2013-09-11 07:35:01 +08:00
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# Aspherical shear demo - 2d line boxes, solvated by SRD particles
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units lj
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atom_style line
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atom_modify first big
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dimension 2
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read_data data.line.srd
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# add small particles as hi density lattice
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lattice sq 0.4
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region plane block INF INF INF INF -0.001 0.001
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lattice sq 10.0
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create_atoms 2 region plane
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group big type 1
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group small type 2
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set group small mass 0.01
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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 1.5
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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
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delete_atoms overlap 1.5 small big
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# SRD run
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reset_timestep 0
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velocity small create 1.44 87287 loop geom
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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 molecule big include big
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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 line/lj 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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fix 1 big rigid molecule
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fix 2 small srd 20 big 1.0 0.25 49894 &
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search 0.2 cubic warn 0.0001 shift yes 49829 &
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overlap yes collision noslip
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fix 3 all deform 1 x scale 0.35 y scale 0.35
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fix 4 all enforce2d
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# diagnostics
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compute tsmall small temp/deform
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compute tbig big temp
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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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compute 1 big erotate/asphere
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compute 2 all ke
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compute 3 all pe
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variable toteng equal (c_1+c_2+c_3)/atoms
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thermo 1000
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thermo_style custom step temp c_tsmall f_2[9] c_1 etotal &
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v_pebig v_ebig press
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thermo_modify temp tbig
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compute 10 big property/atom end1x end1y end2x end2y
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#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump1.line.srd id type &
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# c_10[1] c_10[2] c_10[3] c_10[4]
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run 10000
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#undump 1
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#undump 2
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unfix 3
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change_box all triclinic
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fix 2 small srd 20 big 1.0 0.25 49894 &
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search 0.2 cubic warn 0.0001 shift yes 49829 &
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overlap yes collision noslip tstat yes
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#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
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#dump 2 all custom 500 dump2.line.srd id type &
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# c_10[1] c_10[2] c_10[3] c_10[4]
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fix 3 all deform 1 xy erate 0.05 units box remap v
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run 40000
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