diff --git a/examples/airebo/data.airebo b/examples/airebo/data.airebo new file mode 100644 index 0000000000000000000000000000000000000000..90e20b2388db29ceac1d93c176c82eab2f27ac86 --- /dev/null +++ b/examples/airebo/data.airebo @@ -0,0 +1,78 @@ +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 + diff --git a/examples/airebo/in.airebo b/examples/airebo/in.airebo new file mode 100644 index 0000000000000000000000000000000000000000..5b0e36ff4a0028247f07efbfebe53018586d7805 --- /dev/null +++ b/examples/airebo/in.airebo @@ -0,0 +1,22 @@ +# 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 diff --git a/examples/airebo/in.airebo-m b/examples/airebo/in.airebo-m new file mode 100644 index 0000000000000000000000000000000000000000..3ec29482a72dbef673db5532ecca4cec74ccc253 --- /dev/null +++ b/examples/airebo/in.airebo-m @@ -0,0 +1,22 @@ +# 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 diff --git a/examples/airebo/log.23Jun17.airebo-m.g++.1 b/examples/airebo/log.23Jun17.airebo-m.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..1483fcb4a659f96014b55382ed20783ccba5e3b3 --- /dev/null +++ b/examples/airebo/log.23Jun17.airebo-m.g++.1 @@ -0,0 +1,86 @@ +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 diff --git a/examples/airebo/log.23Jun17.airebo-m.g++.4 b/examples/airebo/log.23Jun17.airebo-m.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..3a3d922bcbed242e7fa6541a5b0b3120101767ba --- /dev/null +++ b/examples/airebo/log.23Jun17.airebo-m.g++.4 @@ -0,0 +1,86 @@ +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 diff --git a/examples/airebo/log.23Jun17.airebo.g++.1 b/examples/airebo/log.23Jun17.airebo.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..0ef895dc28d5fccc9a3fb344466825bb8e6d437b --- /dev/null +++ b/examples/airebo/log.23Jun17.airebo.g++.1 @@ -0,0 +1,86 @@ +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 diff --git a/examples/airebo/log.23Jun17.airebo.g++.4 b/examples/airebo/log.23Jun17.airebo.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..486b48a0045c66894e4d35abb5e6706c77766c2c --- /dev/null +++ b/examples/airebo/log.23Jun17.airebo.g++.4 @@ -0,0 +1,86 @@ +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