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update log files for peptide, peri, pour and python examples

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This commit is contained in:
Axel Kohlmeyer
2018-11-29 14:51:25 -05:00
parent cef4164460
commit 46bf4b7efb
39 changed files with 1843 additions and 1353 deletions
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000678539 secs
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
python end_of_step_callback here """
from __future__ import print_function
from lammps import lammps
def end_of_step_callback(lmp):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### END OF STEP ###", t)
def post_force_callback(lmp, v):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### POST_FORCE ###", t)
"""
fix 1 all nve
fix 2 all python/invoke 50 end_of_step end_of_step_callback
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.732007 on 1 procs for 250 steps with 4000 atoms
Performance: 147539.519 tau/day, 341.527 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60651 | 0.60651 | 0.60651 | 0.0 | 82.86
Neigh | 0.092702 | 0.092702 | 0.092702 | 0.0 | 12.66
Comm | 0.013686 | 0.013686 | 0.013686 | 0.0 | 1.87
Output | 0.00016069 | 0.00016069 | 0.00016069 | 0.0 | 0.02
Modify | 0.016055 | 0.016055 | 0.016055 | 0.0 | 2.19
Other | | 0.00289 | | | 0.39
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000408888 secs
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
python end_of_step_callback here """
from __future__ import print_function
from lammps import lammps
def end_of_step_callback(lmp):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### END OF STEP ###", t)
def post_force_callback(lmp, v):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### POST_FORCE ###", t)
"""
fix 1 all nve
fix 2 all python/invoke 50 end_of_step end_of_step_callback
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.227907 on 4 procs for 250 steps with 4000 atoms
Performance: 473877.870 tau/day, 1096.940 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15923 | 0.16507 | 0.17227 | 1.2 | 72.43
Neigh | 0.02438 | 0.025177 | 0.025757 | 0.4 | 11.05
Comm | 0.022418 | 0.030157 | 0.036685 | 2.9 | 13.23
Output | 0.00052595 | 0.00092125 | 0.0011675 | 0.0 | 0.40
Modify | 0.0053911 | 0.0057266 | 0.006294 | 0.5 | 2.51
Other | | 0.0008523 | | | 0.37
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000658989 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 12.0574 on 1 procs for 250 steps with 4000 atoms
Performance: 8957.186 tau/day, 20.734 timesteps/s
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.61686 | 0.61686 | 0.61686 | 0.0 | 5.12
Neigh | 0.094026 | 0.094026 | 0.094026 | 0.0 | 0.78
Comm | 0.015743 | 0.015743 | 0.015743 | 0.0 | 0.13
Output | 0.00021815 | 0.00021815 | 0.00021815 | 0.0 | 0.00
Modify | 11.328 | 11.328 | 11.328 | 0.0 | 93.95
Other | | 0.002812 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:12

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00041604 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 3.60532 on 4 procs for 250 steps with 4000 atoms
Performance: 29955.711 tau/day, 69.342 timesteps/s
95.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15953 | 0.16556 | 0.16945 | 0.9 | 4.59
Neigh | 0.024014 | 0.024431 | 0.024704 | 0.2 | 0.68
Comm | 0.10837 | 0.26844 | 0.38063 | 19.1 | 7.45
Output | 0.00021553 | 0.0063262 | 0.0088348 | 4.5 | 0.18
Modify | 3.0299 | 3.138 | 3.3038 | 5.7 | 87.04
Other | | 0.002585 | | | 0.07
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:03

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000703096 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE_Opt
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.806998 on 1 procs for 250 steps with 4000 atoms
Performance: 133829.286 tau/day, 309.790 timesteps/s
95.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60639 | 0.60639 | 0.60639 | 0.0 | 75.14
Neigh | 0.092807 | 0.092807 | 0.092807 | 0.0 | 11.50
Comm | 0.013782 | 0.013782 | 0.013782 | 0.0 | 1.71
Output | 0.00021243 | 0.00021243 | 0.00021243 | 0.0 | 0.03
Modify | 0.091672 | 0.091672 | 0.091672 | 0.0 | 11.36
Other | | 0.00213 | | | 0.26
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000407457 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE_Opt
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.283796 on 4 procs for 250 steps with 4000 atoms
Performance: 380554.630 tau/day, 880.913 timesteps/s
93.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16068 | 0.16297 | 0.167 | 0.6 | 57.42
Neigh | 0.024281 | 0.02511 | 0.027018 | 0.7 | 8.85
Comm | 0.033199 | 0.035637 | 0.03814 | 1.3 | 12.56
Output | 0.00044489 | 0.00057381 | 0.00065589 | 0.0 | 0.20
Modify | 0.056902 | 0.058489 | 0.06128 | 0.7 | 20.61
Other | | 0.001018 | | | 0.36
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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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)
1 by 1 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) = 25.18 | 25.18 | 25.18 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 5.78394 on 1 procs for 100 steps with 4500 atoms
Performance: 1.494 ns/day, 16.066 hours/ns, 17.289 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.4417 | 5.4417 | 5.4417 | 0.0 | 94.08
Bond | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.00
Neigh | 0.26895 | 0.26895 | 0.26895 | 0.0 | 4.65
Comm | 0.019179 | 0.019179 | 0.019179 | 0.0 | 0.33
Output | 0.00039768 | 0.00039768 | 0.00039768 | 0.0 | 0.01
Modify | 0.050508 | 0.050508 | 0.050508 | 0.0 | 0.87
Other | | 0.003098 | | | 0.05
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21269 ave 21269 max 21269 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.59772e+06 ave 2.59772e+06 max 2.59772e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
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: 0:00:06

178
examples/python/log.27Nov18.pair_python_coulomb.g++.4 Normal file
View File

@ -0,0 +1,178 @@
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

111
examples/python/log.4May17.pair_python_hybrid.g++.1 → examples/python/log.27Nov18.pair_python_hybrid.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00073123 secs
mass * 1.0
region half block -0.1 4.9 0 10 0 10
set region half type 2
@ -53,7 +54,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@ -61,20 +62,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms
Loop time of 5.56562 on 1 procs for 250 steps with 4000 atoms
Performance: 10758.705 tau/day, 24.904 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 19404.856 tau/day, 44.919 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.913 | 9.913 | 9.913 | 0.0 | 98.75
Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95
Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13
Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00
Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14
Other | | 0.003027 | | | 0.03
Pair | 5.4305 | 5.4305 | 5.4305 | 0.0 | 97.57
Neigh | 0.10441 | 0.10441 | 0.10441 | 0.0 | 1.88
Comm | 0.013915 | 0.013915 | 0.013915 | 0.0 | 0.25
Output | 0.00019979 | 0.00019979 | 0.00019979 | 0.0 | 0.00
Modify | 0.014502 | 0.014502 | 0.014502 | 0.0 | 0.26
Other | | 0.002061 | | | 0.04
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -89,14 +90,60 @@ Neighbor list builds = 12
Dangerous builds not checked
write_data hybrid.data
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
write_restart hybrid.restart
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
clear
using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
restoring pair style hybrid from restart
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
@ -129,7 +176,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.281 | 4.281 | 4.281 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
300 1.645592 -4.7496711 0 -2.2819002 5.8734193
@ -137,20 +184,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms
Loop time of 5.56525 on 1 procs for 250 steps with 4000 atoms
Performance: 10713.932 tau/day, 24.801 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 19406.123 tau/day, 44.922 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69
Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98
Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14
Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00
Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13
Other | | 0.004348 | | | 0.04
Pair | 5.3122 | 5.3122 | 5.3122 | 0.0 | 95.45
Neigh | 0.21918 | 0.21918 | 0.21918 | 0.0 | 3.94
Comm | 0.015959 | 0.015959 | 0.015959 | 0.0 | 0.29
Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00
Modify | 0.014443 | 0.014443 | 0.014443 | 0.0 | 0.26
Other | | 0.00326 | | | 0.06
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -211,7 +258,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.781 | 3.781 | 3.781 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6275257 -4.7224992 0 -2.281821 5.9567365
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
@ -219,20 +266,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms
Loop time of 5.44427 on 1 procs for 250 steps with 4000 atoms
Performance: 10868.626 tau/day, 25.159 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 19837.379 tau/day, 45.920 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74
Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97
Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13
Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00
Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13
Other | | 0.002994 | | | 0.03
Pair | 5.3082 | 5.3082 | 5.3082 | 0.0 | 97.50
Neigh | 0.10536 | 0.10536 | 0.10536 | 0.0 | 1.94
Comm | 0.01346 | 0.01346 | 0.01346 | 0.0 | 0.25
Output | 0.00019431 | 0.00019431 | 0.00019431 | 0.0 | 0.00
Modify | 0.015079 | 0.015079 | 0.015079 | 0.0 | 0.28
Other | | 0.002012 | | | 0.04
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -247,4 +294,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:00:30
Total wall time: 0:00:16

111
examples/python/log.4May17.pair_python_hybrid.g++.4 → examples/python/log.27Nov18.pair_python_hybrid.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000420809 secs
mass * 1.0
region half block -0.1 4.9 0 10 0 10
set region half type 2
@ -53,7 +54,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.968 | 3.968 | 3.968 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
@ -61,20 +62,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms
Loop time of 1.53377 on 4 procs for 250 steps with 4000 atoms
Performance: 39742.745 tau/day, 91.997 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 70414.718 tau/day, 162.997 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35
Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93
Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53
Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01
Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13
Other | | 0.001337 | | | 0.05
Pair | 1.3644 | 1.406 | 1.4448 | 3.2 | 91.67
Neigh | 0.027066 | 0.027591 | 0.028437 | 0.3 | 1.80
Comm | 0.055296 | 0.095109 | 0.13733 | 12.4 | 6.20
Output | 0.00022817 | 0.00030088 | 0.00042033 | 0.0 | 0.02
Modify | 0.0037878 | 0.0038549 | 0.0040336 | 0.2 | 0.25
Other | | 0.0008861 | | | 0.06
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@ -89,14 +90,60 @@ Neighbor list builds = 12
Dangerous builds not checked
write_data hybrid.data
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
write_restart hybrid.restart
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
clear
using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
restoring pair style hybrid from restart
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
@ -129,7 +176,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.626 | 3.626 | 3.626 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
@ -137,20 +184,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms
Loop time of 1.51785 on 4 procs for 250 steps with 4000 atoms
Performance: 39155.038 tau/day, 90.637 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 71153.411 tau/day, 164.707 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13
Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90
Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76
Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01
Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13
Other | | 0.002039 | | | 0.07
Pair | 1.2893 | 1.3741 | 1.416 | 4.2 | 90.53
Neigh | 0.055474 | 0.056676 | 0.057363 | 0.3 | 3.73
Comm | 0.039187 | 0.081666 | 0.16742 | 17.6 | 5.38
Output | 0.00014877 | 0.0002687 | 0.00061893 | 0.0 | 0.02
Modify | 0.003741 | 0.0037862 | 0.0038075 | 0.0 | 0.25
Other | | 0.001315 | | | 0.09
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@ -211,7 +258,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.126 | 3.126 | 3.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
@ -219,20 +266,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms
Loop time of 1.53622 on 4 procs for 250 steps with 4000 atoms
Performance: 39715.257 tau/day, 91.933 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 70302.534 tau/day, 162.737 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52
Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92
Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37
Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01
Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13
Other | | 0.001215 | | | 0.04
Pair | 1.2893 | 1.3875 | 1.4506 | 5.1 | 90.32
Neigh | 0.026512 | 0.02714 | 0.027651 | 0.2 | 1.77
Comm | 0.053684 | 0.11665 | 0.21515 | 17.6 | 7.59
Output | 0.00017214 | 0.00029582 | 0.0006547 | 0.0 | 0.02
Modify | 0.0037682 | 0.0037964 | 0.0038147 | 0.0 | 0.25
Other | | 0.0008581 | | | 0.06
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
@ -247,4 +294,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:00:08
Total wall time: 0:00:04

60
examples/python/log.4May17.pair_python_long.g++.1 → examples/python/log.27Nov18.pair_python_long.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
@ -48,8 +48,8 @@ fix 2 all nvt temp 300.0 300.0 100.0
# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
@ -69,11 +69,13 @@ pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 1 table 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)
thermo 10
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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
@ -98,35 +100,35 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes
Per MPI rank memory allocation (min/avg/max) = 36.57 | 36.57 | 36.57 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16690.032 0 -16690.032 -1268.9538
10 120.58553 -17767.504 0 -16689.536 -4063.8589
20 136.11736 -17882.557 0 -16665.742 -5124.6758
30 137.00764 -17872.318 0 -16647.545 -5337.2022
40 153.38868 -17999.269 0 -16628.059 -5213.6001
50 167.70342 -18103.06 0 -16603.883 -4460.6632
60 163.07134 -18034.856 0 -16577.088 -3285.0037
70 169.59286 -18064.636 0 -16548.57 -2606.407
80 182.92893 -18153.499 0 -16518.215 -2385.5152
90 191.2793 -18195.356 0 -16485.425 -2235.3701
100 194.68587 -18192.458 0 -16452.073 -1948.3746
Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms
0 0 -16690.019 0 -16690.019 -1268.9124
10 120.58553 -17767.489 0 -16689.521 -4063.8136
20 136.11736 -17882.538 0 -16665.724 -5124.6194
30 137.00764 -17872.302 0 -16647.529 -5337.1515
40 153.38867 -17999.256 0 -16628.046 -5213.5616
50 167.70342 -18103.046 0 -16603.87 -4460.6216
60 163.07134 -18034.842 0 -16577.074 -3284.9621
70 169.59286 -18064.622 0 -16548.556 -2606.3642
80 182.92892 -18153.485 0 -16518.202 -2385.4747
90 191.2793 -18195.343 0 -16485.411 -2235.3292
100 194.68587 -18192.446 0 -16452.061 -1948.3379
Loop time of 7.00522 on 1 procs for 100 steps with 4500 atoms
Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.233 ns/day, 19.459 hours/ns, 14.275 timesteps/s
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32
Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00
Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36
Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11
Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30
Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01
Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83
Other | | 0.005364 | | | 0.07
Pair | 5.5664 | 5.5664 | 5.5664 | 0.0 | 79.46
Bond | 0.00011444 | 0.00011444 | 0.00011444 | 0.0 | 0.00
Kspace | 1.0814 | 1.0814 | 1.0814 | 0.0 | 15.44
Neigh | 0.28011 | 0.28011 | 0.28011 | 0.0 | 4.00
Comm | 0.020573 | 0.020573 | 0.020573 | 0.0 | 0.29
Output | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01
Modify | 0.052692 | 0.052692 | 0.052692 | 0.0 | 0.75
Other | | 0.003407 | | | 0.05
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -135,7 +137,7 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2601769
Total # of neighbors = 2601768
Ave neighs/atom = 578.171
Ave special neighs/atom = 2
Neighbor list builds = 3
@ -143,4 +145,4 @@ Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:08
Total wall time: 0:00:07

60
examples/python/log.4May17.pair_python_long.g++.4 → examples/python/log.27Nov18.pair_python_long.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
@ -48,8 +48,8 @@ fix 2 all nvt temp 300.0 300.0 100.0
# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
@ -69,11 +69,13 @@ pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 1 table 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)
thermo 10
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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
@ -98,44 +100,44 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes
Per MPI rank memory allocation (min/avg/max) = 13.5 | 13.5 | 13.5 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16690.032 0 -16690.032 -1268.9538
10 120.58553 -17767.504 0 -16689.536 -4063.8589
20 136.11736 -17882.557 0 -16665.742 -5124.6758
30 137.00764 -17872.318 0 -16647.545 -5337.2022
40 153.38868 -17999.269 0 -16628.059 -5213.6001
50 167.70342 -18103.06 0 -16603.883 -4460.6632
60 163.07134 -18034.856 0 -16577.088 -3285.0037
70 169.59286 -18064.636 0 -16548.57 -2606.407
80 182.92893 -18153.499 0 -16518.215 -2385.5152
90 191.2793 -18195.356 0 -16485.425 -2235.3701
100 194.68587 -18192.458 0 -16452.073 -1948.3746
Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms
0 0 -16690.019 0 -16690.019 -1268.9124
10 120.58553 -17767.489 0 -16689.521 -4063.8136
20 136.11736 -17882.538 0 -16665.724 -5124.6194
30 137.00764 -17872.302 0 -16647.529 -5337.1515
40 153.38867 -17999.256 0 -16628.046 -5213.5616
50 167.70342 -18103.046 0 -16603.87 -4460.6216
60 163.07134 -18034.842 0 -16577.074 -3284.9621
70 169.59286 -18064.622 0 -16548.556 -2606.3642
80 182.92892 -18153.485 0 -16518.202 -2385.4747
90 191.2793 -18195.343 0 -16485.411 -2235.3292
100 194.68587 -18192.446 0 -16452.061 -1948.3379
Loop time of 2.26946 on 4 procs for 100 steps with 4500 atoms
Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 3.807 ns/day, 6.304 hours/ns, 44.063 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49
Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01
Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86
Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83
Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68
Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02
Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95
Other | | 0.003775 | | | 0.16
Pair | 1.4676 | 1.53 | 1.6054 | 4.5 | 67.42
Bond | 9.7752e-05 | 0.00012088 | 0.00013947 | 0.0 | 0.01
Kspace | 0.51974 | 0.59375 | 0.65496 | 7.2 | 26.16
Neigh | 0.075271 | 0.075279 | 0.075287 | 0.0 | 3.32
Comm | 0.028602 | 0.029937 | 0.031052 | 0.5 | 1.32
Output | 0.00035477 | 0.00062722 | 0.0014365 | 0.0 | 0.03
Modify | 0.03581 | 0.035956 | 0.036059 | 0.1 | 1.58
Other | | 0.003819 | | | 0.17
Nlocal: 1125 ave 1154 max 1092 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 12256.2 ave 12296 max 12213 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 650442 ave 678831 max 626373 min
Neighs: 650442 ave 678830 max 626373 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 2601769
Total # of neighbors = 2601768
Ave neighs/atom = 578.171
Ave special neighs/atom = 2
Neighbor list builds = 3

67
examples/python/log.4May17.pair_python_melt.g++.1 → examples/python/log.27Nov18.pair_python_melt.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000694513 secs
mass * 1.0
velocity all create 3.0 87287
@ -39,7 +40,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@ -47,20 +48,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 20.9283 on 1 procs for 250 steps with 4000 atoms
Loop time of 11.5979 on 1 procs for 250 steps with 4000 atoms
Performance: 5160.475 tau/day, 11.946 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 9312.020 tau/day, 21.556 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.809 | 20.809 | 20.809 | 0.0 | 99.43
Neigh | 0.088638 | 0.088638 | 0.088638 | 0.0 | 0.42
Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.06
Output | 0.0002737 | 0.0002737 | 0.0002737 | 0.0 | 0.00
Modify | 0.014334 | 0.014334 | 0.014334 | 0.0 | 0.07
Other | | 0.003089 | | | 0.01
Pair | 11.474 | 11.474 | 11.474 | 0.0 | 98.94
Neigh | 0.092903 | 0.092903 | 0.092903 | 0.0 | 0.80
Comm | 0.01373 | 0.01373 | 0.01373 | 0.0 | 0.12
Output | 0.00021935 | 0.00021935 | 0.00021935 | 0.0 | 0.00
Modify | 0.014506 | 0.014506 | 0.014506 | 0.0 | 0.13
Other | | 0.002072 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -81,8 +82,10 @@ clear
using 1 OpenMP thread(s) per MPI task
read_restart melt.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
pair_style python 2.5
@ -104,7 +107,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.36 | 3.36 | 3.36 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.396 | 3.396 | 3.396 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
300 1.645592 -4.7496711 0 -2.2819002 5.8734193
@ -112,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
Loop time of 21.1422 on 1 procs for 250 steps with 4000 atoms
Loop time of 11.6299 on 1 procs for 250 steps with 4000 atoms
Performance: 5108.279 tau/day, 11.825 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 9286.409 tau/day, 21.496 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.925 | 20.925 | 20.925 | 0.0 | 98.97
Neigh | 0.18452 | 0.18452 | 0.18452 | 0.0 | 0.87
Comm | 0.014836 | 0.014836 | 0.014836 | 0.0 | 0.07
Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.00
Modify | 0.01366 | 0.01366 | 0.01366 | 0.0 | 0.06
Other | | 0.004355 | | | 0.02
Pair | 11.403 | 11.403 | 11.403 | 0.0 | 98.05
Neigh | 0.19289 | 0.19289 | 0.19289 | 0.0 | 1.66
Comm | 0.015828 | 0.015828 | 0.015828 | 0.0 | 0.14
Output | 0.00018644 | 0.00018644 | 0.00018644 | 0.0 | 0.00
Modify | 0.014582 | 0.014582 | 0.014582 | 0.0 | 0.13
Other | | 0.003107 | | | 0.03
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -175,7 +178,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.86 | 2.86 | 2.86 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.896 | 2.896 | 2.896 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6275257 -4.7224992 0 -2.281821 5.9567365
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
@ -183,20 +186,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
Loop time of 21.1026 on 1 procs for 250 steps with 4000 atoms
Loop time of 11.6243 on 1 procs for 250 steps with 4000 atoms
Performance: 5117.845 tau/day, 11.847 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 9290.855 tau/day, 21.507 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.984 | 20.984 | 20.984 | 0.0 | 99.44
Neigh | 0.088639 | 0.088639 | 0.088639 | 0.0 | 0.42
Comm | 0.012881 | 0.012881 | 0.012881 | 0.0 | 0.06
Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00
Modify | 0.013523 | 0.013523 | 0.013523 | 0.0 | 0.06
Other | | 0.003033 | | | 0.01
Pair | 11.501 | 11.501 | 11.501 | 0.0 | 98.94
Neigh | 0.093333 | 0.093333 | 0.093333 | 0.0 | 0.80
Comm | 0.013483 | 0.013483 | 0.013483 | 0.0 | 0.12
Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.00
Modify | 0.014475 | 0.014475 | 0.014475 | 0.0 | 0.12
Other | | 0.001968 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -211,4 +214,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:01:05
Total wall time: 0:00:35

67
examples/python/log.4May17.pair_python_melt.g++.4 → examples/python/log.27Nov18.pair_python_melt.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000413418 secs
mass * 1.0
velocity all create 3.0 87287
@ -39,7 +40,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
@ -47,20 +48,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 5.65922 on 4 procs for 250 steps with 4000 atoms
Loop time of 3.21263 on 4 procs for 250 steps with 4000 atoms
Performance: 19083.895 tau/day, 44.176 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 33617.340 tau/day, 77.818 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.4529 | 5.5207 | 5.5575 | 1.7 | 97.55
Neigh | 0.023164 | 0.023376 | 0.023883 | 0.2 | 0.41
Comm | 0.073318 | 0.1099 | 0.17804 | 12.2 | 1.94
Output | 0.00023365 | 0.00026143 | 0.00030684 | 0.0 | 0.00
Modify | 0.0036483 | 0.0037143 | 0.003896 | 0.2 | 0.07
Other | | 0.001274 | | | 0.02
Pair | 2.9309 | 2.9942 | 3.1071 | 3.9 | 93.20
Neigh | 0.024111 | 0.024518 | 0.024765 | 0.2 | 0.76
Comm | 0.075799 | 0.1889 | 0.25258 | 15.5 | 5.88
Output | 0.00018406 | 0.00030106 | 0.00065088 | 0.0 | 0.01
Modify | 0.0038259 | 0.0038511 | 0.0038726 | 0.0 | 0.12
Other | | 0.0009047 | | | 0.03
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@ -81,8 +82,10 @@ clear
using 1 OpenMP thread(s) per MPI task
read_restart melt.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
pair_style python 2.5
@ -104,7 +107,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.815 | 2.816 | 2.816 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.829 | 2.83 | 2.83 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
@ -112,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 5.70169 on 4 procs for 250 steps with 4000 atoms
Loop time of 3.16401 on 4 procs for 250 steps with 4000 atoms
Performance: 18941.760 tau/day, 43.847 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 34133.894 tau/day, 79.014 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3919 | 5.4905 | 5.6136 | 3.7 | 96.30
Neigh | 0.046791 | 0.047817 | 0.048795 | 0.3 | 0.84
Comm | 0.034221 | 0.1575 | 0.25635 | 22.1 | 2.76
Output | 0.00020409 | 0.00023448 | 0.00026131 | 0.0 | 0.00
Modify | 0.0035028 | 0.0035674 | 0.0036926 | 0.1 | 0.06
Other | | 0.002079 | | | 0.04
Pair | 2.9254 | 2.9723 | 3.0639 | 3.2 | 93.94
Neigh | 0.04915 | 0.050266 | 0.050704 | 0.3 | 1.59
Comm | 0.044051 | 0.13579 | 0.18379 | 15.0 | 4.29
Output | 0.00016141 | 0.00028008 | 0.00063109 | 0.0 | 0.01
Modify | 0.0037544 | 0.003895 | 0.0041802 | 0.3 | 0.12
Other | | 0.001474 | | | 0.05
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@ -175,7 +178,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.315 | 2.316 | 2.316 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.329 | 2.33 | 2.33 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
@ -183,20 +186,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 5.69568 on 4 procs for 250 steps with 4000 atoms
Loop time of 3.16461 on 4 procs for 250 steps with 4000 atoms
Performance: 18961.751 tau/day, 43.893 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 34127.383 tau/day, 78.999 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.4041 | 5.5245 | 5.6139 | 3.2 | 96.99
Neigh | 0.022658 | 0.022986 | 0.023398 | 0.2 | 0.40
Comm | 0.053521 | 0.14309 | 0.26385 | 20.2 | 2.51
Output | 0.00027037 | 0.00029504 | 0.00033665 | 0.0 | 0.01
Modify | 0.0035288 | 0.0035585 | 0.0035827 | 0.0 | 0.06
Other | | 0.001275 | | | 0.02
Pair | 2.9135 | 2.9842 | 3.0594 | 3.1 | 94.30
Neigh | 0.024132 | 0.024319 | 0.024553 | 0.1 | 0.77
Comm | 0.075955 | 0.15106 | 0.22174 | 13.9 | 4.77
Output | 0.00016856 | 0.00028443 | 0.00062919 | 0.0 | 0.01
Modify | 0.0037944 | 0.0038335 | 0.0038977 | 0.1 | 0.12
Other | | 0.0008717 | | | 0.03
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
@ -211,4 +214,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:00:17
Total wall time: 0:00:09

30
examples/python/log.4May17.pair_python_spce.g++.1 → examples/python/log.27Nov18.pair_python_spce.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
@ -52,7 +52,7 @@ fix 2 all nvt temp 300.0 300.0 100.0
thermo 10
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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
@ -77,7 +77,7 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 Mbytes
Per MPI rank memory allocation (min/avg/max) = 41.15 | 41.15 | 41.15 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16692.369 0 -16692.369 -1289.222
10 120.56861 -17769.719 0 -16691.902 -4082.7098
@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916
Loop time of 23.5385 on 1 procs for 100 steps with 4500 atoms
Loop time of 15.3744 on 1 procs for 100 steps with 4500 atoms
Performance: 0.367 ns/day, 65.385 hours/ns, 4.248 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.562 ns/day, 42.707 hours/ns, 6.504 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.642 | 21.642 | 21.642 | 0.0 | 91.94
Bond | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.00
Kspace | 1.5436 | 1.5436 | 1.5436 | 0.0 | 6.56
Neigh | 0.25623 | 0.25623 | 0.25623 | 0.0 | 1.09
Comm | 0.024325 | 0.024325 | 0.024325 | 0.0 | 0.10
Output | 0.00064301 | 0.00064301 | 0.00064301 | 0.0 | 0.00
Modify | 0.065919 | 0.065919 | 0.065919 | 0.0 | 0.28
Other | | 0.005401 | | | 0.02
Pair | 13.914 | 13.914 | 13.914 | 0.0 | 90.50
Bond | 0.00013375 | 0.00013375 | 0.00013375 | 0.0 | 0.00
Kspace | 1.0852 | 1.0852 | 1.0852 | 0.0 | 7.06
Neigh | 0.29811 | 0.29811 | 0.29811 | 0.0 | 1.94
Comm | 0.020503 | 0.020503 | 0.020503 | 0.0 | 0.13
Output | 0.00045133 | 0.00045133 | 0.00045133 | 0.0 | 0.00
Modify | 0.052513 | 0.052513 | 0.052513 | 0.0 | 0.34
Other | | 0.00348 | | | 0.02
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -119,4 +119,4 @@ Ave neighs/atom = 578.169
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:15

30
examples/python/log.4May17.pair_python_spce.g++.4 → examples/python/log.27Nov18.pair_python_spce.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
@ -52,7 +52,7 @@ fix 2 all nvt temp 300.0 300.0 100.0
thermo 10
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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
@ -77,7 +77,7 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes
Per MPI rank memory allocation (min/avg/max) = 14.64 | 14.64 | 14.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16692.369 0 -16692.369 -1289.222
10 120.56861 -17769.719 0 -16691.902 -4082.7098
@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916
Loop time of 6.4942 on 4 procs for 100 steps with 4500 atoms
Loop time of 4.36104 on 4 procs for 100 steps with 4500 atoms
Performance: 1.330 ns/day, 18.039 hours/ns, 15.398 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1.981 ns/day, 12.114 hours/ns, 22.930 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.4084 | 5.572 | 5.8013 | 7.2 | 85.80
Bond | 0.00012994 | 0.0001421 | 0.00016356 | 0.0 | 0.00
Kspace | 0.52942 | 0.75773 | 0.92078 | 19.5 | 11.67
Neigh | 0.071055 | 0.07116 | 0.071278 | 0.0 | 1.10
Comm | 0.040311 | 0.041255 | 0.041817 | 0.3 | 0.64
Output | 0.00040603 | 0.00048071 | 0.00058675 | 0.0 | 0.01
Modify | 0.047507 | 0.047629 | 0.047772 | 0.1 | 0.73
Other | | 0.003771 | | | 0.06
Pair | 3.5019 | 3.6105 | 3.738 | 4.4 | 82.79
Bond | 0.00010133 | 0.00013196 | 0.00017118 | 0.0 | 0.00
Kspace | 0.47082 | 0.59641 | 0.70417 | 10.8 | 13.68
Neigh | 0.081036 | 0.081042 | 0.081047 | 0.0 | 1.86
Comm | 0.030113 | 0.03092 | 0.03135 | 0.3 | 0.71
Output | 0.00034952 | 0.00064117 | 0.001514 | 0.0 | 0.01
Modify | 0.036583 | 0.037553 | 0.038021 | 0.3 | 0.86
Other | | 0.00388 | | | 0.09
Nlocal: 1125 ave 1154 max 1092 min
Histogram: 1 0 0 0 1 0 0 1 0 1
@ -119,4 +119,4 @@ Ave neighs/atom = 578.169
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:06
Total wall time: 0:00:04

27
examples/python/log.4May17.pair_python_table.g++.1 → examples/python/log.27Nov18.pair_python_table.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000697136 secs
mass * 1.0
velocity all create 3.0 87287
@ -38,7 +39,7 @@ Neighbor list info ...
pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
Should only be flagged at inflection points (src/pair_table.cpp:481)
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
@ -59,7 +60,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733629 0 -2.2744879 -3.7032813
50 1.6758731 -4.7953067 0 -2.2821255 5.6706553
@ -67,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.632425 -4.7284533 0 -2.2804279 5.9595684
200 1.6631578 -4.7749889 0 -2.2808759 5.7365839
250 1.6277062 -4.7224727 0 -2.2815238 5.9572913
Loop time of 0.996739 on 1 procs for 250 steps with 4000 atoms
Loop time of 0.94897 on 1 procs for 250 steps with 4000 atoms
Performance: 108353.298 tau/day, 250.818 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 113807.650 tau/day, 263.444 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87985 | 0.87985 | 0.87985 | 0.0 | 88.27
Neigh | 0.08799 | 0.08799 | 0.08799 | 0.0 | 8.83
Comm | 0.012301 | 0.012301 | 0.012301 | 0.0 | 1.23
Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01
Modify | 0.013656 | 0.013656 | 0.013656 | 0.0 | 1.37
Other | | 0.002808 | | | 0.28
Pair | 0.82415 | 0.82415 | 0.82415 | 0.0 | 86.85
Neigh | 0.093798 | 0.093798 | 0.093798 | 0.0 | 9.88
Comm | 0.013542 | 0.013542 | 0.013542 | 0.0 | 1.43
Output | 0.00017834 | 0.00017834 | 0.00017834 | 0.0 | 0.02
Modify | 0.014418 | 0.014418 | 0.014418 | 0.0 | 1.52
Other | | 0.002882 | | | 0.30
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -96,4 +97,4 @@ Dangerous builds not checked
shell rm lj_1_1.table
Total wall time: 0:00:01
Total wall time: 0:00:00

25
examples/python/log.4May17.pair_python_table.g++.4 → examples/python/log.27Nov18.pair_python_table.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000404596 secs
mass * 1.0
velocity all create 3.0 87287
@ -38,7 +39,7 @@ Neighbor list info ...
pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
Should only be flagged at inflection points (src/pair_table.cpp:481)
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
@ -59,7 +60,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733629 0 -2.2744879 -3.7032813
50 1.675395 -4.7945736 0 -2.2821094 5.6620623
@ -67,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6595852 -4.7697199 0 -2.2809644 5.7837898
200 1.6371471 -4.7363942 0 -2.2812874 5.924977
250 1.6315623 -4.7278268 0 -2.2810951 5.9807196
Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms
Loop time of 0.285577 on 4 procs for 250 steps with 4000 atoms
Performance: 370058.286 tau/day, 856.616 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 378181.086 tau/day, 875.419 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06
Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96
Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30
Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05
Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22
Other | | 0.001211 | | | 0.42
Pair | 0.2111 | 0.21779 | 0.22447 | 1.0 | 76.26
Neigh | 0.024165 | 0.024465 | 0.0247 | 0.1 | 8.57
Comm | 0.03147 | 0.038356 | 0.044902 | 2.5 | 13.43
Output | 0.00016117 | 0.00022227 | 0.00040102 | 0.0 | 0.08
Modify | 0.0037565 | 0.0038704 | 0.0040345 | 0.2 | 1.36
Other | | 0.0008699 | | | 0.30
Nlocal: 1000 ave 1010 max 981 min
Histogram: 1 0 0 0 0 0 1 0 0 2

231
examples/python/log.5Oct16.python.g++.1 → examples/python/log.27Nov18.python.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt with Python functions added
units lj
@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00072813 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@ -26,30 +28,35 @@ fix 1 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12
Memory usage per processor = 2.69271 Mbytes
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.721 | 3.721 | 3.721 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.0323398 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.0312054 on 1 procs for 10 steps with 4000 atoms
Performance: 133581.484 tau/day, 309.216 timesteps/s
102.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 138437.508 tau/day, 320.457 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.024638 | 0.024638 | 0.024638 | 0.0 | 76.18
Neigh | 0.0063899 | 0.0063899 | 0.0063899 | 0.0 | 19.76
Comm | 0.00049949 | 0.00049949 | 0.00049949 | 0.0 | 1.54
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.06
Modify | 0.00050044 | 0.00050044 | 0.00050044 | 0.0 | 1.55
Other | | 0.0002944 | | | 0.91
Pair | 0.022328 | 0.022328 | 0.022328 | 0.0 | 71.55
Neigh | 0.0073318 | 0.0073318 | 0.0073318 | 0.0 | 23.50
Comm | 0.0006578 | 0.0006578 | 0.0006578 | 0.0 | 2.11
Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.09
Modify | 0.00057721 | 0.00057721 | 0.00057721 | 0.0 | 1.85
Other | | 0.0002832 | | | 0.91
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -67,13 +74,14 @@ Dangerous builds = 0
# example of catching a syntax error
python simple here """
from __future__ import print_function
def simple():
import exceptions
print "Inside simple function"
foo = 0
print("Inside simple function")
try:
foo += 1
except Exception, e:
print "FOO error:",e
except Exception as e:
print("FOO error:", e)
"""
python simple invoke
@ -110,31 +118,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 26 26 26
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.0046258 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.00488138 on 1 procs for 10 steps with 4000 atoms
Performance: 933893.067 tau/day, 2161.790 timesteps/s
86.4% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 884995.276 tau/day, 2048.600 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001574 | 0.001574 | 0.001574 | 0.0 | 34.03
Neigh | 0.0020421 | 0.0020421 | 0.0020421 | 0.0 | 44.14
Comm | 0.00025463 | 0.00025463 | 0.00025463 | 0.0 | 5.50
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.39
Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 10.73
Other | | 0.000241 | | | 5.21
Pair | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 35.17
Neigh | 0.0020256 | 0.0020256 | 0.0020256 | 0.0 | 41.50
Comm | 0.00028539 | 0.00028539 | 0.00028539 | 0.0 | 5.85
Output | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.55
Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 11.76
Other | | 0.0002532 | | | 5.19
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -151,31 +152,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.4
ghost atom cutoff = 1.4
binsize = 0.7 -> bins = 24 24 24
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.00619817 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.00647616 on 1 procs for 10 steps with 4000 atoms
Performance: 696980.162 tau/day, 1613.380 timesteps/s
96.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 667061.565 tau/day, 1544.124 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0029786 | 0.0029786 | 0.0029786 | 0.0 | 48.06
Neigh | 0.002203 | 0.002203 | 0.002203 | 0.0 | 35.54
Comm | 0.00025678 | 0.00025678 | 0.00025678 | 0.0 | 4.14
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.29
Modify | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 7.98
Other | | 0.0002472 | | | 3.99
Pair | 0.0030439 | 0.0030439 | 0.0030439 | 0.0 | 47.00
Neigh | 0.002295 | 0.002295 | 0.002295 | 0.0 | 35.44
Comm | 0.00028467 | 0.00028467 | 0.00028467 | 0.0 | 4.40
Output | 2.3842e-05 | 2.3842e-05 | 2.3842e-05 | 0.0 | 0.37
Modify | 0.0005753 | 0.0005753 | 0.0005753 | 0.0 | 8.88
Other | | 0.0002534 | | | 3.91
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -192,31 +186,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75 -> bins = 23 23 23
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.00750899 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.00802207 on 1 procs for 10 steps with 4000 atoms
Performance: 575310.153 tau/day, 1331.736 timesteps/s
93.2% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 538514.378 tau/day, 1246.561 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.004189 | 0.004189 | 0.004189 | 0.0 | 55.79
Neigh | 0.0022991 | 0.0022991 | 0.0022991 | 0.0 | 30.62
Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 3.45
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.24
Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 6.61
Other | | 0.0002475 | | | 3.30
Pair | 0.0044219 | 0.0044219 | 0.0044219 | 0.0 | 55.12
Neigh | 0.0024219 | 0.0024219 | 0.0024219 | 0.0 | 30.19
Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 3.75
Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.32
Modify | 0.00059366 | 0.00059366 | 0.00059366 | 0.0 | 7.40
Other | | 0.0002577 | | | 3.21
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -233,31 +220,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6
ghost atom cutoff = 1.6
binsize = 0.8 -> bins = 21 21 21
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.00869107 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.00908327 on 1 procs for 10 steps with 4000 atoms
Performance: 497061.786 tau/day, 1150.606 timesteps/s
103.5% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 475599.593 tau/day, 1100.925 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0049038 | 0.0049038 | 0.0049038 | 0.0 | 56.42
Neigh | 0.0027289 | 0.0027289 | 0.0027289 | 0.0 | 31.40
Comm | 0.00028753 | 0.00028753 | 0.00028753 | 0.0 | 3.31
Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.23
Modify | 0.00049758 | 0.00049758 | 0.00049758 | 0.0 | 5.73
Other | | 0.0002532 | | | 2.91
Pair | 0.0049157 | 0.0049157 | 0.0049157 | 0.0 | 54.12
Neigh | 0.0029771 | 0.0029771 | 0.0029771 | 0.0 | 32.78
Comm | 0.00033617 | 0.00033617 | 0.00033617 | 0.0 | 3.70
Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.25
Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 6.34
Other | | 0.0002553 | | | 2.81
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -274,31 +254,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7
ghost atom cutoff = 1.7
binsize = 0.85 -> bins = 20 20 20
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.00934482 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.0096159 on 1 procs for 10 steps with 4000 atoms
Performance: 462288.386 tau/day, 1070.112 timesteps/s
96.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 449256.007 tau/day, 1039.944 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0055761 | 0.0055761 | 0.0055761 | 0.0 | 59.67
Neigh | 0.002676 | 0.002676 | 0.002676 | 0.0 | 28.64
Comm | 0.00032163 | 0.00032163 | 0.00032163 | 0.0 | 3.44
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.19
Modify | 0.00049901 | 0.00049901 | 0.00049901 | 0.0 | 5.34
Other | | 0.0002542 | | | 2.72
Pair | 0.0054793 | 0.0054793 | 0.0054793 | 0.0 | 56.98
Neigh | 0.0028973 | 0.0028973 | 0.0028973 | 0.0 | 30.13
Comm | 0.00038075 | 0.00038075 | 0.00038075 | 0.0 | 3.96
Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.24
Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 5.97
Other | | 0.0002615 | | | 2.72
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -315,31 +288,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9 -> bins = 19 19 19
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.0103869 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.0107083 on 1 procs for 10 steps with 4000 atoms
Performance: 415906.746 tau/day, 962.747 timesteps/s
96.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 403424.172 tau/day, 933.852 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0063703 | 0.0063703 | 0.0063703 | 0.0 | 61.33
Neigh | 0.002893 | 0.002893 | 0.002893 | 0.0 | 27.85
Comm | 0.00034499 | 0.00034499 | 0.00034499 | 0.0 | 3.32
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.17
Modify | 0.00050139 | 0.00050139 | 0.00050139 | 0.0 | 4.83
Other | | 0.0002594 | | | 2.50
Pair | 0.0062652 | 0.0062652 | 0.0062652 | 0.0 | 58.51
Neigh | 0.0031667 | 0.0031667 | 0.0031667 | 0.0 | 29.57
Comm | 0.00041771 | 0.00041771 | 0.00041771 | 0.0 | 3.90
Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.21
Modify | 0.0005734 | 0.0005734 | 0.0005734 | 0.0 | 5.35
Other | | 0.0002627 | | | 2.45
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -356,31 +322,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.9
ghost atom cutoff = 1.9
binsize = 0.95 -> bins = 18 18 18
Memory usage per processor = 2.78761 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.0116282 on 1 procs for 10 steps with 4000 atoms
Loop time of 0.0121632 on 1 procs for 10 steps with 4000 atoms
Performance: 371512.205 tau/day, 859.982 timesteps/s
103.2% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 355170.795 tau/day, 822.155 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0074186 | 0.0074186 | 0.0074186 | 0.0 | 63.80
Neigh | 0.0030658 | 0.0030658 | 0.0030658 | 0.0 | 26.37
Comm | 0.00036025 | 0.00036025 | 0.00036025 | 0.0 | 3.10
Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.15
Modify | 0.0005033 | 0.0005033 | 0.0005033 | 0.0 | 4.33
Other | | 0.000263 | | | 2.26
Pair | 0.0074623 | 0.0074623 | 0.0074623 | 0.0 | 61.35
Neigh | 0.0033951 | 0.0033951 | 0.0033951 | 0.0 | 27.91
Comm | 0.00043678 | 0.00043678 | 0.00043678 | 0.0 | 3.59
Output | 2.408e-05 | 2.408e-05 | 2.408e-05 | 0.0 | 0.20
Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 4.73
Other | | 0.0002692 | | | 2.21
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

231
examples/python/log.5Oct16.python.g++.4 → examples/python/log.27Nov18.python.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt with Python functions added
units lj
@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000517368 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
@ -26,30 +28,35 @@ fix 1 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12
Memory usage per processor = 2.60344 Mbytes
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.00930309 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00902343 on 4 procs for 10 steps with 4000 atoms
Performance: 464361.693 tau/day, 1074.911 timesteps/s
96.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 478753.753 tau/day, 1108.226 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0064399 | 0.0064787 | 0.0065157 | 0.0 | 69.64
Neigh | 0.0017071 | 0.0017205 | 0.0017281 | 0.0 | 18.49
Comm | 0.00073171 | 0.00077122 | 0.00081086 | 0.1 | 8.29
Output | 1.9789e-05 | 2.3663e-05 | 2.9087e-05 | 0.1 | 0.25
Modify | 0.00012827 | 0.00012904 | 0.00013018 | 0.0 | 1.39
Other | | 0.0001799 | | | 1.93
Pair | 0.0058084 | 0.0058863 | 0.0059605 | 0.1 | 65.23
Neigh | 0.0019183 | 0.0019591 | 0.0020542 | 0.1 | 21.71
Comm | 0.00081086 | 0.00084025 | 0.00090694 | 0.0 | 9.31
Output | 2.1458e-05 | 2.9743e-05 | 4.53e-05 | 0.0 | 0.33
Modify | 0.00015211 | 0.00015229 | 0.00015259 | 0.0 | 1.69
Other | | 0.0001558 | | | 1.73
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 1 0 0 1 0 0 0 1
@ -67,13 +74,14 @@ Dangerous builds = 0
# example of catching a syntax error
python simple here """
from __future__ import print_function
def simple():
import exceptions
print "Inside simple function"
foo = 0
print("Inside simple function")
try:
foo += 1
except Exception, e:
print "FOO error:",e
except Exception as e:
print("FOO error:", e)
"""
python simple invoke
@ -110,31 +118,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 26 26 26
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.00152922 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00153601 on 4 procs for 10 steps with 4000 atoms
Performance: 2824975.566 tau/day, 6539.295 timesteps/s
130.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 2812478.584 tau/day, 6510.367 timesteps/s
91.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00040293 | 0.0004105 | 0.00041485 | 0.0 | 26.84
Neigh | 0.00057507 | 0.00060332 | 0.00062108 | 0.1 | 39.45
Comm | 0.0002377 | 0.00025356 | 0.00026774 | 0.1 | 16.58
Output | 1.9073e-05 | 1.9789e-05 | 2.1935e-05 | 0.0 | 1.29
Modify | 0.00012994 | 0.00013161 | 0.00013328 | 0.0 | 8.61
Other | | 0.0001104 | | | 7.22
Pair | 0.00042677 | 0.00043494 | 0.00044322 | 0.0 | 28.32
Neigh | 0.00051236 | 0.00051689 | 0.00052524 | 0.0 | 33.65
Comm | 0.00025344 | 0.00026941 | 0.00027728 | 0.0 | 17.54
Output | 1.7881e-05 | 2.3544e-05 | 3.9339e-05 | 0.0 | 1.53
Modify | 0.00015187 | 0.00015521 | 0.00016356 | 0.0 | 10.10
Other | | 0.000136 | | | 8.86
Nlocal: 1000 ave 1015 max 987 min
Histogram: 1 0 0 1 0 1 0 0 0 1
@ -151,31 +152,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.4
ghost atom cutoff = 1.4
binsize = 0.7 -> bins = 24 24 24
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.00186676 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00198567 on 4 procs for 10 steps with 4000 atoms
Performance: 2314172.647 tau/day, 5356.881 timesteps/s
107.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 2175589.035 tau/day, 5036.086 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00075388 | 0.00077951 | 0.00079727 | 0.1 | 41.76
Neigh | 0.00057292 | 0.00058091 | 0.00058484 | 0.0 | 31.12
Comm | 0.00022578 | 0.00024849 | 0.00028563 | 0.1 | 13.31
Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 1.00
Modify | 0.00012493 | 0.00012845 | 0.00013137 | 0.0 | 6.88
Other | | 0.0001107 | | | 5.93
Pair | 0.00076985 | 0.00078291 | 0.00079393 | 0.0 | 39.43
Neigh | 0.0005703 | 0.00057709 | 0.00058103 | 0.0 | 29.06
Comm | 0.00030351 | 0.00031525 | 0.00033665 | 0.0 | 15.88
Output | 1.9073e-05 | 2.4378e-05 | 4.0054e-05 | 0.0 | 1.23
Modify | 0.00014806 | 0.00015008 | 0.00015354 | 0.0 | 7.56
Other | | 0.000136 | | | 6.85
Nlocal: 1000 ave 1019 max 983 min
Histogram: 1 0 1 0 0 0 1 0 0 1
@ -192,31 +186,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75 -> bins = 23 23 23
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.00224304 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00232226 on 4 procs for 10 steps with 4000 atoms
Performance: 1925955.918 tau/day, 4458.231 timesteps/s
89.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1860259.570 tau/day, 4306.156 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010781 | 0.0011036 | 0.0011303 | 0.1 | 49.20
Neigh | 0.00060606 | 0.00060952 | 0.00061703 | 0.0 | 27.17
Comm | 0.00023556 | 0.0002715 | 0.00029659 | 0.1 | 12.10
Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.83
Modify | 0.00012541 | 0.00012833 | 0.00013351 | 0.0 | 5.72
Other | | 0.0001114 | | | 4.97
Pair | 0.0010829 | 0.0010984 | 0.0011158 | 0.0 | 47.30
Neigh | 0.00060892 | 0.00061285 | 0.00062037 | 0.0 | 26.39
Comm | 0.00027418 | 0.00030226 | 0.00031734 | 0.0 | 13.02
Output | 1.7881e-05 | 2.3305e-05 | 3.8624e-05 | 0.0 | 1.00
Modify | 0.00014758 | 0.00014979 | 0.0001533 | 0.0 | 6.45
Other | | 0.0001357 | | | 5.84
Nlocal: 1000 ave 1013 max 984 min
Histogram: 1 0 0 1 0 0 0 0 1 1
@ -233,31 +220,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6
ghost atom cutoff = 1.6
binsize = 0.8 -> bins = 21 21 21
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.00257862 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00268328 on 4 procs for 10 steps with 4000 atoms
Performance: 1675317.210 tau/day, 3878.049 timesteps/s
77.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1609968.749 tau/day, 3726.780 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012422 | 0.0012776 | 0.0013103 | 0.1 | 49.55
Neigh | 0.0007019 | 0.00072145 | 0.00073099 | 0.0 | 27.98
Comm | 0.00027132 | 0.00031221 | 0.00036168 | 0.2 | 12.11
Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.74
Modify | 0.00012279 | 0.00012654 | 0.00012875 | 0.0 | 4.91
Other | | 0.0001217 | | | 4.72
Pair | 0.0012326 | 0.0012579 | 0.0012789 | 0.1 | 46.88
Neigh | 0.00073671 | 0.00076056 | 0.00077105 | 0.0 | 28.34
Comm | 0.00031805 | 0.00035089 | 0.0003984 | 0.0 | 13.08
Output | 1.7405e-05 | 2.2769e-05 | 3.8147e-05 | 0.0 | 0.85
Modify | 0.00014949 | 0.00015247 | 0.00015497 | 0.0 | 5.68
Other | | 0.0001387 | | | 5.17
Nlocal: 1000 ave 1013 max 974 min
Histogram: 1 0 0 0 0 0 0 1 0 2
@ -274,31 +254,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7
ghost atom cutoff = 1.7
binsize = 0.85 -> bins = 20 20 20
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.00283062 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00504404 on 4 procs for 10 steps with 4000 atoms
Performance: 1526164.943 tau/day, 3532.789 timesteps/s
97.1% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 856455.812 tau/day, 1982.537 timesteps/s
88.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0014381 | 0.0014688 | 0.0015128 | 0.1 | 51.89
Neigh | 0.00070405 | 0.000714 | 0.00071907 | 0.0 | 25.22
Comm | 0.00032473 | 0.00037426 | 0.0004046 | 0.2 | 13.22
Output | 1.8835e-05 | 1.961e-05 | 2.1935e-05 | 0.0 | 0.69
Modify | 0.00012612 | 0.00012892 | 0.00013089 | 0.0 | 4.55
Other | | 0.000125 | | | 4.42
Pair | 0.0013909 | 0.001602 | 0.0021472 | 0.8 | 31.76
Neigh | 0.00074077 | 0.00075352 | 0.00076365 | 0.0 | 14.94
Comm | 0.00083065 | 0.0018672 | 0.0025668 | 1.7 | 37.02
Output | 2.1458e-05 | 2.7359e-05 | 4.4346e-05 | 0.0 | 0.54
Modify | 0.00014758 | 0.0001505 | 0.00015235 | 0.0 | 2.98
Other | | 0.0006434 | | | 12.76
Nlocal: 1000 ave 1016 max 981 min
Histogram: 1 0 0 0 1 0 1 0 0 1
@ -315,31 +288,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9 -> bins = 19 19 19
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.00313491 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.003398 on 4 procs for 10 steps with 4000 atoms
Performance: 1378031.621 tau/day, 3189.888 timesteps/s
87.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1271335.633 tau/day, 2942.907 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016167 | 0.001663 | 0.0016985 | 0.1 | 53.05
Neigh | 0.00075388 | 0.00076818 | 0.00078201 | 0.0 | 24.50
Comm | 0.00037456 | 0.00042272 | 0.00048018 | 0.2 | 13.48
Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.61
Modify | 0.00012636 | 0.00012881 | 0.00013304 | 0.0 | 4.11
Other | | 0.0001331 | | | 4.25
Pair | 0.0015702 | 0.0016137 | 0.001651 | 0.1 | 47.49
Neigh | 0.00080371 | 0.00082165 | 0.00084138 | 0.0 | 24.18
Comm | 0.0005908 | 0.00064844 | 0.00071096 | 0.0 | 19.08
Output | 1.7643e-05 | 2.3365e-05 | 4.0293e-05 | 0.0 | 0.69
Modify | 0.00014853 | 0.00015211 | 0.00015593 | 0.0 | 4.48
Other | | 0.0001387 | | | 4.08
Nlocal: 1000 ave 1022 max 982 min
Histogram: 1 0 0 1 0 1 0 0 0 1
@ -356,31 +322,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.9
ghost atom cutoff = 1.9
binsize = 0.95 -> bins = 18 18 18
Memory usage per processor = 2.63679 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.00345927 on 4 procs for 10 steps with 4000 atoms
Loop time of 0.00420767 on 4 procs for 10 steps with 4000 atoms
Performance: 1248816.671 tau/day, 2890.779 timesteps/s
79.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 1026696.317 tau/day, 2376.612 timesteps/s
95.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0019331 | 0.0019561 | 0.0019834 | 0.0 | 56.55
Neigh | 0.00081587 | 0.00081897 | 0.00082588 | 0.0 | 23.67
Comm | 0.00037837 | 0.00040215 | 0.00041842 | 0.1 | 11.63
Output | 1.812e-05 | 1.9312e-05 | 2.1935e-05 | 0.0 | 0.56
Modify | 0.00012708 | 0.00013059 | 0.00013423 | 0.0 | 3.78
Other | | 0.0001321 | | | 3.82
Pair | 0.0019023 | 0.00194 | 0.0019965 | 0.1 | 46.11
Neigh | 0.00088286 | 0.00088775 | 0.00089431 | 0.0 | 21.10
Comm | 0.0010023 | 0.0010559 | 0.0010967 | 0.1 | 25.09
Output | 2.0027e-05 | 2.6524e-05 | 4.53e-05 | 0.0 | 0.63
Modify | 0.00014782 | 0.00015038 | 0.00015473 | 0.0 | 3.57
Other | | 0.0001471 | | | 3.50
Nlocal: 1000 ave 1013 max 987 min
Histogram: 1 0 1 0 0 0 0 1 0 1

178
examples/python/log.4May17.pair_python_coulomb.1
View File

@ -1,178 +0,0 @@
LAMMPS (4 May 2017)
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)
1 by 1 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 python 12.0 coul/long 12.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff * * python potentials.LJCutSPCE OW NULL
pair_modify table 0
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
PPPM initialization ...
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
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 python, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
PPPM initialization ...
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
PPPM initialization ...
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
thermo 10
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../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 = 103823 64000
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) = 35.26 | 35.26 | 35.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -100272.97 0 -100272.97 -1282.0708
10 120.61568 -101350.63 0 -100272.39 -4077.5051
20 136.11379 -101465.43 0 -100248.65 -5136.5677
30 137.01602 -101455.3 0 -100230.46 -5347.8311
40 153.424 -101582.46 0 -100210.93 -5223.1676
50 167.73654 -101686.24 0 -100186.77 -4468.6687
60 163.11642 -101618.16 0 -100159.99 -3291.7815
70 169.64512 -101647.89 0 -100131.35 -2611.638
80 182.9979 -101737.01 0 -100101.11 -2390.6293
90 191.33873 -101778.71 0 -100068.24 -2239.386
100 194.7458 -101775.84 0 -100034.92 -1951.9128
Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms
Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51
Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00
Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24
Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02
Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32
Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01
Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83
Other | | 0.005243 | | | 0.07
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21216 ave 21216 max 21216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2601766
Ave neighs/atom = 578.17
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:07

138
examples/python/log.4May17.pair_python_coulomb.g++.1
View File

@ -1,138 +0,0 @@
LAMMPS (4 May 2017)
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)
1 by 1 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
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
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) = 25.08 | 25.08 | 25.08 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -18284.922 0 -18284.922 -2080.7739
10 146.83806 -19552.072 0 -18239.421 -4865.31
20 183.15761 -18706.872 0 -17069.543 -4865.6695
30 205.96203 -18901.541 0 -17060.354 -4454.8634
40 241.62768 -18323.117 0 -16163.099 -3269.1475
50 265.98384 -19883.562 0 -17505.813 -2788.5194
60 274.01897 -21320.575 0 -18870.996 -2387.0708
70 288.7601 -19849.269 0 -17267.913 -1235.818
80 300.64724 -20958.602 0 -18270.981 -1714.7988
90 304.19113 -21580.4 0 -18861.099 -2144.1614
100 304.22027 -21239.014 0 -18519.452 -2092.6759
Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms
Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.698 | 5.698 | 5.698 | 0.0 | 94.67
Bond | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.00
Neigh | 0.23235 | 0.23235 | 0.23235 | 0.0 | 3.86
Comm | 0.018961 | 0.018961 | 0.018961 | 0.0 | 0.32
Output | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.01
Modify | 0.063452 | 0.063452 | 0.063452 | 0.0 | 1.05
Other | | 0.005146 | | | 0.09
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21285 ave 21285 max 21285 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2597662
Ave neighs/atom = 577.258
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:06

138
examples/python/log.4May17.pair_python_coulomb.g++.4
View File

@ -1,138 +0,0 @@
LAMMPS (4 May 2017)
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
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
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) = 9.962 | 9.963 | 9.963 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -18284.922 0 -18284.922 -2080.7739
10 146.83806 -19552.072 0 -18239.421 -4865.31
20 183.15761 -18706.872 0 -17069.543 -4865.6695
30 205.96203 -18901.541 0 -17060.354 -4454.8634
40 241.62768 -18323.117 0 -16163.099 -3269.1475
50 265.98384 -19883.562 0 -17505.813 -2788.5194
60 274.01897 -21320.575 0 -18870.996 -2387.0708
70 288.7601 -19849.269 0 -17267.913 -1235.818
80 300.64724 -20958.602 0 -18270.981 -1714.7988
90 304.19113 -21580.4 0 -18861.099 -2144.1614
100 304.22027 -21239.014 0 -18519.452 -2092.6759
Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26
Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01
Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70
Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65
Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02
Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18
Other | | 0.003148 | | | 0.18
Nlocal: 1125 ave 1162 max 1098 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 12267.8 ave 12302 max 12238 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 649416 ave 681458 max 630541 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 2597662
Ave neighs/atom = 577.258
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:01