diff --git a/bench/log.1Feb14.chain.fixed.linux.1 b/bench/log.1Feb14.chain.fixed.linux.1 new file mode 100644 index 000000000..9d35f3fb8 --- /dev/null +++ b/bench/log.1Feb14.chain.fixed.linux.1 @@ -0,0 +1,63 @@ +LAMMPS (1 Feb 2014) +# FENE beadspring benchmark + +units lj +atom_style bond +special_bonds fene + +read_data data.chain + 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 1.00129 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.201344 (20.1083) +Bond time (%) = 0.0870376 (8.69251) +Neigh time (%) = 0.45714 (45.6549) +Comm time (%) = 0.0338521 (3.38083) +Outpt time (%) = 0.000102043 (0.0101911) +Other time (%) = 0.221819 (22.1532) + +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.1Feb14.chain.fixed.linux.4 b/bench/log.1Feb14.chain.fixed.linux.4 new file mode 100644 index 000000000..c1622f405 --- /dev/null +++ b/bench/log.1Feb14.chain.fixed.linux.4 @@ -0,0 +1,63 @@ +LAMMPS (1 Feb 2014) +# FENE beadspring benchmark + +units lj +atom_style bond +special_bonds fene + +read_data data.chain + 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 0.274804 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.0507675 (18.4741) +Bond time (%) = 0.0225385 (8.20169) +Neigh time (%) = 0.121537 (44.2269) +Comm time (%) = 0.0207262 (7.54219) +Outpt time (%) = 8.74996e-05 (0.0318408) +Other time (%) = 0.0591468 (21.5233) + +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.1Feb14.chain.scaled.linux.4 b/bench/log.1Feb14.chain.scaled.linux.4 new file mode 100644 index 000000000..0b2062bf4 --- /dev/null +++ b/bench/log.1Feb14.chain.scaled.linux.4 @@ -0,0 +1,79 @@ +LAMMPS (1 Feb 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 + 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 1.16627 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 0.224354 (19.2369) +Bond time (%) = 0.0961447 (8.24378) +Neigh time (%) = 0.510646 (43.7846) +Comm time (%) = 0.0876382 (7.5144) +Outpt time (%) = 0.000156462 (0.0134156) +Other time (%) = 0.24733 (21.207) + +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.1Feb14.chute.fixed.linux.1 b/bench/log.1Feb14.chute.fixed.linux.1 new file mode 100644 index 000000000..6fe0cbe06 --- /dev/null +++ b/bench/log.1Feb14.chute.fixed.linux.1 @@ -0,0 +1,65 @@ +LAMMPS (1 Feb 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 = 21.4184 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 0.540977 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.330571 (61.1064) +Neigh time (%) = 0.0416589 (7.70067) +Comm time (%) = 0.018239 (3.3715) +Outpt time (%) = 0.000189066 (0.034949) +Other time (%) = 0.150319 (27.7865) + +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.1Feb14.chute.fixed.linux.4 b/bench/log.1Feb14.chute.fixed.linux.4 new file mode 100644 index 000000000..0acf14ded --- /dev/null +++ b/bench/log.1Feb14.chute.fixed.linux.4 @@ -0,0 +1,65 @@ +LAMMPS (1 Feb 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 = 10.7034 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 0.133553 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.0669281 (50.1135) +Neigh time (%) = 0.01061 (7.9444) +Comm time (%) = 0.0142241 (10.6505) +Outpt time (%) = 9.28044e-05 (0.0694888) +Other time (%) = 0.041698 (31.2221) + +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.1Feb14.chute.scaled.linux.4 b/bench/log.1Feb14.chute.scaled.linux.4 new file mode 100644 index 000000000..804f04128 --- /dev/null +++ b/bench/log.1Feb14.chute.scaled.linux.4 @@ -0,0 +1,75 @@ +LAMMPS (1 Feb 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 $y 1 +replicate 2 2 1 + orthogonal box = (0 0 0) to (80 40 37.2923) + 2 by 2 by 1 MPI processor grid + 128000 atoms + +pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 +pair_coeff * * + +neighbor 0.1 bin +neigh_modify every 1 delay 0 + +timestep 0.0001 + +group bottom type 2 +3648 atoms in group bottom +group active subtract all bottom +124352 atoms in group active +neigh_modify exclude group bottom bottom + +fix 1 all gravity 1.0 chute 26.0 +fix 2 bottom freeze +fix 3 active nve/sphere + +compute 1 all erotate/sphere +thermo_style custom step atoms ke c_1 vol +thermo_modify norm no +thermo 100 + +run 100 +Memory usage per processor = 22.3334 Mbytes +Step Atoms KinEng 1 Volume + 0 128000 3136556.5 6404.5051 119335.13 + 100 128000 3137168.3 6284.3873 119338.83 +Loop time of 0.862817 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 0.518524 (60.0966) +Neigh time (%) = 0.0441293 (5.11455) +Comm time (%) = 0.057479 (6.66178) +Outpt time (%) = 0.000286222 (0.0331729) +Other time (%) = 0.242399 (28.0939) + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5463 ave 5463 max 5463 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 115133 ave 115133 max 115133 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 460532 +Ave neighs/atom = 3.59791 +Neighbor list builds = 2 +Dangerous builds = 0 diff --git a/bench/log.1Feb14.eam.fixed.linux.1 b/bench/log.1Feb14.eam.fixed.linux.1 new file mode 100644 index 000000000..98446148b --- /dev/null +++ b/bench/log.1Feb14.eam.fixed.linux.1 @@ -0,0 +1,67 @@ +LAMMPS (1 Feb 2014) +# bulk Cu lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + +pair_style eam +pair_coeff 1 1 Cu_u3.eam + +velocity all create 1600.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +timestep 0.005 +thermo 50 + +run 100 +Memory usage per processor = 15.3727 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -113280 0 -106662.09 18703.573 + 50 781.69049 -109873.35 0 -106640.13 52273.088 + 100 801.832 -109957.3 0 -106640.77 51322.821 +Loop time of 5.93175 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 5.20741 (87.7887) +Neigh time (%) = 0.618579 (10.4283) +Comm time (%) = 0.0310862 (0.524064) +Outpt time (%) = 0.000214815 (0.00362144) +Other time (%) = 0.0744634 (1.25533) + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19909 ave 19909 max 19909 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1207784 +Ave neighs/atom = 37.7433 +Neighbor list builds = 13 +Dangerous builds = 0 diff --git a/bench/log.1Feb14.eam.fixed.linux.4 b/bench/log.1Feb14.eam.fixed.linux.4 new file mode 100644 index 000000000..02ea03515 --- /dev/null +++ b/bench/log.1Feb14.eam.fixed.linux.4 @@ -0,0 +1,67 @@ +LAMMPS (1 Feb 2014) +# bulk Cu lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + +pair_style eam +pair_coeff 1 1 Cu_u3.eam + +velocity all create 1600.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +timestep 0.005 +thermo 50 + +run 100 +Memory usage per processor = 4.92441 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -113280 0 -106662.09 18703.573 + 50 781.69049 -109873.35 0 -106640.13 52273.088 + 100 801.832 -109957.3 0 -106640.77 51322.821 +Loop time of 1.57335 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 1.35199 (85.9304) +Neigh time (%) = 0.160176 (10.1806) +Comm time (%) = 0.0413526 (2.62832) +Outpt time (%) = 0.000119448 (0.00759193) +Other time (%) = 0.0197157 (1.2531) + +Nlocal: 8000 ave 8008 max 7993 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 9130.25 ave 9138 max 9122 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 301946 ave 302392 max 301360 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 1207784 +Ave neighs/atom = 37.7433 +Neighbor list builds = 13 +Dangerous builds = 0 diff --git a/bench/log.1Feb14.eam.scaled.linux.4 b/bench/log.1Feb14.eam.scaled.linux.4 new file mode 100644 index 000000000..350c397a6 --- /dev/null +++ b/bench/log.1Feb14.eam.scaled.linux.4 @@ -0,0 +1,67 @@ +LAMMPS (1 Feb 2014) +# bulk Cu lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 40 0 40 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (144.6 144.6 72.3) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 128000 atoms + +pair_style eam +pair_coeff 1 1 Cu_u3.eam + +velocity all create 1600.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +timestep 0.005 +thermo 50 + +run 100 +Memory usage per processor = 15.2891 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -453120 0 -426647.73 18704.012 + 50 779.50001 -439457.02 0 -426560.06 52355.276 + 100 797.97828 -439764.76 0 -426562.07 51474.74 +Loop time of 6.55459 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 5.63064 (85.9037) +Neigh time (%) = 0.698691 (10.6596) +Comm time (%) = 0.123277 (1.88077) +Outpt time (%) = 0.000314116 (0.00479231) +Other time (%) = 0.101672 (1.55115) + +Nlocal: 32000 ave 32092 max 31914 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 19910 ave 19997 max 19818 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 4829126 +Ave neighs/atom = 37.7275 +Neighbor list builds = 14 +Dangerous builds = 0 diff --git a/bench/log.1Feb14.lj.fixed.linux.1 b/bench/log.1Feb14.lj.fixed.linux.1 new file mode 100644 index 000000000..d0e616e23 --- /dev/null +++ b/bench/log.1Feb14.lj.fixed.linux.1 @@ -0,0 +1,64 @@ +LAMMPS (1 Feb 2014) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +run 100 +Memory usage per processor = 13.2266 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 + 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 +Loop time of 2.26599 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 1.92891 (85.1244) +Neigh time (%) = 0.252641 (11.1493) +Comm time (%) = 0.0243704 (1.07549) +Outpt time (%) = 0.000110865 (0.00489256) +Other time (%) = 0.059957 (2.64596) + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19657 ave 19657 max 19657 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1202833 +Ave neighs/atom = 37.5885 +Neighbor list builds = 5 +Dangerous builds = 0 diff --git a/bench/log.1Feb14.lj.fixed.linux.4 b/bench/log.1Feb14.lj.fixed.linux.4 new file mode 100644 index 000000000..dfcb7e924 --- /dev/null +++ b/bench/log.1Feb14.lj.fixed.linux.4 @@ -0,0 +1,64 @@ +LAMMPS (1 Feb 2014) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +run 100 +Memory usage per processor = 4.31282 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 + 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 +Loop time of 0.628341 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.505093 (80.3851) +Neigh time (%) = 0.0659957 (10.5032) +Comm time (%) = 0.0406293 (6.46611) +Outpt time (%) = 8.43406e-05 (0.0134227) +Other time (%) = 0.016539 (2.63216) + +Nlocal: 8000 ave 8037 max 7964 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 9007.5 ave 9050 max 8968 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 300708 ave 305113 max 297203 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 1202833 +Ave neighs/atom = 37.5885 +Neighbor list builds = 5 +Dangerous builds = 0 diff --git a/bench/log.1Feb14.lj.scaled.linux.4 b/bench/log.1Feb14.lj.scaled.linux.4 new file mode 100644 index 000000000..6fc614af2 --- /dev/null +++ b/bench/log.1Feb14.lj.scaled.linux.4 @@ -0,0 +1,64 @@ +LAMMPS (1 Feb 2014) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 = 13.1495 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 2.54147 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 2.08305 (81.9623) +Neigh time (%) = 0.258072 (10.1545) +Comm time (%) = 0.116279 (4.57528) +Outpt time (%) = 0.000139415 (0.00548562) +Other time (%) = 0.0839326 (3.30252) + +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.1Feb14.rhodo.fixed.linux.1 b/bench/log.1Feb14.rhodo.fixed.linux.1 new file mode 100644 index 000000000..08af73ac1 --- /dev/null +++ b/bench/log.1Feb14.rhodo.fixed.linux.1 @@ -0,0 +1,109 @@ +LAMMPS (1 Feb 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 + 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 = 17.8100 (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 = 36.2348 (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 36.2348 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 26.0418 (71.8696) +Bond time (%) = 1.26644 (3.4951) +Kspce time (%) = 3.24933 (8.96742) +Neigh time (%) = 4.47968 (12.3629) +Comm time (%) = 0.0700378 (0.193289) +Outpt time (%) = 0.000230074 (0.000634953) +Other time (%) = 1.12729 (3.11108) + +FFT time (% of Kspce) = 0.276809 (8.51896) +FFT Gflps 3d (1d only) = 1.87746 3.23903 + +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.1Feb14.rhodo.fixed.linux.4 b/bench/log.1Feb14.rhodo.fixed.linux.4 new file mode 100644 index 000000000..1cb4138e4 --- /dev/null +++ b/bench/log.1Feb14.rhodo.fixed.linux.4 @@ -0,0 +1,109 @@ +LAMMPS (1 Feb 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 + 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 = 4.7061 (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 = 9.5889 (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 9.58898 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 6.62576 (69.0976) +Bond time (%) = 0.317414 (3.31019) +Kspce time (%) = 1.04771 (10.9262) +Neigh time (%) = 1.15891 (12.0859) +Comm time (%) = 0.0844751 (0.88096) +Outpt time (%) = 0.00015074 (0.00157201) +Other time (%) = 0.354558 (3.69756) + +FFT time (% of Kspce) = 0.0967343 (9.23289) +FFT Gflps 3d (1d only) = 5.37243 12.7459 + +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.1Feb14.rhodo.scaled.linux.4 b/bench/log.1Feb14.rhodo.scaled.linux.4 new file mode 100644 index 000000000..d44aa9ced --- /dev/null +++ b/bench/log.1Feb14.rhodo.scaled.linux.4 @@ -0,0 +1,130 @@ +LAMMPS (1 Feb 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 + 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 = 18.9852 (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 = 38.9161 (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 38.9162 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 27.1908 (69.8701) +Bond time (%) = 1.30758 (3.35999) +Kspce time (%) = 3.99359 (10.262) +Neigh time (%) = 4.65272 (11.9557) +Comm time (%) = 0.216829 (0.557168) +Outpt time (%) = 0.000280738 (0.000721391) +Other time (%) = 1.55441 (3.99426) + +FFT time (% of Kspce) = 0.448314 (11.2258) +FFT Gflps 3d (1d only) = 5.34183 11.5795 + +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