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provide reference output for python pair style inputs

This commit is contained in:
Axel Kohlmeyer 2017-05-15 00:25:11 -04:00
parent d662f5d429
commit 6a1f7e61f2
4 changed files with 934 additions and 0 deletions
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250
examples/python/log.4May2017.pair_python_hybrid.g++.1 Normal file
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LAMMPS (4 May 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid
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 2 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
mass * 1.0
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python lj-melt-potential.py lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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
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
Per MPI rank memory allocation (min/avg/max) = 4.828 | 4.828 | 4.828 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 41.3888 on 1 procs for 250 steps with 4000 atoms
Performance: 2609.399 tau/day, 6.040 timesteps/s
48.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 41.135 | 41.135 | 41.135 | 0.0 | 99.39
Neigh | 0.17089 | 0.17089 | 0.17089 | 0.0 | 0.41
Comm | 0.032175 | 0.032175 | 0.032175 | 0.0 | 0.08
Output | 0.000513 | 0.000513 | 0.000513 | 0.0 | 0.00
Modify | 0.046448 | 0.046448 | 0.046448 | 0.0 | 0.11
Other | | 0.003913 | | | 0.01
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: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 12
Dangerous builds not checked
write_data hybrid.data
write_restart hybrid.restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python lj-melt-potential.py lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 1 steps, delay 10 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
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
Per MPI rank memory allocation (min/avg/max) = 4.626 | 4.626 | 4.626 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
350 1.6514972 -4.7580756 0 -2.2814491 5.810167
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 41.5677 on 1 procs for 250 steps with 4000 atoms
Performance: 2598.172 tau/day, 6.014 timesteps/s
48.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 41.124 | 41.124 | 41.124 | 0.0 | 98.93
Neigh | 0.35605 | 0.35605 | 0.35605 | 0.0 | 0.86
Comm | 0.034799 | 0.034799 | 0.034799 | 0.0 | 0.08
Output | 0.000473 | 0.000473 | 0.000473 | 0.0 | 0.00
Modify | 0.046841 | 0.046841 | 0.046841 | 0.0 | 0.11
Other | | 0.005854 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5472 ave 5472 max 5472 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 25
Dangerous builds = 25
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data hybrid.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python lj-melt-potential.py lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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
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
Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.126 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
100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
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 41.7098 on 1 procs for 250 steps with 4000 atoms
Performance: 2589.318 tau/day, 5.994 timesteps/s
48.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 41.458 | 41.458 | 41.458 | 0.0 | 99.40
Neigh | 0.16992 | 0.16992 | 0.16992 | 0.0 | 0.41
Comm | 0.031355 | 0.031355 | 0.031355 | 0.0 | 0.08
Output | 0.000537 | 0.000537 | 0.000537 | 0.0 | 0.00
Modify | 0.046569 | 0.046569 | 0.046569 | 0.0 | 0.11
Other | | 0.003735 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5487 ave 5487 max 5487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:02:07

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examples/python/log.4May2017.pair_python_hybrid.g++.4 Normal file
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LAMMPS (4 May 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid
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 2 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass * 1.0
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python lj-melt-potential.py lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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
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
Per MPI rank memory allocation (min/avg/max) = 4.044 | 4.044 | 4.044 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 33.3499 on 2 procs for 250 steps with 4000 atoms
Performance: 3238.386 tau/day, 7.496 timesteps/s
31.8% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.739 | 32.45 | 33.16 | 12.5 | 97.30
Neigh | 0.12882 | 0.1292 | 0.12959 | 0.1 | 0.39
Comm | 0.04094 | 0.75173 | 1.4625 | 82.0 | 2.25
Output | 0.000352 | 0.0004115 | 0.000471 | 0.0 | 0.00
Modify | 0.014923 | 0.01509 | 0.015257 | 0.1 | 0.05
Other | | 0.003902 | | | 0.01
Nlocal: 2000 ave 2006 max 1994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 3942 ave 3967 max 3917 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 12
Dangerous builds not checked
write_data hybrid.data
write_restart hybrid.restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 2 MPI processor grid
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python lj-melt-potential.py lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 1 steps, delay 10 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
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
Per MPI rank memory allocation (min/avg/max) = 3.747 | 3.747 | 3.747 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
350 1.6514972 -4.7580756 0 -2.2814491 5.810167
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 33.4436 on 2 procs for 250 steps with 4000 atoms
Performance: 3229.315 tau/day, 7.475 timesteps/s
31.8% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.79 | 32.446 | 33.101 | 11.5 | 97.02
Neigh | 0.26891 | 0.26902 | 0.26912 | 0.0 | 0.80
Comm | 0.051997 | 0.70764 | 1.3633 | 77.9 | 2.12
Output | 0.000332 | 0.000396 | 0.00046 | 0.0 | 0.00
Modify | 0.01539 | 0.015553 | 0.015717 | 0.1 | 0.05
Other | | 0.005483 | | | 0.02
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 3912 ave 3920 max 3904 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 25
Dangerous builds = 25
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data hybrid.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 2 MPI processor grid
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python lj-melt-potential.py lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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
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
Per MPI rank memory allocation (min/avg/max) = 3.247 | 3.247 | 3.247 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
100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
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 33.0043 on 2 procs for 250 steps with 4000 atoms
Performance: 3272.302 tau/day, 7.575 timesteps/s
31.8% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 31.676 | 32.248 | 32.819 | 10.1 | 97.71
Neigh | 0.12725 | 0.12751 | 0.12778 | 0.1 | 0.39
Comm | 0.038764 | 0.60973 | 1.1807 | 73.1 | 1.85
Output | 0.000359 | 0.000424 | 0.000489 | 0.0 | 0.00
Modify | 0.015441 | 0.01555 | 0.01566 | 0.1 | 0.05
Other | | 0.003519 | | | 0.01
Nlocal: 2000 ave 2004 max 1996 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 3923.5 ave 3927 max 3920 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:01:42

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LAMMPS (4 May 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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
mass * 1.0
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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 python, 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) = 3.184 | 3.184 | 3.184 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 62.2396 on 1 procs for 250 steps with 4000 atoms
Performance: 1735.231 tau/day, 4.017 timesteps/s
31.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 61.865 | 61.865 | 61.865 | 0.0 | 99.40
Neigh | 0.24651 | 0.24651 | 0.24651 | 0.0 | 0.40
Comm | 0.049505 | 0.049505 | 0.049505 | 0.0 | 0.08
Output | 0.000738 | 0.000738 | 0.000738 | 0.0 | 0.00
Modify | 0.071444 | 0.071444 | 0.071444 | 0.0 | 0.11
Other | | 0.005964 | | | 0.01
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
write_data melt.data
write_restart melt.restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
read_restart melt.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
4000 atoms
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 1 steps, delay 10 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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 3.36 | 3.36 | 3.36 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
350 1.6514972 -4.7580756 0 -2.2814491 5.810167
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 62.6472 on 1 procs for 250 steps with 4000 atoms
Performance: 1723.939 tau/day, 3.991 timesteps/s
31.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 61.994 | 61.994 | 61.994 | 0.0 | 98.96
Neigh | 0.519 | 0.519 | 0.519 | 0.0 | 0.83
Comm | 0.052574 | 0.052574 | 0.052574 | 0.0 | 0.08
Output | 0.000804 | 0.000804 | 0.000804 | 0.0 | 0.00
Modify | 0.071878 | 0.071878 | 0.071878 | 0.0 | 0.11
Other | | 0.009016 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5472 ave 5472 max 5472 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 = 25
Dangerous builds = 25
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data melt.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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 python, 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) = 2.86 | 2.86 | 2.86 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
100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
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 62.6778 on 1 procs for 250 steps with 4000 atoms
Performance: 1723.098 tau/day, 3.989 timesteps/s
31.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 62.298 | 62.298 | 62.298 | 0.0 | 99.39
Neigh | 0.25251 | 0.25251 | 0.25251 | 0.0 | 0.40
Comm | 0.04911 | 0.04911 | 0.04911 | 0.0 | 0.08
Output | 0.000797 | 0.000797 | 0.000797 | 0.0 | 0.00
Modify | 0.071729 | 0.071729 | 0.071729 | 0.0 | 0.11
Other | | 0.005419 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5487 ave 5487 max 5487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151490 ave 151490 max 151490 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151490
Ave neighs/atom = 37.8725
Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:03:12

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examples/python/log.4May2017.pair_python_melt.g++.4 Normal file
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LAMMPS (4 May 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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
mass * 1.0
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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 python, 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) = 2.69 | 2.69 | 2.69 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 18.0035 on 4 procs for 250 steps with 4000 atoms
Performance: 5998.838 tau/day, 13.886 timesteps/s
31.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.784 | 17.18 | 17.611 | 8.9 | 95.43
Neigh | 0.066257 | 0.066613 | 0.066967 | 0.1 | 0.37
Comm | 0.31192 | 0.74265 | 1.1386 | 42.7 | 4.13
Output | 0.000344 | 0.00076 | 0.001983 | 0.0 | 0.00
Modify | 0.010618 | 0.010763 | 0.010947 | 0.1 | 0.06
Other | | 0.00278 | | | 0.02
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
write_data melt.data
write_restart melt.restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
read_restart melt.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
4000 atoms
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 1 steps, delay 10 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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 2.815 | 2.816 | 2.816 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
350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
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 17.8516 on 4 procs for 250 steps with 4000 atoms
Performance: 6049.891 tau/day, 14.004 timesteps/s
31.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.549 | 17.138 | 17.615 | 9.3 | 96.00
Neigh | 0.1326 | 0.13573 | 0.13709 | 0.5 | 0.76
Comm | 0.083467 | 0.56179 | 1.1533 | 51.4 | 3.15
Output | 0.000353 | 0.000703 | 0.00173 | 0.0 | 0.00
Modify | 0.011229 | 0.011437 | 0.011847 | 0.2 | 0.06
Other | | 0.004124 | | | 0.02
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 2699 ave 2706 max 2693 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 37930.8 ave 39292 max 36264 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 151723
Ave neighs/atom = 37.9308
Neighbor list builds = 25
Dangerous builds = 25
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data melt.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style python 2.5
pair_coeff * * lj-melt-potential.py lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all 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 python, 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) = 2.315 | 2.316 | 2.316 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
100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
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 17.5277 on 4 procs for 250 steps with 4000 atoms
Performance: 6161.664 tau/day, 14.263 timesteps/s
31.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.46 | 17.032 | 17.348 | 8.3 | 97.17
Neigh | 0.063784 | 0.06495 | 0.065515 | 0.3 | 0.37
Comm | 0.10004 | 0.41613 | 0.98807 | 53.0 | 2.37
Output | 0.000331 | 0.00081525 | 0.002223 | 0.0 | 0.00
Modify | 0.010998 | 0.011169 | 0.011264 | 0.1 | 0.06
Other | | 0.002774 | | | 0.02
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 2695.5 ave 2706 max 2682 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 37927.2 ave 39002 max 36400 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 151709
Ave neighs/atom = 37.9273
Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:00:55