Commit 2f32fb7f authored by Steve Plimpton's avatar Steve Plimpton
Browse files

patch 13Apr17

parent cb867ea9

doc/src/Manual.txt

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<!-- HTML_ONLY -->

<HEAD>

<TITLE>LAMMPS Users Manual</TITLE>

<META NAME="docnumber" CONTENT="11 Apr 2017 version">

<META NAME="docnumber" CONTENT="13 Apr 2017 version">

<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">

<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">

</HEAD>
@@ -21,7 +21,7 @@ 
<H1></H1>



LAMMPS Documentation :c,h3

11 Apr 2017 version :c,h4

13 Apr 2017 version :c,h4



Version info: :h4

examples/cmap/log.11Apr17.cmap.g++.1

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LAMMPS (31 Mar 2017)

# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016



units           real

neigh_modify    delay 2 every 1

#newton          off



boundary        p p p



atom_style      full

bond_style      harmonic

angle_style     charmm

dihedral_style  charmmfsw

improper_style  harmonic



pair_style      lj/charmmfsw/coul/charmmfsh 8 12

pair_modify     mix arithmetic



fix             cmap all cmap charmm22.cmap

Reading potential file charmm22.cmap with DATE: 2016-09-26

fix_modify      cmap energy yes



read_data       gagg.data fix cmap crossterm CMAP

  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)

  1 by 1 by 1 MPI processor grid

  reading atoms ...

  34 atoms

  scanning bonds ...

  4 = max bonds/atom

  scanning angles ...

  6 = max angles/atom

  scanning dihedrals ...

  12 = max dihedrals/atom

  scanning impropers ...

  1 = max impropers/atom

  reading bonds ...

  33 bonds

  reading angles ...

  57 angles

  reading dihedrals ...

  75 dihedrals

  reading impropers ...

  7 impropers

  4 = max # of 1-2 neighbors

  7 = max # of 1-3 neighbors

  13 = max # of 1-4 neighbors

  16 = max # of special neighbors



special_bonds   charmm

fix             1 all nve



#fix             1 all nvt temp 300 300 100.0

#fix             2 all shake 1e-9 500 0 m 1.0



velocity        all create 0.0 12345678 dist uniform



thermo          1000

thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp

timestep        2.0



run             100000

Neighbor list info ...

  update every 1 steps, delay 2 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 14

  ghost atom cutoff = 14

  binsize = 7, bins = 12 12 12

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/charmmfsw/coul/charmmfsh, 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) = 14.96 | 14.96 | 14.96 Mbytes

Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 

       0    16.287573  -0.85933785    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 

    1000    18.816462  -0.84379243   0.78931817    2.7554247    4.4371421   -2.7762038   0.12697656 

    2000    18.091571    -1.045888   0.72306589    3.0951524    4.6725102   -2.3580092   0.22712496 

    3000    17.835596   -1.2171641   0.72666403    2.6696491    5.4373798   -2.0737041  0.075101693 

    4000    16.211232  -0.42713611   0.99472642    3.8961462    5.2009895   -2.5626866   0.17356243 

    5000     17.72183  -0.57081189   0.90733068    3.4376382    4.5457582   -2.3727543   0.12354518 

    6000    18.753977   -1.5772499   0.81468321    2.9236782    4.6033216   -2.3380859   0.12835782 

    7000    18.186024  -0.84205608   0.58996182    3.0329585    4.7221473   -2.5733243   0.10047631 

    8000    18.214306   -1.1360938   0.72597611    3.7493028    4.7319958   -2.8957969    0.2006046 

    9000    17.248408  -0.48641993   0.90266229    2.9721743    4.7651056   -2.1473354    0.1302043 

   10000    17.760655   -1.2968444   0.92384663    3.7007455    4.7378947   -2.2147779   0.06940579 

   11000    17.633929  -0.57368413   0.84872849    3.4277114     4.285393    -2.236944   0.17204973 

   12000    18.305835   -1.0675148   0.75879532    2.8853173     4.685027    -2.409087  0.087538866 

   13000    17.391558   -0.9975291   0.66671947    3.8065638    5.2285578   -2.4198822   0.06253594 

   14000    17.483387  -0.67727643   0.91966477    3.7317031    4.7770445   -2.6080027   0.11487095 

   15000    18.131749   -1.1918751    1.0025684    3.1238131     4.789742   -2.2546745   0.13782813 

   16000    16.972343  -0.43926531   0.60644597    3.7551592    4.8658618   -2.2627659   0.12353145 

   17000    18.080785   -1.2073565    0.7867072    3.5671106      4.43754   -2.5092904   0.17429146 

   18000    17.474576  -0.97836065    0.8678524    3.7961537    4.3409032   -1.8922572     0.134048 

   19000    17.000911   -1.2286864   0.83615834    3.9322908    4.9319492   -2.3281576  0.056689619 

   20000    17.043286   -0.8506561   0.80966589    3.5087339    4.8603878   -2.3365263  0.096794824 

   21000    17.314495   -1.1430889   0.95363892    4.2446032    4.2756745   -2.1829483   0.17119518 

   22000    18.954881    -0.998673   0.58688334      2.71536    4.6634319   -2.6862804   0.20328442 

   23000    17.160427  -0.97803282   0.86894041    4.0897736    4.3146238   -2.1962289  0.075339092 

   24000    17.602026   -1.0833323   0.94888776    3.7341878    4.3084335   -2.1640414  0.081493681 

   25000    17.845584   -1.3432612   0.93497086    3.8911043     4.468032   -2.3475883  0.093204333 

   26000    17.833261   -1.1020534   0.77931087    3.7628141     4.512381   -2.3134761   0.15568465 

   27000     17.68607   -1.3222026    1.1985872    3.5817624    4.6360755   -2.3492774   0.08427906 

   28000    18.326649   -1.2669291   0.74809075    3.2624429    4.4698564   -2.3679076   0.14677293 

   29000    17.720933   -1.0773886   0.83099482    3.7652834    4.6584594   -2.8255303   0.23092596 

   30000    18.201999   -1.0168706    1.0637455     3.453095    4.3738593   -2.8063214   0.18658217 

   31000    17.823502   -1.2685768   0.84805585    3.8600661    4.2195821   -2.1169716   0.12517101 

   32000    16.883133  -0.62062648   0.84434922    3.5042683    5.1264906   -2.2674699  0.030138165 

   33000    17.805715    -1.679553    1.2430372     4.314677    4.2523894   -2.3008321   0.18591872 

   34000    16.723767  -0.54189072    1.1282827    3.8542159    4.3026559   -2.2186336   0.05392425 

   35000    17.976909  -0.72092075    0.5876319    2.9726396    5.0881439    -2.491692   0.17356291 

   36000    18.782492    -1.514246   0.63237955    3.2777164    4.6077164    -2.502574  0.082537318 

   37000    17.247716   -0.6344626   0.79885976     3.452491    4.7618281   -2.3902444   0.11450271 

   38000    17.996494   -1.6712877    1.0111769    4.1689136      4.46963   -2.4076725   0.11875756 

   39000    17.586857  -0.74508086   0.95970486    3.7395038    4.6011357   -2.9854953   0.30143284 

   40000    17.494879  -0.30772446   0.72047991    3.2604877    4.7283734   -2.3812495   0.16399034 

   41000    15.855772  -0.49642605   0.82496448    4.5139653      4.76884    -2.214141   0.10899661 

   42000    17.898568   -1.3078863    1.1505144    4.0429873    4.3889581   -2.8696559   0.23336417 

   43000    19.014372   -1.6325979    1.1553166    3.5660772    4.4047997   -2.9302044   0.13672127 

   44000    18.250782  -0.97211613   0.72714301    3.2258362    4.7257298   -2.5533613   0.11968073 

   45000    17.335174   0.24746331    1.0415866    3.3220992    4.5251095   -3.0415216   0.24453084 

   46000     17.72846   -0.9541418   0.88153841    3.7893452    4.5251883   -2.4003613  0.051809816 

   47000    18.226762  -0.67057787   0.84352989    3.0609522    4.5449078   -2.4694254  0.073703949 

   48000    17.838074  -0.88768441    1.3812262    3.5890492    4.5827868   -3.0137515   0.21417113 

   49000    17.973733  -0.75118705   0.69667886    3.3989025    4.7058886   -2.8243945   0.26665792 

   50000    17.461583  -0.65040016   0.68943524    2.9374743    5.6971777   -2.4438011    0.1697603 

   51000     16.79766 -0.010684434   0.89795555     3.959039      4.56763   -2.5101098   0.15048853 

   52000    17.566543   -0.7262764   0.74354418    3.3423185    4.8426523   -2.4187649   0.16908776 

   53000    17.964274   -0.9270914     1.065952    3.0397181    4.4682262   -2.2179503   0.07873406 

   54000    17.941256   -0.5807578   0.76516121    3.7262371    4.6975126    -3.179899   0.24433708 

   55000    17.079478  -0.48559832   0.95364453    3.0414645    5.2811414   -2.7064882   0.30102814 

   56000    17.632179  -0.75403299   0.97577942    3.3672363    4.4851336   -2.3683659  0.051117638 

   57000     16.17128  -0.44699325   0.76341543     4.267716    5.0881056   -2.4122329   0.16671692 

   58000    16.899276  -0.76481024    1.0400825     3.973493    4.8823309   -2.4270284  0.048716383 

   59000    18.145412  -0.84968335   0.71698306    3.2024358    4.6115739   -2.2520353   0.19466966 

   60000    17.578258   -1.0067331   0.72822527    3.5375208    4.9110255   -2.2319607   0.11922362 

   61000    17.434762   -1.0244393   0.90593099    3.8446915    4.8571191   -2.6228357   0.23259208 

   62000    17.580489   -1.1135917   0.79577432    3.7043524    4.6058114    -2.351492  0.042904152 

   63000    18.207335   -1.1512268   0.82684507    3.4114738     4.351069   -2.1878441  0.082922105 

   64000    18.333083   -1.1182287   0.74058959    3.6905164    4.3226172   -2.7110393   0.14721704 

   65000    16.271579   -0.7122151    1.0200168    4.6983643    4.3681131    -2.194921   0.12831024 

   66000    17.316444   -0.5729385   0.85254108    3.5769963    4.5526705   -2.3321328  0.040452643 

   67000     17.19011   -0.8814312    1.1381258    3.8605789    4.4183813    -2.299607  0.091527355 

   68000    18.223367    -1.362189   0.74472056     3.259165     4.486512   -2.2181134  0.048952796 

   69000    17.646348  -0.91647162   0.73990335    3.9313692    5.2663097   -3.3816778   0.27769877 

   70000    18.173493   -1.3107718   0.96484426     3.219728    4.5045124   -2.3349534  0.082327407 

   71000      17.0627  -0.58509083   0.85964129    3.8490884     4.437895   -2.1673348   0.24151404 

   72000    17.809764  -0.35128902   0.65479258    3.3945008    4.6160508   -2.5486166   0.10829531 

   73000     18.27769   -1.0739758   0.80890957    3.6070901    4.6256762   -2.4576547  0.080025736 

   74000    18.109437   -1.0691837   0.66679323    3.5923203    4.4825716   -2.5048169   0.21372319 

   75000    17.914569   -1.3500765    1.2993494     3.362421    4.4160377   -2.1278163   0.19397641 

   76000    16.563928  -0.16539261    1.0067302    3.5742755    4.8581915   -2.1362429  0.059822408 

   77000    18.130477  -0.38361279   0.43406954    3.4725995    4.7005855   -2.8836242   0.11958174 

   78000    16.746204   -1.1732959    0.7455507    3.6296638    5.6344113    -2.459208   0.16099803 

   79000    18.243999   -1.5850155    1.0108545    3.4727867    4.3367411    -2.316686  0.070480814 

   80000    16.960715  -0.84100929   0.91604996     3.862215     4.780949   -2.3711596  0.073916605 

   81000    17.697722   -1.1126605     0.952804    3.7114455    4.4216316   -2.2770085  0.091372066 

   82000    17.835901   -1.3091474   0.71867629    3.8168122    5.0150205   -2.4730634  0.062592852 

   83000    19.168418    -1.476938   0.75592316    3.2304519    4.3946471   -2.2991395   0.13083324 

   84000    17.945778   -1.5223622    1.0859941    3.4334011    5.0286682   -2.7550892    0.2476269 

   85000    17.950251  -0.85843846   0.86888218    3.3101287    4.5511879   -2.3640013   0.12080834 

   86000    17.480699  -0.97493649   0.85049761    3.4973085    4.6344922    -2.343121    0.2009677 

   87000    17.980244    -1.114983   0.88796989    3.4113329    4.3535853   -2.2535412   0.14494917 

   88000    18.023866    -1.226683   0.62339706    3.7649269    4.5923973   -2.3923523   0.10464375 

   89000    16.362829    -0.311462    1.0265375    4.0101723    4.4184777   -2.0314129  0.056570704 

   90000    17.533149  -0.41526788    1.0362029    3.4247412    4.2734431   -2.4776658   0.16960663 

   91000    17.719099   -1.1956801    1.0069945    3.2380672    4.8982805   -2.2154906   0.12950936 

   92000    17.762654    -1.170027   0.95814525    3.5217717    4.5405343   -2.5983677   0.15037754 

   93000    17.393958  -0.45641026    0.6579069    3.6002204    4.5942053   -2.5559641   0.12026544 

   94000      16.8182  -0.92962066   0.86801362    4.2914398     4.659848   -2.5251987   0.18000415 

   95000    17.642086   -0.7994896    0.7003756    3.8036697    4.5252487   -2.4166307   0.15686517 

   96000    18.114292   -1.5102104    1.2635908    3.2764427    5.0659496   -2.2777806  0.054309645 

   97000    18.575765   -1.6015311   0.69500699    3.1649317    4.9945742   -2.4012125  0.067373724 

   98000    16.578893  -0.78030229   0.91524222    4.4429655    4.4622392   -2.4052655   0.15355705 

   99000     17.26063  -0.57832833    0.7098846    3.9000046    4.5576484   -2.5333026   0.25517222 

  100000    18.377235  -0.89109577   0.68988617    2.8751751    4.4115591   -2.3560731   0.12185212 

Loop time of 2.96043 on 1 procs for 100000 steps with 34 atoms



Performance: 5836.990 ns/day, 0.004 hours/ns, 33778.875 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    | 1.074      | 1.074      | 1.074      |   0.0 | 36.28

Bond    | 1.6497     | 1.6497     | 1.6497     |   0.0 | 55.72

Neigh   | 0.007576   | 0.007576   | 0.007576   |   0.0 |  0.26

Comm    | 0.012847   | 0.012847   | 0.012847   |   0.0 |  0.43

Output  | 0.0010746  | 0.0010746  | 0.0010746  |   0.0 |  0.04

Modify  | 0.16485    | 0.16485    | 0.16485    |   0.0 |  5.57

Other   |            | 0.05037    |            |       |  1.70



Nlocal:    34 ave 34 max 34 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:    395 ave 395 max 395 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 395

Ave neighs/atom = 11.6176

Ave special neighs/atom = 9.52941

Neighbor list builds = 253

Dangerous builds = 0

Total wall time: 0:00:02

examples/cmap/log.11Apr17.cmap.g++.4

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File added.

Preview size limit exceeded, changes collapsed.

src/KOKKOS/verlet_kokkos.cpp

+9 −6
Original line number Diff line number Diff line
@@ -64,15 +64,18 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) : 
   setup before run

------------------------------------------------------------------------- */



void VerletKokkos::setup()

void VerletKokkos::setup(int flag)

{

  if (comm->me == 0 && screen) {

    fprintf(screen,"Setting up Verlet run ...\n");

    if (flag) {

      fprintf(screen,"  Unit style    : %s\n", update->unit_style);

    fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n", update->ntimestep);

      fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n",

              update->ntimestep);

      fprintf(screen,"  Time step     : %g\n", update->dt);

      timer->print_timeout(screen);

    }

  }



  update->setupflag = 1;

  lmp->kokkos->auto_sync = 0;
@@ -169,7 +172,7 @@ void VerletKokkos::setup() 
  if (force->newton) comm->reverse_comm();



  modify->setup(vflag);

  output->setup();

  output->setup(flag);

  lmp->kokkos->auto_sync = 1;

  update->setupflag = 1;

}

src/KOKKOS/verlet_kokkos.h

+1 −1
Original line number Diff line number Diff line
@@ -29,7 +29,7 @@ class VerletKokkos : public Verlet { 
 public:

  VerletKokkos(class LAMMPS *, int, char **);

  ~VerletKokkos() {}

  void setup();

  void setup(int flag=1);

  void setup_minimal(int);

  void run(int);

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