Module calculator

This module contains different classes used to define a new calculator for specific spectroscopies understood by MsSpec.

These spectroscopies are listed here.

There is one calculator class for each spectroscopy. The class name is based on the spectroscopy name. For instance, the class for PhotoElectron Diffraction is called _PED.

The helper function calculator.MSSPEC() is used to create objects from these classes by passing the kind of spectroscopy as a keyword argument.

For more information on MsSpec, follow this link

calculator.MSSPEC(spectroscopy='PED', **kwargs)[source]

The MsSpec calculator constructor.

Instanciates a calculator for the given spectroscopy.

Parameters

  • spectroscopy – See spectroscopy.

  • kwargs – Other keywords are passed to the spectroscopy-specific constructor.

Returns

A calculator._MSCALCULATOR object.

class calculator._EIG(algorithm='inversion', polarization=None, dichroism=None, spinpol=False, folder='./calc', txt='-')[source]

Bases: calculator._MSCALCULATOR

Note

This class constructor is not meant to be called directly by the user. Use the MSSPEC() to instanciate any calculator.

class calculator._MSCALCULATOR(spectroscopy='PED', algorithm='expansion', polarization=None, dichroism=None, spinpol=False, folder='./calc', txt='-', **kwargs)[source]

Bases: ase.calculators.calculator.Calculator

This class defines an ASE calculator for doing Multiple scattering calculations.

get_parameters()[source]

Get all the defined parameters in the calculator.

Returns

A list of all parameters objects.

Return type

List of parameters.Parameter

set_atoms(atoms)[source]

Defines the cluster on which the calculator will work.

Parameters

atoms (ase.Atoms) – The cluster to attach the calculator to.

shutdown()[source]

Removes the temporary folder and all its content.

The user may whish to keep the calculation folder (see folder) so it is not removed at the end of the calculation. The calculation folder contains raw results from Phagen and Spec programs as well as their input files and configuration. It allows the program to save some time by not repeating some tasks (such as the Fortran code generation, building the binaries, computing things that did not changed between runs…). Calling this function at the end of the calculation will erase this calculation folder.

Warning

Calling this function will erase the produced data without prompting you for confirmation, so take care of explicitly saving your results in your script, by using the iodata.Data.save() method for example.

class calculator._PED(algorithm='expansion', polarization=None, dichroism=None, spinpol=False, folder='./calc', txt='-')[source]

Bases: calculator._MSCALCULATOR

This class creates a calculator object for PhotoElectron DIffraction spectroscopy.

Parameters

  • algorithm – The algorithm to use for the computation. See algorithm for more details about the allowed values and the type.

  • polarization – The incoming light polarization (see polarization)

  • dichroism – Wether to enable or not the dichroism (see dichroism)

  • spinpol – Enable or disable the spin polarization in the calculation (see spinpol)

  • folder – The path to the temporary folder for the calculations. See folder

  • txt (str) – The name of a file where to redirect standard output. The string ‘-’ will redirect the standard output to the screen (default).

Note

This class constructor is not meant to be called directly by the user. Use the MSSPEC() to instanciate any calculator.

get_energy_scan(phi=0, theta=0, level=None, kinetic_energy=None, data=None, **kwargs)[source]

Computes an energy scan of the emitted photoelectrons.

Parameters

  • phi – All the values of the azimuthal angle to be computed. See phi.

  • theta – The polar angle in degrees. See theta.

  • level – The electronic level. See level.

  • kinetic_energy – see kinetic_energy.

  • data – a iodata.Data object to append the results to or None.

Returns

The modified iodata.Data object passed as an argument or a new iodata.Data object.

get_phi_scan(phi=array([0.0, 1.0, 2.01, ..., 356.99, 358.0, 359.0]), theta=0, level=None, kinetic_energy=None, data=None, **kwargs)[source]

Computes an azimuthal scan of the emitted photoelectrons.

Parameters

  • phi – All the values of the azimuthal angle to be computed. See phi.

  • theta – The polar angle in degrees. See theta.

  • level – The electronic level. See level.

  • kinetic_energy – see kinetic_energy.

  • data – a iodata.Data object to append the results to or None.

Returns

The modified iodata.Data object passed as an argument or a new iodata.Data object.

get_potential(atom_index=None, data=None, units={'energy': 'eV', 'space': 'angstrom'})[source]

Computes the coulombic part of the atomic potential.

Parameters

  • atom_index – The atom indices to get the potential of, either as a list or as a single integer

  • data – The data object to store the results to

  • units – The units to be used. A dictionary with the keys ‘energy’ and ‘space’

Returns

A Data object

get_scattering_factors(level='1s', kinetic_energy=None, data=None, **kwargs)[source]

Computes the scattering factors of all prototypical atoms in the cluster.

This function computes the real and imaginery parts of the scattering factor as well as its modulus for each non symetrically equivalent atom in the cluster. The results are stored in the data object if provided as a parameter.

Parameters
Returns

The modified iodata.Data object passed as an argument or a new iodata.Data object.

get_theta_phi_scan(phi=array([0.0, 7.35, 14.69, ..., 345.31, 352.65, 360.0]), theta=array([0.0, 2.05, 4.09, ..., 85.91, 87.95, 90.0]), level=None, kinetic_energy=None, data=None, **kwargs)[source]

Computes a stereographic scan of the emitted photoelectrons.

The azimuth ranges from 0 to 360° and the polar angle ranges from 0 to 90°.

Parameters
Returns

The modified iodata.Data object passed as an argument or a new iodata.Data object.

get_theta_scan(phi=0, theta=array([- 70.0, - 69.0, - 68.0, ..., 68.0, 69.0, 70.0]), level=None, kinetic_energy=None, data=None, **kwargs)[source]

Computes a polar scan of the emitted photoelectrons.

Parameters

  • phi – The azimuthal angle in degrees. See phi.

  • theta – All the values of the polar angle to be computed. See theta.

  • level – The electronic level. See level.

  • kinetic_energy – see kinetic_energy.

  • data – a iodata.Data object to append the results to or None.

Returns

The modified iodata.Data object passed as an argument or a new iodata.Data object.