142 lines
6.2 KiB
Groff
142 lines
6.2 KiB
Groff
LAMMPS (21 Nov 2023)
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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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# REAX potential for CHO system
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# .....
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units real
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atom_style charge
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read_data data.CHO
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Reading data file ...
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orthogonal box = (0 0 0) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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105 atoms
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read_data CPU = 0.001 seconds
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pair_style reaxff lmp_control
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pair_coeff * * ffield.reax.cho H C O
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Reading potential file ffield.reax.cho with DATE: 2011-02-18
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neighbor 2 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
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fix 3 all temp/berendsen 500.0 500.0 100.0
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timestep 0.25
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thermo 100
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#dump 1 all atom 30 dump.reax.cho
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run 3000
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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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- pair reaxff command: doi:10.1016/j.parco.2011.08.005
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@Article{Aktulga12,
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author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
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title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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number = {4--5},
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pages = {245--259}
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}
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- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
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@Article{Aktulga12,
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author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
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title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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pages = {245--259}
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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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Neighbor list info ...
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update: every = 10 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair reaxff, perpetual
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attributes: half, newton off, ghost
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pair build: half/bin/newtoff/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) fix qeq/reax, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 10.47 | 11.39 | 12.19 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -10226.557 0 -10226.557 -106.09736
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100 54.051902 -10207.393 0 -10190.636 -291.39467
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200 134.81172 -10200.411 0 -10158.619 -1637.1599
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300 140.91215 -10177.136 0 -10133.452 -1668.5676
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400 254.70123 -10189.927 0 -10110.968 -2522.3655
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500 228.22204 -10162.396 0 -10091.646 403.98879
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600 393.48756 -10197.284 0 -10075.301 394.11243
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700 305.82625 -10156.707 0 -10061.9 362.73212
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800 375.95634 -10170.288 0 -10053.74 -664.10079
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900 361.59143 -10155.847 0 -10043.752 458.52018
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1000 445.4582 -10176.601 0 -10038.507 251.4509
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1100 475.47 -10180.12 0 -10032.722 840.09331
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1200 406.77476 -10155.496 0 -10029.394 62.656622
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1300 461.06079 -10167.123 0 -10024.192 265.91062
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1400 408.15869 -10148.621 0 -10022.09 -1187.4869
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1500 514.43021 -10178.337 0 -10018.862 -616.07216
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1600 432.22013 -10151.168 0 -10017.178 -678.01121
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1700 521.0846 -10175.605 0 -10014.067 98.591699
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1800 409.72383 -10138.803 0 -10011.787 1884.7989
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1900 481.86369 -10160.152 0 -10010.773 1058.5554
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2000 423.60058 -10138.532 0 -10007.214 -437.22408
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2100 520.96555 -10169.169 0 -10007.668 376.18619
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2200 477.21351 -10153.089 0 -10005.15 -113.43512
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2300 477.86263 -10153.309 0 -10005.17 868.89369
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2400 471.46466 -10149.152 0 -10002.996 688.76379
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2500 482.61616 -10153.025 0 -10003.412 350.03715
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2600 505.68439 -10159.544 0 -10002.78 -810.94974
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2700 498.37307 -10156.441 0 -10001.944 -460.12105
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2800 535.06218 -10167.029 0 -10001.157 152.85379
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2900 432.98591 -10134.778 0 -10000.55 -170.46638
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3000 547.92956 -10170.199 0 -10000.339 60.201766
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Loop time of 2.03179 on 4 procs for 3000 steps with 105 atoms
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Performance: 31.893 ns/day, 0.753 hours/ns, 1476.533 timesteps/s, 155.036 katom-step/s
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99.0% 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 | 1.213 | 1.2396 | 1.2505 | 1.4 | 61.01
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Neigh | 0.074765 | 0.08966 | 0.10323 | 4.3 | 4.41
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Comm | 0.12894 | 0.14116 | 0.16833 | 4.2 | 6.95
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Output | 0.0006079 | 0.00066664 | 0.00083802 | 0.0 | 0.03
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Modify | 0.54589 | 0.55836 | 0.57217 | 1.6 | 27.48
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Other | | 0.002368 | | | 0.12
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Nlocal: 26.25 ave 45 max 6 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 380.75 ave 495 max 261 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 1269.5 ave 2197 max 179 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Total # of neighbors = 5078
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Ave neighs/atom = 48.361905
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Neighbor list builds = 300
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Dangerous builds not checked
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Total wall time: 0:00:02
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