Loading doc/src/pair_fep_soft.rst +5 −3 Original line number Diff line number Diff line Loading @@ -161,11 +161,11 @@ Examples pair_style coul/long/soft 1.0 10.0 9.5 pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 pair_coeff 1 1 1.0 pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 pair_coeff 1 1 1.0 pair_style morse/soft 4 0.9 10.0 pair_coeff * * 100.0 2.0 1.5 1.0 Loading Loading @@ -284,7 +284,9 @@ core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if :math:`\lambda = 1`, a singularity may occur. These sub-styles are suitable to represent charges embedded in the Lennard-Jones radius of another site (for example hydrogen atoms in several water models). example hydrogen atoms in several water models). The :math:`\lambda` must be defined for each pair, and *coul/cut/soft* can accept an optional cutoff as the second coefficient. .. note:: Loading unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml +79 −71 Original line number Diff line number Diff line --- lammps_version: 30 Jun 2020 date_generated: Sun Jul 12 19:14:20 202 lammps_version: 21 Jul 2020 date_generated: Mon Aug 10 17:03:53 202 epsilon: 1e-13 prerequisites: ! | atom full pair hybrid/overlay pair tip4p/long/soft pair lj/cut pre_commands: ! | variable newton_pair delete variable newton_pair index on Loading @@ -15,83 +17,89 @@ post_commands: ! | kspace_modify gewald 0.3 kspace_modify compute no input_file: in.fourmol pair_style: tip4p/long/soft 5 2 5 1 0.15 10.0 pair_style: hybrid/overlay tip4p/long/soft 5 2 5 1 0.15 4.0 2.5 10.0 lj/cut 8.0 pair_coeff: ! | * * 1 1 lj/cut 0.02 2.5 2 2 lj/cut 0.005 1.0 2 4 lj/cut 0.005 0.5 3 3 lj/cut 0.02 3.2 4 4 lj/cut 0.015 3.1 5 5 lj/cut 0.015 3.1 * * tip4p/long/soft 0.83 extract: ! | cut_coul 0 qdist 0 typeO 0 typeH 0 typeA 0 typeB 0 lambda 2 natoms: 29 init_vdwl: 0 init_coul: 220.904555359383 init_stress: ! |- -3.1383522071804158e+01 -4.1960152113677644e+01 -3.8477634382983439e+01 1.2128496669147679e-01 -1.1198183080297536e+01 6.5268065842458656e+00 init_vdwl: 8.07036960332134 init_coul: 100.236229731909 init_stress: ! |2- 2.0560777882594444e+01 2.1654965423904063e+01 1.0056493693519297e+01 -2.4240063285208659e+00 -1.3467251681546395e+01 -1.4781331319647906e+01 init_forces: ! |2 1 2.6118798121573339e+00 -5.1644240368157168e-01 1.8001437196967410e-01 2 -1.9557407939667784e-01 -2.8434279090485344e+00 -1.2037666274486341e+00 3 1.3516729385656326e-02 -8.3981675119811638e-02 1.3800938031093543e-02 4 -7.9314978889013857e-02 1.6212643266693107e-02 -2.3663785465653561e-01 5 -5.4637120859630939e-01 6.5600989679059629e-01 -6.8980117595427104e-02 6 1.4667908736646822e+00 -3.8991837337279565e+00 -2.5411858592494596e+00 7 -6.7512752271559159e-02 8.9321193431929236e-01 3.8067644595952399e+00 8 -1.4944738413316052e+00 4.5568557152238283e+00 2.3556173395822269e+00 9 1.5618105874324246e+00 -5.8578891996706437e+00 1.3701350515471384e+00 10 -2.6110782215753048e-01 3.6476179750311333e-01 -2.2728997157574121e-01 11 -9.3766462457826905e-01 1.0563563299185068e+00 -5.5775022539970631e-01 12 2.8818522397941928e+00 -5.4162419106234894e-01 1.4389000151728266e+00 13 -7.5720425159299595e-02 3.8772041103398963e-02 -1.8346431648817585e-01 14 -1.0557020156519512e+00 3.6717714938726143e-01 -1.0728817695848940e-01 15 3.5162907632314466e-01 -1.9165325094615621e-01 -1.0148660141104417e+00 16 -9.0625899241785468e-01 -4.0978261630457780e-01 2.0869169313568565e+00 17 -2.2809774497744830e+00 6.2063926325737908e+00 -6.6646229271776178e+00 18 3.7211451024737952e-01 4.7949556440316261e+00 -7.9026298092983307e+00 19 1.9911596893384120e+00 -7.2195675725850206e-01 5.5334689749229105e+00 20 -2.9127135301570397e+00 -4.0021946638596519e+00 4.1375019377447915e+00 21 1.5279890933802478e+00 3.2050983299936133e+00 -6.7676269505726276e+00 22 4.4657588078956723e+00 1.0585032152255676e+00 5.8268290139589860e+00 23 -6.2938601634201303e+00 -3.9616631352879410e+00 1.3192732707154482e+00 24 -1.0816004906486070e+00 6.8108467987003323e+00 -3.6672013590293373e+00 25 4.9746167445264264e+00 -5.2361422570157790e-01 3.9262159421100877e+00 26 -4.3769290854851999e+00 -6.4816134554785325e+00 -8.1534775153570904e-01 27 -1.5366446134631597e+00 7.3612903591829397e+00 -2.7208483294328234e+00 28 6.4035032875423159e+00 -2.1779017025677483e+00 4.1727109672631357e+00 29 -4.5201953782892055e+00 -5.1735155675050022e+00 -1.4886429234413563e+00 run_vdwl: 0 run_coul: 220.048510859325 run_stress: ! |- -3.2535424832930019e+01 -4.2286524075903131e+01 -3.8162313208279478e+01 -4.1743354710271896e-01 -1.2139232458029813e+01 5.8729467776122277e+00 1 1.1274640438568120e+00 -2.7751438713476445e-01 1.8790157920119499e-01 2 -8.1752474659205140e-03 -1.2699647841871851e+00 -6.6459159127307632e-01 3 -1.0359163487629111e+01 1.0628743132498057e+01 6.9531443122386021e+00 4 -3.8774507719289648e-02 6.8713592138544667e-03 -1.1229959830689475e-01 5 -2.5662749622784636e-01 3.0016453264313309e-01 -3.0975775200070998e-02 6 1.0960634574125447e+01 -1.2382387659312155e+01 -8.0618970130884442e+00 7 -2.2832342249723914e-02 4.0208606857513818e-01 1.6920699571811064e+00 8 -6.8521757840727771e-01 2.0368233934687781e+00 9.7118125999477067e-01 9 7.4909470156608438e-01 -2.6744666902612630e+00 7.6981273184827481e-01 10 -2.6708236457335047e+01 -2.3350711235384516e+00 -3.2210899693251669e+00 11 -4.3462661520328849e-01 4.9338265093982914e-01 -2.5789183190888032e-01 12 1.8728378079288682e+01 1.6353733318327308e+01 -1.0844583731336934e+01 13 -2.4463327596094566e-02 1.2857926819797217e-02 -8.6110469907762582e-02 14 -4.9151265846168884e-01 1.7025446557900215e-01 -6.2082087769697814e-02 15 1.6354568305672246e-01 -7.7698250077885903e-02 -4.6974575369116089e-01 16 8.8587570764212451e+00 -1.4378065918299963e+01 1.5533451154012512e+01 17 -1.0936837040746663e+00 2.9076882464810643e+00 -3.0280186326297125e+00 18 1.4165835835894441e-01 2.1223098841030583e+00 -3.2865754977449257e+00 19 7.5955373016364403e-01 -4.4338928207346051e-01 2.3485104425164778e+00 20 -1.1613012874078987e+00 -1.6523434765045006e+00 1.7676741920085632e+00 21 6.0531811555082471e-01 1.3729063968893083e+00 -2.7923868706589650e+00 22 1.7600151197582461e+00 3.8208254002861425e-01 2.3799251532831041e+00 23 -2.5067133471709186e+00 -1.6128262839507992e+00 5.9072667161630799e-01 24 -4.3247234229563630e-01 2.8558353857286596e+00 -1.5284257874942948e+00 25 1.9422682067556065e+00 -2.8471459149302958e-01 1.5547858160286778e+00 26 -1.7355243132931133e+00 -2.6615580136173165e+00 -2.8544328258369955e-01 27 -6.6046529049546032e-01 3.0880567198108069e+00 -1.1428285831811784e+00 28 2.5715778047995865e+00 -9.5077350547568862e-01 1.6962019769146084e+00 29 -1.7484754906688658e+00 -2.1330220551799459e+00 -5.7043877074333793e-01 run_vdwl: 7.24904956330063 run_coul: 99.911855870525 run_stress: ! |2- 1.7268554752664841e+01 1.7311029436658394e+01 7.4057024614157427e+00 -2.3588244888881453e+00 -1.3227628622475972e+01 -1.2896658593010248e+01 run_forces: ! |2 1 2.6131680688578154e+00 -4.8342036562208102e-01 1.7840269686868443e-01 2 -2.6939190738423663e-01 -2.8744087695580736e+00 -1.1967949910131610e+00 3 1.2241135645135771e-02 -8.6362308224595855e-02 1.1995426233952385e-02 4 -7.0078081577080231e-02 1.4086570549491383e-02 -2.4078706748322398e-01 5 -5.3142632409359181e-01 6.5625319261530102e-01 -7.2314716767237025e-02 6 1.4298787244106805e+00 -3.8679855040858215e+00 -2.4359356032175739e+00 7 -2.8086280811704004e-02 8.7464586204498906e-01 3.6888214179346623e+00 8 -1.4124231673653769e+00 4.5103522011087218e+00 2.3342920102440403e+00 9 1.5527910417285362e+00 -5.9309328825446554e+00 1.4750790176848587e+00 10 -2.6235523448699766e-01 3.5757233063187277e-01 -2.3417827221851351e-01 11 -9.3594524483215680e-01 1.0583932974703241e+00 -5.4054985783631648e-01 12 2.8734736478986935e+00 -5.2369178235061564e-01 1.4455704041055824e+00 13 -8.4886264911342699e-02 2.7649029763421085e-02 -1.8007451630217339e-01 14 -1.0584924718013251e+00 3.7660596014862868e-01 -9.7984064821398389e-02 15 3.6566431724606685e-01 -2.1408413234424195e-01 -1.0347874829171970e+00 16 -9.0367323048165127e-01 -4.2277164147395230e-01 2.1071808187769565e+00 17 -2.3201090242227158e+00 6.3375931983791283e+00 -6.7748042498550483e+00 18 -1.0367666932119959e-01 4.2968689902744623e+00 -7.6416292443809883e+00 19 2.4130269465315481e+00 -3.6969316688457571e-01 5.7255888895370948e+00 20 -2.8499218759756748e+00 -3.8615438627050023e+00 3.6703556042733458e+00 21 1.6073193457487478e+00 3.0641132400813054e+00 -6.7626431241090277e+00 22 4.7465924706127307e+00 1.2150404360141627e+00 5.8893302084534209e+00 23 -6.6490042695559275e+00 -3.9871914593958206e+00 1.2434831896174121e+00 24 -1.2659428719544588e+00 6.9952347078745021e+00 -3.8287643151949902e+00 25 5.4119777555846147e+00 -3.6930902052235925e-01 4.3221517005393322e+00 26 -4.6115306062268111e+00 -6.7996016068395502e+00 -1.0144993079163778e+00 27 -1.6939299606678804e+00 7.5603905691193454e+00 -2.6741555445541247e+00 28 6.6722824605425552e+00 -2.2264192462822541e+00 4.2717918034742217e+00 29 -4.6475424291369931e+00 -5.3273838372420599e+00 -1.6341408291562105e+00 1 1.1278716657036829e+00 -2.6258678041342415e-01 1.9538437509672252e-01 2 -3.9676823681212982e-02 -1.2850233836949423e+00 -6.6803498770516612e-01 3 -9.4760567468241792e+00 9.6957989045886777e+00 6.2944176336550850e+00 4 -3.3168171571644096e-02 5.7704850010495169e-03 -1.1426546444723396e-01 5 -2.5048894068746391e-01 3.0038236609978475e-01 -3.3751199287618265e-02 6 1.0055350163583444e+01 -1.1431044936813379e+01 -7.3653563187915854e+00 7 -4.6209803855489368e-03 3.8543231435584174e-01 1.6515226454394019e+00 8 -6.5234607389721311e-01 2.0255440893673859e+00 9.5127903951105719e-01 9 7.4452791812005681e-01 -2.7066417590171179e+00 8.1503724100149588e-01 10 -2.3829098729829035e+01 -2.2599021701791333e+00 -2.6314817812596623e+00 11 -4.3274368894391779e-01 4.9145021406791028e-01 -2.4945411427223665e-01 12 1.6980364542766559e+01 1.4489682516099752e+01 -9.6372227483708528e+00 13 -3.0499236362302704e-02 8.5704383262029168e-03 -8.4575528296466557e-02 14 -4.8927749265401771e-01 1.7489541546329301e-01 -5.6958241413008877e-02 15 1.7309877483511280e-01 -8.8541792285525320e-02 -4.8073433757675438e-01 16 7.7170020069871450e+00 -1.2582802138795630e+01 1.3749590325801609e+01 17 -1.1014220836499897e+00 2.9517040521006654e+00 -3.0758280750634763e+00 18 -5.3109684989899320e-02 1.9235656396790723e+00 -3.1515066237287179e+00 19 9.2467038597949081e-01 -3.0844991584141779e-01 2.4155443336900446e+00 20 -1.1282027113852207e+00 -1.5870971471270534e+00 1.5624094409756832e+00 21 6.2530066466767331e-01 1.3012413310446329e+00 -2.7547234320822804e+00 22 1.8558491629776710e+00 4.4201627758048212e-01 2.3787636307402855e+00 23 -2.6209180821234201e+00 -1.6054037314698315e+00 5.5158435669485273e-01 24 -5.0167023518445786e-01 2.8919413595177517e+00 -1.5751546389610793e+00 25 2.0828183410931089e+00 -2.2433373855840710e-01 1.6879138663646718e+00 26 -1.7999157459828961e+00 -2.7490806231475635e+00 -3.5718231595876937e-01 27 -7.1445352480310931e-01 3.1361391652740100e+00 -1.1076521775768413e+00 28 2.6447579347741770e+00 -9.6083364912278246e-01 1.7125826632673491e+00 29 -1.7739426085325893e+00 -2.1723928021003038e+00 -6.2214756744651156e-01 ... Loading
doc/src/pair_fep_soft.rst +5 −3 Original line number Diff line number Diff line Loading @@ -161,11 +161,11 @@ Examples pair_style coul/long/soft 1.0 10.0 9.5 pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 pair_coeff 1 1 1.0 pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 pair_coeff 1 1 1.0 pair_style morse/soft 4 0.9 10.0 pair_coeff * * 100.0 2.0 1.5 1.0 Loading Loading @@ -284,7 +284,9 @@ core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if :math:`\lambda = 1`, a singularity may occur. These sub-styles are suitable to represent charges embedded in the Lennard-Jones radius of another site (for example hydrogen atoms in several water models). example hydrogen atoms in several water models). The :math:`\lambda` must be defined for each pair, and *coul/cut/soft* can accept an optional cutoff as the second coefficient. .. note:: Loading
unittest/force-styles/tests/mol-pair-tip4p_long_soft.yaml +79 −71 Original line number Diff line number Diff line --- lammps_version: 30 Jun 2020 date_generated: Sun Jul 12 19:14:20 202 lammps_version: 21 Jul 2020 date_generated: Mon Aug 10 17:03:53 202 epsilon: 1e-13 prerequisites: ! | atom full pair hybrid/overlay pair tip4p/long/soft pair lj/cut pre_commands: ! | variable newton_pair delete variable newton_pair index on Loading @@ -15,83 +17,89 @@ post_commands: ! | kspace_modify gewald 0.3 kspace_modify compute no input_file: in.fourmol pair_style: tip4p/long/soft 5 2 5 1 0.15 10.0 pair_style: hybrid/overlay tip4p/long/soft 5 2 5 1 0.15 4.0 2.5 10.0 lj/cut 8.0 pair_coeff: ! | * * 1 1 lj/cut 0.02 2.5 2 2 lj/cut 0.005 1.0 2 4 lj/cut 0.005 0.5 3 3 lj/cut 0.02 3.2 4 4 lj/cut 0.015 3.1 5 5 lj/cut 0.015 3.1 * * tip4p/long/soft 0.83 extract: ! | cut_coul 0 qdist 0 typeO 0 typeH 0 typeA 0 typeB 0 lambda 2 natoms: 29 init_vdwl: 0 init_coul: 220.904555359383 init_stress: ! |- -3.1383522071804158e+01 -4.1960152113677644e+01 -3.8477634382983439e+01 1.2128496669147679e-01 -1.1198183080297536e+01 6.5268065842458656e+00 init_vdwl: 8.07036960332134 init_coul: 100.236229731909 init_stress: ! |2- 2.0560777882594444e+01 2.1654965423904063e+01 1.0056493693519297e+01 -2.4240063285208659e+00 -1.3467251681546395e+01 -1.4781331319647906e+01 init_forces: ! |2 1 2.6118798121573339e+00 -5.1644240368157168e-01 1.8001437196967410e-01 2 -1.9557407939667784e-01 -2.8434279090485344e+00 -1.2037666274486341e+00 3 1.3516729385656326e-02 -8.3981675119811638e-02 1.3800938031093543e-02 4 -7.9314978889013857e-02 1.6212643266693107e-02 -2.3663785465653561e-01 5 -5.4637120859630939e-01 6.5600989679059629e-01 -6.8980117595427104e-02 6 1.4667908736646822e+00 -3.8991837337279565e+00 -2.5411858592494596e+00 7 -6.7512752271559159e-02 8.9321193431929236e-01 3.8067644595952399e+00 8 -1.4944738413316052e+00 4.5568557152238283e+00 2.3556173395822269e+00 9 1.5618105874324246e+00 -5.8578891996706437e+00 1.3701350515471384e+00 10 -2.6110782215753048e-01 3.6476179750311333e-01 -2.2728997157574121e-01 11 -9.3766462457826905e-01 1.0563563299185068e+00 -5.5775022539970631e-01 12 2.8818522397941928e+00 -5.4162419106234894e-01 1.4389000151728266e+00 13 -7.5720425159299595e-02 3.8772041103398963e-02 -1.8346431648817585e-01 14 -1.0557020156519512e+00 3.6717714938726143e-01 -1.0728817695848940e-01 15 3.5162907632314466e-01 -1.9165325094615621e-01 -1.0148660141104417e+00 16 -9.0625899241785468e-01 -4.0978261630457780e-01 2.0869169313568565e+00 17 -2.2809774497744830e+00 6.2063926325737908e+00 -6.6646229271776178e+00 18 3.7211451024737952e-01 4.7949556440316261e+00 -7.9026298092983307e+00 19 1.9911596893384120e+00 -7.2195675725850206e-01 5.5334689749229105e+00 20 -2.9127135301570397e+00 -4.0021946638596519e+00 4.1375019377447915e+00 21 1.5279890933802478e+00 3.2050983299936133e+00 -6.7676269505726276e+00 22 4.4657588078956723e+00 1.0585032152255676e+00 5.8268290139589860e+00 23 -6.2938601634201303e+00 -3.9616631352879410e+00 1.3192732707154482e+00 24 -1.0816004906486070e+00 6.8108467987003323e+00 -3.6672013590293373e+00 25 4.9746167445264264e+00 -5.2361422570157790e-01 3.9262159421100877e+00 26 -4.3769290854851999e+00 -6.4816134554785325e+00 -8.1534775153570904e-01 27 -1.5366446134631597e+00 7.3612903591829397e+00 -2.7208483294328234e+00 28 6.4035032875423159e+00 -2.1779017025677483e+00 4.1727109672631357e+00 29 -4.5201953782892055e+00 -5.1735155675050022e+00 -1.4886429234413563e+00 run_vdwl: 0 run_coul: 220.048510859325 run_stress: ! 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