Calculations

This module contains the basic implementation of the matrix formalism as detailed in Drits and Tchoubar (1990) and Plançon (2001).

It was chosen to implement this using ‘loose’ function calls. The disadvantage of this approach is that the functions are no longer bound to class instances, which makes them less intuitive to use. The advantage is we can more easily call these functions asynchronously (e.g. using Pool)

Despite all this, most function calls in this module do expect to be passed a DataObject sub-class, which wraps all the data in a single object. These DataObject s map onto the different models used. As such this module is also largely independent from the MVC framework used.

Drits, V.A., and Tchoubar, C., 1990. X-Ray Diffraction by Disordered Lamellar Structures: Theory and Applications to Microdivided Silicates and Carbons. Springer-Verlag, Berlin, Germany. Plançon, A., 2001. Order-disorder in clay mineral structures. Clay Miner 36, 1–14.

Atoms

Components

Phases and CSDS

Goniometer

Specimen

Statistics

Improve

Exceptions

exception pyxrd.calculations.exceptions.WrapException

A wrapped exception used by the wrap_exceptions() decorator.

pyxrd.calculations.exceptions.wrap_exceptions(func)

Function decorator that allows to provide useable tracebacks when the function is called asynchronously and raises an error.

Data Objects

The following classes are not meant to be used directly, rather you should create the corresponding model instances and retrieve the DataObject from them.

The rationale behind not using the model instances directly is that they are difficult to serialize or pickle (memory-)efficiently. This is mainly due to all of the boiler-plate code that takes care of references, saving, loading, calculating properties from other properties etc. A lot of this is not needed for the actual calculation. The data objects below, on the other hand, only contain the data needed to be able to calculate XRD patterns.

class pyxrd.calculations.data_objects.DataObject(**kwargs)

The base class for all DataObject instances.

The constructor takes any number of keyword arguments it will set as attributes on the instance.

class pyxrd.calculations.data_objects.AtomTypeData(**kwargs)

The DataObject describing an AtomType.

par_a = None

a numpy array of a scattering factors

par_b = None

a numpy array of b scattering factors

par_c = None

the c scattering constant

debye = None

the debye-waller temperature factor

class pyxrd.calculations.data_objects.AtomData(**kwargs)

The DataObject describing an Atom.

atom_type = None

an AtomTypeData instance

pn = None

the # of atoms projected to this z coordinate

default_z = None

the default z coordinate

z = None

the actual z coordinate

class pyxrd.calculations.data_objects.ComponentData(**kwargs)

The DataObject describing an Atom

layer_atoms = None

a list of AtomData instances

interlayer_atoms = None

a list of AtomData instances

volume = None

the component volume

weight = None

the component weight

d001 = None

the d-spacing of the component

default_c = None

the default d-spacing of the component

delta_c = None

the variation in d-spacing of the component

lattice_d = None

the height of the silicate lattice (excluding the interlayer space)

class pyxrd.calculations.data_objects.CSDSData(**kwargs)

The DataObject describing the CSDS distribution.

average = None

average CSDS

maximum = None

maximum CSDS

minimum = None

minimum CSDS

alpha_scale = None

the alpha scale factor for the log-normal distribution

alpha_offset = None

the alpha offset factor for the log-normal distribution

beta_scale = None

the beta scale factor for the log-normal distribution

beta_offset = None

the beta offset factor for the log-normal distribution

class pyxrd.calculations.data_objects.GonioData(**kwargs)

The DataObject describing the Goniometer setup.

min_2theta = None

Lower 2-theta bound for calculated patterns

max_2theta = None

Upper 2-theta bound for calculated patterns

steps = None

The number of steps in between the lower and upper 2-theta bounds

has_soller1 = False

If the first soller slits are present

soller1 = None

The first soller slit size

has_soller2 = False

If the first soller slits are present

soller2 = None

The second soller slit size

divergence_mode = 'FIXED'

The divergence slit mode

divergence = None

The divergence size (degrees (fixed) or mm (auto))

mcr_2theta = 0

The Bragg angle of the monochromator (or 0° if not present)

has_absorption_correction = None

Flag indicating if intensities need to be corrected for absorption

absorption = 45.0

The sample mass absorption coefficient (mg/cm²)

sample_surf_density = 20.0

The sample surface density (cm²/g)

radius = None

The goniometer radius

wavelength = None

The goniometer wavelength

wavelength_distribution = None

The goniometer wavelength distribution

sample_length = None

The sample length

class pyxrd.calculations.data_objects.ProbabilityData(**kwargs)

The DataObject describing the layer stacking probabilities

valid = None

Whether this probability is really a valid one

G = None

The number of components this probability describes

W = None

The weight fractions matrix

P = None

The probabilities matrix

class pyxrd.calculations.data_objects.PhaseData(**kwargs)

The DataObject describing a phase

apply_lpf = True

A flag indicating whether to apply Lorentz-polarization factor or not

apply_correction = True

A flag indicating whether to apply machine corrections or not

components = None

A list of ComponentData instances

probability = None

A ProbabilityData instance

sigma_star = None

The sigma start value

csds = None

A CSDSData instance

class pyxrd.calculations.data_objects.SpecimenData(**kwargs)

The DataObject describing a specimen

goniometer = None

A GonioData instance

absorption = None

The sample absorption

phases = None

A list of PhaseData instances

observed_intensity = None

A numpy array with the observed intensities

total_intensity = None

A numpy array with the calculated intensity

phase_intensities = None

A nummpy array with the calculated phase profiles

class pyxrd.calculations.data_objects.MixtureData(**kwargs)

The DataObject describing a mixture

specimens = None

A list of SpecimenData instances

fractions = None

A numpy array with the phase fractions

bgshifts = None

A numpy array with the specimen background shifts

scales = None

A numpy array with the specimen absolute scales

parsed = False

Whether this MixtureData object has been parsed (internal flag)

calculated = False

Whether this MixtureData object has been calculated (internal flag)

optimized = False

Whether this MixtureData object has been optimized (internal flag)

n = 0

The number of specimens

m = 0

The number of phases