Loading examples/USER/misc/mesocnt/cnt.indeleted 100644 → 0 +0 −37 Original line number Diff line number Diff line #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify vel no cutoff 33.0 neighbor 7.80 bin newton on #Read data read_data cnt.data #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt #Output thermo 10000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 100000 examples/USER/misc/mesocnt/in.cnt 0 → 100644 +38 −0 Original line number Diff line number Diff line #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify cutoff 11.0 neighbor 7.80 bin newton on #Read data read_data cnt.data replicate 1 2 2 #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt #Output thermo 1000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 10000 examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1 0 → 100644 +126 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify cutoff 11.0 neighbor 7.80 bin newton on #Read data read_data cnt.data orthogonal box = (0 0 0) to (600 600 60) 1 by 1 by 1 MPI processor grid reading atoms ... 500 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 498 bonds reading angles ... 496 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000180006 secs read_data CPU = 0.00125766 secs replicate 1 2 2 orthogonal box = (0 0 0) to (600 1200 120) 1 by 1 by 1 MPI processor grid 2000 atoms 1992 bonds 1984 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.00054121 secs replicate CPU = 0.000902414 secs #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt Reading potential file 10_10.cnt with DATE: 2020-01-13 #Output thermo 1000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 10000 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.177 ghost atom cutoff = 11 binsize = 5.0885, bins = 118 236 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair mesocnt, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304 1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182 2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757 3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539 4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866 5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738 6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986 7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796 8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885 9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197 10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903 Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38 Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57 Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03 Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05 Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52 Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37 Other | | 0.04409 | | | 1.09 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 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: 13320 ave 13320 max 13320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13320 Ave neighs/atom = 6.66 Ave special neighs/atom = 5.952 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:05 examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4 0 → 100644 +126 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify cutoff 11.0 neighbor 7.80 bin newton on #Read data read_data cnt.data orthogonal box = (0 0 0) to (600 600 60) 2 by 2 by 1 MPI processor grid reading atoms ... 500 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 498 bonds reading angles ... 496 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000354767 secs read_data CPU = 0.00286365 secs replicate 1 2 2 orthogonal box = (0 0 0) to (600 1200 120) 1 by 4 by 1 MPI processor grid 2000 atoms 1992 bonds 1984 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.00019598 secs replicate CPU = 0.00055337 secs #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt Reading potential file 10_10.cnt with DATE: 2020-01-13 #Output thermo 1000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 10000 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.177 ghost atom cutoff = 11 binsize = 5.0885, bins = 118 236 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair mesocnt, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 2.725 | 2.725 | 2.725 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304 1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182 2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738 3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513 4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101 5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633 6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686 7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831 8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264 9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773 10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282 Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s 96.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34 Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80 Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04 Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32 Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59 Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45 Other | | 0.04279 | | | 3.46 Nlocal: 500 ave 504 max 496 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 22 ave 24 max 20 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 3330 ave 3368 max 3292 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 13320 Ave neighs/atom = 6.66 Ave special neighs/atom = 5.952 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:02 Loading
examples/USER/misc/mesocnt/cnt.indeleted 100644 → 0 +0 −37 Original line number Diff line number Diff line #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify vel no cutoff 33.0 neighbor 7.80 bin newton on #Read data read_data cnt.data #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt #Output thermo 10000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 100000
examples/USER/misc/mesocnt/in.cnt 0 → 100644 +38 −0 Original line number Diff line number Diff line #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify cutoff 11.0 neighbor 7.80 bin newton on #Read data read_data cnt.data replicate 1 2 2 #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt #Output thermo 1000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 10000
examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1 0 → 100644 +126 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify cutoff 11.0 neighbor 7.80 bin newton on #Read data read_data cnt.data orthogonal box = (0 0 0) to (600 600 60) 1 by 1 by 1 MPI processor grid reading atoms ... 500 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 498 bonds reading angles ... 496 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000180006 secs read_data CPU = 0.00125766 secs replicate 1 2 2 orthogonal box = (0 0 0) to (600 1200 120) 1 by 1 by 1 MPI processor grid 2000 atoms 1992 bonds 1984 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.00054121 secs replicate CPU = 0.000902414 secs #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt Reading potential file 10_10.cnt with DATE: 2020-01-13 #Output thermo 1000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 10000 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.177 ghost atom cutoff = 11 binsize = 5.0885, bins = 118 236 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair mesocnt, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304 1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182 2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757 3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539 4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866 5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738 6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986 7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796 8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885 9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197 10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903 Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38 Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57 Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03 Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05 Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52 Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37 Other | | 0.04409 | | | 1.09 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 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: 13320 ave 13320 max 13320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13320 Ave neighs/atom = 6.66 Ave special neighs/atom = 5.952 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:05
examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4 0 → 100644 +126 −0 Original line number Diff line number Diff line LAMMPS (09 Jan 2020) #Initialisation units nano dimension 3 boundary p p p atom_style full comm_modify cutoff 11.0 neighbor 7.80 bin newton on #Read data read_data cnt.data orthogonal box = (0 0 0) to (600 600 60) 2 by 2 by 1 MPI processor grid reading atoms ... 500 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 498 bonds reading angles ... 496 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000354767 secs read_data CPU = 0.00286365 secs replicate 1 2 2 orthogonal box = (0 0 0) to (600 1200 120) 1 by 4 by 1 MPI processor grid 2000 atoms 1992 bonds 1984 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.00019598 secs replicate CPU = 0.00055337 secs #Force field bond_style harmonic bond_coeff 1 268896.77 2.0 angle_style harmonic angle_coeff 1 46562.17 180.0 pair_style mesocnt pair_coeff * * 10_10.cnt Reading potential file 10_10.cnt with DATE: 2020-01-13 #Output thermo 1000 dump xyz all xyz 1000 cnt.xyz #Simulation setup timestep 1.0e-05 #Nose-Hoover thermostat fix nvt all nvt temp 300 300 0.001 run 10000 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.177 ghost atom cutoff = 11 binsize = 5.0885, bins = 118 236 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair mesocnt, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 2.725 | 2.725 | 2.725 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304 1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182 2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738 3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513 4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101 5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633 6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686 7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831 8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264 9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773 10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282 Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s 96.1% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34 Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80 Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04 Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32 Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59 Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45 Other | | 0.04279 | | | 3.46 Nlocal: 500 ave 504 max 496 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 22 ave 24 max 20 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 3330 ave 3368 max 3292 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 13320 Ave neighs/atom = 6.66 Ave special neighs/atom = 5.952 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:02
