autofile.data_types¶
autofile.data_types.name¶
file namers
- class autofile.data_types.name.Extension¶
file extensions
- autofile.data_types.name.information(file_name)¶
adds information extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.input_file(file_name)¶
adds input file extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.output_file(file_name)¶
adds output file extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.instability(file_name)¶
adds instability extension, if missing
- autofile.data_types.name.run_script(file_name)¶
adds run script extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.energy(file_name)¶
adds energy extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.geometry(file_name)¶
adds geometry extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.trajectory(file_name)¶
adds trajectory extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.zmatrix(file_name)¶
adds zmatrix extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vmatrix(file_name)¶
adds variable zmatrix extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.torsions(file_name)¶
adds variable torsions extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.ring_torsions(file_name)¶
adds variable torsions extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.gradient(file_name)¶
adds gradient extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.hessian(file_name)¶
adds hessian extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.harmonic_zpve(file_name)¶
adds harmonic zpve extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.anharmonic_zpve(file_name)¶
adds anharmonic zpve extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.harmonic_frequencies(file_name)¶
adds harmonic frequencies extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.anharmonic_frequencies(file_name)¶
adds anharmonic frequencies extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.cubic_force_constants(file_name)¶
adds cubic force constants extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.quartic_force_constants(file_name)¶
adds quartic force constants extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.anharmonicity_matrix(file_name)¶
adds anharmonicity maxtrix extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vibro_rot_alpha_matrix(file_name)¶
adds vibro_rot_alpha maxtrix extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.quartic_centrifugal_dist_consts(file_name)¶
adds quartic centrifugal distortion constants, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.lennard_jones_epsilon(file_name)¶
adds lennard-jones epsilon extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.lennard_jones_sigma(file_name)¶
adds lennard-jones sigma extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.lennard_jones_input(file_name)¶
adds lennard-jones input file extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.lennard_jones_elstruct(file_name)¶
adds lennard-jones sigma extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.external_symmetry_factor(file_name)¶
adds external symmetry number extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.internal_symmetry_factor(file_name)¶
adds internal symmetry number extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.dipole_moment(file_name)¶
adds dipole moment extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.polarizability(file_name)¶
adds dipole moment extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.reaction(file_name)¶
adds reaction extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_tst(file_name)¶
adds vrctst_tst extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_divsur(file_name)¶
adds vrctst_divsur extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_molpro(file_name)¶
adds vrctst_molpro extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_tml(file_name)¶
adds vrctst_tml extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_struct(file_name)¶
adds vrctst_struct extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_pot(file_name)¶
adds vrctst_pot extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
- autofile.data_types.name.vrctst_flux(file_name)¶
adds vrctst_flux extension, if missing
- Parameters
file_name (str) – name of file
- Returns
file with extension added
- Return type
str
autofile.data_types.swrite¶
string writers converts properties in internally used units and used data type to properties formatted in strings of externally preferred units dum
- autofile.data_types.swrite.information(inf_obj)¶
write information (any dict/list combination) to a string
- Parameters
inf (Info) – info yaml information
- Returns
info object as a string
- Return type
str
- autofile.data_types.swrite.instability(instab_rxn)¶
write a reaction to a string :param instab_rxn: an automol Reaction object :type instab_rxn: automol.reac.Reaction :return: reaction string :rtype: str
- autofile.data_types.swrite.energy(ene)¶
write an energy (hartree) to a string (hartree)
- Parameters
ene – energy
- Returns
energy
- Return type
str
- autofile.data_types.swrite.geometry(geo)¶
write a geometry (bohr) to a string (angstrom)
- Parameters
geo (tuple) – geometry in autochem tuple format
- Returns
goemetry as xyz format
- Return type
str
- autofile.data_types.swrite.trajectory(traj)¶
write a series of geometries (bohr) to a string (angstrom)
(trajectory is given by a sequence of comment-line, geometry pairs) :param traj: traj object :type traj: tuple :return: trajectory :rtype: str
- autofile.data_types.swrite.zmatrix(zma)¶
write a zmatrix (bohr/radian) to a string (angstroms/degree)
- Parameters
zma (tuple) – zmatrix in autochem tuple format
- Returns
zmatrix as string
- Return type
str
- autofile.data_types.swrite.vmatrix(vma)¶
write a variable zmatrix (bohr/radian) to a string (angstroms/degree)
- Parameters
vma (tuple) – vmatrix in autochem tuple format
- Returns
vmatrix string
- Return type
str
- autofile.data_types.swrite.ring_torsions(ring_tors_dct)¶
Write the torsions and their ranges (radian) to a string (degree).
- Parameters
tors_lst (tuple(automol torsion objects)) – list of torsion objects
- Return type
str
- autofile.data_types.swrite.torsions(tors_lst)¶
Write the torsions and their ranges (radian) to a string (degree).
- Parameters
tors_lst (tuple(automol torsion objects)) – list of torsion objects
- Return type
str
- autofile.data_types.swrite.gradient(grad)¶
write a gradient (hartree bohr^-1) to a string (hartree bohr^-1)
- Parameters
grad (tuple) – gradient tuple
- Returns
gradient string
- Return type
str
- autofile.data_types.swrite.hessian(hess)¶
write a hessian (hartree bohr^-2) to a string (hartree bohr^-2)
- Parameters
hess (tuple) – hessian 3nx3n tuple of floats
- Returns
hessian string
- Return type
str
- autofile.data_types.swrite.harmonic_frequencies(freqs)¶
write harmonic frequencies (cm^-1) to a string (cm^-1)
- Parameters
freqs (tuple) – freq tuple of floats
- Returns
frequencies as string
- Return type
str
- autofile.data_types.swrite.anharmonic_frequencies(freqs)¶
write anharmonic frequencies (cm^-1) to a string (cm^-1)
- Parameters
freqs (tuple) – freq tuple of floats
- Returns
frequencies as string
- Return type
str
- autofile.data_types.swrite.cubic_force_constants(cfcs)¶
Writes cubic force constants () to a string ().
- Parameters
cfcs (numpy.ndarray) – cubic force constants
- Return type
str
- autofile.data_types.swrite.quartic_force_constants(qfcs)¶
Writes quartic force constants () to a string ().
- Parameters
cfcs (numpy.ndarray) – quartic force constants
- Return type
str
- autofile.data_types.swrite.harmonic_zpve(zpve)¶
write the harmonic ZPVE (hartree) to a string (hartree)
- Parameters
harm_zpve (float) – zpve float
- Returns
zpve as string
- Return type
str
- autofile.data_types.swrite.anharmonic_zpve(zpve)¶
write the anharmonic ZPVE (hartree) to a string (hartree)
- Parameters
anh_zpve (float) – zpve float
- Returns
zpve as string
- Return type
str
- autofile.data_types.swrite.anharmonicity_matrix(xmat)¶
write anharmonicity matrix (cm^-1) to a string (cm^-1)
- Parameters
xmat (tuple) – anharmonicity xmatrix as nfreqxnfreq tuple
- Returns
xmat string
- Return type
str
- autofile.data_types.swrite.vibro_rot_alpha_matrix(vibro_rot_mat)¶
write vibro-rot alph matrix (cm^-1) to a string (cm^-1)
- Parameters
vibro_rot (tuple) – matrix as tuple
- Returns
vibro-rot alpha matrix string
- Return type
str
- autofile.data_types.swrite.quartic_centrifugal_dist_consts(qcd_consts)¶
write the quartic centrifugal distortion constant
labels and values (cm^-1) to a string (cm^-1)
- Parameters
qcd_consts (tuple) – constants in a tuple
- Returns
quartic centrifugal dist const string
- Return type
str
- autofile.data_types.swrite.lennard_jones_epsilon(eps)¶
write a lennard-jones epsilon (waveunmbers) to a string (wavenumbers)
- Parameters
eps – epsilon float
- Returns
epsilon string
- Return type
str
- autofile.data_types.swrite.lennard_jones_sigma(sig)¶
write a lennard-jones sigma (angstrom) to a string (angstrom)
- Parameters
sig – sigma float
- Returns
sigma string
- Return type
str
- autofile.data_types.swrite.external_symmetry_factor(esf)¶
write an external symmetry factor to a string
- Parameters
esf – external symmetry factor float
- Returns
external symmetry factor string
- Return type
str
- autofile.data_types.swrite.internal_symmetry_factor(isf)¶
write an internal symmetry factor to a string
- Parameters
isf – internal symmetry factor float
- Returns
internal symmetry factor string
- Return type
str
- autofile.data_types.swrite.dipole_moment(dip_mom)¶
write a dipole moment vector to a string
- Parameters
dip_mom (tuple) – x,y,z dipole moment tuple
- Returns
x, y, z dipole moment vector string
- Return type
str
- autofile.data_types.swrite.polarizability(polar)¶
write a polarizability tensor to a string
- Parameters
polar (tuple) – polarizability tensor
- Returns
polarizability tensor
- Return type
str
- autofile.data_types.swrite.reaction(rxn)¶
write a reaction to a string
- Parameters
rxn (automol.reac.Reaction) – an automol Reaction object
- Returns
reaction string
- Return type
str
- autofile.data_types.swrite.gradient_array(ndarray)¶
transform numpy array into python list
autofile.data_types.sread¶
string readers converts properties formatted in strings of externally preferred units to properties in internally used units and used data type
- autofile.data_types.sread.information(inf_str)¶
read information (any dict/list combination) from a string
- Parameters
inf_str (str) – info yaml information
- Returns
info object class instance
- Return type
- autofile.data_types.sread.instability(instab_str)¶
read information (any dict/list combination) from a string :param inf_str: info yaml information :type inf_str: str :rtype: str
- autofile.data_types.sread.energy(ene_str)¶
read an energy (hartree) from a string (hartree)
- Parameters
ene_str – energy
- Returns
energy
- Return type
float
- autofile.data_types.sread.geometry(xyz_str)¶
read a geometry (bohr) from a string (angstrom)
- Parameters
xyz_str (str) – geometry in xyz format
- Returns
goemetry as internally used tuple object
- Return type
tuple
- autofile.data_types.sread.trajectory(traj_str)¶
read a trajectory of geometries (bohr) from a string (angstrom)
- Parameters
traj_str (str) – traj string
- Returns
trajectory as internally used tuple object
- Return type
tuple
- autofile.data_types.sread.zmatrix(zma_str)¶
read a zmatrix (bohr/radian) from a string (angstrom/degree)
- Parameters
zma_str (str) – zmatrix string
- Returns
zmatrix as internally used tuple object
- Return type
tuple
- autofile.data_types.sread.vmatrix(vma_str)¶
read a variable zmatrix (bohr/radian) from a string (angstrom/degree)
- Parameters
vma_str (str) – vmatrix string
- Returns
vmatrix as internally used tuple object
- Return type
tuple
- autofile.data_types.sread.gradient(grad_str)¶
read a gradient (hartree bohr^-1) from a string (hartree bohr^-1)
- Parameters
grad_str (str) – gradient string
- Returns
gradient as internally used tuple object
- Return type
tuple
- autofile.data_types.sread.gradient_array(grad_list)¶
convert gradient python list to gradient numpy ndarray
- Parameters
grad_list (str) – gradient list
- Returns
gradient list
- Return type
numpy array
- autofile.data_types.sread.ring_torsions(tors_str)¶
Write the torsions and their ranges (radian) to a string (degree).
- Parameters
tors_str (str) – information for each torsion by Z-Matrx names
- Return type
tuple(automol torsion objects)
- autofile.data_types.sread.torsions(tors_str)¶
Write the torsions and their ranges (radian) to a string (degree).
- Parameters
tors_str (str) – information for each torsion by Z-Matrx names
- Return type
tuple(automol torsion objects)
- autofile.data_types.sread.hessian(hess_str)¶
read a hessian (hartree bohr^-2) from a string (hartree bohr^-2)
- Parameters
hess_str (str) – hessian string
- Returns
hessian as 3nx3n tuple
- Return type
tuple
- autofile.data_types.sread.harmonic_frequencies(freq_str)¶
read harmonic frequencies (cm^-1) from a string (cm^-1)
- Parameters
freq_str (str) – freq string
- Returns
tuple of float frequencies
- Return type
tuple
- autofile.data_types.sread.anharmonic_frequencies(freq_str)¶
read anharmonic frequencies (cm^-1) from a string (cm^-1)
- Parameters
freq_str (str) – freq string
- Returns
tuple of float frequencies
- Return type
tuple
- autofile.data_types.sread.cubic_force_constants(cfc_str)¶
Writes cubic force constants () to a string ().
- Parameters
cfc_str (str) – string with cubic force constants
- Return type
numpy.ndarray
- autofile.data_types.sread.quartic_force_constants(qfc_str)¶
Writes quartic force constants () to a string ().
- Parameters
qfc_str (numpy.ndarray) – quartic force constants
- Return type
numpy.ndarray
- autofile.data_types.sread.harmonic_zpve(harm_zpve_str)¶
read the harmonic zpve (hartree) from a string (hartree)
- Parameters
harm_zpve_str (str) – zpve string
- Returns
zpve as float
- Return type
float
- autofile.data_types.sread.anharmonic_zpve(anh_zpve_str)¶
read the anharmonic zpve (hartree) from a string (hartree)
- Parameters
anh_zpve_str (str) – zpve string
- Returns
zpve as float
- Return type
float
- autofile.data_types.sread.anharmonicity_matrix(xmat_str)¶
- read an anharmonicity matrix (cm^-1)
from a string (cm^-1)
- Parameters
xmat_str (str) – xmat string
- Returns
anharmonicity xmatrix as nfreqxnfreq tuple
- Return type
tuple
- autofile.data_types.sread.vibro_rot_alpha_matrix(vibro_rot_str)¶
- read an vibro-rot alpha matrix (cm^-1)
from a string (cm^-1)
- Parameters
vibro_rot_str (str) – vibro-rot alpha matrix string
- Returns
matrix as tuple
- Return type
tuple
- autofile.data_types.sread.quartic_centrifugal_dist_consts(qcd_consts_str)¶
- write the quartic centrifugal distortion constant
labels and values (cm^-1) to a string (cm^-1)
- Parameters
qcd_consts_str (str) – quartic centrifugal dist const string
- Returns
constants in a tuple
- Return type
tuple
- autofile.data_types.sread.lennard_jones_epsilon(eps_str)¶
read a lennard-jones epsilon (waveunmbers) from a string (wavenumbers)
- Parameters
eps_str – epsilon string
- Returns
epsilon float
- Return type
float
- autofile.data_types.sread.lennard_jones_sigma(sig_str)¶
read a lennard-jones sigma (angstrom) from a string (angstrom)
- Parameters
sig_str – sigma string
- Returns
sigma float
- Return type
float
- autofile.data_types.sread.external_symmetry_factor(esf_str)¶
read an external symmetry factor from a string (dimensionless)
- Parameters
esf_str – external symmetry factor string
- Returns
external symmetry factor float
- Return type
float
- autofile.data_types.sread.internal_symmetry_factor(isf_str)¶
read an internal symmetry factor from a string (dimensionless)
- Parameters
isf_str – internal symmetry factor string
- Returns
internal symmetry factor float
- Return type
float
- autofile.data_types.sread.dipole_moment(dip_mom_str)¶
reads the x,y,z dipole moment vector from a string
- Parameters
dip_mom_str (str) – x,y,z dipole moment vector
- Returns
x, y, z dipole moment tuple
- Return type
tuple
- autofile.data_types.sread.polarizability(polar_str)¶
read a polarizability tensor () from a string
- Parameters
polar_str (str) – polarizability tensor
- Returns
polarizability tensor
- Return type
tuple
- autofile.data_types.sread.reaction(rxn_str)¶
read a reaction object from a string
- Parameters
rxn_str (str) – reaction string
- Returns
an automol Reaction object
- Return type
automol.reac.Reaction
