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add polyethylene airebo example for future reference

This commit is contained in:
Axel Kohlmeyer 2017-07-05 17:44:18 -04:00
parent d0a397d6cb
commit fa469ae1d0
7 changed files with 466 additions and 0 deletions
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examples/airebo/data.airebo Normal file
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LAMMPS data file from restart file: timestep = 1, procs = 1
60 atoms
2 atom types
-2.1 2.1 xlo xhi
-2.1 2.1 ylo yhi
0 25.5790000000 zlo zhi
Masses
1 12.01
2 1.00794
Atoms
1 1 0.0000000000 0.0000000000 0.0000000000
2 2 0.9010066786 -0.6310205743 0.0000000000
3 2 -0.9010066786 -0.6310205743 0.0000000000
4 1 0.0000000000 0.8470061967 1.2789591482
5 2 0.9010066786 1.4780267710 1.2789591482
6 2 -0.9010066786 1.4780267710 1.2789591482
7 1 0.0000000000 0.0000000000 2.5579182965
8 2 0.9010066786 -0.6310205743 2.5579182965
9 2 -0.9010066786 -0.6310205743 2.5579182965
10 1 0.0000000000 0.8470061967 3.8368774447
11 2 0.9010066786 1.4780267710 3.8368774447
12 2 -0.9010066786 1.4780267710 3.8368774447
13 1 0.0000000000 0.0000000000 5.1158365929
14 2 0.9010066786 -0.6310205743 5.1158365929
15 2 -0.9010066786 -0.6310205743 5.1158365929
16 1 0.0000000000 0.8470061967 6.3947957411
17 2 0.9010066786 1.4780267710 6.3947957411
18 2 -0.9010066786 1.4780267710 6.3947957411
19 1 0.0000000000 0.0000000000 7.6737548894
20 2 0.9010066786 -0.6310205743 7.6737548894
21 2 -0.9010066786 -0.6310205743 7.6737548894
22 1 0.0000000000 0.8470061967 8.9527140376
23 2 0.9010066786 1.4780267710 8.9527140376
24 2 -0.9010066786 1.4780267710 8.9527140376
25 1 0.0000000000 0.0000000000 10.2316731858
26 2 0.9010066786 -0.6310205743 10.2316731858
27 2 -0.9010066786 -0.6310205743 10.2316731858
28 1 0.0000000000 0.8470061967 11.5106323340
29 2 0.9010066786 1.4780267710 11.5106323340
30 2 -0.9010066786 1.4780267710 11.5106323340
31 1 0.0000000000 0.0000000000 12.7895914823
32 2 0.9010066786 -0.6310205743 12.7895914823
33 2 -0.9010066786 -0.6310205743 12.7895914823
34 1 0.0000000000 0.8470061967 14.0685506305
35 2 0.9010066786 1.4780267710 14.0685506305
36 2 -0.9010066786 1.4780267710 14.0685506305
37 1 0.0000000000 0.0000000000 15.3475097787
38 2 0.9010066786 -0.6310205743 15.3475097787
39 2 -0.9010066786 -0.6310205743 15.3475097787
40 1 0.0000000000 0.8470061967 16.6264689269
41 2 0.9010066786 1.4780267710 16.6264689269
42 2 -0.9010066786 1.4780267710 16.6264689269
43 1 0.0000000000 0.0000000000 17.9054280752
44 2 0.9010066786 -0.6310205743 17.9054280752
45 2 -0.9010066786 -0.6310205743 17.9054280752
46 1 0.0000000000 0.8470061967 19.1843872234
47 2 0.9010066786 1.4780267710 19.1843872234
48 2 -0.9010066786 1.4780267710 19.1843872234
49 1 0.0000000000 0.0000000000 20.4633463716
50 2 0.9010066786 -0.6310205743 20.4633463716
51 2 -0.9010066786 -0.6310205743 20.4633463716
52 1 0.0000000000 0.8470061967 21.7423055198
53 2 0.9010066786 1.4780267710 21.7423055198
54 2 -0.9010066786 1.4780267710 21.7423055198
55 1 0.0000000000 0.0000000000 23.0212646681
56 2 0.9010066786 -0.6310205743 23.0212646681
57 2 -0.9010066786 -0.6310205743 23.0212646681
58 1 0.0000000000 0.8470061967 24.3002238163
59 2 0.9010066786 1.4780267710 24.3002238163
60 2 -0.9010066786 1.4780267710 24.3002238163

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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 1 1
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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examples/airebo/in.airebo-m 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/morse 3.0 1 1
pair_coeff * * ../../potentials/CH.airebo-m C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100

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LAMMPS (23 Jun 2017)
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo/morse 3.0 1 1
pair_coeff * * ../../potentials/CH.airebo-m C H
Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15
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 = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo/morse, 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) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139283.82 0 -138018.14 152.25271
10 166.76148 -138718.75 0 -138015.19 17412.343
20 207.7293 -138891.79 0 -138015.4 -19395.339
30 138.54469 -138596.42 0 -138011.92 -11909.248
40 153.95239 -138661.7 0 -138012.19 -2448.7701
50 126.22907 -138545.12 0 -138012.57 5206.1374
60 181.02757 -138778.28 0 -138014.54 22506.777
70 185.72779 -138799.18 0 -138015.61 -10803.744
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
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
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
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48094 ave 48094 max 48094 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: 2.22109e+07 ave 2.22109e+07 max 2.22109e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:02:00

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LAMMPS (23 Jun 2017)
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo/morse 3.0 1 1
pair_coeff * * ../../potentials/CH.airebo-m C H
Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15
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 = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo/morse, 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) = 29.37 | 29.75 | 30.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139283.82 0 -138018.14 152.25271
10 166.76148 -138718.75 0 -138015.19 17412.343
20 207.7293 -138891.79 0 -138015.4 -19395.339
30 138.54469 -138596.42 0 -138011.92 -11909.248
40 153.95239 -138661.7 0 -138012.19 -2448.7701
50 126.22907 -138545.12 0 -138012.57 5206.1374
60 181.02757 -138778.28 0 -138014.54 22506.777
70 185.72779 -138799.18 0 -138015.61 -10803.744
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
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
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
Nlocal: 8160 ave 8167 max 8153 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22581 ave 22594 max 22569 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55273e+06 ave 5.55908e+06 max 5.54496e+06 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:33

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LAMMPS (23 Jun 2017)
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
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 = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
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) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139300.72 0 -138035.04 7988.6647
10 161.34683 -138712.9 0 -138032.19 33228.921
20 208.59504 -138912.79 0 -138032.74 -3211.8806
30 139.7513 -138618.85 0 -138029.25 10878.143
40 142.14562 -138629.02 0 -138029.32 14601.302
50 114.23401 -138510.95 0 -138029 24691.125
60 164.92002 -138726 0 -138030.21 35125.541
70 162.15256 -138715.9 0 -138031.79 5658.7946
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
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
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
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48190 ave 48190 max 48190 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: 2.22178e+07 ave 2.22178e+07 max 2.22178e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:52

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LAMMPS (23 Jun 2017)
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
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 = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
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) = 29.37 | 29.75 | 30.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139300.72 0 -138035.04 7988.6647
10 161.34683 -138712.9 0 -138032.19 33228.921
20 208.59504 -138912.79 0 -138032.74 -3211.8806
30 139.7513 -138618.85 0 -138029.25 10878.143
40 142.14562 -138629.02 0 -138029.32 14601.302
50 114.23401 -138510.95 0 -138029 24691.125
60 164.92002 -138726 0 -138030.21 35125.541
70 162.15256 -138715.9 0 -138031.79 5658.7946
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
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
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
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22614.5 ave 22629 max 22601 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55446e+06 ave 5.56556e+06 max 5.54192e+06 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:30