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Merge branch 'master' into openmp-master

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This commit is contained in:
Axel Kohlmeyer
2012-01-10 19:18:35 -05:00
parent 68ac4a3356 c3748688aa
commit a0447652a0
183 changed files with 13777 additions and 11080 deletions
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18
bench/log.28Mar11.chain.fixed.linux.1 → bench/log.9Jan12.chain.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# FENE beadspring benchmark
units lj
@ -8,7 +8,7 @@ special_bonds fene
read_data data.chain
1 = max bonds/atom
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
31680 bonds
@ -36,14 +36,14 @@ Memory usage per processor = 11.3536 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 1.87328 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.00598 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.438668 (23.4171)
Bond time (%) = 0.289005 (15.4277)
Neigh time (%) = 0.679554 (36.2761)
Comm time (%) = 0.0552287 (2.94823)
Outpt time (%) = 0.00018096 (0.00966003)
Other time (%) = 0.410646 (21.9212)
Pair time (%) = 0.200669 (19.9477)
Bond time (%) = 0.116349 (11.5657)
Neigh time (%) = 0.434148 (43.1567)
Comm time (%) = 0.0310009 (3.08166)
Outpt time (%) = 9.799e-05 (0.00974076)
Other time (%) = 0.223714 (22.2385)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

18
bench/log.28Mar11.chain.fixed.linux.4 → bench/log.9Jan12.chain.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# FENE beadspring benchmark
units lj
@ -8,7 +8,7 @@ special_bonds fene
read_data data.chain
1 = max bonds/atom
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
31680 bonds
@ -36,14 +36,14 @@ Memory usage per processor = 4.80505 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.97145835 0.43803883 20.502691 22.397872 4.626988
Loop time of 0.436674 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.277092 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0835696 (19.1378)
Bond time (%) = 0.0588097 (13.4677)
Neigh time (%) = 0.157872 (36.1532)
Comm time (%) = 0.047663 (10.915)
Outpt time (%) = 9.69768e-05 (0.0222081)
Other time (%) = 0.0886627 (20.3041)
Pair time (%) = 0.0511394 (18.4557)
Bond time (%) = 0.030314 (10.94)
Neigh time (%) = 0.112937 (40.7578)
Comm time (%) = 0.0222602 (8.03351)
Outpt time (%) = 6.1214e-05 (0.0220915)
Other time (%) = 0.0603806 (21.7908)
Nlocal: 8000 ave 8030 max 7974 min
Histogram: 1 0 0 1 0 1 0 0 0 1

20
bench/log.28Mar11.chain.scaled.linux.4 → bench/log.9Jan12.chain.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# FENE beadspring benchmark
variable x index 1
@ -13,7 +13,7 @@ special_bonds fene
read_data data.chain
1 = max bonds/atom
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
31680 bonds
@ -25,7 +25,7 @@ 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
2 by 2 by 1 MPI processor grid
128000 atoms
126720 bonds
2 = max # of 1-2 neighbors
@ -52,14 +52,14 @@ Memory usage per processor = 13.3552 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
100 0.97682955 0.44239968 20.500229 22.407862 4.6527025
Loop time of 2.4188 on 4 procs for 100 steps with 128000 atoms
Loop time of 1.16957 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 0.507936 (20.9995)
Bond time (%) = 0.340843 (14.0914)
Neigh time (%) = 0.735922 (30.425)
Comm time (%) = 0.228828 (9.46038)
Outpt time (%) = 0.000289202 (0.0119564)
Other time (%) = 0.604987 (25.0118)
Pair time (%) = 0.227149 (19.4215)
Bond time (%) = 0.123806 (10.5856)
Neigh time (%) = 0.472906 (40.4341)
Comm time (%) = 0.0951706 (8.13721)
Outpt time (%) = 0.000224173 (0.0191671)
Other time (%) = 0.250317 (21.4025)
Nlocal: 32000 ave 32015 max 31983 min
Histogram: 1 0 1 0 0 0 0 0 1 1

20
bench/log.28Mar11.chute.fixed.linux.1 → bench/log.9Jan12.chute.fixed.linux.1
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@ -1,16 +1,16 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style granular
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
@ -38,17 +38,17 @@ thermo_modify norm no
thermo 100
run 100
Memory usage per processor = 35.2505 Mbytes
Memory usage per processor = 34.9301 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 1.58777 on 1 procs for 100 steps with 32000 atoms
Loop time of 0.54713 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.887784 (55.9139)
Neigh time (%) = 0.070847 (4.46205)
Comm time (%) = 0.0669501 (4.21661)
Outpt time (%) = 0.000550032 (0.0346418)
Other time (%) = 0.561639 (35.3728)
Pair time (%) = 0.328969 (60.1262)
Neigh time (%) = 0.04423 (8.084)
Comm time (%) = 0.0182245 (3.33092)
Outpt time (%) = 0.00019002 (0.0347302)
Other time (%) = 0.155517 (28.4242)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

20
bench/log.28Mar11.chute.fixed.linux.4 → bench/log.9Jan12.chute.fixed.linux.4
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@ -1,16 +1,16 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style granular
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
2 by 1 by 2 processor grid
2 by 1 by 2 MPI processor grid
32000 atoms
32000 velocities
@ -38,17 +38,17 @@ thermo_modify norm no
thermo 100
run 100
Memory usage per processor = 15.4199 Mbytes
Memory usage per processor = 15.2765 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 0.270323 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.146905 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.135713 (50.2038)
Neigh time (%) = 0.0173983 (6.43611)
Comm time (%) = 0.0378563 (14.0041)
Outpt time (%) = 0.000246227 (0.091086)
Other time (%) = 0.0791097 (29.2649)
Pair time (%) = 0.0729731 (49.6735)
Neigh time (%) = 0.0111947 (7.62035)
Comm time (%) = 0.0153095 (10.4213)
Outpt time (%) = 0.000119746 (0.0815122)
Other time (%) = 0.0473083 (32.2033)
Nlocal: 8000 ave 8010 max 7990 min
Histogram: 2 0 0 0 0 0 0 0 0 2

22
bench/log.28Mar11.chute.scaled.linux.4 → bench/log.9Jan12.chute.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -6,14 +6,14 @@ variable x index 1
variable y index 1
units lj
atom_style granular
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
2 by 1 by 2 processor grid
2 by 1 by 2 MPI processor grid
32000 atoms
32000 velocities
@ -21,7 +21,7 @@ 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
4 by 1 by 1 MPI processor grid
128000 atoms
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
@ -48,17 +48,17 @@ thermo_modify norm no
thermo 100
run 100
Memory usage per processor = 37.3912 Mbytes
Memory usage per processor = 37.0464 Mbytes
Step Atoms KinEng 1 Volume
0 128000 3136556.5 6404.5051 119323.52
100 128000 3137160 6284.0549 119327.22
Loop time of 2.79202 on 4 procs for 100 steps with 128000 atoms
Loop time of 0.893496 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 1.13366 (40.6034)
Neigh time (%) = 0.0699974 (2.50705)
Comm time (%) = 0.24415 (8.74457)
Outpt time (%) = 0.00162953 (0.0583639)
Other time (%) = 1.34259 (48.0866)
Pair time (%) = 0.524706 (58.7251)
Neigh time (%) = 0.0462004 (5.17075)
Comm time (%) = 0.0590464 (6.60847)
Outpt time (%) = 0.00043273 (0.0484311)
Other time (%) = 0.26311 (29.4473)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

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bench/log.28Mar11.eam.fixed.linux.1 → bench/log.9Jan12.eam.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# bulk Cu lattice
variable x index 1
@ -23,7 +23,7 @@ region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
@ -46,13 +46,13 @@ Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 11.4086 on 1 procs for 100 steps with 32000 atoms
Loop time of 5.8924 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 10.2465 (89.814)
Neigh time (%) = 0.893404 (7.83096)
Comm time (%) = 0.0694258 (0.608539)
Outpt time (%) = 0.000409126 (0.00358612)
Other time (%) = 0.198848 (1.74296)
Pair time (%) = 5.20714 (88.3704)
Neigh time (%) = 0.579568 (9.83586)
Comm time (%) = 0.0308812 (0.524085)
Outpt time (%) = 0.000219822 (0.0037306)
Other time (%) = 0.0745952 (1.26596)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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bench/log.28Mar11.eam.fixed.linux.4 → bench/log.9Jan12.eam.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# bulk Cu lattice
variable x index 1
@ -23,7 +23,7 @@ region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
@ -46,13 +46,13 @@ Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 2.84421 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.58434 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 2.47554 (87.0379)
Neigh time (%) = 0.216563 (7.61418)
Comm time (%) = 0.104262 (3.66577)
Outpt time (%) = 0.000251591 (0.00884573)
Other time (%) = 0.0475937 (1.67335)
Pair time (%) = 1.37178 (86.5835)
Neigh time (%) = 0.151559 (9.56606)
Comm time (%) = 0.0399128 (2.5192)
Outpt time (%) = 0.000169277 (0.0106844)
Other time (%) = 0.0209216 (1.32052)
Nlocal: 8000 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1

16
bench/log.28Mar11.eam.scaled.linux.4 → bench/log.9Jan12.eam.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# bulk Cu lattice
variable x index 1
@ -23,7 +23,7 @@ region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (144.6 144.6 72.3)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 128000 atoms
@ -46,13 +46,13 @@ Step Temp E_pair E_mol TotEng Press
0 1600 -453120 0 -426647.73 18704.012
50 779.50001 -439457.02 0 -426560.06 52355.276
100 797.97828 -439764.76 0 -426562.07 51474.74
Loop time of 12.0882 on 4 procs for 100 steps with 128000 atoms
Loop time of 6.64398 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 10.3589 (85.6942)
Neigh time (%) = 0.963713 (7.97234)
Comm time (%) = 0.316817 (2.62088)
Outpt time (%) = 0.000717819 (0.00593818)
Other time (%) = 0.448062 (3.70661)
Pair time (%) = 5.7169 (86.0464)
Neigh time (%) = 0.659102 (9.92029)
Comm time (%) = 0.164221 (2.47173)
Outpt time (%) = 0.000294626 (0.00443448)
Other time (%) = 0.103457 (1.55716)
Nlocal: 32000 ave 32092 max 31914 min
Histogram: 1 0 0 1 0 1 0 0 0 1

16
bench/log.28Mar11.lj.fixed.linux.1 → bench/log.9Jan12.lj.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
variable x index 1
@ -23,7 +23,7 @@ region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
@ -43,13 +43,13 @@ Memory usage per processor = 13.2267 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 4.24155 on 1 procs for 100 steps with 32000 atoms
Loop time of 2.24442 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 3.6555 (86.1832)
Neigh time (%) = 0.359136 (8.4671)
Comm time (%) = 0.0590658 (1.39255)
Outpt time (%) = 0.000212193 (0.00500272)
Other time (%) = 0.167634 (3.95218)
Pair time (%) = 1.92371 (85.7108)
Neigh time (%) = 0.23672 (10.547)
Comm time (%) = 0.0241742 (1.07708)
Outpt time (%) = 0.000104189 (0.00464212)
Other time (%) = 0.059711 (2.66042)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

16
bench/log.28Mar11.lj.fixed.linux.4 → bench/log.9Jan12.lj.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
variable x index 1
@ -23,7 +23,7 @@ region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
@ -43,13 +43,13 @@ Memory usage per processor = 4.31284 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 1.08102 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.62139 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.86205 (79.7443)
Neigh time (%) = 0.0897413 (8.30156)
Comm time (%) = 0.0998399 (9.23573)
Outpt time (%) = 0.000194311 (0.0179748)
Other time (%) = 0.0291918 (2.7004)
Pair time (%) = 0.502622 (80.8866)
Neigh time (%) = 0.0616071 (9.9144)
Comm time (%) = 0.0411073 (6.61538)
Outpt time (%) = 5.79953e-05 (0.00933316)
Other time (%) = 0.0159961 (2.57424)
Nlocal: 8000 ave 8037 max 7964 min
Histogram: 2 0 0 0 0 0 0 0 1 1

16
bench/log.28Mar11.lj.scaled.linux.4 → bench/log.9Jan12.lj.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
variable x index 1
@ -23,7 +23,7 @@ region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 128000 atoms
mass 1 1.0
@ -43,13 +43,13 @@ Memory usage per processor = 13.1495 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6133849 -5.0196788
100 0.75841891 -5.759957 0 -4.6223375 0.20008866
Loop time of 4.71885 on 4 procs for 100 steps with 128000 atoms
Loop time of 2.43423 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 3.70177 (78.4464)
Neigh time (%) = 0.350671 (7.43129)
Comm time (%) = 0.278878 (5.90987)
Outpt time (%) = 0.000279307 (0.00591897)
Other time (%) = 0.387254 (8.20654)
Pair time (%) = 2.04092 (83.8422)
Neigh time (%) = 0.238374 (9.79258)
Comm time (%) = 0.0766696 (3.14964)
Outpt time (%) = 0.000154495 (0.00634677)
Other time (%) = 0.0781193 (3.20919)
Nlocal: 32000 ave 32060 max 31939 min
Histogram: 1 0 1 0 0 0 0 1 0 1

31
bench/log.28Mar11.rhodo.fixed.linux.1 → bench/log.9Jan12.rhodo.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# Rhodopsin model
units real
@ -19,7 +19,7 @@ read_data data.rhodo
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
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
@ -50,6 +50,7 @@ PPPM initialization ...
grid = 25 32 32
stencil order = 5
RMS precision = 7.57143e-05
using double precision FFTs
brick FFT buffer size/proc = 41070 25600 12321
Memory usage per processor = 138.965 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
@ -58,30 +59,30 @@ PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 50 ----- CPU = 32.2123 (sec) ----------------
---------------- Step 50 ----- CPU = 17.8190 (sec) ----------------
TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230
PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753
E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744
Volume = 308031.5641
---------------- Step 100 ----- CPU = 65.3867 (sec) ----------------
---------------- Step 100 ----- CPU = 36.2635 (sec) ----------------
TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
E_coul = 206654.9995 E_long = -270400.7389 Press = 6.9875
E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875
Volume = 308133.9900
Loop time of 65.3868 on 1 procs for 100 steps with 32000 atoms
Loop time of 36.2636 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 46.2231 (70.6918)
Bond time (%) = 2.88711 (4.41543)
Kspce time (%) = 7.06667 (10.8075)
Neigh time (%) = 6.61535 (10.1173)
Comm time (%) = 0.185745 (0.28407)
Outpt time (%) = 0.000392199 (0.000599813)
Other time (%) = 2.4084 (3.68331)
Pair time (%) = 25.8498 (71.283)
Bond time (%) = 1.49598 (4.1253)
Kspce time (%) = 3.27236 (9.02382)
Neigh time (%) = 4.27552 (11.7901)
Comm time (%) = 0.0665278 (0.183456)
Outpt time (%) = 0.000251055 (0.000692305)
Other time (%) = 1.30319 (3.59366)
FFT time (% of Kspce) = 0.430403 (6.0906)
FFT Gflps 3d (1d only) = 1.20747 1.74267
FFT time (% of Kspce) = 0.279837 (8.55152)
FFT Gflps 3d (1d only) = 1.85715 3.22108
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

31
bench/log.28Mar11.rhodo.fixed.linux.4 → bench/log.9Jan12.rhodo.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# Rhodopsin model
units real
@ -19,7 +19,7 @@ read_data data.rhodo
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
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
@ -50,6 +50,7 @@ PPPM initialization ...
grid = 25 32 32
stencil order = 5
RMS precision = 7.57143e-05
using double precision FFTs
brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 54.4744 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
@ -58,30 +59,30 @@ PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 50 ----- CPU = 8.2683 (sec) ----------------
---------------- Step 50 ----- CPU = 4.7389 (sec) ----------------
TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230
PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753
E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744
Volume = 308031.5641
---------------- Step 100 ----- CPU = 16.8728 (sec) ----------------
---------------- Step 100 ----- CPU = 9.6394 (sec) ----------------
TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
E_coul = 206654.9995 E_long = -270400.7389 Press = 6.9875
E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875
Volume = 308133.9900
Loop time of 16.8729 on 4 procs for 100 steps with 32000 atoms
Loop time of 9.63943 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 11.2248 (66.5258)
Bond time (%) = 0.687313 (4.07347)
Kspce time (%) = 2.07329 (12.2877)
Neigh time (%) = 1.59928 (9.47838)
Comm time (%) = 0.410708 (2.43412)
Outpt time (%) = 0.000243425 (0.0014427)
Other time (%) = 0.877245 (5.19914)
Pair time (%) = 6.60502 (68.5208)
Bond time (%) = 0.375643 (3.89695)
Kspce time (%) = 1.09311 (11.3399)
Neigh time (%) = 1.08158 (11.2203)
Comm time (%) = 0.0815379 (0.845879)
Outpt time (%) = 0.000157952 (0.00163861)
Other time (%) = 0.402393 (4.17445)
FFT time (% of Kspce) = 0.223284 (10.7696)
FFT Gflps 3d (1d only) = 2.32752 6.8543
FFT time (% of Kspce) = 0.0966156 (8.83863)
FFT Gflps 3d (1d only) = 5.37903 12.4303
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1

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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# Rhodopsin model
variable x index 1
@ -24,7 +24,7 @@ read_data data.rhodo
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
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
@ -41,7 +41,7 @@ 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
2 by 2 by 1 MPI processor grid
128000 atoms
110892 bonds
161868 angles
@ -71,38 +71,39 @@ PPPM initialization ...
grid = 48 60 36
stencil order = 5
RMS precision = 7.66425e-05
using double precision FFTs
brick FFT buffer size/proc = 41615 25920 12915
Memory usage per processor = 146.135 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4825 KinEng = 85779.3251 Temp = 299.0304
TotEng = -101425.4826 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
E_coul = 827025.3556 E_long = -1080537.3748 Press = -142.3084
E_coul = 827025.3556 E_long = -1080537.3749 Press = -142.3084
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 32.8194 (sec) ----------------
TotEng = -101320.2611 KinEng = 86003.4849 Temp = 299.8118
PotEng = -187323.7460 E_bond = 9887.1072 E_angle = 43346.7920
---------------- Step 50 ----- CPU = 19.1088 (sec) ----------------
TotEng = -101320.2612 KinEng = 86003.4849 Temp = 299.8118
PotEng = -187323.7461 E_bond = 9887.1072 E_angle = 43346.7920
E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456
E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165
Volume = 1232126.1854
---------------- Step 100 ----- CPU = 66.9547 (sec) ----------------
TotEng = -101158.1519 KinEng = 86355.6231 Temp = 301.0394
PotEng = -187513.7749 E_bond = 10272.0700 E_angle = 43128.6453
---------------- Step 100 ----- CPU = 39.1056 (sec) ----------------
TotEng = -101158.1517 KinEng = 86355.6231 Temp = 301.0394
PotEng = -187513.7747 E_bond = 10272.0700 E_angle = 43128.6453
E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196
E_coul = 825555.5006 E_long = -1080544.3306 Press = 15.2192
E_coul = 825555.5009 E_long = -1080544.3307 Press = 15.2192
Volume = 1232535.8453
Loop time of 66.9548 on 4 procs for 100 steps with 128000 atoms
Loop time of 39.1057 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 45.779 (68.373)
Bond time (%) = 2.87439 (4.29303)
Kspce time (%) = 7.5089 (11.2149)
Neigh time (%) = 6.52016 (9.73816)
Comm time (%) = 0.765243 (1.14293)
Outpt time (%) = 0.000411808 (0.000615055)
Other time (%) = 3.50669 (5.2374)
Pair time (%) = 27.0353 (69.1339)
Bond time (%) = 1.5462 (3.9539)
Kspce time (%) = 4.17715 (10.6817)
Neigh time (%) = 4.37974 (11.1997)
Comm time (%) = 0.208052 (0.532026)
Outpt time (%) = 0.000296533 (0.000758287)
Other time (%) = 1.75896 (4.49797)
FFT time (% of Kspce) = 1.17001 (15.5816)
FFT Gflps 3d (1d only) = 2.04683 6.15771
FFT time (% of Kspce) = 0.535835 (12.8278)
FFT Gflps 3d (1d only) = 4.46931 11.0706
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

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@ -0,0 +1,13 @@
\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
\phi\left(r\right) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
E\left(r\right) & = & \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
\end{eqnarray*}
\end{document}

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12
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@ -426,12 +426,12 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -665,6 +665,7 @@ potentials. Click on the style itself for a full description:
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/smooth"_pair_lj_smooth.html,
"lj/smooth/linear"_pair_lj_smooth_linear.html,
"lj96/cut"_pair_lj96.html,
"lubricate"_pair_lubricate.html,
"lubricate/poly"_pair_lubricate.html,

1
doc/Section_intro.html
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@ -109,6 +109,7 @@ it to LAMMPS.
<LI> open-source distribution
<LI> highly portable C++
<LI> optional libraries used: MPI and single-processor FFT
<LI> GPU (CUDA and OpenCL) and OpenMP support for many code features
<LI> easy to extend with new features and functionality
<LI> runs from an input script
<LI> syntax for defining and using variables and formulas

1
doc/Section_intro.txt
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@ -105,6 +105,7 @@ General features :h4
open-source distribution
highly portable C++
optional libraries used: MPI and single-processor FFT
GPU (CUDA and OpenCL) and OpenMP support for many code features
easy to extend with new features and functionality
runs from an input script
syntax for defining and using variables and formulas

12
doc/Section_packages.html
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@ -49,14 +49,14 @@ packages, more details are provided.
<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">howto</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_1">howto</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_1">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
@ -97,16 +97,16 @@ E.g. "peptide" refers to the examples/peptide directory.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EWALDN</TD><TD > Ewald for 1/R^n</TD><TD > Pieter in' t Veld (BASF)</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_2">accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_2">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">SPH_LAMMPS_userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>

12
doc/Section_packages.txt
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@ -44,14 +44,14 @@ CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
GPU, GPU-enabled potentials, Mike Brown (ORNL), "accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu
GPU, GPU-enabled potentials, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu
GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, -
KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
MOLECULE, molecular system force fields, -, "howto"_Section_howto.html#howto_3, peptide, -
OPT, optimized pair potentials, Fischer & Richie & Natoli (2), "howto"_Section_accelerate.html#acc_1, -, -
OPT, optimized pair potentials, Fischer & Richie & Natoli (2), "Section accelerate"_Section_accelerate.html#acc_1, -, -
PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
@ -89,16 +89,16 @@ The "Library" column lists an external library which must be built first and whi
The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
USER-MISC, single-file contributions, USER-MISC/README, -, -, -, -
USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "accelerate"_Section_accelerate.html#acc_4, USER/cuda, -, lib/cuda
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_Section_accelerate.html#acc_4, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-EWALDN, Ewald for 1/R^n, Pieter in' t Veld (BASF), "kspace_style"_kspace_style.html, -, -, -
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "accelerate"_Section_accelerate.html#acc_2, -, -, -
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_Section_accelerate.html#acc_2, -, -, -
USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH_LAMMPS_userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
:tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc)

1
doc/pair_coeff.html
View File

@ -134,6 +134,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity

1
doc/pair_coeff.txt
View File

@ -131,6 +131,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity

111
doc/pair_lj_cut_smooth.html Normal file
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@ -0,0 +1,111 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/cut/smooth command
</H3>
<H3>pair_style lj/cut/smooth/cuda command
</H3>
<H3>pair_style lj/cut/smooth/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/cut/smooth Rc
</PRE>
<UL><LI>Rc = cutoff for lj/cut/smooth interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut/smooth 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/cut/smooth</I> computes a LJ interaction that combines the standard
12/6 Lennard-Jones function and subtracts a linear term that includes a
cutoff distance Rc.
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_cut_smooth.jpg">
</CENTER>
<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>If not specified, the global value for Rc is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients and
cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

3
doc/pair_lj_smooth.html
View File

@ -121,7 +121,8 @@ to be specified in an input script that reads a restart file.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lj_smooth_linear.html">pair
lj/smooth/linear</A>
</P>
<P><B>Default:</B> none
</P>

3
doc/pair_lj_smooth.txt
View File

@ -116,6 +116,7 @@ This pair style can only be used via the {pair} keyword of the
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_coeff"_pair_coeff.html, "pair
lj/smooth/linear"_pair_lj_smooth_linear.html
[Default:] none

86
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@ -0,0 +1,86 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/smooth/linear command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/smooth/linear Rc
</PRE>
<UL><LI>Rc = cutoff for lj/smooth/linear interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/smooth/linear</I> computes a LJ interaction that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term that
includes the cutoff distance Rc, as in this formula:
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_cut_smooth.jpg">
</CENTER>
<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global value
for Rc is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lj_smooth.html">pair lj/smooth</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

81
doc/pair_lj_smooth_linear.txt Normal file
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@ -0,0 +1,81 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/smooth/linear command :h3
[Syntax:]
pair_style lj/smooth/linear Rc :pre
Rc = cutoff for lj/smooth/linear interactions (distance units) :ul
[Examples:]
pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0 :pre
[Description:]
Style {lj/smooth/linear} computes a LJ interaction that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term that
includes the cutoff distance Rc, as in this formula:
:c,image(Eqs/pair_lj_cut_smooth.jpg)
At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global value
for Rc is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant for
this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html
[Default:] none

1
doc/pair_style.html
View File

@ -136,6 +136,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity

1
doc/pair_style.txt
View File

@ -133,6 +133,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity

120
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@ -1,120 +0,0 @@
LAMMPS (27 Mar 2011)
# Big colloid particles and small LJ particles
units lj
atom_style atomic
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
mass 1 9
mass 2 1
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.20285 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.012748525 2.156691 0.073994939 28660.577
6000 2.1073992 0.0076702482 2.1127279 0.097655994 21544.211
7000 2.0845788 -0.0022301947 2.0800324 0.1101457 17791.284
8000 2.0651397 0.0033390713 2.0661842 0.12822835 15494.655
9000 2.0578744 0.0021876274 2.0577755 0.14877329 13860.573
10000 2.050871 0.0074002268 2.0559924 0.16711807 12582.351
11000 2.0393903 0.02180458 2.0589289 0.21757395 11491.106
12000 2.0417078 0.014064648 2.0535038 0.21091044 10565.52
13000 2.0453265 0.0142046 2.0572586 0.23958431 9773.8989
14000 2.0241495 0.030159631 2.05206 0.25409138 9178.076
15000 2.0352822 0.019352462 2.0523732 0.26816816 8601.8792
16000 2.0396728 0.013649097 2.0510556 0.2897209 8117.7222
17000 2.0021829 0.051638556 2.0515968 0.35978072 7694.4722
18000 2.0323755 0.021980006 2.0520973 0.33886022 7331.3619
19000 2.012523 0.039400171 2.049687 0.38829143 7030.9065
20000 2.0210256 0.032912604 2.0516927 0.4026689 6790.5438
21000 2.0347446 0.019902556 2.0523864 0.4007124 6532.5107
22000 2.0264802 0.027247056 2.0514756 0.41874743 6310.6473
23000 2.0284647 0.030679317 2.0568901 0.4253006 6110.0448
24000 1.9937762 0.06381727 2.0553781 0.49092603 5923.5093
25000 2.0353922 0.027248288 2.0603789 0.45091442 5737.0476
26000 2.0237478 0.037618141 2.0591174 0.53619978 5562.6505
27000 2.0242618 0.033821875 2.0558345 0.4959782 5460.2661
28000 2.0482322 0.01320251 2.0591589 0.44939498 5345.4687
29000 2.0287333 0.03621241 2.0626916 0.55562251 5180.2806
30000 2.0040988 0.059211727 2.0610838 0.61808251 5068.541
31000 2.0042212 0.061798172 2.0637924 0.64370526 4957.2604
32000 2.0245435 0.035546139 2.0578402 0.59067342 4872.1932
33000 1.9919557 0.078345663 2.0680881 0.68910022 4765.4334
34000 2.0262779 0.047027618 2.0710541 0.65966618 4657.8074
35000 1.9912139 0.080509163 2.0695106 0.69023472 4598.459
36000 2.0190325 0.053614947 2.0704041 0.67782728 4531.4932
37000 2.0131766 0.063296775 2.0742365 0.74369947 4450.7232
38000 2.0192742 0.059523787 2.0765544 0.72790998 4369.6931
39000 2.0259464 0.057405211 2.0811006 0.76212505 4290.5877
40000 2.0257778 0.050559606 2.0740865 0.75709818 4241.812
41000 2.0210186 0.056870746 2.0756437 0.76054223 4186.8833
42000 1.9726145 0.10828461 2.0787073 0.96623593 4130.8878
43000 2.0163335 0.068098169 2.0821913 0.7724108 4088.3897
44000 1.9702837 0.11909487 2.0871894 0.978469 4023.8067
45000 2.003942 0.090213491 2.0919289 0.92974367 3981.7386
46000 2.0200434 0.069364002 2.0871629 0.8297056 3926.0172
47000 2.041283 0.050439502 2.0894544 0.84552678 3880.6095
48000 2.0172704 0.082594045 2.097623 0.97243304 3823.5355
49000 2.0208893 0.082783178 2.101427 0.97976434 3742.0596
50000 1.9739277 0.11636826 2.0881027 1.0449823 3710.4102
Loop time of 14.2309 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 7.41369 (52.0957)
Neigh time (%) = 1.58633 (11.1471)
Comm time (%) = 0.34565 (2.42887)
Outpt time (%) = 0.344466 (2.42055)
Other time (%) = 4.54078 (31.9079)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 585 ave 585 max 585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6048 ave 6048 max 6048 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6048
Ave neighs/atom = 6.72
Neighbor list builds = 3124
Dangerous builds = 0

120
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@ -1,120 +0,0 @@
LAMMPS (27 Mar 2011)
# Big colloid particles and small LJ particles
units lj
atom_style atomic
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
mass 1 9
mass 2 1
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.10785 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
6000 2.1073955 0.0076739854 2.1127279 0.09765736 21544.21
7000 2.084383 -0.002011532 2.0800555 0.11035732 17791.249
8000 2.0697462 -0.0035908236 2.0638557 0.12727264 15495.564
9000 2.0565713 0.005100289 2.0593865 0.14847835 13885.03
10000 2.0498621 0.0063267281 2.0539112 0.15879624 12601.99
11000 2.0438679 0.018955755 2.0605527 0.18959409 11490.646
12000 2.053458 0.0044167998 2.0555932 0.19336438 10572.921
13000 2.0429256 0.013698073 2.0543538 0.21707695 9791.7501
14000 2.0132501 0.042422704 2.0534359 0.27926827 9147.46
15000 2.0501152 0.0064708164 2.0543081 0.25954559 8659.5624
16000 2.0371395 0.017291634 2.0521676 0.27240923 8172.3226
17000 2.0267747 0.025623672 2.0501464 0.32046495 7767.5953
18000 2.0422824 0.014182115 2.0541954 0.30856342 7387.0945
19000 2.0027128 0.050847835 2.0513354 0.39430768 7044.3881
20000 2.0325646 0.021042471 2.0513486 0.35372598 6769.9838
21000 2.0124313 0.042181593 2.0523768 0.4063794 6509.7544
22000 2.0156252 0.041583224 2.0549689 0.49055441 6281.6377
23000 2.0075157 0.050694007 2.0559791 0.45052595 6080.274
24000 2.0154057 0.036452118 2.0496185 0.48202632 5968.6572
25000 2.0327476 0.029856988 2.060346 0.45561293 5789.7049
26000 1.9897031 0.073921207 2.0614135 0.60112592 5586.2292
27000 2.0440727 0.021849226 2.0636507 0.4825674 5413.6275
28000 2.0045554 0.055337087 2.0576652 0.5591706 5298.2659
29000 2.027287 0.038894068 2.0639286 0.56087137 5177.1542
30000 2.0205914 0.043248372 2.0615947 0.53487433 5070.7318
31000 2.0184388 0.050748054 2.0669441 0.57538446 4976.0508
32000 2.0204751 0.051328968 2.0695591 0.64728677 4878.005
33000 2.0111467 0.060162066 2.0690742 0.62331567 4778.195
34000 2.0284013 0.037363433 2.0635109 0.59724203 4697.3593
35000 1.9845749 0.089467073 2.0718369 0.80254883 4596.7715
36000 2.0062209 0.06902456 2.0730164 0.7322564 4510.2606
37000 2.0232674 0.050125477 2.0711448 0.67066837 4442.9312
38000 2.0347246 0.038024633 2.0704884 0.64951947 4386.1564
39000 2.036067 0.047110384 2.0809151 0.69569962 4289.3392
40000 2.0172137 0.061776712 2.0767491 0.83452283 4219.7458
41000 2.0169547 0.064700391 2.079414 0.89024009 4172.0666
42000 1.9900577 0.089235744 2.0770823 0.85956089 4130.4701
43000 2.0171326 0.075093255 2.0899846 0.86806073 4054.2948
44000 2.0245424 0.062474807 2.0847677 0.87695757 3994.1455
45000 1.9781553 0.10428775 2.0802451 1.0152832 3960.5022
46000 2.0360719 0.056999986 2.0908095 0.78346649 3913.7871
47000 2.0117075 0.078216122 2.0876884 0.95590478 3872.147
48000 1.9995682 0.090946084 2.0882926 0.94568469 3834.7404
49000 1.9904732 0.10585353 2.0941151 0.97553505 3797.357
50000 2.0135224 0.080467977 2.0917532 0.94694354 3769.7374
Loop time of 6.07169 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.86265 (30.6775)
Neigh time (%) = 0.397185 (6.54159)
Comm time (%) = 1.58736 (26.1436)
Outpt time (%) = 0.248944 (4.10007)
Other time (%) = 1.97556 (32.5373)
Nlocal: 225 ave 237 max 201 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 316.25 ave 350 max 291 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1511.25 ave 1653 max 1354 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 6045
Ave neighs/atom = 6.71667
Neighbor list builds = 3136
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.96579 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.012748525 2.156691 0.073994939 28660.577
6000 2.1073992 0.0076702482 2.1127279 0.097655994 21544.211
7000 2.0845788 -0.0022301947 2.0800324 0.1101457 17791.284
8000 2.0651397 0.0033390713 2.0661842 0.12822835 15494.655
9000 2.0578744 0.0021876274 2.0577755 0.14877329 13860.573
10000 2.050871 0.0074002268 2.0559924 0.16711807 12582.351
11000 2.0393903 0.02180458 2.0589289 0.21757395 11491.106
12000 2.0417078 0.014064648 2.0535038 0.21091044 10565.52
13000 2.0453265 0.0142046 2.0572586 0.23958431 9773.8989
14000 2.0241495 0.030159631 2.05206 0.25409138 9178.076
15000 2.0352822 0.019352462 2.0523732 0.26816816 8601.8792
16000 2.0396728 0.013649097 2.0510556 0.2897209 8117.7222
17000 2.0021829 0.051638556 2.0515968 0.35978072 7694.4722
18000 2.0323755 0.021980006 2.0520973 0.33886022 7331.3619
19000 2.012523 0.039400171 2.049687 0.38829143 7030.9065
20000 2.0210256 0.032912605 2.0516927 0.4026689 6790.5438
21000 2.0346845 0.01996079 2.0523846 0.40076736 6532.5103
22000 2.024663 0.027946479 2.0503599 0.42145195 6305.942
23000 2.019905 0.039007463 2.0566681 0.48378424 6097.1834
24000 2.0128761 0.043306652 2.0539462 0.49890589 5931.4039
25000 2.0426669 0.01677892 2.0571762 0.43582414 5761.8463
26000 2.0048718 0.055983728 2.0586279 0.56571575 5567.6133
27000 2.0444253 0.020459712 2.0626134 0.48337889 5415.7979
28000 1.9933145 0.065049949 2.0561496 0.54116421 5309.9562
29000 2.0046319 0.055203466 2.057608 0.59270605 5195.3249
30000 2.008193 0.057534886 2.0634966 0.601137 5072.6056
31000 1.999698 0.06580978 2.0632859 0.67924433 4956.2611
32000 2.0122296 0.055833298 2.0658271 0.59245863 4874.1707
33000 2.0007781 0.069519235 2.0680742 0.6326113 4802.2499
34000 2.0066804 0.064593938 2.0690447 0.63378518 4717.4744
35000 2.0326851 0.042701702 2.0731283 0.62301292 4626.0976
36000 2.024922 0.048686129 2.0713582 0.63389098 4542.6291
37000 1.9933918 0.084026218 2.0752031 0.72269199 4452.0399
38000 2.0286434 0.05351806 2.0799074 0.73016095 4351.0179
39000 2.0047353 0.070614231 2.073122 0.80274462 4289.5501
40000 2.0379085 0.038227025 2.0738712 0.71338936 4246.7929
41000 1.9952571 0.088622162 2.0816623 0.81307645 4200.0671
42000 2.0042363 0.073467747 2.0754771 0.79982857 4148.4054
43000 2.0189089 0.066082632 2.0827483 0.7951291 4081.3285
44000 2.0380445 0.051364672 2.0871447 0.77601424 4031.596
45000 2.0176888 0.071201051 2.086648 0.8814278 3973.177
46000 2.0315294 0.062175754 2.0914479 0.80448793 3920.2923
47000 1.999217 0.091219176 2.0882149 0.97776147 3870.1695
48000 2.0031904 0.091014449 2.0919791 0.9661011 3813.1611
49000 1.9880642 0.10889214 2.0947474 1.0234859 3760.5992
50000 2.0236194 0.078957514 2.1003284 0.99741945 3720.1333
Loop time of 8.99595 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 4.17826 (46.446)
Neigh time (%) = 1.11062 (12.3457)
Comm time (%) = 0.42667 (4.74291)
Outpt time (%) = 0.171033 (1.90122)
Other time (%) = 3.10937 (34.5641)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 564 ave 564 max 564 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6061 ave 6061 max 6061 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6061
Ave neighs/atom = 6.73444
Neighbor list builds = 3122
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.87079 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
6000 2.1073955 0.0076739854 2.1127279 0.09765736 21544.21
7000 2.084383 -0.002011532 2.0800555 0.11035732 17791.249
8000 2.0697462 -0.0035908236 2.0638557 0.12727264 15495.564
9000 2.0565713 0.005100289 2.0593865 0.14847835 13885.03
10000 2.0498621 0.0063267281 2.0539112 0.15879624 12601.99
11000 2.0438679 0.018955755 2.0605527 0.18959409 11490.646
12000 2.053458 0.0044167998 2.0555932 0.19336438 10572.921
13000 2.0429256 0.013698073 2.0543538 0.21707695 9791.7501
14000 2.0132501 0.042422704 2.0534359 0.27926827 9147.46
15000 2.0501152 0.0064708164 2.0543081 0.25954559 8659.5624
16000 2.0371395 0.017291634 2.0521676 0.27240923 8172.3226
17000 2.0267747 0.025623672 2.0501464 0.32046495 7767.5953
18000 2.0422824 0.014182115 2.0541954 0.30856342 7387.0945
19000 2.002713 0.050847562 2.0513354 0.3943075 7044.3881
20000 2.028578 0.02503956 2.0513636 0.35569094 6770.0283
21000 2.0222359 0.033814924 2.0538039 0.42126528 6523.5394
22000 2.0312713 0.024739786 2.0537541 0.41123899 6289.3329
23000 1.9999306 0.055831167 2.0535396 0.46845747 6092.6534
24000 2.0082371 0.050865049 2.0568708 0.45467368 5945.5344
25000 2.0184402 0.039542114 2.0557396 0.46077228 5776.9458
26000 2.0197538 0.046732692 2.0642423 0.57349226 5587.6764
27000 2.0225605 0.036043629 2.0563569 0.48998661 5465.5575
28000 2.0282806 0.029362245 2.0553892 0.46801488 5344.7841
29000 2.025716 0.035993945 2.0594592 0.53066607 5238.028
30000 2.0121673 0.054545747 2.0644773 0.62001526 5107.2201
31000 2.0208128 0.048119988 2.0666874 0.54439146 4994.3653
32000 2.0272104 0.045076806 2.0700348 0.63197584 4872.4903
33000 2.0107761 0.060072558 2.0686144 0.63025398 4766.141
34000 1.9980266 0.075358195 2.0711648 0.67880824 4677.1269
35000 2.0253327 0.048362443 2.0714448 0.64004324 4599.5201
36000 2.0118504 0.058973713 2.0685888 0.67459858 4529.9483
37000 2.0104548 0.065481203 2.0737022 0.80781793 4463.1985
38000 2.0125078 0.066003564 2.0762752 0.78305688 4377.6954
39000 2.0174905 0.063736966 2.0789858 0.70398438 4293.5819
40000 2.0275434 0.05243574 2.0777263 0.78595198 4236.8235
41000 1.9680044 0.10509725 2.070915 0.84301968 4224.0137
42000 2.0169009 0.071278882 2.0859388 0.78081027 4160.3455
43000 2.0404682 0.05026415 2.0884652 0.75914083 4061.9873
44000 2.016673 0.068784573 2.0832168 0.80476991 3996.8686
45000 1.9857998 0.10014888 2.0837422 0.90863992 3939.2325
46000 2.0071737 0.075441094 2.0803846 0.86595933 3918.6894
47000 2.0371945 0.055594532 2.0905255 0.88572726 3889.3681
48000 1.9981195 0.097729669 2.093629 1.0507251 3846.1939
49000 2.0047164 0.089245076 2.091734 0.96126669 3809.5319
50000 2.0028203 0.1069487 2.1075437 1.0114594 3741.7317
Loop time of 4.07413 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.10861 (27.2108)
Neigh time (%) = 0.293286 (7.19874)
Comm time (%) = 0.97903 (24.0304)
Outpt time (%) = 0.13185 (3.23627)
Other time (%) = 1.56136 (38.3238)
Nlocal: 225 ave 241 max 200 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 301 ave 311 max 289 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 1463 ave 1565 max 1310 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 5852
Ave neighs/atom = 6.50222
Neighbor list builds = 3126
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.80471 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
Loop time of 0.802534 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.80151 (99.8723)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000503063 (0.0626843)
Outpt time (%) = 0.000286579 (0.0357093)
Other time (%) = 0.000234842 (0.0292626)
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.29838 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
Loop time of 0.202334 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.197941 (97.8289)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0038377 (1.89672)
Outpt time (%) = 0.000359058 (0.177458)
Other time (%) = 0.000196099 (0.0969187)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 384.277 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -8.502354 -8.5036544 -8.5036544 0 -870253.95 3023.4645 14.46 14.46 14.46 0
1 10.099586 -8.502354 -8.5036544 -8.5036544 0 -870253.93 3023.4645 14.46 14.46 14.46 0
2 10.098343 -8.502354 -8.5036542 -8.5036542 0 -870253.88 3023.4645 14.46 14.46 14.46 0
3 10.096272 -8.502354 -8.5036539 -8.5036539 0 -870253.79 3023.4645 14.46 14.46 14.46 0
4 10.093374 -8.502354 -8.5036536 -8.5036536 0 -870253.67 3023.4645 14.46 14.46 14.46 0
5 10.089648 -8.502354 -8.5036531 -8.5036531 0 -870253.51 3023.4645 14.46 14.46 14.46 0
6 10.085096 -8.502354 -8.5036525 -8.5036525 0 -870253.31 3023.4645 14.46 14.46 14.46 0
7 10.079718 -8.502354 -8.5036518 -8.5036518 0 -870253.08 3023.4645 14.46 14.46 14.46 0
8 10.073516 -8.502354 -8.503651 -8.503651 0 -870252.82 3023.4645 14.46 14.46 14.46 0
9 10.06649 -8.502354 -8.5036501 -8.5036501 0 -870252.52 3023.4645 14.46 14.46 14.46 0
10 10.058642 -8.502354 -8.5036491 -8.5036491 0 -870252.18 3023.4645 14.46 14.46 14.46 0
Loop time of 0.174859 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.174268 (99.6621)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000328779 (0.188025)
Outpt time (%) = 0.000133038 (0.0760827)
Other time (%) = 0.000128984 (0.0737648)
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 383.77 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -8.502354 -8.5036544 -8.5036544 0 -870253.95 3023.4645 14.46 14.46 14.46 0
1 10.09959 -8.502354 -8.5036544 -8.5036544 0 -870253.93 3023.4645 14.46 14.46 14.46 0
2 10.098359 -8.502354 -8.5036542 -8.5036542 0 -870253.88 3023.4645 14.46 14.46 14.46 0
3 10.096308 -8.502354 -8.5036539 -8.5036539 0 -870253.79 3023.4645 14.46 14.46 14.46 0
4 10.093437 -8.502354 -8.5036536 -8.5036536 0 -870253.66 3023.4645 14.46 14.46 14.46 0
5 10.089747 -8.502354 -8.5036531 -8.5036531 0 -870253.49 3023.4645 14.46 14.46 14.46 0
6 10.085238 -8.502354 -8.5036525 -8.5036525 0 -870253.29 3023.4645 14.46 14.46 14.46 0
7 10.079911 -8.502354 -8.5036518 -8.5036518 0 -870253.06 3023.4645 14.46 14.46 14.46 0
8 10.073767 -8.502354 -8.503651 -8.503651 0 -870252.79 3023.4645 14.46 14.46 14.46 0
9 10.066807 -8.502354 -8.5036501 -8.5036501 0 -870252.48 3023.4645 14.46 14.46 14.46 0
10 10.059033 -8.502354 -8.5036491 -8.5036491 0 -870252.13 3023.4645 14.46 14.46 14.46 0
Loop time of 0.0476552 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.0449591 (94.3424)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0022549 (4.7317)
Outpt time (%) = 0.000302732 (0.635255)
Other time (%) = 0.000138521 (0.290674)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

315
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LAMMPS (27 Mar 2011)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 5.54555 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.72421193 -1.4484239 25.62 25.62 25.62 16816.568
1 0.99888668 -3.8382371 -3.8383662 -0.98185761 -2.8565085 0.72421093 -1.4484219 25.62 25.62 25.62 16816.568
2 0.99630957 -3.8382376 -3.8383663 -0.98186477 -2.8565015 0.7242097 -1.4484194 25.62 25.62 25.62 16816.568
Loop time of 2.50572 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.309569 (12.3545)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000235319 (0.00939126)
Outpt time (%) = 0.000140905 (0.00562334)
Other time (%) = 2.19578 (87.6305)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization
Memory usage per processor = 6.84256 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99630957 -3.845015 -3.8451437 -0.97307269 -2.872071 0.7242097 -1.4484194 25.62 25.62 25.62 16816.568
3 0.99630957 -3.8450358 -3.8451645 -0.96977625 -2.8753882 0.7242097 -1.4484194 25.59438 25.594381 25.59438 16766.17
4 0.99630957 -3.8450358 -3.8451645 -0.96977625 -2.8753882 0.7242097 -1.4484194 25.59438 25.594381 25.59438 16766.17
Loop time of 2.3633 on 1 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.8451437267 -3.84516448476 -3.84516448476
Force two-norm initial, final = 14.0243 26.0587
Force max component initial, final = 8.07088 15.0312
Final line search alpha, max atom move = 1.62423e-08 2.44141e-07
Iterations, force evaluations = 2 14
Pair time (%) = 2.35645 (99.7102)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00155354 (0.0657359)
Outpt time (%) = 6.8903e-05 (0.00291554)
Other time (%) = 0.00522709 (0.221178)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 5.7222 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.99630957 -3.8450358 -3.8451645 -0.96977625 -2.8753882 0.72227767 -1.4445553 25.59438 25.594381 25.59438 16766.17
5 0.99306642 -3.8417608 -3.8418891 -0.98316073 -2.8587283 0.7222782 -1.4445564 25.59438 25.594381 25.59438 16766.17
Loop time of 1.11878 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.159516 (14.258)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000136137 (0.0121683)
Outpt time (%) = 8.70228e-05 (0.00777836)
Other time (%) = 0.959042 (85.722)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost
run 10
Memory usage per processor = 5.98075 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.59438 25.594381 25.59438 0 0 0 -23857347 -23854274 -23856348 -44222.028 -67044.325 -59938.384
6 25.594636 25.594381 25.59438 0 0 0 -23857347 -23854274 -23856348 -44222.028 -67044.325 -59938.384
7 25.594892 25.594381 25.59438 0 0 0 -23528290 -23833303 -23835377 -44220.96 -67042.938 -59932.976
8 25.595148 25.594381 25.59438 0 0 0 -23199233 -23812337 -23814412 -44219.892 -67041.552 -59927.569
9 25.595404 25.594381 25.59438 0 0 0 -22870176 -23791377 -23793451 -44218.824 -67040.166 -59922.162
10 25.59566 25.594381 25.59438 0 0 0 -22541119 -23770422 -23772497 -44217.757 -67038.78 -59916.756
11 25.595916 25.594381 25.59438 0 0 0 -22212062 -23749473 -23751547 -44216.69 -67037.395 -59911.349
12 25.596172 25.594381 25.59438 0 0 0 -21883006 -23728529 -23730604 -44215.624 -67036.01 -59905.943
13 25.596428 25.594381 25.59438 0 0 0 -21553950 -23707591 -23709665 -44214.559 -67034.624 -59900.537
14 25.596684 25.594381 25.59438 0 0 0 -21224894 -23686658 -23688732 -44213.493 -67033.238 -59895.132
15 25.59694 25.594381 25.59438 0 0 0 -20895838 -23665731 -23667805 -44212.427 -67031.853 -59889.727
Loop time of 1.73011 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.72171 (99.5144)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0015142 (0.0875201)
Outpt time (%) = 0.00608492 (0.351706)
Other time (%) = 0.000802755 (0.046399)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 6.49784 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.59694 25.594381 25.59438 0 0 0 -20566782 -23644809 -23646883 -44211.362 -67030.467 -59884.323
16 25.59694 25.594381 25.594636 0 0 0 -20566782 -23644809 -23646883 -44211.362 -67030.467 -59884.323
17 25.59694 25.594381 25.594892 0 0 0 -20545864 -23623833 -23317879 -44205.686 -67029.08 -59883.21
18 25.59694 25.594381 25.595148 0 0 0 -20524951 -23602862 -22988874 -44200.011 -67027.694 -59882.097
19 25.59694 25.594381 25.595404 0 0 0 -20504043 -23581897 -22659870 -44194.336 -67026.307 -59880.984
20 25.59694 25.594381 25.59566 0 0 0 -20483141 -23560937 -22330866 -44188.661 -67024.921 -59879.872
21 25.59694 25.594381 25.595916 0 0 0 -20462244 -23539983 -22001862 -44182.986 -67023.535 -59878.76
22 25.59694 25.594381 25.596172 0 0 0 -20441353 -23519034 -21672859 -44177.311 -67022.148 -59877.647
23 25.59694 25.594381 25.596428 0 0 0 -20420468 -23498091 -21343855 -44171.636 -67020.762 -59876.536
24 25.59694 25.594381 25.596683 0 0 0 -20399588 -23477153 -21014852 -44165.962 -67019.375 -59875.424
25 25.59694 25.594381 25.596939 0 0 0 -20378713 -23456221 -20685849 -44160.287 -67017.989 -59874.312
Loop time of 1.72041 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.71271 (99.5523)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00122261 (0.0710651)
Outpt time (%) = 0.00582957 (0.338848)
Other time (%) = 0.000650644 (0.0378192)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 7.01493 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.59694 25.594381 25.596939 0 0 0 -20357844 -23435294 -20356846 -44154.613 -67016.603 -59873.2
26 25.59694 25.594381 25.596939 0 0 5.1193879e-07 -20357844 -23435294 -20356846 -44154.613 -67016.603 -59873.2
27 25.59694 25.594381 25.596939 0 0 1.0238776e-06 -20357844 -23435294 -20356846 -44154.607 -67016.597 -59608.802
28 25.59694 25.594381 25.596939 0 0 1.5358164e-06 -20357844 -23435294 -20356846 -44154.601 -67016.592 -59344.404
29 25.59694 25.594381 25.596939 0 0 2.0477552e-06 -20357844 -23435294 -20356846 -44154.595 -67016.586 -59080.005
30 25.59694 25.594381 25.596939 0 0 2.5596939e-06 -20357844 -23435294 -20356846 -44154.589 -67016.58 -58815.607
31 25.59694 25.594381 25.596939 0 0 3.0716327e-06 -20357844 -23435294 -20356845 -44154.583 -67016.575 -58551.209
32 25.59694 25.594381 25.596939 0 0 3.5835715e-06 -20357844 -23435294 -20356845 -44154.577 -67016.569 -58286.811
33 25.59694 25.594381 25.596939 0 0 4.0955103e-06 -20357844 -23435294 -20356845 -44154.571 -67016.563 -58022.413
34 25.59694 25.594381 25.596939 0 0 4.6074491e-06 -20357844 -23435294 -20356845 -44154.565 -67016.558 -57758.014
35 25.59694 25.594381 25.596939 0 0 5.1193879e-06 -20357844 -23435294 -20356845 -44154.559 -67016.552 -57493.616
Loop time of 1.71669 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.70907 (99.5561)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00118637 (0.0691079)
Outpt time (%) = 0.00573516 (0.334082)
Other time (%) = 0.000698328 (0.0406787)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 7.53202 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.59694 25.594381 25.596939 0 0 5.1193879e-06 -20357844 -23435294 -20356845 -44154.553 -67016.546 -57229.218
36 25.59694 25.594381 25.596939 5.1188761e-07 0 5.1193879e-06 -20357844 -23435294 -20356845 -44154.553 -67016.546 -57229.218
37 25.59694 25.594381 25.596939 1.0237752e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43890.216 -67016.542 -57229.211
38 25.59694 25.594381 25.596939 1.5356628e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43625.88 -67016.537 -57229.203
39 25.59694 25.594381 25.596939 2.0475505e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43361.543 -67016.533 -57229.196
40 25.59694 25.594381 25.596939 2.5594381e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43097.206 -67016.528 -57229.189
41 25.59694 25.594381 25.596939 3.0713257e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42832.87 -67016.523 -57229.181
42 25.59694 25.594381 25.596939 3.5832133e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42568.533 -67016.519 -57229.174
43 25.59694 25.594381 25.596939 4.0951009e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42304.196 -67016.514 -57229.167
44 25.59694 25.594381 25.596939 4.6069885e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42039.86 -67016.51 -57229.159
45 25.59694 25.594381 25.596939 5.1188761e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -41775.523 -67016.505 -57229.152
Loop time of 1.7178 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.71014 (99.5539)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00127482 (0.0742126)
Outpt time (%) = 0.00568557 (0.33098)
Other time (%) = 0.000703096 (0.0409301)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

315
examples/comb/log.comb.Cu2O.elastic.28Mar11.linux.4
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@ -1,315 +0,0 @@
LAMMPS (27 Mar 2011)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 2.98849 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7250204 -1.4500408 25.62 25.62 25.62 16816.568
1 0.99832063 -3.8339963 -3.8341252 -0.98121146 -2.8529137 0.72501959 -1.4500392 25.62 25.62 25.62 16816.568
2 0.99477315 -3.8339968 -3.8341253 -0.98121736 -2.8529079 0.72501849 -1.450037 25.62 25.62 25.62 16816.568
Loop time of 0.649422 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.0756464 (11.6483)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00136131 (0.209619)
Outpt time (%) = 0.000139356 (0.0214584)
Other time (%) = 0.572275 (88.1207)
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization
Memory usage per processor = 4.17364 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99477315 -3.8448334 -3.8449619 -0.96671781 -2.8782441 0.72501849 -1.450037 25.62 25.62 25.62 16816.568
3 0.99477315 -3.8448541 -3.8449826 -0.96342109 -2.8815615 0.72501849 -1.450037 25.594519 25.594381 25.59438 16766.261
4 0.99477315 -3.8448541 -3.8449826 -0.96342109 -2.8815615 0.72501849 -1.450037 25.594519 25.594381 25.59438 16766.261
Loop time of 0.600445 on 4 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.8449619337 -3.84498261759 -3.84498261759
Force two-norm initial, final = 13.89 26.1585
Force max component initial, final = 7.99462 15.1024
Final line search alpha, max atom move = 1.61657e-08 2.44141e-07
Iterations, force evaluations = 2 14
Pair time (%) = 0.58064 (96.7016)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0166085 (2.76603)
Outpt time (%) = 5.75781e-05 (0.00958924)
Other time (%) = 0.00313872 (0.522733)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 3.14651 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.99477315 -3.8448541 -3.8449826 -0.96342109 -2.8815615 0.7219669 -1.4439338 25.594519 25.594381 25.59438 16766.261
5 0.99149942 -3.839274 -3.839402 -0.9840769 -2.8553251 0.72196775 -1.4439355 25.594519 25.594381 25.59438 16766.261
Loop time of 0.308691 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.038758 (12.5556)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00141472 (0.458295)
Outpt time (%) = 7.1466e-05 (0.0231513)
Other time (%) = 0.268447 (86.963)
Nlocal: 324 ave 333 max 320 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 4943 ave 4947 max 4934 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 200056 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost
run 10
Memory usage per processor = 3.38354 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.594519 25.594381 25.59438 0 0 0 -23724673 -23883860 -23885828 -18837.532 -68466.96 -61872.751
6 25.594775 25.594381 25.59438 0 0 0 -23724673 -23883860 -23885828 -18837.532 -68466.96 -61872.751
7 25.595031 25.594381 25.59438 0 0 0 -23395545 -23862932 -23864900 -18836.656 -68465.521 -61867.388
8 25.595287 25.594381 25.59438 0 0 0 -23066417 -23842010 -23843978 -18835.782 -68464.082 -61862.025
9 25.595543 25.594381 25.59438 0 0 0 -22737289 -23821093 -23823061 -18834.907 -68462.645 -61856.662
10 25.595799 25.594381 25.59438 0 0 0 -22408162 -23800182 -23802150 -18834.033 -68461.207 -61851.299
11 25.596055 25.594381 25.59438 0 0 0 -22079034 -23779276 -23781244 -18833.16 -68459.769 -61845.937
12 25.596311 25.594381 25.59438 0 0 0 -21749907 -23758375 -23760343 -18832.287 -68458.331 -61840.575
13 25.596567 25.594381 25.59438 0 0 0 -21420780 -23737480 -23739449 -18831.414 -68456.893 -61835.213
14 25.596822 25.594381 25.59438 0 0 0 -21091653 -23716591 -23718559 -18830.541 -68455.455 -61829.852
15 25.597078 25.594381 25.59438 0 0 0 -20762526 -23695707 -23697675 -18829.669 -68454.017 -61824.492
Loop time of 0.438967 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415694 (94.6982)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0144061 (3.28183)
Outpt time (%) = 0.00844461 (1.92375)
Other time (%) = 0.000422597 (0.0962708)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 3.8576 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.597078 25.594381 25.59438 0 0 0 -20433400 -23674828 -23676797 -18828.796 -68452.579 -61819.131
16 25.597078 25.594381 25.594636 0 0 0 -20433400 -23674828 -23676797 -18828.796 -68452.579 -61819.131
17 25.597078 25.594381 25.594892 0 0 0 -20412525 -23653892 -23347726 -18823.344 -68451.141 -61818.018
18 25.597078 25.594381 25.595148 0 0 0 -20391655 -23632962 -23018656 -18817.892 -68449.702 -61816.905
19 25.597078 25.594381 25.595404 0 0 0 -20370791 -23612037 -22689585 -18812.441 -68448.264 -61815.793
20 25.597078 25.594381 25.59566 0 0 0 -20349932 -23591118 -22360515 -18806.99 -68446.826 -61814.68
21 25.597078 25.594381 25.595916 0 0 0 -20329079 -23570204 -22031445 -18801.538 -68445.388 -61813.567
22 25.597078 25.594381 25.596172 0 0 0 -20308231 -23549295 -21702375 -18796.087 -68443.95 -61812.455
23 25.597078 25.594381 25.596428 0 0 0 -20287389 -23528392 -21373306 -18790.636 -68442.512 -61811.343
24 25.597078 25.594381 25.596683 0 0 0 -20266552 -23507494 -21044236 -18785.185 -68441.074 -61810.231
25 25.597078 25.594381 25.596939 0 0 0 -20245721 -23486602 -20715167 -18779.734 -68439.636 -61809.119
Loop time of 0.438571 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415724 (94.7906)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0140231 (3.19746)
Outpt time (%) = 0.00841451 (1.91862)
Other time (%) = 0.000409245 (0.0933134)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 4.33166 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.597078 25.594381 25.596939 0 0 0 -20224895 -23465716 -20386098 -18774.283 -68438.199 -61808.007
26 25.597078 25.594381 25.596939 0 0 5.1193879e-07 -20224895 -23465716 -20386098 -18774.283 -68438.199 -61808.007
27 25.597078 25.594381 25.596939 0 0 1.0238776e-06 -20224895 -23465716 -20386098 -18774.277 -68438.194 -61543.649
28 25.597078 25.594381 25.596939 0 0 1.5358164e-06 -20224895 -23465716 -20386098 -18774.271 -68438.189 -61279.291
29 25.597078 25.594381 25.596939 0 0 2.0477552e-06 -20224895 -23465716 -20386098 -18774.264 -68438.185 -61014.933
30 25.597078 25.594381 25.596939 0 0 2.5596939e-06 -20224895 -23465716 -20386098 -18774.258 -68438.18 -60750.575
31 25.597078 25.594381 25.596939 0 0 3.0716327e-06 -20224895 -23465716 -20386098 -18774.252 -68438.175 -60486.217
32 25.597078 25.594381 25.596939 0 0 3.5835715e-06 -20224895 -23465716 -20386098 -18774.245 -68438.171 -60221.859
33 25.597078 25.594381 25.596939 0 0 4.0955103e-06 -20224895 -23465716 -20386098 -18774.239 -68438.166 -59957.501
34 25.597078 25.594381 25.596939 0 0 4.6074491e-06 -20224895 -23465716 -20386098 -18774.233 -68438.161 -59693.142
35 25.597078 25.594381 25.596939 0 0 5.1193879e-06 -20224895 -23465716 -20386098 -18774.227 -68438.157 -59428.784
Loop time of 0.438326 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415411 (94.772)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0141624 (3.23101)
Outpt time (%) = 0.00836039 (1.90734)
Other time (%) = 0.000393033 (0.0896667)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 4.80572 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.597078 25.594381 25.596939 0 0 5.1193879e-06 -20224895 -23465716 -20386098 -18774.22 -68438.152 -59164.426
36 25.597078 25.594381 25.596939 5.1188762e-07 0 5.1193879e-06 -20224895 -23465716 -20386098 -18774.22 -68438.152 -59164.426
37 25.597078 25.594381 25.596939 1.0237752e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -18509.926 -68438.147 -59164.419
38 25.597078 25.594381 25.596939 1.5356628e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -18245.633 -68438.143 -59164.411
39 25.597078 25.594381 25.596939 2.0475505e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17981.339 -68438.138 -59164.403
40 25.597078 25.594381 25.596939 2.5594381e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17717.045 -68438.134 -59164.396
41 25.597078 25.594381 25.596939 3.0713257e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17452.751 -68438.129 -59164.388
42 25.597078 25.594381 25.596939 3.5832133e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17188.458 -68438.124 -59164.38
43 25.597078 25.594381 25.596939 4.0951009e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -16924.164 -68438.12 -59164.373
44 25.597078 25.594381 25.596939 4.6069885e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -16659.87 -68438.115 -59164.365
45 25.597078 25.594381 25.596939 5.1188762e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -16395.577 -68438.111 -59164.357
Loop time of 0.438004 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415312 (94.8193)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0140703 (3.21238)
Outpt time (%) = 0.00822508 (1.87786)
Other time (%) = 0.000396073 (0.0904268)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

340
examples/comb/log.comb.Cu2O.elastic.9Jan12.linux.1 Normal file
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@ -0,0 +1,340 @@
LAMMPS (10 Jan 2012)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 492.454 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -5.307041 -5.3071702 -2.6165358 -2.6906344 0.65426811 -1.3085362 25.62 25.62 25.62 16816.568
1 1.0009873 -5.3550555 -5.3551848 -2.9567646 -2.3984202 0.65426879 -1.3085376 25.62 25.62 25.62 16816.568
2 1.0026929 -5.3550537 -5.3551832 -2.9567602 -2.3984231 0.65426936 -1.3085387 25.62 25.62 25.62 16816.568
Loop time of 0.759578 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.101777 (13.3992)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00014329 (0.0188644)
Outpt time (%) = 6.62804e-05 (0.00872595)
Other time (%) = 0.657591 (86.5732)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 493.751 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0026929 -5.3334035 -5.333533 -2.9696799 -2.3638531 0.65426936 -1.3085387 25.62 25.62 25.62 16816.568
3 1.0026929 -5.3366561 -5.3367856 -2.9701261 -2.3666596 0.65426936 -1.3085387 25.594382 25.59438 25.59438 16766.17
4 1.0026929 -5.3398622 -5.3399917 -2.9705203 -2.3694714 0.65426936 -1.3085387 25.568763 25.56876 25.56876 16715.873
5 1.0026929 -5.3430214 -5.3431509 -2.9708622 -2.3722886 0.65426936 -1.3085387 25.543145 25.543141 25.54314 16665.677
6 1.0026929 -5.346133 -5.3462625 -2.9711512 -2.3751113 0.65426936 -1.3085387 25.517527 25.517521 25.51752 16615.581
7 1.0026929 -5.3491964 -5.349326 -2.9713866 -2.3779393 0.65426936 -1.3085387 25.491909 25.491901 25.4919 16565.585
8 1.0026929 -5.3522113 -5.3523408 -2.971568 -2.3807728 0.65426936 -1.3085387 25.46629 25.466281 25.46628 16515.69
9 1.0026929 -5.3660227 -5.3661522 -2.9825701 -2.3835821 0.65426936 -1.3085387 25.440672 25.440662 25.44066 16465.896
10 1.0026929 -5.4362377 -5.4363673 -3.0499986 -2.3863686 0.65426936 -1.3085387 25.415054 25.415042 25.41504 16416.201
11 1.0026929 -5.5662016 -5.5663312 -3.1771711 -2.3891601 0.65426936 -1.3085387 25.389436 25.389422 25.38942 16366.607
12 1.0026929 -5.7519309 -5.7520604 -3.360104 -2.3919564 0.65426936 -1.3085387 25.363818 25.363802 25.3638 16317.113
13 1.0026929 -5.9874068 -5.9875363 -3.5927786 -2.3947577 0.65426936 -1.3085387 25.3382 25.338183 25.33818 16267.718
14 1.0026929 -6.2647792 -6.2649087 -3.8673448 -2.3975639 0.65426936 -1.3085387 25.312582 25.312563 25.31256 16218.423
15 1.0026929 -6.5746359 -6.5747654 -4.1743903 -2.400375 0.65426936 -1.3085387 25.286963 25.286943 25.28694 16169.228
16 1.0026929 -6.9063303 -6.9064598 -4.5032687 -2.4031911 0.65426936 -1.3085387 25.261343 25.261323 25.26132 16120.131
17 1.0026929 -7.2483579 -7.2484874 -4.8424753 -2.4060121 0.65426936 -1.3085387 25.235723 25.235703 25.2357 16071.134
18 1.0026929 -7.5887656 -7.5888951 -5.1800571 -2.408838 0.65426936 -1.3085387 25.210104 25.210083 25.21008 16022.236
19 1.0026929 -7.9155773 -7.9157068 -5.504038 -2.4116688 0.65426936 -1.3085387 25.184484 25.184463 25.18446 15973.438
20 1.0026929 -8.217244 -8.2173735 -5.8028522 -2.4145213 0.65426936 -1.3085387 25.158864 25.158844 25.15884 15924.739
21 1.0026929 -8.4831885 -8.483318 -6.0657645 -2.4175535 0.65426936 -1.3085387 25.133244 25.133224 25.133221 15876.139
22 1.0026929 -8.7037271 -8.7038566 -6.2832612 -2.4205954 0.65426936 -1.3085387 25.107624 25.107605 25.107602 15827.639
23 1.0026929 -8.8709155 -8.8710451 -6.4474006 -2.4236444 0.65426936 -1.3085387 25.082004 25.081986 25.081984 15779.238
24 1.0026929 -8.978681 -8.9788105 -6.55211 -2.4267005 0.65426936 -1.3085387 25.056384 25.056368 25.056366 15730.937
25 1.0026929 -9.0230511 -9.0231807 -6.593417 -2.4297637 0.65426936 -1.3085387 25.030764 25.030751 25.030749 15682.736
26 1.0026929 -9.0240292 -9.0241587 -6.5940118 -2.430147 0.65426936 -1.3085387 25.027561 25.027551 25.027549 15676.72
27 1.0026929 -9.0241357 -9.0242652 -6.5939267 -2.4303385 0.65426936 -1.3085387 25.02596 25.025952 25.025951 15673.715
28 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.65426936 -1.3085387 25.026059 25.026052 25.026051 15673.902
29 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.65426936 -1.3085387 25.026059 25.026052 25.026051 15673.902
Loop time of 5.88834 on 1 procs for 27 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.33353304985 -9.02426597894 -9.02426597894
Force two-norm initial, final = 2433.53 179.132
Force max component initial, final = 1405.03 103.699
Final line search alpha, max atom move = 2.94289e-10 3.05176e-08
Iterations, force evaluations = 27 57
Pair time (%) = 5.50607 (93.508)
Neigh time (%) = 0.363057 (6.16569)
Comm time (%) = 0.00463033 (0.0786355)
Outpt time (%) = 0.000666857 (0.011325)
Other time (%) = 0.0139146 (0.236307)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 4
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 492.631 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
29 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.63678555 -1.2735711 25.026059 25.026052 25.026051 15673.902
30 0.88741647 -9.0386219 -9.0387365 -6.7151088 -2.3236278 0.63678579 -1.2735716 25.026059 25.026052 25.026051 15673.902
Loop time of 0.476254 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.100822 (21.1698)
Neigh time (%) = 0 (0)
Comm time (%) = 6.79493e-05 (0.0142674)
Outpt time (%) = 2.69413e-05 (0.00565692)
Other time (%) = 0.375337 (78.8103)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 492.89 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
30 25.026059 25.026052 25.026051 0 0 0 -1.504334e+08 -1.5326204e+08 -1.5372549e+08 1064068.9 -599765.62 414723.34
31 25.026309 25.026052 25.026051 0 0 0 -1.504334e+08 -1.5326204e+08 -1.5372549e+08 1064068.9 -599765.62 414723.34
32 25.026559 25.026052 25.026051 0 0 0 65979938 -45173439 -45636876 1064082.2 -599660.21 414715.59
33 25.02681 25.026052 25.026051 0 0 0 2.8240082e+08 62914604 62451183 1064095.4 -599554.81 414707.84
34 25.02706 25.026052 25.026051 0 0 0 4.98829e+08 1.7100197e+08 1.7053856e+08 1064108.6 -599449.41 414700.08
35 25.02731 25.026052 25.026051 0 0 0 7.1526424e+08 2.7908854e+08 2.7862515e+08 1064121.9 -599344.01 414692.33
36 25.02756 25.026052 25.026051 0 0 0 9.3170631e+08 3.8717419e+08 3.8671082e+08 1064135.1 -599238.61 414684.58
37 25.027811 25.026052 25.026051 0 0 0 1.148155e+09 4.9525881e+08 4.9479545e+08 1064148.4 -599133.22 414676.83
38 25.028061 25.026052 25.026051 0 0 0 1.36461e+09 6.0334227e+08 6.0287893e+08 1064161.6 -599027.84 414669.08
39 25.028311 25.026052 25.026051 0 0 0 1.5810711e+09 7.1142446e+08 7.1096114e+08 1064174.9 -598922.45 414661.33
40 25.028561 25.026052 25.026051 0 0 0 1.7975381e+09 8.1950525e+08 8.1904196e+08 1064188.2 -598817.07 414653.58
Loop time of 1.1738 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16988 (99.6661)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000679731 (0.0579088)
Outpt time (%) = 0.00296259 (0.252394)
Other time (%) = 0.000277042 (0.0236022)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 493.407 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
40 25.028561 25.026052 25.026051 0 0 0 2.0140107e+09 9.2758454e+08 9.2712126e+08 1064201.4 -598711.69 414645.83
41 25.028561 25.026052 25.026302 0 0 0 2.0140107e+09 9.2758454e+08 9.2712126e+08 1064201.4 -598711.69 414645.83
42 25.028561 25.026052 25.026552 0 0 0 2.1220992e+09 1.0356731e+09 1.1435342e+09 1064179.7 -598601.58 414637.81
43 25.028561 25.026052 25.026802 0 0 0 2.2301859e+09 1.1437611e+09 1.3599535e+09 1064158 -598491.46 414629.79
44 25.028561 25.026052 25.027052 0 0 0 2.3382708e+09 1.2518485e+09 1.576379e+09 1064136.3 -598381.35 414621.77
45 25.028561 25.026052 25.027303 0 0 0 2.4463536e+09 1.359935e+09 1.7928103e+09 1064114.7 -598271.25 414613.74
46 25.028561 25.026052 25.027553 0 0 0 2.5544344e+09 1.4680207e+09 2.0092472e+09 1064093 -598161.15 414605.7
47 25.028561 25.026052 25.027803 0 0 0 2.662513e+09 1.5761053e+09 2.2256896e+09 1064071.3 -598051.06 414597.67
48 25.028561 25.026052 25.028053 0 0 0 2.7705891e+09 1.6841887e+09 2.4421371e+09 1064049.6 -597940.97 414589.63
49 25.028561 25.026052 25.028304 0 0 0 2.8786629e+09 1.7922709e+09 2.6585895e+09 1064027.9 -597830.89 414581.58
50 25.028561 25.026052 25.028554 0 0 0 2.986734e+09 1.9003517e+09 2.8750466e+09 1064006.2 -597720.81 414573.53
Loop time of 1.17224 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16836 (99.6691)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000671864 (0.0573147)
Outpt time (%) = 0.00293803 (0.250635)
Other time (%) = 0.000269175 (0.0229625)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 493.924 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
50 25.028561 25.026052 25.028554 0 0 0 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.74 414565.48
51 25.028561 25.026052 25.028554 0 0 5.0057108e-07 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.74 414565.48
52 25.028561 25.026052 25.028554 0 0 1.0011422e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.79 631065.93
53 25.028561 25.026052 25.028554 0 0 1.5017132e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.83 847566.39
54 25.028561 25.026052 25.028554 0 0 2.0022843e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.88 1064066.8
55 25.028561 25.026052 25.028554 0 0 2.5028554e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597610.93 1280567.3
56 25.028561 25.026052 25.028554 0 0 3.0034265e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597610.97 1497067.7
57 25.028561 25.026052 25.028554 0 0 3.5039975e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.02 1713568.2
58 25.028561 25.026052 25.028554 0 0 4.0045686e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.06 1930068.7
59 25.028561 25.026052 25.028554 0 0 4.5051397e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.11 2146569.1
60 25.028561 25.026052 25.028554 0 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.16 2363069.6
Loop time of 1.17218 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16831 (99.6701)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000669956 (0.0571549)
Outpt time (%) = 0.00293446 (0.250342)
Other time (%) = 0.000262737 (0.0224145)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 494.441 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
60 25.028561 25.026052 25.028554 0 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.2 2579570
61 25.028561 25.026052 25.028554 5.0052105e-07 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.2 2579570
62 25.028561 25.026052 25.028554 1.0010421e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1280463.3 -597611.17 2579570
63 25.028561 25.026052 25.028554 1.5015631e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1496942 -597611.15 2579570
64 25.028561 25.026052 25.028554 2.0020842e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1713420.7 -597611.12 2579570.1
65 25.028561 25.026052 25.028554 2.5026052e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1929899.5 -597611.09 2579570.1
66 25.028561 25.026052 25.028554 3.0031263e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2146378.2 -597611.06 2579570.1
67 25.028561 25.026052 25.028554 3.5036473e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2362856.9 -597611.03 2579570.1
68 25.028561 25.026052 25.028554 4.0041684e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2579335.6 -597611 2579570.1
69 25.028561 25.026052 25.028554 4.5046894e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2795814.4 -597610.97 2579570.1
70 25.028561 25.026052 25.028554 5.0052105e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 3012293.1 -597610.95 2579570.1
Loop time of 1.17232 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16846 (99.6703)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000672817 (0.0573919)
Outpt time (%) = 0.00292802 (0.249763)
Other time (%) = 0.000264168 (0.0225338)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0

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examples/comb/log.comb.Cu2O.elastic.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 412.257 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -5.307041 -5.3071702 -2.6165358 -2.6906344 0.65350507 -1.3070101 25.62 25.62 25.62 16816.568
1 1.0020305 -5.3673359 -5.3674653 -2.9542297 -2.4132356 0.65350576 -1.3070115 25.62 25.62 25.62 16816.568
2 1.0060932 -5.3673341 -5.367464 -2.9542249 -2.4132391 0.65350631 -1.3070126 25.62 25.62 25.62 16816.568
Loop time of 0.199257 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.025626 (12.8608)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000734687 (0.368714)
Outpt time (%) = 6.24657e-05 (0.0313494)
Other time (%) = 0.172834 (86.7391)
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 413.442 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0060932 -5.3330786 -5.3332085 -2.974622 -2.3585866 0.65350631 -1.3070126 25.62 25.62 25.62 16816.568
3 1.0060932 -5.3363314 -5.3364614 -2.9750737 -2.3613876 0.65350631 -1.3070126 25.594384 25.59438 25.594381 16766.172
4 1.0060932 -5.3395378 -5.3396678 -2.9754737 -2.3641941 0.65350631 -1.3070126 25.568768 25.56876 25.568762 16715.877
5 1.0060932 -5.3426973 -5.3428272 -2.9758213 -2.3670059 0.65350631 -1.3070126 25.543152 25.54314 25.543143 16665.683
6 1.0060932 -5.3458091 -5.3459391 -2.976116 -2.3698231 0.65350631 -1.3070126 25.517536 25.51752 25.517525 16615.589
7 1.0060932 -5.3488729 -5.3490029 -2.9763572 -2.3726457 0.65350631 -1.3070126 25.49192 25.4919 25.491906 16565.596
8 1.0060932 -5.3518881 -5.352018 -2.9765443 -2.3754737 0.65350631 -1.3070126 25.466304 25.46628 25.466287 16515.703
9 1.0060932 -5.3656903 -5.3658203 -2.9875426 -2.3782777 0.65350631 -1.3070126 25.440688 25.44066 25.440668 16465.91
10 1.0060932 -5.4358893 -5.4360193 -3.0549604 -2.3810589 0.65350631 -1.3070126 25.415072 25.41504 25.415049 16416.218
11 1.0060932 -5.5658375 -5.5659675 -3.1821225 -2.383845 0.65350631 -1.3070126 25.389457 25.38942 25.389431 16366.626
12 1.0060932 -5.7515526 -5.7516825 -3.3650465 -2.386636 0.65350631 -1.3070126 25.363842 25.3638 25.363812 16317.134
13 1.0060932 -5.9870179 -5.9871478 -3.5977159 -2.389432 0.65350631 -1.3070126 25.338226 25.33818 25.338193 16267.742
14 1.0060932 -6.2643867 -6.2645166 -3.8722838 -2.3922328 0.65350631 -1.3070126 25.312609 25.31256 25.312574 16218.448
15 1.0060932 -6.5742496 -6.5743796 -4.1793409 -2.3950387 0.65350631 -1.3070126 25.286991 25.28694 25.286955 16169.253
16 1.0060932 -6.9059598 -6.9060897 -4.5082402 -2.3978495 0.65350631 -1.3070126 25.261372 25.26132 25.261335 16120.158
17 1.0060932 -7.2480121 -7.248142 -4.8474768 -2.4006652 0.65350631 -1.3070126 25.235753 25.2357 25.235715 16071.161
18 1.0060932 -7.5884527 -7.5885827 -5.1850968 -2.4034859 0.65350631 -1.3070126 25.210133 25.21008 25.210095 16022.263
19 1.0060932 -7.9153023 -7.9154322 -5.5091208 -2.4063115 0.65350631 -1.3070126 25.184513 25.18446 25.184476 15973.465
20 1.0060932 -8.2170093 -8.2171392 -5.8079805 -2.4091587 0.65350631 -1.3070126 25.158893 25.158841 25.158856 15924.766
21 1.0060932 -8.4829952 -8.4831252 -6.0709401 -2.4121851 0.65350631 -1.3070126 25.133273 25.133223 25.133237 15876.167
22 1.0060932 -8.7035764 -8.7037064 -6.2884852 -2.4152212 0.65350631 -1.3070126 25.107653 25.107605 25.107619 15827.668
23 1.0060932 -8.8708084 -8.8709383 -6.4526739 -2.4182644 0.65350631 -1.3070126 25.082033 25.081988 25.082001 15779.269
24 1.0060932 -8.9786185 -8.9787484 -6.5574338 -2.4213146 0.65350631 -1.3070126 25.056413 25.056373 25.056384 15730.97
25 1.0060932 -9.0230363 -9.0231663 -6.5987945 -2.4243718 0.65350631 -1.3070126 25.030793 25.030761 25.03077 15682.774
26 1.0060932 -9.0240207 -9.0241507 -6.5993965 -2.4247541 0.65350631 -1.3070126 25.027591 25.027564 25.027572 15676.761
27 1.0060932 -9.0241307 -9.0242606 -6.5993156 -2.424945 0.65350631 -1.3070126 25.02599 25.02597 25.025976 15673.76
28 1.0060932 -9.0241311 -9.024261 -6.5993219 -2.4249391 0.65350631 -1.3070126 25.026038 25.02602 25.026025 15673.853
29 1.0060932 -9.0241311 -9.0242611 -6.5993235 -2.4249376 0.65350631 -1.3070126 25.02605 25.026033 25.026038 15673.876
30 1.0060932 -9.0241312 -9.0242611 -6.5993242 -2.4249369 0.65350631 -1.3070126 25.026056 25.026039 25.026044 15673.888
31 1.0060932 -9.0241312 -9.0242611 -6.5993242 -2.4249369 0.65350631 -1.3070126 25.026056 25.026039 25.026044 15673.888
Loop time of 2.31824 on 4 procs for 29 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.33320852891 -9.02426111934 -9.02426111934
Force two-norm initial, final = 2433.86 193.581
Force max component initial, final = 1405.28 113.287
Final line search alpha, max atom move = 2.69382e-10 3.05176e-08
Iterations, force evaluations = 29 83
Pair time (%) = 2.07482 (89.4999)
Neigh time (%) = 0.173133 (7.46831)
Comm time (%) = 0.0567805 (2.44929)
Outpt time (%) = 0.000948668 (0.0409219)
Other time (%) = 0.0125538 (0.541521)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 4
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 412.415 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
31 1.0060932 -9.0241312 -9.0242611 -6.5993242 -2.4249369 0.63638209 -1.2727642 25.026056 25.026039 25.026044 15673.888
32 0.89047585 -9.039436 -9.0395511 -6.7149991 -2.3245519 0.63638241 -1.2727648 25.026056 25.026039 25.026044 15673.888
Loop time of 0.12376 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0256067 (20.6905)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000612259 (0.494713)
Outpt time (%) = 9.44734e-05 (0.0763357)
Other time (%) = 0.097447 (78.7384)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 412.652 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
32 25.026056 25.026039 25.026044 0 0 0 -1.6161297e+08 -1.6914237e+08 -1.6702142e+08 1071968.8 1327464.7 391905.86
33 25.026307 25.026039 25.026044 0 0 0 -1.6161297e+08 -1.6914237e+08 -1.6702142e+08 1071968.8 1327464.7 391905.86
34 25.026557 25.026039 25.026044 0 0 0 54810325 -61048772 -58927789 1071982.1 1327546.1 391898.77
35 25.026807 25.026039 25.026044 0 0 0 2.7124117e+08 47044270 49165285 1071995.3 1327627.6 391891.69
36 25.027057 25.026039 25.026044 0 0 0 4.8767934e+08 1.5513664e+08 1.5725769e+08 1072008.6 1327709.1 391884.6
37 25.027308 25.026039 25.026044 0 0 0 7.0412458e+08 2.6322823e+08 2.653493e+08 1072021.8 1327790.5 391877.51
38 25.027558 25.026039 25.026044 0 0 0 9.2057666e+08 3.713189e+08 3.7344e+08 1072035.1 1327872 391870.43
39 25.027808 25.026039 25.026044 0 0 0 1.1370353e+09 4.7940855e+08 4.8152966e+08 1072048.4 1327953.4 391863.34
40 25.028058 25.026039 25.026044 0 0 0 1.3535004e+09 5.8749704e+08 5.8961818e+08 1072061.7 1328034.8 391856.26
41 25.028309 25.026039 25.026044 0 0 0 1.5699715e+09 6.9558428e+08 6.9770543e+08 1072075 1328116.2 391849.18
42 25.028559 25.026039 25.026044 0 0 0 1.7864486e+09 8.0367013e+08 8.057913e+08 1072088.3 1328197.7 391842.09
Loop time of 0.310848 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.299549 (96.3652)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00796747 (2.56314)
Outpt time (%) = 0.00319105 (1.02656)
Other time (%) = 0.00014019 (0.0450993)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 413.126 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
42 25.028559 25.026039 25.026044 0 0 0 2.0029313e+09 9.1175447e+08 9.1387565e+08 1072101.6 1328279.1 391835.01
43 25.028559 25.026039 25.026294 0 0 0 2.0029313e+09 9.1175447e+08 9.1387565e+08 1072101.6 1328279.1 391835.01
44 25.028559 25.026039 25.026544 0 0 0 2.1110248e+09 1.019848e+09 1.1302984e+09 1072079.3 1328365.3 391827.47
45 25.028559 25.026039 25.026795 0 0 0 2.2191166e+09 1.127941e+09 1.3467276e+09 1072057 1328451.5 391819.92
46 25.028559 25.026039 25.027045 0 0 0 2.3272065e+09 1.2360334e+09 1.5631629e+09 1072034.7 1328537.8 391812.38
47 25.028559 25.026039 25.027295 0 0 0 2.4352945e+09 1.3441249e+09 1.7796041e+09 1072012.3 1328624 391804.83
48 25.028559 25.026039 25.027545 0 0 0 2.5433803e+09 1.4522156e+09 1.9960509e+09 1071990 1328710.2 391797.28
49 25.028559 25.026039 25.027796 0 0 0 2.6514639e+09 1.5603052e+09 2.2125031e+09 1071967.7 1328796.4 391789.72
50 25.028559 25.026039 25.028046 0 0 0 2.7595452e+09 1.6683937e+09 2.4289605e+09 1071945.4 1328882.6 391782.17
51 25.028559 25.026039 25.028296 0 0 0 2.867624e+09 1.776481e+09 2.6454229e+09 1071923.1 1328968.8 391774.61
52 25.028559 25.026039 25.028546 0 0 0 2.9757003e+09 1.8845668e+09 2.8618899e+09 1071900.8 1329054.9 391767.05
Loop time of 0.315019 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.302888 (96.1492)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00890404 (2.82651)
Outpt time (%) = 0.00307637 (0.976569)
Other time (%) = 0.000150442 (0.0477566)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 413.6 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
52 25.028559 25.026039 25.028546 0 0 0 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.5 1329141.1 391759.48
53 25.028559 25.026039 25.028546 0 0 5.0057093e-07 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.5 1329141.1 391759.48
54 25.028559 25.026039 25.028546 0 0 1.0011419e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.4 1329141.1 608269.82
55 25.028559 25.026039 25.028546 0 0 1.5017128e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.3 1329141 824780.16
56 25.028559 25.026039 25.028546 0 0 2.0022837e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.2 1329141 1041290.5
57 25.028559 25.026039 25.028546 0 0 2.5028546e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.2 1329140.9 1257800.8
58 25.028559 25.026039 25.028546 0 0 3.0034256e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.1 1329140.9 1474311.2
59 25.028559 25.026039 25.028546 0 0 3.5039965e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878 1329140.8 1690821.5
60 25.028559 25.026039 25.028546 0 0 4.0045674e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878 1329140.8 1907331.8
61 25.028559 25.026039 25.028546 0 0 4.5051384e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.9 1329140.7 2123842.2
62 25.028559 25.026039 25.028546 0 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.8 1329140.7 2340352.5
Loop time of 0.314847 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.302369 (96.0368)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0093742 (2.97739)
Outpt time (%) = 0.00294709 (0.93604)
Other time (%) = 0.00015682 (0.0498083)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 414.075 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
62 25.028559 25.026039 25.028546 0 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.8 1329140.6 2556862.9
63 25.028559 25.026039 25.028546 5.0052078e-07 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.8 1329140.6 2556862.9
64 25.028559 25.026039 25.028546 1.0010416e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1288366.3 1329140.7 2556862.8
65 25.028559 25.026039 25.028546 1.5015623e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1504854.8 1329140.7 2556862.7
66 25.028559 25.026039 25.028546 2.0020831e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1721343.4 1329140.7 2556862.6
67 25.028559 25.026039 25.028546 2.5026039e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1937831.9 1329140.8 2556862.5
68 25.028559 25.026039 25.028546 3.0031247e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2154320.4 1329140.8 2556862.4
69 25.028559 25.026039 25.028546 3.5036454e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2370809 1329140.8 2556862.3
70 25.028559 25.026039 25.028546 4.0041662e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2587297.5 1329140.8 2556862.2
71 25.028559 25.026039 25.028546 4.504687e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2803786 1329140.9 2556862.1
72 25.028559 25.026039 25.028546 5.0052078e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 3020274.6 1329140.9 2556862
Loop time of 0.314899 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.302122 (95.9424)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00967807 (3.07338)
Outpt time (%) = 0.00294942 (0.936622)
Other time (%) = 0.000149965 (0.0476232)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0

193
examples/comb/log.comb.HfO2.9Jan12.linux.1 Normal file
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@ -0,0 +1,193 @@
LAMMPS (10 Jan 2012)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 1 by 1 MPI processor grid
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 1771.07 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -10.375148 -10.375148 4.2805776 -14.655726 -402517.96 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.120123 on 1 procs for 1 steps with 1500 atoms
Pair time (%) = 0.119944 (99.8509)
Neigh time (%) = 0 (0)
Comm time (%) = 8.41618e-05 (0.070063)
Outpt time (%) = 3.40939e-05 (0.0283825)
Other time (%) = 6.07967e-05 (0.0506121)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 1771.89 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 2.7464939 -1.373247
2 1.2795093 -11.722657 -11.722823 -2.5378829 -9.1849398 -1178231.8 17627.802 25.642 25.957 26.4845 -4.46691 2.7464939 -1.373247
3 3.9305261 -11.722662 -11.72317 -2.5381759 -9.1849941 -1176818.8 17627.802 25.642 25.957 26.4845 -4.46691 2.7464667 -1.3732333
4 8.163283 -11.722618 -11.723672 -2.5386819 -9.1849902 -1174685 17627.802 25.642 25.957 26.4845 -4.46691 2.7464056 -1.3732028
5 13.960256 -11.722526 -11.724329 -2.5394249 -9.1849042 -1171826.4 17627.802 25.642 25.957 26.4845 -4.46691 2.7463184 -1.3731592
6 21.29783 -11.722408 -11.72516 -2.5403916 -9.184768 -1168232.6 17627.802 25.642 25.957 26.4845 -4.46691 2.7462211 -1.3731106
Loop time of 2.40353 on 1 procs for 5 steps with 1500 atoms
Pair time (%) = 0.598113 (24.8847)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000421047 (0.0175178)
Outpt time (%) = 0.000158072 (0.00657663)
Other time (%) = 1.80484 (75.0912)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 1773.36 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 21.29783 -11.670408 -11.673159 -2.8765459 -8.7966134 -1265631.7 17627.802 25.642 25.957 26.4845 -4.46691 2.7462211 -1.3731106
7 21.29783 -11.675131 -11.677882 -2.881099 -8.7967827 -1253486.8 17619.929 25.636872 25.952496 26.482562 -4.46691 2.7462211 -1.3731106
8 21.29783 -11.679808 -11.68256 -2.8856058 -8.7969538 -1240999.6 17612.041 25.631743 25.947989 26.480601 -4.46691 2.7462211 -1.3731106
9 21.29783 -11.684439 -11.68719 -2.8900654 -8.7971248 -1228174.4 17604.137 25.626615 25.943479 26.478617 -4.46691 2.7462211 -1.3731106
10 21.29783 -11.689021 -11.691773 -2.8944766 -8.797296 -1215016.6 17596.218 25.621486 25.938967 26.476607 -4.46691 2.7462211 -1.3731106
11 21.29783 -11.693555 -11.696306 -2.8988384 -8.7974677 -1201528.9 17588.281 25.616358 25.934452 26.474572 -4.46691 2.7462211 -1.3731106
12 21.29783 -11.698037 -11.700788 -2.9031496 -8.7976389 -1187674.4 17580.327 25.61123 25.929934 26.472509 -4.46691 2.7462211 -1.3731106
13 21.29783 -11.70247 -11.705221 -2.9074093 -8.7978121 -1173415.2 17572.353 25.606101 25.925412 26.470418 -4.46691 2.7462211 -1.3731106
14 21.29783 -11.707235 -11.709986 -2.9120023 -8.7979838 -1158172.5 17564.36 25.600973 25.920887 26.468297 -4.46691 2.7462211 -1.3731106
15 21.29783 -11.713863 -11.716614 -2.9184576 -8.7981563 -1142098.6 17556.347 25.595844 25.916358 26.466147 -4.46691 2.7462211 -1.3731106
16 21.29783 -11.722779 -11.72553 -2.9272014 -8.7983285 -1129422 17548.315 25.590716 25.911823 26.463971 -4.46691 2.7462211 -1.3731106
17 21.29783 -11.741011 -11.743762 -2.9452614 -8.7985004 -1124627 17540.249 25.585588 25.90728 26.46175 -4.46691 2.7462211 -1.3731106
18 21.29783 -11.748152 -11.750903 -2.9522304 -8.7986728 -1124520.6 17532.121 25.580459 25.902721 26.459445 -4.46691 2.7462211 -1.3731106
19 21.29783 -11.75378 -11.756532 -2.9576857 -8.7988459 -1119185 17523.917 25.575331 25.898158 26.457028 -4.46691 2.7462211 -1.3731106
20 21.29783 -11.758859 -11.761611 -2.9625911 -8.7990195 -1104339.2 17515.652 25.570202 25.89359 26.45452 -4.46691 2.7462211 -1.3731106
21 21.29783 -11.76349 -11.766241 -2.9670486 -8.7991922 -1076322.1 17507.352 25.565074 25.889017 26.451959 -4.46691 2.7462211 -1.3731106
22 21.29783 -11.767701 -11.770452 -2.9710158 -8.7994367 -1048872.9 17499.053 25.559946 25.884435 26.449405 -4.46691 2.7462211 -1.3731106
23 21.29783 -11.775875 -11.778626 -2.9749154 -8.8037107 -1025626.1 17490.752 25.554817 25.879846 26.446854 -4.46691 2.7462211 -1.3731106
24 21.29783 -11.813826 -11.816577 -2.9785903 -8.8379868 -1008756.2 17482.437 25.549689 25.875251 26.444283 -4.46691 2.7462211 -1.3731106
25 21.29783 -11.910194 -11.912945 -2.982199 -8.9307461 -995245.49 17474.1 25.54456 25.870662 26.441668 -4.46691 2.7462211 -1.3731106
26 21.29783 -11.910731 -11.913482 -2.982422 -8.9310604 -994153.58 17473.579 25.54424 25.870377 26.441502 -4.46691 2.7462211 -1.3731106
27 21.29783 -11.910731 -11.913482 -2.982422 -8.9310604 -994153.58 17473.579 25.54424 25.870377 26.441502 -4.46691 2.7462211 -1.3731106
Loop time of 5.40827 on 1 procs for 21 steps with 1500 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-11.6731593188 -11.9134824619 -11.9134824619
Force two-norm initial, final = 25697.5 19505.2
Force max component initial, final = 18706.6 13710.2
Final line search alpha, max atom move = 2.78239e-14 3.8147e-10
Iterations, force evaluations = 21 44
Pair time (%) = 5.39078 (99.6768)
Neigh time (%) = 0 (0)
Comm time (%) = 0.003757 (0.0694677)
Outpt time (%) = 0.000648499 (0.0119909)
Other time (%) = 0.0130765 (0.241788)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
velocity all create 300.1 2398378
run 10
Memory usage per processor = 1771.89 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
27 300.1 -11.874717 -11.913482 -2.982422 -8.9310604 -990851.4 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
28 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
29 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
30 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
31 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
32 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
33 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
34 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
35 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
36 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
37 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
Loop time of 1.66635 on 1 procs for 10 steps with 1500 atoms
Pair time (%) = 1.19877 (71.9397)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000849009 (0.0509501)
Outpt time (%) = 0.00031805 (0.0190866)
Other time (%) = 0.466416 (27.9902)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.045e+06 ave 1.045e+06 max 1.045e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1045000
Ave neighs/atom = 696.667
Neighbor list builds = 0
Dangerous builds = 0

291
examples/comb/log.comb.HfO2.9Jan12.linux.4 Normal file
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@ -0,0 +1,291 @@
LAMMPS (10 Jan 2012)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 2 by 2 MPI processor grid
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 416.525 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -10.375148 -10.375148 4.2805776 -14.655726 -402517.96 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.0318046 on 4 procs for 1 steps with 1500 atoms
Pair time (%) = 0.030692 (96.502)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00102538 (3.224)
Outpt time (%) = 3.89218e-05 (0.122378)
Other time (%) = 4.82202e-05 (0.151614)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 416.923 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 2.480664 -1.240332
2 1.332821 -11.209515 -11.209687 -3.2054666 -8.0042207 -1191111.8 17627.802 25.642 25.957 26.4845 -4.46691 2.480664 -1.240332
3 4.354723 -11.20952 -11.210083 -3.2057752 -8.0043075 -1189669.1 17627.802 25.642 25.957 26.4845 -4.46691 2.4806442 -1.2403221
4 9.3099681 -11.2095 -11.210703 -3.206296 -8.0044071 -1187480.4 17627.802 25.642 25.957 26.4845 -4.46691 2.4805928 -1.2402964
5 16.179541 -11.209458 -11.211548 -3.2070561 -8.0044916 -1184541.9 17627.802 25.642 25.957 26.4845 -4.46691 2.4805273 -1.2402636
6 24.937669 -11.209421 -11.212642 -3.2080101 -8.0046317 -1180839.7 17627.802 25.642 25.957 26.4845 -4.46691 2.4804545 -1.2402272
Loop time of 0.665697 on 4 procs for 5 steps with 1500 atoms
Pair time (%) = 0.150524 (22.6115)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00534689 (0.803202)
Outpt time (%) = 0.000192285 (0.0288847)
Other time (%) = 0.509634 (76.5564)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 417.638 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 24.937669 -11.119392 -11.122613 -3.7917885 -7.3308248 -1331535.2 17627.802 25.642 25.957 26.4845 -4.46691 2.4804545 -1.2402272
7 24.937669 -11.124364 -11.127585 -3.7966203 -7.3309649 -1319068.8 17619.914 25.636872 25.952494 26.482541 -4.46691 2.4804545 -1.2402272
8 24.937669 -11.12929 -11.132511 -3.8014047 -7.3311063 -1306249 17612.011 25.631743 25.947986 26.480559 -4.46691 2.4804545 -1.2402272
9 24.937669 -11.134167 -11.137388 -3.8061404 -7.3312478 -1293080.4 17604.094 25.626615 25.943476 26.478554 -4.46691 2.4804545 -1.2402272
10 24.937669 -11.138994 -11.142216 -3.8108264 -7.3313893 -1279568.8 17596.16 25.621486 25.938963 26.476524 -4.46691 2.4804545 -1.2402272
11 24.937669 -11.143771 -11.146993 -3.8154614 -7.3315313 -1265720.4 17588.21 25.616358 25.934448 26.474468 -4.46691 2.4804545 -1.2402272
12 24.937669 -11.148496 -11.151717 -3.8200446 -7.3316729 -1251540.8 17580.241 25.61123 25.92993 26.472385 -4.46691 2.4804545 -1.2402272
13 24.937669 -11.153513 -11.156734 -3.8249183 -7.3318161 -1237144.2 17572.254 25.606101 25.925408 26.470273 -4.46691 2.4804545 -1.2402272
14 24.937669 -11.16005 -11.163272 -3.8313134 -7.3319582 -1222915.3 17564.247 25.600973 25.920884 26.46813 -4.46691 2.4804545 -1.2402272
15 24.937669 -11.16669 -11.169911 -3.8378099 -7.332101 -1208411.1 17556.216 25.595844 25.916354 26.465954 -4.46691 2.4804545 -1.2402272
16 24.937669 -11.176313 -11.179534 -3.8472905 -7.3322435 -1194529.9 17548.16 25.590716 25.911819 26.463742 -4.46691 2.4804545 -1.2402272
17 24.937669 -11.189963 -11.193184 -3.8607982 -7.3323858 -1181590.6 17540.074 25.585588 25.907276 26.461489 -4.46691 2.4804545 -1.2402272
18 24.937669 -11.198449 -11.20167 -3.8691419 -7.332528 -1166711 17531.951 25.580459 25.902722 26.459188 -4.46691 2.4804545 -1.2402272
19 24.937669 -11.205262 -11.208484 -3.8758138 -7.3326699 -1151023.9 17523.796 25.575331 25.89816 26.456843 -4.46691 2.4804545 -1.2402272
20 24.937669 -11.212314 -11.215535 -3.8827236 -7.3328117 -1135134.5 17515.611 25.570202 25.893592 26.454455 -4.46691 2.4804545 -1.2402272
21 24.937669 -11.218016 -11.221237 -3.8882845 -7.3329526 -1118552.5 17507.392 25.565074 25.889016 26.45202 -4.46691 2.4804545 -1.2402272
22 24.937669 -11.222659 -11.225881 -3.8927875 -7.333093 -1101383.9 17499.139 25.559946 25.884434 26.449538 -4.46691 2.4804545 -1.2402272
23 24.937669 -11.226952 -11.230173 -3.8969397 -7.3332337 -1083865.1 17490.854 25.554817 25.879846 26.447008 -4.46691 2.4804545 -1.2402272
24 24.937669 -11.231023 -11.234244 -3.9008707 -7.3333736 -1066045.2 17482.533 25.549689 25.875252 26.444426 -4.46691 2.4804545 -1.2402272
25 24.937669 -11.235033 -11.238254 -3.9047394 -7.3335144 -1047983.4 17474.175 25.54456 25.870652 26.441792 -4.46691 2.4804545 -1.2402272
26 24.937669 -11.238979 -11.242201 -3.9085455 -7.333655 -1029686.9 17465.779 25.539432 25.866046 26.4391 -4.46691 2.4804545 -1.2402272
27 24.937669 -11.242863 -11.246084 -3.9122887 -7.3337956 -1011163.7 17457.34 25.534304 25.861433 26.436349 -4.46691 2.4804545 -1.2402272
28 24.937669 -11.246686 -11.249907 -3.9159688 -7.3339381 -992422.88 17448.858 25.529175 25.856812 26.433534 -4.46691 2.4804545 -1.2402272
29 24.937669 -11.250446 -11.253668 -3.9195856 -7.3340819 -973472.02 17440.328 25.524047 25.852184 26.430652 -4.46691 2.4804545 -1.2402272
30 24.937669 -11.254146 -11.257367 -3.923139 -7.3342279 -954319.47 17431.749 25.518918 25.847547 26.427699 -4.46691 2.4804545 -1.2402272
31 24.937669 -11.257781 -11.261003 -3.9266292 -7.3343734 -934971.89 17423.116 25.51379 25.842902 26.424669 -4.46691 2.4804545 -1.2402272
32 24.937669 -11.261355 -11.264576 -3.9300563 -7.3345201 -915438.13 17414.426 25.508662 25.838247 26.421559 -4.46691 2.4804545 -1.2402272
33 24.937669 -11.264868 -11.268089 -3.9334206 -7.3346683 -895726.51 17405.675 25.503533 25.833583 26.418362 -4.46691 2.4804545 -1.2402272
34 24.937669 -11.268319 -11.27154 -3.9367223 -7.3348175 -875844.65 17396.86 25.498405 25.828908 26.415072 -4.46691 2.4804545 -1.2402272
35 24.937669 -11.271708 -11.27493 -3.9399621 -7.3349676 -855800.42 17387.974 25.493276 25.824221 26.411684 -4.46691 2.4804545 -1.2402272
36 24.937669 -11.275035 -11.278257 -3.9431406 -7.3351162 -835600.16 17379.014 25.488148 25.819523 26.40819 -4.46691 2.4804545 -1.2402272
37 24.937669 -11.278302 -11.281523 -3.9462585 -7.3352643 -815252.4 17369.973 25.48302 25.814811 26.404583 -4.46691 2.4804545 -1.2402272
38 24.937669 -11.281508 -11.284729 -3.949317 -7.3354119 -794764.78 17360.845 25.477891 25.810085 26.400852 -4.46691 2.4804545 -1.2402272
39 24.937669 -11.284657 -11.287878 -3.9523172 -7.335561 -774146.03 17351.623 25.472763 25.805345 26.396989 -4.46691 2.4804545 -1.2402272
40 24.937669 -11.28775 -11.290971 -3.9552606 -7.3357107 -753402.85 17342.3 25.467634 25.800587 26.392983 -4.46691 2.4804545 -1.2402272
41 24.937669 -11.290789 -11.294011 -3.9581487 -7.3358619 -732542.91 17332.865 25.462506 25.795813 26.388822 -4.46691 2.4804545 -1.2402272
42 24.937669 -11.293778 -11.296999 -3.9609838 -7.3360152 -711573.18 17323.31 25.457378 25.791019 26.384491 -4.46691 2.4804545 -1.2402272
43 24.937669 -11.296716 -11.299937 -3.9637679 -7.3361695 -690499.53 17313.623 25.452249 25.786204 26.379975 -4.46691 2.4804545 -1.2402272
44 24.937669 -11.299611 -11.302832 -3.966504 -7.3363285 -669329.96 17303.791 25.447121 25.781367 26.375256 -4.46691 2.4804545 -1.2402272
45 24.937669 -11.302465 -11.305686 -3.9691953 -7.336491 -648069.16 17293.8 25.441992 25.776504 26.370314 -4.46691 2.4804545 -1.2402272
46 24.937669 -11.30528 -11.308502 -3.9718455 -7.3366562 -626720.99 17283.632 25.436864 25.771614 26.365124 -4.46691 2.4804545 -1.2402272
47 24.937669 -11.307978 -11.311199 -3.9743804 -7.3368185 -605946.37 17273.585 25.431893 25.766844 26.359827 -4.46691 2.4804545 -1.2402272
48 24.937669 -11.310512 -11.313733 -3.9767586 -7.3369747 -586171.83 17263.86 25.427179 25.76229 26.35453 -4.46691 2.4804545 -1.2402272
49 24.937669 -11.312898 -11.31612 -3.978995 -7.3371247 -567358.74 17254.444 25.422709 25.757942 26.349233 -4.46691 2.4804545 -1.2402272
50 24.937669 -11.315151 -11.318372 -3.9811032 -7.337269 -549468.1 17245.321 25.418472 25.753791 26.343936 -4.46691 2.4804545 -1.2402272
51 24.937669 -11.317282 -11.320503 -3.9830955 -7.3374078 -532460.71 17236.477 25.414458 25.749827 26.33864 -4.46691 2.4804545 -1.2402272
52 24.937669 -11.319303 -11.322525 -3.9849831 -7.3375416 -516297.54 17227.899 25.410655 25.746041 26.333343 -4.46691 2.4804545 -1.2402272
53 24.937669 -11.321225 -11.324447 -3.9867761 -7.3376707 -500940.12 17219.573 25.407053 25.742425 26.328046 -4.46691 2.4804545 -1.2402272
54 24.937669 -11.323058 -11.326279 -3.9884836 -7.3377956 -486350.73 17211.488 25.403642 25.738971 26.322749 -4.46691 2.4804545 -1.2402272
55 24.937669 -11.32481 -11.328031 -3.9901141 -7.3379171 -472493.07 17203.631 25.400413 25.735671 26.317452 -4.46691 2.4804545 -1.2402272
56 24.937669 -11.326489 -11.32971 -3.9916749 -7.3380352 -459331.31 17195.991 25.397358 25.732517 26.312155 -4.46691 2.4804545 -1.2402272
57 24.937669 -11.328102 -11.331323 -3.9931729 -7.3381501 -446830.89 17188.558 25.394466 25.729502 26.306858 -4.46691 2.4804545 -1.2402272
58 24.937669 -11.329654 -11.332876 -3.9946142 -7.3382614 -434958.48 17181.322 25.391731 25.72662 26.301561 -4.46691 2.4804545 -1.2402272
59 24.937669 -11.331153 -11.334374 -3.9960043 -7.3383695 -423682.29 17174.272 25.389145 25.723864 26.296264 -4.46691 2.4804545 -1.2402272
60 24.937669 -11.332601 -11.335823 -3.9973482 -7.3384745 -412971.91 17167.399 25.386699 25.721228 26.290967 -4.46691 2.4804545 -1.2402272
61 24.937669 -11.334006 -11.337227 -3.9986504 -7.3385765 -402798.3 17160.695 25.384388 25.718706 26.285671 -4.46691 2.4804545 -1.2402272
62 24.937669 -11.335369 -11.338591 -3.999915 -7.3386757 -393133.76 17154.152 25.382205 25.716293 26.280374 -4.46691 2.4804545 -1.2402272
63 24.937669 -11.336696 -11.339918 -4.0011456 -7.3387722 -383951.94 17147.76 25.380142 25.713983 26.275077 -4.46691 2.4804545 -1.2402272
64 24.937669 -11.33799 -11.341212 -4.0023455 -7.3388662 -375227.79 17141.513 25.378195 25.711772 26.26978 -4.46691 2.4804545 -1.2402272
65 24.937669 -11.339254 -11.342475 -4.0035177 -7.3389578 -366937.52 17135.404 25.376357 25.709653 26.264483 -4.46691 2.4804545 -1.2402272
66 24.937669 -11.340491 -11.343712 -4.0046649 -7.3390471 -359058.56 17129.426 25.374623 25.707624 26.259186 -4.46691 2.4804545 -1.2402272
67 24.937669 -11.341702 -11.344924 -4.0057895 -7.3391342 -351569.51 17123.572 25.372988 25.70568 26.253889 -4.46691 2.4804545 -1.2402272
68 24.937669 -11.342892 -11.346113 -4.0068937 -7.3392192 -344450.1 17117.836 25.371447 25.703816 26.248592 -4.46691 2.4804545 -1.2402272
69 24.937669 -11.344061 -11.347282 -4.0079795 -7.3393023 -337681.13 17112.212 25.369995 25.702029 26.243295 -4.46691 2.4804545 -1.2402272
70 24.937669 -11.345211 -11.348432 -4.0090487 -7.3393835 -331244.45 17106.696 25.368628 25.700315 26.237998 -4.46691 2.4804545 -1.2402272
71 24.937669 -11.346345 -11.349567 -4.0101029 -7.3394638 -325123.5 17101.281 25.367342 25.698671 26.232702 -4.46691 2.4804545 -1.2402272
72 24.937669 -11.347464 -11.350685 -4.0111435 -7.3395417 -319300.89 17095.963 25.366132 25.697093 26.227405 -4.46691 2.4804545 -1.2402272
73 24.937669 -11.34857 -11.351791 -4.0121718 -7.3396197 -313762.69 17090.736 25.364996 25.695578 26.222108 -4.46691 2.4804545 -1.2402272
74 24.937669 -11.349662 -11.352883 -4.0131891 -7.3396939 -308492.11 17085.598 25.363929 25.694123 26.216811 -4.46691 2.4804545 -1.2402272
75 24.937669 -11.350742 -11.353963 -4.0141963 -7.3397671 -303476.96 17080.542 25.362927 25.692725 26.211514 -4.46691 2.4804545 -1.2402272
76 24.937669 -11.351812 -11.355033 -4.0151946 -7.3398386 -298703.85 17075.566 25.361989 25.691382 26.206217 -4.46691 2.4804545 -1.2402272
77 24.937669 -11.352873 -11.356094 -4.0161846 -7.3399096 -294161.04 17070.665 25.36111 25.690091 26.20092 -4.46691 2.4804545 -1.2402272
78 24.937669 -11.353926 -11.357147 -4.0171674 -7.3399796 -289836.52 17065.836 25.360288 25.688849 26.195623 -4.46691 2.4804545 -1.2402272
79 24.937669 -11.35497 -11.358192 -4.0181434 -7.3400483 -285719.12 17061.075 25.35952 25.687655 26.190326 -4.46691 2.4804545 -1.2402272
80 24.937669 -11.356008 -11.35923 -4.0191135 -7.340116 -281798.55 17056.379 25.358803 25.686506 26.185029 -4.46691 2.4804545 -1.2402272
81 24.937669 -11.357041 -11.360262 -4.0200782 -7.340184 -278065.73 17051.745 25.358135 25.685399 26.179733 -4.46691 2.4804545 -1.2402272
82 24.937669 -11.358068 -11.361289 -4.0210379 -7.3402515 -274510.78 17047.17 25.357514 25.684334 26.174436 -4.46691 2.4804545 -1.2402272
83 24.937669 -11.35909 -11.362311 -4.0219933 -7.340318 -271124.57 17042.651 25.356936 25.683307 26.169139 -4.46691 2.4804545 -1.2402272
84 24.937669 -11.360107 -11.363329 -4.0229447 -7.3403841 -267898.97 17038.186 25.356401 25.682318 26.163842 -4.46691 2.4804545 -1.2402272
85 24.937669 -11.36112 -11.364342 -4.0238925 -7.3404492 -264825.72 17033.771 25.355905 25.681365 26.158545 -4.46691 2.4804545 -1.2402272
86 24.937669 -11.362129 -11.36535 -4.0248371 -7.3405133 -261897.31 17029.405 25.355448 25.680445 26.153248 -4.46691 2.4804545 -1.2402272
87 24.937669 -11.363134 -11.366355 -4.0257788 -7.3405765 -259106.64 17025.085 25.355027 25.679558 26.147951 -4.46691 2.4804545 -1.2402272
88 24.937669 -11.364135 -11.367357 -4.0267179 -7.3406387 -256446.95 17020.808 25.35464 25.678702 26.142654 -4.46691 2.4804545 -1.2402272
89 24.937669 -11.365133 -11.368355 -4.0276546 -7.3407001 -253911.89 17016.574 25.354285 25.677875 26.137357 -4.46691 2.4804545 -1.2402272
90 24.937669 -11.366129 -11.36935 -4.0285893 -7.3407607 -251495.4 17012.379 25.353962 25.677076 26.13206 -4.46691 2.4804545 -1.2402272
91 24.937669 -11.367121 -11.370342 -4.029522 -7.3408204 -249191.74 17008.223 25.353669 25.676304 26.126764 -4.46691 2.4804545 -1.2402272
92 24.937669 -11.368111 -11.371333 -4.0304531 -7.3408794 -246995.48 17004.103 25.353403 25.675558 26.121467 -4.46691 2.4804545 -1.2402272
93 24.937669 -11.369099 -11.37232 -4.0313827 -7.3409374 -244901.4 17000.017 25.353165 25.674837 26.11617 -4.46691 2.4804545 -1.2402272
94 24.937669 -11.370084 -11.373306 -4.032311 -7.3409945 -242904.51 16995.964 25.352951 25.674139 26.110873 -4.46691 2.4804545 -1.2402272
95 24.937669 -11.371068 -11.374289 -4.0332381 -7.3410509 -241000.35 16991.942 25.352762 25.673463 26.105576 -4.46691 2.4804545 -1.2402272
96 24.937669 -11.372049 -11.37527 -4.0341641 -7.3411063 -239184.32 16987.95 25.352596 25.672809 26.100279 -4.46691 2.4804545 -1.2402272
97 24.937669 -11.373029 -11.37625 -4.0350892 -7.341161 -237452.42 16983.987 25.352452 25.672175 26.094982 -4.46691 2.4804545 -1.2402272
98 24.937669 -11.374007 -11.377229 -4.0360135 -7.341215 -235800.7 16980.05 25.352329 25.671561 26.089685 -4.46691 2.4804545 -1.2402272
99 24.937669 -11.374985 -11.378206 -4.0369371 -7.3412694 -234226.03 16976.14 25.352225 25.670965 26.084388 -4.46691 2.4804545 -1.2402272
100 24.937669 -11.375963 -11.379184 -4.0378601 -7.341324 -232724.75 16972.254 25.352141 25.670388 26.079091 -4.46691 2.4804545 -1.2402272
101 24.937669 -11.37694 -11.380161 -4.0387826 -7.3413784 -231293.15 16968.391 25.352074 25.669827 26.073795 -4.46691 2.4804545 -1.2402272
102 24.937669 -11.377915 -11.381137 -4.0397046 -7.3414322 -229927.75 16964.551 25.352024 25.669283 26.068498 -4.46691 2.4804545 -1.2402272
103 24.937669 -11.37889 -11.382112 -4.0406262 -7.3414855 -228625.48 16960.733 25.35199 25.668755 26.063201 -4.46691 2.4804545 -1.2402272
104 24.937669 -11.379864 -11.383086 -4.0415475 -7.3415382 -227383.42 16956.934 25.351972 25.668242 26.057904 -4.46691 2.4804545 -1.2402272
105 24.937669 -11.380838 -11.384059 -4.0424685 -7.3415903 -226198.79 16953.155 25.351968 25.667743 26.052607 -4.46691 2.4804545 -1.2402272
106 24.937669 -11.38181 -11.385031 -4.0433894 -7.3416419 -225068.97 16949.395 25.351978 25.667258 26.04731 -4.46691 2.4804545 -1.2402272
107 24.937669 -11.382783 -11.386004 -4.0443101 -7.3416939 -223992.05 16945.652 25.352001 25.666786 26.042013 -4.46691 2.4804545 -1.2402272
108 24.937669 -11.383755 -11.386976 -4.0452307 -7.3417454 -222965.04 16941.926 25.352037 25.666326 26.036716 -4.46691 2.4804545 -1.2402272
109 24.937669 -11.384727 -11.387948 -4.0461513 -7.3417972 -221986.16 16938.216 25.352084 25.665879 26.031419 -4.46691 2.4804545 -1.2402272
110 24.937669 -11.385699 -11.38892 -4.0470718 -7.3418485 -221052.74 16934.521 25.352143 25.665444 26.026122 -4.46691 2.4804545 -1.2402272
111 24.937669 -11.38667 -11.389892 -4.0479923 -7.3418993 -220162.75 16930.841 25.352212 25.665019 26.020826 -4.46691 2.4804545 -1.2402272
112 24.937669 -11.387641 -11.390863 -4.048913 -7.3419496 -219314.21 16927.174 25.352291 25.664605 26.015529 -4.46691 2.4804545 -1.2402272
113 24.937669 -11.388612 -11.391833 -4.0498336 -7.3419995 -218505.28 16923.521 25.35238 25.664202 26.010232 -4.46691 2.4804545 -1.2402272
114 24.937669 -11.389582 -11.392803 -4.0507545 -7.3420489 -217734.19 16919.88 25.352478 25.663808 26.004935 -4.46691 2.4804545 -1.2402272
115 24.937669 -11.390553 -11.393774 -4.0516754 -7.3420988 -216999.89 16916.252 25.352585 25.663424 25.999638 -4.46691 2.4804545 -1.2402272
116 24.937669 -11.391524 -11.394745 -4.0525965 -7.3421486 -216300.32 16912.635 25.3527 25.663049 25.994341 -4.46691 2.4804545 -1.2402272
117 24.937669 -11.39201 -11.395231 -4.0530571 -7.3421737 -215967.06 16910.832 25.352761 25.662866 25.991693 -4.46691 2.4804545 -1.2402272
118 24.937669 -11.392232 -11.395453 -4.0532686 -7.3421844 -215803.49 16909.932 25.352792 25.662775 25.990368 -4.46691 2.4804545 -1.2402272
119 24.937669 -11.392243 -11.395465 -4.0532786 -7.342186 -215784.41 16909.819 25.352796 25.662764 25.990203 -4.46691 2.4804545 -1.2402272
120 24.937669 -11.392247 -11.395468 -4.0532822 -7.3421862 -215782.06 16909.805 25.352797 25.662763 25.990182 -4.46691 2.4804545 -1.2402272
121 24.937669 -11.392249 -11.39547 -4.053284 -7.3421863 -215780.89 16909.798 25.352797 25.662762 25.990172 -4.46691 2.4804545 -1.2402272
122 24.937669 -11.392249 -11.395471 -4.0532845 -7.3421863 -215780.6 16909.796 25.352797 25.662762 25.990169 -4.46691 2.4804545 -1.2402272
123 24.937669 -11.39225 -11.395471 -4.0532847 -7.3421863 -215780.45 16909.796 25.352797 25.662762 25.990168 -4.46691 2.4804545 -1.2402272
124 24.937669 -11.39225 -11.395471 -4.0532847 -7.3421863 -215780.41 16909.795 25.352797 25.662762 25.990168 -4.46691 2.4804545 -1.2402272
125 24.937669 -11.39225 -11.395471 -4.0532847 -7.3421863 -215780.41 16909.795 25.352797 25.662762 25.990168 -4.46691 2.4804545 -1.2402272
Loop time of 6.48088 on 4 procs for 119 steps with 1500 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-11.1226132511 -11.3954710611 -11.3954710611
Force two-norm initial, final = 27009.2 6698.47
Force max component initial, final = 19644.3 6673.92
Final line search alpha, max atom move = 2.28633e-13 1.52588e-09
Iterations, force evaluations = 119 198
Pair time (%) = 6.18186 (95.3861)
Neigh time (%) = 0.13631 (2.10326)
Comm time (%) = 0.121525 (1.87513)
Outpt time (%) = 0.00443709 (0.0684643)
Other time (%) = 0.0367464 (0.566998)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 268488 ave 268492 max 268483 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 1073950
Ave neighs/atom = 715.967
Neighbor list builds = 2
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
velocity all create 300.1 2398378
run 10
Memory usage per processor = 416.923 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
125 300.1 -11.356706 -11.395471 -4.0532847 -7.3421863 -212412.69 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
126 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
127 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
128 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
129 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
130 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
131 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
132 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
133 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
134 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
135 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
Loop time of 0.445023 on 4 procs for 10 steps with 1500 atoms
Pair time (%) = 0.314639 (70.7017)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00810659 (1.82161)
Outpt time (%) = 0.000411868 (0.0925499)
Other time (%) = 0.121866 (27.3841)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 271875 ave 271875 max 271875 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1087500
Ave neighs/atom = 725
Neighbor list builds = 0
Dangerous builds = 0

69
examples/comb/log.comb.Si.28Mar11.linux.1
View File

@ -1,69 +0,0 @@
LAMMPS (27 Mar 2011)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 3.18525 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
Loop time of 0.449238 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.447972 (99.7182)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000600338 (0.133635)
Outpt time (%) = 0.000299215 (0.0666051)
Other time (%) = 0.000366449 (0.0815713)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.33625 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
Loop time of 0.118667 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.112987 (95.2134)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00507617 (4.27764)
Outpt time (%) = 0.000378549 (0.319)
Other time (%) = 0.000225365 (0.189913)
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 384.657 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -5.2974091 -5.2987121 -5.2987121 0 -71570.238 10246.592 21.72 21.72 21.72 0
1 10.098269 -5.2974091 -5.2987119 -5.2987119 0 -71570.213 10246.592 21.72 21.72 21.72 0
2 10.093077 -5.2974091 -5.2987112 -5.2987112 0 -71570.137 10246.592 21.72 21.72 21.72 0
3 10.08443 -5.2974091 -5.2987101 -5.2987101 0 -71570.011 10246.592 21.72 21.72 21.72 0
4 10.072338 -5.2974091 -5.2987085 -5.2987085 0 -71569.835 10246.592 21.72 21.72 21.72 0
5 10.056815 -5.2974091 -5.2987065 -5.2987065 0 -71569.609 10246.592 21.72 21.72 21.72 0
6 10.037878 -5.2974091 -5.2987041 -5.2987041 0 -71569.334 10246.592 21.72 21.72 21.72 0
7 10.015548 -5.2974091 -5.2987012 -5.2987012 0 -71569.01 10246.592 21.72 21.72 21.72 0
8 9.9898514 -5.2974091 -5.2986979 -5.2986979 0 -71568.636 10246.592 21.72 21.72 21.72 0
9 9.9608163 -5.2974091 -5.2986941 -5.2986941 0 -71568.215 10246.592 21.72 21.72 21.72 0
10 9.9284757 -5.2974091 -5.29869 -5.29869 0 -71567.746 10246.592 21.72 21.72 21.72 0
Loop time of 0.131721 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.131023 (99.47)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000367165 (0.278744)
Outpt time (%) = 0.000140667 (0.106792)
Other time (%) = 0.000190258 (0.14444)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 383.808 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -5.2974091 -5.2987121 -5.2987121 0 -71570.238 10246.592 21.72 21.72 21.72 0
1 10.098254 -5.2974091 -5.2987119 -5.2987119 0 -71570.212 10246.592 21.72 21.72 21.72 0
2 10.093019 -5.2974091 -5.2987112 -5.2987112 0 -71570.136 10246.592 21.72 21.72 21.72 0
3 10.0843 -5.2974091 -5.2987101 -5.2987101 0 -71570.008 10246.592 21.72 21.72 21.72 0
4 10.072108 -5.2974091 -5.2987085 -5.2987085 0 -71569.83 10246.592 21.72 21.72 21.72 0
5 10.056457 -5.2974091 -5.2987065 -5.2987065 0 -71569.601 10246.592 21.72 21.72 21.72 0
6 10.037364 -5.2974091 -5.298704 -5.298704 0 -71569.322 10246.592 21.72 21.72 21.72 0
7 10.014852 -5.2974091 -5.2987011 -5.2987011 0 -71568.993 10246.592 21.72 21.72 21.72 0
8 9.9889464 -5.2974091 -5.2986978 -5.2986978 0 -71568.614 10246.592 21.72 21.72 21.72 0
9 9.9596766 -5.2974091 -5.298694 -5.298694 0 -71568.187 10246.592 21.72 21.72 21.72 0
10 9.927076 -5.2974091 -5.2986898 -5.2986898 0 -71567.712 10246.592 21.72 21.72 21.72 0
Loop time of 0.0353957 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0332664 (93.9841)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00170434 (4.81509)
Outpt time (%) = 0.000266969 (0.754241)
Other time (%) = 0.000158072 (0.446583)
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization
Memory usage per processor = 3.87189 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.768104 on 1 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.763957 (99.46)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0010047 (0.130802)
Outpt time (%) = 7.00951e-05 (0.00912572)
Other time (%) = 0.00307274 (0.400042)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move
Memory usage per processor = 2.88007 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0448351 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0447428 (99.7942)
Neigh time (%) = 0 (0)
Comm time (%) = 5.81741e-05 (0.129751)
Outpt time (%) = 1.5974e-05 (0.0356284)
Other time (%) = 1.81198e-05 (0.0404144)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost
run 10
Memory usage per processor = 3.33784 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.9450404e-06 2.4752556e-06 -1.6071587e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.8110987e-06 2.6015226e-06 -1.1358357e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 -4.4966424e-06 1.848553e-07 -2.2958737e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 2.4287963e-06 2.6615821e-06 -1.9832618e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 2.4447348e-06 2.4469323e-06 -8.4990897e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 4.0363922e-06 -5.9982754e-06 -2.3201799e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 2.8253812e-06 2.5964234e-06 -8.931554e-07
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 2.3933505e-06 2.283704e-06 -3.9266049e-07
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.2037259e-06 2.6987214e-06 3.737462e-07
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 2.6802555e-06 2.9969439e-06 1.7521287e-07
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 4.4634386e-06 -4.2738918e-06 3.2367003e-07
Loop time of 0.48314 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479521 (99.2508)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000623703 (0.129094)
Outpt time (%) = 0.0027349 (0.566067)
Other time (%) = 0.000261068 (0.0540357)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 3.7956 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 1.3848713e-06 1.8198295e-06 -3.1488289e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 1.4477769e-06 2.1276907e-06 -2.7563351e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.1162843e-06 -3.0681281e-06 -1.8698946e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 1.5226892e-06 3.1081802e-06 -2.6821714e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -7.5700513e-07 1.7188656e-06 4.1051196e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -1.4391091e-06 2.0797417e-06 3.9123487e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -1.5213551e-06 1.9181068e-06 -2.1773741e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -1.4238005e-06 1.7984361e-06 -2.0333083e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 4.4088785e-06 2.5805071e-06 -2.1480169e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -9.3407459e-07 2.1740278e-06 -1.3082692e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -1.7972725e-06 2.108669e-06 -1.6910019e-06
Loop time of 0.48289 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479337 (99.2643)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000632048 (0.130889)
Outpt time (%) = 0.0026505 (0.548883)
Other time (%) = 0.00026989 (0.0558906)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 4.25336 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -1.7548117e-06 3.6087566e-06 -3.6198628e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -1.7167978e-06 3.4304272e-06 -2.9804569e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -1.8729445e-06 4.5840765e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -1.2316967e-06 2.6286266e-06 487.30276
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -1.3251453e-06 2.7225014e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -8.5464495e-07 -6.3592996e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -1.7272259e-06 2.0497545e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -4.6626464e-07 2.1955509e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -1.1296433e-06 2.2397275e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -1.388603e-06 1.2425658e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.1793341e-06 1.7092936e-06 2192.8625
Loop time of 0.483123 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479436 (99.2368)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000645638 (0.133638)
Outpt time (%) = 0.00276113 (0.571516)
Other time (%) = 0.00028038 (0.058035)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 4.71113 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.7294679e-06 4.8293026e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.4630595e-06 4.5052213e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012576585 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025542614 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038565598 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051669611 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064706412 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.0007779958 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090716273 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.001038008 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011663311 2436.5138
Loop time of 0.484576 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.480966 (99.255)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000598431 (0.123496)
Outpt time (%) = 0.00274968 (0.567441)
Other time (%) = 0.000261784 (0.0540232)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

273
examples/comb/log.comb.Si.elastic.28Mar11.linux.4
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@ -1,273 +0,0 @@
LAMMPS (27 Mar 2011)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization
Memory usage per processor = 3.02671 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.250542 on 4 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.191762 (76.5388)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0565124 (22.556)
Outpt time (%) = 5.87702e-05 (0.0234572)
Other time (%) = 0.00220919 (0.881761)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move
Memory usage per processor = 2.03489 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0146563 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.01146 (78.1916)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00314051 (21.4277)
Outpt time (%) = 3.39746e-05 (0.231809)
Other time (%) = 2.18153e-05 (0.148846)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost
run 10
Memory usage per processor = 2.49265 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 -5.331517e-06 3.0239293e-06 -4.7684649e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 -4.2797025e-06 2.0730342e-06 -3.2414474e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 6.7462199e-07 1.6210516e-06 -2.8184106e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 -3.9337607e-06 2.4599063e-06 -4.2531358e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 -3.6805931e-06 3.0030584e-06 -2.6648247e-06
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 1.0867248e-05 -8.1694237e-06 -1.7161938e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 -3.2850644e-06 1.3204575e-06 -1.5057612e-06
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 -3.6006336e-06 2.4158409e-06 -2.7959314e-06
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 -3.3313125e-06 1.4697892e-06 -2.7046099e-06
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 -4.1963855e-06 1.8017491e-06 -2.3957259e-06
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 8.2405636e-06 -9.2080568e-06 -2.6979061e-06
Loop time of 0.162016 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.123017 (75.9293)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0340899 (21.0411)
Outpt time (%) = 0.00473952 (2.92535)
Other time (%) = 0.000169039 (0.104335)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 2.95041 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 -4.8604756e-06 3.7251477e-06 -2.9550019e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 -3.8939866e-06 2.9223391e-06 -2.2819697e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 -3.6671782e-06 -3.9050298e-06 -2.216407e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 -3.9258267e-06 2.221206e-06 -2.1819285e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -3.1570557e-06 8.2160424e-07 4.7018758e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -3.572314e-06 1.2809206e-06 4.3456208e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -2.6839761e-06 1.8703615e-06 -2.1448559e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -2.7199703e-06 1.6784208e-06 -2.426873e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 -2.5654468e-06 2.0648963e-06 -1.6998995e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -3.3044419e-06 2.6103683e-06 -2.5246759e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -3.5025824e-06 1.2024729e-06 -1.5524318e-06
Loop time of 0.161845 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.122915 (75.946)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0340765 (21.055)
Outpt time (%) = 0.00468802 (2.89661)
Other time (%) = 0.000165582 (0.102309)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 3.40818 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -2.4048644e-06 3.3513607e-06 -2.8722185e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -2.481322e-06 3.6480379e-06 -3.1092437e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -3.0751506e-06 5.8376744e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -2.7247323e-06 2.3340173e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -2.8719517e-06 4.5249397e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -2.6310243e-06 -6.3464035e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -2.5635976e-06 3.5771871e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -3.2260573e-06 2.5233788e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -3.0611909e-06 3.1329051e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -2.6095826e-06 1.3805022e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.8236839e-06 1.8352159e-06 2192.8625
Loop time of 0.161851 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.122992 (75.9912)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0339996 (21.0068)
Outpt time (%) = 0.00469309 (2.89964)
Other time (%) = 0.000165641 (0.102342)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 3.86594 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.4937771e-06 4.8352356e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.6268441e-06 5.4186954e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012459169 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025416174 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038484627 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051633193 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064696028 2436.5138
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00077648633 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090632398 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010366567 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011656542 2436.5138
Loop time of 0.150393 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.123172 (81.9005)
Neigh time (%) = 0 (0)
Comm time (%) = 0.022368 (14.8731)
Outpt time (%) = 0.0046854 (3.11545)
Other time (%) = 0.000166953 (0.111011)
Nlocal: 128 ave 152 max 112 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 3073 ave 3089 max 3049 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 63232 max 46592 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

296
examples/comb/log.comb.Si.elastic.9Jan12.linux.1 Normal file
View File

@ -0,0 +1,296 @@
LAMMPS (10 Jan 2012)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 385.344 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -5.298087 -5.298216 -5.298216 0
1 1 -5.3007406 -5.3008696 -5.3008696 0
2 1 -5.3032941 -5.3034231 -5.3034231 0
3 1 -5.3057463 -5.3058753 -5.3058753 0
4 1 -5.3080963 -5.3082253 -5.3082253 0
5 1 -5.310343 -5.310472 -5.310472 0
6 1 -5.3124852 -5.3126142 -5.3126142 0
7 1 -5.3145219 -5.3146509 -5.3146509 0
8 1 -5.316452 -5.3165811 -5.3165811 0
9 1 -5.3182744 -5.3184034 -5.3184034 0
10 1 -5.319988 -5.320117 -5.320117 0
11 1 -5.3215916 -5.3217206 -5.3217206 0
12 1 -5.3230841 -5.3232131 -5.3232131 0
13 1 -5.3244643 -5.3245933 -5.3245933 0
14 1 -5.3257312 -5.3258602 -5.3258602 0
15 1 -5.3268835 -5.3270126 -5.3270126 0
16 1 -5.3279202 -5.3280492 -5.3280492 0
17 1 -5.3288399 -5.3289689 -5.3289689 0
18 1 -5.3296416 -5.3297706 -5.3297706 0
19 1 -5.330324 -5.330453 -5.330453 0
20 1 -5.3308859 -5.3310149 -5.3310149 0
21 1 -5.3313261 -5.3314551 -5.3314551 0
22 1 -5.3316434 -5.3317725 -5.3317725 0
23 1 -5.3318366 -5.3319656 -5.3319656 0
24 1 -5.3319044 -5.3320335 -5.3320335 0
25 1 -5.3319045 -5.3320335 -5.3320335 0
26 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.641141 on 1 procs for 26 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.29821600825 -5.33203354013 -5.33203354013
Force two-norm initial, final = 799.113 0.221963
Force max component initial, final = 461.368 0.12815
Final line search alpha, max atom move = 0.000121927 1.5625e-05
Iterations, force evaluations = 26 37
Pair time (%) = 0.512635 (79.9566)
Neigh time (%) = 0.121496 (18.95)
Comm time (%) = 0.00175428 (0.273619)
Outpt time (%) = 0.00022912 (0.0357363)
Other time (%) = 0.00502706 (0.78408)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 3
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
Memory usage per processor = 384.352 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
26 1 -5.3319045 -5.3320335 -5.3320335 0
27 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.0137792 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0137219 (99.5847)
Neigh time (%) = 0 (0)
Comm time (%) = 3.69549e-05 (0.268194)
Outpt time (%) = 9.77516e-06 (0.0709416)
Other time (%) = 1.04904e-05 (0.0761325)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 384.81 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 21.201945 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -8.8447721e-06 -8.4498844e-06 -3.4721654e-06
28 21.202157 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -9.2168914e-06 -8.6256272e-06 -2.98407e-06
29 21.202369 21.201945 21.201945 0 0 0 310358.27 310352.06 310352.06 -8.4833253e-06 -7.9020222e-06 -2.5493378e-06
30 21.202581 21.201945 21.201945 0 0 0 420331.84 420315.03 420315.03 -8.8006585e-06 -8.0215558e-06 -3.3761116e-06
31 21.202793 21.201945 21.201945 0 0 0 530306.27 530274.45 530274.45 -8.5096512e-06 -7.6252451e-06 -5.0268132e-06
32 21.203005 21.201945 21.201945 0 0 0 640281.55 640230.33 640230.33 -8.1652807e-06 -8.8525987e-06 -6.7073981e-06
33 21.203217 21.201945 21.201945 0 0 0 750257.69 750182.67 750182.67 -8.0727845e-06 -7.9112719e-06 -5.5575991e-06
34 21.203429 21.201945 21.201945 0 0 0 860234.68 860131.46 860131.46 -8.7195464e-06 -8.420001e-06 -3.5539889e-06
35 21.203641 21.201945 21.201945 0 0 0 970212.53 970076.71 970076.71 -9.1912771e-06 -8.7423147e-06 -6.3680082e-06
36 21.203853 21.201945 21.201945 0 0 0 1080191.2 1080018.4 1080018.4 -8.7416032e-06 -8.6889515e-06 -6.1602475e-06
37 21.204065 21.201945 21.201945 0 0 0 1190170.8 1189956.6 1189956.6 -8.263469e-06 -8.460557e-06 -2.753541e-06
Loop time of 0.165838 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.163672 (98.694)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000379562 (0.228875)
Outpt time (%) = 0.00165892 (1.00032)
Other time (%) = 0.000127316 (0.076771)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 385.268 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 21.204065 21.201945 21.201945 0 0 0 1300151.2 1299891.2 1299891.2 -8.5068051e-06 -8.341735e-06 -1.0682601e-05
38 21.204065 21.201945 21.202157 0 0 0 1300151.2 1299891.2 1299891.2 -8.6917976e-06 -8.5608798e-06 -9.949746e-06
39 21.204065 21.201945 21.202369 0 0 0 1410093.3 1409811.3 1409839.5 -3.943896e-06 -5.7881281e-06 -1.2222307e-05
40 21.204065 21.201945 21.202581 0 0 0 1520031.8 1519727.8 1519788.6 5.9268724e-07 -7.7433557e-06 -1.0823479e-05
41 21.204065 21.201945 21.202793 0 0 0 1629966.8 1629640.8 1629738.6 -4.0790828e-06 -7.9582315e-06 -8.9045388e-06
42 21.204065 21.201945 21.203005 0 0 0 1739898.2 1739550.3 1739689.4 -7.4637325e-06 -7.3819089e-06 -1.0844825e-05
43 21.204065 21.201945 21.203217 0 0 0 1849826.1 1849456.2 1849641.1 -1.3091771e-07 -7.8351404e-06 -1.0877554e-05
44 21.204065 21.201945 21.203429 0 0 0 1959750.5 1959358.6 1959593.7 5.9909083e-06 -6.7621843e-06 -1.1562738e-05
45 21.204065 21.201945 21.203641 0 0 0 2069671.3 2069257.4 2069547.1 5.3697607e-06 -7.5476906e-06 -1.0171025e-05
46 21.204065 21.201945 21.203853 0 0 0 2179588.5 2179152.7 2179501.4 7.4559059e-06 -8.3858486e-06 -1.0113393e-05
47 21.204065 21.201945 21.204065 0 0 0 2289502.3 2289044.4 2289456.5 8.1389548e-06 -7.1328807e-06 -1.1707174e-05
Loop time of 0.1659 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.163715 (98.6829)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000379801 (0.228934)
Outpt time (%) = 0.00167823 (1.01159)
Other time (%) = 0.000127077 (0.0765986)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 385.725 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 21.204065 21.201945 21.204065 0 0 0 2399412.4 2398932.6 2399412.4 1.2782265e-05 -8.2784107e-06 -1.164883e-05
48 21.204065 21.201945 21.204065 0 0 4.2408131e-07 2399412.4 2398932.6 2399412.4 1.2881164e-05 -7.8749849e-06 -1.141759e-05
49 21.204065 21.201945 21.204065 0 0 8.4816261e-07 2399412.4 2398932.6 2399412.4 1.3132327e-05 -8.5857827e-06 219.84282
50 21.204065 21.201945 21.204065 0 0 1.2722439e-06 2399412.4 2398932.6 2399412.4 1.3429026e-05 -6.4875418e-06 439.68565
51 21.204065 21.201945 21.204065 0 0 1.6963252e-06 2399412.4 2398932.6 2399412.4 1.3087502e-05 -5.472218e-06 659.52848
52 21.204065 21.201945 21.204065 0 0 2.1204065e-06 2399412.4 2398932.6 2399412.4 1.331305e-05 -1.5510903e-07 879.37131
53 21.204065 21.201945 21.204065 0 0 2.5444878e-06 2399412.4 2398932.6 2399412.4 1.3029158e-05 1.0452072e-06 1099.2141
54 21.204065 21.201945 21.204065 0 0 2.9685691e-06 2399412.4 2398932.6 2399412.4 1.245497e-05 3.791633e-06 1319.057
55 21.204065 21.201945 21.204065 0 0 3.3926505e-06 2399412.4 2398932.6 2399412.4 1.2748824e-05 8.154608e-06 1538.8998
56 21.204065 21.201945 21.204065 0 0 3.8167318e-06 2399412.4 2398932.6 2399412.4 1.3488082e-05 1.0240753e-05 1758.7426
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1.2915317e-05 1.3717899e-05 1978.5855
Loop time of 0.165923 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.163732 (98.6796)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000390053 (0.235081)
Outpt time (%) = 0.00167251 (1.008)
Other time (%) = 0.000128269 (0.0773065)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 386.183 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1.2363897e-05 1.9987719e-05 2198.4283
58 21.204065 21.201945 21.204065 4.240389e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1.2859108e-05 1.9237788e-05 2198.4283
59 21.204065 21.201945 21.204065 8.480778e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 219.84283 -0.00012237462 2198.4283
60 21.204065 21.201945 21.204065 1.2721167e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 439.68565 -0.00026263658 2198.4283
61 21.204065 21.201945 21.204065 1.6961556e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 659.52847 -0.00040342648 2198.4283
62 21.204065 21.201945 21.204065 2.1201945e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 879.37129 -0.00054391257 2198.4283
63 21.204065 21.201945 21.204065 2.5442334e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1099.2141 -0.00068552355 2198.4283
64 21.204065 21.201945 21.204065 2.9682723e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1319.0569 -0.00082718719 2198.4283
65 21.204065 21.201945 21.204065 3.3923112e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1538.8998 -0.00096788602 2198.4283
66 21.204065 21.201945 21.204065 3.8163501e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1758.7426 -0.0011099011 2198.4283
67 21.204065 21.201945 21.204065 4.240389e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1978.5854 -0.0012526114 2198.4283
Loop time of 0.166279 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.164098 (98.6882)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000380278 (0.228698)
Outpt time (%) = 0.00167036 (1.00455)
Other time (%) = 0.000130653 (0.0785748)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0

296
examples/comb/log.comb.Si.elastic.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 384.499 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -5.298087 -5.298216 -5.298216 0
1 1 -5.3007406 -5.3008696 -5.3008696 0
2 1 -5.3032941 -5.3034231 -5.3034231 0
3 1 -5.3057463 -5.3058753 -5.3058753 0
4 1 -5.3080963 -5.3082253 -5.3082253 0
5 1 -5.310343 -5.310472 -5.310472 0
6 1 -5.3124852 -5.3126142 -5.3126142 0
7 1 -5.3145219 -5.3146509 -5.3146509 0
8 1 -5.316452 -5.3165811 -5.3165811 0
9 1 -5.3182744 -5.3184034 -5.3184034 0
10 1 -5.319988 -5.320117 -5.320117 0
11 1 -5.3215916 -5.3217206 -5.3217206 0
12 1 -5.3230841 -5.3232131 -5.3232131 0
13 1 -5.3244643 -5.3245933 -5.3245933 0
14 1 -5.3257312 -5.3258602 -5.3258602 0
15 1 -5.3268835 -5.3270126 -5.3270126 0
16 1 -5.3279202 -5.3280492 -5.3280492 0
17 1 -5.3288399 -5.3289689 -5.3289689 0
18 1 -5.3296416 -5.3297706 -5.3297706 0
19 1 -5.330324 -5.330453 -5.330453 0
20 1 -5.3308859 -5.3310149 -5.3310149 0
21 1 -5.3313261 -5.3314551 -5.3314551 0
22 1 -5.3316434 -5.3317725 -5.3317725 0
23 1 -5.3318366 -5.3319656 -5.3319656 0
24 1 -5.3319044 -5.3320335 -5.3320335 0
25 1 -5.3319045 -5.3320335 -5.3320335 0
26 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.250753 on 4 procs for 26 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.29821600825 -5.33203354012 -5.33203354012
Force two-norm initial, final = 799.113 0.221963
Force max component initial, final = 461.368 0.12815
Final line search alpha, max atom move = 0.000121927 1.5625e-05
Iterations, force evaluations = 26 37
Pair time (%) = 0.132469 (52.8283)
Neigh time (%) = 0.0654684 (26.1087)
Comm time (%) = 0.0481624 (19.2071)
Outpt time (%) = 0.000469863 (0.187381)
Other time (%) = 0.00418389 (1.66853)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 3
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
Memory usage per processor = 383.507 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
26 1 -5.3319045 -5.3320335 -5.3320335 0
27 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.00479984 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.00358206 (74.6287)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00118113 (24.6076)
Outpt time (%) = 2.31266e-05 (0.48182)
Other time (%) = 1.35303e-05 (0.28189)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 383.965 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 21.201945 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -7.7070687e-06 -3.8058632e-06 -1.3983292e-05
28 21.202157 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -7.6074574e-06 -3.7702878e-06 -1.3585558e-05
29 21.202369 21.201945 21.201945 0 0 0 310358.27 310352.06 310352.06 -6.6668421e-06 -3.6792146e-06 -7.5669014e-06
30 21.202581 21.201945 21.201945 0 0 0 420331.84 420315.03 420315.03 -7.1762828e-06 -3.9709334e-06 -8.7117198e-06
31 21.202793 21.201945 21.201945 0 0 0 530306.27 530274.45 530274.45 -7.4146384e-06 -3.7098095e-06 -8.0407666e-06
32 21.203005 21.201945 21.201945 0 0 0 640281.55 640230.33 640230.33 -6.9144473e-06 -3.671388e-06 -9.8821526e-06
33 21.203217 21.201945 21.201945 0 0 0 750257.69 750182.67 750182.67 -6.8219511e-06 -3.598814e-06 -9.722063e-06
34 21.203429 21.201945 21.201945 0 0 0 860234.68 860131.46 860131.46 -5.8386453e-06 -4.1658869e-06 -1.1708597e-05
35 21.203641 21.201945 21.201945 0 0 0 970212.53 970076.71 970076.71 -6.7991828e-06 -4.0449303e-06 -1.4273588e-05
36 21.203853 21.201945 21.201945 0 0 0 1080191.2 1080018.4 1080018.4 -6.9471768e-06 -4.0342577e-06 -6.4647735e-06
37 21.204065 21.201945 21.201945 0 0 0 1190170.8 1189956.6 1189956.6 -6.5373474e-06 -3.5354897e-06 -7.4680016e-06
Loop time of 0.0582895 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0428118 (73.4468)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0132927 (22.8047)
Outpt time (%) = 0.00210714 (3.61496)
Other time (%) = 7.78437e-05 (0.133547)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 384.423 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 21.204065 21.201945 21.201945 0 0 0 1300151.2 1299891.2 1299891.2 -7.732683e-06 -3.9915672e-06 -1.0324e-05
38 21.204065 21.201945 21.202157 0 0 0 1300151.2 1299891.2 1299891.2 -7.6593976e-06 -3.7304432e-06 -1.0456341e-05
39 21.204065 21.201945 21.202369 0 0 0 1410093.3 1409811.3 1409839.5 -8.7024702e-06 -2.759233e-06 -1.2029488e-05
40 21.204065 21.201945 21.202581 0 0 0 1520031.8 1519727.8 1519788.6 -1.2521141e-05 -3.7197706e-06 -1.131869e-05
41 21.204065 21.201945 21.202793 0 0 0 1629966.8 1629640.8 1629738.6 -1.5294604e-05 -4.3451873e-06 -1.0193082e-05
42 21.204065 21.201945 21.203005 0 0 0 1739898.2 1739550.3 1739689.4 -2.1207246e-05 -2.4511495e-06 -1.127173e-05
43 21.204065 21.201945 21.203217 0 0 0 1849826.1 1849456.2 1849641.1 -2.2560537e-05 -4.0741022e-06 -1.0863324e-05
44 21.204065 21.201945 21.203429 0 0 0 1959750.5 1959358.6 1959593.7 -2.5883997e-05 -3.9545687e-06 -9.4637851e-06
45 21.204065 21.201945 21.203641 0 0 0 2069671.3 2069257.4 2069547.1 -3.1642953e-05 -3.5852953e-06 -1.0898899e-05
46 21.204065 21.201945 21.203853 0 0 0 2179588.5 2179152.7 2179501.4 -2.3043652e-05 -4.3067658e-06 -9.9049209e-06
47 21.204065 21.201945 21.204065 0 0 0 2289502.3 2289044.4 2289456.5 -2.4092416e-05 -3.0054153e-06 -1.0928783e-05
Loop time of 0.0580854 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0426171 (73.3696)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0133364 (22.96)
Outpt time (%) = 0.00205803 (3.54311)
Other time (%) = 7.39098e-05 (0.127243)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 384.88 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 21.204065 21.201945 21.204065 0 0 0 2399412.4 2398932.6 2399412.4 -2.394798e-05 -4.7607087e-06 -9.6708344e-06
48 21.204065 21.201945 21.204065 0 0 4.2408131e-07 2399412.4 2398932.6 2399412.4 -2.4658066e-05 -3.597391e-06 -1.0876843e-05
49 21.204065 21.201945 21.204065 0 0 8.4816261e-07 2399412.4 2398932.6 2399412.4 -2.4053995e-05 -6.6063638e-06 219.84282
50 21.204065 21.201945 21.204065 0 0 1.2722439e-06 2399412.4 2398932.6 2399412.4 -2.4549205e-05 -9.9312468e-06 439.68565
51 21.204065 21.201945 21.204065 0 0 1.6963252e-06 2399412.4 2398932.6 2399412.4 -2.4068225e-05 -1.3762013e-05 659.52848
52 21.204065 21.201945 21.204065 0 0 2.1204065e-06 2399412.4 2398932.6 2399412.4 -2.4051149e-05 -1.3256841e-05 879.37131
53 21.204065 21.201945 21.204065 0 0 2.5444878e-06 2399412.4 2398932.6 2399412.4 -2.387754e-05 -1.4584518e-05 1099.2141
54 21.204065 21.201945 21.204065 0 0 2.9685691e-06 2399412.4 2398932.6 2399412.4 -2.4606126e-05 -1.4511944e-05 1319.057
55 21.204065 21.201945 21.204065 0 0 3.3926505e-06 2399412.4 2398932.6 2399412.4 -2.4684392e-05 -1.3372817e-05 1538.8998
56 21.204065 21.201945 21.204065 0 0 3.8167318e-06 2399412.4 2398932.6 2399412.4 -2.4492996e-05 -1.3092483e-05 1758.7426
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 -2.4132261e-05 -1.5846735e-05 1978.5855
Loop time of 0.0582204 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0425564 (73.0954)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0134656 (23.1287)
Outpt time (%) = 0.00212365 (3.64761)
Other time (%) = 7.46846e-05 (0.128279)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 385.338 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 -2.3903155e-05 -1.5495249e-05 2198.4283
58 21.204065 21.201945 21.204065 4.240389e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 -2.4564147e-05 -1.6061611e-05 2198.4283
59 21.204065 21.201945 21.204065 8.480778e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 219.8428 -0.00015851218 2198.4283
60 21.204065 21.201945 21.204065 1.2721167e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 439.68561 -0.0003005522 2198.4283
61 21.204065 21.201945 21.204065 1.6961556e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 659.52844 -0.00044221512 2198.4283
62 21.204065 21.201945 21.204065 2.1201945e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 879.37126 -0.0005848827 2198.4283
63 21.204065 21.201945 21.204065 2.5442334e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1099.2141 -0.00072538515 2198.4283
64 21.204065 21.201945 21.204065 2.9682723e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1319.0569 -0.00086665461 2198.4283
65 21.204065 21.201945 21.204065 3.3923112e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1538.8997 -0.0010079945 2198.4283
66 21.204065 21.201945 21.204065 3.8163501e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1758.7425 -0.0011483945 2198.4283
67 21.204065 21.201945 21.204065 4.240389e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1978.5854 -0.0012892271 2198.4283
Loop time of 0.0581976 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0426993 (73.3695)
Neigh time (%) = 0 (0)
Comm time (%) = 0.013256 (22.7775)
Outpt time (%) = 0.00216591 (3.72165)
Other time (%) = 7.64728e-05 (0.131402)
Nlocal: 128 ave 164 max 104 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 3073 ave 3097 max 3037 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 45760 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0

18
examples/crack/log.crack.28Mar11.linux.1 → examples/crack/log.crack.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d LJ crack simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 8141 atoms
@ -76,7 +76,7 @@ fix 2 boundary setforce NULL 0.0 0.0
timestep 0.003
thermo 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
@ -109,13 +109,13 @@ Step Temp E_pair E_mol TotEng Press Volume
4600 0.086766447 -3.0437627 0 -2.9634443 -1.0212664 9358.4367
4800 0.088195149 -3.0328502 0 -2.9512093 -1.0275959 9392.0495
5000 0.089415266 -3.0228825 0 -2.9401122 -1.0219203 9432.5928
Loop time of 12.7818 on 1 procs for 5000 steps with 8141 atoms
Loop time of 6.90229 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 10.9406 (85.5951)
Neigh time (%) = 0.403301 (3.15527)
Comm time (%) = 0.00951362 (0.0744309)
Outpt time (%) = 0.125842 (0.984542)
Other time (%) = 1.30255 (10.1906)
Pair time (%) = 5.71184 (82.7529)
Neigh time (%) = 0.270525 (3.91935)
Comm time (%) = 0.00593114 (0.0859301)
Outpt time (%) = 0.063314 (0.91729)
Other time (%) = 0.850676 (12.3246)
Nlocal: 8141 ave 8141 max 8141 min
Histogram: 1 0 0 0 0 0 0 0 0 0

18
examples/crack/log.crack.28Mar11.linux.4 → examples/crack/log.crack.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d LJ crack simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 8141 atoms
@ -76,7 +76,7 @@ fix 2 boundary setforce NULL 0.0 0.0
timestep 0.003
thermo 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
@ -109,13 +109,13 @@ Step Temp E_pair E_mol TotEng Press Volume
4600 0.088763719 -3.0446018 0 -2.9624346 -1.0280829 9388.1338
4800 0.089467982 -3.0337452 0 -2.950926 -1.0235966 9423.847
5000 0.089910902 -3.0237571 0 -2.9405279 -1.0178644 9448.4573
Loop time of 3.4854 on 4 procs for 5000 steps with 8141 atoms
Loop time of 1.91453 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 2.6865 (77.0788)
Neigh time (%) = 0.106176 (3.04632)
Comm time (%) = 0.220427 (6.3243)
Outpt time (%) = 0.102362 (2.93688)
Other time (%) = 0.36993 (10.6137)
Pair time (%) = 1.43427 (74.9148)
Neigh time (%) = 0.0727076 (3.79767)
Comm time (%) = 0.107613 (5.62085)
Outpt time (%) = 0.051915 (2.71163)
Other time (%) = 0.248028 (12.955)
Nlocal: 2035.25 ave 2064 max 2015 min
Histogram: 1 1 0 0 0 1 0 0 0 1

84
examples/dipole/log.dipole.28Mar11.linux.1
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@ -1,84 +0,0 @@
LAMMPS (27 Mar 2011)
# Point dipoles in a 2d box
units lj
atom_style dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 200 atoms
mass 1 1.0
shape 1 1 1 1
dipole 1 0.75
set group all dipole/random 98934
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz
run 10000
Memory usage per processor = 3.0531 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019061 0.19532181 -2.3829095 0.18067142
2000 0.39019935 -2.791487 0.22407032 -2.4032386 -0.40913692
2500 0.40240606 -2.8139309 0.24275491 -2.4135369 -0.33839305
3000 0.41889117 -2.8310674 0.24638389 -2.4142707 -0.071480473
3500 0.41664896 -2.7505011 0.17937876 -2.3359354 -0.34413079
4000 0.4399873 -2.8093287 0.22438034 -2.3715414 -0.16626012
4500 0.43361189 -2.8162656 0.24187231 -2.3848217 0.13489299
5000 0.39259055 -2.7471068 0.21065822 -2.3564792 -0.15485345
5500 0.42121291 -2.7676815 0.21145234 -2.3485747 -0.085961294
6000 0.46934915 -2.8576035 0.26500223 -2.3906011 -0.21441119
6500 0.41344307 -2.7863091 0.2478621 -2.3749333 -0.12807499
7000 0.45597995 -2.7959254 0.22846639 -2.3422254 -0.47086714
7500 0.39910433 -2.7779885 0.25742031 -2.3808797 -0.19465195
8000 0.46690622 -2.7777549 0.19323901 -2.3131832 -0.063292514
8500 0.45022765 -2.814943 0.25463601 -2.3669665 0.15612777
9000 0.47294866 -2.7986322 0.2117454 -2.3280483 0.21776933
9500 0.50062288 -2.8318393 0.22438459 -2.3337195 -0.20077418
10000 0.48531399 -2.8185842 0.23564567 -2.3356968 -0.1417187
Loop time of 1.86084 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 1.50143 (80.6853)
Neigh time (%) = 0.0485067 (2.60671)
Comm time (%) = 0.0729742 (3.92157)
Outpt time (%) = 0.0331767 (1.78288)
Other time (%) = 0.204759 (11.0035)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 150 ave 150 max 150 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1673 ave 1673 max 1673 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1673
Ave neighs/atom = 8.365
Neighbor list builds = 683
Dangerous builds = 0

84
examples/dipole/log.dipole.28Mar11.linux.4
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@ -1,84 +0,0 @@
LAMMPS (27 Mar 2011)
# Point dipoles in a 2d box
units lj
atom_style dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 processor grid
create_atoms 1 box
Created 200 atoms
mass 1 1.0
shape 1 1 1 1
dipole 1 0.75
set group all dipole/random 98934
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz
run 10000
Memory usage per processor = 3.05241 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067142
2000 0.39019888 -2.7914865 0.22407033 -2.4032386 -0.40913106
2500 0.4023511 -2.81393 0.24280405 -2.4135906 -0.33881491
3000 0.38615692 -2.818646 0.26460202 -2.4344198 -0.0079725577
3500 0.42122454 -2.8127945 0.23501007 -2.3936761 -0.12887917
4000 0.44161593 -2.8007801 0.20799836 -2.3613722 -0.079523244
4500 0.4231261 -2.7826844 0.22673018 -2.361674 -0.55083706
5000 0.4440514 -2.799822 0.22995936 -2.3579908 -0.28425958
5500 0.45033043 -2.7886448 0.21727591 -2.340566 0.0059789839
6000 0.45676909 -2.8007108 0.23936573 -2.3462256 0.12294031
6500 0.52050628 -2.8509712 0.2362808 -2.3330675 -0.22427307
7000 0.41855625 -2.8254088 0.31121935 -2.4089453 -0.48809423
7500 0.36025589 -2.7101495 0.25308278 -2.3516949 -0.29426489
8000 0.44494177 -2.7665688 0.23326231 -2.3238517 -0.57748114
8500 0.4336595 -2.7378567 0.2235799 -2.3063655 0.030370416
9000 0.41942743 -2.6901214 0.19875084 -2.2727911 0.18043421
9500 0.42853326 -2.7396334 0.23748738 -2.3132428 -0.01076467
10000 0.46672835 -2.7582561 0.22673928 -2.2938614 -0.16751321
Loop time of 0.861498 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.374077 (43.4217)
Neigh time (%) = 0.0131148 (1.52232)
Comm time (%) = 0.346431 (40.2127)
Outpt time (%) = 0.0234395 (2.72078)
Other time (%) = 0.104435 (12.1225)
Nlocal: 50 ave 56 max 41 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 87.5 ave 91 max 85 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 411.25 ave 502 max 304 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 1645
Ave neighs/atom = 8.225
Neighbor list builds = 686
Dangerous builds = 0

86
examples/dipole/log.dipole.9Jan12.linux.1 Normal file
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@ -0,0 +1,86 @@
LAMMPS (10 Jan 2012)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz
run 10000
Memory usage per processor = 3.28198 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019973 -2.7914873 0.22407026 -2.4032386 -0.40914143
2500 0.40242274 -2.8142159 0.24281467 -2.4138053 -0.3391299
3000 0.42771065 -2.8535488 0.25848739 -2.4279767 -0.2500108
3500 0.44706195 -2.7890555 0.18446345 -2.3442289 -0.1005632
4000 0.4041733 -2.7741037 0.22161024 -2.3719512 -0.13373446
4500 0.47549052 -2.8368758 0.21740299 -2.3637627 -0.14246916
5000 0.42071015 -2.7518085 0.20821432 -2.3332019 -0.047522754
5500 0.43520504 -2.8042986 0.24366805 -2.3712696 -0.22180582
6000 0.42802195 -2.7822398 0.24060881 -2.3563579 -0.35350862
6500 0.4479767 -2.8175363 0.25806495 -2.3717994 0.07885849
7000 0.39538519 -2.7246562 0.23766993 -2.331248 -0.098542228
7500 0.40716663 -2.7115371 0.21917238 -2.3064063 -0.14844207
8000 0.42814546 -2.7318282 0.23188976 -2.3058235 -0.37209482
8500 0.46175735 -2.7607768 0.23020837 -2.3013282 -0.33381513
9000 0.48360992 -2.758533 0.21927619 -2.2773411 -0.016767257
9500 0.47646809 -2.7812073 0.24046809 -2.3071216 -0.12582235
10000 0.48207466 -2.7437285 0.20973254 -2.2640642 0.51612253
Loop time of 1.0464 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 0.83996 (80.2713)
Neigh time (%) = 0.0338588 (3.23573)
Comm time (%) = 0.0464656 (4.44051)
Outpt time (%) = 0.0178115 (1.70217)
Other time (%) = 0.108306 (10.3503)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1673 ave 1673 max 1673 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1673
Ave neighs/atom = 8.365
Neighbor list builds = 679
Dangerous builds = 0

86
examples/dipole/log.dipole.9Jan12.linux.4 Normal file
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@ -0,0 +1,86 @@
LAMMPS (10 Jan 2012)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz
run 10000
Memory usage per processor = 3.28129 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019968 -2.7914873 0.22407029 -2.4032386 -0.4091395
2500 0.40237391 -2.8138968 0.24276582 -2.4135348 -0.33901619
3000 0.42595202 -2.8621684 0.26812111 -2.4383462 -0.19493812
3500 0.41153448 -2.8070419 0.23860803 -2.397565 -0.032395966
4000 0.40867238 -2.7790568 0.22331133 -2.3724278 0.014462986
4500 0.39803378 -2.7718651 0.23536245 -2.3758215 -0.25429533
5000 0.42736901 -2.8476039 0.2824171 -2.4223718 0.12187395
5500 0.41115816 -2.7810177 0.24508517 -2.3719153 -0.1925336
6000 0.43184788 -2.8015292 0.24726776 -2.3718406 -0.014489672
6500 0.45955478 -2.8340069 0.26105652 -2.3767499 -0.16015969
7000 0.43826613 -2.7488226 0.20031236 -2.3127478 0.071480756
7500 0.45738321 -2.7892162 0.23337255 -2.3341199 -0.17245012
8000 0.46107991 -2.7322063 0.18569571 -2.2734318 -0.21563894
8500 0.40367385 -2.7623279 0.27023252 -2.3606724 -0.038576129
9000 0.43104207 -2.7672424 0.25452132 -2.3383555 0.044351007
9500 0.38924411 -2.7231541 0.24926613 -2.3358562 -0.21910634
10000 0.44421944 -2.7677489 0.23376321 -2.3257506 0.034770807
Loop time of 0.446674 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.213113 (47.7111)
Neigh time (%) = 0.00897831 (2.01004)
Comm time (%) = 0.149779 (33.532)
Outpt time (%) = 0.0130295 (2.91701)
Other time (%) = 0.0617741 (13.8298)
Nlocal: 50 ave 55 max 41 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 87.75 ave 92 max 78 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 415 ave 481 max 301 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 1660
Ave neighs/atom = 8.3
Neighbor list builds = 671
Dangerous builds = 0

10
examples/dreiding/log.dreiding.11Oct11.linux.1 → examples/dreiding/log.dreiding.9Jan12.linux.1
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@ -1,4 +1,4 @@
LAMMPS (10 Oct 2011)
LAMMPS (10 Jan 2012)
units real
atom_style full
boundary p p p
@ -18,7 +18,7 @@ read_data data.dreiding
3 = max dihedrals/atom
0 = max impropers/atom
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
384 atoms
320 bonds
448 angles
@ -54,7 +54,7 @@ thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:204)
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:216)
G vector = 0.142075
grid = 3 3 3
stencil order = 5
@ -68,7 +68,7 @@ PotEng = 113.723443 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.224193 E_long = -361.169476 E_hbond = -69.322152
C_hbond = 235.000000 Press = -847.552598 Volume = 7447.236335
Loop time of 0 on 1 procs for 0 steps with 384 atoms
Loop time of 2.14577e-06 on 1 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
@ -76,7 +76,7 @@ Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 0 (0)
Other time (%) = 2.14577e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0

18
examples/dreiding/log.dreiding.11Oct11.linux.4 → examples/dreiding/log.dreiding.9Jan12.linux.4
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@ -1,4 +1,4 @@
LAMMPS (10 Oct 2011)
LAMMPS (10 Jan 2012)
units real
atom_style full
boundary p p p
@ -18,7 +18,7 @@ read_data data.dreiding
3 = max dihedrals/atom
0 = max impropers/atom
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 processor grid
2 by 1 by 2 MPI processor grid
384 atoms
320 bonds
448 angles
@ -54,31 +54,31 @@ thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:204)
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:216)
G vector = 0.142075
grid = 3 3 3
stencil order = 5
RMS precision = 0.000329493
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.143211
grid = 3 3 3
stencil order = 4
RMS precision = 0.000315601
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.140124
grid = 3 3 3
stencil order = 3
RMS precision = 0.000354326
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.127333
grid = 3 3 3
stencil order = 2
RMS precision = 0.00055716
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.113516
grid = 9 9 9
stencil order = 1
@ -92,7 +92,7 @@ PotEng = 118.484313 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 529.430008 E_long = -288.614421 E_hbond = -69.322152
C_hbond = 235.000000 Press = -803.848888 Volume = 7447.236335
Loop time of 1.43051e-06 on 4 procs for 0 steps with 384 atoms
Loop time of 1.09673e-05 on 4 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
@ -100,7 +100,7 @@ Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 1.43051e-06 (100)
Other time (%) = 1.09673e-05 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0

16
examples/eim/log.eim.28Mar11.linux.1 → examples/eim/log.eim.9Jan12.linux.1
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# NaCl test problem for embedded atom method (EIM) potential
units metal
@ -10,7 +10,7 @@ lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
2000 atoms
2000 velocities
@ -33,13 +33,13 @@ Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5774.4337 865.73356 874.29837 679.99459 888.89401
100 -5752.6028 652.10345 601.94922 670.57848 780.52664
Loop time of 1.97708 on 1 procs for 100 steps with 2000 atoms
Loop time of 1.19197 on 1 procs for 100 steps with 2000 atoms
Pair time (%) = 1.76707 (89.3779)
Neigh time (%) = 0.176 (8.90203)
Comm time (%) = 0.00904274 (0.457379)
Outpt time (%) = 0.000144005 (0.00728372)
Other time (%) = 0.0248206 (1.25542)
Pair time (%) = 1.05228 (88.2801)
Neigh time (%) = 0.119006 (9.98397)
Comm time (%) = 0.00567245 (0.475887)
Outpt time (%) = 6.00815e-05 (0.0050405)
Other time (%) = 0.0149598 (1.25504)
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

16
examples/eim/log.eim.28Mar11.linux.4 → examples/eim/log.eim.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# NaCl test problem for embedded atom method (EIM) potential
units metal
@ -10,7 +10,7 @@ lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
2000 atoms
2000 velocities
@ -33,13 +33,13 @@ Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5774.4337 865.73356 874.29837 679.99459 888.89401
100 -5752.6028 652.10345 601.94922 670.57848 780.52664
Loop time of 0.527222 on 4 procs for 100 steps with 2000 atoms
Loop time of 0.324442 on 4 procs for 100 steps with 2000 atoms
Pair time (%) = 0.448031 (84.9795)
Neigh time (%) = 0.0419526 (7.9573)
Comm time (%) = 0.0275348 (5.22263)
Outpt time (%) = 0.000249505 (0.0473245)
Other time (%) = 0.00945419 (1.79321)
Pair time (%) = 0.275492 (84.9125)
Neigh time (%) = 0.0300437 (9.26011)
Comm time (%) = 0.0126455 (3.89763)
Outpt time (%) = 5.33462e-05 (0.0164424)
Other time (%) = 0.00620759 (1.91331)
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0

97
examples/ellipse/log.ellipse.gayberne.28Mar11.linux.1 → examples/ellipse/log.ellipse.gayberne.9Jan12.linux.1
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@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# GayBerne ellipsoids in LJ background fluid
units lj
@ -10,20 +10,23 @@ Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
@ -50,9 +53,11 @@ thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse.gayberne id type x y z quatw quati quatj quatk
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
@ -63,7 +68,7 @@ compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.06749 Mbytes
Memory usage per processor = 3.71598 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
@ -86,13 +91,13 @@ Step rot E_pair TotEng Press Volume
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.73157369 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615
Loop time of 1.28801 on 1 procs for 2000 steps with 400 atoms
Loop time of 0.744775 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.936182 (72.6843)
Neigh time (%) = 0.0181944 (1.4126)
Comm time (%) = 0.0219097 (1.70105)
Outpt time (%) = 0.0356205 (2.76554)
Other time (%) = 0.276105 (21.4365)
Pair time (%) = 0.5056 (67.8863)
Neigh time (%) = 0.0121155 (1.62673)
Comm time (%) = 0.0133355 (1.79054)
Outpt time (%) = 0.0179069 (2.40434)
Other time (%) = 0.195817 (26.2921)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -112,45 +117,45 @@ unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.0695 Mbytes
Memory usage per processor = 3.72613 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981977 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720134 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222378 1187.4615
2400 2.1323063 -3.3152815 -1.1669961 0.7609986 1187.4615
2500 2.0866911 -3.269205 -1.1766061 0.67971558 1187.4615
2600 2.0982823 -3.277443 -1.1869915 0.90454873 1187.4615
2700 2.0482785 -3.2229463 -1.1928887 0.69425526 1187.4615
2800 1.9676368 -3.1400446 -1.1685879 0.75779083 1187.4615
2900 2.0421383 -3.2182299 -1.1866946 0.7937753 1187.4615
3000 2.1073889 -3.2869759 -1.2013081 0.18890292 1187.4615
3100 2.0467451 -3.2228328 -1.1821281 0.70497485 1187.4615
3200 2.1166717 -3.2985096 -1.1590407 0.51905745 1187.4615
3300 2.1526773 -3.3388713 -1.1806099 0.4510048 1187.4615
3400 2.0962387 -3.2790768 -1.1607666 0.7517609 1187.4615
3500 2.0602553 -3.2409952 -1.1416561 0.79266623 1187.4615
3600 2.0251393 -3.2024628 -1.1698576 0.51604302 1187.4615
3700 2.0147428 -3.1885349 -1.1821832 0.26661154 1187.4615
3800 1.9640896 -3.1344959 -1.1907397 0.52870297 1187.4615
3900 2.042533 -3.2187558 -1.1810341 0.71118836 1187.4615
4000 2.0882357 -3.2628943 -1.18488 0.69781619 1187.4615
Loop time of 1.42811 on 1 procs for 2000 steps with 400 atoms
2100 2.0350673 -3.2084761 -1.1823685 0.33981976 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720135 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222385 1187.4615
2400 2.1323063 -3.3152815 -1.1669962 0.76099867 1187.4615
2500 2.0866912 -3.269205 -1.176606 0.67971578 1187.4615
2600 2.0982825 -3.2774432 -1.1869918 0.90454676 1187.4615
2700 2.0482779 -3.2229456 -1.1928884 0.69425859 1187.4615
2800 1.9676351 -3.1400429 -1.1685864 0.7577946 1187.4615
2900 2.0421413 -3.2182319 -1.1866955 0.79375204 1187.4615
3000 2.1074018 -3.2869882 -1.2013002 0.18882145 1187.4615
3100 2.0467315 -3.2228162 -1.1821143 0.70508986 1187.4615
3200 2.1165018 -3.2983333 -1.1590455 0.5195734 1187.4615
3300 2.1523232 -3.3384994 -1.1803176 0.45229381 1187.4615
3400 2.0966131 -3.2797219 -1.1608863 0.75030508 1187.4615
3500 2.0623035 -3.2433952 -1.1409405 0.78443505 1187.4615
3600 2.0110509 -3.1874756 -1.1629634 0.54103399 1187.4615
3700 2.0105927 -3.1835726 -1.1894401 0.27445727 1187.4615
3800 1.9528229 -3.1230718 -1.1908005 0.53926039 1187.4615
3900 2.0657038 -3.2420623 -1.1608259 0.56113492 1187.4615
4000 2.0354627 -3.2069944 -1.2073941 0.5668484 1187.4615
Loop time of 0.780395 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.16699 (81.7159)
Neigh time (%) = 0.00850844 (0.595783)
Comm time (%) = 0.0236228 (1.65413)
Outpt time (%) = 0.0354347 (2.48123)
Other time (%) = 0.193552 (13.553)
Pair time (%) = 0.622527 (79.7707)
Neigh time (%) = 0.00560331 (0.71801)
Comm time (%) = 0.0139475 (1.78723)
Outpt time (%) = 0.0179484 (2.29991)
Other time (%) = 0.120369 (15.4241)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 222 ave 222 max 222 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2912 ave 2912 max 2912 min
Neighs: 2914 ave 2914 max 2914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2912
Ave neighs/atom = 7.28
Total # of neighbors = 2914
Ave neighs/atom = 7.285
Neighbor list builds = 47
Dangerous builds = 0

109
examples/ellipse/log.ellipse.gayberne.28Mar11.linux.4 → examples/ellipse/log.ellipse.gayberne.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# GayBerne ellipsoids in LJ background fluid
units lj
@ -10,20 +10,23 @@ Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
@ -50,9 +53,11 @@ thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse.gayberne id type x y z quatw quati quatj quatk
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
@ -63,7 +68,7 @@ compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.05653 Mbytes
Memory usage per processor = 3.70503 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
@ -85,14 +90,14 @@ Step rot E_pair TotEng Press Volume
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.73157369 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615
Loop time of 0.471032 on 4 procs for 2000 steps with 400 atoms
2000 2.0794708 -3.253147 -1.2230906 0.49491311 1187.4615
Loop time of 0.276916 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.233772 (49.6298)
Neigh time (%) = 0.0046134 (0.979424)
Comm time (%) = 0.0967541 (20.5409)
Outpt time (%) = 0.0360661 (7.65683)
Other time (%) = 0.0998262 (21.1931)
Pair time (%) = 0.13188 (47.6245)
Neigh time (%) = 0.00327903 (1.18413)
Comm time (%) = 0.0477025 (17.2263)
Outpt time (%) = 0.0184636 (6.66759)
Other time (%) = 0.0755909 (27.2974)
Nlocal: 100 ave 113 max 79 min
Histogram: 1 0 0 0 0 1 0 0 1 1
@ -112,45 +117,45 @@ unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.05737 Mbytes
Memory usage per processor = 3.70587 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615
2000 2.0794708 -3.253147 -1.2230906 0.49491311 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981977 1187.4615
2200 1.9674878 -3.1385618 -1.1467435 1.1720135 1187.4615
2300 2.0160348 -3.1912829 -1.1652126 0.98222401 1187.4615
2400 2.1323062 -3.3152814 -1.1669962 0.7609989 1187.4615
2500 2.0866913 -3.2692051 -1.1766059 0.67971628 1187.4615
2600 2.0982825 -3.2774432 -1.1869919 0.90454622 1187.4615
2700 2.0482776 -3.2229453 -1.192888 0.69426696 1187.4615
2800 1.9676403 -3.1400511 -1.1685935 0.75777885 1187.4615
2900 2.0421568 -3.2182511 -1.1867014 0.79371143 1187.4615
3000 2.1074324 -3.2870215 -1.201353 0.18881974 1187.4615
3100 2.0468246 -3.2229216 -1.1821138 0.70504941 1187.4615
3200 2.1169492 -3.2986856 -1.1589351 0.51871921 1187.4615
3300 2.1536413 -3.3397682 -1.180639 0.44887653 1187.4615
3400 2.0978165 -3.280631 -1.1610415 0.75128792 1187.4615
3500 2.0587882 -3.2398235 -1.1433609 0.80394373 1187.4615
3600 2.0255166 -3.2025649 -1.1720208 0.54192507 1187.4615
3700 2.0154027 -3.1893307 -1.1657023 0.28402513 1187.4615
3800 1.9277814 -3.0960105 -1.1854881 0.77670745 1187.4615
3900 2.0112013 -3.1831546 -1.1850665 0.67676688 1187.4615
4000 2.0284348 -3.2011574 -1.1772834 0.41947147 1187.4615
Loop time of 0.539757 on 4 procs for 2000 steps with 400 atoms
2200 1.9674878 -3.1385619 -1.1467435 1.1720134 1187.4615
2300 2.0160348 -3.1912829 -1.1652127 0.98222397 1187.4615
2400 2.1323061 -3.3152813 -1.1669962 0.76099924 1187.4615
2500 2.0866909 -3.2692047 -1.1766059 0.67971739 1187.4615
2600 2.0982828 -3.2774435 -1.1869916 0.90454525 1187.4615
2700 2.0482779 -3.2229456 -1.1928882 0.69426441 1187.4615
2800 1.9676376 -3.1400474 -1.1685904 0.7577817 1187.4615
2900 2.0421364 -3.2182286 -1.1866999 0.79377489 1187.4615
3000 2.1074314 -3.2870216 -1.2013314 0.18876892 1187.4615
3100 2.0467964 -3.2228886 -1.1821044 0.70505639 1187.4615
3200 2.1167631 -3.298607 -1.1590547 0.51900634 1187.4615
3300 2.1528874 -3.339087 -1.1804887 0.45092936 1187.4615
3400 2.0979325 -3.2807362 -1.1607408 0.75035729 1187.4615
3500 2.0604373 -3.2416646 -1.1425421 0.7913285 1187.4615
3600 2.013392 -3.1897322 -1.1643385 0.56365647 1187.4615
3700 1.9922643 -3.1651575 -1.1883771 0.3074551 1187.4615
3800 1.9456148 -3.1160905 -1.1794166 0.73639236 1187.4615
3900 2.0237054 -3.1999536 -1.1869795 0.77500395 1187.4615
4000 2.0613642 -3.2364067 -1.2375068 0.53583637 1187.4615
Loop time of 0.294889 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.289897 (53.7087)
Neigh time (%) = 0.00209838 (0.388764)
Comm time (%) = 0.148968 (27.599)
Outpt time (%) = 0.0367653 (6.81144)
Other time (%) = 0.0620289 (11.492)
Pair time (%) = 0.158921 (53.8917)
Neigh time (%) = 0.00147468 (0.500079)
Comm time (%) = 0.0758675 (25.7275)
Outpt time (%) = 0.0184799 (6.26672)
Other time (%) = 0.0401463 (13.614)
Nlocal: 100 ave 119 max 68 min
Nlocal: 100 ave 120 max 68 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 137.25 ave 151 max 128 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 735.25 ave 965 max 403 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 136 ave 151 max 126 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 732.5 ave 972 max 402 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 2941
Ave neighs/atom = 7.3525
Neighbor list builds = 46
Total # of neighbors = 2930
Ave neighs/atom = 7.325
Neighbor list builds = 47
Dangerous builds = 0

75
examples/ellipse/log.ellipse.resquared.28Mar11.linux.1 → examples/ellipse/log.ellipse.resquared.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# RESquared ellipsoids in LJ background fluid
units lj
@ -10,20 +10,23 @@ Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
@ -50,9 +53,11 @@ thermo 100
timestep 0.002
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z quatw quati quatj quatk
compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared id type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
dump 1 all custom 100 dump.ellipse.resquared id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
@ -63,7 +68,7 @@ compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.06749 Mbytes
Memory usage per processor = 3.71598 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
@ -86,13 +91,13 @@ Step rot E_pair TotEng Press Volume
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 2.35265 on 1 procs for 2000 steps with 400 atoms
Loop time of 1.45024 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.99574 (84.8295)
Neigh time (%) = 0.0173743 (0.738497)
Comm time (%) = 0.0161958 (0.688404)
Outpt time (%) = 0.0359209 (1.52682)
Other time (%) = 0.287418 (12.2168)
Pair time (%) = 1.21183 (83.5607)
Neigh time (%) = 0.0117629 (0.811095)
Comm time (%) = 0.00985646 (0.679641)
Outpt time (%) = 0.0178938 (1.23385)
Other time (%) = 0.198897 (13.7147)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -112,7 +117,7 @@ unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.0695 Mbytes
Memory usage per processor = 3.718 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
@ -121,27 +126,27 @@ Step rot E_pair TotEng Press Volume
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635013 2.1016576 1.5081781 1657.9242
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384026 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242
2800 1.9512215 0.15099708 2.0988078 1.2134332 1657.9242
2900 1.9211262 0.18279164 2.0994516 1.3620722 1657.9242
3000 1.9067873 0.19775138 2.0931298 1.4157493 1657.9242
3100 1.9114597 0.19296345 2.1126573 1.4113468 1657.9242
3200 1.9427389 0.15998512 2.0865326 1.3075164 1657.9242
3300 1.9111615 0.19317464 2.1216596 1.4309791 1657.9242
3400 1.9538373 0.14833011 2.1210138 1.2276235 1657.9242
3500 1.9244333 0.17929245 2.0825151 1.3186853 1657.9242
3600 1.9511827 0.151075 2.1197983 1.2271865 1657.9242
3700 1.9369709 0.16601302 2.0970219 1.281288 1657.9242
3800 1.9418076 0.16093985 2.1231367 1.2354776 1657.9242
3900 1.9450409 0.1576083 2.139479 1.239228 1657.9242
4000 1.935011 0.16819134 2.1142338 1.2676432 1657.9242
Loop time of 4.09014 on 1 procs for 2000 steps with 400 atoms
3000 1.9067873 0.19775142 2.0931298 1.4157494 1657.9242
3100 1.9114596 0.19296349 2.1126573 1.411347 1657.9242
3200 1.9427389 0.15998518 2.0865326 1.3075167 1657.9242
3300 1.9111615 0.19317456 2.1216596 1.4309787 1657.9242
3400 1.9538371 0.14833029 2.1210138 1.2276245 1657.9242
3500 1.9244333 0.17929251 2.082515 1.3186851 1657.9242
3600 1.9511825 0.15107526 2.1197982 1.2271872 1657.9242
3700 1.9369717 0.16601219 2.0970211 1.2812847 1657.9242
3800 1.9418085 0.16093887 2.1231359 1.2354724 1657.9242
3900 1.9450402 0.15760907 2.139479 1.2392343 1657.9242
4000 1.9350094 0.16819308 2.1142355 1.2676502 1657.9242
Loop time of 2.46236 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.82004 (93.3962)
Neigh time (%) = 0.00708961 (0.173334)
Comm time (%) = 0.0222418 (0.543791)
Outpt time (%) = 0.0359786 (0.879641)
Other time (%) = 0.204794 (5.00702)
Pair time (%) = 2.30114 (93.4523)
Neigh time (%) = 0.00465512 (0.189051)
Comm time (%) = 0.0134063 (0.544447)
Outpt time (%) = 0.0178988 (0.726895)
Other time (%) = 0.125267 (5.08728)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0

83
examples/ellipse/log.ellipse.resquared.28Mar11.linux.4 → examples/ellipse/log.ellipse.resquared.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# RESquared ellipsoids in LJ background fluid
units lj
@ -10,20 +10,23 @@ Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
@ -50,9 +53,11 @@ thermo 100
timestep 0.002
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z quatw quati quatj quatk
compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared id type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
dump 1 all custom 100 dump.ellipse.resquared id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
@ -63,7 +68,7 @@ compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.05653 Mbytes
Memory usage per processor = 3.70503 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
@ -86,13 +91,13 @@ Step rot E_pair TotEng Press Volume
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 0.739788 on 4 procs for 2000 steps with 400 atoms
Loop time of 0.700645 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.503251 (68.0264)
Neigh time (%) = 0.00446272 (0.603243)
Comm time (%) = 0.0924973 (12.5032)
Outpt time (%) = 0.0361266 (4.88337)
Other time (%) = 0.10345 (13.9837)
Pair time (%) = 0.315776 (45.0694)
Neigh time (%) = 0.00318927 (0.45519)
Comm time (%) = 0.202914 (28.961)
Outpt time (%) = 0.0198641 (2.83512)
Other time (%) = 0.158901 (22.6793)
Nlocal: 100 ave 109 max 96 min
Histogram: 2 0 1 0 0 0 0 0 0 1
@ -112,36 +117,36 @@ unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.05737 Mbytes
Memory usage per processor = 3.70587 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635013 2.1016576 1.5081781 1657.9242
2600 1.9450942 0.15744768 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066635 2.1170012 1.3384024 1657.9242
2800 1.9512215 0.15099707 2.0988078 1.2134332 1657.9242
2900 1.9211262 0.18279164 2.0994516 1.3620722 1657.9242
3000 1.9067872 0.19775145 2.0931298 1.4157496 1657.9242
3100 1.9114596 0.19296351 2.1126573 1.4113471 1657.9242
3200 1.9427387 0.15998532 2.0865326 1.3075175 1657.9242
3300 1.9111617 0.19317443 2.1216596 1.4309782 1657.9242
3400 1.9538372 0.14833016 2.1210136 1.227624 1657.9242
3500 1.9244336 0.17929216 2.0825143 1.3186829 1657.9242
3600 1.9511833 0.15107439 2.1197975 1.2271826 1657.9242
3700 1.936968 0.16601605 2.0970224 1.281307 1657.9242
3800 1.9418139 0.16093313 2.1231352 1.2354467 1657.9242
3900 1.9450405 0.15760875 2.1394706 1.2392359 1657.9242
4000 1.9350206 0.16818121 2.1142436 1.2676066 1657.9242
Loop time of 1.18441 on 4 procs for 2000 steps with 400 atoms
2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384026 1657.9242
2800 1.9512215 0.15099708 2.0988078 1.2134332 1657.9242
2900 1.9211262 0.18279165 2.0994516 1.3620722 1657.9242
3000 1.9067873 0.19775135 2.0931298 1.4157491 1657.9242
3100 1.9114597 0.19296344 2.1126573 1.4113468 1657.9242
3200 1.942739 0.15998509 2.0865326 1.3075162 1657.9242
3300 1.9111617 0.19317434 2.1216595 1.4309773 1657.9242
3400 1.9538374 0.14833002 2.121014 1.2276232 1657.9242
3500 1.9244329 0.17929295 2.0825158 1.3186873 1657.9242
3600 1.9511828 0.1510749 2.1197985 1.227186 1657.9242
3700 1.9369672 0.16601695 2.0970237 1.2813052 1657.9242
3800 1.9418088 0.16093858 2.1231366 1.2354749 1657.9242
3900 1.9450382 0.15761114 2.1394772 1.2392412 1657.9242
4000 1.9350119 0.16819038 2.1142388 1.2676423 1657.9242
Loop time of 0.718566 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.955088 (80.6381)
Neigh time (%) = 0.00181705 (0.153414)
Comm time (%) = 0.131738 (11.1227)
Outpt time (%) = 0.03601 (3.04033)
Other time (%) = 0.0597591 (5.04546)
Pair time (%) = 0.588593 (81.9121)
Neigh time (%) = 0.00123084 (0.171291)
Comm time (%) = 0.0711493 (9.90156)
Outpt time (%) = 0.0183669 (2.55604)
Other time (%) = 0.0392267 (5.45902)
Nlocal: 100 ave 107 max 97 min
Histogram: 1 2 0 0 0 0 0 0 0 1

20
examples/flow/log.flow.couette.28Mar11.linux.1 → examples/flow/log.flow.couette.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -61,7 +61,7 @@ velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poisseuille flow
# Poiseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
@ -75,7 +75,7 @@ fix 4 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 50 dump.flow
run 10000
@ -102,13 +102,13 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.47706517 0 0.23483959 2.3965332 571.43371
9500 1.034152 -0.43908184 0 0.29713592 2.0674205 571.43371
10000 1 -0.42405289 0 0.28785187 2.0333283 571.43371
Loop time of 0.586487 on 1 procs for 10000 steps with 420 atoms
Loop time of 0.345332 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.211832 (36.1187)
Neigh time (%) = 0.0697327 (11.8899)
Comm time (%) = 0.0170028 (2.8991)
Outpt time (%) = 0.128883 (21.9754)
Other time (%) = 0.159037 (27.1169)
Pair time (%) = 0.123751 (35.8355)
Neigh time (%) = 0.0470059 (13.6118)
Comm time (%) = 0.00936413 (2.71163)
Outpt time (%) = 0.0644042 (18.6499)
Other time (%) = 0.100806 (29.1912)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

20
examples/flow/log.flow.couette.28Mar11.linux.4 → examples/flow/log.flow.couette.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -61,7 +61,7 @@ velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poisseuille flow
# Poiseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
@ -75,7 +75,7 @@ fix 4 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 50 dump.flow
run 10000
@ -102,13 +102,13 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.4381772 0 0.27372756 2.4112541 571.43371
9500 1.0233668 -0.40460424 0 0.32393546 2.4071091 571.43371
10000 1 -0.4130336 0 0.29887116 2.3859891 571.43371
Loop time of 0.41448 on 4 procs for 10000 steps with 420 atoms
Loop time of 0.240091 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0529404 (12.7727)
Neigh time (%) = 0.0177063 (4.27193)
Comm time (%) = 0.159481 (38.4773)
Outpt time (%) = 0.0909385 (21.9404)
Other time (%) = 0.0934139 (22.5376)
Pair time (%) = 0.0312895 (13.0323)
Neigh time (%) = 0.0124956 (5.20452)
Comm time (%) = 0.0893214 (37.2031)
Outpt time (%) = 0.0469025 (19.5353)
Other time (%) = 0.0600821 (25.0247)
Nlocal: 105 ave 113 max 93 min
Histogram: 1 0 0 0 1 0 0 0 0 2

20
examples/flow/log.flow.pois.28Mar11.linux.1 → examples/flow/log.flow.pois.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -61,7 +61,7 @@ fix_modify 2 temp mobile
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poisseuille flow
# Poiseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
@ -75,7 +75,7 @@ fix 7 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 25 dump.flow
run 10000
@ -102,13 +102,13 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.79193368 0 -0.080028922 2.4413256 499.77059
9500 1.2151255 -0.75195108 0 0.11310255 2.4315907 500.33116
10000 1 -0.76066018 0 -0.048755416 2.4113886 502.50751
Loop time of 0.765119 on 1 procs for 10000 steps with 420 atoms
Loop time of 0.440015 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.230286 (30.0981)
Neigh time (%) = 0.0396361 (5.18039)
Comm time (%) = 0.0152719 (1.99602)
Outpt time (%) = 0.258458 (33.7801)
Other time (%) = 0.221467 (28.9454)
Pair time (%) = 0.136467 (31.0142)
Neigh time (%) = 0.0267653 (6.08282)
Comm time (%) = 0.00789261 (1.79371)
Outpt time (%) = 0.128578 (29.2214)
Other time (%) = 0.140311 (31.8879)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

20
examples/flow/log.flow.pois.28Mar11.linux.4 → examples/flow/log.flow.pois.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -61,7 +61,7 @@ fix_modify 2 temp mobile
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poisseuille flow
# Poiseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
@ -75,7 +75,7 @@ fix 7 all enforce2d
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 25 dump.flow
run 10000
@ -102,13 +102,13 @@ Step Temp E_pair E_mol TotEng Press Volume
9000 1 -0.75191705 0 -0.040012285 2.521768 509.91505
9500 1.2149548 -0.71491732 0 0.15001477 2.3827722 508.86228
10000 1 -0.71239141 0 -0.00048664424 2.3193862 508.75244
Loop time of 0.623361 on 4 procs for 10000 steps with 420 atoms
Loop time of 0.334578 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0576158 (9.24276)
Neigh time (%) = 0.0104457 (1.6757)
Comm time (%) = 0.179585 (28.8092)
Outpt time (%) = 0.173133 (27.7741)
Other time (%) = 0.202582 (32.4983)
Pair time (%) = 0.034201 (10.2221)
Neigh time (%) = 0.00749511 (2.24017)
Comm time (%) = 0.0808396 (24.1616)
Outpt time (%) = 0.0899565 (26.8865)
Other time (%) = 0.122086 (36.4895)
Nlocal: 105 ave 107 max 104 min
Histogram: 2 0 0 1 0 0 0 0 0 1

18
examples/friction/log.friction.28Mar11.linux.1 → examples/friction/log.friction.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d friction simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
mass 1 1.0
mass 2 1.0
@ -93,7 +93,7 @@ fix_modify 3 temp new
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 500 dump.friction
run 20000
@ -120,13 +120,13 @@ Step Temp E_pair E_mol TotEng Press Volume
18000 0.11194476 -3.0440786 0 -2.9979112 -0.35902467 2444.4558
19000 0.11200621 -3.0473992 0 -3.0012064 -0.25540459 2444.4558
20000 0.10818968 -3.0456459 0 -3.0010271 -0.29452342 2444.4558
Loop time of 10.6353 on 1 procs for 20000 steps with 1724 atoms
Loop time of 5.76747 on 1 procs for 20000 steps with 1724 atoms
Pair time (%) = 8.85169 (83.2295)
Neigh time (%) = 0.454272 (4.27137)
Comm time (%) = 0.0700171 (0.658347)
Outpt time (%) = 0.106286 (0.999372)
Other time (%) = 1.15302 (10.8415)
Pair time (%) = 4.63048 (80.2861)
Neigh time (%) = 0.297429 (5.15701)
Comm time (%) = 0.0432248 (0.749459)
Outpt time (%) = 0.0548413 (0.950872)
Other time (%) = 0.741497 (12.8565)
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0

18
examples/friction/log.friction.28Mar11.linux.4 → examples/friction/log.friction.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d friction simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
mass 1 1.0
mass 2 1.0
@ -93,7 +93,7 @@ fix_modify 3 temp new
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 500 dump.friction
run 20000
@ -120,13 +120,13 @@ Step Temp E_pair E_mol TotEng Press Volume
18000 0.11632659 -3.0376748 0 -2.9897002 -0.2781061 2444.4558
19000 0.11302219 -3.0324168 0 -2.985805 -0.35512798 2444.4558
20000 0.11916746 -3.0379931 0 -2.9888469 -0.30162295 2444.4558
Loop time of 3.65225 on 4 procs for 20000 steps with 1724 atoms
Loop time of 1.9566 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 2.22406 (60.8956)
Neigh time (%) = 0.111846 (3.06239)
Comm time (%) = 0.684649 (18.7459)
Outpt time (%) = 0.240481 (6.58446)
Other time (%) = 0.391215 (10.7116)
Pair time (%) = 1.17991 (60.3041)
Neigh time (%) = 0.0769351 (3.93207)
Comm time (%) = 0.391056 (19.9865)
Outpt time (%) = 0.0432984 (2.21293)
Other time (%) = 0.265402 (13.5644)
Nlocal: 431 ave 486 max 376 min
Histogram: 1 0 0 1 0 0 1 0 0 1

2
examples/gpu/in.melt_2.5.gpu → examples/gpu/in.gpu.melt.2.5
View File

@ -31,4 +31,4 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 5000
run 1000

2
examples/gpu/in.melt_5.0.gpu → examples/gpu/in.gpu.melt.5.0
View File

@ -31,4 +31,4 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 5000
run 1000

2
examples/gpu/in.phosphate.gpu → examples/gpu/in.gpu.phosphate
View File

@ -27,5 +27,5 @@ thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 1000
run 200
unfix 1

2
examples/gpu/in.rhodo.gpu → examples/gpu/in.gpu.rhodo
View File

@ -33,4 +33,4 @@ thermo 100
thermo_style multi
timestep 2.0
run 1000
run 200

77
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.1 Normal file
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@ -0,0 +1,77 @@
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI 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/gpu 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
thermo 100
run 1000
Memory usage per processor = 46.8382 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
100 0.75865618 -5.760326 0 -4.6223462 0.19586078
200 0.75643081 -5.7572862 0 -4.6226445 0.22641252
300 0.74927357 -5.7463992 0 -4.6224932 0.2973801
400 0.7404924 -5.7329247 0 -4.6221905 0.37767073
500 0.73092032 -5.7182616 0 -4.6218854 0.46900679
600 0.72315678 -5.706314 0 -4.621583 0.5348031
700 0.71597165 -5.6952207 0 -4.6212675 0.59549602
800 0.71194748 -5.6889042 0 -4.6209871 0.63784817
900 0.70596464 -5.6796285 0 -4.6206857 0.68573109
1000 0.70323336 -5.67534 0 -4.6204941 0.7069076
Loop time of 20.1772 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 12.8361 (63.6167)
Neigh time (%) = 7.34329e-05 (0.00036394)
Comm time (%) = 1.08434 (5.3741)
Outpt time (%) = 0.0102942 (0.051019)
Other time (%) = 6.24641 (30.9578)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69905 ave 69905 max 69905 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.2.5.9Jan12.linux.4 Normal file
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@ -0,0 +1,77 @@
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI 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/gpu 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
thermo 100
run 1000
Memory usage per processor = 14.5128 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
100 0.75865619 -5.7603258 0 -4.622346 0.19586113
200 0.75643076 -5.7572857 0 -4.6226439 0.22641355
300 0.74927365 -5.7463989 0 -4.6224928 0.29738053
400 0.74049513 -5.7329265 0 -4.6221881 0.37765479
500 0.73092165 -5.7182628 0 -4.6218846 0.46899675
600 0.72307341 -5.7061845 0 -4.6215786 0.53536825
700 0.71593631 -5.6951696 0 -4.6212694 0.59644919
800 0.71106107 -5.6875486 0 -4.6209611 0.6450072
900 0.70789378 -5.6825117 0 -4.6206752 0.67079907
1000 0.70324302 -5.6753075 0 -4.6204471 0.71004301
Loop time of 8.45152 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 5.1208 (60.5903)
Neigh time (%) = 5.52535e-05 (0.00065377)
Comm time (%) = 1.60643 (19.0076)
Outpt time (%) = 0.032979 (0.390213)
Other time (%) = 1.69126 (20.0113)
Nlocal: 64000 ave 64090 max 63900 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 30521 ave 30604 max 30461 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.1 Normal file
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@ -0,0 +1,77 @@
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI 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/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 58.5637 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
100 0.7599844 -6.1430228 0 -5.0030506 -0.43702259
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563905
300 0.7502998 -6.1286575 0 -5.0032122 -0.33104598
400 0.73999173 -6.1132483 0 -5.003265 -0.24002836
500 0.73224837 -6.101694 0 -5.0033257 -0.16523366
600 0.72448052 -6.0900828 0 -5.0033662 -0.099466624
700 0.71878723 -6.0815904 0 -5.0034138 -0.044361885
800 0.71444388 -6.0751019 0 -5.0034403 -0.0083893389
900 0.70949961 -6.0676978 0 -5.0034525 0.032534654
1000 0.70480647 -6.0606748 0 -5.0034693 0.067358025
Loop time of 43.8997 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 35.1574 (80.0858)
Neigh time (%) = 8.29697e-05 (0.000188998)
Comm time (%) = 1.61756 (3.68467)
Outpt time (%) = 0.011915 (0.0271413)
Other time (%) = 7.1127 (16.2022)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 141753 ave 141753 max 141753 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.5.0.9Jan12.linux.4 Normal file
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@ -0,0 +1,77 @@
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI 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/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 20.3741 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
100 0.75998442 -6.1430228 0 -5.0030506 -0.4370226
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563885
300 0.75029998 -6.1286577 0 -5.0032121 -0.33104745
400 0.73999268 -6.1132497 0 -5.003265 -0.24002923
500 0.73223459 -6.1016733 0 -5.0033257 -0.16512674
600 0.72450196 -6.0901153 0 -5.0033666 -0.099408327
700 0.71915302 -6.0821406 0 -5.0034153 -0.045922554
800 0.71398822 -6.0744174 0 -5.0034392 -0.0064880998
900 0.70918338 -6.0672194 0 -5.0034485 0.032885247
1000 0.70513415 -6.0611556 0 -5.0034585 0.063293271
Loop time of 20.8409 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 14.4203 (69.1925)
Neigh time (%) = 5.91874e-05 (0.000283997)
Comm time (%) = 4.66054 (22.3625)
Outpt time (%) = 0.0455028 (0.218335)
Other time (%) = 1.71444 (8.22633)
Nlocal: 64000 ave 64103 max 63848 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 64409.2 ave 64479 max 64338 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

74
examples/gpu/log.gpu.phosphate.9Jan12.linux.1 Normal file
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@ -0,0 +1,74 @@
LAMMPS (10 Jan 2012)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 1 by 1 MPI processor grid
10950 atoms
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
1 by 1 by 1 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector = 0.210111
grid = 108 108 108
stencil order = 5
RMS precision = 8.76251e-06
using double precision FFTs
brick FFT buffer size/proc = 1520875 1259712 158700
Memory usage per processor = 266.913 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.5 0 -2366643.7 -449.93537 4242016.4
100 411.69679 -2392428.5 0 -2376695.2 7046.7022 4308883.6
200 401.28406 -2394152.4 0 -2378817.1 3243.2514 4334284.6
Loop time of 174.691 on 1 procs for 200 steps with 295650 atoms
Pair time (%) = 12.053 (6.89962)
Kspce time (%) = 80.9936 (46.3638)
Neigh time (%) = 0.013356 (0.00764546)
Comm time (%) = 0.347907 (0.199155)
Outpt time (%) = 0.00172615 (0.000988114)
Other time (%) = 81.2818 (46.5288)
FFT time (% of Kspce) = 56.1923 (69.3786)
FFT Gflps 3d (1d only) = 1.25956 2.99555
Nlocal: 295650 ave 295650 max 295650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 226982 ave 226982 max 226982 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1

74
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LAMMPS (10 Jan 2012)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 2 by 2 MPI processor grid
10950 atoms
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
2 by 1 by 2 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector = 0.210111
grid = 108 108 108
stencil order = 5
RMS precision = 8.76251e-06
using double precision FFTs
brick FFT buffer size/proc = 427915 314928 84180
Memory usage per processor = 80.0627 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.5 0 -2366643.7 -449.93522 4242016.4
100 411.69683 -2392428.5 0 -2376695.2 7046.7136 4308883.6
200 401.28395 -2394152.4 0 -2378817.1 3243.2713 4334284.6
Loop time of 62.4573 on 4 procs for 200 steps with 295650 atoms
Pair time (%) = 5.04743 (8.08141)
Kspce time (%) = 35.3904 (56.6633)
Neigh time (%) = 0.00620693 (0.00993788)
Comm time (%) = 0.473388 (0.757939)
Outpt time (%) = 0.000503302 (0.000805833)
Other time (%) = 21.5394 (34.4866)
FFT time (% of Kspce) = 22.1085 (62.4703)
FFT Gflps 3d (1d only) = 3.20138 11.8522
Nlocal: 73912.5 ave 74223 max 73638 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 105257 ave 105797 max 104698 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1

121
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LAMMPS (10 Jan 2012)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
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/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 1 by 1 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector = 0.245952
grid = 48 64 60
stencil order = 5
RMS precision = 8.7421e-05
using double precision FFTs
brick FFT buffer size/proc = 237705 184320 40365
Memory usage per processor = 757.714 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157025.0401 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15767.5754 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894235.3907 E_long = -2130427.5409 Press = 9562.2425
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.8336 (sec) ----------------
TotEng = -233301.4802 KinEng = 123222.6026 Temp = 214.7785
PotEng = -356524.0828 E_bond = 13098.4631 E_angle = 56766.9481
E_dihed = 45556.8121 E_impro = 1313.9420 E_vdwl = -40863.8988
E_coul = 1705023.3608 E_long = -2137419.7102 Press = -1634.3633
Volume = 2522232.7977
---------------- Step 200 ----- CPU = 72.2618 (sec) ----------------
TotEng = -308340.6857 KinEng = 108944.3257 Temp = 189.8913
PotEng = -417285.0114 E_bond = 9579.0680 E_angle = 47373.8383
E_dihed = 39847.6180 E_impro = 967.6100 E_vdwl = -23634.8218
E_coul = 1646565.2623 E_long = -2137983.5863 Press = -1185.9778
Volume = 2554683.5150
Loop time of 72.2618 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.1078 (13.9878)
Bond time (%) = 29.9182 (41.4025)
Kspce time (%) = 7.29844 (10.1)
Neigh time (%) = 1.64225 (2.27264)
Comm time (%) = 0.614946 (0.850997)
Outpt time (%) = 0.00137877 (0.00190803)
Other time (%) = 22.6787 (31.3841)
FFT time (% of Kspce) = 5.23688 (71.7535)
FFT Gflps 3d (1d only) = 1.70695 3.00498
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161678 ave 161678 max 161678 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

121
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LAMMPS (10 Jan 2012)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
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/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 2 by 2 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector = 0.245952
grid = 48 64 60
stencil order = 5
RMS precision = 8.7421e-05
using double precision FFTs
brick FFT buffer size/proc = 68635 46080 17649
Memory usage per processor = 249.821 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157025.0390 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15767.5765 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894235.3896 E_long = -2130427.5409 Press = 9562.2425
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 12.2605 (sec) ----------------
TotEng = -233301.4713 KinEng = 123222.6058 Temp = 214.7785
PotEng = -356524.0771 E_bond = 13098.4614 E_angle = 56766.9463
E_dihed = 45556.8096 E_impro = 1313.9414 E_vdwl = -40863.8548
E_coul = 1705023.3285 E_long = -2137419.7095 Press = -1634.3527
Volume = 2522232.7976
---------------- Step 200 ----- CPU = 23.7724 (sec) ----------------
TotEng = -308340.7251 KinEng = 108941.9220 Temp = 189.8871
PotEng = -417282.6471 E_bond = 9579.0415 E_angle = 47373.9551
E_dihed = 39847.5174 E_impro = 967.5823 E_vdwl = -23636.2292
E_coul = 1646568.9776 E_long = -2137983.4917 Press = -1186.1181
Volume = 2554683.4248
Loop time of 23.7725 on 4 procs for 200 steps with 256000 atoms
Pair time (%) = 4.55113 (19.1446)
Bond time (%) = 7.43137 (31.2604)
Kspce time (%) = 3.8699 (16.2789)
Neigh time (%) = 0.51208 (2.15409)
Comm time (%) = 0.544156 (2.28902)
Outpt time (%) = 0.000452995 (0.00190555)
Other time (%) = 6.86337 (28.8711)
FFT time (% of Kspce) = 1.94085 (50.1524)
FFT Gflps 3d (1d only) = 4.60577 11.8123
Nlocal: 64000 ave 64003 max 63997 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 70640.8 ave 70645 max 70636 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

6
examples/hugoniostat/in.nphug → examples/hugoniostat/in.hugoniostat
View File

@ -82,7 +82,7 @@ variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 10
thermo 100
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
@ -122,7 +122,7 @@ variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 10
thermo 100
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
@ -162,7 +162,7 @@ variable pzz equal pzz # axial stress
variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
variable time equal dt*step
thermo 10
thermo 100
thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'

90
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LAMMPS (10 Jan 2012)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.80047 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.4422116e-13 -4.919366e-13 -4.9777247e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.082279 on 1 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.78407e-10
Force max component initial, final = 1960.27 3.42777e-10
Final line search alpha, max atom move = 1 3.42777e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0646594 (78.5855)
Neigh time (%) = 0.00100803 (1.22514)
Comm time (%) = 0.00203061 (2.46796)
Outpt time (%) = 2.09808e-05 (0.0254996)
Other time (%) = 0.01456 (17.6959)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

90
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@ -0,0 +1,90 @@
LAMMPS (10 Jan 2012)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.77702 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.5540246e-13 -4.9541511e-13 -5.0200254e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0306363 on 4 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.85569e-10
Force max component initial, final = 1960.27 3.45689e-10
Final line search alpha, max atom move = 1 3.45689e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0165715 (54.0909)
Neigh time (%) = 0.000261545 (0.85371)
Comm time (%) = 0.00607055 (19.8149)
Outpt time (%) = 2.06828e-05 (0.0675108)
Other time (%) = 0.00771207 (25.173)
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6350 max 4305 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

30
examples/indent/log.indent.28Mar11.linux.1 → examples/indent/log.indent.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d indenter simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -57,7 +57,7 @@ fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 250 dump.indent
run 30000
@ -94,13 +94,13 @@ Step Temp E_pair E_mol TotEng Press Volume
28000 0.11149859 -3.0023437 0 -2.907039 1.3034926 476.52895
29000 0.12150147 -2.9856999 0 -2.8818451 1.576077 476.13435
30000 0.11570444 -2.9624626 0 -2.8635628 1.5924214 479.30483
Loop time of 4.48839 on 1 procs for 30000 steps with 420 atoms
Loop time of 2.37765 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.32296 (74.0347)
Neigh time (%) = 0.0993707 (2.21395)
Comm time (%) = 0.0551386 (1.22847)
Outpt time (%) = 0.0783148 (1.74483)
Other time (%) = 0.932601 (20.7781)
Pair time (%) = 1.74991 (73.5984)
Neigh time (%) = 0.0673277 (2.83169)
Comm time (%) = 0.0314863 (1.32426)
Outpt time (%) = 0.041635 (1.7511)
Other time (%) = 0.487288 (20.4945)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -151,13 +151,13 @@ Step Temp E_pair E_mol TotEng Press Volume
58000 0.11424257 -3.0506964 0 -2.9530462 -0.24886576 481.40236
59000 0.11626176 -3.0423269 0 -2.9429508 -0.3377255 484.34589
60000 0.11322673 -3.0398445 0 -2.9430626 -0.0027517474 481.19045
Loop time of 4.02696 on 1 procs for 30000 steps with 420 atoms
Loop time of 2.15946 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.30979 (82.1908)
Neigh time (%) = 0.0998025 (2.47836)
Comm time (%) = 0.0567474 (1.40919)
Outpt time (%) = 0.078594 (1.95169)
Other time (%) = 0.482025 (11.97)
Pair time (%) = 1.73037 (80.1299)
Neigh time (%) = 0.067282 (3.11568)
Comm time (%) = 0.0314145 (1.45474)
Outpt time (%) = 0.039238 (1.81703)
Other time (%) = 0.291153 (13.4827)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

30
examples/indent/log.indent.28Mar11.linux.4 → examples/indent/log.indent.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d indenter simulation
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -57,7 +57,7 @@ fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 250 dump.indent
run 30000
@ -94,13 +94,13 @@ Step Temp E_pair E_mol TotEng Press Volume
28000 0.12260647 -2.9956772 0 -2.8908779 1.7319832 470.55197
29000 0.12231691 -2.9866104 0 -2.8820586 1.9114487 468.06771
30000 0.1134125 -2.9719856 0 -2.8750449 1.735366 474.78395
Loop time of 2.15339 on 4 procs for 30000 steps with 420 atoms
Loop time of 1.0663 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.834652 (38.76)
Neigh time (%) = 0.0253125 (1.17548)
Comm time (%) = 0.6108 (28.3646)
Outpt time (%) = 0.207858 (9.6526)
Other time (%) = 0.474765 (22.0474)
Pair time (%) = 0.451498 (42.3424)
Neigh time (%) = 0.0176335 (1.6537)
Comm time (%) = 0.308133 (28.8973)
Outpt time (%) = 0.0310341 (2.91044)
Other time (%) = 0.258004 (24.1961)
Nlocal: 105 ave 116 max 91 min
Histogram: 1 0 0 1 0 0 0 0 1 1
@ -151,13 +151,13 @@ Step Temp E_pair E_mol TotEng Press Volume
58000 0.11901212 -3.0460985 0 -2.9443714 -0.2523838 484.38143
59000 0.11452134 -3.0424137 0 -2.9445252 -0.13008427 481.35053
60000 0.1121022 -3.0402301 0 -2.9444094 -0.21943641 488.19161
Loop time of 1.76434 on 4 procs for 30000 steps with 420 atoms
Loop time of 0.960824 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.824768 (46.7466)
Neigh time (%) = 0.0261157 (1.4802)
Comm time (%) = 0.6177 (35.0103)
Outpt time (%) = 0.0596796 (3.38255)
Other time (%) = 0.236074 (13.3803)
Pair time (%) = 0.445671 (46.3843)
Neigh time (%) = 0.0183511 (1.90994)
Comm time (%) = 0.31143 (32.4128)
Outpt time (%) = 0.030867 (3.21255)
Other time (%) = 0.154504 (16.0804)
Nlocal: 105 ave 115 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2

102
examples/indent/log.indent.min.28Mar11.linux.1 → examples/indent/log.indent.min.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -52,7 +52,7 @@ dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
@ -64,7 +64,7 @@ Step Temp E_pair E_mol TotEng Press Volume
60 0 -3.1906458 0 -3.1906458 -0.78391531 435.53833
70 0 -3.190782 0 -3.190782 -0.75177925 435.53833
74 0 -3.1908431 0 -3.1908431 -0.73891705 435.53833
Loop time of 0.0884922 on 1 procs for 74 steps with 420 atoms
Loop time of 0.0452979 on 1 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -75,11 +75,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.00643442 0.00042405
Iterations, force evaluations = 74 411
Pair time (%) = 0.0747404 (84.4599)
Neigh time (%) = 0.000659704 (0.745495)
Comm time (%) = 0.000694275 (0.784561)
Outpt time (%) = 0.00545716 (6.16683)
Other time (%) = 0.0069406 (7.84318)
Pair time (%) = 0.0378823 (83.6294)
Neigh time (%) = 0.0004251 (0.938456)
Comm time (%) = 0.00039506 (0.872137)
Outpt time (%) = 0.0027256 (6.01706)
Other time (%) = 0.00386977 (8.54295)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -100,7 +100,7 @@ fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.246435 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624129 -0.73821499 435.95254
@ -113,7 +113,7 @@ Step Temp E_pair E_mol TotEng Press Volume
140 0 -3.1811622 0 -3.180374 -0.18867263 434.93784
150 0 -3.1811721 0 -3.1804507 -0.17763419 433.08677
156 0 -3.1811921 0 -3.1804771 -0.17272768 433.95891
Loop time of 0.0995409 on 1 procs for 82 steps with 420 atoms
Loop time of 0.050761 on 1 procs for 82 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -124,11 +124,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.00298294 0.000487467
Iterations, force evaluations = 82 418
Pair time (%) = 0.0757627 (76.1121)
Neigh time (%) = 0.00378561 (3.80307)
Comm time (%) = 0.000819445 (0.823224)
Outpt time (%) = 0.00627327 (6.3022)
Other time (%) = 0.0128999 (12.9594)
Pair time (%) = 0.0383368 (75.5241)
Neigh time (%) = 0.00255942 (5.04211)
Comm time (%) = 0.000461578 (0.909317)
Outpt time (%) = 0.00308037 (6.06838)
Other time (%) = 0.00632286 (12.4561)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -146,7 +146,7 @@ fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
156 0 -3.1811921 0 -0.18185886 -0.17245392 434.6478
@ -161,7 +161,7 @@ Step Temp E_pair E_mol TotEng Press Volume
240 0 -3.1039956 0 -3.0965499 1.310294 431.25237
250 0 -3.1041599 0 -3.0968021 1.3296476 432.71979
251 0 -3.1041297 0 -3.0968045 1.3346958 431.22872
Loop time of 0.107578 on 1 procs for 95 steps with 420 atoms
Loop time of 0.0553658 on 1 procs for 95 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -172,11 +172,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.00129143 0.0003215
Iterations, force evaluations = 95 443
Pair time (%) = 0.0807207 (75.0345)
Neigh time (%) = 0.00420499 (3.90878)
Comm time (%) = 0.000867605 (0.806489)
Outpt time (%) = 0.00791669 (7.35902)
Other time (%) = 0.0138681 (12.8912)
Pair time (%) = 0.0411718 (74.3632)
Neigh time (%) = 0.00282073 (5.09472)
Comm time (%) = 0.000554085 (1.00077)
Outpt time (%) = 0.0038321 (6.92142)
Other time (%) = 0.00698709 (12.6199)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -194,7 +194,7 @@ fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
251 0 -3.1041297 0 2.0179509 1.3331076 431.74246
@ -206,7 +206,7 @@ Step Temp E_pair E_mol TotEng Press Volume
310 0 -2.9633194 0 -2.9509764 3.0506152 453.58916
320 0 -2.9656103 0 -2.9548573 3.0261904 453.95834
328 0 -2.9669235 0 -2.9563046 3.008729 453.95834
Loop time of 0.0679569 on 1 procs for 77 steps with 420 atoms
Loop time of 0.0352268 on 1 procs for 77 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -217,11 +217,11 @@ Minimization stats:
Final line search alpha, max atom move = 1.61036e-06 3.04651e-06
Iterations, force evaluations = 77 268
Pair time (%) = 0.0498948 (73.4212)
Neigh time (%) = 0.0028069 (4.13041)
Comm time (%) = 0.000552416 (0.812891)
Outpt time (%) = 0.00547743 (8.06015)
Other time (%) = 0.00922537 (13.5753)
Pair time (%) = 0.0257685 (73.1503)
Neigh time (%) = 0.00191307 (5.43072)
Comm time (%) = 0.000335932 (0.953625)
Outpt time (%) = 0.00268078 (7.61005)
Other time (%) = 0.00452852 (12.8553)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -239,7 +239,7 @@ fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
328 0 -2.9669235 0 7.5568154 3.0093541 453.86405
@ -263,7 +263,7 @@ Step Temp E_pair E_mol TotEng Press Volume
500 0 -2.9943854 0 -2.9875383 3.1955071 480.5305
510 0 -2.9952148 0 -2.9880037 3.1698354 480.5305
517 0 -2.9952859 0 -2.9880707 3.1663812 480.5305
Loop time of 0.176604 on 1 procs for 189 steps with 420 atoms
Loop time of 0.0913372 on 1 procs for 189 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -274,11 +274,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.000217837 5.67363e-05
Iterations, force evaluations = 189 705
Pair time (%) = 0.131893 (74.683)
Neigh time (%) = 0.00583577 (3.30444)
Comm time (%) = 0.00148368 (0.840116)
Outpt time (%) = 0.0149209 (8.44882)
Other time (%) = 0.0224705 (12.7236)
Pair time (%) = 0.0679402 (74.384)
Neigh time (%) = 0.0040462 (4.42996)
Comm time (%) = 0.00089097 (0.975474)
Outpt time (%) = 0.0072484 (7.93587)
Other time (%) = 0.0112114 (12.2747)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -296,7 +296,7 @@ fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74082 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
517 0 -2.9952859 0 -2.4853146 3.1725652 479.59385
@ -314,7 +314,7 @@ Step Temp E_pair E_mol TotEng Press Volume
630 0 -2.9389523 0 -2.9243365 4.0118887 479.60846
640 0 -2.9389486 0 -2.9244942 3.9965251 481.89847
647 0 -2.9390355 0 -2.9245617 4.0040398 480.57245
Loop time of 0.170806 on 1 procs for 130 steps with 420 atoms
Loop time of 0.0892859 on 1 procs for 130 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -325,11 +325,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.000879757 0.000125345
Iterations, force evaluations = 130 703
Pair time (%) = 0.13136 (76.906)
Neigh time (%) = 0.0067091 (3.92791)
Comm time (%) = 0.00150347 (0.88022)
Outpt time (%) = 0.010102 (5.91433)
Other time (%) = 0.0211313 (12.3715)
Pair time (%) = 0.068279 (76.4724)
Neigh time (%) = 0.00469089 (5.25378)
Comm time (%) = 0.000895262 (1.00269)
Outpt time (%) = 0.00496078 (5.55606)
Other time (%) = 0.0104599 (11.7151)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -347,7 +347,7 @@ fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74082 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
647 0 -2.9390355 0 -2.2881675 4.004627 480.50198
@ -374,7 +374,7 @@ Step Temp E_pair E_mol TotEng Press Volume
850 0 -2.8846306 0 -2.8640867 4.2891586 499.70114
860 0 -2.8891911 0 -2.8698441 4.2003836 499.39278
866 0 -2.8894083 0 -2.870152 4.2061476 498.42046
Loop time of 0.239795 on 1 procs for 219 steps with 420 atoms
Loop time of 0.125655 on 1 procs for 219 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -385,11 +385,11 @@ Minimization stats:
Final line search alpha, max atom move = 6.43213e-05 4.82973e-05
Iterations, force evaluations = 219 962
Pair time (%) = 0.182819 (76.2399)
Neigh time (%) = 0.00830817 (3.4647)
Comm time (%) = 0.00199533 (0.832096)
Outpt time (%) = 0.0170641 (7.11612)
Other time (%) = 0.029608 (12.3472)
Pair time (%) = 0.0958545 (76.2839)
Neigh time (%) = 0.00576615 (4.58888)
Comm time (%) = 0.00116706 (0.928781)
Outpt time (%) = 0.0083425 (6.63922)
Other time (%) = 0.0145247 (11.5592)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

102
examples/indent/log.indent.min.28Mar11.linux.4 → examples/indent/log.indent.min.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
@ -15,7 +15,7 @@ Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
@ -52,7 +52,7 @@ dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
@ -64,7 +64,7 @@ Step Temp E_pair E_mol TotEng Press Volume
60 0 -3.1906458 0 -3.1906458 -0.78391528 435.53833
70 0 -3.190782 0 -3.190782 -0.75177926 435.53833
74 0 -3.1908431 0 -3.1908431 -0.73891675 435.53833
Loop time of 0.0379065 on 4 procs for 74 steps with 420 atoms
Loop time of 0.0206316 on 4 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -75,11 +75,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.00643452 0.000423891
Iterations, force evaluations = 74 411
Pair time (%) = 0.0186192 (49.1188)
Neigh time (%) = 0.000171363 (0.452068)
Comm time (%) = 0.00722551 (19.0614)
Outpt time (%) = 0.00571096 (15.0659)
Other time (%) = 0.00617945 (16.3018)
Pair time (%) = 0.00988287 (47.9017)
Neigh time (%) = 0.000116825 (0.566245)
Comm time (%) = 0.00376642 (18.2556)
Outpt time (%) = 0.00290936 (14.1015)
Other time (%) = 0.00395608 (19.1749)
Nlocal: 105 ave 110 max 99 min
Histogram: 1 1 0 0 0 0 0 0 0 2
@ -100,7 +100,7 @@ fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.246435 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624137 -0.73821469 435.95253
@ -113,7 +113,7 @@ Step Temp E_pair E_mol TotEng Press Volume
140 0 -3.1811242 0 -3.1804145 -0.1823656 433.48453
150 0 -3.1812451 0 -3.1805047 -0.16049814 432.87389
154 0 -3.1812423 0 -3.1805491 -0.15211702 432.87389
Loop time of 0.0430946 on 4 procs for 80 steps with 420 atoms
Loop time of 0.024414 on 4 procs for 80 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -124,11 +124,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.00540441 0.0010507
Iterations, force evaluations = 80 406
Pair time (%) = 0.0184599 (42.8358)
Neigh time (%) = 0.000846982 (1.9654)
Comm time (%) = 0.00861949 (20.0013)
Outpt time (%) = 0.00648999 (15.0599)
Other time (%) = 0.00867826 (20.1377)
Pair time (%) = 0.00969785 (39.7225)
Neigh time (%) = 0.000582635 (2.38648)
Comm time (%) = 0.00488079 (19.9917)
Outpt time (%) = 0.00335246 (13.7317)
Other time (%) = 0.00590026 (24.1675)
Nlocal: 105 ave 111 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
@ -146,7 +146,7 @@ fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
154 0 -3.1812423 0 -0.19846921 -0.15159029 434.378
@ -162,7 +162,7 @@ Step Temp E_pair E_mol TotEng Press Volume
250 0 -3.1041911 0 -3.0968745 1.3470137 430.97789
260 0 -3.1041223 0 -3.0970712 1.386564 430.92355
262 0 -3.1041329 0 -3.0970762 1.3846332 431.51763
Loop time of 0.0572262 on 4 procs for 108 steps with 420 atoms
Loop time of 0.032465 on 4 procs for 108 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -173,11 +173,11 @@ Minimization stats:
Final line search alpha, max atom move = 0.00390625 0.00102649
Iterations, force evaluations = 108 532
Pair time (%) = 0.024202 (42.2918)
Neigh time (%) = 0.00122923 (2.14801)
Comm time (%) = 0.0118026 (20.6245)
Outpt time (%) = 0.00885069 (15.4661)
Other time (%) = 0.0111417 (19.4696)
Pair time (%) = 0.0128388 (39.5466)
Neigh time (%) = 0.00085789 (2.64251)
Comm time (%) = 0.00652206 (20.0895)
Outpt time (%) = 0.00459975 (14.1683)
Other time (%) = 0.0076465 (23.5531)
Nlocal: 105 ave 111 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
@ -195,7 +195,7 @@ fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
262 0 -3.1041329 0 1.9882182 1.3862425 431.01668
@ -215,7 +215,7 @@ Step Temp E_pair E_mol TotEng Press Volume
400 0 -3.1036401 0 -3.1004924 1.2216848 469.7629
410 0 -3.1132635 0 -3.1105323 1.0773999 469.945
418 0 -3.1149693 0 -3.1123334 1.0362325 472.71946
Loop time of 0.062937 on 4 procs for 156 steps with 420 atoms
Loop time of 0.0366988 on 4 procs for 156 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -226,11 +226,11 @@ Minimization stats:
Final line search alpha, max atom move = 2.56426e-05 9.5386e-05
Iterations, force evaluations = 156 527
Pair time (%) = 0.0241739 (38.4096)
Neigh time (%) = 0.0016433 (2.61102)
Comm time (%) = 0.0132205 (21.006)
Outpt time (%) = 0.0120705 (19.1787)
Other time (%) = 0.0118288 (18.7947)
Pair time (%) = 0.0129628 (35.322)
Neigh time (%) = 0.00114769 (3.12731)
Comm time (%) = 0.00773114 (21.0665)
Outpt time (%) = 0.00628912 (17.1371)
Other time (%) = 0.00856811 (23.3471)
Nlocal: 105 ave 119 max 88 min
Histogram: 1 1 0 0 0 0 0 0 0 2
@ -248,7 +248,7 @@ fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
418 0 -3.1149693 0 3.9695775 1.0398804 471.06117
@ -270,7 +270,7 @@ Step Temp E_pair E_mol TotEng Press Volume
570 0 -3.0754999 0 -3.068936 1.5508329 495.84223
580 0 -3.0791924 0 -3.0725672 1.5199839 497.9288
589 0 -3.0795685 0 -3.0729707 1.5102713 497.95469
Loop time of 0.0711412 on 4 procs for 171 steps with 420 atoms
Loop time of 0.044094 on 4 procs for 171 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -281,11 +281,11 @@ Minimization stats:
Final line search alpha, max atom move = 6.02041e-05 2.44137e-05
Iterations, force evaluations = 171 578
Pair time (%) = 0.0263076 (36.9794)
Neigh time (%) = 0.00178152 (2.50421)
Comm time (%) = 0.0165319 (23.2382)
Outpt time (%) = 0.0136525 (19.1907)
Other time (%) = 0.0128677 (18.0875)
Pair time (%) = 0.0140276 (31.8129)
Neigh time (%) = 0.001252 (2.83938)
Comm time (%) = 0.0106812 (24.2237)
Outpt time (%) = 0.00707901 (16.0543)
Other time (%) = 0.0110542 (25.0696)
Nlocal: 105 ave 124 max 88 min
Histogram: 2 0 0 0 0 0 0 0 1 1
@ -303,7 +303,7 @@ fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74743 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
589 0 -3.0795685 0 -2.5645649 1.5134157 496.92009
@ -314,7 +314,7 @@ Step Temp E_pair E_mol TotEng Press Volume
630 0 -3.0162496 0 -3.0004658 2.3321472 496.68198
640 0 -3.0163782 0 -3.0017964 2.3448435 496.43329
650 0 -3.0170272 0 -3.0035125 2.3710061 495.40836
Loop time of 0.0300033 on 4 procs for 61 steps with 420 atoms
Loop time of 0.0185835 on 4 procs for 61 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -325,11 +325,11 @@ Minimization stats:
Final line search alpha, max atom move = 6.69976e-05 4.95299e-05
Iterations, force evaluations = 61 252
Pair time (%) = 0.0115876 (38.6211)
Neigh time (%) = 0.000545442 (1.81794)
Comm time (%) = 0.00724971 (24.163)
Outpt time (%) = 0.00480968 (16.0305)
Other time (%) = 0.00581086 (19.3674)
Pair time (%) = 0.00620061 (33.3662)
Neigh time (%) = 0.000388563 (2.0909)
Comm time (%) = 0.00460953 (24.8043)
Outpt time (%) = 0.00249505 (13.4261)
Other time (%) = 0.00488979 (26.3125)
Nlocal: 105 ave 122 max 88 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -347,7 +347,7 @@ fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74743 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
650 0 -3.0170272 0 -2.3648009 2.3681511 496.00561
@ -356,7 +356,7 @@ Step Temp E_pair E_mol TotEng Press Volume
680 0 -2.9028036 0 -2.874857 3.5600205 495.73432
690 0 -2.9040138 0 -2.8811237 3.5847696 495.73432
695 0 -2.9044182 0 -2.8814536 3.5808985 495.92978
Loop time of 0.0232177 on 4 procs for 45 steps with 420 atoms
Loop time of 0.0143149 on 4 procs for 45 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
@ -367,11 +367,11 @@ Minimization stats:
Final line search alpha, max atom move = 6.0444e-06 3.05084e-06
Iterations, force evaluations = 45 198
Pair time (%) = 0.00926459 (39.9032)
Neigh time (%) = 0.000253439 (1.09158)
Comm time (%) = 0.00583363 (25.1258)
Outpt time (%) = 0.00319672 (13.7685)
Other time (%) = 0.00466931 (20.111)
Pair time (%) = 0.00502551 (35.1068)
Neigh time (%) = 0.00018084 (1.2633)
Comm time (%) = 0.00382853 (26.7451)
Outpt time (%) = 0.00163871 (11.4476)
Other time (%) = 0.00364131 (25.4372)
Nlocal: 105 ave 125 max 85 min
Histogram: 2 0 0 0 0 0 0 0 0 2

16
examples/meam/log.meam.28Mar11.linux.1 → examples/meam/log.meam.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# Test of MEAM potential for SiC system
units metal
@ -8,7 +8,7 @@ atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
128 atoms
pair_style meam
@ -37,13 +37,13 @@ Step Temp E_pair E_mol TotEng Press
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.129397 on 1 procs for 100 steps with 128 atoms
Loop time of 0.0790551 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.122473 (94.6495)
Neigh time (%) = 0.00316429 (2.44541)
Comm time (%) = 0.000795126 (0.614486)
Outpt time (%) = 0.0022583 (1.74525)
Other time (%) = 0.000705719 (0.545391)
Pair time (%) = 0.0747664 (94.5751)
Neigh time (%) = 0.00214291 (2.71065)
Comm time (%) = 0.000567198 (0.717472)
Outpt time (%) = 0.0012064 (1.52602)
Other time (%) = 0.000372171 (0.470775)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0

16
examples/meam/log.meam.28Mar11.linux.4 → examples/meam/log.meam.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# Test of MEAM potential for SiC system
units metal
@ -8,7 +8,7 @@ atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
128 atoms
pair_style meam
@ -37,13 +37,13 @@ Step Temp E_pair E_mol TotEng Press
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.073782 on 4 procs for 100 steps with 128 atoms
Loop time of 0.03332 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.0618048 (83.7668)
Neigh time (%) = 0.000865817 (1.17348)
Comm time (%) = 0.00796497 (10.7953)
Outpt time (%) = 0.00274181 (3.7161)
Other time (%) = 0.000404596 (0.548367)
Pair time (%) = 0.0281992 (84.6316)
Neigh time (%) = 0.000612736 (1.83895)
Comm time (%) = 0.00279725 (8.39511)
Outpt time (%) = 0.00148147 (4.44621)
Other time (%) = 0.000229299 (0.688174)
Nlocal: 32 ave 36 max 30 min
Histogram: 1 2 0 0 0 0 0 0 0 1

80
examples/meam/log.meam.shear.28Mar11.linux.1 → examples/meam/log.meam.shear.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
@ -10,7 +10,7 @@ Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
@ -60,7 +60,7 @@ fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
@ -71,13 +71,13 @@ Step Temp E_pair E_mol TotEng Press Volume
50 300 -8149.7654 0 -8096.1353 10637.302 19676.681
75 304.80657 -8163.4557 0 -8108.9665 7048.2094 19752.029
100 300 -8173.6884 0 -8120.0584 5954.839 19878.848
Loop time of 2.5416 on 1 procs for 100 steps with 1912 atoms
Loop time of 1.46607 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 2.50755 (98.6603)
Neigh time (%) = 0.0220699 (0.868349)
Comm time (%) = 0.00254846 (0.10027)
Outpt time (%) = 0.000214577 (0.00844259)
Other time (%) = 0.00921631 (0.362619)
Pair time (%) = 1.44517 (98.5743)
Neigh time (%) = 0.0143578 (0.979338)
Comm time (%) = 0.00156951 (0.107055)
Outpt time (%) = 6.38962e-05 (0.00435832)
Other time (%) = 0.00490999 (0.334908)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -105,7 +105,7 @@ fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
@ -123,43 +123,43 @@ Step Temp E_pair E_mol TotEng Press Volume
900 303.87706 -8128.16 0 -8091.9576 4388.821 20631.103
1000 300 -8113.4908 0 -8077.7503 6189.061 20747.117
1100 306.13486 -8097.1731 0 -8060.7018 8908.048 20871.68
1200 309.15673 -8081.8589 0 -8045.0276 10527.674 20988.916
1300 304.48416 -8064.5597 0 -8028.2851 10066.832 21118.364
1400 300 -8046.7607 0 -8011.0202 10976.597 21230.714
1500 300 -8041.3545 0 -8005.6141 11944.043 21366.268
1600 309.60362 -8035.2271 0 -7998.3426 11344.441 21522.036
1700 300 -8029.1688 0 -7993.4283 11303.125 21627.406
1800 300 -8034.2214 0 -7998.4809 9637.4925 21728.966
1900 307.8766 -8037.1068 0 -8000.428 6165.8684 21849.865
2000 307.93939 -8029.9415 0 -7993.2552 3171.4159 22004.863
2100 300 -8032.6008 0 -7996.8604 1295.9263 22098.991
2200 300 -8042.3739 0 -8006.6334 1615.3416 22223.554
2300 309.98225 -8040.4009 0 -8003.4713 3571.2277 22340.79
2400 295.53749 -8036.0363 0 -8000.8275 5496.7006 22470.237
2500 300 -8038.9034 0 -8003.163 6990.6617 22588.694
2600 300 -8039.3156 0 -8003.5751 8774.3909 22712.036
2700 300 -8041.8829 0 -8006.1425 8212.4486 22830.493
2800 300 -8041.7538 0 -8006.0133 7007.2322 22956.277
2900 308.45087 -8041.8224 0 -8005.0752 6596.7027 23078.397
3000 304.66557 -8039.5734 0 -8003.2772 3648.991 23201.739
Loop time of 80.2078 on 1 procs for 3000 steps with 1912 atoms
1200 309.15672 -8081.8589 0 -8045.0276 10527.674 20988.916
1300 304.48415 -8064.5597 0 -8028.2851 10066.833 21118.364
1400 300 -8046.7607 0 -8011.0202 10976.596 21230.714
1500 300 -8041.3546 0 -8005.6141 11944.043 21366.268
1600 309.60321 -8035.2271 0 -7998.3426 11344.414 21522.036
1700 300 -8029.1687 0 -7993.4283 11303.058 21627.405
1800 300 -8034.2245 0 -7998.4841 9635.5534 21728.966
1900 307.86145 -8037.1072 0 -8000.4302 6167.8738 21849.865
2000 307.81899 -8029.9421 0 -7993.2701 3170.0159 22004.862
2100 300 -8032.7539 0 -7997.0135 1311.0313 22098.991
2200 300 -8042.5128 0 -8006.7724 1644.7181 22223.554
2300 309.60919 -8041.3003 0 -8004.415 3447.4419 22344.453
2400 303.51436 -8036.8571 0 -8000.698 5476.9727 22461.689
2500 309.82464 -8036.3148 0 -7999.4039 6946.3833 22589.915
2600 308.45257 -8038.9157 0 -8002.1683 9164.9017 22713.257
2700 306.90752 -8041.0584 0 -8004.495 8144.5283 22836.599
2800 308.64671 -8042.8933 0 -8006.1228 8314.2343 22957.498
2900 300 -8044.2363 0 -8008.4959 6534.6291 23077.176
3000 308.55125 -8045.1049 0 -8008.3457 2319.2124 23193.191
Loop time of 46.7216 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 78.7984 (98.2427)
Neigh time (%) = 0.961029 (1.19817)
Comm time (%) = 0.0793548 (0.0989364)
Outpt time (%) = 0.0915716 (0.114168)
Other time (%) = 0.277497 (0.345972)
Pair time (%) = 45.8546 (98.1444)
Neigh time (%) = 0.622606 (1.33259)
Comm time (%) = 0.0498846 (0.10677)
Outpt time (%) = 0.0463471 (0.0991986)
Other time (%) = 0.148106 (0.316996)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1658 ave 1658 max 1658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23414 ave 23414 max 23414 min
Neighs: 23394 ave 23394 max 23394 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46828 ave 46828 max 46828 min
FullNghs: 46788 ave 46788 max 46788 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46828
Ave neighs/atom = 24.4916
Neighbor list builds = 225
Total # of neighbors = 46788
Ave neighs/atom = 24.4707
Neighbor list builds = 222
Dangerous builds = 0

80
examples/meam/log.meam.shear.28Mar11.linux.4 → examples/meam/log.meam.shear.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
@ -10,7 +10,7 @@ Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 processor grid
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
@ -60,7 +60,7 @@ fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
@ -71,13 +71,13 @@ Step Temp E_pair E_mol TotEng Press Volume
50 300 -8152.0635 0 -8098.4335 10060.658 19678.279
75 308.13652 -8164.4552 0 -8109.3706 6520.8872 19773.8
100 300 -8178.2806 0 -8124.6506 4001.6051 19951.128
Loop time of 0.680185 on 4 procs for 100 steps with 1912 atoms
Loop time of 0.400293 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.660636 (97.1258)
Neigh time (%) = 0.00543064 (0.798406)
Comm time (%) = 0.0110168 (1.61968)
Outpt time (%) = 0.000174105 (0.0255967)
Other time (%) = 0.00292808 (0.430482)
Pair time (%) = 0.387236 (96.7382)
Neigh time (%) = 0.00367391 (0.917806)
Comm time (%) = 0.00746405 (1.86465)
Outpt time (%) = 9.32813e-05 (0.0233033)
Other time (%) = 0.00182539 (0.456014)
Nlocal: 478 ave 486 max 469 min
Histogram: 1 0 1 0 0 0 0 0 1 1
@ -105,7 +105,7 @@ fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
@ -126,40 +126,40 @@ Step Temp E_pair E_mol TotEng Press Volume
1200 300.37461 -8081.159 0 -8045.3739 9988.7374 20999.907
1300 307.55251 -8065.2275 0 -8028.5873 10516.036 21126.912
1400 303.2639 -8051.2915 0 -8015.1623 11668.072 21235.599
1500 300 -8039.6298 0 -8003.8893 12498.159 21361.383
1500 300 -8039.6298 0 -8003.8893 12498.158 21361.383
1600 300 -8032.3339 0 -7996.5935 13558.654 21487.167
1700 300 -8021.6093 0 -7985.8689 13720.959 21608.067
1700 300 -8021.6093 0 -7985.8689 13720.956 21608.067
1800 300 -8013.5338 0 -7977.7933 10671.997 21727.745
1900 300 -8014.5801 0 -7978.8397 6968.6165 21849.865
2000 300 -8026.6564 0 -7990.916 3269.5142 21974.428
2100 300 -8033.104 0 -7997.3635 1537.6968 22102.655
2200 306.76458 -8028.5483 0 -7992.002 3816.212 22221.112
2300 300 -8028.9662 0 -7993.2258 3429.3646 22348.117
2400 300 -8035.5372 0 -7999.7968 2897.9007 22464.131
2500 300 -8039.4612 0 -8003.7208 1164.0875 22581.367
2600 303.83211 -8036.4648 0 -8000.2678 2956.6036 22710.815
2700 300 -8037.9929 0 -8002.2524 3272.0339 22824.387
2800 308.111 -8042.3302 0 -8005.6235 1981.3196 22951.392
2900 300 -8039.5639 0 -8003.8235 2710.0878 23079.619
3000 300 -8038.5652 0 -8002.8248 1297.2939 23190.748
Loop time of 21.7748 on 4 procs for 3000 steps with 1912 atoms
1900 300 -8014.5801 0 -7978.8396 6968.6386 21849.865
2000 300 -8026.6571 0 -7990.9167 3269.4443 21974.428
2100 300 -8033.1013 0 -7997.3609 1537.4207 22102.655
2200 307.36281 -8028.6497 0 -7992.0321 3817.5435 22222.333
2300 300 -8027.913 0 -7992.1726 3488.2549 22348.117
2400 300 -8035.0837 0 -7999.3433 2982.0314 22465.353
2500 304.59101 -8038.8331 0 -8002.5457 1690.5828 22581.367
2600 300 -8038.555 0 -8002.8146 1526.8827 22699.824
2700 300 -8040.1447 0 -8004.4043 736.6537 22824.387
2800 308.16594 -8041.4384 0 -8004.7252 -602.64831 22948.95
2900 300 -8038.5929 0 -8002.8524 -884.13202 23067.406
3000 300 -8037.9149 0 -8002.1744 -1850.8904 23201.739
Loop time of 13.031 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 20.9228 (96.087)
Neigh time (%) = 0.237493 (1.09068)
Comm time (%) = 0.435934 (2.00201)
Outpt time (%) = 0.0909243 (0.417566)
Other time (%) = 0.0876888 (0.402707)
Pair time (%) = 12.489 (95.8408)
Neigh time (%) = 0.16103 (1.23574)
Comm time (%) = 0.275773 (2.11628)
Outpt time (%) = 0.049704 (0.381428)
Other time (%) = 0.0554834 (0.425779)
Nlocal: 478 ave 510 max 445 min
Nlocal: 478 ave 511 max 445 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 786 ave 821 max 750 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5752.25 ave 6082 max 5380 min
Histogram: 1 0 0 0 1 0 0 1 0 1
FullNghs: 11504.5 ave 12167 max 10785 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 789 ave 828 max 753 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 5745.75 ave 6118 max 5418 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 11491.5 ave 12238 max 10833 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 46018
Ave neighs/atom = 24.068
Neighbor list builds = 224
Total # of neighbors = 45966
Ave neighs/atom = 24.0408
Neighbor list builds = 222
Dangerous builds = 0

16
examples/melt/log.melt.28Mar11.linux.1 → examples/melt/log.melt.9Jan12.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
units lj
@ -9,7 +9,7 @@ Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 processor grid
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
@ -36,13 +36,13 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 1.26498 on 1 procs for 250 steps with 4000 atoms
Loop time of 0.734027 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 1.06745 (84.3844)
Neigh time (%) = 0.114981 (9.0895)
Comm time (%) = 0.0207102 (1.63719)
Outpt time (%) = 0.0310349 (2.45339)
Other time (%) = 0.0308092 (2.43554)
Pair time (%) = 0.608454 (82.8925)
Neigh time (%) = 0.0777593 (10.5935)
Comm time (%) = 0.0137377 (1.87155)
Outpt time (%) = 0.0153244 (2.08771)
Other time (%) = 0.0187521 (2.55469)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

16
examples/melt/log.melt.28Mar11.linux.4 → examples/melt/log.melt.9Jan12.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (27 Mar 2011)
LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
units lj
@ -9,7 +9,7 @@ Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 processor grid
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
@ -36,13 +36,13 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.404644 on 4 procs for 250 steps with 4000 atoms
Loop time of 0.233054 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.270148 (66.7619)
Neigh time (%) = 0.0298547 (7.37801)
Comm time (%) = 0.0646951 (15.9881)
Outpt time (%) = 0.0312538 (7.72378)
Other time (%) = 0.00869256 (2.1482)
Pair time (%) = 0.160472 (68.8563)
Neigh time (%) = 0.0206246 (8.84973)
Comm time (%) = 0.0306477 (13.1505)
Outpt time (%) = 0.0157282 (6.74875)
Other time (%) = 0.00558102 (2.39473)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2

Some files were not shown because too many files have changed in this diff Show More