Loading examples/controller/in.controller 100755 → 100644 +0 −0 File mode changed from 100755 to 100644. View file examples/crack/log.5Oct16.crack.g++.1→examples/crack/log.27Nov18.crack.g++.1 +22 −15 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d LJ crack simulation dimension 2 Loading @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8141 atoms Time spent = 0.00162196 secs mass 1 1.0 mass 2 1.0 Loading Loading @@ -76,7 +78,7 @@ fix 2 boundary setforce NULL 0.0 0.0 timestep 0.003 thermo 200 thermo_modify temp new WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) neigh_modify exclude type 2 3 Loading @@ -90,13 +92,18 @@ neigh_modify exclude type 2 3 run 5000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 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 = 80 56 1 Memory usage per processor = 2.48017 Mbytes binsize = 1.4, bins = 80 56 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917 200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101 Loading Loading @@ -124,20 +131,20 @@ Step Temp E_pair E_mol TotEng Press Volume 4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925 4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122 5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637 Loop time of 6.89346 on 1 procs for 5000 steps with 8141 atoms Loop time of 7.02888 on 1 procs for 5000 steps with 8141 atoms Performance: 188004.255 tau/day, 725.325 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 184382.046 tau/day, 711.350 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 | 5.8036 | 5.8036 | 5.8036 | 0.0 | 84.19 Neigh | 0.37434 | 0.37434 | 0.37434 | 0.0 | 5.43 Comm | 0.004128 | 0.004128 | 0.004128 | 0.0 | 0.06 Output | 0.00077105 | 0.00077105 | 0.00077105 | 0.0 | 0.01 Modify | 0.53619 | 0.53619 | 0.53619 | 0.0 | 7.78 Other | | 0.1744 | | | 2.53 Pair | 5.8668 | 5.8668 | 5.8668 | 0.0 | 83.47 Neigh | 0.29717 | 0.29717 | 0.29717 | 0.0 | 4.23 Comm | 0.0045955 | 0.0045955 | 0.0045955 | 0.0 | 0.07 Output | 0.0011108 | 0.0011108 | 0.0011108 | 0.0 | 0.02 Modify | 0.65277 | 0.65277 | 0.65277 | 0.0 | 9.29 Other | | 0.2064 | | | 2.94 Nlocal: 8141 ave 8141 max 8141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -150,4 +157,4 @@ Total # of neighbors = 71389 Ave neighs/atom = 8.76907 Neighbor list builds = 100 Dangerous builds = 0 Total wall time: 0:00:06 Total wall time: 0:00:07 examples/crack/log.5Oct16.crack.g++.4→examples/crack/log.27Nov18.crack.g++.4 +22 −15 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d LJ crack simulation dimension 2 Loading @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 8141 atoms Time spent = 0.00064826 secs mass 1 1.0 mass 2 1.0 Loading Loading @@ -76,7 +78,7 @@ fix 2 boundary setforce NULL 0.0 0.0 timestep 0.003 thermo 200 thermo_modify temp new WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) neigh_modify exclude type 2 3 Loading @@ -90,13 +92,18 @@ neigh_modify exclude type 2 3 run 5000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 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 = 80 56 1 Memory usage per processor = 2.48163 Mbytes binsize = 1.4, bins = 80 56 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.069 | 3.069 | 3.069 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917 200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331 Loading Loading @@ -124,20 +131,20 @@ Step Temp E_pair E_mol TotEng Press Volume 4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949 4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155 5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031 Loop time of 1.97398 on 4 procs for 5000 steps with 8141 atoms Loop time of 2.06204 on 4 procs for 5000 steps with 8141 atoms Performance: 656540.037 tau/day, 2532.948 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads Performance: 628504.111 tau/day, 2424.784 timesteps/s 97.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4909 | 1.5203 | 1.5671 | 2.3 | 77.02 Neigh | 0.10125 | 0.10271 | 0.10657 | 0.7 | 5.20 Comm | 0.076516 | 0.13066 | 0.15771 | 8.8 | 6.62 Output | 0.00077796 | 0.00082064 | 0.00091672 | 0.2 | 0.04 Modify | 0.13725 | 0.14082 | 0.14325 | 0.6 | 7.13 Other | | 0.07865 | | | 3.98 Pair | 1.4844 | 1.5266 | 1.5909 | 3.6 | 74.03 Neigh | 0.081047 | 0.085878 | 0.093027 | 1.5 | 4.16 Comm | 0.12993 | 0.19571 | 0.25179 | 11.6 | 9.49 Output | 0.00072265 | 0.00096798 | 0.0016601 | 0.0 | 0.05 Modify | 0.16787 | 0.17024 | 0.17234 | 0.4 | 8.26 Other | | 0.0826 | | | 4.01 Nlocal: 2035.25 ave 2064 max 2015 min Histogram: 1 1 0 0 0 1 0 0 0 1 Loading @@ -150,4 +157,4 @@ Total # of neighbors = 71400 Ave neighs/atom = 8.77042 Neighbor list builds = 106 Dangerous builds = 0 Total wall time: 0:00:01 Total wall time: 0:00:02 examples/deposit/log.5Oct16.deposit.atom.g++.1→examples/deposit/log.27Nov18.deposit.atom.g++.1 +23 −16 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj Loading @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms Time spent = 0.000444174 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 Loading @@ -30,7 +32,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp compute_modify add dynamic yes extra 0 compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 Loading @@ -43,7 +45,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom Loading @@ -55,13 +57,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65 -> bins = 3 3 6 Memory usage per processor = 2.54053 Mbytes binsize = 2.65, bins = 3 3 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, 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) = 3.126 | 3.126 | 3.126 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746 Loading Loading @@ -164,20 +171,20 @@ Step Atoms Temp E_pair TotEng Press 9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109 9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384 10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643 Loop time of 5.63963 on 1 procs for 10000 steps with 450 atoms Loop time of 6.17726 on 1 procs for 10000 steps with 450 atoms Performance: 766007.688 tau/day, 1773.166 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 699339.360 tau/day, 1618.841 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 | 3.1973 | 3.1973 | 3.1973 | 0.0 | 56.69 Neigh | 2.1646 | 2.1646 | 2.1646 | 0.0 | 38.38 Comm | 0.11922 | 0.11922 | 0.11922 | 0.0 | 2.11 Output | 0.00081301 | 0.00081301 | 0.00081301 | 0.0 | 0.01 Modify | 0.11702 | 0.11702 | 0.11702 | 0.0 | 2.07 Other | | 0.04063 | | | 0.72 Pair | 3.1708 | 3.1708 | 3.1708 | 0.0 | 51.33 Neigh | 2.6376 | 2.6376 | 2.6376 | 0.0 | 42.70 Comm | 0.18927 | 0.18927 | 0.18927 | 0.0 | 3.06 Output | 0.0013239 | 0.0013239 | 0.0013239 | 0.0 | 0.02 Modify | 0.13663 | 0.13663 | 0.13663 | 0.0 | 2.21 Other | | 0.04162 | | | 0.67 Nlocal: 450 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -190,4 +197,4 @@ Total # of neighbors = 29176 Ave neighs/atom = 64.8356 Neighbor list builds = 1143 Dangerous builds = 0 Total wall time: 0:00:05 Total wall time: 0:00:06 examples/deposit/log.5Oct16.deposit.atom.g++.4→examples/deposit/log.27Nov18.deposit.atom.g++.4 +23 −16 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj Loading @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms Time spent = 0.000353813 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 Loading @@ -30,7 +32,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp compute_modify add dynamic yes extra 0 compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 Loading @@ -43,7 +45,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom Loading @@ -55,13 +57,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65 -> bins = 3 3 6 Memory usage per processor = 2.60645 Mbytes binsize = 2.65, bins = 3 3 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, 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) = 0.4396 | 2.389 | 3.192 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131 Loading Loading @@ -164,20 +171,20 @@ Step Atoms Temp E_pair TotEng Press 9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592 9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329 10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403 Loop time of 4.38653 on 4 procs for 10000 steps with 450 atoms Loop time of 5.30178 on 4 procs for 10000 steps with 450 atoms Performance: 984832.436 tau/day, 2279.705 timesteps/s 98.5% CPU use with 4 MPI tasks x no OpenMP threads Performance: 814820.053 tau/day, 1886.158 timesteps/s 94.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0022979 | 0.81396 | 2.0831 | 95.7 | 18.56 Neigh | 0.0083807 | 0.57856 | 1.7676 | 93.7 | 13.19 Comm | 0.3792 | 2.1868 | 3.8575 | 85.0 | 49.85 Output | 0.001919 | 0.008881 | 0.025856 | 10.5 | 0.20 Modify | 0.0053477 | 0.035994 | 0.08146 | 16.2 | 0.82 Other | | 0.7623 | | | 17.38 Pair | 0.0030358 | 0.8503 | 2.2484 | 100.1 | 16.04 Neigh | 0.0085447 | 0.74813 | 2.3721 | 111.4 | 14.11 Comm | 0.50519 | 2.6696 | 4.6851 | 95.8 | 50.35 Output | 0.0024836 | 0.012219 | 0.029616 | 9.5 | 0.23 Modify | 0.014966 | 0.047625 | 0.094656 | 14.8 | 0.90 Other | | 0.9739 | | | 18.37 Nlocal: 112.5 ave 250 max 9 min Histogram: 2 0 0 0 0 0 1 0 0 1 Loading @@ -190,4 +197,4 @@ Total # of neighbors = 29661 Ave neighs/atom = 65.9133 Neighbor list builds = 1164 Dangerous builds = 0 Total wall time: 0:00:04 Total wall time: 0:00:05 Loading
examples/controller/in.controller 100755 → 100644 +0 −0 File mode changed from 100755 to 100644. View file
examples/crack/log.5Oct16.crack.g++.1→examples/crack/log.27Nov18.crack.g++.1 +22 −15 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d LJ crack simulation dimension 2 Loading @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8141 atoms Time spent = 0.00162196 secs mass 1 1.0 mass 2 1.0 Loading Loading @@ -76,7 +78,7 @@ fix 2 boundary setforce NULL 0.0 0.0 timestep 0.003 thermo 200 thermo_modify temp new WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) neigh_modify exclude type 2 3 Loading @@ -90,13 +92,18 @@ neigh_modify exclude type 2 3 run 5000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 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 = 80 56 1 Memory usage per processor = 2.48017 Mbytes binsize = 1.4, bins = 80 56 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917 200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101 Loading Loading @@ -124,20 +131,20 @@ Step Temp E_pair E_mol TotEng Press Volume 4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925 4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122 5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637 Loop time of 6.89346 on 1 procs for 5000 steps with 8141 atoms Loop time of 7.02888 on 1 procs for 5000 steps with 8141 atoms Performance: 188004.255 tau/day, 725.325 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 184382.046 tau/day, 711.350 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 | 5.8036 | 5.8036 | 5.8036 | 0.0 | 84.19 Neigh | 0.37434 | 0.37434 | 0.37434 | 0.0 | 5.43 Comm | 0.004128 | 0.004128 | 0.004128 | 0.0 | 0.06 Output | 0.00077105 | 0.00077105 | 0.00077105 | 0.0 | 0.01 Modify | 0.53619 | 0.53619 | 0.53619 | 0.0 | 7.78 Other | | 0.1744 | | | 2.53 Pair | 5.8668 | 5.8668 | 5.8668 | 0.0 | 83.47 Neigh | 0.29717 | 0.29717 | 0.29717 | 0.0 | 4.23 Comm | 0.0045955 | 0.0045955 | 0.0045955 | 0.0 | 0.07 Output | 0.0011108 | 0.0011108 | 0.0011108 | 0.0 | 0.02 Modify | 0.65277 | 0.65277 | 0.65277 | 0.0 | 9.29 Other | | 0.2064 | | | 2.94 Nlocal: 8141 ave 8141 max 8141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -150,4 +157,4 @@ Total # of neighbors = 71389 Ave neighs/atom = 8.76907 Neighbor list builds = 100 Dangerous builds = 0 Total wall time: 0:00:06 Total wall time: 0:00:07
examples/crack/log.5Oct16.crack.g++.4→examples/crack/log.27Nov18.crack.g++.4 +22 −15 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 2d LJ crack simulation dimension 2 Loading @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 8141 atoms Time spent = 0.00064826 secs mass 1 1.0 mass 2 1.0 Loading Loading @@ -76,7 +78,7 @@ fix 2 boundary setforce NULL 0.0 0.0 timestep 0.003 thermo 200 thermo_modify temp new WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) neigh_modify exclude type 2 3 Loading @@ -90,13 +92,18 @@ neigh_modify exclude type 2 3 run 5000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 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 = 80 56 1 Memory usage per processor = 2.48163 Mbytes binsize = 1.4, bins = 80 56 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.069 | 3.069 | 3.069 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917 200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331 Loading Loading @@ -124,20 +131,20 @@ Step Temp E_pair E_mol TotEng Press Volume 4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949 4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155 5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031 Loop time of 1.97398 on 4 procs for 5000 steps with 8141 atoms Loop time of 2.06204 on 4 procs for 5000 steps with 8141 atoms Performance: 656540.037 tau/day, 2532.948 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads Performance: 628504.111 tau/day, 2424.784 timesteps/s 97.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4909 | 1.5203 | 1.5671 | 2.3 | 77.02 Neigh | 0.10125 | 0.10271 | 0.10657 | 0.7 | 5.20 Comm | 0.076516 | 0.13066 | 0.15771 | 8.8 | 6.62 Output | 0.00077796 | 0.00082064 | 0.00091672 | 0.2 | 0.04 Modify | 0.13725 | 0.14082 | 0.14325 | 0.6 | 7.13 Other | | 0.07865 | | | 3.98 Pair | 1.4844 | 1.5266 | 1.5909 | 3.6 | 74.03 Neigh | 0.081047 | 0.085878 | 0.093027 | 1.5 | 4.16 Comm | 0.12993 | 0.19571 | 0.25179 | 11.6 | 9.49 Output | 0.00072265 | 0.00096798 | 0.0016601 | 0.0 | 0.05 Modify | 0.16787 | 0.17024 | 0.17234 | 0.4 | 8.26 Other | | 0.0826 | | | 4.01 Nlocal: 2035.25 ave 2064 max 2015 min Histogram: 1 1 0 0 0 1 0 0 0 1 Loading @@ -150,4 +157,4 @@ Total # of neighbors = 71400 Ave neighs/atom = 8.77042 Neighbor list builds = 106 Dangerous builds = 0 Total wall time: 0:00:01 Total wall time: 0:00:02
examples/deposit/log.5Oct16.deposit.atom.g++.1→examples/deposit/log.27Nov18.deposit.atom.g++.1 +23 −16 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj Loading @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms Time spent = 0.000444174 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 Loading @@ -30,7 +32,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp compute_modify add dynamic yes extra 0 compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 Loading @@ -43,7 +45,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom Loading @@ -55,13 +57,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65 -> bins = 3 3 6 Memory usage per processor = 2.54053 Mbytes binsize = 2.65, bins = 3 3 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, 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) = 3.126 | 3.126 | 3.126 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746 Loading Loading @@ -164,20 +171,20 @@ Step Atoms Temp E_pair TotEng Press 9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109 9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384 10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643 Loop time of 5.63963 on 1 procs for 10000 steps with 450 atoms Loop time of 6.17726 on 1 procs for 10000 steps with 450 atoms Performance: 766007.688 tau/day, 1773.166 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads Performance: 699339.360 tau/day, 1618.841 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 | 3.1973 | 3.1973 | 3.1973 | 0.0 | 56.69 Neigh | 2.1646 | 2.1646 | 2.1646 | 0.0 | 38.38 Comm | 0.11922 | 0.11922 | 0.11922 | 0.0 | 2.11 Output | 0.00081301 | 0.00081301 | 0.00081301 | 0.0 | 0.01 Modify | 0.11702 | 0.11702 | 0.11702 | 0.0 | 2.07 Other | | 0.04063 | | | 0.72 Pair | 3.1708 | 3.1708 | 3.1708 | 0.0 | 51.33 Neigh | 2.6376 | 2.6376 | 2.6376 | 0.0 | 42.70 Comm | 0.18927 | 0.18927 | 0.18927 | 0.0 | 3.06 Output | 0.0013239 | 0.0013239 | 0.0013239 | 0.0 | 0.02 Modify | 0.13663 | 0.13663 | 0.13663 | 0.0 | 2.21 Other | | 0.04162 | | | 0.67 Nlocal: 450 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading @@ -190,4 +197,4 @@ Total # of neighbors = 29176 Ave neighs/atom = 64.8356 Neighbor list builds = 1143 Dangerous builds = 0 Total wall time: 0:00:05 Total wall time: 0:00:06
examples/deposit/log.5Oct16.deposit.atom.g++.4→examples/deposit/log.27Nov18.deposit.atom.g++.4 +23 −16 Original line number Diff line number Diff line LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj Loading @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms Time spent = 0.000353813 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 Loading @@ -30,7 +32,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp compute_modify add dynamic yes extra 0 compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 Loading @@ -43,7 +45,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom Loading @@ -55,13 +57,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 binsize = 2.65 -> bins = 3 3 6 Memory usage per processor = 2.60645 Mbytes binsize = 2.65, bins = 3 3 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, 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) = 0.4396 | 2.389 | 3.192 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131 Loading Loading @@ -164,20 +171,20 @@ Step Atoms Temp E_pair TotEng Press 9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592 9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329 10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403 Loop time of 4.38653 on 4 procs for 10000 steps with 450 atoms Loop time of 5.30178 on 4 procs for 10000 steps with 450 atoms Performance: 984832.436 tau/day, 2279.705 timesteps/s 98.5% CPU use with 4 MPI tasks x no OpenMP threads Performance: 814820.053 tau/day, 1886.158 timesteps/s 94.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0022979 | 0.81396 | 2.0831 | 95.7 | 18.56 Neigh | 0.0083807 | 0.57856 | 1.7676 | 93.7 | 13.19 Comm | 0.3792 | 2.1868 | 3.8575 | 85.0 | 49.85 Output | 0.001919 | 0.008881 | 0.025856 | 10.5 | 0.20 Modify | 0.0053477 | 0.035994 | 0.08146 | 16.2 | 0.82 Other | | 0.7623 | | | 17.38 Pair | 0.0030358 | 0.8503 | 2.2484 | 100.1 | 16.04 Neigh | 0.0085447 | 0.74813 | 2.3721 | 111.4 | 14.11 Comm | 0.50519 | 2.6696 | 4.6851 | 95.8 | 50.35 Output | 0.0024836 | 0.012219 | 0.029616 | 9.5 | 0.23 Modify | 0.014966 | 0.047625 | 0.094656 | 14.8 | 0.90 Other | | 0.9739 | | | 18.37 Nlocal: 112.5 ave 250 max 9 min Histogram: 2 0 0 0 0 0 1 0 0 1 Loading @@ -190,4 +197,4 @@ Total # of neighbors = 29661 Ave neighs/atom = 65.9133 Neighbor list builds = 1164 Dangerous builds = 0 Total wall time: 0:00:04 Total wall time: 0:00:05
