def __init__(self,
ff_file_path,
label='reaxff',
specorder=None,
implementation='C',
update_charges=True,
save_bond_orders=False,
debug_energy=False,
**kwargs):
LAMMPSBase.__init__(self,
label,
update_charges=update_charges,
**kwargs)
self.parameters.atom_style = 'charge'
self.parameters.pair_style = 'reax'
if implementation == 'C':
self.parameters.pair_style += '/c NULL'
self.parameters.extra_cmds.append(
'fix qeq all qeq/reax 1 0.0 10.0 1.0e-6 reax/c')
self.parameters.units = 'real'
if not specorder:
self.specorder = get_element_order(ff_file_path)
else:
self.specorder = specorder
self.ff_file = ff_file_path
self.ff_data = FFData()
self.save_bond_orders = save_bond_orders
"""
mhg oh ho 30.0 109.47
cao oh ho 30.0 109.47
cah oh ho 30.0 109.47
feo oh ho 30.0 109.47
lio oh ho 30.0 109.47
ao ohs ho 30.0 109.47
at ohs ho 30.0 109.47
mgo ohs ho 30.0 109.47
mhg ohs ho 30.0 109.47
cao ohs ho 30.0 109.47
cah ohs ho 30.0 109.47
feo ohs ho 30.0 109.47
lio ohs ho 30.0 109.47
'''
ff_data = FFData()
rho_fac = 2**(-1. / 6)
charges = {}
for line in nonbond_data.strip().split('\n'):
fields = line.split()
charges[fields[0]] = float(fields[1])
parameters = [float(fields[2]), float(fields[3]) * rho_fac]
ff_data.add('atom', fields[0], 'Pair Coeffs', parameters)
for line in bond_stretch_data.strip().split('\n'):
fields = line.split()
parameters = map(float, fields[2:4])
ff_data.add('bond', SequenceType(fields[:2]), 'Bond Coeffs', parameters)
for line in angle_bend_data.strip().split('\n'):
mhg oh ho 30.0 109.47
cao oh ho 30.0 109.47
cah oh ho 30.0 109.47
feo oh ho 30.0 109.47
lio oh ho 30.0 109.47
ao ohs ho 30.0 109.47
at ohs ho 30.0 109.47
mgo ohs ho 30.0 109.47
mhg ohs ho 30.0 109.47
cao ohs ho 30.0 109.47
cah ohs ho 30.0 109.47
feo ohs ho 30.0 109.47
lio ohs ho 30.0 109.47
'''
ff_data = FFData()
rho_fac = 2**(-1./6)
charges = {}
for line in nonbond_data.strip().split('\n'):
fields = line.split()
charges[fields[0]] = float(fields[1])
parameters = [float(fields[2]), float(fields[3])*rho_fac]
ff_data.add('atom', fields[0], 'Pair Coeffs', parameters)
for line in bond_stretch_data.strip().split('\n'):
fields = line.split()
parameters = map(float, fields[2:4])
ff_data.add('bond', SequenceType(fields[:2]), 'Bond Coeffs', parameters)
for line in angle_bend_data.strip().split('\n'):
def read(infile):
result = FFData()
def parser(infile):
for line in infile:
if line.startswith('BONDS') or \
line.startswith('ANGLES') or \
line.startswith('DIHEDRALS') or \
line.startswith('IMPROPERS') or \
line.startswith('NONBONDED') or \
line.startswith('HBOND'):
break
line = line.replace('!HGTIP', 'HGTIP')
line = line.replace('!OGTIP', 'OGTIP')
yield line.split('!')[0].split()
# Skip masses
for item in parser(infile): pass
# Bonds
for fields in parser(infile):
if len(fields) != 4: continue
type = SequenceType(fields[0:2])
parameters = [float(f) for f in fields[2:]]
result.bond[type] = {'Bond Coeffs': parameters}
# Angles
for fields in parser(infile):
if len(fields) == 5: fields += [0, 0]
if len(fields) != 7: continue
type = SequenceType(fields[0:3])
parameters = [float(f) for f in fields[3:]]
result.angle[type] = {'Angle Coeffs': parameters}
# Dihedrals
for fields in parser(infile):
if len(fields) == 7: fields += [0]
if len(fields) != 8: continue
type = SequenceType(fields[0:4])
parameters = [float(fields[4]), int(fields[5]), int(float(fields[6])), float(fields[7])]
result.dihedral[type] = {'Dihedral Coeffs': parameters}
# Impropers
for fields in parser(infile):
if len(fields) != 7: continue
type = ImproperType(central_type=fields[0], other_types=fields[1:4])
parameters = [float(f) for f in fields[4:7:2]]
result.improper[type] = {'Improper Coeffs': parameters}
# Nonbonded
for fields in parser(infile):
if len(fields) == 4: fields += [0, 0, 0]
if len(fields) != 7: continue
eps = -float(fields[2])
rmin = float(fields[3])*2
sigma = rmin*2**(-1./6)
type = fields[0]
parameters = [eps, sigma]
result.atom[type] = {'Pair Coeffs': parameters}
return result
def read(infile):
result = FFData()
def parser(infile):
for line in infile:
if line.startswith('BONDS') or \
line.startswith('ANGLES') or \
line.startswith('DIHEDRALS') or \
line.startswith('IMPROPERS') or \
line.startswith('NONBONDED') or \
line.startswith('HBOND'):
break
line = line.replace('!HGTIP', 'HGTIP')
line = line.replace('!OGTIP', 'OGTIP')
yield line.split('!')[0].split()
# Skip masses
for item in parser(infile):
pass
# Bonds
for fields in parser(infile):
if len(fields) != 4: continue
type = SequenceType(fields[0:2])
parameters = [float(f) for f in fields[2:]]
result.bond[type] = {'Bond Coeffs': parameters}
# Angles
for fields in parser(infile):
if len(fields) == 5: fields += [0, 0]
if len(fields) != 7: continue
type = SequenceType(fields[0:3])
parameters = [float(f) for f in fields[3:]]
result.angle[type] = {'Angle Coeffs': parameters}
# Dihedrals
for fields in parser(infile):
if len(fields) == 7: fields += [0]
if len(fields) != 8: continue
type = SequenceType(fields[0:4])
parameters = [
float(fields[4]),
int(fields[5]),
int(float(fields[6])),
float(fields[7])
]
result.dihedral[type] = {'Dihedral Coeffs': parameters}
# Impropers
for fields in parser(infile):
if len(fields) != 7: continue
type = ImproperType(central_type=fields[0], other_types=fields[1:4])
parameters = [float(f) for f in fields[4:7:2]]
result.improper[type] = {'Improper Coeffs': parameters}
# Nonbonded
for fields in parser(infile):
if len(fields) == 4: fields += [0, 0, 0]
if len(fields) != 7: continue
eps = -float(fields[2])
rmin = float(fields[3]) * 2
sigma = rmin * 2**(-1. / 6)
type = fields[0]
parameters = [eps, sigma]
result.atom[type] = {'Pair Coeffs': parameters}
return result