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Updated data processing and viz documentation to include examples
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nhorelik
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3 changed files with 96 additions and 12 deletions
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@ -5,11 +5,11 @@ Data Processing and Visualization
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=================================
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This section is intended to explain in detail the recommended procedures for
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carrying out common tasks with OpenMC. While several utilities of varying
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complexity are provided to help automate the process, in many cases it will be
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extremely beneficial to do some coding in Python to quickly obtain results. In
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these cases, and for many of the provided utilities, it is necessary for your
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Python installation to contain:
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carrying out common post-processing tasks with OpenMC. While several utilities
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of varying complexity are provided to help automate the process, in many cases
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it will be extremely beneficial to do some coding in Python to quickly obtain
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results. In these cases, and for many of the provided utilities, it is necessary
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for your Python installation to contain:
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* [1]_ `Numpy <http://www.numpy.org/>`_
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* [1]_ `Scipy <http://www.scipy.org/>`_
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@ -41,6 +41,55 @@ Plotting in 2D
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.. image:: ../_images/atr.png
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:height: 200px
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See below for a simple example of a plots xml file that demonstrates the
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capabilities of 2D slice plots. Here we assume that there is a ``geometry.xml``
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file containing 7 cells.
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.. code-block:: xml
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<?xml version="1.0" encoding="UTF-8"?>
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<plots>
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<plot id="1" type="slice" color="cell" basis="xy">
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<filename> myplot </filename>
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<origin> 0 0 </origin>
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<width> 10 10 </width>
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<pixels> 2000 2000 </pixels>
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<background> 0 0 0 </background>
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<col_spec id="1" rgb="198 226 255"/>
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<col_spec id="2" rgb="255 218 185"/>
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<col_spec id="3" rgb="255 255 255"/>
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<col_spec id="4" rgb="101 101 101"/>
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<col_spec id="7" rgb="123 123 231"/>
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<mask background="255 255 255">
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<components> 1 3 4 5 6 </components>
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</mask>
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</plot>
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</plots>
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In this example, OpenMC will produce a plot named ``myplot.ppm`` when run in
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plotting mode. The picture will be on the xy-plane, depicting the rectangle
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between points (-5,-5) and (5,5) with 2000 pixels along each dimension. The
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color of each pixel is determined by placing a particle at the center of that
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pixel and using OpenMC's internal ``find_cell`` routine (the same one used for
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particle tracking during simulation) to determine the cell and material at that
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location. In this example, pixels are 10/2000=0.005 cm wide, so points will be
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at (-4.9975,-4.9975), (-4.9950,-4.9975), (-4.9925,-4.9975), etc. This is pointed
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out to demonstrate that this plot may miss any features smaller than 0.005 cm,
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since they could exist between pixel centers. More pixels can be used to resolve
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finer features, but could result in larger files.
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The ``background``, ``col_spec``, and ``mask`` elements define how to set pixel
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colors based on the cell ids at each pixel center. In this example, RGB colors
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are specified for cells 1,2,3,4, and 7, a random color will be assigned to cells
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5 and 6, and a black background color (``rgb="0 0 0"``) will be applied to
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locations where no cell is defined. However, the ``mask`` element here says that
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only cells 1,3,4,5, and 6 should be displayed, with other cells taking a white
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color (``rgb="255 255 255"``), which overrides the ``col_spec`` for cell 2 and
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the random color assigned to cell 7.
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After running OpenMC to obtain PPM files, images should be saved to another
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format before using them elsewhere. This cuts down the size of the file by
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orders of magnitude. Most image viewers and editors that can view PPM images
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@ -53,7 +102,7 @@ Ubuntu: ``sudo apt-get install imagemagick``). Images are then converted like:
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.. code-block:: sh
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convert plot.ppm plot.png
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convert myplot.ppm myplot.png
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Plotting in 3D
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--------------
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@ -61,10 +110,37 @@ Plotting in 3D
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.. image:: ../_images/3dgeomplot.png
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:height: 200px
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See below for a simple example of a plots xml file that demonstrates the
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capabilities of 3D voxel plots.
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.. code-block:: xml
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<?xml version="1.0" encoding="UTF-8"?>
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<plots>
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<plot id="1" type="voxel" color="mat">
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<filename> myplot </filename>
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<origin> 0 0 0 </origin>
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<width> 10 10 10 </width>
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<pixels> 500 500 500 </pixels>
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</plot>
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</plots>
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Voxel plots are built the same way 2D slice plots are, by determining the cell
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or material id of a particle at the center of each voxel. In this example, the
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space covered is the cube between the points (-5,-5,-5) and (5,5,5), with voxel
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centers 10/500 = 0.02 cm apart. The binary VOXEL files that are produced do not
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specify any color - instead containing only material or cell ids (material id
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in this example) - and thus the ``background``, ``col_spec``, and ``mask``
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elements are not used. If no cell is found at a voxel center, an id of -1 is
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stored.
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The binary VOXEL files output by OpenMC can not be viewed directly by any
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existing viewers. In order to view them, they must be converted into a standard
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mesh format that can be viewed in ParaView, Visit, etc. The provided utility
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voxel.py accomplishes this for SILO:
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mesh format that can be viewed in ParaView, Visit, etc. This typically will
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compress the size of the file significantly. The provided utility voxel.py
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accomplishes this for SILO:
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.. code-block:: sh
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@ -88,13 +164,21 @@ or
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Users can process the binary into any other format if desired by following the
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example of voxel.py. For the binary file structure, see :ref:`devguide_voxel`.
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Once processed into a standard 3D file format, colors and masks can be defined
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using the stored id numbers to better explore the geometry. The process for
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doing this will depend on the 3D viewer, but should be straightforward.
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.. image:: ../_images/3dba.png
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:height: 200px
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.. note:: 3D voxel plotting can be very computer intensive for the viewing
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program (Visit, Paraview, etc.) if the number of voxels is large (>10
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million or so). Thus if you want an accurate picture that renders
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smoothly, consider using only one voxel in a certain direction. For
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instance, the 3D pin lattice figure above was generated with a
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500x500x1 voxel mesh, which allows for resolution of the cylinders
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without wasting too many voxels on the axial dimension.
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instance, the 3D pin lattice figure at the beginning of this section
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was generated with a 500x500x1 voxel mesh, which allows for resolution
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of the cylinders without wasting too many voxels on the axial
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dimension.
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-------------------
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