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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@647 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-06-22 23:47:25 +00:00
parent e3fa1c4ef6
commit f95ccaf035
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examples/colloid/log.colloid.22Jun07.liberty.4 Normal file
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LAMMPS (22 June 2007)
# 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
868 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
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 10000
Memory usage per processor = 1.45054 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4376 0.0009584 900000
1000 1.8470142 0.0048357172 1.8487715 0.017163086 74830.331
2000 1.9719939 0.18486401 2.1535713 0.79205274 4710.4215
3000 1.8512583 0.19478206 2.0429549 1.2638229 3348.993
4000 2.0197762 0.085599862 2.1020098 0.44423307 6289.5217
5000 2.1100188 0.066582351 2.1730844 0.30071147 7797.8952
6000 2.122322 0.080537323 2.1993221 0.47114461 5829.3235
7000 2.0053017 0.17924225 2.1812018 0.82372251 4418.5393
8000 1.9850765 0.16081341 2.1425814 0.86380905 4218.1246
9000 2.0229633 0.14063325 2.1602249 0.8620141 4223.7169
10000 2.0133665 0.16380502 2.173816 0.95385436 3995.0006
Loop time of 4.86636 on 4 procs for 10000 steps with 900 atoms
Pair time (%) = 1.32706 (27.27)
Neigh time (%) = 0.274084 (5.63221)
Comm time (%) = 1.98481 (40.7863)
Outpt time (%) = 0.0898068 (1.84546)
Other time (%) = 1.1906 (24.466)
Nlocal: 225 ave 232 max 218 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 411.5 ave 428 max 388 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 2307 ave 2410 max 2183 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 9228
Ave neighs/atom = 10.2533
Neighbor list builds = 773
Dangerous builds = 0

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examples/colloid/log.colloid.22Jun07.linux.1 Normal file
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LAMMPS (22 June 2007)
# 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
868 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
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 10000
Memory usage per processor = 1.47629 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4376 0.0009584 900000
1000 1.8470142 0.0048357172 1.8487715 0.017163086 74830.331
2000 1.9719939 0.18486401 2.1535713 0.79205271 4710.4215
3000 1.8760117 0.16888745 2.0417724 1.2866805 3349.4362
4000 2.0084889 0.10591744 2.1110589 0.41080478 6315.195
5000 2.0845189 0.074837406 2.1558821 0.32123703 7787.3569
6000 2.0635646 0.12699208 2.1871174 0.55212245 5811.0643
7000 2.0511741 0.13194486 2.1797003 0.75534937 4447.7483
8000 2.0057569 0.14524464 2.1476586 0.93321505 4260.455
9000 1.9863917 0.16294985 2.1460309 0.85687596 4264.0791
10000 1.9867944 0.17403524 2.1575183 1.019418 3985.5163
Loop time of 13.1171 on 1 procs for 10000 steps with 900 atoms
Pair time (%) = 8.49344 (64.7507)
Neigh time (%) = 1.7079 (13.0204)
Comm time (%) = 0.409296 (3.12032)
Outpt time (%) = 0.224203 (1.70924)
Other time (%) = 2.28229 (17.3993)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9057 ave 9057 max 9057 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9057
Ave neighs/atom = 10.0633
Neighbor list builds = 777
Dangerous builds = 0

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examples/crack/log.crack.22Jun07.liberty.4 Normal file
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LAMMPS (22 June 2007)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
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
create_atoms 1 box
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
820 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
820 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 200
thermo_modify temp new
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 1.59725 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065996472 -3.2595015 0 -3.1984136 -0.04302381 4792.6107
200 0.060047239 -3.2531973 0 -3.1976162 -0.27194148 4811.0322
400 0.060540328 -3.2510659 0 -3.1950283 -0.51122765 4832.8487
600 0.060577107 -3.2468136 0 -3.190742 -0.71796559 4855.0481
800 0.060812364 -3.241354 0 -3.1850647 -0.89095308 4876.899
1000 0.061815921 -3.2349951 0 -3.1777768 -1.0418483 4899.229
1200 0.063180751 -3.227761 0 -3.1692795 -1.1726472 4913.5762
1400 0.065132588 -3.2198103 0 -3.1595221 -1.279378 4933.6517
1600 0.067270882 -3.2111519 0 -3.1488844 -1.3695054 4952.9497
1800 0.0693778 -3.201954 0 -3.1377363 -1.4352657 4975.6762
2000 0.071252815 -3.1921529 0 -3.1261996 -1.4841334 4994.9699
2200 0.073149176 -3.181847 0 -3.1141384 -1.5151492 5011.4455
2400 0.074908709 -3.1710714 0 -3.1017341 -1.5320377 5034.0712
2600 0.076683014 -3.1599865 0 -3.0890069 -1.5392632 5049.8449
2800 0.078565789 -3.1486031 0 -3.0758808 -1.5361716 5070.8919
3000 0.080066913 -3.1368161 0 -3.0627043 -1.5207043 5089.9281
3200 0.081471767 -3.1247706 0 -3.0493584 -1.4971581 5105.9878
3400 0.08330546 -3.1128524 0 -3.035743 -1.4631308 5124.3294
3600 0.08531273 -3.1009259 0 -3.0219584 -1.4242782 5139.7334
3800 0.086420792 -3.0884931 0 -3.0085 -1.3812881 5151.9744
4000 0.085220498 -3.0759708 0 -2.9970887 -1.3501547 5163.5493
4200 0.08235554 -3.0634364 0 -2.9872062 -1.341062 5178.82
4400 0.08347755 -3.0521602 0 -2.9748914 -1.3473183 5192.4176
4600 0.084114334 -3.0389835 0 -2.9611253 -1.3384039 5209.5435
4800 0.085414901 -3.0273902 0 -2.9483282 -1.3365973 5232.9505
5000 0.087614902 -3.0176386 0 -2.9365402 -1.337001 5251.075
Loop time of 7.15681 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 4.67775 (65.3608)
Neigh time (%) = 0.180912 (2.52784)
Comm time (%) = 1.1892 (16.6164)
Outpt time (%) = 0.174089 (2.4325)
Other time (%) = 0.934854 (13.0624)
Nlocal: 2035.25 ave 2062 max 2008 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 204.5 ave 246 max 175 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 17860.5 ave 18270 max 17548 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 71442
Ave neighs/atom = 8.77558
Neighbor list builds = 98
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
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
create_atoms 1 box
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
820 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
820 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 200
thermo_modify temp new
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 2.04243 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065655433 -3.2595015 0 -3.1987293 -0.043381291 4792.6107
200 0.060090071 -3.2531939 0 -3.1975731 -0.27682436 4811.1142
400 0.060537254 -3.2509976 0 -3.1949629 -0.51538634 4833.6384
600 0.060833381 -3.2466952 0 -3.1903864 -0.72165405 4854.5327
800 0.061681012 -3.2413218 0 -3.1842284 -0.89573177 4876.5182
1000 0.062387584 -3.2349276 0 -3.1771802 -1.046532 4897.0644
1200 0.063713197 -3.2276097 0 -3.1686353 -1.1733596 4916.992
1400 0.065408625 -3.2196611 0 -3.1591173 -1.2802996 4937.9378
1600 0.067583821 -3.2110381 0 -3.1484809 -1.3713947 4956.9814
1800 0.069328584 -3.2018539 0 -3.1376817 -1.4389808 4974.9955
2000 0.071019398 -3.192111 0 -3.1263738 -1.4879518 4992.2457
2200 0.072997487 -3.1818704 0 -3.1143022 -1.5204135 5014.7654
2400 0.075005457 -3.1712316 0 -3.1018048 -1.5359222 5031.8024
2600 0.076848328 -3.1601006 0 -3.088968 -1.5313163 5052.4867
2800 0.078676694 -3.148775 0 -3.07595 -1.5154187 5070.2113
3000 0.080718743 -3.137326 0 -3.0626108 -1.4892046 5087.256
3200 0.083100049 -3.1260245 0 -3.0491051 -1.4538734 5106.4445
3400 0.085430328 -3.1146626 0 -3.0355863 -1.4172254 5127.5606
3600 0.087402049 -3.1029496 0 -3.0220482 -1.3687184 5142.5301
3800 0.089013695 -3.0908222 0 -3.0084291 -1.3168466 5156.5957
4000 0.089818767 -3.079408 0 -2.9962696 -1.2722766 5169.2872
4200 0.085852921 -3.0668561 0 -2.9873886 -1.2424995 5184.3213
4400 0.086203112 -3.0559681 0 -2.9761765 -1.2315726 5195.5481
4600 0.086772028 -3.0437629 0 -2.9634447 -1.2220387 5213.9452
4800 0.088200815 -3.0328504 0 -2.9512097 -1.2296115 5232.6714
5000 0.08942145 -3.0228831 0 -2.9401125 -1.2228214 5255.2593
Loop time of 45.1427 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 36.1309 (80.0372)
Neigh time (%) = 1.29244 (2.86301)
Comm time (%) = 0.075937 (0.168216)
Outpt time (%) = 0.437291 (0.968687)
Other time (%) = 7.20605 (15.9628)
Nlocal: 8141 ave 8141 max 8141 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 71389 ave 71389 max 71389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 71389
Ave neighs/atom = 8.76907
Neighbor list builds = 100
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 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/dipole
fix 2 all enforce2d
timestep 0.005
thermo_style dipole
thermo 500
dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
run 10000
Memory usage per processor = 2.32239 Mbytes
Step Temp E_pair RotKEdip TotEng Press
0 0 -2.1284412 0 -2.1284412 -0.98973217
500 0.38229437 -2.703408 0.24548268 -2.3239808 -0.073894217
1000 0.41156476 -2.7426733 0.25757681 -2.3341953 0.05919685
1500 0.43191585 -2.8089326 0.33203347 -2.3802561 -0.16059384
2000 0.43337741 -2.7836977 0.30755109 -2.3535707 -0.050258895
2500 0.41025746 -2.7704617 0.31976882 -2.3632812 -0.040387583
3000 0.4343462 -2.7853843 0.32540887 -2.3542957 -0.040773878
3500 0.4516216 -2.7378372 0.25848559 -2.2896027 0.01498558
4000 0.46812215 -2.7531454 0.25653816 -2.2885341 -0.015167924
4500 0.41857472 -2.7022096 0.27078871 -2.2867742 0.040384474
5000 0.42275097 -2.7173978 0.28129865 -2.2978174 0.08127607
5500 0.39689205 -2.6755268 0.28694074 -2.2816114 -0.063519745
6000 0.40712229 -2.6810855 0.29780556 -2.2770166 -0.010331415
6500 0.42401695 -2.7099716 0.32599472 -2.2891348 -0.080194492
7000 0.46557586 -2.7235207 0.277596 -2.2614366 -0.025483686
7500 0.4634213 -2.7520289 0.33385569 -2.2920833 -0.07670048
8000 0.44330991 -2.6937045 0.28515119 -2.2537194 0.063037221
8500 0.46501497 -2.7192191 0.31059999 -2.2576917 -0.12974997
9000 0.48895857 -2.7113963 0.27823171 -2.2261049 -0.032792109
9500 0.5206475 -2.7393465 0.2997953 -2.2226039 0.15436407
10000 0.47111871 -2.6818528 0.2936091 -2.2142675 -0.18366919
Loop time of 2.70823 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.644681 (23.8045)
Neigh time (%) = 0.0255789 (0.944486)
Comm time (%) = 1.55045 (57.2495)
Outpt time (%) = 0.0430555 (1.5898)
Other time (%) = 0.444467 (16.4117)
Nlocal: 50 ave 53 max 46 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 88.75 ave 91 max 86 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 402.25 ave 443 max 365 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 1609
Ave neighs/atom = 8.045
Neighbor list builds = 700
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 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/dipole
fix 2 all enforce2d
timestep 0.005
thermo_style dipole
thermo 500
dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
run 10000
Memory usage per processor = 2.33154 Mbytes
Step Temp E_pair RotKEdip TotEng Press
0 0 -2.1284412 0 -2.1284412 -0.98973217
500 0.38229437 -2.703408 0.24548268 -2.3239808 -0.073894217
1000 0.41156476 -2.7426733 0.25757681 -2.3341953 0.05919685
1500 0.43191583 -2.8089326 0.33203347 -2.3802561 -0.16059384
2000 0.43342192 -2.7837445 0.30758527 -2.3535733 -0.050298945
2500 0.40678173 -2.7608212 0.32070295 -2.3570903 -0.066209676
3000 0.44085008 -2.7740637 0.3050664 -2.33652 -0.033394791
3500 0.44821249 -2.7478981 0.27867563 -2.3030472 0.0084562338
4000 0.45333935 -2.7563404 0.3084146 -2.3064011 -0.10934119
4500 0.45156284 -2.723795 0.27757494 -2.2756189 -0.23949041
5000 0.48926457 -2.7653696 0.29559023 -2.2797745 0.038474281
5500 0.47000827 -2.7286039 0.28271513 -2.2621207 -0.01679705
6000 0.49865525 -2.7247669 0.24383453 -2.2298516 -0.028697894
6500 0.46877605 -2.6998151 0.25730063 -2.2345548 -0.034887111
7000 0.38249447 -2.6298198 0.31407559 -2.250194 0.010153416
7500 0.4674564 -2.667655 0.25360513 -2.2037046 -0.14832
8000 0.46214985 -2.6953164 0.31284004 -2.2366327 -0.13077442
8500 0.45348969 -2.6629085 0.30178085 -2.21282 0.014011681
9000 0.45748811 -2.6903116 0.33394285 -2.2362547 -0.093496105
9500 0.49014698 -2.7127804 0.32910939 -2.2263096 -0.013973624
10000 0.39914132 -2.6368493 0.35529835 -2.2407016 -0.12272941
Loop time of 6.7855 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 5.39439 (79.4989)
Neigh time (%) = 0.164115 (2.41861)
Comm time (%) = 0.264522 (3.89834)
Outpt time (%) = 0.1165 (1.7169)
Other time (%) = 0.845967 (12.4673)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1615 ave 1615 max 1615 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1615
Ave neighs/atom = 8.075
Neighbor list builds = 697
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
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
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
38 settings made for type/fraction
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
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.3262 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1910653 0 2.391 0.0045085128 141421.36
100 1.9478792 0 2.1256232 0.004563496 124210.22
200 2.3700495 -3.3319106e-05 2.5862832 0.013268829 51975.461
300 1.8455677 -0.099549795 1.8705975 0.043367291 11254.795
400 4.7673362 -0.63680144 4.1000403 2.5967285 2117.5435
500 2.0914283 -3.1875966 -0.98127813 15.054185 716.60631
600 0.16670993 -6.5302264 -6.3521489 -1.2408868 763.95532
700 0.61510434 -6.2651546 -5.6130844 -1.7391671 850.63471
800 4.2400887 -4.7665917 -0.37668829 4.3628579 893.62251
900 0.56540605 -4.0704259 -3.4850161 -1.2625042 1339.0962
1000 4.1072215 -3.5049913 0.78871853 1.3994916 1581.8306
1100 1.002839 -3.4270693 -2.3625765 -0.34931088 2002.5983
1200 2.3739586 -3.2294296 -0.73953462 0.47928761 2137.475
1300 1.755069 -3.2886568 -1.4395111 0.24365268 2147.7339
1400 1.4374762 -3.597546 -2.0874512 0.26707014 1976.8436
1500 2.7207484 -3.4893404 -0.67636594 1.4873069 1672.6682
1600 1.0385312 -4.3747776 -3.2807384 0.10681629 1506.5847
1700 3.3252787 -4.3839001 -0.91852241 1.7513361 1235.5246
1800 1.2745712 -4.7993978 -3.4903396 0.16468564 1129.5996
1900 2.2642602 -4.906129 -2.5944276 2.1651713 988.12263
2000 1.807468 -5.0525829 -3.1803091 0.86237508 964.0263
Loop time of 1.6379 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.785513 (47.9584)
Neigh time (%) = 0.00847417 (0.517379)
Comm time (%) = 0.494713 (30.204)
Outpt time (%) = 0.0563657 (3.44133)
Other time (%) = 0.292839 (17.8789)
Nlocal: 100 ave 109 max 89 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 188.5 ave 199 max 184 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 1116 ave 1233 max 921 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 4464
Ave neighs/atom = 11.16
Neighbor list builds = 106
Dangerous builds = 43
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.3271 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.807468 -5.0525829 -3.1803091 0.86237508 964.0263
2100 1.8124564 -5.0575946 -3.1482012 0.70216467 964.0263
2200 1.7626774 -5.0023408 -3.1505535 0.895245 964.0263
2300 1.7196825 -4.9521 -3.1438517 1.0459072 964.0263
2400 1.7461817 -4.9798462 -3.1713534 0.81729653 964.0263
2500 1.7613354 -4.9981109 -3.1720957 0.75962477 964.0263
2600 1.7938723 -5.0329298 -3.1542958 0.6834629 964.0263
2700 1.6845575 -4.9156511 -3.1602763 1.018788 964.0263
2800 1.8106845 -5.0514857 -3.1552486 0.82016251 964.0263
2900 1.7106648 -4.9415742 -3.172624 0.9661594 964.0263
3000 1.7191328 -4.9501009 -3.1633969 0.68191191 964.0263
3100 1.7105373 -4.9420092 -3.17246 0.54874965 964.0263
3200 1.7495364 -4.9843342 -3.1275575 0.77248303 964.0263
3300 1.7698509 -5.0087562 -3.1389426 0.8145502 964.0263
3400 1.7335983 -4.9691262 -3.1854084 0.79184554 964.0263
3500 1.7048596 -4.9344286 -3.1656937 0.81686942 964.0263
3600 1.759633 -4.9973343 -3.1654564 0.82451312 964.0263
3700 1.8497696 -5.0949098 -3.1884636 0.78672739 964.0263
3800 1.7619814 -4.997269 -3.1385271 1.0176047 964.0263
3900 1.7634023 -5.0041064 -3.1775639 1.058629 964.0263
4000 1.8327776 -5.0805738 -3.2201943 0.76054519 964.0263
Loop time of 1.88218 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 1.11996 (59.5032)
Neigh time (%) = 0.00454992 (0.241736)
Comm time (%) = 0.533296 (28.3339)
Outpt time (%) = 0.0546536 (2.90374)
Other time (%) = 0.169724 (9.01738)
Nlocal: 100 ave 105 max 90 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 188.75 ave 201 max 182 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 1128.75 ave 1184 max 1035 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Total # of neighbors = 4515
Ave neighs/atom = 11.2875
Neighbor list builds = 43
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
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
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
38 settings made for type/fraction
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
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.3468 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1910653 0 2.391 0.0045085128 141421.36
100 1.9478792 0 2.1256232 0.004563496 124210.22
200 2.3700495 -3.3319106e-05 2.5862832 0.013268829 51975.461
300 1.8455677 -0.099549795 1.8705975 0.043367291 11254.795
400 4.7673362 -0.63680144 4.1000403 2.5967285 2117.5435
500 2.0914283 -3.1875966 -0.98127813 15.054185 716.60631
600 0.16670993 -6.5302264 -6.3521489 -1.2408868 763.95532
700 0.61510434 -6.2651546 -5.6130844 -1.7391671 850.63471
800 4.2400887 -4.7665917 -0.37668829 4.3628579 893.62251
900 0.56540605 -4.0704259 -3.4850161 -1.2625042 1339.0962
1000 4.1072215 -3.5049913 0.78871853 1.3994916 1581.8306
1100 1.002839 -3.4270693 -2.3625765 -0.34931088 2002.5983
1200 2.3739586 -3.2294296 -0.73953462 0.47928761 2137.475
1300 1.755069 -3.2886568 -1.4395111 0.24365268 2147.7339
1400 1.4374762 -3.597546 -2.0874512 0.26707014 1976.8436
1500 2.7207484 -3.4893404 -0.67636594 1.4873069 1672.6682
1600 1.0385312 -4.3747776 -3.2807384 0.10681629 1506.5847
1700 3.3252787 -4.3839001 -0.91852241 1.7513361 1235.5246
1800 1.2745711 -4.7993978 -3.4903396 0.16468567 1129.5996
1900 2.2642603 -4.9061291 -2.5944276 2.1651712 988.12263
2000 1.8074681 -5.0525831 -3.180309 0.86237472 964.0263
Loop time of 5.79084 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 4.47783 (77.3261)
Neigh time (%) = 0.055152 (0.9524)
Comm time (%) = 0.092337 (1.59453)
Outpt time (%) = 0.101419 (1.75137)
Other time (%) = 1.0641 (18.3756)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 345 ave 345 max 345 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4464 ave 4464 max 4464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4464
Ave neighs/atom = 11.16
Neighbor list builds = 106
Dangerous builds = 43
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.35512 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.8074681 -5.0525831 -3.180309 0.86237472 964.0263
2100 1.8124563 -5.0575946 -3.1482012 0.70216509 964.0263
2200 1.7626781 -5.0023416 -3.1505538 0.89524393 964.0263
2300 1.7196822 -4.9520998 -3.1438526 1.045906 964.0263
2400 1.7461825 -4.9798453 -3.1713506 0.81731176 964.0263
2500 1.7613208 -4.9980929 -3.1720863 0.75968573 964.0263
2600 1.7938507 -5.0328997 -3.1542798 0.68355324 964.0263
2700 1.6845018 -4.9157085 -3.1604062 1.0187342 964.0263
2800 1.8107758 -5.0515881 -3.1552159 0.8201522 964.0263
2900 1.7106214 -4.9415299 -3.1727682 0.96607251 964.0263
3000 1.7174173 -4.9483503 -3.1634164 0.68480916 964.0263
3100 1.713011 -4.9449497 -3.1743883 0.5448844 964.0263
3200 1.7540834 -4.988469 -3.1263823 0.78165991 964.0263
3300 1.7916136 -5.0322754 -3.1513102 0.74578197 964.0263
3400 1.7470198 -4.9834088 -3.1838699 0.74098826 964.0263
3500 1.6950853 -4.9232007 -3.1647376 0.96347072 964.0263
3600 1.7317637 -4.9664612 -3.1496825 0.91204136 964.0263
3700 1.7217782 -4.9544926 -3.1343126 1.0385551 964.0263
3800 1.8248397 -5.0685779 -3.172072 0.96728742 964.0263
3900 1.7621697 -4.9966809 -3.1392953 0.99972394 964.0263
4000 1.6909581 -4.9165496 -3.1646954 0.85776161 964.0263
Loop time of 7.49334 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 6.37188 (85.0339)
Neigh time (%) = 0.030365 (0.405227)
Comm time (%) = 0.110936 (1.48046)
Outpt time (%) = 0.100005 (1.33459)
Other time (%) = 0.880153 (11.7458)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 334 ave 334 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4415 ave 4415 max 4415 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4415
Ave neighs/atom = 11.0375
Neighbor list builds = 44
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
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
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
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
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.44615 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.0967867 -0.3465085 0 0.43299345 3.3754137 366.96236
1000 1 -0.36129869 0 0.3494156 3.254923 366.96236
1500 1.1299217 -0.37859354 0 0.42445794 3.0386512 366.96236
2000 1 -0.34287549 0 0.3678388 3.1412475 366.96236
2500 1.0894638 -0.38358068 0 0.3907168 2.9575357 366.96236
3000 1 -0.38250431 0 0.32820997 2.9128345 366.96236
3500 1.1577825 -0.41389292 0 0.40895962 3.0892503 366.96236
4000 1 -0.42306155 0 0.28765273 2.5216835 366.96236
4500 1.0340697 -0.39435146 0 0.34057665 2.5709158 366.96236
5000 1 -0.43445662 0 0.27625767 2.7074512 366.96236
5500 1.1091102 -0.45430683 0 0.33395366 2.451199 366.96236
6000 1 -0.41166346 0 0.29905082 2.7464633 366.96236
6500 1.0003563 -0.40533723 0 0.30563029 2.5834633 366.96236
7000 1 -0.3904519 0 0.32026238 2.5201459 366.96236
7500 1.1170747 -0.40190088 0 0.39202009 2.6487896 366.96236
8000 1 -0.46477384 0 0.24594045 2.6442771 366.96236
8500 1.1344912 -0.38276439 0 0.4235347 2.7888644 366.96236
9000 1 -0.39709912 0 0.31361516 2.4730908 366.96236
9500 0.99852413 -0.45682444 0 0.25284093 2.3290285 366.96236
10000 1 -0.45069251 0 0.26002177 2.5361799 366.96236
Loop time of 1.99299 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0893506 (4.48324)
Neigh time (%) = 0.0427105 (2.14304)
Comm time (%) = 1.34109 (67.2904)
Outpt time (%) = 0.165156 (8.28685)
Other time (%) = 0.354682 (17.7964)
Nlocal: 105 ave 115 max 96 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 40.25 ave 44 max 37 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 237.5 ave 296 max 179 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 950
Ave neighs/atom = 2.2619
Neighbor list builds = 984
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
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
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
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
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.0604224 -0.31549525 0 0.4381621 3.1208962 366.96236
1000 1 -0.34356865 0 0.36714563 3.0305145 366.96236
1500 1.1738082 -0.382026 0 0.45221626 2.9197883 366.96236
2000 1 -0.42682511 0 0.28388918 2.8469183 366.96236
2500 1.0256109 -0.41905835 0 0.30985794 2.9371918 366.96236
3000 1 -0.47521752 0 0.23549677 2.5062527 366.96236
3500 1.1314909 -0.4206347 0 0.38353207 2.7478302 366.96236
4000 1 -0.43576251 0 0.27495178 2.6141195 366.96236
4500 1.0005992 -0.42588084 0 0.28525931 2.7421664 366.96236
5000 1 -0.42282912 0 0.28788516 2.7688981 366.96236
5500 1.0686835 -0.4761288 0 0.28339982 2.5689028 366.96236
6000 1 -0.42978507 0 0.28092922 2.6551983 366.96236
6500 1.0786904 -0.43713715 0 0.3295035 2.5141669 366.96236
7000 1 -0.4121221 0 0.29859218 2.594973 366.96236
7500 1.0939854 -0.40293252 0 0.37457856 2.6974983 366.96236
8000 1 -0.45181425 0 0.25890004 2.6049049 366.96236
8500 1.0257333 -0.400669 0 0.32833428 2.5577387 366.96236
9000 1 -0.42858125 0 0.28213304 2.5725646 366.96236
9500 1.0823613 -0.38920599 0 0.38004366 2.6543624 366.96236
10000 1 -0.42341732 0 0.28729697 2.4806728 366.96236
Loop time of 2.27165 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.707011 (31.1232)
Neigh time (%) = 0.278071 (12.2409)
Comm time (%) = 0.108514 (4.77687)
Outpt time (%) = 0.425657 (18.7377)
Other time (%) = 0.752402 (33.1213)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 50 ave 50 max 50 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 955 ave 955 max 955 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 955
Ave neighs/atom = 2.27381
Neighbor list builds = 1003
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
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
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#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
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.44615 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.0778761 -0.35048279 0 0.41557918 2.8792129 369.20271
1000 1 -0.38740705 0 0.32330724 2.2684877 375.93354
1500 1.2052679 -0.37768559 0 0.47891551 1.6193029 376.17118
2000 1 -0.38060118 0 0.33011311 1.4972142 371.27032
2500 1.2211446 -0.39689946 0 0.47098548 1.5612989 364.09539
3000 1 -0.46394625 0 0.24676803 1.5629864 356.17691
3500 1.2338136 -0.5721878 0 0.30470115 1.8177807 344.96808
4000 1 -0.69530976 0 0.015404522 2.3144776 333.06418
4500 1.2279548 -0.72662695 0 0.14609808 2.9985939 323.55709
5000 1 -0.81185506 0 -0.10114077 3.1833009 321.19482
5500 1.2171627 -0.73966198 0 0.12539291 2.711954 325.39659
6000 1 -0.66983997 0 0.040874311 2.1579634 329.73937
6500 1.2267682 -0.66743744 0 0.20444422 2.1114545 331.88829
7000 1 -0.64509348 0 0.065620807 1.9028431 332.49532
7500 1.2202538 -0.6816503 0 0.18560148 2.1227978 329.88213
8000 1 -0.72110847 0 -0.010394181 2.3587956 327.78501
8500 1.2103845 -0.76502979 0 0.095207788 2.5823624 325.21722
9000 1 -0.75191645 0 -0.041202164 2.4020904 324.81713
9500 1.2094179 -0.74196652 0 0.11758403 2.5289414 326.12345
10000 1 -0.7568777 0 -0.046163412 2.5601376 326.60462
Loop time of 2.41079 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.099645 (4.13329)
Neigh time (%) = 0.0237269 (0.984194)
Comm time (%) = 1.25536 (52.0723)
Outpt time (%) = 0.306114 (12.6977)
Other time (%) = 0.725951 (30.1125)
Nlocal: 105 ave 106 max 103 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 43.75 ave 45 max 41 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 276.5 ave 291 max 256 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 1106
Ave neighs/atom = 2.63333
Neighbor list builds = 553
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
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
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#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
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.1036177 -0.37435595 0 0.4100009 2.6003586 369.52344
1000 1 -0.40278179 0 0.30793249 2.0566706 375.56836
1500 1.2346487 -0.41204291 0 0.46543956 1.6254791 376.55032
2000 1 -0.40773469 0 0.3029796 1.5174808 374.73899
2500 1.2225527 -0.43831258 0 0.43057311 1.538442 366.48806
3000 1 -0.49535282 0 0.21536146 1.5818917 355.29347
3500 1.2493993 -0.59973642 0 0.28822953 1.7491905 344.52279
4000 1 -0.67338979 0 0.037324493 2.0787539 332.81149
4500 1.1956948 -0.72693321 0 0.12286419 3.0234335 322.85596
5000 1 -0.74958096 0 -0.038866674 3.2864093 320.05477
5500 1.1735028 -0.73256028 0 0.10146491 2.7725647 321.70778
6000 1 -0.68197653 0 0.028737759 2.4161345 328.01856
6500 1.1989708 -0.63163198 0 0.2204937 2.0979387 331.80767
7000 1 -0.65810386 0 0.052610422 2.1889649 331.12128
7500 1.2335065 -0.65237655 0 0.22429412 2.1016554 330.36358
8000 1 -0.68661166 0 0.024102628 2.1253504 327.99967
8500 1.2297323 -0.72995326 0 0.14403503 2.4289517 324.51364
9000 1 -0.72767623 0 -0.016961948 2.4354045 323.49316
9500 1.2252226 -0.75893761 0 0.1118456 2.5476916 324.00783
10000 1 -0.73637225 0 -0.025657963 2.3491973 324.64848
Loop time of 2.80857 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.736941 (26.239)
Neigh time (%) = 0.15112 (5.38067)
Comm time (%) = 0.100391 (3.57445)
Outpt time (%) = 1.02177 (36.3805)
Other time (%) = 0.798347 (28.4254)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 53 ave 53 max 53 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1128 ave 1128 max 1128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1128
Ave neighs/atom = 2.68571
Neighbor list builds = 558
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
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
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 110 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
860 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1422 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 1.46023 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128
1000 0.088860957 -3.0636883 0 -3.0270758 0.0047805196 1384.4128
2000 0.087112073 -3.066344 0 -3.030452 -0.63632956 1384.4128
3000 0.10058239 -3.0642114 0 -3.0227694 -0.25555813 1384.4128
4000 0.093260137 -3.0555323 0 -3.0171072 -0.40761447 1384.4128
5000 0.11067201 -3.0399212 0 -2.994322 0.066689705 1384.4128
6000 0.10526463 -3.0390544 0 -2.9956832 -0.51522958 1384.4128
7000 0.11541593 -3.0403447 0 -2.992791 -0.41397003 1384.4128
8000 0.10197576 -3.0347747 0 -2.9927585 -0.5486861 1384.4128
9000 0.11134064 -3.0333357 0 -2.9874611 -0.35496419 1384.4128
10000 0.11080628 -3.0436254 0 -2.9979709 -0.46700659 1384.4128
11000 0.11943821 -3.0413975 0 -2.9921865 -0.30699848 1384.4128
12000 0.10413208 -3.0510277 0 -3.0081231 -0.36572201 1384.4128
13000 0.099296169 -3.039397 0 -2.9984849 -0.4947437 1384.4128
14000 0.10330462 -3.0420671 0 -2.9995034 -0.39995589 1384.4128
15000 0.10870951 -3.038746 0 -2.9939554 -0.50477181 1384.4128
16000 0.11417657 -3.0464982 0 -2.9994551 -0.32657064 1384.4128
17000 0.10800189 -3.047902 0 -3.0034029 -0.41936081 1384.4128
18000 0.10829723 -3.0458306 0 -3.0012098 -0.41668893 1384.4128
19000 0.10404908 -3.0526816 0 -3.0098112 -0.41121519 1384.4128
20000 0.10691019 -3.0411759 0 -2.9971266 -0.23642395 1384.4128
Loop time of 8.68844 on 4 procs for 20000 steps with 1722 atoms
Pair time (%) = 3.88408 (44.704)
Neigh time (%) = 0.210725 (2.42535)
Comm time (%) = 3.2323 (37.2023)
Outpt time (%) = 0.152017 (1.74965)
Other time (%) = 1.20932 (13.9187)
Nlocal: 430.5 ave 482 max 375 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 92 ave 117 max 76 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 3601.25 ave 4057 max 3129 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 14405
Ave neighs/atom = 8.36527
Neighbor list builds = 750
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
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
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 110 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
860 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1422 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 1.53816 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128
1000 0.088253389 -3.0560474 0 -3.0196852 0.050420633 1384.4128
2000 0.087864125 -3.0547262 0 -3.0185243 -0.67004561 1384.4128
3000 0.10557467 -3.0607837 0 -3.0172848 -0.221612 1384.4128
4000 0.085491315 -3.0478702 0 -3.012646 -0.42154648 1384.4128
5000 0.10534884 -3.051862 0 -3.0084561 -0.087935136 1384.4128
6000 0.10556767 -3.0559544 0 -3.0124583 -0.54210169 1384.4128
7000 0.098711954 -3.0590419 0 -3.0183705 -0.42838742 1384.4128
8000 0.11529691 -3.0366296 0 -2.9891248 -0.4457814 1384.4128
9000 0.1 -3.0333227 0 -2.9921206 -0.49174903 1384.4128
10000 0.11644796 -3.04181 0 -2.993831 -0.41991946 1384.4128
11000 0.1051652 -3.0340308 0 -2.9907005 -0.61535665 1384.4128
12000 0.10761127 -3.0351207 0 -2.9907826 -0.30937044 1384.4128
13000 0.11361189 -3.0354003 0 -2.9885898 -0.44289723 1384.4128
14000 0.11530172 -3.037545 0 -2.9900383 -0.31673329 1384.4128
15000 0.098629121 -3.0397602 0 -2.9991229 -0.44569024 1384.4128
16000 0.10525229 -3.0429476 0 -2.9995815 -0.29935796 1384.4128
17000 0.10467455 -3.0381932 0 -2.9950651 -0.48920299 1384.4128
18000 0.10817926 -3.0402364 0 -2.9956643 -0.37596363 1384.4128
19000 0.10816167 -3.0452456 0 -3.0006808 -0.35822139 1384.4128
20000 0.11364667 -3.0448494 0 -2.9980246 -0.40159119 1384.4128
Loop time of 36.1633 on 1 procs for 20000 steps with 1722 atoms
Pair time (%) = 28.7323 (79.4516)
Neigh time (%) = 1.38031 (3.81689)
Comm time (%) = 0.367905 (1.01734)
Outpt time (%) = 0.372357 (1.02965)
Other time (%) = 5.31041 (14.6845)
Nlocal: 1722 ave 1722 max 1722 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 146 ave 146 max 146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14398 ave 14398 max 14398 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14398
Ave neighs/atom = 8.36121
Neighbor list builds = 728
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
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
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.44615 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282
1000 0.11576832 -3.0966334 0 -2.9978168 -0.24095347 250.17681
2000 0.11528823 -3.0962223 0 -2.9978155 -0.45030047 250.45856
3000 0.11379051 -3.0840496 0 -2.9869213 -0.5022142 251.7439
4000 0.11595816 -3.085882 0 -2.9869034 -0.047829504 249.09265
5000 0.11272851 -3.0844605 0 -2.9882386 -0.57244294 252.48573
6000 0.12387775 -3.0900283 0 -2.9842898 0.0072734648 249.1402
7000 0.1113616 -3.0914902 0 -2.9964351 -0.12742916 250.29327
8000 0.1167364 -3.0879355 0 -2.9882926 0.20678001 250.17825
9000 0.11504768 -3.0918767 0 -2.9936753 0.35261539 249.40265
10000 0.11864876 -3.0776022 0 -2.976327 0.45724638 249.80407
11000 0.12749806 -3.0769801 0 -2.9681514 0.7106404 248.1776
12000 0.11068569 -3.0664256 0 -2.9719474 0.77940328 248.88714
13000 0.11341039 -3.0596733 0 -2.9628694 1.1566167 249.36303
14000 0.1176102 -3.058063 0 -2.9576743 1.2083863 249.05567
15000 0.12582683 -3.054119 0 -2.9467168 1.052489 254.01804
16000 0.11716129 -3.0359809 0 -2.9359753 1.1111189 259.94912
17000 0.11836208 -3.0276209 0 -2.9265904 1.0821166 257.9832
18000 0.12271609 -3.0171547 0 -2.9124077 1.511924 264.99507
19000 0.11746326 -3.0102961 0 -2.9100328 1.6305608 267.60875
20000 0.12091083 -2.996777 0 -2.893571 1.7996398 268.87085
21000 0.1263182 -2.9950013 0 -2.8871797 1.8539429 271.55393
22000 0.12425331 -2.9761891 0 -2.87013 1.5415686 276.54337
23000 0.11563313 -2.9874945 0 -2.8887934 1.2018805 279.40748
24000 0.11553831 -2.9945403 0 -2.8959201 1.5305748 278.38798
25000 0.11085112 -2.9896742 0 -2.8950548 1.8815906 275.87487
26000 0.12077848 -2.986181 0 -2.883088 1.9122673 275.91918
27000 0.12399848 -2.9814354 0 -2.8755938 1.9167983 278.64025
28000 0.12143106 -3.0225278 0 -2.9188777 0.56589243 290.55803
29000 0.11959029 -3.0121799 0 -2.9101011 0.49660855 295.49221
30000 0.11931566 -3.0215043 0 -2.9196598 0.83146141 294.35452
Loop time of 7.02654 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.4371 (20.4525)
Neigh time (%) = 0.0463696 (0.659921)
Comm time (%) = 4.19698 (59.7304)
Outpt time (%) = 0.106641 (1.51768)
Other time (%) = 1.23945 (17.6395)
Nlocal: 105 ave 125 max 79 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 92.75 ave 104 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 901 ave 1133 max 620 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3604
Ave neighs/atom = 8.58095
Neighbor list builds = 622
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.4468 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11931566 -3.0215043 0 -2.9196598 0.83281489 293.87614
31000 0.1167364 -3.0429651 0 -2.9433222 -0.36091255 293.88145
32000 0.12641731 -3.0639714 0 -2.9560652 -0.46898184 290.09909
33000 0.10706313 -3.0741804 0 -2.9827944 0.00022078579 285.15883
34000 0.11367315 -3.0688054 0 -2.9717772 -0.76240201 289.87707
35000 0.10655807 -3.0627342 0 -2.9717793 -0.26051048 288.22641
36000 0.11703008 -3.0716705 0 -2.971777 -0.1853764 285.83663
37000 0.11221734 -3.0675632 0 -2.9717776 -0.73386022 290.12632
38000 0.11874224 -3.0731334 0 -2.9717784 -0.12687563 285.36376
39000 0.1189778 -3.0733361 0 -2.9717801 -0.25499323 287.084
40000 0.11898338 -3.0620885 0 -2.9605277 -0.62541843 288.73621
41000 0.1167364 -3.0735602 0 -2.9739173 -0.11692923 283.98124
42000 0.11266172 -3.0700831 0 -2.9739183 -0.39632943 286.59658
43000 0.11902827 -3.0755188 0 -2.9739196 -0.57312115 287.53858
44000 0.12554232 -3.0810812 0 -2.9739219 -0.070954433 286.20995
45000 0.11075688 -3.0684563 0 -2.9739174 -0.55071995 288.55119
46000 0.12586051 -3.0707391 0 -2.9633081 -0.48923571 289.30041
47000 0.11671697 -3.0736442 0 -2.9740179 -0.12378289 285.31819
48000 0.10853944 -3.0666634 0 -2.9740172 -0.57661015 289.17231
49000 0.1167364 -3.0679033 0 -2.9682604 -0.28913991 286.84813
50000 0.10777198 -3.0602483 0 -2.9682572 -0.2607135 286.76228
51000 0.10971818 -3.0619099 0 -2.9682576 -0.50602899 289.54807
52000 0.12283301 -3.0731069 0 -2.9682602 -0.17101974 286.39074
53000 0.11323492 -3.0762744 0 -2.9796203 -0.39853784 289.81061
54000 0.12076965 -3.0709553 0 -2.9678698 -0.3939254 288.24037
55000 0.12319168 -3.0730238 0 -2.9678709 -0.17986864 284.15611
56000 0.12040501 -3.0706451 0 -2.9678708 -0.34825544 286.68764
57000 0.12192823 -3.0719452 0 -2.9678707 -0.42539274 287.8374
58000 0.11878678 -3.0692629 0 -2.9678699 -0.24575165 286.73167
59000 0.11418711 -3.0653342 0 -2.9678674 -0.51388179 287.99512
60000 0.11462897 -3.0657114 0 -2.9678673 -0.4538483 288.11403
Loop time of 6.86808 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.4141 (20.5895)
Neigh time (%) = 0.0468405 (0.682003)
Comm time (%) = 4.16007 (60.5711)
Outpt time (%) = 0.107103 (1.55943)
Other time (%) = 1.13996 (16.5979)
Nlocal: 105 ave 122 max 82 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 92 ave 101 max 82 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 888.5 ave 1097 max 643 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3554
Ave neighs/atom = 8.4619
Neighbor list builds = 630
Dangerous builds = 0

169
examples/indent/log.indent.22Jun07.linux.1 Normal file
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LAMMPS (22 June 2007)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
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
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282
1000 0.11979027 -3.0878285 0 -2.9855789 -0.043690155 249.58001
2000 0.12095292 -3.0888211 0 -2.9855791 -0.46999358 251.6098
3000 0.1167364 -3.0841547 0 -2.9845118 -0.41054969 250.8041
4000 0.12249143 -3.1004175 0 -2.9958623 -0.060853986 248.47717
5000 0.10957873 -3.0886367 0 -2.9951034 -0.57642649 251.31708
6000 0.12346008 -3.0985964 0 -2.9932144 -0.072968634 250.46216
7000 0.10994736 -3.0850721 0 -2.9912241 -0.20324168 251.37979
8000 0.11557891 -3.086042 0 -2.9873871 0.22717975 249.49714
9000 0.12016755 -3.084536 0 -2.9819645 0.33218396 248.89256
10000 0.12659552 -3.0852403 0 -2.977182 0.40666454 249.67836
11000 0.12524777 -3.0736607 0 -2.9667528 0.77561215 248.69926
12000 0.11844672 -3.0571177 0 -2.9560149 0.77334207 249.761
13000 0.12031568 -3.0583679 0 -2.9556699 1.2700141 247.59077
14000 0.1167364 -3.0548463 0 -2.9552034 1.0859392 250.18904
15000 0.1167364 -3.0549235 0 -2.9552806 1.2995977 251.78491
16000 0.12471796 -3.0524621 0 -2.9460064 1.6452633 249.66328
17000 0.12078141 -3.0356474 0 -2.9325519 1.9172375 248.00713
18000 0.11737951 -3.0294793 0 -2.9292875 1.984307 254.03132
19000 0.12273273 -3.016492 0 -2.9117309 1.9954892 251.8583
20000 0.12551089 -3.0011944 0 -2.8940619 1.7797455 260.26155
21000 0.12037224 -2.9934253 0 -2.890679 1.3694744 269.07586
22000 0.12174807 -3.0193123 0 -2.9153916 0.94134986 270.00347
23000 0.12706029 -3.0244275 0 -2.9159725 1.1867392 266.05204
24000 0.11467621 -3.0095158 0 -2.9116314 0.73011254 267.48776
25000 0.11535618 -3.0158848 0 -2.91742 1.2611256 266.59514
26000 0.10710521 -3.0133947 0 -2.9219727 0.67441358 268.32045
27000 0.12422208 -3.0164988 0 -2.9104663 1.1543726 268.18532
28000 0.11139527 -3.0072089 0 -2.9121251 1.4607146 265.23157
29000 0.1167364 -3.0085086 0 -2.9088658 1.6594744 265.37526
30000 0.11102647 -3.0064551 0 -2.9116861 1.3943384 268.60718
Loop time of 14.1353 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 10.7241 (75.8675)
Neigh time (%) = 0.304084 (2.15125)
Comm time (%) = 0.321909 (2.27735)
Outpt time (%) = 0.401015 (2.83699)
Other time (%) = 2.38419 (16.867)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 109 ave 109 max 109 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3655 ave 3655 max 3655 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3655
Ave neighs/atom = 8.70238
Neighbor list builds = 616
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11102647 -3.0064551 0 -2.9116861 1.3929673 268.87157
31000 0.12620212 -3.0510755 0 -2.943353 -0.18214813 273.9697
32000 0.11450566 -3.0412855 0 -2.9435467 -0.36947207 273.74363
33000 0.11300395 -3.0666261 0 -2.9701691 -0.36891232 262.29844
34000 0.11360641 -3.0910465 0 -2.9940753 -0.2930611 263.47461
35000 0.11792208 -3.0826962 0 -2.9820413 -0.53020156 264.92677
36000 0.1167364 -3.0791913 0 -2.9795484 -0.28901516 264.42654
37000 0.11195363 -3.075108 0 -2.9795476 -0.35271906 264.6512
38000 0.11608571 -3.0786363 0 -2.9795489 -0.5028598 264.60065
39000 0.1177969 -3.0800557 0 -2.9795076 -0.32434056 263.66269
40000 0.11466668 -3.0774252 0 -2.979549 -0.40950185 263.65927
41000 0.11118976 -3.0744545 0 -2.9795461 -0.58454381 264.39108
42000 0.11460312 -3.0773684 0 -2.9795464 -0.20755902 262.35795
43000 0.11677527 -3.0792261 0 -2.97955 -0.49949012 264.53893
44000 0.11158159 -3.0747894 0 -2.9795466 -0.37452501 263.88851
45000 0.12176422 -3.0834855 0 -2.979551 -0.16070447 262.66164
46000 0.11682005 -3.0792615 0 -2.9795472 -0.63716759 266.07809
47000 0.11262188 -3.0756805 0 -2.9795497 -0.15500292 263.19673
48000 0.12119234 -3.0829975 0 -2.9795512 -0.39672723 263.37224
49000 0.11784014 -3.0801322 0 -2.9795473 -0.42268487 265.07121
50000 0.11675902 -3.0792108 0 -2.9795486 -0.1111771 261.69863
51000 0.11170649 -3.0748959 0 -2.9795465 -0.46340258 263.55401
52000 0.12175858 -3.0834809 0 -2.9795513 -0.48539416 263.47789
53000 0.12074224 -3.0964747 0 -2.9934126 -0.4846085 262.58631
54000 0.11099551 -3.0767379 0 -2.9819953 -0.39099317 263.38816
55000 0.11519489 -3.0803219 0 -2.9819948 -0.38576064 263.5242
56000 0.11716036 -3.0820002 0 -2.9819954 -0.26199121 262.69272
57000 0.10872156 -3.0792099 0 -2.9864083 -0.49564243 267.348
58000 0.12397214 -3.0923068 0 -2.9864877 -0.37680531 262.14403
59000 0.11456625 -3.0842744 0 -2.9864839 -0.30718293 263.3254
60000 0.11413467 -3.0839074 0 -2.9864853 -0.54302442 263.54231
Loop time of 13.6011 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 10.6377 (78.2117)
Neigh time (%) = 0.311073 (2.28711)
Comm time (%) = 0.330723 (2.43159)
Outpt time (%) = 0.267656 (1.9679)
Other time (%) = 2.054 (15.1017)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 101 ave 101 max 101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3570 ave 3570 max 3570 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3570
Ave neighs/atom = 8.5
Neighbor list builds = 630
Dangerous builds = 0

382
examples/indent/log.indent.min.22Jun07.liberty.4 Normal file
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LAMMPS (22 June 2007)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
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
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90392 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.8810645 251.71282
10 0 -3.1820434 0 -3.1820434 -1.3321628 249.7446
20 0 -3.1892762 0 -3.1892762 -1.030012 247.85333
30 0 -3.1906231 0 -3.1906231 -0.90653473 247.85333
38 0 -3.1909329 0 -3.1909329 -0.81496712 247.85333
Loop time of 0.05091 on 4 procs for 38 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -3.17276 -3.19093 -3.19093
Gradient 2-norm init/final= 6.74302 0.251767
Gradient inf-norm init/final= 1.46877 0.0232337
Iterations = 38
Force evaluations = 148
Pair time (%) = 0.00834811 (16.3978)
Neigh time (%) = 0.00015372 (0.301945)
Comm time (%) = 0.0218924 (43.0021)
Outpt time (%) = 0.00391895 (7.69779)
Other time (%) = 0.0165969 (32.6004)
Nlocal: 105 ave 110 max 100 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 84 ave 89 max 79 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 895 ave 900 max 885 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 2
Dangerous builds = 0
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90395 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
38 0 -3.1909329 0 -2.1718641 -0.81877351 246.70109
40 0 -3.169091 0 -2.8877594 -0.54943778 246.70107
50 0 -3.1711852 0 -3.1696057 -0.39685207 246.70204
60 0 -3.1780204 0 -3.1769046 -0.39225544 246.81048
70 0 -3.1800811 0 -3.1793038 -0.31260477 246.81048
80 0 -3.1809088 0 -3.1801828 -0.23455796 246.81048
90 0 -3.1811924 0 -3.1805002 -0.17000885 246.18491
100 0 -3.1812635 0 -3.1805822 -0.14393015 246.18491
103 0 -3.1812545 0 -3.180591 -0.14136212 246.18491
Loop time of 0.080998 on 4 procs for 65 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.17186 -3.18059 -3.18059
Gradient 2-norm init/final= 1621.12 0.469022
Gradient inf-norm init/final= 1193.11 0.272199
Iterations = 65
Force evaluations = 211
Pair time (%) = 0.0118939 (14.6842)
Neigh time (%) = 0.000379205 (0.468166)
Comm time (%) = 0.0308498 (38.0871)
Outpt time (%) = 0.00909978 (11.2346)
Other time (%) = 0.0287753 (35.5259)
Nlocal: 105 ave 111 max 98 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 87 ave 91 max 84 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 896.5 ave 999 max 789 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3586
Ave neighs/atom = 8.5381
Neighbor list builds = 5
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90399 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
103 0 -3.1812545 0 -0.21951029 -0.14159267 245.78405
110 0 -2.9284097 0 -2.6466557 2.4269773 245.78334
120 0 -3.0511214 0 -3.0267128 1.7637829 245.78215
130 0 -3.0919408 0 -3.0831141 1.4860665 245.92571
140 0 -3.1001312 0 -3.0930458 1.4234791 245.92571
150 0 -3.102631 0 -3.0950311 1.4404842 246.21073
160 0 -3.1037978 0 -3.09648 1.5609439 244.44101
170 0 -3.1041785 0 -3.0969724 1.6411134 244.44101
180 0 -3.1042622 0 -3.0971039 1.6655381 244.44101
186 0 -3.1042077 0 -3.0971259 1.6700959 244.44101
Loop time of 0.103969 on 4 procs for 83 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -0.21951 -3.09712 -3.09713
Gradient 2-norm init/final= 1753.54 0.525185
Gradient inf-norm init/final= 923.56 0.20363
Iterations = 83
Force evaluations = 279
Pair time (%) = 0.0159835 (15.3734)
Neigh time (%) = 0.000830472 (0.798769)
Comm time (%) = 0.039287 (37.7872)
Outpt time (%) = 0.0104416 (10.043)
Other time (%) = 0.0374264 (35.9976)
Nlocal: 105 ave 111 max 98 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 95 ave 97 max 92 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 910.5 ave 1001 max 816 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3642
Ave neighs/atom = 8.67143
Neighbor list builds = 11
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90399 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
186 0 -3.1042077 0 1.9876467 1.6726187 244.07233
190 0 -2.7684954 0 -1.1554028 4.8385981 243.82123
200 0 -2.7738026 0 -2.6431045 5.3693642 246.38337
210 0 -2.892911 0 -2.863976 4.4322106 250.63896
220 0 -2.9428319 0 -2.9275563 3.8976868 253.54966
230 0 -2.9566576 0 -2.9427828 3.7470914 255.96648
240 0 -2.9622154 0 -2.9537038 3.6488191 256.62718
250 0 -2.9685121 0 -2.9588966 3.5333392 257.75615
260 0 -2.9851957 0 -2.9793281 3.2459764 258.1143
270 0 -3.0137593 0 -3.0035449 2.8836141 257.01204
280 0 -3.0182039 0 -3.0121893 2.7594651 257.4611
290 0 -3.0271401 0 -3.0194953 2.4173885 260.04588
300 0 -3.0332671 0 -3.0255652 2.4243877 260.04588
310 0 -3.0346445 0 -3.0270706 2.4432531 258.57203
320 0 -3.0355796 0 -3.0277669 2.4110728 258.57203
330 0 -3.0359691 0 -3.0280778 2.3724675 258.57203
340 0 -3.0358963 0 -3.0281771 2.350355 258.57203
350 0 -3.0359324 0 -3.0282261 2.3336342 258.57203
Loop time of 0.229392 on 4 procs for 164 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 1.98765 -3.02822 -3.02823
Gradient 2-norm init/final= 2323.65 0.605547
Gradient inf-norm init/final= 1037.31 0.14972
Iterations = 164
Force evaluations = 579
Pair time (%) = 0.0342199 (14.9176)
Neigh time (%) = 0.00194269 (0.846887)
Comm time (%) = 0.0764942 (33.3465)
Outpt time (%) = 0.0237187 (10.3398)
Other time (%) = 0.0930168 (40.5492)
Nlocal: 105 ave 110 max 100 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 97.5 ave 103 max 92 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 947.25 ave 1037 max 857 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3789
Ave neighs/atom = 9.02143
Neighbor list builds = 25
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90403 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
350 0 -3.0359324 0 6.9766773 2.3291833 259.06614
360 0 -2.335093 0 -1.5707757 8.8885569 259.07026
370 0 -2.5599881 0 -2.4347598 7.565773 259.34078
380 0 -2.7844216 0 -2.7584649 5.7681807 262.33347
390 0 -2.8656166 0 -2.8440742 4.9699457 263.34253
400 0 -2.9109956 0 -2.8923852 4.2490464 265.32325
410 0 -2.9467505 0 -2.9334194 3.7795578 267.03801
420 0 -2.9744267 0 -2.9577148 3.6538838 266.60412
430 0 -2.9926456 0 -2.9736412 3.47796 267.0876
440 0 -2.997545 0 -2.9801205 3.4033732 266.91219
450 0 -2.999611 0 -2.9820253 3.3516037 267.52197
460 0 -2.9987285 0 -2.9829306 3.3110334 267.52197
470 0 -2.9987287 0 -2.9846017 3.1122307 268.32025
480 0 -3.0028832 0 -2.9903847 2.7073161 271.2535
490 0 -3.0065428 0 -2.9942342 2.5293968 272.93505
500 0 -3.0095717 0 -2.996454 2.3893318 274.49155
510 0 -3.0115719 0 -2.9991889 2.3031093 274.994
520 0 -3.0127377 0 -3.0033432 2.2510198 275.25753
530 0 -3.0246486 0 -3.0155041 2.1233648 276.13644
540 0 -3.0313871 0 -3.0223311 2.0234035 276.99491
550 0 -3.0347292 0 -3.024608 1.9491149 277.7476
560 0 -3.0414445 0 -3.0318447 1.8709947 278.24973
570 0 -3.0430604 0 -3.0339769 1.8661497 278.31951
580 0 -3.0439059 0 -3.0348806 1.8551822 278.31951
590 0 -3.0447011 0 -3.0361812 1.8528222 277.66633
600 0 -3.0459159 0 -3.0371266 1.8221349 277.61268
610 0 -3.046738 0 -3.0376993 1.8002546 277.61268
620 0 -3.0485294 0 -3.0387662 1.7551062 278.38429
630 0 -3.0502895 0 -3.0409144 1.6978737 278.68446
631 0 -3.050959 0 -3.0413239 1.6846776 279.02342
Loop time of 0.386644 on 4 procs for 281 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 6.97668 -3.04091 -3.04132
Gradient 2-norm init/final= 3559.61 8.94131
Gradient inf-norm init/final= 1438.88 3.48783
Iterations = 281
Force evaluations = 1001
Pair time (%) = 0.0592298 (15.3189)
Neigh time (%) = 0.00355858 (0.920375)
Comm time (%) = 0.141013 (36.4711)
Outpt time (%) = 0.0428388 (11.0797)
Other time (%) = 0.140004 (36.2099)
Nlocal: 105 ave 121 max 91 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 93 ave 100 max 86 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 918.5 ave 1110 max 728 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3674
Ave neighs/atom = 8.74762
Neighbor list builds = 45
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90445 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
631 0 -3.050959 0 -2.6512973 1.6846776 279.02342
640 0 -2.9724763 0 -2.9385365 2.6808269 279.01768
650 0 -2.9831473 0 -2.9603508 2.6529278 279.3157
660 0 -2.9883088 0 -2.9688882 2.6455144 279.19287
670 0 -2.9901301 0 -2.9719337 2.6833537 279.19287
680 0 -2.9901469 0 -2.973945 2.7672171 278.35898
690 0 -2.9914393 0 -2.9758977 2.8347562 277.52757
700 0 -2.9948972 0 -2.9783768 2.8254108 276.61918
710 0 -2.998313 0 -2.9811357 2.6879262 278.27732
720 0 -3.0011637 0 -2.9837006 2.6342646 278.77996
730 0 -3.0018221 0 -2.9859645 2.6867882 278.53266
740 0 -3.0027142 0 -2.9869511 2.7039706 278.53266
750 0 -3.0033059 0 -2.9872782 2.703748 278.53266
760 0 -3.0033193 0 -2.9872481 2.6988534 278.53266
766 0 -3.0034118 0 -2.987267 2.6950367 278.53266
Loop time of 0.177757 on 4 procs for 135 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.6513 -2.98727 -2.98727
Gradient 2-norm init/final= 390.148 0.682374
Gradient inf-norm init/final= 173.709 0.209763
Iterations = 135
Force evaluations = 454
Pair time (%) = 0.0266486 (14.9915)
Neigh time (%) = 0.000991344 (0.557695)
Comm time (%) = 0.0658523 (37.0461)
Outpt time (%) = 0.0170659 (9.60066)
Other time (%) = 0.0671993 (37.804)
Nlocal: 105 ave 120 max 90 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 93.25 ave 101 max 84 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 951.75 ave 1140 max 744 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3807
Ave neighs/atom = 9.06429
Neighbor list builds = 12
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90445 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
766 0 -3.0034118 0 -2.4108045 2.7094764 277.04827
770 0 -2.8791192 0 -2.7876589 4.0283682 277.04934
780 0 -2.8893782 0 -2.8546005 4.1023299 277.26539
790 0 -2.89497 0 -2.8651108 4.0749194 277.26539
800 0 -2.8939699 0 -2.8709228 4.1282326 277.3396
810 0 -2.9013871 0 -2.8864339 3.9178823 283.50328
820 0 -2.9229391 0 -2.9084604 3.5302579 287.65327
830 0 -2.9466199 0 -2.9297134 3.0931452 288.09455
840 0 -2.9731215 0 -2.9592738 2.6847913 287.70955
850 0 -2.9914172 0 -2.9815521 2.4955367 287.80661
860 0 -3.0193833 0 -3.0131192 2.2721938 289.11983
870 0 -3.0346779 0 -3.0266442 2.0697315 289.28859
880 0 -3.0438692 0 -3.0351998 1.9227994 289.55602
890 0 -3.0586749 0 -3.0486877 1.6182639 291.71842
900 0 -3.0709615 0 -3.0616412 1.451258 292.90302
910 0 -3.0739192 0 -3.0643475 1.4689297 293.25346
920 0 -3.0744679 0 -3.064872 1.4814698 293.25346
930 0 -3.0745289 0 -3.0654103 1.5231812 293.25346
940 0 -3.0747725 0 -3.0657629 1.563189 292.6074
950 0 -3.0747162 0 -3.0658229 1.5643522 292.6074
952 0 -3.0747117 0 -3.0658271 1.564168 292.6074
Loop time of 0.265928 on 4 procs for 186 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.4108 -3.06583 -3.06583
Gradient 2-norm init/final= 492.496 0.683919
Gradient inf-norm init/final= 186.143 0.307738
Iterations = 186
Force evaluations = 690
Pair time (%) = 0.0411488 (15.4737)
Neigh time (%) = 0.00259405 (0.975474)
Comm time (%) = 0.104417 (39.2652)
Outpt time (%) = 0.0248856 (9.35804)
Other time (%) = 0.0928821 (34.9276)
Nlocal: 105 ave 129 max 80 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 95 ave 107 max 83 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 895 ave 1166 max 606 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 33
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
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
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.8810645 251.71282
10 0 -3.1820434 0 -3.1820434 -1.3321628 249.7446
20 0 -3.1892762 0 -3.1892762 -1.030012 247.85333
30 0 -3.1906231 0 -3.1906231 -0.90653473 247.85333
38 0 -3.1909329 0 -3.1909329 -0.81496712 247.85333
Loop time of 0.083943 on 1 procs for 38 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -3.17276 -3.19093 -3.19093
Gradient 2-norm init/final= 6.74302 0.251767
Gradient inf-norm init/final= 1.46877 0.0232337
Iterations = 38
Force evaluations = 148
Pair time (%) = 0.062235 (74.1396)
Neigh time (%) = 0.000978 (1.16508)
Comm time (%) = 0.001545 (1.84053)
Outpt time (%) = 0.006357 (7.573)
Other time (%) = 0.012828 (15.2818)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3580 ave 3580 max 3580 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 2
Dangerous builds = 0
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
38 0 -3.1909329 0 -2.1718641 -0.81877351 246.70109
40 0 -3.169091 0 -2.8877594 -0.54943778 246.70107
50 0 -3.1711852 0 -3.1696057 -0.39685207 246.70204
60 0 -3.1780204 0 -3.1769046 -0.39225544 246.81048
70 0 -3.1800811 0 -3.1793038 -0.31260477 246.81048
80 0 -3.1809088 0 -3.1801828 -0.23455796 246.81048
90 0 -3.1811924 0 -3.1805002 -0.17000885 246.18491
100 0 -3.1812635 0 -3.1805822 -0.14393015 246.18491
103 0 -3.1812545 0 -3.180591 -0.14136212 246.18491
Loop time of 0.130711 on 1 procs for 65 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.17186 -3.18059 -3.18059
Gradient 2-norm init/final= 1621.12 0.469022
Gradient inf-norm init/final= 1193.11 0.272199
Iterations = 65
Force evaluations = 211
Pair time (%) = 0.089035 (68.1159)
Neigh time (%) = 0.002389 (1.8277)
Comm time (%) = 0.002298 (1.75808)
Outpt time (%) = 0.015673 (11.9906)
Other time (%) = 0.021316 (16.3077)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3586 ave 3586 max 3586 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3586
Ave neighs/atom = 8.5381
Neighbor list builds = 5
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
103 0 -3.1812545 0 -0.21951029 -0.14159267 245.78405
110 0 -2.9284097 0 -2.6466557 2.4269773 245.78334
120 0 -3.0511214 0 -3.0267128 1.7637829 245.78215
130 0 -3.0919408 0 -3.0831141 1.4860665 245.92571
140 0 -3.1001312 0 -3.0930458 1.4234791 245.92571
150 0 -3.102631 0 -3.0950311 1.4404842 246.21073
160 0 -3.1037978 0 -3.09648 1.5609439 244.44101
170 0 -3.1041785 0 -3.0969724 1.6411134 244.44101
180 0 -3.1042622 0 -3.0971039 1.6655381 244.44101
186 0 -3.1042077 0 -3.0971259 1.6700959 244.44101
Loop time of 0.174012 on 1 procs for 83 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -0.21951 -3.09712 -3.09713
Gradient 2-norm init/final= 1753.54 0.525185
Gradient inf-norm init/final= 923.56 0.20363
Iterations = 83
Force evaluations = 279
Pair time (%) = 0.119678 (68.7757)
Neigh time (%) = 0.005353 (3.07622)
Comm time (%) = 0.003228 (1.85504)
Outpt time (%) = 0.017629 (10.1309)
Other time (%) = 0.028124 (16.1621)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 107 ave 107 max 107 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3642 ave 3642 max 3642 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3642
Ave neighs/atom = 8.67143
Neighbor list builds = 11
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
186 0 -3.1042077 0 1.9876467 1.6726187 244.07233
190 0 -2.7684954 0 -1.1554028 4.8385981 243.82123
200 0 -2.7738026 0 -2.6431045 5.3693642 246.38337
210 0 -2.892911 0 -2.863976 4.4322106 250.63896
220 0 -2.9428319 0 -2.9275563 3.8976868 253.54966
230 0 -2.9566576 0 -2.9427828 3.7470914 255.96648
240 0 -2.9622154 0 -2.9537038 3.6488191 256.62718
250 0 -2.9685121 0 -2.9588966 3.5333392 257.75615
260 0 -2.9851957 0 -2.9793281 3.2459764 258.1143
270 0 -3.0137593 0 -3.0035449 2.8836141 257.01204
280 0 -3.0182039 0 -3.0121893 2.7594651 257.4611
290 0 -3.0271401 0 -3.0194953 2.4173885 260.04588
300 0 -3.0332671 0 -3.0255652 2.4243877 260.04588
310 0 -3.0346445 0 -3.0270706 2.4432531 258.57203
320 0 -3.0355796 0 -3.0277669 2.4110728 258.57203
330 0 -3.0359691 0 -3.0280778 2.3724675 258.57203
340 0 -3.0358963 0 -3.0281771 2.350355 258.57203
350 0 -3.0359324 0 -3.0282261 2.3336342 258.57203
Loop time of 0.364823 on 1 procs for 164 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 1.98765 -3.02822 -3.02823
Gradient 2-norm init/final= 2323.65 0.605547
Gradient inf-norm init/final= 1037.31 0.149722
Iterations = 164
Force evaluations = 579
Pair time (%) = 0.254752 (69.8289)
Neigh time (%) = 0.012437 (3.40905)
Comm time (%) = 0.007036 (1.92861)
Outpt time (%) = 0.035757 (9.80119)
Other time (%) = 0.054841 (15.0322)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 109 ave 109 max 109 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3789 ave 3789 max 3789 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3789
Ave neighs/atom = 9.02143
Neighbor list builds = 25
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
350 0 -3.0359324 0 6.9766773 2.3291833 259.06614
360 0 -2.335093 0 -1.5707757 8.8885568 259.07026
370 0 -2.5599881 0 -2.4347598 7.565773 259.34078
380 0 -2.7844216 0 -2.7584649 5.7681809 262.33347
390 0 -2.8656166 0 -2.8440742 4.9699456 263.34254
400 0 -2.9109956 0 -2.8923852 4.2490464 265.32325
410 0 -2.9467505 0 -2.9334194 3.7795578 267.03801
420 0 -2.9744267 0 -2.9577148 3.6538839 266.60412
430 0 -2.9926459 0 -2.9736415 3.4779579 267.0876
440 0 -2.9975444 0 -2.9801207 3.4033949 266.91222
450 0 -2.9996115 0 -2.9820253 3.3516145 267.52149
460 0 -2.99873 0 -2.9829304 3.3110697 267.52149
470 0 -2.9987502 0 -2.984601 3.1122612 268.31993
480 0 -3.0028144 0 -2.990299 2.7066551 271.25603
490 0 -3.0064815 0 -2.9941922 2.5269217 272.94586
500 0 -3.0096474 0 -2.9965356 2.3795554 274.42313
510 0 -3.0123415 0 -2.999981 2.2773683 275.06513
520 0 -3.0153983 0 -3.0059828 2.2054397 275.17639
530 0 -3.0265326 0 -3.0171295 2.0959919 276.89139
540 0 -3.0324549 0 -3.0227829 2.0207038 276.89139
550 0 -3.0338293 0 -3.0240046 1.9861902 277.47265
560 0 -3.0373141 0 -3.027647 1.8982732 278.61063
570 0 -3.0418824 0 -3.0325541 1.8690028 278.55645
580 0 -3.0429662 0 -3.0340728 1.8795056 278.36003
590 0 -3.0447406 0 -3.0359543 1.8652644 277.68832
600 0 -3.045522 0 -3.0368802 1.8599157 277.68832
610 0 -3.0461885 0 -3.0374215 1.8228959 277.68832
620 0 -3.0469853 0 -3.0377678 1.7959291 277.9626
630 0 -3.0480444 0 -3.038612 1.7335705 278.37443
631 0 -3.0484588 0 -3.0387787 1.724502 278.37443
Loop time of 0.627039 on 1 procs for 281 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 6.97668 -3.03861 -3.03878
Gradient 2-norm init/final= 3559.61 6.9459
Gradient inf-norm init/final= 1438.88 2.75216
Iterations = 281
Force evaluations = 1000
Pair time (%) = 0.440883 (70.3119)
Neigh time (%) = 0.02191 (3.4942)
Comm time (%) = 0.012146 (1.93704)
Outpt time (%) = 0.060133 (9.58999)
Other time (%) = 0.091967 (14.6669)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 115 ave 115 max 115 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3702 ave 3702 max 3702 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3702
Ave neighs/atom = 8.81429
Neighbor list builds = 43
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
631 0 -3.0484588 0 -2.604481 1.7235776 278.52373
640 0 -2.9643579 0 -2.928693 2.785548 278.5501
650 0 -2.9743774 0 -2.9520339 2.7702732 278.80038
660 0 -2.9814575 0 -2.9643711 2.777993 278.70742
670 0 -2.9873942 0 -2.9725414 2.8285795 277.74776
680 0 -2.9939115 0 -2.9787385 2.8153784 277.37112
690 0 -3.0030163 0 -2.9852712 2.7060285 277.07917
700 0 -3.0038477 0 -2.9869319 2.6884535 277.07917
710 0 -3.0038815 0 -2.9874213 2.6896219 277.07917
720 0 -3.0038761 0 -2.9875543 2.701217 277.07917
730 0 -3.003858 0 -2.9875861 2.7091036 277.07917
740 0 -3.00415 0 -2.987852 2.7243361 276.81523
750 0 -3.0041764 0 -2.9882589 2.7318353 276.72141
760 0 -3.0044009 0 -2.9883898 2.7254417 276.72141
770 0 -3.0045687 0 -2.9885435 2.7179258 276.72141
780 0 -3.00483 0 -2.988598 2.7038145 276.72141
784 0 -3.0048523 0 -2.9886088 2.7008904 276.72141
Loop time of 0.341197 on 1 procs for 153 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.60448 -2.98861 -2.98861
Gradient 2-norm init/final= 419.523 0.776857
Gradient inf-norm init/final= 175.55 0.266814
Iterations = 153
Force evaluations = 523
Pair time (%) = 0.228625 (67.0067)
Neigh time (%) = 0.006238 (1.82827)
Comm time (%) = 0.006256 (1.83354)
Outpt time (%) = 0.050744 (14.8723)
Other time (%) = 0.049334 (14.4591)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 115 ave 115 max 115 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3810 ave 3810 max 3810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3810
Ave neighs/atom = 9.07143
Neighbor list builds = 12
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 1.90811 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
784 0 -3.0048523 0 -2.4268246 2.7001678 276.79547
790 0 -2.8807915 0 -2.8212034 4.0892175 276.79878
800 0 -2.8950546 0 -2.8611291 4.082591 277.02332
810 0 -2.9005828 0 -2.8735631 4.0937007 277.23062
820 0 -2.9033388 0 -2.880864 4.0724241 277.48631
830 0 -2.9144679 0 -2.896527 3.8087147 281.95887
840 0 -2.9296668 0 -2.9129029 3.4437246 286.37863
850 0 -2.9523068 0 -2.9344645 2.7938894 290.46463
860 0 -2.9752409 0 -2.9623271 2.4497341 291.16741
870 0 -2.9878386 0 -2.9774613 2.3988152 288.45049
880 0 -3.0168937 0 -3.0094002 2.2534858 289.05328
890 0 -3.0298392 0 -3.0215958 2.118575 289.37008
900 0 -3.0361898 0 -3.0276031 2.0386889 289.68806
910 0 -3.0444205 0 -3.035322 1.8601706 291.35702
920 0 -3.0593366 0 -3.0505717 1.6181397 291.67077
930 0 -3.0654752 0 -3.0565939 1.571603 292.044
940 0 -3.0712476 0 -3.0620886 1.5718668 291.77651
950 0 -3.0727487 0 -3.0641228 1.5614938 291.98714
960 0 -3.0743601 0 -3.0655064 1.560509 292.20323
970 0 -3.0748867 0 -3.0659016 1.5496073 292.20323
980 0 -3.0752084 0 -3.0661516 1.5372769 292.25778
990 0 -3.0751243 0 -3.0662155 1.5394404 292.25778
991 0 -3.075136 0 -3.0662166 1.5393777 292.25778
Loop time of 0.470478 on 1 procs for 207 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.42682 -3.06622 -3.06622
Gradient 2-norm init/final= 483.942 0.629476
Gradient inf-norm init/final= 212.858 0.27039
Iterations = 207
Force evaluations = 759
Pair time (%) = 0.325699 (69.2273)
Neigh time (%) = 0.01922 (4.08521)
Comm time (%) = 0.009439 (2.00626)
Outpt time (%) = 0.046274 (9.83553)
Other time (%) = 0.069846 (14.8458)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 120 ave 120 max 120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3579 ave 3579 max 3579 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3579
Ave neighs/atom = 8.52143
Neighbor list builds = 38
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Test of MEAM potential for SiC system
units metal
boundary p p p
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
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.55272 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.93784 0 -636.93784 -76401.859
10 1777.5718 -666.27518 0 -637.0945 -150596.32
20 1908.6646 -668.42203 0 -637.08932 -120846.06
30 1937.3373 -668.90047 0 -637.09706 -101367.81
40 2110.906 -671.75978 0 -637.10706 -110475.14
50 2057.8682 -670.89589 0 -637.11385 -107817.44
60 1887.9614 -668.08977 0 -637.09693 -108906.46
70 2036.4427 -670.53667 0 -637.10635 -113836.91
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
Loop time of 0.18309 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.155092 (84.7084)
Neigh time (%) = 0.00145948 (0.797139)
Comm time (%) = 0.0187557 (10.244)
Outpt time (%) = 0.00630403 (3.44313)
Other time (%) = 0.00147808 (0.807296)
Nlocal: 32 ave 35 max 29 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 292.25 ave 307 max 279 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 384.25 ave 432 max 327 min
Histogram: 1 0 0 0 1 0 0 1 0 1
FullNghs: 768.5 ave 859 max 657 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 3074
Ave neighs/atom = 24.0156
Neighbor list builds = 10
Dangerous builds = 10

60
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LAMMPS (22 June 2007)
# Test of MEAM potential for SiC system
units metal
boundary p p p
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
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.65579 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.93784 0 -636.93784 -76401.859
10 1777.5718 -666.27518 0 -637.0945 -150596.32
20 1908.6646 -668.42203 0 -637.08932 -120846.06
30 1937.3373 -668.90047 0 -637.09706 -101367.81
40 2110.906 -671.75978 0 -637.10706 -110475.14
50 2057.8682 -670.89589 0 -637.11385 -107817.44
60 1887.9614 -668.08977 0 -637.09693 -108906.46
70 2036.4427 -670.53667 0 -637.10635 -113836.91
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
Loop time of 0.447923 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.422714 (94.372)
Neigh time (%) = 0.008859 (1.9778)
Comm time (%) = 0.003976 (0.887653)
Outpt time (%) = 0.0087 (1.9423)
Other time (%) = 0.003674 (0.82023)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 541 ave 541 max 541 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1537 ave 1537 max 1537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3074 ave 3074 max 3074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3074
Ave neighs/atom = 24.0156
Neighbor list builds = 10
Dangerous builds = 10

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LAMMPS (22 June 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
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
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
create_atoms 1 box
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 5.05583 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
25 223.02513 -8188.2962 0 -8148.4267 8998.4716 19539.346
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 1.74057 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 1.69932 (97.6299)
Neigh time (%) = 0.00826591 (0.474896)
Comm time (%) = 0.022138 (1.27188)
Outpt time (%) = 0.000750303 (0.0431067)
Other time (%) = 0.0100996 (0.580245)
Nlocal: 478 ave 486 max 469 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 809 ave 818 max 801 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 5932.75 ave 6076 max 5807 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 11865.5 ave 12111 max 11653 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 47462
Ave neighs/atom = 24.8232
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 5.10101 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
100 304.48468 -8173.0606 0 -8136.7859 425.54216 19949.638
200 292.7057 -8176.0355 0 -8141.1641 -420.37567 19967.921
300 300 -8174.2457 0 -8138.5052 -2225.0957 20035.454
400 301.8783 -8169.8228 0 -8133.8586 -954.54062 20072.806
500 297.3529 -8163.9704 0 -8128.5453 -636.90863 20224.627
600 300.21575 -8158.4937 0 -8122.7275 426.04354 20300.212
700 294.62668 -8149.3419 0 -8114.2416 2914.3315 20397.69
800 297.68293 -8140.221 0 -8104.7566 4382.9813 20500.434
900 307.34872 -8129.6288 0 -8093.0129 6273.2975 20626.218
1000 299.54856 -8114.9745 0 -8079.2878 9036.1509 20758.108
1100 298.61047 -8098.7531 0 -8063.1782 10485.79 20872.901
1200 293.03092 -8082.1069 0 -8047.1967 11405.523 21004.792
1300 307.76805 -8065.4274 0 -8028.7615 11979.925 21120.806
1400 300 -8051.592 0 -8015.8516 12466.399 21238.042
1500 308.53314 -8037.7116 0 -8000.9546 15186.116 21363.826
1600 300 -8031.857 0 -7996.1166 16229.579 21487.167
1700 300 -8022.9424 0 -7987.202 18187.876 21605.624
1800 300 -8009.2389 0 -7973.4984 18721.834 21735.072
1900 300.26712 -7997.956 0 -7962.1837 18855.604 21848.644
2000 300 -7987.6035 0 -7951.8631 18711.312 21976.871
2100 300 -7996.1806 0 -7960.4401 16424.414 22100.212
2200 305.54436 -8006.7713 0 -7970.3703 13205.691 22211.342
2300 300 -8010.5965 0 -7974.8561 11455.319 22342.011
2400 300 -8012.9434 0 -7977.2029 12543.014 22469.016
2500 300 -8014.3999 0 -7978.6595 12003.377 22583.809
2600 296.98849 -8009.1337 0 -7973.7521 11080.253 22707.151
2700 300 -8002.4065 0 -7966.666 8890.8608 22836.599
2800 300 -8005.4907 0 -7969.7503 7724.8308 22956.277
2900 308.79197 -8003.0392 0 -7966.2514 8308.48 23072.291
3000 300 -8014.1797 0 -7978.4393 5468.9701 23199.297
Loop time of 54.7884 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 53.2791 (97.2452)
Neigh time (%) = 0.365944 (0.667922)
Comm time (%) = 0.69469 (1.26795)
Outpt time (%) = 0.151946 (0.277333)
Other time (%) = 0.29672 (0.541574)
Nlocal: 478 ave 521 max 447 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 790.5 ave 838 max 745 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 5842.25 ave 6343 max 5608 min
Histogram: 1 2 0 0 0 0 0 0 0 1
FullNghs: 11684.5 ave 12654 max 11231 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 46738
Ave neighs/atom = 24.4446
Neighbor list builds = 225
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
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
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
create_atoms 1 box
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 5.90372 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
25 222.78953 -8188.1215 0 -8148.2941 9099.4735 19539.346
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 8.49319 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 8.38065 (98.6749)
Neigh time (%) = 0.058524 (0.68907)
Comm time (%) = 0.014651 (0.172503)
Outpt time (%) = 0.001071 (0.0126101)
Other time (%) = 0.038294 (0.450879)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1672 ave 1672 max 1672 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23806 ave 23806 max 23806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47612 ave 47612 max 47612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47612
Ave neighs/atom = 24.9017
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 6.13252 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
100 292.43462 -8178.5214 0 -8143.6823 2595.8245 19846.142
200 302.79029 -8177.5966 0 -8141.5238 928.09995 20038.569
300 291.68573 -8173.4974 0 -8138.7474 -1202.8487 20113.221
400 300 -8170.0629 0 -8134.3225 -1617.1537 20115.738
500 308.49792 -8164.7324 0 -8127.9796 -346.62656 20250.005
600 308.95879 -8159.1257 0 -8122.3179 1160.1349 20280.432
700 303.02599 -8150.2418 0 -8114.1409 2807.9227 20434.583
800 305.36804 -8140.8077 0 -8104.4278 3218.2338 20500.434
900 305.593 -8128.943 0 -8092.5363 3121.7248 20628.661
1000 308.39114 -8113.6413 0 -8076.9012 5180.0491 20758.108
1100 304.62199 -8096.7999 0 -8060.5088 8173.3442 20874.123
1200 293.41155 -8082.676 0 -8047.7205 9884.2077 20987.695
1300 303.32764 -8066.7733 0 -8030.6365 10196.38 21108.594
1400 304.17521 -8049.5115 0 -8013.2736 11518.937 21249.033
1500 300 -8038.1747 0 -8002.4342 12554.583 21361.383
1600 304.95273 -8030.5805 0 -7994.2501 12166.296 21483.504
1700 302.82122 -8019.1918 0 -7983.1152 11726.855 21604.403
1800 300 -8010.2021 0 -7974.4617 11039.327 21737.514
1900 309.75034 -7999.8523 0 -7962.9503 10360.771 21859.635
2000 303.95534 -7995.5876 0 -7959.3759 11106.855 21974.428
2100 300 -7998.4845 0 -7962.7441 9592.4431 22092.885
2200 300 -8010.3787 0 -7974.6383 7011.3257 22223.554
2300 300 -8013.8118 0 -7978.0714 7206.5123 22334.684
2400 300 -8016.5277 0 -7980.7872 8333.0814 22469.016
2500 309.73732 -8019.4133 0 -7982.5128 8734.2461 22586.252
2600 300 -8018.1897 0 -7982.4492 9088.9471 22702.266
2700 300.98484 -8016.4337 0 -7980.576 11358.168 22821.944
2800 309.26899 -8013.3976 0 -7976.5529 11582.101 22956.277
2900 305.82563 -8013.711 0 -7977.2765 8649.9858 23077.176
3000 309.93922 -8013.2879 0 -7976.3634 6488.7794 23187.085
Loop time of 270.752 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 266.289 (98.3517)
Neigh time (%) = 2.51321 (0.928236)
Comm time (%) = 0.465902 (0.172077)
Outpt time (%) = 0.345781 (0.127711)
Other time (%) = 1.13779 (0.420235)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1659 ave 1659 max 1659 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23351 ave 23351 max 23351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46702 ave 46702 max 46702 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46702
Ave neighs/atom = 24.4257
Neighbor list builds = 216
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 3d Lennard-Jones melt
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 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
2 by 1 by 2 processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 50 dump.melt
thermo 50
run 250
Memory usage per processor = 1.52225 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6557237 -4.7655254 0 -2.2825608 5.7884064
100 1.6549846 -4.7636783 0 -2.281822 5.7819801
150 1.6390665 -4.7393685 0 -2.2813835 5.925551
200 1.6294936 -4.7247826 0 -2.2811533 5.9482013
250 1.6468354 -4.7510951 0 -2.2814595 5.8749319
Loop time of 0.777116 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.466133 (59.9824)
Neigh time (%) = 0.0471849 (6.0718)
Comm time (%) = 0.186014 (23.9365)
Outpt time (%) = 0.0529453 (6.81305)
Other time (%) = 0.0248383 (3.19622)
Nlocal: 1000 ave 1005 max 995 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 2714.75 ave 2724 max 2701 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 37856.2 ave 38434 max 37299 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 151425
Ave neighs/atom = 37.8563
Neighbor list builds = 12
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 3d Lennard-Jones melt
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 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
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 50 dump.melt
thermo 50
run 250
Memory usage per processor = 2.28877 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
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 4.4047 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 3.68702 (83.7066)
Neigh time (%) = 0.345328 (7.83999)
Comm time (%) = 0.110895 (2.51765)
Outpt time (%) = 0.095988 (2.17922)
Other time (%) = 0.165464 (3.75653)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 1.84779 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673
50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428
100 0.45 0.73037684 0.054821983 1.2346363 7.730955
150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616
200 0.45 0.78466058 0.076912805 1.3110109 10.136457
250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975
300 0.45 0.76794745 0.066716745 1.2841017 12.618422
350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774
400 0.45 0.68493339 0.090717081 1.225088 14.904536
450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896
500 0.45 0.64764573 0.078468194 1.1755514 15.970391
550 0.56476697 0.58160926 0.080519682 1.22619 16.573931
600 0.45 0.58331363 0.088243449 1.1209946 17.103627
650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826
700 0.45 0.52374674 0.085166964 1.0583512 17.640835
750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674
800 0.45 0.50467091 0.090255509 1.0443639 18.600542
850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713
900 0.45 0.48352312 0.097223467 1.0301841 19.049897
950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988
1000 0.45 0.46260893 0.10106179 1.0131082 19.538971
Loop time of 0.292184 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0816203 (27.9345)
Bond time (%) = 0.00599533 (2.0519)
Neigh time (%) = 0.015554 (5.32335)
Comm time (%) = 0.14458 (49.4825)
Outpt time (%) = 0.00397557 (1.36064)
Other time (%) = 0.040459 (13.8471)
Nlocal: 300 ave 302 max 294 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 101.75 ave 105 max 100 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 794 ave 811 max 774 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 3176
Ave neighs/atom = 2.64667
Ave special neighs/atom = 0.5
Neighbor list builds = 93
Dangerous builds = 0
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
dump 1 all atom 500 dump.micelle
reset_timestep 0
run 60000
Memory usage per processor = 1.85934 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785
1000 0.44914716 -1.9350719 0.071373764 -1.4151124 7.1568301
2000 0.45 -2.017979 0.070742172 -1.4977993 4.8375385
3000 0.46278827 -2.0089553 0.058330549 -1.488415 4.820275
4000 0.46714531 -2.0210549 0.057888529 -1.496605 4.2962188
5000 0.44804799 -2.0254175 0.06916971 -1.5087599 4.4157997
6000 0.45761629 -2.0368567 0.076990577 -1.5028219 4.6540238
7000 0.44640723 -2.0461339 0.064790763 -1.5354939 4.4179413
8000 0.45177284 -2.0324404 0.047705359 -1.5335269 4.54304
9000 0.43975305 -2.06401 0.069375126 -1.5554315 3.2833286
10000 0.45308355 -2.0423211 0.056575039 -1.5332289 4.1729746
11000 0.44229664 -2.0436958 0.065042761 -1.5369092 4.3783133
12000 0.4688876 -2.0591494 0.058270214 -1.5325777 3.6811782
13000 0.45151162 -2.0633938 0.053917641 -1.5585289 3.1767412
14000 0.44571931 -2.0503046 0.0570333 -1.5481092 3.5096724
15000 0.45 -2.0837399 0.060991769 -1.5733106 3.1370759
16000 0.45307444 -2.0804646 0.0670541 -1.5609024 3.2516824
17000 0.45880865 -2.072733 0.061534139 -1.5529637 3.3828133
18000 0.45650845 -2.0811023 0.057626785 -1.5675377 2.8631577
19000 0.45645839 -2.1137579 0.058378793 -1.5994913 2.6678277
20000 0.44760402 -2.109567 0.06512585 -1.5973966 2.3558292
21000 0.43651289 -2.0863769 0.057529291 -1.5928803 3.0018852
22000 0.43440649 -2.0950161 0.063482231 -1.5976704 2.3233803
23000 0.44572794 -2.0887627 0.061323772 -1.5822681 2.9579923
24000 0.44306777 -2.0843912 0.050176466 -1.5917008 2.8496622
25000 0.45 -2.1051658 0.061328265 -1.5944 2.1179388
26000 0.45552583 -2.119375 0.058663998 -1.6057546 2.2945202
27000 0.43912671 -2.1066914 0.051902852 -1.6162108 2.1491613
28000 0.45168054 -2.1078102 0.067816662 -1.5888776 2.4300025
29000 0.44173014 -2.0804191 0.05137384 -1.5878673 3.0500294
30000 0.44407338 -2.0998759 0.053922142 -1.6024355 2.7183453
31000 0.4431566 -2.1102821 0.061544598 -1.6061349 2.7379786
32000 0.45 -2.1163285 0.060739023 -1.606152 2.0727532
33000 0.46444105 -2.1050315 0.062866914 -1.5783041 1.9114822
34000 0.44581302 -2.0954209 0.063239112 -1.5869261 2.3525995
35000 0.45 -2.1261175 0.060452019 -1.616228 2.014967
36000 0.43470345 -2.1034119 0.063748152 -1.6055037 2.6086075
37000 0.44671396 -2.093898 0.057613863 -1.5901286 2.9715819
38000 0.45751276 -2.1085734 0.058845472 -1.592787 2.5044165
39000 0.44786323 -2.1130108 0.056041424 -1.609666 2.1432
40000 0.43937694 -2.1125665 0.04967594 -1.6240628 2.5594741
41000 0.45 -2.1083933 0.0547275 -1.6042283 2.4651511
42000 0.43287348 -2.1009617 0.054318981 -1.6143103 2.1496725
43000 0.44945469 -2.1285428 0.05863553 -1.6210144 2.2786034
44000 0.44737235 -2.0967009 0.058373014 -1.5915148 2.7502707
45000 0.45401167 -2.110646 0.059341015 -1.5978608 1.9203458
46000 0.43451455 -2.1077912 0.060728016 -1.6130918 2.3294588
47000 0.44822719 -2.1295807 0.061997031 -1.6199168 2.1463667
48000 0.43300738 -2.1029353 0.064025843 -1.6064433 2.1373309
49000 0.44657342 -2.1237489 0.060905756 -1.616828 2.0319341
50000 0.4677882 -2.1242266 0.059790209 -1.597233 2.5375996
51000 0.45536082 -2.0986081 0.052858152 -1.5909583 2.562239
52000 0.45919514 -2.1064277 0.057955 -1.5898515 2.3499751
53000 0.46449938 -2.1195508 0.060178993 -1.595453 2.5406265
54000 0.43682602 -2.1035311 0.069334917 -1.5979162 2.6919587
55000 0.45 -2.0965463 0.055320603 -1.5917882 2.5110927
56000 0.44913495 -2.1210973 0.058848556 -1.6136752 1.8246708
57000 0.44307699 -2.1361861 0.066761708 -1.6269012 2.4928119
58000 0.45181349 -2.1311357 0.05656415 -1.6233228 2.1515038
59000 0.45 -2.1345398 0.060573082 -1.6245292 1.715299
60000 0.45068289 -2.1230762 0.055943523 -1.6170131 2.1657885
Loop time of 22.1561 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 7.33887 (33.1235)
Bond time (%) = 0.358887 (1.61981)
Neigh time (%) = 1.42228 (6.41939)
Comm time (%) = 10.1198 (45.675)
Outpt time (%) = 0.320405 (1.44613)
Other time (%) = 2.59584 (11.7162)
Nlocal: 300 ave 308 max 291 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 207 ave 218 max 195 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 2467.25 ave 2570 max 2397 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 9869
Ave neighs/atom = 8.22417
Ave special neighs/atom = 0.5
Neighbor list builds = 4885
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 1.7704 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673
50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428
100 0.45 0.73037684 0.054821983 1.2346363 7.730955
150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616
200 0.45 0.78466058 0.076912805 1.3110109 10.136457
250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975
300 0.45 0.76794745 0.066716745 1.2841017 12.618422
350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774
400 0.45 0.68493339 0.090717081 1.225088 14.904536
450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896
500 0.45 0.64764573 0.078468194 1.1755514 15.970391
550 0.56476697 0.58160926 0.080519682 1.22619 16.573931
600 0.45 0.58331363 0.088243449 1.1209946 17.103627
650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826
700 0.45 0.52374674 0.085166964 1.0583512 17.640835
750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674
800 0.45 0.50467091 0.090255509 1.0443639 18.600542
850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713
900 0.45 0.48352312 0.097223467 1.0301841 19.049897
950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988
1000 0.45 0.46260893 0.10106179 1.0131082 19.538971
Loop time of 0.846992 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.503286 (59.4204)
Bond time (%) = 0.041896 (4.94645)
Neigh time (%) = 0.107992 (12.7501)
Comm time (%) = 0.026696 (3.15186)
Outpt time (%) = 0.00491 (0.579699)
Other time (%) = 0.162212 (19.1515)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 193 ave 193 max 193 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3176 ave 3176 max 3176 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3176
Ave neighs/atom = 2.64667
Ave special neighs/atom = 0.5
Neighbor list builds = 93
Dangerous builds = 0
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
dump 1 all atom 500 dump.micelle
reset_timestep 0
run 60000
Memory usage per processor = 1.85432 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785
1000 0.44914708 -1.9350711 0.071372351 -1.4151131 7.156807
2000 0.45270543 -2.0004904 0.066419058 -1.4819318 5.5702827
3000 0.46916283 -2.0213933 0.065872359 -1.4869445 5.0060597
4000 0.43945376 -2.0166598 0.067641209 -1.5101142 4.6396644
5000 0.45495437 -2.0447226 0.066285498 -1.5240515 3.9305266
6000 0.44963328 -2.056045 0.068450242 -1.5385235 3.8603798
7000 0.44856129 -2.0414287 0.058586674 -1.5348414 3.9952578
8000 0.43667749 -2.0567464 0.065334814 -1.5552799 4.2727683
9000 0.45682384 -2.0679034 0.060201786 -1.5514488 3.9267838
10000 0.45 -2.0518982 0.055746513 -1.5467142 4.0952215
11000 0.45708142 -2.0867219 0.069796539 -1.5604153 2.9408563
12000 0.45241478 -2.0660119 0.05984197 -1.5543207 3.1690286
13000 0.44107393 -2.0641661 0.05983938 -1.5638041 3.505816
14000 0.44110861 -2.097022 0.051901352 -1.6045634 3.1530067
15000 0.46350177 -2.0714176 0.060468155 -1.548027 3.1473645
16000 0.44655044 -2.1091366 0.063286789 -1.5998576 3.01513
17000 0.4669612 -2.0818303 0.06033586 -1.5551169 3.5882255
18000 0.46094826 -2.1157008 0.066505672 -1.5888231 2.3269852
19000 0.44560596 -2.0990576 0.065162589 -1.5888461 2.8984257
20000 0.44208903 -2.0909757 0.059515289 -1.589924 2.8119311
21000 0.45155589 -2.0997977 0.059798723 -1.5890075 2.8373688
22000 0.4454493 -2.1064356 0.057219664 -1.6043234 2.5646073
23000 0.44607005 -2.0965713 0.061416631 -1.5896422 2.4608998
24000 0.46538564 -2.1045166 0.05774363 -1.5819691 2.3150363
25000 0.45936625 -2.1067378 0.056323997 -1.5916218 2.048119
26000 0.44475849 -2.1039936 0.062084383 -1.5977067 2.6218634
27000 0.44698457 -2.0984145 0.055709014 -1.5962797 2.9317131
28000 0.43517932 -2.0913271 0.064117709 -1.5925741 2.8086074
29000 0.45647804 -2.1041742 0.062494065 -1.5857727 3.1137153
30000 0.46315669 -2.0956986 0.062535694 -1.5705852 2.7393652
31000 0.45 -2.1057734 0.06440468 -1.5919312 2.6231226
32000 0.45070852 -2.1035845 0.058447795 -1.5949916 2.4537766
33000 0.45666657 -2.1082739 0.062668872 -1.5895093 2.3000181
34000 0.45 -2.1016598 0.058047346 -1.594175 2.7045891
35000 0.45761633 -2.1166321 0.05661317 -1.6029746 2.4867114
36000 0.4472238 -2.1032503 0.058087856 -1.5984977 2.5708579
37000 0.45 -2.0862798 0.060216086 -1.5766262 3.0682877
38000 0.46457862 -2.111786 0.050899355 -1.5968888 2.3837735
39000 0.4461965 -2.0958328 0.065822692 -1.5843713 2.9356665
40000 0.44099466 -2.1082333 0.052068542 -1.6157214 2.7461117
41000 0.44708215 -2.1138114 0.061595428 -1.6056927 2.7512054
42000 0.45300055 -2.1160106 0.060484049 -1.6030923 2.1170549
43000 0.44584477 -2.1016681 0.065545873 -1.5908347 2.7168769
44000 0.44874855 -2.0962255 0.060190909 -1.587847 2.4701379
45000 0.43208001 -2.0985058 0.059429899 -1.607536 3.4135814
46000 0.43328324 -2.068705 0.062466255 -1.5734971 3.1729387
47000 0.46070055 -2.1056376 0.054706613 -1.5908063 2.4710329
48000 0.44818286 -2.1037138 0.060858877 -1.5952323 2.2822087
49000 0.43421688 -2.0920093 0.05524275 -1.6030924 2.9802749
50000 0.44919305 -2.118617 0.054774617 -1.6152108 2.1728215
51000 0.44744615 -2.1090016 0.059814306 -1.6023004 2.3189772
52000 0.45486735 -2.1082261 0.055067991 -1.5988594 2.2933516
53000 0.46483852 -2.1205596 0.059875293 -1.5964269 2.4109235
54000 0.43582273 -2.0939722 0.056892621 -1.6018017 2.9757336
55000 0.45654728 -2.1024753 0.062836674 -1.583662 2.3343503
56000 0.45942073 -2.0961849 0.053090528 -1.584248 2.8313158
57000 0.44650252 -2.092082 0.052991549 -1.5931461 3.0447824
58000 0.46418464 -2.1277093 0.060472378 -1.6036325 1.7271421
59000 0.45 -2.1304819 0.057808836 -1.6232356 1.6864115
60000 0.45599586 -2.1338576 0.053131762 -1.6253 2.201508
Loop time of 81.32 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 56.0068 (68.8721)
Bond time (%) = 2.55027 (3.1361)
Neigh time (%) = 9.86523 (12.1314)
Comm time (%) = 2.19366 (2.69756)
Outpt time (%) = 0.727356 (0.894437)
Other time (%) = 9.97665 (12.2684)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 396 ave 396 max 396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9650 ave 9650 max 9650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9650
Ave neighs/atom = 8.04167
Ave special neighs/atom = 0.5
Neighbor list builds = 4890
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 1.44958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.6248859 0 2.3657391 10.863748
100 3.3056095 -0.90010417 0 2.3993073 34.161569
200 3.3179673 -0.91237776 0 2.3993683 33.885931
300 3.2898718 -0.88383768 0 2.3998656 34.100539
400 3.3040789 -0.8979868 0 2.3998969 33.870872
500 3.3858715 -0.98323293 0 2.39629 33.00502
600 3.3016075 -0.89577331 0 2.3996436 34.094211
700 3.3530103 -0.94642636 0 2.4002971 33.706321
800 3.2765339 -0.87171428 0 2.3986761 34.272397
900 3.4084164 -1.0031926 0 2.398833 32.606983
1000 3.3077995 -0.90272314 0 2.3988743 33.989676
Loop time of 0.362762 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0987712 (27.2276)
Neigh time (%) = 0.0306859 (8.45897)
Comm time (%) = 0.164804 (45.4305)
Outpt time (%) = 0.0234722 (6.47043)
Other time (%) = 0.0450281 (12.4126)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 170.75 ave 175 max 167 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 1943 ave 1984 max 1900 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 7772
Ave neighs/atom = 9.715
Neighbor list builds = 204
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 5
thermo 5
minimize 0.001 100 1000
Memory usage per processor = 1.90765 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3077995 -0.90272314 0 2.3988743 33.989676
1005 3.3077995 -2.4349846 0 0.86661284 12.143512
1010 3.3077995 -2.7077137 0 0.59388372 7.3653436
1015 3.3077995 -2.8095165 0 0.49208093 5.52331
1020 3.3077995 -2.8698628 0 0.43173457 4.5567353
1025 3.3077995 -2.9017222 0 0.3998752 4.1175547
1030 3.3077995 -2.9229662 0 0.37863118 3.8267031
1034 3.3077995 -2.9342146 0 0.36738284 3.7139314
Loop time of 0.072973 on 4 procs for 34 steps with 800 atoms
Minimization stats:
E initial, next-to-last, final = -0.902723 -2.93279 -2.93421
Gradient 2-norm init/final= 1904.03 19.9961
Gradient inf-norm init/final= 304.285 6.47018
Iterations = 34
Force evaluations = 140
Pair time (%) = 0.0167579 (22.9645)
Neigh time (%) = 0.00157726 (2.16143)
Comm time (%) = 0.0223088 (30.5713)
Outpt time (%) = 0.0142592 (19.5404)
Other time (%) = 0.0180699 (24.7624)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 171 ave 172 max 170 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1828.5 ave 1839 max 1816 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 7314
Ave neighs/atom = 9.1425
Neighbor list builds = 10
Dangerous builds = 0

107
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LAMMPS (22 June 2007)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 1.47247 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.6248859 0 2.3657391 10.863748
100 3.3056095 -0.90010417 0 2.3993073 34.161569
200 3.3179673 -0.91237776 0 2.3993683 33.885931
300 3.2898718 -0.88383768 0 2.3998656 34.100539
400 3.3040789 -0.8979868 0 2.3998969 33.870872
500 3.3858715 -0.98323293 0 2.39629 33.00502
600 3.3016074 -0.89577327 0 2.3996436 34.094211
700 3.3530108 -0.94642681 0 2.4002971 33.706316
800 3.2765414 -0.87172188 0 2.398676 34.272332
900 3.4086632 -1.003472 0 2.3988 32.603903
1000 3.3011881 -0.89596181 0 2.3990365 34.054429
Loop time of 1.1982 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.771744 (64.4089)
Neigh time (%) = 0.216457 (18.0653)
Comm time (%) = 0.034888 (2.91171)
Outpt time (%) = 0.051374 (4.28762)
Other time (%) = 0.123732 (10.3265)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 314 ave 314 max 314 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7777 ave 7777 max 7777 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7777
Ave neighs/atom = 9.72125
Neighbor list builds = 204
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 5
thermo 5
minimize 0.001 100 1000
Memory usage per processor = 1.96838 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3011881 -0.89596181 0 2.3990365 34.054429
1005 3.3011881 -2.4401696 0 0.85482874 12.041862
1010 3.3011881 -2.7166328 0 0.5783655 7.1580172
1015 3.3011881 -2.8220746 0 0.47292374 5.2831538
1020 3.3011881 -2.8767531 0 0.41824521 4.4303385
1025 3.3011881 -2.9059245 0 0.3890739 4.0379055
1030 3.3011881 -2.9263769 0 0.36862144 3.7665159
1033 3.3011881 -2.9347626 0 0.3602357 3.6756741
Loop time of 0.181051 on 1 procs for 33 steps with 800 atoms
Minimization stats:
E initial, next-to-last, final = -0.895962 -2.93317 -2.93476
Gradient 2-norm init/final= 1920.78 20.9248
Gradient inf-norm init/final= 304.283 7.73109
Iterations = 33
Force evaluations = 134
Pair time (%) = 0.1206 (66.6111)
Neigh time (%) = 0.01161 (6.41256)
Comm time (%) = 0.003518 (1.9431)
Outpt time (%) = 0.025866 (14.2866)
Other time (%) = 0.019457 (10.7467)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 317 ave 317 max 317 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7334 ave 7334 max 7334 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7334
Ave neighs/atom = 9.1675
Neighbor list builds = 10
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
2 by 2 by 1 processor grid
create_atoms 1 box
Created 160 atoms
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
40 settings made for type
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000
Memory usage per processor = 1.55792 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.4265 0.52159515 291.72051
1000 1.0781851 0.3767373 0 1.4448145 3.341071 291.72051
2000 1.1353421 0.31826705 0 1.4429653 3.0572956 291.72051
3000 1.030567 0.33822461 0 1.35913 3.0754292 291.72051
4000 1.084434 0.22978281 0 1.3040503 2.9985039 291.72051
5000 1.0301138 0.29805878 0 1.3185153 2.9303247 291.72051
6000 1.0077497 0.25076216 0 1.2490642 2.6414909 291.72051
7000 0.94139392 0.25553029 0 1.1880986 2.5455354 291.72051
8000 0.99185449 0.20276353 0 1.1853194 2.3004842 291.72051
9000 0.98667899 0.19320088 0 1.1706297 2.3286929 291.72051
10000 0.8694539 0.30351063 0 1.1648134 2.8869823 291.72051
11000 0.91957626 0.26311283 0 1.1740681 2.482322 291.72051
12000 0.96816147 0.24842003 0 1.207505 2.5968204 291.72051
13000 0.99305932 0.27827402 0 1.2620234 2.6008086 291.72051
14000 0.96964013 0.32524077 0 1.2857905 2.7589889 291.72051
15000 1.0406234 0.27494524 0 1.3058128 2.9745583 291.72051
16000 1.0563876 0.30415531 0 1.3506393 2.9591999 291.72051
17000 1.1546609 0.26606543 0 1.4099014 2.6835151 291.72051
18000 1.1446667 0.23591973 0 1.3698552 2.5639461 291.72051
19000 1.0933319 0.32022608 0 1.403308 2.9400962 291.72051
20000 1.0496919 0.27302946 0 1.3128805 2.8111569 291.72051
21000 1.0045344 0.30920696 0 1.3043239 2.9781411 291.72051
22000 1.1738476 0.17013633 0 1.3329791 2.1044152 291.72051
23000 1.0772052 0.30975242 0 1.3768589 3.0931004 291.72051
24000 1.0736648 0.25699966 0 1.3205988 2.7170813 291.72051
25000 0.97012122 0.32820484 0 1.2892312 2.7960758 291.72051
26000 1.0135594 0.22519064 0 1.2292479 2.2619809 291.72051
27000 0.86643886 0.26495984 0 1.1232758 2.6357446 291.72051
28000 0.87485679 0.21153951 0 1.0781945 2.3944736 291.72051
29000 0.8794958 0.20903385 0 1.0802844 2.4996412 291.72051
30000 0.95021338 0.1785099 0 1.119815 2.1001022 291.72051
31000 0.89467667 0.30930983 0 1.1955989 2.7732651 291.72051
32000 0.9996451 0.27049753 0 1.260771 2.5230927 291.72051
33000 1.1456535 0.19262378 0 1.3275368 2.5191339 291.72051
34000 1.1172695 0.30009096 0 1.4068861 2.9083508 291.72051
35000 1.1782712 0.33658625 0 1.5038112 3.2710349 291.72051
36000 1.2175616 0.33888092 0 1.5450279 2.9095564 291.72051
37000 1.1251235 0.46373017 0 1.5783056 3.5548553 291.72051
38000 1.258536 0.33742417 0 1.5841613 2.9829523 291.72051
39000 1.1674319 0.35037031 0 1.5068575 3.4103837 291.72051
40000 1.1300951 0.30391857 0 1.4234191 2.9007945 291.72051
41000 1.0079916 0.33954008 0 1.3380817 2.7537688 291.72051
42000 0.98741084 0.28566374 0 1.2638176 2.7612619 291.72051
43000 0.97625215 0.22170786 0 1.1888077 2.4375962 291.72051
44000 0.93659924 0.23779606 0 1.1656147 2.4336161 291.72051
45000 0.95304289 0.25561996 0 1.1997281 2.6384297 291.72051
46000 1.0028816 0.2345278 0 1.2280074 2.0876811 291.72051
47000 0.93735189 0.28467325 0 1.2132375 2.7980605 291.72051
48000 0.94622747 0.24014997 0 1.1775066 2.307812 291.72051
49000 0.89706269 0.31167999 0 1.2003327 3.0336271 291.72051
50000 0.91583019 0.29328288 0 1.2005272 2.6667222 291.72051
Loop time of 9.10519 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.15942 (1.75087)
Neigh time (%) = 0.107759 (1.18349)
Comm time (%) = 5.86661 (64.4315)
Outpt time (%) = 0.052742 (0.579252)
Other time (%) = 2.91866 (32.0549)
Nlocal: 40 ave 43 max 37 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 36.75 ave 39 max 32 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 86.75 ave 97 max 75 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 347
Ave neighs/atom = 2.16875
Neighbor list builds = 5065
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 160 atoms
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
40 settings made for type
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000
Memory usage per processor = 1.5625 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.4265 0.52159515 291.72051
1000 1.1192431 0.32152228 0 1.4302725 3.0849273 291.72051
2000 1.0722145 0.32792208 0 1.3900846 2.7359267 291.72051
3000 1.0803269 0.21497546 0 1.2851743 2.2834162 291.72051
4000 1.083557 0.23095583 0 1.3043545 2.5848777 291.72051
5000 1.0659096 0.23578138 0 1.2916981 2.7308093 291.72051
6000 0.97914922 0.28414151 0 1.2541112 2.8350724 291.72051
7000 0.94345331 0.24801991 0 1.1826283 2.2781061 291.72051
8000 0.91284482 0.21572014 0 1.120007 2.3373662 291.72051
9000 0.90773857 0.20179507 0 1.1010236 2.0423789 291.72051
10000 0.88145472 0.18125755 0 1.0544486 2.3362039 291.72051
11000 0.87571013 0.12262143 0 0.99012178 1.6880068 291.72051
12000 0.80074028 0.22956229 0 1.0227956 2.6468191 291.72051
13000 0.7825286 0.26841268 0 1.0436051 2.4945056 291.72051
14000 0.79211256 0.25282461 0 1.0375111 2.5466413 291.72051
15000 0.86932228 0.19819701 0 1.0593694 2.2687924 291.72051
16000 0.95832898 0.20737909 0 1.1567237 2.4392205 291.72051
17000 0.8874087 0.27245064 0 1.1515399 2.6651657 291.72051
18000 0.92215327 0.22555391 0 1.139062 2.3727549 291.72051
19000 0.93403801 0.28658997 0 1.2118714 2.6635906 291.72051
20000 1.0282451 0.28503838 0 1.3036437 2.8944077 291.72051
21000 1.1053745 0.30936149 0 1.4043731 3.050874 291.72051
22000 1.1681036 0.33179109 0 1.4889437 2.963996 291.72051
23000 1.0853893 0.39394314 0 1.4691569 3.1671499 291.72051
24000 1.1704699 0.35809955 0 1.5175963 2.8419242 291.72051
25000 1.1918317 0.37475072 0 1.5554089 3.0968822 291.72051
26000 1.168098 0.34965423 0 1.5068013 3.1272861 291.72051
27000 1.1354617 0.31857532 0 1.443392 3.0609084 291.72051
28000 1.1876004 0.23206863 0 1.4085352 2.7389154 291.72051
29000 1.079827 0.36142889 0 1.4311325 3.191018 291.72051
30000 1.0753913 0.33649265 0 1.4018022 3.0008887 291.72051
31000 1.0696975 0.24250732 0 1.3021764 2.5570239 291.72051
32000 0.98836403 0.27036659 0 1.2494647 2.6083143 291.72051
33000 0.88065423 0.36359233 0 1.2359904 3.1970968 291.72051
34000 0.98597162 0.25219858 0 1.2289267 2.498528 291.72051
35000 1.0112914 0.22672846 0 1.228539 2.493751 291.72051
36000 0.93127567 0.28243389 0 1.2049789 2.7373743 291.72051
37000 0.82187438 0.35141767 0 1.165587 3.1778458 291.72051
38000 0.9521639 0.25784465 0 1.201082 2.5899557 291.72051
39000 0.95037029 0.29516101 0 1.2366216 2.4676855 291.72051
40000 0.95260903 0.27577233 0 1.2194507 2.6339219 291.72051
41000 1.0486929 0.22025027 0 1.2591117 2.542758 291.72051
42000 1.0345116 0.25222001 0 1.2770331 2.4358793 291.72051
43000 0.98585285 0.26611246 0 1.2427229 2.5447851 291.72051
44000 0.97750213 0.28088531 0 1.2492234 2.7728279 291.72051
45000 0.89570157 0.3129666 0 1.200271 2.4704519 291.72051
46000 0.98786766 0.20874738 0 1.1873538 2.2601725 291.72051
47000 0.88635928 0.31043687 0 1.1884865 2.7900499 291.72051
48000 0.9178394 0.24146658 0 1.1507012 2.6352068 291.72051
49000 0.96622547 0.17283616 0 1.1300033 1.9782123 291.72051
50000 0.90751608 0.19739424 0 1.0964024 2.2519054 291.72051
Loop time of 5.69224 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 1.09039 (19.1556)
Neigh time (%) = 0.683712 (12.0113)
Comm time (%) = 0.57192 (10.0474)
Outpt time (%) = 0.09878 (1.73535)
Other time (%) = 3.24744 (57.0503)
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 348 ave 348 max 348 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 348
Ave neighs/atom = 2.175
Neighbor list builds = 5070
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
4 by 1 by 1 processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 35 atoms, new total = 805
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 770
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.44234 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0006918 0 0 0.68683847 0.48039951 733.92473
1000 1 -0.3603446 0 0.32601904 1.5725867 779.90508
2000 1 -0.42832732 0 0.25803632 1.3587382 813.11821
3000 1 -0.47232806 0 0.21403558 1.4341388 844.88084
4000 1 -0.52763648 0 0.15872716 1.5459739 875.13499
5000 1 -0.48314311 0 0.20322052 1.4357888 907.02154
6000 1 -0.472141 0 0.21422264 1.3030726 924.98416
7000 1 -0.44830722 0 0.23805641 1.2882909 928.95817
8000 1 -0.43371728 0 0.25264635 1.132775 927.35692
9000 1 -0.41463177 0 0.27173186 1.1209309 921.76003
10000 1 -0.38315652 0 0.30320712 1.0966664 922.24088
11000 1 -0.37156486 0 0.31479878 1.1423804 919.78903
12000 1 -0.3742195 0 0.31214414 1.0593775 928.05099
13000 1 -0.38124076 0 0.30512288 1.1256769 929.73097
14000 1 -0.38555026 0 0.30081337 1.0946739 933.53885
15000 1 -0.40703488 0 0.27932876 1.0764066 930.2934
16000 1 -0.3725232 0 0.31384044 1.0011147 931.1519
17000 1 -0.38470452 0 0.30165912 0.99838577 928.91833
18000 1 -0.40199729 0 0.28436634 1.0888096 932.68523
19000 1 -0.37259199 0 0.31377165 0.97032094 938.58622
20000 1 -0.44719826 0 0.23916537 1.0118322 936.68972
21000 1 -0.39518804 0 0.29117559 1.0584198 935.59526
22000 1 -0.36368989 0 0.32267374 1.0593392 935.25352
23000 1 -0.41084354 0 0.27552009 0.9952792 936.90123
24000 1 -0.39025763 0 0.29610601 1.014413 941.44567
25000 1 -0.36909647 0 0.31726717 0.9812463 940.90255
Loop time of 4.74776 on 4 procs for 25000 steps with 770 atoms
Pair time (%) = 0.368852 (7.76898)
Neigh time (%) = 0.124334 (2.6188)
Comm time (%) = 1.96391 (41.365)
Outpt time (%) = 0.360654 (7.59629)
Other time (%) = 1.93001 (40.6509)
Nlocal: 192.5 ave 240 max 158 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 42.5 ave 45 max 37 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 401.25 ave 559 max 288 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 1605
Ave neighs/atom = 2.08442
Neighbor list builds = 1636
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 35 atoms, new total = 805
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 770
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.4637 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0087541 0 0 0.69237216 0.48426997 733.92473
1000 1 -0.37498059 0 0.31138304 1.5619007 780.16609
2000 1 -0.42018277 0 0.26618087 1.381975 813.7446
3000 1 -0.49158436 0 0.19477928 1.4950838 846.60042
4000 1 -0.50974647 0 0.17661717 1.6968335 877.90837
5000 1 -0.48739676 0 0.19896688 1.372862 906.72222
6000 1 -0.45489776 0 0.23146588 1.1850408 922.1588
7000 1 -0.44298261 0 0.24338103 1.2353271 922.55214
8000 1 -0.39106076 0 0.29530287 1.2129774 923.79013
9000 1 -0.36894699 0 0.31741665 1.1022787 925.88908
10000 1 -0.40366483 0 0.28269881 1.0425088 924.55991
11000 1 -0.37662826 0 0.30973537 1.0605386 924.15634
12000 1 -0.39748408 0 0.28887956 1.1069709 926.1591
13000 1 -0.40533845 0 0.28102518 1.0999422 931.71451
14000 1 -0.39364952 0 0.29271412 0.98434706 935.98322
15000 1 -0.38545757 0 0.30090607 1.0288972 936.10741
16000 1 -0.34970581 0 0.33665783 1.0686207 939.12879
17000 1 -0.35935376 0 0.32700987 0.96188021 939.41127
18000 1 -0.38218429 0 0.30417934 0.97219528 939.42804
19000 1 -0.35002145 0 0.33634218 0.96884865 941.93045
20000 1 -0.37936966 0 0.30699398 1.0604325 935.73258
21000 1 -0.3797544 0 0.30660924 1.0525308 936.59648
22000 1 -0.37015981 0 0.31620383 1.0908613 935.05927
23000 1 -0.39940438 0 0.28695925 1.0860163 932.28118
24000 1 -0.36738604 0 0.3189776 0.97212319 936.04359
25000 1 -0.36023241 0 0.32613123 1.0971047 938.21817
Loop time of 9.91214 on 1 procs for 25000 steps with 770 atoms
Pair time (%) = 3.48576 (35.1666)
Neigh time (%) = 0.841295 (8.48752)
Comm time (%) = 0.288146 (2.907)
Outpt time (%) = 0.994089 (10.029)
Other time (%) = 4.30285 (43.4099)
Nlocal: 770 ave 770 max 770 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1637 ave 1637 max 1637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1637
Ave neighs/atom = 2.12597
Neighbor list builds = 1632
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-05
brick FFT buffer size/proc = 4312 960 3696
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 8.97394 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2794 E_long = -33907.9417 Press = -845.4771
---------------- Step 50 ----- CPU = 1.0767 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774
E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80748e-07
6 0.997 1.06201e-06
8 1.08 6.20434e-07
10 1.111 6.23399e-07
12 1.08 2.68045e-07
14 0.96 0
18 0.957201 5.38002e-06
31 104.52 0.000502303
---------------- Step 100 ----- CPU = 2.1741 (sec) ----------------
TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656
PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271
E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634
---------------- Step 150 ----- CPU = 3.3006 (sec) ----------------
TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698
E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18831e-07
6 0.997 1.50909e-07
8 1.08 6.58563e-08
10 1.111 5.56695e-07
12 1.08 1.99338e-07
14 0.96 0
18 0.957201 3.59689e-06
31 104.52 0.000388134
---------------- Step 200 ----- CPU = 4.4047 (sec) ----------------
TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480
PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209
E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571
---------------- Step 250 ----- CPU = 5.5320 (sec) ----------------
TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530
PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972
E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340
E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78173e-06
6 0.997001 3.51761e-06
8 1.08 2.09202e-06
10 1.111 5.64179e-06
12 1.08 2.10252e-06
14 0.96 0
18 0.957202 7.62675e-06
31 104.52 0.00080599
---------------- Step 300 ----- CPU = 6.6418 (sec) ----------------
TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484
PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644
E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075
E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013
Loop time of 6.64219 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 3.83138 (57.6825)
Bond time (%) = 0.0190526 (0.286843)
Kspce time (%) = 1.23672 (18.6191)
Neigh time (%) = 0.383302 (5.77072)
Comm time (%) = 0.699462 (10.5306)
Outpt time (%) = 0.0126947 (0.191122)
Other time (%) = 0.459581 (6.91913)
FFT time (% of Kspce) = 0.217534 (17.5896)
FFT Gflps 3d 1d-only = 0.756267 3.92102
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177008 ave 180559 max 170208 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-05
brick FFT buffer size/proc = 10648 3375 5808
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 20.1003 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2794 E_long = -33907.9417 Press = -845.4771
---------------- Step 50 ----- CPU = 7.7456 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774
E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80748e-07
6 0.997 1.06201e-06
8 1.08 6.20434e-07
10 1.111 6.23399e-07
12 1.08 2.68045e-07
14 0.96 0
18 0.957201 5.38002e-06
31 104.52 0.000502303
---------------- Step 100 ----- CPU = 15.4121 (sec) ----------------
TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656
PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271
E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634
---------------- Step 150 ----- CPU = 23.2155 (sec) ----------------
TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698
E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18831e-07
6 0.997 1.50909e-07
8 1.08 6.58563e-08
10 1.111 5.56695e-07
12 1.08 1.99338e-07
14 0.96 0
18 0.957201 3.59689e-06
31 104.52 0.000388134
---------------- Step 200 ----- CPU = 30.6635 (sec) ----------------
TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480
PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209
E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571
---------------- Step 250 ----- CPU = 38.4972 (sec) ----------------
TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530
PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972
E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340
E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78173e-06
6 0.997001 3.51761e-06
8 1.08 2.09202e-06
10 1.111 5.64179e-06
12 1.08 2.10252e-06
14 0.96 0
18 0.957202 7.62675e-06
31 104.52 0.00080599
---------------- Step 300 ----- CPU = 46.2639 (sec) ----------------
TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484
PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644
E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075
E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013
Loop time of 46.2643 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 37.5374 (81.1369)
Bond time (%) = 0.079241 (0.171279)
Kspce time (%) = 3.3838 (7.31405)
Neigh time (%) = 4.46671 (9.65476)
Comm time (%) = 0.320268 (0.692257)
Outpt time (%) = 0.01816 (0.0392527)
Other time (%) = 0.458701 (0.991479)
FFT time (% of Kspce) = 1.13484 (33.5375)
FFT Gflps 3d 1d-only = 0.144967 0.198071
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708030 ave 708030 max 708030 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
Memory usage per processor = 0.335693 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1424.6738 13.243803 6600
4000 804 1725.4319 47.250762 6600
5000 804 1605.2015 60.084404 6600
6000 804 1371.3425 69.247899 6600
7000 1206 1524.3574 74.071529 6600
8000 1206 1418.8997 60.727536 6600
9000 1206 1258.0238 52.045974 6600
10000 1608 1387.2361 50.17452 6600
11000 1608 1226.8131 50.547962 6600
12000 1608 1195.97 41.951622 6600
13000 2010 1312.7197 51.888514 6600
14000 2010 1176.2242 43.086598 6600
15000 2010 972.7316 46.053358 6600
16000 2412 1040.0907 45.535472 6600
17000 2412 1033.3053 37.798831 6600
18000 2412 929.20314 37.574869 6600
19000 2814 1010.9926 38.716555 6600
20000 2814 953.49259 41.76949 6600
21000 2814 768.81045 45.76655 6600
22000 2814 501.98827 42.18076 6600
23000 3000 428.98535 35.914834 6600
24000 3000 365.81359 22.320118 6600
25000 3000 227.404 23.276402 6600
Loop time of 12.9955 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 4.94591 (38.0586)
Neigh time (%) = 0.678777 (5.22316)
Comm time (%) = 3.9515 (30.4066)
Outpt time (%) = 0.122208 (0.940388)
Other time (%) = 3.29713 (25.3713)
Nlocal: 750 ave 766 max 734 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 388.75 ave 395 max 386 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 3588.5 ave 3661 max 3520 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 14354
Ave neighs/atom = 4.78467
Neighbor list builds = 1154
Dangerous builds = 0
unfix ins
fix 2 all gravity chute 26.0
run 25000
Memory usage per processor = 6.82838 Mbytes
Step Atoms KinEng RotKEgrn Volume
25000 3000 227.404 23.276402 6600
26000 3000 106.43826 18.101442 6600
27000 3000 113.05348 12.760864 6600
28000 3000 205.07328 11.584573 6600
29000 3000 358.43804 15.113582 6600
30000 3000 598.64933 20.578979 6600
31000 3000 873.5316 28.461109 6600
32000 3000 1170.5204 31.532882 6600
33000 3000 1527.4366 38.434515 6600
34000 3000 1984.9084 46.821444 6600
35000 3000 2510.0466 50.236977 6600
36000 3000 3115.8979 66.529363 6600
37000 3000 3828.8672 78.585843 6600
38000 3000 4614.202 90.003111 6600
39000 3000 5443.9784 97.5867 6600
40000 3000 6277.0696 109.40245 6600
41000 3000 7205.7543 116.90896 6600
42000 3000 8231.9822 123.54846 6600
43000 3000 9341.3262 139.91668 6600
44000 3000 10540.217 154.5832 6600
45000 3000 11634.026 163.89013 6600
46000 3000 12939.113 172.01293 6600
47000 3000 14117.982 183.04471 6600
48000 3000 15405.59 211.29982 6600
49000 3000 16780.191 197.48907 6600
50000 3000 18147.971 232.52213 6600
Loop time of 23.7168 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 10.9603 (46.2134)
Neigh time (%) = 1.05963 (4.46785)
Comm time (%) = 5.99627 (25.2828)
Outpt time (%) = 0.196248 (0.827465)
Other time (%) = 5.5043 (23.2085)
Nlocal: 750 ave 757 max 742 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 401.5 ave 412 max 390 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 3645.75 ave 3775 max 3584 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 14583
Ave neighs/atom = 4.861
Neighbor list builds = 825
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
Memory usage per processor = 0.335693 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1424.6738 13.243803 6600
4000 804 1725.9135 47.193854 6600
5000 804 1605.9404 61.336034 6600
6000 804 1364.6108 67.554058 6600
7000 1206 1511.4113 74.376707 6600
8000 1206 1418.8901 57.72159 6600
9000 1206 1256.2845 48.910044 6600
10000 1608 1398.3246 51.447622 6600
11000 1608 1247.546 48.387594 6600
12000 1608 1182.5307 42.323247 6600
13000 2010 1308.4067 48.900862 6600
14000 2010 1184.2874 44.83509 6600
15000 2010 1005.943 39.943887 6600
16000 2412 1031.9872 47.786837 6600
17000 2412 1032.5851 40.540687 6600
18000 2412 919.78138 36.200329 6600
19000 2814 1017.0854 35.573349 6600
20000 2814 964.17268 41.63371 6600
21000 2814 748.30864 44.884418 6600
22000 2814 531.66082 40.886555 6600
23000 3000 415.96265 35.009259 6600
24000 3000 363.92132 18.910655 6600
25000 3000 223.50386 24.163325 6600
Loop time of 75.6189 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 40.9621 (54.1691)
Neigh time (%) = 4.96025 (6.55953)
Comm time (%) = 2.47589 (3.27417)
Outpt time (%) = 0.225462 (0.298155)
Other time (%) = 26.9953 (35.6991)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 675 ave 675 max 675 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13637 ave 13637 max 13637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13637
Ave neighs/atom = 4.54567
Neighbor list builds = 1153
Dangerous builds = 0
unfix ins
fix 2 all gravity chute 26.0
run 25000
Memory usage per processor = 7.24008 Mbytes
Step Atoms KinEng RotKEgrn Volume
25000 3000 223.50386 24.163325 6600
26000 3000 116.7995 18.613728 6600
27000 3000 122.40388 11.057402 6600
28000 3000 231.29589 11.189183 6600
29000 3000 394.03717 14.367314 6600
30000 3000 647.20427 22.016262 6600
31000 3000 908.91364 28.607326 6600
32000 3000 1271.4653 30.481316 6600
33000 3000 1667.4275 41.693229 6600
34000 3000 2165.6715 50.388564 6600
35000 3000 2742.9875 52.867314 6600
36000 3000 3313.9686 64.802217 6600
37000 3000 4043.4311 73.963901 6600
38000 3000 4826.4345 82.469868 6600
39000 3000 5665.19 95.419726 6600
40000 3000 6555.0312 105.12519 6600
41000 3000 7541.9934 121.4346 6600
42000 3000 8632.6663 129.37799 6600
43000 3000 9666.568 132.68521 6600
44000 3000 10825.138 153.12413 6600
45000 3000 12010.686 165.13241 6600
46000 3000 13364.225 184.80686 6600
47000 3000 14694.757 196.08109 6600
48000 3000 16083.771 220.53678 6600
49000 3000 17548.113 228.11249 6600
50000 3000 19103.087 244.48465 6600
Loop time of 155.24 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 93.0545 (59.9425)
Neigh time (%) = 7.81717 (5.03555)
Comm time (%) = 5.47774 (3.52857)
Outpt time (%) = 0.403527 (0.259938)
Other time (%) = 48.4867 (31.2335)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 766 ave 766 max 766 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13994 ave 13994 max 13994 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13994
Ave neighs/atom = 4.66467
Neighbor list builds = 833
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
2 by 2 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 90.0 -90.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
Memory usage per processor = 0.335693 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3240.26 51.002089 5000
7000 672 3375.857 86.854847 5000
8000 672 3218.9668 120.74194 5000
9000 672 3042.428 99.125785 5000
10000 896 2986.9988 88.590035 5000
11000 896 2829.9982 65.795595 5000
12000 896 2742.1752 65.335529 5000
13000 1000 2701.7207 61.182084 5000
14000 1000 2478.5724 53.465798 5000
15000 1000 2079.7846 63.176195 5000
16000 1000 1440.481 54.982049 5000
17000 1000 809.4817 47.009446 5000
18000 1000 588.67412 33.215005 5000
19000 1000 259.55248 27.403802 5000
20000 1000 39.743003 14.941136 5000
21000 1000 20.085002 8.8303457 5000
22000 1000 11.861124 6.1014125 5000
23000 1000 11.065631 3.3946532 5000
24000 1000 5.1323063 2.011498 5000
25000 1000 2.6809517 1.3185775 5000
Loop time of 7.24504 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.30585 (18.024)
Neigh time (%) = 0.24281 (3.35139)
Comm time (%) = 1.61472 (22.2872)
Outpt time (%) = 0.187656 (2.59012)
Other time (%) = 3.89401 (53.7472)
Nlocal: 250 ave 501 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5.75 ave 13 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 620 ave 1246 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2480
Ave neighs/atom = 2.48
Neighbor list builds = 1606
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 90.0 -90.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
Memory usage per processor = 0.320435 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3240.26 51.002089 5000
7000 672 3375.857 86.854847 5000
8000 672 3218.9668 120.74194 5000
9000 672 3042.428 99.125785 5000
10000 896 2986.9988 88.590036 5000
11000 896 2829.9925 65.792313 5000
12000 896 2742.7084 65.819834 5000
13000 1000 2708.5986 57.322444 5000
14000 1000 2465.496 61.169722 5000
15000 1000 2053.8397 61.691032 5000
16000 1000 1462.2958 51.138602 5000
17000 1000 829.85835 42.214656 5000
18000 1000 598.95282 32.11476 5000
19000 1000 246.95726 30.259864 5000
20000 1000 36.390829 15.37906 5000
21000 1000 16.970773 8.7787109 5000
22000 1000 11.318963 5.9319445 5000
23000 1000 5.8086775 3.5214371 5000
24000 1000 4.5594534 2.588639 5000
25000 1000 2.1765737 0.75876888 5000
Loop time of 24.7627 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 9.848 (39.7695)
Neigh time (%) = 1.90215 (7.68151)
Comm time (%) = 0.123851 (0.500152)
Outpt time (%) = 0.407864 (1.64709)
Other time (%) = 12.4808 (50.4017)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2469 ave 2469 max 2469 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2469
Ave neighs/atom = 2.469
Neighbor list builds = 1600
Dangerous builds = 0

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LAMMPS (22 June 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.41797 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722842e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.02681437 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.058989 0 5269.4979 12.062708
9750 16738.013 0.1355011 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270524 0 5269.5237 11.395098
9900 16738.489 -0.00024984559 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 1.84118 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0128225 (0.696429)
Neigh time (%) = 0.0221436 (1.20268)
Comm time (%) = 1.1992 (65.1324)
Outpt time (%) = 0.0962372 (5.22693)
Other time (%) = 0.510773 (27.7416)
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 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 = 998
Dangerous builds = 997

306
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LAMMPS (22 June 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.50411 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722836e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.1355012 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270518 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.92229 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.079705 (8.64208)
Neigh time (%) = 0.123638 (13.4055)
Comm time (%) = 0.108608 (11.7759)
Outpt time (%) = 0.176786 (19.1682)
Other time (%) = 0.433553 (47.0083)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 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 = 998
Dangerous builds = 997

306
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LAMMPS (22 June 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.49443 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384276
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.86699164
1200 21815.003 45.317416 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36505 0 3680.8286 6.0538621
1350 20558.972 254.3648 0 3680.8601 -3.6773984
1400 21485.029 99.812952 0 3680.6511 -16.185471
1450 21771.108 52.159597 0 3680.6775 -2.4756679
1500 21520.948 93.503946 0 3680.3286 2.1023577
1550 21351.418 121.68139 0 3680.2511 5.5159972
1600 20778.805 216.92173 0 3680.0559 15.089183
1650 21477.639 100.21821 0 3679.8247 -1.1045931
1700 18501.343 596.4785 0 3680.0357 -15.679631
1750 18563.643 587.3477 0 3681.2882 33.53217
1800 19110.189 494.82277 0 3679.8543 18.024037
1850 21364.196 119.23462 0 3679.9339 2.529149
1900 20146.64 322.14631 0 3679.9197 5.7311673
1950 20692.671 231.25338 0 3680.0319 4.2977687
2000 20943.903 189.11238 0 3679.7629 -22.645639
2050 19668.148 401.81475 0 3679.8394 3.6256063
2100 20280.572 299.73979 0 3679.8351 7.4809366
2150 19182.127 483.47805 0 3680.4992 22.615355
2200 21299.767 130.77158 0 3680.7327 4.7114063
2250 20487.762 266.50325 0 3681.1302 -8.6408345
2300 18655.048 571.92772 0 3681.1023 -5.266975
2350 21512.632 95.763771 0 3681.2025 -9.3526622
2400 21467.744 103.31997 0 3681.2773 -29.599491
2450 20097.033 332.78544 0 3682.291 35.886632
2500 20761.514 222.1498 0 3682.4021 -12.52654
2550 20410.179 280.57555 0 3682.272 -22.280218
2600 21469.95 103.95758 0 3682.2826 -10.039024
2650 20711.858 230.38535 0 3682.3616 5.3554349
2700 18584.052 585.19766 0 3682.5397 21.807604
2750 20511.368 263.53176 0 3682.0931 -4.7085799
2800 20592.991 249.9677 0 3682.1328 -6.5329985
2850 17078.939 835.43473 0 3681.9245 16.780854
2900 19704.624 397.94471 0 3682.0488 -0.87435077
2950 19282.968 468.43149 0 3682.2595 7.0271622
3000 20552.037 256.84085 0 3682.1804 -2.9282943
3050 20934.711 193.08576 0 3682.2043 3.8942358
3100 21703.768 64.8113 0 3682.106 0.063237279
3150 18722.82 561.7019 0 3682.172 -1.4520091
3200 18284.044 634.53317 0 3681.8739 6.3415584
3250 21255.255 139.48628 0 3682.0288 2.6455564
3300 20558.956 255.77083 0 3682.2636 -3.9152408
3350 20373.309 286.62048 0 3682.1719 4.5400971
3400 20618.175 245.81811 0 3682.1806 5.7100283
3450 19473.455 436.70128 0 3682.2771 11.870427
3500 18903.565 531.91776 0 3682.5119 -9.3476901
3550 21030.252 177.18619 0 3682.2282 -14.260278
3600 19942.611 357.98433 0 3681.7528 11.183792
3650 20388.541 283.86156 0 3681.9518 -8.2736257
3700 20724.985 226.58383 0 3680.748 -13.429981
3750 21586.121 84.456333 0 3682.1432 -2.7515188
3800 21478.159 102.70951 0 3682.4027 -2.5874121
3850 18107.437 665.11995 0 3683.0262 11.062091
3900 19602.682 415.48105 0 3682.5947 17.867347
3950 19208.319 480.73213 0 3682.1186 0.55405471
4000 20700.944 232.01332 0 3682.1706 4.2790356
4050 18241.028 641.65227 0 3681.8236 14.819974
4100 16330.098 961.03753 0 3682.7206 -8.1781858
4150 20507.949 263.34806 0 3681.3396 -5.2032219
4200 21620.592 79.051795 0 3682.4838 -11.796063
4250 20841.315 209.02052 0 3682.573 -5.781042
4300 21378.616 119.44038 0 3682.5431 -3.0055326
4350 21391.4 116.89963 0 3682.133 1.2620601
4400 20092.07 333.32793 0 3682.0062 11.429014
4450 19315.512 461.83055 0 3681.0825 1.3462703
4500 20839.628 208.21416 0 3681.4855 4.709479
4550 14522.388 1263.1063 0 3683.5043 -20.816537
4600 21284.581 134.21556 0 3681.6457 -4.8183612
4650 20126.198 327.1439 0 3681.5103 -5.5395838
4700 21764.236 54.44036 0 3681.813 3.4863656
4750 21095.836 165.90339 0 3681.876 6.1541649
4800 20619.747 245.94729 0 3682.5718 2.5595916
4850 20763.177 222.12286 0 3682.6523 -8.6266804
4900 20537.14 259.67462 0 3682.5313 -15.421035
4950 21422.584 112.253 0 3682.6837 -1.4727022
5000 16257.411 972.68578 0 3682.2542 2.3147962
5050 19857.171 373.56369 0 3683.0922 -15.300375
5100 15635.264 1076.6903 0 3682.5676 36.8946
5150 21553.911 90.645813 0 3682.9642 1.5400926
5200 21559.956 89.704166 0 3683.0302 2.0981184
5250 19117.968 496.85067 0 3683.1787 29.282193
5300 21330.342 127.91971 0 3682.9767 2.4699055
5350 21829.625 44.595903 0 3682.8667 -11.606558
5400 21789.041 51.183465 0 3682.6902 -3.8674971
5450 19143.18 491.7975 0 3682.3275 -0.6880826
5500 19773.011 386.55132 0 3682.0532 -0.39276859
5550 21170.746 153.72971 0 3682.1873 -0.039885143
5600 20634.546 243.05851 0 3682.1496 -10.510731
5650 18940.14 525.80138 0 3682.4913 -8.4026702
5700 18137.059 658.45807 0 3681.3012 1.8086854
5750 18402.492 614.81681 0 3681.8988 18.121726
5800 15725.316 1060.3153 0 3681.2013 32.3919
5850 21350.969 122.71085 0 3681.2057 1.6244497
5900 20596.373 248.09794 0 3680.8268 -10.287271
5950 19586.195 416.65918 0 3681.0251 7.1327258
6000 20566.394 252.63425 0 3680.3666 9.3309712
6050 18063.299 667.31886 0 3677.8687 -10.246241
6100 17305.121 797.2545 0 3681.4414 14.554146
6150 19696.433 395.50284 0 3678.2416 4.1990406
6200 20908.19 195.69314 0 3680.3915 -9.0297611
6250 20767.885 219.35847 0 3680.6727 -5.4239147
6300 20271.076 302.48547 0 3680.9981 7.5881011
6350 21510.748 96.348849 0 3681.4736 -0.28663642
6400 21731.982 60.504382 0 3682.5014 -3.5673143
6450 19495.709 434.28569 0 3683.5706 4.7979099
6500 18668.623 571.92754 0 3683.3647 1.5185672
6550 16004.711 1016.2903 0 3683.7422 8.1972253
6600 20629.015 244.44595 0 3682.615 3.8351386
6650 21647.055 75.493996 0 3683.3365 -0.10989704
6700 19793.226 384.41402 0 3683.2851 7.7597696
6750 20441.55 275.94512 0 3682.8702 3.6110747
6800 21623.66 79.350309 0 3683.2936 -6.3458991
6850 21644.786 75.922535 0 3683.3869 -22.166786
6900 18150.965 657.76117 0 3682.9219 -14.903565
6950 21192.162 150.83369 0 3682.8607 -7.6579085
7000 20481.657 268.91866 0 3682.5281 -10.728925
7050 19265.165 471.58584 0 3682.4467 -3.1547895
7100 20241.165 308.92052 0 3682.4479 10.770847
7150 20883.514 201.92495 0 3682.5106 12.276271
7200 20675.066 236.51208 0 3682.3564 4.0653811
7250 21464.099 105.01329 0 3682.3631 -4.2891409
7300 19279.539 469.63353 0 3682.89 19.415276
7350 20266.489 304.68631 0 3682.4344 -0.15439874
7400 18978.717 519.39579 0 3682.5153 19.185958
7450 20816.852 213.20924 0 3682.6845 18.435432
7500 20655.662 240.16805 0 3682.7785 -4.4996568
7550 19061.292 506.0418 0 3682.9238 -1.7545473
7600 20564.235 255.25251 0 3682.625 -5.3903401
7650 21273.693 137.41485 0 3683.0303 -6.9034645
7700 20999.106 183.2458 0 3683.0968 -5.9941062
7750 18886.194 534.2212 0 3681.9202 5.9891004
7800 20327.925 294.85306 0 3682.8405 -2.5902629
7850 19533.408 427.77688 0 3683.3448 -4.9977086
7900 20973.609 187.37509 0 3682.9765 0.11759117
7950 18164.635 654.02996 0 3681.4691 16.402128
8000 20938.276 193.48738 0 3683.2 -5.9311301
8050 20819.498 213.21616 0 3683.1324 1.3392987
8100 19553.561 424.27379 0 3683.2006 -2.5040641
8150 17524.659 759.26187 0 3680.0384 -37.279253
8200 21104.916 165.88837 0 3683.3744 -3.8952964
8250 19614.453 414.27984 0 3683.3553 -2.9352541
8300 13365.081 1457.0212 0 3684.5347 100.4608
8350 20920.925 197.0494 0 3683.8702 -11.661629
8400 19724.857 396.41163 0 3683.8878 0.74045509
8450 21751.144 58.967512 0 3684.1583 -4.095218
8500 21283.998 136.40954 0 3683.7425 -5.4781843
8550 19255.08 474.01022 0 3683.1903 0.61248835
8600 20786.099 219.06078 0 3683.4107 9.7864578
8650 20801.493 216.74923 0 3683.6647 7.1280503
8700 19893.433 368.11056 0 3683.6827 -9.5312543
8750 21072.739 171.47966 0 3683.6028 -17.222136
8800 18791.068 551.89466 0 3683.7394 -13.425301
8850 20323.723 296.58355 0 3683.8708 1.2544121
8900 19160.522 487.13728 0 3680.5575 7.5449432
8950 20247.9 309.46468 0 3684.1146 -11.397923
9000 20721.089 230.36979 0 3683.8846 11.354348
9050 21798.873 51.104409 0 3684.25 -9.645863
9100 21093.423 168.78605 0 3684.3565 -1.2127948
9150 20954.177 191.65626 0 3684.0191 0.61911701
9200 17054.376 842.546 0 3684.942 41.714389
9250 19253.515 475.58375 0 3684.5029 13.186069
9300 21681.124 71.036838 0 3684.5575 -4.139581
9350 21796.739 51.725799 0 3684.5157 -8.5902286
9400 21631.679 79.362722 0 3684.6425 -8.7541514
9450 18537.758 595.38459 0 3685.011 -6.2719267
9500 17152.352 824.77642 0 3683.5018 46.593524
9550 20928.938 196.82808 0 3684.9843 -1.5521829
9600 15991.62 1020.98 0 3686.25 -3.8314742
9650 19629.68 414.15513 0 3685.7685 32.867017
9700 20900.569 201.75492 0 3685.183 6.1694301
9750 17072.588 841.426 0 3686.8573 -4.0468499
9800 21939.049 29.032402 0 3685.5406 -9.1896877
9850 21261.674 141.7745 0 3685.3869 -13.02325
9900 19393.195 452.88226 0 3685.0814 1.4304574
9950 17226.824 814.05288 0 3685.1902 19.353254
10000 20630.15 245.97222 0 3684.3306 0.61583151
Loop time of 16.3618 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.125099 (0.764576)
Neigh time (%) = 0.0542815 (0.331757)
Comm time (%) = 1.68193 (10.2796)
Outpt time (%) = 0.102797 (0.628274)
Other time (%) = 14.3977 (87.9958)
Nlocal: 20.25 ave 74 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 42 ave 90 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 211.25 ave 769 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 845
Ave neighs/atom = 10.4321
Neighbor list builds = 991
Dangerous builds = 929

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LAMMPS (22 June 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.58102 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699156
1200 21815.003 45.317415 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064077
1300 20780.781 217.36506 0 3680.8286 6.053862
1350 20558.972 254.36481 0 3680.8601 -3.6773966
1400 21485.029 99.812935 0 3680.6511 -16.185472
1450 21771.107 52.159605 0 3680.6775 -2.4756675
1500 21520.948 93.503934 0 3680.3286 2.1023577
1550 21351.418 121.68138 0 3680.2511 5.5159957
1600 20778.805 216.92176 0 3680.0559 15.089186
1650 21477.638 100.2183 0 3679.8247 -1.1045812
1700 18501.341 596.47889 0 3680.0357 -15.67966
1750 18563.642 587.34786 0 3681.2882 33.532195
1800 19110.187 494.82315 0 3679.8543 18.024044
1850 21364.193 119.2351 0 3679.9339 2.5291255
1900 20146.632 322.14766 0 3679.9197 5.7312569
1950 20692.671 231.25335 0 3680.0319 4.2977718
2000 20943.904 189.1123 0 3679.7629 -22.645328
2050 19668.094 401.82367 0 3679.8394 3.625351
2100 20280.495 299.75279 0 3679.8352 7.4808501
2150 19181.964 483.50484 0 3680.4989 22.618437
2200 21300.002 130.73207 0 3680.7324 4.7107204
2250 20487.278 266.58364 0 3681.13 -8.6436788
2300 18653.922 572.11506 0 3681.102 -5.2650803
2350 21513.162 95.675284 0 3681.2022 -9.358275
2400 21466.87 103.46516 0 3681.2768 -29.576898
2450 20098.852 332.48096 0 3682.2896 35.802574
2500 20763.224 221.86356 0 3682.401 -12.492465
2550 20425.308 278.04709 0 3682.265 -22.360414
2600 21467.742 104.32441 0 3682.2815 -10.062558
2650 20774.17 220.00066 0 3682.3623 5.2193436
2700 18569.233 587.73881 0 3682.6109 22.145192
2750 20654.466 239.78519 0 3682.1961 -6.9106068
2800 20814.792 213.06343 0 3682.1954 -6.9316614
2850 16353.471 956.9648 0 3682.5433 34.229058
2900 19519.089 429.00752 0 3682.189 8.7072031
2950 20171.665 320.18684 0 3682.1309 2.7223515
3000 20470.108 270.26106 0 3681.9457 -8.2674499
3050 20359.511 288.83368 0 3682.0856 -4.69092
3100 19856.099 372.69336 0 3682.0432 9.3653131
3150 20561.401 254.89391 0 3681.794 6.7807193
3200 18974.717 519.59328 0 3682.0462 14.028207
3250 17201.03 816.05668 0 3682.895 30.827229
3300 21032.748 176.57229 0 3682.0304 -8.8776478
3350 17299.203 798.82174 0 3682.0222 -6.5474977
3400 16871.128 870.67484 0 3682.5295 -23.235008
3450 19319.303 462.06051 0 3681.9443 -11.811901
3500 17860.126 705.48294 0 3682.1705 -15.992033
3550 21874.357 36.186306 0 3681.9124 -2.4098493
3600 21393.595 116.22067 0 3681.8199 -10.262929
3650 20544.718 257.71089 0 3681.8306 0.55484185
3700 20330.417 293.63761 0 3682.0404 16.661746
3750 21244.461 141.09081 0 3681.8343 4.9615754
3800 19958.592 355.64853 0 3682.0806 13.979713
3850 21497.423 98.927167 0 3681.8309 -6.621684
3900 21769.359 53.67612 0 3681.9026 -1.926207
3950 19975.772 352.52452 0 3681.8198 9.245817
4000 21113.483 163.03078 0 3681.9446 2.7569744
4050 19709.067 397.27579 0 3682.1202 -3.0811456
4100 21815.578 46.077634 0 3682.0073 -12.520188
4150 21642.428 74.997052 0 3682.0685 -1.1460009
4200 19928.01 360.19492 0 3681.53 8.857095
4250 17863.117 703.82283 0 3681.009 33.346649
4300 20382.848 284.9686 0 3682.1099 -7.0563493
4350 21589.546 83.691599 0 3681.9492 -6.3466935
4400 21561.341 88.259907 0 3681.8167 -0.05858595
4450 19016.303 512.39829 0 3681.7821 43.125503
4500 20065.798 337.40858 0 3681.7083 1.7677159
4550 19263.771 471.03594 0 3681.6644 -23.462523
4600 20845.688 207.74162 0 3682.023 0.16598388
4650 19646.643 407.84353 0 3682.2841 11.884842
4700 20692.329 233.43094 0 3682.1524 -14.265029
4750 17999.182 682.2895 0 3682.1531 -25.09426
4800 20585.117 251.43776 0 3682.2906 10.111397
4850 19368.488 453.98051 0 3682.0618 6.199069
4900 20416.868 279.66263 0 3682.474 7.5050136
4950 21376.045 119.55597 0 3682.2302 -9.6343892
5000 21346.337 124.42913 0 3682.1519 -3.6930357
5050 19787.72 384.70087 0 3682.6542 -5.855159
5100 20440.061 275.27592 0 3681.9528 1.7528745
5150 15625.189 1079.1543 0 3683.3525 19.539205
5200 20308.779 297.80498 0 3682.6014 8.9223119
5250 21044.849 175.43646 0 3682.9113 5.2785373
5300 20543.584 258.744 0 3682.6747 1.2007699
5350 21171.39 154.69163 0 3683.2566 -12.896011
5400 19626.405 409.45045 0 3680.518 16.150799
5450 20550.071 258.26489 0 3683.2766 -21.262685
5500 19104.84 499.01387 0 3683.1539 11.949545
5550 19559.267 422.41448 0 3682.2923 3.8829356
5600 20044.332 342.61709 0 3683.3391 -1.7700503
5650 21953.27 25.016694 0 3683.8951 -22.754979
5700 21639.986 77.352619 0 3684.017 -15.578393
5750 21144.414 159.81932 0 3683.8884 -9.0956708
5800 19267.59 472.68582 0 3683.9509 12.517057
5850 21221.184 146.53726 0 3683.4012 -0.35975116
5900 21141.226 159.83342 0 3683.371 0.79471018
5950 20417.806 280.84037 0 3683.808 -4.380384
6000 15946.467 1025.7528 0 3683.4973 -2.9233738
6050 20307.785 299.10545 0 3683.7362 -7.6865743
6100 18110.389 663.98174 0 3682.3799 4.1591862
6150 19958.364 357.9562 0 3684.3502 0.64161306
6200 18283.091 637.04273 0 3684.2246 1.3409324
6250 17081.956 837.9693 0 3684.962 -6.7113704
6300 21382.883 120.98513 0 3684.7989 -13.987822
6350 19952.702 359.01391 0 3684.4642 6.3550454
6400 20832.557 212.50673 0 3684.5995 -1.5787609
6450 18646.002 577.10671 0 3684.7738 7.7299342
6500 18261.033 641.30218 0 3684.8076 17.386854
6550 18426.877 613.53329 0 3684.6794 -3.3462219
6600 20349.993 293.18762 0 3684.8531 -12.422327
6650 21112.2 166.06059 0 3684.7606 -6.7451773
6700 20046.245 343.52129 0 3684.5621 -4.0057021
6750 20834.1 212.52233 0 3684.8724 -1.5556583
6800 21150.619 159.68754 0 3684.7908 -1.5850612
6850 20008.249 350.12255 0 3684.8308 6.4872768
6900 18654.888 575.51473 0 3684.6627 -17.992304
6950 19708.289 400.17932 0 3684.8942 7.0106327
7000 20437.426 278.17876 0 3684.4164 6.2019137
7050 19604.082 416.96446 0 3684.3114 -3.924055
7100 18301.87 633.03111 0 3683.3428 19.029745
7150 18558.782 591.49191 0 3684.6222 25.690348
7200 16746.788 894.4891 0 3685.6204 9.3897347
7250 19956.035 358.65844 0 3684.6642 2.9307876
7300 21612.74 82.596669 0 3684.7199 -6.0761772
7350 21082.361 170.97104 0 3684.6979 -1.6531911
7400 21447.623 110.03038 0 3684.6342 -9.6680921
7450 21815.262 48.645261 0 3684.5222 -2.4194461
7500 21586.807 86.513539 0 3684.3147 0.80475725
7550 21432.021 112.08344 0 3684.087 3.7213279
7600 18765.76 557.30844 0 3684.9351 25.566982
7650 19237.591 477.51887 0 3683.784 -0.93181342
7700 20058.61 340.75274 0 3683.8544 4.1984966
7750 21689.282 69.4903 0 3684.3707 -8.0484797
7800 21149.046 159.71259 0 3684.5537 7.1881243
7850 19334.412 461.23349 0 3683.6355 14.066324
7900 21263.983 140.83705 0 3684.8343 -14.739146
7950 20871.691 206.2356 0 3684.8508 -11.575259
8000 18916.496 531.93786 0 3684.6872 -20.395653
8050 20703.238 233.97858 0 3684.5183 4.2191304
8100 19544.399 426.74441 0 3684.1442 15.563275
8150 17578.916 755.02603 0 3684.8454 23.23474
8200 18121.828 663.35414 0 3683.6588 -23.277149
8250 19000.859 515.63274 0 3682.4425 8.1499185
8300 16312.856 965.20527 0 3684.0147 69.340264
8350 17908.285 699.50533 0 3684.2195 -13.64631
8400 19971.59 355.22033 0 3683.8187 6.2163041
8450 13617.129 1415.4014 0 3684.9229 -9.1829017
8500 20374.985 288.34097 0 3684.1719 1.0194401
8550 21452.212 108.96717 0 3684.3359 -8.0882838
8600 17196.613 818.7652 0 3684.8674 -2.1874477
8650 21510.389 99.326067 0 3684.3909 -3.5449392
8700 21446.623 109.76972 0 3684.2068 -0.76115037
8750 20700.162 234.50311 0 3684.5301 2.0551713
8800 21686.769 69.759974 0 3684.2215 -3.6322891
8850 20892.916 201.69594 0 3683.8486 0.57163157
8900 18095.714 668.44418 0 3684.3965 19.055292
8950 21325.044 129.56368 0 3683.7377 2.2916549
9000 20739.771 227.15562 0 3683.7842 -6.4759144
9050 20683.885 235.94003 0 3683.2543 1.8163478
9100 21432.386 111.08386 0 3683.1483 -9.5573949
9150 21686.43 69.315468 0 3683.7205 2.1854565
9200 16916.728 864.20897 0 3683.6636 7.2632357
9250 20122.374 329.80422 0 3683.5332 6.2589988
9300 20621.693 246.58967 0 3683.5386 -20.210043
9350 20343.792 292.92921 0 3683.5612 0.47974589
9400 20334.062 294.47957 0 3683.4899 -5.5269222
9450 20971.669 188.26826 0 3683.5464 1.5825497
9500 20948.938 191.99574 0 3683.4855 1.7294775
9550 21557.149 90.697719 0 3683.5559 4.5248095
9600 21121.109 162.83027 0 3683.0151 -3.8673505
9650 21306.551 132.27859 0 3683.3704 -0.05028404
9700 21064.24 172.82072 0 3683.5273 1.7248916
9750 18962.129 523.71798 0 3684.0729 17.93568
9800 21192.894 151.77036 0 3683.9193 -0.2514556
9850 20585.229 252.91402 0 3683.7855 9.2033197
9900 21584.165 86.429361 0 3683.7902 -5.4686156
9950 21190.652 151.98402 0 3683.7593 -3.5815764
10000 20061.072 340.24042 0 3683.7525 -2.2008049
Loop time of 26.3326 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.951727 (3.61425)
Neigh time (%) = 0.339969 (1.29106)
Comm time (%) = 0.117033 (0.444442)
Outpt time (%) = 0.166224 (0.631248)
Other time (%) = 24.7576 (94.019)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 721 ave 721 max 721 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 721
Ave neighs/atom = 8.90123
Neighbor list builds = 989
Dangerous builds = 911

307
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LAMMPS (22 June 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.83851 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444672
1400 18549.582 329.31436 0 3764.4221 10.738304
1450 15163.926 957.47583 0 3765.6103 -17.923459
1500 19223.688 204.15164 0 3764.0939 -1.6134548
1550 18147.996 404.12675 0 3764.8668 8.419476
1600 18615.043 317.42462 0 3764.6548 -2.3289018
1650 20120.654 38.887963 0 3764.935 -8.7620159
1700 19450.904 162.98318 0 3765.0025 2.3254642
1750 19374.634 177.37922 0 3765.2744 8.932879
1800 19424.403 167.93984 0 3765.0514 0.081244414
1850 17936.476 442.80024 0 3764.3699 6.6004381
1900 19982.598 64.405734 0 3764.8868 -2.9530867
1950 16216.207 761.84618 0 3764.8475 13.99299
2000 18584.309 322.14125 0 3763.6799 7.1657135
2050 20107.968 41.025323 0 3764.723 -0.31100219
2100 20002.381 60.584283 0 3764.7288 -6.7918769
2150 16949.202 626.70007 0 3765.4412 3.5108751
2200 20010.949 58.809053 0 3764.5403 -10.862469
2250 18982.71 247.01257 0 3762.3292 -0.53760308
2300 18401.513 354.84007 0 3762.5277 1.0915424
2350 19390.418 172.96117 0 3763.7793 -3.3530683
2400 16084.09 785.7786 0 3764.3137 -16.190023
2450 18871.606 268.52952 0 3763.2713 11.177432
2500 19686.081 117.99211 0 3763.5626 4.4022105
2550 18875.819 267.86112 0 3763.3831 -5.644853
2600 17010.705 613.30983 0 3763.4405 6.339113
2650 18797.741 282.8114 0 3763.8745 2.3556876
2700 19726.505 110.11368 0 3763.1701 -0.24505394
2750 19436.803 164.0424 0 3763.4504 -1.5253044
2800 18357.485 362.53565 0 3762.0699 22.084345
2850 19004.145 243.73317 0 3763.0192 2.2627686
2900 20108.185 39.496053 0 3763.234 -0.48500324
2950 15919.562 814.90854 0 3762.9756 15.610955
3000 17654.881 493.61172 0 3763.0342 2.6630007
3050 18711.769 298.14871 0 3763.2911 2.9706053
3100 16038.72 793.07314 0 3763.2064 8.0214715
3150 19925.087 73.363563 0 3763.1945 -11.409754
3200 19305.94 187.89701 0 3763.0711 0.57287469
3250 19779.251 100.11507 0 3762.9394 -10.121237
3300 17922.539 444.12789 0 3763.1166 6.2204358
3350 18967.646 250.37413 0 3762.9011 6.3180053
3400 16940.148 625.60864 0 3762.673 35.103295
3450 19284.152 191.53891 0 3762.6781 2.3570968
3500 19321.512 184.58448 0 3762.6423 2.2709682
3550 19631.049 126.97845 0 3762.358 -0.65897943
3600 18494.976 337.74154 0 3762.7371 -2.419701
3650 19117.634 222.45812 0 3762.7607 0.050198383
3700 19400.367 170.05551 0 3762.716 -0.60552841
3750 19912.752 75.322358 0 3762.869 -3.6525006
3800 18564.109 325.06781 0 3762.8658 5.4109379
3850 19846.304 87.655562 0 3762.8971 2.5946736
3900 19476.444 156.1165 0 3762.8653 -8.9729351
3950 19647.738 124.43854 0 3762.9085 0.82844488
4000 18123.616 406.3511 0 3762.5762 8.2661512
4050 16574.617 693.99841 0 3763.372 0.84625476
4100 18946.287 254.50552 0 3763.0773 -0.39624245
4150 18466.555 343.35133 0 3763.0837 -10.151094
4200 19477.739 156.04727 0 3763.0359 -0.73208547
4250 19680.9 118.38024 0 3762.9913 1.4563423
4300 18320.329 369.90558 0 3762.5591 -1.1852345
4350 18767.214 286.789 0 3762.199 6.3326391
4400 16894.629 634.49312 0 3763.1281 10.255417
4450 17915.848 444.62515 0 3762.3748 -4.633212
4500 19487.927 154.02671 0 3762.9021 -2.8383574
4550 19880.496 81.301302 0 3762.8746 2.9361031
4600 19872.228 82.669863 0 3762.7122 -3.2788098
4650 15769.89 843.11924 0 3763.4693 8.5209519
4700 19720.045 110.85283 0 3762.7129 -0.52445088
4750 19764.607 102.5192 0 3762.6317 2.1798609
4800 17562.467 510.78691 0 3763.0956 7.3629583
4850 19463.538 158.32481 0 3762.6836 -3.9920666
4900 17932.952 441.75053 0 3762.6675 6.9598399
4950 19084.979 228.62301 0 3762.8785 6.4376261
5000 19472.38 156.9411 0 3762.9375 4.4983114
5050 19453.908 160.3778 0 3762.9533 4.6612574
5100 19521.287 147.96055 0 3763.0137 2.904162
5150 18128.471 405.81521 0 3762.9394 5.3809492
5200 17049.524 605.73212 0 3763.0514 -6.0390166
5250 19645.014 125.0255 0 3762.991 -6.8246205
5300 18281.054 377.45844 0 3762.8388 13.32637
5350 19457.083 159.77948 0 3762.9429 0.21762328
5400 18431.165 349.7041 0 3762.8827 -5.7191385
5450 19431.127 164.51144 0 3762.8682 -8.6635331
5500 19538.523 144.42775 0 3762.6727 -1.6610416
5550 16105.678 780.35525 0 3762.8882 48.462329
5600 20038.616 51.570638 0 3762.4254 -1.5590991
5650 19774.413 100.34213 0 3762.2704 -3.4571242
5700 19210.59 204.66324 0 3762.18 1.851606
5750 19146.331 216.47595 0 3762.0928 2.0721573
5800 19058.521 232.88706 0 3762.2428 -1.9839575
5850 19195.04 207.81355 0 3762.4506 -10.269192
5900 18304.113 372.73776 0 3762.3882 -5.7543087
5950 19936.776 70.443763 0 3762.4393 3.6659806
6000 19413.016 167.50961 0 3762.5125 2.5981288
6050 19169.847 212.36264 0 3762.3343 2.9324328
6100 19873.513 82.452317 0 3762.7325 -0.5468764
6150 18911.794 260.42784 0 3762.6119 -2.1216521
6200 19153.7 215.69884 0 3762.6802 -1.0975226
6250 18802.916 280.37164 0 3762.3932 4.7012709
6300 19385.046 172.8566 0 3762.6799 3.7637577
6350 20042.403 51.159768 0 3762.7159 -0.15040693
6400 17671.74 490.05042 0 3762.5948 9.0126067
6450 18092.22 412.77197 0 3763.1832 -2.8594764
6500 19953.711 67.838094 0 3762.9698 3.7323378
6550 19818.338 92.883562 0 3762.9461 -1.9994936
6600 19323.833 183.93088 0 3762.4184 -0.95695044
6650 18642.816 310.35894 0 3762.7323 15.264581
6700 16246.778 753.95834 0 3762.6209 26.618472
6750 19362.672 176.94037 0 3762.6204 -4.6442606
6800 18813.849 278.64468 0 3762.6908 2.5699369
6850 19386.278 172.79274 0 3762.8443 -10.400863
6900 19206.609 206.02588 0 3762.8054 -2.680536
6950 18068.847 416.85422 0 3762.9369 -9.0106209
7000 18369.805 360.43314 0 3762.249 13.735008
7050 18426.189 350.61688 0 3762.8741 8.3714758
7100 17656.982 492.79834 0 3762.6098 4.4583118
7150 18141.722 402.98387 0 3762.562 8.3258153
7200 18621.905 313.92925 0 3762.4301 -5.8742464
7250 18374.083 360.03493 0 3762.6429 -13.815946
7300 18040.277 421.82567 0 3762.6177 -4.6905029
7350 19146.198 217.01003 0 3762.6023 5.1451068
7400 18826.989 276.1892 0 3762.6686 6.5391972
7450 16067.243 787.1796 0 3762.5949 8.3754041
7500 18419.546 351.11771 0 3762.1448 7.7248275
7550 18446.346 346.8971 0 3762.8871 13.350672
7600 18944.672 254.13521 0 3762.4077 3.6554152
7650 18736.984 292.8881 0 3762.7 -14.958085
7700 18741.654 291.39068 0 3762.0673 -2.1933562
7750 18220.361 388.04072 0 3762.1816 9.7868422
7800 19348.223 178.96147 0 3761.9658 -0.26463817
7850 19401.949 169.04328 0 3761.9968 -1.5022009
7900 18577.957 321.63399 0 3761.9965 1.4151292
7950 17739.892 476.69976 0 3761.865 5.1996225
8000 17512.557 519.37266 0 3762.4387 5.2453534
8050 19168.123 212.38445 0 3762.0369 -3.9960482
8100 17916.044 443.46573 0 3761.2517 -5.9817899
8150 18601.23 316.95165 0 3761.6238 3.8327542
8200 17791.805 467.15931 0 3761.9381 -2.6931191
8250 18321.607 369.09405 0 3761.9843 1.4342349
8300 17334.957 552.06316 0 3762.2404 4.1774271
8350 17207.467 575.31923 0 3761.8872 1.1785558
8400 18225.217 387.22593 0 3762.2662 9.0197316
8450 19004.047 243.03694 0 3762.3048 7.664125
8500 18952.876 252.61597 0 3762.4078 -3.9713236
8550 19127.437 220.08856 0 3762.2066 -10.686924
8600 19542.154 143.35104 0 3762.2684 -1.9189815
8650 19294.525 189.17898 0 3762.2392 -1.4875507
8700 18832.532 274.05387 0 3761.5598 -1.9519412
8750 18591.931 318.93488 0 3761.885 9.928625
8800 18576.38 322.04174 0 3762.1121 -3.8846944
8850 19922.086 72.972833 0 3762.248 -0.56032546
8900 18892.839 263.55803 0 3762.2319 4.9733954
8950 16486.736 708.70288 0 3761.8022 37.965254
9000 18628.335 312.81773 0 3762.5094 6.0750689
9050 19286.823 190.4938 0 3762.1278 -2.2862927
9100 18973.378 247.96414 0 3761.5526 5.0771442
9150 17256.927 566.17648 0 3761.9038 5.7456977
9200 18507.288 334.66416 0 3761.9398 1.1406887
9250 18961.534 250.42427 0 3761.8194 -5.8909163
9300 19206.115 205.203 0 3761.8911 1.0922244
9350 19401.191 168.92055 0 3761.7336 -1.921044
9400 18069.392 415.54646 0 3761.7301 5.0565694
9450 18828.428 274.89551 0 3761.6415 10.024306
9500 18295.323 373.66825 0 3761.691 -1.4888703
9550 17709.338 482.22946 0 3761.7365 -9.028568
9600 19512.39 148.31281 0 3761.7184 -4.2133026
9650 19742.351 105.74048 0 3761.7315 -0.57801883
9700 19892.658 77.898869 0 3761.7245 1.2005091
9750 19035.044 236.65131 0 3761.6595 2.87911
9800 17443.415 531.71826 0 3761.9802 23.5179
9850 19545.912 141.99994 0 3761.6133 1.3493021
9900 19542.173 142.22929 0 3761.1503 3.087434
9950 19794.356 96.034607 0 3761.6561 -3.1844994
10000 19058.563 232.34496 0 3761.7085 -7.1466609
Loop time of 17.168 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0928572 (0.540875)
Neigh time (%) = 0.0403583 (0.235079)
Comm time (%) = 1.50369 (8.75868)
Outpt time (%) = 0.0945153 (0.550533)
Other time (%) = 15.4366 (89.9148)
Nlocal: 20.25 ave 42 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 20.5 ave 37 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 164.25 ave 401 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 657
Ave neighs/atom = 8.11111
Neighbor list builds = 991
Dangerous builds = 930

307
examples/rigid/log.rigid.poems2.22Jun07.linux.1 Normal file
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@ -0,0 +1,307 @@
LAMMPS (22 June 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.92712 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444672
1400 18549.582 329.31436 0 3764.4221 10.738304
1450 15163.926 957.47582 0 3765.6103 -17.923459
1500 19223.689 204.15156 0 3764.0939 -1.6134559
1550 18147.996 404.12674 0 3764.8668 8.4194748
1600 18615.043 317.42458 0 3764.6548 -2.3289073
1650 20120.654 38.887996 0 3764.935 -8.7620081
1700 19450.903 162.98348 0 3765.0025 2.3254585
1750 19374.636 177.37893 0 3765.2744 8.93288
1800 19424.402 167.93995 0 3765.0514 0.081253537
1850 17936.625 442.77274 0 3764.3699 6.60003
1900 19982.599 64.405428 0 3764.8868 -2.9531558
1950 16216.44 761.80238 0 3764.8469 13.991862
2000 18584.234 322.15493 0 3763.6798 7.1659198
2050 20107.969 41.025039 0 3764.723 -0.31106422
2100 20002.411 60.57861 0 3764.7288 -6.7918086
2150 16948.844 626.76647 0 3765.4413 3.512116
2200 20010.946 58.809564 0 3764.5403 -10.862667
2250 18982.703 247.01388 0 3762.3292 -0.5373304
2300 18401.642 354.81637 0 3762.5279 1.0912175
2350 19390.361 172.97181 0 3763.7793 -3.3533924
2400 16086.125 785.40108 0 3764.3132 -16.183657
2450 18872.351 268.39211 0 3763.2718 11.164657
2500 19684.688 118.25055 0 3763.5632 4.4144806
2550 18878.925 267.2853 0 3763.3825 -5.6338978
2600 17005.407 614.29162 0 3763.441 6.3575302
2650 18827.389 277.31059 0 3763.8641 2.3182614
2700 19715.461 112.12451 0 3763.1358 -0.19109773
2750 19319.449 185.79269 0 3763.4684 -1.3550374
2800 18120.942 406.44184 0 3762.1719 26.654821
2850 19401.627 170.17075 0 3763.0647 0.73603491
2900 20106.157 39.874788 0 3763.2371 -1.1342032
2950 16814.814 649.4335 0 3763.288 12.415015
3000 16200.577 761.45184 0 3761.5588 21.599685
3050 18396.676 356.11264 0 3762.9044 7.6140431
3100 17582.958 506.67523 0 3762.7786 -14.766278
3150 18362.109 362.43838 0 3762.8289 3.2782729
3200 17008.785 613.88943 0 3763.6645 5.070376
3250 19614.194 130.81389 0 3763.072 1.1021521
3300 18995.955 245.31261 0 3763.0821 -8.6889904
3350 18215.815 389.87474 0 3763.1737 2.7550234
3400 18068.71 417.08655 0 3763.144 17.578891
3450 19352.914 179.0126 0 3762.8855 8.4058764
3500 18738.818 292.55665 0 3762.7082 3.8415777
3550 19469.912 157.36508 0 3762.9044 2.5399078
3600 18431.706 349.41269 0 3762.6916 2.3088878
3650 18819.962 277.76095 0 3762.9392 5.1521358
3700 19813.675 93.945731 0 3763.1449 -0.34475825
3750 18075.078 415.77801 0 3763.0146 -1.8968333
3800 19422.14 166.53886 0 3763.2315 -2.2150672
3850 18013.209 427.44475 0 3763.2243 -6.0428819
3900 19193.889 208.87526 0 3763.2991 -3.9692972
3950 16568.188 695.64549 0 3763.8284 13.243843
4000 17993.623 430.51008 0 3762.6626 5.0888559
4050 19625.511 128.63837 0 3762.9922 -0.70241793
4100 19069.298 231.35736 0 3762.7088 -5.6365968
4150 18033.877 424.02231 0 3763.6292 -6.8518969
4200 19950.626 68.482279 0 3763.0426 -1.8524059
4250 18786.19 284.10677 0 3763.0309 5.811473
4300 19526.067 146.81821 0 3762.7565 -9.5811432
4350 16343.335 736.72783 0 3763.2714 30.281083
4400 18759.668 288.81939 0 3762.8319 5.5918027
4450 18633.251 312.20135 0 3762.8033 3.8618473
4500 18079.31 414.80535 0 3762.8256 2.2481588
4550 18288.498 376.11039 0 3762.8693 4.1087615
4600 18315.887 371.16083 0 3762.9918 -3.5412078
4650 18901.901 262.59396 0 3762.9459 -7.3155419
4700 19311.704 186.85051 0 3763.092 -5.9856651
4750 19426.54 165.69302 0 3763.2005 -7.0519961
4800 18347.933 365.43611 0 3763.2015 5.0195241
4850 19952.067 68.477491 0 3763.3047 3.3126678
4900 19224.549 203.14962 0 3763.2513 -2.8437357
4950 19857.322 85.89601 0 3763.1779 -1.4381085
5000 19592.925 134.86246 0 3763.182 0.8610879
5050 19472.16 157.37877 0 3763.3343 -0.31578957
5100 19814.831 93.787624 0 3763.2008 5.3970415
5150 18211.407 390.82193 0 3763.3047 8.4423278
5200 18828.994 276.3271 0 3763.1778 10.441024
5250 20121.332 37.261735 0 3763.4344 -2.2672502
5300 17755.337 475.75071 0 3763.7761 3.3792401
5350 20033.05 53.761483 0 3763.5855 -3.031072
5400 19332.059 183.54479 0 3763.5557 6.0877875
5450 19964.421 66.56191 0 3763.677 0.034467069
5500 19838.257 89.969443 0 3763.7207 -3.5800893
5550 19202.804 207.40212 0 3763.4769 8.5123136
5600 19855.825 86.760789 0 3763.7654 1.3832846
5650 19060.478 234.22396 0 3763.9421 2.6116735
5700 20124.587 37.161564 0 3763.937 3.4519842
5750 19304.489 189.01672 0 3763.9221 -0.096371392
5800 18516.206 335.07659 0 3764.0036 -4.9526268
5850 18093.127 413.01533 0 3763.5945 -3.6663927
5900 17303.637 559.08088 0 3763.458 -4.805237
5950 19818.733 93.796285 0 3763.932 0.043875363
6000 18162.182 400.57864 0 3763.9457 7.4143797
6050 18439.177 349.30792 0 3763.9703 -0.92601434
6100 18899.456 263.84185 0 3763.741 8.018437
6150 17317.004 556.71789 0 3763.5704 10.764267
6200 18991.81 246.89696 0 3763.8989 -4.0990586
6250 19868.798 84.388048 0 3763.795 0.58061118
6300 18989.135 247.26992 0 3763.7763 12.682799
6350 15978.578 804.89 0 3763.8858 6.3163773
6400 18967.47 251.22915 0 3763.7236 1.3481515
6450 19294.369 190.87058 0 3763.9019 -8.5139829
6500 19826.451 92.014872 0 3763.5798 1.0125001
6550 17480.845 526.28717 0 3763.4807 5.9053655
6600 17806.087 465.8384 0 3763.262 21.004433
6650 17942.192 439.48981 0 3762.118 2.0212326
6700 16468.094 712.95472 0 3762.6018 6.6618901
6750 19305.119 188.34815 0 3763.3703 1.8765297
6800 19988.201 62.004452 0 3763.5231 -1.6652967
6850 20193.079 24.117041 0 3763.5761 -4.1748266
6900 20011.596 57.729546 0 3763.5806 -3.6774766
6950 18419.577 352.48285 0 3763.5157 -3.8710136
7000 19178.531 212.01179 0 3763.5917 5.2484112
7050 18754.875 289.8693 0 3762.9942 7.5083851
7100 19179.381 211.26035 0 3762.9975 1.8325782
7150 18221.392 388.75188 0 3763.0837 -9.4596464
7200 19508.765 150.73861 0 3763.4729 -8.4154341
7250 16779.268 656.19712 0 3763.4689 3.9284063
7300 19184.405 210.6069 0 3763.2744 -7.0049508
7350 17914.948 445.90458 0 3763.4876 1.9922265
7400 14040.559 1164.2709 0 3764.3744 -25.198045
7450 17680.643 489.04226 0 3763.2354 4.6678876
7500 15575.048 879.11471 0 3763.3829 5.3335325
7550 16738.339 663.36831 0 3763.0607 10.735452
7600 18927.126 258.2804 0 3763.3038 -1.3289622
7650 17033.929 610.18818 0 3764.6195 15.51609
7700 17800.589 463.84003 0 3760.2454 -9.8344679
7750 18337.643 367.47891 0 3763.3388 -3.4235631
7800 20102.521 40.465427 0 3763.1544 -2.5622118
7850 18854.307 271.72975 0 3763.2681 16.38529
7900 18769.869 287.08151 0 3762.9832 8.285443
7950 19530.556 146.69214 0 3763.4618 2.5699618
8000 17967.757 436.48149 0 3763.8439 -13.724493
8050 19995.451 60.489084 0 3763.3503 -6.7296549
8100 17668.554 491.39156 0 3763.346 -1.5877323
8150 17041.937 607.0112 0 3762.9255 29.132719
8200 19634.282 127.02828 0 3763.0064 5.4245146
8250 19464.43 158.26891 0 3762.7929 -1.0959737
8300 18262.088 380.75171 0 3762.6199 -9.5161603
8350 19154.678 214.95549 0 3762.118 1.4904442
8400 18631.904 312.04844 0 3762.4011 6.200446
8450 17326.79 552.9849 0 3761.6497 0.58133511
8500 18262.986 380.59746 0 3762.6319 -1.5859109
8550 16355.636 733.37813 0 3762.1995 -6.8040182
8600 17652.805 494.50385 0 3763.5419 2.9981184
8650 16589.75 690.94159 0 3763.1175 -0.61681982
8700 18767.632 287.52175 0 3763.0091 -0.15112824
8750 19530.676 145.40209 0 3762.194 3.6106484
8800 16209.935 760.89243 0 3762.7323 -12.504448
8850 19909.854 75.790768 0 3762.8008 1.4759603
8900 19162.868 213.40033 0 3762.0797 6.8118408
8950 17996.377 429.38719 0 3762.0496 11.126692
9000 17366.686 545.41384 0 3761.4667 -5.089277
9050 16976.454 618.54424 0 3762.332 -5.533809
9100 19419.965 166.18943 0 3762.4793 3.7595663
9150 17900.022 448.30981 0 3763.1287 -6.2299514
9200 18662.637 306.89813 0 3762.942 -2.0816787
9250 19806.478 95.487105 0 3763.3534 -19.715374
9300 19065.731 233.31844 0 3764.0093 0.66896622
9350 15347.66 921.21669 0 3763.3759 10.777468
9400 18056.449 416.32084 0 3760.1078 13.580271
9450 19104.743 225.75045 0 3763.6658 -0.57249212
9500 18193.488 394.55096 0 3763.7154 -3.8896144
9550 17005.07 614.383 0 3763.4701 20.544154
9600 18956.557 253.26137 0 3763.7349 1.0366132
9650 18278.345 379.38464 0 3764.2634 -11.945363
9700 19791.354 98.864736 0 3763.9303 1.0827422
9750 19840.264 89.82519 0 3763.9482 -2.1741548
9800 19120.304 222.91513 0 3763.7122 -3.392839
9850 15643.719 866.53246 0 3763.5175 1.2278747
9900 16998.456 616.53609 0 3764.3983 -8.3833815
9950 19670.981 121.07532 0 3763.8496 0.76591747
10000 16544.589 699.98952 0 3763.8022 -21.503512
Loop time of 26.9591 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.70095 (2.60005)
Neigh time (%) = 0.258285 (0.958063)
Comm time (%) = 0.131733 (0.488641)
Outpt time (%) = 0.175157 (0.649714)
Other time (%) = 25.693 (95.3035)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 528 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 528
Ave neighs/atom = 6.51852
Neighbor list builds = 993
Dangerous builds = 946

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examples/shear/log.shear.22Jun07.liberty.4 Normal file
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LAMMPS (22 June 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
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
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
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.68686 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
25 220.91849 -8272.7063 0 -8233.2134 5171.0015 19539.346
50 300 -8239.0761 0 -8185.446 13404.703 19669.87
75 295.11708 -8231.4059 0 -8178.6488 13741.993 19743.549
100 300 -8250.5856 0 -8196.9555 6735.754 19818.526
Loop time of 0.207772 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.172011 (82.7884)
Neigh time (%) = 0.0050208 (2.4165)
Comm time (%) = 0.0227784 (10.9632)
Outpt time (%) = 0.000707865 (0.340693)
Other time (%) = 0.00725383 (3.49125)
Nlocal: 478 ave 490 max 468 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1033.75 ave 1043 max 1021 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 11508.8 ave 12218 max 10874 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 46035
Ave neighs/atom = 24.0769
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 1.70559 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781
100 297.48776 -8255.7637 0 -8220.3225 1519.5936 19869.252
200 300 -8259.5191 0 -8223.7786 407.14026 19843.233
300 306.85093 -8252.9546 0 -8216.3979 -1452.8459 19987.791
400 303.87074 -8246.296 0 -8210.0945 1276.3308 20128.061
500 299.00581 -8241.6473 0 -8206.0253 943.44685 20226.281
600 300 -8228.0773 0 -8192.3369 3740.0009 20307.41
700 302.55478 -8222.4773 0 -8186.4325 6034.1752 20412.441
800 291.55934 -8208.4477 0 -8173.7129 9870.4071 20534.96
900 300.04405 -8197.8106 0 -8162.0649 11858.874 20635.988
1000 303.4363 -8185.1721 0 -8149.0223 15860.089 20755.666
1100 300 -8172.7372 0 -8136.9967 19064.863 20868.017
1200 300 -8163.6948 0 -8127.9543 20503.74 20997.464
1300 300 -8157.774 0 -8122.0336 19017.48 21108.594
1400 301.23169 -8148.1245 0 -8112.2373 19838.433 21245.369
1500 300 -8137.0376 0 -8101.2972 19618.234 21361.383
1600 300 -8129.5673 0 -8093.8269 17832.316 21493.274
1700 300 -8131.9086 0 -8096.1682 15651.56 21609.288
1800 300 -8154.2629 0 -8118.5225 9602.8973 21725.302
1900 300 -8166.6747 0 -8130.9342 7079.4166 21855.971
2000 297.56913 -8164.1963 0 -8128.7455 6008.7168 21970.765
2100 307.18117 -8162.4989 0 -8125.903 5339.1594 22100.212
2200 307.91443 -8165.8526 0 -8129.1693 4903.917 22218.669
2300 307.29809 -8166.6561 0 -8130.0463 4057.1866 22343.232
2400 306.14212 -8165.725 0 -8129.2529 4381.5236 22462.91
2500 306.62123 -8166.8443 0 -8130.3151 2924.8251 22583.809
2600 300 -8166.6003 0 -8130.8598 2179.9998 22701.045
2700 309.89171 -8168.2224 0 -8131.3035 3044.4626 22836.599
2800 305.74412 -8166.2652 0 -8129.8404 1099.7498 22952.613
2900 301.2671 -8170.7739 0 -8134.8825 -2699.4417 23073.512
3000 300 -8171.8299 0 -8136.0895 -3656.4591 23189.527
Loop time of 6.63055 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 5.21397 (78.6355)
Neigh time (%) = 0.273334 (4.12235)
Comm time (%) = 0.765037 (11.5381)
Outpt time (%) = 0.153763 (2.31901)
Other time (%) = 0.224447 (3.38504)
Nlocal: 478 ave 508 max 449 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1006.75 ave 1064 max 959 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 11284 ave 12171 max 10415 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 45136
Ave neighs/atom = 23.6067
Neighbor list builds = 216
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
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
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
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.92854 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
25 220.34459 -8272.5701 0 -8233.1798 5170.6956 19539.346
50 300 -8237.7876 0 -8184.1576 13746.642 19678.792
75 292.67269 -8229.8093 0 -8177.4891 14324.984 19737.233
100 300 -8245.8191 0 -8192.189 9038.4055 19770.872
Loop time of 1.25061 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 1.16404 (93.0782)
Neigh time (%) = 0.037578 (3.00478)
Comm time (%) = 0.012906 (1.03198)
Outpt time (%) = 0.001262 (0.100911)
Other time (%) = 0.034818 (2.78409)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2122 ave 2122 max 2122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45975 ave 45975 max 45975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45975
Ave neighs/atom = 24.0455
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 2.00339 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399
100 300 -8263.5777 0 -8227.8373 2795.3643 19788.083
200 295.48797 -8257.8787 0 -8222.6759 2179.0845 19913.732
300 292.48667 -8250.5584 0 -8215.7131 2.9847512 20043.736
400 304.93883 -8245.9033 0 -8209.5745 179.50544 20125.384
500 294.27283 -8241.2854 0 -8206.2272 829.41012 20145.713
600 302.25208 -8230.3821 0 -8194.3734 4273.5024 20285.46
700 300 -8223.3443 0 -8187.6038 6565.4269 20406.893
800 303.62781 -8211.0391 0 -8174.8665 8116.0638 20515.088
900 297.87427 -8197.7869 0 -8162.2997 10317.159 20621.333
1000 300 -8181.081 0 -8145.3406 13621.801 20748.339
1100 307.26338 -8166.9162 0 -8130.3105 17420.976 20877.786
1200 300.29796 -8153.8084 0 -8118.0325 20385.904 20986.474
1300 300 -8147.0071 0 -8111.2667 21178.857 21115.921
1400 300 -8137.1276 0 -8101.3872 21423.889 21246.59
1500 308.75316 -8131.6139 0 -8094.8306 20067.792 21365.047
1600 300 -8133.2906 0 -8097.5501 16682.824 21477.398
1700 308.52741 -8149.3473 0 -8112.5909 11697.908 21599.518
1800 300 -8152.6978 0 -8116.9573 9550.2281 21737.514
1900 308.57591 -8146.2494 0 -8109.4873 9662.4382 21859.635
2000 308.26812 -8146.4139 0 -8109.6884 9661.2057 21976.871
2100 302.17107 -8146.0627 0 -8110.0636 8521.2058 22094.106
2200 305.08447 -8151.7703 0 -8115.4241 4427.9711 22218.669
2300 300 -8166.2097 0 -8130.4693 -1334.8828 22346.896
2400 304.42128 -8165.4861 0 -8129.219 -931.52307 22464.131
2500 291.59698 -8160.1078 0 -8125.3684 2248.0287 22592.358
2600 304.33702 -8161.3244 0 -8125.0673 3566.8213 22704.709
2700 308.4539 -8163.6628 0 -8126.9152 1887.5801 22825.608
2800 309.42404 -8163.7723 0 -8126.9092 -395.06508 22946.507
2900 307.81471 -8165.3682 0 -8128.6967 -3460.652 23077.176
3000 299.7731 -8165.3688 0 -8129.6554 -5437.2745 23191.969
Loop time of 41.7807 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 38.0687 (91.1155)
Neigh time (%) = 2.03169 (4.86276)
Comm time (%) = 0.401437 (0.960819)
Outpt time (%) = 0.279676 (0.66939)
Other time (%) = 0.999203 (2.39154)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2089 ave 2089 max 2089 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45088 ave 45088 max 45088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45088
Ave neighs/atom = 23.5816
Neighbor list builds = 216
Dangerous builds = 0

160
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LAMMPS (22 June 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
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
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
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.67464 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
25 221.73981 -7320.8381 0 -7287.0455 1130.0476 19599.582
50 300 -7293.1759 0 -7247.4566 8052.1835 19662.062
75 293.25753 -7287.1687 0 -7242.4769 7429.1313 19732.777
100 300 -7300.0537 0 -7254.3344 1198.4581 19807.395
Loop time of 0.17824 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.14804 (83.0562)
Neigh time (%) = 0.00533068 (2.99073)
Comm time (%) = 0.0173439 (9.73062)
Outpt time (%) = 0.000686049 (0.384901)
Other time (%) = 0.00684005 (3.83754)
Nlocal: 427 ave 435 max 419 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 780.25 ave 792 max 769 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 9878.75 ave 10203 max 9534 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 39515
Ave neighs/atom = 23.1352
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 1.69123 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521
100 307.23986 -7307.219 0 -7276.0171 -5006.3499 19862.724
200 300 -7309.7515 0 -7279.2849 -9319.6187 19862.401
300 298.46847 -7303.3937 0 -7273.0826 -9727.416 20012.256
400 298.27255 -7299.2458 0 -7268.9546 -7916.7896 20056.15
500 297.5947 -7299.7495 0 -7269.5271 -6499.9287 20136.515
600 299.11571 -7294.7189 0 -7264.342 -4738.4592 20278.808
700 299.12204 -7285.1912 0 -7254.8138 -1900.5818 20396.287
800 300 -7279.6074 0 -7249.1408 -601.56409 20516.31
900 300 -7272.2062 0 -7241.7396 372.01695 20624.997
1000 297.17814 -7265.7734 0 -7235.5934 -1620.5152 20750.781
1100 300 -7257.7175 0 -7227.2509 -1422.3295 20870.459
1200 300 -7254.9538 0 -7224.4872 -2924.6246 20990.137
1300 300 -7257.9757 0 -7227.5091 -4069.1414 21123.248
1400 300 -7265.0693 0 -7234.6027 -6549.1146 21249.033
1500 305.40659 -7268.4 0 -7237.3844 -9980.0284 21360.162
1600 307.73328 -7272.8967 0 -7241.6447 -12845.156 21479.84
1700 308.89481 -7272.8308 0 -7241.4609 -14742.73 21599.518
1800 301.22537 -7272.7599 0 -7242.1688 -15363.965 21736.293
1900 294.08915 -7269.2219 0 -7239.3555 -17918.885 21854.75
2000 300 -7267.3723 0 -7236.9057 -22110.158 21970.765
2100 303.71749 -7266.6269 0 -7235.7828 -24452.593 22103.876
2200 305.09813 -7260.5568 0 -7229.5724 -22990.432 22219.89
2300 302.38637 -7258.8153 0 -7228.1063 -21646.154 22335.905
2400 305.66165 -7262.3039 0 -7231.2623 -21131.332 22458.025
2500 298.90421 -7257.9905 0 -7227.6352 -21269.206 22592.358
2600 300.16888 -7256.8469 0 -7226.3631 -23698.687 22699.824
2700 296.33302 -7251.3734 0 -7221.2792 -26655.74 22826.829
2800 296.22091 -7248.3427 0 -7218.2599 -30008.453 22947.728
2900 301.32756 -7250.3222 0 -7219.7207 -28370.97 23080.84
3000 300 -7252.9148 0 -7222.4482 -28938.171 23201.739
Loop time of 5.65794 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 4.48969 (79.352)
Neigh time (%) = 0.226591 (4.00482)
Comm time (%) = 0.582767 (10.3)
Outpt time (%) = 0.15564 (2.75081)
Other time (%) = 0.203256 (3.5924)
Nlocal: 427 ave 441 max 415 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 784 ave 845 max 718 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 9597.25 ave 10151 max 9269 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 38389
Ave neighs/atom = 22.476
Neighbor list builds = 211
Dangerous builds = 0

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LAMMPS (22 June 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
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
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
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.91124 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
25 222.66197 -7321.4403 0 -7287.5071 562.50939 19539.346
50 300 -7292.2273 0 -7246.508 7558.4629 19680.84
75 292.67603 -7286.2016 0 -7241.5984 6828.0763 19738.503
100 300 -7297.4174 0 -7251.698 1627.881 19767.928
Loop time of 1.06407 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 0.989223 (92.9663)
Neigh time (%) = 0.030778 (2.89249)
Comm time (%) = 0.01177 (1.10613)
Outpt time (%) = 0.001512 (0.142096)
Other time (%) = 0.030783 (2.89296)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39444 ave 39444 max 39444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39444
Ave neighs/atom = 23.0937
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 1.97639 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704
100 300 -7311.9184 0 -7281.4518 -5944.573 19791.679
200 298.46333 -7306.5409 0 -7276.2304 -6669.0732 19903.341
300 298.05646 -7303.4774 0 -7273.2081 -10334.9 20033.654
400 297.71277 -7298.5998 0 -7268.3655 -7644.8753 20112.791
500 300 -7301.3145 0 -7270.8479 -6327.722 20143.842
600 306.29328 -7291.192 0 -7260.0863 -1482.3063 20281.66
700 308.44794 -7289.4349 0 -7258.1103 -3026.5046 20394.034
800 300 -7282.5733 0 -7252.1067 -3555.2034 20513.867
900 300 -7273.9966 0 -7243.53 -1850.9526 20622.554
1000 300 -7266.6095 0 -7236.1429 -1119.6046 20741.011
1100 301.26482 -7261.9024 0 -7231.3073 -1647.8612 20874.123
1200 299.17066 -7259.2281 0 -7228.8457 -1938.4437 20998.686
1300 300 -7263.9553 0 -7233.4887 -3376.9235 21112.258
1400 300 -7270.1139 0 -7239.6473 -5846.3511 21249.033
1500 307.98903 -7273.6991 0 -7242.4211 -6121.5944 21366.268
1600 300 -7278.9972 0 -7248.5306 -9389.2139 21484.725
1700 300 -7279.8403 0 -7249.3737 -14440.631 21615.394
1800 309.55921 -7284.1875 0 -7252.7501 -14795.954 21727.745
1900 299.29406 -7282.5749 0 -7252.18 -15392.232 21848.644
2000 299.964 -7271.7156 0 -7241.2526 -19451.05 21968.322
2100 308.54552 -7272.2334 0 -7240.8989 -23685.178 22100.212
2200 308.49102 -7271.1314 0 -7239.8025 -20630.136 22219.89
2300 290.31543 -7268.9828 0 -7239.4997 -19028.307 22342.011
2400 299.15433 -7259.7686 0 -7229.3878 -14272.769 22459.246
2500 299.15088 -7260.7963 0 -7230.4159 -14923.448 22576.482
2600 301.27999 -7258.5805 0 -7227.9839 -15706.203 22702.266
2700 307.83121 -7254.9828 0 -7223.7209 -19761.07 22830.493
2800 300 -7254.6086 0 -7224.142 -23849.892 22944.065
2900 303.23126 -7256.0886 0 -7225.2938 -23451.705 23080.84
3000 290.86402 -7255.5292 0 -7225.9904 -20678.136 23202.96
Loop time of 33.1295 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 29.994 (90.5356)
Neigh time (%) = 1.58958 (4.79809)
Comm time (%) = 0.381225 (1.15071)
Outpt time (%) = 0.25781 (0.778188)
Other time (%) = 0.906904 (2.73745)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1882 ave 1882 max 1882 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38801 ave 38801 max 38801 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38801
Ave neighs/atom = 22.7172
Neighbor list builds = 205
Dangerous builds = 0