shadow4.physical_models.mlayer package

Submodules

shadow4.physical_models.mlayer.mlayer module

python version of the multilayer code in shadow.

The stack is as follows: Vacuum+[Odd,Even]xn+Substrate

>>> #                  vacuum   ")
>>> #       |------------------------------|  >>> #       |          odd (n)             |  |
>>> #       |------------------------------|  | BILAYER # n
>>> #       |          even (n)            |  |
>>> #       |------------------------------|  /
>>> #       |          .                   |
>>> #       |          .                   |
>>> #       |          .                   |
>>> #       |------------------------------|  >>> #       |          odd (1)             |  |
>>> #       |------------------------------|  | BILAYER # 1
>>> #       |          even (1)            |  |
>>> #       |------------------------------|  /
>>> #       |                              |
>>> #       |///////// substrate //////////|
>>> #       |                              |

>>> #      gamma = thickness_even / (thickness_even + thickness_odd)
class shadow4.physical_models.mlayer.mlayer.MLayer[source]

Bases: object

Constructor.

Several ways of using MLayer: * ml = MLayer.pre_mlayer(<keywords>) * ml = MLayer(); ml.read_preprocessor_file(‘mymlayer.dat’) * ml = MLayer.initialize_from_bilayer_stack(<keywords>)

classmethod initialize_from_bilayer_stack(material_S='Si', density_S=None, roughness_S=0.0, material_E='B4C', density_E=None, roughness_E=0.0, material_O='Ru', density_O=None, roughness_O=0.0, bilayer_pairs=70, bilayer_thickness=33.1, bilayer_gamma=0.483, GRADE_SURFACE=0, AA0=1.0, AA1=0.0, AA2=0.0, AA3=0.0, ell_p=10.0, ell_q=3.0, ell_theta_grazing_deg=0.1, ell_length=0.1, ell_photon_energy=10000.0, GRADE_DEPTH=0, LIST_N_THICK_GAMMA_ROUGHE_ROUGHO_FROM_TOP_TO_BOTTOM=None, use_xraylib_or_dabax=0, dabax=None)[source]

Creates an instance of MLayer with the main parameters of a multilater. In this case, the calculations are done without using the preprocessor data, and the optical constants are supplied by xraylib at run time.

Parameters:

  • material_S (str, optional) – The symbol of the SUBSTRATE material.

  • density_S (float, optional) – The density in g/cm3 for the SUBSTRATE layers.

  • roughness_S (float, optional) – The roughness in A for the SUBSTRATE layers.

  • material_E (str, optional) – The symbol of the EVEN layer material.

  • density_E (float, optional) – The density in g/cm3 for the EVEN layers.

  • roughness_E (float, optional) – The roughness in A for the EVEN layers.

  • material_O (str, optional) – The symbol of the ODD layer material.

  • density_O (float, optional) – The density in g/cm3 for the ODD layers.

  • roughness_O (float, optional) – The roughness in A for the ODD layers.

  • bilayer_pairs (int, optional) – The number of bilayers.

  • bilayer_thickness (float, optional) – The thickness in A of the bilayers.

  • bilayer_gamma (float, optional) – The gamma factor of the bilayer thickness(even) / (thichness(odd) + thichness(even)).

  • GRADE_SURFACE (int, optional) –

    Flag for multilayer graded over the surface:

    • 0: No.

    • 1: Not used (for compatibility with SHADOW3).

    • 2: Not used (for compatibility with SHADOW3).

    • 3: t graded over the surface (input quadratic fit to t gradient in meters).

    • 4: t graded over the surface for an elliptical multilayer (quadratic coefficients are calculated from

      the ellipse design parameters).

  • AA0 (float, optional) – Coefficient (constant); used when GRADED_SURFACE=2

  • AA1 (float, optional) – Coefficient (linear) in m^-1; used when GRADED_SURFACE=2

  • AA2 (float, optional) – Coefficient (quadratic) in m^-2; used when GRADED_SURFACE=2

  • AA3 (float, optional) – Coefficient (cubic) in m^-3; used when GRADED_SURFACE=2

  • ell_p (float, optional) – The ellipse design parameters p in m; used when GRADED_SURFACE=3.

  • ell_q (float, optional) – The ellipse design parameters q in m; used when GRADED_SURFACE=3.

  • ell_theta_grazing_deg (float, optional) – The ellipse design grazing angle in deg; used when GRADED_SURFACE=3.

  • ell_length (float, optional) – The ellipse length in m; used when GRADED_SURFACE=3.

  • ell_photon_energy (float, optional) – The photon energy in eV at the center of the ellipse; used when GRADED_SURFACE=3.

  • use_xraylib_or_dabax (int, optional) – 0=use xraylib, 1=use dabax for the optical constabrs.

  • dabax (None or instance of DabaxXraylib,) – The pointer to the dabax library (used for use_xraylib_or_dabax = 1).

Return type:

instance of MLayer

classmethod initialize_from_bilayer_stack_in_compressed_format(structure='[Pd/B4C]x150+Si', density_O=None, roughness_O=0.0, density_E=None, roughness_E=0.0, density_S=None, roughness_S=0.0, bilayer_thickness=33.1, bilayer_gamma=0.483, GRADE_SURFACE=0, AA0=1.0, AA1=0.0, AA2=0.0, AA3=0.0, ell_p=10.0, ell_q=3.0, ell_theta_grazing_deg=0.1, ell_length=0.1, ell_photon_energy=10000.0, GRADE_DEPTH=0, LIST_N_THICK_GAMMA_ROUGHE_ROUGHO_FROM_TOP_TO_BOTTOM=None, use_xraylib_or_dabax=0, dabax=None)[source]

Creates an instance of MLayer with the main parameters of a multilater. In this case, the calculations are done without using the preprocessor data, and the optical constants are supplied by xraylib at run time.

Parameters:

  • material_S (str, optional) – The symbol of the SUBSTRATE material.

  • density_S (float, optional) – The density in g/cm3 for the SUBSTRATE layers.

  • roughness_S (float, optional) – The roughness in A for the SUBSTRATE layers.

  • material_E (str, optional) – The symbol of the EVEN layer material.

  • density_E (float, optional) – The density in g/cm3 for the EVEN layers.

  • roughness_E (float, optional) – The roughness in A for the EVEN layers.

  • material_O (str, optional) – The symbol of the ODD layer material.

  • density_O (float, optional) – The density in g/cm3 for the ODD layers.

  • roughness_O (float, optional) – The roughness in A for the ODD layers.

  • bilayer_pairs (int, optional) – The number of bilayers.

  • bilayer_thickness (float, optional) – The thickness in A of the bilayers.

  • bilayer_gamma (float, optional) – The gamma factor of the bilayer thickness(even) / (thichness(odd) + thichness(even)).

  • GRADE_SURFACE (int, optional) –

    Flag for multilayer graded over the surface:

    • 0: No.

    • 1: Not used (for compatibility with SHADOW3).

    • 2: Not used (for compatibility with SHADOW3).

    • 3: t graded over the surface (input quadratic fit to t gradient in meters).

    • 4: t graded over the surface for an elliptical multilayer (quadratic coefficients are calculated from

      the ellipse design parameters).

  • AA0 (float, optional) – Coefficient (constant); used when GRADED_SURFACE=2

  • AA1 (float, optional) – Coefficient (linear) in m^-1; used when GRADED_SURFACE=2

  • AA2 (float, optional) – Coefficient (quadratic) in m^-2; used when GRADED_SURFACE=2

  • AA3 (float, optional) – Coefficient (cubic) in m^-3; used when GRADED_SURFACE=2

  • ell_p (float, optional) – The ellipse design parameters p in m; used when GRADED_SURFACE=3.

  • ell_q (float, optional) – The ellipse design parameters q in m; used when GRADED_SURFACE=3.

  • ell_theta_grazing_deg (float, optional) – The ellipse design grazing angle in deg; used when GRADED_SURFACE=3.

  • ell_length (float, optional) – The ellipse length in m; used when GRADED_SURFACE=3.

  • ell_photon_energy (float, optional) – The photon energy in eV at the center of the ellipse; used when GRADED_SURFACE=3.

  • use_xraylib_or_dabax (int, optional) – 0=use xraylib, 1=use dabax for the optical constabrs.

  • dabax (None or instance of DabaxXraylib,) – The pointer to the dabax library (used for use_xraylib_or_dabax = 1).

Return type:

instance of MLayer

is_depth_graded()[source]

Returns True if the multilayes is depth-graded.

Return type:

bool

is_laterally_graded()[source]

Returns True if the multilayes is laterally-graded.

Return type:

bool

classmethod pre_mlayer(FILE='pre_mlayer.dat', E_MIN=5000.0, E_MAX=20000.0, S_DENSITY=2.33, S_MATERIAL='Si', E_DENSITY=2.4, E_MATERIAL='B4C', O_DENSITY=9.4, O_MATERIAL='Ru', N_PAIRS=70, THICKNESS=33.1, GAMMA=0.483, ROUGHNESS_EVEN=3.3, ROUGHNESS_ODD=3.1, GRADE_SURFACE=0, AA0=1.0, AA1=0.0, AA2=0.0, AA3=0.0, ell_p=10.0, ell_q=3.0, ell_theta_grazing_deg=0.1, ell_length=0.1, ell_photon_energy=10000.0, GRADE_DEPTH=0, LIST_N_THICK_GAMMA_ROUGHE_ROUGHO_FROM_TOP_TO_BOTTOM=None, use_xraylib_or_dabax=0, dabax=None)[source]

Creates an instance of MLayer with parameters initialized from the keyword parameters and the pre_mlayer preprocessor file. It uses xraylib for accessing the optical constants.

Parameters:

  • FILE (str, optional) – File name to be created (preprocessor pre_mlayer file).

  • E_MIN (float, optional) – The minimum photon energy in eV (for creating the tabulated refraction index).

  • E_MAX (float, optional) – The maximum photon energy in eV (for creating the tabulated refraction index).

  • S_DENSITY (float, optional) – Density (in g/cm3) for the SUBSTRATE material.

  • S_MATERIAL (float, optional) – Material formula for the SUBSTRATE material.

  • E_DENSITY (float, optional) – Density (in g/cm3) for the EVEN material.

  • E_MATERIAL (float, optional) – Material formula for the EVEN material.

  • O_DENSITY (float, optional) – Density (in g/cm3) for the ODD material.

  • O_MATERIAL (float, optional) – Material formula for the ODD material.

  • N_PAIRS (int, optional) – The number of bilayers of the multilayer. Not used if GRADE_DEPTH=1.

  • THICKNESS (float, optional) – The thickness of a bilayer in Angstroms. Not used if GRADE_DEPTH=1.

  • GAMMA (float, optional) – The gamma factor thickness(even) / (thickness(odd) + thickness(even)) for the multilayer. Not used if GRADE_DEPTH=1.

  • ROUGHNESS_EVEN (float, optional) – The rounghness of the EVEN layers in A. Not used if GRADE_DEPTH=1.

  • ROUGHNESS_ODD (float, optional) – The rounghness of the ODD layers in A. Not used if GRADE_DEPTH=1.

  • GRADE_SURFACE (int, optional) –

    Flag for multilayer graded over the surface:

    • 0: No.

    • 1: Not used (for compatibility with SHADOW3).

    • 2: Not used (for compatibility with SHADOW3).

    • 3: t graded over the surface (input quadratic fit to t gradient in meters).

    • 4: t graded over the surface for an elliptical multilayer (quadratic coefficients are calculated from

      the ellipse design parameters).

  • AA0 (float, optional) – Coefficient (constant); used when GRADED_SURFACE=2

  • AA1 (float, optional) – Coefficient (linear) in m^-1; used when GRADED_SURFACE=2

  • AA2 (float, optional) – Coefficient (quadratic) in m^-2; used when GRADED_SURFACE=2

  • AA3 (float, optional) – Coefficient (cubic) in m^-3; used when GRADED_SURFACE=2

  • ell_p (float, optional) – The ellipse design parameters p in m; used when GRADED_SURFACE=3.

  • ell_q (float, optional) – The ellipse design parameters q in m; used when GRADED_SURFACE=3.

  • ell_theta_grazing_deg (float, optional) – The ellipse design grazing angle in deg; used when GRADED_SURFACE=3.

  • ell_length (float, optional) – The ellipse length in m; used when GRADED_SURFACE=3.

  • ell_photon_energy (float, optional) – The photon energy in eV at the center of the ellipse; used when GRADED_SURFACE=3.

  • GRADE_DEPTH (int, optional) – Flag to indicate if the multilayes has a graded thickness (1) or not (0).

  • LIST_N_THICK_GAMMA_ROUGHE_ROUGHO_FROM_TOP_TO_BOTTOM (None or str) – A str with a list definition of multilayers blocks in the form: [block1, block2, …] with each block defined as [Nbilayers, BilayerThickness, BilayerGamma, roughnessEven, roughnessOdd].

  • use_xraylib_or_dabax (int, optional) – 0=use xraylib, 1=use dabax for the optical constabrs.

  • dabax (None or instance of DabaxXraylib,) – The pointer to the dabax library (used for use_xraylib_or_dabax = 1).

Returns:

It contains a dictionary in MLayer.pre_mlayer_dict with the data in the following keys:

  • np : number of photon energy points,

  • energy : numpy array with photon energy,

  • delta_s : numpy array with refraction index (delta) for substrate,

  • beta_s : numpy array with refraction index (beta) for substrate,

  • delta_e : numpy array with refraction index (delta) for even sublayer,

  • beta_e : numpy array with refraction index (beta) for even sublayer,

  • delta_o : numpy array with refraction index (delta) for odd sublayer,

  • beta_o : numpy array with refraction index (beta) for odd sublayer,

  • npair : number of bilayer paits,

  • thick : numpy array with bilayer thicknesses,

  • gamma1 : numpy array with bilayer gamma,

  • mlroughness1 : numpy array with roughness for even sublayer,

  • mlroughness2 : numpy array with roughness for odd sublayer,

  • igrade : GRADE_SURFACE flag,

  • a0, a1, a2, a3 : polynomial coefficients for laterally graded multilayers (GRADE_SURFACE=3),

  • ell_p, ell_q, ell_theta_grazing_deg, ell_length, ell_photon_energyellipse settings for laterally

    graded multilayers (GRADE_SURFACE=4).

Return type:

instance of MLayer

Notes

This method requires xraylib to access to the optical constants.

read_preprocessor_file(filename)[source]

Reads a preprocessor (pre_mlayer) file. It has the same file format as in shadow3.

Parameters:

filename (str) – The name of the filename.

reflectivity(grazing_angle_deg, photon_energy_ev, Y=0.0)[source]

Computes the reflectivity (in amplitude) as a function of the incident angle and photon energy.

Parameters:

  • grazing_angle_deg (numpy array) – The array with the incident gracing angle in deg.

  • photon_energy_ev (numpy array) – The array with the photon energy in eV.

  • Y (numpy array) – The array of coordinates along the Y direction (tangential). This is used only in the case of laterally graded multilayers.

Returns:

(R_S_array, R_P_array, phase_S, phase_P) arrays with reflectivities (in amplitude) and phases.

Return type:

tuple

scan(h5file='', energyN=51, energy1=5000.0, energy2=20000.0, thetaN=1, theta1=0.75, theta2=0.75, verbose=0)[source]

this method computes the multilayer reflectivity vs photon energy and/or angle. The reflectivity values are for amplitude.

Parameters:

  • energyN (int, optional) – Number of points in photon energy.

  • energy1 (float, optional) – The minimum photon energy in eV.

  • energy2 (float, optional) – The maximum photon energy in eV.

  • thetaN (int, optional) – Number of points in incident grazing angle.

  • theta1 (float, optional) – The minimum value of the incident grazing angle in deg.

  • theta2 (float, optional) – The minimum value of the incident grazing angle in deg.

  • h5file (str, optional) – Name of the h5 file to dump calculated data. Set to “” to avoid creating file.

  • verbose (int, optional) – if verbose=1, and thetaN=angleN=1 a text with results is printed .

Returns:

(R_S_array, R_P_array, energy_array, theta_array) numpy arrays for the sigma reflectivity (energyN, thetaN), pi reflectivity (energyN, thetaN), photon energy (energyN) and incident grazing angle (thetaN).

Return type:

tuple

Module contents