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rayosborn committed Mar 14, 2024
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5 changes: 5 additions & 0 deletions docs/source/index.rst
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NXRefine
========
.. figure:: /images/nxrefine-index-image.png
:align: right
:width: 100%
:figwidth: 40%

Recent advances in synchrotron x-ray instrumentation have enabled the
rapid acquisition of x-ray diffraction data from single crystals,
allowing large contiguous volumes of scattering in reciprocal space to
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19 changes: 9 additions & 10 deletions docs/source/introduction.rst
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:align: center
:width: 80%

*Example of the eperimental geometry used in NXRefine, with the
*Example of the experimental geometry used in NXRefine, with the
Φ-axis horizontal (χ = -90°).*

The sample is at the center of a χ-circle, which can be rotated about
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To transform data collected in this experimental geometry, it is
necessary to determine an orientation matrix using Bragg peaks measured
in the course of the sample rotation. With high-energy x-rays, the area
detector covers reciprocal space volumes that can exceed
10×10×10Å\ :sup:`3`. Depending on the size of the crystal unit cell,
such volumes contain hundreds, if not thousands, of Brillouin Zones.
*NXRefine* has a peak-search algorithm for identifying all the peaks
above a certain intensity threshold, which are then used to generate an
orientation matrix, :math:`\mathcal{U}`, which is refined using the
positions of a large number of Bragg peaks.
detector covers reciprocal space volumes that can exceed 10×10×10Å\
:sup:`-3`. Depending on the size of the crystal unit cell, such volumes
contain hundreds, if not thousands, of Brillouin Zones. *NXRefine* has a
peak-search algorithm for identifying all the peaks above a certain
intensity threshold. These peaks are then used to generate and then
refine an orientation matrix, :math:`\mathcal{U}`.

Each Bragg peak is defined by its coordinates on the detector,
:math:`x_p` and :math:`y_p`, and the goniometer angles :math:`\theta`,
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number of peaks are used to refine both the instrumental and sample
parameters in order to minimize discrepancies between the calculated and
measured peak positions, allowing :math:`\mathcal{U}` to be optimized.
If too few peaks are assigned by the initial peak selection, it is
necessary to select different peaks.
If few peaks are assigned with reasonable accuracy by the selection of
the initial two peaks, it is necessary to select two different peaks.

The refinement process, along with the tools that *NXRefine* provide to
facilitate peak assignments, are described in a later section.
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