267 lines
12 KiB
Groff
267 lines
12 KiB
Groff
LAMMPS (27 Jun 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable sname index ch4
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units electron
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newton on
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boundary f f f
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atom_style electron
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read_data data.${sname}
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read_data data.ch4
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Reading data file ...
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orthogonal box = (-500 -500 -500) to (500 500 500)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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15 atoms
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read_data CPU = 0.000 seconds
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pair_style eff/cut 100.0
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pair_coeff * *
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comm_modify vel yes
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# Minimize
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min_style cg
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compute 1 all property/atom spin eradius
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dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
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dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
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min_modify line quadratic dmax 0.1
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minimize 0 1.0e-6 1000 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- EFF package: doi:10.1002/jcc.21637
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@Article{Jaramillo-Botero11,
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author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
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title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
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journal = {J.~Comp.\ Chem.},
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year = 2011,
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volume = 32,
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number = 3,
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pages = {497--512}
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}
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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 102
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ghost atom cutoff = 102
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binsize = 51, bins = 20 20 20
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair eff/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.385 | 5.385 | 5.385 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -27.314082 0 -27.314082 -56588.53
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1000 0 -34.07448 0 -34.07448 0.39495391
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Loop time of 0.0230482 on 4 procs for 1000 steps with 15 atoms
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97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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-27.3140820331249 -34.0744796901924 -34.0744796901707
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Force two-norm initial, final = 10.728716 0.00024139276
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Force max component initial, final = 6.1727999 0.00017091779
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Final line search alpha, max atom move = 1 0.00017091779
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Iterations, force evaluations = 1000 1946
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0015331 | 0.0032095 | 0.0046681 | 2.0 | 13.93
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0037211 | 0.0053887 | 0.0069902 | 1.6 | 23.38
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Output | 0.0062087 | 0.0079064 | 0.011172 | 2.2 | 34.30
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.006544 | | | 28.39
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Nlocal: 3.75 ave 6 max 3 min
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Histogram: 3 0 0 0 0 0 0 0 0 1
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Nghost: 11.25 ave 12 max 9 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Neighs: 26.25 ave 39 max 12 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Total # of neighbors = 105
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Ave neighs/atom = 7
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Neighbor list builds = 0
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Dangerous builds = 0
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# Dynamics
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compute effTemp all temp/eff
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thermo 1000
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thermo_style custom step pe temp press
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thermo_modify temp effTemp
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velocity all create 300.0 4928459 dist gaussian rot yes mom yes
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timestep 0.005
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fix 1 all nve/eff
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# the custom dump includes the radii
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dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
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dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
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dump 3 all xyz 1000 ${sname}.nve.xyz
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dump 3 all xyz 1000 ch4.nve.xyz
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run 100000
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes
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Step PotEng Temp Press
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1000 -34.07448 1050 391.71277
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2000 -34.065618 583.70724 -617.78946
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3000 -34.063563 475.53779 661.75865
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4000 -34.06119 350.74901 -449.8917
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5000 -34.065201 561.76559 -130.73147
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6000 -34.065798 593.21893 753.94281
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7000 -34.067408 677.86552 -409.14034
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8000 -34.065662 586.02658 446.74947
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9000 -34.062939 442.6953 413.93386
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10000 -34.060101 293.35262 -1202.4169
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11000 -34.064946 548.37877 344.89658
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12000 -34.067324 673.52389 444.40605
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13000 -34.063275 460.44923 -854.41022
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14000 -34.064667 533.59655 1541.2922
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15000 -34.063344 464.01572 -777.83895
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16000 -34.064461 522.76554 -2.2050586
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17000 -34.061202 351.31261 -148.09486
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18000 -34.066534 631.89021 -236.72076
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19000 -34.065169 560.16576 1359.8928
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20000 -34.063042 448.14707 -663.76152
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21000 -34.060695 324.66945 -168.3252
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22000 -34.065376 570.90677 -831.8481
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23000 -34.063127 452.62391 767.31463
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24000 -34.064572 528.62018 -108.63204
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25000 -34.06584 595.41818 610.87995
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26000 -34.066885 650.4263 -894.11862
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27000 -34.062035 395.1876 1754.1737
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28000 -34.060697 324.71187 -2621.333
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29000 -34.066777 644.68166 1550.7046
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30000 -34.066421 625.9368 -507.12512
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31000 -34.066163 612.3605 610.12993
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32000 -34.063108 451.66459 -48.049967
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33000 -34.062834 437.21062 -606.58502
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34000 -34.061656 375.26971 -158.76936
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35000 -34.064938 547.90576 273.26572
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36000 -34.067508 683.20936 360.05973
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37000 -34.067582 686.96938 -385.62265
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38000 -34.063213 457.13708 412.74004
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39000 -34.06272 431.16474 -595.05437
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40000 -34.062285 408.38247 456.29631
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41000 -34.064078 502.65934 -1149.196
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42000 -34.066408 625.33356 1402.5676
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43000 -34.065948 601.04311 -772.96544
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44000 -34.064113 504.47553 179.83988
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45000 -34.060572 318.08821 222.85125
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46000 -34.063614 478.25613 -409.06152
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47000 -34.064813 541.37361 613.37159
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48000 -34.065602 582.88704 -743.72019
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49000 -34.063922 494.52189 475.22811
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50000 -34.064616 530.95516 288.46302
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51000 -34.062038 395.30091 -479.68548
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52000 -34.06497 549.50477 -305.82851
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53000 -34.065577 581.56927 964.95886
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54000 -34.06766 691.14533 -437.95563
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55000 -34.064707 535.85441 1058.0886
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56000 -34.062481 418.62259 -1010.5517
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57000 -34.064996 551.02074 -33.54291
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58000 -34.064281 513.27818 375.07194
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59000 -34.066177 613.11494 -464.71576
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60000 -34.064718 536.306 1010.9545
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61000 -34.065746 590.47317 -1056.9192
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62000 -34.063252 459.22005 1525.6789
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63000 -34.06226 407.05859 -1743.9974
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64000 -34.063836 489.91026 762.61836
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65000 -34.069569 791.63831 322.35333
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66000 -34.065557 580.46799 875.11714
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67000 -34.064916 546.74052 -1349.5741
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68000 -34.062962 443.93438 1178.1978
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69000 -34.063064 449.3052 -1659.8695
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70000 -34.063596 477.36452 1322.0559
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71000 -34.065424 573.49586 -131.11749
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72000 -34.06521 562.24612 -415.25895
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73000 -34.06339 466.38351 724.08642
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74000 -34.062286 408.37673 -1093.6751
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75000 -34.065545 579.81257 586.8907
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76000 -34.066774 644.62609 -356.7044
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77000 -34.064479 523.75235 1545.8498
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78000 -34.065506 577.88123 -1014.0878
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79000 -34.062875 439.30997 241.55748
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80000 -34.06306 449.06553 -799.58139
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81000 -34.063338 463.64261 1528.4412
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82000 -34.066812 646.55603 -1350.9377
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83000 -34.064724 536.63793 1338.2148
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84000 -34.063774 486.717 -875.60363
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85000 -34.06156 370.19433 617.85579
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86000 -34.063628 478.9961 -135.13703
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87000 -34.065141 558.62541 -756.91518
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88000 -34.066732 642.27743 1158.5797
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89000 -34.067351 674.92164 -300.79164
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90000 -34.063624 478.70378 386.44004
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91000 -34.061884 387.27577 -774.22945
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92000 -34.061364 359.79856 500.36442
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93000 -34.065723 589.31234 -469.57015
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94000 -34.065006 551.46665 819.01826
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95000 -34.065409 572.7351 -676.74519
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96000 -34.06233 410.60509 1382.9732
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97000 -34.0615 366.99019 -1714.2302
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98000 -34.061152 348.67783 352.89211
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99000 -34.066217 615.29222 193.8722
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100000 -34.067739 695.32836 206.03841
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101000 -34.067313 672.90918 928.0541
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Loop time of 1.62544 on 4 procs for 100000 steps with 15 atoms
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Performance: 26577371.575 fs/day, 0.000 hours/fs, 61521.693 timesteps/s, 922.825 katom-step/s
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93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.066581 | 0.15332 | 0.25928 | 21.7 | 9.43
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.18521 | 0.29733 | 0.3879 | 16.1 | 18.29
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Output | 0.66513 | 0.81838 | 1.1333 | 20.4 | 50.35
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Modify | 0.01285 | 0.014237 | 0.016092 | 1.0 | 0.88
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Other | | 0.3422 | | | 21.05
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Nlocal: 3.75 ave 5 max 3 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Nghost: 11.25 ave 12 max 10 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Neighs: 26.25 ave 47 max 10 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Total # of neighbors = 105
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Ave neighs/atom = 7
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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