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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@301 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-02-12 17:55:40 +00:00
parent efd7b8e8ff
commit 941093187f
16 changed files with 258 additions and 233 deletions
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16
bench/log.1Oct06.chain.lmp.fixed.liberty.8 → bench/log.12Feb07.chain.lmp.fixed.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# FENE beadspring benchmark
units lj
@ -35,14 +35,14 @@ Memory usage per processor = 2.55132 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 0.558263 on 8 procs for 100 steps with 32000 atoms
Loop time of 0.567145 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0848848 (15.2052)
Bond time (%) = 0.0478233 (8.56643)
Neigh time (%) = 0.136857 (24.5147)
Comm time (%) = 0.17255 (30.9083)
Outpt time (%) = 0.000431776 (0.0773427)
Other time (%) = 0.115718 (20.7281)
Pair time (%) = 0.0830945 (14.6514)
Bond time (%) = 0.0505197 (8.90772)
Neigh time (%) = 0.133964 (23.6207)
Comm time (%) = 0.176345 (31.0935)
Outpt time (%) = 0.000548124 (0.0966462)
Other time (%) = 0.122674 (21.6301)
Nlocal: 4000 ave 4029 max 3985 min
Histogram: 2 0 2 1 2 0 0 0 0 1

16
bench/log.1Oct06.chain.lmp.fixed.linux.1 → bench/log.12Feb07.chain.lmp.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# FENE beadspring benchmark
units lj
@ -35,14 +35,14 @@ Memory usage per processor = 8.45251 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 7.46203 on 1 procs for 100 steps with 32000 atoms
Loop time of 7.89679 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 2.27111 (30.4355)
Bond time (%) = 0.614795 (8.23898)
Neigh time (%) = 2.60854 (34.9576)
Comm time (%) = 0.387562 (5.19379)
Outpt time (%) = 0.00133 (0.0178236)
Other time (%) = 1.57869 (21.1563)
Pair time (%) = 2.2188 (28.0975)
Bond time (%) = 0.694979 (8.80078)
Neigh time (%) = 2.6686 (33.7934)
Comm time (%) = 0.334908 (4.24106)
Outpt time (%) = 0.000815 (0.0103206)
Other time (%) = 1.97869 (25.0569)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

18
bench/log.1Oct06.chain.lmp.scaled.liberty.8 → bench/log.12Feb07.chain.lmp.scaled.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# FENE beadspring benchmark
variable x index 1
@ -46,18 +46,18 @@ thermo 100
timestep 0.012
run 100
Memory usage per processor = 10.1502 Mbytes
Memory usage per processor = 10.0158 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 5.67904 on 8 procs for 100 steps with 256000 atoms
Loop time of 5.82027 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 1.11213 (19.5831)
Bond time (%) = 0.547845 (9.64677)
Neigh time (%) = 1.54568 (27.2173)
Comm time (%) = 1.02577 (18.0624)
Outpt time (%) = 0.00302154 (0.0532051)
Other time (%) = 1.44459 (25.4372)
Pair time (%) = 1.10706 (19.0208)
Bond time (%) = 0.553447 (9.50897)
Neigh time (%) = 1.48756 (25.5583)
Comm time (%) = 1.07831 (18.5267)
Outpt time (%) = 0.0030714 (0.0527707)
Other time (%) = 1.59082 (27.3325)
Nlocal: 32000 ave 32058 max 31953 min
Histogram: 1 1 0 1 2 1 1 0 0 1

16
bench/log.1Oct06.chute.lmp.fixed.liberty.8 → bench/log.12Feb07.chute.lmp.fixed.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -34,16 +34,16 @@ thermo 100
run 100
Memory usage per processor = 9.31091 Mbytes
Step Atoms Trans-KE Rot-KE Volume
Step Atoms KinEng RotKEgrn Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 0.696548 on 8 procs for 100 steps with 32000 atoms
Loop time of 0.712546 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 0.306387 (43.9864)
Neigh time (%) = 0.0181609 (2.60727)
Comm time (%) = 0.160018 (22.9731)
Outpt time (%) = 0.000968486 (0.139041)
Other time (%) = 0.211014 (30.2942)
Pair time (%) = 0.318114 (44.6448)
Neigh time (%) = 0.0166372 (2.33489)
Comm time (%) = 0.164817 (23.1307)
Outpt time (%) = 0.000648975 (0.0910784)
Other time (%) = 0.212329 (29.7986)
Nlocal: 4000 ave 4005 max 3995 min
Histogram: 4 0 0 0 0 0 0 0 0 4

16
bench/log.1Oct06.chute.lmp.fixed.linux.1 → bench/log.12Feb07.chute.lmp.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -34,16 +34,16 @@ thermo 100
run 100
Memory usage per processor = 30.7824 Mbytes
Step Atoms Trans-KE Rot-KE Volume
Step Atoms KinEng RotKEgrn Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 7.0548 on 1 procs for 100 steps with 32000 atoms
Loop time of 6.95992 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 4.59052 (65.0694)
Neigh time (%) = 0.444649 (6.30278)
Comm time (%) = 0.263586 (3.73626)
Outpt time (%) = 0.002312 (0.032772)
Other time (%) = 1.75374 (24.8588)
Pair time (%) = 4.73089 (67.9733)
Neigh time (%) = 0.454631 (6.53213)
Comm time (%) = 0.250711 (3.60221)
Outpt time (%) = 0.00157 (0.0225577)
Other time (%) = 1.52212 (21.8698)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

67
bench/log.12Feb07.chute.lmp.scaled.liberty.8 Normal file
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@ -0,0 +1,67 @@
LAMMPS (12 Feb 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
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
replicate $x $y 1
replicate 2 $y 1
replicate 2 4 1
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 = 32.76 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 256000 6273113 12809.01 238647.04
100 256000 6274319.9 12568.11 238654.43
Loop time of 5.47474 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 2.62579 (47.9619)
Neigh time (%) = 0.159791 (2.9187)
Comm time (%) = 0.68137 (12.4457)
Outpt time (%) = 0.00449485 (0.0821015)
Other time (%) = 2.0033 (36.5916)
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

29
bench/log.1Oct06.eam.lmp.fixed.liberty.8 → bench/log.12Feb07.eam.lmp.fixed.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# bulk Cu lattice
variable x index 20
@ -9,6 +9,7 @@ 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
@ -35,25 +36,25 @@ thermo 50
run 100
Memory usage per processor = 2.51765 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.35 18700.769
50 781.34228 -109870.68 0 -106639.02 52610.512
100 792.17919 -109916.28 0 -106639.81 51732.452
Loop time of 2.76732 on 8 procs for 100 steps with 32000 atoms
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 2.74317 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 2.17097 (78.4503)
Neigh time (%) = 0.18389 (6.64505)
Comm time (%) = 0.337954 (12.2123)
Outpt time (%) = 0.000817209 (0.0295307)
Other time (%) = 0.0736872 (2.66277)
Pair time (%) = 2.15412 (78.5268)
Neigh time (%) = 0.18556 (6.76443)
Comm time (%) = 0.321706 (11.7275)
Outpt time (%) = 0.00110888 (0.0404235)
Other time (%) = 0.0806725 (2.94085)
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 150650 min
Histogram: 2 1 0 0 3 0 1 0 0 1
Neighs: 151237 ave 152083 max 150648 min
Histogram: 2 1 0 0 3 1 0 0 0 1
Total # of neighbors = 1209898
Ave neighs/atom = 37.8093
Total # of neighbors = 1209894
Ave neighs/atom = 37.8092
Neighbor list builds = 13
Dangerous builds = 0

27
bench/log.1Oct06.eam.lmp.fixed.linux.1 → bench/log.12Feb07.eam.lmp.fixed.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# bulk Cu lattice
variable x index 20
@ -9,6 +9,7 @@ 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
@ -35,25 +36,25 @@ thermo 50
run 100
Memory usage per processor = 15.1091 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.35 18700.769
50 781.34228 -109870.68 0 -106639.02 52610.512
100 792.17919 -109916.28 0 -106639.81 51732.452
Loop time of 31.1581 on 1 procs for 100 steps with 32000 atoms
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 30.7455 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 27.3229 (87.6912)
Neigh time (%) = 2.60888 (8.37301)
Comm time (%) = 0.368158 (1.18158)
Outpt time (%) = 0.001816 (0.00582833)
Other time (%) = 0.85635 (2.7484)
Pair time (%) = 26.8708 (87.3973)
Neigh time (%) = 2.73064 (8.88142)
Comm time (%) = 0.334074 (1.08658)
Outpt time (%) = 0.00196 (0.00637491)
Other time (%) = 0.808084 (2.6283)
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: 1.2099e+06 ave 1.2099e+06 max 1.2099e+06 min
Neighs: 1.20989e+06 ave 1.20989e+06 max 1.20989e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209898
Ave neighs/atom = 37.8093
Total # of neighbors = 1209894
Ave neighs/atom = 37.8092
Neighbor list builds = 13
Dangerous builds = 0

29
bench/log.1Oct06.eam.lmp.scaled.liberty.8 → bench/log.12Feb07.eam.lmp.scaled.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# bulk Cu lattice
variable x index 20
@ -9,6 +9,7 @@ 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
@ -35,25 +36,25 @@ thermo 50
run 100
Memory usage per processor = 14.9873 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -906240 0 -853297.36 18701.28
50 799.87665 -879587.33 0 -853120.09 51528.346
100 784.7092 -879087.36 0 -853121.99 51929.574
Loop time of 23.074 on 8 procs for 100 steps with 256000 atoms
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 23.2889 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 18.7307 (81.1765)
Neigh time (%) = 1.95514 (8.47332)
Comm time (%) = 1.47881 (6.40896)
Outpt time (%) = 0.00384498 (0.0166636)
Other time (%) = 0.905552 (3.92455)
Pair time (%) = 19.0116 (81.6336)
Neigh time (%) = 1.94885 (8.36816)
Comm time (%) = 1.4661 (6.29526)
Outpt time (%) = 0.00339171 (0.0145637)
Other time (%) = 0.85899 (3.68841)
Nlocal: 32000 ave 32128 max 31853 min
Histogram: 1 0 1 1 0 1 1 2 0 1
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 1.20305e+06 min
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 = 9669468
Ave neighs/atom = 37.7714
Total # of neighbors = 9669450
Ave neighs/atom = 37.7713
Neighbor list builds = 14
Dangerous builds = 0

16
bench/log.1Oct06.lj.lmp.fixed.liberty.8 → bench/log.12Feb07.lj.lmp.fixed.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# 3d Lennard-Jones melt
variable x index 20
@ -9,6 +9,7 @@ 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
@ -35,13 +36,13 @@ Memory usage per processor = 2.13618 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 1.2329 on 8 procs for 100 steps with 32000 atoms
Loop time of 1.30724 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 0.803863 (65.2008)
Neigh time (%) = 0.0741274 (6.01243)
Comm time (%) = 0.294729 (23.9053)
Outpt time (%) = 0.000427932 (0.0347093)
Other time (%) = 0.059756 (4.84677)
Pair time (%) = 0.816335 (62.4473)
Neigh time (%) = 0.0767174 (5.86866)
Comm time (%) = 0.352994 (27.003)
Outpt time (%) = 0.000502974 (0.0384761)
Other time (%) = 0.060688 (4.64247)
Nlocal: 4000 ave 4038 max 3962 min
Histogram: 2 1 0 1 0 0 2 0 0 2
@ -54,4 +55,3 @@ Total # of neighbors = 1203529
Ave neighs/atom = 37.6103
Neighbor list builds = 5
Dangerous builds = 0

16
bench/log.1Oct06.lj.lmp.fixed.linux.1 → bench/log.12Feb07.lj.lmp.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# 3d Lennard-Jones melt
variable x index 20
@ -9,6 +9,7 @@ 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
@ -35,13 +36,13 @@ Memory usage per processor = 13.278 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 15.8447 on 1 procs for 100 steps with 32000 atoms
Loop time of 14.3764 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 13.7396 (86.7142)
Neigh time (%) = 1.07461 (6.78214)
Comm time (%) = 0.327973 (2.06993)
Outpt time (%) = 0.001538 (0.00970674)
Other time (%) = 0.700972 (4.42403)
Pair time (%) = 11.9406 (83.0576)
Neigh time (%) = 1.49862 (10.4242)
Comm time (%) = 0.27036 (1.88059)
Outpt time (%) = 0.000846 (0.00588466)
Other time (%) = 0.665877 (4.63175)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -54,4 +55,3 @@ Total # of neighbors = 1203529
Ave neighs/atom = 37.6103
Neighbor list builds = 5
Dangerous builds = 0

16
bench/log.1Oct06.lj.lmp.scaled.liberty.8 → bench/log.12Feb07.lj.lmp.scaled.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# 3d Lennard-Jones melt
variable x index 20
@ -9,6 +9,7 @@ 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
@ -35,13 +36,13 @@ Memory usage per processor = 13.1944 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 9.80536 on 8 procs for 100 steps with 256000 atoms
Loop time of 9.93393 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 7.10165 (72.4262)
Neigh time (%) = 0.641534 (6.54269)
Comm time (%) = 1.25001 (12.7483)
Outpt time (%) = 0.00192311 (0.0196129)
Other time (%) = 0.810236 (8.2632)
Pair time (%) = 7.17714 (72.2488)
Neigh time (%) = 0.639012 (6.43262)
Comm time (%) = 1.32449 (13.333)
Outpt time (%) = 0.00168276 (0.0169395)
Other time (%) = 0.791604 (7.96869)
Nlocal: 32000 ave 32077 max 31945 min
Histogram: 2 2 0 1 0 0 0 1 1 1
@ -54,4 +55,3 @@ Total # of neighbors = 9628940
Ave neighs/atom = 37.613
Neighbor list builds = 5
Dangerous builds = 0

54
bench/log.1Oct06.rhodo.lmp.fixed.liberty.8 → bench/log.12Feb07.rhodo.lmp.fixed.liberty.8
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@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# Rhodopsin model
units real
@ -51,35 +51,35 @@ PPPM initialization ...
brick FFT buffer size/proc = 7140 3072 3780
Memory usage per processor = 29.8784 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8070 KinEng = 21444.8287 Temp = 299.0420
PotEng = -46800.6357 E_bond = 2537.9940 E_angle = 10921.3742
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 = 203819.9996 E_long = -267197.4382 Press = -142.0854
E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456
Volume = 307995.0335
---------------- Step 50 ----- CPU = 10.3500 (sec) ----------------
TotEng = -25330.0515 KinEng = 21500.8719 Temp = 299.8235
PotEng = -46830.9234 E_bond = 2471.7510 E_angle = 10836.5171
E_dihed = 5239.6981 E_impro = 227.1295 E_vdwl = -1992.9813
E_coul = 203591.2432 E_long = -267204.2808 Press = 238.5401
Volume = 308031.8248
---------------- Step 100 ----- CPU = 21.1191 (sec) ----------------
TotEng = -25291.9828 KinEng = 21589.3087 Temp = 301.0567
PotEng = -46881.2915 E_bond = 2568.0314 E_angle = 10781.6607
E_dihed = 5198.3574 E_impro = 216.6809 E_vdwl = -1898.4756
E_coul = 203451.1288 E_long = -267198.6749 Press = 10.7061
Volume = 308134.7569
Loop time of 21.1201 on 8 procs for 100 steps with 32000 atoms
---------------- Step 50 ----- CPU = 9.4108 (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 = 19.1853 (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 19.1859 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 13.2797 (62.8773)
Bond time (%) = 0.57078 (2.70255)
Kspce time (%) = 3.77787 (17.8876)
Neigh time (%) = 1.58397 (7.49984)
Comm time (%) = 0.793642 (3.75777)
Outpt time (%) = 0.00181401 (0.00858903)
Other time (%) = 1.11227 (5.2664)
Pair time (%) = 12.5105 (65.2066)
Bond time (%) = 0.52636 (2.74347)
Kspce time (%) = 2.62125 (13.6624)
Neigh time (%) = 1.56684 (8.16665)
Comm time (%) = 0.816595 (4.25623)
Outpt time (%) = 0.00121596 (0.00633781)
Other time (%) = 1.14317 (5.95836)
FFT time (% of Kspce) = 0.459179 (12.1545)
FFT Gflps 3d 1d-only = 1.00804 7.35704
FFT time (% of Kspce) = 0.501384 (19.1277)
FFT Gflps 3d 1d-only = 0.92319 7.31311
Nlocal: 4000 ave 4083 max 3940 min
Histogram: 2 1 0 1 2 0 0 0 1 1
@ -88,7 +88,7 @@ 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 = 12027974
Total # of neighbors = 12027978
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11

54
bench/log.1Oct06.rhodo.lmp.fixed.linux.1 → bench/log.12Feb07.rhodo.lmp.fixed.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# Rhodopsin model
units real
@ -51,35 +51,35 @@ PPPM initialization ...
brick FFT buffer size/proc = 37555 23040 11655
Memory usage per processor = 134.397 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8070 KinEng = 21444.8287 Temp = 299.0420
PotEng = -46800.6357 E_bond = 2537.9940 E_angle = 10921.3742
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 = 203819.9996 E_long = -267197.4382 Press = -142.0854
E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456
Volume = 307995.0335
---------------- Step 50 ----- CPU = 158.6744 (sec) ----------------
TotEng = -25330.0515 KinEng = 21500.8719 Temp = 299.8235
PotEng = -46830.9234 E_bond = 2471.7510 E_angle = 10836.5171
E_dihed = 5239.6981 E_impro = 227.1295 E_vdwl = -1992.9813
E_coul = 203591.2432 E_long = -267204.2808 Press = 238.5401
Volume = 308031.8248
---------------- Step 100 ----- CPU = 322.3292 (sec) ----------------
TotEng = -25291.9828 KinEng = 21589.3087 Temp = 301.0567
PotEng = -46881.2915 E_bond = 2568.0314 E_angle = 10781.6607
E_dihed = 5198.3574 E_impro = 216.6809 E_vdwl = -1898.4756
E_coul = 203451.1288 E_long = -267198.6749 Press = 10.7061
Volume = 308134.7569
Loop time of 322.329 on 1 procs for 100 steps with 32000 atoms
---------------- Step 50 ----- CPU = 156.2625 (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 = 317.1181 (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 317.119 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 239.178 (74.203)
Bond time (%) = 7.33387 (2.27527)
Kspce time (%) = 19.0626 (5.914)
Neigh time (%) = 49.7111 (15.4224)
Comm time (%) = 0.930179 (0.28858)
Outpt time (%) = 0.003927 (0.00121832)
Other time (%) = 6.10957 (1.89544)
Pair time (%) = 232.058 (73.177)
Bond time (%) = 7.36005 (2.32091)
Kspce time (%) = 19.7418 (6.22536)
Neigh time (%) = 51.2461 (16.1599)
Comm time (%) = 0.820785 (0.258825)
Outpt time (%) = 0.002893 (0.000912275)
Other time (%) = 5.88915 (1.85708)
FFT time (% of Kspce) = 4.06694 (21.3347)
FFT Gflps 3d 1d-only = 0.113814 0.261395
FFT time (% of Kspce) = 3.83548 (19.4282)
FFT Gflps 3d 1d-only = 0.120682 0.247042
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -88,7 +88,7 @@ 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 = 12027974
Total # of neighbors = 12027978
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11

56
bench/log.1Oct06.rhodo.lmp.scaled.liberty.8 → bench/log.12Feb07.rhodo.lmp.scaled.liberty.8
View File

@ -1,4 +1,4 @@
LAMMPS (1 Oct 2006)
LAMMPS (12 Feb 2007)
# Rhodopsin model
variable x index 1
@ -69,37 +69,37 @@ PPPM initialization ...
grid = 48 64 60
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 37555 24576 11655
Memory usage per processor = 140.353 Mbytes
Memory usage per processor = 138.693 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -202846.4560 KinEng = 171558.6298 Temp = 299.0311
PotEng = -374405.0858 E_bond = 20303.9521 E_angle = 87370.9937
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 = 1630559.9965 E_long = -2137579.5054 Press = -142.0854
E_coul = 1630560.5366 E_long = -2137580.2135 Press = -142.0456
Volume = 2463960.2680
---------------- Step 50 ----- CPU = 80.3339 (sec) ----------------
TotEng = -202634.6400 KinEng = 172010.0889 Temp = 299.8180
PotEng = -374644.7289 E_bond = 19774.2719 E_angle = 86693.1834
E_dihed = 41917.7603 E_impro = 1817.0606 E_vdwl = -15943.4739
E_coul = 1628730.7042 E_long = -2137634.2354 Press = 238.6347
Volume = 2464254.6396
---------------- Step 100 ----- CPU = 165.2014 (sec) ----------------
TotEng = -202318.7870 KinEng = 172723.1177 Temp = 301.0609
PotEng = -375041.9047 E_bond = 20545.0687 E_angle = 86256.5048
E_dihed = 41587.4799 E_impro = 1733.5220 E_vdwl = -15187.0971
E_coul = 1627611.9671 E_long = -2137589.3501 Press = 10.9015
Volume = 2465078.6410
Loop time of 165.202 on 8 procs for 100 steps with 256000 atoms
---------------- Step 50 ----- CPU = 72.8553 (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 = 150.8302 (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 150.831 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 109.485 (66.2732)
Bond time (%) = 4.55416 (2.75672)
Kspce time (%) = 26.1207 (15.8114)
Neigh time (%) = 14.7538 (8.93074)
Comm time (%) = 2.72842 (1.65156)
Outpt time (%) = 0.00508916 (0.00308057)
Other time (%) = 7.55527 (4.57335)
Pair time (%) = 101.656 (67.3972)
Bond time (%) = 4.32254 (2.86581)
Kspce time (%) = 20.0325 (13.2814)
Neigh time (%) = 14.8069 (9.81688)
Comm time (%) = 2.77154 (1.83751)
Outpt time (%) = 0.00373158 (0.00247401)
Other time (%) = 7.23789 (4.79867)
FFT time (% of Kspce) = 6.32901 (24.2299)
FFT Gflps 3d 1d-only = 0.7062 7.01015
FFT time (% of Kspce) = 5.40172 (26.9648)
FFT Gflps 3d 1d-only = 0.827431 7.20053
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 8 0 0 0 0 0 0 0 0 0
@ -108,7 +108,7 @@ 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 = 96223728
Total # of neighbors = 96223696
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11

45
bench/log.1Oct06.chute.lmp.scaled.liberty.8
View File

@ -1,45 +0,0 @@
LAMMPS (1 Oct 2006)
# 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
2 by 2 by 2 processor grid
32000 atoms
32000 velocities
replicate $x $y 1
replicate 2 $y 1
replicate 2 4 1
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
ERROR: Pair style peri requires atoms have IDs