131 lines
4.5 KiB
Groff
131 lines
4.5 KiB
Groff
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
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using 1 OpenMP thread(s) per MPI task
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# ACKS2 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 0 0) 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 (src/read_data.cpp:1548)
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3000 atoms
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read_data CPU = 0.009 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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Replication is creating a 1x1x1 = 1 times larger system...
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orthogonal box = (0 0 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 = 0.001 seconds
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pair_style reaxff NULL safezone 3.0 mincap 150
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pair_coeff * * acks2_ff.water O H
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Reading potential file acks2_ff.water with DATE: 2021-09-21
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WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
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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 acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
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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: 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 acks2/reaxff command: doi:10.1137/18M1224684
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@Article{O'Hearn2020,
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author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga},
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title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
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journal = {SIAM J.\ Sci.\ Comput.},
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year = 2020,
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volume = 42,
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number = 1,
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pages = {1--22}
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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/ghost/newtoff
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stencil: full/ghost/bin/3d
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bin: standard
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(2) fix acks2/reaxff, 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) = 198.5 | 199.3 | 199.9 Mbytes
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Step Temp Press Density Volume
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0 300 -20760.178 0.99996859 29916.212
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10 396.27472 -18425.294 1.0000143 29914.845
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20 518.59015 -10012.352 1.0000209 29914.647
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Loop time of 3.14386 on 4 procs for 20 steps with 3000 atoms
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Performance: 0.275 ns/day, 87.329 hours/ns, 6.362 timesteps/s, 19.085 katom-step/s
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99.2% 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 | 0.66121 | 0.66884 | 0.68146 | 1.0 | 21.27
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Neigh | 0.095801 | 0.09707 | 0.098006 | 0.3 | 3.09
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Comm | 0.0018538 | 0.014557 | 0.022268 | 6.8 | 0.46
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Output | 3.5758e-05 | 4.0192e-05 | 5.2801e-05 | 0.0 | 0.00
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Modify | 2.3621 | 2.3631 | 2.3644 | 0.1 | 75.17
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Other | | 0.0002583 | | | 0.01
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Nlocal: 750 ave 758 max 737 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 4219.5 ave 4233 max 4198 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Neighs: 230733 ave 233430 max 225532 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Total # of neighbors = 922931
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Ave neighs/atom = 307.64367
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Neighbor list builds = 7
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Dangerous builds = 0
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Total wall time: 0:00:03
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