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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1395 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2008-01-18 21:48:26 +00:00
parent cd1297d507
commit fd0e404679
64 changed files with 2644 additions and 2937 deletions
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examples/ellipse/log.ellipse.22Jan08.linux.1 Normal file
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LAMMPS (22 Jan 2008)
# 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
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 = 2.5914 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 2.1320898 -0.00053003398 2.3634243 0.067260787 14046.57
500 2.0125529 -0.044948035 2.1687617 0.10245426 8750.3467
600 2.0786425 -0.23406014 1.9442479 0.22613511 4851.3617
700 2.2133435 -0.69014988 1.5954372 0.54309778 2612.3736
800 1.9098353 -1.4850103 0.51347537 1.3704181 1483.4256
900 2.1260352 -2.8142501 -0.59067406 3.1656374 962.6457
1000 1.6045695 -4.3144152 -2.6174061 2.546312 768.15096
1100 1.8583682 -4.7215526 -2.7550345 2.2351608 721.1814
1200 2.0033979 -4.4224318 -2.3394492 1.497766 762.68534
1300 1.9444498 -3.9403965 -1.8821931 0.71183994 853.44376
1400 2.0389741 -3.5330024 -1.3903083 0.56027235 953.42519
1500 1.9557022 -3.3648518 -1.315844 0.5652338 1045.7045
1600 2.0224945 -3.2441781 -1.0982354 0.54437381 1120.6403
1700 2.0299156 -3.0845458 -0.92406001 0.48408419 1184.9462
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
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)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 241 ave 241 max 241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2899 ave 2899 max 2899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2899
Ave neighs/atom = 7.2475
Neighbor list builds = 116
Dangerous builds = 66
# 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 1.9665091 -3.2421939 -1.2158182 0.66817261 1162.3788
2100 1.8708937 -3.1339765 -1.2087845 0.65485928 1162.3788
2200 1.9126691 -3.1751558 -1.1398886 0.64965308 1162.3788
2300 1.8486671 -3.106799 -1.1627689 0.7992831 1162.3788
2400 1.9064396 -3.1727593 -1.1529333 0.65253656 1162.3788
2500 1.9271407 -3.196764 -1.170919 0.69672634 1162.3788
2600 1.9128576 -3.1780462 -1.1737268 0.49259816 1162.3788
2700 1.8577605 -3.1183107 -1.1469431 0.69798298 1162.3788
2800 1.8968015 -3.1635109 -1.1706025 0.72238772 1162.3788
2900 1.9243377 -3.1936655 -1.2164049 0.71602441 1162.3788
3000 1.9744936 -3.2522509 -1.1675852 0.973599 1162.3788
3100 1.9958325 -3.2744643 -1.1947121 0.74284674 1162.3788
3200 1.970421 -3.2446567 -1.1999887 0.82553849 1162.3788
3300 2.0258625 -3.3090808 -1.1388773 0.92883543 1162.3788
3400 1.8890826 -3.1558929 -1.1949006 0.79651332 1162.3788
3500 1.995457 -3.2762027 -1.1679919 0.56633624 1162.3788
3600 1.931652 -3.2051941 -1.1993639 0.64332962 1162.3788
3700 1.9274391 -3.1996536 -1.1892997 0.30677766 1162.3788
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
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)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 240 ave 240 max 240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2941 ave 2941 max 2941 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2941
Ave neighs/atom = 7.3525
Neighbor list builds = 46
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
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 = 2.55985 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 2.1320898 -0.00053003398 2.3634243 0.067260787 14046.57
500 2.0125529 -0.044948035 2.1687617 0.10245426 8750.3467
600 2.0786425 -0.23406014 1.9442479 0.22613511 4851.3617
700 2.2133435 -0.69014988 1.5954372 0.54309778 2612.3736
800 1.9098353 -1.4850103 0.51347537 1.3704181 1483.4256
900 2.1260352 -2.8142501 -0.59067406 3.1656374 962.6457
1000 1.6045695 -4.3144152 -2.6174061 2.546312 768.15096
1100 1.8583682 -4.7215526 -2.7550345 2.2351608 721.1814
1200 2.0033979 -4.4224318 -2.3394492 1.497766 762.68534
1300 1.9444498 -3.9403965 -1.8821931 0.71183994 853.44376
1400 2.0389741 -3.5330024 -1.3903083 0.56027235 953.42519
1500 1.9557022 -3.3648518 -1.315844 0.5652338 1045.7045
1600 2.0224945 -3.2441781 -1.0982355 0.54437381 1120.6403
1700 2.0299156 -3.0845458 -0.92406001 0.48408419 1184.9462
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
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)
Nlocal: 100 ave 114 max 89 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 143.75 ave 150 max 134 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 724.75 ave 888 max 603 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 2899
Ave neighs/atom = 7.2475
Neighbor list builds = 116
Dangerous builds = 66
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.56108 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9665091 -3.2421939 -1.2158181 0.66817261 1162.3788
2100 1.8708938 -3.1339766 -1.2087845 0.65485904 1162.3788
2200 1.9126692 -3.1751559 -1.1398886 0.64965265 1162.3788
2300 1.8486668 -3.1067986 -1.1627689 0.79928388 1162.3788
2400 1.9064384 -3.172758 -1.1529331 0.65253881 1162.3788
2500 1.9271407 -3.1967644 -1.170919 0.69672795 1162.3788
2600 1.9128672 -3.1780573 -1.173728 0.49255026 1162.3788
2700 1.8577651 -3.118316 -1.1469407 0.69794398 1162.3788
2800 1.896808 -3.1635198 -1.1706185 0.72233802 1162.3788
2900 1.9244369 -3.1937775 -1.2164447 0.71557304 1162.3788
3000 1.9743523 -3.2520956 -1.1675977 0.97482809 1162.3788
3100 1.996246 -3.2749273 -1.194868 0.74170535 1162.3788
3200 1.9705094 -3.2447603 -1.1997475 0.8278483 1162.3788
3300 2.0273054 -3.3108123 -1.1389432 0.92136684 1162.3788
3400 1.8906596 -3.1579072 -1.1949426 0.76619179 1162.3788
3500 1.9983053 -3.2795554 -1.1695681 0.60352395 1162.3788
3600 1.9635271 -3.2409899 -1.2167445 0.4863415 1162.3788
3700 1.9144359 -3.1843815 -1.2155475 0.42825617 1162.3788
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
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)
Nlocal: 100 ave 112 max 86 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 152.5 ave 161 max 131 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 740.5 ave 888 max 623 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 2962
Ave neighs/atom = 7.405
Neighbor list builds = 46
Dangerous builds = 0

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LAMMPS (5 Oct 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 = 2.24808 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1910653 0 2.391 0.04782 20000
100 1.8095627 0 1.9746853 0.038390446 20574.757
200 2.2122326 0 2.4140988 0.046564771 20737.556
300 1.9063379 -1.214926e-05 2.0802791 0.044571535 18668.848
400 2.14459 -0.00065227227 2.3396287 0.067112127 13932.123
500 1.9839619 -0.027216549 2.1106955 0.097030863 8670.8439
600 2.1813245 -0.22525728 1.9958423 0.22257746 4767.8119
700 2.1573483 -0.58326488 1.5801843 0.84713222 2584.519
800 1.597355 -1.396491 0.18782136 0.97433767 1507.2721
900 2.437693 -2.7450948 -0.224847 2.3554255 974.53876
1000 1.4397708 -4.3642585 -2.8750355 2.3391635 758.96341
1100 2.0019719 -5.0196156 -2.9228438 3.4499334 690.43198
1200 1.8533049 -4.6254312 -2.676135 0.32615846 747.72266
1300 2.1345511 -4.0901956 -1.8707205 1.2073927 822.89299
1400 1.8835579 -3.7674375 -1.7862324 0.15959829 916.22676
1500 2.1664981 -3.601865 -1.3511416 0.43163361 988.61927
1600 1.8804439 -3.403727 -1.4501073 0.71137234 1048.0854
1700 2.1047833 -3.4408214 -1.2233404 0.68547035 1090.6363
1800 1.9209703 -3.4235716 -1.425094 0.66306974 1116.0986
1900 2.0782358 -3.4434636 -1.2999904 0.85753296 1123.1083
2000 1.913813 -3.4337877 -1.4476809 0.76521957 1122.0104
Loop time of 1.34096 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.998966 (74.4963)
Neigh time (%) = 0.0142684 (1.06404)
Comm time (%) = 0.0232384 (1.73297)
Outpt time (%) = 0.0350761 (2.61574)
Other time (%) = 0.269413 (20.091)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 289 ave 289 max 289 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2982 ave 2982 max 2982 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2982
Ave neighs/atom = 7.455
Neighbor list builds = 117
Dangerous builds = 68
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.24907 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.913813 -3.4337877 -1.4476809 0.76521957 1122.0104
2100 1.9392734 -3.4624792 -1.4465536 0.55728534 1122.0104
2200 1.9484372 -3.4756538 -1.4300779 0.85520705 1122.0104
2300 1.9932144 -3.5292307 -1.4614194 1.0101492 1122.0104
2400 1.9870773 -3.5233349 -1.4623489 0.84050703 1122.0104
2500 2.008909 -3.5472136 -1.4365552 0.62243452 1122.0104
2600 1.9248384 -3.4544998 -1.4277814 0.62904921 1122.0104
2700 1.9676982 -3.5014783 -1.4163428 0.93455061 1122.0104
2800 1.9634201 -3.4965253 -1.4437866 0.60426251 1122.0104
2900 1.8942982 -3.4183082 -1.4610915 0.96307431 1122.0104
3000 1.9507023 -3.4763696 -1.4868716 0.66418626 1122.0104
3100 1.9692369 -3.4976199 -1.4313664 0.52025108 1122.0104
3200 1.9061527 -3.4236291 -1.4320272 0.21933983 1122.0104
3300 1.8522206 -3.3654471 -1.4250894 0.68162268 1122.0104
3400 1.8435473 -3.3579876 -1.4294877 0.53218256 1122.0104
3500 1.8652812 -3.3822322 -1.4306304 0.64363163 1122.0104
3600 1.906713 -3.4263208 -1.4368148 0.34955899 1122.0104
3700 1.8921623 -3.4096991 -1.4272177 0.49670614 1122.0104
3800 1.8440869 -3.358654 -1.4404377 0.66324137 1122.0104
3900 1.8658234 -3.3813354 -1.4486617 0.65460693 1122.0104
4000 1.7952836 -3.3059557 -1.4696545 0.61997638 1122.0104
Loop time of 1.50554 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.22338 (81.2585)
Neigh time (%) = 0.0090003 (0.597811)
Comm time (%) = 0.0273209 (1.81468)
Outpt time (%) = 0.0354002 (2.35132)
Other time (%) = 0.210441 (13.9777)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 252 ave 252 max 252 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2979 ave 2979 max 2979 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2979
Ave neighs/atom = 7.4475
Neighbor list builds = 47
Dangerous builds = 0

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LAMMPS (5 Oct 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 = 2.21653 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1910653 0 2.391 0.04782 20000
100 1.8095627 0 1.9746853 0.038390446 20574.757
200 2.2122326 0 2.4140988 0.046564771 20737.556
300 1.9063379 -1.214926e-05 2.0802791 0.044571535 18668.848
400 2.14459 -0.00065227227 2.3396287 0.067112127 13932.123
500 1.9839619 -0.027216549 2.1106955 0.097030863 8670.8439
600 2.1813245 -0.22525728 1.9958423 0.22257746 4767.8119
700 2.1573483 -0.58326488 1.5801843 0.84713222 2584.519
800 1.597355 -1.396491 0.18782136 0.97433767 1507.2721
900 2.437693 -2.7450948 -0.224847 2.3554255 974.53876
1000 1.4397708 -4.3642585 -2.8750355 2.3391635 758.96341
1100 2.0019719 -5.0196156 -2.9228438 3.4499334 690.43198
1200 1.8533049 -4.6254312 -2.676135 0.32615846 747.72266
1300 2.1345511 -4.0901956 -1.8707205 1.2073927 822.89299
1400 1.8835579 -3.7674375 -1.7862324 0.15959829 916.22676
1500 2.1664981 -3.601865 -1.3511416 0.43163361 988.61927
1600 1.8804439 -3.403727 -1.4501073 0.71137235 1048.0854
1700 2.1047833 -3.4408214 -1.2233404 0.68547035 1090.6363
1800 1.9209703 -3.4235716 -1.425094 0.66306973 1116.0986
1900 2.0782358 -3.4434636 -1.2999903 0.85753294 1123.1083
2000 1.913813 -3.4337877 -1.4476809 0.7652196 1122.0104
Loop time of 1.47109 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.268236 (18.2338)
Neigh time (%) = 0.00441265 (0.299958)
Comm time (%) = 0.695434 (47.2734)
Outpt time (%) = 0.0549261 (3.7337)
Other time (%) = 0.448082 (30.4592)
Nlocal: 100 ave 108 max 82 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Nghost: 146.25 ave 154 max 139 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 745.5 ave 843 max 560 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 2982
Ave neighs/atom = 7.455
Neighbor list builds = 117
Dangerous builds = 68
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.21749 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.913813 -3.4337877 -1.4476809 0.7652196 1122.0104
2100 1.9392734 -3.4624792 -1.4465536 0.55728527 1122.0104
2200 1.9484372 -3.4756538 -1.430078 0.85520698 1122.0104
2300 1.9932147 -3.5292311 -1.4614196 1.0101481 1122.0104
2400 1.9870766 -3.5233342 -1.4623482 0.84050897 1122.0104
2500 2.0089076 -3.5472127 -1.4365562 0.62243991 1122.0104
2600 1.9248404 -3.4545027 -1.4277817 0.62903775 1122.0104
2700 1.9676964 -3.5014778 -1.4163444 0.93454271 1122.0104
2800 1.9634123 -3.4965184 -1.4437805 0.6042572 1122.0104
2900 1.8942778 -3.4182826 -1.4610692 0.96320768 1122.0104
3000 1.9508272 -3.4765008 -1.4870311 0.66384122 1122.0104
3100 1.9693971 -3.4977959 -1.4314692 0.51799815 1122.0104
3200 1.9061859 -3.4235391 -1.4320175 0.21930105 1122.0104
3300 1.8507455 -3.3642208 -1.4253415 0.68947825 1122.0104
3400 1.8475658 -3.3622885 -1.4300297 0.51439111 1122.0104
3500 1.8686479 -3.3851861 -1.4239649 0.65619019 1122.0104
3600 1.9045242 -3.4225094 -1.4283796 0.3990323 1122.0104
3700 1.8508053 -3.3647144 -1.4275746 0.63320963 1122.0104
3800 1.8686968 -3.3861007 -1.450784 0.53652248 1122.0104
3900 1.9279105 -3.4508746 -1.4489514 0.41331452 1122.0104
4000 1.8881881 -3.4077594 -1.4471586 0.48356986 1122.0104
Loop time of 1.25137 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.335973 (26.8483)
Neigh time (%) = 0.00260264 (0.207982)
Comm time (%) = 0.674996 (53.9404)
Outpt time (%) = 0.055564 (4.44024)
Other time (%) = 0.182239 (14.5631)
Nlocal: 100 ave 115 max 76 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 142.5 ave 157 max 133 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 736.75 ave 891 max 512 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 2947
Ave neighs/atom = 7.3675
Neighbor list builds = 47
Dangerous builds = 0

147
examples/ellipse/log.resquared.5Oct07.linux.1
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@ -1,147 +0,0 @@
LAMMPS (5 Oct 2007)
# 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
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
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 = 2.24808 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1910653 0 2.391 0.04782 20000
100 1.8095627 0 1.9746853 0.038390446 20574.757
200 2.2122326 0 2.4140988 0.046564771 20737.556
300 1.9063376 -5.7129771e-07 2.0802903 0.044572407 18668.848
400 2.1443027 -4.1525764e-05 2.3399288 0.067177103 13932.17
500 1.9935737 0.020739237 2.1709918 0.11614411 8676.7091
600 2.0758546 0.14241195 2.2377541 0.42402912 4825.6843
700 2.0126007 0.13606636 2.1889045 0.70828423 2838.8217
800 1.6462918 0.2046157 1.8512218 1.2376454 1892.2685
900 2.190847 0.30083633 2.5138928 2.2184314 1514.3405
1000 1.3598624 0.091198957 1.4911943 0.88175797 1539.8707
1100 2.8445227 0.11328079 3.0592352 1.2795802 1730.3911
1200 1.3382362 0.040390813 1.4257646 0.42380767 2154.7415
1300 2.7512047 0.077319995 2.9113574 0.65020381 2663.8909
1400 1.5020205 0.036823371 1.5702929 0.29246763 3222.4577
1500 2.3675283 0.038543836 2.4356404 0.40520771 3466.977
1600 1.7835072 0.093405966 1.9051993 0.45990301 3303.3659
1700 1.9533673 0.12927983 2.1439979 0.65856182 2800.1559
1800 2.1374757 0.13952435 2.3364613 0.88232342 2276.3173
1900 1.5819658 0.19418472 1.784052 1.1003878 1899.366
2000 2.3775502 0.31125894 2.8031834 1.9866756 1686.1093
Loop time of 2.19601 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.87699 (85.4727)
Neigh time (%) = 0.0140491 (0.639752)
Comm time (%) = 0.015686 (0.714296)
Outpt time (%) = 0.0341499 (1.55508)
Other time (%) = 0.255136 (11.6181)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1817 ave 1817 max 1817 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1817
Ave neighs/atom = 4.5425
Neighbor list builds = 152
Dangerous builds = 83
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.24907 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.3775502 0.31125894 2.8031834 1.9866756 1686.1093
2100 2.4704706 0.20979826 2.8181123 1.5528216 1686.1093
2200 2.4870518 0.19166309 2.8234014 1.5033296 1686.1093
2300 2.4979294 0.17991997 2.8150474 1.4820467 1686.1093
2400 2.4528898 0.22907402 2.8177607 1.6359713 1686.1093
2500 2.4736478 0.20644427 2.8205459 1.5542491 1686.1093
2600 2.4459311 0.23690159 2.7285446 1.7818242 1686.1093
2700 2.5049454 0.17219678 2.7322165 1.4206231 1686.1093
2800 2.4375688 0.2457243 2.7808663 1.7703798 1686.1093
2900 2.4809391 0.19837454 2.7666384 1.5039555 1686.1093
3000 2.4057445 0.28017977 2.8000918 2.0077193 1686.1093
3100 2.501681 0.175622 2.7685873 1.5086241 1686.1093
3200 2.5137428 0.16265329 2.7993588 1.4172503 1686.1093
3300 2.4554425 0.22611273 2.8045787 1.701504 1686.1093
3400 2.4748543 0.20510794 2.8207304 1.6366181 1686.1093
3500 2.4759985 0.20389249 2.8002404 1.6521669 1686.1093
3600 2.4758346 0.20403353 2.7711828 1.5710022 1686.1093
3700 2.4787227 0.20086917 2.770613 1.5403745 1686.1093
3800 2.446548 0.23584146 2.7262009 1.6718807 1686.1093
3900 2.4748471 0.20500365 2.7587198 1.5545469 1686.1093
4000 2.4462716 0.23631996 2.8256605 1.7138586 1686.1093
Loop time of 3.82609 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.55299 (92.8621)
Neigh time (%) = 0.00729918 (0.190774)
Comm time (%) = 0.0212815 (0.556221)
Outpt time (%) = 0.0343854 (0.89871)
Other time (%) = 0.210135 (5.49216)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1802 ave 1802 max 1802 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1802
Ave neighs/atom = 4.505
Neighbor list builds = 55
Dangerous builds = 0

147
examples/ellipse/log.resquared.5Oct07.linux.4
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LAMMPS (5 Oct 2007)
# 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
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
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 = 2.21653 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1910653 0 2.391 0.04782 20000
100 1.8095627 0 1.9746853 0.038390446 20574.757
200 2.2122326 0 2.4140988 0.046564771 20737.556
300 1.9063376 -5.7129771e-07 2.0802903 0.044572407 18668.848
400 2.1443027 -4.1525764e-05 2.3399288 0.067177103 13932.17
500 1.9935737 0.020739237 2.1709918 0.11614411 8676.7091
600 2.0758546 0.14241195 2.2377541 0.42402912 4825.6843
700 2.0126007 0.13606636 2.1889045 0.70828423 2838.8217
800 1.6462918 0.2046157 1.8512218 1.2376454 1892.2685
900 2.190847 0.30083633 2.5138928 2.2184314 1514.3405
1000 1.3598624 0.091198957 1.4911943 0.88175797 1539.8707
1100 2.8445227 0.11328079 3.0592352 1.2795802 1730.3911
1200 1.3382362 0.040390813 1.4257646 0.42380767 2154.7415
1300 2.7512047 0.077319995 2.9113574 0.65020381 2663.8909
1400 1.5020205 0.036823371 1.5702929 0.29246763 3222.4577
1500 2.3675283 0.038543836 2.4356404 0.40520771 3466.977
1600 1.7835072 0.093405966 1.9051993 0.45990301 3303.3659
1700 1.9533673 0.12927983 2.1439979 0.65856182 2800.1559
1800 2.1374757 0.13952435 2.3364613 0.88232342 2276.3173
1900 1.5819658 0.19418472 1.784052 1.1003878 1899.366
2000 2.3775502 0.31125894 2.8031834 1.9866756 1686.1093
Loop time of 1.82386 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.505425 (27.7118)
Neigh time (%) = 0.00490487 (0.268927)
Comm time (%) = 0.801568 (43.9489)
Outpt time (%) = 0.0571777 (3.13498)
Other time (%) = 0.454788 (24.9354)
Nlocal: 100 ave 110 max 93 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 109.25 ave 112 max 102 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 454.25 ave 500 max 436 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 1817
Ave neighs/atom = 4.5425
Neighbor list builds = 152
Dangerous builds = 83
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.21749 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.3775502 0.31125894 2.8031834 1.9866756 1686.1093
2100 2.4704706 0.20979826 2.8181123 1.5528216 1686.1093
2200 2.4870518 0.19166309 2.8234014 1.5033296 1686.1093
2300 2.4979294 0.17991997 2.8150474 1.4820467 1686.1093
2400 2.4528898 0.22907402 2.8177607 1.6359713 1686.1093
2500 2.4736478 0.20644425 2.8205459 1.554249 1686.1093
2600 2.4459311 0.23690157 2.7285446 1.7818242 1686.1093
2700 2.5049455 0.17219675 2.7322165 1.420623 1686.1093
2800 2.4375688 0.24572427 2.7808663 1.7703797 1686.1093
2900 2.4809392 0.19837443 2.7666384 1.503955 1686.1093
3000 2.4057443 0.28017993 2.8000919 2.0077203 1686.1093
3100 2.5016814 0.17562158 2.7685872 1.5086217 1686.1093
3200 2.5137429 0.16265319 2.7993589 1.41725 1686.1093
3300 2.4554427 0.22611244 2.8045792 1.7015029 1686.1093
3400 2.4748517 0.20511081 2.8207301 1.6366328 1686.1093
3500 2.4760054 0.20388481 2.8002348 1.6521255 1686.1093
3600 2.475846 0.20402109 2.7711827 1.5709354 1686.1093
3700 2.4787517 0.20083747 2.7705896 1.5401804 1686.1093
3800 2.4465961 0.23578893 2.7261788 1.6715972 1686.1093
3900 2.474922 0.20492158 2.758706 1.5538029 1686.1093
4000 2.4461703 0.23642775 2.8255095 1.7141916 1686.1093
Loop time of 2.04081 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.93536 (45.8329)
Neigh time (%) = 0.00250566 (0.122778)
Comm time (%) = 0.843584 (41.3358)
Outpt time (%) = 0.0581496 (2.84934)
Other time (%) = 0.201209 (9.85927)
Nlocal: 100 ave 106 max 91 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 112.5 ave 115 max 109 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 450.5 ave 512 max 374 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 1802
Ave neighs/atom = 4.505
Neighbor list builds = 55
Dangerous builds = 0