132 lines
5.4 KiB
Groff
132 lines
5.4 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 Nitroamines 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.AB
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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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104 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.AB H B N
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Reading potential file ffield.reax.AB with DATE: 2011-02-18
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WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:289)
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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.ab
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run 2000
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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) = 11.06 | 11.68 | 11.96 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -8505.1816 0 -8505.1816 -673.36566
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100 83.873123 -8497.0031 0 -8471.252 -609.71119
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200 125.23001 -8479.8879 0 -8441.4394 -1069.4122
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300 202.34219 -8479.1319 0 -8417.0081 -707.82246
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400 260.52726 -8476.7906 0 -8396.8026 221.14446
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500 282.4624 -8466.8556 0 -8380.133 -223.17501
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600 288.8059 -8452.9729 0 -8364.3028 679.38441
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700 378.87007 -8467.429 0 -8351.107 920.99401
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800 382.10004 -8458.7194 0 -8341.4058 256.06383
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900 379.69698 -8449.4416 0 -8332.8657 1266.1715
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1000 379.63496 -8440.9584 0 -8324.4015 -604.987
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1100 372.82256 -8428.7507 0 -8314.2854 -1236.8451
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1200 397.12809 -8427.4286 0 -8305.501 -356.42394
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1300 413.36951 -8425.3861 0 -8298.472 -47.619729
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1400 428.68835 -8424.4328 0 -8292.8154 -812.52975
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1500 403.59408 -8411.0829 0 -8287.1701 71.054401
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1600 448.76276 -8419.8186 0 -8282.0379 -339.19148
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1700 450.87444 -8416.1981 0 -8277.769 -44.043208
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1800 485.33509 -8421.3776 0 -8272.3684 -848.94941
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1900 481.36374 -8416.1719 0 -8268.382 -282.62675
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2000 437.25967 -8398.9233 0 -8264.6743 -217.40762
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Loop time of 1.44368 on 4 procs for 2000 steps with 104 atoms
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Performance: 29.924 ns/day, 0.802 hours/ns, 1385.350 timesteps/s, 144.076 katom-step/s
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99.1% 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 | 0.77999 | 0.87212 | 0.96576 | 8.1 | 60.41
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Neigh | 0.054058 | 0.059726 | 0.06287 | 1.4 | 4.14
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Comm | 0.031767 | 0.12609 | 0.21802 | 21.3 | 8.73
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Output | 0.00041377 | 0.00045661 | 0.00058001 | 0.0 | 0.03
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Modify | 0.3805 | 0.38348 | 0.3894 | 0.6 | 26.56
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Other | | 0.001808 | | | 0.13
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Nlocal: 26 ave 34 max 14 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Nghost: 429.25 ave 457 max 386 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Neighs: 922.5 ave 1238 max 496 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 3690
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Ave neighs/atom = 35.480769
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Neighbor list builds = 200
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Dangerous builds not checked
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Total wall time: 0:00:01
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