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modernize example for dumping ellipsoid info to visualize with OVITO

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This commit is contained in:
Axel Kohlmeyer
2023-07-06 09:16:58 -04:00
parent 146245e6ae
commit fcf30f4c58
2 changed files with 132 additions and 122 deletions
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127
examples/ASPHERE/ellipsoid/in.ellipsoid
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@ -1,23 +1,23 @@
# SRD diffusion demo - ellipsoids # SRD diffusion demo - ellipsoids
units lj units lj
atom_style ellipsoid atom_style ellipsoid
atom_modify first big atom_modify first big
dimension 2 dimension 2
# create big ellipsoidal particles # create big ellipsoidal particles
lattice sq 0.14 lattice sq 0.14
region box block 0 10 0 10 -0.5 0.5 region box block 0 10 0 10 -0.5 0.5
create_box 2 box create_box 2 box
create_atoms 1 region box create_atoms 1 region box
set type 1 mass 1.0 set type 1 mass 1.0
set type 1 shape 3.0 1.0 1.0 set type 1 shape 3.0 1.0 1.0
group big type 1 group big type 1
set group big quat/random 29898 set group big quat/random 29898
velocity big create 1.44 87287 loop geom velocity big create 1.44 87287 loop geom
# equilibrate big particles # equilibrate big particles
@ -26,57 +26,60 @@ pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere fix 1 big nve/asphere
fix 2 all enforce2d fix 2 all enforce2d
compute rot big temp/asphere compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z & #dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
# quatw quati quatj quatk # c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press thermo_style custom step temp c_rot epair etotal press
thermo 100 thermo 100
run 1000 run 1000
#undump 1 #undump 1
unfix 1 unfix 1
unfix 2 unfix 2
# add small particles as hi density lattice # add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0 lattice sq 120.0
create_atoms 2 region plane create_atoms 2 region plane
set type 2 mass 0.01 set type 2 mass 0.01
group small type 2 group small type 2
velocity small create 1.0 593849 loop geom velocity small create 1.0 593849 loop geom
# delete overlaps # delete overlaps
# must set 1-2 cutoff to non-zero value # must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0 pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0 pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000 neigh_modify one 10000
delete_atoms overlap 1.6 small big delete_atoms overlap 1.6 small big
# SRD run # SRD run
reset_timestep 0 reset_timestep 0
neighbor 0.3 multi neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes comm_modify mode multi group big vel yes
neigh_modify include big neigh_modify include big
# no pairwise interactions with small particles # no pairwise interactions with small particles
@ -88,29 +91,31 @@ pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones # use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles # if comment out, big particles won't see SRD particles
timestep 0.0005 timestep 0.0005
fix 1 big nve/asphere fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
collision noslip search 0.2 inside ignore exact no bounce 50 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 all enforce2d fix 3 all enforce2d
# diagnostics # diagnostics
compute tbig big temp/asphere compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big) variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big) variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & 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] 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_modify temp tbig
thermo 1000 thermo 1000
#dump 1 all custom 1000 dump.ellipsoid id type x y z & #dump 1 all custom 1000 dump.ellipsoid id type x y z &
# quatw quati quatj quatk # c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 1 all image 1000 image.*.jpg type type zoom 1.6 #dump 2 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 #dump_modify 2 pad 6 adiam 1 1 adiam 2 0.2
run 100000 run 100000

127
examples/ASPHERE/ellipsoid/in.ellipsoid.mp
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@ -1,23 +1,23 @@
# SRD viscosity demo - ellipsoids # SRD viscosity demo - ellipsoids
units lj units lj
atom_style ellipsoid atom_style ellipsoid
atom_modify first big atom_modify first big
dimension 2 dimension 2
# create big ellipsoidal particles # create big ellipsoidal particles
lattice sq 0.14 lattice sq 0.14
region box block 0 10 0 10 -0.5 0.5 region box block 0 10 0 10 -0.5 0.5
create_box 2 box create_box 2 box
create_atoms 1 region box create_atoms 1 region box
set type 1 mass 1.0 set type 1 mass 1.0
set type 1 shape 3.0 1.0 1.0 set type 1 shape 3.0 1.0 1.0
group big type 1 group big type 1
set group big quat/random 29898 set group big quat/random 29898
velocity big create 1.44 87287 loop geom velocity big create 1.44 87287 loop geom
# equilibrate big particles # equilibrate big particles
@ -26,57 +26,60 @@ pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere fix 1 big nve/asphere
fix 2 all enforce2d fix 2 all enforce2d
compute rot big temp/asphere compute rot big temp/asphere
compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z & #dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
# quatw quati quatj quatk # c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
thermo_style custom step temp c_rot epair etotal press thermo_style custom step temp c_rot epair etotal press
thermo 100 thermo 100
run 1000 run 1000
#undump 1 #undump 1
unfix 1 unfix 1
unfix 2 unfix 2
# add small particles as hi density lattice # add small particles as hi density lattice
region plane block INF INF INF INF -0.001 0.001 units box region plane block INF INF INF INF -0.001 0.001 units box
lattice sq 120.0 lattice sq 120.0
create_atoms 2 region plane create_atoms 2 region plane
set type 2 mass 0.01 set type 2 mass 0.01
group small type 2 group small type 2
velocity small create 1.0 593849 loop geom velocity small create 1.0 593849 loop geom
# delete overlaps # delete overlaps
# must set 1-2 cutoff to non-zero value # must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0 pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 2.0 pair_coeff 1 2 0.0 1.0 2.0
neigh_modify one 10000 neigh_modify one 10000
delete_atoms overlap 1.6 small big delete_atoms overlap 1.6 small big
# SRD run # SRD run
reset_timestep 0 reset_timestep 0
neighbor 0.3 multi neighbor 0.3 multi
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes comm_modify mode multi group big vel yes
neigh_modify include big neigh_modify include big
# no pairwise interactions with small particles # no pairwise interactions with small particles
@ -88,30 +91,32 @@ pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
# use fix SRD to push small particles out from inside big ones # use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles # if comment out, big particles won't see SRD particles
timestep 0.0005 timestep 0.0005
fix 1 big nve/asphere fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 & fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
collision noslip search 0.2 inside ignore exact no bounce 50 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 small viscosity 20 x y 50 fix 3 small viscosity 20 x y 50
fix 4 all enforce2d fix 4 all enforce2d
# diagnostics # diagnostics
compute tbig big temp/asphere compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big) variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big) variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press & thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] & 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] 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_modify temp tbig
thermo 1000 thermo 1000
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z & #dump 1 all custom 500 dump.ellipsoid id type x y z &
# quatw quati quatj quatk # c_0[1] c_0[2] c_0[3] c_0[4] c_0[5] c_0[6] c_0[7]
#dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk &
# colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
#dump 1 all image 500 image.*.jpg type type zoom 1.6 #dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 #dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000 run 50000