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update AIREBO/REBO examples and provide references for rebo and airebo with LJ and TORSION turned off

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This commit is contained in:
Axel Kohlmeyer
2018-11-20 13:48:49 -05:00
parent 1235e77199
commit dcffeb546f
10 changed files with 448 additions and 44 deletions
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examples/airebo/in.airebo-0-0 Normal file
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# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
replicate 17 16 2
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 0 0
pair_coeff * * ../../potentials/CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100

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# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
replicate 17 16 2
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * ../../potentials/CH.rebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100

88
examples/airebo/log.29Jun18.airebo-0-0.g++.1 Normal file
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LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00136042 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 0 0
pair_coeff * * ../../potentials/CH.airebo C H
Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0756
10 179.38448 -137931.29 0 -137174.48 15656.689
20 206.89283 -138047.05 0 -137174.19 -24047.407
30 150.81289 -137807.48 0 -137171.21 -16524.191
40 173.24289 -137902.32 0 -137171.42 -5721.7187
50 151.80722 -137812.37 0 -137171.91 3489.8954
60 199.06038 -138013.7 0 -137173.88 17887.024
70 217.84848 -138093.82 0 -137174.73 -12266.16
80 202.34667 -138029.28 0 -137175.59 -7623.6635
90 194.92367 -137997.12 0 -137174.75 -32277.173
100 185.2078 -137954.64 0 -137173.26 -6888.5104
Loop time of 5.00753 on 1 procs for 100 steps with 32640 atoms
Performance: 0.863 ns/day, 27.820 hours/ns, 19.970 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 | 3.4898 | 3.4898 | 3.4898 | 0.0 | 69.69
Neigh | 1.4697 | 1.4697 | 1.4697 | 0.0 | 29.35
Comm | 0.015885 | 0.015885 | 0.015885 | 0.0 | 0.32
Output | 0.00096607 | 0.00096607 | 0.00096607 | 0.0 | 0.02
Modify | 0.021901 | 0.021901 | 0.021901 | 0.0 | 0.44
Other | | 0.009297 | | | 0.19
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460 ave 26460 max 26460 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
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000609159 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 0 0
pair_coeff * * ../../potentials/CH.airebo C H
Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0756
10 179.38448 -137931.29 0 -137174.48 15656.689
20 206.89283 -138047.05 0 -137174.19 -24047.407
30 150.81289 -137807.48 0 -137171.21 -16524.191
40 173.24289 -137902.32 0 -137171.42 -5721.7187
50 151.80722 -137812.37 0 -137171.91 3489.8954
60 199.06038 -138013.7 0 -137173.88 17887.024
70 217.84848 -138093.82 0 -137174.73 -12266.16
80 202.34667 -138029.28 0 -137175.59 -7623.6635
90 194.92367 -137997.12 0 -137174.75 -32277.173
100 185.2078 -137954.64 0 -137173.26 -6888.5104
Loop time of 1.50369 on 4 procs for 100 steps with 32640 atoms
Performance: 2.873 ns/day, 8.354 hours/ns, 66.503 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 | 0.92943 | 0.95749 | 0.97327 | 1.8 | 63.68
Neigh | 0.456 | 0.46115 | 0.46657 | 0.7 | 30.67
Comm | 0.048775 | 0.068415 | 0.10077 | 8.2 | 4.55
Output | 0.00044918 | 0.00073665 | 0.0015814 | 0.0 | 0.05
Modify | 0.0087936 | 0.0089477 | 0.0091038 | 0.1 | 0.60
Other | | 0.006951 | | | 0.46
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01

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examples/airebo/log.23Jun17.airebo-m.g++.1 → examples/airebo/log.29Jun18.airebo-m.g++.1
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LAMMPS (23 Jun 2017)
LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +16,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00136828 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +57,20 @@ Step Temp E_pair E_mol TotEng Press
80 164.28396 -138709.5 0 -138016.4 -1524.7353
90 180.26403 -138776.42 0 -138015.9 -27143.467
100 164.05694 -138706.58 0 -138014.44 5157.5516
Loop time of 117.672 on 1 procs for 100 steps with 32640 atoms
Loop time of 64.9938 on 1 procs for 100 steps with 32640 atoms
Performance: 0.037 ns/day, 653.734 hours/ns, 0.850 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.066 ns/day, 361.077 hours/ns, 1.539 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 | 108.31 | 108.31 | 108.31 | 0.0 | 92.04
Neigh | 9.2199 | 9.2199 | 9.2199 | 0.0 | 7.84
Comm | 0.052942 | 0.052942 | 0.052942 | 0.0 | 0.04
Output | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.00
Modify | 0.060962 | 0.060962 | 0.060962 | 0.0 | 0.05
Other | | 0.02656 | | | 0.02
Pair | 60.289 | 60.289 | 60.289 | 0.0 | 92.76
Neigh | 4.6445 | 4.6445 | 4.6445 | 0.0 | 7.15
Comm | 0.025577 | 0.025577 | 0.025577 | 0.0 | 0.04
Output | 0.00097752 | 0.00097752 | 0.00097752 | 0.0 | 0.00
Modify | 0.022412 | 0.022412 | 0.022412 | 0.0 | 0.03
Other | | 0.01114 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -83,4 +85,4 @@ Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:02:00
Total wall time: 0:01:06

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examples/airebo/log.23Jun17.airebo-m.g++.4 → examples/airebo/log.29Jun18.airebo-m.g++.4
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@ -1,4 +1,5 @@
LAMMPS (23 Jun 2017)
LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +16,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000688076 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +57,20 @@ Step Temp E_pair E_mol TotEng Press
80 164.28396 -138709.5 0 -138016.4 -1524.7353
90 180.26403 -138776.42 0 -138015.9 -27143.467
100 164.05694 -138706.58 0 -138014.44 5157.5516
Loop time of 32.9268 on 4 procs for 100 steps with 32640 atoms
Loop time of 18.0388 on 4 procs for 100 steps with 32640 atoms
Performance: 0.131 ns/day, 182.927 hours/ns, 3.037 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.239 ns/day, 100.216 hours/ns, 5.544 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.045 | 28.537 | 29.42 | 10.4 | 86.67
Neigh | 3.163 | 3.237 | 3.3761 | 4.7 | 9.83
Comm | 0.09883 | 1.1206 | 1.6862 | 60.4 | 3.40
Output | 0.00099325 | 0.0011329 | 0.0012462 | 0.3 | 0.00
Modify | 0.016013 | 0.016726 | 0.017257 | 0.4 | 0.05
Other | | 0.01459 | | | 0.04
Pair | 15.983 | 16.085 | 16.285 | 2.9 | 89.17
Neigh | 1.5975 | 1.6116 | 1.6215 | 0.8 | 8.93
Comm | 0.11408 | 0.32424 | 0.43065 | 21.7 | 1.80
Output | 0.00062895 | 0.0012782 | 0.0018394 | 1.2 | 0.01
Modify | 0.0089653 | 0.0090135 | 0.0090837 | 0.0 | 0.05
Other | | 0.007664 | | | 0.04
Nlocal: 8160 ave 8167 max 8153 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -83,4 +85,4 @@ Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:33
Total wall time: 0:00:18

24
examples/airebo/log.23Jun17.airebo.g++.1 → examples/airebo/log.29Jun18.airebo.g++.1
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@ -1,4 +1,5 @@
LAMMPS (23 Jun 2017)
LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +16,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00137973 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +57,20 @@ Step Temp E_pair E_mol TotEng Press
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8462
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 110.107 on 1 procs for 100 steps with 32640 atoms
Loop time of 58.178 on 1 procs for 100 steps with 32640 atoms
Performance: 0.039 ns/day, 611.705 hours/ns, 0.908 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.074 ns/day, 323.211 hours/ns, 1.719 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 | 100.76 | 100.76 | 100.76 | 0.0 | 91.51
Neigh | 9.1909 | 9.1909 | 9.1909 | 0.0 | 8.35
Comm | 0.058134 | 0.058134 | 0.058134 | 0.0 | 0.05
Output | 0.0015941 | 0.0015941 | 0.0015941 | 0.0 | 0.00
Modify | 0.062212 | 0.062212 | 0.062212 | 0.0 | 0.06
Other | | 0.03123 | | | 0.03
Pair | 53.477 | 53.477 | 53.477 | 0.0 | 91.92
Neigh | 4.6405 | 4.6405 | 4.6405 | 0.0 | 7.98
Comm | 0.025745 | 0.025745 | 0.025745 | 0.0 | 0.04
Output | 0.00097823 | 0.00097823 | 0.00097823 | 0.0 | 0.00
Modify | 0.022715 | 0.022715 | 0.022715 | 0.0 | 0.04
Other | | 0.01117 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -83,4 +85,4 @@ Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:52
Total wall time: 0:00:59

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examples/airebo/log.23Jun17.airebo.g++.4 → examples/airebo/log.29Jun18.airebo.g++.4
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@ -1,4 +1,5 @@
LAMMPS (23 Jun 2017)
LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
@ -15,6 +16,7 @@ replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000712872 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -55,20 +57,20 @@ Step Temp E_pair E_mol TotEng Press
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8462
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 30.1916 on 4 procs for 100 steps with 32640 atoms
Loop time of 16.4409 on 4 procs for 100 steps with 32640 atoms
Performance: 0.143 ns/day, 167.731 hours/ns, 3.312 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.263 ns/day, 91.338 hours/ns, 6.082 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 | 26.083 | 26.31 | 26.795 | 5.5 | 87.14
Neigh | 3.1781 | 3.2134 | 3.2775 | 2.2 | 10.64
Comm | 0.086296 | 0.63643 | 0.88995 | 40.2 | 2.11
Output | 0.00074124 | 0.0010698 | 0.0013616 | 0.7 | 0.00
Modify | 0.015335 | 0.016373 | 0.017565 | 0.8 | 0.05
Other | | 0.01457 | | | 0.05
Pair | 14.212 | 14.384 | 14.487 | 3.0 | 87.49
Neigh | 1.5943 | 1.615 | 1.6263 | 1.0 | 9.82
Comm | 0.30944 | 0.42389 | 0.61698 | 19.2 | 2.58
Output | 0.00065231 | 0.00094843 | 0.0018184 | 0.0 | 0.01
Modify | 0.0092347 | 0.0093143 | 0.0094111 | 0.1 | 0.06
Other | | 0.007456 | | | 0.05
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -83,4 +85,4 @@ Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:30
Total wall time: 0:00:16

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LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00153542 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * ../../potentials/CH.rebo C H
Reading potential file ../../potentials/CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0748
10 179.37985 -137931.27 0 -137174.48 15655.936
20 206.87654 -138046.99 0 -137174.19 -24042.627
30 150.80122 -137807.43 0 -137171.21 -16524.118
40 173.24945 -137902.35 0 -137171.42 -5716.9118
50 151.80455 -137812.36 0 -137171.91 3480.4584
60 199.08777 -138013.82 0 -137173.88 17881.372
70 217.85748 -138093.86 0 -137174.73 -12270.999
80 202.37482 -138029.39 0 -137175.59 -7622.732
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 5.03541 on 1 procs for 100 steps with 32640 atoms
Performance: 0.858 ns/day, 27.975 hours/ns, 19.859 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 | 3.5083 | 3.5083 | 3.5083 | 0.0 | 69.67
Neigh | 1.4785 | 1.4785 | 1.4785 | 0.0 | 29.36
Comm | 0.016176 | 0.016176 | 0.016176 | 0.0 | 0.32
Output | 0.0009644 | 0.0009644 | 0.0009644 | 0.0 | 0.02
Modify | 0.02224 | 0.02224 | 0.02224 | 0.0 | 0.44
Other | | 0.009286 | | | 0.18
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460 ave 26460 max 26460 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
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.00151467 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * ../../potentials/CH.rebo C H
Reading potential file ../../potentials/CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0748
10 179.37985 -137931.27 0 -137174.48 15655.936
20 206.87654 -138046.99 0 -137174.19 -24042.627
30 150.80122 -137807.43 0 -137171.21 -16524.118
40 173.24945 -137902.35 0 -137171.42 -5716.9118
50 151.80455 -137812.36 0 -137171.91 3480.4584
60 199.08777 -138013.82 0 -137173.88 17881.372
70 217.85748 -138093.86 0 -137174.73 -12270.999
80 202.37482 -138029.39 0 -137175.59 -7622.732
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 1.49632 on 4 procs for 100 steps with 32640 atoms
Performance: 2.887 ns/day, 8.313 hours/ns, 66.831 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 | 0.93275 | 0.95717 | 0.97367 | 1.6 | 63.97
Neigh | 0.45634 | 0.46084 | 0.46749 | 0.6 | 30.80
Comm | 0.038283 | 0.062074 | 0.090508 | 7.6 | 4.15
Output | 0.00046492 | 0.00072992 | 0.0015128 | 0.0 | 0.05
Modify | 0.0088651 | 0.0090639 | 0.0093012 | 0.2 | 0.61
Other | | 0.006436 | | | 0.43
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01