pow(t,constraints[i][4])* + exp(-constraints[i][5]/(force->boltz*t)); + if (prrhob < rrhandom[(int) constraints[i][2]]->uniform()) return 0; + } } } return 1; } +/* ---------------------------------------------------------------------- +compute local temperature: average over all atoms in reaction template +------------------------------------------------------------------------- */ + +double FixBondReact::get_temperature() +{ + int i,ilocal; + double adof = domain->dimension; + + double **v = atom->v; + double *mass = atom->mass; + double *rmass = atom->rmass; + int *type = atom->type; + + double t = 0.0; + + if (rmass) { + for (i = 0; i < onemol->natoms; i++) { + ilocal = atom->map(glove[i][1]); + t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] + + v[ilocal][2]*v[ilocal][2]) * rmass[ilocal]; + } + } else { + for (i = 0; i < onemol->natoms; i++) { + ilocal = atom->map(glove[i][1]); + t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] + + v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]]; + } + } + + // final temperature + double dof = adof*onemol->natoms; + double tfactor = force->mvv2e / (dof * force->boltz); + t *= tfactor; + return t; +} + /* ---------------------------------------------------------------------- Get xspecials for current molecule templates ------------------------------------------------------------------------- */ @@ -1801,7 +1910,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) if (dedup_mode == 1) ghostly_rxn_count[i] = 0; } - int dedup_size; + int dedup_size = 0; if (dedup_mode == 0) { dedup_size = local_num_mega; } else if (dedup_mode == 1) { @@ -2750,15 +2859,20 @@ void FixBondReact::read(int myrxn) if (strspn(line," \t\n\r") == strlen(line)) continue; if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge); - else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent); + else if (strstr(line,"equivalences")) { + sscanf(line,"%d",&nequivalent); + if (nequivalent != onemol->natoms) + error->one(FLERR,"Bond/react: Number of equivalences in map file must " + "equal number of atoms in reaction templates"); + } else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom); else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); - else if (strstr(line,"constraints")) sscanf(line,"%d",&nconstraints[myrxn]); - else break; + else if (strstr(line,"constraints")) { + sscanf(line,"%d",&nconstr); + memory->grow(constraints,nconstraints+nconstr,MAXCONARGS,"bond/react:constraints"); + } else break; } - //count = NULL; - // grab keyword and skip next line parse_keyword(0,line,keyword); @@ -2766,7 +2880,7 @@ void FixBondReact::read(int myrxn) // loop over sections of superimpose file - int equivflag = 0, edgeflag = 0, bondflag = 0, customedgesflag = 0; + int equivflag = 0, bondflag = 0, customedgesflag = 0; while (strlen(keyword)) { if (strcmp(keyword,"BondingIDs") == 0) { bondflag = 1; @@ -2775,7 +2889,6 @@ void FixBondReact::read(int myrxn) readline(line); sscanf(line,"%d",&jbonding[myrxn]); } else if (strcmp(keyword,"EdgeIDs") == 0) { - edgeflag = 1; EdgeIDs(line, myrxn); } else if (strcmp(keyword,"Equivalences") == 0) { equivflag = 1; @@ -2867,18 +2980,36 @@ void FixBondReact::Constraints(char *line, int myrxn) double tmp[MAXCONARGS]; int n = strlen("distance") + 1; char *constraint_type = new char[n]; - for (int i = 0; i < nconstraints[myrxn]; i++) { + for (int i = 0; i < nconstr; i++) { readline(line); sscanf(line,"%s",constraint_type); + constraints[nconstraints][0] = myrxn; if (strcmp(constraint_type,"distance") == 0) { - constraints[myrxn][0] = 0; // 0 = 'distance' ...maybe use another enum eventually + constraints[nconstraints][1] = DISTANCE; sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]); - constraints[myrxn][1] = tmp[0]; - constraints[myrxn][2] = tmp[1]; - constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance - constraints[myrxn][4] = tmp[3]*tmp[3]; + constraints[nconstraints][2] = tmp[0]; + constraints[nconstraints][3] = tmp[1]; + constraints[nconstraints][4] = tmp[2]*tmp[2]; // using square of distance + constraints[nconstraints][5] = tmp[3]*tmp[3]; + } else if (strcmp(constraint_type,"angle") == 0) { + constraints[nconstraints][1] = ANGLE; + sscanf(line,"%*s %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3],&tmp[4]); + constraints[nconstraints][2] = tmp[0]; + constraints[nconstraints][3] = tmp[1]; + constraints[nconstraints][4] = tmp[2]; + constraints[nconstraints][5] = tmp[3]/180.0 * MY_PI; + constraints[nconstraints][6] = tmp[4]/180.0 * MY_PI; + } else if (strcmp(constraint_type,"arrhenius") == 0) { + constraints[nconstraints][1] = ARRHENIUS; + constraints[nconstraints][2] = narrhenius++; + sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]); + constraints[nconstraints][3] = tmp[0]; + constraints[nconstraints][4] = tmp[1]; + constraints[nconstraints][5] = tmp[2]; + constraints[nconstraints][6] = tmp[3]; } else error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file"); + nconstraints++; } delete [] constraint_type; } @@ -3098,6 +3229,42 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) } } +/* ---------------------------------------------------------------------- + write Set data to restart file +------------------------------------------------------------------------- */ + +void FixBondReact::write_restart(FILE *fp) +{ + set[0].nreacts = nreacts; + for (int i = 0; i < nreacts; i++) { + set[i].reaction_count_total = reaction_count_total[i]; + strncpy(set[i].rxn_name,rxn_name[i],MAXLINE); + set[i].rxn_name[MAXLINE-1] = '\0'; + } + + if (me == 0) { + int size = nreacts*sizeof(Set); + fwrite(&size,sizeof(int),1,fp); + fwrite(set,sizeof(Set),nreacts,fp); + } +} + +/* ---------------------------------------------------------------------- + use selected state info from restart file to restart the Fix +------------------------------------------------------------------------- */ + +void FixBondReact::restart(char *buf) +{ + Set *set_restart = (Set *) buf; + for (int i = 0; i < set_restart[0].nreacts; i++) { + for (int j = 0; j < nreacts; j++) { + if (strcmp(set_restart[i].rxn_name,rxn_name[j]) == 0) { + reaction_count_total[j] = set_restart[i].reaction_count_total; + } + } + } +} + /* ---------------------------------------------------------------------- memory usage of local atom-based arrays ------------------------------------------------------------------------- */ diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h index 1ac8d624a926226c7ac49d596d7f951e07cd037f..f59e051ed184d81ccafa5cf4885a8ffb6633733a 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-MISC/fix_bond_react.h @@ -30,6 +30,9 @@ namespace LAMMPS_NS { class FixBondReact : public Fix { public: + + enum {MAXLINE=256}; + FixBondReact(class LAMMPS *, int, char **); ~FixBondReact(); int setmask(); @@ -61,7 +64,8 @@ class FixBondReact : public Fix { int custom_exclude_flag; int *stabilize_steps_flag; int *update_edges_flag; - int *nconstraints; + int nconstraints; + int narrhenius; double **constraints; int status; int *groupbits; @@ -85,7 +89,8 @@ class FixBondReact : public Fix { Fix *fix2; // properties/atom used to indicate 1) relaxing atoms // 2) to which 'react' atom belongs Fix *fix3; // property/atom used for system-wide thermostat - class RanMars **random; + class RanMars **random; // random number for 'prob' keyword + class RanMars **rrhandom; // random number for Arrhenius constraint class NeighList *list; int *reacted_mol,*unreacted_mol; @@ -105,7 +110,7 @@ class FixBondReact : public Fix { int *ibonding,*jbonding; int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors - int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file + int nedge,nequivalent,ncustom,ndelete,nconstr; // # edge, equivalent, custom atoms in mapping file int attempted_rxn; // there was an attempt! int *local_rxn_count; int *ghostly_rxn_count; @@ -153,6 +158,7 @@ class FixBondReact : public Fix { void inner_crosscheck_loop(); void ring_check(); int check_constraints(); + double get_temperature(); void open(char *); void readline(char *); @@ -170,6 +176,15 @@ class FixBondReact : public Fix { void unlimit_bond(); void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove + virtual void write_restart(FILE *); + virtual void restart(char *buf); + + struct Set { + int nreacts; + char rxn_name[MAXLINE]; + int reaction_count_total; + }; + Set *set; // DEBUG diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 55526a914940099a2c9995053c6622c60c178d96..49e9cc02a64c9952096ffe2cd0a767fe36efc727 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -32,6 +32,7 @@ #include "error.h" #include "citeme.h" #include "math_const.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -93,10 +94,11 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0) error->all(FLERR,"Fix ttm/mod number of nodes must be > 0"); - FILE *fpr = force->open_potential(arg[8]); + const char *filename = arg[8]; + FILE *fpr = force->open_potential(filename); if (fpr == NULL) { char str[128]; - snprintf(str,128,"Cannot open file %s",arg[8]); + snprintf(str,128,"Cannot open file %s",filename); error->all(FLERR,str); } @@ -117,113 +119,113 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) : double tresh_d; int tresh_i; // C0 (metal) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_0 = tresh_d; // C1 (metal*10^3) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_1 = tresh_d; // C2 (metal*10^6) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_2 = tresh_d; // C3 (metal*10^9) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_3 = tresh_d; // C4 (metal*10^12) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); esheat_4 = tresh_d; // C_limit - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); C_limit = tresh_d; //Temperature damping factor - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); T_damp = tresh_d; // rho_e - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); electronic_density = tresh_d; //thermal_diffusion - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); el_th_diff = tresh_d; // gamma_p - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); gamma_p = tresh_d; // gamma_s - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); gamma_s = tresh_d; // v0 - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); v_0 = tresh_d; // average intensity of pulse (source of energy) (metal units) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); intensity = tresh_d; // coordinate of 1st surface in x-direction (in box units) - constant - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); surface_l = tresh_i; // coordinate of 2nd surface in x-direction (in box units) - constant - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); surface_r = tresh_i; // skin_layer = intensity is reduced (I=I0*exp[-x/skin_layer]) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); skin_layer = tresh_i; // width of pulse (picoseconds) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); width = tresh_d; // factor of electronic pressure (PF) Pe = PF*Ce*Te - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); pres_factor = tresh_d; // effective free path of electrons (angstrom) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); free_path = tresh_d; // ionic density (ions*angstrom^{-3}) - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); ionic_density = tresh_d; // if movsur = 0: surface is freezed - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%d",&tresh_i); movsur = tresh_i; // electron_temperature_min - fgets(linee,MAXLINE,fpr_2); - fgets(linee,MAXLINE,fpr_2); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); + utils::sfgets(FLERR,linee,MAXLINE,fpr_2,filename,error); sscanf(linee,"%lg",&tresh_d); electron_temperature_min = tresh_d; fclose(fpr_2); diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 2ea804b95d8754cdea78bf8425a52b5bb4f87543..c5556b746d172adcb775d19f82e6002b9b9f27db 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -26,6 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "math_const.h" using namespace LAMMPS_NS; @@ -301,8 +302,8 @@ void ImproperCossq::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 2efab8b5f81e5f5ba30638896b7de3165c7b9909..146bd344f1a65c56b2cd9e799cba79a474762280 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -25,6 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -247,8 +248,8 @@ void ImproperDistance::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index a0ef3a205859d72434c010b8eaeffd628191e22f..beb473d78cc17e200b3aa567daf9ad9de756ff42 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -26,6 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -325,11 +326,11 @@ void ImproperFourier::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&C0[1],sizeof(double),atom->nimpropertypes,fp); - fread(&C1[1],sizeof(double),atom->nimpropertypes,fp); - fread(&C2[1],sizeof(double),atom->nimpropertypes,fp); - fread(&all[1],sizeof(int),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&C0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&C1[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&C2[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&all[1],sizeof(int),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&C0[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 48db5a41e9e22d6fa85612888b726fd781887994..7f818595a2e04af8f2259e9319440e696877f170 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -47,6 +47,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -325,8 +326,8 @@ void ImproperRing::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index e9771975229074650df22b72a45dd7fb9242a5a1..6339f7d1359e672dac4f4c33f50a45254e5f4f66 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -25,6 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -302,14 +303,14 @@ void PairBuckMDF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -338,10 +339,10 @@ void PairBuckMDF::write_restart_settings(FILE *fp) void PairBuckMDF::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 4544a6db4391281a6ea776195a966d615055e1ce..ffa8a6603ce6e7bbe49372bd710ab12ebddba097 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -30,6 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -275,14 +276,14 @@ void PairCosineSquared::read_restart(FILE *fp) for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { if (me == 0) - fread(&setflag[i][j], sizeof(int), 1, fp); + utils::sfread(FLERR,&setflag[i][j], sizeof(int), 1, fp,NULL,error); MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j], sizeof(double), 1, fp); - fread(&sigma[i][j], sizeof(double), 1, fp); - fread(&cut[i][j], sizeof(double), 1, fp); - fread(&wcaflag[i][j], sizeof(int), 1, fp); + utils::sfread(FLERR,&epsilon[i][j], sizeof(double), 1, fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j], sizeof(double), 1, fp,NULL,error); + utils::sfread(FLERR,&cut[i][j], sizeof(double), 1, fp,NULL,error); + utils::sfread(FLERR,&wcaflag[i][j], sizeof(int), 1, fp,NULL,error); } MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); @@ -310,7 +311,7 @@ void PairCosineSquared::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global, sizeof(double), 1, fp); + utils::sfread(FLERR,&cut_global, sizeof(double), 1, fp,NULL,error); } MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); } diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index a375901ecde082219428823a80ced918223b0823..bdb605f547a9db5a983b6a3016171ab3ab89c6ae 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -24,6 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -282,9 +283,9 @@ void PairCoulDiel::read_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { if (setflag[i][j]) { if (me == 0) { - fread(&rme[i][j],sizeof(double),1,fp); - fread(&sigmae[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&rme[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigmae[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&rme[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world); @@ -311,9 +312,9 @@ void PairCoulDiel::write_restart_settings(FILE *fp) void PairCoulDiel::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 9264e51287f745523dfeeb06399ea2291a14e259..980b4a71d5d852c0d4f44abe79a7ca7fba26d854 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -28,6 +28,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -298,8 +299,8 @@ void PairCoulShield::read_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { if (setflag[i][j]) { if (me == 0) { - fread(&sigmae[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&sigmae[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -325,9 +326,9 @@ void PairCoulShield::write_restart_settings(FILE *fp) void PairCoulShield::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index e6cfc02f631125eeb98698544601c707af2706a0..2a4f61cce3c99f1b07b95fd58b380b9ae296c246 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -24,6 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "math_const.h" using namespace LAMMPS_NS; @@ -300,14 +301,14 @@ void PairGaussCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&hgauss[i][j],sizeof(double),1,fp); - fread(&rmh[i][j],sizeof(double),1,fp); - fread(&sigmah[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&hgauss[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rmh[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigmah[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&hgauss[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rmh[i][j],1,MPI_DOUBLE,0,world); @@ -336,9 +337,9 @@ void PairGaussCut::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 47412636036b480c5c6a8025dd274f1a0fcc2c91..e09287ae2322b80c7f6a31893db2c562128ba641 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -446,9 +446,9 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag) van der Waals forces and energy ------------------------------------------------------------------------- */ -void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag) +void PairILPGrapheneHBN::calc_FvdW(int eflag, int /* vflag */) { - int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll; + int i,j,ii,jj,inum,jnum,itype,jtype; tagint itag,jtag; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vilp,TSvdw,TSvdw2inv,fsum; @@ -544,15 +544,15 @@ void PairILPGrapheneHBN::calc_FvdW(int eflag, int vflag) Repulsive forces and energy ------------------------------------------------------------------------- */ -void PairILPGrapheneHBN::calc_FRep(int eflag, int vflag) +void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */) { int i,j,ii,jj,inum,jnum,itype,jtype,k,kk; double prodnorm1,fkcx,fkcy,fkcz; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1; - double rsq,r,Rcut,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vilp; - double frho1,TSvdw,TSvdw2inv,Erep,fsum,rdsq1; + double rsq,r,Rcut,rhosq1,exp0,exp1,Tap,dTap,Vilp; + double frho1,Erep,fsum,rdsq1; int *ilist,*jlist,*numneigh,**firstneigh; - int *ILP_neighs_i,*ILP_neighs_j; + int *ILP_neighs_i; evdwl = 0.0; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h index ec6146fa33efe5cee7647469a41dfa1e7fad858b..5ca8eb64a78ca044c9ea85b5d6e83240a20add0b 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.h +++ b/src/USER-MISC/pair_ilp_graphene_hbn.h @@ -48,7 +48,7 @@ class PairILPGrapheneHBN : public Pair { MyPage *ipage; // neighbor list pages int *ILP_numneigh; // # of pair neighbors for each atom int **ILP_firstneigh; // ptr to 1st neighbor of each atom - int tap_flag; // flag to turn on/off taper function + int tap_flag; // flag to turn on/off taper function struct Param { double z0,alpha,epsilon,C,delta,d,sR,reff,C6,S; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 7bfbedfa1c6213dbc437e60f0c4c1daa4a0ccf17..8ba3dc9db30909d300820b68928e4e883ea70613 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -448,9 +448,9 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) van der Waals forces and energy ------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag) +void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int /* vflag */) { - int i,j,ii,jj,inum,jnum,itype,jtype,k,l,kk,ll; + int i,j,ii,jj,inum,jnum,itype,jtype; tagint itag,jtag; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r,Rcut,r2inv,r6inv,r8inv,Tap,dTap,Vkc,fsum; @@ -544,15 +544,15 @@ void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int vflag) Repulsive forces and energy ------------------------------------------------------------------------- */ -void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag) +void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */) { int i,j,ii,jj,inum,jnum,itype,jtype,k,kk; double prodnorm1,fkcx,fkcy,fkcz; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,fpair1; - double rsq,r,rhosq1,exp0,exp1,r2inv,r6inv,r8inv,Tap,dTap,Vkc; + double rsq,r,rhosq1,exp0,exp1,Tap,dTap,Vkc; double frho_ij,sumC1,sumC11,sumCff,fsum,rho_ij; int *ilist,*jlist,*numneigh,**firstneigh; - int *KC_neighs_i,*KC_neighs_j; + int *KC_neighs_i; evdwl = 0.0; @@ -606,9 +606,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int vflag) Param& p = params[iparam_ij]; r = sqrt(rsq); - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - r8inv = r2inv*r6inv; + // turn on/off taper function if (tap_flag) { Tap = calc_Tap(r,sqrt(cutsq[itype][jtype])); diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h index d2971e3fbc65a53f8c592ddd3f3442b1d45068d4..c579788110a134e9964a70a341b20162ac37097e 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h @@ -48,7 +48,7 @@ class PairKolmogorovCrespiFull : public Pair { MyPage *ipage; // neighbor list pages int *KC_numneigh; // # of pair neighbors for each atom int **KC_firstneigh; // ptr to 1st neighbor of each atom - int tap_flag; // flag to turn on/off taper function + int tap_flag; // flag to turn on/off taper function struct Param { diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index 50f59107a0b7d3b0280b5f2999cfc6c4dca16319..c539bb30e27b87080454f1bd2c7a285293e7d9ac 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -302,14 +303,14 @@ void PairLJ_AB_MDF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&aparm[i][j],sizeof(double),1,fp); - fread(&bparm[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&aparm[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&bparm[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&aparm[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&bparm[i][j],1,MPI_DOUBLE,0,world); @@ -336,7 +337,7 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index ffa828826f4d38bd3c43ba3c4d98c095309c5ede..957173bf7f2e25e466cfa708cd631df4400f9b38 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -31,6 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -828,14 +829,14 @@ void PairLJExpandCoulLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&shift[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shift[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -867,13 +868,13 @@ void PairLJExpandCoulLong::write_restart_settings(FILE *fp) void PairLJExpandCoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index 3fe0fa6bf9c04f4c70d4fb8fae6ea0b6283d0331..51e24639b931139c12112cc78413373dc20e28e0 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -310,14 +311,14 @@ void PairLJMDF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -344,7 +345,7 @@ void PairLJMDF::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index 758962ce297096378dcd981627a2606b60713c54..19bc66bdcb63cb6c037cef93afc3ef337969bf4f 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -27,6 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "update.h" using namespace LAMMPS_NS; @@ -486,15 +487,15 @@ void PairLJSFDipoleSF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); - fread(&scale[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&scale[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -523,9 +524,9 @@ void PairLJSFDipoleSF::write_restart_settings(FILE *fp) void PairLJSFDipoleSF::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp new file mode 100644 index 0000000000000000000000000000000000000000..97aa3dcaca0ea5aba0645291a7017ac4ef342f98 --- /dev/null +++ b/src/USER-MISC/pair_local_density.cpp @@ -0,0 +1,894 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: + Tanmoy Sanyal, M.Scott Shell, UC Santa Barbara + David Rosenberger, TU Darmstadt +------------------------------------------------------------------------- */ + +#include "pair_local_density.h" +#include +#include +#include +#include +#include +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include "domain.h" +#include "citeme.h" +#include "utils.h" + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 + +static const char cite_pair_local_density[] = + "pair_style local/density command:\n\n" + "@Article{Sanyal16,\n" + " author = {T.Sanyal and M.Scott Shell},\n" + " title = {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},\n" + " journal = {J.~Chem.~Phys.},\n" + " year = 2016,\n" + " DOI = doi.org/10.1063/1.4958629" + "}\n\n" + "@Article{Sanyal18,\n" + " author = {T.Sanyal and M.Scott Shell},\n" + " title = {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},\n" + " journal = {J.~Phys.~Chem. B},\n" + " year = 2018,\n" + " DOI = doi.org/10.1021/acs.jpcb.7b12446" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +PairLocalDensity::PairLocalDensity(LAMMPS *lmp) : Pair(lmp) +{ + restartinfo = 0; + one_coeff = 1; + single_enable = 1; + + // stuff read from tabulated file + nLD = 0; + nrho = 0; + rho_min = NULL; + rho_max = NULL; + a = NULL; + b = NULL; + c0 = NULL; + c2 = NULL; + c4 = NULL; + c6 = NULL; + uppercut = NULL; + lowercut = NULL; + uppercutsq = NULL; + lowercutsq = NULL; + frho = NULL; + rho = NULL; + + // splined arrays + frho_spline = NULL; + + // per-atom arrays + nmax = 0; + fp = NULL; + localrho = NULL; + + // set comm size needed by this pair + comm_forward = 1; + comm_reverse = 1; + + // cite publication + if (lmp->citeme) lmp->citeme->add(cite_pair_local_density); +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairLocalDensity::~PairLocalDensity() +{ + + memory->destroy(localrho); + memory->destroy(fp); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + } + + memory->destroy(frho_spline); + + memory->destroy(rho_min); + memory->destroy(rho_max); + memory->destroy(delta_rho); + memory->destroy(c0); + memory->destroy(c2); + memory->destroy(c4); + memory->destroy(c6); + memory->destroy(uppercut); + memory->destroy(lowercut); + memory->destroy(uppercutsq); + memory->destroy(lowercutsq); + memory->destroy(frho); + memory->destroy(rho); + + memory->destroy(a); + memory->destroy(b); +} + +/* ---------------------------------------------------------------------- */ + +void PairLocalDensity::compute(int eflag, int vflag) +{ + + int i,j,ii,jj,m,k,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + double rsqinv, phi, uLD, dphi, evdwl,fpair; + double p, *coeff; + int *ilist,*jlist,*numneigh,**firstneigh; + + phi = uLD = evdwl = fpair = rsqinv = 0.0; + + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + + /* localrho = LD at each atom + fp = derivative of embedding energy at each atom for each LD potential + uLD = embedding energy of each atom due to each LD potential*/ + + // grow LD and fp arrays if necessary + // need to be atom->nmax in length + + if (atom->nmax > nmax) { + memory->destroy(localrho); + memory->destroy(fp); + nmax = atom->nmax; + memory->create(localrho, nLD, nmax, "pairLD:localrho"); + memory->create(fp, nLD, nmax, "pairLD:fp"); + } + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // zero out LD and fp + + if (newton_pair) { + m = nlocal + atom->nghost; + for (k = 0; k < nLD; k++) { + for (i = 0; i < m; i++) { + localrho[k][i] = 0.0; + fp[k][i] = 0.0; + } + } + } + else { + for (k = 0; k < nLD; k++){ + for (i = 0; i < nlocal; i++) { + localrho[k][i] = 0.0; + fp[k][i] = 0.0; + } + } + } + + // loop over neighs of central atoms and types of LDs + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + // calculate distance-squared between i,j atom-types + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + // calculating LDs based on central and neigh filters + + for (k = 0; k < nLD; k++) { + if (rsq < lowercutsq[k]) { + phi = 1.0; + } + else if (rsq > uppercutsq[k]) { + phi = 0.0; + } + else { + phi = c0[k] + rsq * (c2[k] + rsq * (c4[k] + c6[k]*rsq)); + } + localrho[k][i] += (phi * b[k][jtype]); + + /*checking for both i,j is necessary + since a half neighbor list is processed.*/ + + if (newton_pair || jreverse_comm_pair(this); + + // + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + uLD = 0.0; + + for (k = 0; k < nLD; k++) { + + /*skip over this loop if the LD potential + is not intendend for central atomtype */ + if (!(a[k][itype])) continue; + + // linear extrapolation at rho_min and rho_max + + if (localrho[k][i] <= rho_min[k]) { + coeff = frho_spline[k][0]; + fp[k][i] = coeff[2]; + uLD += a[k][itype] * ( coeff[6] + fp[k][i]*(localrho[k][i] - rho_min[k]) ); + } + else if (localrho[k][i] >= rho_max[k]) { + coeff = frho_spline[k][nrho-2]; + fp[k][i] = coeff[0] + coeff[1] + coeff[2]; + uLD += a[k][itype] * ( (coeff[3] + coeff[4] + coeff[5] + coeff[6]) + fp[k][i]*(localrho[k][i] - rho_max[k]) ); + } + else { + p = (localrho[k][i] - rho_min[k]) / delta_rho[k]; + m = static_cast (p); + m = MAX(0, MIN(m, nrho-2)); + p -= m; + p = MIN(p, 1.0); + coeff = frho_spline[k][m]; + fp[k][i] = (coeff[0]*p + coeff[1])*p + coeff[2]; + uLD += a[k][itype] * (((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]); + } + } + + if (eflag) { + if (eflag_global) eng_vdwl += uLD; + if (eflag_atom) eatom[i] += uLD; + } + } + + // communicate LD and fp to all procs + + comm->forward_comm_pair(this); + + // compute forces on each atom + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + // calculate square of distance between i,j atoms + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + // calculate force between two atoms + fpair = 0.0; + if (rsq < cutforcesq) { // global cutoff check + rsqinv = 1.0/rsq; + for (k = 0; k < nLD; k++) { + if (rsq >= lowercutsq[k] && rsq < uppercutsq[k]) { + dphi = rsq * (2.0*c2[k] + rsq * (4.0*c4[k] + 6.0*c6[k]*rsq)); + fpair += -(a[k][itype]*b[k][jtype]*fp[k][i] + a[k][jtype]*b[k][itype]*fp[k][j]) * dphi; + } + } + fpair *= rsqinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + /*eng_vdwl has already been completely built, + so no need to add anything here*/ + + if (eflag) evdwl = 0.0; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLocalDensity::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLocalDensity::settings(int narg, char ** /* arg */) +{ + if (narg > 0) error->all(FLERR,"Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for all type pairs + read tabulated LD input file +------------------------------------------------------------------------- */ + +void PairLocalDensity::coeff(int narg, char **arg) +{ + int i, j; + if (!allocated) allocate(); + + if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients"); + + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + // parse LD file + + parse_file(arg[2]); + + + // clear setflag since coeff() called once with I,J = * * + + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + setflag[i][j] = 0; + + // set setflag for all i,j type pairs + + int count = 0; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + setflag[i][j] = 1; + count++; + } + } + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLocalDensity::init_style() +{ + // spline rho and frho arrays + // request half neighbor list + + array2spline(); + + // half neighbor request + neighbor->request(this); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLocalDensity::init_one(int /* i */, int /* j */) +{ + // single global cutoff = max of all uppercuts read in from LD file + + cutmax = 0.0; + for (int k = 0; k < nLD; k++) + cutmax = MAX(cutmax,uppercut[k]); + + cutforcesq = cutmax*cutmax; + + return cutmax; +} + + +/*-------------------------------------------------------------------------- + pair_write functionality for this pair style that gives just a snap-shot + of the LD potential without doing an actual MD run + ---------------------------------------------------------------------------*/ + +double PairLocalDensity::single(int /* i */, int /* j */, int itype, int jtype, + double rsq, double /* factor_coul */, + double /* factor_lj */, double &fforce) +{ + int m, k, index; + double rsqinv, p, uLD; + double *coeff, **LD; + double dFdrho, phi, dphi; + + uLD = dFdrho = dphi = 0.0; + + memory->create(LD, nLD, 3, "pairLD:LD"); + for (k = 0; k < nLD; k++) { + LD[k][1] = 0.0; // itype:- 1 + LD[k][2] = 0.0; // jtype:- 2 + } + + rsqinv = 1.0/rsq; + for (k = 0; k < nLD; k++) { + if (rsq < lowercutsq[k]) { + phi = 1.0; + } + else if (rsq > uppercutsq[k]) { + phi = 0.0; + } + else { + phi = c0[k] + rsq * (c2[k] + rsq * (c4[k] + c6[k]*rsq)); + } + LD[k][1] += (phi * b[k][jtype]); + LD[k][2] += (phi * b[k][itype]); + } + + for (k = 0; k < nLD; k++) { + if (a[k][itype]) index = 1; + if (a[k][jtype]) index = 2; + + if (LD[k][index] <= rho_min[k]) { + coeff = frho_spline[k][0]; + dFdrho = coeff[2]; + uLD += a[k][itype] * ( coeff[6] + dFdrho*(LD[k][index] - rho_min[k]) ); + } + else if (LD[k][index] >= rho_max[k]) { + coeff = frho_spline[k][nrho-1]; + dFdrho = coeff[0] + coeff[1] + coeff[2]; + uLD += a[k][itype] * ( (coeff[3] + coeff[4] + coeff[5] + coeff[6]) + dFdrho*(LD[k][index] - rho_max[k]) ); + } + else { + p = (LD[k][index] - rho_min[k]) / delta_rho[k]; + m = static_cast (p); + m = MAX(0, MIN(m, nrho-2)); + p -= m; + p = MIN(p, 1.0); + coeff = frho_spline[k][m]; + dFdrho = (coeff[0]*p + coeff[1])*p + coeff[2]; + uLD += a[k][itype] * (((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]); + } + + if (rsq < lowercutsq[k]) { + dphi = 0.0; + } + else if (rsq > uppercutsq[k]) { + dphi = 0.0; + } + else { + dphi = rsq * (2.0*c2[k] + rsq * (4.0*c4[k] + 6.0*c6[k]*rsq)); + } + fforce += -(a[k][itype]*b[k][jtype]*dFdrho + a[k][jtype]*b[k][itype]*dFdrho) * dphi *rsqinv; + } + memory->destroy(LD); + + return uLD; +} + +/*-------------------------------------------------------------------- + spline the array frho read in from the file to create + frho_spline +---------------------------------------------------------------------- */ + +void PairLocalDensity::array2spline() { + memory->destroy(frho_spline); + memory->create(frho_spline, nLD, nrho, 7, "pairLD:frho_spline"); + + for (int k = 0; k < nLD; k++) + interpolate_cbspl(nrho, delta_rho[k], frho[k], frho_spline[k]); + +} + +/* ---------------------------------------------------------------------- + (one-dimensional) cubic spline interpolation sub-routine, + which determines the coeffs for a clamped cubic spline + given tabulated data + ------------------------------------------------------------------------*/ + +void PairLocalDensity::interpolate_cbspl(int n, double delta, + double *f, double **spline) +{ +/* inputs: + n number of interpolating points + + f array containing function values to + be interpolated; f[i] is the function + value corresponding to x[i] + ('x' refers to the independent var) + + delta difference in tabulated values of x + + outputs: (packaged as columns of the coeff matrix) + coeff_b coeffs of linear terms + coeff_c coeffs of quadratic terms + coeff_d coeffs of cubic terms + spline matrix that collects b,c,d + + + other parameters: + fpa derivative of function at x=a + fpb derivative of function at x=b +*/ + + double *dl, *dd, *du; + double *coeff_b, *coeff_c, *coeff_d; + double fpa, fpb; + + int i; + + coeff_b = new double [n]; + coeff_c = new double [n]; + coeff_d = new double [n]; + dl = new double [n]; + dd = new double [n]; + du = new double [n]; + + // initialize values + for ( i = 0; i= 0; i-- ) + coeff_c[i] -= coeff_c[i+1] * du[i]; + + for ( i = 0; i < n-1; i++ ) { + coeff_d[i] = ( coeff_c[i+1] - coeff_c[i] ) / ( 3.0 * delta ); + coeff_b[i] = ( f[i+1] - f[i] ) / delta - delta * ( coeff_c[i+1] + 2.0*coeff_c[i] ) / 3.0; + } + + // normalize + for ( i = 0; i < n-1; i++ ) { + coeff_b[i] = coeff_b[i] * delta ; + coeff_c[i] = coeff_c[i] * delta*delta ; + coeff_d[i] = coeff_d[i] * delta*delta*delta; + } + + //copy to coefficient matrix + for ( i = 0; i < n; i++) { + spline[i][3] = coeff_d[i]; + spline[i][4] = coeff_c[i]; + spline[i][5] = coeff_b[i]; + spline[i][6] = f[i]; + spline[i][2] = spline[i][5]/delta; + spline[i][1] = 2.0*spline[i][4]/delta; + spline[i][0] = 3.0*spline[i][3]/delta; + } + + delete [] coeff_b; + delete [] coeff_c; + delete [] coeff_d; + delete [] du; + delete [] dd; + delete [] dl; +} + +/* ---------------------------------------------------------------------- + read potential values from tabulated LD input file +------------------------------------------------------------------------- */ + +void PairLocalDensity::parse_file(char *filename) { + + int k, n; + int me = comm->me; + FILE *fptr; + char line[MAXLINE]; + double ratio, lc2, uc2, denom; + + + if (me == 0) { + fptr = fopen(filename, "r"); + if (fptr == NULL) { + char str[128]; + sprintf(str,"Cannot open Local Density potential file %s",filename); + error->one(FLERR,str); + } + } + + double *ftmp; // tmp var to extract the complete 2D frho array from file + + // broadcast number of LD potentials and number of (rho,frho) pairs + if (me == 0) { + + // first 2 comment lines ignored + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + + // extract number of potentials and number of (frho, rho) points + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + sscanf(line, "%d %d", &nLD, &nrho); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + } + + MPI_Bcast(&nLD,1,MPI_INT,0,world); + MPI_Bcast(&nrho,1,MPI_INT,0,world); + + // setting up all arrays to be read from files and broadcasted + memory->create(uppercut, nLD, "pairLD:uppercut"); + memory->create(lowercut, nLD, "pairLD:lowercut"); + memory->create(uppercutsq, nLD, "pairLD:uppercutsq"); + memory->create(lowercutsq, nLD, "pairLD:lowercutsq"); + memory->create(c0, nLD, "pairLD:c0"); + memory->create(c2, nLD, "pairLD:c2"); + memory->create(c4, nLD, "pairLD:c4"); + memory->create(c6, nLD, "pairLD:c6"); + memory->create(rho_min, nLD, "pairLD:rho_min"); + memory->create(rho_max, nLD, "pairLD:rho_max"); + memory->create(delta_rho, nLD,"pairLD:delta_rho"); + memory->create(ftmp, nrho*nLD, "pairLD:ftmp"); + + // setting up central and neighbor atom filters + memory->create(a, nLD, atom->ntypes+1 , "pairLD:a"); + memory->create(b, nLD, atom->ntypes+1, "pairLD:b"); + if (me == 0) { + for (n = 1; n <= atom->ntypes; n++){ + for (k = 0; k < nLD; k++) { + a[k][n] = 0; + b[k][n] = 0; + } + } + } + + // read file block by block + + if (me == 0) { + for (k = 0; k < nLD; k++) { + + // parse upper and lower cut values + if (fgets(line,MAXLINE,fptr)==NULL) break; + sscanf(line, "%lf %lf", &lowercut[k], &uppercut[k]); + + // parse and broadcast central atom filter + utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); + char *tmp = strtok(line, " /t/n/r/f"); + while (tmp != NULL) { + a[k][atoi(tmp)] = 1; + tmp = strtok(NULL, " /t/n/r/f"); + } + + // parse neighbor atom filter + utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); + tmp = strtok(line, " /t/n/r/f"); + while (tmp != NULL) { + b[k][atoi(tmp)] = 1; + tmp = strtok(NULL, " /t/n/r/f"); + } + + // parse min, max and delta rho values + utils::sfgets(FLERR,line, MAXLINE, fptr,filename,error); + sscanf(line, "%lf %lf %lf", &rho_min[k], &rho_max[k], &delta_rho[k]); + // recompute delta_rho from scratch for precision + delta_rho[k] = (rho_max[k] - rho_min[k]) / (nrho - 1); + + // parse tabulated frho values from each line into temporary array + for (n = 0; n < nrho; n++) { + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + sscanf(line, "%lf", &ftmp[k*nrho + n]); + } + + // ignore blank line at the end of every block + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + + // set coefficients for local density indicator function + uc2 = uppercut[k] * uppercut[k]; + uppercutsq[k] = uc2; + lc2 = lowercut[k] * lowercut[k]; + lowercutsq[k] = lc2; + ratio = lc2/uc2; + denom = 1.0 - ratio; + denom = denom*denom*denom; + c0[k] = (1 - 3.0 * ratio) / denom; + c2[k] = (6.0 * ratio) / (uc2 * denom); + c4[k] = -(3.0 + 3.0*ratio) / (uc2*uc2 * denom); + c6[k] = 2.0 / (uc2*uc2*uc2 * denom); + } + } + + // Broadcast all parsed arrays + MPI_Bcast(&lowercut[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&uppercut[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&lowercutsq[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&uppercutsq[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&c0[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&c2[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&c4[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&c6[0], nLD, MPI_DOUBLE, 0, world); + for (k = 0; k < nLD; k++) { + MPI_Bcast(&a[k][1], atom->ntypes, MPI_INT, 0, world); + MPI_Bcast(&b[k][1], atom->ntypes, MPI_INT, 0, world); + } + MPI_Bcast(&rho_min[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&rho_max[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&delta_rho[0], nLD, MPI_DOUBLE, 0, world); + MPI_Bcast(&ftmp[0], nLD*nrho, MPI_DOUBLE, 0, world); + + if (me == 0) fclose(fptr); + + // set up rho and frho arrays + memory->create(rho, nLD, nrho, "pairLD:rho"); + memory->create(frho, nLD, nrho, "pairLD:frho"); + + for (k = 0; k < nLD; k++) { + for (n = 0; n < nrho; n++) { + rho[k][n] = rho_min[k] + n*delta_rho[k]; + frho[k][n] = ftmp[k*nrho + n]; + } + } + + // delete temporary array + memory->destroy(ftmp); +} + +/* ---------------------------------------------------------------------- + communication routines +------------------------------------------------------------------------- */ + +int PairLocalDensity::pack_comm(int n, int *list, double *buf, + int /* pbc_flag */, int * /* pbc */) { + int i,j,k; + int m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + for (k = 0; k < nLD; k++) { + buf[m++] = fp[k][j]; + } + } + + return nLD; +} + +/* ---------------------------------------------------------------------- */ + +void PairLocalDensity::unpack_comm(int n, int first, double *buf) { + + int i,k,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + for (k = 0; k < nLD; k++) { + fp[k][i] = buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int PairLocalDensity::pack_reverse_comm(int n, int first, double *buf) { + + int i,k,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + for (k = 0; k < nLD; k++) { + buf[m++] = localrho[k][i]; + } + } + return nLD; +} + +/* ---------------------------------------------------------------------- */ + +void PairLocalDensity::unpack_reverse_comm(int n, int *list, double *buf) { + + int i,j,k; + int m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + for (k = 0; k < nLD; k++) { + localrho[k][j] += buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double PairLocalDensity::memory_usage() +{ + double bytes = maxeatom * sizeof(double); + bytes += maxvatom*6 * sizeof(double); + bytes += 2 * (nmax*nLD) * sizeof(double); + return bytes; +} + diff --git a/src/USER-MISC/pair_local_density.h b/src/USER-MISC/pair_local_density.h new file mode 100644 index 0000000000000000000000000000000000000000..77aab1399b0a1d1fe25197d6d336bae56f0dfe1f --- /dev/null +++ b/src/USER-MISC/pair_local_density.h @@ -0,0 +1,88 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- + pair_LocalDensity written by: + Tanmoy Sanyal and M. Scott Shell from UC Santa Barbara + David Rosenberger: TU Darmstadt +-------------------------------------------------------------------------*/ + + +#ifdef PAIR_CLASS + +PairStyle(local/density,PairLocalDensity) + +#else + +#ifndef LMP_PAIR_LOCAL_DENSITY_H +#define LMP_PAIR_LOCAL_DENSITY_H + +#include "pair.h" + + +namespace LAMMPS_NS { + +class PairLocalDensity : public Pair { + public: + PairLocalDensity(class LAMMPS *); + virtual ~PairLocalDensity(); + virtual void compute(int, int); + void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + double single(int, int, int, int, double, double, double, double &); + + virtual int pack_comm(int, int *, double *, int, int *); + virtual void unpack_comm(int, int, double *); + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + double memory_usage(); + + + protected: + //------------------------------------------------------------------------ + //This information is read from the tabulated input file + + int nLD, nrho; // number of LD types + int **a, **b; // central and neigh atom filters + double *uppercut, *lowercut; // upper and lower cutoffs + double *uppercutsq, *lowercutsq; // square of above cutoffs + double *c0, *c2, *c4, *c6; // coeffs for indicator function + double *rho_min, *rho_max, *delta_rho; // min, max & grid-size for LDs + double **rho, **frho; // LD and LD function tables + + //------------------------------------------------------------------------ + + double ***frho_spline; // splined LD potentials + double cutmax; // max cutoff for all elements + double cutforcesq; // square of global upper cutoff + + int nmax; // max size of per-atom arrays + double **localrho; // per-atom LD + double **fp; // per-atom LD potential function derivative + + void allocate(); + + // read tabulated input file + void parse_file(char *); + + // convert array to spline + void array2spline(); + + // cubic spline interpolation + void interpolate_cbspl(int, double, double *, double **); +}; + +} + +#endif +#endif diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 79e7ac7e092f1cc33de4962e3178234d3a3ed9e1..27deff9a6ec3ee780af13751d6834587b4d1e500 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -43,6 +43,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -439,13 +440,13 @@ void PairMEAMSpline::read_file(const char* filename) // Skip first line of file. It's a comment. char line[MAXLINE]; char *ptr; - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); // Second line holds potential type ("meam/spline") // in new potential format. bool isNewFormat = false; - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); ptr = strtok(line, " \t\n\r\f"); if (strcmp(ptr, "meam/spline") == 0) { @@ -475,7 +476,7 @@ void PairMEAMSpline::read_file(const char* filename) elements[0] = new char[1]; strcpy(elements[0], ""); rewind(fp); - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); } nmultichoose2 = ((nelements+1)*nelements)/2; @@ -639,27 +640,27 @@ void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error, // If new format, read the spline format. Should always be "spline3eq" for now. if (isNewFormat) - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); // Parse number of spline knots. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); int n = atoi(line); if(n < 2) error->one(FLERR,"Invalid number of spline knots in MEAM potential file"); // Parse first derivatives at beginning and end of spline. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); double d0 = atof(strtok(line, " \t\n\r\f")); double dN = atof(strtok(NULL, " \t\n\r\f")); init(n, d0, dN); // Skip line in old format if (!isNewFormat) - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); // Parse knot coordinates. for(int i=0; ione(FLERR,"Invalid knot line in MEAM potential file"); diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index eeadacf33a81e6c209eaa44d51100a162d255469..73d6c81004392ae042cf84df6e5a168d5f3cf88a 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -35,6 +35,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -468,7 +469,7 @@ void PairMEAMSWSpline::read_file(const char* filename) // Skip first line of file. char line[MAXLINE]; - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); // Parse spline functions. phi.parse(fp, error); @@ -600,23 +601,23 @@ void PairMEAMSWSpline::SplineFunction::parse(FILE* fp, Error* error) char line[MAXLINE]; // Parse number of spline knots. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); int n = atoi(line); if(n < 2) error->one(FLERR,"Invalid number of spline knots in MEAM potential file"); // Parse first derivatives at beginning and end of spline. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); double d0 = atof(strtok(line, " \t\n\r\f")); double dN = atof(strtok(NULL, " \t\n\r\f")); init(n, d0, dN); // Skip line. - fgets(line, MAXLINE, fp); + utils::sfgets(FLERR,line,MAXLINE,fp,NULL,error); // Parse knot coordinates. for(int i=0; ione(FLERR,"Invalid knot line in MEAM potential file"); diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 29d5715302c14863d75d2ab02f621ba45cfd58d4..8786394221d3e7ba2330591af72644348666007a 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -25,6 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "citeme.h" using namespace LAMMPS_NS; @@ -307,16 +308,16 @@ void PairMomb::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&d0[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&rr[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rr[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); @@ -348,11 +349,11 @@ void PairMomb::write_restart_settings(FILE *fp) void PairMomb::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&sscale,sizeof(double),1,fp); - fread(&dscale,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sscale,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&dscale,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&sscale,1,MPI_DOUBLE,0,world); diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index c3cbe39db70596ab9c270524ce3897e5529493dc..bbdae231f87b81c516666c16a04953b8765396b1 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -21,6 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -273,14 +274,14 @@ void PairMorseSmoothLinear::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&d0[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); @@ -307,8 +308,8 @@ void PairMorseSmoothLinear::write_restart_settings(FILE *fp) void PairMorseSmoothLinear::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 416ace81321f12ef6859cfaab3b0fa3211f47485..606fdc9fc54b18b8c09119a877300ac4da99c96a 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -44,6 +44,7 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "thermo.h" #include "output.h" #include "citeme.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -698,13 +699,12 @@ void PairSRP::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - printf(" i %d j %d \n",i,j); - fread(&a0[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -732,12 +732,12 @@ void PairSRP::write_restart_settings(FILE *fp) void PairSRP::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&bptype,sizeof(int),1,fp); - fread(&btype,sizeof(int),1,fp); - fread(&min,sizeof(int),1,fp); - fread(&midpoint,sizeof(int),1,fp); - fread(&exclude,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&bptype,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&btype,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&min,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&midpoint,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&exclude,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); } diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index bb0a01d546548830f271b2229128243bf5e9df07..839148bc13922fff3086e5f75db2ea4694993d4b 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -28,6 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -385,21 +386,21 @@ void AngleClass2P6::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); - fread(&k2[1],sizeof(double),atom->nangletypes,fp); - fread(&k3[1],sizeof(double),atom->nangletypes,fp); - fread(&k4[1],sizeof(double),atom->nangletypes,fp); - fread(&k5[1],sizeof(double),atom->nangletypes,fp); - fread(&k6[1],sizeof(double),atom->nangletypes,fp); - - fread(&bb_k[1],sizeof(double),atom->nangletypes,fp); - fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp); - fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp); - - fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp); - fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp); - fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp); - fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k3[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k4[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k5[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&k6[1],sizeof(double),atom->nangletypes,fp,NULL,error); + + utils::sfread(FLERR,&bb_k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&bb_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&bb_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + + utils::sfread(FLERR,&ba_k1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ba_k2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ba_r1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&ba_r2[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index c17b2a1dba6469af89197cf09147a4022908f3ca..a6643601c145d57b4fce651dfa270e787d34280d 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -28,6 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -331,9 +332,9 @@ void AngleCosineBuck6d::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nangletypes,fp); - fread(&multiplicity[1],sizeof(int),atom->nangletypes,fp); - fread(&th0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&multiplicity[1],sizeof(int),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&th0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 12f7062ccc9eca3ab385ad1e35a9d094013aa1cc..e38b82067d4e6408218813701a33f1aa5c2c814f 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -29,6 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -312,8 +313,8 @@ void ImproperInversionHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&kw[1],sizeof(double),atom->nimpropertypes,fp); - fread(&w0[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&kw[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&w0[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&kw[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&w0[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 9c917d1c191ed97a925fdf1437f7a77adf009633..57a935a0b343f015adedeb63a65c9ad03e8c5076 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -29,6 +29,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" +#include "utils.h" #include "math_special.h" using namespace LAMMPS_NS; @@ -414,16 +415,16 @@ void PairBuck6dCoulGaussDSF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&buck6d1[i][j],sizeof(double),1,fp); - fread(&buck6d2[i][j],sizeof(double),1,fp); - fread(&buck6d3[i][j],sizeof(double),1,fp); - fread(&buck6d4[i][j],sizeof(double),1,fp); - fread(&alpha_ij[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&buck6d1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck6d2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck6d3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck6d4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha_ij[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world); @@ -456,12 +457,12 @@ void PairBuck6dCoulGaussDSF::write_restart_settings(FILE *fp) void PairBuck6dCoulGaussDSF::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&vdwl_smooth,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&vdwl_smooth,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 953507ce21396eca7e76292b957fffe5db9faf57..d3ccec3a55cd8869d16cdb6273cf30bd58d48b70 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -29,6 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" #include "math_special.h" using namespace LAMMPS_NS; @@ -446,16 +447,16 @@ void PairBuck6dCoulGaussLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&buck6d1[i][j],sizeof(double),1,fp); - fread(&buck6d2[i][j],sizeof(double),1,fp); - fread(&buck6d3[i][j],sizeof(double),1,fp); - fread(&buck6d4[i][j],sizeof(double),1,fp); - fread(&alpha_ij[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&buck6d1[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck6d2[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck6d3[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&buck6d4[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha_ij[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world); @@ -489,13 +490,13 @@ void PairBuck6dCoulGaussLong::write_restart_settings(FILE *fp) void PairBuck6dCoulGaussLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&vdwl_smooth,sizeof(double),1,fp); - fread(&coul_smooth,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&vdwl_smooth,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&coul_smooth,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world); MPI_Bcast(&coul_smooth,1,MPI_DOUBLE,0,world); diff --git a/src/USER-OMP/domain_omp.cpp b/src/USER-OMP/domain_omp.cpp index a18931c551fb39714f7bc2bebfcf0c4ff91cd6fc..18d2a587ca87cfc26df9e342321aa3617ef8e4ae 100644 --- a/src/USER-OMP/domain_omp.cpp +++ b/src/USER-OMP/domain_omp.cpp @@ -44,11 +44,10 @@ void DomainOMP::pbc() imageint * _noalias const image = atom->image; const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { imageint idim,otherdims; if (xperiodic) { @@ -142,12 +141,11 @@ void DomainOMP::lamda2x(int n) { dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0]; const int num = n; - int i; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < num; i++) { + for (int i = 0; i < num; i++) { x[i].x = h[0]*x[i].x + h[5]*x[i].y + h[4]*x[i].z + boxlo[0]; x[i].y = h[1]*x[i].y + h[3]*x[i].z + boxlo[1]; x[i].z = h[2]*x[i].z + boxlo[2]; @@ -163,12 +161,11 @@ void DomainOMP::x2lamda(int n) { dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0]; const int num = n; - int i; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < num; i++) { + for (int i = 0; i < num; i++) { double delta0 = x[i].x - boxlo[0]; double delta1 = x[i].y - boxlo[1]; double delta2 = x[i].z - boxlo[2]; diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index fa6b698821aeb11690b7035eec43a440728dd065..5bc1085f34c7f6ccaf139545eb3728ffb7d0a074 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -63,19 +63,17 @@ void FixGravityOMP::post_force(int /* vflag */) const double xacc_thr = xacc; const double yacc_thr = yacc; const double zacc_thr = zacc; - double massone; - int i; eflag = 0; double grav = 0.0; if (rmass) { #if defined(_OPENMP) -#pragma omp parallel for private(i,massone) default(none) reduction(-:grav) +#pragma omp parallel for default(none) reduction(-:grav) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - massone = rmass[i]; + const double massone = rmass[i]; f[i][0] += massone*xacc_thr; f[i][1] += massone*yacc_thr; f[i][2] += massone*zacc_thr; @@ -83,11 +81,11 @@ void FixGravityOMP::post_force(int /* vflag */) } } else { #if defined(_OPENMP) -#pragma omp parallel for private(i,massone) default(none) reduction(-:grav) +#pragma omp parallel for default(none) reduction(-:grav) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - massone = mass[type[i]]; + const double massone = mass[type[i]]; f[i][0] += massone*xacc_thr; f[i][1] += massone*yacc_thr; f[i][2] += massone*zacc_thr; diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index b0967bf7f78c7a2ca8f883c92c7b3558ddc2936d..185eab5f47c756b152344318aa1521d19573e215 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -77,15 +77,14 @@ void FixNHAsphereOMP::nve_v() const double * _noalias const rmass = atom->rmass; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; // standard nve_v velocity update. for efficiency the loop is // merged with FixNHOMP instead of calling it for the COM update. #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i].x += dtfm*f[i].x; @@ -112,7 +111,6 @@ void FixNHAsphereOMP::nve_x() AtomVecEllipsoid::Bonus * _noalias const bonus = avec->bonus; const int * _noalias const ellipsoid = atom->ellipsoid; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; // set timestep here since dt may have changed or come via rRESPA @@ -124,9 +122,9 @@ void FixNHAsphereOMP::nve_x() // principal moments of inertia #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { double omega[3], inertia[3]; @@ -162,13 +160,12 @@ void FixNHAsphereOMP::nh_v_temp() dbl3_t * _noalias const angmom = (dbl3_t *) atom->angmom[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (which == NOBIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { v[i].x *= factor_eta; v[i].y *= factor_eta; @@ -180,9 +177,9 @@ void FixNHAsphereOMP::nh_v_temp() } } else if (which == BIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { double buf[3]; if (mask[i] & groupbit) { temperature->remove_bias_thr(i,&v[i].x,buf); diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp index 2abd739f717368165c6d7371dc30f73af0abc71b..d584bcd11f0c73740d01ad1c5fb8a6f5ac746885 100644 --- a/src/USER-OMP/fix_nh_omp.cpp +++ b/src/USER-OMP/fix_nh_omp.cpp @@ -56,11 +56,10 @@ void FixNHOMP::remap() if (allremap) domain->x2lamda(nlocal); else { - int i; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & dilate_group_bit) domain->x2lamda(x[i],x[i]); } @@ -207,11 +206,10 @@ void FixNHOMP::remap() if (allremap) domain->lamda2x(nlocal); else { - int i; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & dilate_group_bit) domain->lamda2x(x[i],x[i]); } @@ -234,13 +232,12 @@ void FixNHOMP::nh_v_press() dbl3_t * _noalias const v = (dbl3_t *) atom->v[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (which == NOBIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { v[i].x *= factor0; v[i].y *= factor1; @@ -256,9 +253,9 @@ void FixNHOMP::nh_v_press() } } else if (which == BIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { double buf[3]; if (mask[i] & groupbit) { temperature->remove_bias_thr(i,&v[i].x,buf); @@ -288,14 +285,13 @@ void FixNHOMP::nve_v() const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (atom->rmass) { const double * _noalias const rmass = atom->rmass; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i].x += dtfm*f[i].x; @@ -307,9 +303,9 @@ void FixNHOMP::nve_v() const double *_noalias const mass = atom->mass; const int * _noalias const type = atom->type; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { const double dtfm = dtf / mass[type[i]]; v[i].x += dtfm*f[i].x; @@ -330,14 +326,13 @@ void FixNHOMP::nve_x() const dbl3_t * _noalias const v = (dbl3_t *) atom->v[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; // x update by full step only for atoms in group #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { x[i].x += dtv * v[i].x; x[i].y += dtv * v[i].y; @@ -354,13 +349,12 @@ void FixNHOMP::nh_v_temp() dbl3_t * _noalias const v = (dbl3_t *) atom->v[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (which == NOBIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { v[i].x *= factor_eta; v[i].y *= factor_eta; @@ -369,9 +363,9 @@ void FixNHOMP::nh_v_temp() } } else if (which == BIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { double buf[3]; if (mask[i] & groupbit) { temperature->remove_bias_thr(i,&v[i].x,buf); diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp index 64bc536bb0e3ac792eecf00276d53b1173b76b3b..0048ae7ff746bcad79398469810154266807273c 100644 --- a/src/USER-OMP/fix_nh_sphere_omp.cpp +++ b/src/USER-OMP/fix_nh_sphere_omp.cpp @@ -76,7 +76,6 @@ void FixNHSphereOMP::nve_v() const double dtfrotate = dtf / INERTIA; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; // standard nve_v velocity update. for efficiency the loop is // merged with FixNHOMP instead of calling it for the COM update. @@ -86,9 +85,9 @@ void FixNHSphereOMP::nve_v() // 4 cases depending on radius vs shape and rmass vs mass #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i].x += dtfm*f[i].x; @@ -113,13 +112,12 @@ void FixNHSphereOMP::nh_v_temp() dbl3_t * _noalias const omega = (dbl3_t *) atom->omega[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (which == NOBIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { v[i].x *= factor_eta; v[i].y *= factor_eta; @@ -131,9 +129,9 @@ void FixNHSphereOMP::nh_v_temp() } } else if (which == BIAS) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { double buf[3]; if (mask[i] & groupbit) { temperature->remove_bias_thr(i,&v[i].x,buf); diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp index 61ed82b16fbc1b918fede4c5632617c9137c9b11..f693c2fa20cc019df2a375ebf7ae324bf836091c 100644 --- a/src/USER-OMP/fix_nve_omp.cpp +++ b/src/USER-OMP/fix_nve_omp.cpp @@ -37,14 +37,13 @@ void FixNVEOMP::initial_integrate(int /* vflag */) const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0]; const int * const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (atom->rmass) { const double * const rmass = atom->rmass; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i].x += dtfm * f[i].x; @@ -59,9 +58,9 @@ void FixNVEOMP::initial_integrate(int /* vflag */) const double * const mass = atom->mass; const int * const type = atom->type; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { const double dtfm = dtf / mass[type[i]]; v[i].x += dtfm * f[i].x; @@ -84,14 +83,13 @@ void FixNVEOMP::final_integrate() const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0]; const int * const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (atom->rmass) { const double * const rmass = atom->rmass; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i].x += dtfm * f[i].x; @@ -103,9 +101,9 @@ void FixNVEOMP::final_integrate() const double * const mass = atom->mass; const int * const type = atom->type; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { const double dtfm = dtf / mass[type[i]]; v[i].x += dtfm * f[i].x; diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index ccdd65487445d3ee9735a78ca02386a2f6a6c4a2..bc7be4019ca79d87eff405780f88953f03b45481 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -42,7 +42,6 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */) const double * const rmass = atom->rmass; const int * const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; // set timestep here since dt may have changed or come via rRESPA const double dtfrotate = dtf / INERTIA; @@ -50,9 +49,9 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */) // update v,x,omega for all particles // d_omega/dt = torque / inertia #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) +#pragma omp parallel for default(none) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i][0] += dtfm * f[i][0]; @@ -77,9 +76,9 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */) double * const * const mu = atom->mu; if (dlm == NODLM) { #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) +#pragma omp parallel for default(none) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { double g0,g1,g2,msq,scale; if (mask[i] & groupbit) { if (mu[i][3] > 0.0) { @@ -96,10 +95,10 @@ void FixNVESphereOMP::initial_integrate(int /* vflag */) } } else { #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) +#pragma omp parallel for default(none) #endif // Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { vector w, w_temp, a; matrix Q, Q_temp, R; @@ -215,7 +214,6 @@ void FixNVESphereOMP::final_integrate() const double * const radius = atom->radius; const int * const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; // set timestep here since dt may have changed or come via rRESPA @@ -225,9 +223,9 @@ void FixNVESphereOMP::final_integrate() // d_omega/dt = torque / inertia #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) +#pragma omp parallel for default(none) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { const double dtfm = dtf / rmass[i]; v[i][0] += dtfm * f[i][0]; diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index 208dfb943202389da052d1bac6fcd4191f1e755d..9b3b5154157e6b2cc55f59c2942973ef4f1eb3f9 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -107,7 +107,6 @@ void FixNVTSllodOMP::nh_v_temp() dbl3_t * _noalias const v = (dbl3_t *) atom->v[0]; const int * _noalias const mask = atom->mask; const int nlocal = (igroup == atom->firstgroup) ? atom->nfirst : atom->nlocal; - int i; if (nondeformbias) temperature->compute_scalar(); @@ -115,9 +114,9 @@ void FixNVTSllodOMP::nh_v_temp() MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two); #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) shared(h_two) schedule(static) +#pragma omp parallel for default(none) shared(h_two) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { double vdelu0,vdelu1,vdelu2,buf[3]; if (mask[i] & groupbit) { vdelu0 = h_two[0]*v[i].x + h_two[5]*v[i].y + h_two[4]*v[i].z; diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index f7945b55793ffea910aad4c4e97ef6715ca12efd..a10d3127a9a9c7992ca61c4b931a2c80e320d86d 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -188,7 +188,7 @@ void FixQEqReaxOMP::compute_H() #pragma omp parallel default(shared) #endif { - int i, j, ii, jj, mfill, jnum, flag; + int mfill, jnum, flag; int *jlist; double dx, dy, dz, r_sqr; @@ -197,15 +197,15 @@ void FixQEqReaxOMP::compute_H() #if defined(_OPENMP) #pragma omp for schedule(guided) #endif - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; + for (int ii = 0; ii < inum; ii++) { + int i = ilist[ii]; if (mask[i] & groupbit) { jlist = firstneigh[i]; jnum = numneigh[i]; mfill = H.firstnbr[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; + for (int jj = 0; jj < jnum; jj++) { + int j = jlist[jj]; dx = x[j][0] - x[i][0]; dy = x[j][1] - x[i][1]; @@ -450,13 +450,13 @@ void FixQEqReaxOMP::init_matvec() int FixQEqReaxOMP::CG( double *b, double *x) { - int i, ii, imax; + int i, imax; double alpha, beta, b_norm; double sig_old, sig_new; double my_buf[2], buf[2]; - int nn, jj; + int nn; int *ilist; if (reaxc) { nn = reaxc->list->inum; @@ -476,16 +476,16 @@ int FixQEqReaxOMP::CG( double *b, double *x) tmp1 = tmp2 = 0.0; #if defined(_OPENMP) -#pragma omp parallel for schedule(dynamic,50) private(i) reduction(+:tmp1,tmp2) +#pragma omp parallel for schedule(dynamic,50) reduction(+:tmp1,tmp2) #endif - for (jj = 0; jj < nn; ++jj) { - i = ilist[jj]; - if (atom->mask[i] & groupbit) { - r[i] = b[i] - q[i]; - d[i] = r[i] * Hdia_inv[i]; //pre-condition - - tmp1 += b[i] * b[i]; - tmp2 += r[i] * d[i]; + for (int jj = 0; jj < nn; ++jj) { + int ii = ilist[jj]; + if (atom->mask[ii] & groupbit) { + r[ii] = b[ii] - q[ii]; + d[ii] = r[ii] * Hdia_inv[ii]; //pre-condition + + tmp1 += b[ii] * b[ii]; + tmp2 += r[ii] * d[ii]; } } @@ -509,10 +509,10 @@ int FixQEqReaxOMP::CG( double *b, double *x) { #if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1) +#pragma omp for schedule(dynamic,50) reduction(+:tmp1) #endif - for (jj = 0; jj < nn; jj++) { - ii = ilist[jj]; + for (int jj = 0; jj < nn; jj++) { + int ii = ilist[jj]; if (atom->mask[ii] & groupbit) tmp1 += d[ii] * q[ii]; } @@ -529,10 +529,10 @@ int FixQEqReaxOMP::CG( double *b, double *x) #if defined(_OPENMP) #pragma omp barrier -#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1) +#pragma omp for schedule(dynamic,50) reduction(+:tmp1) #endif - for (jj = 0; jj < nn; jj++) { - ii = ilist[jj]; + for (int jj = 0; jj < nn; jj++) { + int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { x[ii] += alpha * d[ii]; r[ii] -= alpha * q[ii]; @@ -552,10 +552,10 @@ int FixQEqReaxOMP::CG( double *b, double *x) beta = sig_new / sig_old; #if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) private(ii) +#pragma omp for schedule(dynamic,50) #endif - for (jj = 0; jj < nn; jj++) { - ii = ilist[jj]; + for (int jj = 0; jj < nn; jj++) { + int ii = ilist[jj]; if (atom->mask[ii] & groupbit) d[ii] = p[ii] + beta * d[ii]; } } @@ -765,13 +765,13 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) startTimeBase = MPI_Wtime(); #endif - int i, imax; + int i, imax; double alpha_s, alpha_t, beta_s, beta_t, b_norm_s, b_norm_t; double sig_old_s, sig_old_t, sig_new_s, sig_new_t; double my_buf[4], buf[4]; - int nn, ii, jj; + int nn; int *ilist; if (reaxc) { nn = reaxc->list->inum; @@ -785,26 +785,26 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) pack_flag = 5; // forward 2x d and reverse 2x q dual_sparse_matvec( &H, x1, x2, q ); - comm->reverse_comm_fix( this); //Coll_Vector( q ); + comm->reverse_comm_fix(this); //Coll_Vector( q ); double tmp1, tmp2, tmp3, tmp4; tmp1 = tmp2 = tmp3 = tmp4 = 0.0; #if defined(_OPENMP) -#pragma omp parallel for schedule(dynamic,50) private(i) reduction(+:tmp1,tmp2,tmp3,tmp4) +#pragma omp parallel for schedule(dynamic,50) reduction(+:tmp1,tmp2,tmp3,tmp4) #endif - for (jj = 0; jj < nn; ++jj) { - i = ilist[jj]; - if (atom->mask[i] & groupbit) { - int indxI = 2 * i; - r[indxI ] = b1[i] - q[indxI ]; - r[indxI+1] = b2[i] - q[indxI+1]; + for (int jj = 0; jj < nn; ++jj) { + int ii = ilist[jj]; + if (atom->mask[ii] & groupbit) { + int indxI = 2 * ii; + r[indxI ] = b1[ii] - q[indxI ]; + r[indxI+1] = b2[ii] - q[indxI+1]; - d[indxI ] = r[indxI ] * Hdia_inv[i]; //pre-condition - d[indxI+1] = r[indxI+1] * Hdia_inv[i]; + d[indxI ] = r[indxI ] * Hdia_inv[ii]; //pre-condition + d[indxI+1] = r[indxI+1] * Hdia_inv[ii]; - tmp1 += b1[i] * b1[i]; - tmp2 += b2[i] * b2[i]; + tmp1 += b1[ii] * b1[ii]; + tmp2 += b2[ii] * b2[ii]; tmp3 += r[indxI ] * d[indxI ]; tmp4 += r[indxI+1] * d[indxI+1]; @@ -836,10 +836,10 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) { #if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1,tmp2) +#pragma omp for schedule(dynamic,50) reduction(+:tmp1,tmp2) #endif - for (jj = 0; jj < nn; jj++) { - ii = ilist[jj]; + for (int jj = 0; jj < nn; jj++) { + int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; tmp1 += d[indxI ] * q[indxI ]; @@ -865,10 +865,10 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) #if defined(_OPENMP) #pragma omp barrier -#pragma omp for schedule(dynamic,50) private(ii) reduction(+:tmp1,tmp2) +#pragma omp for schedule(dynamic,50) reduction(+:tmp1,tmp2) #endif - for (jj = 0; jj < nn; jj++) { - ii = ilist[jj]; + for (int jj = 0; jj < nn; jj++) { + int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; x1[ii] += alpha_s * d[indxI ]; @@ -905,10 +905,10 @@ int FixQEqReaxOMP::dual_CG( double *b1, double *b2, double *x1, double *x2) beta_t = sig_new_t / sig_old_t; #if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) private(ii) +#pragma omp for schedule(dynamic,50) #endif - for (jj = 0; jj < nn; jj++) { - ii = ilist[jj]; + for (int jj = 0; jj < nn; jj++) { + int ii = ilist[jj]; if (atom->mask[ii] & groupbit) { int indxI = 2 * ii; diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 74b2a9277541dcabddf1786b1f57259506737bbc..d92a82a6bff94b37b46669704294beab95ee1024 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -38,15 +38,12 @@ #include "math_extra.h" #include "math_const.h" +#include "rigid_const.h" using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; - -enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid -enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid - -#define EINERTIA 0.4 // moment of inertia prefactor for ellipsoid +using namespace RigidConst; typedef struct { double x,y,z; } dbl3_t; @@ -90,12 +87,11 @@ void FixRigidNHOMP::initial_integrate(int vflag) // update xcm, vcm, quat, conjqm and angmom double akt=0.0, akr=0.0; - int ibody; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr) +#pragma omp parallel for default(none) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { double mbody[3],tbody[3],fquat[4]; const double dtf2 = dtf * 2.0; @@ -393,7 +389,6 @@ void FixRigidNHOMP::compute_forces_and_torques() void FixRigidNHOMP::final_integrate() { - int ibody; double scale_t[3],scale_r; // compute scale variables @@ -425,9 +420,9 @@ void FixRigidNHOMP::final_integrate() const double dtf2 = dtf * 2.0; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr) +#pragma omp parallel for default(none) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { double mbody[3],tbody[3],fquat[4]; // update vcm by 1/2 step @@ -545,11 +540,10 @@ void FixRigidNHOMP::remap() if (allremap) domain->x2lamda(nlocal); else { - int i; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & dilate_group_bit) domain->x2lamda(x[i],x[i]); } @@ -578,11 +572,10 @@ void FixRigidNHOMP::remap() if (allremap) domain->lamda2x(nlocal); else { - int i; #if defined (_OPENMP) -#pragma omp parallel for private(i) default(none) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (i = 0; i < nlocal; i++) + for (int i = 0; i < nlocal; i++) if (mask[i] & dilate_group_bit) domain->lamda2x(x[i],x[i]); } @@ -770,8 +763,8 @@ void FixRigidNHOMP::set_xv_thr() if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]); else theta_body = -2.0*acos(quat[ibody][0]); theta = orient[i][0] + theta_body; - while (theta <= MINUSPI) theta += TWOPI; - while (theta > MY_PI) theta -= TWOPI; + while (theta <= -MY_PI) theta += MY_2PI; + while (theta > MY_PI) theta -= MY_2PI; lbonus[line[i]].theta = theta; omega_one[i][0] = omega[ibody][0]; omega_one[i][1] = omega[ibody][1]; diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index b807ddba7c0432edf7b37d69bc342f32783c556a..20d3009d40e4223898d9e3d25f638a7c1e2cc727 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -33,14 +33,12 @@ #include "math_extra.h" #include "math_const.h" +#include "rigid_const.h" using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; - -enum{SINGLE,MOLECULE,GROUP}; // same as in FixRigid - -#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid +using namespace RigidConst; typedef struct { double x,y,z; } dbl3_t; @@ -48,12 +46,10 @@ typedef struct { double x,y,z; } dbl3_t; void FixRigidOMP::initial_integrate(int vflag) { - int ibody; - #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { // update vcm by 1/2 step @@ -122,12 +118,11 @@ void FixRigidOMP::compute_forces_and_torques() if (rstyle == SINGLE) { // we have just one rigid body. use OpenMP reduction to get sum[] double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0; - int i; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) reduction(+:s0,s1,s2,s3,s4,s5) +#pragma omp parallel for default(none) reduction(+:s0,s1,s2,s3,s4,s5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = body[i]; if (ibody < 0) continue; @@ -161,12 +156,11 @@ void FixRigidOMP::compute_forces_and_torques() for (int ib = 0; ib < nbody; ++ib) { double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0; - int i; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5) +#pragma omp parallel for default(none) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = body[i]; if (ibody != ib) continue; @@ -250,12 +244,11 @@ void FixRigidOMP::compute_forces_and_torques() // update vcm and angmom // include Langevin thermostat forces // fflag,tflag = 0 for some dimensions in 2d - int ibody; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; fcm[ibody][1] = all[ibody][1] + langextra[ibody][1]; fcm[ibody][2] = all[ibody][2] + langextra[ibody][2]; @@ -269,16 +262,14 @@ void FixRigidOMP::compute_forces_and_torques() void FixRigidOMP::final_integrate() { - int ibody; - if (!earlyflag) compute_forces_and_torques(); // update vcm and angmom #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nbody; ibody++) { + for (int ibody = 0; ibody < nbody; ibody++) { // update vcm by 1/2 step @@ -340,12 +331,11 @@ void FixRigidOMP::set_xv_thr() // set x and v of each atom const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) +#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = body[i]; if (ibody < 0) continue; @@ -488,8 +478,8 @@ void FixRigidOMP::set_xv_thr() if (quat[ibody][3] >= 0.0) theta_body = 2.0*acos(quat[ibody][0]); else theta_body = -2.0*acos(quat[ibody][0]); theta = orient[i][0] + theta_body; - while (theta <= MINUSPI) theta += TWOPI; - while (theta > MY_PI) theta -= TWOPI; + while (theta <= -MY_PI) theta += MY_2PI; + while (theta > MY_PI) theta -= MY_2PI; lbonus[line[i]].theta = theta; omega_one[i][0] = omega[ibody][0]; omega_one[i][1] = omega[ibody][1]; @@ -541,12 +531,11 @@ void FixRigidOMP::set_v_thr() // set v of each atom const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) +#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = body[i]; if (ibody < 0) continue; diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 41f6c53e40bcdf366bb01ee85f23adac692b08e6..705f0e6bd070673a39de4d257f11382226e223f3 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -31,14 +31,12 @@ #include "math_extra.h" #include "math_const.h" +#include "rigid_const.h" using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; - -#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid - -enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF}; +using namespace RigidConst; typedef struct { double x,y,z; } dbl3_t; @@ -46,12 +44,11 @@ typedef struct { double x,y,z; } dbl3_t; void FixRigidSmallOMP::initial_integrate(int vflag) { - int ibody; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nlocal_body; ibody++) { + for (int ibody = 0; ibody < nlocal_body; ibody++) { Body &b = body[ibody]; @@ -118,12 +115,11 @@ void FixRigidSmallOMP::compute_forces_and_torques() const double * const * const torque_one = atom->torque; const int nlocal = atom->nlocal; const int nthreads=comm->nthreads; - int i, ibody; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) { + for (int ibody = 0; ibody < nlocal_body+nghost_body; ibody++) { double * _noalias const fcm = body[ibody].fcm; fcm[0] = fcm[1] = fcm[2] = 0.0; double * _noalias const tcm = body[ibody].torque; @@ -136,7 +132,7 @@ void FixRigidSmallOMP::compute_forces_and_torques() // and then each thread only processes some bodies. #if defined(_OPENMP) -#pragma omp parallel default(none) private(i,ibody) +#pragma omp parallel default(none) #endif { #if defined(_OPENMP) @@ -145,8 +141,8 @@ void FixRigidSmallOMP::compute_forces_and_torques() const int tid = 0; #endif - for (i = 0; i < nlocal; i++) { - ibody = atom2body[i]; + for (int i = 0; i < nlocal; i++) { + int ibody = atom2body[i]; if ((ibody < 0) || (ibody % nthreads != tid)) continue; Body &b = body[ibody]; @@ -187,9 +183,9 @@ void FixRigidSmallOMP::compute_forces_and_torques() if (langflag) { #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nlocal_body; ibody++) { + for (int ibody = 0; ibody < nlocal_body; ibody++) { double * _noalias const fcm = body[ibody].fcm; fcm[0] += langextra[ibody][0]; fcm[1] += langextra[ibody][1]; @@ -206,16 +202,14 @@ void FixRigidSmallOMP::compute_forces_and_torques() void FixRigidSmallOMP::final_integrate() { - int ibody; - if (!earlyflag) compute_forces_and_torques(); // update vcm and angmom, recompute omega #if defined(_OPENMP) -#pragma omp parallel for default(none) private(ibody) schedule(static) +#pragma omp parallel for default(none) schedule(static) #endif - for (ibody = 0; ibody < nlocal_body; ibody++) { + for (int ibody = 0; ibody < nlocal_body; ibody++) { Body &b = body[ibody]; // update vcm by 1/2 step @@ -283,12 +277,11 @@ void FixRigidSmallOMP::set_xv_thr() // set x and v of each atom const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) +#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = atom2body[i]; if (ibody < 0) continue; @@ -427,8 +420,8 @@ void FixRigidSmallOMP::set_xv_thr() if (b.quat[3] >= 0.0) theta_body = 2.0*acos(b.quat[0]); else theta_body = -2.0*acos(b.quat[0]); theta = orient[i][0] + theta_body; - while (theta <= MINUSPI) theta += TWOPI; - while (theta > MY_PI) theta -= TWOPI; + while (theta <= -MY_PI) theta += MY_2PI; + while (theta > MY_PI) theta -= MY_2PI; lbonus[line[i]].theta = theta; omega[i][0] = b.omega[0]; omega[i][1] = b.omega[1]; @@ -479,12 +472,11 @@ void FixRigidSmallOMP::set_v_thr() // set v of each atom const int nlocal = atom->nlocal; - int i; #if defined(_OPENMP) -#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) +#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { const int ibody = atom2body[i]; if (ibody < 0) continue; diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index 78b4735863d8a58f0c49bfbe00c836a28a697f3f..d36574713f81cbcf6d55b747f23c4d735e07600f 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMAlloyOMP::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMAlloyOMP::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -184,7 +185,7 @@ void PairEAMAlloyOMP::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 17fecf9b4f1bf122d7f81642c8bfacdb8195c7ef..d1014c5a1446589f84efd3830beff0fcd054875d 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -136,10 +137,10 @@ void PairEAMFSOMP::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -164,7 +165,7 @@ void PairEAMFSOMP::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -186,7 +187,7 @@ void PairEAMFSOMP::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index aedd4380661c4d2946d057aa01f3cd0d79502fcc..8743fb8e4aa77a489cff9c282a6474a37b409d2e 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -285,14 +285,13 @@ void PairReaxCOMP::compute(int eflag, int vflag) if (vflag_fdotr) virial_fdotr_compute(); -// Set internal timestep counter to that of LAMMPS + // Set internal timestep counter to that of LAMMPS data->step = update->ntimestep; Output_Results( system, control, data, &lists, out_control, mpi_data ); // populate tmpid and tmpbo arrays for fix reax/c/species - int i, j; if(fixspecies_flag) { if (system->N > nmax) { @@ -306,8 +305,8 @@ void PairReaxCOMP::compute(int eflag, int vflag) #if defined(_OPENMP) #pragma omp parallel for collapse(2) schedule(static) default(shared) #endif - for (i = 0; i < system->N; i ++) - for (j = 0; j < MAXSPECBOND; j ++) { + for (int i = 0; i < system->N; i++) + for (int j = 0; j < MAXSPECBOND; j++) { tmpbo[i][j] = 0.0; tmpid[i][j] = 0; } @@ -325,9 +324,10 @@ void PairReaxCOMP::init_style( ) // firstwarn = 1; - int iqeq = modify->find_fix_by_style("qeq/reax/omp"); - if (iqeq < 0 && qeqflag == 1) - error->all(FLERR,"Pair reax/c/omp requires use of fix qeq/reax/omp"); + bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1) + || (modify->find_fix_by_style("^qeq/shielded") != -1)); + if (!have_qeq && qeqflag == 1) + error->all(FLERR,"Pair reax/c requires use of fix qeq/reax or qeq/shielded"); system->n = atom->nlocal; // my atoms system->N = atom->nlocal + atom->nghost; // mine + ghosts @@ -612,13 +612,11 @@ void PairReaxCOMP::read_reax_forces(int /* vflag */) void PairReaxCOMP::FindBond() { const double bo_cut = 0.10; - int i; #if defined(_OPENMP) -#pragma omp parallel for schedule(static) default(shared) \ - private(i) +#pragma omp parallel for schedule(static) default(shared) #endif - for (i = 0; i < system->n; i++) { + for (int i = 0; i < system->n; i++) { int j, pj, nj; double bo_tmp; bond_data *bo_ij; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index de902b1a57289343b61ae0785d36f86593d49869..6b2c180a3fe8fabd56a7088b6805bfb6208fb5c6 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -364,11 +364,11 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv, if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions. Simulation unstable."); - int i, flag = 0; + int flag = 0; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static) +#pragma omp parallel for default(none) reduction(+:flag) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { // (nx,ny,nz) = global coords of grid pt to "lower left" of charge // current particle coord can be outside global and local box diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index fc9466e395ab333627e0fc8f1b41a12fcac1471a..bdd8f23ee4fe20c66966bdd7ba1398d34cf99751 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -356,11 +356,11 @@ void PPPMDispTIP4POMP::particle_map_c(double dxinv, double dyinv, if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); - int i, flag = 0; + int flag = 0; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static) +#pragma omp parallel for default(none) reduction(+:flag) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { dbl3_t xM; int iH1,iH2; @@ -432,11 +432,11 @@ void PPPMDispTIP4POMP::particle_map(double dxinv, double dyinv, const int nyhi_out = nyhi_o; const int nzhi_out = nzhi_o; - int i, flag = 0; + int flag = 0; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static) +#pragma omp parallel for default(none) reduction(+:flag) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { // (nx,ny,nz) = global coords of grid pt to "lower left" of charge // current particle coord can be outside global and local box diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index 3ef3de1ab7aec2ce22bd22367f068e93ea1c29aa..c6aaafaa3139d6869d204e72e14061b42e1191e7 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -48,7 +48,7 @@ using namespace MathSpecial; PPPMOMP::PPPMOMP(LAMMPS *lmp) : PPPM(lmp), ThrOMP(lmp, THR_KSPACE) { - triclinic_support = 0; + triclinic_support = 1; suffix_flag |= Suffix::OMP; } diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index d7c12613d96660ecf2610687f04a1318056ba318..322730b57301633435dbbe61c288020b36e553d8 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -353,11 +353,11 @@ void PPPMTIP4POMP::particle_map() if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2])) error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); - int i, flag = 0; + int flag = 0; #if defined(_OPENMP) -#pragma omp parallel for private(i) default(none) reduction(+:flag) schedule(static) +#pragma omp parallel for default(none) reduction(+:flag) schedule(static) #endif - for (i = 0; i < nlocal; i++) { + for (int i = 0; i < nlocal; i++) { dbl3_t xM; int iH1,iH2; @@ -750,11 +750,18 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM) // since local atoms are in lambda coordinates, but ghosts are not. int *sametag = atom->sametag; - double xo[3],xh1[3],xh2[3]; + double xo[3],xh1[3],xh2[3],xm[3]; + const int nlocal = atom->nlocal; - domain->lamda2x(x[i],xo); - domain->lamda2x(x[iH1],xh1); - domain->lamda2x(x[iH2],xh2); + for (int ii = 0; ii < 3; ++ii) { + xo[ii] = x[i][ii]; + xh1[ii] = x[iH1][ii]; + xh2[ii] = x[iH2][ii]; + } + + if (i < nlocal) domain->lamda2x(x[i],xo); + if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1); + if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2); double delx = xo[0] - xh1[0]; double dely = xo[1] - xh1[1]; @@ -763,6 +770,7 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM) double rsq; int closest = iH1; + // no need to run lamda2x here -> ghost atoms while (sametag[iH1] >= 0) { iH1 = sametag[iH1]; delx = xo[0] - x[iH1][0]; @@ -811,13 +819,13 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM) double dely2 = xh2[1] - xo[1]; double delz2 = xh2[2] - xo[2]; - xM.x = xo[0] + alpha * 0.5 * (delx1 + delx2); - xM.y = xo[1] + alpha * 0.5 * (dely1 + dely2); - xM.z = xo[2] + alpha * 0.5 * (delz1 + delz2); + xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2); + xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2); + xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2); // ... and convert M to lamda space for PPPM - domain->x2lamda((double *)&xM,(double *)&xM); + domain->x2lamda(xm,(double *)&xM); } else { diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 971667cc2db889cedc1482c9ceacfd073f4a7c8b..2ebfcea1e0d19bf2e200b7c8a17d8b7c96071353 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -265,12 +265,12 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control, void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list **lists, int step, int n, int N, int numH, MPI_Comm /*comm*/) { - int i, comp, Hindex; + int comp, Hindex; reax_list *bonds, *hbonds; double saferzone = system->saferzone; #if defined(_OPENMP) -#pragma omp parallel default(shared) private(i, comp, Hindex) +#pragma omp parallel default(shared) private(comp,Hindex) #endif { @@ -281,7 +281,7 @@ void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list * #if defined(_OPENMP) #pragma omp for schedule(guided) #endif - for( i = 0; i < N; ++i ) { + for(int i = 0; i < N; ++i ) { system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); if (i < N-1) @@ -305,7 +305,7 @@ void Validate_ListsOMP(reax_system *system, storage * /*workspace*/, reax_list * #if defined(_OPENMP) #pragma omp for schedule(guided) #endif - for( i = 0; i < n; ++i ) { + for(int i = 0; i < n; ++i ) { Hindex = system->my_atoms[i].Hindex; if (Hindex > -1) { system->my_atoms[i].num_hbonds = @@ -338,7 +338,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, startTimeBase = MPI_Wtime(); #endif - int i, j, pj; + int j, pj; int start_i, end_i; int type_i, type_j; int ihb, jhb, ihb_top, jhb_top; @@ -367,8 +367,8 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, #if defined(_OPENMP) #pragma omp parallel default(shared) \ - private(i, atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \ - j, atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp) + private(atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \ + atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp) #endif { @@ -382,9 +382,9 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, long totalReductionSize = system->N * nthreads; #if defined(_OPENMP) -#pragma omp for schedule(dynamic,50) reduction(+ : num_bonds) +#pragma omp for schedule(dynamic,50) reduction(+:num_bonds) #endif - for (i = 0; i < system->N; ++i) { + for (int i = 0; i < system->N; ++i) { atom_i = &(system->my_atoms[i]); type_i = atom_i->type; sbp_i = &(system->reax_param.sbp[type_i]); @@ -395,7 +395,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, for( pj = start_i; pj < end_i; ++pj ) { nbr_pj = &( far_nbrs->select.far_nbr_list[pj] ); if (nbr_pj->d <= cutoff) { - j = nbr_pj->nbr; + int j = nbr_pj->nbr; atom_j = &(system->my_atoms[j]); type_j = atom_j->type; sbp_j = &(system->reax_param.sbp[type_j]); @@ -490,7 +490,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, #if defined(_OPENMP) #pragma omp for schedule(dynamic,50) #endif - for(i=0; iN; i++) + for(int i=0; iN; i++) for(int t=0; tN + i; workspace->dDeltap_self[i][0] += tmp_ddelta[indx][0]; @@ -506,7 +506,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, #if defined(_OPENMP) #pragma omp for schedule(dynamic,50) reduction(+ : num_hbonds) #endif - for (i = 0; i < system->n; ++i) { + for (int i = 0; i < system->n; ++i) { atom_i = &(system->my_atoms[i]); type_i = atom_i->type; sbp_i = &(system->reax_param.sbp[type_i]); @@ -572,7 +572,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, #if defined(_OPENMP) #pragma omp for schedule(guided) #endif - for(i=0; imincap; double safezone = system->safezone; double saferzone = system->saferzone; - comm = mpi_data->world; bond_top = (int*) calloc( system->total_cap, sizeof(int) ); hb_top = (int*) calloc( system->local_cap, sizeof(int) ); Estimate_Storages( system, control, lists, diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh index 26104b45cfe676da5fa573f4cefee9df145aad27..a73f529cfadd0c6fa8e062fe0c936dbd01fc890f 100755 --- a/src/USER-PHONON/Install.sh +++ b/src/USER-PHONON/Install.sh @@ -42,3 +42,5 @@ action fix_phonon.cpp fft3d_wrap.h action fix_phonon.h fft3d_wrap.h action dynamical_matrix.cpp action dynamical_matrix.h +action third_order.cpp +action third_order.h diff --git a/src/USER-PHONON/README b/src/USER-PHONON/README index b554eacd5e203e39fd0ef4b1bfd8cc8475423567..d5ed666c0c070194ee6f3951e7ef6948fe8512be 100644 --- a/src/USER-PHONON/README +++ b/src/USER-PHONON/README @@ -3,11 +3,11 @@ matrices from finite temperature MD simulations, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. -It also contains a command to compute the dynamical matrix at -pre-optimized positions through finite differences. +It also contains commands to compute the dynamical matrix and third +order tensor at pre-optimized positions through finite differences. See the doc page for the fix phonon command or the dynamical_matrix -command for detailed usage instructions. +or third_order commands for detailed usage instructions. Use of this package requires building LAMMPS with FFT suppport, as described in doc/Section_start.html. diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index 559ef4c36f5378500a6f0f3b7afe605aee4ee166..fe266fba76f525a6e75562e30c942591d62d787e 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -66,11 +66,6 @@ void DynamicalMatrix::setup() domain->image_check(); domain->box_too_small_check(); neighbor->build(1); - neighbor->ncalls = 0; - neighbor->every = 2; // build every this many steps - neighbor->delay = 1; - neighbor->ago = 0; - neighbor->ndanger = 0; // compute all forces external_force_clear = 0; @@ -273,7 +268,7 @@ void DynamicalMatrix::calculateMatrix() local_idx = atom->map(i); if (gm[i-1] < 0) continue; - for (bigint alpha=0; alpha<3; alpha++){ + for (int alpha=0; alpha<3; alpha++){ displace_atom(local_idx, alpha, 1); update_force(); for (bigint j=1; j<=natoms; j++){ @@ -291,7 +286,7 @@ void DynamicalMatrix::calculateMatrix() local_jdx = atom->map(j); if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal && gm[j-1] >= 0){ - for (bigint beta=0; beta<3; beta++){ + for (int beta=0; beta<3; beta++){ if (atom->rmass_flag == 1) imass = sqrt(m[local_idx] * m[local_jdx]); else diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp new file mode 100644 index 0000000000000000000000000000000000000000..7764287337ff186a3fe292b27f582d3b00b48367 --- /dev/null +++ b/src/USER-PHONON/third_order.cpp @@ -0,0 +1,575 @@ +// +// Created by charlie sievers on 7/5/18. +// + +#include "third_order.h" +#include +#include +#include +#include "atom.h" +#include "domain.h" +#include "comm.h" +#include "error.h" +#include "group.h" +#include "force.h" +#include "memory.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "update.h" +#include "neighbor.h" +#include "pair.h" +#include "timer.h" +#include "finish.h" +#include "math_special.h" +#include +#include + +using namespace LAMMPS_NS; +using namespace MathSpecial; +enum{REGULAR,BALLISTICO}; + +/* ---------------------------------------------------------------------- */ + +ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(NULL) +{ + external_force_clear = 1; +} + +/* ---------------------------------------------------------------------- */ + +ThirdOrder::~ThirdOrder() +{ + if (fp && me == 0) fclose(fp); + fp = NULL; + memory->destroy(groupmap); +} + +/* ---------------------------------------------------------------------- + setup without output or one-time post-init setup + flag = 0 = just force calculation + flag = 1 = reneighbor and force calculation +------------------------------------------------------------------------- */ + +void ThirdOrder::setup() +{ + // setup domain, communication and neighboring + // acquire ghosts + // build neighbor lists + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + domain->reset_box(); + comm->setup(); + if (neighbor->style) neighbor->setup_bins(); + comm->exchange(); + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + domain->image_check(); + domain->box_too_small_check(); + neighbor->build(1); + + // compute all forces + external_force_clear = 0; + eflag=0; + vflag=0; + update_force(); + + if (gcount == atom->natoms) + for (bigint i=0; inatoms; i++) + groupmap[i] = i; + else + create_groupmap(); +} + +/* ---------------------------------------------------------------------- */ + +void ThirdOrder::command(int narg, char **arg) +{ + MPI_Comm_rank(world,&me); + + if (domain->box_exist == 0) + error->all(FLERR,"third_order command before simulation box is defined"); + if (narg < 2) error->all(FLERR,"Illegal third_order command"); + + lmp->init(); + + // orthogonal vs triclinic simulation box + + triclinic = domain->triclinic; + + if (force->pair && force->pair->compute_flag) pair_compute_flag = 1; + else pair_compute_flag = 0; + if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1; + else kspace_compute_flag = 0; + + // group and style + + igroup = group->find(arg[0]); + if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID"); + groupbit = group->bitmask[igroup]; + gcount = group->count(igroup); + dynlen = (gcount)*3; + memory->create(groupmap,atom->natoms,"total_group_map:totalgm"); + update->setupflag = 1; + + int style = -1; + if (strcmp(arg[1],"regular") == 0) style = REGULAR; + else if (strcmp(arg[1],"eskm") == 0) style = BALLISTICO; + else error->all(FLERR,"Illegal Dynamical Matrix command"); + + // set option defaults + + binaryflag = 0; + scaleflag = 0; + compressed = 0; + file_flag = 0; + file_opened = 0; + conversion = 1; + + // read options from end of input line + if (style == REGULAR) options(narg-3,&arg[3]); //COME BACK + else if (style == BALLISTICO) options(narg-3,&arg[3]); //COME BACK + else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n"); + del = force->numeric(FLERR, arg[2]); + + if (atom->map_style == 0) + error->all(FLERR,"third_order command requires an atom map, see atom_modify"); + + // move atoms by 3-vector or specified variable(s) + + if (style == REGULAR) { + setup(); + timer->init(); + timer->barrier_start(); + calculateMatrix(); + timer->barrier_stop(); + } + + if (style == BALLISTICO) { + setup(); + convert_units(update->unit_style); + conversion = conv_energy/conv_distance/conv_distance; + timer->init(); + timer->barrier_start(); + calculateMatrix(); + timer->barrier_stop(); + } + + Finish finish(lmp); + finish.end(1); +} + +/* ---------------------------------------------------------------------- + parse optional parameters +------------------------------------------------------------------------- */ + +void ThirdOrder::options(int narg, char **arg) +{ + if (narg < 0) error->all(FLERR,"Illegal third_order command"); + int iarg = 0; + const char *filename = "third_order.dat"; + std::stringstream fss; + + while (iarg < narg) { + if (strcmp(arg[iarg],"file") == 0) { + if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command"); + fss << arg[iarg + 1]; + filename = fss.str().c_str(); + file_flag = 1; + iarg += 2; + } else if (strcmp(arg[iarg],"binary") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal third_order command"); + if (strcmp(arg[iarg+1],"gzip") == 0) { + compressed = 1; + } else if (strcmp(arg[iarg+1],"yes") == 0) { + binaryflag = 1; + } + iarg += 2; + } else error->all(FLERR,"Illegal third_order command"); + } + if (file_flag == 1 and me == 0) { + openfile(filename); + } +} + +/* ---------------------------------------------------------------------- + generic opening of a file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void ThirdOrder::openfile(const char* filename) +{ + // if file already opened, return + if (file_opened) return; + + if (compressed) { +#ifdef LAMMPS_GZIP + char gzip[128]; + sprintf(gzip,"gzip -6 > %s",filename); +#ifdef _WIN32 + fp = _popen(gzip,"wb"); +#else + fp = popen(gzip,"w"); +#endif +#else + error->one(FLERR,"Cannot open gzipped file"); +#endif + } else if (binaryflag) { + fp = fopen(filename,"wb"); + } else { + fp = fopen(filename,"w"); + } + + if (fp == NULL) error->one(FLERR,"Cannot open dump file"); + + file_opened = 1; +} + +/* ---------------------------------------------------------------------- + create dynamical matrix +------------------------------------------------------------------------- */ + +void ThirdOrder::calculateMatrix() +{ + int local_idx; // local index + int local_jdx; // second local index + int local_kdx; // third local index + int nlocal = atom->nlocal; + bigint natoms = atom->natoms; + bigint *gm = groupmap; + double **f = atom->f; + + double *dynmat = new double[3*dynlen]; + double *fdynmat = new double[3*dynlen]; + memset(&dynmat[0],0,dynlen*sizeof(double)); + memset(&fdynmat[0],0,dynlen*sizeof(double)); + + if (comm->me == 0 && screen) { + fprintf(screen,"Calculating Third Order ...\n"); + fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms); + fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount); + fprintf(screen," Total third order elements = " + BIGINT_FORMAT "\n", (dynlen*dynlen*dynlen) ); + } + + update->nsteps = 0; + int prog = 0; + for (bigint i=1; i<=natoms; i++){ + local_idx = atom->map(i); + for (int alpha=0; alpha<3; alpha++){ + for (bigint j=1; j<=natoms; j++){ + local_jdx = atom->map(j); + for (int beta=0; beta<3; beta++){ + displace_atom(local_idx, alpha, 1); + displace_atom(local_jdx, beta, 1); + update_force(); + for (bigint k=1; k<=natoms; k++){ + local_kdx = atom->map(k); + for (int gamma=0; gamma<3; gamma++){ + if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0 + && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0 + && local_kdx < nlocal) { + dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma]; + } + } + } + displace_atom(local_jdx, beta, -2); + update_force(); + for (bigint k=1; k<=natoms; k++){ + local_kdx = atom->map(k); + for (int gamma=0; gamma<3; gamma++){ + if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0 + && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0 + && local_kdx < nlocal) { + dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma]; + } + } + } + displace_atom(local_jdx, beta, 1); + displace_atom(local_idx,alpha,-2); + displace_atom(local_jdx, beta, 1); + update_force(); + for (bigint k=1; k<=natoms; k++){ + local_kdx = atom->map(k); + for (int gamma=0; gamma<3; gamma++){ + if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0 + && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0 + && local_kdx < nlocal) { + dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma]; + } + } + } + displace_atom(local_jdx, beta, -2); + update_force(); + for (bigint k=1; k<=natoms; k++){ + local_kdx = atom->map(k); + for (int gamma=0; gamma<3; gamma++){ + if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0 + && gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0 + && local_kdx < nlocal) { + dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma]; + dynmat[gm[k-1]*3+gamma] /= (4 * del * del); + } + } + } + displace_atom(local_jdx, beta, 1); + displace_atom(local_idx, alpha, 1); + MPI_Reduce(dynmat,fdynmat,3*dynlen,MPI_DOUBLE,MPI_SUM,0,world); + if (me == 0){ + writeMatrix(fdynmat, gm[i-1], alpha, gm[j-1], beta); + } + memset(&dynmat[0],0,dynlen*sizeof(double)); + } + } + } + if (comm->me == 0 && screen) { + int p = 10 * gm[i-1] / gcount; + if (p > prog) { + prog = p; + fprintf(screen," %d%%",p*10); + fflush(screen); + } + } + } + + delete [] dynmat; + delete [] fdynmat; + + if (screen && me ==0 ) + fprintf(screen,"Finished Calculating Third Order Tensor\n"); +} + +/* ---------------------------------------------------------------------- + write dynamical matrix +------------------------------------------------------------------------- */ + +void ThirdOrder::writeMatrix(double *dynmat, bigint i, int a, bigint j, int b) +{ + if (me != 0) + return; + + double norm; + if (!binaryflag && fp) { + clearerr(fp); + for (int k = 0; k < gcount; k++){ + norm = square(dynmat[k*3])+ + square(dynmat[k*3+1])+ + square(dynmat[k*3+2]); + if (norm > 1.0e-16) + fprintf(fp, + BIGINT_FORMAT " %d " BIGINT_FORMAT " %d " BIGINT_FORMAT + " %7.8f %7.8f %7.8f\n", + i+1, a + 1, j+1, b + 1, groupmap[k]+1, + dynmat[k*3] * conversion, + dynmat[k*3+1] * conversion, + dynmat[k*3+2] * conversion); + } + } else if (binaryflag && fp){ + clearerr(fp); + fwrite(&dynmat[0], sizeof(double), dynlen, fp); + } + if (ferror(fp)) error->one(FLERR,"Error writing to file"); + +} + +/* ---------------------------------------------------------------------- + Displace atoms + ---------------------------------------------------------------------- */ + +void ThirdOrder::displace_atom(int local_idx, int direction, int magnitude) +{ + if (local_idx < 0) return; + + double **x = atom->x; + int *sametag = atom->sametag; + int j = local_idx; + + x[local_idx][direction] += del*magnitude; + + while (sametag[j] >= 0){ + j = sametag[j]; + x[j][direction] += del*magnitude; + } +} + +/* ---------------------------------------------------------------------- + evaluate potential energy and forces + may migrate atoms due to reneighboring + return new energy, which should include nextra_global dof + return negative gradient stored in atom->f + return negative gradient for nextra_global dof in fextra +------------------------------------------------------------------------- */ + +void ThirdOrder::update_force() +{ + force_clear(); + + if (pair_compute_flag) { + force->pair->compute(eflag,vflag); + timer->stamp(Timer::PAIR); + } + if (atom->molecular) { + if (force->bond) force->bond->compute(eflag,vflag); + if (force->angle) force->angle->compute(eflag,vflag); + if (force->dihedral) force->dihedral->compute(eflag,vflag); + if (force->improper) force->improper->compute(eflag,vflag); + timer->stamp(Timer::BOND); + } + if (kspace_compute_flag) { + force->kspace->compute(eflag,vflag); + timer->stamp(Timer::KSPACE); + } + if (force->newton) { + comm->reverse_comm(); + timer->stamp(Timer::COMM); + } + ++ update->nsteps; +} + +/* ---------------------------------------------------------------------- + clear force on own & ghost atoms + clear other arrays as needed +------------------------------------------------------------------------- */ + +void ThirdOrder::force_clear() +{ + if (external_force_clear) return; + + // clear global force array + // if either newton flag is set, also include ghosts + + size_t nbytes = sizeof(double) * atom->nlocal; + if (force->newton) nbytes += sizeof(double) * atom->nghost; + + if (nbytes) { + memset(&atom->f[0][0],0,3*nbytes); + } +} + +/* ---------------------------------------------------------------------- */ + +void ThirdOrder::convert_units(const char *style) +{ + // physical constants from: + // http://physics.nist.gov/cuu/Constants/Table/allascii.txt + // using thermochemical calorie = 4.184 J + + if (strcmp(style,"lj") == 0) { + error->all(FLERR,"Conversion Not Set"); + //conversion = 1; // lj -> 10 J/mol + + } else if (strcmp(style,"real") == 0) { + conv_energy = 418.4; // kcal/mol -> 10 J/mol + conv_mass = 1; // g/mol -> g/mol + conv_distance = 1; // angstrom -> angstrom + + } else if (strcmp(style,"metal") == 0) { + conv_energy = 9648.5; // eV -> 10 J/mol + conv_mass = 1; // g/mol -> g/mol + conv_distance = 1; // angstrom -> angstrom + + } else if (strcmp(style,"si") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float"); + conv_energy = 6.022E22; // J -> 10 J/mol + conv_mass = 6.022E26; // kg -> g/mol + conv_distance = 1E-10; // meter -> angstrom + + } else if (strcmp(style,"cgs") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float"); + conv_energy = 6.022E12; // Erg -> 10 J/mol + conv_mass = 6.022E23; // g -> g/mol + conv_distance = 1E-7; // centimeter -> angstrom + + } else if (strcmp(style,"electron") == 0) { + conv_energy = 262550; // Hartree -> 10 J/mol + conv_mass = 1; // amu -> g/mol + conv_distance = 0.529177249; // bohr -> angstrom + + } else if (strcmp(style,"micro") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion"); + conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol + conv_mass = 6.022E11; // pg -> g/mol + conv_distance = 1E-4; // micrometer -> angstrom + + } else if (strcmp(style,"nano") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion"); + conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol + conv_mass = 6.022E5; // ag -> g/mol + conv_distance = 0.1; // angstrom -> angstrom + + } else error->all(FLERR,"Units Type Conversion Not Found"); + +} + +/* ---------------------------------------------------------------------- */ + +void ThirdOrder::create_groupmap() +{ + //Create a group map which maps atom order onto group + // groupmap[global atom index-1] = output column/row + + int local_idx; // local index + int gid = 0; //group index + int nlocal = atom->nlocal; + int *mask = atom->mask; + bigint natoms = atom->natoms; + int *recv = new int[comm->nprocs]; + int *displs = new int[comm->nprocs]; + bigint *temp_groupmap = new bigint[natoms]; + + //find number of local atoms in the group (final_gid) + for (bigint i=1; i<=natoms; i++){ + local_idx = atom->map(i); + if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit) + gid += 1; // gid at the end of loop is final_Gid + } + //create an array of length final_gid + bigint *sub_groupmap = new bigint[gid]; + + gid = 0; + //create a map between global atom id and group atom id for each proc + for (bigint i=1; i<=natoms; i++){ + local_idx = atom->map(i); + if ((local_idx >= 0) && (local_idx < nlocal) + && (mask[local_idx] & groupbit)){ + sub_groupmap[gid] = i; + gid += 1; + } + } + + //populate arrays for Allgatherv + for (int i=0; inprocs; i++){ + recv[i] = 0; + } + recv[comm->me] = gid; + MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world); + for (int i=0; inprocs; i++){ + recv[i]=displs[i]; + if (i>0) displs[i] = displs[i-1]+recv[i-1]; + else displs[i] = 0; + } + + //combine subgroup maps into total temporary groupmap + MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT, + temp_groupmap,recv,displs,MPI_LMP_BIGINT,world); + std::sort(temp_groupmap,temp_groupmap+gcount); + + //populate member groupmap based on temp groupmap + bigint j = 0; + for (bigint i=1; i<=natoms; i++){ + // flag groupmap contents that are in temp_groupmap + if (j < gcount && i == temp_groupmap[j]) + groupmap[i-1] = j++; + else + groupmap[i-1] = -1; + } + + //free that memory! + delete[] recv; + delete[] displs; + delete[] sub_groupmap; + delete[] temp_groupmap; +} diff --git a/src/USER-PHONON/third_order.h b/src/USER-PHONON/third_order.h new file mode 100644 index 0000000000000000000000000000000000000000..83062b6b1f9e173c7727023b303aa0499afac90a --- /dev/null +++ b/src/USER-PHONON/third_order.h @@ -0,0 +1,76 @@ +// +// Created by charlie sievers on 7/5/18. +// + + +#ifdef COMMAND_CLASS + +CommandStyle(third_order,ThirdOrder) + +#else + +#ifndef LMP_THIRD_ORDER_H +#define LMP_THIRD_ORDER_H + +#include "pointers.h" + +namespace LAMMPS_NS { + + class ThirdOrder : protected Pointers { + public: + ThirdOrder(class LAMMPS *); + virtual ~ThirdOrder(); + void command(int, char **); + void setup(); + + protected: + int eflag,vflag; // flags for energy/virial computation + int external_force_clear; // clear forces locally or externally + + + int triclinic; // 0 if domain is orthog, 1 if triclinic + int pairflag; + + int pair_compute_flag; // 0 if pair->compute is skipped + int kspace_compute_flag; // 0 if kspace->compute is skipped + + int nvec; // local atomic dof = length of xvec + + void update_force(); + void force_clear(); + virtual void openfile(const char* filename); + + + private: + void options(int, char **); + void create_groupmap(); + void calculateMatrix(); + void convert_units(const char *style); + void displace_atom(int local_idx, int direction, int magnitude); + void writeMatrix(double *, bigint, int, bigint, int); + + double conversion; + double conv_energy; + double conv_distance; + double conv_mass; + double del; + int igroup,groupbit; + bigint dynlen; + int scaleflag; + int me; + bigint gcount; // number of atoms in group + bigint *groupmap; + + int compressed; // 1 if dump file is written compressed, 0 no + int binaryflag; // 1 if dump file is written binary, 0 no + int file_opened; // 1 if openfile method has been called, 0 no + int file_flag; // 1 custom file name, 0 dynmat.dat + + FILE *fp; + }; +} + + +#endif //LMP_THIRD_ORDER_H +#endif + diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index ad3d3facdb86fe43ef1872cdcf2ef372b3ce891a..3a2c8daac4ec00434ece72eb4a3ead350a417d16 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -23,6 +23,7 @@ under #include #include "atom.h" +#include "citeme.h" #include "comm.h" #include "error.h" #include "force.h" @@ -82,6 +83,9 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) PTM_CHECK_ALL, PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; + if (lmp->citeme) + lmp->citeme->add(cite_user_ptm_package); + input_flags = 0; while (*ptr != '\0') { diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp index dc4ce4e747a8b0c3e16a079f8a95c15cccd1ae09..60ef4cf87b3fb58bc472d9d38c49646581627187 100644 --- a/src/USER-PTM/ptm_voronoi_cell.cpp +++ b/src/USER-PTM/ptm_voronoi_cell.cpp @@ -210,13 +210,15 @@ void voronoicell_base::add_memory_vorder(vc_class &vc) { fprintf(stderr,"Vertex order memory scaled up to %d\n",i); #endif p1=new int[i]; - for(j=0;jnfix; iqeq++) - if (strstr(modify->fix[iqeq]->style,"qeq/reax") - || strstr(modify->fix[iqeq]->style,"qeq/shielded")) break; - if (iqeq == modify->nfix && qeqflag == 1) - error->all(FLERR,"Pair reax/c requires use of fix qeq/reax"); + bool have_qeq = ((modify->find_fix_by_style("^qeq/reax") != -1) + || (modify->find_fix_by_style("^qeq/shielded") != -1)); + if (!have_qeq && qeqflag == 1) + error->all(FLERR,"Pair reax/c requires use of fix qeq/reax or qeq/shielded"); system->n = atom->nlocal; // my atoms system->N = atom->nlocal + atom->nghost; // mine + ghosts diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 88e95dd338382fc2d620ba25bfe313f267711356..7f1443c6545d6fe303b56dc65a939efff2008914 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -166,13 +166,6 @@ DumpVTK::DumpVTK(LAMMPS *lmp, int narg, char **arg) : header_choice = NULL; write_choice = NULL; boxcorners = NULL; - - // unsupported feature by dump vtk - delete [] vformat; - vformat = NULL; - - delete [] format_column_user; - format_column_user = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 0f8861cdf5efbe6eaa341400ba21fa6ef7a95c78..3d5715c23e28e080cc4eec9f3bc062d6750159ca 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -278,12 +279,12 @@ void AngleCross::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&kss[1],sizeof(double),atom->nangletypes,fp); - fread(&kbs0[1],sizeof(double),atom->nangletypes,fp); - fread(&kbs1[1],sizeof(double),atom->nangletypes,fp); - fread(&r00[1],sizeof(double),atom->nangletypes,fp); - fread(&r01[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&kss[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&kbs0[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&kbs1[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&r00[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&r01[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&kss[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index b90db37afac4069fe2bc232aca7cbc24fbe8e34d..cb3010e97c8d41d20dc9bc9a9332194a3dc82055 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -225,8 +226,8 @@ void AngleMM3::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k2[1],sizeof(double),atom->nangletypes,fp); - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->nangletypes,fp,NULL,error); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index 2a7d5d184305f810a6d83f56d5fd680a29bcd65c..8001e35d74c8a831617fe2109049beb30a90b60f 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -24,6 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -178,8 +179,8 @@ void BondMM3::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k2[1],sizeof(double),atom->nbondtypes,fp); - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&k2[1],sizeof(double),atom->nbondtypes,fp,NULL,error); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world); MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index 2b62f827e771afd38c0f1b769275e748d0370505..751e6e19c275cbf252d838118a5727c4746e220a 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -26,6 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -256,8 +257,8 @@ void ImproperDistHarm::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index bcc0549f7ec4ca58fcdd1423c83a6f3bed4dc59a..82bf4a1755f9eaab9721614cb80c594c89529d1a 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -26,6 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -256,8 +257,8 @@ void ImproperSQDistHarm::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&k[1],sizeof(double),atom->nimpropertypes,fp); - fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + utils::sfread(FLERR,&k[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); + utils::sfread(FLERR,&chi[1],sizeof(double),atom->nimpropertypes,fp,NULL,error); } MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index ab983a78bca0fa1cfd2e78fe18b0d4d0d5de40bd..77a25db7cc103b4de5587b021010300672805cc9 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -31,6 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -520,14 +521,14 @@ void PairLJSwitch3CoulGaussLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -560,14 +561,14 @@ void PairLJSwitch3CoulGaussLong::write_restart_settings(FILE *fp) void PairLJSwitch3CoulGaussLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&truncw,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&truncw,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 4175ef915d5cf3d421f7f30c3d804c80b5ff69a1..3a4a49c880dbb40ee544b821302522b0954c7b4a 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -31,6 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -520,14 +521,14 @@ void PairMM3Switch3CoulGaussLong::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -560,16 +561,15 @@ void PairMM3Switch3CoulGaussLong::write_restart_settings(FILE *fp) void PairMM3Switch3CoulGaussLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&truncw,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - fread(&ncoultablebits,sizeof(int),1,fp); - fread(&tabinner,sizeof(double),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&truncw,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } - printf("Reading from restart, trunc = %f\n",truncw); MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); MPI_Bcast(&truncw,1,MPI_DOUBLE,0,world); diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index 6ffbc19d08eae3814e634982e8dc3d4639e41ed4..b8535e692ec50ba22d7a1beffd1a5cc701bcf343 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -334,7 +335,7 @@ void AngleHybrid::write_restart(FILE *fp) void AngleHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) fread(&nstyles,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nstyles,1,MPI_INT,0,world); styles = new Angle*[nstyles]; keywords = new char*[nstyles]; @@ -343,10 +344,10 @@ void AngleHybrid::read_restart(FILE *fp) int n,dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); keywords[m] = new char[n]; - if (me == 0) fread(keywords[m],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_angle(keywords[m],0,dummy); styles[m]->read_restart_settings(fp); diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index 3c92b852b39b54abfd2fb47431eebf65daed68be..5da8e9d5bc96fdcd832878b4c6369e904510c357 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -24,6 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -128,7 +129,7 @@ void AngleZero::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,NULL,error); } MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); diff --git a/src/atom.cpp b/src/atom.cpp index 24ad2d40da26e547200483b3b9c829aa5a468177..de5d30930a5542235dc4d116a612f0aaf08b5da6 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -211,7 +211,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) tag_enable = 1; map_style = map_user = 0; map_tag_max = -1; - map_maxarray = map_nhash = -1; + map_maxarray = map_nhash = map_nbucket = -1; max_same = 0; sametag = NULL; diff --git a/src/atom_map.cpp b/src/atom_map.cpp index 7949e327a910d107c417cc0d73eaed0654668075..c23aeec83cd442186e71a1acdffc75d5de756943 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -335,7 +335,7 @@ void Atom::map_delete() map_bucket = NULL; map_hash = NULL; } - map_nhash = 0; + map_nhash = map_nbucket = 0; } } diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 2b365014cfb2e88aa37c02872e5adf121c88133b..c66d2c1425b8918fcffcf13983b31cbbf6d1a2c7 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -335,7 +336,7 @@ void BondHybrid::write_restart(FILE *fp) void BondHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) fread(&nstyles,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nstyles,1,MPI_INT,0,world); styles = new Bond*[nstyles]; keywords = new char*[nstyles]; @@ -344,10 +345,10 @@ void BondHybrid::read_restart(FILE *fp) int n,dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); keywords[m] = new char[n]; - if (me == 0) fread(keywords[m],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_bond(keywords[m],0,dummy); styles[m]->read_restart_settings(fp); diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 9be37c13be8bfded37bcfc6d28b89f95fd558f02..428fd0ace2d54c94563a785aca02dbc19d8e009d 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -23,6 +23,7 @@ #include "comm.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -126,7 +127,7 @@ void BondZero::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,NULL,error); } MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index d579772384333cb178d8a87e2aecf0b01fc7ed8b..e14f188e62c2fc37e622056f8197b91515f03fc5 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -33,7 +33,7 @@ using namespace LAMMPS_NS; #define DELTA 10000 #define EPSILON 1.0e-12 -enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,VARIABLE}; +enum{DIST,VELVIB,OMEGA,ENGTRANS,ENGVIB,ENGROT,ENGPOT,FORCE,FX,FY,FZ,VARIABLE}; /* ---------------------------------------------------------------------- */ @@ -64,6 +64,9 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg],"dist") == 0) bstyle[nvalues++] = DIST; else if (strcmp(arg[iarg],"engpot") == 0) bstyle[nvalues++] = ENGPOT; else if (strcmp(arg[iarg],"force") == 0) bstyle[nvalues++] = FORCE; + else if (strcmp(arg[iarg],"fx") == 0) bstyle[nvalues++] = FX; + else if (strcmp(arg[iarg],"fy") == 0) bstyle[nvalues++] = FY; + else if (strcmp(arg[iarg],"fz") == 0) bstyle[nvalues++] = FZ; else if (strcmp(arg[iarg],"engvib") == 0) bstyle[nvalues++] = ENGVIB; else if (strcmp(arg[iarg],"engrot") == 0) bstyle[nvalues++] = ENGROT; else if (strcmp(arg[iarg],"engtrans") == 0) bstyle[nvalues++] = ENGTRANS; @@ -127,7 +130,8 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : singleflag = 0; velflag = 0; for (int i = 0; i < nvalues; i++) { - if (bstyle[i] == ENGPOT || bstyle[i] == FORCE) singleflag = 1; + if (bstyle[i] == ENGPOT || bstyle[i] == FORCE || bstyle[i] == FX || + bstyle[i] == FY || bstyle[i] == FZ) singleflag = 1; if (bstyle[i] == VELVIB || bstyle[i] == OMEGA || bstyle[i] == ENGTRANS || bstyle[i] == ENGVIB || bstyle[i] == ENGROT) velflag = 1; } @@ -393,6 +397,15 @@ int ComputeBondLocal::compute_bonds(int flag) case FORCE: ptr[n] = sqrt(rsq)*fbond; break; + case FX: + ptr[n] = dx*fbond; + break; + case FY: + ptr[n] = dy*fbond; + break; + case FZ: + ptr[n] = dz*fbond; + break; case ENGVIB: ptr[n] = engvib; break; diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index 266df575f91c2cbbc25413704889824cb4554072..0a783561272299e7fa726f1387e6f9e7f9e3b5ab 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -43,12 +43,14 @@ using namespace std; #define MY_EPSILON (10.0*2.220446049250313e-16) #endif +#define QEPSILON 1.0e-6 + /* ---------------------------------------------------------------------- */ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), qlist(NULL), distsq(NULL), nearest(NULL), rlist(NULL), - qnarray(NULL), qnm_r(NULL), qnm_i(NULL) + qnarray(NULL), qnm_r(NULL), qnm_i(NULL), cglist(NULL) { if (narg < 3 ) error->all(FLERR,"Illegal compute orientorder/atom command"); @@ -56,6 +58,8 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg nnn = 12; cutsq = 0.0; + wlflag = 0; + wlhatflag = 0; qlcompflag = 0; // specify which orders to request @@ -96,27 +100,39 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg if (iarg+nqlist > narg) error->all(FLERR,"Illegal compute orientorder/atom command"); qmax = 0; - for (int iw = 0; iw < nqlist; iw++) { - qlist[iw] = force->numeric(FLERR,arg[iarg+iw]); - if (qlist[iw] < 0) + for (int il = 0; il < nqlist; il++) { + qlist[il] = force->numeric(FLERR,arg[iarg+il]); + if (qlist[il] < 0) error->all(FLERR,"Illegal compute orientorder/atom command"); - if (qlist[iw] > qmax) qmax = qlist[iw]; + if (qlist[il] > qmax) qmax = qlist[il]; } iarg += nqlist; + } else if (strcmp(arg[iarg],"wl") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute orientorder/atom command"); + if (strcmp(arg[iarg+1],"yes") == 0) wlflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) wlflag = 0; + else error->all(FLERR,"Illegal compute orientorder/atom command"); + iarg += 2; + } else if (strcmp(arg[iarg],"wl/hat") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute orientorder/atom command"); + if (strcmp(arg[iarg+1],"yes") == 0) wlhatflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) wlhatflag = 0; + else error->all(FLERR,"Illegal compute orientorder/atom command"); + iarg += 2; } else if (strcmp(arg[iarg],"components") == 0) { qlcompflag = 1; if (iarg+2 > narg) error->all(FLERR,"Illegal compute orientorder/atom command"); qlcomp = force->numeric(FLERR,arg[iarg+1]); - if (qlcomp <= 0) - error->all(FLERR,"Illegal compute orientorder/atom command"); iqlcomp = -1; - for (int iw = 0; iw < nqlist; iw++) - if (qlcomp == qlist[iw]) { - iqlcomp = iw; + for (int il = 0; il < nqlist; il++) + if (qlcomp == qlist[il]) { + iqlcomp = il; break; } - if (iqlcomp < 0) + if (iqlcomp == -1) error->all(FLERR,"Illegal compute orientorder/atom command"); iarg += 2; } else if (strcmp(arg[iarg],"cutoff") == 0) { @@ -130,8 +146,10 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg } else error->all(FLERR,"Illegal compute orientorder/atom command"); } - if (qlcompflag) ncol = nqlist + 2*(2*qlcomp+1); - else ncol = nqlist; + ncol = nqlist; + if (wlflag) ncol += nqlist; + if (wlhatflag) ncol += nqlist; + if (qlcompflag) ncol += 2*(2*qlcomp+1); peratom_flag = 1; size_peratom_cols = ncol; @@ -151,7 +169,7 @@ ComputeOrientOrderAtom::~ComputeOrientOrderAtom() memory->destroy(qlist); memory->destroy(qnm_r); memory->destroy(qnm_i); - + memory->destroy(cglist); } /* ---------------------------------------------------------------------- */ @@ -166,8 +184,8 @@ void ComputeOrientOrderAtom::init() error->all(FLERR,"Compute orientorder/atom cutoff is " "longer than pairwise cutoff"); - memory->create(qnm_r,qmax,2*qmax+1,"orientorder/atom:qnm_r"); - memory->create(qnm_i,qmax,2*qmax+1,"orientorder/atom:qnm_i"); + memory->create(qnm_r,nqlist,2*qmax+1,"orientorder/atom:qnm_r"); + memory->create(qnm_i,nqlist,2*qmax+1,"orientorder/atom:qnm_i"); // need an occasional full neighbor list @@ -183,6 +201,8 @@ void ComputeOrientOrderAtom::init() if (strcmp(modify->compute[i]->style,"orientorder/atom") == 0) count++; if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one compute orientorder/atom"); + + if (wlflag || wlhatflag) init_clebsch_gordan(); } /* ---------------------------------------------------------------------- */ @@ -274,8 +294,8 @@ void ComputeOrientOrderAtom::compute_peratom() // if not nnn neighbors, order parameter = 0; if ((ncount == 0) || (ncount < nnn)) { - for (int iw = 0; iw < nqlist; iw++) - qn[iw] = 0.0; + for (int jj = 0; jj < ncol; jj++) + qn[jj] = 0.0; continue; } @@ -287,6 +307,7 @@ void ComputeOrientOrderAtom::compute_peratom() } calc_boop(rlist, ncount, qn, qlist, nqlist); + } } } @@ -403,13 +424,12 @@ void ComputeOrientOrderAtom::select3(int k, int n, double *arr, int *iarr, doubl void ComputeOrientOrderAtom::calc_boop(double **rlist, int ncount, double qn[], int qlist[], int nqlist) { - for (int iw = 0; iw < nqlist; iw++) { - int n = qlist[iw]; - qn[iw] = 0.0; - for(int m = 0; m < 2*n+1; m++) { - qnm_r[iw][m] = 0.0; - qnm_i[iw][m] = 0.0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m = 0; m < 2*l+1; m++) { + qnm_r[il][m] = 0.0; + qnm_i[il][m] = 0.0; } } @@ -433,24 +453,24 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, expphi_i *= rxymaginv; } - for (int iw = 0; iw < nqlist; iw++) { - int n = qlist[iw]; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; - qnm_r[iw][n] += polar_prefactor(n, 0, costheta); + qnm_r[il][l] += polar_prefactor(l, 0, costheta); double expphim_r = expphi_r; double expphim_i = expphi_i; - for(int m = 1; m <= +n; m++) { - double prefactor = polar_prefactor(n, m, costheta); + for(int m = 1; m <= +l; m++) { + double prefactor = polar_prefactor(l, m, costheta); double c_r = prefactor * expphim_r; double c_i = prefactor * expphim_i; - qnm_r[iw][m+n] += c_r; - qnm_i[iw][m+n] += c_i; + qnm_r[il][m+l] += c_r; + qnm_i[il][m+l] += c_i; if(m & 1) { - qnm_r[iw][-m+n] -= c_r; - qnm_i[iw][-m+n] += c_i; + qnm_r[il][-m+l] -= c_r; + qnm_i[il][-m+l] += c_i; } else { - qnm_r[iw][-m+n] += c_r; - qnm_i[iw][-m+n] -= c_i; + qnm_r[il][-m+l] += c_r; + qnm_i[il][-m+l] -= c_i; } double tmp_r = expphim_r*expphi_r - expphim_i*expphi_i; double tmp_i = expphim_r*expphi_i + expphim_i*expphi_r; @@ -461,30 +481,110 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, } } - double fac = sqrt(MY_4PI) / ncount; - double normfac = 0.0; - for (int iw = 0; iw < nqlist; iw++) { - int n = qlist[iw]; + // convert sums to averages + + double facn = 1.0 / ncount; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m = 0; m < 2*l+1; m++) { + qnm_r[il][m] *= facn; + qnm_i[il][m] *= facn; + } + } + + // calculate Q_l + // NOTE: optional W_l_hat and components of Q_qlcomp use these stored Q_l values + + int jj = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + double qnormfac = sqrt(MY_4PI/(2*l+1)); double qm_sum = 0.0; - for(int m = 0; m < 2*n+1; m++) { - qm_sum += qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]; - // printf("Ylm^2 = %d %d %g\n",n,m, - // qnm_r[iw][m]*qnm_r[iw][m] + qnm_i[iw][m]*qnm_i[iw][m]); + for(int m = 0; m < 2*l+1; m++) + qm_sum += qnm_r[il][m]*qnm_r[il][m] + qnm_i[il][m]*qnm_i[il][m]; + qn[jj++] = qnormfac * sqrt(qm_sum); + } + + // TODO: + // 1. [done]Need to allocate extra memory in qnarray[] for this option + // 2. [done]Need to add keyword option + // 3. [done]Need to caclulate Clebsch-Gordan/Wigner 3j coefficients + // (Can try getting them from boop.py first) + // 5. [done]Compare to bcc values in /Users/athomps/netapp/codes/MatMiner/matminer/matminer/featurizers/boop.py + // 6. [done]I get the right answer for W_l, but need to make sure that factor of 1/sqrt(l+1) is right for cglist + // 7. Add documentation + // 8. [done] run valgrind + // 9. [done] Add Wlhat + // 10. Update memory_usage() + // 11. Add exact FCC values for W_4, W_4_hat + + // calculate W_l + + if (wlflag) { + int idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + double wlsum = 0.0; + for(int m1 = 0; m1 < 2*l+1; m1++) { + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { + int m = m1 + m2 - l; + double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2]; + double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2]; + wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count]; + idxcg_count++; + } + } + qn[jj++] = wlsum/sqrt(2*l+1); } - qn[iw] = fac * sqrt(qm_sum / (2*n+1)); - if (qlcompflag && iqlcomp == iw) normfac = 1.0/sqrt(qm_sum); + } + // calculate W_l_hat + + if (wlhatflag) { + int idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + double wlsum = 0.0; + for(int m1 = 0; m1 < 2*l+1; m1++) { + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { + int m = m1 + m2 - l; + double qm1qm2_r = qnm_r[il][m1]*qnm_r[il][m2] - qnm_i[il][m1]*qnm_i[il][m2]; + double qm1qm2_i = qnm_r[il][m1]*qnm_i[il][m2] + qnm_i[il][m1]*qnm_r[il][m2]; + wlsum += (qm1qm2_r*qnm_r[il][m] + qm1qm2_i*qnm_i[il][m])*cglist[idxcg_count]; + idxcg_count++; + } + } + // Whats = [w/(q/np.sqrt(np.pi * 4 / (2 * l + 1)))**3 if abs(q) > 1.0e-6 else 0.0 for l,q,w in zip(range(1,max_l+1),Qs,Ws)] + if (qn[il] < QEPSILON) + qn[jj++] = 0.0; + else { + double qnormfac = sqrt(MY_4PI/(2*l+1)); + double qnfac = qnormfac/qn[il]; + qn[jj++] = wlsum/sqrt(2*l+1)*(qnfac*qnfac*qnfac); + } + } } - // output of the complex vector + // Calculate components of Q_l, for l=qlcomp if (qlcompflag) { - int j = nqlist; - for(int m = 0; m < 2*qlcomp+1; m++) { - qn[j++] = qnm_r[iqlcomp][m] * normfac; - qn[j++] = qnm_i[iqlcomp][m] * normfac; + int il = iqlcomp; + int l = qlcomp; + if (qn[il] < QEPSILON) + for(int m = 0; m < 2*l+1; m++) { + qn[jj++] = 0.0; + qn[jj++] = 0.0; + } + else { + double qnormfac = sqrt(MY_4PI/(2*l+1)); + double qnfac = qnormfac/qn[il]; + for(int m = 0; m < 2*l+1; m++) { + qn[jj++] = qnm_r[il][m] * qnfac; + qn[jj++] = qnm_i[il][m] * qnfac; + } } } + } /* ---------------------------------------------------------------------- @@ -542,3 +642,258 @@ double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x) return p; } + +/* ---------------------------------------------------------------------- + assign Clebsch-Gordan coefficients + using the quasi-binomial formula VMK 8.2.1(3) + specialized for case j1=j2=j=l +------------------------------------------------------------------------- */ + +void ComputeOrientOrderAtom::init_clebsch_gordan() +{ + double sum,dcg,sfaccg, sfac1, sfac2; + int m, aa2, bb2, cc2; + int ifac, idxcg_count; + + idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m1 = 0; m1 < 2*l+1; m1++) + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) + idxcg_count++; + } + idxcg_max = idxcg_count; + memory->create(cglist, idxcg_max, "computeorientorderatom:cglist"); + + idxcg_count = 0; + for (int il = 0; il < nqlist; il++) { + int l = qlist[il]; + for(int m1 = 0; m1 < 2*l+1; m1++) { + aa2 = m1 - l; + for(int m2 = MAX(0,l-m1); m2 < MIN(2*l+1,3*l-m1+1); m2++) { + bb2 = m2 - l; + m = aa2 + bb2 + l; + + sum = 0.0; + for (int z = MAX(0, MAX(-aa2, bb2)); + z <= MIN(l, MIN(l - aa2, l + bb2)); z++) { + ifac = z % 2 ? -1 : 1; + sum += ifac / + (factorial(z) * + factorial(l - z) * + factorial(l - aa2 - z) * + factorial(l + bb2 - z) * + factorial(aa2 + z) * + factorial(-bb2 + z)); + } + + cc2 = m - l; + sfaccg = sqrt(factorial(l + aa2) * + factorial(l - aa2) * + factorial(l + bb2) * + factorial(l - bb2) * + factorial(l + cc2) * + factorial(l - cc2) * + (2*l + 1)); + + sfac1 = factorial(3*l + 1); + sfac2 = factorial(l); + dcg = sqrt(sfac2*sfac2*sfac2 / sfac1); + + cglist[idxcg_count] = sum * dcg * sfaccg; + idxcg_count++; + } + } + } +} + +/* ---------------------------------------------------------------------- + factorial n, wrapper for precomputed table +------------------------------------------------------------------------- */ + +double ComputeOrientOrderAtom::factorial(int n) +{ + if (n < 0 || n > nmaxfactorial) { + char str[128]; + sprintf(str, "Invalid argument to factorial %d", n); + error->all(FLERR, str); + } + + return nfac_table[n]; +} + +/* ---------------------------------------------------------------------- + factorial n table, size SNA::nmaxfactorial+1 +------------------------------------------------------------------------- */ + +const double ComputeOrientOrderAtom::nfac_table[] = { + 1, + 1, + 2, + 6, + 24, + 120, + 720, + 5040, + 40320, + 362880, + 3628800, + 39916800, + 479001600, + 6227020800, + 87178291200, + 1307674368000, + 20922789888000, + 355687428096000, + 6.402373705728e+15, + 1.21645100408832e+17, + 2.43290200817664e+18, + 5.10909421717094e+19, + 1.12400072777761e+21, + 2.5852016738885e+22, + 6.20448401733239e+23, + 1.5511210043331e+25, + 4.03291461126606e+26, + 1.08888694504184e+28, + 3.04888344611714e+29, + 8.8417619937397e+30, + 2.65252859812191e+32, + 8.22283865417792e+33, + 2.63130836933694e+35, + 8.68331761881189e+36, + 2.95232799039604e+38, + 1.03331479663861e+40, + 3.71993326789901e+41, + 1.37637530912263e+43, + 5.23022617466601e+44, + 2.03978820811974e+46, + 8.15915283247898e+47, + 3.34525266131638e+49, + 1.40500611775288e+51, + 6.04152630633738e+52, + 2.65827157478845e+54, + 1.1962222086548e+56, + 5.50262215981209e+57, + 2.58623241511168e+59, + 1.24139155925361e+61, + 6.08281864034268e+62, + 3.04140932017134e+64, + 1.55111875328738e+66, + 8.06581751709439e+67, + 4.27488328406003e+69, + 2.30843697339241e+71, + 1.26964033536583e+73, + 7.10998587804863e+74, + 4.05269195048772e+76, + 2.35056133128288e+78, + 1.3868311854569e+80, + 8.32098711274139e+81, + 5.07580213877225e+83, + 3.14699732603879e+85, + 1.98260831540444e+87, + 1.26886932185884e+89, + 8.24765059208247e+90, + 5.44344939077443e+92, + 3.64711109181887e+94, + 2.48003554243683e+96, + 1.71122452428141e+98, + 1.19785716699699e+100, + 8.50478588567862e+101, + 6.12344583768861e+103, + 4.47011546151268e+105, + 3.30788544151939e+107, + 2.48091408113954e+109, + 1.88549470166605e+111, + 1.45183092028286e+113, + 1.13242811782063e+115, + 8.94618213078297e+116, + 7.15694570462638e+118, + 5.79712602074737e+120, + 4.75364333701284e+122, + 3.94552396972066e+124, + 3.31424013456535e+126, + 2.81710411438055e+128, + 2.42270953836727e+130, + 2.10775729837953e+132, + 1.85482642257398e+134, + 1.65079551609085e+136, + 1.48571596448176e+138, + 1.3520015276784e+140, + 1.24384140546413e+142, + 1.15677250708164e+144, + 1.08736615665674e+146, + 1.03299784882391e+148, + 9.91677934870949e+149, + 9.61927596824821e+151, + 9.42689044888324e+153, + 9.33262154439441e+155, + 9.33262154439441e+157, + 9.42594775983835e+159, + 9.61446671503512e+161, + 9.90290071648618e+163, + 1.02990167451456e+166, + 1.08139675824029e+168, + 1.14628056373471e+170, + 1.22652020319614e+172, + 1.32464181945183e+174, + 1.44385958320249e+176, + 1.58824554152274e+178, + 1.76295255109024e+180, + 1.97450685722107e+182, + 2.23119274865981e+184, + 2.54355973347219e+186, + 2.92509369349301e+188, + 3.3931086844519e+190, + 3.96993716080872e+192, + 4.68452584975429e+194, + 5.5745857612076e+196, + 6.68950291344912e+198, + 8.09429852527344e+200, + 9.8750442008336e+202, + 1.21463043670253e+205, + 1.50614174151114e+207, + 1.88267717688893e+209, + 2.37217324288005e+211, + 3.01266001845766e+213, + 3.8562048236258e+215, + 4.97450422247729e+217, + 6.46685548922047e+219, + 8.47158069087882e+221, + 1.118248651196e+224, + 1.48727070609069e+226, + 1.99294274616152e+228, + 2.69047270731805e+230, + 3.65904288195255e+232, + 5.01288874827499e+234, + 6.91778647261949e+236, + 9.61572319694109e+238, + 1.34620124757175e+241, + 1.89814375907617e+243, + 2.69536413788816e+245, + 3.85437071718007e+247, + 5.5502938327393e+249, + 8.04792605747199e+251, + 1.17499720439091e+254, + 1.72724589045464e+256, + 2.55632391787286e+258, + 3.80892263763057e+260, + 5.71338395644585e+262, + 8.62720977423323e+264, + 1.31133588568345e+267, + 2.00634390509568e+269, + 3.08976961384735e+271, + 4.78914290146339e+273, + 7.47106292628289e+275, + 1.17295687942641e+278, + 1.85327186949373e+280, + 2.94670227249504e+282, + 4.71472363599206e+284, + 7.59070505394721e+286, + 1.22969421873945e+289, + 2.0044015765453e+291, + 3.28721858553429e+293, + 5.42391066613159e+295, + 9.00369170577843e+297, + 1.503616514865e+300, // nmaxfactorial = 167 +}; + diff --git a/src/compute_orientorder_atom.h b/src/compute_orientorder_atom.h index d5905df63bd170eedd0cb1d4ae6dcf6d3b18e3a9..643875ccd01c805720d8a272daf6141652518216 100644 --- a/src/compute_orientorder_atom.h +++ b/src/compute_orientorder_atom.h @@ -33,7 +33,7 @@ class ComputeOrientOrderAtom : public Compute { void compute_peratom(); double memory_usage(); double cutsq; - int iqlcomp, qlcomp, qlcompflag; + int iqlcomp, qlcomp, qlcompflag, wlflag, wlhatflag; int *qlist; int nqlist; @@ -55,6 +55,13 @@ class ComputeOrientOrderAtom : public Compute { double polar_prefactor(int, int, double); double associated_legendre(int, int, double); + + static const int nmaxfactorial = 167; + static const double nfac_table[]; + double factorial(int); + void init_clebsch_gordan(); + double *cglist; // Clebsch-Gordan coeffs + int idxcg_max; }; } diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index fd7b74b43a9db3420c4411f92f43af88a4ae0173..379de0f9de3a4655584f67a1a7da8b0abef50c2b 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -26,6 +26,7 @@ #include "modify.h" #include "domain.h" #include "error.h" +#include "atom_masks.h" using namespace LAMMPS_NS; @@ -65,6 +66,9 @@ ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) : iarg++; } } + + datamask_read = EMPTY_MASK; + datamask_modify = EMPTY_MASK; } /* ---------------------------------------------------------------------- */ diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 8a091ef2ef88561f02462f5b3b505a6a6942ce6b..c7df5ac264f0a009a7f82c8cf61e3b8229efb90e 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -606,8 +606,11 @@ void CreateAtoms::add_random() double *boxlo,*boxhi; // random number generator, same for all procs + // warm up the generator 30x to avoid correlations in first-particle + // positions if runs are repeated with consecutive seeds RanPark *random = new RanPark(lmp,seed); + for (int ii=0; ii < 30; ii++) random->uniform(); // bounding box for atom creation // in real units, even if triclinic diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 5b7c354595e47feb68e8cb597964707abdfa0334..437f5959db38ba5b5c62ad4c4365f58be33cd4b9 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -12,7 +12,9 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Mike Salerno (NRL) added single methods + Contributing authors: + Mike Salerno (NRL) added single methods + Thomas Farmer (ISIS) added single/improper ------------------------------------------------------------------------- */ #include "create_bonds.h" @@ -31,7 +33,7 @@ using namespace LAMMPS_NS; -enum{MANY,SBOND,SANGLE,SDIHEDRAL}; +enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER}; /* ---------------------------------------------------------------------- */ @@ -100,6 +102,18 @@ void CreateBonds::command(int narg, char **arg) (datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4)) error->all(FLERR,"Illegal create_bonds command"); iarg = 6; + } else if (strcmp(arg[0],"single/improper") == 0) { + style = SIMPROPER; + if (narg < 6) error->all(FLERR,"Illegal create_bonds command"); + dtype = force->inumeric(FLERR,arg[1]); + datom1 = force->tnumeric(FLERR,arg[2]); + datom2 = force->tnumeric(FLERR,arg[3]); + datom3 = force->tnumeric(FLERR,arg[4]); + datom4 = force->tnumeric(FLERR,arg[5]); + if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || + (datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4)) + error->all(FLERR,"Illegal create_bonds command"); + iarg = 6; } else error->all(FLERR,"Illegal create_bonds command"); // optional args @@ -132,6 +146,9 @@ void CreateBonds::command(int narg, char **arg) } else if (style == SDIHEDRAL) { if (dtype <= 0 || dtype > atom->ndihedraltypes) error->all(FLERR,"Invalid dihedral type in create_bonds command"); + } else if (style == SIMPROPER) { + if (dtype <= 0 || dtype > atom->nimpropertypes) + error->all(FLERR,"Invalid improper type in create_bonds command"); } // invoke creation method @@ -140,6 +157,7 @@ void CreateBonds::command(int narg, char **arg) else if (style == SBOND) single_bond(); else if (style == SANGLE) single_angle(); else if (style == SDIHEDRAL) single_dihedral(); + else if (style == SIMPROPER) single_improper(); // trigger special list build @@ -512,3 +530,89 @@ void CreateBonds::single_dihedral() num_dihedral[m]++; } } + +/* ---------------------------------------------------------------------- */ + +void CreateBonds::single_improper() +{ + int m; + + // check that 4 atoms exist + + const int nlocal = atom->nlocal; + const int idx1 = atom->map(datom1); + const int idx2 = atom->map(datom2); + const int idx3 = atom->map(datom3); + const int idx4 = atom->map(datom4); + + int count = 0; + if ((idx1 >= 0) && (idx1 < nlocal)) count++; + if ((idx2 >= 0) && (idx2 < nlocal)) count++; + if ((idx3 >= 0) && (idx3 < nlocal)) count++; + if ((idx4 >= 0) && (idx4 < nlocal)) count++; + + int allcount; + MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world); + if (allcount != 4) + error->all(FLERR,"Create_bonds single/improper atoms do not exist"); + + // create bond once or 4x if newton_bond set + + int *num_improper = atom->num_improper; + int **improper_type = atom->improper_type; + tagint **improper_atom1 = atom->improper_atom1; + tagint **improper_atom2 = atom->improper_atom2; + tagint **improper_atom3 = atom->improper_atom3; + tagint **improper_atom4 = atom->improper_atom4; + + if ((m = idx2) >= 0) { + if (num_improper[m] == atom->improper_per_atom) + error->one(FLERR, + "New improper exceeded impropers per atom in create_bonds"); + improper_type[m][num_improper[m]] = dtype; + improper_atom1[m][num_improper[m]] = datom1; + improper_atom2[m][num_improper[m]] = datom2; + improper_atom3[m][num_improper[m]] = datom3; + improper_atom4[m][num_improper[m]] = datom4; + num_improper[m]++; + } + atom->nimpropers++; + + if (force->newton_bond) return; + + if ((m = idx1) >= 0) { + if (num_improper[m] == atom->improper_per_atom) + error->one(FLERR, + "New improper exceeded impropers per atom in create_bonds"); + improper_type[m][num_improper[m]] = dtype; + improper_atom1[m][num_improper[m]] = datom1; + improper_atom2[m][num_improper[m]] = datom2; + improper_atom3[m][num_improper[m]] = datom3; + improper_atom4[m][num_improper[m]] = datom4; + num_improper[m]++; + } + + if ((m = idx3) >= 0) { + if (num_improper[m] == atom->improper_per_atom) + error->one(FLERR, + "New improper exceeded impropers per atom in create_bonds"); + improper_type[m][num_improper[m]] = dtype; + improper_atom1[m][num_improper[m]] = datom1; + improper_atom2[m][num_improper[m]] = datom2; + improper_atom3[m][num_improper[m]] = datom3; + improper_atom4[m][num_improper[m]] = datom4; + num_improper[m]++; + } + + if ((m = idx4) >= 0) { + if (num_improper[m] == atom->improper_per_atom) + error->one(FLERR, + "New improper exceeded impropers per atom in create_bonds"); + improper_type[m][num_improper[m]] = dtype; + improper_atom1[m][num_improper[m]] = datom1; + improper_atom2[m][num_improper[m]] = datom2; + improper_atom3[m][num_improper[m]] = datom3; + improper_atom4[m][num_improper[m]] = datom4; + num_improper[m]++; + } +} diff --git a/src/create_bonds.h b/src/create_bonds.h index 0c71242ed9001d2a0426fe0f52efe9f30b0fe39a..eea99b0113d501a7709ff16c682bbb3cad4a8264 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -39,6 +39,7 @@ class CreateBonds : protected Pointers { void single_bond(); void single_angle(); void single_dihedral(); + void single_improper(); }; } @@ -87,6 +88,10 @@ E: Invalid dihedral type in create_bonds command UNDOCUMENTED +E: Invalid improper type in create_bonds command + +UNDOCUMENTED + E: Create_bonds requires a pair style be defined Self-explanatory. @@ -135,4 +140,12 @@ E: New dihedral exceeded dihedrals per atom in create_bonds UNDOCUMENTED +E: Create_bonds single/improper atoms do not exist + +UNDOCUMENTED + +E: New improper exceeded impropers per atom in create_bonds + +UNDOCUMENTED + */ diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 6c0a4338ae4ebc15dd37ceb5ecb0bf5a7de87c36..fe755ab85b66f2834f58f9436405fe0bf215f323 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -21,9 +21,11 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; + #define EXTRA 1000 /* ---------------------------------------------------------------------- */ @@ -319,7 +321,7 @@ void DihedralHybrid::write_restart(FILE *fp) void DihedralHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) fread(&nstyles,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nstyles,1,MPI_INT,0,world); styles = new Dihedral*[nstyles]; keywords = new char*[nstyles]; @@ -328,10 +330,10 @@ void DihedralHybrid::read_restart(FILE *fp) int n,dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); keywords[m] = new char[n]; - if (me == 0) fread(keywords[m],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_dihedral(keywords[m],0,dummy); styles[m]->read_restart_settings(fp); diff --git a/src/domain.cpp b/src/domain.cpp index 372b264013ff0620b4eb7b8ea287be8e8893e368..e8946825569abb46ec311fb385f8e9cd353b41a9 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -352,6 +352,11 @@ void Domain::set_local_box() void Domain::reset_box() { // perform shrink-wrapping + + // nothing to do for empty systems + + if (atom->natoms == 0) return; + // compute extent of atoms on this proc // for triclinic, this is done in lamda space diff --git a/src/dump.cpp b/src/dump.cpp index 57a8decbb0dccf28dda89a7b658ee082b3e75040..83b74f1bbca24b7a7c0b046787d4fc001c1866c0 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -87,6 +87,9 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp) buffer_flag = 0; padflag = 0; pbcflag = 0; + time_flag = 0; + unit_flag = 0; + unit_count = 0; delay_flag = 0; maxfiles = -1; @@ -545,6 +548,8 @@ void Dump::openfile() if (singlefile_opened) return; if (multifile == 0) singlefile_opened = 1; + unit_count = 0; + // if one file per timestep, replace '*' with current timestep char *filecurrent = filename; @@ -1119,6 +1124,20 @@ void Dump::modify_params(int narg, char **arg) } iarg += 2; + } else if (strcmp(arg[iarg],"time") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command"); + if (strcmp(arg[iarg+1],"yes") == 0) time_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) time_flag = 0; + else error->all(FLERR,"Illegal dump_modify command"); + iarg += 2; + + } else if (strcmp(arg[iarg],"units") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command"); + if (strcmp(arg[iarg+1],"yes") == 0) unit_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) unit_flag = 0; + else error->all(FLERR,"Illegal dump_modify command"); + iarg += 2; + } else { int n = modify_param(narg-iarg,&arg[iarg]); if (n == 0) error->all(FLERR,"Illegal dump_modify command"); @@ -1127,6 +1146,12 @@ void Dump::modify_params(int narg, char **arg) } } +/* ---------------------------------------------------------------------- */ + +double Dump::compute_time() +{ + return update->atime + (update->ntimestep - update->atimestep)*update->dt; +} /* ---------------------------------------------------------------------- return # of bytes of allocated memory ------------------------------------------------------------------------- */ diff --git a/src/dump.h b/src/dump.h index bc7fd2d5a50a56e59a877cf74f52b62d9ef94fa2..17e9434faa6a7e493967b7f26434062f8bcbc865 100644 --- a/src/dump.h +++ b/src/dump.h @@ -75,6 +75,9 @@ class Dump : protected Pointers { int sortcol; // 0 to sort on ID, 1-N on columns int sortcolm1; // sortcol - 1 int sortorder; // ASCEND or DESCEND + int time_flag; // 1 if output accumulated time + int unit_flag; // 1 if dump should contain unit information + int unit_count; // # of times the unit information was written int delay_flag; // 1 if delay output until delaystep bigint delaystep; @@ -143,6 +146,7 @@ class Dump : protected Pointers { virtual int convert_string(int, double *) {return 0;} virtual void write_data(int, double *) = 0; void pbc_allocate(); + double compute_time(); void sort(); #if defined(LMP_QSORT) diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp index e2e77cfb770fa93b4ad37a949163e66f1dd3b012..401b47051dad2768a412760ee7d953c3cc9e5b0b 100644 --- a/src/dump_atom.cpp +++ b/src/dump_atom.cpp @@ -15,9 +15,9 @@ #include #include "domain.h" #include "atom.h" -#include "update.h" #include "memory.h" #include "error.h" +#include "update.h" using namespace LAMMPS_NS; @@ -209,6 +209,12 @@ void DumpAtom::header_binary_triclinic(bigint ndump) void DumpAtom::header_item(bigint ndump) { + if (unit_flag && !unit_count) { + ++unit_count; + fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time()); + fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); @@ -224,6 +230,12 @@ void DumpAtom::header_item(bigint ndump) void DumpAtom::header_item_triclinic(bigint ndump) { + if (unit_flag && !unit_count) { + ++unit_count; + fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time()); + fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index ce83e442c9e296ac8b3bbdc7adc7d4845e5b0095..4b25896d79a6f31c5631e542d85f4b75661c5e78 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -20,14 +20,14 @@ #include "region.h" #include "group.h" #include "input.h" -#include "variable.h" -#include "update.h" #include "modify.h" #include "compute.h" #include "fix.h" #include "fix_store.h" #include "memory.h" #include "error.h" +#include "update.h" +#include "variable.h" using namespace LAMMPS_NS; @@ -248,8 +248,10 @@ DumpCustom::~DumpCustom() delete [] vformat; } - for (int i = 0; i < size_one; i++) delete [] format_column_user[i]; - delete [] format_column_user; + if (format_column_user) { + for (int i = 0; i < size_one; i++) delete [] format_column_user[i]; + delete [] format_column_user; + } delete [] columns; } @@ -420,6 +422,12 @@ void DumpCustom::header_binary_triclinic(bigint ndump) void DumpCustom::header_item(bigint ndump) { + if (unit_flag && !unit_count) { + ++unit_count; + fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time()); + fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); @@ -435,6 +443,12 @@ void DumpCustom::header_item(bigint ndump) void DumpCustom::header_item_triclinic(bigint ndump) { + if (unit_flag && !unit_count) { + ++unit_count; + fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time()); + fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF ATOMS\n"); diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 9f021a7b6aa373c552a876b3cd2855b4c481a711..21a96d1e8ae8e621c1bc97de1cc0c30d7d2e2ea4 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -256,6 +256,12 @@ int DumpLocal::modify_param(int narg, char **arg) void DumpLocal::write_header(bigint ndump) { if (me == 0) { + if (unit_flag && !unit_count) { + ++unit_count; + fprintf(fp,"ITEM: UNITS\n%s\n",update->unit_style); + } + if (time_flag) fprintf(fp,"ITEM: TIME\n%.16g\n",compute_time()); + fprintf(fp,"ITEM: TIMESTEP\n"); fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep); fprintf(fp,"ITEM: NUMBER OF %s\n",label); diff --git a/src/dump_local.h b/src/dump_local.h index 91381ba1ece389a5904dd412585318937032793f..9b150829958dc842e65865ef4b85a9cd478e12c5 100644 --- a/src/dump_local.h +++ b/src/dump_local.h @@ -29,7 +29,7 @@ class DumpLocal : public Dump { DumpLocal(LAMMPS *, int, char **); virtual ~DumpLocal(); - private: + protected: int nevery; // dump frequency to check Fix against char *label; // string for dump file header @@ -55,11 +55,11 @@ class DumpLocal : public Dump { void init_style(); int modify_param(int, char **); - void write_header(bigint); + virtual void write_header(bigint); int count(); void pack(tagint *); int convert_string(int, double *); - void write_data(int, double *); + virtual void write_data(int, double *); void parse_fields(int, char **); int add_compute(char *); diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index 45eb38f5c2625e8e3ade8238260eab5ccfd496bd..0ebdddb9df88a5adc4beb9806c95de73060f603d 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -1055,7 +1055,8 @@ void FixAveChunk::end_of_step() if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } } diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index f65b53efc8111dc05656d8090321d895414677df..0a8a4cd17fd3bed33346fb15a3d6b33578168e85 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -535,7 +535,8 @@ void FixAveCorrelate::end_of_step() if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 5a5de6d0b62068a40bf3273e15c2c55c6bef3af8..1a292bf8d259a8fa79c77e0960390e97e9b68b62 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -851,7 +851,8 @@ void FixAveHisto::end_of_step() fflush(fp); if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } } diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index f4ff0ae55fb193834a59afa8ef6b3c4e52a1da1d..4b86681153d0175d5d60184bc60a79d86acce661 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -493,7 +493,8 @@ void FixAveHistoWeight::end_of_step() fflush(fp); if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } } diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 05d556d0c81aae5c2433f67660a84b3d7c8e90f6..9b8dd13f05bf7dda84d63bb8cc7988952d41ae4f 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -698,7 +698,8 @@ void FixAveTime::invoke_scalar(bigint ntimestep) if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } } @@ -909,7 +910,8 @@ void FixAveTime::invoke_vector(bigint ntimestep) fflush(fp); if (overwrite) { long fileend = ftell(fp); - if (fileend > 0) ftruncate(fileno(fp),fileend); + if ((fileend > 0) && (ftruncate(fileno(fp),fileend))) + perror("Error while tuncating output"); } } } diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index a050e5a13a2d4d51c9a8f104e1117d6588833eca..f8f85fcf30d32c633d2666bd7bb72248a444fb88 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -14,6 +14,9 @@ /* ---------------------------------------------------------------------- Contributing authors: Carolyn Phillips (U Mich), reservoir energy tally Aidan Thompson (SNL) GJF formulation + Charles Sievers & Niels Gronbech-Jensen (UC Davis) + updated GJF formulation and included + statistically correct 2GJ velocity ------------------------------------------------------------------------- */ #include "fix_langevin.h" @@ -35,6 +38,7 @@ #include "memory.h" #include "error.h" #include "group.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -50,7 +54,7 @@ enum{CONSTANT,EQUAL,ATOM}; FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), gjfflag(0), gfactor1(NULL), gfactor2(NULL), ratio(NULL), tstr(NULL), - flangevin(NULL), tforce(NULL), franprev(NULL), id_temp(NULL), random(NULL) + flangevin(NULL), tforce(NULL), franprev(NULL), lv(NULL), id_temp(NULL), random(NULL) { if (narg < 7) error->all(FLERR,"Illegal fix langevin command"); @@ -92,9 +96,11 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0; ascale = 0.0; gjfflag = 0; + nvalues = 0; oflag = 0; tallyflag = 0; zeroflag = 0; + osflag = 0; int iarg = 7; while (iarg < narg) { @@ -105,8 +111,18 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else if (strcmp(arg[iarg],"gjf") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command"); - if (strcmp(arg[iarg+1],"no") == 0) gjfflag = 0; - else if (strcmp(arg[iarg+1],"yes") == 0) gjfflag = 1; + if (strcmp(arg[iarg+1],"no") == 0) { + gjfflag = 0; + osflag = 0; + } + else if (strcmp(arg[iarg+1],"vfull") == 0) { + gjfflag = 1; + osflag = 1; + } + else if (strcmp(arg[iarg+1],"vhalf") == 0) { + gjfflag = 1; + osflag = 0; + } else error->all(FLERR,"Illegal fix langevin command"); iarg += 2; } else if (strcmp(arg[iarg],"omega") == 0) { @@ -152,6 +168,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : flangevin = NULL; flangevin_allocated = 0; franprev = NULL; + lv = NULL; tforce = NULL; maxatom1 = maxatom2 = 0; @@ -160,7 +177,6 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : // no need to set peratom_flag, b/c data is for internal use only if (gjfflag) { - nvalues = 3; grow_arrays(atom->nmax); atom->add_callback(0); @@ -171,6 +187,9 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : franprev[i][0] = 0.0; franprev[i][1] = 0.0; franprev[i][2] = 0.0; + lv[i][0] = 0.0; + lv[i][1] = 0.0; + lv[i][2] = 0.0; } } @@ -191,6 +210,7 @@ FixLangevin::~FixLangevin() if (gjfflag) { memory->destroy(franprev); + memory->destroy(lv); atom->delete_callback(id,0); } } @@ -200,6 +220,7 @@ FixLangevin::~FixLangevin() int FixLangevin::setmask() { int mask = 0; + if (gjfflag) mask |= INITIAL_INTEGRATE; mask |= POST_FORCE; mask |= POST_FORCE_RESPA; mask |= END_OF_STEP; @@ -211,6 +232,21 @@ int FixLangevin::setmask() void FixLangevin::init() { + if (gjfflag) { + if (t_period*2 == update->dt) + error->all(FLERR,"Fix langevin gjf cannot have t_period equal to dt/2"); + + // warn if any integrate fix comes after this one + int before = 1; + int flag = 0; + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(id,modify->fix[i]->id) == 0) before = 0; + else if ((modify->fmask[i] && utils::strmatch(modify->fix[i]->style,"^nve")) && before) flag = 1; + } + if (flag) + error->all(FLERR,"Fix langevin gjf should come before fix nve"); + } + if (oflag && !atom->sphere_flag) error->all(FLERR,"Fix langevin omega requires atom style sphere"); if (ascale && !atom->ellipsoid_flag) @@ -260,9 +296,14 @@ void FixLangevin::init() if (!atom->rmass) { for (int i = 1; i <= atom->ntypes; i++) { gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v; - gfactor2[i] = sqrt(atom->mass[i]) * - sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / - force->ftm2v; + if (gjfflag) + gfactor2[i] = sqrt(atom->mass[i]) * + sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) / + force->ftm2v; + else + gfactor2[i] = sqrt(atom->mass[i]) * + sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / + force->ftm2v; gfactor1[i] *= 1.0/ratio[i]; gfactor2[i] *= 1.0/sqrt(ratio[i]); } @@ -274,14 +315,60 @@ void FixLangevin::init() if (strstr(update->integrate_style,"respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; - if (gjfflag) gjffac = 1.0/(1.0+update->dt/2.0/t_period); + if (utils::strmatch(update->integrate_style,"^respa") && gjfflag) + error->all(FLERR,"Fix langevin gjf and respa are not compatible"); + if (gjfflag) gjfa = (1.0-update->dt/2.0/t_period)/(1.0+update->dt/2.0/t_period); + if (gjfflag) gjfsib = sqrt(1.0+update->dt/2.0/t_period); } /* ---------------------------------------------------------------------- */ void FixLangevin::setup(int vflag) { + if (gjfflag) { + double dtfm; + double dt = update->dt; + double **v = atom->v; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / rmass[i]; + v[i][0] -= dtfm * f[i][0]; + v[i][1] -= dtfm * f[i][1]; + v[i][2] -= dtfm * f[i][2]; + if (tbiasflag) + temperature->remove_bias(i,v[i]); + v[i][0] /= gjfa*gjfsib*gjfsib; + v[i][1] /= gjfa*gjfsib*gjfsib; + v[i][2] /= gjfa*gjfsib*gjfsib; + if (tbiasflag) + temperature->restore_bias(i,v[i]); + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / mass[type[i]]; + v[i][0] -= dtfm * f[i][0]; + v[i][1] -= dtfm * f[i][1]; + v[i][2] -= dtfm * f[i][2]; + if (tbiasflag) + temperature->remove_bias(i,v[i]); + v[i][0] /= gjfa*gjfsib*gjfsib; + v[i][1] /= gjfa*gjfsib*gjfsib; + v[i][2] /= gjfa*gjfsib*gjfsib; + if (tbiasflag) + temperature->restore_bias(i,v[i]); + } + } + } if (strstr(update->integrate_style,"verlet")) post_force(vflag); else { @@ -289,6 +376,61 @@ void FixLangevin::setup(int vflag) post_force_respa(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); } + if (gjfflag) { + double dtfm; + double dt = update->dt; + double **f = atom->f; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + lv[i][0] = v[i][0]; + lv[i][1] = v[i][1]; + lv[i][2] = v[i][2]; + } +// + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + lv[i][0] = v[i][0]; + lv[i][1] = v[i][1]; + lv[i][2] = v[i][2]; + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevin::initial_integrate(int /* vflag */) +{ + double **v = atom->v; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + f[i][0] /= gjfa; + f[i][1] /= gjfa; + f[i][2] /= gjfa; + v[i][0] = lv[i][0]; + v[i][1] = lv[i][1]; + v[i][2] = lv[i][2]; + } } /* ---------------------------------------------------------------------- */ @@ -303,7 +445,7 @@ void FixLangevin::post_force(int /*vflag*/) if (tstyle == ATOM) if (gjfflag) - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass) if (zeroflag) post_force_templated<1,1,1,1,1,1>(); @@ -334,7 +476,7 @@ void FixLangevin::post_force(int /*vflag*/) if (zeroflag) post_force_templated<1,1,0,0,0,1>(); else post_force_templated<1,1,0,0,0,0>(); else - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass) if (zeroflag) post_force_templated<1,0,1,1,1,1>(); @@ -366,7 +508,7 @@ void FixLangevin::post_force(int /*vflag*/) else post_force_templated<1,0,0,0,0,0>(); else if (gjfflag) - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass) if (zeroflag) post_force_templated<0,1,1,1,1,1>(); @@ -397,7 +539,7 @@ void FixLangevin::post_force(int /*vflag*/) if (zeroflag) post_force_templated<0,1,0,0,0,1>(); else post_force_templated<0,1,0,0,0,0>(); else - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass) if (zeroflag) post_force_templated<0,0,1,1,1,1>(); @@ -510,7 +652,10 @@ void FixLangevin::post_force_templated() if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]); if (Tp_RMASS) { gamma1 = -rmass[i] / t_period / ftm2v; - gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v; + if (Tp_GJF) + gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v; + else + gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v; gamma1 *= 1.0/ratio[type[i]]; gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt; } else { @@ -518,9 +663,15 @@ void FixLangevin::post_force_templated() gamma2 = gfactor2[type[i]] * tsqrt; } - fran[0] = gamma2*(random->uniform()-0.5); - fran[1] = gamma2*(random->uniform()-0.5); - fran[2] = gamma2*(random->uniform()-0.5); + if (Tp_GJF) { + fran[0] = gamma2*random->gaussian(); + fran[1] = gamma2*random->gaussian(); + fran[2] = gamma2*random->gaussian(); + } else { + fran[0] = gamma2*(random->uniform()-0.5); + fran[1] = gamma2*(random->uniform()-0.5); + fran[2] = gamma2*(random->uniform()-0.5); + } if (Tp_BIAS) { temperature->remove_bias(i,v[i]); @@ -538,6 +689,16 @@ void FixLangevin::post_force_templated() } if (Tp_GJF) { + if (Tp_BIAS) + temperature->remove_bias(i,v[i]); + lv[i][0] = gjfsib*v[i][0]; + lv[i][1] = gjfsib*v[i][1]; + lv[i][2] = gjfsib*v[i][2]; + if (Tp_BIAS) + temperature->restore_bias(i,v[i]); + if (Tp_BIAS) + temperature->restore_bias(i,lv[i]); + fswap = 0.5*(fran[0]+franprev[i][0]); franprev[i][0] = fran[0]; fran[0] = fswap; @@ -548,31 +709,43 @@ void FixLangevin::post_force_templated() franprev[i][2] = fran[2]; fran[2] = fswap; - fdrag[0] *= gjffac; - fdrag[1] *= gjffac; - fdrag[2] *= gjffac; - fran[0] *= gjffac; - fran[1] *= gjffac; - fran[2] *= gjffac; - f[i][0] *= gjffac; - f[i][1] *= gjffac; - f[i][2] *= gjffac; + fdrag[0] *= gjfa; + fdrag[1] *= gjfa; + fdrag[2] *= gjfa; + fran[0] *= gjfa; + fran[1] *= gjfa; + fran[2] *= gjfa; + f[i][0] *= gjfa; + f[i][1] *= gjfa; + f[i][2] *= gjfa; } f[i][0] += fdrag[0] + fran[0]; f[i][1] += fdrag[1] + fran[1]; f[i][2] += fdrag[2] + fran[2]; + if (Tp_ZERO) { + fsum[0] += fran[0]; + fsum[1] += fran[1]; + fsum[2] += fran[2]; + } + if (Tp_TALLY) { + if (Tp_GJF) { + fdrag[0] = gamma1*lv[i][0]/gjfsib/gjfsib; + fdrag[1] = gamma1*lv[i][1]/gjfsib/gjfsib; + fdrag[2] = gamma1*lv[i][2]/gjfsib/gjfsib; + fswap = (2*fran[0]/gjfa - franprev[i][0])/gjfsib; + fran[0] = fswap; + fswap = (2*fran[1]/gjfa - franprev[i][1])/gjfsib; + fran[1] = fswap; + fswap = (2*fran[2]/gjfa - franprev[i][2])/gjfsib; + fran[2] = fswap; + } flangevin[i][0] = fdrag[0] + fran[0]; flangevin[i][1] = fdrag[1] + fran[1]; flangevin[i][2] = fdrag[2] + fran[2]; - } - if (Tp_ZERO) { - fsum[0] += fran[0]; - fsum[1] += fran[1]; - fsum[2] += fran[2]; } } } @@ -753,18 +926,71 @@ void FixLangevin::angmom_thermostat() void FixLangevin::end_of_step() { - if (!tallyflag) return; + if (!tallyflag && !gjfflag) return; double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; + double dtfm; + double dt = update->dt; + double *mass = atom->mass; + double *rmass = atom->rmass; + double **f = atom->f; + int *type = atom->type; energy_onestep = 0.0; - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] + - flangevin[i][2]*v[i][2]; + if (tallyflag) { + if (gjfflag) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (tbiasflag) + temperature->remove_bias(i, lv[i]); + energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] + + flangevin[i][2]*lv[i][2]; + if (tbiasflag) + temperature->restore_bias(i, lv[i]); + } + } + else + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] + + flangevin[i][2]*v[i][2]; + } + + if (gjfflag) { + double tmp[3]; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + tmp[0] = v[i][0]; + tmp[1] = v[i][1]; + tmp[2] = v[i][2]; + if (!osflag) { + v[i][0] = lv[i][0]; + v[i][1] = lv[i][1]; + v[i][2] = lv[i][2]; + } else { + if (atom->rmass) { + dtfm = force->ftm2v * 0.5 * dt / rmass[i]; + } else { + dtfm = force->ftm2v * 0.5 * dt / mass[type[i]]; + } + v[i][0] = 0.5 * gjfsib*gjfsib*(v[i][0] + dtfm * f[i][0] / gjfa) + + dtfm * 0.5 * (gjfsib * flangevin[i][0] - franprev[i][0]) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][0]; + v[i][1] = 0.5 * gjfsib*gjfsib*(v[i][1] + dtfm * f[i][1] / gjfa) + + dtfm * 0.5 * (gjfsib * flangevin[i][1] - franprev[i][1]) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][1]; + v[i][2] = 0.5 * gjfsib*gjfsib*(v[i][2] + dtfm * f[i][2] / gjfa) + + dtfm * 0.5 * (gjfsib * flangevin[i][2] - franprev[i][2]) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][2]; + } + lv[i][0] = tmp[0]; + lv[i][1] = tmp[1]; + lv[i][2] = tmp[2]; + } + } energy += energy_onestep*update->dt; } @@ -782,12 +1008,21 @@ void FixLangevin::reset_dt() { if (atom->mass) { for (int i = 1; i <= atom->ntypes; i++) { - gfactor2[i] = sqrt(atom->mass[i]) * - sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / - force->ftm2v; + if (gjfflag) + gfactor2[i] = sqrt(atom->mass[i]) * + sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) / + force->ftm2v; + else + gfactor2[i] = sqrt(atom->mass[i]) * + sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / + force->ftm2v; gfactor2[i] *= 1.0/sqrt(ratio[i]); } } + if (gjfflag) { + gjfa = (1.0-update->dt/2.0/t_period)/(1.0+update->dt/2.0/t_period); + gjfsib = sqrt(1.0+update->dt/2.0/t_period); + } } /* ---------------------------------------------------------------------- */ @@ -830,11 +1065,24 @@ double FixLangevin::compute_scalar() if (update->ntimestep == update->beginstep) { energy_onestep = 0.0; - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] + - flangevin[i][2]*v[i][2]; - energy = 0.5*energy_onestep*update->dt; + if (!gjfflag) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] + + flangevin[i][2]*v[i][2]; + energy = 0.5*energy_onestep*update->dt; + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (tbiasflag) + temperature->remove_bias(i, lv[i]); + energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] + + flangevin[i][2]*lv[i][2]; + if (tbiasflag) + temperature->restore_bias(i, lv[i]); + } + energy = -0.5*energy_onestep*update->dt; + } } // convert midstep energy back to previous fullstep energy @@ -866,8 +1114,8 @@ void *FixLangevin::extract(const char *str, int &dim) double FixLangevin::memory_usage() { double bytes = 0.0; - if (gjfflag) bytes += atom->nmax*3 * sizeof(double); - if (tallyflag) bytes += atom->nmax*3 * sizeof(double); + if (gjfflag) bytes += atom->nmax*6 * sizeof(double); + if (tallyflag || osflag) bytes += atom->nmax*3 * sizeof(double); if (tforce) bytes += atom->nmax * sizeof(double); return bytes; } @@ -879,6 +1127,7 @@ double FixLangevin::memory_usage() void FixLangevin::grow_arrays(int nmax) { memory->grow(franprev,nmax,3,"fix_langevin:franprev"); + memory->grow(lv,nmax,3,"fix_langevin:lv"); } /* ---------------------------------------------------------------------- @@ -887,8 +1136,12 @@ void FixLangevin::grow_arrays(int nmax) void FixLangevin::copy_arrays(int i, int j, int /*delflag*/) { - for (int m = 0; m < nvalues; m++) - franprev[j][m] = franprev[i][m]; + franprev[j][0] = franprev[i][0]; + franprev[j][1] = franprev[i][1]; + franprev[j][2] = franprev[i][2]; + lv[j][0] = lv[i][0]; + lv[j][1] = lv[i][1]; + lv[j][2] = lv[i][2]; } /* ---------------------------------------------------------------------- @@ -897,8 +1150,14 @@ void FixLangevin::copy_arrays(int i, int j, int /*delflag*/) int FixLangevin::pack_exchange(int i, double *buf) { - for (int m = 0; m < nvalues; m++) buf[m] = franprev[i][m]; - return nvalues; + int n = 0; + buf[n++] = franprev[i][0]; + buf[n++] = franprev[i][1]; + buf[n++] = franprev[i][2]; + buf[n++] = lv[i][0]; + buf[n++] = lv[i][1]; + buf[n++] = lv[i][2]; + return n; } /* ---------------------------------------------------------------------- @@ -907,6 +1166,12 @@ int FixLangevin::pack_exchange(int i, double *buf) int FixLangevin::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < nvalues; m++) franprev[nlocal][m] = buf[m]; - return nvalues; + int n = 0; + franprev[nlocal][0] = buf[n++]; + franprev[nlocal][1] = buf[n++]; + franprev[nlocal][2] = buf[n++]; + lv[nlocal][0] = buf[n++]; + lv[nlocal][1] = buf[n++]; + lv[nlocal][2] = buf[n++]; + return n; } diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 4b5570ac2ed18866a4a0726e111fbc59488a3e39..868b71a44d5d19176b5b226dc7b601651db3c692 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -31,6 +31,7 @@ class FixLangevin : public Fix { int setmask(); void init(); void setup(int); + virtual void initial_integrate(int); virtual void post_force(int); void post_force_respa(int, int, int); virtual void end_of_step(); @@ -46,7 +47,7 @@ class FixLangevin : public Fix { int unpack_exchange(int, double *); protected: - int gjfflag,oflag,tallyflag,zeroflag,tbiasflag; + int gjfflag,nvalues,osflag,oflag,tallyflag,zeroflag,tbiasflag; int flangevin_allocated; double ascale; double t_start,t_stop,t_period,t_target; @@ -54,7 +55,7 @@ class FixLangevin : public Fix { double energy,energy_onestep; double tsqrt; int tstyle,tvar; - double gjffac; + double gjfa, gjfsib; //gjf a and gjf sqrt inverse b char *tstr; class AtomVecEllipsoid *avec; @@ -63,7 +64,7 @@ class FixLangevin : public Fix { double **flangevin; double *tforce; double **franprev; - int nvalues; + double **lv; //half step velocity char *id_temp; class Compute *temperature; @@ -139,6 +140,18 @@ E: Fix_modify temperature ID does not compute temperature The compute ID assigned to the fix must compute temperature. +E: Fix langevin gjf cannot have period equal to dt/2 + +If the period is equal to dt/2 then division by zero will happen. + +E: Fix langevin gjf should come before fix nve + +Self-explanatory + +E: Fix langevin gjf and respa are not compatible + +Self-explanatory + W: Group for fix_modify temp != fix group The fix_modify command is specifying a temperature computation that diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp index df2dfb02a777dc22ed51786966a42364d2416c7b..93b13fac49aacd87efbad45301453c712272da89 100644 --- a/src/fix_minimize.cpp +++ b/src/fix_minimize.cpp @@ -42,8 +42,10 @@ FixMinimize::~FixMinimize() // delete locally stored data memory->destroy(peratom); - for (int m = 0; m < nvector; m++) memory->destroy(vectors[m]); - memory->sfree(vectors); + if (vectors) { + for (int m = 0; m < nvector; m++) memory->destroy(vectors[m]); + memory->sfree(vectors); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_minimize.h b/src/fix_minimize.h index 7b9f571628df1870959ad8f2489ed711d76df973..615eb6a0952dbf79762dc1a4d1b71b7720a2cc54 100644 --- a/src/fix_minimize.h +++ b/src/fix_minimize.h @@ -29,22 +29,22 @@ class FixMinimize : public Fix { public: FixMinimize(class LAMMPS *, int, char **); - ~FixMinimize(); + virtual ~FixMinimize(); int setmask(); - void init() {} + virtual void init() {} double memory_usage(); - void grow_arrays(int); - void copy_arrays(int, int, int); - int pack_exchange(int, double *); - int unpack_exchange(int, double *); + virtual void grow_arrays(int); + virtual void copy_arrays(int, int, int); + virtual int pack_exchange(int, double *); + virtual int unpack_exchange(int, double *); - void add_vector(int); + virtual void add_vector(int); double *request_vector(int); void store_box(); void reset_coords(); - private: + protected: int nvector; int *peratom; double **vectors; diff --git a/src/force.cpp b/src/force.cpp index 1a826b2843269d99647247e2ef97ef99c74ff853..cc121a5f801d1d6bf9ee951811bf206f642a3702 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -21,6 +21,7 @@ #include "style_improper.h" #include "style_pair.h" #include "style_kspace.h" +#include "atom.h" #include "comm.h" #include "pair.h" #include "pair_hybrid.h" @@ -196,6 +197,28 @@ void Force::init() if (angle) angle->init(); if (dihedral) dihedral->init(); if (improper) improper->init(); + + // print warnings if topology and force field are inconsistent + + if (comm->me == 0) { + if (!bond && (atom->nbonds > 0)) { + error->warning(FLERR,"Bonds are defined but no bond style is set"); + if ((special_lj[1] != 1.0) || (special_coul[1] != 1.0)) + error->warning(FLERR,"Likewise 1-2 special neighbor interactions != 1.0"); + } + if (!angle && (atom->nangles > 0)) { + error->warning(FLERR,"Angles are defined but no angle style is set"); + if ((special_lj[2] != 1.0) || (special_coul[2] != 1.0)) + error->warning(FLERR,"Likewise 1-3 special neighbor interactions != 1.0"); + } + if (!dihedral && (atom->ndihedrals > 0)) { + error->warning(FLERR,"Dihedrals are defined but no dihedral style is set"); + if ((special_lj[3] != 1.0) || (special_coul[3] != 1.0)) + error->warning(FLERR,"Likewise 1-4 special neighbor interactions != 1.0"); + } + if (!improper && (atom->nimpropers > 0)) + error->warning(FLERR,"Impropers are defined but no improper style is set"); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/force.h b/src/force.h index 26a3ecdfb837239077169b4ad43f7188be52ddbb..2dcbdbdd7570a124c2d953f484257cbff8c8f8a2 100644 --- a/src/force.h +++ b/src/force.h @@ -226,4 +226,48 @@ A command with an argument that specifies an integer or range of integers is using a value that is less than 1 or greater than the maximum allowed limit. +W: Bonds are defined but no bond style is set + +The topology contains bonds, but there are no bond forces computed +since there was no bond_style command. + +W: Angles are defined but no angle style is set + +The topology contains angles, but there are no angle forces computed +since there was no angle_style command. + +W: Dihedrals are defined but no dihedral style is set + +The topology contains dihedrals, but there are no dihedral forces computed +since there was no dihedral_style command. + +W: Impropers are defined but no improper style is set + +The topology contains impropers, but there are no improper forces computed +since there was no improper_style command. + +W: Likewise 1-2 special neighbor interactions != 1.0 + +The topology contains bonds, but there is no bond style defined +and a 1-2 special neighbor scaling factor was not 1.0. This +means that pair style interactions may have scaled or missing +pairs in the neighbor list in expectation of interactions for +those pairs being computed from the bond style. + +W: Likewise 1-3 special neighbor interactions != 1.0 + +The topology contains angles, but there is no angle style defined +and a 1-3 special neighbor scaling factor was not 1.0. This +means that pair style interactions may have scaled or missing +pairs in the neighbor list in expectation of interactions for +those pairs being computed from the angle style. + +W: Likewise 1-4 special neighbor interactions != 1.0 + +The topology contains dihedrals, but there is no dihedral style defined +and a 1-4 special neighbor scaling factor was not 1.0. This +means that pair style interactions may have scaled or missing +pairs in the neighbor list in expectation of interactions for +those pairs being computed from the dihedral style. + */ diff --git a/src/group.cpp b/src/group.cpp index d119964ea17d1df3cb0565213dced5deb1f2b1a0..93cd6681949a15d39f2280f27309df242607da8a 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -31,6 +31,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" +#include "utils.h" #include @@ -735,7 +736,7 @@ void Group::read_restart(FILE *fp) for (i = 0; i < MAX_GROUP; i++) delete [] names[i]; - if (me == 0) fread(&ngroup,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&ngroup,sizeof(int),1,fp,NULL,error); MPI_Bcast(&ngroup,1,MPI_INT,0,world); // use count to not change restart format with deleted groups @@ -747,11 +748,11 @@ void Group::read_restart(FILE *fp) names[i] = NULL; continue; } - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); if (n) { names[i] = new char[n]; - if (me == 0) fread(names[i],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,names[i],sizeof(char),n,fp,NULL,error); MPI_Bcast(names[i],n,MPI_CHAR,0,world); count++; } else names[i] = NULL; diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 730a75766c81e8884a13fd43315cf9a97fc387f0..fe524b838a0e5b03ed08536abae6c2c0308ee449 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -21,6 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -316,7 +317,7 @@ void ImproperHybrid::write_restart(FILE *fp) void ImproperHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) fread(&nstyles,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nstyles,1,MPI_INT,0,world); styles = new Improper*[nstyles]; keywords = new char*[nstyles]; @@ -325,10 +326,10 @@ void ImproperHybrid::read_restart(FILE *fp) int n,dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); keywords[m] = new char[n]; - if (me == 0) fread(keywords[m],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_improper(keywords[m],0,dummy); styles[m]->read_restart_settings(fp); diff --git a/src/info.cpp b/src/info.cpp index caa2d6fdd034bab61450ad79d7385b1b1a90f8c0..4b4c9a6a75648b4ae1511f44ac192a7e786de60d 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -281,6 +281,7 @@ void Info::command(int narg, char **arg) infobuf = get_compiler_info(); fprintf(out,"\nCompiler: %s with %s\n",infobuf,get_openmp_info()); delete[] infobuf; + fprintf(out,"C++ standard: %s\n",get_cxx_info()); fputs("\nActive compile time flags:\n\n",out); if (has_gzip_support()) fputs("-DLAMMPS_GZIP\n",out); @@ -1208,6 +1209,23 @@ const char *Info::get_openmp_info() #endif } +const char *Info::get_cxx_info() +{ +#if __cplusplus > 201703L + return (const char *)"newer than C++17"; +#elif __cplusplus == 201703L + return (const char *)"C++17"; +#elif __cplusplus == 201402L + return (const char *)"C++14"; +#elif __cplusplus == 201103L + return (const char *)"C++11"; +#elif __cplusplus == 199711L + return (const char *)"C++98"; +#else + return (const char *)"unknown"; +#endif +} + /* ---------------------------------------------------------------------- */ char **Info::get_variable_names(int &num) { diff --git a/src/info.h b/src/info.h index ff8f15676d5d543af229b51da45f88a6ba17bf22..8ac931aa6834d248d174950cac15a9c6d07054a8 100644 --- a/src/info.h +++ b/src/info.h @@ -43,6 +43,7 @@ class Info : protected Pointers { static char *get_os_info(); static char *get_compiler_info(); static const char *get_openmp_info(); + static const char *get_cxx_info(); char **get_variable_names(int &num); diff --git a/src/input.cpp b/src/input.cpp index 6871ee23f5396fcffe556b48a1fdbd108d0b8a17..6adf37e847d7b4cd15ddd2e6baea76fb25b0fb18 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1672,7 +1672,7 @@ void Input::min_style() { if (domain->box_exist == 0) error->all(FLERR,"Min_style command before simulation box is defined"); - update->create_minimize(narg,arg); + update->create_minimize(narg,arg,1); } /* ---------------------------------------------------------------------- */ diff --git a/src/kspace.h b/src/kspace.h index c04a0db989308d7894bac0acec59d9bf58763966..60df2345fd24043f4d6572a2e9f02d63ec2aae73 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -44,7 +44,7 @@ class KSpace : protected Pointers { int dispersionflag; // 1 if a LJ/dispersion solver int tip4pflag; // 1 if a TIP4P solver int dipoleflag; // 1 if a dipole solver - int spinflag; // 1 if a spin solver + int spinflag; // 1 if a spin solver int differentiation_flag; int neighrequest_flag; // used to avoid obsolete construction // of neighbor lists diff --git a/src/lammps.cpp b/src/lammps.cpp index 5ddc1600a4145f36ca6e953a643a85bfce59aedb..b3f420b03da780c9288816a590599079d2a31082 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -444,6 +444,19 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : if ((universe->me == 0) && !helpflag) { if (screen) fprintf(screen,"LAMMPS (%s)\n",universe->version); if (logfile) fprintf(logfile,"LAMMPS (%s)\n",universe->version); +#if defined(LAMMPS_CXX98) + const char warning[] = "\nWARNING-WARNING-WARNING-WARNING-WARNING\n" + "This LAMMPS executable was compiled using C++98 compatibility.\n" + "Please report the compiler info below at https://github.com/lammps/lammps/issues/1659\n"; + const char *infobuf = Info::get_compiler_info(); + if (screen) + fprintf(screen,"%s%s\nWARNING-WARNING-WARNING-WARNING-WARNING\n\n", + warning,infobuf); + if (logfile) + fprintf(logfile,"%s%s\nWARNING-WARNING-WARNING-WARNING-WARNING\n\n", + warning,infobuf); + delete[] infobuf; +#endif } // universe is one or more worlds, as setup by partition switch @@ -1263,8 +1276,9 @@ void LAMMPS::print_config(FILE *fp) delete[] infobuf; infobuf = Info::get_compiler_info(); - fprintf(fp,"Compiler: %s with %s\n\n",infobuf,Info::get_openmp_info()); + fprintf(fp,"Compiler: %s with %s\n",infobuf,Info::get_openmp_info()); delete[] infobuf; + fprintf(fp,"C++ standard: %s\n\n",Info::get_cxx_info()); fputs("Active compile time flags:\n\n",fp); if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp); diff --git a/src/library.h b/src/library.h index 59b68b9502a0b334e6a5ffe860ec4bef763f2a3c..5ff10faf6f6c8affa9be1c04350e98ca6c14b0cc 100644 --- a/src/library.h +++ b/src/library.h @@ -17,7 +17,7 @@ */ #include -#ifdef LAMMPS_BIGBIG +#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG) #include /* for int64_t */ #endif @@ -61,6 +61,9 @@ void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); #ifdef LAMMPS_BIGBIG typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **); void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); +#elif LAMMPS_SMALLBIG +typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **); +void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); #else typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **); void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*); diff --git a/src/lmptype.h b/src/lmptype.h index 65e46535fc489ccdd8ee6b48692b61c80e6d8895..c1902e7ebeea4dbdf69d9393a1f22b3f21c129a5 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -28,6 +28,13 @@ #ifndef LMP_LMPTYPE_H #define LMP_LMPTYPE_H +// C++11 check +#ifndef LAMMPS_CXX98 +#if __cplusplus <= 199711L + #error LAMMPS is planning to transition to C++11. To disable this error please use a C++11 compliant compiler, enable C++11 (or later) compliance, or define LAMMPS_CXX98 in your makefile +#endif +#endif + #ifndef __STDC_LIMIT_MACROS #define __STDC_LIMIT_MACROS #endif diff --git a/src/memory.cpp b/src/memory.cpp index a513dde6c2e82590226aec8e16cb3affdc0f5c58..4374882efec3ca08b66768c5d6a8108a9a58ffe4 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -20,6 +20,7 @@ #define LMP_USE_TBB_ALLOCATOR #include "tbb/scalable_allocator.h" #else +#include #include #endif #endif diff --git a/src/min.cpp b/src/min.cpp index 408954edb8d37c3ba1a5c3c8c2e7e84e5fd50221..5721d5ab3ea246c2b37ba088b4b00d0e95831a35 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -42,10 +42,12 @@ #include "output.h" #include "thermo.h" #include "timer.h" +#include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; +using namespace MathConst; /* ---------------------------------------------------------------------- */ @@ -54,6 +56,7 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp) dmax = 0.1; searchflag = 0; linestyle = 1; + normstyle = TWO; elist_global = elist_atom = NULL; vlist_global = vlist_atom = NULL; @@ -68,6 +71,8 @@ Min::Min(LAMMPS *lmp) : Pointers(lmp) requestor = NULL; external_force_clear = 0; + + kokkosable = 0; } /* ---------------------------------------------------------------------- */ @@ -93,6 +98,10 @@ Min::~Min() void Min::init() { + if (lmp->kokkos && !kokkosable) + error->all(FLERR,"Must use a Kokkos-enabled min style (e.g. min_style cg/kk) " + "with Kokkos minimize"); + // create fix needed for storing atom-based quantities // will delete it at end of run @@ -653,6 +662,15 @@ void Min::modify_params(int narg, char **arg) if (strcmp(arg[iarg+1],"backtrack") == 0) linestyle = 0; else if (strcmp(arg[iarg+1],"quadratic") == 0) linestyle = 1; else if (strcmp(arg[iarg+1],"forcezero") == 0) linestyle = 2; + else if (strcmp(arg[iarg+1],"spin_cubic") == 0) linestyle = 3; + else if (strcmp(arg[iarg+1],"spin_none") == 0) linestyle = 4; + else error->all(FLERR,"Illegal min_modify command"); + iarg += 2; + } else if (strcmp(arg[iarg],"norm") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal min_modify command"); + if (strcmp(arg[iarg+1],"two") == 0) normstyle = TWO; + else if (strcmp(arg[iarg+1],"max") == 0) normstyle = MAX; + else if (strcmp(arg[iarg+1],"inf") == 0) normstyle = INF; else error->all(FLERR,"Illegal min_modify command"); iarg += 2; } else { @@ -816,6 +834,139 @@ double Min::fnorm_inf() return norm_inf; } +/* ---------------------------------------------------------------------- + compute and return ||force||_max (inf norm per-vector) +------------------------------------------------------------------------- */ + +double Min::fnorm_max() +{ + int i,n; + double fdotf,*fatom; + + double local_norm_max = 0.0; + for (i = 0; i < nvec; i+=3) { + fdotf = fvec[i]*fvec[i]+fvec[i+1]*fvec[i+1]+fvec[i+2]*fvec[i+2]; + local_norm_max = MAX(fdotf,local_norm_max); + } + if (nextra_atom) { + for (int m = 0; m < nextra_atom; m++) { + fatom = fextra_atom[m]; + n = extra_nlen[m]; + for (i = 0; i < n; i+=3) { + fdotf = fatom[i]*fatom[i]+fatom[i+1]*fatom[i+1]+fatom[i+2]*fatom[i+2]; + local_norm_max = MAX(fdotf,local_norm_max); + } + } + } + + double norm_max = 0.0; + MPI_Allreduce(&local_norm_max,&norm_max,1,MPI_DOUBLE,MPI_MAX,world); + + if (nextra_global) { + for (i = 0; i < nextra_global; i+=3) { + fdotf = fextra[i]*fextra[i]; + norm_max = MAX(fdotf,norm_max); + } + } + return norm_max; +} + +/* ---------------------------------------------------------------------- + compute and return sum_i||mag. torque_i||_2 (in eV) +------------------------------------------------------------------------- */ + +double Min::total_torque() +{ + double fmsq,ftotsqone,ftotsqall; + int nlocal = atom->nlocal; + double hbar = force->hplanck/MY_2PI; + double tx,ty,tz; + double **sp = atom->sp; + double **fm = atom->fm; + + fmsq = ftotsqone = ftotsqall = 0.0; + for (int i = 0; i < nlocal; i++) { + tx = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]; + ty = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]; + tz = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]; + fmsq = tx*tx + ty*ty + tz*tz; + ftotsqone += fmsq; + } + + // summing all fmsqtot on this replica + + MPI_Allreduce(&ftotsqone,&ftotsqall,1,MPI_DOUBLE,MPI_SUM,world); + + // multiply it by hbar so that units are in eV + + return sqrt(ftotsqall) * hbar; +} + +/* ---------------------------------------------------------------------- + compute and return max_i ||mag. torque components|| (in eV) +------------------------------------------------------------------------- */ + +double Min::inf_torque() +{ + double fmaxsqone,fmaxsqall; + int nlocal = atom->nlocal; + double hbar = force->hplanck/MY_2PI; + double tx,ty,tz; + double **sp = atom->sp; + double **fm = atom->fm; + + fmaxsqone = fmaxsqall = 0.0; + for (int i = 0; i < nlocal; i++) { + tx = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]; + ty = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]; + tz = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]; + fmaxsqone = MAX(fmaxsqone,tx*tx); + fmaxsqone = MAX(fmaxsqone,ty*ty); + fmaxsqone = MAX(fmaxsqone,tz*tz); + } + + // finding max fm on this replica + + fmaxsqall = fmaxsqone; + MPI_Allreduce(&fmaxsqone,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,world); + + // multiply it by hbar so that units are in eV + + return sqrt(fmaxsqall) * hbar; +} + +/* ---------------------------------------------------------------------- + compute and return max_i ||mag. torque_i|| (in eV) +------------------------------------------------------------------------- */ + +double Min::max_torque() +{ + double fmsq,fmaxsqone,fmaxsqall; + int nlocal = atom->nlocal; + double hbar = force->hplanck/MY_2PI; + double tx,ty,tz; + double **sp = atom->sp; + double **fm = atom->fm; + + fmsq = fmaxsqone = fmaxsqall = 0.0; + for (int i = 0; i < nlocal; i++) { + tx = fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]; + ty = fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]; + tz = fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]; + fmsq = tx*tx + ty*ty + tz*tz; + fmaxsqone = MAX(fmaxsqone,fmsq); + } + + // finding max fm on this replica + + fmaxsqall = fmaxsqone; + MPI_Allreduce(&fmaxsqone,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,world); + + // multiply it by hbar so that units are in eV + + return sqrt(fmaxsqall) * hbar; +} + /* ---------------------------------------------------------------------- possible stop conditions ------------------------------------------------------------------------- */ diff --git a/src/min.h b/src/min.h index a63254231cde662e6f0ed2676308643e35815b6f..61f9ce0bda5b384e9e95b2883861662b68ddd594 100644 --- a/src/min.h +++ b/src/min.h @@ -31,9 +31,9 @@ class Min : protected Pointers { Min(class LAMMPS *); virtual ~Min(); virtual void init(); - void setup(int flag=1); - void setup_minimal(int); - void run(int); + virtual void setup(int flag=1); + virtual void setup_minimal(int); + virtual void run(int); void cleanup(); int request(class Pair *, int, double); virtual bigint memory_usage() {return 0;} @@ -41,6 +41,14 @@ class Min : protected Pointers { virtual int modify_param(int, char **) {return 0;} double fnorm_sqr(); double fnorm_inf(); + double fnorm_max(); + + enum{TWO,MAX,INF}; + + // methods for spin minimizers + double total_torque(); + double inf_torque(); + double max_torque(); virtual void init_style() {} virtual void setup_style() = 0; @@ -56,8 +64,11 @@ class Min : protected Pointers { int virial_style; // compute virial explicitly or implicitly int external_force_clear; // clear forces locally or externally - double dmax; // max dist to move any atom in one step - int linestyle; // 0 = backtrack, 1 = quadratic, 2 = forcezero + double dmax; // max dist to move any atom in one step + int linestyle; // 0 = backtrack, 1 = quadratic, 2 = forcezero + // 3 = spin_cubic, 4 = spin_none + + int normstyle; // TWO, MAX or INF flag for force norm evaluation int nelist_global,nelist_atom; // # of PE,virial computes to check int nvlist_global,nvlist_atom; @@ -97,13 +108,12 @@ class Min : protected Pointers { double *extra_max; // max allowed change per iter for atom's var class Pair **requestor; // Pair that stores/manipulates the variable - int neigh_every,neigh_delay,neigh_dist_check; // neighboring params + int kokkosable; // 1 if this min style supports Kokkos - double energy_force(int); - void force_clear(); + int neigh_every,neigh_delay,neigh_dist_check; // neighboring params - double compute_force_norm_sqr(); - double compute_force_norm_inf(); + virtual double energy_force(int); + virtual void force_clear(); void ev_setup(); void ev_set(bigint); diff --git a/src/min_cg.cpp b/src/min_cg.cpp index ff318d23da689109fd97cbe84e476a461ed93bfd..80dde25f51feb28fada737f806b262b3cf5329db 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -14,6 +14,7 @@ #include "min_cg.h" #include #include +#include "error.h" #include "update.h" #include "output.h" #include "timer.h" @@ -35,7 +36,7 @@ MinCG::MinCG(LAMMPS *lmp) : MinLineSearch(lmp) {} int MinCG::iterate(int maxiter) { int i,m,n,fail,ntimestep; - double beta,gg,dot[2],dotall[2]; + double beta,gg,dot[2],dotall[2],fmax; double *fatom,*gatom,*hatom; // nlimit = max # of CG iterations before restarting @@ -90,6 +91,7 @@ int MinCG::iterate(int maxiter) dot[0] += fvec[i]*fvec[i]; dot[1] += fvec[i]*g[i]; } + if (nextra_atom) for (m = 0; m < nextra_atom; m++) { fatom = fextra_atom[m]; @@ -98,6 +100,7 @@ int MinCG::iterate(int maxiter) for (i = 0; i < n; i++) { dot[0] += fatom[i]*fatom[i]; dot[1] += fatom[i]*gatom[i]; + fmax = MAX(fmax,fatom[i]*fatom[i]); } } MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world); @@ -107,7 +110,16 @@ int MinCG::iterate(int maxiter) dotall[1] += fextra[i]*gextra[i]; } - if (dotall[0] < update->ftol*update->ftol) return FTOL; + fmax = 0.0; + if (normstyle == MAX) { // max force norm + fmax = fnorm_max(); + if (fmax < update->ftol*update->ftol) return FTOL; + } else if (normstyle == INF) { // infinite force norm + fmax = fnorm_inf(); + if (fmax < update->ftol*update->ftol) return FTOL; + } else if (normstyle == TWO) { // Euclidean force 2-norm + if (dotall[0] < update->ftol*update->ftol) return FTOL; + } else error->all(FLERR,"Illegal min_modify command"); // update new search direction h from new f = -Grad(x) and old g // this is Polak-Ribieri formulation diff --git a/src/min_fire.cpp b/src/min_fire.cpp index b7f853afd27681ebfc368608a474bf40e2dff6e5..b4b0f14534cea9fab23028d4d925fa76bbcbd4b3 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -16,6 +16,7 @@ #include #include "universe.h" #include "atom.h" +#include "error.h" #include "force.h" #include "update.h" #include "output.h" @@ -250,7 +251,10 @@ int MinFire::iterate(int maxiter) // sync across replicas if running multi-replica minimization if (update->ftol > 0.0) { - fdotf = fnorm_sqr(); + if (normstyle == MAX) fdotf = fnorm_max(); // max force norm + else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm + else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + else error->all(FLERR,"Illegal min_modify command"); if (update->multireplica == 0) { if (fdotf < update->ftol*update->ftol) return FTOL; } else { diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index dcfed10fefae11b47e1bb2d143746d84ee9ad83e..63432aab63593c3c0499f65226d7ce787c4707c7 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -22,6 +22,7 @@ #include #include #include "atom.h" +#include "error.h" #include "fix_minimize.h" #include "modify.h" #include "output.h" @@ -112,6 +113,9 @@ void MinHFTN::init() { Min::init(); + if (normstyle == MAX) + error->all(FLERR,"Incorrect min_modify option"); + for (int i = 1; i < NUM_HFTN_ATOM_BASED_VECTORS; i++) { if (_daExtraGlobal[i] != NULL) delete [] _daExtraGlobal[i]; diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 04e72b046d15d258e089d69454f7967067f92873..5f3728153aa2307b01fd89121d2987be322a83cc 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -16,6 +16,7 @@ #include #include "universe.h" #include "atom.h" +#include "error.h" #include "force.h" #include "update.h" #include "output.h" @@ -215,7 +216,10 @@ int MinQuickMin::iterate(int maxiter) // sync across replicas if running multi-replica minimization if (update->ftol > 0.0) { - fdotf = fnorm_sqr(); + if (normstyle == MAX) fdotf = fnorm_max(); // max force norm + else if (normstyle == INF) fdotf = fnorm_inf(); // inf force norm + else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + else error->all(FLERR,"Illegal min_modify command"); if (update->multireplica == 0) { if (fdotf < update->ftol*update->ftol) return FTOL; } else { diff --git a/src/min_sd.cpp b/src/min_sd.cpp index e4e159003f46df61b794b4f7bbc8ee04c3f957ff..627a3b3cf3517139bcbad23397e8a243cf8913db 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -13,6 +13,7 @@ #include "min_sd.h" #include +#include "error.h" #include "update.h" #include "output.h" #include "timer.h" @@ -77,7 +78,10 @@ int MinSD::iterate(int maxiter) // force tolerance criterion - fdotf = fnorm_sqr(); + if (normstyle == MAX) fdotf = fnorm_max(); // max force norm + else if (normstyle == INF) fdotf = fnorm_inf(); // infinite force norm + else if (normstyle == TWO) fdotf = fnorm_sqr(); // Euclidean force 2-norm + else error->all(FLERR,"Illegal min_modify command"); if (fdotf < update->ftol*update->ftol) return FTOL; // set new search direction h to f = -Grad(x) diff --git a/src/minimize.cpp b/src/minimize.cpp index e1af92401941ebda6dac402ca54e715886137da7..94fdcd86810c12bad1c3df4b33daeb6367ec8d0c 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -52,9 +52,6 @@ void Minimize::command(int narg, char **arg) if (update->laststep < 0) error->all(FLERR,"Too many iterations"); - if (lmp->kokkos) - error->all(FLERR,"Cannot yet use minimize with Kokkos"); - lmp->init(); timer->init_timeout(); update->minimize->setup(); diff --git a/src/modify.cpp b/src/modify.cpp index 109571d531a5d86a60df8f97ec70289725aaa16c..101540f78655a91f177cb518ed7651ec81ba6b24 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -1029,7 +1029,7 @@ int Modify::find_fix_by_style(const char *style) { int ifix; for (ifix = 0; ifix < nfix; ifix++) - if (strcmp(style,fix[ifix]->style) == 0) break; + if (utils::strmatch(fix[ifix]->style,style)) break; if (ifix == nfix) return -1; return ifix; } @@ -1364,7 +1364,7 @@ int Modify::read_restart(FILE *fp) // nfix_restart_global = # of restart entries with global state info int me = comm->me; - if (me == 0) fread(&nfix_restart_global,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nfix_restart_global,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nfix_restart_global,1,MPI_INT,0,world); // allocate space for each entry @@ -1381,22 +1381,22 @@ int Modify::read_restart(FILE *fp) int n; for (int i = 0; i < nfix_restart_global; i++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); id_restart_global[i] = new char[n]; - if (me == 0) fread(id_restart_global[i],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,id_restart_global[i],sizeof(char),n,fp,NULL,error); MPI_Bcast(id_restart_global[i],n,MPI_CHAR,0,world); - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); style_restart_global[i] = new char[n]; - if (me == 0) fread(style_restart_global[i],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,style_restart_global[i],sizeof(char),n,fp,NULL,error); MPI_Bcast(style_restart_global[i],n,MPI_CHAR,0,world); - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); state_restart_global[i] = new char[n]; - if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,state_restart_global[i],sizeof(char),n,fp,NULL,error); MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world); used_restart_global[i] = 0; @@ -1406,7 +1406,7 @@ int Modify::read_restart(FILE *fp) int maxsize = 0; - if (me == 0) fread(&nfix_restart_peratom,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nfix_restart_peratom,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nfix_restart_peratom,1,MPI_INT,0,world); // allocate space for each entry @@ -1423,19 +1423,19 @@ int Modify::read_restart(FILE *fp) // set index = which set of extra data this fix represents for (int i = 0; i < nfix_restart_peratom; i++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); id_restart_peratom[i] = new char[n]; - if (me == 0) fread(id_restart_peratom[i],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,id_restart_peratom[i],sizeof(char),n,fp,NULL,error); MPI_Bcast(id_restart_peratom[i],n,MPI_CHAR,0,world); - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); style_restart_peratom[i] = new char[n]; - if (me == 0) fread(style_restart_peratom[i],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,style_restart_peratom[i],sizeof(char),n,fp,NULL,error); MPI_Bcast(style_restart_peratom[i],n,MPI_CHAR,0,world); - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); maxsize += n; diff --git a/src/neighbor.cpp b/src/neighbor.cpp index d38aed08c0dd1eb7e8712e0b0212e2f074a3b189..2c77a1325831ba0676601c35c79b979dc6750c63 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -1941,6 +1941,7 @@ int Neighbor::decide() conservative shrink procedure: compute distance each of 8 corners of box has moved since last reneighbor reduce skin distance by sum of 2 largest of the 8 values + if reduced skin distance is negative, set to zero new trigger = 1/2 of reduced skin distance for orthogonal box, only need 2 lo/hi corners for triclinic, need all 8 corners since deformations can displace all 8 @@ -1962,6 +1963,7 @@ int Neighbor::check_distance() delz = bboxhi[2] - boxhi_hold[2]; delta2 = sqrt(delx*delx + dely*dely + delz*delz); delta = 0.5 * (skin - (delta1+delta2)); + if (delta < 0.0) delta = 0.0; deltasq = delta*delta; } else { domain->box_corners(); @@ -1975,6 +1977,7 @@ int Neighbor::check_distance() else if (delta > delta2) delta2 = delta; } delta = 0.5 * (skin - (delta1+delta2)); + if (delta < 0.0) delta = 0.0; deltasq = delta*delta; } } else deltasq = triggersq; diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index b94436b696e750550333d7d8b1c79c85fe2fac7a..1f058b9bd5ff143b56a69754488ec4d6f2acb220 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -25,6 +25,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathSpecial; @@ -277,16 +278,16 @@ void PairBeck::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&AA[i][j],sizeof(double),1,fp); - fread(&BB[i][j],sizeof(double),1,fp); - fread(&aa[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&beta[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&AA[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&BB[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&aa[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&beta[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world); @@ -316,8 +317,8 @@ void PairBeck::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/pair_born.cpp b/src/pair_born.cpp index bd993acb569b5e3a5d93266ff6e0ccfd1b199d72..b0aba57df5e2e9d33fa0bda70005da91d8b27e0e 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -329,16 +330,16 @@ void PairBorn::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&d[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -369,10 +370,10 @@ void PairBorn::write_restart_settings(FILE *fp) void PairBorn::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index f7e139c750e5455038a21d7a38248a00bd33bb12..3e8c76696bbf880273d23a4f62054555545da7b0 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -28,6 +28,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -360,16 +361,16 @@ void PairBornCoulDSF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&d[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -401,11 +402,11 @@ void PairBornCoulDSF::write_restart_settings(FILE *fp) void PairBornCoulDSF::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&alpha,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&alpha,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index f4d533bdb029b806229cd10ec9b2e968c68ed281..dc4e4b8e3ffbaef87abf8de3c5774928804ffde5 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -359,16 +360,16 @@ void PairBornCoulWolf::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&d[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&d[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -400,11 +401,11 @@ void PairBornCoulWolf::write_restart_settings(FILE *fp) void PairBornCoulWolf::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&alf,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&alf,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&alf,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index a94ce87891c5c4d95f42259a6fd489460351e344..4a7740e0344dbaf57da176a1c795e7b1201b3efa 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -307,14 +308,14 @@ void PairBuck::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -343,10 +344,10 @@ void PairBuck::write_restart_settings(FILE *fp) void PairBuck::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index d05c139f7188e6b3907d26c88b2f5d7e0331bdaf..d74945aa57e767ab811845adc30152bf22b8cea9 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -363,15 +364,15 @@ void PairBuckCoulCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&rho[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&rho[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); @@ -402,11 +403,11 @@ void PairBuckCoulCut::write_restart_settings(FILE *fp) void PairBuckCoulCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 9e6f238ebaf5c4cae72ea47d6755c160f666682b..ebb3d8ca0dcf84da6fcb42bb318b77bb4c1a178b 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -22,6 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -244,10 +245,10 @@ void PairCoulCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) fread(&cut[i][j],sizeof(double),1,fp); + if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } } @@ -271,9 +272,9 @@ void PairCoulCut::write_restart_settings(FILE *fp) void PairCoulCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 1b87a9370118cf26a38174261589ac3cc40b5364..b45353837a3592e4a53841f269b3fedc0ff41078 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -19,6 +19,7 @@ #include "force.h" #include "neigh_list.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -145,10 +146,10 @@ void PairCoulDebye::write_restart_settings(FILE *fp) void PairCoulDebye::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&kappa,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&kappa,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world); diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 22230182b05e144af209015402b348e2ebb47f7b..0a248e3084b92286152801dd3a3b1c508f2876ba 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -28,6 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -252,7 +253,7 @@ void PairCoulDSF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); } } @@ -276,10 +277,10 @@ void PairCoulDSF::write_restart_settings(FILE *fp) void PairCoulDSF::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&alpha,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&alpha,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 15c7839fc6981bd8238ebe85248ca267bdc9048c..9c48137270f014473d32f1754be30e5463e6f9e1 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -248,7 +249,7 @@ void PairCoulWolf::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); } } @@ -272,10 +273,10 @@ void PairCoulWolf::write_restart_settings(FILE *fp) void PairCoulWolf::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&alf,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&alf,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&alf,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index ec65eaafd6ba35a659ed95b17f588baf359e094f..ef0b7dd21d708987dd14eaf732feef6f9ad99616 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -27,6 +27,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -313,13 +314,13 @@ void PairDPD::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a0[i][j],sizeof(double),1,fp); - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); @@ -347,10 +348,10 @@ void PairDPD::write_restart_settings(FILE *fp) void PairDPD::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&temperature,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&temperature,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 15d7c90b277148f02d861f574034649b8b33d4b7..8366ff459fa8f9ab473841a682d4d237af00890b 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -21,6 +21,7 @@ #include "comm.h" #include "random_mars.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -231,12 +232,12 @@ void PairDPDTstat::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&gamma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -264,11 +265,11 @@ void PairDPDTstat::write_restart_settings(FILE *fp) void PairDPDTstat::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&t_start,sizeof(double),1,fp); - fread(&t_stop,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&seed,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&t_start,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&t_stop,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&seed,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&t_start,1,MPI_DOUBLE,0,world); MPI_Bcast(&t_stop,1,MPI_DOUBLE,0,world); diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index 7fd3233f4c4b0ddbee64f1d89de4ee64c17392cb..dcc3ac5f514a7b9e18d41342ee48120b92656639 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -25,6 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -279,13 +280,13 @@ void PairGauss::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&b[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&b[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&b[i][j],1,MPI_DOUBLE,0,world); @@ -312,9 +313,9 @@ void PairGauss::write_restart_settings(FILE *fp) void PairGauss::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 762b9fe8fc6ab2aa646a99fa70969209fde568b3..b853ef1db136a757e44f34561c44a853b034fa64 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -26,6 +26,7 @@ #include "memory.h" #include "error.h" #include "respa.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -362,13 +363,21 @@ void PairHybrid::flags() if (styles[m]->tip4pflag) tip4pflag = 1; if (styles[m]->compute_flag) compute_flag = 1; } + init_svector(); +} - // single_extra = min of all sub-style single_extra +/* ---------------------------------------------------------------------- + initialize Pair::svector array +------------------------------------------------------------------------- */ + +void PairHybrid::init_svector() +{ + // single_extra = list all sub-style single_extra // allocate svector - single_extra = styles[0]->single_extra; - for (m = 1; m < nstyles; m++) - single_extra = MIN(single_extra,styles[m]->single_extra); + single_extra = 0; + for (int m = 0; m < nstyles; m++) + single_extra = MAX(single_extra,styles[m]->single_extra); if (single_extra) { delete [] svector; @@ -673,7 +682,7 @@ void PairHybrid::write_restart(FILE *fp) void PairHybrid::read_restart(FILE *fp) { int me = comm->me; - if (me == 0) fread(&nstyles,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&nstyles,sizeof(int),1,fp,NULL,error); MPI_Bcast(&nstyles,1,MPI_INT,0,world); // allocate list of sub-styles @@ -696,32 +705,32 @@ void PairHybrid::read_restart(FILE *fp) // each sub-style is created via new_pair() // each reads its settings, but no coeff info - if (me == 0) fread(compute_tally,sizeof(int),nstyles,fp); + if (me == 0) utils::sfread(FLERR,compute_tally,sizeof(int),nstyles,fp,NULL,error); MPI_Bcast(compute_tally,nstyles,MPI_INT,0,world); int n,dummy; for (int m = 0; m < nstyles; m++) { - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); keywords[m] = new char[n]; - if (me == 0) fread(keywords[m],sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,keywords[m],sizeof(char),n,fp,NULL,error); MPI_Bcast(keywords[m],n,MPI_CHAR,0,world); styles[m] = force->new_pair(keywords[m],0,dummy); styles[m]->read_restart_settings(fp); // read back per style special settings, if present special_lj[m] = special_coul[m] = NULL; - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); if (n > 0 ) { special_lj[m] = new double[4]; - if (me == 0) fread(special_lj[m],sizeof(double),4,fp); + if (me == 0) utils::sfread(FLERR,special_lj[m],sizeof(double),4,fp,NULL,error); MPI_Bcast(special_lj[m],4,MPI_DOUBLE,0,world); } - if (me == 0) fread(&n,sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); MPI_Bcast(&n,1,MPI_INT,0,world); if (n > 0 ) { special_coul[m] = new double[4]; - if (me == 0) fread(special_coul[m],sizeof(double),4,fp); + if (me == 0) utils::sfread(FLERR,special_coul[m],sizeof(double),4,fp,NULL,error); MPI_Bcast(special_coul[m],4,MPI_DOUBLE,0,world); } } @@ -772,18 +781,29 @@ double PairHybrid::single(int i, int j, int itype, int jtype, esum += styles[map[itype][jtype][m]]-> single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone); fforce += fone; - - // copy substyle extra values into hybrid's svector - - if (single_extra && styles[map[itype][jtype][m]]->single_extra) - for (m = 0; m < single_extra; m++) - svector[m] = styles[map[itype][jtype][m]]->svector[m]; } } + if (single_extra) copy_svector(itype,jtype); return esum; } +/* ---------------------------------------------------------------------- + copy Pair::svector data +------------------------------------------------------------------------- */ + +void PairHybrid::copy_svector(int itype, int jtype) +{ + memset(svector,0,single_extra*sizeof(double)); + + // there is only one style in pair style hybrid for a pair of atom types + Pair *this_style = styles[map[itype][jtype][0]]; + + for (int l = 0; this_style->single_extra; ++l) { + svector[l] = this_style->svector[l]; + } +} + /* ---------------------------------------------------------------------- modify parameters of the pair style and its sub-styles ------------------------------------------------------------------------- */ diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 074517a85902bc18304ca7baa93477ce385fcca7..61e961ddcb1730c194d44f05847edb8ac88de360 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -77,6 +77,9 @@ class PairHybrid : public Pair { void allocate(); void flags(); + virtual void init_svector(); + virtual void copy_svector(int,int); + void modify_special(int, int, char**); double *save_special(); void set_special(int); diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index e67cb677afbfbe7f39d07d03ad708722060823d9..4c2acfe8ba4bb6ac9ede7cbf805da04da3e1b488 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -102,3 +102,52 @@ void PairHybridOverlay::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } + + +/* ---------------------------------------------------------------------- + we need to handle Pair::svector special for hybrid/overlay +------------------------------------------------------------------------- */ + +void PairHybridOverlay::init_svector() +{ + // single_extra = list all sub-style single_extra + // allocate svector + + single_extra = 0; + for (int m = 0; m < nstyles; m++) + single_extra += styles[m]->single_extra; + + if (single_extra) { + delete [] svector; + svector = new double[single_extra]; + } +} + +/* ---------------------------------------------------------------------- + we need to handle Pair::svector special for hybrid/overlay +------------------------------------------------------------------------- */ + +void PairHybridOverlay::copy_svector(int itype, int jtype) +{ + int n=0; + Pair *this_style; + + // fill svector array. + // copy data from active styles and use 0.0 for inactive ones + for (int m = 0; m < nstyles; m++) { + for (int k = 0; k < nmap[itype][jtype]; ++k) { + if (m == map[itype][jtype][k]) { + this_style = styles[m]; + } else { + this_style = NULL; + } + } + for (int l = 0; l < styles[m]->single_extra; ++l) { + if (this_style) { + svector[n++] = this_style->svector[l]; + } else { + svector[n++] = 0.0; + } + } + } +} diff --git a/src/pair_hybrid_overlay.h b/src/pair_hybrid_overlay.h index 934be05365d53da75e91470ebe7a12309bee385d..f1514ea079894c61f5ecb23e6b96421a185d3ce6 100644 --- a/src/pair_hybrid_overlay.h +++ b/src/pair_hybrid_overlay.h @@ -29,6 +29,9 @@ class PairHybridOverlay : public PairHybrid { PairHybridOverlay(class LAMMPS *); virtual ~PairHybridOverlay() {} void coeff(int, char **); + + void init_svector(); + void copy_svector(int,int); }; } diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index c27038900d0ae6a0024a012b330f90d14268f57f..f5548729650efeef3bf52924a8b4205e23a71362 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -30,6 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -605,13 +606,13 @@ void PairLJ96Cut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -640,10 +641,10 @@ void PairLJ96Cut::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 79909524945ad9a724ec9b66b69f8f05f1c0d878..98f221b689b2088e8e4b2b97ea4dd6acc4122e23 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -25,6 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace PairLJCubicConstants; @@ -276,14 +277,14 @@ void PairLJCubic::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -310,7 +311,7 @@ void PairLJCubic::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 0302858adbe3e26f61e905e95c94acf71ff6eeec..8765ba4313219db156add6b9caf4d52aa5af06a5 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -30,6 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -599,13 +600,13 @@ void PairLJCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -634,10 +635,10 @@ void PairLJCut::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index d4640bee3a009b299b771ea7897f66f51647d055..621148dc9b6a336d1cf2d85b032e6266e1c351c1 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -23,6 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -352,14 +353,14 @@ void PairLJCutCoulCut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -389,11 +390,11 @@ void PairLJCutCoulCut::write_restart_settings(FILE *fp) void PairLJCutCoulCut::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index 4ef533a7432157451206c3cd3b075b251d726477..a65d7aa50f3b909b24f0fc308d8b42482fd124f5 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -19,6 +19,7 @@ #include "force.h" #include "comm.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -170,11 +171,11 @@ void PairLJCutCoulDebye::write_restart_settings(FILE *fp) void PairLJCutCoulDebye::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_global,sizeof(double),1,fp); - fread(&kappa,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&kappa,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index 778f9f2fb4cf5e6de17dc2227f94357ff8a9a2d0..3b78b8ad1ddc6d3d3ae95ac372d32436234486e7 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -28,6 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -375,13 +376,13 @@ void PairLJCutCoulDSF::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -411,12 +412,12 @@ void PairLJCutCoulDSF::write_restart_settings(FILE *fp) void PairLJCutCoulDSF::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&alpha,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&alpha,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&alpha,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index 00a58325292ca620f3769f8381a9d21071a1cde5..b4eaa070a7d26d4246e29e66a8ebccc531614360 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -26,6 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -367,13 +368,13 @@ void PairLJCutCoulWolf::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -404,12 +405,12 @@ void PairLJCutCoulWolf::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&alf,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&alf,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&alf,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index a5184bc2f5f049a81ce6f5dbd65c376842c48695..16c8d586a25d354a92c99a353d24add7e6f91b16 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -323,14 +324,14 @@ void PairLJExpand::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&shift[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&shift[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -359,10 +360,10 @@ void PairLJExpand::write_restart_settings(FILE *fp) void PairLJExpand::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index baef482ef9262abdc6ab42c038266bf0199da2f3..73f4307d62af148bbba6adae2d911ddce69f1e55 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -24,6 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -338,14 +339,14 @@ void PairLJGromacs::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -375,10 +376,10 @@ void PairLJGromacs::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index c62944b6a11feecfdec84880e62f9441b9b48425..53b62bfdbdd1f956a92f7d07152cdcc8ac7de787 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -25,6 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -377,12 +378,12 @@ void PairLJGromacsCoulGromacs::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -411,12 +412,12 @@ void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp) void PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_lj_inner,sizeof(double),1,fp); - fread(&cut_lj,sizeof(double),1,fp); - fread(&cut_coul_inner,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul_inner,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 7c7eb51b5349f727d85460307fcf13ea3d329f3c..8c906dee466bb4b94f67cd63efb0119461aa5b99 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -24,6 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -351,14 +352,14 @@ void PairLJSmooth::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -388,10 +389,10 @@ void PairLJSmooth::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index bc2904c26277e6c8c8327edcd690bdc4682fa66b..16d5e96c12c0f973ce36a56b1d2a92bb9a2af62b 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -24,6 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -284,13 +285,13 @@ void PairLJSmoothLinear::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -317,8 +318,8 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index 46657687f67d4a7bbe287bd2b12e74d3fa6eb446..4ce82381f3aabf769c01c866e2cfa371a2d9df42 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -30,6 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -626,15 +627,15 @@ void PairMIECut::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&gamR[i][j],sizeof(double),1,fp); - fread(&gamA[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamR[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&gamA[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -665,10 +666,10 @@ void PairMIECut::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index d088f98bf42221f21fbadc0f71afbdfada398f90..86f0e34bf8f832a0f77adf50c7d280d77c07facb 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -21,6 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -264,14 +265,14 @@ void PairMorse::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&d0[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&d0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); @@ -299,9 +300,9 @@ void PairMorse::write_restart_settings(FILE *fp) void PairMorse::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 6f821e684bc6d219a49af05281b3d64b75bcd444..ddfc4476dc49291d48c877c4c920b38ca16dcc35 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -22,6 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -244,12 +245,12 @@ void PairSoft::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&prefactor[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -274,8 +275,8 @@ void PairSoft::write_restart_settings(FILE *fp) void PairSoft::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&mix_flag,1,MPI_INT,0,world); diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 9fcbc3ee9f7549ecc46cac21e1fd76c05e2a46cf..9cb86b4123e1c4fd224404c4160fb58b33e1373d 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -976,13 +976,13 @@ void PairTable::write_restart_settings(FILE *fp) void PairTable::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&tabstyle,sizeof(int),1,fp); - fread(&tablength,sizeof(int),1,fp); - fread(&ewaldflag,sizeof(int),1,fp); - fread(&pppmflag,sizeof(int),1,fp); - fread(&msmflag,sizeof(int),1,fp); - fread(&dispersionflag,sizeof(int),1,fp); - fread(&tip4pflag,sizeof(int),1,fp); + utils::sfread(FLERR,&tabstyle,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tablength,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&ewaldflag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&pppmflag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&msmflag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&dispersionflag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&tip4pflag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index 8cc4d2796f267261e3643103935af7b3188a95bc..ba3ad9ee504453d507c0a87a175f1b2a2643ba30 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -27,6 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -278,13 +279,13 @@ void PairUFM::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); @@ -312,9 +313,9 @@ void PairUFM::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&offset_flag,1,MPI_INT,0,world); diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index e8775c96688f0d9dde43e27fc4f8893987b139b0..d1e06fdb8484822e2571e3baa136224c0c305c80 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -20,6 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -252,12 +253,12 @@ void PairYukawa::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&a[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); @@ -284,10 +285,10 @@ void PairYukawa::write_restart_settings(FILE *fp) void PairYukawa::read_restart_settings(FILE *fp) { if (comm->me == 0) { - fread(&kappa,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&kappa,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index 403bd73944c42b73cea6cddbeac249ac870457dc..6ab108ff4f8e5d26a1dad8ec2ae8fe55f356d777 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -23,6 +23,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -31,6 +32,8 @@ using namespace LAMMPS_NS; PairZero::PairZero(LAMMPS *lmp) : Pair(lmp) { coeffflag=1; writedata=1; + single_enable=1; + respa_enable=1; } /* ---------------------------------------------------------------------- */ @@ -49,10 +52,16 @@ PairZero::~PairZero() void PairZero::compute(int eflag, int vflag) { ev_init(eflag,vflag); - if (vflag_fdotr) virial_fdotr_compute(); } +/* ---------------------------------------------------------------------- */ + +void PairZero::compute_outer(int eflag, int vflag) +{ + ev_init(eflag,vflag); +} + /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ @@ -170,11 +179,11 @@ void PairZero::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } @@ -199,8 +208,8 @@ void PairZero::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&coeffflag,sizeof(int),1,fp); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error); + utils::sfread(FLERR,&coeffflag,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&coeffflag,1,MPI_INT,0,world); @@ -227,4 +236,13 @@ void PairZero::write_data_all(FILE *fp) fprintf(fp,"%d %d %g\n",i,j,cut[i][j]); } +/* ---------------------------------------------------------------------- */ + +double PairZero::single(int /*i*/, int /*j*/, int /* itype */, int /* jtype */, + double /* rsq */, double /*factor_coul*/, + double /* factor_lj */, double &fforce) +{ + fforce = 0.0; + return 0.0; +} diff --git a/src/pair_zero.h b/src/pair_zero.h index b980ed89d1acc021ce234823862340d04ee62984..058edbd05308fa42ee663a63e3f14b3f8f91e3b7 100644 --- a/src/pair_zero.h +++ b/src/pair_zero.h @@ -39,6 +39,7 @@ class PairZero : public Pair { PairZero(class LAMMPS *); virtual ~PairZero(); virtual void compute(int, int); + virtual void compute_outer(int, int); void settings(int, char **); void coeff(int, char **); double init_one(int, int); @@ -48,6 +49,7 @@ class PairZero : public Pair { void read_restart_settings(FILE *); void write_data(FILE *); void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); protected: double cut_global; diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 3d2e2b6592d4921ce7f69d062b1e9a32278c453d..a31700990d532a888d1d067e0bdfbf878d9cdcd3 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -35,6 +35,7 @@ #include "mpiio.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -302,24 +303,24 @@ void ReadRestart::command(int narg, char **arg) error->one(FLERR,str); } - fread(&flag,sizeof(int),1,fp); + utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error); if (flag != PROCSPERFILE) error->one(FLERR,"Invalid flag in peratom section of restart file"); int procsperfile; - fread(&procsperfile,sizeof(int),1,fp); + utils::sfread(FLERR,&procsperfile,sizeof(int),1,fp,NULL,error); for (int i = 0; i < procsperfile; i++) { - fread(&flag,sizeof(int),1,fp); + utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error); if (flag != PERPROC) error->one(FLERR,"Invalid flag in peratom section of restart file"); - fread(&n,sizeof(int),1,fp); + utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); if (n > maxbuf) { maxbuf = n; memory->destroy(buf); memory->create(buf,maxbuf,"read_restart:buf"); } - fread(buf,sizeof(double),n,fp); + utils::sfread(FLERR,buf,sizeof(double),n,fp,NULL,error); m = 0; while (m < n) m += avec->unpack_restart(&buf[m]); @@ -379,10 +380,10 @@ void ReadRestart::command(int narg, char **arg) int flag,procsperfile; if (filereader) { - fread(&flag,sizeof(int),1,fp); + utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error); if (flag != PROCSPERFILE) error->one(FLERR,"Invalid flag in peratom section of restart file"); - fread(&procsperfile,sizeof(int),1,fp); + utils::sfread(FLERR,&procsperfile,sizeof(int),1,fp,NULL,error); } MPI_Bcast(&procsperfile,1,MPI_INT,0,clustercomm); @@ -391,17 +392,17 @@ void ReadRestart::command(int narg, char **arg) for (int i = 0; i < procsperfile; i++) { if (filereader) { - fread(&flag,sizeof(int),1,fp); + utils::sfread(FLERR,&flag,sizeof(int),1,fp,NULL,error); if (flag != PERPROC) error->one(FLERR,"Invalid flag in peratom section of restart file"); - fread(&n,sizeof(int),1,fp); + utils::sfread(FLERR,&n,sizeof(int),1,fp,NULL,error); if (n > maxbuf) { maxbuf = n; memory->destroy(buf); memory->create(buf,maxbuf,"read_restart:buf"); } - fread(buf,sizeof(double),n,fp); + utils::sfread(FLERR,buf,sizeof(double),n,fp,NULL,error); if (i % nclusterprocs) { iproc = me + (i % nclusterprocs); @@ -734,8 +735,12 @@ void ReadRestart::header(int incompatible) } else if (flag == NPROCS) { nprocs_file = read_int(); - if (nprocs_file != comm->nprocs && me == 0) - error->warning(FLERR,"Restart file used different # of processors"); + if (nprocs_file != comm->nprocs && me == 0) { + char msg[128]; + snprintf(msg,128,"Restart file used different # of processors: %d vs. %d", + nprocs_file,comm->nprocs); + error->warning(FLERR,msg); + } // don't set procgrid, warn if different @@ -1101,7 +1106,7 @@ void ReadRestart::file_layout() memory->create(nproc_chunk_number,nprocs, "write_restart:nproc_chunk_number"); - fread(all_written_send_sizes,sizeof(int),nprocs_file,fp); + utils::sfread(FLERR,all_written_send_sizes,sizeof(int),nprocs_file,fp,NULL,error); if ((nprocs != nprocs_file) && !(atom->nextra_store)) { // nprocs differ, but atom sizes are fixed length, yeah! @@ -1283,7 +1288,7 @@ char *ReadRestart::read_string() int n = read_int(); if (n < 0) error->all(FLERR,"Illegal size string or corrupt restart"); char *value = new char[n]; - if (me == 0) fread(value,sizeof(char),n,fp); + if (me == 0) utils::sfread(FLERR,value,sizeof(char),n,fp,NULL,error); MPI_Bcast(value,n,MPI_CHAR,0,world); return value; } @@ -1295,7 +1300,7 @@ char *ReadRestart::read_string() void ReadRestart::read_int_vec(int n, int *vec) { if (n < 0) error->all(FLERR,"Illegal size integer vector read requested"); - if (me == 0) fread(vec,sizeof(int),n,fp); + if (me == 0) utils::sfread(FLERR,vec,sizeof(int),n,fp,NULL,error); MPI_Bcast(vec,n,MPI_INT,0,world); } @@ -1306,6 +1311,6 @@ void ReadRestart::read_int_vec(int n, int *vec) void ReadRestart::read_double_vec(int n, double *vec) { if (n < 0) error->all(FLERR,"Illegal size double vector read requested"); - if (me == 0) fread(vec,sizeof(double),n,fp); + if (me == 0) utils::sfread(FLERR,vec,sizeof(double),n,fp,NULL,error); MPI_Bcast(vec,n,MPI_DOUBLE,0,world); } diff --git a/src/reader_native.cpp b/src/reader_native.cpp index fba613bdd36b90e743be431a3cdae2f116090cb1..a4b188be5f82dddc9bd32a34dba183be2b23ea52 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -56,12 +56,19 @@ int ReaderNative::read_time(bigint &ntimestep) char *eof = fgets(line,MAXLINE,fp); if (eof == NULL) return 1; + // skip over unit information, if present. + + if (strstr(line,"ITEM: UNITS") == line) + read_lines(2); + if (strstr(line,"ITEM: TIMESTEP") != line) error->one(FLERR,"Dump file is incorrectly formatted"); + read_lines(1); int rv = sscanf(line,BIGINT_FORMAT,&ntimestep); if (rv != 1) error->one(FLERR,"Dump file is incorrectly formatted"); + return 0; } diff --git a/src/update.cpp b/src/update.cpp index 8a3e6f0d1df9104294df68610e2d9f8b57b477ad..c82e2bcf96d6f642e924edf3720123ad301a1b51 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -78,7 +78,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) create_integrate(1,&str,1); str = (char *) "cg"; - create_minimize(1,&str); + create_minimize(1,&str,1); } /* ---------------------------------------------------------------------- */ @@ -376,22 +376,69 @@ Integrate *Update::integrate_creator(LAMMPS *lmp, int narg, char ** arg) /* ---------------------------------------------------------------------- */ -void Update::create_minimize(int narg, char **arg) +void Update::create_minimize(int narg, char **arg, int trysuffix) { - if (narg != 1) error->all(FLERR,"Illegal min_style command"); + if (narg < 1) error->all(FLERR,"Illegal run_style command"); delete [] minimize_style; delete minimize; - if (minimize_map->find(arg[0]) != minimize_map->end()) { - MinimizeCreator minimize_creator = (*minimize_map)[arg[0]]; + int sflag; + new_minimize(arg[0],narg-1,&arg[1],trysuffix,sflag); + + if (sflag) { + char estyle[256]; + if (sflag == 1) snprintf(estyle,256,"%s/%s",arg[0],lmp->suffix); + else snprintf(estyle,256,"%s/%s",arg[0],lmp->suffix2); + int n = strlen(estyle) + 1; + minimize_style = new char[n]; + strcpy(minimize_style,estyle); + } else { + int n = strlen(arg[0]) + 1; + minimize_style = new char[n]; + strcpy(minimize_style,arg[0]); + } +} + +/* ---------------------------------------------------------------------- + create the Minimize style, first with suffix appended +------------------------------------------------------------------------- */ + +void Update::new_minimize(char *style, int /* narg */, char ** /* arg */, + int trysuffix, int &sflag) +{ + if (trysuffix && lmp->suffix_enable) { + if (lmp->suffix) { + sflag = 1; + char estyle[256]; + snprintf(estyle,256,"%s/%s",style,lmp->suffix); + if (minimize_map->find(estyle) != minimize_map->end()) { + MinimizeCreator minimize_creator = (*minimize_map)[estyle]; + minimize = minimize_creator(lmp); + return; + } + } + + if (lmp->suffix2) { + sflag = 2; + char estyle[256]; + snprintf(estyle,256,"%s/%s",style,lmp->suffix2); + if (minimize_map->find(estyle) != minimize_map->end()) { + MinimizeCreator minimize_creator = (*minimize_map)[estyle]; + minimize = minimize_creator(lmp); + return; + } + } + } + + sflag = 0; + if (minimize_map->find(style) != minimize_map->end()) { + MinimizeCreator minimize_creator = (*minimize_map)[style]; minimize = minimize_creator(lmp); + return; } - else error->all(FLERR,"Illegal min_style command"); - int n = strlen(arg[0]) + 1; - minimize_style = new char[n]; - strcpy(minimize_style,arg[0]); + error->all(FLERR,"Illegal minimize style"); } /* ---------------------------------------------------------------------- diff --git a/src/update.h b/src/update.h index d3602ef21e98b0dfcbc036e29625831d3a27be3a..e70325a4984b3e62f6df0bfa247b364533136a7b 100644 --- a/src/update.h +++ b/src/update.h @@ -63,7 +63,7 @@ class Update : protected Pointers { void init(); void set_units(const char *); void create_integrate(int, char **, int); - void create_minimize(int, char **); + void create_minimize(int, char **, int); void reset_timestep(int, char **); void reset_timestep(bigint); void update_time(); @@ -71,6 +71,7 @@ class Update : protected Pointers { private: void new_integrate(char *, int, char **, int, int &); + void new_minimize(char *, int, char **, int, int &); template static Integrate *integrate_creator(LAMMPS *, int, char **); template static Min *minimize_creator(LAMMPS *); diff --git a/src/utils.cpp b/src/utils.cpp index 5e53a3a09dda065b62e44c892b39091611d26434..f6556a3ac8cd72307528f69353b486033cf920b0 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -17,6 +17,10 @@ #include "lammps.h" #include "error.h" +#if defined(__linux) +#include // for readlink +#endif + /*! \file utils.cpp */ /* @@ -103,14 +107,43 @@ int utils::cfvarg(std::string mode, const char *arg, char *&cfv_id) return rv; } +/** \brief try to detect pathname from FILE pointer. Currently only supported on Linux, otherwise will report "(unknown)". + * + * \param buf storage buffer for pathname. output will be truncated if not large enough + * \param len size of storage buffer. output will be truncated to this length - 1 + * \param fp FILE pointer structe from STDIO library for which we want to detect the name + * \return pointer to the storage buffer, i.e. buf + */ +static const char *guesspath(char *buf, int len, FILE *fp) +{ + memset(buf,0,len); + +#if defined(__linux) + char procpath[32]; + int fd = fileno(fp); + snprintf(procpath,32,"/proc/self/fd/%d",fd); + // get pathname from /proc or copy (unknown) + if (readlink(procpath,buf,len-1) <= 0) strcpy(buf,"(unknown)"); +#else + strcpy(buf,"(unknown)"); +#endif + return buf; +} + +#define MAXPATHLENBUF 1024 /* like fgets() but aborts with an error or EOF is encountered */ void utils::sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error) { char *rv = fgets(s,size,fp); if (rv == NULL) { // something went wrong + char buf[MAXPATHLENBUF]; std::string errmsg; + // try to figure out the file name from the file pointer + if (!filename) + filename = guesspath(buf,MAXPATHLENBUF,fp); + if (feof(fp)) { errmsg = "Unexpected end of file while reading file '"; } else if (ferror(fp)) { @@ -127,6 +160,34 @@ void utils::sfgets(const char *srcname, int srcline, char *s, int size, return; } +/* like fread() but aborts with an error or EOF is encountered */ +void utils::sfread(const char *srcname, int srcline, void *s, size_t size, + size_t num, FILE *fp, const char *filename, Error *error) +{ + size_t rv = fread(s,size,num,fp); + if (rv != num) { // something went wrong + char buf[MAXPATHLENBUF]; + std::string errmsg; + + // try to figure out the file name from the file pointer + if (!filename) + filename = guesspath(buf,MAXPATHLENBUF,fp); + + if (feof(fp)) { + errmsg = "Unexpected end of file while reading file '"; + } else if (ferror(fp)) { + errmsg = "Unexpected error while reading file '"; + } else { + errmsg = "Unexpected short read while reading file '"; + } + errmsg += filename; + errmsg += "'"; + + if (error) error->one(srcname,srcline,errmsg.c_str()); + } + return; +} + /* ------------------------------------------------------------------ */ std::string utils::check_packages_for_style(std::string style, diff --git a/src/utils.h b/src/utils.h index 5f71bfae7634b0ee24e2a4dcc10ee433bf6c8cc5..e87aa4bb9189bf0a070d1435c907e09773a71d2f 100644 --- a/src/utils.h +++ b/src/utils.h @@ -63,12 +63,27 @@ namespace LAMMPS_NS { * \param s buffer for storing the result of fgets() * \param size size of buffer s (max number of bytes read by fgets()) * \param fp file pointer used by fgets() - * \param filename file name associated with fp (for error message) + * \param filename file name associated with fp (may be NULL; then LAMMPS will try to detect) * \param error pointer to Error class instance (for abort) */ void sfgets(const char *srcname, int srcline, char *s, int size, FILE *fp, const char *filename, Error *error); + /** \brief safe wrapper around fread() which aborts on errors + * or EOF and prints a suitable error message to help debugging + * + * \param srcname name of the calling source file (from FLERR macro) + * \param srcline line in the calling source file (from FLERR macro) + * \param s buffer for storing the result of fread() + * \param size size of data elements read by fread() + * \param num number of data elements read by fread() + * \param fp file pointer used by fread() + * \param filename file name associated with fp (may be NULL; then LAMMPS will try to detect) + * \param error pointer to Error class instance (for abort) + */ + void sfread(const char *srcname, int srcline, void *s, size_t size, + size_t num, FILE *fp, const char *filename, Error *error); + /** \brief Report if a requested style is in a package or may have a typo * * \param style type of style that is to be checked for diff --git a/src/version.h b/src/version.h index 7387a3a1a4231c46a4c3715c650f4b7b56ffde48..9471c2b951c68a7dd57965d207cf4d34cded0676 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "7 Aug 2019" +#define LAMMPS_VERSION "30 Oct 2019" diff --git a/tools/README b/tools/README index 54f8d86898a37afd5ab8a23ff5c13dd03dac883f..b20e82c53e839459e9eec0d752ac749860c9b36a 100644 --- a/tools/README +++ b/tools/README @@ -38,6 +38,7 @@ polybond Python tool for programmable polymer bonding pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output reax Tools for analyzing output of ReaxFF simulations +replica tool to reorder LAMMPS replica trajectories according to temperature smd convert Smooth Mach Dynamics triangles to VTK spin perform a cubic polynomial interpolation of a GNEB MEP vim add-ons to VIM editor for editing LAMMPS input scripts diff --git a/tools/binary2txt.cpp b/tools/binary2txt.cpp index e0778fbf3c6c6eae52793748be6efa15e7098449..119e9e35743d9991cee105c460d6af0fd7fcff49 100644 --- a/tools/binary2txt.cpp +++ b/tools/binary2txt.cpp @@ -99,9 +99,9 @@ int main(int narg, char **arg) // detect end-of-file if (feof(fp)) { - fclose(fp); - fclose(fptxt); - break; + fclose(fp); + fclose(fptxt); + break; } fread(&natoms,sizeof(bigint),1,fp); @@ -114,13 +114,13 @@ int main(int narg, char **arg) fread(&zlo,sizeof(double),1,fp); fread(&zhi,sizeof(double),1,fp); if (triclinic) { - fread(&xy,sizeof(double),1,fp); - fread(&xz,sizeof(double),1,fp); - fread(&yz,sizeof(double),1,fp); + fread(&xy,sizeof(double),1,fp); + fread(&xz,sizeof(double),1,fp); + fread(&yz,sizeof(double),1,fp); } fread(&size_one,sizeof(int),1,fp); fread(&nchunk,sizeof(int),1,fp); - + fprintf(fptxt,"ITEM: TIMESTEP\n"); fprintf(fptxt,BIGINT_FORMAT "\n",ntimestep); fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n"); @@ -128,26 +128,26 @@ int main(int narg, char **arg) m = 0; for (int idim = 0; idim < 3; idim++) { - for (int iside = 0; iside < 2; iside++) { - if (boundary[idim][iside] == 0) boundstr[m++] = 'p'; - else if (boundary[idim][iside] == 1) boundstr[m++] = 'f'; - else if (boundary[idim][iside] == 2) boundstr[m++] = 's'; - else if (boundary[idim][iside] == 3) boundstr[m++] = 'm'; - } - boundstr[m++] = ' '; + for (int iside = 0; iside < 2; iside++) { + if (boundary[idim][iside] == 0) boundstr[m++] = 'p'; + else if (boundary[idim][iside] == 1) boundstr[m++] = 'f'; + else if (boundary[idim][iside] == 2) boundstr[m++] = 's'; + else if (boundary[idim][iside] == 3) boundstr[m++] = 'm'; + } + boundstr[m++] = ' '; } boundstr[8] = '\0'; - + if (!triclinic) { - fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr); - fprintf(fptxt,"%g %g\n",xlo,xhi); - fprintf(fptxt,"%g %g\n",ylo,yhi); - fprintf(fptxt,"%g %g\n",zlo,zhi); + fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr); + fprintf(fptxt,"%g %g\n",xlo,xhi); + fprintf(fptxt,"%g %g\n",ylo,yhi); + fprintf(fptxt,"%g %g\n",zlo,zhi); } else { - fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr); - fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy); - fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz); - fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz); + fprintf(fptxt,"ITEM: BOX BOUNDS %s xy xz yz\n",boundstr); + fprintf(fptxt,"%g %g %g\n",xlo,xhi,xy); + fprintf(fptxt,"%g %g %g\n",ylo,yhi,xz); + fprintf(fptxt,"%g %g %g\n",zlo,zhi,yz); } fprintf(fptxt,"ITEM: ATOMS\n"); @@ -156,25 +156,25 @@ int main(int narg, char **arg) // loop over processor chunks in file for (i = 0; i < nchunk; i++) { - fread(&n,sizeof(int),1,fp); - - // extend buffer to fit chunk size - - if (n > maxbuf) { - if (buf) delete [] buf; - buf = new double[n]; - maxbuf = n; - } - - // read chunk and write as size_one values per line - - fread(buf,sizeof(double),n,fp); - n /= size_one; - m = 0; - for (j = 0; j < n; j++) { - for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]); - fprintf(fptxt,"\n"); - } + fread(&n,sizeof(int),1,fp); + + // extend buffer to fit chunk size + + if (n > maxbuf) { + if (buf) delete [] buf; + buf = new double[n]; + maxbuf = n; + } + + // read chunk and write as size_one values per line + + fread(buf,sizeof(double),n,fp); + n /= size_one; + m = 0; + for (j = 0; j < n; j++) { + for (k = 0; k < size_one; k++) fprintf(fptxt,"%g ",buf[m++]); + fprintf(fptxt,"\n"); + } } printf(" " BIGINT_FORMAT,ntimestep); diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl index bda9ace2bc3afa835028575aec547fd7daa8c12a..b53bd00541677f9b3d5a536a01a755e56aebb1d0 100755 --- a/tools/ch2lmp/charmm2lammps.pl +++ b/tools/ch2lmp/charmm2lammps.pl @@ -39,6 +39,7 @@ # 20161001 Added instructions in CMAP section to fix problem if 'ter' # is not designated in the .pdb file to identify last amino acid # 20161005 Added tweak to embed command line in generated LAMMPS input +# 20181120 Fix topology parsing bug # # General Many thanks to Paul S. Crozier for checking script validity # against his projects. @@ -86,8 +87,8 @@ my $notes; $program = "charmm2lammps"; - $version = "1.9.1"; - $year = "2016"; + $version = "1.9.2"; + $year = "2018"; $add = 1; $water_dens = 0; $ions = 0; diff --git a/tools/eam_database/create.f b/tools/eam_database/create.f index 2bdf49dd0d906ed922331d02bb1b68dacff6b126..528b4251dbb3d8a263a6676b48ef5865b6f2c5c8 100644 --- a/tools/eam_database/create.f +++ b/tools/eam_database/create.f @@ -73,8 +73,9 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc rhoin(ntypes)=rhol(ntypes)*rhoe(ntypes) rhoout(ntypes)=rhoh(ntypes)*rhoe(ntypes) else - do 1 i=1,27 -1 read(10,*)vtmp + do i=1,27 + read(10,*)vtmp + end do goto 11 endif close(10) @@ -94,28 +95,29 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc rst=0.5 dr=rc/(nr-1.0) fmax=-1.0 - do 3 i1=1,ntypes - do 3 i2=1,i1 - if ( i1 .eq. i2) then - do 4 i=1,nr - r=(i-1.0)*dr - if (r .lt. rst) r=rst - call prof(i1,r,fvalue) - if (fmax .lt. fvalue) fmax=fvalue - rhor(i,i1)=fvalue - call pair(i1,i2,r,psi) - z2r(i,i1,i2)=r*psi -4 continue - else - do 5 i=1,nr - r=(i-1.0)*dr - if (r .lt. rst) r=rst - call pair(i1,i2,r,psi) - z2r(i,i1,i2)=r*psi - z2r(i,i2,i1)=z2r(i,i1,i2) -5 continue - endif -3 continue + do i1=1,ntypes + do i2=1,i1 + if ( i1 .eq. i2) then + do i=1,nr + r=(i-1.0)*dr + if (r .lt. rst) r=rst + call prof(i1,r,fvalue) + if (fmax .lt. fvalue) fmax=fvalue + rhor(i,i1)=fvalue + call pair(i1,i2,r,psi) + z2r(i,i1,i2)=r*psi + end do + else + do i=1,nr + r=(i-1.0)*dr + if (r .lt. rst) r=rst + call pair(i1,i2,r,psi) + z2r(i,i1,i2)=r*psi + z2r(i,i2,i1)=z2r(i,i1,i2) + end do + endif + end do + end do rhom=fmax if (rhom .lt. 2.0*rhoemax) rhom=2.0*rhoemax if (rhom .lt. 100.0) rhom=100.0 @@ -239,10 +241,11 @@ ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc 10 continue 11 format(i5,2g15.5,a8) 12 format(5e24.16) - do 13 i1=1,ntypes - do 13 i2=1,i1 - write(1,12)(z2r(i,i1,i2),i=1,nr) -13 continue + do i1=1,ntypes + do i2=1,i1 + write(1,12)(z2r(i,i1,i2),i=1,nr) + end do + end do close(1) return end diff --git a/tools/python/pizza/cfg.py b/tools/python/pizza/cfg.py index 8cefd38acdc43154f2b05b26fe8967820fc1c016..bbd930ea3cb7e5f3b8dcc2375722405e4c084411 100644 --- a/tools/python/pizza/cfg.py +++ b/tools/python/pizza/cfg.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # cfg tool @@ -11,14 +11,14 @@ oneline = "Convert LAMMPS snapshots to AtomEye CFG format" docstr = """ -c = cfg(d) d = object containing atom coords (dump, data) +c = cfg(d) d = object containing atom coords (dump, data) c.one() write all snapshots to tmp.cfg c.one("new") write all snapshots to new.cfg c.many() write snapshots to tmp0000.cfg, tmp0001.cfg, etc c.many("new") write snapshots to new0000.cfg, new0001.cfg, etc -c.single(N) write snapshot for timestep N to tmp.cfg -c.single(N,"file") write snapshot for timestep N to file.cfg +c.single(N) write snapshot for timestep N to tmp.cfg +c.single(N,"file") write snapshot for timestep N to file.cfg """ # History @@ -46,7 +46,7 @@ class cfg: def __init__(self,data): self.data = data - + # -------------------------------------------------------------------- def one(self,*args): @@ -68,16 +68,16 @@ class cfg: print >>f,"Number of particles = %d " % len(atoms) print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time print >>f,"H0(1,1) = %20.10f A " % xlen - print >>f,"H0(1,2) = 0.0 A " - print >>f,"H0(1,3) = 0.0 A " - print >>f,"H0(2,1) = 0.0 A " + print >>f,"H0(1,2) = 0.0 A " + print >>f,"H0(1,3) = 0.0 A " + print >>f,"H0(2,1) = 0.0 A " print >>f,"H0(2,2) = %20.10f A " % ylen - print >>f,"H0(2,3) = 0.0 A " - print >>f,"H0(3,1) = 0.0 A " - print >>f,"H0(3,2) = 0.0 A " + print >>f,"H0(2,3) = 0.0 A " + print >>f,"H0(3,1) = 0.0 A " + print >>f,"H0(3,2) = 0.0 A " print >>f,"H0(3,3) = %20.10f A " % zlen print >>f,"#" - + for atom in atoms: itype = int(atom[1]) xfrac = (atom[2]-box[0])/xlen @@ -85,14 +85,14 @@ class cfg: zfrac = (atom[4]-box[2])/zlen # print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]) print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac) - + print time, sys.stdout.flush() n += 1 - + f.close() print "\nwrote %d snapshots to %s in CFG format" % (n,file) - + # -------------------------------------------------------------------- def many(self,*args): @@ -104,7 +104,7 @@ class cfg: which,time,flag = self.data.iterator(flag) if flag == -1: break time,box,atoms,bonds,tris,lines = self.data.viz(which) - + if n < 10: file = root + "000" + str(n) elif n < 100: @@ -112,7 +112,7 @@ class cfg: elif n < 1000: file = root + "0" + str(n) else: - file = root + str(n) + file = root + str(n) file += ".cfg" f = open(file,"w") @@ -123,16 +123,16 @@ class cfg: print >>f,"Number of particles = %d " % len(atoms) print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time print >>f,"H0(1,1) = %20.10f A " % xlen - print >>f,"H0(1,2) = 0.0 A " - print >>f,"H0(1,3) = 0.0 A " - print >>f,"H0(2,1) = 0.0 A " + print >>f,"H0(1,2) = 0.0 A " + print >>f,"H0(1,3) = 0.0 A " + print >>f,"H0(2,1) = 0.0 A " print >>f,"H0(2,2) = %20.10f A " % ylen - print >>f,"H0(2,3) = 0.0 A " - print >>f,"H0(3,1) = 0.0 A " - print >>f,"H0(3,2) = 0.0 A " + print >>f,"H0(2,3) = 0.0 A " + print >>f,"H0(3,1) = 0.0 A " + print >>f,"H0(3,2) = 0.0 A " print >>f,"H0(3,3) = %20.10f A " % zlen print >>f,"#" - + for atom in atoms: itype = int(atom[1]) xfrac = (atom[2]-box[0])/xlen @@ -140,14 +140,14 @@ class cfg: zfrac = (atom[4]-box[2])/zlen # print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]) print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac) - + print time, sys.stdout.flush() f.close() n += 1 - + print "\nwrote %s snapshots in CFG format" % n - + # -------------------------------------------------------------------- def single(self,time,*args): @@ -166,16 +166,16 @@ class cfg: print >>f,"Number of particles = %d " % len(atoms) print >>f,"# Timestep %d \n#\nA = 1.0 Angstrom" % time print >>f,"H0(1,1) = %20.10f A " % xlen - print >>f,"H0(1,2) = 0.0 A " - print >>f,"H0(1,3) = 0.0 A " - print >>f,"H0(2,1) = 0.0 A " + print >>f,"H0(1,2) = 0.0 A " + print >>f,"H0(1,3) = 0.0 A " + print >>f,"H0(2,1) = 0.0 A " print >>f,"H0(2,2) = %20.10f A " % ylen - print >>f,"H0(2,3) = 0.0 A " - print >>f,"H0(3,1) = 0.0 A " - print >>f,"H0(3,2) = 0.0 A " + print >>f,"H0(2,3) = 0.0 A " + print >>f,"H0(3,1) = 0.0 A " + print >>f,"H0(3,2) = 0.0 A " print >>f,"H0(3,3) = %20.10f A " % zlen print >>f,"#" - + for atom in atoms: itype = int(atom[1]) xfrac = (atom[2]-box[0])/xlen @@ -183,5 +183,5 @@ class cfg: zfrac = (atom[4]-box[2])/zlen # print >>f,"1.0 %d %15.10f %15.10f %15.10f %15.10f %15.10f %15.10f " % (itype,xfrac,yfrac,zfrac,atom[5],atom[6],atom[7]) print >>f,"1.0 %d %15.10f %15.10f %15.10f 0.0 0.0 0.0 " % (itype,xfrac,yfrac,zfrac) - + f.close() diff --git a/tools/python/pizza/dump.py b/tools/python/pizza/dump.py index 8098a2c4b75bfb66ad5427308a93b7e126ed0ac5..1c6eb5edfd822f604e584cd877715dd7acc94b7f 100644 --- a/tools/python/pizza/dump.py +++ b/tools/python/pizza/dump.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # dump tool @@ -12,15 +12,15 @@ oneline = "Read, write, manipulate dump files and particle attributes" docstr = """ d = dump("dump.one") read in one or more dump files -d = dump("dump.1 dump.2.gz") can be gzipped -d = dump("dump.*") wildcard expands to multiple files -d = dump("dump.*",0) two args = store filenames, but don't read +d = dump("dump.1 dump.2.gz") can be gzipped +d = dump("dump.*") wildcard expands to multiple files +d = dump("dump.*",0) two args = store filenames, but don't read incomplete and duplicate snapshots are deleted atoms will be unscaled if stored in files as scaled - self-describing column names assigned + self-describing column names assigned -time = d.next() read next snapshot from dump files +time = d.next() read next snapshot from dump files used with 2-argument constructor to allow reading snapshots one-at-a-time snapshot will be skipped only if another snapshot has same time stamp @@ -31,21 +31,21 @@ time = d.next() read next snapshot from dump files d.map(1,"id",3,"x") assign names to columns (1-N) not needed if dump file is self-describing - -d.tselect.all() select all timesteps -d.tselect.one(N) select only timestep N -d.tselect.none() deselect all timesteps -d.tselect.skip(M) select every Mth step + +d.tselect.all() select all timesteps +d.tselect.one(N) select only timestep N +d.tselect.none() deselect all timesteps +d.tselect.skip(M) select every Mth step d.tselect.test("$t >= 100 and $t < 10000") select matching timesteps -d.delete() delete non-selected timesteps +d.delete() delete non-selected timesteps selecting a timestep also selects all atoms in the timestep skip() and test() only select from currently selected timesteps test() uses a Python Boolean expression with $t for timestep value Python comparison syntax: == != < > <= >= and or -d.aselect.all() select all atoms in all steps -d.aselect.all(N) select all atoms in one step +d.aselect.all() select all atoms in all steps +d.aselect.all(N) select all atoms in one step d.aselect.test("$id > 100 and $type == 2") select match atoms in all steps d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step @@ -56,24 +56,24 @@ d.aselect.test("$id > 100 and $type == 2",N) select matching atoms in one step Python comparison syntax: == != < > <= >= and or $name must end with a space -d.write("file") write selected steps/atoms to dump file -d.write("file",head,app) write selected steps/atoms to dump file -d.scatter("tmp") write selected steps/atoms to multiple files +d.write("file") write selected steps/atoms to dump file +d.write("file",head,app) write selected steps/atoms to dump file +d.scatter("tmp") write selected steps/atoms to multiple files write() can be specified with 2 additional flags head = 0/1 for no/yes snapshot header, app = 0/1 for write vs append scatter() files are given timestep suffix: e.g. tmp.0, tmp.100, etc -d.scale() scale x,y,z to 0-1 for all timesteps -d.scale(100) scale atom coords for timestep N -d.unscale() unscale x,y,z to box size to all timesteps -d.unscale(1000) unscale atom coords for timestep N -d.wrap() wrap x,y,z into periodic box via ix,iy,iz -d.unwrap() unwrap x,y,z out of box via ix,iy,iz -d.owrap("other") wrap x,y,z to same image as another atom -d.sort() sort atoms by atom ID in all selected steps -d.sort("x") sort atoms by column value in all steps -d.sort(1000) sort atoms in timestep N +d.scale() scale x,y,z to 0-1 for all timesteps +d.scale(100) scale atom coords for timestep N +d.unscale() unscale x,y,z to box size to all timesteps +d.unscale(1000) unscale atom coords for timestep N +d.wrap() wrap x,y,z into periodic box via ix,iy,iz +d.unwrap() unwrap x,y,z out of box via ix,iy,iz +d.owrap("other") wrap x,y,z to same image as another atom +d.sort() sort atoms by atom ID in all selected steps +d.sort("x") sort atoms by column value in all steps +d.sort(1000) sort atoms in timestep N scale(), unscale(), wrap(), unwrap(), owrap() operate on all steps and atoms wrap(), unwrap(), owrap() require ix,iy,iz be defined @@ -85,8 +85,8 @@ d.sort(1000) sort atoms in timestep N m1,m2 = d.minmax("type") find min/max values for a column d.set("$ke = $vx * $vx + $vy * $vy") set a column to a computed value d.setv("type",vector) set a column to a vector of values -d.spread("ke",N,"color") 2nd col = N ints spread over 1st col -d.clone(1000,"color") clone timestep N values to other steps +d.spread("ke",N,"color") 2nd col = N ints spread over 1st col +d.clone(1000,"color") clone timestep N values to other steps minmax() operates on selected timesteps and atoms set() operates on selected timesteps and atoms @@ -107,17 +107,17 @@ d.clone(1000,"color") clone timestep N values to other steps values at every timestep are set to value at timestep N for that atom ID useful for propagating a color map -t = d.time() return vector of selected timestep values +t = d.time() return vector of selected timestep values fx,fy,... = d.atom(100,"fx","fy",...) return vector(s) for atom ID N fx,fy,... = d.vecs(1000,"fx","fy",...) return vector(s) for timestep N atom() returns vectors with one value for each selected timestep vecs() returns vectors with one value for each selected atom in the timestep -index,time,flag = d.iterator(0/1) loop over dump snapshots +index,time,flag = d.iterator(0/1) loop over dump snapshots time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects -d.atype = "color" set column returned as "type" by viz -d.extra(obj) extract bond/tri/line info from obj +d.atype = "color" set column returned as "type" by viz +d.extra(obj) extract bond/tri/line info from obj iterator() loops over selected timesteps iterator() called with arg = 0 first time, with arg = 1 on subsequent calls @@ -137,7 +137,7 @@ d.extra(obj) extract bond/tri/line info from obj if extra() used to define lines, else NULL atype is column name viz() will return as atom type (def = "type") extra() extracts bonds/tris/lines from obj each time viz() is called - obj can be data object for bonds, cdata object for tris and lines, + obj can be data object for bonds, cdata object for tris and lines, bdump object for bonds, tdump object for tris, ldump object for lines. mdump object for tris """ @@ -227,7 +227,7 @@ class dump: for word in words: self.flist += glob.glob(word) if len(self.flist) == 0 and len(list) == 1: raise StandardError,"no dump file specified" - + if len(list) == 1: self.increment = 0 self.read_all() @@ -270,7 +270,7 @@ class dump: self.tselect.all() # print column assignments - + if len(self.names): print "assigned columns:",self.names2str() else: @@ -304,15 +304,15 @@ class dump: snap = self.read_snapshot(f) if not snap: self.nextfile += 1 - if self.nextfile == len(self.flist): return -1 + if self.nextfile == len(self.flist): return -1 f.close() - self.eof = 0 - continue + self.eof = 0 + continue self.eof = f.tell() f.close() try: self.findtime(snap.time) - continue + continue except: break # select the new snapshot with all its atoms @@ -334,7 +334,7 @@ class dump: # assign column names (file must be self-describing) # set scale_original to 0/1/-1 for unscaled/scaled/unknown # convert xs,xu to x in names - + def read_snapshot(self,f): try: snap = Snap() @@ -351,7 +351,7 @@ class dump: else: snap.boxstr = words[1].strip() if "xy" in snap.boxstr: snap.triclinic = 1 else: snap.triclinic = 0 - + words = f.readline().split() if len(words) == 2: snap.xlo,snap.xhi,snap.xy = float(words[0]),float(words[1]),0.0 @@ -372,7 +372,7 @@ class dump: else: snap.zlo,snap.zhi,snap.yz = \ float(words[0]),float(words[1]),float(words[2]) - + item = f.readline() if len(self.names) == 0: self.scale_original = -1 @@ -401,7 +401,7 @@ class dump: else: self.names[words[i]] = i if xflag == 0 and yflag == 0 and zflag == 0: self.scale_original = 0 if xflag == 1 and yflag == 1 and zflag == 1: self.scale_original = 1 - + if snap.natoms: words = f.readline().split() ncol = len(words) @@ -424,7 +424,7 @@ class dump: # -------------------------------------------------------------------- # map atom column names - + def map(self,*pairs): if len(pairs) % 2 != 0: raise StandardError, "dump map() requires pairs of mappings" @@ -509,7 +509,7 @@ class dump: atoms[:,y] = (atoms[:,y] - snap.ylo)*h1inv + \ (atoms[:,z] - snap.zlo)*h3inv atoms[:,z] = (atoms[:,z] - snap.zlo)*h2inv - + # -------------------------------------------------------------------- # unscale coords from 0-1 to box size for all snapshots or just one # use 6 params as h-matrix to treat orthogonal or triclinic boxes @@ -564,7 +564,7 @@ class dump: atoms[:,x] = snap.xlo + atoms[:,x]*h0 + atoms[:,y]*h5 + atoms[:,z]*h4 atoms[:,y] = snap.ylo + atoms[:,y]*h1 + atoms[:,z]*h3 atoms[:,z] = snap.zlo + atoms[:,z]*h2 - + # -------------------------------------------------------------------- # wrap coords from outside box to inside @@ -577,7 +577,7 @@ class dump: ix = self.names["ix"] iy = self.names["iy"] iz = self.names["iz"] - + for snap in self.snaps: xprd = snap.xhi - snap.xlo yprd = snap.yhi - snap.ylo @@ -599,7 +599,7 @@ class dump: ix = self.names["ix"] iy = self.names["iy"] iz = self.names["iz"] - + for snap in self.snaps: xprd = snap.xhi - snap.xlo yprd = snap.yhi - snap.ylo @@ -612,10 +612,10 @@ class dump: # -------------------------------------------------------------------- # wrap coords to same image as atom ID stored in "other" column # if dynamic extra lines or triangles defined, owrap them as well - + def owrap(self,other): print "Wrapping to other ..." - + id = self.names["id"] x = self.names["x"] y = self.names["y"] @@ -641,10 +641,10 @@ class dump: # should bonds also be owrapped ? if self.lineflag == 2 or self.triflag == 2: self.objextra.owrap(snap.time,xprd,yprd,zprd,ids,atoms,iother,ix,iy,iz) - + # -------------------------------------------------------------------- # convert column names assignment to a string, in column order - + def names2str(self): pairs = self.names.items() values = self.names.values() @@ -697,7 +697,7 @@ class dump: else: id = -1 if "type" in self.names: type = self.names["type"] else: type = -1 - + for snap in self.snaps: if not snap.tselect: continue print snap.time, @@ -719,7 +719,7 @@ class dump: print >>f,snap.ylo,snap.yhi print >>f,snap.zlo,snap.zhi print >>f,"ITEM: ATOMS",namestr - + atoms = snap.atoms nvalues = len(atoms[0]) for i in xrange(snap.natoms): @@ -743,7 +743,7 @@ class dump: if not snap.tselect: continue print snap.time, sys.stdout.flush() - + file = root + "." + str(snap.time) f = open(file,"w") print >>f,"ITEM: TIMESTEP" @@ -761,7 +761,7 @@ class dump: print >>f,snap.ylo,snap.yhi print >>f,snap.zlo,snap.zhi print >>f,"ITEM: ATOMS",namestr - + atoms = snap.atoms nvalues = len(atoms[0]) for i in xrange(snap.natoms): @@ -803,7 +803,7 @@ class dump: lhs = list[0][1:] if not self.names.has_key(lhs): self.newcolumn(lhs) - + for item in list: name = item[1:] column = self.names[name] @@ -815,7 +815,7 @@ class dump: if not snap.tselect: continue for i in xrange(snap.natoms): if snap.aselect[i]: exec ceq - + # -------------------------------------------------------------------- # set a column value via an input vec for all selected snapshots/atoms @@ -835,7 +835,7 @@ class dump: if snap.aselect[i]: atoms[i][icol] = vec[m] m += 1 - + # -------------------------------------------------------------------- # clone value in col across selected timesteps for atoms with same ID @@ -901,7 +901,7 @@ class dump: columns.append(self.names[name]) values.append(self.nselect * [0]) ncol = len(columns) - + id = self.names["id"] m = 0 for snap in self.snaps: @@ -917,13 +917,13 @@ class dump: if len(list) == 1: return values[0] else: return values - + # -------------------------------------------------------------------- # extract vector(s) of values for selected atoms at chosen timestep def vecs(self,n,*list): snap = self.snaps[self.findtime(n)] - + if len(list) == 0: raise StandardError, "no columns specified" columns = [] @@ -978,7 +978,7 @@ class dump: del self.snaps[i] else: i += 1 - + # -------------------------------------------------------------------- # iterate over selected snapshots @@ -990,12 +990,12 @@ class dump: self.iterate = i return i,self.snaps[i].time,1 return 0,0,-1 - + # -------------------------------------------------------------------- # return list of atoms to viz for snapshot isnap # if called with flag, then index is timestep, so convert to snapshot index # augment with bonds, tris, lines if extra() was invoked - + def viz(self,index,flag=0): if not flag: isnap = index else: @@ -1019,7 +1019,7 @@ class dump: # create atom list needed by viz from id,type,x,y,z # need Numeric/Numpy mode here - + atoms = [] for i in xrange(snap.natoms): if not snap.aselect[i]: continue @@ -1059,7 +1059,7 @@ class dump: if self.triflag == 1: tris = self.trilist elif self.triflag == 2: tmp1,tmp2,tmp3,tmp4,tris,tmp5 = self.objextra.viz(time,1) - + # create list of lines from static or dynamic tri list # if dynamic, could eliminate lines for unselected atoms @@ -1070,7 +1070,7 @@ class dump: tmp1,tmp2,tmp3,tmp4,tmp5,lines = self.objextra.viz(time,1) return time,box,atoms,bonds,tris,lines - + # -------------------------------------------------------------------- def findtime(self,n): @@ -1115,7 +1115,7 @@ class dump: def extra(self,arg): # data object, grab bonds statically - + if type(arg) is types.InstanceType and ".data" in str(arg.__class__): self.bondflag = 0 try: @@ -1132,7 +1132,7 @@ class dump: raise StandardError,"could not extract bonds from data object" # cdata object, grab tris and lines statically - + elif type(arg) is types.InstanceType and ".cdata" in str(arg.__class__): self.triflag = self.lineflag = 0 try: @@ -1147,32 +1147,32 @@ class dump: raise StandardError,"could not extract tris/lines from cdata object" # mdump object, grab tris dynamically - + elif type(arg) is types.InstanceType and ".mdump" in str(arg.__class__): self.triflag = 2 self.objextra = arg # bdump object, grab bonds dynamically - + elif type(arg) is types.InstanceType and ".bdump" in str(arg.__class__): self.bondflag = 2 self.objextra = arg # ldump object, grab lines dynamically - + elif type(arg) is types.InstanceType and ".ldump" in str(arg.__class__): self.lineflag = 2 self.objextra = arg # tdump object, grab tris dynamically - + elif type(arg) is types.InstanceType and ".tdump" in str(arg.__class__): self.triflag = 2 self.objextra = arg else: raise StandardError,"unrecognized argument to dump.extra()" - + # -------------------------------------------------------------------- def compare_atom(self,a,b): @@ -1181,7 +1181,7 @@ class dump: elif a[0] > b[0]: return 1 else: - return 0 + return 0 # -------------------------------------------------------------------- # one snapshot @@ -1196,7 +1196,7 @@ class tselect: def __init__(self,data): self.data = data - + # -------------------------------------------------------------------- def all(self): @@ -1243,7 +1243,7 @@ class tselect: data.nselect -= 1 data.aselect.all() print "%d snapshots selected out of %d" % (data.nselect,data.nsnaps) - + # -------------------------------------------------------------------- def test(self,teststr): @@ -1289,7 +1289,7 @@ class aselect: data = self.data # replace all $var with snap.atoms references and compile test string - + pattern = "\$\w*" list = re.findall(pattern,teststr) for item in list: diff --git a/tools/python/pizza/gnu.py b/tools/python/pizza/gnu.py index f6f0167330055a0d3f347ff4d2f9d878579ce0fc..d99ab3811d020933077951edf2cbe19962f12a8e 100644 --- a/tools/python/pizza/gnu.py +++ b/tools/python/pizza/gnu.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # gnu tool @@ -11,12 +11,12 @@ oneline = "Create plots via GnuPlot plotting program" docstr = """ -g = gnu() start up GnuPlot -g.stop() shut down GnuPlot process - +g = gnu() start up GnuPlot +g.stop() shut down GnuPlot process + g.plot(a) plot vector A against linear index -g.plot(a,b) plot B against A -g.plot(a,b,c,d,...) plot B against A, D against C, etc +g.plot(a,b) plot B against A +g.plot(a,b,c,d,...) plot B against A, D against C, etc g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc each plot argument can be a tuple, list, or Numeric/NumPy vector @@ -29,21 +29,21 @@ g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot -g.enter() enter GnuPlot shell +g.enter() enter GnuPlot shell gnuplot> plot sin(x) with lines type commands directly to GnuPlot -gnuplot> exit, quit exit GnuPlot shell - +gnuplot> exit, quit exit GnuPlot shell + g.export("data",range(100),a,...) create file with columns of numbers all vectors must be of equal length could plot from file with GnuPlot command: plot 'data' using 1:2 with lines -g.select(N) figure N becomes the current plot - +g.select(N) figure N becomes the current plot + subsequent commands apply to this plot -g.hide(N) delete window for figure N -g.save("file") save current plot as file.eps +g.hide(N) delete window for figure N +g.save("file") save current plot as file.eps Set attributes for current plot: @@ -94,7 +94,7 @@ except: PIZZA_GNUTERM = "x11" # Class definition class gnu: - + # -------------------------------------------------------------------- def __init__(self): @@ -102,7 +102,7 @@ class gnu: self.file = "tmp.gnu" self.figures = [] self.select(1) - + # -------------------------------------------------------------------- def stop(self): @@ -114,7 +114,7 @@ class gnu: def __call__(self,command): self.GNUPLOT.write(command + '\n') self.GNUPLOT.flush() - + # -------------------------------------------------------------------- def enter(self): @@ -152,7 +152,7 @@ class gnu: if i: partial_vecs.append(vec[:i]) else: partial_vecs.append([0]) self.plot(*partial_vecs) - + if n < 10: newfile = file + "000" + str(n) elif n < 100: newfile = file + "00" + str(n) elif n < 1000: newfile = file + "0" + str(n) @@ -160,7 +160,7 @@ class gnu: self.save(newfile) n += 1 - + # -------------------------------------------------------------------- # write list of equal-length vectors to filename @@ -201,7 +201,7 @@ class gnu: # do not continue until plot file is written out # else script could go forward and change data file # use tmp.done as semaphore to indicate plot is finished - + def save(self,file): self.__call__("set terminal postscript enhanced solid lw 2 color portrait") cmd = "set output '%s.eps'" % file @@ -212,7 +212,7 @@ class gnu: while not os.path.exists("tmp.done"): continue self.__call__("set output") self.select(self.current) - + # -------------------------------------------------------------------- # restore default attributes by creating a new fig object @@ -221,7 +221,7 @@ class gnu: fig.ncurves = self.figures[self.current-1].ncurves self.figures[self.current-1] = fig self.draw() - + # -------------------------------------------------------------------- def aspect(self,value): @@ -245,12 +245,12 @@ class gnu: else: self.figures[self.current-1].ylimit = (values[0],values[1]) self.draw() - + # -------------------------------------------------------------------- def label(self,x,y,text): self.figures[self.current-1].labels.append((x,y,text)) - self.figures[self.current-1].nlabels += 1 + self.figures[self.current-1].nlabels += 1 self.draw() # -------------------------------------------------------------------- @@ -259,7 +259,7 @@ class gnu: self.figures[self.current-1].nlabel = 0 self.figures[self.current-1].labels = [] self.draw() - + # -------------------------------------------------------------------- def title(self,*strings): @@ -276,13 +276,13 @@ class gnu: def xtitle(self,label): self.figures[self.current-1].xtitle = label self.draw() - + # -------------------------------------------------------------------- def ytitle(self,label): self.figures[self.current-1].ytitle = label self.draw() - + # -------------------------------------------------------------------- def xlog(self): @@ -291,7 +291,7 @@ class gnu: else: self.figures[self.current-1].xlog = 1 self.draw() - + # -------------------------------------------------------------------- def ylog(self): @@ -300,7 +300,7 @@ class gnu: else: self.figures[self.current-1].ylog = 1 self.draw() - + # -------------------------------------------------------------------- def curve(self,num,color): @@ -316,10 +316,10 @@ class gnu: def draw(self): fig = self.figures[self.current-1] if not fig.ncurves: return - + cmd = 'set size ratio ' + str(1.0/float(fig.aspect)) self.__call__(cmd) - + cmd = 'set title ' + '"' + fig.title + '"' self.__call__(cmd) cmd = 'set xlabel ' + '"' + fig.xtitle + '"' @@ -331,11 +331,11 @@ class gnu: else: self.__call__("unset logscale x") if fig.ylog: self.__call__("set logscale y") else: self.__call__("unset logscale y") - if fig.xlimit: + if fig.xlimit: cmd = 'set xr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']' self.__call__(cmd) else: self.__call__("set xr [*:*]") - if fig.ylimit: + if fig.ylimit: cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']' self.__call__(cmd) else: self.__call__("set yr [*:*]") @@ -365,7 +365,7 @@ class figure: def __init__(self): self.ncurves = 0 - self.colors = [] + self.colors = [] self.title = "" self.xtitle = "" self.ytitle = "" diff --git a/tools/python/pizza/log.py b/tools/python/pizza/log.py index aeca1d8d82f1520c45f3a629463fd05733798b86..a255af203012376e31d2536c93e0c6ccd3c120b0 100644 --- a/tools/python/pizza/log.py +++ b/tools/python/pizza/log.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # log tool @@ -28,7 +28,7 @@ nvec = l.nvec # of vectors of thermo info nlen = l.nlen length of each vectors names = l.names list of vector names t,pe,... = l.get("Time","KE",...) return one or more vectors of values -l.write("file.txt") write all vectors to a file +l.write("file.txt") write all vectors to a file l.write("file.txt","Time","PE",...) write listed vectors to a file get and write allow abbreviated (uniquely) vector names @@ -89,7 +89,7 @@ class log: # -------------------------------------------------------------------- # read all thermo from all files - + def read_all(self): self.read_header(self.flist[0]) if self.nvec == 0: raise StandardError,"log file has no values" @@ -100,7 +100,7 @@ class log: print # sort entries by timestep, cull duplicates - + self.data.sort(self.compare) self.cull() self.nlen = len(self.data) @@ -133,9 +133,9 @@ class log: else: count = 0 for i in range(self.nvec): - if self.names[i].find(key) == 0: - count += 1 - index = i + if self.names[i].find(key) == 0: + count += 1 + index = i if count == 1: map.append(index) else: @@ -161,9 +161,9 @@ class log: else: count = 0 for i in range(self.nvec): - if self.names[i].find(key) == 0: - count += 1 - index = i + if self.names[i].find(key) == 0: + count += 1 + index = i if count == 1: map.append(index) else: @@ -226,7 +226,7 @@ class log: keywords.insert(0,"Step") i = 0 for keyword in keywords: - self.names.append(keyword) + self.names.append(keyword) self.ptr[keyword] = i i += 1 @@ -236,7 +236,7 @@ class log: line = txt[s1:s2] words = line.split() for i in range(len(words)): - self.names.append(words[i]) + self.names.append(words[i]) self.ptr[words[i]] = i self.nvec = len(self.names) @@ -275,43 +275,43 @@ class log: if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2 if self.style == 2: - s1 = txt.find("\n",s1) + 1 + s1 = txt.find("\n",s1) + 1 elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1 s1 = 0 elif s1 == -1 and s2 >= 0: # found s2, but no s1 - last = 1 + last = 1 s1 = 0 elif s1 >= 0 and s2 == -1: # found s1, but no s2 last = 1 if self.style == 1: s2 = txt.rfind("\n--",s1) + 1 else: - s1 = txt.find("\n",s1) + 1 + s1 = txt.find("\n",s1) + 1 s2 = txt.rfind("\n",s1) + 1 - eof -= len(txt) - s2 + eof -= len(txt) - s2 elif s1 == -1 and s2 == -1: # found neither # could be end-of-file section - # or entire read was one chunk + # or entire read was one chunk if txt.find("Loop time of",start) == start: # end of file, so exit - eof -= len(txt) - start # reset eof to "Loop" - break + eof -= len(txt) - start # reset eof to "Loop" + break - last = 1 # entire read is a chunk + last = 1 # entire read is a chunk s1 = 0 if self.style == 1: s2 = txt.rfind("\n--",s1) + 1 else: s2 = txt.rfind("\n",s1) + 1 - eof -= len(txt) - s2 - if s1 == s2: break + eof -= len(txt) - s2 + if s1 == s2: break chunk = txt[s1:s2-1] start = s2 # split chunk into entries # parse each entry for numeric fields, append to data - + if self.style == 1: sections = chunk.split("\n--") pat1 = re.compile("Step\s*(\S*)\s") diff --git a/tools/python/pizza/pdbfile.py b/tools/python/pizza/pdbfile.py index 1713ada0433fee591d00e49f80fceffad4728b21..9b2238cbd6d55f3e88119cc452c7009c20ad6d01 100644 --- a/tools/python/pizza/pdbfile.py +++ b/tools/python/pizza/pdbfile.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # pdb tool @@ -22,7 +22,7 @@ p = pdbfile("3CRO",d) read in single PDB file with snapshot data if only one 4-char file specified and it is not found, it will be downloaded from http://www.rcsb.org as 3CRO.pdb d arg is object with atom coordinates (dump, data) - + p.one() write all output as one big PDB file to tmp.pdb p.one("mine") write to mine.pdb p.many() write one PDB file per snapshot: tmp0000.pdb, ... @@ -36,7 +36,7 @@ p.single(N,"new") write as new.pdb if one file in str arg and d: one new PDB file per snapshot using input PDB file as template multiple input PDB files with a d is not allowed - + index,time,flag = p.iterator(0) index,time,flag = p.iterator(1) @@ -87,7 +87,7 @@ class pdbfile: # flist = full list of all PDB input file names # append .pdb if needed - + if filestr: list = filestr.split() flist = [] @@ -107,7 +107,7 @@ class pdbfile: raise StandardError, "no input PDB file(s)" # grab PDB file from http://rcsb.org if not a local file - + if len(self.files) == 1 and len(self.files[0]) == 8: try: open(self.files[0],'r').close() @@ -117,7 +117,7 @@ class pdbfile: urllib.urlretrieve(fetchstr,self.files[0]) if self.data and len(self.files): self.read_template(self.files[0]) - + # -------------------------------------------------------------------- # write a single large PDB file for concatenating all input data or files # if data exists: @@ -135,7 +135,7 @@ class pdbfile: f = open(file,'w') # use template PDB file with each snapshot - + if self.data: n = flag = 0 while 1: @@ -153,7 +153,7 @@ class pdbfile: print >>f,"END" print file, sys.stdout.flush() - + f.close() print "\nwrote %d datasets to %s in PDB format" % (n,file) @@ -189,7 +189,7 @@ class pdbfile: f = open(file,'w') self.convert(f,which) f.close() - + print time, sys.stdout.flush() n += 1 @@ -206,13 +206,13 @@ class pdbfile: else: file = root + str(n) file += ".pdb" - + f = open(file,'w') f.write(open(infile,'r').read()) f.close() print file, sys.stdout.flush() - + n += 1 print "\nwrote %d datasets to %s*.pdb in PDB format" % (n,root) @@ -239,7 +239,7 @@ class pdbfile: self.convert(f,which) else: f.write(open(self.files[time],'r').read()) - + f.close() # -------------------------------------------------------------------- @@ -258,8 +258,8 @@ class pdbfile: # -------------------------------------------------------------------- # read a PDB file and store ATOM lines - - def read_template(self,file): + + def read_template(self,file): lines = open(file,'r').readlines() self.atomlines = {} for line in lines: diff --git a/tools/python/pizza/xyz.py b/tools/python/pizza/xyz.py index 66699ab5fa26f633eafe434c91a9e4ef0f1e1528..92b681540a2055a6fcc210c9e1d7dacd2b2690b1 100644 --- a/tools/python/pizza/xyz.py +++ b/tools/python/pizza/xyz.py @@ -3,7 +3,7 @@ # # Copyright (2005) Sandia Corporation. Under the terms of Contract # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains -# certain rights in this software. This software is distributed under +# certain rights in this software. This software is distributed under # the GNU General Public License. # xyz tool @@ -11,14 +11,14 @@ oneline = "Convert LAMMPS snapshots to XYZ format" docstr = """ -x = xyz(d) d = object containing atom coords (dump, data) +x = xyz(d) d = object containing atom coords (dump, data) x.one() write all snapshots to tmp.xyz x.one("new") write all snapshots to new.xyz x.many() write snapshots to tmp0000.xyz, tmp0001.xyz, etc x.many("new") write snapshots to new0000.xyz, new0001.xyz, etc -x.single(N) write snapshot for timestep N to tmp.xyz -x.single(N,"file") write snapshot for timestep N to file.xyz +x.single(N) write snapshot for timestep N to tmp.xyz +x.single(N,"file") write snapshot for timestep N to file.xyz """ # History @@ -41,7 +41,7 @@ class xyz: def __init__(self,data): self.data = data - + # -------------------------------------------------------------------- def one(self,*args): @@ -61,14 +61,14 @@ class xyz: for atom in atoms: itype = int(atom[1]) print >>f,itype,atom[2],atom[3],atom[4] - + print time, sys.stdout.flush() n += 1 - + f.close() print "\nwrote %d snapshots to %s in XYZ format" % (n,file) - + # -------------------------------------------------------------------- def many(self,*args): @@ -80,7 +80,7 @@ class xyz: which,time,flag = self.data.iterator(flag) if flag == -1: break time,box,atoms,bonds,tris,lines = self.data.viz(which) - + if n < 10: file = root + "000" + str(n) elif n < 100: @@ -88,7 +88,7 @@ class xyz: elif n < 1000: file = root + "0" + str(n) else: - file = root + str(n) + file = root + str(n) file += ".xyz" f = open(file,"w") print >>f,len(atoms) @@ -100,9 +100,9 @@ class xyz: sys.stdout.flush() f.close() n += 1 - + print "\nwrote %s snapshots in XYZ format" % n - + # -------------------------------------------------------------------- def single(self,time,*args): diff --git a/tools/replica/README.md b/tools/replica/README.md new file mode 100644 index 0000000000000000000000000000000000000000..9205d962b25e1b1dbb576cd2164326891167aa7b --- /dev/null +++ b/tools/replica/README.md @@ -0,0 +1,86 @@ +## reorder_remd_traj + +LAMMPS Replica Exchange Molecular Dynamics (REMD) trajectories (implemented using the temper command) are arranged by replica, i.e., each trajectory is a continuous replica that records all the ups and downs in temperature. However, often the requirement is that trajectories be continuous in temperature. This requires the LAMMPS REMD trajectories to be re-ordered, which LAMMPS does not do automatically. (see the discussion [here](https://lammps.sandia.gov/threads/msg60440.html)). The reorderLAMMPSREMD tool does exactly this in parallel (using MPI) + +(Protein folding trajectories in [Sanyal, Mittal and Shell, JPC, 2019, 151(4), 044111](https://aip.scitation.org/doi/abs/10.1063/1.5108761) were ordered in temperature space using this tool) + +#### Author + +Tanmoy Sanyal, Shell lab, UC Santa Barbara + +(currently at UC San Francisco) + +email: tanmoy dot 7989 at gmail.com + +#### Features + +- reorder LAMMPS REMD trajectories by temperature keeping only desired frames. + Note: this only handles LAMMPS format trajectories (i.e., lammpstrj format) + Trajectories can be gzipped or bz2-compressed. The trajectories are assumed to + be named as \\.%d.lammpstrj[.gz or .bz2] + +- (optionally) calculate configurational weights for each frame at each + temperature if potential energies are supplied (only implemented for the canonical (NVT) ensemble) + +#### Dependencies + +[`mpi4py`](https://mpi4py.readthedocs.io/en/stable/) +[`pymbar`](https://pymbar.readthedocs.io/en/master/) (for getting configurational weights) +[`tqdm`](https://github.com/tqdm/tqdm) (for printing pretty progress bars) +[`StringIO`](https://docs.python.org/2/library/stringio.html) (or [`io`](https://docs.python.org/3/library/io.html) if in Python 3.x) + +#### Example + +###### REMD Simulation specs +Suppose you ran a REMD simulation for the peptide example using the CHARMM forcefield (see lammps/examples/peptide) in Lammps with the following settings: + +- number of replicas = 16 +- temperatures used (in K): 200 209 219 230 241 252 264 276 289 303 317 332 348 365 382 400 (i.e., exponentially distributed in the range 270-400 K) +- timestep = 2 fs +- total number of timesteps simulated using temper = 2000 (i.e. 4 ps) +- swap frequency = temperatures swapped after every this many steps = `ns` = 10 (i.e. 20 fs) +- write frequency = trajectory frame written to disk after this many steps (using the dump command) = `nw` = 20 (i.e. 40 fs) + +###### LAMMPS output +So, when the dust settles, + +- You'll have 16 replica trajectories. For this tool to work, each replica traj must be named: `..lammpstrj[.gz or .bz2]`, where, + - `prefix` = some common prefix for all your trajectories and (say it is called "peptide")` + - `n` = replica number (0-15 in this case). Note: trajectories **must be in default LAMMPS format **(so stuff like dcd won't work) + +- You will also have a master LAMMPS log file (`logfn`) that contains the swap history of all the replicas + (for more details see [here](https://lammps.sandia.gov/doc/temper.html). Assume that this is called `log.peptide` + +- Further you must have a txt file that numpy can read which stores all the temperature values (say this is called `temps.txt`) + +###### Your desired output +- The total number of timesteps you want consider as production (i.e. after equilbration) = 1000 (i.e. last 2 ps) + +- Reordered trajectories at temperatures 200 K, 276 K, 400 K + +- Configurational log-weight calculation (using [`pymbar`](https://github.com/choderalab/pymbar)). Here, this is limited to the canonical (NVT) ensemble **and without biasing restraints** in your simulation. To do this you'd need to have a file (say called `ene.dat`) that stores a 2D (K X N) array of total potential energies, where, + + - K = total number of replicas = 16, and N = total number of frames in each replica trajectory (= 1000 / 20 = 50 in this case) + + - `ene[k,n]` = energy from n-th frame of k-th replica. + +###### Using the tool (description of the workflow) +Assume you have 16 processors at your disposal. When you run the following: + +```bash +mpirun -np 16 python reorder_remd_traj.py peptide -logfn log.peptide -tfn temps.txt -ns 10 -nw 20 -np 1000 -ot 200 276 400 -logw -e ene.peptide -od ./output +``` + +1. First the temperature swap history file (`log.peptide` in this case) is read. This is done on one processor since it is usually fast. +2. Then the (compressed or otherwise) LAMMPS replica trajectories are read in parallel. So if you have less processors than replicas at this stage, it'll be slower. +3. Then using the frame ordering generated in (1), trajectory frames read in (2) are re-ordered and written to disk in parallel. Each processor writes one trajectory. So, If you request reordered trajectories for less temperatures (3 in this case) than the total number of temperatures (16), then 16-3 = 13 processors will be retired. +4. If you have further requested configurational log-weight calculation, then they will be done on a single processor since pymbar is pretty fast. +5. Finally you will have 3 LAMMPS trajectories of the form ``peptide..lammpstrj.gz`` each with 1000 / 20 = 50 frames, where `` = 200, 276, 400. If you request reordering at a temperature like say 280 K which is not present in the supplied temp schedule (as written in `temps.txt`), the closest temperature (276 K) will be chosen. + +For more details, use the help menu generated by the tool by using: +python reorder_remd_traj.py -h + +###### Caveats +- This tool crawls through the replica trajectories and creates index files that are hidden. These are called .byteind_`'.gz files. You may delete these if you want, but subsequent replica reads will be slow in that case. + +- When writing trajectories to disk, the trajectories are first written to a buffer in memory, and then finally dumped all-at-once to the disk. While this makes the tool very fast, it can cause out-of-memory errors for very large trajectories. A useful feature might be to write to the buffer in batches and emptying to disk when some (predefined) max-buffer-size is exceeded. diff --git a/tools/replica/example/data.peptide b/tools/replica/example/data.peptide new file mode 120000 index 0000000000000000000000000000000000000000..f523fc92c199143f0f16724c2444d4d7e779acb3 --- /dev/null +++ b/tools/replica/example/data.peptide @@ -0,0 +1 @@ +../../../examples/peptide/data.peptide \ No newline at end of file diff --git a/tools/replica/example/in.peptide b/tools/replica/example/in.peptide new file mode 100644 index 0000000000000000000000000000000000000000..5d321e34c34a3eb6042d0301e17e47389873c372 --- /dev/null +++ b/tools/replica/example/in.peptide @@ -0,0 +1,50 @@ +# Solvated 5-mer peptide + +#---------------------------------- +# Taken as is from examples/peptide + +units real +atom_style full +boundary p p p + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 +#---------------------------------- + + +# temperature schedule for REMD +variable idx world 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 +variable t world 200.0 209.0 219.0 230.0 241.0 252.0 264.0 276.0 289.0 303.0 317.0 332.0 348.0 365.0 382.0 400.0 + +# thermostat +fix thermostat all langevin $t $t 1000 772530 + +# log-file output before minimization +thermo_style custom step temp ke pe +thermo 20 + +# minimization +minimize 1e-4 0.0 1000 1000 + +# change logfile output after minimization +thermo_style custom step temp pe +thermo 20 + +# trajectory style +dump myDump all atom 20 peptide.${idx}.lammpstrj.gz +dump_modify myDump sort id scale no + +# run REMD (for realistic results run for 100000000 steps with 10000 frequency) +reset_timestep 0 +temper 2000 10 $t thermostat 3847 5382 diff --git a/tools/replica/example/parse_ene.py b/tools/replica/example/parse_ene.py new file mode 100644 index 0000000000000000000000000000000000000000..00cee08d68ea9fec314c404a508ed608d2b2f36a --- /dev/null +++ b/tools/replica/example/parse_ene.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python + +import os, sys, numpy as np + +tempfn = os.path.abspath(sys.argv[1]) +logfnprefix = os.path.abspath(sys.argv[2]) + +temps = np.loadtxt(tempfn) +ntemps = len(temps) +u_kn = [] +start_token = 'Step Temp PotEng' +end_token = 'Loop time' + +for i in range(ntemps): + logfn = '%s.%d' % (logfnprefix, i) + with open(logfn, 'r') as of: + lines = of.readlines() + + # extract relevant lines from logfile + start = [lines.index(line) for line in lines if line.startswith(start_token)][0] + lines = lines[(start+1) : ] + stop = [lines.index(line) for line in lines if line.startswith(end_token)][0] + lines = lines[:stop] + + # store the potential energies + pe = [float(line.strip().split()[-1]) for line in lines] + u_kn.append(pe) + +u_kn = np.array(u_kn) +np.savetxt('ene.peptide', u_kn, fmt = '%5.5f') diff --git a/tools/replica/example/run.sh b/tools/replica/example/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..f190bf5dfa812ab4ada3ad634072b3cc6efdebdf --- /dev/null +++ b/tools/replica/example/run.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +## run REMD using LAMMPS +mpirun -np 16 ~/mysoftware/lammps/src/lmp_mpi -partition 16x1 -in in.peptide -log log.peptide + +## collect all energies from different replica logs +echo ; echo +echo "Parsing energies from replica logs" +python parse_ene.py temps.txt log.peptide + +## run the reordering tool to get reordered trajectories @ 200 K, 276 K, 400 K +echo ; echo +mpirun -np 16 python ../reorder_remd_traj.py peptide -logfn log.peptide -tfn temps.txt -ns 10 -nw 20 -np 1000 -ot 200 276 400 -logw -e ene.peptide -od ./output diff --git a/tools/replica/example/runlog.05Sep19 b/tools/replica/example/runlog.05Sep19 new file mode 100644 index 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3 0 5 2 7 4 9 6 11 8 13 10 15 12 14 + + +Parsing energies from replica logs + + +Getting frames from all replicas at temperature: +200.00 K +209.00 K +219.00 K +230.00 K +241.00 K +252.00 K +264.00 K +276.00 K +289.00 K +303.00 K +317.00 K +332.00 K +348.00 K +365.00 K +382.00 K +400.00 K + +Releasing 13 excess procs +Writing buffer to file + +Running pymbar... +K (total states) = 16, total samples = 800 +N_k = +[50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50] +There are 16 states with samples. +Initializing free energies to zero. +Initial dimensionless free energies with method zeros +f_k = +[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.] +Final dimensionless free energies +f_k = +[ 0. 889.75988663 1792.61111609 2695.06980154 + 3515.14636632 4263.62894529 5009.01862104 5689.59180324 + 6363.10021193 7023.7847743 7626.11234062 8215.09228661 + 8787.37318432 9340.44739436 9844.29510404 10331.10090589] +MBAR initialization complete. + +Extracting log-weights... diff --git a/tools/replica/example/temps.txt b/tools/replica/example/temps.txt new file mode 100644 index 0000000000000000000000000000000000000000..5931ff06c8c965eb3ad086d2bbb9ddadc46c33be --- /dev/null +++ b/tools/replica/example/temps.txt @@ -0,0 +1 @@ +200.0 209.0 219.0 230.0 241.0 252.0 264.0 276.0 289.0 303.0 317.0 332.0 348.0 365.0 382.0 400.0 diff --git a/tools/replica/reorder_remd_traj.py b/tools/replica/reorder_remd_traj.py new file mode 100644 index 0000000000000000000000000000000000000000..5f4f316b14b60b9c8303d33ea3e48319faaf669b --- /dev/null +++ b/tools/replica/reorder_remd_traj.py @@ -0,0 +1,573 @@ +#!/usr/bin/env python + +""" +LAMMPS Replica Exchange Molecular Dynamics (REMD) trajectories are arranged by +replica, i.e., each trajectory is a continuous replica that records all the +ups and downs in temperature. However, often the requirement is trajectories +that are continuous in temperature, which is achieved by this tool. + +Author: +Tanmoy Sanyal, Shell lab, Chemical Engineering, UC Santa Barbara +Email: tanmoy dot 7989 at gmail dot com + +Usage +----- +To get detailed information about the arguments, flags, etc use: +python reorder_remd_traj.py -h or +python reorder_remd_traj.py --help + +Features of this script +----------------------- +a) reorder LAMMPS REMD trajectories by temperature keeping only desired frames. +Note: this only handles LAMMPS format trajectories (i.e. .lammpstrj format) +Trajectories can be gzipped or bz2-compressed. The trajectories are assumed to +be named as .%d.lammpstrj[.gz or .bz2] + +b) (optionally) calculate configurational weights for each frame at each +temperature if potential energies are supplied. But this if for the canonical +(NVT) ensemble only. + +Dependencies +------------ +mpi4py +pymbar (for getting configurational weights) +tqdm (for printing pretty progress bars) +StringIO (or io if in Python 3.x) + +""" + + + +import os, numpy as np, argparse, time, pickle +from scipy.special import logsumexp +from mpi4py import MPI + +from tqdm import tqdm +import gzip, bz2 +try: + # python-2 + from StringIO import StringIO as IOBuffer +except ImportError: + # python-3 + from io import BytesIO as IOBuffer + + + +#### INITIALISE MPI #### +# (note that all output on screen will be printed only on the ROOT proc) +ROOT = 0 +comm = MPI.COMM_WORLD +me = comm.rank # my proc id +nproc = comm.size + + +#### HELPER FUNCTIONS #### +def _get_nearest_temp(temps, query_temp): + """ + Helper function to get the nearest temp in a list + from a given query_temp + + :param temps: list of temps. + + :param query_temp: query temp + + Returns: + idx: index of nearest temp in the list + + out_temp: nearest temp from the list + """ + + if isinstance(temps, list): temps = np.array(temps) + return temps[np.argmin(np.abs(temps-query_temp))] + + +def readwrite(trajfn, mode): + """ + Helper function for input/output LAMMPS traj files. + Trajectories may be plain text, .gz or .bz2 compressed. + + :param trajfn: name of LAMMPS traj + + :param mode: "r" ("w") and "rb" ("wb") depending on read or write + + Returns: file pointer + """ + + if trajfn.endswith(".gz"): + of = gzip.open(trajfn, mode) + #return gzip.GzipFile(trajfn, mode) + elif trajfn.endswith(".bz2"): + of = bz2.open(trajfn, mode) + #return bz2.BZ2File(trajfn, mode) + else: + of = open(trajfn, mode) + return of + + +def get_replica_frames(logfn, temps, nswap, writefreq): + """ + Get a list of frames from each replica that is + at a particular temp. Do this for all temps. + + :param logfn: master LAMMPS log file that contains the temp + swap history of all replicas + + :param temps: list of all temps used in the REMD simulation. + + :param nswap: swap frequency of the REMD simulation + + :param writefreq: traj dump frequency in LAMMPS + + Returns: master_frametuple_dict: + dict containing a tuple (replica #, frame #) for each temp. + """ + + n_rep = len(temps) + swap_history = np.loadtxt(logfn, skiprows = 3) + master_frametuple_dict = dict( (n, []) for n in range(n_rep) ) + + # walk through the replicas + print("Getting frames from all replicas at temperature:") + for n in range(n_rep): + print("%3.2f K" % temps[n]) + rep_inds = [np.where(x[1:] == n)[0][0] for x in swap_history] + + # case-1: when frames are dumped faster than temp. swaps + if writefreq <= nswap: + for ii, i in enumerate(rep_inds[:-1]): + start = int(ii * nswap / writefreq) + stop = int( (ii+1) * nswap / writefreq) + [master_frametuple_dict[n].append( (i,x) ) \ + for x in range(start, stop)] + + # case-2: when temps. are swapped faster than dumping frames + else: + nskip = int(writefreq / nswap) + [master_frametuple_dict[n].append( (i,ii) ) \ + for ii, i in enumerate(rep_inds[0::nskip])] + + return master_frametuple_dict + + +def get_byte_index(rep_inds, byteindfns, intrajfns): + """ + Get byte indices from (un-ordered) trajectories. + + :param rep_inds: indices of replicas to process on this proc + + :param byteindsfns: list of filenames that will contain the byte indices + + :param intrajfns: list of (unordered) input traj filenames + """ + for n in rep_inds: + # check if the byte indices for this traj has aleady been computed + if os.path.isfile(byteindfns[n]): continue + + # extract bytes + fobj = readwrite(intrajfns[n], "rb") + byteinds = [ [0,0] ] + + # place file pointer at first line + nframe = 0 + first_line = fobj.readline() + cur_pos = fobj.tell() + + # status printed only for replica read on root proc + # this assumes that each proc takes roughly the same time + if me == ROOT: + pb = tqdm(desc = "Reading replicas", leave = True, + position = ROOT + 2*me, + unit = "B/replica", unit_scale = True, + unit_divisor = 1024) + + # start crawling through the bytes + while True: + next_line = fobj.readline() + if len(next_line) == 0: break + # this will only work with lammpstrj traj format. + # this condition essentially checks periodic recurrences + # of the token TIMESTEP. Each time it is found, + # we have crawled through a frame (snapshot) + if next_line == first_line: + nframe += 1 + byteinds.append( [nframe, cur_pos] ) + if me == ROOT: pb.update() + cur_pos = fobj.tell() + if me == ROOT: pb.update(0) + if me == ROOT: pb.close() + + # take care of the EOF + cur_pos = fobj.tell() + byteinds.append( [nframe+1, cur_pos] ) # dummy index for the EOF + + # write to file + np.savetxt(byteindfns[n], np.array(byteinds), fmt = "%d") + + # close the trajfile object + fobj.close() + + return + + +def write_reordered_traj(temp_inds, byte_inds, outtemps, temps, + frametuple_dict, nprod, writefreq, + outtrajfns, infobjs): + """ + Reorders trajectories by temp. and writes them to disk + + :param temp_inds: list index of temps (in the list of all temps) for which + reordered trajs will be produced on this proc. + + :param byte_inds: dict containing the (previously stored) byte indices + for each replica file (key = replica number) + + :param outtemps: list of all temps for which to produce reordered trajs. + + :param temps: list of all temps used in the REMD simulation. + + :param outtrajfns: list of filenames for output (ordered) trajs. + + :param frametuple_dict: dict containing a tuple (replica #, frame #) + for each temp. + + :param nprod: number of production timesteps. + Last (nprod / writefreq) frames + from the end will be written to disk. + + :param writefreq: traj dump frequency in LAMMPS + + :param infobjs: list of file pointers to input (unordered) trajs. + """ + + nframes = int(nprod / writefreq) + + for n in temp_inds: + # open string-buffer and file + buf = IOBuffer() + of = readwrite(outtrajfns[n], "wb") + + # get frames + abs_temp_ind = np.argmin( abs(temps - outtemps[n]) ) + frametuple = frametuple_dict[abs_temp_ind][-nframes:] + + # write frames to buffer + if me == ROOT: + pb = tqdm(frametuple, + desc = ("Buffering trajectories for writing"), + leave = True, position = ROOT + 2*me, + unit = 'frame/replica', unit_scale = True) + + iterable = pb + else: + iterable = frametuple + + for i, (rep, frame) in enumerate(iterable): + infobj = infobjs[rep] + start_ptr = int(byte_inds[rep][frame,1]) + stop_ptr = int(byte_inds[rep][frame+1,1]) + byte_len = stop_ptr - start_ptr + infobj.seek(start_ptr) + buf.write(infobj.read(byte_len)) + if me == ROOT: pb.close() + + # write buffer to disk + if me == ROOT: print("Writing buffer to file") + of.write(buf.getvalue()) + of.close() + buf.close() + + for i in infobjs: i.close() + + return + + +def get_canonical_logw(enefn, frametuple_dict, temps, nprod, writefreq, + kB): + """ + Gets configurational log-weights (logw) for each frame and at each temp. + from the REMD simulation. ONLY WRITTEN FOR THE CANONICAL (NVT) ensemble. + + This weights can be used to calculate the + ensemble averaged value of any simulation observable X at a given temp. T : + (T) = \sum_{k=1, ntemps} \sum_{n=1, nframes} w[idx][k,n] X[k,n] + where nframes is the number of frames to use from each *reordered* traj + + :param enefn: ascii file (readable by numpy.loadtxt) containing an array + u[r,n] of *total* potential energy for the n-th frame for + the r-th replica. + + :param frametuple_dict: dict containing a tuple (replica #, frame #) + for each temp. + + :param temps: array of temps. used in the REMD simulation + + :param nprod: number of production timesteps. Last (nprod / writefreq) + frames from the end will be written to disk. + + :param writefreq: traj dump frequency in LAMMPS + + :param kB : Boltzmann constant to set the energy scale. + Default is in kcal/mol + + Returns: logw: dict, logw[l][k,n] gives the log weights from the + n-th frame of the k-th temp. *ordered* trajectory + to reweight to the l-th temp. + + """ + + try: + import pymbar + except ImportError: + print(""" + Configurational log-weight calculation requires pymbar. + Here are some options to install it: + conda install -c omnia pymbar + pip install --user pymbar + sudo pip install pymbar + + To install the dev. version directly from github, use: + pip install pip install git+https://github.com/choderalab/pymbar.git + """) + + u_rn = np.loadtxt(enefn) + ntemps = u_rn.shape[0] # number of temps. + nframes = int(nprod / writefreq) # number of frames at each temp. + + # reorder the temps + u_kn = np.zeros([ntemps, nframes], float) + for k in range(ntemps): + frame_tuple = frametuple_dict[k][-nframes:] + for i, (rep, frame) in enumerate(frame_tuple): + u_kn[k, i] = u_rn[rep, frame] + + # prep input for pymbar + #1) array of frames at each temp. + nframes_k = nframes * np.ones(ntemps, np.uint8) + + #2) inverse temps. for chosen energy scale + beta_k = 1.0 / (kB * temps) + + #3) get reduced energies (*ONLY FOR THE CANONICAL ENSEMBLE*) + u_kln = np.zeros([ntemps, ntemps, nframes], float) + for k in range(ntemps): + u_kln[k] = np.outer(beta_k, u_kn[k]) + + # run pymbar and extract the free energies + print("\nRunning pymbar...") + mbar = pymbar.mbar.MBAR(u_kln, nframes_k, verbose = True) + f_k = mbar.f_k # (1 x k array) + + # calculate the log-weights + print("\nExtracting log-weights...") + log_nframes = np.log(nframes) + logw = dict( (k, np.zeros([ntemps, nframes], float)) for k in range(ntemps) ) + # get log-weights to reweight to this temp. + for k in range(ntemps): + for n in range(nframes): + num = -beta_k[k] * u_kn[k,n] + denom = f_k - beta_k[k] * u_kn[k,n] + for l in range(ntemps): + logw[l][k,n] = num - logsumexp(denom) - log_nframes + + return logw + + + +#### MAIN WORKFLOW #### +if __name__ == "__main__": + # accept user inputs + parser = argparse.ArgumentParser(description = __doc__, + formatter_class = argparse.RawDescriptionHelpFormatter) + + parser.add_argument("prefix", + help = "Prefix of REMD LAMMPS trajectories.\ + Supply full path. Trajectories assumed to be named as \ + .%%d.lammpstrj. \ + Can be in compressed (.gz or .bz2) format. \ + This is a required argument") + + parser.add_argument("-logfn", "--logfn", default = "log.lammps", + help = "LAMMPS log file that contains swap history \ + of temperatures among replicas. \ + Default = 'lammps.log'") + + parser.add_argument("-tfn", "--tempfn", default = "temps.txt", + help = "ascii file (readable by numpy.loadtxt) with \ + the temperatures used in the REMD simulation.") + + parser.add_argument("-ns", "--nswap", type = int, + help = "Swap frequency used in LAMMPS temper command") + + parser.add_argument("-nw", "--nwrite", type = int, default = 1, + help = "Trajectory writing frequency used \ + in LAMMPS dump command") + + parser.add_argument("-np", "--nprod", type = int, default = 0, + help = "Number of timesteps to save in the reordered\ + trajectories.\ + This should be in units of the LAMMPS timestep") + + parser.add_argument("-logw", "--logw", action = 'store_true', + help = "Supplying this flag \ + calculates *canonical* (NVT ensemble) log weights") + + parser.add_argument("-e", "--enefn", + help = "File that has n_replica x n_frames array\ + of total potential energies") + + parser.add_argument("-kB", "--boltzmann_const", + type = float, default = 0.001987, + help = "Boltzmann constant in appropriate units. \ + Default is kcal/mol") + + parser.add_argument("-ot", "--out_temps", nargs = '+', type = np.float64, + help = "Reorder trajectories at these temperatures.\n \ + Default is all temperatures used in the simulation") + + parser.add_argument("-od", "--outdir", default = ".", + help = "All output will be saved to this directory") + + # parse inputs + args = parser.parse_args() + traj_prefix = os.path.abspath(args.prefix) + logfn = os.path.abspath(args.logfn) + tempfn = os.path.abspath(args.tempfn) + + nswap = args.nswap + writefreq = args.nwrite + nprod = args.nprod + + enefn = args.enefn + if not enefn is None: enefn = os.path.abspath(enefn) + get_logw = args.logw + kB = args.boltzmann_const + + out_temps = args.out_temps + outdir = os.path.abspath(args.outdir) + if not os.path.isdir(outdir): + if me == ROOT: os.mkdir(outdir) + + # check that all input files are present (only on the ROOT proc) + if me == ROOT: + if not os.path.isfile(tempfn): + raise IOError("Temperature file %s not found." % tempfn) + elif not os.path.isfile(logfn): + raise IOError("LAMMPS log file %s not found." % logfn) + elif get_logw and not os.path.isfile(enefn): + raise IOError("Canonical log-weight calculation requested but\ + energy file %s not found" % enefn) + + # get (unordered) trajectories + temps = np.loadtxt(tempfn) + ntemps = len(temps) + intrajfns = ["%s.%d.lammpstrj" % (traj_prefix, k) for k in range(ntemps)] + # check if the trajs. (or their zipped versions are present) + for i in range(ntemps): + this_intrajfn = intrajfns[i] + x = this_intrajfn + ".gz" + if os.path.isfile(this_intrajfn): continue + elif os.path.isfile(this_intrajfn + ".gz"): + intrajfns[i] = this_intrajfn + ".gz" + elif os.path.isfile(this_intrajfn + ".bz2"): + intrajfns[i] = this_intrajfn + ".bz2" + else: + if me == ROOT: + raise IOError("Trajectory for replica # %d missing" % i) + + # set output filenames + outprefix = os.path.join(outdir, traj_prefix.split('/')[-1]) + outtrajfns = ["%s.%3.2f.lammpstrj.gz" % \ + (outprefix, _get_nearest_temp(temps, t)) \ + for t in out_temps] + byteindfns = [os.path.join(outdir, ".byteind_%d.gz" % k) \ + for k in range(ntemps)] + frametuplefn = outprefix + '.frametuple.pickle' + if get_logw: + logwfn = outprefix + ".logw.pickle" + + + # get a list of all frames at a particular temp visited by each replica + # this is fast so run only on ROOT proc. + master_frametuple_dict = {} + if me == ROOT: + master_frametuple_dict = get_replica_frames(logfn = logfn, + temps = temps, + nswap = nswap, + writefreq = writefreq) + # save to a pickle from the ROOT proc + with open(frametuplefn, 'wb') as of: + pickle.dump(master_frametuple_dict, of) + + # broadcast to all procs + master_frametuple_dict = comm.bcast(master_frametuple_dict, root = ROOT) + + # define a chunk of replicas to process on each proc + CHUNKSIZE_1 = int(ntemps/nproc) + if me < nproc - 1: + my_rep_inds = range( (me*CHUNKSIZE_1), (me+1)*CHUNKSIZE_1 ) + else: + my_rep_inds = range( (me*CHUNKSIZE_1), ntemps ) + + # get byte indices from replica (un-ordered) trajs. in parallel + get_byte_index(rep_inds = my_rep_inds, + byteindfns = byteindfns, + intrajfns = intrajfns) + + # block until all procs have finished + comm.barrier() + + # open all replica files for reading + infobjs = [readwrite(i, "rb") for i in intrajfns] + + # open all byteindex files + byte_inds = dict( (i, np.loadtxt(fn)) for i, fn in enumerate(byteindfns) ) + + # define a chunk of output trajs. to process for each proc. + # # of reordered trajs. to write may be less than the total # of replicas + # which is usually equal to the requested nproc. If that is indeed the case, + # retire excess procs + n_out_temps = len(out_temps) + CHUNKSIZE_2 = int(n_out_temps / nproc) + if CHUNKSIZE_2 == 0: + nproc_active = n_out_temps + CHUNKSIZE_2 = 1 + if me == ROOT: + print("\nReleasing %d excess procs" % (nproc - nproc_active)) + else: + nproc_active = nproc + if me < nproc_active-1: + my_temp_inds = range( (me*CHUNKSIZE_2), (me+1)*CHUNKSIZE_1 ) + else: + my_temp_inds = range( (me*CHUNKSIZE_2), n_out_temps) + + # retire the excess procs + # dont' forget to close any open file objects + if me >= nproc_active: + for fobj in infobjs: fobj.close() + exit() + + # write reordered trajectories to disk from active procs in parallel + write_reordered_traj(temp_inds = my_temp_inds, + byte_inds = byte_inds, + outtemps = out_temps, temps = temps, + frametuple_dict = master_frametuple_dict, + nprod = nprod, writefreq = writefreq, + outtrajfns = outtrajfns, + infobjs = infobjs) + + # calculate canonical log-weights if requested + # usually this is very fast so retire all but the ROOT proc + if not get_logw: exit() + if not me == ROOT: exit() + + logw = get_canonical_logw(enefn = enefn, temps = temps, + frametuple_dict = master_frametuple_dict, + nprod = nprod, writefreq = writefreq, + kB = kB) + + + # save the logweights to a pickle + with open(logwfn, 'wb') as of: + pickle.dump(logw, of) + + diff --git a/tools/singularity/README.md b/tools/singularity/README.md new file mode 100644 index 0000000000000000000000000000000000000000..d316e629f3563abfeef7bee7efee6036e6cb76be --- /dev/null +++ b/tools/singularity/README.md @@ -0,0 +1,50 @@ +# Singularity container definitions for compiling/testing LAMMPS + +The *.def files in this folder can be used to build container images +for [Singularity](https://sylabs.io) suitable for compiling and testing +LAMMPS on a variety of OS variants with support for most standard packages +and building/spellchecking the manual. This allows to test and debug +LAMMPS code on different OS variants than what is locally installed on +your development workstation, e.g. when bugs are reported that can only +be reproduced on a specific OS or with specific (mostly older) versions +of tools, compilers, or libraries. + +Ready-to-use container images built from these definition files are +occasionally uploaded to the container library at sylabs.io. They +can be found here: https://cloud.sylabs.io/library/lammps/default/lammps_development# +and will be signed with the key fingerprint: EEA103764C6C633EDC8AC428D9B44E93BF0C375A + +Here is a workflow for testing a compilation of LAMMPS with a locally +built CentOS 7.x singularity container. + +``` +cd some/work/directory +git clone --depth 500 git://github.com/lammps/lammps.git lammps +mkdir build-centos7 +cd build-centos7 +sudo singularity build centos7.sif ../tools/singularity/centos7.def +singularity shell centos7.sif +cmake -C ../cmake/presets/most.cmake -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -std=c++11" ../cmake +make +``` + +And here is the equivalent workflow for testing a compilation of LAMMPS +using a pre-built Ubuntu 18.04LTS singularity container. + +``` +cd some/work/directory +git clone --depth 500 git://github.com/lammps/lammps.git lammps +mkdir build-ubuntu18 +cd build-ubuntu18 +singularity pull library://lammps/default/lammps_development:ubuntu18.04 +singularity shell lammps_development_ubuntu18.04.sif +cmake -C ../cmake/presets/most.cmake ../cmake +make +``` + +| Currently available: | | +| --- | --- | +| centos7.def | CentOS 7.x with EPEL enabled | +| centos8.def | CentOS 8.x with EPEL enabled | +| ubuntu16.04.def | Ubuntu 16.04LTS with default MPI == OpenMPI | +| ubuntu18.04.def | Ubuntu 18.04LTS with default MPI == OpenMPI | diff --git a/tools/singularity/centos7.def b/tools/singularity/centos7.def new file mode 100644 index 0000000000000000000000000000000000000000..81601055240a1e64c62ce6fd7337b5cab1ff6a81 --- /dev/null +++ b/tools/singularity/centos7.def @@ -0,0 +1,10 @@ +BootStrap: library +From: centos:7 + +%post + yum -y install epel-release + yum -y update + yum -y install vim-enhanced ccache gcc-c++ gcc-gfortran clang gdb valgrind-openmpi make cmake cmake3 ninja-build patch which file git libpng-devel libjpeg-devel openmpi-devel mpich-devel python-devel python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant + +%labels + Author akohlmey diff --git a/tools/singularity/centos8.def b/tools/singularity/centos8.def new file mode 100644 index 0000000000000000000000000000000000000000..b48979cab108754a78b723b549bad0e74839a216 --- /dev/null +++ b/tools/singularity/centos8.def @@ -0,0 +1,13 @@ +BootStrap: docker +From: centos:8 + +%post + dnf -y install epel-release dnf-utils + dnf config-manager --set-enabled PowerTools + dnf -y update + dnf -y install vim-enhanced ccache gcc-c++ gcc-gfortran clang gdb make cmake patch which file git libpng-devel libjpeg-devel openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel enchant platform-python-devel python3-virtualenv valgrind openblas ninja-build eigen3-devel + +#No match for argument: valgrind-openmpi + +%labels + Author akohlmey diff --git a/tools/singularity/ubuntu16.04.def b/tools/singularity/ubuntu16.04.def new file mode 100644 index 0000000000000000000000000000000000000000..2f7841bd4afc342aeee10d40b7548413847a1794 --- /dev/null +++ b/tools/singularity/ubuntu16.04.def @@ -0,0 +1,9 @@ +BootStrap: docker +From: ubuntu:16.04 + +%post + apt-get update -y + env DEBIAN_FRONTEND=noninteractive apt-get install -y make cmake cmake-curses-gui ninja-build git ccache gcc g++ gfortran libfftw3-dev libjpeg-dev libpng12-dev libblas-dev liblapack-dev mpi-default-bin mpi-default-dev libeigen3-dev libgsl-dev libopenblas-dev virtualenv python-dev enchant vim-nox + +%labels + Author akohlmey diff --git a/tools/singularity/ubuntu18.04.def b/tools/singularity/ubuntu18.04.def new file mode 100644 index 0000000000000000000000000000000000000000..c87daa8de5d834fd3c156060f531bc7fc9f88ad9 --- /dev/null +++ b/tools/singularity/ubuntu18.04.def @@ -0,0 +1,9 @@ +BootStrap: docker +From: ubuntu:18.04 + +%post + apt-get update -y + env DEBIAN_FRONTEND=noninteractive apt-get install -y make cmake cmake-curses-gui ninja-build git ccache gcc g++ gfortran libfftw3-dev libjpeg-dev libpng-dev libblas-dev liblapack-dev mpi-default-bin mpi-default-dev libeigen3-dev libgsl-dev libopenblas-dev virtualenv python-dev enchant vim-nox voro++-dev + +%labels + Author akohlmey