diff --git a/bench/log.30Jul13.chain.fixed.linux.1 b/bench/log.28Jan14.chain.fixed.linux.1 similarity index 75% rename from bench/log.30Jul13.chain.fixed.linux.1 rename to bench/log.28Jan14.chain.fixed.linux.1 index 872e90bfa..34017075d 100644 --- a/bench/log.30Jul13.chain.fixed.linux.1 +++ b/bench/log.28Jan14.chain.fixed.linux.1 @@ -1,59 +1,63 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # FENE beadspring benchmark units lj atom_style bond special_bonds fene read_data data.chain - 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities + scanning bonds ... + 1 = max bonds/atom + reading bonds ... 31680 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors neighbor 0.4 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 pair_style lj/cut 1.12 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12 fix 1 all nve fix 2 all langevin 1.0 1.0 10.0 904297 thermo 100 timestep 0.012 run 100 Memory usage per processor = 11.5156 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.9729966 0.4361122 20.507698 22.40326 4.6548819 -Loop time of 0.992695 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.200438 (20.1913) -Bond time (%) = 0.0872233 (8.78652) -Neigh time (%) = 0.450228 (45.3541) -Comm time (%) = 0.0333259 (3.35712) -Outpt time (%) = 9.58443e-05 (0.00965496) -Other time (%) = 0.221384 (22.3013) +Loop time of 1.00576 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.201571 (20.0416) +Bond time (%) = 0.0877447 (8.7242) +Neigh time (%) = 0.46259 (45.9939) +Comm time (%) = 0.0333455 (3.31544) +Outpt time (%) = 0.000102997 (0.0102407) +Other time (%) = 0.22041 (21.9147) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9493 ave 9493 max 9493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155873 ave 155873 max 155873 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155873 Ave neighs/atom = 4.87103 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.30Jul13.chain.fixed.linux.4 b/bench/log.28Jan14.chain.fixed.linux.4 similarity index 75% rename from bench/log.30Jul13.chain.fixed.linux.4 rename to bench/log.28Jan14.chain.fixed.linux.4 index 68b3ebc4f..2fc81c06e 100644 --- a/bench/log.30Jul13.chain.fixed.linux.4 +++ b/bench/log.28Jan14.chain.fixed.linux.4 @@ -1,59 +1,63 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # FENE beadspring benchmark units lj atom_style bond special_bonds fene read_data data.chain - 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities + scanning bonds ... + 1 = max bonds/atom + reading bonds ... 31680 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors neighbor 0.4 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 pair_style lj/cut 1.12 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12 fix 1 all nve fix 2 all langevin 1.0 1.0 10.0 904297 thermo 100 timestep 0.012 run 100 Memory usage per processor = 4.85536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.97145835 0.43803883 20.502691 22.397872 4.626988 -Loop time of 0.272427 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.0509947 (18.7187) -Bond time (%) = 0.0227102 (8.33625) -Neigh time (%) = 0.116272 (42.6802) -Comm time (%) = 0.0213055 (7.82062) -Outpt time (%) = 7.23004e-05 (0.0265394) -Other time (%) = 0.0610721 (22.4178) +Loop time of 0.273179 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.050166 (18.3638) +Bond time (%) = 0.0222697 (8.15205) +Neigh time (%) = 0.119487 (43.7393) +Comm time (%) = 0.0235835 (8.633) +Outpt time (%) = 5.48959e-05 (0.0200952) +Other time (%) = 0.0576181 (21.0917) Nlocal: 8000 ave 8030 max 7974 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 4177 ave 4191 max 4160 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 38995.8 ave 39169 max 38852 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 155983 Ave neighs/atom = 4.87447 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.30Jul13.chain.scaled.linux.4 b/bench/log.28Jan14.chain.scaled.linux.4 similarity index 79% rename from bench/log.30Jul13.chain.scaled.linux.4 rename to bench/log.28Jan14.chain.scaled.linux.4 index a00958e32..c6c877a07 100644 --- a/bench/log.30Jul13.chain.scaled.linux.4 +++ b/bench/log.28Jan14.chain.scaled.linux.4 @@ -1,75 +1,79 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # FENE beadspring benchmark variable x index 1 variable y index 1 variable z index 1 units lj atom_style bond atom_modify map hash special_bonds fene read_data data.chain - 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities + scanning bonds ... + 1 = max bonds/atom + reading bonds ... 31680 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 1 orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796) 2 by 2 by 1 MPI processor grid 128000 atoms 126720 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors neighbor 0.4 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 pair_style lj/cut 1.12 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12 fix 1 all nve fix 2 all langevin 1.0 1.0 10.0 904297 thermo 100 timestep 0.012 run 100 Memory usage per processor = 13.4806 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97027498 0.44484087 20.494523 22.394765 4.6721833 100 0.97682955 0.44239968 20.500229 22.407862 4.6527025 -Loop time of 1.188 on 4 procs for 100 steps with 128000 atoms +Loop time of 1.22968 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 0.226131 (19.0346) -Bond time (%) = 0.0970581 (8.16985) -Neigh time (%) = 0.506595 (42.6426) -Comm time (%) = 0.107507 (9.04943) -Outpt time (%) = 0.000239134 (0.0201291) -Other time (%) = 0.250472 (21.0834) +Pair time (%) = 0.233808 (19.0137) +Bond time (%) = 0.102124 (8.30491) +Neigh time (%) = 0.535992 (43.5879) +Comm time (%) = 0.103922 (8.45112) +Outpt time (%) = 0.000156224 (0.0127044) +Other time (%) = 0.253678 (20.6296) Nlocal: 32000 ave 32015 max 31983 min Histogram: 1 0 1 0 0 0 0 0 1 1 Nghost: 9492 ave 9522 max 9432 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 155837 ave 156079 max 155506 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 623349 Ave neighs/atom = 4.86991 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.30Jul13.chute.fixed.linux.1 b/bench/log.28Jan14.chute.fixed.linux.1 similarity index 77% rename from bench/log.30Jul13.chute.fixed.linux.1 rename to bench/log.28Jan14.chute.fixed.linux.1 index d91216877..2e56c5e93 100644 --- a/bench/log.30Jul13.chute.fixed.linux.1 +++ b/bench/log.28Jan14.chute.fixed.linux.1 @@ -1,63 +1,65 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees units lj atom_style sphere boundary p p fs newton off communicate single vel yes read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 1 by 1 by 1 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 pair_coeff * * neighbor 0.1 bin neigh_modify every 1 delay 0 timestep 0.0001 group bottom type 2 912 atoms in group bottom group active subtract all bottom 31088 atoms in group active neigh_modify exclude group bottom bottom fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/sphere compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo_modify norm no thermo 100 run 100 -Memory usage per processor = 21.0636 Mbytes +Memory usage per processor = 21.4184 Mbytes Step Atoms KinEng 1 Volume 0 32000 784139.13 1601.1263 29833.783 100 32000 784292.08 1571.0968 29834.707 -Loop time of 0.54007 on 1 procs for 100 steps with 32000 atoms +Loop time of 0.532316 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 0.329372 (60.987) -Neigh time (%) = 0.0422847 (7.82949) -Comm time (%) = 0.0179758 (3.32842) -Outpt time (%) = 0.00019002 (0.0351843) -Other time (%) = 0.150247 (27.8199) +Pair time (%) = 0.323012 (60.6805) +Neigh time (%) = 0.0413709 (7.77186) +Comm time (%) = 0.017947 (3.37149) +Outpt time (%) = 0.000191927 (0.0360551) +Other time (%) = 0.149794 (28.1401) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5463 ave 5463 max 5463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115133 ave 115133 max 115133 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115133 Ave neighs/atom = 3.59791 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.30Jul13.chute.fixed.linux.4 b/bench/log.28Jan14.chute.fixed.linux.4 similarity index 77% rename from bench/log.30Jul13.chute.fixed.linux.4 rename to bench/log.28Jan14.chute.fixed.linux.4 index 03eda1e7e..59e161396 100644 --- a/bench/log.30Jul13.chute.fixed.linux.4 +++ b/bench/log.28Jan14.chute.fixed.linux.4 @@ -1,63 +1,65 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees units lj atom_style sphere boundary p p fs newton off communicate single vel yes read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 2 by 1 by 2 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 pair_coeff * * neighbor 0.1 bin neigh_modify every 1 delay 0 timestep 0.0001 group bottom type 2 912 atoms in group bottom group active subtract all bottom 31088 atoms in group active neigh_modify exclude group bottom bottom fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/sphere compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo_modify norm no thermo 100 run 100 -Memory usage per processor = 10.5226 Mbytes +Memory usage per processor = 10.7034 Mbytes Step Atoms KinEng 1 Volume 0 32000 784139.13 1601.1263 29833.783 100 32000 784292.08 1571.0968 29834.707 -Loop time of 0.135566 on 4 procs for 100 steps with 32000 atoms +Loop time of 0.13025 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 0.0668132 (49.2847) -Neigh time (%) = 0.0107402 (7.9225) -Comm time (%) = 0.0142344 (10.5) -Outpt time (%) = 0.000106156 (0.0783057) -Other time (%) = 0.043672 (32.2145) +Pair time (%) = 0.0655041 (50.291) +Neigh time (%) = 0.0103548 (7.94993) +Comm time (%) = 0.0144752 (11.1134) +Outpt time (%) = 9.47714e-05 (0.072761) +Other time (%) = 0.0398214 (30.573) Nlocal: 8000 ave 8008 max 7992 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 2439 ave 2450 max 2428 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 29500.5 ave 30488 max 28513 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 118002 Ave neighs/atom = 3.68756 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.30Jul13.chute.scaled.linux.4 b/bench/log.28Jan14.chute.scaled.linux.4 similarity index 80% rename from bench/log.30Jul13.chute.scaled.linux.4 rename to bench/log.28Jan14.chute.scaled.linux.4 index fe0406d7d..a7f95fc7d 100644 --- a/bench/log.30Jul13.chute.scaled.linux.4 +++ b/bench/log.28Jan14.chute.scaled.linux.4 @@ -1,73 +1,75 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees variable x index 1 variable y index 1 units lj atom_style sphere boundary p p fs newton off communicate single vel yes read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 2 by 1 by 2 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities replicate $x $y 1 replicate 2 $y 1 replicate 2 2 1 orthogonal box = (0 0 0) to (80 40 37.2923) 2 by 2 by 1 MPI processor grid 128000 atoms pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 pair_coeff * * neighbor 0.1 bin neigh_modify every 1 delay 0 timestep 0.0001 group bottom type 2 3648 atoms in group bottom group active subtract all bottom 124352 atoms in group active neigh_modify exclude group bottom bottom fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/sphere compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo_modify norm no thermo 100 run 100 -Memory usage per processor = 21.8161 Mbytes +Memory usage per processor = 22.3334 Mbytes Step Atoms KinEng 1 Volume 0 128000 3136556.5 6404.5051 119335.13 100 128000 3137168.3 6284.3873 119338.83 -Loop time of 1.01235 on 4 procs for 100 steps with 128000 atoms +Loop time of 0.981477 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 0.508497 (50.2295) -Neigh time (%) = 0.0454835 (4.49288) -Comm time (%) = 0.0667624 (6.59481) -Outpt time (%) = 0.00123399 (0.121894) -Other time (%) = 0.390371 (38.5609) +Pair time (%) = 0.507874 (51.7459) +Neigh time (%) = 0.0444019 (4.52399) +Comm time (%) = 0.065434 (6.6669) +Outpt time (%) = 0.000373006 (0.0380046) +Other time (%) = 0.363394 (37.0252) Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 5463 ave 5463 max 5463 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 115133 ave 115133 max 115133 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460532 Ave neighs/atom = 3.59791 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.30Jul13.eam.fixed.linux.1 b/bench/log.28Jan14.eam.fixed.linux.1 similarity index 81% rename from bench/log.30Jul13.eam.fixed.linux.1 rename to bench/log.28Jan14.eam.fixed.linux.1 index f69e04ca8..71ac3c6b3 100644 --- a/bench/log.30Jul13.eam.fixed.linux.1 +++ b/bench/log.28Jan14.eam.fixed.linux.1 @@ -1,67 +1,67 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # bulk Cu lattice variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units metal atom_style atomic lattice fcc 3.615 Lattice spacing in x,y,z = 3.615 3.615 3.615 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms pair_style eam pair_coeff 1 1 Cu_u3.eam velocity all create 1600.0 376847 loop geom neighbor 1.0 bin neigh_modify every 1 delay 5 check yes fix 1 all nve timestep 0.005 thermo 50 run 100 -Memory usage per processor = 15.3729 Mbytes +Memory usage per processor = 15.3727 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -113280 0 -106662.09 18703.573 50 781.69049 -109873.35 0 -106640.13 52273.088 100 801.832 -109957.3 0 -106640.77 51322.821 -Loop time of 5.89581 on 1 procs for 100 steps with 32000 atoms +Loop time of 5.88636 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 5.20005 (88.1991) -Neigh time (%) = 0.590692 (10.0188) -Comm time (%) = 0.0308192 (0.52273) -Outpt time (%) = 0.000217915 (0.00369609) -Other time (%) = 0.0740323 (1.25568) +Pair time (%) = 5.1909 (88.1853) +Neigh time (%) = 0.590118 (10.0252) +Comm time (%) = 0.0310338 (0.527215) +Outpt time (%) = 0.000212908 (0.00361697) +Other time (%) = 0.0740924 (1.25871) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19909 ave 19909 max 19909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1207784 Ave neighs/atom = 37.7433 Neighbor list builds = 13 Dangerous builds = 0 diff --git a/bench/log.30Jul13.eam.fixed.linux.4 b/bench/log.28Jan14.eam.fixed.linux.4 similarity index 81% rename from bench/log.30Jul13.eam.fixed.linux.4 rename to bench/log.28Jan14.eam.fixed.linux.4 index 82e20d64f..fd7849c27 100644 --- a/bench/log.30Jul13.eam.fixed.linux.4 +++ b/bench/log.28Jan14.eam.fixed.linux.4 @@ -1,67 +1,67 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # bulk Cu lattice variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units metal atom_style atomic lattice fcc 3.615 Lattice spacing in x,y,z = 3.615 3.615 3.615 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms pair_style eam pair_coeff 1 1 Cu_u3.eam velocity all create 1600.0 376847 loop geom neighbor 1.0 bin neigh_modify every 1 delay 5 check yes fix 1 all nve timestep 0.005 thermo 50 run 100 -Memory usage per processor = 4.92459 Mbytes +Memory usage per processor = 4.92441 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -113280 0 -106662.09 18703.573 50 781.69049 -109873.35 0 -106640.13 52273.088 100 801.832 -109957.3 0 -106640.77 51322.821 -Loop time of 1.62415 on 4 procs for 100 steps with 32000 atoms +Loop time of 1.55795 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 1.39691 (86.0084) -Neigh time (%) = 0.157564 (9.70131) -Comm time (%) = 0.0479782 (2.95404) -Outpt time (%) = 0.000121653 (0.00749025) -Other time (%) = 0.0215805 (1.32873) +Pair time (%) = 1.34981 (86.6403) +Neigh time (%) = 0.153546 (9.85563) +Comm time (%) = 0.0348434 (2.23649) +Outpt time (%) = 9.79304e-05 (0.00628584) +Other time (%) = 0.0196509 (1.26133) Nlocal: 8000 ave 8008 max 7993 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 9130.25 ave 9138 max 9122 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 301946 ave 302392 max 301360 min Histogram: 1 0 0 0 1 0 0 0 1 1 Total # of neighbors = 1207784 Ave neighs/atom = 37.7433 Neighbor list builds = 13 Dangerous builds = 0 diff --git a/bench/log.30Jul13.eam.scaled.linux.4 b/bench/log.28Jan14.eam.scaled.linux.4 similarity index 81% rename from bench/log.30Jul13.eam.scaled.linux.4 rename to bench/log.28Jan14.eam.scaled.linux.4 index a2ae4f92b..7682a91b3 100644 --- a/bench/log.30Jul13.eam.scaled.linux.4 +++ b/bench/log.28Jan14.eam.scaled.linux.4 @@ -1,67 +1,67 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # bulk Cu lattice variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*2 variable yy equal 20*$y variable yy equal 20*2 variable zz equal 20*$z variable zz equal 20*1 units metal atom_style atomic lattice fcc 3.615 Lattice spacing in x,y,z = 3.615 3.615 3.615 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 40 0 ${yy} 0 ${zz} region box block 0 40 0 40 0 ${zz} region box block 0 40 0 40 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (144.6 144.6 72.3) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 128000 atoms pair_style eam pair_coeff 1 1 Cu_u3.eam velocity all create 1600.0 376847 loop geom neighbor 1.0 bin neigh_modify every 1 delay 5 check yes fix 1 all nve timestep 0.005 thermo 50 run 100 -Memory usage per processor = 15.2893 Mbytes +Memory usage per processor = 15.2891 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -453120 0 -426647.73 18704.012 50 779.50001 -439457.02 0 -426560.06 52355.276 100 797.97828 -439764.76 0 -426562.07 51474.74 -Loop time of 6.63538 on 4 procs for 100 steps with 128000 atoms +Loop time of 6.49873 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 5.70315 (85.9507) -Neigh time (%) = 0.671065 (10.1134) -Comm time (%) = 0.154897 (2.33441) -Outpt time (%) = 0.0003497 (0.00527024) -Other time (%) = 0.105914 (1.5962) +Pair time (%) = 5.61886 (86.4609) +Neigh time (%) = 0.667741 (10.2749) +Comm time (%) = 0.110698 (1.70337) +Outpt time (%) = 0.000267088 (0.00410985) +Other time (%) = 0.101163 (1.55666) Nlocal: 32000 ave 32092 max 31914 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 19910 ave 19997 max 19818 min Histogram: 1 0 0 0 1 0 1 0 0 1 Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 4829126 Ave neighs/atom = 37.7275 Neighbor list builds = 14 Dangerous builds = 0 diff --git a/bench/log.30Jul13.lj.fixed.linux.1 b/bench/log.28Jan14.lj.fixed.linux.1 similarity index 80% rename from bench/log.30Jul13.lj.fixed.linux.1 rename to bench/log.28Jan14.lj.fixed.linux.1 index 8713a1228..b5b579efa 100644 --- a/bench/log.30Jul13.lj.fixed.linux.1 +++ b/bench/log.28Jan14.lj.fixed.linux.1 @@ -1,64 +1,64 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve run 100 -Memory usage per processor = 13.2267 Mbytes +Memory usage per processor = 13.2266 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 -Loop time of 2.24794 on 1 procs for 100 steps with 32000 atoms +Loop time of 2.25121 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 1.92284 (85.5376) -Neigh time (%) = 0.241012 (10.7215) -Comm time (%) = 0.0244191 (1.08629) -Outpt time (%) = 0.000105858 (0.0047091) -Other time (%) = 0.0595703 (2.64999) +Pair time (%) = 1.92625 (85.5648) +Neigh time (%) = 0.241071 (10.7085) +Comm time (%) = 0.0242682 (1.078) +Outpt time (%) = 0.000102997 (0.00457517) +Other time (%) = 0.0595243 (2.6441) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19657 ave 19657 max 19657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1202833 Ave neighs/atom = 37.5885 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.30Jul13.lj.fixed.linux.4 b/bench/log.28Jan14.lj.fixed.linux.4 similarity index 80% rename from bench/log.30Jul13.lj.fixed.linux.4 rename to bench/log.28Jan14.lj.fixed.linux.4 index a93377b36..8fa8a7e85 100644 --- a/bench/log.30Jul13.lj.fixed.linux.4 +++ b/bench/log.28Jan14.lj.fixed.linux.4 @@ -1,64 +1,64 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve run 100 -Memory usage per processor = 4.31295 Mbytes +Memory usage per processor = 4.31282 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 -Loop time of 0.621459 on 4 procs for 100 steps with 32000 atoms +Loop time of 0.632266 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 0.50556 (81.3506) -Neigh time (%) = 0.0630878 (10.1516) -Comm time (%) = 0.036548 (5.88099) -Outpt time (%) = 5.19753e-05 (0.00836343) -Other time (%) = 0.0162107 (2.60849) +Pair time (%) = 0.509912 (80.6484) +Neigh time (%) = 0.0636757 (10.071) +Comm time (%) = 0.0426416 (6.74425) +Outpt time (%) = 5.04255e-05 (0.00797537) +Other time (%) = 0.015986 (2.52837) Nlocal: 8000 ave 8037 max 7964 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 9007.5 ave 9050 max 8968 min Histogram: 1 1 0 0 0 0 0 1 0 1 Neighs: 300708 ave 305113 max 297203 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 1202833 Ave neighs/atom = 37.5885 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.30Jul13.lj.scaled.linux.4 b/bench/log.28Jan14.lj.scaled.linux.4 similarity index 80% rename from bench/log.30Jul13.lj.scaled.linux.4 rename to bench/log.28Jan14.lj.scaled.linux.4 index 580b9e51d..e6dfcde8e 100644 --- a/bench/log.30Jul13.lj.scaled.linux.4 +++ b/bench/log.28Jan14.lj.scaled.linux.4 @@ -1,64 +1,64 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*2 variable yy equal 20*$y variable yy equal 20*2 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 40 0 ${yy} 0 ${zz} region box block 0 40 0 40 0 ${zz} region box block 0 40 0 40 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 128000 atoms mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve run 100 -Memory usage per processor = 13.1496 Mbytes +Memory usage per processor = 13.1495 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6133849 -5.0196788 100 0.75841891 -5.759957 0 -4.6223375 0.20008866 -Loop time of 2.51513 on 4 procs for 100 steps with 128000 atoms +Loop time of 2.53652 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 2.06373 (82.0527) -Neigh time (%) = 0.246449 (9.79865) -Comm time (%) = 0.122232 (4.85986) -Outpt time (%) = 0.000143051 (0.00568762) -Other time (%) = 0.0825751 (3.28313) +Pair time (%) = 2.08358 (82.1432) +Neigh time (%) = 0.246569 (9.72079) +Comm time (%) = 0.121166 (4.77688) +Outpt time (%) = 0.000156581 (0.00617309) +Other time (%) = 0.0850482 (3.35295) Nlocal: 32000 ave 32060 max 31939 min Histogram: 1 0 1 0 0 0 0 1 0 1 Nghost: 19630.8 ave 19681 max 19562 min Histogram: 1 0 0 0 1 0 0 0 1 1 Neighs: 1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min Histogram: 1 0 0 0 0 0 0 2 0 1 Total # of neighbors = 4807797 Ave neighs/atom = 37.5609 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.30Jul13.rhodo.fixed.linux.1 b/bench/log.28Jan14.rhodo.fixed.linux.1 similarity index 78% rename from bench/log.30Jul13.rhodo.fixed.linux.1 rename to bench/log.28Jan14.rhodo.fixed.linux.1 index 0030e0730..8c96989eb 100644 --- a/bench/log.30Jul13.rhodo.fixed.linux.1 +++ b/bench/log.28Jan14.rhodo.fixed.linux.1 @@ -1,99 +1,109 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # Rhodopsin model units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo - 4 = max bonds/atom - 8 = max angles/atom - 18 = max dihedrals/atom - 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 1 by 1 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 8 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... 27723 bonds + reading angles ... 40467 angles + reading dihedrals ... 56829 dihedrals + reading impropers ... 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # of frozen angles fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248835 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0355478 estimated relative force accuracy = 0.000107051 using double precision FFTs 3d grid and FFT values/proc = 41070 25600 Memory usage per processor = 139.238 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 17.7652 (sec) ---------------- +---------------- Step 50 ----- CPU = 17.7678 (sec) ---------------- TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230 PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975 E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754 E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701 Volume = 308031.5639 ----------------- Step 100 ----- CPU = 36.1527 (sec) ---------------- +---------------- Step 100 ----- CPU = 36.1938 (sec) ---------------- TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920 PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408 E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783 E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960 Volume = 308133.9888 -Loop time of 36.1528 on 1 procs for 100 steps with 32000 atoms +Loop time of 36.1938 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 26.1216 (72.2533) -Bond time (%) = 1.27574 (3.52875) -Kspce time (%) = 3.25689 (9.00869) -Neigh time (%) = 4.3025 (11.9009) -Comm time (%) = 0.0688474 (0.190435) -Outpt time (%) = 0.000230074 (0.000636394) -Other time (%) = 1.127 (3.11732) +Pair time (%) = 25.9243 (71.6264) +Bond time (%) = 1.26808 (3.50358) +Kspce time (%) = 3.25738 (8.99982) +Neigh time (%) = 4.54843 (12.5669) +Comm time (%) = 0.0694413 (0.19186) +Outpt time (%) = 0.000235081 (0.000649505) +Other time (%) = 1.12593 (3.11082) -FFT time (% of Kspce) = 0.277417 (8.51784) -FFT Gflps 3d (1d only) = 1.87335 3.23863 +FFT time (% of Kspce) = 0.27522 (8.44911) +FFT Gflps 3d (1d only) = 1.8883 3.24026 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 47958 ave 47958 max 47958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.30Jul13.rhodo.fixed.linux.4 b/bench/log.28Jan14.rhodo.fixed.linux.4 similarity index 78% rename from bench/log.30Jul13.rhodo.fixed.linux.4 rename to bench/log.28Jan14.rhodo.fixed.linux.4 index 898d61ddf..186a3ad8b 100644 --- a/bench/log.30Jul13.rhodo.fixed.linux.4 +++ b/bench/log.28Jan14.rhodo.fixed.linux.4 @@ -1,99 +1,109 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # Rhodopsin model units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo - 4 = max bonds/atom - 8 = max angles/atom - 18 = max dihedrals/atom - 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 8 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... 27723 bonds + reading angles ... 40467 angles + reading dihedrals ... 56829 dihedrals + reading impropers ... 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # of frozen angles fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248835 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0355478 estimated relative force accuracy = 0.000107051 using double precision FFTs 3d grid and FFT values/proc = 13230 6400 Memory usage per processor = 54.595 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 4.6553 (sec) ---------------- +---------------- Step 50 ----- CPU = 4.8445 (sec) ---------------- TotEng = -25330.0829 KinEng = 21501.0029 Temp = 299.8230 PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975 E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754 E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701 Volume = 308031.5639 ----------------- Step 100 ----- CPU = 9.5123 (sec) ---------------- +---------------- Step 100 ----- CPU = 9.9262 (sec) ---------------- TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920 PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408 E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783 E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960 Volume = 308133.9888 -Loop time of 9.51235 on 4 procs for 100 steps with 32000 atoms +Loop time of 9.92624 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 6.58797 (69.2571) -Bond time (%) = 0.319462 (3.35839) -Kspce time (%) = 1.08263 (11.3813) -Neigh time (%) = 1.08542 (11.4107) -Comm time (%) = 0.0859144 (0.903188) -Outpt time (%) = 0.000161052 (0.00169308) -Other time (%) = 0.350788 (3.68772) +Pair time (%) = 6.65637 (67.0583) +Bond time (%) = 0.320161 (3.2254) +Kspce time (%) = 1.26452 (12.7392) +Neigh time (%) = 1.21993 (12.2899) +Comm time (%) = 0.0982867 (0.99017) +Outpt time (%) = 0.000156939 (0.00158105) +Other time (%) = 0.366824 (3.69549) -FFT time (% of Kspce) = 0.0982845 (9.07835) -FFT Gflps 3d (1d only) = 5.28769 12.8216 +FFT time (% of Kspce) = 0.0959004 (7.58393) +FFT Gflps 3d (1d only) = 5.41914 12.8168 Nlocal: 8000 ave 8143 max 7933 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 22733.5 ave 22769 max 22693 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.30Jul13.rhodo.scaled.linux.4 b/bench/log.28Jan14.rhodo.scaled.linux.4 similarity index 81% rename from bench/log.30Jul13.rhodo.scaled.linux.4 rename to bench/log.28Jan14.rhodo.scaled.linux.4 index 3abfe12af..c2d667303 100644 --- a/bench/log.30Jul13.rhodo.scaled.linux.4 +++ b/bench/log.28Jan14.rhodo.scaled.linux.4 @@ -1,120 +1,130 @@ -LAMMPS (14 Aug 2013) +LAMMPS (30 Jan 2014) # Rhodopsin model variable x index 1 variable y index 1 variable z index 1 units real neigh_modify delay 5 every 1 atom_style full atom_modify map hash bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo - 4 = max bonds/atom - 8 = max angles/atom - 18 = max dihedrals/atom - 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 MPI processor grid + reading atoms ... 32000 atoms + reading velocities ... 32000 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 8 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... 27723 bonds + reading angles ... 40467 angles + reading dihedrals ... 56829 dihedrals + reading impropers ... 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 1 orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615) 2 by 2 by 1 MPI processor grid 128000 atoms 110892 bonds 161868 angles 227316 dihedrals 4136 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 6468 = # of size 2 clusters 14532 = # of size 3 clusters 2988 = # of size 4 clusters 16932 = # of frozen angles fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248593 grid = 48 60 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0359793 estimated relative force accuracy = 0.00010835 using double precision FFTs 3d grid and FFT values/proc = 41615 25920 Memory usage per processor = 146.358 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304 PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968 E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537 E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092 Volume = 1231980.1340 ----------------- Step 50 ----- CPU = 19.2151 (sec) ---------------- +---------------- Step 50 ----- CPU = 19.1272 (sec) ---------------- TotEng = -101320.2676 KinEng = 86003.4837 Temp = 299.8118 PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922 E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457 E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161 Volume = 1232126.1855 ----------------- Step 100 ----- CPU = 39.0436 (sec) ---------------- +---------------- Step 100 ----- CPU = 39.2968 (sec) ---------------- TotEng = -101158.1853 KinEng = 86355.6148 Temp = 301.0393 PotEng = -187513.8001 E_bond = 10272.0693 E_angle = 43128.6453 E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186 E_coul = 825583.7120 E_long = -1080572.5667 Press = 15.2151 Volume = 1232535.8423 -Loop time of 39.0437 on 4 procs for 100 steps with 128000 atoms +Loop time of 39.2969 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 27.1533 (69.546) -Bond time (%) = 1.31501 (3.36805) -Kspce time (%) = 4.35908 (11.1646) -Neigh time (%) = 4.42268 (11.3275) -Comm time (%) = 0.229435 (0.587637) -Outpt time (%) = 0.000313759 (0.00080361) -Other time (%) = 1.56382 (4.00532) +Pair time (%) = 27.1236 (69.0224) +Bond time (%) = 1.30692 (3.32576) +Kspce time (%) = 4.30137 (10.9458) +Neigh time (%) = 4.78495 (12.1764) +Comm time (%) = 0.217593 (0.553716) +Outpt time (%) = 0.000282824 (0.000719711) +Other time (%) = 1.56213 (3.9752) -FFT time (% of Kspce) = 0.466478 (10.7013) -FFT Gflps 3d (1d only) = 5.13382 11.4048 +FFT time (% of Kspce) = 0.505049 (11.7416) +FFT Gflps 3d (1d only) = 4.74174 11.1028 Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 47957 ave 47957 max 47957 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 48112472 Ave neighs/atom = 375.879 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0