def well(well_label, well_data, zero_energy=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_energy: elec+zpve energy relative to PES reference
:rtype: str
"""
# Indent the string containing all of data for the well
well_data = util.indent(well_data, 4)
# Format the precision of the zero energy
if zero_energy is not None:
zero_energy = '{0:<8.2f}'.format(zero_energy)
# Create dictionary to fill template
well_keys = {
'well_label': well_label,
'well_data': well_data,
'zero_energy': zero_energy
}
return build_mako_str(template_file_name='well.mako',
template_src_path=RXNCHAN_PATH,
template_keys=well_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 = util.indent(species1_data, 4)
species2_data = util.indent(species2_data, 4)
# Determine if species is an atom
isatom1 = util.is_atom_in_str(species1_data)
isatom2 = util.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 species(spc_label, spc_data, zero_energy):
""" 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_energy: elec+zpve energy relative to PES reference
:rtype: str
"""
# Indent the string containing all of data for the well
spc_data = util.indent(spc_data, 2)
# Format the precision of the zero energy
zero_energy = '{0:<8.2f}'.format(zero_energy)
# Create dictionary to fill template
spc_keys = {
'spc_label': spc_label,
'spc_data': spc_data,
'zero_energy': zero_energy
}
return build_mako_str(template_file_name='species.mako',
template_src_path=RXNCHAN_PATH,
template_keys=spc_keys)
def configs_union(mol_data_strs):
""" 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
"""
# Add 'End' statment to each of the data strings
mol_data_strs = [string + 'End' 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 = util.indent(union_data, 2)
# Add the tunneling string (seems tunneling goes for all TSs in union)
# if tunnel != '':
# tunnel = util.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 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 input_file(ranseed,
nsamp,
smin,
smax,
target_xyz_name,
bath_xyz_name,
spin_method=2):
""" writes the 1dmin input file for each instance
"""
assert isinstance(ranseed, int) # check size of seed?
assert isinstance(nsamp, int)
assert target_xyz_name.endswith('.xyz')
assert bath_xyz_name.endswith('.xyz')
assert isinstance(smin, float)
assert isinstance(smax, float)
# Set the dictionary for the 1DMin input file
inp_keys = {
"ranseed": ranseed,
"nsamples": nsamp,
"target_xyz_name": target_xyz_name,
"bath_xyz_name": bath_xyz_name,
"smin": smin,
"smax": smax,
"spin_method": spin_method
}
return build_mako_str(template_file_name='onedmin_inp.mako',
template_src_path=TEMPLATE_PATH,
template_keys=inp_keys)
def collision_frequency(eps1, eps2, sig1, sig2, mass1, mass2):
""" Writes the energy transfer section of the MESS input file by
formatting input information into strings a filling Mako template.
:param eps1: A+A Lennard-Jones epsilon parameter of spc 1 (cm-1)
:type eps1: float
:param eps2: A+A Lennard-Jones epsilon parameter of spc 2 (cm-1)
:type eps2: float
:param sig1: A+A Lennard-Jones sigma parameter of spc 1 (Angstrom)
:type sig1: float
:param sig2: A+A Lennard-Jones sigma parameter of spc 2 (Angstrom)
:type sig2: float
:param mass1: mass of Species 1 (amu)
:type mass1: float
:param mass2: mass of Species 2 (amu)
:type mass2: float
:rtype: string
"""
# Convert LJ units and format them into string
eps_str = f'{eps1*phycon.EH2WAVEN:<10.3f} {eps2*phycon.EH2WAVEN:<10.3f}'
sig_str = f'{sig1*phycon.BOHR2ANG:<10.3f} {sig2*phycon.BOHR2ANG:<10.3f}'
mass_str = f'{mass1:<10.3f} {mass2:<10.3f}'
# Create dictionary to fill template
etrans_keys = {
'epsilons': eps_str,
'sigmas': sig_str,
'masses': mass_str
}
return build_mako_str(
template_file_name='collid_freq.mako',
template_src_path=ENE_TRANS_PATH,
template_keys=etrans_keys)
def dummy(dummy_label, aux_id_label=None, zero_ene=None):
""" Writes the string that defines the `Dummy` section,
for dummy reaction products, for a MESS input file by
formatting input information into strings a filling Mako template.
:param dummy_label: label for dummy product used by MESS
:type dummy_label: str
:rtype: str
"""
# Format the label
full_label = messformat.mess_label_format(dummy_label,
aux_id_label=aux_id_label,
calc_dens=False)
# Format energy string if needed
if zero_ene is not None:
zero_ene = f'{zero_ene:6.2f}'
# Create dictionary to fill template
dummy_keys = {
'dummy_label': full_label,
'aux_id_label': aux_id_label,
'zero_ene': zero_ene
}
return build_mako_str(template_file_name='dummy.mako',
template_src_path=RXNCHAN_PATH,
template_keys=dummy_keys)
def input_file(data_train, data_test, num_write, units, range_parameter,
ref_energy, num_ranges, energy_ranges, num_atoms, symbols,
atom_groups, read_basis, factor_order, total_order, imode,
num_channels, fragment_groups):
""" writes the PIPPy input file for each instance
"""
# Set the dictionary for the PIPPy input file
inp_keys = {
'DataTrain': data_train,
'DataTest': data_test,
'NumWrite': num_write,
'Units': units,
'RangeParameter': range_parameter,
'RefEnergy': ref_energy,
'NumRanges': num_ranges,
'EnergyRanges': energy_ranges,
'NumAtoms': num_atoms,
'Symbols': symbols,
'AtomGroups': atom_groups,
'ReadBasis': read_basis,
'FactorOrder': factor_order,
'TotalOrder': total_order,
'IMode': imode,
'NumChannels': num_channels,
'FragmentGroups': fragment_groups
}
return build_mako_str(template_file_name='pippy_inp.mako',
template_src_path=TEMPLATE_PATH,
template_keys=inp_keys)
def mc_species(geom, elec_levels,
flux_mode_str, data_file_name,
ground_energy, reference_energy,
freqs=(), no_qc_corr=False, use_cm_shift=False):
""" Writes a monte carlo species section
:param core: `MonteCarlo` section string in MESS format
:type core: str
:param freqs: vibrational frequencies without fluxional mode (cm-1)
:type freqs: list(float)
:param elec_levels: energy and degeneracy of atom's electronic states
:type elec_levels: list(float)
:param hind_rot: string of MESS-format `Rotor` sections for all rotors
:type hind_rot: str
:param ground_energy: energy relative to reference (kcal.mol-1)
:type ground_energy: float
:param reference_energy: reference energy (kcal.mol-1)
:type reference_energy: float
:param freqs: vibrational frequencies (cm-1)
:type freqs: list(float)
:param no_qc_corr: signal to preclude quantum correction
:type no_qc_corr: bool
:param use_cm_chift: signal to include a CM shift
:type use_cm_shift: bool
:rtype: str
"""
# Format the molecule specification section
atom_list = util.molec_spec_format(geom)
# Build a formatted frequencies and elec levels string
nlevels, levels = util.elec_levels_format(elec_levels)
if freqs:
nfreqs, freqs = util.freqs_format(freqs)
no_qc_corr = True
else:
nfreqs = 0
# Indent various strings string if needed
flux_mode_str = util.indent(flux_mode_str, 4)
# Create dictionary to fill template
monte_carlo_keys = {
'atom_list': atom_list,
'flux_mode_str': flux_mode_str,
'data_file_name': data_file_name,
'ground_energy': ground_energy,
'nlevels': nlevels,
'levels': levels,
'nfreqs': nfreqs,
'freqs': freqs,
'reference_energy': reference_energy,
'no_qc_corr': no_qc_corr,
'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 fluxional_mode(atom_indices, span=360.0):
""" Writes the string that defines the `FluxionalMode` section for a
single fluxional mode (torsion) of a species for a MESS input file by
formatting input information into strings a filling Mako template.
:param atom_idxs: idxs of atoms involved in fluxional mode
:type atom_indices: list(int)
:param span: range from 0.0 to value that mode was sampled over (deg.)
:type span: float
:rtype: str
"""
# Format the aotm indices string
atom_indices = util.format_flux_mode_indices(atom_indices)
# Create dictionary to fill template
flux_mode_keys = {
'atom_indices': atom_indices,
'span': span,
}
return build_mako_str(
template_file_name='fluxional_mode.mako',
template_src_path=MONTE_CARLO_PATH,
template_keys=flux_mode_keys)
def rotor_bundle(enegrid_step=5.0,
enegrid_max=50.0,
quantm_st_max=100.0,
mc_samp_size=2000.0):
""" Write a HinderedRotor Bundle string
:param gride_step: (cm-1)
:type gride_step: float
:param gride_max: (kcal/mol)
:type gride_max: float
:param quantm_st_max: (kcal/mol)
:type quantm_st_max: float
:param mc_samp_size: ??
:type mc_samp_size: ??
:param grid
"""
# Set the Monte Carlo List (just num of flux modes?)
mc_modes_lst = []
# Create dictionary to fill template
rotor_keys = {
'enegrid_step': enegrid_step,
'enegrid_max': enegrid_max,
'quantm_st_max': quantm_st_max,
'mc_mods_lst': mc_modes_lst,
'mc_samp_size': mc_samp_size
}
return build_mako_str(template_file_name='rotor_bundle.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=rotor_keys)
def tunnel_read(imag_freq, tunnel_file, cutoff_energy=2500.0):
""" Writes the string that defines the 'Tunneling' section for a
small curvature tunneling model for a transition state
for a MESS input file by formatting input information into
strings a filling Mako template. Currently requires an additional
auxiliary data file for transmission probabilities generated by
ProjRot code.
:param imag_freq: imaginary frequency of the TS
:type imag_freq: float
:param tunnel_file: name of data file with transmission probabilities
:type tunnel_file: str
:param cutoff_energy: energy to include tunneling density (kcal.mol-1)
:type cutoff_energy: float
:rtype: str
"""
# Format the imaginary frequency value
imag_freq = f'{imag_freq:<8.0f}'
# Create dictionary to fill template
tunnel_keys = {
'imag_freq': imag_freq,
'cutoff_energy': cutoff_energy,
'tunnel_file': tunnel_file
}
return build_mako_str(
template_file_name='tunnel_read.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=tunnel_keys)
def elec_struct(exe_path, lib_path, base_name, npot,
dummy_name='dummy_corr_', lib_name='libcorrpot.so',
geom_ptt='GEOMETRY_HERE', ene_ptt='molpro_energy'):
""" Writes the electronic structure code input file for VaReCoF
Currently code only runs with Molpro
:rtype: string
"""
# Write the correction potential strings
pot_path = os.path.join(lib_path, lib_name)
pot_params_str = ''
for i in range(npot):
pot_params_str += '{0:<42s}{1:<8d}\n'.format(base_name+'_corr_', 1)
pot_params_str += '{0:<42s}{1:<8d}\n'.format('ParameterInteger', i+1)
pot_params_str += '{0:<42s}{1:<8d}\n'.format(dummy_name, 1)
# Create dictionary to fill template
els_keys = {
'exe_path': exe_path,
'geom_ptt': geom_ptt,
'ene_ptt': ene_ptt,
'base_name': base_name,
'pot_path': pot_path,
'pot_params_str': pot_params_str
}
return build_mako_str(
template_file_name='els.mako',
template_src_path=TEMPLATE_PATH,
template_keys=els_keys)
def core_rigidrotor(geo, 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 geo: geometry of species
:type geo: 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, geo = messformat.geometry_format(geo)
# Create dictionary to fill template
core_keys = {
'sym_factor': sym_factor,
'natom': natom,
'geo': geo,
'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 tunnel_eckart(imag_freq, well_depth1, well_depth2):
""" Writes the string that defines the 'Tunneling' section for a
Eckart tunneling model for a transition state for a MESS input file by
formatting input information into strings a filling Mako template.
:param imag_freq: imaginary frequency of the TS
:type imag_freq: float
:param well_depth1: energy difference: E[TS] - E[reactant well]
:type well_depth1: float
:param well_depth2: energy difference: E[TS] - E[product well]
:type well_depth2: float
:rtype: str
"""
# Format the imaginary frequency and well-depth values
imag_freq = f'{imag_freq:<8.0f}'
well_depth1 = f'{well_depth1:<8.2f}'
well_depth2 = f'{well_depth2:<8.2f}'
# Create dictionary to fill template
tunnel_keys = {
'imag_freq': imag_freq,
'well_depth1': well_depth1,
'well_depth2': well_depth2
}
return build_mako_str(
template_file_name='tunnel_eckart.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=tunnel_keys)
def submission_script(njobs, run_dir, exe_path):
""" Writes a special BASH submission script for launching
parallel instances of OneDMin.
:param njobs: number of OneDMin processes to run
:type njobs: int
:param run_dir: directory to run each OneDMin process
:type run_dir: str
:param exe_path: full path to the OneDMin executable
:type exe_path: str
:rtype: str
"""
# Write the string for running all of the job lines
# job_lines = 'mkdir -p {0}/run1\n'.format(run_dir)
job_lines = 'cd {0}/run1\n'.format(run_dir)
job_lines += 'time $ONEDMINEXE < input.dat > output.dat &\n'
for i in range(njobs - 1):
# job_lines += 'mkdir -p ../run{0}\n'.format(str(i+2))
job_lines += 'cd ../run{0}\n'.format(str(i + 2))
job_lines += 'time $ONEDMINEXE < input.dat > output.dat &\n'
job_lines += 'wait\n'
# Set the dictionary for the 1DMin input file
exe_keys = {"exe_path": exe_path, "job_lines": job_lines}
return build_mako_str(template_file_name='onedmin_sub.mako',
template_src_path=TEMPLATE_PATH,
template_keys=exe_keys)
def core_rotd(sym_factor, flux_file_name, stoich):
""" Writes the string that defines the `Core` section for a
variational reaction-coordinate transition-state theory model of a
transition state for a MESS input file by
formatting input information into strings a filling Mako template.
:param sym_factor: symmetry factor of transition state
:type sym_factor: float
:param flux_file_name:
:type flux_file_name: str
:param stoich: combined stoichiometry of dissociation species 1 and 2
:type stoich: str
:rtype: str
"""
# Create dictionary to fill template
core_keys = {
'sym_factor': sym_factor,
'flux_file_name': flux_file_name,
'stoich': stoich
}
return build_mako_str(
template_file_name='core_rotd.mako',
template_src_path=SPEC_INFO_PATH,
template_keys=core_keys)
def collision_frequency(eps1, eps2, sig1, sig2, mass1, mass2):
""" Writes the energy transfer section of the MESS input file by
formatting input information into strings a filling Mako template.
:param eps1: A+A Lennard-Jones epsilon parameter of spc 1 (cm-1)
:type eps1: float
:param eps2: A+A Lennard-Jones epsilon parameter of spc 2 (cm-1)
:type eps2: float
:param sig1: A+A Lennard-Jones sigma parameter of spc 1 (Angstrom)
:type sig1: float
:param sig2: A+A Lennard-Jones sigma parameter of spc 2 (Angstrom)
:type sig2: float
:param mass1: mass of Species 1 (amu)
:type mass1: float
:param mass2: mass of Species 2 (amu)
:type mass2: float
:rtype: string
"""
# Put the values into a string
epsilon_str = '{0:<10.3f} {1:<10.3f}'.format(eps1, eps2)
sigma_str = '{0:<10.3f} {1:<10.3f}'.format(sig1, sig2)
mass_str = '{0:<10.3f} {1:<10.3f}'.format(mass1, mass2)
# Create dictionary to fill template
etrans_keys = {
'epsilons': epsilon_str,
'sigmas': sigma_str,
'masses': mass_str
}
return build_mako_str(template_file_name='collid_freq.mako',
template_src_path=ENE_TRANS_PATH,
template_keys=etrans_keys)
def rpht_input(geoms, grads, hessians,
saddle_idx=1,
rotors_str='',
coord_proj='cartesian',
proj_rxn_coord=False):
""" Writes a string for the input file for ProjRot.
:param geoms: geometry for single species or along a reaction path
:type geoms: list(list(float))
:param grads: gradient for single species or along a reaction path
:type grads: list(list(float))
:param hessians: Hessian for single species or along a reaction path
:type hessians: list(list(float))
:param saddle_idx: idx denoting the saddle point along a reaction path
:type saddle_idx: int
:param rotors_str: ProjRot-format string with all the rotor definitions
:type rotors_str: str
:param coord_proj: choice of coordinate system to perform projections
:type coord_proj: str
:param proj_rxn_coord: whether to project out reaction coordinate
:type proj_rxn_coord: bool
:rtype: str
"""
# Format the molecule info
data_str = util.write_data_str(geoms, grads, hessians)
natoms = len(geoms[0])
# nsteps = len(geoms)
nrotors = rotors_str.count('pivotA')
# Check input into the function (really fix calls to not have this)
if not isinstance(geoms, list):
geoms = [geoms]
if not isinstance(grads, list):
grads = [grads]
if not isinstance(hessians, list):
hessians = [hessians]
nsteps = len(geoms)
assert nsteps == len(hessians)
if len(grads) != 0:
assert len(grads) == nsteps
assert coord_proj in ('cartesian', 'internal')
# Create a fill value dictionary
rpht_keys = {
'natoms': natoms,
'nsteps': nsteps,
'saddle_idx': saddle_idx,
'coord_proj': coord_proj,
'proj_rxn_coord': proj_rxn_coord,
'nrotors': nrotors,
'rotors_str': rotors_str,
'data_str': data_str
}
return build_mako_str(
template_file_name='rpht_input.mako',
template_src_path=TEMPLATE_PATH,
template_keys=rpht_keys)
def structure(geo1, geo2):
""" Writes the structure input file for VaReCoF
:param list geo1: geometry of fragment 1
:param list geo2: geometry of fragment 2
:rtype: string
"""
# Determine linearity of molecule
struct_type1 = util.determine_struct_type(geo1)
struct_type2 = util.determine_struct_type(geo2)
# Format the coordinates of the geoetry
natoms1, coords1 = util.format_coords(geo1)
natoms2, coords2 = util.format_coords(geo2)
# Create dictionary to fill template
struct_keys = {
'struct_type1': struct_type1,
'natoms1': natoms1,
'coords1': coords1,
'struct_type2': struct_type2,
'natoms2': natoms2,
'coords2': coords2,
}
return build_mako_str(template_file_name='struct.mako',
template_src_path=TEMPLATE_PATH,
template_keys=struct_keys)
def energy_down(exp_factor, exp_power, exp_cutoff):
""" Writes the energy transfer section of the MESS input file by
formatting input information into strings a filling Mako template.
:param exp_factor: 300 K energy-down value for collision model (cm-1)
:type exp_factor: float
:param exp_power: n, for [energy-down * (T/300K)^n] for collision model
:type exp_power: float
:param exp_cutoff: cutoff for assuming transition probability is zero
:type exp_cutoff: float
:rtype: string
"""
# Put the values into a string
exp_factor_str = '{0:<10.3f}'.format(exp_factor)
exp_power_str = '{0:<10.3f}'.format(exp_power)
exp_cutoff_str = '{0:<10.3f}'.format(exp_cutoff)
# Create dictionary to fill template
etrans_keys = {
'exp_factor': exp_factor_str,
'exp_power': exp_power_str,
'exp_cutoff': exp_cutoff_str
}
return build_mako_str(template_file_name='edown.mako',
template_src_path=ENE_TRANS_PATH,
template_keys=etrans_keys)
def makefile(fortran_compiler, pot_file_names=()):
""" Writes string for a makefile to compile correction potentials.
:param fortran_compiler: name of compiler to build potentials
:type fortran_compiler: str
:param pot_file_names: names of files with various potentials
:type: pot_file_names: list(str)
:return: string for the makefile
:rtype: string
"""
# Set species name
corr_potential_names = ''
if pot_file_names:
for potential in pot_file_names:
corr_potential_names += f'{potential}_corr.f '
# Create dictionary to fill template
make_keys = {
'fc': fortran_compiler,
'corr_potential_names': corr_potential_names
}
return build_mako_str(template_file_name='makefile.mako',
template_src_path=TEMPLATE_PATH,
template_keys=make_keys)
def tml(memory, basis, wfn, method, inf_sep_energy):
""" writes the tml file used as the template for the electronic structure
calculation
currently, we assume the use of molpro
in particular: method and wfn assume molpro input card structure
"""
# convert the memory
memory_mw = int(memory * (1024.0 / 8.0))
# make the infinite seperation energy positive
inf_sep_energy *= -1.0
# Create dictionary to fill template
tml_keys = {
'memory': memory_mw,
'basis': basis,
'method': method,
'wfn': wfn,
'inf_sep_energy': inf_sep_energy
}
return build_mako_str(
template_file_name='tml.mako',
template_src_path=TEMPLATE_PATH,
template_keys=tml_keys)
def tst(nsamp_max,
nsamp_min,
flux_err,
pes_size,
faces=(0, ),
faces_symm=1,
ener_grid=(),
amom_grid=()):
""" Writes the tst.inp file for VaReCoF
:param nsamp_max: maximum number of samples
:type nsamp_max: int
:param nsamp_min: minimum number of samples
:type nsamp_min: int
:param flux_err: allowed error in flux during sampling
:type flux_err: float
:param pes_size: number of PESs in the calculation ?
:type pes_size: int
:param faces: inde ?
:type fascs: list(int)
:param faces_symm: indices noting symmetry of face
:type faces_symm: list(int)
:param list ener_grid:
:type ener_grid: list(float)
:param amom_grid:
:type amom_grid: list(float)
:rtype: str
"""
# Set the energy and angular momentum grids
if not ener_grid:
ener_grid = [0, 10, 1.05, 179]
else:
assert len(ener_grid) == 4
if not amom_grid:
amom_grid = [0, 4, 1.10, 40]
else:
assert len(amom_grid) == 4
ener_grid = util.format_grids_string(ener_grid, 'ener', 'Kelvin')
amom_grid = util.format_grids_string(amom_grid, 'amom', 'Kelvin')
# Set the faces
print(faces)
faces = util.format_faces_string(faces)
# Create dictionary to fill template
tst_keys = {
'ener_grid': ener_grid,
'amom_grid': amom_grid,
'nsamp_max': nsamp_max,
'nsamp_min': nsamp_min,
'flux_err': flux_err,
'pes_size': pes_size,
'faces': faces,
'faces_symm': faces_symm
}
return build_mako_str(template_file_name='tst.mako',
template_src_path=TEMPLATE_PATH,
template_keys=tst_keys)
def input_file(job_type,
geo,
zero_ene,
ene_grid=100.0,
ene_max=50000.0,
ang_grid=6,
ang_max=300,
h_so=20.0,
qe_scale_factor=3.0,
cuts=False,
comment=None):
""" Writes a string for the input file for NST.
:param geo: guess geometry for a NST TS
:type geo: automol.geom object
:param job_type: NST job to run
:type job_type: str
:param geo: geometry of transition state
:type geo: automol.geom object
:param zero_ene: energy at infinite separation (in Hartrees)
:type zero_ene: float
:param ene_gro: Energy grid spacing (cm-1)
:param ene_max: maximum grid energy (cm-1)
:param so_coup: Spin-orbit coupling in cm-1
:param so_scale: scaling factor for state counts in output
:param cuts: cuts along vibrational modes (only for HESSC and HESSR)
:param comment: comment line at top of file
:rtype: str
"""
# Format the molecule info
natoms, geo_str, mass_str = format_geometry(geo)
# Format flags
cuts_flag = 'T' if cuts else 'F'
# Format comment line
comment = comment if comment is not None else 'NST Run'
# Create a fill value dictionary
inp_keys = {
'comment': comment,
'job_type': job_type,
'natoms': natoms,
'geo_str': geo_str,
'mass_str': mass_str,
'zero_ene': zero_ene,
'ene_grid': ene_grid,
'ene_max': ene_max,
'ang_grid': ang_grid,
'ang_max': ang_max,
'h_so': h_so,
'qe_scale_factor': qe_scale_factor,
'cuts_flag': cuts_flag,
}
return build_mako_str(template_file_name='input.mako',
template_src_path=TEMPLATE_PATH,
template_keys=inp_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_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 dummy():
""" Writes string for the dummy correction potential Fortran file.
:rtype: string
"""
return build_mako_str(template_file_name='dummy_corr.mako',
template_src_path=TEMPLATE_PATH,
template_keys={})
def auxiliary():
""" Writes string for the potential auxiliary functions Fortran file.
:rtype: string
"""
return build_mako_str(template_file_name='pot_aux.mako',
template_src_path=TEMPLATE_PATH,
template_keys={})