All the simulation parameters¶

Contents

Common parameters
Spectroscopy parameters
- PEDParameters
- EIGParameters

Common parameters ¶

GlobalParameters ¶

spectroscopy¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	PED, AED, LEED, EXAFS, EIG
Default	PED

There are 4 choices for the spectroscopy option:

‘PED’, for Photo Electron Diffraction

‘AED’, for Auger Electron Diffraction

‘LEED’, for Low Energy Electron Diffraction

‘EXAFS’, for the Extended X-ray Absorption Fine Structure

Additionally, a 5th keyword EIG is used to get deeper information about the convergence of the eigen values of multiple scattering matrix.

The value is case insensitive.

algorithm¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	expansion, inversion, correlation, power
Default	expansion

You can choose the algorithm used for the computation of the scattering path operator.

‘inversion’, for the classical matrix inversion method

‘expansion’, for the Rehr-Albers series expansion

‘correlation’, for the correlation-expansion algorithm

‘power’, for the power method approximation scheme (only for spectroscopy=’EIG’)

The series expansion algorithm is well suited for high energy since the number of terms required decreases as the energy increases. The exact solution is obtained by the matrix inversion method but should be preferably used for lower energy.

polarization¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, linear_qOz, linear_xOy, circular
Default	None

Specify the polarization of the incident light.

None, for unpolarized light

‘linear_qOz’ for a polarization vector in the \((\vec{q}0z)\) plane

‘linear_xOy’ for a polarization vector in the \((x0y)\) plane

‘circular’ for circular dichroism

dichroism¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, natural, sum_over_spin, spin_resolved
Default	None

Used to perform dichroic calculations. The default (None) is to disable this.

spinpol¶

details

Types	bool
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	False

Enable or disbale spin-resolved calculations.

folder¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	./calc

This parameter is the path to the temporary folder used for the calculations. If you do not change this parameter between calculations, all the content will be overridden. This is usually not a problem, since the whole bunch of data created during a computation is not meant to be saved. But you may want to anyway by changing it to another path.

This folder is not automatically removed after a computation. It is removed when calling the shutdown() calculator method:

calc = MSSPEC() # the './calc' folder is created
# do your calculation here
calc.shutdown() # the folder is removed

MuffintinParameters ¶

charge_relaxation¶

details

Types	bool
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	True

Used to specify whether the charge density of the photoabsorbing atom, which is used to construct the potential, is allowed to relax around the core hole or not.

ionicity¶

details

Types	dict
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	{}

A dictionary to specify the ionicity of each kind of atoms. If empty, the atoms are considered to be neutral. Otherwise, each key must be a chemical symbol and the corresponding value should be the fraction of electrons added (negative) or substracted (positive) with respect to neutrality. As an example for a LaFeO₃ cluster:

>>> calc.muffintin_parameters.ionicity = {'La': 0.15, 'Fe': 0.15, 'O': -0.1}

means that 0.15 electrons have been substracted from La, likewise from Fe. Neutrality implies that 0.3 electrons have to be added to oxygen atoms.

relativistic_mode¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	non_relativistic, scalar_relativistic, spin_orbit_resolved
Default	non_relativistic

To tell whether to use the scalar relativistic approximation or not.

radius_overlapping¶

details

Types	float
Limits	0.0 <= value <= 1.0
Unit	None
Allowed values	None
Default	0.0

to allow atomic spheres to overlapp with each other. The value is a percentage, 1. means 100%.

interstitial_potential¶

details

Types	int, float
Limits	None <= value <= None
Unit	electron_volt
Allowed values	None
Default	0.0

The average interstitial potential (or inner potential) expressed in eV. It is used to compute the refraction at the surface.

hydrogen_radius¶

details

Types	int, float
Limits	0.0 <= value <= None
Unit	angstrom
Allowed values	None
Default	0.9

The program can have difficulties to find the radius of the hydrogen atom (small atom). You can specify here a value for the radius. If you set it to ‘None’, the calculation of the muffin-tin radius of H atoms will be left to the program.

TMatrixParameters ¶

potential¶

details

Types	str, ForeignPotential
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	muffin_tin

This option allows to choose which kind of potential is used to compute the T-Matrix. For now, only the internal Muffin-Tin potential is supported.

exchange_correlation¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	hedin_lundqvist_real, hedin_lundqvist_complex, x_alpha_real, dirac_hara_real, dirac_hara_complex
Default	hedin_lundqvist_complex

Set the type of exchange and correlation potential that will be used.

imaginery_part¶

details

Types	int, float
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	0.0

This value is added to complex potentials to account for core-hole lifetime and experimental resolution broadening effects.

lmax_mode¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	max_ke, true_ke, imposed
Default	true_ke

This allows to control the number of basis functions used to expand the wave function on each atom. It can be:

‘imposed’, and will be equal to the lmaxt parameter (see below). It is therefore independent on both the energy and atom type.
‘max_ke’, in this case \(l_{max}\) is computed according to the formula \(l_{max} = kr_{at} + 1\) where \(k=E^{1/2}_{max}\) with \(E_{max}\) being the maximum kinetic energy. In this case \(l_{max}\) is independent of the energy but depends on the atom number.
‘true_ke’, in this case \(l_{max}\) is computed according to the formula \(l_{max} = kr_{at} + 1\) where \(k=E^{1/2}_k\) with \(E_k\) being the kinetic energy. In this case \(l_{max}\) depends both on the energy and the atom number.

lmaxt¶

details

Types	int
Limits	1 <= value <= None
Unit	None
Allowed values	None
Default	19

The value of \(l_{max}\) if lmax_mode = ‘imposed’

tl_threshold¶

details

Types	NoneType, float
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	None

This option allows to control the number of basis function by defining a threshold value for the tl. For example:

>>> calc.tmatrix_parameters.tl_threshold = 1e-6

will remove all tl with a value \(< 1.10^{-6}\)

Note

This option is compatible with any modes of the lmax_mode option.

max_tl¶

details

Types	NoneType, dict
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	None

max_tl is used to sepcify a maximum number of basis functions to use for each kind of atoms. For example, in the case of an MgO cluster, you could write:

>>> calc.muffintin_parameters.max_tl = {'Mg': 20, 'O', 15}

to tell the program to use at most 20 tl for Mg and 15 for O. It acts like a filter, meaning that if you use this option, you are not required to sepcif a value for each kind of atoms in your cluster. You can restrict the number of tl only for one type of atom for example.

Note

This option is compatible with any modes of the lmax_mode option.

SourceParameters ¶

energy¶

details

Types	list, tuple, int, float
Limits	0 <= value <= None
Unit	electron_volt
Allowed values	None
Default	1253.6

The photon energy in eV.

Common laboratories X-ray source Mg \(K_\alpha\) and Al \(K_\alpha\) lines are defined in the msspec.misc.XRaySource class. For example:

>>> from msspec.calculator import MSSPEC
>>> calc = MSSPEC()
>>> calc.source_parameters.energy = XRaySource.MG_KALPHA
>>> print calc.source_parameters.energy
1253.6

theta¶

details

Types	int, float
Limits	-180.0 <= value <= 180.0
Unit	degree
Allowed values	None
Default	-55.0

The polar angle of the photon incidence (in degrees). Please refer to this figure for questions regarding the proper orientation.

phi¶

details

Types	int, float
Limits	-180.0 <= value <= 180.0
Unit	degree
Allowed values	None
Default	0.0

The azimuthal angle of the photon incidence (in degrees). Please refer to this figure for questions regarding the proper orientation.

DetectorParameters ¶

angular_acceptance¶

details

Types	int, float
Limits	0.0 <= value <= None
Unit	degree
Allowed values	None
Default	0.0

The angular acceptance of the detector in degrees used when the average_sampling option is enabled below.

average_sampling¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, low, medium, high
Default	None

Used to averaged the signal over directions lying in the cone of half-angle angular_acceptance. The number of directions to take into account depends on the choosen value:

None, for no averaging at all
‘low’, to average over 5 directions
‘medium’, to average over 13 directions
‘high’, to average over 49 directions

rotate¶

details

Types	bool
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	False

When False, the sample is rotated when doing a scan (the usual way). Otherwise, the detector is rotated.

ScanParameters ¶

type¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	theta, phi, theta_phi, energy, scatf
Default	theta

Sorry, no more help for this parameter.

theta¶

details

Types	ndarray, list, tuple, int, float
Limits	-90.0 <= value <= 90.0
Unit	degree
Allowed values	None
Default	[0.00 2.00 4.00 … 84.00 86.00 88.00]

Sorry, no more help for this parameter.

phi¶

details

Types	ndarray, list, tuple, int, float
Limits	0.0 <= value <= 360.0
Unit	degree
Allowed values	None
Default	[0.00]

Sorry, no more help for this parameter.

kinetic_energy¶

details

Types	list, tuple, int, float
Limits	0.0 <= value <= None
Unit	electron_volt
Allowed values	None
Default	200.0

if given as a list or tuple:

with 2 elements, 10 points of energy will be generated with the first element as the starting energy and the second element as the stopping energy.
with 3 elements, the first element is the starting energy the second one is the stopping energy and the last one is the number of points.

if given as a float or integer, there will be one point for the kinetic energy.

CalculationParameters ¶

RA_cutoff¶

details

Types	int
Limits	0 <= value <= 8
Unit	None
Allowed values	None
Default	1

The Rehr-Albers cut-off parameter which controls the degree of sphericity introduced in the description of the basis functions used to expand the wave function around each atomic center. It is only meaningful for the series expansion algorithm. Its value is limited to 8 but it is rarely necessary to go beyond 2 or 3.

scattering_order¶

details

Types	int
Limits	1 <= value <= 10
Unit	None
Allowed values	None
Default	3

The scattering order. Only meaningful for the ‘expansion’ algorithm. Its value is limited to 10.

renormalization_mode¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, G_n, Sigma_n, Z_n, Pi_1, Lowdin
Default	None

Enable the calculation of the coefficients for the renormalization of the multiple scattering series. You can choose to renormalize in terms of the \(G_n\), the \(\Sigma_n\), the \(Z_n\), the \(\Pi_1\) or the Lowdin \(K^2\) matrices

renormalization_omega¶

details

Types	int, float, complex
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	(1+0j)

The \(\omega\) coefficient used to initialize the renormalization alogorithm.

RA_cutoff_damping¶

details

Types	int
Limits	0 <= value <= None
Unit	None
Allowed values	None
Default	0

The Rehr-Albers truncation order. If > 0, the RA_cutoff is decreased by 1 every i^th scatterer until 0, where i = RA_cutoff_damping.

spin_flip¶

details

Types	bool
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	False

This parameter tells if spin-flip is authorized or not in the scattering process.

Note

This option works only if the spin polarization is enabled in your calculator object (see spinpol).

integrals¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	all, diagonal
Default	all

This option allows to take into account all four radial integrals (R++, R+-, R-+ and R–) in the calculation or only the diagonal radial integrals (R++ and R–) which are generally much larger.

Note

This option works only if the spin polarization is enabled in your calculator object.

path_filtering¶

details

Types	NoneType, str, tuple, list
Limits	None <= value <= None
Unit	None
Allowed values	None, forward_scattering, backward_scattering, distance_cutoff, plane_wave_normal, plane_wave_spin_averaged
Default	None

Used to activate some filters. It is possible to specify several of them by grouping them in a tuple or a list. For example:

>>> my_filters = ('forward_scattering', 'backward_scattering')
>>> calc.calculation_parameters.path_filtering = my_filters

off_cone_events¶

details

Types	int
Limits	0 <= value <= None
Unit	None
Allowed values	None
Default	1

Used in conjunction with the ‘forward_scattering’ filter. If the number of scattering processes outside the forward (or backward) scattering cone is greater than this number, then the path is rejected and its contribution to the scattering path operator won’t be computed.

scattering_order_cutoff¶

details

Types	int
Limits	0 <= value <= 10
Unit	None
Allowed values	None
Default	2

Used in conjunction with the ‘plane_wave_normal’ filter. It states to activate the plane wave approximation (which is fast but less accurate) to compute the contribution when the scattering order is greater than this value.

distance¶

details

Types	int, float
Limits	0 <= value <= None
Unit	angstrom
Allowed values	None
Default	10.0

Used with the ‘distance_cut_off’ filter. Paths whose length is larger than this value are simply rejected.

vibrational_damping¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, debye_waller, averaged_tl
Default	debye_waller

Tells how to compute the effect of atomic vibrations. It can be:

‘debye_waller’ for using the Debye Waller model.

‘averaged_tl’ to use the more correct averaging over T-matrix elements.

temperature¶

details

Types	int, float
Limits	0 <= value <= None
Unit	kelvin
Allowed values	None
Default	293.0

The temperature of the cluster. Used when use_debye_model = True

debye_temperature¶

details

Types	int, float
Limits	0 <= value <= None
Unit	kelvin
Allowed values	None
Default	420.0

The Debye temperature used for the calculation of the mean square displacements if use_debye_model = True

use_debye_model¶

details

Types	bool
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	False

No matter the way you compute the effect of atomic vibrations, you need the mean square displacements of atoms. It can be computed internally following the Debye model if you set this option to True.

vibration_scaling¶

details

Types	int, float
Limits	0.0 <= value <= None
Unit	None
Allowed values	None
Default	1.2

Used to simulate the fact that surface atoms vibrate more than bulk ones. It is a factor applied to the mean square displacements.

cutoff_factor¶

details

Types	int, float
Limits	0.0001 <= value <= 999.9999
Unit	None
Allowed values	None
Default	0.01

Sorry, no more help for this parameter.

mean_free_path¶

details

Types	int, float, str
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	SeahDench

The electron mean free path value. You can either: - Enter a value (in Angströms), in this case any value <=0 will disable the damping - Enter the keyword ‘mono’ to use a formula valid only for monoelemental samples - Enter the keyword ‘SeahDench’ to use the Seah and Dench formula.

Note

The mean free path is only taken into account when the input T-matrix corresponds to a real potential as, when the potential is complex, this damping is taken care of by the imaginery part othe potential.

Spectroscopy parameters ¶

PEDParameters ¶

level¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	1s

The level is the electronic level where the electron comes from. It is written: nlJ where:

n is the principal quantum number
l is the orbital quantum number
J is the spin-orbit component

Example:

>>> calc.spectroscopy_parameters.level = '2p3/2'
>>> calc.spectroscopy_parameters.level = '2p' # is equivalent to '2p1/2'

final_state¶

details

Types	int
Limits	-1 <= value <= 2
Unit	None
Allowed values	None
Default	2

Sorry, no more help for this parameter.

spin_orbit¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, single, both
Default	None

Sorry, no more help for this parameter.

EIGParameters ¶

level¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	1s

The level is the electronic level where the electron comes from. It is written: nlJ where:

n is the principal quantum number
l is the orbital quantum number
J is the spin-orbit component

Example:

>>> calc.spectroscopy_parameters.level = '2p3/2'
>>> calc.spectroscopy_parameters.level = '2p' # is equivalent to '2p1/2'

final_state¶

details

Types	int
Limits	-1 <= value <= 2
Unit	None
Allowed values	None
Default	2

Sorry, no more help for this parameter.

spin_orbit¶

details

Types	NoneType, str
Limits	None <= value <= None
Unit	None
Allowed values	None, single, both
Default	None

Sorry, no more help for this parameter.

kernel_matrix_spectrum¶

details

Types	bool
Limits	None <= value <= None
Unit	None
Allowed values	None
Default	False

Whether to output the kernel matrix spectrum for each energy point.

method¶

details

Types	str
Limits	None <= value <= None
Unit	None
Allowed values	AITK, RICH, SALZ, EPSI, EPSG, RHOA, THET, LEGE, CHEB, OVER, DURB, DLEV, TLEV, ULEV, VLEV, ELEV, EULE, GBWT, VARI, ITHE, EALG
Default	EPSI

The convergence acceleration scheme to be used.