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This commit is contained in:
Axel Kohlmeyer
@ -1,111 +1,111 @@
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# SRD diffusion demo - rigid box particles
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units lj
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atom_style sphere
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atom_modify map array first big
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dimension 2
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units lj
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atom_style sphere
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atom_modify map array first big
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dimension 2
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# read in clusters of rigid bodies
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fix molprop all property/atom mol
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read_data data.box fix molprop NULL Molecules
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read_data data.box fix molprop NULL Molecules
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set type 1 mass 1.0
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group big type 1
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velocity big create 1.44 87287 loop geom
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set type 1 mass 1.0
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group big type 1
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles
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pair_style soft 1.12
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pair_coeff 1 1 0.0
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pair_coeff 2 2 0.0 0.0
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pair_coeff 1 2 0.0 0.0
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pair_style soft 1.12
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pair_coeff 1 1 0.0
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pair_coeff 2 2 0.0 0.0
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pair_coeff 1 2 0.0 0.0
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variable prefactor equal ramp(0,60)
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fix soft all adapt 1 pair soft a * * v_prefactor
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 big rigid molecule
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fix 2 all enforce2d
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fix 1 big rigid molecule
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.box.equil
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#dump 1 all atom 10 dump.box.equil
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compute tbig all temp/sphere
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thermo_modify temp tbig
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compute tbig all temp/sphere
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thermo_modify temp tbig
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thermo 100
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run 1000
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thermo 100
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run 1000
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#undump 1
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#undump 1
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unfix soft
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unfix 1
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unfix 2
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unfix 1
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unfix 2
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# add small particles as hi density lattice
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region plane block INF INF INF INF -0.001 0.001 units box
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lattice sq 85.0
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create_atoms 2 region plane
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region plane block INF INF INF INF -0.001 0.001 units box
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lattice sq 85.0
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create_atoms 2 region plane
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set type 2 mass 0.1
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group small type 2
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velocity small create 1.0 593849 loop geom
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set type 2 mass 0.1
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group small type 2
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set 1-2 cutoff to non-zero value
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 1.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 1.0
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delete_atoms overlap 1.0 small big
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delete_atoms overlap 1.0 small big
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# SRD run
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reset_timestep 0
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reset_timestep 0
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neighbor 0.3 multi
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neigh_modify delay 0 every 1 check yes
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neighbor 0.3 multi
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neigh_modify delay 0 every 1 check yes
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comm_modify mode multi group big vel yes
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neigh_modify include big
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comm_modify mode multi group big vel yes
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neigh_modify include big
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# no pairwise interactions with small particles
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.0
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.0
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# use fix SRD to push small particles out from inside big ones
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# if comment out, big particles won't see SRD particles
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timestep 0.001
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timestep 0.001
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fix 1 big rigid molecule
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
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search 0.2 collision slip inside ignore overlap yes
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fix 3 all enforce2d
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fix 1 big rigid molecule
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
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search 0.2 collision slip inside ignore overlap yes
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fix 3 all enforce2d
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# diagnostics
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uncompute tbig
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compute tbig big temp/sphere
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
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f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
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f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
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compute tbig big temp/sphere
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
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f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
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f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
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thermo_modify temp tbig
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thermo 1000
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thermo_modify temp tbig
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thermo 1000
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#dump 1 all atom 1000 dump.box
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#dump 1 all atom 1000 dump.box
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#dump 1 all image 1000 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
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#dump 1 all image 1000 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
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run 100000
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run 100000
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