def core_phasespace(geom1,
geom2,
sym_factor,
stoich,
pot_prefactor=10.0,
pot_exp=6.0,
tstlvl='e'):
""" Writes the string that defines the `Core` section for a
phase space theory model of a transition state for a MESS input file by
formatting input information into strings a filling Mako template.
:param geom1: geometry of the dissociation species 1
:type geom1: list
:param geom2: geometry of the dissociation species 2
:type geom2: list
:param sym_factor: symmetry factor of transition state
:type sym_factor: float
:param stoich: combined stoichiometry of dissociation species 1 and 2
:type stoich: str
:param pot_prefator: factor C0 in potential expression V = -C0/R^n (au)
:type pot_prefactor: float
:param pot_exp: power n in potential expression V = -C0/R^n (au)
:type pot_exp: float
:param tstlvl: level to resolve the rate constant
:type tstlvl: str
:rtype: str
"""
assert tstlvl in ('e', 'ej', 't')
# Format the geometry section of each fragment
natom1, geom1 = util.geom_format(geom1)
natom2, geom2 = util.geom_format(geom2)
# Indent the geometry strings
geom1 = indent(geom1, 2)
geom2 = indent(geom2, 2)
# Format the tstlvl string
assert tstlvl in ('e', 'ej', 't')
tstlvl = tstlvl.upper()
# Create dictionary to fill template
core_keys = {
'sym_factor': sym_factor,
'natom1': natom1,
'geom1': geom1,
'natom2': natom2,
'geom2': geom2,
'stoich': stoich,
'pot_prefactor': pot_prefactor,
'pot_exp': pot_exp,
'tstlvl': tstlvl
}
return build_mako_str(template_file_name='core_phasespace.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=core_keys)
def core_rigidrotor(geom, sym_factor, interp_emax=None):
""" Writes the string that defines the 'Core' section for a
rigid-rotor model of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param geom: geometry of species
:type geom: list
:param sym_factor: symmetry factor of species
:type sym_factor: float
:param interp_emax: max energy to calculate num. of states (kcal.mol-1)
:type interp_emax: float
:rtype: str
"""
# Format the geometry section
natom, geom = util.geom_format(geom)
# Create dictionary to fill template
core_keys = {
'sym_factor': sym_factor,
'natom': natom,
'geom': geom,
'interp_emax': interp_emax
}
return build_mako_str(template_file_name='core_rigidrotor.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=core_keys)
def rotor_hindered(group,
axis,
symmetry,
potential,
remdummy=None,
geom=None,
use_quantum_weight=False,
rotor_id=''):
""" Writes the string that defines the `Rotor` section for a
single hindered rotor of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param group: idxs for the atoms of one of the rotational groups
:type group: list(int)
:param axis: idxs for the atoms that make up the rotational axis
:type axis: list(int)
:param symmetry: overall symmetry of the torsional motion (potential)
:type symmetry: int
:param potential: value of the potential along torsion (kcal.mol-1)
:type potential: list(float)
:param remdummy: list of idxs of dummy atoms for shifting values
:type remdummy: list(int)
:param geom: geometry of the species the rotor exists for
:type geom: list
:param use_quantum_weight: toggle weigthing of quantum effects
:type use_quantum_weight: bool
:param rotor_id: name associated with the rotor
:type rotor_id: str
:rtype: str
"""
# Format the rotor sections
rotor_group = util.format_rotor_key_defs(group, remdummy)
rotor_axis = util.format_rotor_key_defs(axis, remdummy)
rotor_npotential, rotor_potential = util.format_rotor_potential(potential)
# Format the geom
natom = 1
if geom is not None:
natom, geom = util.geom_format(geom)
geom = indent(geom, 4)
# Create dictionary to fill template
rotor_keys = {
'group': rotor_group,
'axis': rotor_axis,
'symmetry': symmetry,
'npotential': rotor_npotential,
'potential': rotor_potential,
'natom': natom,
'geom': geom,
'use_quantum_weight': use_quantum_weight,
'rotor_id': rotor_id
}
return build_mako_str(template_file_name='rotor_hindered.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=rotor_keys)
def core_multirotor(geom,
sym_factor,
pot_surf_file,
int_rot_str,
interp_emax=100,
quant_lvl_emax=9):
""" Writes the string that defines the `Core` section for a
multidimensional rotor model of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param geom: geometry of species
:type geom: list
:param sym_factor: symmetry factor of species
:type sym_factor: float
:param pot_surf_file: name of file with PES along rotor (kcal.mol-1)
:type pot_sur_file: str
:param int_rot_str: MESS-format strings that define internal rotors
:type int_rot_str: str
:param interp_emax: max energy to calculate density/number of states
:type interp_emax: float
:param quant_lvl_emax: max energy to calculate quantum energy levels
:type quant_lvl_emax: float
:rtype: str
"""
# Format the geometry section
natom, geom = util.geom_format(geom)
# Indent the internal rotor string
int_rot_str = indent(int_rot_str, 2)
# Create dictionary to fill template
core_keys = {
'sym_factor': sym_factor,
'natom': natom,
'geom': geom,
'pot_surf_file': pot_surf_file,
'int_rot': int_rot_str,
'interp_emax': interp_emax,
'quant_lvl_emax': quant_lvl_emax
}
return build_mako_str(template_file_name='core_multirotor.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=core_keys)
def umbrella_mode(group, plane, ref_atom, potential, remdummy=None, geom=None):
""" Writes the string that defines the `Umbrella` section for a
single umbrella mode of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param group: idxs for the atoms of ?
:type group: list(int)
:param axis: idxs for the atoms that ?
:type axis: list(int)
:param remdummy: list of idxs of dummy atoms for shifting values
:type remdummy: list(int)
:param geom: geometry of the species the umbrella mode exists for
:type geom: list
:rtype: str
"""
# Format the sections
umbr_group = util.format_rotor_key_defs(group, remdummy)
umbr_plane = util.format_rotor_key_defs(plane, remdummy)
umbr_npotential, umbr_potential = util.format_rotor_potential(potential)
# Format the geom
if geom is not None:
natom, geom = util.geom_format(geom)
geom = indent(geom, 4)
else:
natom = None
# Create dictionary to fill template
umbr_keys = {
'group': umbr_group,
'axis': umbr_plane,
'ref_atom': ref_atom,
'npotential': umbr_npotential,
'potential': umbr_potential,
'natom': natom,
'geom': geom,
}
return build_mako_str(template_file_name='umbrella_mode.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=umbr_keys)
def rotor_internal(group,
axis,
symmetry,
grid_size,
mass_exp_size,
pot_exp_size=5,
hmin=13,
hmax=101,
remdummy=None,
geom=None,
rotor_id=''):
""" Writes the string that defines the `Rotor` section for a
single internal rotor of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param group: idxs for the atoms of one of the rotational groups
:type group: list(int)
:param axis: idxs for the atoms that make up the rotational axis
:type axis: list(int)
:param symmetry: overall symmetry of the torsional motion (potential)
:type symmetry: int
:param grid_size: grid_size for statistical weight calculation
:type grid_size: int
:param mass_exp_size: num. mass expansion Fourier harmonics
:type mass_exp_size: int
:param pot_exp_size: num. potential expansion Fourier harmonics
:type pot_exp_size: int
:param hmin: minimum value for quantum phase space dimension
:type hmin: int
:param hmax: maximum value for quantum phase space dimension
:type hmax: int
:param remdummy: list of idxs of dummy atoms for shifting values
:type remdummy: list(int)
:param geom: geometry of the species the rotor exists for
:type geom: list
:param rotor_id: name associated with the rotor
:type rotor_id: str
:rtype: str
"""
assert mass_exp_size > 0 and mass_exp_size % 2 == 1
assert pot_exp_size > 0 and pot_exp_size % 2 == 1
# Format the sections
rotor_group = util.format_rotor_key_defs(group, remdummy)
rotor_axis = util.format_rotor_key_defs(axis, remdummy)
# Format the geom
if geom is not None:
natom, geom = util.geom_format(geom)
geom = indent(geom, 4)
else:
natom = None
# Create dictionary to fill template
rotor_keys = {
'group': rotor_group,
'axis': rotor_axis,
'symmetry': symmetry,
'mass_exp_size': mass_exp_size,
'pot_exp_size': pot_exp_size,
'hmin': hmin,
'hmax': hmax,
'grid_size': grid_size,
'natom': natom,
'geom': geom,
'rotor_id': rotor_id
}
return build_mako_str(template_file_name='rotor_internal.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=rotor_keys)
def rotor_hindered(group,
axis,
symmetry,
potential,
hmin=None,
hmax=None,
lvl_ene_max=None,
therm_pow_max=None,
remdummy=None,
geom=None,
rotor_id=''):
""" Writes the string that defines the `Rotor` section for a
single hindered rotor of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param group: idxs for the atoms of one of the rotational groups
:type group: list(int)
:param axis: idxs for the atoms that make up the rotational axis
:type axis: list(int)
:param symmetry: overall symmetry of the torsional motion (potential)
:type symmetry: int
:param hmin: minimum value for quantum phase space dimension
:type hmin: int
:param hmax: maximum value for quantum phase space dimension
:type hmax: int
:param potential: value of the potential along torsion (kcal.mol-1)
:type potential: list(float)
:param therm_pow_max: max exp't power in Boltzmann weight
:type therm_pow_max: int
:param remdummy: list of idxs of dummy atoms for shifting values
:type remdummy: list(int)
:param geom: geometry of the species the rotor exists for
:type geom: list
:param rotor_id: name associated with the rotor
:type rotor_id: str
:rtype: str
"""
# Format the rotor sections
rotor_group = util.format_rotor_key_defs(group, remdummy)
rotor_axis = util.format_rotor_key_defs(axis, remdummy)
rotor_npotential, rotor_potential = util.format_rotor_potential(potential)
# Format the geom
natom = 1
if geom is not None:
natom, geom = util.geom_format(geom)
geom = indent(geom, 4)
# Create dictionary to fill template
rotor_keys = {
'group': rotor_group,
'axis': rotor_axis,
'symmetry': symmetry,
'npotential': rotor_npotential,
'potential': rotor_potential,
'hmin': hmin,
'hmax': hmax,
'lvl_ene_max': lvl_ene_max,
'therm_pow_max': therm_pow_max,
'natom': natom,
'geom': geom,
'rotor_id': rotor_id
}
return build_mako_str(template_file_name='rotor_hindered.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=rotor_keys)