			# 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

lammps/examples/ASPHERE/box/in.box
c9188c00959eefficient_neuronet

in.box
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lammps/examples/ASPHERE/box/in.boxc9188c00959eefficient_neuronet

in.boxView Options

lammps/examples/ASPHERE/box/in.box
c9188c00959eefficient_neuronet

in.box
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