CyRSoXS Simulation Components#

Cy-RSoXS is a voxel-based forward-scattering simulator calculated in the Born Approximation. This page describes the required files and file structure for use with CyRSoXS.

  • Morphology file

    • .hdf5 format

  • Material optical constant files

    • Material1.txt, Material2.txt, Material3.txt, etc.

  • Configuration file

    • config.txt

Morphology File Structure#

Cy-RSoXS accepts two different types of morphologies: Vector and Euler. A vector morphology will use a vector to assign the direction and amount of alignment in each voxel for each material. A Euler morphology will use a set of Euler angles to assign the direction of alignment. A separate S parameter is used to denote the amount of alignment in each voxel for each material.

The two structures below assume a morphology of size [1, 256, 256] where the dimensions are [Z, Y, X], and two materials in the morphology.

Vector Morphology HDF5 Structure#

NOTE: The Vector Morphology type is included for legacy support and may be deprecated in future releases. Use of the Euler Morphology type is strongly recommended.

Vector_Morphology/
    Mat_1_alignment/
        data = alignment vector array of shape [1, 256, 256, 3] and order [Z, Y, X, (XYZ)]
            dims = ['Z', 'Y', 'X']
    Mat_1_unaligned/
        data = volume fraction array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_2_alignment/
        data = alignment vector array of shape [1, 256, 256, 3] and order [Z, Y, X, (XYZ)]
            dims = ['Z', 'Y', 'X']
    Mat_2_unaligned/
        data = volume fraction array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']

Morphology_Parameters/
*required*
    PhysSize/
        data = size of each voxel edge in nanometers
    NumMaterial/
        data = number of materials in morphology (integer)
*optional*
    creation_date/
        data = date and time
    film_normal/
        data = [Z, Y, X] vector denoting the film normal direction
    morphology_creator/
        data = author of the morphology
    name/
        data = name of morphology

Euler Morphology HDF5 Structure#

The Euler Morphology uses a ZYZ convention. Currently, Cy-RSoXS only supports uniaxial materials and the first Euler rotation (Phi) is unused. Theta is the rotation around the Y axis. Psi is the last rotation around the Z axis.

../_images/Euler_ZYZ-v4.gif 
Euler_Angles/
    Mat_1_Vfrac/
        data = Rotation angle array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_1_S/
        data = alignment magnitude array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_1_Theta/
        data = Rotation angle array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_1_Psi/
        data = Rotation angle array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']

    Mat_2_Vfrac/
        data = Rotation angle array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_2_S/
        data = alignment magnitude array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_2_Theta/
        data = Rotation angle array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']
    Mat_2_Psi/
        data = Rotation angle array of shape [1, 256, 256] and order [Z, Y, X]
            dims = ['Z', 'Y', 'X']

Morphology Parameters/
*required*
    PhysSize/
        data = size of each voxel edge in nanometers
    NumMaterial/
        data = number of materials in morphology (integer)
*optional*
    creation_date/
        data = date and time
    film_normal/
        data = [Z, Y, X] vector denoting the film normal direction
    morphology_creator/
        data = author of the morphology
    name/
        data = name of morphology

Material Optical Constant File Structure#

CyRSoXS currently supports uniaxial optical constants. In tensor form, this can be represented as:

\[\begin{split}\begin{bmatrix} n_{perp} & 0 & 0\\ 0 & n_{perp} & 0\\ 0 & 0 & n_{para} \end{bmatrix}\end{split}\]

where \(n = 1 - \delta + i\beta\). Para is the extraordinary (unique) axis, and perp is the ordinary (degenerate) axis.

For each material in the simulation, we need a corresponding MaterialX.txt file. This file contains the optical constants at each energy for the extraordinary (Para) and ordinary (Perp) axes of the uniaxial dielectric function.

EnergyData0:
{
Energy = 275.0;
BetaPara = 6.388392448251455e-05;
BetaPerp = 6.303899730113871e-05;
DeltaPara = 0.0010635346640931634;
DeltaPerp = 0.0011221433414215483;
}

EnergyData1:
{
Energy = 275.1;
BetaPara = 6.309144102259152e-05;
BetaPerp = 6.304376809350212e-05;
DeltaPara = 0.0010567115883113286;
DeltaPerp = 0.0011157664852560843;
}

.
.
.

EnergyData249:
{
Energy = 299.9;
BetaPara = 0.0024365306249853557;
BetaPerp = 0.0025455166691934236;
DeltaPara = 0.0017547293997892883;
DeltaPerp = 0.001774225207859871;
}

Configuration File Structure#

The config.txt file has a number of options, where each option is written to a separate line in the file:

Energies = [275.0, 275.1, ..., 299.9];
CaseType = 0
EAngleRotation = [0.0, 1.0, 360.0];
MorphologyType = 0

Table of Configuration File Options#

Option

Required

Default

Comment

CaseType

Yes

-

Energies

Yes

-

EAngleRotation

Yes

-

MorphologyType

Yes

-

listKVectors

No

[0, 0, 1]

Required for CaseType = 1, 2

DetectorCoordinates

No

[0, 0, 1]

Required for CaseType = 2

NumThreads

No

4

AlgorithmType

No

0

DumpMorphology

No

False

ScatterApproach

No

0

WindowingType

No

0

RotMask

No

False

EwaldsInterpolation

No

False

Configuration File Option Descriptions#

  • CaseType

    • The scattering configuration

    • 0 : Default configuration. fixed \(\vec k = (0, 0, 1)\) and dectector normal of \(\vec n = (0, 0, 1)\).

    • 1 : Beam Divergence. Supports arbitrary \(\vec k\), but fixed detector normal of \(\vec n = (0, 0, 1)\).

    • 2 : Grazing Incidence. Supports arbitrary \(\vec k\) and \(\vec n\). Currently untested

    • Input datatype: integer

    • Example: CaseType = 1;

  • Energies

    • The list of energies to simulate

    • Input datatype : Real double/float values

    • Example: Energies = [270.0, 271.0, 272.0];

  • EAngleRotation

    • The rotation angle in degrees for the x-ray beam’s \(\vec E\) polarization

    • List of 3 values in order of \([Start, Increment, End]\).

    • Default \(\vec E = (1, 0, 0)\). Rotation is counter-clockwise.

    • Input datatype : Real double/float

    • Example: EAngleRotation = [0.0, 1.0, 360.0];

  • MorphologyType

    • Vector or Euler Morphology

    • 0 : Euler Morphology

    • 1 : Vector Morphology

    • Input datatype: integer

    • Example: MorphologyType = 0;

  • listKVectors

    • The list of \(\vec k\) vectors

    • Specific to CaseType = 1, 2

    • \(\vec k\) vectors are arranged in groups.

    • Input datatype: Real double/float

    • Example: listKVectors = {k0={k=[0.0, 0.0, 1.0]}, k1={k=[0.5, 0.5, 1.0]}};

  • DetectorCoordinates

    • Determines the detector geometry by setting the detector’s vector normal

    • Specific to CaseType = 2

    • List of 3 values in the order \([x, y, z]\). Default is \(\vec n = (0, 0, 1)\)

    • Input datatype: Real double/float

    • Example: DetectorCoordinates = [0.0, 0.0, 1.0];

  • NumThreads

    • number of OpenMP threads

    • Default value = 4

    • Must be \(\geq\) number of GPUs

    • To set in hardware, run in bash export OMP_NUM_THREADS=4 for 4 OpenMP threads

    • Example: NumThreads = 4;

  • AlgorithmType

    • Selects the type of algorithm used by CyRSoXS

    • 0 : Communication minimizing algorithm

    • 1 : Memory minimizing algorithm

    • Default values = 0

    • Input datatype: integer

    • Example: AlgorithmType = 0;

  • DumpMorphology

    • Writes the morphology as seen by CyRSoXS, after any necessary conversions are performed. Useful for double checking morphology construction

    • Writes to XMDF and HDF5 files. The XMDF file can be loaded in Paraview/Visit for 3D visualization. The native CyRSoXS visualizer is Paraview or Visit. Use of other tools is up to the discretion of the user.

    • Default value = False

    • Input datatype : Boolean string

    • Example: DumpMorphology = True;

  • ScatterApproach

    • Option to explicitly calculate the differential scattering cross-section before the Ewald Sphere Projection

    • 0 : Do not compute

    • 1 : Compute

    • Example: ScatterApproach = 0;

  • WindowingType

    • Type of windowing for the FFT

    • 0 : None

    • 1 : Hanning

    • Default value = 0

    • Input datatype : integer

    • Example: WindowingType = 0;

  • EwaldsInterpolation

    • Type of interpolation onto the Ewald Sphere

    • 0 : Nearest neighbor

    • 1 : Trilinear interpolation

    • Default value = 1

    • Example: EwaldsInterpolation = 1;