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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1394 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-01-18 21:22:59 +00:00
parent 2511d4528e
commit cd1297d507
17 changed files with 375 additions and 375 deletions
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18
bench/log.5Oct07.chain.fixed.linux.1 → bench/log.22Jan08.chain.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# FENE beadspring benchmark
units lj
@ -32,18 +32,18 @@ thermo 100
timestep 0.012
run 100
Memory usage per processor = 8.52547 Mbytes
Memory usage per processor = 8.37288 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 1.88106 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.92511 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)
Pair time (%) = 0.479302 (24.8973)
Bond time (%) = 0.244982 (12.7256)
Neigh time (%) = 0.724451 (37.6316)
Comm time (%) = 0.0567744 (2.94914)
Outpt time (%) = 0.000191927 (0.00996964)
Other time (%) = 0.419413 (21.7864)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

18
bench/log.5Oct07.chain.fixed.linux.4 → bench/log.22Jan08.chain.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# FENE beadspring benchmark
units lj
@ -32,18 +32,18 @@ thermo 100
timestep 0.012
run 100
Memory usage per processor = 3.53032 Mbytes
Memory usage per processor = 3.56846 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
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
Loop time of 0.519059 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)
Pair time (%) = 0.0858856 (16.5464)
Bond time (%) = 0.0584659 (11.2638)
Neigh time (%) = 0.164426 (31.6776)
Comm time (%) = 0.10412 (20.0594)
Outpt time (%) = 0.000526488 (0.101431)
Other time (%) = 0.105635 (20.3513)
Nlocal: 8000 ave 8024 max 7973 min
Histogram: 1 0 0 1 0 0 0 1 0 1

18
bench/log.5Oct07.chain.scaled.linux.4 → bench/log.22Jan08.chain.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# FENE beadspring benchmark
variable x index 1
@ -48,18 +48,18 @@ thermo 100
timestep 0.012
run 100
Memory usage per processor = 9.56386 Mbytes
Memory usage per processor = 10.0339 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
Loop time of 2.50452 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)
Pair time (%) = 0.524648 (20.948)
Bond time (%) = 0.266218 (10.6295)
Neigh time (%) = 0.772881 (30.8594)
Comm time (%) = 0.300915 (12.0149)
Outpt time (%) = 0.000822663 (0.0328471)
Other time (%) = 0.63904 (25.5154)
Nlocal: 32000 ave 32015 max 31986 min
Histogram: 2 0 0 0 0 0 0 0 1 1

16
bench/log.5Oct07.chute.fixed.linux.1 → bench/log.22Jan08.chute.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -34,17 +34,17 @@ thermo_style granular
thermo 100
run 100
Memory usage per processor = 32.9693 Mbytes
Memory usage per processor = 34.1137 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 1.91739 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.96253 on 1 procs for 100 steps with 32000 atoms
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)
Pair time (%) = 1.1289 (57.5225)
Neigh time (%) = 0.0840769 (4.2841)
Comm time (%) = 0.100157 (5.10344)
Outpt time (%) = 0.000550032 (0.0280267)
Other time (%) = 0.648851 (33.062)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

16
bench/log.5Oct07.chute.fixed.linux.4 → bench/log.22Jan08.chute.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -34,17 +34,17 @@ thermo_style granular
thermo 100
run 100
Memory usage per processor = 13.5416 Mbytes
Memory usage per processor = 14.9911 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 0.562479 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.380859 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)
Pair time (%) = 0.186777 (49.0411)
Neigh time (%) = 0.0192279 (5.04857)
Comm time (%) = 0.0684672 (17.9771)
Outpt time (%) = 0.000488818 (0.128346)
Other time (%) = 0.105898 (27.8049)
Nlocal: 8000 ave 8010 max 7990 min
Histogram: 2 0 0 0 0 0 0 0 0 2

16
bench/log.5Oct07.chute.scaled.linux.4 → bench/log.22Jan08.chute.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -44,17 +44,17 @@ thermo_style granular
thermo 100
run 100
Memory usage per processor = 35.0123 Mbytes
Memory usage per processor = 36.1567 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
Loop time of 3.47138 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)
Pair time (%) = 1.57714 (45.4327)
Neigh time (%) = 0.0880994 (2.53788)
Comm time (%) = 0.309906 (8.92747)
Outpt time (%) = 0.00190902 (0.054993)
Other time (%) = 1.49432 (43.0469)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

28
bench/log.5Oct07.eam.fixed.linux.1 → bench/log.22Jan08.eam.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# bulk Cu lattice
variable x index 20
@ -34,27 +34,27 @@ timestep 0.005
thermo 50
run 100
Memory usage per processor = 14.6785 Mbytes
Memory usage per processor = 13.3815 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
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
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 11.4861 on 1 procs for 100 steps with 32000 atoms
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)
Pair time (%) = 10.3396 (90.0179)
Neigh time (%) = 0.873706 (7.60662)
Comm time (%) = 0.0718901 (0.625887)
Outpt time (%) = 0.0004282 (0.00372798)
Other time (%) = 0.200537 (1.74591)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19910 ave 19910 max 19910 min
Nghost: 19909 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20857e+06 ave 1.20857e+06 max 1.20857e+06 min
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 = 1208570
Ave neighs/atom = 37.7678
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0

34
bench/log.5Oct07.eam.fixed.linux.4 → bench/log.22Jan08.eam.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# bulk Cu lattice
variable x index 20
@ -34,27 +34,27 @@ timestep 0.005
thermo 50
run 100
Memory usage per processor = 4.42085 Mbytes
Memory usage per processor = 4.30641 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
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
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 3.00533 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)
Pair time (%) = 2.54989 (84.8455)
Neigh time (%) = 0.218561 (7.27242)
Comm time (%) = 0.183583 (6.10856)
Outpt time (%) = 0.00118673 (0.0394874)
Other time (%) = 0.0521147 (1.73407)
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
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 = 1208570
Ave neighs/atom = 37.7678
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0

32
bench/log.5Oct07.eam.scaled.linux.4 → bench/log.22Jan08.eam.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# bulk Cu lattice
variable x index 20
@ -34,27 +34,27 @@ timestep 0.005
thermo 50
run 100
Memory usage per processor = 14.5948 Mbytes
Memory usage per processor = 13.2978 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
50 779.50001 -439457.02 0 -426560.06 52355.276
100 797.97828 -439764.76 0 -426562.07 51474.74
Loop time of 12.4187 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)
Pair time (%) = 10.5898 (85.2731)
Neigh time (%) = 0.97017 (7.81219)
Comm time (%) = 0.390233 (3.14231)
Outpt time (%) = 0.00154972 (0.012479)
Other time (%) = 0.466937 (3.75996)
Nlocal: 32000 ave 32087 max 31920 min
Nlocal: 32000 ave 32092 max 31914 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 19909.8 ave 19989 max 19824 min
Nghost: 19910 ave 19997 max 19818 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
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 = 4832066
Ave neighs/atom = 37.7505
Total # of neighbors = 4829126
Ave neighs/atom = 37.7275
Neighbor list builds = 14
Dangerous builds = 0

26
bench/log.5Oct07.lj.fixed.linux.1 → bench/log.22Jan08.lj.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# 3d Lennard-Jones melt
variable x index 20
@ -32,26 +32,26 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 12.8375 Mbytes
Memory usage per processor = 11.5405 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.77218928 -5.7804197 0 -4.6221719 0.072558996
Loop time of 4.11023 on 1 procs for 100 steps with 32000 atoms
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 4.29901 on 1 procs for 100 steps with 32000 atoms
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)
Pair time (%) = 3.70609 (86.208)
Neigh time (%) = 0.364576 (8.48046)
Comm time (%) = 0.0613043 (1.42601)
Outpt time (%) = 0.000224829 (0.00522977)
Other time (%) = 0.166815 (3.8803)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19665 ave 19665 max 19665 min
Nghost: 19657 ave 19657 max 19657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20232e+06 ave 1.20232e+06 max 1.20232e+06 min
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 = 1202315
Ave neighs/atom = 37.5723
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0

34
bench/log.5Oct07.lj.fixed.linux.4 → bench/log.22Jan08.lj.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# 3d Lennard-Jones melt
variable x index 20
@ -32,26 +32,26 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 3.88556 Mbytes
Memory usage per processor = 3.77112 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.77218928 -5.7804197 0 -4.6221719 0.072558996
Loop time of 1.12636 on 4 procs for 100 steps with 32000 atoms
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 1.13074 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)
Pair time (%) = 0.864449 (76.4498)
Neigh time (%) = 0.0882651 (7.80595)
Comm time (%) = 0.146416 (12.9487)
Outpt time (%) = 0.000469029 (0.0414798)
Other time (%) = 0.0311421 (2.75413)
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
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 = 1202315
Ave neighs/atom = 37.5723
Total # of neighbors = 1202833
Ave neighs/atom = 37.5885
Neighbor list builds = 5
Dangerous builds = 0

34
bench/log.5Oct07.lj.scaled.linux.4 → bench/log.22Jan08.lj.scaled.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# 3d Lennard-Jones melt
variable x index 20
@ -32,26 +32,26 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
run 100
Memory usage per processor = 12.7603 Mbytes
Memory usage per processor = 11.4634 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
100 0.75841891 -5.759957 0 -4.6223375 0.20008866
Loop time of 4.83011 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)
Pair time (%) = 3.73327 (77.2916)
Neigh time (%) = 0.352578 (7.29959)
Comm time (%) = 0.343265 (7.10678)
Outpt time (%) = 0.000744462 (0.0154129)
Other time (%) = 0.400251 (8.28659)
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
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 = 4811274
Ave neighs/atom = 37.5881
Total # of neighbors = 4807797
Ave neighs/atom = 37.5609
Neighbor list builds = 5
Dangerous builds = 0

96
bench/log.22Jan08.rhodo.fixed.linux.1 Normal file
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@ -0,0 +1,96 @@
LAMMPS (22 Jan 2008)
# 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 = 0.248831
grid = 25 32 32
RMS precision = 7.57143e-05
brick FFT buffer size/proc = 41070 25600 12321
Memory usage per processor = 124.369 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055
Volume = 307995.0335
---------------- Step 50 ----- CPU = 37.3083 (sec) ----------------
TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861
E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633
Volume = 308031.6776
---------------- Step 100 ----- CPU = 75.1703 (sec) ----------------
TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920
PotEng = -46882.7493 E_bond = 2567.9820 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962
E_coul = 206655.0353 E_long = -270400.7390 Press = 6.9485
Volume = 308134.2307
Loop time of 75.1704 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 55.4333 (73.7434)
Bond time (%) = 2.73595 (3.63967)
Kspce time (%) = 6.22079 (8.27558)
Neigh time (%) = 8.40617 (11.1828)
Comm time (%) = 0.20465 (0.272248)
Outpt time (%) = 0.000381947 (0.000508108)
Other time (%) = 2.16921 (2.88573)
FFT time (% of Kspce) = 0.4386 (7.05055)
FFT Gflps 3d 1d-only = 1.1849 1.72142
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 = 12028097
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

96
bench/log.22Jan08.rhodo.fixed.linux.4 Normal file
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@ -0,0 +1,96 @@
LAMMPS (22 Jan 2008)
# 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 = 0.248831
grid = 25 32 32
RMS precision = 7.57143e-05
brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 47.7552 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055
Volume = 307995.0335
---------------- Step 50 ----- CPU = 9.2501 (sec) ----------------
TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861
E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633
Volume = 308031.6776
---------------- Step 100 ----- CPU = 18.7659 (sec) ----------------
TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920
PotEng = -46882.7494 E_bond = 2567.9820 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962
E_coul = 206655.0352 E_long = -270400.7391 Press = 6.9485
Volume = 308134.2307
Loop time of 18.7664 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 12.4306 (66.2387)
Bond time (%) = 0.672617 (3.58415)
Kspce time (%) = 2.40555 (12.8184)
Neigh time (%) = 1.92536 (10.2596)
Comm time (%) = 0.438069 (2.33432)
Outpt time (%) = 0.00159127 (0.00847933)
Other time (%) = 0.892596 (4.75635)
FFT time (% of Kspce) = 0.331501 (13.7806)
FFT Gflps 3d 1d-only = 1.56771 6.70967
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: 3.00702e+06 ave 3.0975e+06 max 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028097
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

76
bench/log.5Oct07.rhodo.scaled.linux.4 → bench/log.22Jan08.rhodo.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (5 Oct 2007)
LAMMPS (22 Jan 2008)
# Rhodopsin model
variable x index 1
@ -67,51 +67,51 @@ 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
G vector = 0.248586
grid = 48 60 36
RMS precision = 7.66425e-05
brick FFT buffer size/proc = 41615 25920 12915
Memory usage per processor = 130.497 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
TotEng = -101425.4928 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8179 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
E_coul = 827025.3455 E_long = -1080537.3748 Press = -142.3110
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
---------------- Step 50 ----- CPU = 38.3008 (sec) ----------------
TotEng = -101320.2392 KinEng = 86003.4766 Temp = 299.8118
PotEng = -187323.7158 E_bond = 9887.1093 E_angle = 43346.7930
E_dihed = 20958.7048 E_impro = 908.4715 E_vdwl = -7973.4918
E_coul = 826113.2245 E_long = -1080564.5270 Press = 237.9865
Volume = 1232126.6400
---------------- Step 100 ----- CPU = 78.1279 (sec) ----------------
TotEng = -101158.0378 KinEng = 86355.6419 Temp = 301.0394
PotEng = -187513.6797 E_bond = 10272.0762 E_angle = 43128.6553
E_dihed = 20793.9769 E_impro = 867.0831 E_vdwl = -7586.7842
E_coul = 825555.6424 E_long = -1080544.3294 Press = 15.1826
Volume = 1232536.8037
Loop time of 78.1285 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)
Pair time (%) = 53.1309 (68.0045)
Bond time (%) = 2.72833 (3.49211)
Kspce time (%) = 9.81881 (12.5675)
Neigh time (%) = 8.04447 (10.2965)
Comm time (%) = 0.981682 (1.2565)
Outpt time (%) = 0.00180387 (0.00230886)
Other time (%) = 3.42247 (4.38057)
FFT time (% of Kspce) = 1.57698 (15.8841)
FFT Gflps 3d 1d-only = 1.41574 5.85277
FFT time (% of Kspce) = 1.67033 (17.0115)
FFT Gflps 3d 1d-only = 1.43374 5.81408
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
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 = 48112030
Ave neighs/atom = 375.875
Total # of neighbors = 48112464
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

96
bench/log.5Oct07.rhodo.fixed.linux.1
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@ -1,96 +0,0 @@
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 = 133.859 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 = 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 (%) = 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) = 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 = 12027976
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

96
bench/log.5Oct07.rhodo.fixed.linux.4
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@ -1,96 +0,0 @@
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