def __init__(self, gromacs_dir, label='opls-aa', pair_cutoff=10.0, kspace=False, **kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = 'real'
if kspace:
self.parameters.pair_style = 'lj/cut/coul/long %f' % pair_cutoff
self.parameters.kspace_style = 'ewald 0.0001'
else:
self.parameters.pair_style = 'lj/cut/coul/cut %f' % pair_cutoff
self.parameters.pair_modify = 'mix geometric'
self.parameters.bond_style = 'harmonic'
self.parameters.angle_style = 'harmonic'
self.parameters.dihedral_style = 'multi/harmonic'
#self.parameters.improper_style = 'harmonic'
self.parameters.special_bonds = 'lj/coul 0.0 0.0 0.5'
# Read force field file
ffnonbonded = os.path.join(gromacs_dir, 'oplsaa.ff', 'ffnonbonded.itp')
ffbonded = os.path.join(gromacs_dir, 'oplsaa.ff', 'ffbonded.itp')
self.ff_data, self.charges = read_gromacs_params.read((ffnonbonded, ffbonded), return_charges=True)
self.type_resolver = typing.TypeResolver(oplsaatypes.data)
# Add parameters for flexible TIP3P water
self.ff_data.add('bond', SequenceType(['OW', 'HW']), 'Bond Coeffs', [450, 0.9572])
self.ff_data.add('angle', SequenceType(['HW', 'OW', 'HW']), 'Angle Coeffs', [55, 104.52])
def __init__(self,
ff_file_path,
label='compass',
pair_cutoff=9.5,
kspace=False,
**kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = 'real'
if kspace:
self.parameters.pair_style = 'lj/class2/coul/long %f' % pair_cutoff
self.parameters.kspace_style = 'ewald 0.0001'
else:
self.parameters.pair_style = 'lj/class2/coul/cut %f' % pair_cutoff
self.parameters.bond_style = 'class2'
self.parameters.angle_style = 'class2'
self.parameters.dihedral_style = 'class2'
self.parameters.improper_style = 'class2'
self.parameters.special_bonds = 'lj/coul 0.0 0.0 1.0 dihedral yes'
self.ff_data, self.bond_increments = read_compass_params.read(
open(ff_file_path))
self.type_resolver = typing.TypeResolver(compasstypes.data)
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
"""
def __init__(self, ff_file_path, label='charmm', pair_cutoff=10.0, auto_charges=False, **kwargs): LAMMPSBase.__init__(self, label, **kwargs) self.parameters.units = 'real' self.parameters.pair_style = 'lj/charmm/coul/charmm 8.0 10.0' self.parameters.bond_style = 'harmonic' self.parameters.angle_style = 'charmm' self.parameters.dihedral_style = 'charmm' self.parameters.improper_style = 'harmonic' self.parameters.special_bonds = 'charmm' # Read force field file self.ff_data = read_charmm_params.read(open(ff_file_path)) self.type_resolver = typing.TypeResolver(charmmtypes.data) self.auto_charges = auto_charges
def __init__(self, gromacs_dir, label='amber', inner_cutoff = 8.0, outer_cutoff=10.0, **kwargs): LAMMPSBase.__init__(self, label, **kwargs) self.parameters.units = 'real' self.parameters.pair_style = 'lj/charmm/coul/charmm %f %f' % (inner_cutoff, outer_cutoff) self.parameters.bond_style = 'harmonic' self.parameters.angle_style = 'harmonic' self.parameters.dihedral_style = 'charmm' #self.parameters.improper_style = 'harmonic' self.parameters.special_bonds = 'amber' # Read force field file ffnonbonded = os.path.join(gromacs_dir, 'amber03.ff', 'ffnonbonded.itp') ffbonded = os.path.join(gromacs_dir, 'amber03.ff', 'ffbonded.itp') self.ff_data = read_gromacs_params.read((ffnonbonded, ffbonded)) self.type_resolver = typing.TypeResolver(ambertypes.data)
def __init__(self, ff_file_path, label="pcff", pair_cutoff=10.0, kspace=False, **kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = "real"
if kspace:
self.parameters.pair_style = "lj/class2/coul/long %f" % pair_cutoff
self.parameters.kspace_style = "ewald 0.0001"
else:
self.parameters.pair_style = "lj/class2/coul/cut %f" % pair_cutoff
self.parameters.bond_style = "class2"
self.parameters.angle_style = "class2"
self.parameters.dihedral_style = "class2"
self.parameters.improper_style = "class2"
self.parameters.special_bonds = "lj/coul 0.0 0.0 1.0 dihedral yes"
self.ff_data, self.bond_increments = read_compass_params.read(open(ff_file_path))
self.type_resolver = typing.TypeResolver(pcfftypes.data)
def __init__(self, label='clayff', pair_cutoff=(10.0, 10.0), **kwargs): LAMMPSBase.__init__(self, label, **kwargs) try: ljcut, coulcut = pair_cutoff except: ljcut = pair_cutoff coulcut = pair_cutoff self.parameters.units = 'real' self.parameters.pair_style = 'lj/cut/coul/long %f %f' % (ljcut, coulcut) #self.parameters.pair_style = 'lj/cut/coul/cut %f %f' % (ljcut, coulcut) self.parameters.pair_modify = 'mix arithmetic' self.parameters.bond_style = 'harmonic' self.parameters.angle_style = 'harmonic' self.parameters.kspace_style = 'ewald/disp 0.0001' self.ff_data = ff_data self.type_resolver = typing.TypeResolver(clayff_types)
def __init__(self, label='clayff', pair_cutoff=(10.0, 10.0), **kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
try:
ljcut, coulcut = pair_cutoff
except:
ljcut = pair_cutoff
coulcut = pair_cutoff
self.parameters.units = 'real'
self.parameters.pair_style = 'lj/cut/coul/long %f %f' % (ljcut,
coulcut)
#self.parameters.pair_style = 'lj/cut/coul/cut %f %f' % (ljcut, coulcut)
self.parameters.pair_modify = 'mix arithmetic'
self.parameters.bond_style = 'harmonic'
self.parameters.angle_style = 'harmonic'
self.parameters.kspace_style = 'ewald/disp 0.0001'
self.ff_data = ff_data
self.type_resolver = typing.TypeResolver(clayff_types)
def __init__(self,
ff_file_path,
label='charmm',
pair_cutoff=10.0,
auto_charges=False,
**kwargs):
LAMMPSBase.__init__(self, label, **kwargs)
self.parameters.units = 'real'
self.parameters.pair_style = 'lj/charmm/coul/charmm 8.0 10.0'
self.parameters.bond_style = 'harmonic'
self.parameters.angle_style = 'charmm'
self.parameters.dihedral_style = 'charmm'
self.parameters.improper_style = 'harmonic'
self.parameters.special_bonds = 'charmm'
# Read force field file
self.ff_data = read_charmm_params.read(open(ff_file_path))
self.type_resolver = typing.TypeResolver(charmmtypes.data)
self.auto_charges = auto_charges
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
"""
def read_lammps_trj(self, *args, **kwargs):
LAMMPSBase.read_lammps_trj(self, *args, **kwargs)
def set_dumpfreq(self, freq):
LAMMPSBase.set_dumpfreq(self, freq)
def read_lammps_trj(self, *args, **kwargs): LAMMPSBase.read_lammps_trj(self, *args, **kwargs)
def set_dumpfreq(self, freq): LAMMPSBase.set_dumpfreq(self, freq)
