def configs_union(mol_data_strs, zero_enes, tunnel_strs=None):
""" Writes the string that defines the `Union` section, containing
multiple configurations for a given species, for a MESS input file by
formatting input information into strings a filling Mako template.
:param mol_data_strs: MESS strings with data for all configurations
:type mol_data_strs: list(str)
:rtype: str
"""
# Build the zero energy strings and add them to the union strings
union_data = ''
for idx, (union_str, zero_ene) in enumerate(zip(mol_data_strs, zero_enes)):
zero_ene_str = messformat.zero_energy_format(zero_ene)
zero_ene_str = messformat.indent(zero_ene_str, 2)
union_data += union_str
union_data += zero_ene_str
if tunnel_strs is not None:
_tunnel_str = f'\n{tunnel_strs[idx]}\nEnd ! Tunnel\n'
union_data += messformat.indent(_tunnel_str, 2)
union_data += '\n\n'
union_data += f'End ! Union{idx+1}\n'
# Concatenate all of the molecule strings
union_data = messformat.indent(union_data, 2)
# Create dictionary to fill template
union_keys = {'union_data': union_data}
return build_mako_str(template_file_name='union.mako',
template_src_path=RXNCHAN_PATH,
template_keys=union_keys)
def bimolecular(bimol_label, species1_label, species1_data, species2_label,
species2_data, ground_energy):
""" Writes a Bimolecular section.
"""
# Indent the string containing all of data for each species
species1_data = messformat.indent(species1_data, 4)
species2_data = messformat.indent(species2_data, 4)
# Determine if species is an atom
isatom1 = messformat.is_atom_in_str(species1_data)
isatom2 = messformat.is_atom_in_str(species2_data)
# Format the precision of the ground energy
ground_energy = '{0:<8.2f}'.format(ground_energy)
# Create dictionary to fill template
bimol_keys = {
'bimolec_label': bimol_label,
'species1_label': species1_label,
'species1_data': species1_data,
'isatom1': isatom1,
'species2_label': species2_label,
'species2_data': species2_data,
'isatom2': isatom2,
'ground_energy': ground_energy
}
return build_mako_str(template_file_name='bimolecular.mako',
template_src_path=RXNCHAN_PATH,
template_keys=bimol_keys)
def ts_sadpt(ts_label,
reac_label,
prod_label,
ts_data,
aux_id_label=None,
zero_ene=None,
tunnel=''):
""" Writes the string that defines the `Barrier` section for
for a given transition state, modeled as a PES saddle point,
for fixed transition state theory. MESS input file string built by
formatting input information into strings a filling Mako template.
:param ts_label: label for input TS used by MESS
:type ts_label: str
:param reac_label: label for reactant connected to TS used by MESS
:type reac_label: str
:param prod_label: label for product connected to TS used by MESS
:type prod_label: str
:param ts_data: MESS string with required electronic structure data
:type ts_data: str
:param aux_id_label: label for additional species ID information
:type aux_id_label: str
:param zero_ene: elec+zpve energy relative to PES reference
:type zero_ene: float
:param tunnel: `Tunnel` section MESS-string for TS
:type tunnel: str
:rtype: str
"""
# Format the label
rxn_label = f'{ts_label} {reac_label} {prod_label}'
full_label = messformat.mess_label_format(rxn_label,
aux_id_label=aux_id_label,
calc_dens=False)
# Indent the string containing all of data for the saddle point
ts_data = messformat.indent(ts_data, 2)
if tunnel != '':
tunnel = messformat.indent(tunnel, 4)
# Format the precision of the zero energy
if zero_ene is not None:
zero_ene = f'{zero_ene:<8.2f}'
# Create dictionary to fill template
ts_sadpt_keys = {
'rxn_label': full_label,
'ts_data': ts_data,
'aux_id_label': aux_id_label,
'zero_ene': zero_ene,
'tunnel': tunnel
}
return build_mako_str(template_file_name='ts_sadpt.mako',
template_src_path=RXNCHAN_PATH,
template_keys=ts_sadpt_keys)
def ts_variational(ts_label,
reac_label,
prod_label,
rpath_strs,
zero_enes=None,
tunnel=''):
""" Writes the string that defines the `Barrier` section for
for a given transition state, modeled using points along reaction path,
for varational transition state theory. MESS input file string built by
formatting input information into strings a filling Mako template.
:param ts_label: label for input TS used by MESS
:type ts_label: str
:param reac_label: label for reactant connected to TS used by MESS
:type reac_label: str
:param prod_label: label for product connected to TS used by MESS
:type prod_label: str
:param rpath_pt_strs: MESS strings for each point on reaction path
:type rpath_pt_strs: list(str)
:param tunnel: `Tunnel` section MESS-string for TS
:type tunnel: str
:rtype: str
"""
assert len(rpath_strs) == len(zero_enes), (
'Number of rpath strings ({})'.format(len(rpath_strs)),
'and zero energies ({}) do not match'.format(len(zero_enes)))
# Build the zero energy strings and add them to the rpath strings
full_rpath_str = ''
for rpath_str, zero_ene in zip(rpath_strs, zero_enes):
zero_ene_str = messformat.zero_energy_format(zero_ene)
zero_ene_str = messformat.indent(zero_ene_str, 2)
full_rpath_str += rpath_str
full_rpath_str += zero_ene_str
full_rpath_str += '\n\n'
full_rpath_str += 'End ! RPATH PT\n'
# Concatenate all of the variational point strings and indent them
ts_data = messformat.indent(full_rpath_str, 4)
if tunnel != '':
tunnel = messformat.indent(tunnel, 4)
# Create dictionary to fill template
var_keys = {
'ts_label': ts_label,
'reac_label': reac_label,
'prod_label': prod_label,
'ts_data': ts_data,
'tunnel': tunnel
}
return build_mako_str(template_file_name='ts_var.mako',
template_src_path=RXNCHAN_PATH,
template_keys=var_keys)
def bimolecular(bimol_label,
spc1_label,
spc1_data,
spc2_label,
spc2_data,
ground_ene,
auxbimol_id_label=None,
aux1_id_label=None,
aux2_id_label=None,
calc_spc1_density=False,
calc_spc2_density=False):
""" Writes a Bimolecular section.
"""
# Format the labels
full_bimol_label = messformat.mess_label_format(
bimol_label, aux_id_label=auxbimol_id_label, calc_dens=False)
full_spc1_label = messformat.mess_label_format(spc1_label,
aux_id_label=aux1_id_label,
calc_dens=calc_spc1_density)
full_spc2_label = messformat.mess_label_format(spc2_label,
aux_id_label=aux2_id_label,
calc_dens=calc_spc2_density)
# Indent the string containing all of data for each species
spc1_data = messformat.indent(spc1_data, 4)
spc2_data = messformat.indent(spc2_data, 4)
# Determine if species is an atom
isatom1 = messformat.is_atom_in_str(spc1_data)
isatom2 = messformat.is_atom_in_str(spc2_data)
# Format the precision of the ground energy
ground_ene = f'{ground_ene:<8.2f}'
# Create dictionary to fill template
bimol_keys = {
'bimolec_label': full_bimol_label,
'spc1_label': full_spc1_label,
'spc1_data': spc1_data,
'isatom1': isatom1,
'spc2_label': full_spc2_label,
'spc2_data': spc2_data,
'isatom2': isatom2,
'ground_ene': ground_ene
}
return build_mako_str(template_file_name='bimolecular.mako',
template_src_path=RXNCHAN_PATH,
template_keys=bimol_keys)
def species(spc_label, spc_data, zero_ene=None):
""" Writes the string that defines the `Species` section for
for a given species for a MESS input file by
formatting input information into strings a filling Mako template.
:param spc_label: label for input species used by MESS
:type spc_label: str
:param spc_data: MESS string with required electronic structure data
:type spc_data: str
:param zero_ene: elec+zpve energy relative to PES reference
:rtype: str
"""
# Indent the string containing all of data for the well
spc_data = messformat.indent(spc_data, 2)
# Format the precision of the zero energy
if zero_ene is not None:
zero_ene = '{0:<8.2f}'.format(zero_ene)
# Create dictionary to fill template
spc_keys = {
'spc_label': spc_label,
'spc_data': spc_data,
'zero_ene': zero_ene
}
return build_mako_str(template_file_name='species.mako',
template_src_path=RXNCHAN_PATH,
template_keys=spc_keys)
def well(well_label,
well_data,
zero_ene=None,
edown_str=None,
collid_freq_str=None):
""" Writes the string that defines the `Well` section for
for a given species for a MESS input file by
formatting input information into strings a filling Mako template.
:param well_label: label for input well used by MESS
:type well_label: str
:param well_data: MESS string with required electronic structure data
:type well_data: str
:param zero_ene: elec+zpve energy relative to PES reference
:param edown_str: String for the energy down parameters
:type edown_str: str
:param collid_freq_str: String for the collisional freq parameters
:type collid_freq_str: str
:rtype: str
"""
# Indent the string containing all of data for the well
well_data = messformat.indent(well_data, 4)
# Format the precision of the zero energy
if zero_ene is not None:
zero_ene = '{0:<8.2f}'.format(zero_ene)
# Indent the energy transfer parameter strings if needed
if edown_str is not None:
edown_str = messformat.indent(edown_str, 4)
if collid_freq_str is not None:
collid_freq_str = messformat.indent(collid_freq_str, 4)
# Create dictionary to fill template
well_keys = {
'well_label': well_label,
'well_data': well_data,
'zero_ene': zero_ene,
'edown_str': edown_str,
'collid_freq_str': collid_freq_str
}
return build_mako_str(template_file_name='well.mako',
template_src_path=RXNCHAN_PATH,
template_keys=well_keys)
def configs_union(mol_data_strs, zero_enes, tunnel_strs=None):
""" Writes the string that defines the `Union` section, containing
multiple configurations for a given species, for a MESS input file by
formatting input information into strings a filling Mako template.
:param mol_data_strs: MESS strings with data for all configurations
:type mol_data_strs: list(str)
:rtype: str
"""
# Build the zero energy strings and add them to the union strings
union_data = ''
for idx, (union_str, zero_ene) in enumerate(zip(mol_data_strs, zero_enes)):
zero_ene_str = messformat.zero_energy_format(zero_ene)
zero_ene_str = messformat.indent(zero_ene_str, 2)
union_data += union_str
union_data += zero_ene_str
if tunnel_strs is not None:
union_data += '\n' + tunnel_strs[idx] + '\n'
union_data += '\n\n'
union_data += 'End ! Union1\nEnd ! Union2\n'
# Add 'End' statment to each of the data strings
# mol_data_strs = [string+'End ! UnionN' for string in mol_data_strs]
# mol_data_strs[-1] += '\n'
# Concatenate all of the molecule strings
# union_data = '\n'.join(mol_data_strs)
union_data = messformat.indent(union_data, 2)
# Add the tunneling string (seems tunneling goes for all TSs in union)
# if tunnel != '':
# tunnel = messformat.indent(tunnel, 4)
# Create dictionary to fill template
union_keys = {'union_data': union_data}
return build_mako_str(template_file_name='union.mako',
template_src_path=RXNCHAN_PATH,
template_keys=union_keys)
def mc_species(geo,
sym_factor,
elec_levels,
flux_mode_str,
data_file_name,
ref_config_file_name='',
ground_ene=None,
reference_ene=None,
freqs=(),
use_cm_shift=False):
""" Writes a monte carlo species section
:param geo: geometry of species
:type geo: list
:param sym_factor: symmetry factor of species
:type sym_factor: float
:param elec_levels: energy and degeneracy of atom's electronic states
:type elec_levels: list(float)
:param flux_mode_str: MESS-format `FluxionalMode` sections for rotors
:type flux_mode_str: str
:param data_file_name: Name of data file with molecular info
:type data_file_name: str
:param ground_ene: energy relative to reference n PES (kcal.mol-1)
:type ground_ene: float
:param reference_ene: harmonic ZPVE used for MC PF (kcal.mol-1)
:type reference_ene: float
:param freqs: vibrational frequencies (cm-1)
:type freqs: list(float)
:param use_cm_chift: signal to include a CM shift
:type use_cm_shift: bool
:rtype: str
"""
# Format the molecule specification section
atom_list = messformat.molec_spec_format(geo)
# Build a formatted frequencies and elec levels string
nlevels, levels = messformat.elec_levels_format(elec_levels)
levels = indent(levels, 2)
if freqs:
nfreqs, freqs = messformat.freqs_format(freqs)
else:
nfreqs = 0
# Check if reference config name is present
if nfreqs > 0:
assert ref_config_file_name, (
'Must provide a reference configuration file if no Hessians given')
# Indent various strings string if needed
flux_mode_str = messformat.indent(flux_mode_str, 4)
# Create dictionary to fill template
monte_carlo_keys = {
'atom_list': atom_list,
'sym_factor': sym_factor,
'flux_mode_str': flux_mode_str,
'data_file_name': data_file_name,
'ref_config_file_name': ref_config_file_name,
'reference_ene': reference_ene,
'ground_ene': ground_ene,
'nlevels': nlevels,
'levels': levels,
'nfreqs': nfreqs,
'freqs': freqs,
'use_cm_shift': use_cm_shift
}
return build_mako_str(template_file_name='monte_carlo.mako',
template_src_path=MONTE_CARLO_PATH,
template_keys=monte_carlo_keys)
def molecule(core,
elec_levels,
freqs=(),
hind_rot='',
xmat=(),
rovib_coups=(),
rot_dists=(),
inf_intens=(),
freq_scale_factor=None,
use_harmfreqs_key=False):
""" Writes the string that defines the `Species` section
for a molecule for a MESS input file by
formatting input information into strings and filling Mako template.
:param core: `Core` section string in MESS format
:type core: str
:param elec_levels: energy and degeneracy of atom's electronic states
:type elec_levels: list(float)
:param freqs: Harmonic/Anharmonic vibrational frequencies
:type freqs: list(float)
:param elec_levels: energy and degeneracy of atom's electronic states
:param hind_rot: string of MESS-format `Rotor` sections for all rotors
:type hind_rot: str
:param xmat: anharmonicity matrix (cm-1)
:type xmat: list(list(float))
:param inf_intens: Harmonic Infrared Intensities for vibrational modes
:type inf_intens: list(float)
:param rovib_coups: rovibrational coupling matrix
:type rovib_coups: numpy.ndarray
:param rot_dists: rotational distortion constants: [['aaa'], [val]]
:type rot_dists: list(list(str), list(float))
:rtype: str
"""
# Add in infrared intensities at some point
# Build formatted frequencies, infrared intensities and elec levels string
nfreqs, freqs = messformat.freqs_format(freqs)
nintens, intens = messformat.intensities_format(inf_intens)
nlevels, levels = messformat.elec_levels_format(elec_levels)
# Format the rovib couplings and rotational distortions if needed
if rovib_coups:
rovib_coups = messformat.format_rovib_coups(rovib_coups)
else:
rovib_coups = ''
if rot_dists:
rot_dists = messformat.format_rot_dist_consts(rot_dists)
else:
rot_dists = ''
if xmat:
anharm = messformat.format_xmat(xmat)
else:
anharm = ''
# Indent various strings string if needed
if hind_rot != '':
hind_rot = messformat.indent(hind_rot, 2)
# Create dictionary to fill template
molec_keys = {
'core': core,
'nlevels': nlevels,
'levels': levels,
'nfreqs': nfreqs,
'freqs': freqs,
'hind_rot': hind_rot,
'anharm': anharm,
'nintens': nintens,
'intens': intens,
'rovib_coups': rovib_coups,
'rot_dists': rot_dists,
'freq_scale_factor': freq_scale_factor,
'use_harmfreqs_key': use_harmfreqs_key
}
return build_mako_str(template_file_name='molecule.mako',
template_src_path=SPECIES_PATH,
template_keys=molec_keys)
def well(well_label,
well_data,
aux_id_label=None,
zero_ene=None,
well_cap=None,
edown_str=None,
collid_freq_str=None):
""" Writes the string that defines the `Well` section for
for a given species for a MESS input file by
formatting input information into strings a filling Mako template.
:param well_label: label for input well used by MESS
:type well_label: str
:param well_data: MESS string with required electronic structure data
:type well_data: str
:param aux_id_label: label for additional species ID information
:type aux_id_label: str
:param zero_ene: elec+zpve energy relative to PES reference
:type zero_ene: float
:param well_cap: value for the well extension cap keyword
:type well_cap: float
:param edown_str: String for the energy down parameters
:type edown_str: str
:param collid_freq_str: String for the collisional freq parameters
:type collid_freq_str: str
:rtype: str
"""
# Format the label
full_label = messformat.mess_label_format(well_label,
aux_id_label=aux_id_label,
calc_dens=False)
# Indent the string containing all of data for the well
well_data = messformat.indent(well_data, 4)
# Format the precision of the zero energy and well extension cap
if zero_ene is not None:
zero_ene = f'{zero_ene:<8.2f}'
if well_cap is not None:
well_cap = f'{well_cap:<8.2f}'
# Indent the energy transfer parameter strings, if needed
if edown_str is not None:
edown_str = messformat.indent(edown_str, 4)
if collid_freq_str is not None:
collid_freq_str = messformat.indent(collid_freq_str, 4)
# Create dictionary to fill template
well_keys = {
'well_label': full_label,
'well_data': well_data,
'zero_ene': zero_ene,
'well_cap': well_cap,
'edown_str': edown_str,
'collid_freq_str': collid_freq_str
}
return build_mako_str(template_file_name='well.mako',
template_src_path=RXNCHAN_PATH,
template_keys=well_keys)
