129 lines
4.3 KiB
Groff
129 lines
4.3 KiB
Groff
LAMMPS (29 Sep 2021)
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# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
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boundary p p s
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units real
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atom_style charge
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read_data data.water
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
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WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
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WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
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3000 atoms
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read_data CPU = 0.017 seconds
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variable x index 1
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variable y index 1
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variable z index 1
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replicate $x $y $z
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replicate 1 $y $z
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replicate 1 1 $z
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replicate 1 1 1
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Replicating atoms ...
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orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
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2 by 1 by 2 MPI processor grid
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3000 atoms
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replicate CPU = 0.002 seconds
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pair_style reaxff NULL safezone 3.0 mincap 150
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pair_coeff * * qeq_ff.water O H
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WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
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neighbor 0.5 bin
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neigh_modify every 1 delay 0 check yes
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velocity all create 300.0 4928459 rot yes dist gaussian
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fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
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fix 2 all nvt temp 300 300 50.0
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fix 3 all efield 0.0 0.0 1.0
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fix 4 all wall/reflect zlo EDGE zhi EDGE
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timestep 0.5
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thermo 10
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thermo_style custom step temp press density vol
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run 20
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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:
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@Article{Aktulga12,
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author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
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title = {Parallel reactive molecular dynamics: Numerical 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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- fix qeq/reaxff command:
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@Article{Aktulga12,
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author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
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title = {Parallel reactive molecular dynamics: Numerical 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 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 = 10.5
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ghost atom cutoff = 10.5
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binsize = 5.25, bins = 6 6 6
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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/reaxff, perpetual, copy from (1)
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attributes: half, newton off, ghost
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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) = 188.9 | 189.5 | 190.1 Mbytes
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Step Temp Press Density Volume
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0 300 25015.837 0.99996859 29916.212
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10 348.83356 31131.298 0.99964273 29925.965
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20 414.67243 27564.999 0.99979791 29921.32
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Loop time of 5.71549 on 4 procs for 20 steps with 3000 atoms
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Performance: 0.151 ns/day, 158.764 hours/ns, 3.499 timesteps/s
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94.1% CPU use with 4 MPI tasks x no 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 | 3.6678 | 3.8126 | 4.1402 | 9.8 | 66.71
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Neigh | 0.31449 | 0.34639 | 0.38898 | 5.5 | 6.06
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Comm | 0.032125 | 0.35935 | 0.50408 | 31.9 | 6.29
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Output | 7.643e-05 | 0.00015959 | 0.00039876 | 0.0 | 0.00
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Modify | 1.1534 | 1.1959 | 1.2283 | 3.0 | 20.92
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Other | | 0.001099 | | | 0.02
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Nlocal: 750.000 ave 757 max 738 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Nghost: 4219.00 ave 4232 max 4198 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 230549.0 ave 233374 max 225849 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Total # of neighbors = 922196
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Ave neighs/atom = 307.39867
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Neighbor list builds = 6
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Dangerous builds = 0
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Total wall time: 0:00:06
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