forked from lijiext/lammps
Revert "use neighbor list exclusions instead of a zero cutoff"
This reverts commit bbb4d63db9
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This commit is contained in:
parent
bc5186bc30
commit
d9186c8fde
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@ -1,115 +1,114 @@
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# SRD diffusion demo - poydisperse spheres
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units lj
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atom_style sphere
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atom_modify 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 first big
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dimension 2
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# create big particles with 3 different types and diameters
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lattice sq 0.3
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region box block 0 10 0 10 -0.5 0.5
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create_box 4 box
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create_atoms 1 region box
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lattice sq 0.3
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region box block 0 10 0 10 -0.5 0.5
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create_box 4 box
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create_atoms 1 region box
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group big type 1
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set group big type/fraction 2 0.33 394895
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set group big type/fraction 3 0.5 989894
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group big type 2 3
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group big type 1
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set group big type/fraction 2 0.33 394895
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set group big type/fraction 3 0.5 989894
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group big type 2 3
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set type 1*3 mass 1.0
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velocity big create 1.44 87287 loop geom
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set type 1*3 mass 1.0
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles, repulsive only to prevent aggregation
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.1
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.0
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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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neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
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fix 1 big nve
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fix 2 all enforce2d
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fix 1 big nve
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.poly.equil
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#dump 1 all atom 10 dump.poly.equil
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run 1000
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run 1000
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#undump 1
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unfix 1
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unfix 2
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#undump 1
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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 250.0
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create_atoms 4 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 250.0
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create_atoms 4 region plane
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set type 4 mass 0.1
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group small type 4
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velocity small create 1.0 593849 loop geom
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set type 4 mass 0.1
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group small type 4
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set *-4 cutoffs to non-zero values
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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 1.0 2.0
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pair_coeff 3 3 1.0 1.5
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pair_coeff 4 4 0.0 1.0 0.1
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neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
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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 1.0 2.0
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pair_coeff 3 3 1.0 1.5
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pair_coeff 1 4 0.0 1.0 0.5
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pair_coeff 2 4 0.0 1.0 1.0
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pair_coeff 3 4 0.0 1.0 0.75
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pair_coeff 4 4 0.0 1.0 0.0
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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 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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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 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.1
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neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 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 nve
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
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fix 1 big nve
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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 inside ignore
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fix 3 all enforce2d
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fix 3 all enforce2d
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# diagnostics
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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]
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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]
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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.poly
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#dump 1 all atom 1000 dump.poly
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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 2.0 adiam 3 1.5 adiam 4 0.1
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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 2.0 adiam 3 1.5 adiam 4 0.1
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run 100000
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run 100000
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@ -1,116 +1,115 @@
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# SRD viscosity demo - poydisperse spheres
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units lj
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atom_style sphere
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atom_modify 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 first big
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dimension 2
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# create big particles with 3 different types and diameters
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lattice sq 0.3
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region box block 0 10 0 10 -0.5 0.5
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create_box 4 box
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create_atoms 1 region box
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lattice sq 0.3
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region box block 0 10 0 10 -0.5 0.5
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create_box 4 box
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create_atoms 1 region box
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group big type 1
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set group big type/fraction 2 0.33 394895
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set group big type/fraction 3 0.5 989894
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group big type 2 3
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group big type 1
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set group big type/fraction 2 0.33 394895
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set group big type/fraction 3 0.5 989894
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group big type 2 3
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set type 1*3 mass 1.0
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velocity big create 1.44 87287 loop geom
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set type 1*3 mass 1.0
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles, repulsive only to prevent aggregation
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.1
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.0
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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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neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
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fix 1 big nve
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fix 2 all enforce2d
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fix 1 big nve
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.poly.equil
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#dump 1 all atom 10 dump.poly.equil
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run 1000
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run 1000
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#undump 1
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unfix 1
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unfix 2
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#undump 1
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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 250.0
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create_atoms 4 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 250.0
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create_atoms 4 region plane
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set type 4 mass 0.1
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group small type 4
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velocity small create 1.0 593849 loop geom
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set type 4 mass 0.1
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group small type 4
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set *-4 cutoffs to non-zero values
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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 1.0 2.0
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pair_coeff 3 3 1.0 1.5
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pair_coeff 4 4 0.0 1.0 0.1
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neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
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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 1.0 2.0
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pair_coeff 3 3 1.0 1.5
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pair_coeff 1 4 0.0 1.0 0.5
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pair_coeff 2 4 0.0 1.0 1.0
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pair_coeff 3 4 0.0 1.0 0.75
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pair_coeff 4 4 0.0 1.0 0.0
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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 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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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 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.1
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neigh_modify exclude type 1 4 exclude type 2 4 exclude type 3 4 exclude type 4 4
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 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 nve
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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 inside ignore
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fix 3 small viscosity 10 x y 50
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fix 4 all enforce2d
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fix 1 big nve
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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 inside ignore
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fix 3 small viscosity 10 x y 50
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fix 4 all enforce2d
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# diagnostics
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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]
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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]
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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 500 dump.poly.mp
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#dump 1 all atom 500 dump.poly.mp
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#dump 1 all image 500 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
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#dump 1 all image 500 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
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run 50000
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run 50000
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