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lammps/examples/ASPHERE/tri/in.tri.srd
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# 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
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