pymatgen.io.gaussian module

This module implements input and output processing from Gaussian.

class GaussianInput(mol, charge=None, spin_multiplicity=None, title=None, functional='HF', basis_set='6-31G(d)', route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag='#P', gen_basis=None)

Bases: object

An object representing a Gaussian input file.

Parameters:

• mol – Input molecule. It can either be a Molecule object, a string giving the geometry in a format supported by Gaussian, or None. If the molecule is None, you will need to use read it in from a checkpoint. Consider adding CHK to the link0_parameters.

• charge – Charge of the molecule. If None, charge on molecule is used. Defaults to None. This allows the input file to be set a charge independently from the molecule itself. If mol is not a Molecule object, then you must specify a charge.

• spin_multiplicity –

  Spin multiplicity of molecule. Defaults to None, which means that the spin multiplicity is set to 1 if the molecule has no unpaired electrons and to 2 if there are unpaired electrons. If mol is not a Molecule object, then you

  must specify the multiplicity

• title – Title for run. Defaults to formula of molecule if None.

• functional – Functional for run.

• basis_set – Basis set for run.

• route_parameters – Additional route parameters as a dict. For example, {‘SP’:””, “SCF”:”Tight”}

• input_parameters – Additional input parameters for run as a dict. Used for example, in PCM calculations. E.g., {“EPS”:12}

• link0_parameters – Link0 parameters as a dict. E.g., {“%mem”: “1000MW”}

• dieze_tag – # preceding the route line. E.g. “#p”

• gen_basis – allows a user-specified basis set to be used in a Gaussian calculation. If this is not None, the attribute basis_set will be set to “Gen”.

as_dict()

Returns:

MSONable dict

classmethod from_dict(d)

Parameters:

d – dict

Returns:

GaussianInput

static from_file(filename)

Creates GaussianInput from a file.

Parameters:

filename – Gaussian input filename

Returns:

GaussianInput object

static from_string(contents)

Creates GaussianInput from a string.

Parameters:

contents – String representing an Gaussian input file.

Returns:

GaussianInput object

get_cart_coords() → str

Return the Cartesian coordinates of the molecule

get_zmatrix()

Returns a z-matrix representation of the molecule.

property molecule

Returns molecule associated with this GaussianInput.

to_string(cart_coords=False)

Return GaussianInput string.

Parameters:

cart_coords (bool) – If True, return Cartesian coordinates instead of z-matrix. Defaults to False.

write_file(filename, cart_coords=False)

Write the input string into a file

Option: see __str__ method

class GaussianOutput(filename)

Bases: object

Parser for Gaussian output files.

Note

Still in early beta.

Attributes: .. attribute:: structures

All structures from the calculation in the standard orientation. If the symmetry is not considered, the standard orientation is not printed out and the input orientation is used instead. Check the standard_orientation attribute.

structures_input_orientation

All structures from the calculation in the input orientation or the Z-matrix orientation (if an opt=z-matrix was requested).

opt_structures

All optimized structures from the calculation in the standard orientation, if the attribute ‘standard_orientation’ is True, otherwise in the input or the Z-matrix orientation.

energies

All energies from the calculation.

eigenvalues

List of eigenvalues for the last geometry

MO_coefficients

Matrix of MO coefficients for the last geometry

cart_forces

All Cartesian forces from the calculation.

frequencies

A list for each freq calculation and for each mode of a dict with {

“frequency”: freq in cm-1, “symmetry”: symmetry tag “r_mass”: Reduce mass, “f_constant”: force constant, “IR_intensity”: IR Intensity, “mode”: normal mode

}

The normal mode is a 1D vector of dx, dy dz of each atom.

hessian

Matrix of second derivatives of the energy with respect to cartesian coordinates in the input orientation frame. Need #P in the route section in order to be in the output.

properly_terminated

True if run has properly terminated

is_pcm

True if run is a PCM run.

is_spin

True if it is an unrestricted run

stationary_type

If it is a relaxation run, indicates whether it is a minimum (Minimum) or a saddle point (“Saddle”).

corrections

Thermochemical corrections if this run is a Freq run as a dict. Keys are “Zero-point”, “Thermal”, “Enthalpy” and “Gibbs Free Energy”

functional

Functional used in the run.

basis_set

Basis set used in the run

route

Additional route parameters as a dict. For example,

{‘SP’:””, “SCF”:”Tight”}

dieze_tag

# preceding the route line, e.g. “#P”

link0

Link0 parameters as a dict. E.g., {“%mem”: “1000MW”}

charge

Charge for structure

spin_multiplicity

Spin multiplicity for structure

num_basis_func

Number of basis functions in the run.

electrons

number of alpha and beta electrons as (N alpha, N beta)

pcm

PCM parameters and output if available.

errors

error if not properly terminated (list to be completed in error_defs)

Mulliken_charges

Mulliken atomic charges

eigenvectors

Matrix of shape (num_basis_func, num_basis_func). Each column is an eigenvectors and contains AO coefficients of an MO.

eigenvectors[Spin] = mat(num_basis_func, num_basis_func)

molecular_orbital

MO development coefficients on AO in a more convenient array dict for each atom and basis set label.

mo[Spin][OM j][atom i] = {AO_k: coeff, AO_k: coeff … }

atom_basis_labels

Labels of AO for each atoms. These labels are those used in the output of molecular orbital coefficients (POP=Full) and in the molecular_orbital array dict.

atom_basis_labels[iatom] = [AO_k, AO_k, …]

resumes

List of gaussian data resume given at the end of the output file before the quotation. The resumes are given as string.

title

Title of the gaussian run.

standard_orientation

If True, the geometries stored in the structures are in the standard orientation. Else, the geometries are in the input orientation.

bond_orders

Dict of bond order values read in the output file such as: {(0, 1): 0.8709, (1, 6): 1.234, …}

The keys are the atom indexes and the values are the Wiberg bond indexes that are printed using pop=NBOREAD and $nbo bndidx $end.

Methods: .. method:: to_input()

Return a GaussianInput object using the last geometry and the same calculation parameters.

read_scan()

Read a potential energy surface from a gaussian scan calculation.

get_scan_plot()

Get a matplotlib plot of the potential energy surface

save_scan_plot()

Save a matplotlib plot of the potential energy surface to a file

Parameters:

filename – Filename of Gaussian output file.

as_dict()

JSON-serializable dict representation.

property final_energy

Final energy in Gaussian output.

Type:

return

property final_structure

Final structure in Gaussian output.

Type:

return

get_scan_plot(coords=None)

Get a matplotlib plot of the potential energy surface.

Parameters:

coords – internal coordinate name to use as abscissa.

get_spectre_plot(sigma=0.05, step=0.01)

Get a matplotlib plot of the UV-visible xas. Transitions are plotted as vertical lines and as a sum of normal functions with sigma with. The broadening is applied in energy and the xas is plotted as a function of the wavelength.

Parameters:

• sigma – Full width at half maximum in eV for normal functions.

• step – bin interval in eV

Returns:

{“energies”: values, “lambda”: values, “xas”: values}

where values are lists of abscissa (energies, lamba) and the sum of gaussian functions (xas).

A matplotlib plot.

Return type:

A dict

read_excitation_energies()

Read a excitation energies after a TD-DFT calculation.

Returns:

A list of tuple for each transition such as

[(energie (eV), lambda (nm), oscillatory strength), … ]

Return type:

A list

read_scan()

Read a potential energy surface from a gaussian scan calculation.

Returns:

{“energies”: [ values ],

”coords”: {“d1”: [ values ], “A2”, [ values ], … }}

”energies” are the energies of all points of the potential energy surface. “coords” are the internal coordinates used to compute the potential energy surface and the internal coordinates optimized, labelled by their name as defined in the calculation.

Return type:

A dict

save_scan_plot(filename='scan.pdf', img_format='pdf', coords=None)

Save matplotlib plot of the potential energy surface to a file.

Parameters:

• filename – Filename to write to.

• img_format – Image format to use. Defaults to EPS.

• coords – internal coordinate name to use as abcissa.

save_spectre_plot(filename='spectre.pdf', img_format='pdf', sigma=0.05, step=0.01)

Save matplotlib plot of the spectre to a file.

Parameters:

• filename – Filename to write to.

• img_format – Image format to use. Defaults to EPS.

• sigma – Full width at half maximum in eV for normal functions.

• step – bin interval in eV

to_input(mol=None, charge=None, spin_multiplicity=None, title=None, functional=None, basis_set=None, route_parameters=None, input_parameters=None, link0_parameters=None, dieze_tag=None, cart_coords=False)

Create a new input object using by default the last geometry read in the output file and with the same calculation parameters. Arguments are the same as GaussianInput class.

Returns:

the gaussian input object

Return type:

gaunip (GaussianInput)

read_route_line(route)

read route line in gaussian input/output and return functional basis_set and a dictionary of other route parameters

Parameters:

route (str) – the route line

Returns:

the method (HF, PBE …) basis_set (str) : the basis set route (dict) : dictionary of parameters

Return type:

functional (str)