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Ray tracing in x-ray regime, primarily meant for modeling synchrotron beamlines and beamline elements

Project Description

Package xrt (XRayTracer) is a python software library for ray tracing in
x-ray regime. It is primarily meant for modeling synchrotron beamlines and
beamline elements.

Why another ray tracing program?

Indeed, there are several good programs for ray tracing, like `Shadow`, `Ray`,
`McXtrace`. These have been extremely useful in modeling synchrotron beamlines
and/or individual beamline components. However, they all have the following

* Limited graphical output, where the images are composed of dots representing
individual rays. A color map, if ever implemented, can encode a physical
property *not* weighted with intensity (unless it is intensity itself).

* The choice of surface shapes is very limited. Closed shapes, like wave-guides
or capillaries, are not possible.

* Multiple reflections at a single surface, as it happens in a multi-bounce
capillary, are not possible.

* Non-sequential optical elements, as poly-capillaries or multi-mirror arrays,
are not possible.

* There are many restrictive limitations on energy range and energy mesh
points, spatial mesh size etc.

* The execution cannot be parallelized (except may be in `McXtrace`).

The above issues are resolved in xrt.

Features of xrt

* *Publication quality graphics*. 1D and 2D position histograms are
*simultaneously* coded by hue and brightness. Typically, colors represent
energy and brightness represents beam intensity. The user may select other
quantities to be encoded by colors: angular and positional distributions,
various polarization properties, beam categories, number of reflections,
incidence angle etc. Brightness can also encode partial flux for a selected
polarization and incident or absorbed power. Publication quality plots are
provided by `matplotlib` with image formats PNG, PostScript, PDF, SVG.

* *Unlimited number of rays*. The colored histograms are *cumulative*. The
accumulation can be stopped and resumed.

* *Parallel execution*. xrt can be run in parallel in several
threads or processes (can be opted), which accelerates the execution on
multi-core computers. It can run on an external server (supercomputer), also
without X window system (X11) support.

* *Scripting in Python*. xrt can be run within Python scripts to generate a
series of images under changing geometrical or physical parameters. The image
brightness and 1D histograms can be normalized to the global maximum
throughout the series.

* *Sources*. xrt can have several light sources. For example, an ID beamline
has 3 sources: one ID and two BM. This feature allows exploring the influence
of out-of-focus sources.

* Synchrotron sources. Bending magnet, wiggler,
undulator and elliptic undulator are calculated internally within xrt. There
is also a legacy approach to sampling synchrotron sources using the codes
`ws` and `urgent` which are parts of XOP package. Please look the section
`Comparison of synchrotron source codes` for the comparison between the
implementations. If the photon source is one of the synchrotron sources, the
total flux in the beam is reported not just in number of rays but in physical
units of ph/s. The total power or absorbed power can be opted instead of flux
and is reported in W. The power density can be visualized by isolines.
Tapering of the magnetic gap has been added (0.9.2). Undulators can now be
calculated on GPU, with a high gain in computation speed (0.9.2).

* *Shapes*. There are several predefined shapes of optical elements implemented
as python classes. The inheritance mechanism simplifies creation of other
shapes. The user specifies methods for the surface and the surface normal.
For asymmetric crystals, the normal to the atomic planes can be additionally
given. The surface and the normals are defined either in local (x, y)
coordinates or in user-defined parametric coordinates. Parametric
representation enables closed shapes like capillaries. The methods of finding
the intersections of rays with the surface are very robust and can cope with
pathological cases like sharp surface kinks. Any surface can be combined with
a (differently and variably oriented) crystal structure and/or (variable)
grating vector. Surfaces can be faceted.

* *Energy dispersive elements*. Implemented are crystals in dynamical
gratings (so far, without efficiency calculations), Fresnel zone plates and
Bragg-Fresnel optics. Crystals can work in Bragg or Laue cases, in reflection
or in transmission. The two-field polarization phenomena are fully preserved,
also within the Darwin diffraction plateau, thus enabling the ray tracing of
crystal-based phase retarders. As compared to XOP/Shadow, xrt works correctly
for asymmetric crystals in transmission regime.

* *Materials*. The material properties are incorporated using three
different tabulations of the
scattering factors, with differently wide and differently dense energy
meshes. Refraction index and absorption coefficient are calculated from the
scattering factors. Two-surface bodies, like plates or refractive lenses,
are treated with both refraction and absorption.

* *Multiple reflections*. xrt can trace multiple reflections in a single
optical element. This is useful, for example in 'whispering gallery' optics
or in Montel or Wolter mirrors. Here, very handy is the histogramming over
the number of reflections, incidence angle and elevation over the surface.

* *Non-sequential optics*. xrt can trace non-sequential optics where different
parts of the incoming beam meet different surfaces. Examples of such optics
are poly-capillaries and Wolter mirrors.

* *Global coordinate system*. The optical elements are positioned in a global
coordinate system. This is convenient for modeling a real synchrotron
beamline. The coordinates in this system can be directly taken from a CAD
library. The optical surfaces are defined in local systems for the user's

* *Beam categories*. xrt discriminates rays by several categories: `good`,
`out`, `over` and `dead`. This distinction simplifies the adjustment of
entrance and exit slits. An alarm is triggered if the fraction of dead rays
exceeds a specified level.

* *Portability*. xrt runs on Windows and Unix-like platforms, wherever you can
run python.

* *Examples*. xrt comes with many examples; see the gallery.

The histogramming is done by means of `numpy`; `matplotlib` is used
for plotting. If you use calculations on GPU (so far, only for calculating
undulators), you need AMD/NVIDIA drivers, Intel SDK for OpenCL, a CPU only
OpenCL runtime, pytools and pyopencl.

Python 3
The code can be fully automatically converted to Python 3 with ``2to3`` at its
default options.

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