Merge branch 'source_interval' into read_sourcefile

.gitignore

@@ -29,3 +29,6 @@ src/templates/*.f90
 
 # Test results error file
 results_error.dat
+
+# HDF5 files
+*.h5

data/get_nndc_data.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import os
+import shutil
+import subprocess
+import sys
+import tarfile
+
+try:
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen
+
+baseUrl = 'http://www.nndc.bnl.gov/endf/b7.1/aceFiles/'
+files = ['ENDF-B-VII.1-neutron-293.6K.tar.gz',
+         'ENDF-B-VII.1-neutron-300K.tar.gz',
+         'ENDF-B-VII.1-neutron-900K.tar.gz',
+         'ENDF-B-VII.1-neutron-1500K.tar.gz',
+         'ENDF-B-VII.1-tsl.tar.gz']
+block_size = 16384
+
+# ==============================================================================
+# DOWNLOAD FILES FROM NNDC SITE
+
+filesComplete = []
+for f in files:
+    # Establish connection to URL
+    url = baseUrl + f
+    req = urlopen(url)
+
+    # Get file size from header
+    file_size = int(req.info().getheaders('Content-Length')[0])
+    downloaded = 0
+
+    # Check if file already downloaded
+    if os.path.exists(f):
+        if os.path.getsize(f) == file_size:
+            print('Skipping ' + f)
+            filesComplete.append(f)
+            continue
+        else:
+            if sys.version_info[0] < 3:
+                overwrite = raw_input('Overwrite {0}? ([y]/n) '.format(f))
+            else:
+                overwrite = input('Overwrite {0}? ([y]/n) '.format(f))
+            if overwrite.lower().startswith('n'):
+                continue
+
+    # Copy file to disk
+    print('Downloading {0}... '.format(f), end='')
+    with open(f, 'wb') as fh:
+        while True:
+            chunk = req.read(block_size)
+            if not chunk: break
+            fh.write(chunk)
+            downloaded += len(chunk)
+            status = '{0:10}  [{1:3.2f}%]'.format(downloaded, downloaded * 100. / file_size)
+            print(status + chr(8)*len(status), end='')
+        print('')
+        filesComplete.append(f)
+
+# ==============================================================================
+# EXTRACT FILES FROM TGZ
+
+for f in files:
+    if not f in filesComplete:
+        continue
+
+    # Extract files
+    suffix = f[f.rindex('-') + 1:].rstrip('.tar.gz')
+    with tarfile.open(f, 'r') as tgz:
+        print('Extracting {0}...'.format(f))
+        tgz.extractall(path='nndc/' + suffix)
+
+# ==============================================================================
+# COPY CROSS_SECTIONS.XML
+
+print('Copying cross_sections_nndc.xml...')
+shutil.copyfile('cross_sections_nndc.xml', 'nndc/cross_sections.xml')
+
+# ==============================================================================
+# PROMPT USER TO DELETE .TAR.GZ FILES
+
+# Ask user to delete
+if sys.version_info[0] < 3:
+    response = raw_input('Delete *.tar.gz files? ([y]/n) ')
+else:
+    response = input('Delete *.tar.gz files? ([y]/n) ')
+
+# Delete files if requested
+if not response or response.lower().startswith('y'):
+    for f in files:
+        if os.path.exists(f):
+            print('Removing {0}...'.format(f))
+            os.remove(f)

data/readme.rst

@@ -15,6 +15,9 @@ work with a few common cross section sources.
 - **cross_sections_ascii.xml** -- This file matches ENDF/B-VII.0 cross sections
     distributed with MCNP5 / MCNP6 beta.
 
+- **cross_sections_nndc.xml** -- This file matches ENDF/B-VII.1 cross sections
+    distributed from the `NNDC website`_.
+
 - **cross_sections_serpent.xml** -- This file matches ENDF/B-VII.0 cross
     sections distributed with Serpent 1.1.7.
 
@@ -31,3 +34,4 @@ element in your settings.xml, or set the CROSS_SECTIONS environment variable to
 the full path of the cross_sections.xml file.
 
 .. _user's guide: http://mit-crpg.github.io/openmc/usersguide/install.html#cross-section-configuration
+.. _NNDC website: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html

docs/source/usersguide/input.rst

@@ -348,8 +348,10 @@ attributes/sub-elements:
 
 The ``<state_point>`` element indicates at what batches a state point file
 should be written. A state point file can be used to restart a run or to get
-tally results at any batch. This element has the following
-attributes/sub-elements:
+tally results at any batch. The default behavior when using this tag is to 
+write out the source bank in the state_point file. This behavior can be 
+customized by using the ``<source_point>`` element. This element has the
+following attributes/sub-elements:
 
   :batches:
     A list of integers separated by spaces indicating at what batches a state
@@ -364,19 +366,52 @@ attributes/sub-elements:
 
     *Default*: None
 
+``<source_point>`` Element
+--------------------------
+
+The ``<source_point>`` element indicates at what batches the source bank 
+should be written. The source bank can be either written out within a state  
+point file or separately in a source point file. This element has the following
+attributes/sub-elements:
+
+  :batches:
+    A list of integers separated by spaces indicating at what batches a state
+    point file should be written. It should be noted that if source_separate
+    tag is not set to "true", this list must be a subset of state point batches.
+
+    *Default*: Last batch only
+
+  :interval:
+    A single integer :math:`n` indicating that a state point should be written
+    every :math:`n` batches. This option can be given in lieu of listing
+    batches explicitly. It should be noted that if source_separate tag is not
+    set to "true", this value should produce a list of batches that is a subset
+    of state point batches.
+
+    *Default*: None
+
   :source_separate:
-    If this element is set to "true", a separate binary source file will be
+    If this element is set to "true", a separate binary source point file will be
     written. Otherwise, the source sites will be written in the state point
     directly.
 
     *Default*: false
 
-  :source_write: If this element is set to "false", source sites are not written
-    to the state point file. This can substantially reduce the size of state
-    points if large numbers of particles per batch are used.
+  :source_write:
+    If this element is set to "false", source sites are not written
+    to the state point or source point file. This can substantially reduce the 
+    size of state points if large numbers of particles per batch are used.
 
     *Default*: true
 
+  :overwrite_latest:
+    If this element is set to "true", a source point file containing
+    the source bank will be written out to a separate file named 
+    ``source.binary`` or ``source.h5`` depending on if HDF5 is enabled. 
+    This file will be overwritten at every single batch so that the latest
+    source bank will be available. It should be noted that a user can set both 
+    this element to "true" and specify batches to write a permanent source bank.
+
 ``<survival_biasing>`` Element
 ------------------------------
 

docs/source/usersguide/install.rst

@@ -264,10 +264,27 @@ Cross Section Configuration
 
 In order to run a simulation with OpenMC, you will need cross section data for
 each nuclide in your problem. Since OpenMC uses ACE format cross sections, you
-can use nuclear data that was processed with NJOY, such as that distributed with
-MCNP_ or Serpent_. The TALYS-based evaluated nuclear data library, TENDL_, is
+can use nuclear data that was processed with NJOY_, such as that distributed
+with MCNP_ or Serpent_. Several sources provide free processed ACE data as
+described below. The TALYS-based evaluated nuclear data library, TENDL_, is also
 openly available in ACE format.
 
+Using ENDF/B-VII.1 Cross Sections from NNDC
+-------------------------------------------
+
+The NNDC_ provides ACE data from the ENDF/B-VII.1 neutron and thermal scattering
+sublibraries at four temperatures processed using NJOY_. To use this data with
+OpenMC, a script is provided with OpenMC that will automatically download,
+extract, and set up a confiuration file:
+
+.. code-block:: sh
+
+    cd openmc/data
+    python get_nndc_data.py
+
+At this point, you should set the :envvar:`CROSS_SECTIONS` environment variable
+to the absolute path of the file ``openmc/data/nndc/cross_sections.xml``.
+
 Using JEFF Cross Sections from OECD/NEA
 ---------------------------------------
 
@@ -314,6 +331,8 @@ distribution to the location of the Serpent cross sections. Then, either set the
 environment variable to the absolute path of the ``cross_sections_serpent.xml``
 file.
 
+.. _NJOY: http://t2.lanl.gov/nis/codes.shtml
+.. _NNDC: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
 .. _NEA: http://www.oecd-nea.org
 .. _JEFF: http://www.oecd-nea.org/dbdata/jeff/
 .. _here: http://www.oecd-nea.org/dbdata/pubs/jeff312-cd.html

docs/source/usersguide/processing.rst

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

tests/cleanup.bash

@@ -0,0 +1,14 @@
+# This simple script ensures that all binary
+# output files have been deleted in all the
+# folders. This can occur if a previous error
+# occurred and the test suite was rerun without
+# deleting left over binary files. This will
+# cause an assertion error in some of the 
+# tests.
+for i in ./*; do
+  if [ -d "$i" ]; then
+    cd $i
+    rm -f *.binary *.h5
+    cd ..
+  fi
+done

tests/test_sourcepoint_latest/results_test.dat

@@ -1,2 +0,0 @@
-k-combined:
-3.011353E-01 2.854556E-03

tests/test_sourcepoint_latest/results_true.dat

@@ -1,3 +1,2 @@
 k-combined:
-0.000000E+00 0.000000E+00
--9.438655E-02 -4.436810E+00 -2.416825E+00 
+3.011353E-01 2.854556E-03

tests/test_sourcepoint_restart/results.py

@@ -11,7 +11,7 @@ import statepoint
 if len(sys.argv) > 1:
     sp = statepoint.StatePoint(sys.argv[1])
 else:
-    sp = statepoint.StatePoint('statepoint.7.binary')
+    sp = statepoint.StatePoint('statepoint.10.binary')
 sp.read_results()
 
 # extract tally results and convert to vector

tests/test_sourcepoint_restart/settings.xml

@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <settings>
 
-  <state_point batches="7" />
-  <source_point source_separate="true" />
+  <state_point batches="7 10" />
+  <source_point batches="7" source_separate="true" />
 
   <eigenvalue>
     <batches>10</batches>

tests/test_sourcepoint_restart/test_sourcepoint_restart.py

@@ -24,49 +24,49 @@ def test_run():
     assert returncode == 0
 
 def test_created_statepoint():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
-    assert len(statepoint) == 1
+    statepoint = glob.glob(pwd + '/statepoint.*')
+    assert len(statepoint) == 2
     assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
     sourcepoint = glob.glob(pwd + '/source.7.*')
     assert len(sourcepoint) == 1
     assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5')
 
 def test_results():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     call(['python', 'results.py', statepoint[0]])
     compare = filecmp.cmp('results_test.dat', 'results_true.dat')
     if not compare:
       os.rename('results_test.dat', 'results_error.dat')
     assert compare
+    os.remove(statepoint[0])
 
 def test_restart_form1():
     statepoint = glob.glob(pwd + '/statepoint.7.*')
+    sourcepoint = glob.glob(pwd + '/source.7.*')
     openmc_path = pwd + '/../../src/openmc'
     if int(NoseMPI.mpi_np) > 0:
         proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path, 
-                      '-r', statepoint[0]],
+                      '-r', statepoint[0], sourcepoint[0]],
                stderr=STDOUT, stdout=PIPE)
     else:
-        proc = Popen([openmc_path, '-r', statepoint[0]], stderr=STDOUT, stdout=PIPE)
+        proc = Popen([openmc_path, '-r', statepoint[0], sourcepoint[0]], stderr=STDOUT, stdout=PIPE)
     print(proc.communicate()[0])
     returncode = proc.returncode
     assert returncode == 0
 
 def test_created_statepoint_form1():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     assert len(statepoint) == 1
     assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
-    sourcepoint = glob.glob(pwd + '/source.7.*')
-    assert len(sourcepoint) == 1
-    assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5')
 
 def test_results_form1():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     call(['python', 'results.py', statepoint[0]])
     compare = filecmp.cmp('results_test.dat', 'results_true.dat')
     if not compare:
       os.rename('results_test.dat', 'results_error.dat')
     assert compare
+    os.remove(statepoint[0])
 
 def test_restart_form2():
     statepoint = glob.glob(pwd + '/statepoint.7.*')
@@ -74,50 +74,46 @@ def test_restart_form2():
     openmc_path = pwd + '/../../src/openmc'
     if int(NoseMPI.mpi_np) > 0:
         proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path, 
-                      '--restart', statepoint[0], source[0]],
+                      '--restart', statepoint[0], sourcepoint[0]],
                stderr=STDOUT, stdout=PIPE)
     else:
-        proc = Popen([openmc_path, '--restart', statepoint[0]], 
+        proc = Popen([openmc_path, '--restart', statepoint[0], sourcepoint[0]],
                      stderr=STDOUT, stdout=PIPE)
     print(proc.communicate()[0])
     returncode = proc.returncode
     assert returncode == 0
 
 def test_created_statepoint_form2():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     assert len(statepoint) == 1
     assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
-    sourcepoint = glob.glob(pwd + '/source.7.*')
-    assert len(sourcepoint) == 1
-    assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5')
 
 def test_results_form2():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     call(['python', 'results.py', statepoint[0]])
     compare = filecmp.cmp('results_test.dat', 'results_true.dat')
     if not compare:
       os.rename('results_test.dat', 'results_error.dat')
     assert compare
+    os.remove(statepoint[0])
 
 def test_restart_serial():
     statepoint = glob.glob(pwd + '/statepoint.7.*')
+    sourcepoint = glob.glob(pwd + '/source.7.*')
     openmc_path = pwd + '/../../src/openmc'
-    proc = Popen([openmc_path, '--restart', statepoint[0]], 
+    proc = Popen([openmc_path, '--restart', statepoint[0], sourcepoint[0]], 
                  stderr=STDOUT, stdout=PIPE)
     print(proc.communicate()[0])
     returncode = proc.returncode
     assert returncode == 0
 
 def test_created_statepoint_serial():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     assert len(statepoint) == 1
     assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
-    sourcepoint = glob.glob(pwd + '/source.7.*')
-    assert len(sourcepoint) == 1
-    assert sourcepoint[0].endswith('binary') or sourcepoint[0].endswith('h5')
 
 def test_results_serial():
-    statepoint = glob.glob(pwd + '/statepoint.7.*')
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
     call(['python', 'results.py', statepoint[0]])
     compare = filecmp.cmp('results_test.dat', 'results_true.dat')
     if not compare:
@@ -125,8 +121,8 @@ def test_results_serial():
     assert compare
 
 def teardown():
-    output = glob.glob(pwd + '/statepoint.7.*')
-    output += glob.glob(pwd + '/sourcepoint.7.*')
+    output = glob.glob(pwd + '/statepoint.*')
+    output += glob.glob(pwd + '/source.*')
     output.append(pwd + '/results_test.dat')
     for f in output:
         if os.path.exists(f):