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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1079 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-10-22 21:18:55 +00:00
parent d87689d8b8
commit c07107c8ba
6 changed files with 362 additions and 3 deletions
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13
examples/ellipse/in.ellipse → examples/ellipse/in.gayberne
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@ -1,4 +1,4 @@
# Ellipsoids in LJ background fluid
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
@ -25,6 +25,11 @@ 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
@ -32,9 +37,12 @@ thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse &
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
@ -48,4 +56,3 @@ unfix 1
fix 1 all nve/asphere
run 2000

58
examples/ellipse/in.resquared Normal file
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@ -0,0 +1,58 @@
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
create_atoms 1 box
set group all type/fraction 2 0.1 95392
set group all quat/random 18238
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
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000

0
examples/ellipse/log.ellipse.5Oct07.linux.1 → examples/ellipse/log.gayberne.5Oct07.linux.1
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0
examples/ellipse/log.ellipse.5Oct07.linux.4 → examples/ellipse/log.gayberne.5Oct07.linux.4
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147
examples/ellipse/log.resquared.5Oct07.linux.1 Normal file
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@ -0,0 +1,147 @@
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

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examples/ellipse/log.resquared.5Oct07.linux.4 Normal file
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@ -0,0 +1,147 @@
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