diff --git a/bench/log.22Jun07.chain.scaled.liberty.8 b/bench/log.22Jun07.chain.scaled.liberty.8 deleted file mode 100644 index 9ed3c088d..000000000 --- a/bench/log.22Jun07.chain.scaled.liberty.8 +++ /dev/null @@ -1,75 +0,0 @@ -LAMMPS (22 June 2007) -# 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 0.0 1.0 1.0 - -read_data data.chain - 1 = max bonds/atom - orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) - 2 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 2 - orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 50.388) - 2 by 2 by 2 processor grid - 256000 atoms - 253440 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 = 10.0921 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.97027119 0.44484087 20.494523 22.394765 4.6721833 - 100 0.97424237 0.44152909 20.501694 22.404581 4.6873411 -Loop time of 5.43268 on 8 procs for 100 steps with 256000 atoms - -Pair time (%) = 1.0989 (20.2275) -Bond time (%) = 0.542015 (9.97692) -Neigh time (%) = 1.49201 (27.4635) -Comm time (%) = 0.922278 (16.9765) -Outpt time (%) = 0.00245366 (0.0451647) -Other time (%) = 1.37503 (25.3104) - -Nlocal: 32000 ave 32058 max 31953 min -Histogram: 1 1 0 1 2 1 1 0 0 1 -Nghost: 9505.38 ave 9533 max 9479 min -Histogram: 2 0 0 1 0 2 1 1 0 1 -Neighs: 155776 ave 156274 max 155380 min -Histogram: 1 0 1 1 3 1 0 0 0 1 - -Total # of neighbors = 1246208 -Ave neighs/atom = 4.868 -Ave special neighs/atom = 1.98 -Neighbor list builds = 25 -Dangerous builds = 0 diff --git a/bench/log.22Jun07.chute.scaled.liberty.8 b/bench/log.22Jun07.chute.scaled.liberty.8 deleted file mode 100644 index 9cb9e5df1..000000000 --- a/bench/log.22Jun07.chute.scaled.liberty.8 +++ /dev/null @@ -1,69 +0,0 @@ -LAMMPS (22 June 2007) -# 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 - -read_data data.chute - orthogonal box = (0 0 0) to (40 20 37.2886) - 2 by 2 by 2 processor grid - 32000 atoms - 32000 velocities - -replicate $x $y 1 -replicate 2 $y 1 -replicate 2 4 1 - orthogonal box = (0 0 0) to (80 80 37.2887) - 2 by 4 by 1 processor grid - 256000 atoms - -pair_style gran/history 200000.0 50.0 0.5 0 - -neighbor 0.1 bin -neigh_modify every 1 delay 0 - -timestep 0.0001 - -group bottom type 2 -7296 atoms in group bottom -group active subtract all bottom -248704 atoms in group active -neigh_modify exclude group bottom bottom - -fix 1 all gravity chute 26.0 -fix 2 bottom freeze -fix 3 active nve/gran - -thermo_style granular -thermo 100 - -run 100 -Memory usage per processor = 32.9126 Mbytes -Step Atoms KinEng RotKEgrn Volume - 0 256000 6273113 12809.01 238647.04 - 100 256000 6274319.9 12568.11 238654.43 -Loop time of 5.21764 on 8 procs for 100 steps with 256000 atoms - -Pair time (%) = 2.551 (48.8918) -Neigh time (%) = 0.174133 (3.3374) -Comm time (%) = 0.643821 (12.3393) -Outpt time (%) = 0.00319499 (0.0612344) -Other time (%) = 1.84549 (35.3702) - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 5463 ave 5463 max 5463 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 115133 ave 115133 max 115133 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 921064 -Ave neighs/atom = 3.59791 -Neighbor list builds = 2 -Dangerous builds = 0 diff --git a/bench/log.22Jun07.eam.scaled.liberty.8 b/bench/log.22Jun07.eam.scaled.liberty.8 deleted file mode 100644 index 186d8d015..000000000 --- a/bench/log.22Jun07.eam.scaled.liberty.8 +++ /dev/null @@ -1,60 +0,0 @@ -LAMMPS (22 June 2007) -# bulk Cu lattice - -variable x index 20 -variable y index 20 -variable z index 20 - -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 $x 0 $y 0 $z -region box block 0 40 0 $y 0 $z -region box block 0 40 0 40 0 $z -region box block 0 40 0 40 0 40 -create_box 1 box -Created orthogonal box = (0 0 0) to (144.6 144.6 144.6) - 2 by 2 by 2 processor grid -create_atoms 1 box -Created 256000 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 = 15.1399 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1600 -906240 0 -853295.25 18704.085 - 50 799.88728 -879586.61 0 -853117.96 51535.434 - 100 784.70888 -879086.24 0 -853119.86 51937.46 -Loop time of 23.2141 on 8 procs for 100 steps with 256000 atoms - -Pair time (%) = 18.9744 (81.7368) -Neigh time (%) = 1.94597 (8.38272) -Comm time (%) = 1.45154 (6.25285) -Outpt time (%) = 0.0030815 (0.0132743) -Other time (%) = 0.839045 (3.61439) - -Nlocal: 32000 ave 32128 max 31853 min -Histogram: 1 0 0 2 0 1 1 2 0 1 -Nghost: 19909.9 ave 20057 max 19782 min -Histogram: 1 0 2 1 1 0 1 1 0 1 -Neighs: 1.20868e+06 ave 1.21395e+06 max 1.20304e+06 min -Histogram: 1 2 0 0 0 0 2 2 0 1 - -Total # of neighbors = 9669450 -Ave neighs/atom = 37.7713 -Neighbor list builds = 14 -Dangerous builds = 0 diff --git a/bench/log.22Jun07.lj.scaled.liberty.8 b/bench/log.22Jun07.lj.scaled.liberty.8 deleted file mode 100644 index 3d618f3cc..000000000 --- a/bench/log.22Jun07.lj.scaled.liberty.8 +++ /dev/null @@ -1,57 +0,0 @@ -LAMMPS (22 June 2007) -# 3d Lennard-Jones melt - -variable x index 20 -variable y index 20 -variable z index 20 - -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 $x 0 $y 0 $z -region box block 0 40 0 $y 0 $z -region box block 0 40 0 40 0 $z -region box block 0 40 0 40 0 40 -create_box 1 box -Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838) - 2 by 2 by 2 processor grid -create_atoms 1 box -Created 256000 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 = 13.347 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 -6.7733681 0 -4.6133765 -5.019674 - 100 0.7616931 -5.7642895 0 -4.6217544 0.20907141 -Loop time of 9.57871 on 8 procs for 100 steps with 256000 atoms - -Pair time (%) = 7.12462 (74.3797) -Neigh time (%) = 0.635592 (6.63546) -Comm time (%) = 1.05576 (11.0219) -Outpt time (%) = 0.00168183 (0.017558) -Other time (%) = 0.761061 (7.94533) - -Nlocal: 32000 ave 32077 max 31945 min -Histogram: 2 2 0 1 0 0 0 1 1 1 -Nghost: 19666.1 ave 19728 max 19582 min -Histogram: 1 0 1 1 0 1 0 2 0 2 -Neighs: 1.20362e+06 ave 1.20977e+06 max 1.19745e+06 min -Histogram: 1 2 0 0 1 0 2 0 0 2 - -Total # of neighbors = 9628940 -Ave neighs/atom = 37.613 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/bench/log.22Jun07.rhodo.fixed.liberty.8 b/bench/log.22Jun07.rhodo.fixed.liberty.8 deleted file mode 100644 index 88a3d55b3..000000000 --- a/bench/log.22Jun07.rhodo.fixed.liberty.8 +++ /dev/null @@ -1,96 +0,0 @@ -LAMMPS (22 June 2007) -# 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) - 2 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 - -special_bonds charmm - -thermo 50 -thermo_style multi -timestep 2.0 - -run 100 -PPPM initialization ... - G vector = 0.245875 - grid = 24 32 30 - RMS precision = 8.76365e-05 - brick FFT buffer size/proc = 7140 3072 3780 -Memory usage per processor = 30.031 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397 -PotEng = -46800.6567 E_bond = 2537.9940 E_angle = 10921.3742 -E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 -E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456 -Volume = 307995.0335 ----------------- Step 50 ----- CPU = 10.1023 (sec) ---------------- -TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223 -PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458 -E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669 -E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815 -Volume = 308031.8243 ----------------- Step 100 ----- CPU = 20.8372 (sec) ---------------- -TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576 -PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480 -E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511 -E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451 -Volume = 308134.7692 -Loop time of 20.8381 on 8 procs for 100 steps with 32000 atoms - -Pair time (%) = 13.4637 (64.6111) -Bond time (%) = 0.525574 (2.52218) -Kspce time (%) = 3.3461 (16.0576) -Neigh time (%) = 1.63546 (7.84842) -Comm time (%) = 0.770115 (3.69571) -Outpt time (%) = 0.00124443 (0.00597188) -Other time (%) = 1.09588 (5.25903) - -FFT time (% of Kspce) = 0.715048 (21.3696) -FFT Gflps 3d 1d-only = 0.647331 7.04904 - -Nlocal: 4000 ave 4083 max 3940 min -Histogram: 2 1 0 1 2 0 0 0 1 1 -Nghost: 16028.4 ave 16084 max 15941 min -Histogram: 1 0 0 2 0 1 0 0 2 2 -Neighs: 1.5035e+06 ave 1.55024e+06 max 1.46322e+06 min -Histogram: 2 0 1 0 2 1 0 0 0 2 - -Total # of neighbors = 12027978 -Ave neighs/atom = 375.874 -Ave special neighs/atom = 7.43187 -Neighbor list builds = 11 -Dangerous builds = 0 diff --git a/bench/log.22Jun07.rhodo.scaled.liberty.8 b/bench/log.22Jun07.rhodo.scaled.liberty.8 deleted file mode 100644 index a42959a31..000000000 --- a/bench/log.22Jun07.rhodo.scaled.liberty.8 +++ /dev/null @@ -1,117 +0,0 @@ -LAMMPS (22 June 2007) -# 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) - 2 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 2 - orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 109.088) - 2 by 2 by 2 processor grid - 256000 atoms - 221784 bonds - 323736 angles - 454632 dihedrals - 8272 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 - 12936 = # of size 2 clusters - 29064 = # of size 3 clusters - 5976 = # of size 4 clusters - 33864 = # of frozen angles -fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 - -special_bonds charmm - -thermo 50 -thermo_style multi -timestep 2.0 - -run 100 -PPPM initialization ... - G vector = 0.245875 - grid = 48 64 60 - RMS precision = 8.76365e-05 - brick FFT buffer size/proc = 37555 24576 11655 -Memory usage per processor = 139.074 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -202846.6035 KinEng = 171558.6503 Temp = 299.0288 -PotEng = -374405.2538 E_bond = 20303.9521 E_angle = 87370.9937 -E_dihed = 41694.2920 E_impro = 1708.0927 E_vdwl = -18462.9073 -E_coul = 1630560.5366 E_long = -2137580.2135 Press = -142.0456 -Volume = 2463960.2680 ----------------- Step 50 ----- CPU = 74.8537 (sec) ---------------- -TotEng = -202633.5610 KinEng = 172010.7811 Temp = 299.8169 -PotEng = -374644.3420 E_bond = 19774.3302 E_angle = 86693.4128 -E_dihed = 41917.7989 E_impro = 1817.0662 E_vdwl = -15943.3555 -E_coul = 1628731.3465 E_long = -2137634.9412 Press = 238.5780 -Volume = 2464254.6355 ----------------- Step 100 ----- CPU = 155.1037 (sec) ---------------- -TotEng = -202315.0204 KinEng = 172724.9944 Temp = 301.0618 -PotEng = -375040.0148 E_bond = 20545.2484 E_angle = 86257.2003 -E_dihed = 41587.6129 E_impro = 1733.5368 E_vdwl = -15186.8930 -E_coul = 1627613.3289 E_long = -2137590.0491 Press = 10.9720 -Volume = 2465078.7315 -Loop time of 155.104 on 8 procs for 100 steps with 256000 atoms - -Pair time (%) = 102.817 (66.2892) -Bond time (%) = 4.29529 (2.76929) -Kspce time (%) = 22.4796 (14.4932) -Neigh time (%) = 15.5455 (10.0226) -Comm time (%) = 2.68199 (1.72915) -Outpt time (%) = 0.00327626 (0.00211229) -Other time (%) = 7.28125 (4.69442) - -FFT time (% of Kspce) = 6.0543 (26.9324) -FFT Gflps 3d 1d-only = 0.738243 7.05801 - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 47962 ave 47962 max 47962 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 1.2028e+07 ave 1.2057e+07 max 1.19989e+07 min -Histogram: 4 0 0 0 0 0 0 0 0 4 - -Total # of neighbors = 96223696 -Ave neighs/atom = 375.874 -Ave special neighs/atom = 7.43187 -Neighbor list builds = 11 -Dangerous builds = 0 diff --git a/bench/log.22Jun07.chain.fixed.linux.1 b/bench/log.5Oct07.chain.fixed.linux.1 similarity index 76% rename from bench/log.22Jun07.chain.fixed.linux.1 rename to bench/log.5Oct07.chain.fixed.linux.1 index 917f3d97e..023e89407 100644 --- a/bench/log.22Jun07.chain.fixed.linux.1 +++ b/bench/log.5Oct07.chain.fixed.linux.1 @@ -1,59 +1,59 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # FENE beadspring benchmark units lj atom_style bond special_bonds 0.0 1.0 1.0 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 = 8.52881 Mbytes +Memory usage per processor = 8.52547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.97434451 0.439712 20.499596 22.400779 4.6558589 -Loop time of 7.13438 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 2.21672 (31.0709) -Bond time (%) = 0.614869 (8.61839) -Neigh time (%) = 2.68187 (37.5908) -Comm time (%) = 0.329216 (4.6145) -Outpt time (%) = 0.001037 (0.0145353) -Other time (%) = 1.29067 (18.0908) +Loop time of 1.88106 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.470788 (25.0278) +Bond time (%) = 0.240855 (12.8042) +Neigh time (%) = 0.701759 (37.3066) +Comm time (%) = 0.0541713 (2.87983) +Outpt time (%) = 0.000169992 (0.00903705) +Other time (%) = 0.413318 (21.9726) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9537 ave 9537 max 9537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155877 ave 155877 max 155877 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155877 Ave neighs/atom = 4.87116 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.22Jun07.chain.fixed.liberty.8 b/bench/log.5Oct07.chain.fixed.linux.4 similarity index 51% rename from bench/log.22Jun07.chain.fixed.liberty.8 rename to bench/log.5Oct07.chain.fixed.linux.4 index 4e23432e0..adc61aafa 100644 --- a/bench/log.22Jun07.chain.fixed.liberty.8 +++ b/bench/log.5Oct07.chain.fixed.linux.4 @@ -1,59 +1,59 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # FENE beadspring benchmark units lj atom_style bond special_bonds 0.0 1.0 1.0 read_data data.chain 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) - 2 by 2 by 2 processor grid + 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 = 2.62762 Mbytes +Memory usage per processor = 3.53032 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 - 100 0.97000691 0.44751221 20.498199 22.400676 4.7159344 -Loop time of 0.559036 on 8 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.0874849 (15.6492) -Bond time (%) = 0.0473607 (8.47185) -Neigh time (%) = 0.138014 (24.6879) -Comm time (%) = 0.167274 (29.9218) -Outpt time (%) = 0.000471383 (0.0843207) -Other time (%) = 0.118431 (21.1848) - -Nlocal: 4000 ave 4029 max 3985 min -Histogram: 2 0 2 1 2 0 0 0 0 1 -Nghost: 2592.25 ave 2602 max 2566 min -Histogram: 1 0 0 0 0 1 1 1 0 4 -Neighs: 19477.4 ave 19776 max 19279 min -Histogram: 1 2 2 0 0 0 1 1 0 1 - -Total # of neighbors = 155819 -Ave neighs/atom = 4.86934 + 100 0.96717514 0.4422441 20.503712 22.396674 4.6686541 +Loop time of 0.550458 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.092812 (16.8609) +Bond time (%) = 0.06107 (11.0944) +Neigh time (%) = 0.169702 (30.8293) +Comm time (%) = 0.113217 (20.5678) +Outpt time (%) = 0.000525832 (0.0955263) +Other time (%) = 0.113131 (20.5521) + +Nlocal: 8000 ave 8024 max 7973 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 4169 ave 4212 max 4141 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 38936.2 ave 39212 max 38690 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 155745 +Ave neighs/atom = 4.86703 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.5Oct07.chain.scaled.linux.4 b/bench/log.5Oct07.chain.scaled.linux.4 new file mode 100644 index 000000000..efbbd37eb --- /dev/null +++ b/bench/log.5Oct07.chain.scaled.linux.4 @@ -0,0 +1,75 @@ +LAMMPS (5 Oct 2007) +# 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 0.0 1.0 1.0 + +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 = 9.56386 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.97027498 0.44484087 20.494523 22.394765 4.6721833 + 100 0.97400897 0.44134715 20.501052 22.403401 4.6879813 +Loop time of 2.98639 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 0.56241 (18.8325) +Bond time (%) = 0.284682 (9.53266) +Neigh time (%) = 0.780229 (26.1262) +Comm time (%) = 0.48756 (16.3261) +Outpt time (%) = 0.00329143 (0.110214) +Other time (%) = 0.868214 (29.0724) + +Nlocal: 32000 ave 32015 max 31986 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 9499 ave 9524 max 9446 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +Neighs: 155798 ave 156103 max 155422 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 623193 +Ave neighs/atom = 4.8687 +Ave special neighs/atom = 1.98 +Neighbor list builds = 25 +Dangerous builds = 0 diff --git a/bench/log.22Jun07.chute.fixed.linux.1 b/bench/log.5Oct07.chute.fixed.linux.1 similarity index 76% rename from bench/log.22Jun07.chute.fixed.linux.1 rename to bench/log.5Oct07.chute.fixed.linux.1 index 993ad6258..c20377eb3 100644 --- a/bench/log.22Jun07.chute.fixed.linux.1 +++ b/bench/log.5Oct07.chute.fixed.linux.1 @@ -1,59 +1,59 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # 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 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/history 200000.0 50.0 0.5 0 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 chute 26.0 +fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/gran thermo_style granular thermo 100 run 100 -Memory usage per processor = 30.935 Mbytes +Memory usage per processor = 32.9693 Mbytes Step Atoms KinEng RotKEgrn Volume 0 32000 784139.13 1601.1263 29830.88 100 32000 784289.99 1571.0137 29831.804 -Loop time of 6.87253 on 1 procs for 100 steps with 32000 atoms +Loop time of 1.91739 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 4.6578 (67.7741) -Neigh time (%) = 0.45709 (6.65097) -Comm time (%) = 0.247749 (3.60492) -Outpt time (%) = 0.001582 (0.0230192) -Other time (%) = 1.50831 (21.9469) +Pair time (%) = 1.09812 (57.2715) +Neigh time (%) = 0.0856261 (4.46577) +Comm time (%) = 0.0961592 (5.01512) +Outpt time (%) = 0.000524998 (0.0273809) +Other time (%) = 0.63696 (33.2202) 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.22Jun07.chute.fixed.liberty.8 b/bench/log.5Oct07.chute.fixed.linux.4 similarity index 55% rename from bench/log.22Jun07.chute.fixed.liberty.8 rename to bench/log.5Oct07.chute.fixed.linux.4 index cb983e432..0fea207a9 100644 --- a/bench/log.22Jun07.chute.fixed.liberty.8 +++ b/bench/log.5Oct07.chute.fixed.linux.4 @@ -1,59 +1,59 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # 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 read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) - 2 by 2 by 2 processor grid + 2 by 1 by 2 processor grid 32000 atoms 32000 velocities pair_style gran/history 200000.0 50.0 0.5 0 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 chute 26.0 +fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/gran thermo_style granular thermo 100 run 100 -Memory usage per processor = 9.4635 Mbytes +Memory usage per processor = 13.5416 Mbytes Step Atoms KinEng RotKEgrn Volume 0 32000 784139.13 1601.1263 29830.88 100 32000 784289.99 1571.0137 29831.804 -Loop time of 0.672613 on 8 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.302915 (45.0355) -Neigh time (%) = 0.0175665 (2.61168) -Comm time (%) = 0.158755 (23.6026) -Outpt time (%) = 0.000497788 (0.0740081) -Other time (%) = 0.19288 (28.6762) - -Nlocal: 4000 ave 4005 max 3995 min -Histogram: 4 0 0 0 0 0 0 0 0 4 -Nghost: 1736.5 ave 1739 max 1734 min -Histogram: 4 0 0 0 0 0 0 0 0 4 -Neighs: 15093 ave 15610 max 14576 min -Histogram: 4 0 0 0 0 0 0 0 0 4 - -Total # of neighbors = 120744 -Ave neighs/atom = 3.77325 +Loop time of 0.562479 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.227851 (40.5084) +Neigh time (%) = 0.0203491 (3.61776) +Comm time (%) = 0.102512 (18.225) +Outpt time (%) = 0.000804424 (0.143014) +Other time (%) = 0.210963 (37.5058) + +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.5Oct07.chute.scaled.linux.4 b/bench/log.5Oct07.chute.scaled.linux.4 new file mode 100644 index 000000000..76d07be42 --- /dev/null +++ b/bench/log.5Oct07.chute.scaled.linux.4 @@ -0,0 +1,69 @@ +LAMMPS (5 Oct 2007) +# 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 + +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/history 200000.0 50.0 0.5 0 + +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/gran + +thermo_style granular +thermo 100 + +run 100 +Memory usage per processor = 35.0123 Mbytes +Step Atoms KinEng RotKEgrn Volume + 0 128000 3136556.5 6404.5051 119323.52 + 100 128000 3137160 6284.0549 119327.22 +Loop time of 3.77144 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 1.685 (44.6779) +Neigh time (%) = 0.0923538 (2.44877) +Comm time (%) = 0.346049 (9.17553) +Outpt time (%) = 0.00418776 (0.111039) +Other time (%) = 1.64385 (43.5867) + +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.22Jun07.eam.fixed.linux.1 b/bench/log.5Oct07.eam.fixed.linux.1 similarity index 60% rename from bench/log.22Jun07.eam.fixed.linux.1 rename to bench/log.5Oct07.eam.fixed.linux.1 index 6444c5932..f49155ae6 100644 --- a/bench/log.22Jun07.eam.fixed.linux.1 +++ b/bench/log.5Oct07.eam.fixed.linux.1 @@ -1,60 +1,60 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # bulk Cu lattice variable x index 20 variable y index 20 variable z index 20 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 $x 0 $y 0 $z region box block 0 20 0 $y 0 $z region box block 0 20 0 20 0 $z 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 = 15.2616 Mbytes +Memory usage per processor = 14.6785 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -113280 0 -106662.09 18703.573 - 50 781.37184 -109870.67 0 -106638.76 52616.84 - 100 792.19277 -109916.21 0 -106639.54 51739.67 -Loop time of 31.0146 on 1 procs for 100 steps with 32000 atoms + 50 781.55267 -109870.85 0 -106638.19 52764.534 + 100 805.29574 -109970.16 0 -106639.3 51178.427 +Loop time of 11.2999 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 27.1822 (87.6433) -Neigh time (%) = 2.71986 (8.76962) -Comm time (%) = 0.338775 (1.09231) -Outpt time (%) = 0.002124 (0.00684839) -Other time (%) = 0.771616 (2.48791) +Pair time (%) = 10.1502 (89.8261) +Neigh time (%) = 0.871946 (7.71642) +Comm time (%) = 0.0720956 (0.638021) +Outpt time (%) = 0.000406027 (0.00359319) +Other time (%) = 0.205194 (1.81589) 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 +Nghost: 19910 ave 19910 max 19910 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.20989e+06 ave 1.20989e+06 max 1.20989e+06 min +Neighs: 1.20857e+06 ave 1.20857e+06 max 1.20857e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 1209894 -Ave neighs/atom = 37.8092 +Total # of neighbors = 1208570 +Ave neighs/atom = 37.7678 Neighbor list builds = 13 Dangerous builds = 0 diff --git a/bench/log.22Jun07.eam.fixed.liberty.8 b/bench/log.5Oct07.eam.fixed.linux.4 similarity index 50% rename from bench/log.22Jun07.eam.fixed.liberty.8 rename to bench/log.5Oct07.eam.fixed.linux.4 index b70139e3e..c0a685523 100644 --- a/bench/log.22Jun07.eam.fixed.liberty.8 +++ b/bench/log.5Oct07.eam.fixed.linux.4 @@ -1,60 +1,60 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # bulk Cu lattice variable x index 20 variable y index 20 variable z index 20 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 $x 0 $y 0 $z region box block 0 20 0 $y 0 $z region box block 0 20 0 20 0 $z 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) - 2 by 2 by 2 processor grid + 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 = 2.51765 Mbytes +Memory usage per processor = 4.42085 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -113280 0 -106662.09 18703.573 - 50 781.37184 -109870.67 0 -106638.76 52616.84 - 100 792.19277 -109916.21 0 -106639.54 51739.67 -Loop time of 2.7327 on 8 procs for 100 steps with 32000 atoms - -Pair time (%) = 2.16792 (79.3324) -Neigh time (%) = 0.187726 (6.86961) -Comm time (%) = 0.306913 (11.2311) -Outpt time (%) = 0.000829369 (0.0303498) -Other time (%) = 0.0693147 (2.53649) - -Nlocal: 4000 ave 4026 max 3981 min -Histogram: 1 1 0 2 1 2 0 0 0 1 -Nghost: 5840.62 ave 5860 max 5815 min -Histogram: 1 0 0 0 3 0 2 0 1 1 -Neighs: 151237 ave 152083 max 150648 min -Histogram: 2 1 0 0 3 1 0 0 0 1 - -Total # of neighbors = 1209894 -Ave neighs/atom = 37.8092 + 50 781.55267 -109870.85 0 -106638.19 52764.534 + 100 805.29574 -109970.16 0 -106639.3 51178.427 +Loop time of 3.11047 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 2.61131 (83.9521) +Neigh time (%) = 0.222731 (7.1607) +Comm time (%) = 0.20405 (6.56012) +Outpt time (%) = 0.000865459 (0.0278241) +Other time (%) = 0.0715173 (2.29925) + +Nlocal: 8000 ave 8023 max 7981 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 9130 ave 9150 max 9105 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 302142 ave 303202 max 300766 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 1208570 +Ave neighs/atom = 37.7678 Neighbor list builds = 13 Dangerous builds = 0 diff --git a/bench/log.5Oct07.eam.scaled.linux.4 b/bench/log.5Oct07.eam.scaled.linux.4 new file mode 100644 index 000000000..d004b93c6 --- /dev/null +++ b/bench/log.5Oct07.eam.scaled.linux.4 @@ -0,0 +1,60 @@ +LAMMPS (5 Oct 2007) +# bulk Cu lattice + +variable x index 20 +variable y index 20 +variable z index 20 + +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 $x 0 $y 0 $z +region box block 0 40 0 $y 0 $z +region box block 0 40 0 40 0 $z +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 = 14.5948 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1600 -453120 0 -426647.73 18704.012 + 50 772.46776 -439343 0 -426562.39 52646.044 + 100 798.31788 -439771.6 0 -426563.3 51493.923 +Loop time of 13.0599 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 10.8899 (83.3838) +Neigh time (%) = 0.99729 (7.63627) +Comm time (%) = 0.631329 (4.8341) +Outpt time (%) = 0.00184333 (0.0141144) +Other time (%) = 0.539597 (4.13171) + +Nlocal: 32000 ave 32087 max 31920 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 19909.8 ave 19989 max 19824 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 1.20802e+06 ave 1.21174e+06 max 1.20443e+06 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 4832066 +Ave neighs/atom = 37.7505 +Neighbor list builds = 14 +Dangerous builds = 0 diff --git a/bench/log.22Jun07.lj.fixed.linux.1 b/bench/log.5Oct07.lj.fixed.linux.1 similarity index 63% rename from bench/log.22Jun07.lj.fixed.linux.1 rename to bench/log.5Oct07.lj.fixed.linux.1 index b425eeff5..080923dfa 100644 --- a/bench/log.22Jun07.lj.fixed.linux.1 +++ b/bench/log.5Oct07.lj.fixed.linux.1 @@ -1,57 +1,57 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # 3d Lennard-Jones melt variable x index 20 variable y index 20 variable z index 20 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 $x 0 $y 0 $z region box block 0 20 0 $y 0 $z region box block 0 20 0 20 0 $z 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 = 13.4306 Mbytes +Memory usage per processor = 12.8375 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 - 100 0.77196819 -5.7795465 0 -4.6216304 0.079908069 -Loop time of 13.8981 on 1 procs for 100 steps with 32000 atoms + 100 0.77218928 -5.7804197 0 -4.6221719 0.072558996 +Loop time of 4.11023 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 12.0067 (86.3907) -Neigh time (%) = 1.07342 (7.72346) -Comm time (%) = 0.271477 (1.95334) -Outpt time (%) = 0.000835 (0.00600801) -Other time (%) = 0.545714 (3.92653) +Pair time (%) = 3.54178 (86.1699) +Neigh time (%) = 0.351553 (8.55311) +Comm time (%) = 0.0573781 (1.39598) +Outpt time (%) = 0.000291109 (0.00708254) +Other time (%) = 0.159229 (3.87395) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 19715 ave 19715 max 19715 min +Nghost: 19665 ave 19665 max 19665 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.20353e+06 ave 1.20353e+06 max 1.20353e+06 min +Neighs: 1.20232e+06 ave 1.20232e+06 max 1.20232e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 1203529 -Ave neighs/atom = 37.6103 +Total # of neighbors = 1202315 +Ave neighs/atom = 37.5723 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.22Jun07.lj.fixed.liberty.8 b/bench/log.5Oct07.lj.fixed.linux.4 similarity index 53% rename from bench/log.22Jun07.lj.fixed.liberty.8 rename to bench/log.5Oct07.lj.fixed.linux.4 index 3ef1ad13f..17a80c081 100644 --- a/bench/log.22Jun07.lj.fixed.liberty.8 +++ b/bench/log.5Oct07.lj.fixed.linux.4 @@ -1,57 +1,57 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # 3d Lennard-Jones melt variable x index 20 variable y index 20 variable z index 20 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 $x 0 $y 0 $z region box block 0 20 0 $y 0 $z region box block 0 20 0 20 0 $z 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) - 2 by 2 by 2 processor grid + 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 = 2.13618 Mbytes +Memory usage per processor = 3.88556 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 - 100 0.77196819 -5.7795465 0 -4.6216304 0.079908069 -Loop time of 1.25475 on 8 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.816538 (65.0759) -Neigh time (%) = 0.0738717 (5.88738) -Comm time (%) = 0.30246 (24.1053) -Outpt time (%) = 0.000414073 (0.0330006) -Other time (%) = 0.061462 (4.89836) - -Nlocal: 4000 ave 4038 max 3962 min -Histogram: 2 1 0 1 0 0 2 0 0 2 -Nghost: 5778.12 ave 5820 max 5742 min -Histogram: 2 0 2 0 0 1 0 2 0 1 -Neighs: 150441 ave 152219 max 147904 min -Histogram: 1 0 0 2 0 1 0 2 0 2 - -Total # of neighbors = 1203529 -Ave neighs/atom = 37.6103 + 100 0.77218928 -5.7804197 0 -4.6221719 0.072558996 +Loop time of 1.12636 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.867727 (77.0383) +Neigh time (%) = 0.0890129 (7.90273) +Comm time (%) = 0.138108 (12.2615) +Outpt time (%) = 0.00042218 (0.0374819) +Other time (%) = 0.0310873 (2.75999) + +Nlocal: 8000 ave 8049 max 7971 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Nghost: 9015.5 ave 9051 max 8966 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 300579 ave 304810 max 298185 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 1202315 +Ave neighs/atom = 37.5723 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.5Oct07.lj.scaled.linux.4 b/bench/log.5Oct07.lj.scaled.linux.4 new file mode 100644 index 000000000..db698690f --- /dev/null +++ b/bench/log.5Oct07.lj.scaled.linux.4 @@ -0,0 +1,57 @@ +LAMMPS (5 Oct 2007) +# 3d Lennard-Jones melt + +variable x index 20 +variable y index 20 +variable z index 20 + +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 $x 0 $y 0 $z +region box block 0 40 0 $y 0 $z +region box block 0 40 0 40 0 $z +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 = 12.7603 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -6.7733681 0 -4.6133849 -5.0196788 + 100 0.75341035 -5.7518267 0 -4.62172 0.2612672 +Loop time of 5.14761 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 3.82234 (74.2548) +Neigh time (%) = 0.361516 (7.02299) +Comm time (%) = 0.496529 (9.64583) +Outpt time (%) = 0.000954211 (0.018537) +Other time (%) = 0.466263 (9.05786) + +Nlocal: 32000 ave 32038 max 31942 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 19629.8 ave 19675 max 19594 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 1.20282e+06 ave 1.20573e+06 max 1.20081e+06 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 4811274 +Ave neighs/atom = 37.5881 +Neighbor list builds = 5 +Dangerous builds = 0 diff --git a/bench/log.22Jun07.rhodo.fixed.linux.1 b/bench/log.5Oct07.rhodo.fixed.linux.1 similarity index 57% rename from bench/log.22Jun07.rhodo.fixed.linux.1 rename to bench/log.5Oct07.rhodo.fixed.linux.1 index 5d056391a..24b48e329 100644 --- a/bench/log.22Jun07.rhodo.fixed.linux.1 +++ b/bench/log.5Oct07.rhodo.fixed.linux.1 @@ -1,96 +1,96 @@ -LAMMPS (22 June 2007) +LAMMPS (5 Oct 2007) # 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector = 0.245875 grid = 24 32 30 RMS precision = 8.76365e-05 brick FFT buffer size/proc = 37555 23040 11655 -Memory usage per processor = 134.779 Mbytes +Memory usage per processor = 133.859 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397 -PotEng = -46800.6567 E_bond = 2537.9940 E_angle = 10921.3742 +TotEng = -25355.8260 KinEng = 21444.8313 Temp = 299.0397 +PotEng = -46800.6573 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 -E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456 +E_coul = 203820.0665 E_long = -267197.5267 Press = -142.0485 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 152.6104 (sec) ---------------- -TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223 -PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458 -E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669 -E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815 -Volume = 308031.8243 ----------------- Step 100 ----- CPU = 309.5271 (sec) ---------------- -TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576 -PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480 -E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511 -E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451 -Volume = 308134.7692 -Loop time of 309.527 on 1 procs for 100 steps with 32000 atoms +---------------- Step 50 ----- CPU = 37.2652 (sec) ---------------- +TotEng = -25329.9165 KinEng = 21500.9587 Temp = 299.8223 +PotEng = -46830.8751 E_bond = 2471.7583 E_angle = 10836.5458 +E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9667 +E_coul = 203591.3235 E_long = -267204.3691 Press = 238.4820 +Volume = 308031.8242 +---------------- Step 100 ----- CPU = 75.6253 (sec) ---------------- +TotEng = -25291.5444 KinEng = 21589.5406 Temp = 301.0576 +PotEng = -46881.0850 E_bond = 2568.0538 E_angle = 10781.7478 +E_dihed = 5198.3743 E_impro = 216.6829 E_vdwl = -1898.4506 +E_coul = 203451.2690 E_long = -267198.7621 Press = 10.7475 +Volume = 308134.7686 +Loop time of 75.6254 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 231.215 (74.6994) -Bond time (%) = 6.3242 (2.04318) -Kspce time (%) = 19.1711 (6.19366) -Neigh time (%) = 46.0779 (14.8865) -Comm time (%) = 0.796922 (0.257464) -Outpt time (%) = 0.002562 (0.000827714) -Other time (%) = 5.93944 (1.91888) +Pair time (%) = 56.2927 (74.4362) +Bond time (%) = 2.58034 (3.41201) +Kspce time (%) = 6.11111 (8.08076) +Neigh time (%) = 8.38886 (11.0927) +Comm time (%) = 0.208683 (0.275943) +Outpt time (%) = 0.000406027 (0.000536892) +Other time (%) = 2.0433 (2.70186) -FFT time (% of Kspce) = 3.96566 (20.6857) -FFT Gflps 3d 1d-only = 0.11672 0.259612 +FFT time (% of Kspce) = 0.42448 (6.94605) +FFT Gflps 3d 1d-only = 1.09045 1.58681 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 47962 ave 47962 max 47962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.2028e+07 ave 1.2028e+07 max 1.2028e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 12027978 +Total # of neighbors = 12027976 Ave neighs/atom = 375.874 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.5Oct07.rhodo.fixed.linux.4 b/bench/log.5Oct07.rhodo.fixed.linux.4 new file mode 100644 index 000000000..9dde6bc3b --- /dev/null +++ b/bench/log.5Oct07.rhodo.fixed.linux.4 @@ -0,0 +1,96 @@ +LAMMPS (5 Oct 2007) +# 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 + +special_bonds charmm + +thermo 50 +thermo_style multi +timestep 2.0 + +run 100 +PPPM initialization ... + G vector = 0.245875 + grid = 24 32 30 + RMS precision = 8.76365e-05 + brick FFT buffer size/proc = 12180 6144 5481 +Memory usage per processor = 50.2175 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -25355.8260 KinEng = 21444.8313 Temp = 299.0397 +PotEng = -46800.6573 E_bond = 2537.9940 E_angle = 10921.3742 +E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 +E_coul = 203820.0665 E_long = -267197.5267 Press = -142.0485 +Volume = 307995.0335 +---------------- Step 50 ----- CPU = 9.6422 (sec) ---------------- +TotEng = -25329.9165 KinEng = 21500.9586 Temp = 299.8223 +PotEng = -46830.8752 E_bond = 2471.7583 E_angle = 10836.5458 +E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9667 +E_coul = 203591.3235 E_long = -267204.3691 Press = 238.4820 +Volume = 308031.8242 +---------------- Step 100 ----- CPU = 19.4814 (sec) ---------------- +TotEng = -25291.5443 KinEng = 21589.5406 Temp = 301.0576 +PotEng = -46881.0849 E_bond = 2568.0538 E_angle = 10781.7478 +E_dihed = 5198.3743 E_impro = 216.6829 E_vdwl = -1898.4506 +E_coul = 203451.2690 E_long = -267198.7621 Press = 10.7475 +Volume = 308134.7686 +Loop time of 19.4821 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 12.9977 (66.7161) +Bond time (%) = 0.64311 (3.30104) +Kspce time (%) = 2.5143 (12.9057) +Neigh time (%) = 1.95058 (10.0122) +Comm time (%) = 0.480013 (2.46387) +Outpt time (%) = 0.0015353 (0.00788057) +Other time (%) = 0.894842 (4.59316) + +FFT time (% of Kspce) = 0.315807 (12.5604) +FFT Gflps 3d 1d-only = 1.46568 6.19563 + +Nlocal: 8000 ave 8143 max 7933 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 22735.5 ave 22770 max 22697 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 3.00699e+06 ave 3.0975e+06 max 2.96494e+06 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 12027976 +Ave neighs/atom = 375.874 +Ave special neighs/atom = 7.43187 +Neighbor list builds = 11 +Dangerous builds = 0 diff --git a/bench/log.5Oct07.rhodo.scaled.linux.4 b/bench/log.5Oct07.rhodo.scaled.linux.4 new file mode 100644 index 000000000..59e072778 --- /dev/null +++ b/bench/log.5Oct07.rhodo.scaled.linux.4 @@ -0,0 +1,117 @@ +LAMMPS (5 Oct 2007) +# 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 + +special_bonds charmm + +thermo 50 +thermo_style multi +timestep 2.0 + +run 100 +PPPM initialization ... + G vector = 0.246338 + grid = 45 60 36 + RMS precision = 8.56639e-05 + brick FFT buffer size/proc = 40180 24840 17220 +Memory usage per processor = 137.911 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -101423.5112 KinEng = 85779.3251 Temp = 299.0304 +PotEng = -187202.8364 E_bond = 10151.9760 E_angle = 43685.4968 +E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538 +E_coul = 817284.2513 E_long = -1070794.2991 Press = -141.9925 +Volume = 1231980.1340 +---------------- Step 50 ----- CPU = 38.9431 (sec) ---------------- +TotEng = -101316.6996 KinEng = 86004.2667 Temp = 299.8145 +PotEng = -187320.9663 E_bond = 9887.1225 E_angle = 43346.5775 +E_dihed = 20958.7139 E_impro = 908.4248 E_vdwl = -7973.9399 +E_coul = 816372.0088 E_long = -1070819.8739 Press = 238.0995 +Volume = 1232127.0570 +---------------- Step 100 ----- CPU = 79.6546 (sec) ---------------- +TotEng = -101158.1182 KinEng = 86360.5576 Temp = 301.0566 +PotEng = -187518.6758 E_bond = 10272.2506 E_angle = 43128.8182 +E_dihed = 20794.4833 E_impro = 867.0824 E_vdwl = -7591.0566 +E_coul = 815810.2886 E_long = -1070800.5424 Press = 13.1624 +Volume = 1232538.4006 +Loop time of 79.6554 on 4 procs for 100 steps with 128000 atoms + +Pair time (%) = 54.0019 (67.7944) +Bond time (%) = 2.60068 (3.26491) +Kspce time (%) = 9.92803 (12.4637) +Neigh time (%) = 8.09826 (10.1666) +Comm time (%) = 1.17806 (1.47895) +Outpt time (%) = 0.00191575 (0.00240505) +Other time (%) = 3.84657 (4.82902) + +FFT time (% of Kspce) = 1.57698 (15.8841) +FFT Gflps 3d 1d-only = 1.41574 5.85277 + +Nlocal: 32000 ave 32001 max 31999 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 47957.5 ave 47959 max 47956 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 1.2028e+07 ave 1.20576e+07 max 1.19984e+07 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 48112030 +Ave neighs/atom = 375.875 +Ave special neighs/atom = 7.43187 +Neighbor list builds = 11 +Dangerous builds = 0