# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles units lj atom_style tri atom_modify first big read_data data.tri.srd # add small particles as hi density lattice lattice sc 0.4 region box block INF INF INF INF INF INF lattice sc 20.0 create_atoms 2 region box group big type 1 group small type 2 set group small mass 0.01 # delete overlaps # must set 1-2 cutoff to non-zero value pair_style lj/cut 1.5 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 delete_atoms overlap 1.5 small big # SRD run reset_timestep 0 velocity small create 1.44 87287 loop geom neighbor 0.3 bin neigh_modify delay 0 every 1 check yes neigh_modify exclude molecule big include big comm_modify mode multi group big vel yes neigh_modify include big # no pairwise interactions with small particles pair_style tri/lj 3.5 pair_coeff 1 1 0.1 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 #langevin 1.0 1.0 0.1 12398 fix 2 small srd 20 big 1.0 0.25 49894 & search 0.2 cubic warn 0.0001 shift yes 49829 & overlap yes collision noslip fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6 # diagnostics compute tsmall small temp/deform compute tbig big temp variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) compute 1 big erotate/asphere compute 2 all ke compute 3 all pe variable toteng equal (c_1+c_2+c_3)/atoms thermo 1000 thermo_style custom step f_1 c_tsmall f_2[9] temp press thermo_modify temp tbig compute 10 all property/atom corner1x corner1y corner1z & corner2x corner2y corner2z corner3x corner3y corner3z #dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz #dump 2 all custom 500 dump1.tri.srd id type & # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] & # c_10[7] c_10[8] c_10[9] run 10000 #undump 1 #undump 2 unfix 3 change_box all triclinic fix 2 small srd 20 big 1.0 0.25 49894 & search 0.2 cubic warn 0.0001 shift yes 49829 & overlap yes collision noslip tstat yes #dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz #dump 2 all custom 500 dump2.tri.srd id type & # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] & # c_10[7] c_10[8] c_10[9] fix 3 all deform 1 xy erate 0.05 units box remap v run 40000