diff --git a/bench/log.28Mar11.chain.fixed.linux.1 b/bench/log.28Mar11.chain.fixed.linux.1 deleted file mode 100644 index a656eb9e7..000000000 --- a/bench/log.28Mar11.chain.fixed.linux.1 +++ /dev/null @@ -1,59 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 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 1.87328 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.438668 (23.4171) -Bond time (%) = 0.289005 (15.4277) -Neigh time (%) = 0.679554 (36.2761) -Comm time (%) = 0.0552287 (2.94823) -Outpt time (%) = 0.00018096 (0.00966003) -Other time (%) = 0.410646 (21.9212) - -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.28Mar11.chain.fixed.linux.4 b/bench/log.28Mar11.chain.fixed.linux.4 deleted file mode 100644 index 0d9a9854f..000000000 --- a/bench/log.28Mar11.chain.fixed.linux.4 +++ /dev/null @@ -1,59 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 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 0.436674 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.0835696 (19.1378) -Bond time (%) = 0.0588097 (13.4677) -Neigh time (%) = 0.157872 (36.1532) -Comm time (%) = 0.047663 (10.915) -Outpt time (%) = 9.69768e-05 (0.0222081) -Other time (%) = 0.0886627 (20.3041) - -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.28Mar11.chain.scaled.linux.4 b/bench/log.28Mar11.chain.scaled.linux.4 deleted file mode 100644 index fcef10320..000000000 --- a/bench/log.28Mar11.chain.scaled.linux.4 +++ /dev/null @@ -1,75 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 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 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 2.4188 on 4 procs for 100 steps with 128000 atoms - -Pair time (%) = 0.507936 (20.9995) -Bond time (%) = 0.340843 (14.0914) -Neigh time (%) = 0.735922 (30.425) -Comm time (%) = 0.228828 (9.46038) -Outpt time (%) = 0.000289202 (0.0119564) -Other time (%) = 0.604987 (25.0118) - -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.28Mar11.chute.fixed.linux.1 b/bench/log.28Mar11.chute.fixed.linux.1 deleted file mode 100644 index e16830ffd..000000000 --- a/bench/log.28Mar11.chute.fixed.linux.1 +++ /dev/null @@ -1,63 +0,0 @@ -LAMMPS (27 Mar 2011) -# LAMMPS benchmark of granular flow -# chute flow of 32000 atoms with frozen base at 26 degrees - -units lj -atom_style granular -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 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 = 35.2505 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 1.58777 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.887784 (55.9139) -Neigh time (%) = 0.070847 (4.46205) -Comm time (%) = 0.0669501 (4.21661) -Outpt time (%) = 0.000550032 (0.0346418) -Other time (%) = 0.561639 (35.3728) - -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.28Mar11.chute.fixed.linux.4 b/bench/log.28Mar11.chute.fixed.linux.4 deleted file mode 100644 index 59efa4a12..000000000 --- a/bench/log.28Mar11.chute.fixed.linux.4 +++ /dev/null @@ -1,63 +0,0 @@ -LAMMPS (27 Mar 2011) -# LAMMPS benchmark of granular flow -# chute flow of 32000 atoms with frozen base at 26 degrees - -units lj -atom_style granular -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 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 = 15.4199 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 0.270323 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.135713 (50.2038) -Neigh time (%) = 0.0173983 (6.43611) -Comm time (%) = 0.0378563 (14.0041) -Outpt time (%) = 0.000246227 (0.091086) -Other time (%) = 0.0791097 (29.2649) - -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.28Mar11.chute.scaled.linux.4 b/bench/log.28Mar11.chute.scaled.linux.4 deleted file mode 100644 index 318511002..000000000 --- a/bench/log.28Mar11.chute.scaled.linux.4 +++ /dev/null @@ -1,73 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 granular -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 processor grid - 32000 atoms - 32000 velocities - -replicate $x $y 1 -replicate 2 $y 1 -replicate 2 2 1 - orthogonal box = (0 0 0) to (80 40 37.2887) - 4 by 1 by 1 processor grid - 128000 atoms - -pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 -pair_coeff * * - -neighbor 0.1 bin -neigh_modify every 1 delay 0 - -timestep 0.0001 - -group bottom type 2 -3648 atoms in group bottom -group active subtract all bottom -124352 atoms in group active -neigh_modify exclude group bottom bottom - -fix 1 all gravity 1.0 chute 26.0 -fix 2 bottom freeze -fix 3 active nve/sphere - -compute 1 all erotate/sphere -thermo_style custom step atoms ke c_1 vol -thermo_modify norm no -thermo 100 - -run 100 -Memory usage per processor = 37.3912 Mbytes -Step Atoms KinEng 1 Volume - 0 128000 3136556.5 6404.5051 119323.52 - 100 128000 3137160 6284.0549 119327.22 -Loop time of 2.79202 on 4 procs for 100 steps with 128000 atoms - -Pair time (%) = 1.13366 (40.6034) -Neigh time (%) = 0.0699974 (2.50705) -Comm time (%) = 0.24415 (8.74457) -Outpt time (%) = 0.00162953 (0.0583639) -Other time (%) = 1.34259 (48.0866) - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 5456 ave 5456 max 5456 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 115135 ave 115135 max 115135 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 460540 -Ave neighs/atom = 3.59797 -Neighbor list builds = 2 -Dangerous builds = 0 diff --git a/bench/log.28Mar11.eam.fixed.linux.1 b/bench/log.28Mar11.eam.fixed.linux.1 deleted file mode 100644 index 4303ebf43..000000000 --- a/bench/log.28Mar11.eam.fixed.linux.1 +++ /dev/null @@ -1,67 +0,0 @@ -LAMMPS (27 Mar 2011) -# bulk Cu lattice - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$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 ${zz} -region box block 0 20 0 20 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) - 1 by 1 by 1 processor grid -create_atoms 1 box -Created 32000 atoms - -pair_style eam -pair_coeff 1 1 Cu_u3.eam - -velocity all create 1600.0 376847 loop geom - -neighbor 1.0 bin -neigh_modify every 1 delay 5 check yes - -fix 1 all nve - -timestep 0.005 -thermo 50 - -run 100 -Memory usage per processor = 15.3728 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1600 -113280 0 -106662.09 18703.573 - 50 781.69049 -109873.35 0 -106640.13 52273.088 - 100 801.832 -109957.3 0 -106640.77 51322.821 -Loop time of 11.4086 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 10.2465 (89.814) -Neigh time (%) = 0.893404 (7.83096) -Comm time (%) = 0.0694258 (0.608539) -Outpt time (%) = 0.000409126 (0.00358612) -Other time (%) = 0.198848 (1.74296) - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19909 ave 19909 max 19909 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1207784 -Ave neighs/atom = 37.7433 -Neighbor list builds = 13 -Dangerous builds = 0 diff --git a/bench/log.28Mar11.eam.fixed.linux.4 b/bench/log.28Mar11.eam.fixed.linux.4 deleted file mode 100644 index 22fb1cf05..000000000 --- a/bench/log.28Mar11.eam.fixed.linux.4 +++ /dev/null @@ -1,67 +0,0 @@ -LAMMPS (27 Mar 2011) -# bulk Cu lattice - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$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 ${zz} -region box block 0 20 0 20 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) - 1 by 2 by 2 processor grid -create_atoms 1 box -Created 32000 atoms - -pair_style eam -pair_coeff 1 1 Cu_u3.eam - -velocity all create 1600.0 376847 loop geom - -neighbor 1.0 bin -neigh_modify every 1 delay 5 check yes - -fix 1 all nve - -timestep 0.005 -thermo 50 - -run 100 -Memory usage per processor = 4.92442 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1600 -113280 0 -106662.09 18703.573 - 50 781.69049 -109873.35 0 -106640.13 52273.088 - 100 801.832 -109957.3 0 -106640.77 51322.821 -Loop time of 2.84421 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 2.47554 (87.0379) -Neigh time (%) = 0.216563 (7.61418) -Comm time (%) = 0.104262 (3.66577) -Outpt time (%) = 0.000251591 (0.00884573) -Other time (%) = 0.0475937 (1.67335) - -Nlocal: 8000 ave 8008 max 7993 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 9130.25 ave 9138 max 9122 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 301946 ave 302392 max 301360 min -Histogram: 1 0 0 0 1 0 0 0 1 1 - -Total # of neighbors = 1207784 -Ave neighs/atom = 37.7433 -Neighbor list builds = 13 -Dangerous builds = 0 diff --git a/bench/log.28Mar11.eam.scaled.linux.4 b/bench/log.28Mar11.eam.scaled.linux.4 deleted file mode 100644 index 08f93dca8..000000000 --- a/bench/log.28Mar11.eam.scaled.linux.4 +++ /dev/null @@ -1,67 +0,0 @@ -LAMMPS (27 Mar 2011) -# bulk Cu lattice - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$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 ${zz} -region box block 0 40 0 40 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (144.6 144.6 72.3) - 2 by 2 by 1 processor grid -create_atoms 1 box -Created 128000 atoms - -pair_style eam -pair_coeff 1 1 Cu_u3.eam - -velocity all create 1600.0 376847 loop geom - -neighbor 1.0 bin -neigh_modify every 1 delay 5 check yes - -fix 1 all nve - -timestep 0.005 -thermo 50 - -run 100 -Memory usage per processor = 15.2892 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1600 -453120 0 -426647.73 18704.012 - 50 779.50001 -439457.02 0 -426560.06 52355.276 - 100 797.97828 -439764.76 0 -426562.07 51474.74 -Loop time of 12.0882 on 4 procs for 100 steps with 128000 atoms - -Pair time (%) = 10.3589 (85.6942) -Neigh time (%) = 0.963713 (7.97234) -Comm time (%) = 0.316817 (2.62088) -Outpt time (%) = 0.000717819 (0.00593818) -Other time (%) = 0.448062 (3.70661) - -Nlocal: 32000 ave 32092 max 31914 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Nghost: 19910 ave 19997 max 19818 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min -Histogram: 1 0 0 1 1 0 0 0 0 1 - -Total # of neighbors = 4829126 -Ave neighs/atom = 37.7275 -Neighbor list builds = 14 -Dangerous builds = 0 diff --git a/bench/log.28Mar11.lj.fixed.linux.1 b/bench/log.28Mar11.lj.fixed.linux.1 deleted file mode 100644 index 1daa53dd3..000000000 --- a/bench/log.28Mar11.lj.fixed.linux.1 +++ /dev/null @@ -1,64 +0,0 @@ -LAMMPS (27 Mar 2011) -# 3d Lennard-Jones melt - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$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 ${zz} -region box block 0 20 0 20 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) - 1 by 1 by 1 processor grid -create_atoms 1 box -Created 32000 atoms -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 20 check no - -fix 1 all nve - -run 100 -Memory usage per processor = 13.2267 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 - 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 -Loop time of 4.24155 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 3.6555 (86.1832) -Neigh time (%) = 0.359136 (8.4671) -Comm time (%) = 0.0590658 (1.39255) -Outpt time (%) = 0.000212193 (0.00500272) -Other time (%) = 0.167634 (3.95218) - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19657 ave 19657 max 19657 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1202833 -Ave neighs/atom = 37.5885 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/bench/log.28Mar11.lj.fixed.linux.4 b/bench/log.28Mar11.lj.fixed.linux.4 deleted file mode 100644 index 1886e2060..000000000 --- a/bench/log.28Mar11.lj.fixed.linux.4 +++ /dev/null @@ -1,64 +0,0 @@ -LAMMPS (27 Mar 2011) -# 3d Lennard-Jones melt - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$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 ${zz} -region box block 0 20 0 20 0 20 -create_box 1 box -Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) - 1 by 2 by 2 processor grid -create_atoms 1 box -Created 32000 atoms -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 20 check no - -fix 1 all nve - -run 100 -Memory usage per processor = 4.31284 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 - 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 -Loop time of 1.08102 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.86205 (79.7443) -Neigh time (%) = 0.0897413 (8.30156) -Comm time (%) = 0.0998399 (9.23573) -Outpt time (%) = 0.000194311 (0.0179748) -Other time (%) = 0.0291918 (2.7004) - -Nlocal: 8000 ave 8037 max 7964 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 9007.5 ave 9050 max 8968 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 300708 ave 305113 max 297203 min -Histogram: 1 0 0 1 1 0 0 0 0 1 - -Total # of neighbors = 1202833 -Ave neighs/atom = 37.5885 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/bench/log.28Mar11.lj.scaled.linux.4 b/bench/log.28Mar11.lj.scaled.linux.4 deleted file mode 100644 index c74c76403..000000000 --- a/bench/log.28Mar11.lj.scaled.linux.4 +++ /dev/null @@ -1,64 +0,0 @@ -LAMMPS (27 Mar 2011) -# 3d Lennard-Jones melt - -variable x index 1 -variable y index 1 -variable z index 1 - -variable xx equal 20*$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 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 4.71885 on 4 procs for 100 steps with 128000 atoms - -Pair time (%) = 3.70177 (78.4464) -Neigh time (%) = 0.350671 (7.43129) -Comm time (%) = 0.278878 (5.90987) -Outpt time (%) = 0.000279307 (0.00591897) -Other time (%) = 0.387254 (8.20654) - -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.28Mar11.rhodo.fixed.linux.1 b/bench/log.28Mar11.rhodo.fixed.linux.1 deleted file mode 100644 index eb669ae71..000000000 --- a/bench/log.28Mar11.rhodo.fixed.linux.1 +++ /dev/null @@ -1,97 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 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 - 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 = 32.2123 (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 = 65.3867 (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 = -270400.7389 Press = 6.9875 -Volume = 308133.9900 -Loop time of 65.3868 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 46.2231 (70.6918) -Bond time (%) = 2.88711 (4.41543) -Kspce time (%) = 7.06667 (10.8075) -Neigh time (%) = 6.61535 (10.1173) -Comm time (%) = 0.185745 (0.28407) -Outpt time (%) = 0.000392199 (0.000599813) -Other time (%) = 2.4084 (3.68331) - -FFT time (% of Kspce) = 0.430403 (6.0906) -FFT Gflps 3d (1d only) = 1.20747 1.74267 - -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.28Mar11.rhodo.fixed.linux.4 b/bench/log.28Mar11.rhodo.fixed.linux.4 deleted file mode 100644 index f78c4872a..000000000 --- a/bench/log.28Mar11.rhodo.fixed.linux.4 +++ /dev/null @@ -1,97 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 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 - 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 = 8.2683 (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 = 16.8728 (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 = -270400.7389 Press = 6.9875 -Volume = 308133.9900 -Loop time of 16.8729 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 11.2248 (66.5258) -Bond time (%) = 0.687313 (4.07347) -Kspce time (%) = 2.07329 (12.2877) -Neigh time (%) = 1.59928 (9.47838) -Comm time (%) = 0.410708 (2.43412) -Outpt time (%) = 0.000243425 (0.0014427) -Other time (%) = 0.877245 (5.19914) - -FFT time (% of Kspce) = 0.223284 (10.7696) -FFT Gflps 3d (1d only) = 2.32752 6.8543 - -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.28Mar11.rhodo.scaled.linux.4 b/bench/log.28Mar11.rhodo.scaled.linux.4 deleted file mode 100644 index 55e3d6649..000000000 --- a/bench/log.28Mar11.rhodo.scaled.linux.4 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (27 Mar 2011) -# 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 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 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 - brick FFT buffer size/proc = 41615 25920 12915 -Memory usage per processor = 146.135 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -101425.4825 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 = -1080537.3748 Press = -142.3084 -Volume = 1231980.1340 ----------------- Step 50 ----- CPU = 32.8194 (sec) ---------------- -TotEng = -101320.2611 KinEng = 86003.4849 Temp = 299.8118 -PotEng = -187323.7460 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 = 66.9547 (sec) ---------------- -TotEng = -101158.1519 KinEng = 86355.6231 Temp = 301.0394 -PotEng = -187513.7749 E_bond = 10272.0700 E_angle = 43128.6453 -E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196 -E_coul = 825555.5006 E_long = -1080544.3306 Press = 15.2192 -Volume = 1232535.8453 -Loop time of 66.9548 on 4 procs for 100 steps with 128000 atoms - -Pair time (%) = 45.779 (68.373) -Bond time (%) = 2.87439 (4.29303) -Kspce time (%) = 7.5089 (11.2149) -Neigh time (%) = 6.52016 (9.73816) -Comm time (%) = 0.765243 (1.14293) -Outpt time (%) = 0.000411808 (0.000615055) -Other time (%) = 3.50669 (5.2374) - -FFT time (% of Kspce) = 1.17001 (15.5816) -FFT Gflps 3d (1d only) = 2.04683 6.15771 - -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