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fix example problems

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This commit is contained in:
Steve Plimpton
2021-08-26 15:09:27 -06:00
parent 9c095e8d76
commit 9f46071226
14 changed files with 4196 additions and 77 deletions
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1980
examples/amoeba/data.water_box.amoeba Normal file
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1980
examples/amoeba/data.water_box.hippo Normal file
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18
examples/amoeba/data.water_dimer.amoeba
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@ -1,4 +1,4 @@
LAMMPS data file created from Tinker water_dimer.xyz and water03.prm files LAMMPS data file created from Tinker ../TINKER_TESTS/water_dimer/water_dimer.xyz and ../TINKER_TESTS/water_dimer/amoeba.prm files
6 atoms 6 atoms
4 bonds 4 bonds
@ -38,17 +38,17 @@ Angles
Bond Coeffs Bond Coeffs
1 556.85 0.9572 1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs Angle Coeffs
1 48.70 108.50 1 0 108.5 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
Tinker Types Tinker Types
1 1 1 1 1
2 2 1 2 2
3 2 1 3 2
4 1 2 4 1
5 2 2 5 2
6 2 2 6 2

18
examples/amoeba/data.water_dimer.hippo
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@ -1,4 +1,4 @@
LAMMPS data file created from Tinker water_dimer.xyz and water19.prm files LAMMPS data file created from Tinker water_dimer.xyz and hippo.prm files
6 atoms 6 atoms
4 bonds 4 bonds
@ -38,17 +38,17 @@ Angles
Bond Coeffs Bond Coeffs
1 556.85 0.9572 1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs Angle Coeffs
1 48.70 107.70 1 0 107.7 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
Tinker Types Tinker Types
1 1 1 1 1
2 2 1 2 2
3 2 1 3 2
4 1 2 4 1
5 2 2 5 2
6 2 2 6 2

42
examples/amoeba/data.water_hexamer.amoeba
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@ -1,4 +1,4 @@
LAMMPS data file created from Tinker water_hexamer.xyz and water03.prm files LAMMPS data file created from Tinker water_hexamer.xyz and amoeba.prm files
18 atoms 18 atoms
12 bonds 12 bonds
@ -62,29 +62,29 @@ Angles
Bond Coeffs Bond Coeffs
1 556.85 0.9572 1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs Angle Coeffs
1 48.70 108.50 1 0 108.5 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
Tinker Types Tinker Types
1 1 1 1 1
2 2 1 2 2
3 2 1 3 2
4 1 2 4 1
5 2 2 5 2
6 2 2 6 2
7 1 3 7 1
8 2 3 8 2
9 2 3 9 2
10 1 4 10 1
11 2 4 11 2
12 2 4 12 2
13 1 5 13 1
14 2 5 14 2
15 2 5 15 2
16 1 6 16 1
17 2 6 17 2
18 2 6 18 2

42
examples/amoeba/data.water_hexamer.hippo
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@ -1,4 +1,4 @@
LAMMPS data file created from Tinker water_hexamer.xyz and water19.prm files LAMMPS data file created from Tinker water_hexamer.xyz and hippo.prm files
18 atoms 18 atoms
12 bonds 12 bonds
@ -62,29 +62,29 @@ Angles
Bond Coeffs Bond Coeffs
1 556.85 0.9572 1 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs Angle Coeffs
1 48.70 107.70 1 0 107.7 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
Tinker Types Tinker Types
1 1 1 1 1
2 2 1 2 2
3 2 1 3 2
4 1 2 4 1
5 2 2 5 2
6 2 2 6 2
7 1 3 7 1
8 2 3 8 2
9 2 3 9 2
10 1 4 10 1
11 2 4 11 2
12 2 4 12 2
13 1 5 13 1
14 2 5 14 2
15 2 5 15 2
16 1 6 16 1
17 2 6 17 2
18 2 6 18 2

11
examples/amoeba/in.ubiquitin
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@ -30,6 +30,15 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp & thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*] emol etotal press c_virial[*]
# 0-step run # DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0 run 0

15
examples/amoeba/in.water_box → examples/amoeba/in.water_box.amoeba
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@ -18,16 +18,12 @@ fix extra2 all property/atom i_polaxe
# read data file # read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types" read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
#read_data data.water_box.hippo fix amtype NULL "Tinker Types"
# force field # force field
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
#pair_style hippo
#pair_coeff * * hippo_water.prm hippo_water.key
# thermo output # thermo output
compute virial all pressure NULL virial compute virial all pressure NULL virial
@ -35,6 +31,15 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp & thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*] emol etotal press c_virial[*]
# 0-step run # DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0 run 0

45
examples/amoeba/in.water_box.hippo Normal file
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@ -0,0 +1,45 @@
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
# DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0

15
examples/amoeba/in.water_dimer → examples/amoeba/in.water_dimer.amoeba
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@ -18,16 +18,12 @@ fix extra2 all property/atom i_polaxe
# read data file # read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types" read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
#read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
# force field # force field
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
#pair_style hippo
#pair_coeff * * hippo_water.prm hippo_water.key
# thermo output # thermo output
compute virial all pressure NULL virial compute virial all pressure NULL virial
@ -35,6 +31,15 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp & thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*] emol etotal press c_virial[*]
# 0-step run # DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0 run 0

45
examples/amoeba/in.water_dimer.hippo Normal file
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@ -0,0 +1,45 @@
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
# DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0

15
examples/amoeba/in.water_hexamer → examples/amoeba/in.water_hexamer.amoeba
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@ -18,16 +18,12 @@ fix extra2 all property/atom i_polaxe
# read data file # read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types" read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
#read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
# force field # force field
pair_style amoeba pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key pair_coeff * * amoeba_water.prm amoeba_water.key
#pair_style hippo
#pair_coeff * * hippo_water.prm hippo_water.key
# thermo output # thermo output
compute virial all pressure NULL virial compute virial all pressure NULL virial
@ -35,6 +31,15 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp & thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*] emol etotal press c_virial[*]
# 0-step run # DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0 run 0

45
examples/amoeba/in.water_hexamer.hippo Normal file
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@ -0,0 +1,45 @@
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
# DEBUG: setup force components this way so can dump them
fix fhal all store/state 0 fx fy fz
fix frepulse all store/state 0 fx fy fz
fix fdisp all store/state 0 fx fy fz
fix fpolar all store/state 0 fx fy fz
fix fmpole all store/state 0 fx fy fz
fix fqxfer all store/state 0 fx fy fz
# zero step run
run 0

2
src/fix_property_atom.cpp
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@ -223,7 +223,7 @@ FixPropertyAtom::~FixPropertyAtom()
} }
} }
delete [] style; delete [] styles;
delete [] cols; delete [] cols;
delete [] index; delete [] index;
delete [] astyle; delete [] astyle;