125 lines
4.0 KiB
Groff
125 lines
4.0 KiB
Groff
LAMMPS (29 Sep 2021)
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# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
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boundary p p p
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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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3000 atoms
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read_data CPU = 0.013 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 0.0000000) to (31.043046 31.043046 31.043046)
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1 by 2 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 * * 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 (../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 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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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 acks2/reaxff command:
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@Article{O'Hearn2020,
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author = {K. A. O'Hearn, 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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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/newtoff/ghost
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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, 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) = 271.9 | 273.6 | 275.1 Mbytes
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Step Temp Press Density Volume
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0 300 1572.3807 1 29915.273
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10 300.6152 8252.4834 1 29915.273
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20 294.73868 2502.5661 1 29915.273
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Loop time of 11.1133 on 4 procs for 20 steps with 3000 atoms
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Performance: 0.078 ns/day, 308.702 hours/ns, 1.800 timesteps/s
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92.7% 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 | 4.3609 | 4.7715 | 5.4812 | 19.5 | 42.94
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Neigh | 0.15797 | 0.17176 | 0.19405 | 3.5 | 1.55
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Comm | 0.21014 | 0.922 | 1.3353 | 44.6 | 8.30
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Output | 8.815e-05 | 0.0002 | 0.00030501 | 0.0 | 0.00
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Modify | 5.2267 | 5.2468 | 5.2584 | 0.5 | 47.21
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Other | | 0.001074 | | | 0.01
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Nlocal: 750.000 ave 760 max 735 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Nghost: 6231.50 ave 6255 max 6192 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Neighs: 277006.0 ave 280567 max 271394 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Total # of neighbors = 1108026
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Ave neighs/atom = 369.34200
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:12
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