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