add two examples for regression testing

This commit is contained in:
alphataubio
2024-10-07 17:15:09 -04:00
parent b16ddfcdd4
commit 941b3dd566
3 changed files with 142 additions and 0 deletions

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units real
molecule water tip3p.mol
atom_style full
variable radius equal 100.0
region box block $(-v_radius) $(v_radius) $(-v_radius) $(v_radius) $(-v_radius) $(v_radius)
create_box 2 box bond/types 1 angle/types 1 &
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
mass 1 15.9994
mass 2 1.008
bond_style zero
bond_coeff 1 0.9574
angle_style zero
angle_coeff 1 104.52
region block1 block -80 80 -80 80 -80 80
region block2 block -70 70 -70 70 -70 70
create_atoms 0 random 5000 12345 block2 mol water 12345 overlap 2
thermo 1
thermo_style custom step time spcpu temp press etotal pe
fix wall all wall/region block1 harmonic 1000.0 0.0 2.5
fix_modify wall energy yes
pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1521 3.1507
pair_coeff 2 2 0.0 1.0
velocity all create 300.0 12345
fix 1 all nvt temp 300 300 100.0
fix 2 all shake 0.001 10 10000 b 1 a 1
dump 2 all movie 10 wall.block.mpg type type size 1500 1500 fsaa yes
dump_modify 2 pad 4 acolor * white/red/green/blue/aqua/magenta
run 100

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units real
molecule water tip3p.mol
atom_style full
variable radius equal 100.0
region box block $(-v_radius) $(v_radius) $(-v_radius) $(v_radius) $(-v_radius) $(v_radius)
create_box 2 box bond/types 1 angle/types 1 &
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
mass 1 15.9994
mass 2 1.008
bond_style zero
bond_coeff 1 0.9574
angle_style zero
angle_coeff 1 104.52
region sphere1 sphere 0 0 0 $(v_radius-10) side in
region sphere2 sphere 0 0 0 $(v_radius-20) side in
create_atoms 0 random 1000 12345 sphere2 mol water 12345 overlap 1.33
thermo 1
thermo_style custom step time spcpu temp press etotal pe
fix wall all wall/region sphere1 harmonic 1000.0 0.0 2.5
fix_modify wall energy yes
pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1521 3.1507
pair_coeff 2 2 0.0 1.0
velocity all create 300.0 12345
fix 1 all nvt temp 300 300 100.0
fix 2 all shake 0.001 10 10000 b 1 a 1
dump 2 all movie 10 wall.sphere.mpg type type size 1500 1500 fsaa yes
dump_modify 2 pad 4 acolor * white/red/green/blue/aqua/magenta
run 100

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examples/wall/tip3p.mol Normal file
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# Water molecule. TIP3P geometry
3 atoms
2 bonds
1 angles
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1
2 2
3 2
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Shake Flags
1 1
2 1
3 1
Shake Atoms
1 1 2 3
2 1 2 3
3 1 2 3
Shake Bond Types
1 1 1 1
2 1 1 1
3 1 1 1
Special Bond Counts
1 2 0 0
2 1 1 0
3 1 1 0
Special Bonds
1 2 3
2 1 3
3 1 2