diff --git a/examples/ellipse/in.ellipse b/examples/ellipse/in.gayberne similarity index 74% rename from examples/ellipse/in.ellipse rename to examples/ellipse/in.gayberne index 147c54714a..ac4d8bf249 100644 --- a/examples/ellipse/in.ellipse +++ b/examples/ellipse/in.gayberne @@ -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 - diff --git a/examples/ellipse/in.resquared b/examples/ellipse/in.resquared new file mode 100644 index 0000000000..1486a3fd0f --- /dev/null +++ b/examples/ellipse/in.resquared @@ -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 diff --git a/examples/ellipse/log.ellipse.5Oct07.linux.1 b/examples/ellipse/log.gayberne.5Oct07.linux.1 similarity index 100% rename from examples/ellipse/log.ellipse.5Oct07.linux.1 rename to examples/ellipse/log.gayberne.5Oct07.linux.1 diff --git a/examples/ellipse/log.ellipse.5Oct07.linux.4 b/examples/ellipse/log.gayberne.5Oct07.linux.4 similarity index 100% rename from examples/ellipse/log.ellipse.5Oct07.linux.4 rename to examples/ellipse/log.gayberne.5Oct07.linux.4 diff --git a/examples/ellipse/log.resquared.5Oct07.linux.1 b/examples/ellipse/log.resquared.5Oct07.linux.1 new file mode 100644 index 0000000000..00cb11f93a --- /dev/null +++ b/examples/ellipse/log.resquared.5Oct07.linux.1 @@ -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 diff --git a/examples/ellipse/log.resquared.5Oct07.linux.4 b/examples/ellipse/log.resquared.5Oct07.linux.4 new file mode 100644 index 0000000000..68fbfb7d93 --- /dev/null +++ b/examples/ellipse/log.resquared.5Oct07.linux.4 @@ -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