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write_molecule_files.py
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write_molecule_files.py
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from textwrap import dedent
def water(last_atom_ID, last_bond_ID, last_angle_ID, model='TIP4P_cutoff'):
ID_O = last_atom_ID + 1
ID_H = ID_O + 1
BT = last_bond_ID + 1
AT = last_angle_ID + 1
charge_dict = {
'TIP4P_cutoff': (-1.0400, 0.5200),
'TIP4P_2005': (-1.1128, 0.5564),
'TIP4P_long': (-1.0484, 0.5242),
'TIP3P_long': (-0.8300, 0.4150)
}
M_site_dist_dict = {
'TIP4P_cutoff': 0.1500,
'TIP4P_2005': 0.1546,
'TIP4P_long': 0.1250,
'TIP3P_long': None
}
LJ_dict = {
# LAMMPS has a special TIP4P pair_style that automatically adds the M site
'TIP4P_cutoff': {ID_O: ('lj/cut/tip4p/cut' , 0.15500, 3.15360), ID_H: ('lj/cut/tip4p/cut' , 0.0, 0.0), 'style': 'lj/cut/tip4p/cut' , 'comments': {ID_O:['O_water', 'O_water'], ID_H:['H_water', 'H_water']}},
'TIP4P_2005': {ID_O: ('lj/cut/tip4p/long', 0.18520, 3.15890), ID_H: ('lj/cut/tip4p/long', 0.0, 0.0), 'style': 'lj/cut/tip4p/long', 'comments': {ID_O:['O_water', 'O_water'], ID_H:['H_water', 'H_water']}},
'TIP4P_long': {ID_O: ('lj/cut/tip4p/long', 0.16275, 3.16435), ID_H: ('lj/cut/tip4p/long', 0.0, 0.0), 'style': 'lj/cut/tip4p/long', 'comments': {ID_O:['O_water', 'O_water'], ID_H:['H_water', 'H_water']}},
'TIP3P_long': {ID_O: ('lj/cut/coul/long' , 0.10200, 3.18800), ID_H: ('lj/cut/coul/long' , 0.0, 0.0), 'style': 'lj/cut/coul/long' , 'comments': {ID_O:['O_water', 'O_water'], ID_H:['H_water', 'H_water']}}
}
bond_dict = {
# TIP4P is a rigid model (use fix shake), force constants should just be reasonable values
# TIP3P has force constants if a flexible model is desired
'TIP4P_cutoff': {BT: {'style':'harmonic', 'params':(100.0, 0.9572), 'comments':'# O_water H_water'}},
'TIP4P_2005': {BT: {'style':'harmonic', 'params':(100.0, 0.9572), 'comments':'# O_water H_water'}},
'TIP4P_long': {BT: {'style':'harmonic', 'params':(100.0, 0.9572), 'comments':'# O_water H_water'}},
'TIP3P_long': {BT: {'style':'harmonic', 'params':(450.0, 0.9572), 'comments':'# O_water H_water'}}
}
angle_dict = {
# TIP4P is a rigid model (use fix shake), force constants should just be reasonable values
# TIP3P has force constants if a flexible model is desired
'TIP4P_cutoff': {AT: {'style':'harmonic', 'params':(50.0, 104.52), 'comments':'# H_water O_water H_water'}},
'TIP4P_2005': {AT: {'style':'harmonic', 'params':(50.0, 104.52), 'comments':'# H_water O_water H_water'}},
'TIP4P_long': {AT: {'style':'harmonic', 'params':(50.0, 104.52), 'comments':'# H_water O_water H_water'}},
'TIP3P_long': {AT: {'style':'harmonic', 'params':(55.0, 104.52), 'comments':'# H_water O_water H_water'}}
}
qO,qH = charge_dict[model]
LJ_params = LJ_dict[model]
bond_params = bond_dict[model]
angle_params = angle_dict[model]
if 'TIP4P' in model:
molfile = dedent("""# Water molecule. useable for TIP3P or TIP4P in LAMMPS.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 {ID_O}
2 {ID_H}
3 {ID_H}
Charges
1 {qO}
2 {qH}
3 {qH}
Bonds
1 {BT} 1 2
2 {BT} 1 3
Angles
1 {AT} 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 {BT} {BT} {AT}
2 {BT} {BT} {AT}
3 {BT} {BT} {AT}""".format(**locals())).strip()
if 'TIP3P' in model:
molfile = dedent("""# Water molecule. useable for TIP3P or TIP4P in LAMMPS.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 {ID_O}
2 {ID_H}
3 {ID_H}
Charges
1 {qO}
2 {qH}
3 {qH}
Bonds
1 {BT} 1 2
2 {BT} 1 3
Angles
1 {AT} 2 1 3""".format(**locals())).strip()
mass_dict = {ID_O:15.9994, ID_H:1.00794}
molnames = ('H2O_mol', 'H2O.txt')
extra_types = (2,1,1,None,None)
return molfile, LJ_params, bond_params, angle_params, molnames, mass_dict, M_site_dist_dict[model], extra_types