FileReader class

Any data parsed from by a FileReader can be accessed much like a dictiory (i.e. some_filereader["energy"]). A nearly complete list of keys for various file types is at the bottom of this page.

class AaronTools.fileIO.FileReader(fname, get_all=False, just_geom=True, oniom=False, scan_read_all=False, freq_name=None, conf_name=None, nbo_name=None, max_length=10000000)

class for reading files

Attributes

• name

• file_type

• comment

• atoms list(Atom) or list(OniomAtom)

• other dict

__init__(fname, get_all=False, just_geom=True, oniom=False, scan_read_all=False, freq_name=None, conf_name=None, nbo_name=None, max_length=10000000)

Parameters:

• fname (str|tuple) – either a string specifying the file name of the file to read or a tuple of (str(name), str(file_type), str(content))

• get_all (bool) – if true, optimization steps are also saved in self.all_geom; otherwise only saves last geometry

• just_geom (bool) – if true, does not store other information, such as frequencies, only what is needed to construct a Geometry() obj

• freq_name (str) – Name of the file containing the frequency output. Only use if this information is in a different file than fname (eg: xtb runs using the –hess runtype option)

• nbo_name (str) – Name of the file containing the NBO orbital coefficients in the AO basis. Only used when reading .47 files.

• max_length (int) –

  maximum array size to store from FCHK files

  any array that would be larger than this will be the size the array would be ignored

read_file(get_all=False, just_geom=True, scan_read_all=False, freq_name=None, conf_name=None, nbo_name=None, oniom=False, max_length=10000000)

Reads geometry information from fname.

Parameters:

• get_all (bool) – If false (default), only keep the last geom If true, self is last geom, but return list of all others encountered

• nbo_name (str) – nbo output file containing coefficients to map AO’s to orbitals

• max_length (int) – max. array size for arrays to store in FCHK files - anything larger will be the size the array would not be stored

read_xyz(f, get_all=False, oniom=False)

read xyz files

read_sd(f, get_all=False)

read sdf file

read_mol2(f, get_all=False)

read TRIPOS mol2

read_psi4_out(f, get_all=False, just_geom=True)

read psi4 output file

read_orca_out(f, get_all=False, just_geom=True, scan_read_all=False)

read orca output file

read_qchem_out(f, get_all=False, just_geom=True)

read qchem output file

read_log(f, get_all=False, just_geom=True, scan_read_all=False)

read gaussian output file

read_com(f)

read gaussian input file

read_fchk(f, just_geom=True, max_length=10000000)

read formatted checkpoint file

read_pdb(f, qt=False)

read pdb or pdbqt file

read_mmcif(f)

read mmcif

read_nbo(f)

read nbo data

read_crest(f, conf_name=None)

conf_name = False to skip conformer loading (doesn’t get written until crest job is done)

read_xtb(f, freq_name=None)

read xtb output

read_sqm(f)

read sqm output

read_nbo_47(f, nbo_name=None)

read nbo .47 file

read_nbo_31(f, nbo_name=None)

read nbo .31 file

FileReader keys for various output files

CREST output

key	description
finished	boolean for whether the job finished without error
best_pop	population of the lowest energy structure
free_energy	free energy of the ensemble in Eh
entropy	entropy of the ensemble
avg_energy	average energy of the ensemble in Eh
energy	energy of the lowest structure (Eh)
temperature	temperature in K
error	AaronTools error code if the job errored out
error_msg	error message if the job errored out
charge	charge of the system
multiplicity	spin multiplicity of the system
finished	boolean for whether the job finished without error
conformers	structures for all of the conformers CREST found

Gaussian Output

key	description
energy	energy of the system (Eh), might be TD-DFT energy for TD-DFT jobs
charge	total charge of the system
multiplicity	spin multiplicity of the system
archive	archive entry of the computation
opt_steps	number of steps for geometry optimizations
ECP	elements that are using an effective core potential
gradient	optimization convergence status
params	coordinates that are used for geometry optimization
scf_energy	energy from SCF
E(TD-DF/TD-DFT)	energy from TD
E(method)	energy from the specified method after SCF
mass	mass of the system in kg
n_basis	number of basis functions
n_frozen	number of basis functions that are frozen
n_occupied_alpha	number of basis functions that occupied by alpha electrons
n_virtual_beta	number of basis functions that unoccupied by alpha electrons
n_virtual_beta	number of basis functions that unoccupied by beta electrons
hpmodes	boolean for whether freq=HPModes or equivalent was requested
frequency	Frequency object for the vibrational data
X_matrix	anharmonic vibrations X matrix
X0	anharmonic vibrations X0
uv_vis	ValenceExciations object for the excitation data
S^2 before	spin before annihilation
S^2 annihilated	spin after annihilation
temperature	temperature for thermochemistry in K
rotational_temperature	rotational constants in K
equilibrium_rotational_temperature	rotational constants in K from anharmonic frequency jobs
ground_rotational_temperature	rotational constants in K from anharmonic frequency jobs
centr_rotational_temperature	rotational constants in K from anharmonic frequency jobs
E_ZPVE	zero-point vibrational energy in Eh
enthalpy	enthalpy in Eh
free_energy	RRHO free energy in Eh
ZPVE	zero-point vibrational energy correction to the electronic energy in Eh
rotational_symmetry_number	rotational symmetry number
electric_potential	electric potential for each
electric_field	electric field vector
optical_rotation_(number)	optical rotation at the given wavelength
full_point_group	point group
abelian_subgroup	Abelian subgroup of point group
concise_abelian_subgroup	concise Abelian subgroup of point group
forces	force vectors for each nucleus in Eh/Bohr
X Charges	partial atomic charges calculated using X scheme (e.g., NBO)
error	AaronTools error code if the job errored out
error_msg	error message if the job errored out
theory	Theory object for this job type (might not be perfect)
finished	boolean for whether the job finished without error

Gaussian Formatted Checkpoint File

The keys for .fchk files are mostly the same as the labels in the .fchk file. No string entries are parsed from .fchk files. There is also an orbitals key with an Orbitals object.

NBO Output

key	description
ao_types	type of each orbital
ao_atom_ndx	index of the atom for each atomic orbital
nao_type	description for the natural orbitals
ao_occ	orbital occupancies
ao_nrg	orbital energies
Natural Charges	partial atomic charges based on natural population analysis
core_occ	core occupancies
valence_occ	valence occupancies
rydberg_occ	Rydberg occupancies
wiberg_nao	Wiberg bond orders
wiberg_nao	Wiberg bond orders
shell_to_atom	maps each shell to an atom
momentum_label	angular momentum label for each atomic orbital
orbit_kinds	description for the orbitals (e.g., C 1-O 2 bond)
alpha_coefficients	orbital coefficients
funcs_per_shell	number of primitive functions in each shell
orbitals	Orbitals object
n_prim_per_shell	number of primitive functions in each shell
n_prim_per_shell	number of primitive functions in each shell

ORCA Output

key	description
energy	energy of the system (Eh)
scf_energy	energy from SCF (Eh) - might not include dispersion corrections
SOC CIS/TD root energy	TD energy for the specified root from a TD-DFT computation with SOC
CIS/TD root energy	TD energy for the specified root from a TD-DFT computation
X correlation energy	correlation energy from X method (e.g., MP2)
forces	force vectors for each atom in Eh/Bohr
frequency	Frequency object for the vibrational modes
temperature	temperature for thermochemistry
mass	mass of the system in kg
charge	charge of the system
multiplicity	spin multiplicity of the system
rotational_symmetry_number	rotational symmetry number
ZPVE	zero-point energy correction in Eh
enthalpy	enthalpy in Eh
free_energy	free energy in Eh(ORCA prints Quasi-RRHO)
rotational_temperature	rotational constants in K
full_point_group	point group
gradient	optimization convergence status
Löwdin Charges	partial atomic charges based on Löwdin population analysis
Mulliken Charges	partial atomic charges based on Mulliken population analysis
basis_set_by_ele	basis set parameters for each element
n_basis	number of basis functions
SOC GS stabilization energy	ground state stabilization due to SOC (Eh)
soc x	X component of the SOC (cm-1)
soc y	Y component of the SOC (cm-1)
soc z	Z component of the SOC (cm-1)
soc (cm^-1)	magnitude of the SOC for each pair of roots from TD-DFT (cm-1)
uv_vis	ValenceExciations object for excitation data
alpha_coefficients	alpha molecular orbital coefficients
beta_coefficients	beta molecular orbital coefficients
alpha_nrgs	alpha molecular orbital energies
beta_nrgs	beta molecular orbital energies
alpha_occupancies	molecular orbital occupancies
beta_occupancies	molecular orbital occupancies
shell_to_atom	maps each basis set function to an atom index
n_alpha	number of alpha electrons
n_beta	number of beta electrons
opt_steps	number of optimization steps
ao_overlap	atomic orbital overlap matrix
finished	whether the job finished without error
error	AaronTools error code if the job errored out
error_msg	error message if the job errored out
orbitals	Orbitals instace

Psi4 Output

key	description
key	description
energy	energy of the system (Eh)
charge	charge of the system
multiplicity	spin multiplicity of the system
mass	mass of the system (kg)
ZPVE	zero-point energy correction (Eh)
E_ZPVE	zero-point energy (Eh)
enthalpy	enthalpy (Eh)
free_energy	RRHO free energy (Eh)
rotational_symmetry_number	rotational symmetry number
rotational_temperature	rotational constants in K
frequency	Frequency object for the vibrational modes
finished	whether the job finished without error
gradient	geometry optimization convergence status
forces	force vector for each atom (Eh/Bohr)
scf_energy	energy from SCF (Eh/Bohr)
X correlation energy	correlation energy from method X (e.g., MP2)
full_point_group	point group
molecular_point_group	point group that Psi4 could take advantage of
uv_vis	ValenceExciations object for excitation data
error	AaronTools error job if the job errored out
error_msg	error message

Q-Chem Output

key	description
energy	energy of the system (Eh)
scf_energy	SCF energy of the system (Eh)
E(corr)	correlation energy (Eh)
full_point_group	point group
abelian_subgroup	Abelian point group subgroup
Mulliken Charges	partial atomic charges based on Mulliken population analysis
gradient	geometry optimization convergence status
frequency	Frequency object for vibrational data
temperature	temperature for thermochemistry
rotational_symmetry_number	rotational symmetry number
mass	mass of the system in kg
charge	net charge of the system
multiplicity	spin multiplicity of the system
uv_vis	ValenceExciations object for excitation data
forces	force on each atom in Eh/Bohr (only parsed from analytic force computations)
finished	whether the job finished without error
error	AaronTools error code if the job errored out

SQM Output

key	description
energy	energy of the system (Eh)
finished	whether the job finished without error
error	AaronTools error code if the job errored out (currently only UNKNOWN)
error_msg	error message if the job errored out

xTB Output

key	description
energy	energy of the system (Eh)
error	AaronTools error code if the job errored out
error_msg	error message if the job errored out
finished	whether the job finished without error
charge	net charge of the system
multiplicity	spin multiplicity of the system
ZPVE	zero-point energy correction (Eh)
free_energy	free energy (Eh)
temperature	temperature for thermochemistry
frequency	Frequency object for vibrational modes