diff --git a/examples/ASPHERE/box/in.box b/examples/ASPHERE/box/in.box index 289fc6c6a..2ec09faf5 100644 --- a/examples/ASPHERE/box/in.box +++ b/examples/ASPHERE/box/in.box @@ -1,107 +1,111 @@ # SRD diffusion demo - rigid box particles units lj atom_style sphere atom_modify map array first big dimension 2 # read in clusters of rigid bodies fix molprop all property/atom mol read_data data.box fix molprop NULL Molecules set type 1 mass 1.0 group big type 1 velocity big create 1.44 87287 loop geom # equilibrate big particles pair_style soft 1.12 pair_coeff 1 1 0.0 pair_coeff 2 2 0.0 0.0 pair_coeff 1 2 0.0 0.0 variable prefactor equal ramp(0,60) fix soft all adapt 1 pair soft a * * v_prefactor neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 big rigid molecule fix 2 all enforce2d #dump 1 all atom 10 dump.box.equil +compute tbig all temp/sphere +thermo_modify temp tbig + thermo 100 run 1000 #undump 1 unfix soft 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 85.0 create_atoms 2 region plane set type 2 mass 0.1 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 1.0 delete_atoms overlap 1.0 small big # SRD run reset_timestep 0 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes neigh_modify include big # no pairwise interactions with small particles 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 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 0.001 fix 1 big rigid molecule fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & search 0.2 collision slip inside ignore overlap yes fix 3 all enforce2d # diagnostics +uncompute tbig compute tbig big temp/sphere variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) thermo_style custom step temp f_2[8] 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 #dump 1 all atom 1000 dump.box #dump 1 all image 1000 image.*.jpg type type zoom 1.6 #dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 run 100000 diff --git a/examples/ASPHERE/box/in.box.mp b/examples/ASPHERE/box/in.box.mp index 2d6a2d2df..295355259 100644 --- a/examples/ASPHERE/box/in.box.mp +++ b/examples/ASPHERE/box/in.box.mp @@ -1,108 +1,112 @@ # SRD viscosity demo - rigid box particles units lj atom_style sphere atom_modify map array first big dimension 2 # read in clusters of rigid bodies fix molprop all property/atom mol read_data data.box fix molprop NULL Molecules set type 1 mass 1.0 group big type 1 velocity big create 1.44 87287 loop geom # equilibrate big particles pair_style soft 1.12 pair_coeff 1 1 0.0 pair_coeff 2 2 0.0 0.0 pair_coeff 1 2 0.0 0.0 variable prefactor equal ramp(0,60) fix soft all adapt 1 pair soft a * * v_prefactor neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 big rigid molecule fix 2 all enforce2d #dump 1 all atom 10 dump.box.equil +compute tbig all temp/sphere +thermo_modify temp tbig + thermo 100 run 1000 #undump 1 unfix soft 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 85.0 create_atoms 2 region plane set type 2 mass 0.1 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 1.0 delete_atoms overlap 1.0 small big # SRD run reset_timestep 0 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes neigh_modify include big # no pairwise interactions with small particles 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 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 0.001 fix 1 big rigid molecule fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & search 0.2 collision slip inside ignore overlap yes fix 3 small viscosity 10 x y 50 fix 4 all enforce2d # diagnostics +uncompute tbig compute tbig big temp/sphere variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) thermo_style custom step temp f_2[8] 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 #dump 1 all atom 1000 dump.box.mp #dump 1 all image 1000 image.*.jpg type type zoom 1.6 #dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 run 100000