pyviblib.io.writers

Module for writing files

Classes

AbstractFileWriter

abstract base class for the writers

FCHKFileWriter

Gaussian Formatted Checkpoint files

VOAVIEWFileWriter

VOAVIEW files

MOLDENFileWriter

MOLDEN files

XMolXYZFileWriter

XMol XYZ files

GaussianInputFileWriter

Gaussian input files

HESFileWriter

Hessian files of DALTON 1.x or 2.0

SpectraMixtureFileWriter

spectra mixture files (ini-based)

RamanROAExpSpectraFileWriter

Raman/ROA experimental files

PyVib2MolFileWriter

PyVib2 molecule files

Author:Maxim Fedorovsky

class pyviblib.io.writers.AbstractFileWriter(filename, **data)

Abstract base class for all writers.

The following protected method is called in the constructor:

_check_consistency()

check the data supplied by the user

The following public method is exported:

write()

write the data and close the file

Subclasses must override these two methods. Otherwise a NotImplementedError is raised.

The following read-only property is exposed:

filename

filename argument supplied in the constructor

Initializer of the class.

Parameters:

• filename – file name of file object
• data – data to be written

write()

Write the data to a file.

class pyviblib.io.writers.FCHKFileWriter(filename, **data)

Writer for Gaussian formatted checkpoint files.

The following items are written:

• Comment
• Dummy job line (always ‘JobType Method Basis’)
• Number of atoms
• Charge (always ‘0’)
• Multiplicity (always ‘1’)
• Atomic numbers
• Cartesian coordinates
• Hessian (if available)
• Derivatives of the polarizability tensor [alpha] (if available)
• Derivatives of the optical rotation tensor [G’] (if available)
• Derivatives of the D-Q polarizability tensor [A] (if available)
• Derivatives of the electric dipole moment [APT] (if available)
• Derivatives of the magnetic dipole moment [AAT] (if available)

Initializer of the class.

Parameters:

• filename – file name of file object
• molecule – pyviblib.molecule.Molecule (required)
• comment – comment (default None)
• hessian – hessian matrix (default None)

write()

Write the data.

class pyviblib.io.writers.VOAVIEWFileWriter(filename, **data)

Writer for VOAVIEW files.

Initializer of the class.

Parameters:

• filename – file name of file object
• molecule – pyviblib.molecule.Molecule (required)

write()

Write the data.

class pyviblib.io.writers.MOLDENFileWriter(filename, **data)

Writer for MOLDEN files.

Initializer of the class.

Parameters:

• filename – file name of file object
• molecule – pyviblib.molecule.Molecule (required)
• comment – comment

write()

Write the data.

class pyviblib.io.writers.XMolXYZFileWriter(filename, **data)

Writer for XMol XYZ files.

Initializer of the class.

Parameters:

• filename – file name of file object
• molecule – pyviblib.molecule.Molecule (required)
• comment – comment

write()

Write the data.

class pyviblib.io.writers.GaussianInputFileWriter(filename, **data)

Writer for Gaussian input files.

Example is given bellow:

%chk=filebase.chk
%mem=256MB
%nproc=1
# B3LYP/6-31G* OPT

molecule_name <generated by PyVib2-version>

0 1
atomic coordinates (in angstrom)...

Initializer of the class.

Parameters:

• filename – file name of file object
• molecule – pyviblib.molecule.Molecule (required)
• comment – comment

write()

Write the data.

class pyviblib.io.writers.HESFileWriter(filename, **data)

Writer for hessian files of DALTON 1.x or 2.0 (*.hes).

Initializer of the class.

Parameters:

• filename – file name of file object
• hessian – hessian matrix (required)
• coords – cartesian coordinates (required)
• inbohr – whether coordinates are given in a.u. (default False)

write()

Write the data.

class pyviblib.io.writers.SpectraMixtureFileWriter(filename, **data)

Writer for spectra mixture files (ini-based).

Initializer of the class.

Parameters:

• filename – file name of file object
• molecules – list of molecules (required)
• composition – composition (required)
• ramanroa – this parameter is True for Raman/ROA spectra (default False)

write()

Write the data.

class pyviblib.io.writers.RamanROAExpSpectraFileWriter(filename, **data)

Writer for Raman/ROA experimental files.

Example contents:

laser_power=200,total_exposure_time=60
nu1, raman1, roa1, degcirc1(optional)
.
.
.
nuM, ramanM, roaM, degcircM(optional)

Initializer of the class.

Parameters:

• filename – file name of file object
• scattering – scattering as string
• laser_power – laser power in mW (required)
• total_exposure_time – total exposure time in minutes (required)
• X – wavenumbers in cm**(-1) (required)
• raman – raman (required)
• roa – roa (required)
• degcirc – degree of circularity (required)

write()

Write the data.

class pyviblib.io.writers.PyVib2MolFileWriter(filename, **data)

Writer for PyVib2 molecule files.

Initializer of the class.

Parameters:

• filename – file name of file object
• molecule – pyviblib.molecule.Molecule (required)
• NBasis – number of basis functions (default None)
• Etotal – total electronic energy in hartree (default None)

write()

Write (pickle) the data.