Gaussian files (`chemistry_files.gaussian`)

Files from the Gaussian software.

class qcip_tools.chemistry_files.gaussian.BasisSet

File containing a basis set in the gaussian format.

This file format does not exists, but lets say that copy/paste from ESML basis set exchange should work.

self.basis_set: the basis_set (qcip_tools.basis_set.BasisSet)

read(f, fail_for_same_atom=False)

Parameters:

f (file) – f
fail_for_same_atom (bool) – raise an exception is the same atom is defined more than once

to_string(for_molecule=None)

Give basis set

Parameters:: for_molecule (qcip_tools.molecule.Molecule) – if defined, only output for the atoms contained in the molecule
Return type:: str

exception qcip_tools.chemistry_files.gaussian.BasisSetFormatError

class qcip_tools.chemistry_files.gaussian.ChargeTransferInformation(charge, barycenter_m, barycenter_p)

Analyzed charge transfer.

In it, charge is the amount of charge (in e) transfered from barycenter_m to barycenter_p, linked by vector, which lead to a certain charge transfer distance.

Parameters:

charge (float) – charge
barycenter_m (numpy.array) – barycenter of the negative charges
barycenter_p (numpy.array) – barycenter of the positive charges

class qcip_tools.chemistry_files.gaussian.Cube

Gaussian cube.

Documentation on that format can be found here.

Note

Increments and origin are stored as found, in bohr.

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.cube_type: set to MO if the cube contains MOs (str)
self.records_per_directions: number of point in the grid (list of int)
self.origin: origin of the grid (3x1 numpy.ndarray)
self.increments: increments between each point (3x1 numpy.ndarray)
self.data_per_records: data per point (int)
self.records: the records (numpy.ndarray)
self.title: the title (str)
self.subtitle: the second line (str)
self.MOs: the MOs contained in the file, if any (list of int)

alike(other)

Compare two cubes to check if they have the same size

Parameters:: other (Cube) – the other cube
Return type:: bool

classmethod attempt_identification(f): A cube file contains, in line 3-6, quadruplets of numbers, the first one being an integer, then 3 floats. Then, after the different atoms, line should contains numbers in scientific notation.

compute_charge_transfer(index=0)

Analyse CT by computing:

Transferred charge ;
Barycenter positions (the negative one being the starting point of the transfer) ;
Distance between the two barycenters.

Made according to J. Chem. Theory. Comput. 7, 2498 (2011).

Parameters:: index (int) – slice of the record to use
Return type:: ChargeTransferInformation

dV()

Return the size of the smallest unit of volume in the cube, in angstrom**3.

Return type:: float

file_type = 'GAUSSIAN_CUBE': The identifier

classmethod from_molecule(molecule, *args, **kwargs)

Create an object out of a molecule

Parameters:: molecule (qcip_tools.molecule.Molecule) – the molecule
Return type:: WithMoleculeMixin

number_of_data()

Number of points in the file

Return type:: int

number_of_records()

Number of records in the file

Note

According to the documentation:

Cube files have one row per record (i.e., N1*N2 records each of length N3*NVal) (where N1 and N2 are the record per direction in the X and Y direction, while N3 is for the Z direction, the fastest running index).

So it returns the number of rows, and should not be mistaken with number_of_data().

Return type:: int

positions()

Return an array with the position (in angstrom) of each point.

Return type:: numpy.array

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:: list

read(f)

Warning

The charge/multiplicity may be wrong !

Parameters:: f (file) – File

slice(index=0)

Get a specific part of the data

Parameters:: index (int) – index of the record
Return type:: Cube

sum_density_of_sets(bounding_sets, index=0)

Sum the density in a given space, defined by the bounding boxes

Parameters:

bounding_sets (dict) – sets of bounding boxes
index (int) – slice of the record to use

Returns:

dictionary with the sum of the density

Return type:

dict

to_string()

Return type:: str

exception qcip_tools.chemistry_files.gaussian.CubeFormatError

class qcip_tools.chemistry_files.gaussian.FCHK

A FCHK file. Based on the same principle as DataFile (split into chunks, interpret and store after).

Most of the information are found in the “FChk file” part of the “Interfacing” documentation of Gaussian.

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.title: the title (str)
self.calculation_type: the type of calculation (str)
self.calculation_method: the method used (str)
self.basis_set: the basis set (str)
self.chunks_information: information about every chunk (dict of FCHKChunkInformation)
self.chunks_parsed: parsed chunks are stored here (dict of int|float|str|numpy.ndarray)
self.lines: the different lines of the file, used for interpretation (list of str)

classmethod attempt_identification(f): A gaussian fchk starts with two two line of info, then “Number of atoms”

file_type = 'GAUSSIAN_FCHK': The identifier

classmethod from_molecule(molecule, *args, **kwargs)

Create an object out of a molecule

Parameters:: molecule (qcip_tools.molecule.Molecule) – the molecule
Return type:: WithMoleculeMixin

get(key)

Get the content from a given keyword

Parameters:: key (str) – the keyword
Return type:: list|int|float|str

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:: list

read(f)

Parameters:: f (file) – File

class qcip_tools.chemistry_files.gaussian.FCHKChunkInformation(keyword, data_type, data_length, line_start, line_end, is_matrix=True)

Where to find a given keyword in the FCHK file

Parameters:

keyword (str) – keyword related to this piece of information
data_type (str) – type of this piece of information
data_length (int) – length of this data
line_start (int|object) – start in the source file
line_end (int|object) – end in the source file
is_matrix (bool) – is it a matrix ?

exception qcip_tools.chemistry_files.gaussian.FCHKFormatError

class qcip_tools.chemistry_files.gaussian.Input

Gaussian input file.

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.options: the different options (starting with % in the file, dict of str [if %xxx=yyy, key is xxx and value is yyy])
self.input_card: the input card (starting with # in the file, list of str [the different lines])
self.title: the title (str)
self.other_blocks: the additionnal blocks after the molecule (list of list of str [the different lines])

classmethod attempt_identification(f): A gaussian input should contains ‘%’ or ‘#’ as the first character of the line of the “first block”

file_type = 'GAUSSIAN_INP': The identifier

classmethod from_molecule(molecule, title='', input_card='', options=None, other_blocks=None, *args, **kwargs)

Create a file from molecule

Parameters:

molecule (qcip_tools.molecule.Molecule) – the molecule
title (str) – title of the run
input_card (str|list) – the input card (starting with #P)
options (dict) – calculation options
other_blocks (list) – the other input blocks

Return type:

qcip_tools.chemistry_files.gaussian.Input

classmethod possible_file_extensions()

Return the common extention of this kind of files

Return type:: list

read(f)

Parameters:: f (file) – File

to_string(chk='', original_chk=False)

Parameters:

chk (str) – new chk name if needed
original_chk (bool) – use original chk name

Return type:

str

write(f, chk=None, original_chk=False)

Parameters:: f (file) – File

exception qcip_tools.chemistry_files.gaussian.InputFormatError

class qcip_tools.chemistry_files.gaussian.LinkCalled(link, line_start, line_end)

Remind when a link is called

Parameters:: link (int) – number of the link called

class qcip_tools.chemistry_files.gaussian.Output

Log file of Gaussian. Contains a lot of informations, but not well printed or located. If possible, rely on the FCHK rather than on the LOG file.

Note

self.geometry contains the input geometry, but it may be reoriented according to the symmetry if nosym was not provided. If it was not reoriented, self.input_orientation is set to True.

Warning

Results are not guaranteed if the job ran without #P.

self.molecule: the molecule (qcip_tools.molecule.Molecule)
self.input_orientation: wether the molecule has been reoriented w.r.t. input (bool)
self.chunks: the different links called (list of LinkCalled)
self.lines: the lines of the file (list of str)

classmethod attempt_identification(f): A gaussian log … Contains a lot of “gaussian” in the beginning (limit to the 150 first lines)”

file_type = 'GAUSSIAN_LOG': The identifier

read(f)

Parameters:: f (file) – File

exception qcip_tools.chemistry_files.gaussian.OutputFormatError

qcip_tools.chemistry_files.gaussian.beta_EOP_from_fchk(compressed_tensor, offset=0)

EOP beta tensor in FCHK is a bit messed up

Parameters:: offset (int) – frequency offset
Return type:: numpy.ndarray

qcip_tools.chemistry_files.gaussian.beta_SHG_from_fchk(compressed_tensor, offset=0)

SHG beta tensor in FCHK is a bit messed up

Parameters:: offset (int) – frequency offset
Return type:: numpy.ndarray

qcip_tools.chemistry_files.gaussian.gamma_from_gaussian(compressed_tensor, offset=0, exchange_23=False)

gamma tensor in FCHK is (also) a bit messed up

Parameters:

offset (int) – frequency offset
exchange_23 (bool) – exchange the third and the fourth component if True (second and third otherwise)

Return type:

numpy.ndarray

qcip_tools.chemistry_files.gaussian.gaussian__fchk__property__computed_energies(obj, *args, **kwargs)

Get the energies. Returns a dictionary of the energies at different level of approximation.

Parameters:: obj (qcip_tools.chemistry_files.gaussian.FCHK plots)) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.gaussian__fchk__property__electrical_derivatives(obj, *args, **kwargs)

Get electrical derivatives in FCHK. Returns a dictionary of dictionary:

+ "F"
    + static : ElectricDipole
+ "FF":
    + static : PolarizabilityTensor
+ "FD":
    + 0.042 : PolarizabilityTensor
    + ...
+ "FDD":
    + static : FirstHyperpolarizabilityTensor
    + ...
+ ...

Note that the dipole moment is present in more or less every cases.

Does not fetch (yet?) the second hyperpolarizability, stored as Derivative Beta(-w,w,0) and Derivative Beta(w,w,-2w) (that will be fun for reorganisation).

Parameters:: obj (qcip_tools.chemistry_files.gaussian.FCHK) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.gaussian__fchk__property__excitations(obj, *args, **kwargs)

Get excitation properties in FCHK. Returns a dictionary:

+ "!" : Tensor
+ "!F" : Tensor

Parameters:: obj (qcip_tools.chemistry_files.gaussian.FCHK) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.gaussian__fchk__property__geometrical_derivatives(obj, *args, **kwargs)

Get geometrical derivatives in FCHK. Returns a dictionary of dictionary:

+ "G": BaseGeometricalDerivativeTensor
+ "GG": BaseGeometricalDerivativeTensor

Does not fetch (yet?) the cubic force constants.

Parameters:: obj (qcip_tools.chemistry_files.gaussian.FCHK) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.gaussian__output__get_computed_energies(obj, *args, **kwargs)

Get the energies… Actually, “only” + HF and DFT energy (in link 502/503/506/508) + MP2 energy (in link 804/903/905/906) + MP3, CCSD and CCSD(T) energy (in link 913)

Parameters:: obj (qcip_tools.chemistry_files.gaussian.Output) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.gaussian__output__property__electrical_derivatives(obj, *args, **kwargs)

Parameters:: obj (gaussian.Output) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.gaussian__output__property__excitations(obj, *args, **kwargs)

Get excitation properties in FCHK. Returns a dictionary:

+ "!" : Tensor
+ "!F" : Tensor

Parameters:: obj (qcip_tools.chemistry_files.gaussian.Output) – object
Return type:: dict

qcip_tools.chemistry_files.gaussian.make_cartesian_hessian_from_fchk(half_cartesian_hessian, spacial_dof)

Half the hessian is stored in fchk, get full hessian back

Parameters:

half_cartesian_hessian (list) – the half of the hessian, as retrieved from FCHK
spacial_dof (int) – spacial degree of freedom (DOF)

Returns:

Gaussian files (chemistry_files.gaussian)

Gaussian files (`chemistry_files.gaussian`)