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Merge remote-tracking branch 'upstream/develop' into python-api

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Will Boyd 2015-03-19 11:40:56 -04:00
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docs/source/usersguide/processing.rst
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@ -22,7 +22,7 @@ Most of these are easily obtainable in Ubuntu through the package manager, or
are easily installed with distutils.
.. [1] Required for tally data extraction from statepoints with statepoint.py
.. [2] Required only if reading HDF5 statepoint files.
.. [2] Required only if reading HDF5 statepoint files.
.. [3] Optional for plotting utilities
----------------------
@ -265,18 +265,18 @@ two heatmaps in the previous figure.
.. code-block:: python
#!/usr/bin/env python
import os
import statepoint
# load and parse the statepoint file
sp = statepoint.StatePoint('statepoint.300.binary')
sp.read_results()
tallyid = 0 # This is tally 1
score = 0 # This corresponds to flux (see tally.scores)
# get mesh dimensions
meshid = sp.tallies[tallyid].filters['mesh'].bins[0]
for i,m in enumerate(sp.meshes):
@ -299,7 +299,7 @@ two heatmaps in the previous figure.
[('mesh',(x,y,z)),('energyin',1)],
score)
fast[(x,y,z)] = val
# sum up the axial values and write datafile for gnuplot
with open('meshdata.dat','w') as fh:
for x in range(1,nx+1):
@ -336,7 +336,7 @@ Plotting in 3D
As with 3D plots of the geometry, meshtally data needs to be put into a standard
format for viewing. The utility statepoint_3d.py is provided to accomplish this
for both VTK and SILO. By default statepoint_3d.py processes a statepoint into a
3D file with all mesh tallies and filter/score combinations,
3D file with all mesh tallies and filter/score combinations,
.. code-block:: sh
@ -348,8 +348,8 @@ certain data arrays in order to keep file sizes down.
.. code-block:: sh
<openmc_root>/src/utils/statepoint_3d.py <statepoint_file> --tallies 2,4 --scores 4.1,4.3 -o output.silo
<openmc_root>/src/utils/statepoint_3d.py <statepoint_file> --filters 2.energyin.1 --vtk -o output.vtm
statepoint_3d.py <statepoint_file> --tallies 2,4 --scores 4.1,4.3 -o output.silo
statepoint_3d.py <statepoint_file> --filters 2.energyin.1 --vtk -o output.vtm
All available options for specifying a subset of tallies, scores, and filters
can be listed with the ``--list`` or ``-l`` command line options.
@ -358,7 +358,7 @@ can be listed with the ``--list`` or ``-l`` command line options.
VTK needs to use a multi-block dataset, which stores each mesh piece
in a different file in a subfolder. All meshes can be loaded at once
with the main VTM file, or each VTI file in the subfolder can be
loaded individually.
loaded individually.
Alternatively, the user can write their own Python script to manipulate the data
appropriately before insertion into a SILO or VTK file. For instance, if the
@ -396,7 +396,7 @@ and the equivalent VTK file with:
grid.SetOrigin(*mesh.lower_left)
grid.SetSpacing(*mesh.width)
# vtk cell arrays have x on the inners, so we need to reorder the data
# vtk cell arrays have x on the inners, so we need to reorder the data
idata = {}
for x in range(nx):
for y in range(ny):
@ -416,7 +416,7 @@ and the equivalent VTK file with:
grid.GetCellData().AddArray(vtkfastdata)
grid.GetCellData().AddArray(vtkthermaldata)
writer = vtk.vtkXMLImageDataWriter()
writer.SetInput(grid)
writer.SetFileName('tally.vti')
@ -486,16 +486,16 @@ example of an interactive ipython session using the statepoint.py Python module:
.. code-block:: python
In [1]: import statepoint
In [2]: sp = statepoint.StatePoint('statepoint.100.h5')
In [3]: sp.read_source()
In [4]: len(sp.source)
Out[4]: 1000
In [5]: sp.source[0:10]
Out[5]:
Out[5]:
[<SourceSite: xyz=[ 2.21980946 -8.92686048 87.93720485] at E=0.932923263566>,
<SourceSite: xyz=[ 2.21980946 -8.92686048 87.93720485] at E=0.349240220512>,
<SourceSite: xyz=[-31.21542213 -30.26762771 72.10845757] at E=3.75843584486>,
@ -506,17 +506,17 @@ example of an interactive ipython session using the statepoint.py Python module:
<SourceSite: xyz=[ -32.80427668 -15.49316628 125.26301151] at E=1.61907104162>,
<SourceSite: xyz=[ 53.20376026 -15.38643708 120.58071044] at E=3.33962024907>,
<SourceSite: xyz=[ 53.20376026 -15.38643708 120.58071044] at E=1.90185680329>]
In [6]: site = sp.source[0]
In [7]: site.weight
Out[7]: 1.0
In [8]: site.xyz
Out[8]: array([ 2.21980946, -8.92686048, 87.93720485])
In [9]: site.uvw
Out[9]: array([ 0.06740523, 0.50612814, 0.85982024])
In [10]: site.E
Out[10]: 0.93292326356564159