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fixes for sphinx doc
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@PrometheusPi
PrometheusPi committed Jul 16, 2020
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53 changes: 27 additions & 26 deletions docs/source/usage/plugins/xrayScattering.rst
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Expand Up @@ -56,16 +56,16 @@ The orientation can be then fine adjusted with the `RotationParam` setting.
.. TODO: Add other parameters after the coordinate transform has been fixed and the settings have been moved back to the .param file.
================ ===============================================================================================================================
================= ===============================================================================================================================
Setting Description
================ ===============================================================================================================================
================= ===============================================================================================================================
``ProbingSide`` The side from which the x-ray is propagated.
Set `X`, `Y` or `Z` for propagation along one of the PIC coordinate system axes;
`XR`, `YR` or `ZR` for propagation in an opposite direction.

``RotationParam`` Rotation of the beam axis, :math:`z_{\text{beam}}`, from the default orientation ( perpendicular the the simulation box side ).
Set the beam yaw and pitch angles in radians.
================ ===============================================================================================================================
================= ===============================================================================================================================

.. TODO: Add BEAM_OFFSET in between after the coordinate transform has been fixed.
Expand All @@ -78,36 +78,36 @@ rotation to one of the default orientations (``ProbingSide`` setting), additiona

For a specific (charged) species ``<species>`` e.g. ``e``, the scattering can be computed by the following commands.

========================================= ============================================================================================================================================
Command line option Description
========================================= ============================================================================================================================================
``--<species>_xrayScattering.period`` Period at which the plugin is enabled (PIC period syntax). Only the intensity from this steps is accumulated.
Default is `0`, which means that the scattering intensity in never calculated and therefor off.

``--<species>_xrayScattering.outputPeriod`` Period at which the accumulated amplitude is written to the output file (PIC period syntax). Usually set close to the x-ray coherence time.

``--<species>_xrayScattering.qx_max`` Upper bound of reciprocal space range in qx direction. The unit is :math:`Å^{-1}`. Default is `5`.
============================================ ============================================================================================================================================
Command line option Description
============================================ ============================================================================================================================================
``--<species>_xrayScattering.period`` Period at which the plugin is enabled (PIC period syntax). Only the intensity from this steps is accumulated.
Default is `0`, which means that the scattering intensity in never calculated and therefor off

``--<species>_xrayScattering.qy_max`` Upper bound of reciprocal space range in qy direction. The unit is :math:`Å^{-1}` Default is `5`.

``--<species>_xrayScattering.qx_min`` Lower bound of reciprocal space range in qx direction. The unit is :math:`Å^{-1}` Default is `-5`.

``--<species>_xrayScattering.qy_min`` Lower bound of reciprocal space range in qy direction. The unit is :math:`Å^{-1}` Default is `-5`.
``--<species>_xrayScattering.outputPeriod`` Period at which the accumulated amplitude is written to the output file (PIC period syntax). Usually set close to the x-ray coherence time.

``--<species>_xrayScattering.n_qx`` Number of scattering vectors needed to be calculated in qx direction. Default is `100`,
``--<species>_xrayScattering.qx_max`` Upper bound of reciprocal space range in qx direction. The unit is :math:`Å^{-1}`. Default is `5`.

``--<species>_xrayScattering.n_qy`` Number of scattering vectors needed to be calculated in qy direction. Default is '100'.
``--<species>_xrayScattering.qy_max`` Upper bound of reciprocal space range in qy direction. The unit is :math:`Å^{-1}` Default is `5`.

``--<species>_xrayScattering.file`` Output file name. Default is `<species>_xrayScatteringOutput`.
``--<species>_xrayScattering.qx_min`` Lower bound of reciprocal space range in qx direction. The unit is :math:`Å^{-1}` Default is `-5`.

``--<species>_xrayScattering.ext`` `openPMD` filename extension. This controls the backend picked by the `openPMD` API. Default is `bp` for adios backend.
``--<species>_xrayScattering.qy_min`` Lower bound of reciprocal space range in qy direction. The unit is :math:`Å^{-1}` Default is `-5`.

``--<species>_xrayScattering.compression`` Backend-specific `openPMD` compression method (e.g.) zlib.
``--<species>_xrayScattering.n_qx`` Number of scattering vectors needed to be calculated in qx direction. Default is `100`,

``--<species>_xrayScattering.memoryLayout`` Possible values: `mirror` and `split`. Output can be mirrored on all Host+Device pairs or uniformly split, in chunks, over all nodes.
Use split when the output array is too big to store the complete computed q-space on one device.
For small output grids the `mirror` setting could turn out to be more efficient.
========================================= ============================================================================================================================================
``--<species>_xrayScattering.n_qy`` Number of scattering vectors needed to be calculated in qy direction. Default is '100'.

``--<species>_xrayScattering.file`` Output file name. Default is `<species>_xrayScatteringOutput`.

``--<species>_xrayScattering.ext`` `openPMD` filename extension. This controls the backend picked by the `openPMD` API. Default is `bp` for adios backend.

``--<species>_xrayScattering.compression`` Backend-specific `openPMD` compression method (e.g.) zlib.

``--<species>_xrayScattering.memoryLayout`` Possible values: `mirror` and `split`. Output can be mirrored on all Host+Device pairs or uniformly split, in chunks, over all nodes.
Use split when the output array is too big to store the complete computed q-space on one device.
For small output grids the `mirror` setting could turn out to be more efficient.
============================================ ============================================================================================================================================


Output
Expand All @@ -131,6 +131,7 @@ When you don't want to use the python reader keep in mind that:
* All iterations are saved in a single file
* The mesh containing the output is called `'amplitude'`
* This mesh has 2 components, `'x'` is the real part and `'y'` is the imaginary part.

.. note::
The amplitude is not zeroed on ``outputPeriod`` so one has to subtract the output from the iteration one period before and then calculate :math:`\left|\Phi\right|^2` and sum it with the intensities from other coherence periods.

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