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 1 by 1 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) = 5.405 | 5.405 | 5.405 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 1.3464499
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Loop time of 0.0308104 on 1 procs for 1000 steps with 15 atoms
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88.9% CPU use with 1 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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-27.3140820331247 -34.0744796893375 -34.0744796893447
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Force two-norm initial, final = 10.728716 0.00017815706
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Force max component initial, final = 6.1727999 8.2675815e-05
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Final line search alpha, max atom move = 1 8.2675815e-05
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Iterations, force evaluations = 1000 1943
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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 | 0.012522 | 0.012522 | 0.012522 | 0.0 | 40.64
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00012209 | 0.00012209 | 0.00012209 | 0.0 | 0.40
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Output | 0.016563 | 0.016563 | 0.016563 | 0.0 | 53.76
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.001604 | | | 5.20
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Nlocal: 15 ave 15 max 15 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 105 ave 105 max 105 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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) = 5.406 | 5.406 | 5.406 Mbytes
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Step PotEng Temp Press
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1000 -34.07448 1050 392.66426
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2000 -34.065618 583.71716 -618.55027
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3000 -34.063563 475.54605 661.95076
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4000 -34.06119 350.76183 -449.64687
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5000 -34.0652 561.71223 -131.2575
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6000 -34.065798 593.21728 754.38406
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7000 -34.067408 677.86019 -409.21139
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8000 -34.065663 586.03411 446.32573
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9000 -34.06294 442.71136 414.41408
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10000 -34.060101 293.33406 -1203.0131
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11000 -34.064946 548.39598 345.29601
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12000 -34.067323 673.49043 444.55927
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13000 -34.063275 460.43973 -854.83884
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14000 -34.064666 533.57265 1542.0127
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15000 -34.063343 463.97449 -778.73252
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16000 -34.064462 522.77625 -1.5339614
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17000 -34.061203 351.37068 -148.19163
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18000 -34.066534 631.87837 -237.0746
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19000 -34.065169 560.16772 1360.7348
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20000 -34.063042 448.13104 -664.72128
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21000 -34.060696 324.68723 -167.83333
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22000 -34.065376 570.90279 -831.73853
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23000 -34.063127 452.61143 766.59984
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24000 -34.064572 528.62282 -107.80755
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25000 -34.06584 595.42175 610.33075
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26000 -34.066886 650.43579 -894.20521
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27000 -34.062035 395.20224 1754.7666
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28000 -34.060696 324.66878 -2622.013
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29000 -34.066777 644.66282 1551.3147
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30000 -34.066421 625.94614 -507.44173
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31000 -34.066163 612.36658 610.11907
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32000 -34.063109 451.70185 -47.463209
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33000 -34.062833 437.16794 -607.25848
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34000 -34.061657 375.30056 -158.28097
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35000 -34.064937 547.86519 272.75585
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36000 -34.067509 683.23088 359.91072
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37000 -34.067582 686.96461 -384.97405
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38000 -34.063213 457.13191 411.86349
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39000 -34.06272 431.13187 -594.23723
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40000 -34.062286 408.41212 456.09079
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41000 -34.064078 502.64096 -1149.8496
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42000 -34.066408 625.33334 1403.4937
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43000 -34.065948 601.03876 -773.40678
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44000 -34.064113 504.49498 179.93456
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45000 -34.060573 318.11433 223.38679
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46000 -34.063614 478.24588 -409.99081
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47000 -34.064814 541.38544 614.25246
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48000 -34.065602 582.87984 -743.92184
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49000 -34.063923 494.52673 474.88127
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50000 -34.064616 530.94533 288.81199
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51000 -34.062038 395.2991 -480.07513
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52000 -34.06497 549.5123 -305.53764
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53000 -34.065578 581.59919 964.80956
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54000 -34.06766 691.12707 -437.99603
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55000 -34.064707 535.85658 1058.6734
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56000 -34.062481 418.58003 -1011.5341
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57000 -34.064997 551.06731 -32.91724
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58000 -34.064281 513.25358 374.91628
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59000 -34.066177 613.1188 -464.85124
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60000 -34.064718 536.29803 1011.6698
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61000 -34.065746 590.46955 -1057.9241
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62000 -34.063253 459.23293 1526.2698
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63000 -34.062261 407.08636 -1743.6652
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64000 -34.063835 489.88286 761.60266
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65000 -34.069569 791.614 323.26812
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66000 -34.065557 580.45685 874.52459
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67000 -34.064917 546.77223 -1349.3606
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68000 -34.062963 443.96697 1178.4319
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69000 -34.063063 449.26418 -1660.686
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70000 -34.063597 477.39716 1323.13
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71000 -34.065424 573.47914 -131.55428
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72000 -34.065211 562.31067 -415.56361
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73000 -34.06339 466.38097 724.92885
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74000 -34.062286 408.34027 -1094.3845
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75000 -34.065545 579.79767 587.58121
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76000 -34.066774 644.61685 -357.22241
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77000 -34.064479 523.74831 1545.6628
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78000 -34.065506 577.88405 -1013.2409
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79000 -34.062874 439.24856 240.66725
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80000 -34.06306 449.09678 -799.14252
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81000 -34.063338 463.66067 1528.3351
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82000 -34.066812 646.52985 -1351.1758
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83000 -34.064724 536.65114 1338.595
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84000 -34.063774 486.67172 -876.0475
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85000 -34.06156 370.19256 617.89915
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86000 -34.063628 478.95398 -134.40164
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87000 -34.065141 558.60424 -758.03942
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88000 -34.066732 642.27865 1159.5992
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89000 -34.067349 674.83453 -301.45201
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90000 -34.063623 478.69626 386.87752
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91000 -34.061885 387.30728 -774.32296
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92000 -34.061363 359.77745 500.06117
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93000 -34.065724 589.32209 -469.10399
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94000 -34.065006 551.42796 818.92294
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95000 -34.06541 572.75191 -677.20865
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96000 -34.062331 410.64868 1383.8935
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97000 -34.061499 366.95753 -1715.2058
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98000 -34.061153 348.68703 353.63545
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99000 -34.066217 615.27816 193.79593
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100000 -34.067739 695.36238 205.35389
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101000 -34.067314 672.94727 929.41223
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Loop time of 2.23163 on 1 procs for 100000 steps with 15 atoms
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Performance: 19358038.198 fs/day, 0.000 hours/fs, 44810.274 timesteps/s, 672.154 katom-step/s
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85.0% CPU use with 1 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 | 0.59187 | 0.59187 | 0.59187 | 0.0 | 26.52
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0061524 | 0.0061524 | 0.0061524 | 0.0 | 0.28
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Output | 1.5983 | 1.5983 | 1.5983 | 0.0 | 71.62
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Modify | 0.017759 | 0.017759 | 0.017759 | 0.0 | 0.80
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Other | | 0.01755 | | | 0.79
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Nlocal: 15 ave 15 max 15 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 105 ave 105 max 105 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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: 0:00:02
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