diff --git a/bench/log.9Jan12.chain.fixed.linux.1 b/bench/log.9Jan12.chain.fixed.linux.1 new file mode 100644 index 0000000000..a229d70148 --- /dev/null +++ b/bench/log.9Jan12.chain.fixed.linux.1 @@ -0,0 +1,59 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + 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 = 11.3536 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 1.00598 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.200669 (19.9477) +Bond time (%) = 0.116349 (11.5657) +Neigh time (%) = 0.434148 (43.1567) +Comm time (%) = 0.0310009 (3.08166) +Outpt time (%) = 9.799e-05 (0.00974076) +Other time (%) = 0.223714 (22.2385) + +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.9Jan12.chain.fixed.linux.4 b/bench/log.9Jan12.chain.fixed.linux.4 new file mode 100644 index 0000000000..858dc4477a --- /dev/null +++ b/bench/log.9Jan12.chain.fixed.linux.4 @@ -0,0 +1,59 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + 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 = 4.80505 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 0.277092 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.0511394 (18.4557) +Bond time (%) = 0.030314 (10.94) +Neigh time (%) = 0.112937 (40.7578) +Comm time (%) = 0.0222602 (8.03351) +Outpt time (%) = 6.1214e-05 (0.0220915) +Other time (%) = 0.0603806 (21.7908) + +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.9Jan12.chain.scaled.linux.4 b/bench/log.9Jan12.chain.scaled.linux.4 new file mode 100644 index 0000000000..a03171c3c0 --- /dev/null +++ b/bench/log.9Jan12.chain.scaled.linux.4 @@ -0,0 +1,75 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + 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 = 13.3552 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 1.16957 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 0.227149 (19.4215) +Bond time (%) = 0.123806 (10.5856) +Neigh time (%) = 0.472906 (40.4341) +Comm time (%) = 0.0951706 (8.13721) +Outpt time (%) = 0.000224173 (0.0191671) +Other time (%) = 0.250317 (21.4025) + +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.9Jan12.chute.fixed.linux.1 b/bench/log.9Jan12.chute.fixed.linux.1 new file mode 100644 index 0000000000..683915ee95 --- /dev/null +++ b/bench/log.9Jan12.chute.fixed.linux.1 @@ -0,0 +1,63 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 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 = 34.9301 Mbytes +Step Atoms KinEng 1 Volume + 0 32000 784139.13 1601.1263 29830.88 + 100 32000 784289.99 1571.0137 29831.804 +Loop time of 0.54713 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.328969 (60.1262) +Neigh time (%) = 0.04423 (8.084) +Comm time (%) = 0.0182245 (3.33092) +Outpt time (%) = 0.00019002 (0.0347302) +Other time (%) = 0.155517 (28.4242) + +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.9Jan12.chute.fixed.linux.4 b/bench/log.9Jan12.chute.fixed.linux.4 new file mode 100644 index 0000000000..06869eedd8 --- /dev/null +++ b/bench/log.9Jan12.chute.fixed.linux.4 @@ -0,0 +1,63 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 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 = 15.2765 Mbytes +Step Atoms KinEng 1 Volume + 0 32000 784139.13 1601.1263 29830.88 + 100 32000 784289.99 1571.0137 29831.804 +Loop time of 0.146905 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.0729731 (49.6735) +Neigh time (%) = 0.0111947 (7.62035) +Comm time (%) = 0.0153095 (10.4213) +Outpt time (%) = 0.000119746 (0.0815122) +Other time (%) = 0.0473083 (32.2033) + +Nlocal: 8000 ave 8010 max 7990 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2439 ave 2452 max 2426 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 29503.5 ave 30500 max 28507 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 118014 +Ave neighs/atom = 3.68794 +Neighbor list builds = 2 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.chute.scaled.linux.4 b/bench/log.9Jan12.chute.scaled.linux.4 new file mode 100644 index 0000000000..c47cef6fee --- /dev/null +++ b/bench/log.9Jan12.chute.scaled.linux.4 @@ -0,0 +1,73 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + +replicate $x $y 1 +replicate 2 $y 1 +replicate 2 2 1 + orthogonal box = (0 0 0) to (80 40 37.2887) + 4 by 1 by 1 MPI processor grid + 128000 atoms + +pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 +pair_coeff * * + +neighbor 0.1 bin +neigh_modify every 1 delay 0 + +timestep 0.0001 + +group bottom type 2 +3648 atoms in group bottom +group active subtract all bottom +124352 atoms in group active +neigh_modify exclude group bottom bottom + +fix 1 all gravity 1.0 chute 26.0 +fix 2 bottom freeze +fix 3 active nve/sphere + +compute 1 all erotate/sphere +thermo_style custom step atoms ke c_1 vol +thermo_modify norm no +thermo 100 + +run 100 +Memory usage per processor = 37.0464 Mbytes +Step Atoms KinEng 1 Volume + 0 128000 3136556.5 6404.5051 119323.52 + 100 128000 3137160 6284.0549 119327.22 +Loop time of 0.893496 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 0.524706 (58.7251) +Neigh time (%) = 0.0462004 (5.17075) +Comm time (%) = 0.0590464 (6.60847) +Outpt time (%) = 0.00043273 (0.0484311) +Other time (%) = 0.26311 (29.4473) + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5456 ave 5456 max 5456 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 115135 ave 115135 max 115135 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 460540 +Ave neighs/atom = 3.59797 +Neighbor list builds = 2 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.eam.fixed.linux.1 b/bench/log.9Jan12.eam.fixed.linux.1 new file mode 100644 index 0000000000..0a28a05c75 --- /dev/null +++ b/bench/log.9Jan12.eam.fixed.linux.1 @@ -0,0 +1,67 @@ +LAMMPS (10 Jan 2012) +# bulk Cu lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + +pair_style eam +pair_coeff 1 1 Cu_u3.eam + +velocity all create 1600.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +timestep 0.005 +thermo 50 + +run 100 +Memory usage per processor = 15.3728 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -113280 0 -106662.09 18703.573 + 50 781.69049 -109873.35 0 -106640.13 52273.088 + 100 801.832 -109957.3 0 -106640.77 51322.821 +Loop time of 5.8924 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 5.20714 (88.3704) +Neigh time (%) = 0.579568 (9.83586) +Comm time (%) = 0.0308812 (0.524085) +Outpt time (%) = 0.000219822 (0.0037306) +Other time (%) = 0.0745952 (1.26596) + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19909 ave 19909 max 19909 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1207784 +Ave neighs/atom = 37.7433 +Neighbor list builds = 13 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.eam.fixed.linux.4 b/bench/log.9Jan12.eam.fixed.linux.4 new file mode 100644 index 0000000000..6c3999a470 --- /dev/null +++ b/bench/log.9Jan12.eam.fixed.linux.4 @@ -0,0 +1,67 @@ +LAMMPS (10 Jan 2012) +# bulk Cu lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + +pair_style eam +pair_coeff 1 1 Cu_u3.eam + +velocity all create 1600.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +timestep 0.005 +thermo 50 + +run 100 +Memory usage per processor = 4.92442 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -113280 0 -106662.09 18703.573 + 50 781.69049 -109873.35 0 -106640.13 52273.088 + 100 801.832 -109957.3 0 -106640.77 51322.821 +Loop time of 1.58434 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 1.37178 (86.5835) +Neigh time (%) = 0.151559 (9.56606) +Comm time (%) = 0.0399128 (2.5192) +Outpt time (%) = 0.000169277 (0.0106844) +Other time (%) = 0.0209216 (1.32052) + +Nlocal: 8000 ave 8008 max 7993 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 9130.25 ave 9138 max 9122 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 301946 ave 302392 max 301360 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 1207784 +Ave neighs/atom = 37.7433 +Neighbor list builds = 13 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.eam.scaled.linux.4 b/bench/log.9Jan12.eam.scaled.linux.4 new file mode 100644 index 0000000000..ecaf1bd709 --- /dev/null +++ b/bench/log.9Jan12.eam.scaled.linux.4 @@ -0,0 +1,67 @@ +LAMMPS (10 Jan 2012) +# bulk Cu lattice + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 40 0 40 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (144.6 144.6 72.3) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 128000 atoms + +pair_style eam +pair_coeff 1 1 Cu_u3.eam + +velocity all create 1600.0 376847 loop geom + +neighbor 1.0 bin +neigh_modify every 1 delay 5 check yes + +fix 1 all nve + +timestep 0.005 +thermo 50 + +run 100 +Memory usage per processor = 15.2892 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -453120 0 -426647.73 18704.012 + 50 779.50001 -439457.02 0 -426560.06 52355.276 + 100 797.97828 -439764.76 0 -426562.07 51474.74 +Loop time of 6.64398 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 5.7169 (86.0464) +Neigh time (%) = 0.659102 (9.92029) +Comm time (%) = 0.164221 (2.47173) +Outpt time (%) = 0.000294626 (0.00443448) +Other time (%) = 0.103457 (1.55716) + +Nlocal: 32000 ave 32092 max 31914 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 19910 ave 19997 max 19818 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 4829126 +Ave neighs/atom = 37.7275 +Neighbor list builds = 14 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.lj.fixed.linux.1 b/bench/log.9Jan12.lj.fixed.linux.1 new file mode 100644 index 0000000000..8e69e57aeb --- /dev/null +++ b/bench/log.9Jan12.lj.fixed.linux.1 @@ -0,0 +1,64 @@ +LAMMPS (10 Jan 2012) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +run 100 +Memory usage per processor = 13.2267 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 + 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 +Loop time of 2.24442 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 1.92371 (85.7108) +Neigh time (%) = 0.23672 (10.547) +Comm time (%) = 0.0241742 (1.07708) +Outpt time (%) = 0.000104189 (0.00464212) +Other time (%) = 0.059711 (2.66042) + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19657 ave 19657 max 19657 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1202833 +Ave neighs/atom = 37.5885 +Neighbor list builds = 5 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.lj.fixed.linux.4 b/bench/log.9Jan12.lj.fixed.linux.4 new file mode 100644 index 0000000000..be2afe74a1 --- /dev/null +++ b/bench/log.9Jan12.lj.fixed.linux.4 @@ -0,0 +1,64 @@ +LAMMPS (10 Jan 2012) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 20 check no + +fix 1 all nve + +run 100 +Memory usage per processor = 4.31284 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 + 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 +Loop time of 0.62139 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.502622 (80.8866) +Neigh time (%) = 0.0616071 (9.9144) +Comm time (%) = 0.0411073 (6.61538) +Outpt time (%) = 5.79953e-05 (0.00933316) +Other time (%) = 0.0159961 (2.57424) + +Nlocal: 8000 ave 8037 max 7964 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 9007.5 ave 9050 max 8968 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 300708 ave 305113 max 297203 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 1202833 +Ave neighs/atom = 37.5885 +Neighbor list builds = 5 +Dangerous builds = 0 diff --git a/bench/log.9Jan12.lj.scaled.linux.4 b/bench/log.9Jan12.lj.scaled.linux.4 new file mode 100644 index 0000000000..8b4cf65cd0 --- /dev/null +++ b/bench/log.9Jan12.lj.scaled.linux.4 @@ -0,0 +1,64 @@ +LAMMPS (10 Jan 2012) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 2.43423 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 2.04092 (83.8422) +Neigh time (%) = 0.238374 (9.79258) +Comm time (%) = 0.0766696 (3.14964) +Outpt time (%) = 0.000154495 (0.00634677) +Other time (%) = 0.0781193 (3.20919) + +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.9Jan12.rhodo.fixed.linux.1 b/bench/log.9Jan12.rhodo.fixed.linux.1 new file mode 100644 index 0000000000..a8a0c37ca1 --- /dev/null +++ b/bench/log.9Jan12.rhodo.fixed.linux.1 @@ -0,0 +1,98 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + 27723 bonds + 40467 angles + 56829 dihedrals + 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 = 0.248831 + grid = 25 32 32 + stencil order = 5 + RMS precision = 7.57143e-05 + using double precision FFTs + brick FFT buffer size/proc = 41070 25600 12321 +Memory usage per processor = 138.965 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397 +PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742 +E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 +E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030 +Volume = 307995.0335 +---------------- Step 50 ----- CPU = 17.8190 (sec) ---------------- +TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230 +PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977 +E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753 +E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744 +Volume = 308031.5641 +---------------- Step 100 ----- CPU = 36.2635 (sec) ---------------- +TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920 +PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408 +E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804 +E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875 +Volume = 308133.9900 +Loop time of 36.2636 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 25.8498 (71.283) +Bond time (%) = 1.49598 (4.1253) +Kspce time (%) = 3.27236 (9.02382) +Neigh time (%) = 4.27552 (11.7901) +Comm time (%) = 0.0665278 (0.183456) +Outpt time (%) = 0.000251055 (0.000692305) +Other time (%) = 1.30319 (3.59366) + +FFT time (% of Kspce) = 0.279837 (8.55152) +FFT Gflps 3d (1d only) = 1.85715 3.22108 + +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.9Jan12.rhodo.fixed.linux.4 b/bench/log.9Jan12.rhodo.fixed.linux.4 new file mode 100644 index 0000000000..4b500aa5c9 --- /dev/null +++ b/bench/log.9Jan12.rhodo.fixed.linux.4 @@ -0,0 +1,98 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + 27723 bonds + 40467 angles + 56829 dihedrals + 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 = 0.248831 + grid = 25 32 32 + stencil order = 5 + RMS precision = 7.57143e-05 + using double precision FFTs + brick FFT buffer size/proc = 13230 6400 5670 +Memory usage per processor = 54.4744 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397 +PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742 +E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 +E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030 +Volume = 307995.0335 +---------------- Step 50 ----- CPU = 4.7389 (sec) ---------------- +TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230 +PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977 +E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753 +E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744 +Volume = 308031.5641 +---------------- Step 100 ----- CPU = 9.6394 (sec) ---------------- +TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920 +PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408 +E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804 +E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875 +Volume = 308133.9900 +Loop time of 9.63943 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 6.60502 (68.5208) +Bond time (%) = 0.375643 (3.89695) +Kspce time (%) = 1.09311 (11.3399) +Neigh time (%) = 1.08158 (11.2203) +Comm time (%) = 0.0815379 (0.845879) +Outpt time (%) = 0.000157952 (0.00163861) +Other time (%) = 0.402393 (4.17445) + +FFT time (% of Kspce) = 0.0966156 (8.83863) +FFT Gflps 3d (1d only) = 5.37903 12.4303 + +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.9Jan12.rhodo.scaled.linux.4 b/bench/log.9Jan12.rhodo.scaled.linux.4 new file mode 100644 index 0000000000..dffa4d9bf2 --- /dev/null +++ b/bench/log.9Jan12.rhodo.scaled.linux.4 @@ -0,0 +1,119 @@ +LAMMPS (10 Jan 2012) +# 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 + 32000 atoms + 32000 velocities + 27723 bonds + 40467 angles + 56829 dihedrals + 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 = 0.248586 + grid = 48 60 36 + stencil order = 5 + RMS precision = 7.66425e-05 + using double precision FFTs + brick FFT buffer size/proc = 41615 25920 12915 +Memory usage per processor = 146.135 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -101425.4826 KinEng = 85779.3251 Temp = 299.0304 +PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968 +E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537 +E_coul = 827025.3556 E_long = -1080537.3749 Press = -142.3084 +Volume = 1231980.1340 +---------------- Step 50 ----- CPU = 19.1088 (sec) ---------------- +TotEng = -101320.2612 KinEng = 86003.4849 Temp = 299.8118 +PotEng = -187323.7461 E_bond = 9887.1072 E_angle = 43346.7920 +E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456 +E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165 +Volume = 1232126.1854 +---------------- Step 100 ----- CPU = 39.1056 (sec) ---------------- +TotEng = -101158.1517 KinEng = 86355.6231 Temp = 301.0394 +PotEng = -187513.7747 E_bond = 10272.0700 E_angle = 43128.6453 +E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196 +E_coul = 825555.5009 E_long = -1080544.3307 Press = 15.2192 +Volume = 1232535.8453 +Loop time of 39.1057 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 27.0353 (69.1339) +Bond time (%) = 1.5462 (3.9539) +Kspce time (%) = 4.17715 (10.6817) +Neigh time (%) = 4.37974 (11.1997) +Comm time (%) = 0.208052 (0.532026) +Outpt time (%) = 0.000296533 (0.000758287) +Other time (%) = 1.75896 (4.49797) + +FFT time (% of Kspce) = 0.535835 (12.8278) +FFT Gflps 3d (1d only) = 4.46931 11.0706 + +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 = 48112468 +Ave neighs/atom = 375.879 +Ave special neighs/atom = 7.43187 +Neighbor list builds = 11 +Dangerous builds = 0