The `FluoCrystal` Component

Sample model handling absorption, fluorescence, Compton, Rayleigh scattering and single crystal diffraction.

Identification

Site:
Author: Emmanuel Farhi (emmanuel.farhi.synchrotron-soleil.fr)
Origin: Synchrotron SOLEIL
Date: April 2025

Description

Sample that models multiple photon-matter interactions:
- absorption          (photon excites an electron and creates a hole)
- fluorescence        (excited electrons emit light while falling into lower states)
- Compton scattering  (inelastic, incoherent)
- Rayleigh scattering (elastic,   coherent)
- crystal diffraction (elastic,   coherent)

The 'material' specification is given as a chemical formulae, e.g. "LaB6". It
may also be given as a file name (CIF/LAU/LAZ/FullProf format) in which case
the formulae is guessed (but may be approximative), and the crystal
diffraction is computed, following same options as the PowderN
sample component. The fluorescence is handled for atoms from Z=5 to Z=90.

By setting the 'order' to 1, the absorption along the scattered path is handled.
A higher 'order' will handle multiple scattering events, and final absorption.
For instance, a value order>=2 handles e.g. fluorescence iterative cascades
in the material. Leaving 'order=0' handles the single scattering only.

The single crystal diffraction model is simplified wrt the Single_crystal
component. Use that latter with a Fluorescence in a GROUP for more complex features.

Example: FluoCrystal(material="LaB6.cif",
xwidth=0.001,yheight=0.001,zdepth=0.0001, p_interact=0.99, mosaic=3)

Sample shape:
Sample shape may be a cylinder, a sphere, a box or any other shape
box/plate:       xwidth x yheight x zdepth (thickness=0)
hollow box/plate:xwidth x yheight x zdepth and thickness>0
cylinder:        radius x yheight (thickness=0)
hollow cylinder: radius x yheight and thickness>0
sphere:          radius (yheight=0 thickness=0)
hollow sphere:   radius and thickness>0 (yheight=0)
any shape:       geometry=OFF file

The complex geometry option handles any closed non-convex polyhedra.
It computes the intersection points of the photon ray with the object
transparently, so that it can be used like a regular sample object.
It supports the OFF, PLY and NOFF file format but not COFF (colored faces).
Such files may be generated from XYZ data using:
qhull < coordinates.xyz Qx Qv Tv o > geomview.off
or
powercrust coordinates.xyz
and viewed with geomview or java -jar jroff.jar (see below).
The default size of the object depends of the OFF file data, but its
bounding box may be resized using xwidth,yheight and zdepth.

Concentric components:
This component has the ability to contain other components when used in
hollow cylinder geometry (namely sample environment, e.g. cryostat and
furnace structure). Such component 'shells' should be split into input and
output side surrounding the 'inside' components. First part must then use
'concentric=1' flag to enter the inside part. The component itself must be
repeated to mark the end of the concentric zone. The number of concentric
shells and number of components inside is not limited.

COMPONENT F_in = FluoCrystal(material="Al", concentric=1, ...)
AT (0,0,0) RELATIVE sample_position

COMPONENT something_inside ... // e.g. the sample itself or other materials

COMPONENT F_out = COPY(F_in)(concentric=0)
AT (0,0,0) RELATIVE sample_position

Enhancing computation efficiency:
An important option to enhance statistics is to set 'p_interact' to, say,
30 percent (0.3) in order to force a fraction of the beam to scatter. This
will result on a larger number of scattered events, retaining intensity.

In addition, it may be desirable to define a 'target' for the fluorescence
processes via e.g. the 'target_index' and the 'focus_xw / focus_yh' options.
This target should e.g. be the SDD area.

The SPLIT feature is currently BROKEN with this component. Do not use it.

If you get strange results, check the crystal mosaicity and delta(d)/d parameters,
as this component is not suited for ideal/perfect mosaic crystals.

The fluorescence is computed via the XRayLib (apt install libxrl-dev) https://github.com/tschoonj/xraylib.

Input parameters

Parameters in boldface are required; the others are optional.

Name	Unit	Description	Default
geometry	str	Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust.	0
radius	m	Outer radius of sample in (x,z) plane. cylinder/sphere.	0
thickness	m	Thickness of hollow sample Negative value extends the hollow volume outside of the box/cylinder.	0
xwidth	m	Width for a box sample shape.	0
yheight	m	Height of sample in vertical direction for box/cylinder shapes.	0
zdepth	m	Depth for a box sample shape.	0
concentric	1	Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere).	0
material	str	A CIF/LAZ/LAU file e.g. "LaB6.cif" to handle diffraction or chemical formulae, e.g. "Pb2SnO4" (no diffraction).	"LaB6.cif"
packing_factor	1	How dense is the material compared to bulk 0-1.	0
density	g/cm^3	Density of material. V_rho=density/weight/1e24*N_A at/Angs^3.	0
weight	g/mol	Atomic/molecular weight of material.	0
p_interact	1	Force a given fraction of the beam to scatter, keeping intensity right, to enhance small signals (-1 inactivate).	0
target_x	m	Position of target to focus at, along X (for fluorescence).	0
target_y	m	Position of target to focus at, along Y (for fluorescence).	0
target_z	m	Position of target to focus at, along Z (for fluorescence).	0
focus_r	m	Radius of disk containing target. Use 0 for full space (for fluorescence).	0
focus_xw	m	Horiz. dimension of a rectangular area (for fluorescence).	0
focus_yh	m	Vert. dimension of a rectangular area (for fluorescence).	0
focus_aw	deg	Horiz. angular dimension of a rectangular area (for fluorescence).	0
focus_ah	deg	Vert. angular dimension of a rectangular area (for fluorescence).	0
target_index	1	Relative index of component to focus at, e.g. next is +1 (for fluorescence).	0
flag_compton	1	When 0, the Compton scattering is ignored.	1
flag_rayleigh	1	When 0, the Rayleigh scattering is ignored.	1
flag_lorentzian	1	When 1, the fluorescence line shapes are assumed to be Lorentzian, else Gaussian.	0
flag_kissel	1	When 1 (slower), handle M-lines XRF from Kissel for Z>=52 Te (else only K and L-lines).	0
sx_refl	str	A CIF/LAZ/LAU reflection file as for PowderN. When not given, 'material' is used. Specify it when 'material' is a chemical formula.	""
int flag_sx			1
delta_d_d	1	Lattice spacing variance, gaussian RMS (longitudinal mosaic) e.g. 1e-4 to 1e-3.	1e-3
int barns			1
recip_cell	1	Choice of direct/reciprocal (0/1) unit cell definition	0
ax	AA or AA^-1	Coordinates of first (direct/recip) unit cell vector	0
ay	AA or AA^-1	a on y axis	0
az	AA or AA^-1	a on z axis	0
bx	AA or AA^-1	Coordinates of second (direct/recip) unit cell vector	0
by	AA or AA^-1	b on y axis	0
bz	AA or AA^-1	b on z axis	0
cx	AA or AA^-1	Coordinates of third (direct/recip) unit cell vector	0
cy	AA or AA^-1	c on y axis	0
cz	AA or AA^-1	c on z axis	0
aa			0
bb			0
cc			0
mosaic_AB	arc_minutes, arc_minutes,1, 1, 1, 1, 1, 1	In Plane mosaic rotation and plane vectors (anisotropic), mosaic_A, mosaic_B, A_h,A_k,A_l, B_h,B_k,B_l. Puts the crystal in the in-plane mosaic state. Vectors A and B define plane in which the crystal roation is defined, and mosaic_A, mosaic_B, denotes the resp. mosaicities (gaussian RMS) with respect to the two reflections chosen by A and B (Miller indices).	{0,0, 0,0,0, 0,0,0}
mosaic	arc min	Crystal mosaic (isotropic), gaussian RMS. Puts the crystal in the isotropic mosaic model state, thus disregarding other mosaicity parameters, e.g. 1-10.	3
mosaic_a	arc min	Horizontal (rotation around lattice vector a) mosaic (anisotropic), gaussian RMS. Put the crystal in the anisotropic crystal vector state. I.e. model mosaicity through rotation around the crystal lattice vectors. Has precedence over in-plane mosaic model.	-1
mosaic_b	arc min	Vertical (rotation around lattice vector b) mosaic (anisotropic), gaussian RMS.	-1
mosaic_c	arc min	Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), gaussian RMS	-1

AT (	,	,		) RELATIVE
ROTATED (	,	,		) RELATIVE

McXtrace - An X-ray ray-trace simulation package

The FluoCrystal Component

Identification

Description

Input parameters

Links

The `FluoCrystal` Component