diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid b/examples/ASPHERE/ellipsoid/in.ellipsoid index 2dda95a029..1ee59597da 100644 --- a/examples/ASPHERE/ellipsoid/in.ellipsoid +++ b/examples/ASPHERE/ellipsoid/in.ellipsoid @@ -35,8 +35,7 @@ fix 2 all enforce2d compute rot big temp/asphere compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez -#dump 1 all custom 10 dump.ellipsoid.equil id type x y z & -# c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7] +#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*] #dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk & # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez @@ -110,8 +109,7 @@ thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & thermo_modify temp tbig thermo 1000 -#dump 1 all custom 1000 dump.ellipsoid id type x y z & -# c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7] +#dump 1 all custom 1000 dump.ellipsoid id type x y z c_0[*] #dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk & # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp index e950cc86f5..31fe79eb58 100644 --- a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp +++ b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp @@ -35,8 +35,7 @@ fix 2 all enforce2d compute rot big temp/asphere compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez -#dump 1 all custom 10 dump.ellipsoid.equil id type x y z & -# c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7] +#dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*] #dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk & # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez @@ -111,8 +110,7 @@ thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & thermo_modify temp tbig thermo 1000 -#dump 1 all custom 500 dump.ellipsoid id type x y z & -# c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7] +#dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*] #dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk & # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez diff --git a/examples/ellipse/in.ellipse.gayberne b/examples/ellipse/in.ellipse.gayberne index fe783ac6de..0e6b21797a 100644 --- a/examples/ellipse/in.ellipse.gayberne +++ b/examples/ellipse/in.ellipse.gayberne @@ -1,23 +1,23 @@ # GayBerne ellipsoids in LJ background fluid -units lj +units lj atom_style ellipsoid dimension 2 -lattice sq 0.02 -region box block 0 20 0 20 -0.5 0.5 +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 type 1 mass 1.0 -set type 2 mass 1.5 -set type 1 shape 1 1 1 -set type 2 shape 3 1 1 -set group all quat/random 18238 +set group all type/fraction 2 0.1 95392 +set type 1 mass 1.0 +set type 2 mass 1.5 +set type 1 shape 1 1 1 +set type 2 shape 3 1 1 +set group all quat/random 18238 -compute rot all temp/asphere -group spheroid type 1 +compute rot all temp/asphere +group spheroid type 1 variable dof equal count(spheroid)+2 compute_modify rot extra/dof ${dof} @@ -31,36 +31,37 @@ 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 +thermo 100 timestep 0.002 -compute q all property/atom quatw quati quatj quatk +compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez -#dump 1 all custom 100 dump.ellipse.gayberne & -# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] +dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_0[*] +dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk & + colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez -#dump 2 all image 100 image.*.jpg type type & -# zoom 1.6 center d 0.5 0.5 0.5 +#dump 2 all image 100 image.*.jpg type type & +# zoom 1.6 center d 0.5 0.5 0.5 #dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 -#dump 3 all movie 100 movie.mpg type type & -# zoom 1.6 center d 0.5 0.5 0.5 +#dump 3 all movie 100 movie.mpg type type & +# zoom 1.6 center d 0.5 0.5 0.5 #dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & - mtk no pchain 0 tchain 1 -fix 2 all enforce2d +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d compute_modify 1_temp extra/dof ${dof} # equilibrate to shrink box around dilute system -run 2000 +run 2000 # run dynamics on dense system -unfix 1 -fix 1 all nve/asphere +unfix 1 +fix 1 all nve/asphere -run 2000 +run 2000 diff --git a/examples/ellipse/in.ellipse.resquared b/examples/ellipse/in.ellipse.resquared index 82398987f8..d5bc8897cb 100644 --- a/examples/ellipse/in.ellipse.resquared +++ b/examples/ellipse/in.ellipse.resquared @@ -1,23 +1,23 @@ # RESquared ellipsoids in LJ background fluid -units lj +units lj atom_style ellipsoid dimension 2 -lattice sq 0.02 -region box block 0 20 0 20 -0.5 0.5 +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 type 1 mass 1.0 -set type 2 mass 1.5 -set type 1 shape 1 1 1 -set type 2 shape 3 1 1 -set group all quat/random 18238 +set group all type/fraction 2 0.1 95392 +set type 1 mass 1.0 +set type 2 mass 1.5 +set type 1 shape 1 1 1 +set type 2 shape 3 1 1 +set group all quat/random 18238 -compute rot all temp/asphere -group spheroid type 1 +compute rot all temp/asphere +group spheroid type 1 variable dof equal count(spheroid)+2 compute_modify rot extra/dof ${dof} @@ -31,36 +31,40 @@ 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 +thermo 100 timestep 0.002 -compute q all property/atom quatw quati quatj quatk +compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez -#dump 1 all custom 100 dump.ellipse.resquared & -# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] +dump 1 all custom 100 dump.ellipse.resquared id type x y z c_0[*] +dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk & + colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez -#dump 2 all image 100 image.*.jpg type type & -# zoom 1.6 center d 0.5 0.5 0.5 +#dump 1 all custom 100 dump.ellipse.resquared & +# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type & +# zoom 1.6 center d 0.5 0.5 0.5 #dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 -#dump 3 all movie 100 movie.mpg type type & -# zoom 1.6 center d 0.5 0.5 0.5 +#dump 3 all movie 100 movie.mpg type type & +# zoom 1.6 center d 0.5 0.5 0.5 #dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & - mtk no pchain 0 tchain 1 -fix 2 all enforce2d +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & + mtk no pchain 0 tchain 1 +fix 2 all enforce2d compute_modify 1_temp extra/dof ${dof} # equilibrate to shrink box around dilute system -run 2000 +run 2000 # run dynamics on dense system -unfix 1 -fix 1 all nve/asphere +unfix 1 +fix 1 all nve/asphere -run 2000 +run 2000