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update remaining ellipsoid example dump output for OVITO compatibility

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This commit is contained in:
Axel Kohlmeyer
2023-07-10 19:42:48 -04:00
parent a4b3306b7c
commit c63c9711d5
4 changed files with 61 additions and 60 deletions
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6
examples/ASPHERE/ellipsoid/in.ellipsoid
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@ -35,8 +35,7 @@ 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 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 c_0[*]
# 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 & #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 # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
@ -110,8 +109,7 @@ thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
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 c_0[*]
# 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 & #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 # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez

6
examples/ASPHERE/ellipsoid/in.ellipsoid.mp
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@ -35,8 +35,7 @@ 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 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 c_0[*]
# 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 & #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 # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez
@ -111,8 +110,7 @@ thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
thermo_modify temp tbig thermo_modify temp tbig
thermo 1000 thermo 1000
#dump 1 all custom 500 dump.ellipsoid id type x y z & #dump 1 all custom 500 dump.ellipsoid id type x y z c_0[*]
# 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 & #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 # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez

53
examples/ellipse/in.ellipse.gayberne
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@ -1,23 +1,23 @@
# GayBerne ellipsoids in LJ background fluid # GayBerne ellipsoids in LJ background fluid
units lj units lj
atom_style ellipsoid atom_style ellipsoid
dimension 2 dimension 2
lattice sq 0.02 lattice sq 0.02
region box block 0 20 0 20 -0.5 0.5 region box block 0 20 0 20 -0.5 0.5
create_box 2 box create_box 2 box
create_atoms 1 box create_atoms 1 box
set group all type/fraction 2 0.1 95392 set group all type/fraction 2 0.1 95392
set type 1 mass 1.0 set type 1 mass 1.0
set type 2 mass 1.5 set type 2 mass 1.5
set type 1 shape 1 1 1 set type 1 shape 1 1 1
set type 2 shape 3 1 1 set type 2 shape 3 1 1
set group all quat/random 18238 set group all quat/random 18238
compute rot all temp/asphere compute rot all temp/asphere
group spheroid type 1 group spheroid type 1
variable dof equal count(spheroid)+2 variable dof equal count(spheroid)+2
compute_modify rot extra/dof ${dof} compute_modify rot extra/dof ${dof}
@ -31,36 +31,37 @@ pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol thermo_style custom step c_rot epair etotal press vol
thermo 100 thermo 100
timestep 0.002 timestep 0.002
compute q all property/atom quatw quati quatj quatk compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 100 dump.ellipse.gayberne & dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_0[*]
# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] 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 2 all image 100 image.*.jpg type type & #dump 2 all image 100 image.*.jpg type type &
# zoom 1.6 center d 0.5 0.5 0.5 # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 #dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type & #dump 3 all movie 100 movie.mpg type type &
# zoom 1.6 center d 0.5 0.5 0.5 # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 #dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
mtk no pchain 0 tchain 1 mtk no pchain 0 tchain 1
fix 2 all enforce2d fix 2 all enforce2d
compute_modify 1_temp extra/dof ${dof} compute_modify 1_temp extra/dof ${dof}
# equilibrate to shrink box around dilute system # equilibrate to shrink box around dilute system
run 2000 run 2000
# run dynamics on dense system # run dynamics on dense system
unfix 1 unfix 1
fix 1 all nve/asphere fix 1 all nve/asphere
run 2000 run 2000

56
examples/ellipse/in.ellipse.resquared
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@ -1,23 +1,23 @@
# RESquared ellipsoids in LJ background fluid # RESquared ellipsoids in LJ background fluid
units lj units lj
atom_style ellipsoid atom_style ellipsoid
dimension 2 dimension 2
lattice sq 0.02 lattice sq 0.02
region box block 0 20 0 20 -0.5 0.5 region box block 0 20 0 20 -0.5 0.5
create_box 2 box create_box 2 box
create_atoms 1 box create_atoms 1 box
set group all type/fraction 2 0.1 95392 set group all type/fraction 2 0.1 95392
set type 1 mass 1.0 set type 1 mass 1.0
set type 2 mass 1.5 set type 2 mass 1.5
set type 1 shape 1 1 1 set type 1 shape 1 1 1
set type 2 shape 3 1 1 set type 2 shape 3 1 1
set group all quat/random 18238 set group all quat/random 18238
compute rot all temp/asphere compute rot all temp/asphere
group spheroid type 1 group spheroid type 1
variable dof equal count(spheroid)+2 variable dof equal count(spheroid)+2
compute_modify rot extra/dof ${dof} compute_modify rot extra/dof ${dof}
@ -31,36 +31,40 @@ pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol thermo_style custom step c_rot epair etotal press vol
thermo 100 thermo 100
timestep 0.002 timestep 0.002
compute q all property/atom quatw quati quatj quatk compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez
#dump 1 all custom 100 dump.ellipse.resquared & dump 1 all custom 100 dump.ellipse.resquared id type x y z c_0[*]
# id type x y z c_q[1] c_q[2] c_q[3] c_q[4] 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 2 all image 100 image.*.jpg type type & #dump 1 all custom 100 dump.ellipse.resquared &
# zoom 1.6 center d 0.5 0.5 0.5 # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type &
# zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 #dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type & #dump 3 all movie 100 movie.mpg type type &
# zoom 1.6 center d 0.5 0.5 0.5 # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 #dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 & fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
mtk no pchain 0 tchain 1 mtk no pchain 0 tchain 1
fix 2 all enforce2d fix 2 all enforce2d
compute_modify 1_temp extra/dof ${dof} compute_modify 1_temp extra/dof ${dof}
# equilibrate to shrink box around dilute system # equilibrate to shrink box around dilute system
run 2000 run 2000
# run dynamics on dense system # run dynamics on dense system
unfix 1 unfix 1
fix 1 all nve/asphere fix 1 all nve/asphere
run 2000 run 2000