forked from lijiext/lammps
179 lines
6.1 KiB
Groff
179 lines
6.1 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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pair_style hybrid/overlay coul/cut 12.0 python 12.0
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pair_coeff * * coul/cut
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pair_coeff * * python py_pot.LJCutSPCE OW NULL
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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# create combined lj/coul table for all atom types
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# generate tabulated potential from python variant
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair coul/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair python, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair coul/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair python, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair coul/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair python, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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# switch to tabulated potential
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pair_style table linear 2000 pppm
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pair_coeff 1 1 spce.table OW-OW
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WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (src/pair_table.cpp:481)
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pair_coeff 1 2 spce.table OW-HW
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WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (src/pair_table.cpp:481)
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pair_coeff 2 2 spce.table HW-HW
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WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (src/pair_table.cpp:481)
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thermo 10
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run 100
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair table, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 10.01 | 10.01 | 10.01 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -18173.499 0 -18173.499 -2019.6011
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10 146.87683 -19431.334 0 -18118.336 -4804.774
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20 183.13008 -19192.694 0 -17555.612 -5105.075
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30 205.91102 -18124.567 0 -16283.836 -4052.5955
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40 241.34432 -18154.089 0 -15996.604 -3187.3994
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50 265.93905 -19712.779 0 -17335.431 -2716.3264
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60 273.67861 -21092.479 0 -18645.943 -2266.2648
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70 288.39213 -19794.592 0 -17216.526 -1207.5782
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80 300.36209 -20235.73 0 -17550.658 -1345.2669
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90 303.8567 -21670.331 0 -18954.02 -2207.0831
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100 304.10875 -19847.214 0 -17128.649 -1431.7749
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Loop time of 1.64676 on 4 procs for 100 steps with 4500 atoms
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Performance: 5.247 ns/day, 4.574 hours/ns, 60.725 timesteps/s
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98.4% 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 | 1.4241 | 1.4506 | 1.5134 | 3.0 | 88.09
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Bond | 9.8705e-05 | 0.00010312 | 0.00010729 | 0.0 | 0.01
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Neigh | 0.071698 | 0.071712 | 0.07172 | 0.0 | 4.35
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Comm | 0.027696 | 0.090501 | 0.11691 | 12.1 | 5.50
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Output | 0.00032783 | 0.00048846 | 0.00096679 | 0.0 | 0.03
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Modify | 0.030543 | 0.030691 | 0.030788 | 0.1 | 1.86
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Other | | 0.002627 | | | 0.16
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Nlocal: 1125 ave 1163 max 1097 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Nghost: 12265.5 ave 12299 max 12233 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Neighs: 649430 ave 681781 max 630283 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 2597720
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Ave neighs/atom = 577.271
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Ave special neighs/atom = 2
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Neighbor list builds = 3
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Dangerous builds = 0
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shell rm spce.table
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Total wall time: 0:00:01
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