2013-09-11 07:35:01 +08:00
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# SRD diffusion demo - ellipsoids
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units lj
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atom_style ellipsoid
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atom_modify first big
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dimension 2
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# create big ellipsoidal particles
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lattice sq 0.14
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region box block 0 10 0 10 -0.5 0.5
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create_box 2 box
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create_atoms 1 region box
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set type 1 mass 1.0
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set type 1 shape 3.0 1.0 1.0
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group big type 1
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set group big quat/random 29898
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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 gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
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pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
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pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 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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fix 1 big nve/asphere
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fix 2 all enforce2d
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compute rot big temp/asphere
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#dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
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# quatw quati quatj quatk
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thermo_style custom step temp c_rot epair etotal press
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thermo 100
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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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# 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 120.0
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create_atoms 2 region plane
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set type 2 mass 0.01
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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 2.0
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neigh_modify one 10000
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delete_atoms overlap 1.6 small big
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# SRD run
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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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2014-06-05 20:52:27 +08:00
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comm_modify mode multi group big vel yes
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2013-09-11 07:35:01 +08:00
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neigh_modify include big
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# no pairwise interactions with small particles
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pair_style gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
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pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
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pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 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 0.0005
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fix 1 big nve/asphere
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
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collision noslip search 0.2 inside ignore exact no bounce 50
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fix 3 all enforce2d
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# diagnostics
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compute tbig big temp/asphere
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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 c_rot f_2[9] 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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#dump 1 all custom 1000 dump.ellipsoid id type x y z &
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# quatw quati quatj quatk
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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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