115 lines
3.8 KiB
Groff
115 lines
3.8 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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# QTPIE Water
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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 0 0) to (31.043046 31.043046 31.043046)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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3000 atoms
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read_data CPU = 0.008 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) to (31.043046 31.043046 31.043046)
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1 by 1 by 1 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 * * qeq_ff.water O H
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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 qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff gauss_exp.txt
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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: 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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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 qtpie/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) = 539.2 | 539.2 | 539.2 Mbytes
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Step Temp Press Density Volume
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0 300 10138.375 1 29915.273
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10 295.97879 3575.2769 1 29915.273
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20 292.76583 10309.128 1 29915.273
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Loop time of 5.70229 on 1 procs for 20 steps with 3000 atoms
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Performance: 0.152 ns/day, 158.397 hours/ns, 3.507 timesteps/s, 10.522 katom-step/s
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99.6% CPU use with 1 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 | 2.4269 | 2.4269 | 2.4269 | 0.0 | 42.56
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Neigh | 0.084723 | 0.084723 | 0.084723 | 0.0 | 1.49
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Comm | 0.00093159 | 0.00093159 | 0.00093159 | 0.0 | 0.02
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Output | 7.4061e-05 | 7.4061e-05 | 7.4061e-05 | 0.0 | 0.00
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Modify | 3.1894 | 3.1894 | 3.1894 | 0.0 | 55.93
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Other | | 0.0002537 | | | 0.00
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Nlocal: 3000 ave 3000 max 3000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11077 ave 11077 max 11077 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 971830 ave 971830 max 971830 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 971830
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Ave neighs/atom = 323.94333
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:06
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