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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1398 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-01-18 22:12:52 +00:00
parent 8cbf38c2ba
commit 59f821e981
4 changed files with 336 additions and 30 deletions

36
examples/ellipse/log.ellipse.22Jan08.linux.1 → examples/ellipse/log.gayberne.22Jan08.linux.1
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@ -1,5 +1,5 @@
LAMMPS (22 Jan 2008)
# Ellipsoids in LJ background fluid
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
@ -32,6 +32,11 @@ 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
#pair_style resquared 4.0
#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
@ -39,7 +44,9 @@ thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.gayberne tag type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.resquared # 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
@ -70,13 +77,13 @@ Step rot E_pair TotEng Press Volume
1800 2.0251982 -2.9795387 -0.83247158 0.52149705 1215.081
1900 2.0206629 -3.159343 -1.0374344 0.72829367 1196.1151
2000 1.9665091 -3.2421939 -1.2158182 0.66817261 1162.3788
Loop time of 1.24727 on 1 procs for 2000 steps with 400 atoms
Loop time of 1.24429 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.9127 (73.1756)
Neigh time (%) = 0.0137322 (1.10098)
Comm time (%) = 0.0217996 (1.74778)
Outpt time (%) = 0.0341289 (2.73628)
Other time (%) = 0.264913 (21.2394)
Pair time (%) = 0.909927 (73.1284)
Neigh time (%) = 0.0135996 (1.09297)
Comm time (%) = 0.0220442 (1.77163)
Outpt time (%) = 0.0341184 (2.74201)
Other time (%) = 0.264597 (21.2649)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -119,13 +126,13 @@ Step rot E_pair TotEng Press Volume
3800 1.9107307 -3.1825901 -1.2150398 0.76019944 1162.3788
3900 2.0003232 -3.2826031 -1.2144381 0.69551187 1162.3788
4000 1.9971268 -3.2783688 -1.2104061 0.67606395 1162.3788
Loop time of 1.42325 on 1 procs for 2000 steps with 400 atoms
Loop time of 1.41674 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.13466 (79.7228)
Neigh time (%) = 0.0079174 (0.55629)
Comm time (%) = 0.0247726 (1.74057)
Outpt time (%) = 0.0347703 (2.44301)
Other time (%) = 0.221135 (15.5373)
Pair time (%) = 1.12906 (79.6942)
Neigh time (%) = 0.00786209 (0.554944)
Comm time (%) = 0.0250032 (1.76484)
Outpt time (%) = 0.0342295 (2.41608)
Other time (%) = 0.220585 (15.5699)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -138,4 +145,3 @@ Total # of neighbors = 2941
Ave neighs/atom = 7.3525
Neighbor list builds = 46
Dangerous builds = 0

36
examples/ellipse/log.ellipse.22Jan08.linux.4 → examples/ellipse/log.gayberne.22Jan08.linux.4
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@ -1,5 +1,5 @@
LAMMPS (22 Jan 2008)
# Ellipsoids in LJ background fluid
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
@ -32,6 +32,11 @@ 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
#pair_style resquared 4.0
#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
@ -39,7 +44,9 @@ thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.gayberne tag type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.resquared # 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
@ -70,13 +77,13 @@ Step rot E_pair TotEng Press Volume
1800 2.0251982 -2.9795387 -0.83247158 0.52149705 1215.081
1900 2.0206629 -3.159343 -1.0374344 0.72829366 1196.1151
2000 1.9665091 -3.2421939 -1.2158181 0.66817261 1162.3788
Loop time of 1.48207 on 4 procs for 2000 steps with 400 atoms
Loop time of 1.46444 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.262188 (17.6907)
Neigh time (%) = 0.00443518 (0.299256)
Comm time (%) = 0.704064 (47.5055)
Outpt time (%) = 0.0561122 (3.78607)
Other time (%) = 0.45527 (30.7185)
Pair time (%) = 0.262376 (17.9165)
Neigh time (%) = 0.00438559 (0.299471)
Comm time (%) = 0.695195 (47.4716)
Outpt time (%) = 0.0550858 (3.76155)
Other time (%) = 0.447401 (30.5509)
Nlocal: 100 ave 114 max 89 min
Histogram: 1 0 0 1 1 0 0 0 0 1
@ -119,13 +126,13 @@ Step rot E_pair TotEng Press Volume
3800 1.9125088 -3.1825738 -1.2078829 0.58850208 1162.3788
3900 1.9607643 -3.2375105 -1.2043099 0.50399343 1162.3788
4000 1.9199974 -3.1924774 -1.1937016 1.0992901 1162.3788
Loop time of 1.30075 on 4 procs for 2000 steps with 400 atoms
Loop time of 1.30653 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.334192 (25.6922)
Neigh time (%) = 0.00251496 (0.193347)
Comm time (%) = 0.706741 (54.3333)
Outpt time (%) = 0.0571193 (4.39126)
Other time (%) = 0.200183 (15.3898)
Pair time (%) = 0.327121 (25.0374)
Neigh time (%) = 0.00245857 (0.188176)
Comm time (%) = 0.719629 (55.0794)
Outpt time (%) = 0.0561987 (4.30137)
Other time (%) = 0.201123 (15.3937)
Nlocal: 100 ave 112 max 86 min
Histogram: 1 0 1 0 0 0 0 0 1 1
@ -138,4 +145,3 @@ Total # of neighbors = 2962
Ave neighs/atom = 7.405
Neighbor list builds = 46
Dangerous builds = 0

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examples/ellipse/log.resquared.22Jan08.linux.1 Normal file
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LAMMPS (22 Jan 2008)
# RESquared 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
45 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
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 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.gayberne # tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.resquared 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 = 2.5914 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1564825 0 2.391 0.04782 20000
100 1.838411 0 2.0383382 0.039613219 20582.404
200 2.1840926 0 2.4216127 0.046586295 20792.49
300 1.9277991 0 2.1374472 0.045558261 18766.715
400 2.1319531 -2.8942919e-05 2.363774 0.067309702 14046.61
500 2.0159993 0.025003198 2.192142 0.12365516 8758.5309
600 2.0502951 0.082711121 2.1869989 0.2914997 4953.8346
700 2.1346857 0.19349894 2.4259271 0.83641851 2850.8843
800 1.7500542 0.31713085 2.1311843 1.7957167 1886.6112
900 1.7954476 0.2020433 2.0534119 1.5200892 1555.0105
1000 1.9617502 0.11559302 2.1882642 1.2192863 1547.216
1100 2.029642 0.11732822 2.28763 1.0329822 1776.5022
1200 1.932547 0.055745664 2.0771327 0.56592224 2220.4328
1300 2.1273555 0.022049267 2.2406619 0.39671812 2776.2006
1400 1.9348031 0.041576451 2.0680195 0.34763372 3284.7889
1500 2.145937 0.05819306 2.2958826 0.39414678 3503.5721
1600 1.925752 0.13306059 2.1690861 0.54488654 3303.1224
1700 2.1312499 0.14010948 2.3616269 0.69736084 2818.368
1800 1.9625036 0.1767238 2.2308375 0.96298372 2310.965
1900 1.9411448 0.23022702 2.301414 1.3620231 1895.482
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
Loop time of 2.25316 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.93077 (85.6918)
Neigh time (%) = 0.0138793 (0.615992)
Comm time (%) = 0.0163372 (0.725077)
Outpt time (%) = 0.0341411 (1.51525)
Other time (%) = 0.258029 (11.4518)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 208 ave 208 max 208 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1896 ave 1896 max 1896 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1896
Ave neighs/atom = 4.74
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.5924 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
2100 2.0653748 0.15379429 2.3138055 1.2692328 1665.9849
2200 2.0296751 0.19333047 2.3431266 1.4194185 1665.9849
2300 2.031445 0.19134884 2.3346008 1.4455022 1665.9849
2400 2.0416873 0.17998527 2.3055585 1.3819478 1665.9849
2500 1.9732771 0.25585123 2.3498283 1.7058898 1665.9849
2600 2.0186547 0.2054707 2.2994266 1.5413429 1665.9849
2700 2.0300352 0.19285781 2.2682949 1.384344 1665.9849
2800 2.0258032 0.1974685 2.3003298 1.4218564 1665.9849
2900 2.0506397 0.16996513 2.3131175 1.3967849 1665.9849
3000 1.9768248 0.251823 2.3267822 1.6698709 1665.9849
3100 2.0005064 0.22563045 2.2868834 1.540767 1665.9849
3200 2.0309162 0.19193638 2.3082578 1.4597896 1665.9849
3300 2.0483286 0.17251967 2.3200717 1.3676295 1665.9849
3400 2.0019218 0.22424333 2.3467104 1.6024582 1665.9849
3500 2.0060182 0.21959616 2.3235298 1.582482 1665.9849
3600 2.0000757 0.22586393 2.3411772 1.5632004 1665.9849
3700 2.0293619 0.1936261 2.3426439 1.4262837 1665.9849
3800 2.0256136 0.19784063 2.3112499 1.5090404 1665.9849
3900 2.0554399 0.16475477 2.3129868 1.281966 1665.9849
4000 2.0845029 0.13253315 2.3282445 1.2142775 1665.9849
Loop time of 4.02238 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.74757 (93.1678)
Neigh time (%) = 0.00655437 (0.162947)
Comm time (%) = 0.0214994 (0.534494)
Outpt time (%) = 0.0341754 (0.849631)
Other time (%) = 0.212587 (5.2851)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 206 ave 206 max 206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1869 ave 1869 max 1869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1869
Ave neighs/atom = 4.6725
Neighbor list builds = 50
Dangerous builds = 0

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examples/ellipse/log.resquared.22Jan08.linux.4 Normal file
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LAMMPS (22 Jan 2008)
# RESquared 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
45 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
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 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.gayberne # tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.resquared 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 = 2.55985 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1564825 0 2.391 0.04782 20000
100 1.838411 0 2.0383382 0.039613219 20582.404
200 2.1840926 0 2.4216127 0.046586295 20792.49
300 1.9277991 0 2.1374472 0.045558261 18766.715
400 2.1319531 -2.8942919e-05 2.363774 0.067309702 14046.61
500 2.0159993 0.025003198 2.192142 0.12365516 8758.5309
600 2.0502951 0.082711121 2.1869989 0.2914997 4953.8346
700 2.1346857 0.19349894 2.4259271 0.83641851 2850.8843
800 1.7500542 0.31713085 2.1311843 1.7957167 1886.6112
900 1.7954476 0.2020433 2.0534119 1.5200892 1555.0105
1000 1.9617502 0.11559302 2.1882642 1.2192863 1547.216
1100 2.029642 0.11732822 2.28763 1.0329822 1776.5022
1200 1.932547 0.055745664 2.0771327 0.56592224 2220.4328
1300 2.1273555 0.022049267 2.2406619 0.39671812 2776.2006
1400 1.9348031 0.041576451 2.0680195 0.34763372 3284.7889
1500 2.145937 0.05819306 2.2958826 0.39414678 3503.5721
1600 1.925752 0.13306059 2.1690861 0.54488654 3303.1224
1700 2.1312499 0.14010948 2.3616269 0.69736084 2818.368
1800 1.9625036 0.1767238 2.2308375 0.96298372 2310.965
1900 1.9411448 0.23022702 2.301414 1.3620231 1895.482
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
Loop time of 1.70624 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.53287 (31.2306)
Neigh time (%) = 0.00461602 (0.270537)
Comm time (%) = 0.702465 (41.1703)
Outpt time (%) = 0.0564025 (3.30566)
Other time (%) = 0.40989 (24.0229)
Nlocal: 100 ave 103 max 98 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 118.25 ave 121 max 114 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 474 ave 509 max 460 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 1896
Ave neighs/atom = 4.74
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.56054 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
2100 2.0653748 0.15379429 2.3138055 1.2692328 1665.9849
2200 2.0296751 0.19333047 2.3431266 1.4194185 1665.9849
2300 2.031445 0.19134884 2.3346008 1.4455022 1665.9849
2400 2.0416873 0.17998527 2.3055585 1.3819478 1665.9849
2500 1.9732771 0.25585123 2.3498283 1.7058898 1665.9849
2600 2.0186547 0.2054707 2.2994266 1.5413428 1665.9849
2700 2.0300352 0.19285781 2.2682949 1.384344 1665.9849
2800 2.0258032 0.19746848 2.3003298 1.4218563 1665.9849
2900 2.0506396 0.16996525 2.3131178 1.3967855 1665.9849
3000 1.9768248 0.25182299 2.3267824 1.6698709 1665.9849
3100 2.0005068 0.22563005 2.286884 1.5407669 1665.9849
3200 2.0309161 0.19193653 2.3082598 1.4597915 1665.9849
3300 2.0483373 0.1725101 2.3200665 1.3675732 1665.9849
3400 2.0019136 0.22425249 2.3467007 1.6025191 1665.9849
3500 2.0060157 0.21959893 2.3235339 1.5824949 1665.9849
3600 2.0000689 0.22587176 2.3411757 1.5633105 1665.9849
3700 2.0292856 0.19371118 2.342629 1.4266405 1665.9849
3800 2.0255614 0.19789877 2.3112561 1.5093285 1665.9849
3900 2.0554045 0.16479373 2.3130089 1.2821629 1665.9849
4000 2.0844571 0.13258442 2.3284091 1.2146999 1665.9849
Loop time of 1.94966 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 1.01464 (52.0418)
Neigh time (%) = 0.00212574 (0.109032)
Comm time (%) = 0.695318 (35.6636)
Outpt time (%) = 0.0557072 (2.85728)
Other time (%) = 0.181869 (9.32825)
Nlocal: 100 ave 108 max 90 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 122.25 ave 128 max 114 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 467.25 ave 524 max 403 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 1869
Ave neighs/atom = 4.6725
Neighbor list builds = 50
Dangerous builds = 0