diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid b/examples/ASPHERE/ellipsoid/in.ellipsoid index 5e9a20f6e0..2dda95a029 100644 --- a/examples/ASPHERE/ellipsoid/in.ellipsoid +++ b/examples/ASPHERE/ellipsoid/in.ellipsoid @@ -1,23 +1,23 @@ # SRD diffusion demo - ellipsoids -units lj -atom_style ellipsoid -atom_modify first big -dimension 2 +units lj +atom_style ellipsoid +atom_modify first big +dimension 2 # create big ellipsoidal particles -lattice sq 0.14 -region box block 0 10 0 10 -0.5 0.5 -create_box 2 box -create_atoms 1 region box +lattice sq 0.14 +region box block 0 10 0 10 -0.5 0.5 +create_box 2 box +create_atoms 1 region box -set type 1 mass 1.0 -set type 1 shape 3.0 1.0 1.0 -group big type 1 -set group big quat/random 29898 +set type 1 mass 1.0 +set type 1 shape 3.0 1.0 1.0 +group big type 1 +set group big quat/random 29898 -velocity big create 1.44 87287 loop geom +velocity big create 1.44 87287 loop geom # equilibrate big particles @@ -26,57 +26,60 @@ pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1 pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes -fix 1 big nve/asphere -fix 2 all enforce2d +fix 1 big nve/asphere +fix 2 all enforce2d -compute rot big temp/asphere +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 & -# quatw quati quatj quatk +#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_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 -thermo_style custom step temp c_rot epair etotal press -thermo 100 +thermo_style custom step temp c_rot epair etotal press +thermo 100 -run 1000 +run 1000 -#undump 1 -unfix 1 -unfix 2 +#undump 1 +unfix 1 +unfix 2 # add small particles as hi density lattice -region plane block INF INF INF INF -0.001 0.001 units box -lattice sq 120.0 -create_atoms 2 region plane +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 120.0 +create_atoms 2 region plane -set type 2 mass 0.01 -group small type 2 -velocity small create 1.0 593849 loop geom +set type 2 mass 0.01 +group small type 2 +velocity small create 1.0 593849 loop geom # delete overlaps # must set 1-2 cutoff to non-zero value -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 2.0 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 2.0 -neigh_modify one 10000 +neigh_modify one 10000 -delete_atoms overlap 1.6 small big +delete_atoms overlap 1.6 small big # SRD run -reset_timestep 0 +reset_timestep 0 -neighbor 0.3 multi -neigh_modify delay 0 every 1 check yes +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes -comm_modify mode multi group big vel yes -neigh_modify include big +comm_modify mode multi group big vel yes +neigh_modify include big # no pairwise interactions with small particles @@ -88,29 +91,31 @@ pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 # use fix SRD to push small particles out from inside big ones # if comment out, big particles won't see SRD particles -timestep 0.0005 +timestep 0.0005 -fix 1 big nve/asphere -fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & - collision noslip search 0.2 inside ignore exact no bounce 50 -fix 3 all enforce2d +fix 1 big nve/asphere +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & + collision noslip search 0.2 inside ignore exact no bounce 50 +fix 3 all enforce2d # diagnostics -compute tbig big temp/asphere -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & - f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & - f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +compute tbig big temp/asphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & + f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & + f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] -thermo_modify temp tbig -thermo 1000 +thermo_modify temp tbig +thermo 1000 -#dump 1 all custom 1000 dump.ellipsoid id type x y z & -# quatw quati quatj quatk +#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_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 1 all image 1000 image.*.jpg type type zoom 1.6 -#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 +#dump 2 all image 1000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2 -run 100000 +run 100000 diff --git a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp index 7ce01ad4e1..e950cc86f5 100644 --- a/examples/ASPHERE/ellipsoid/in.ellipsoid.mp +++ b/examples/ASPHERE/ellipsoid/in.ellipsoid.mp @@ -1,23 +1,23 @@ # SRD viscosity demo - ellipsoids -units lj -atom_style ellipsoid -atom_modify first big -dimension 2 +units lj +atom_style ellipsoid +atom_modify first big +dimension 2 # create big ellipsoidal particles -lattice sq 0.14 -region box block 0 10 0 10 -0.5 0.5 -create_box 2 box -create_atoms 1 region box +lattice sq 0.14 +region box block 0 10 0 10 -0.5 0.5 +create_box 2 box +create_atoms 1 region box -set type 1 mass 1.0 -set type 1 shape 3.0 1.0 1.0 -group big type 1 -set group big quat/random 29898 +set type 1 mass 1.0 +set type 1 shape 3.0 1.0 1.0 +group big type 1 +set group big quat/random 29898 -velocity big create 1.44 87287 loop geom +velocity big create 1.44 87287 loop geom # equilibrate big particles @@ -26,57 +26,60 @@ pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1 pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes -fix 1 big nve/asphere -fix 2 all enforce2d +fix 1 big nve/asphere +fix 2 all enforce2d -compute rot big temp/asphere +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 & -# quatw quati quatj quatk +#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_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 -thermo_style custom step temp c_rot epair etotal press -thermo 100 +thermo_style custom step temp c_rot epair etotal press +thermo 100 -run 1000 +run 1000 -#undump 1 -unfix 1 -unfix 2 +#undump 1 +unfix 1 +unfix 2 # add small particles as hi density lattice -region plane block INF INF INF INF -0.001 0.001 units box -lattice sq 120.0 -create_atoms 2 region plane +region plane block INF INF INF INF -0.001 0.001 units box +lattice sq 120.0 +create_atoms 2 region plane -set type 2 mass 0.01 -group small type 2 -velocity small create 1.0 593849 loop geom +set type 2 mass 0.01 +group small type 2 +velocity small create 1.0 593849 loop geom # delete overlaps # must set 1-2 cutoff to non-zero value -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 2.0 +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 2.0 -neigh_modify one 10000 +neigh_modify one 10000 -delete_atoms overlap 1.6 small big +delete_atoms overlap 1.6 small big # SRD run -reset_timestep 0 +reset_timestep 0 -neighbor 0.3 multi -neigh_modify delay 0 every 1 check yes +neighbor 0.3 multi +neigh_modify delay 0 every 1 check yes -comm_modify mode multi group big vel yes -neigh_modify include big +comm_modify mode multi group big vel yes +neigh_modify include big # no pairwise interactions with small particles @@ -88,30 +91,32 @@ pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 # use fix SRD to push small particles out from inside big ones # if comment out, big particles won't see SRD particles -timestep 0.0005 +timestep 0.0005 -fix 1 big nve/asphere -fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & +fix 1 big nve/asphere +fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & collision noslip search 0.2 inside ignore exact no bounce 50 -fix 3 small viscosity 20 x y 50 -fix 4 all enforce2d +fix 3 small viscosity 20 x y 50 +fix 4 all enforce2d # diagnostics -compute tbig big temp/asphere -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & - f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & - f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] +compute tbig big temp/asphere +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & + f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & + f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12] -thermo_modify temp tbig -thermo 1000 +thermo_modify temp tbig +thermo 1000 -#dump 1 all custom 500 dump.ellipsoid.mp id type x y z & -# quatw quati quatj quatk +#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_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 1 all image 500 image.*.jpg type type zoom 1.6 -#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 +#dump 1 all image 500 image.*.jpg type type zoom 1.6 +#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 -run 50000 +run 50000