lammps/examples/rdf-adf/log.27Nov18.spce.g++.4

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom)
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 lj/cut/coul/long 12.0 12.0
pair_coeff * * 0.0 1.0
pair_coeff 1 1 0.15535 3.166
kspace_style pppm 1.0e-6
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
# need to set bond/angle inclusion to > 0.0
# so that intramolecular pairs are included in neighbor lists (required for second ADF)
special_bonds lj/coul 1.0e-100 1.0e-100 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
timestep 2.0
neigh_modify every 1 delay 2 check yes
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
velocity all create 300.0 6244325
thermo 100
run 500
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394674
estimated relative force accuracy = 1.18855e-06
using double precision FFTs
3d grid and FFT values/proc = 34263 16000
Neighbor list info ...
update every 1 steps, delay 2 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 lj/cut/coul/long, 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) = 13.1 | 13.1 | 13.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -16692.369 0 -14010.534 -112.83562
100 283.44729 -17008.717 0 -14474.854 -162.06378
200 298.75279 -16765.543 0 -14094.858 428.79175
300 296.65013 -16589.155 0 -13937.267 547.40809
400 303.82993 -16625.014 0 -13908.942 237.957
500 298.00206 -16716.893 0 -14052.919 231.33112
Loop time of 12.5516 on 4 procs for 500 steps with 4500 atoms
Performance: 6.884 ns/day, 3.487 hours/ns, 39.836 timesteps/s
94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.739 | 7.9051 | 8.2663 | 7.5 | 62.98
Bond | 0.00061631 | 0.00064486 | 0.00070524 | 0.0 | 0.01
Kspace | 2.7001 | 3.0573 | 3.2239 | 11.9 | 24.36
Neigh | 1.1736 | 1.174 | 1.1743 | 0.0 | 9.35
Comm | 0.18222 | 0.1869 | 0.19248 | 0.8 | 1.49
Output | 0.00017595 | 0.00032246 | 0.00076079 | 0.0 | 0.00
Modify | 0.20354 | 0.20467 | 0.20652 | 0.2 | 1.63
Other | | 0.02259 | | | 0.18
Nlocal: 1125 ave 1132 max 1114 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 12241 ave 12298 max 12196 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 650366 ave 671163 max 631441 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 2601464
Ave neighs/atom = 578.103
Ave special neighs/atom = 2
Neighbor list builds = 45
Dangerous builds = 0
reset_timestep 0
compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O
fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394674
estimated relative force accuracy = 1.18855e-06
using double precision FFTs
3d grid and FFT values/proc = 34263 16000
Neighbor list info ...
update every 1 steps, delay 2 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
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute rdf, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(3) compute adf, occasional
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.96 | 13.96 | 13.96 Mbytes
Step Temp E_pair E_mol TotEng Press
0 298.00206 -16716.893 0 -14052.919 231.44272
100 307.28155 -16760.647 0 -14013.72 452.38436
200 299.05168 -16674.695 0 -14001.338 177.44237
300 292.7564 -16573.946 0 -13956.865 122.27796
400 299.2644 -16578.318 0 -13903.059 482.03304
500 296.04028 -16623.179 0 -13976.742 89.968145
600 300.30911 -16664.206 0 -13979.608 132.70079
700 292.39517 -16703.749 0 -14089.897 825.267
800 298.75851 -16661.684 0 -13990.948 468.68671
900 301.55689 -16644.846 0 -13949.093 -72.16965
1000 298.2852 -16682.077 0 -14015.572 0.69725342
Loop time of 32.3106 on 4 procs for 1000 steps with 4500 atoms
Performance: 5.348 ns/day, 4.488 hours/ns, 30.950 timesteps/s
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.647 | 15.876 | 16.119 | 4.3 | 49.13
Bond | 0.0011718 | 0.0012704 | 0.001348 | 0.2 | 0.00
Kspace | 5.286 | 5.5364 | 5.7729 | 7.5 | 17.13
Neigh | 2.3892 | 2.3962 | 2.3991 | 0.3 | 7.42
Comm | 0.34641 | 0.35514 | 0.35988 | 0.9 | 1.10
Output | 0.00047851 | 0.00069892 | 0.0013568 | 0.0 | 0.00
Modify | 8.0882 | 8.0963 | 8.1047 | 0.3 | 25.06
Other | | 0.04887 | | | 0.15
Nlocal: 1125 ave 1137 max 1114 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 12206.2 ave 12239 max 12169 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 650464 ave 655962 max 641444 min
Histogram: 1 0 0 0 0 0 0 2 0 1
FullNghs: 1.30095e+06 ave 1.31925e+06 max 1.28413e+06 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 5203786
Ave neighs/atom = 1156.4
Ave special neighs/atom = 2
Neighbor list builds = 94
Dangerous builds = 0
Total wall time: 0:00:45