Merge commit 'upstream/develop' into res_scat

.gitignore

@@ -19,6 +19,7 @@ src/openmc
 
 # Documentation builds
 docs/build
+docs/source/_images/*.pdf
 
 # xml-fortran reader
 src/xml-fortran/xmlreader
@@ -28,3 +29,6 @@ src/templates/*.f90
 
 # Test results error file
 results_error.dat
+
+# HDF5 files
+*.h5

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2011-2013 Massachusetts Institute of Technology
+Copyright (c) 2011-2014 Massachusetts Institute of Technology
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

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/Makefile

@@ -6,13 +6,19 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
+IMAGEDIR      = source/_images
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
 ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+# SVG to PDF conversion
+SVG2PDF = inkscape
+PDFS    = $(patsubst %.svg,%.pdf,$(wildcard $(IMAGEDIR)/*.svg))
+
+
+.PHONY: help images clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
@@ -33,8 +39,16 @@ help:
 	@echo "  linkcheck  to check all external links for integrity"
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
+# Pattern rule for converting SVG to PDF
+%.pdf: %.svg
+	$(SVG2PDF) -f $< -A $@
+
+# Rule to build PDFs
+images: $(PDFS)
+
 clean:
 	-rm -rf $(BUILDDIR)/*
+	-rm $(PDFS)
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@@ -91,14 +105,14 @@ epub:
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
-latex:
+latex: images
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
 	@echo "Run \`make' in that directory to run these through (pdf)latex" \
 	      "(use \`make latexpdf' here to do that automatically)."
 
-latexpdf:
+latexpdf: images
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through pdflatex..."
 	make -C $(BUILDDIR)/latex all-pdf

docs/source/conf.py

@@ -39,7 +39,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'OpenMC'
-copyright = u'2011-2013, Massachusetts Institute of Technology'
+copyright = u'2011-2014, Massachusetts Institute of Technology'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -121,7 +121,7 @@ html_title = "OpenMC Documentation"
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = '../img/openmc.png'
+html_logo = '_images/openmc.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -188,6 +188,8 @@ latex_documents = [
    u'Massachusetts Institute of Technology', 'manual'),
 ]
 
+latex_elements = {'preamble': '\\usepackage{enumitem}\\setlistdepth{9}'}
+
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
 #latex_logo = None

docs/source/devguide/workflow.rst

@@ -60,7 +60,7 @@ features and bug fixes. The general steps for contributing are as follows:
    repository with the same name under your personal account. As such, you can
    commit to it as you please without disrupting other developers.
 
-   .. image:: ../../img/fork.png
+   .. image:: ../_images/fork.png
 
 2. Clone your fork of OpenMC and create a branch that branches off of *develop*:
 
@@ -77,7 +77,7 @@ features and bug fixes. The general steps for contributing are as follows:
 4. Issue a pull request from GitHub and select the *develop* branch of
    mit-crpg/openmc as the target.
 
-   .. image:: ../../img/pullrequest.png
+   .. image:: ../_images/pullrequest.png
 
    At a minimum, you should describe what the changes you've made are and why
    you are making them. If the changes are related to an oustanding issue, make

docs/source/license.rst

@@ -4,7 +4,7 @@
 License Agreement
 =================
 
-Copyright © 2011-2013 Massachusetts Institute of Technology
+Copyright © 2011-2014 Massachusetts Institute of Technology
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

docs/source/methods/cross_sections.rst

@@ -80,7 +80,7 @@ dashed box would need to be stored on a per-nuclide basis, and the union grid
 would need to be stored once. This method is also referred to as *double
 indexing* and is available as an option in Serpent (see paper by Leppanen_).
 
-.. figure:: ../../img/uniongrid.svg
+.. figure:: ../_images/uniongrid.*
     :width: 600px
     :align: center
     :figclass: align-center

docs/source/methods/eigenvalue.rst

@@ -108,6 +108,40 @@ at plots of :math:`k_{eff}` and the Shannon entropy. A number of methods have
 been proposed (see e.g. [Romano]_, [Ueki]_), but each of these is not without
 problems.
 
+---------------------------
+Uniform Fission Site Method
+---------------------------
+
+Generally speaking, the variance of a Monte Carlo tally will be inversely
+proportional to the number of events that score to the tally. In a reactor
+problem, this implies that regions with low relative power density will have
+higher variance that regions with high relative power density. One method to
+circumvent the uneven distribution of relative errors is the uniform fission
+site (UFS) method introduced by [Sutton]_. In this method, the portion of the
+problem containing fissionable material is subdivided into a number of cells
+(typically using a structured mesh). Rather than producing
+
+.. math::
+
+    m = \frac{w}{k} \frac{\nu\Sigma_f}{\Sigma_t}
+
+fission sites at each collision where :math:`w` is the weight of the neutron,
+:math:`k` is the previous-generation estimate of the neutron multiplication
+factor, :math:`\nu\Sigma_f` is the neutron production cross section, and
+:math:`\Sigma_t` is the total cross section, in the UFS method we produce
+
+.. math::
+
+    m_{UFS} = \frac{w}{k} \frac{\nu\Sigma_f}{\Sigma_t} \frac{v_i}{s_i}
+
+fission sites at each collision where :math:`v_i` is the fraction of the total
+volume occupied by cell :math:`i` and :math:`s_i` is the fraction of the fission
+source contained in cell :math:`i`. To ensure that no bias is introduced, the
+weight of each fission site stored in the fission bank is :math:`s_i/v_i` rather
+than unity. By ensuring that the expected number of fission sites in each mesh
+cell is constant, the collision density across all cells, and hence the variance
+of tallies, is more uniform than it would be otherwise.
+
 .. _Shannon entropy: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-06-3737_entropy.pdf
 
 .. [Lieberoth] J. Lieberoth, "A Monte Carlo Technique to Solve the Static
@@ -119,5 +153,9 @@ problems.
    *Proc. International Conference on Mathematics, Computational Methods, and
    Reactor Physics*, Saratoga Springs, New York (2009).
 
+.. [Sutton] Daniel J. Kelly, Thomas M. Sutton, and Stephen C. Wilson, "MC21
+   Analysis of the Nuclear Energy Agency Monte Carlo Performance Benchmark
+   Problem," *Proc. PHYSOR 2012*, Knoxville, Tennessee, Apr. 15--20 (2012).
+
 .. [Ueki] Taro Ueki, "On-the-Fly Judgments of Monte Carlo Fission Source
    Convergence," *Trans. Am. Nucl. Soc.*, **98**, 512 (2008).

docs/source/methods/geometry.rst

@@ -45,7 +45,7 @@ surface by a combination of the unique ID of the surface and a positive/negative
 sign. The following illustration shows an example of an ellipse with unique ID 1
 dividing space into two half-spaces.
 
-.. figure:: ../../img/halfspace.svg
+.. figure:: ../_images/halfspace.*
    :align: center
    :figclass: align-center
 
@@ -60,7 +60,7 @@ half-space references whose intersection defines the region. The region is then
 assigned a material defined elsewhere. The following illustration shows an
 example of a cell defined as the intersection of an ellipse and two planes.
    
-.. figure:: ../../img/union.svg
+.. figure:: ../_images/union.*
    :align: center
    :figclass: align-center
 

docs/source/methods/parallelization.rst

@@ -65,7 +65,7 @@ in the case of an eigenvalue calculation). This idea is illustrated in
 
 .. _figure-master-slave:
 
-.. figure:: ../../img/master-slave.png
+.. figure:: ../_images/master-slave.png
     :align: center
     :figclass: align-center
 
@@ -122,7 +122,7 @@ needed. This concept is illustrated in :ref:`Figure 2
 
 .. _figure-nearest-neighbor:
 
-.. figure:: ../../img/nearest-neighbor.png
+.. figure:: ../_images/nearest-neighbor.png
     :align: center
     :figclass: align-center
 
@@ -203,7 +203,7 @@ communicated between adjacent nodes.
 
 .. _figure-neighbor-example:
 
-.. figure:: ../../img/nearest-neighbor-example.png
+.. figure:: ../_images/nearest-neighbor-example.png
     :align: center
     :figclass: align-center
 

docs/source/publications.rst

@@ -48,8 +48,8 @@ Publications
 
 - Andrew R. Siegel, Kord Smith, Paul K. Romano, Benoit Forget, and Kyle Felker,
   "Multi-core performance studies of a Monte Carlo neutron transport code,"
-  *Int. J. High Perform. Comput. Appl.*
-  (2013). `<http://dx.doi.org/10.1177/1094342013492179>`_
+  *Int. J. High Perform. Comput. Appl.*, **28** (1), 87--96
+  (2014). `<http://dx.doi.org/10.1177/1094342013492179>`_
 
 - Paul K. Romano, Andrew R. Siegel, Benoit Forget, and Kord Smith, "Data
   decomposition of Monte Carlo particle transport simulations via tally

docs/source/quickinstall.rst

@@ -48,7 +48,12 @@ following commands in a terminal:
     sudo make install
 
 This will build an executable named ``openmc`` and install it (by default in
-/usr/local/bin).
+/usr/local/bin). If you do not have administrator privileges, the last command
+can be replaced with a local install, e.g.
+
+.. code-block:: sh
+
+    make install -e prefix=$HOME/.local
 
 .. _GitHub: https://github.com/mit-crpg/openmc
 .. _git: http://git-scm.com

docs/source/releasenotes/index.rst

@@ -10,6 +10,7 @@ bugs fixed, and known issues for each successive release.
 .. toctree::
     :maxdepth: 1
 
+    notes_0.5.4
     notes_0.5.3
     notes_0.5.2
     notes_0.5.1

docs/source/releasenotes/notes_0.5.4.rst

@@ -0,0 +1,63 @@
+.. _notes_0.5.4:
+
+==============================
+Release Notes for OpenMC 0.5.4
+==============================
+
+.. note::
+    These release notes are for an upcoming release of OpenMC and are still
+    subject to change.
+
+-------------------
+System Requirements
+-------------------
+
+There are no special requirements for running the OpenMC code. As of this
+release, OpenMC has been tested on a variety of Linux distributions, Mac OS X,
+and Microsoft Windows 7. Memory requirements will vary depending on the size of
+the problem at hand (mostly on the number of nuclides in the problem).
+
+------------
+New Features
+------------
+
+- New XML parsing backend (FoX)
+- Ability to write particle track files
+- Handle lost particles more gracefully (via particle track files)
+- Source sites outside geometry are resampled
+- Multiple random number generator streams
+- plot_mesh_tally.py utility converted to use Tkinter rather than PyQt
+- Script added to download ACE data from NNDC
+- Mixed ASCII/binary cross_sections.xml now allowed
+- Expanded options for writing source bank
+- Re-enabled ability to use source file as starting source
+
+---------
+Bug Fixes
+---------
+
+- 32c03c_: Check for valid data in cross_sections.xml
+- c71ef5_: Fix bug in statepoint.py
+- 8884fb_: Check for all ZAIDs for S(a,b) tables
+- b38af0_: Fix XML reading on multiple levels of input
+- d28750_: Fix bug in convert_xsdir.py
+
+.. _32c03c: https://github.com/mit-crpg/openmc/commit/32c03c
+.. _c71ef5: https://github.com/mit-crpg/openmc/commit/c71ef5
+.. _8884fb: https://github.com/mit-crpg/openmc/commit/8884fb
+.. _b38af0: https://github.com/mit-crpg/openmc/commit/b38af0
+.. _d28750: https://github.com/mit-crpg/openmc/commit/d28750
+
+------------
+Contributors
+------------
+
+This release contains new contributions from the following people:
+
+- `Sterling Harper <smharper@mit.edu>`_
+- `Bryan Herman <bherman@mit.edu>`_
+- `Nick Horelik <nhorelik@mit.edu>`_
+- `Adam Nelson <nelsonag@umich.edu>`_
+- `Paul Romano <paul.k.romano@gmail.com>`_
+- `Tuomas Viitanen <tuomas.viitanen@vtt.fi>`_
+- `Jon Walsh <walshjon@mit.edu>`_

docs/source/usersguide/input.rst

@@ -264,7 +264,9 @@ attributes/sub-elements:
 
   :file:
     If this attribute is given, it indicates that the source is to be read from
-    a binary source file whose path is given by the value of this element
+    a binary source file whose path is given by the value of this element. Note,
+    the number of source sites needs to be the same as the number of particles
+    simulated in a fission source generation.
 
     *Default*: None
 
@@ -348,8 +350,10 @@ 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 +368,52 @@ 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
 ------------------------------
 
@@ -1052,7 +1089,7 @@ sub-elements:
               the PNG format can often times reduce the file size by orders of
               magnitude without any loss of image quality. Likewise,
               high-resolution voxel files produced by OpenMC can be quite large,
-              but the equivalent SILO files will by significantly smaller.
+              but the equivalent SILO files will be significantly smaller.
 
     *Default*: "slice"
 

docs/source/usersguide/install.rst

@@ -189,7 +189,15 @@ the root directory of the source code:
     sudo make install
 
 This will build an executable named ``openmc`` and install it (by default in
-/usr/local/bin).
+/usr/local/bin). If you do not have administrative privileges, you can install
+OpenMC locally by replacing the last command with:
+
+.. code-block:: sh
+
+    make install -e prefix=$HOME/.local
+
+The ``prefix`` variable can be changed to any path for which you have
+write-access.
 
 Compiling on Windows
 --------------------
@@ -264,10 +272,27 @@ 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 +339,8 @@ 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/>`_
@@ -38,9 +38,58 @@ running OpenMC with the -plot or -p command-line option (See
 Plotting in 2D
 --------------
 
-.. image:: ../../img/atr.png
+.. 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
@@ -53,18 +102,45 @@ 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
 --------------
 
-.. image:: ../../img/3dgeomplot.png
+.. 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.
 
 
 -------------------
@@ -162,7 +246,7 @@ tasks will be described here in the following sections.
 Plotting in 2D
 --------------
 
-.. image:: ../../img/plotmeshtally.png
+.. image:: ../_images/plotmeshtally.png
    :height: 200px
 
 For simple viewing of 2D slices of a mesh plot, the utility plot_mesh_tally.py
@@ -170,7 +254,7 @@ is provided.  This utility provides an interactive GUI to explore and plot
 mesh tallies for any scores and filter bins.  It requires statepoint.py, as well
 as `PyQt <http://www.riverbankcomputing.com/software/pyqt>`_.
 
-.. image:: ../../img/fluxplot.png
+.. image:: ../_images/fluxplot.png
    :height: 200px
 
 Alternatively, the user can write their own Python script to manipulate the data
@@ -249,7 +333,7 @@ two heatmaps in the previous figure.
 Plotting in 3D
 --------------
 
-.. image:: ../../img/3dcore.png
+.. image:: ../_images/3dcore.png
    :height: 200px
 
 As with 3D plots of the geometry, meshtally data needs to be put into a standard
@@ -357,7 +441,7 @@ and dumped to MATLAB in one step.
 Particle Track Visualization
 ----------------------------
 
-.. image:: ../../img/Tracks.png
+.. image:: ../_images/Tracks.png
    :height: 200px
 
 OpenMC can dump particle tracks—the position of particles as they are

docs/source/usersguide/troubleshoot.rst

@@ -79,6 +79,14 @@ with the :envvar:`CROSS_SECTIONS` environment variable. It is recommended to add
 a line in your ``.profile`` or ``.bash_profile`` setting the
 :envvar:`CROSS_SECTIONS` environment variable.
 
+ERROR: Invalid usage of L(I) in ACE data; Consider using more recent data set.
+******************************************************************************
+
+The cross-sections requested in ``materials.xml`` do not conform to the current
+standard format.  This typically happens with fissionable nuclides in a ``.6*c``
+library as distributed with MCNP.  Please try a newer library such as any from
+the ``.7*c`` set.
+
 Geometry Debugging
 ******************
 
@@ -107,8 +115,8 @@ have many particles travelling through them there will not be many locations
 where overlaps are checked for in that region.  The user should refer to the
 output after a geometry debug run to see how many checks were performed in each
 cell, and then adjust the number of starting particles or starting source
-distributions accordingly to achieve good coverage. 
- 
+distributions accordingly to achieve good coverage.
+
 ERROR: After particle __ crossed surface __ it could not be located in any cell and it did not leak.
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

man/man1/openmc.1

@@ -46,7 +46,7 @@ to locate ACE format cross section libraries if the user has not specified the
 <cross_sections> tag in
 .I settings.xml\fP.
 .SH LICENSE
-Copyright \(co 2011-2013 Massachusetts Institute of Technology.
+Copyright \(co 2011-2014 Massachusetts Institute of Technology.
 .PP
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

src/Makefile

@@ -181,17 +181,17 @@ endif
 
 ifeq ($(OPENMP),yes)
   ifeq ($(COMPILER),intel)
-    F90FLAGS += -openmp -DOPENMP
+    F90FLAGS += -openmp
     LDFLAGS += -openmp
   endif
 
   ifeq ($(COMPILER),gnu)
-    F90FLAGS += -fopenmp -DOPENMP
+    F90FLAGS += -fopenmp
     LDFLAGS += -fopenmp
   endif
 
   ifeq ($(COMPILER),ibm)
-    F90FLAGS += -qsmp=omp -WF,-DOPENMP
+    F90FLAGS += -qsmp=omp
     LDFLAGS += -qsmp=omp
   endif
 endif
@@ -218,7 +218,7 @@ endif
 
 ifeq ($(MACHINE),bluegene)
   F90 = /bgsys/drivers/ppcfloor/comm/xl/bin/mpixlf2003
-  F90FLAGS = -WF,-DNO_F2008,-DMPI -O3
+  F90FLAGS = -WF,-DNO_F2008,-DMPI,-DRESTRICTED_ASSOCIATED_BUG -O3
   LDFLAGS = -lmpich.cnkf90
 endif
 
@@ -233,7 +233,7 @@ endif
 
 ifeq ($(MACHINE),bluegeneq)
   F90 = mpixlf2003
-  F90FLAGS = -WF,-DNO_F2008,-DMPI -O5
+  F90FLAGS = -WF,-DNO_F2008,-DMPI,-DRESTRICTED_ASSOCIATED_BUG -O5
 endif
 
 #===============================================================================

src/ace.F90

@@ -1015,6 +1015,7 @@ contains
     integer :: NEa   ! number of energies for Watt 'a'
     integer :: NRb   ! number of interpolation regions for Watt 'b'
     integer :: NEb   ! number of energies for Watt 'b'
+    real(8), allocatable :: L(:)  ! locations of distributions for each Ein
 
     ! initialize length
     length = 0
@@ -1039,6 +1040,22 @@ contains
       ! Continuous tabular distribution
       NR = int(XSS(lc + 1))
       NE = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       length = length + 2 + 2*NR + 2*NE
       do i = 1,NE
         ! determine length
@@ -1081,6 +1098,22 @@ contains
       ! Kalbach-Mann correlated scattering
       NR = int(XSS(lc + 1))
       NE = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       length = length + 2 + 2*NR + 2*NE
       do i = 1,NE
         NP = int(XSS(lc + length + 2))
@@ -1095,6 +1128,22 @@ contains
       ! Correlated energy and angle distribution
       NR = int(XSS(lc + 1))
       NE = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       length = length + 2 + 2*NR + 2*NE
       do i = 1,NE
         ! outgoing energy distribution
@@ -1127,6 +1176,22 @@ contains
       ! Laboratory energy-angle law
       NR  = int(XSS(lc + 1))
       NE  = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       NMU = int(XSS(lc + 4 + 2*NR + 2*NE))
       length = 4 + 2*(NR + NE + NMU)
 

src/cmfd_input.F90

@@ -577,7 +577,9 @@ contains
     end do
 
     ! Put cmfd tallies into active tally array and turn tallies on
+!$omp parallel
     call setup_active_cmfdtallies()
+!$omp end parallel
     tallies_on = .true.
 
   end subroutine create_cmfd_tally

src/constants.F90

@@ -11,13 +11,14 @@ module constants
   integer, parameter :: VERSION_RELEASE = 3
 
   ! Revision numbers for binary files
-  integer, parameter :: REVISION_STATEPOINT       = 10
+  integer, parameter :: REVISION_STATEPOINT       = 11
   integer, parameter :: REVISION_PARTICLE_RESTART = 1
 
   ! Binary file types
   integer, parameter :: &
        FILETYPE_STATEPOINT       = -1, &
-       FILETYPE_PARTICLE_RESTART = -2
+       FILETYPE_PARTICLE_RESTART = -2, &
+       FILETYPE_SOURCE           = -3
 
   ! ============================================================================
   ! ADJUSTABLE PARAMETERS

src/eigenvalue.F90

@@ -17,7 +17,7 @@ module eigenvalue
   use random_lcg,   only: prn, set_particle_seed, prn_skip
   use search,       only: binary_search
   use source,       only: get_source_particle
-  use state_point,  only: write_state_point
+  use state_point,  only: write_state_point, write_source_point
   use string,       only: to_str
   use tally,        only: synchronize_tallies, setup_active_usertallies, &
                           reset_result
@@ -166,7 +166,7 @@ contains
 
   subroutine finalize_generation()
 
-#ifdef OPENMP
+#ifdef _OPENMP
     ! Join the fission bank from each thread into one global fission bank
     call join_bank_from_threads()
 #endif
@@ -222,6 +222,12 @@ contains
       call write_state_point()
     end if
 
+    ! Write out source point if it's been specified for this batch
+    if ((sourcepoint_batch % contains(current_batch) .or. source_latest) .and. &
+        source_write) then
+      call write_source_point()
+    end if
+
     if (master .and. current_batch == n_batches) then
       ! Make sure combined estimate of k-effective is calculated at the last
       ! batch in case no state point is written
@@ -821,7 +827,7 @@ contains
 
   end subroutine replay_batch_history
 
-#ifdef OPENMP
+#ifdef _OPENMP
 !===============================================================================
 ! JOIN_BANK_FROM_THREADS
 !===============================================================================

src/global.F90

@@ -158,7 +158,7 @@ module global
   ! Source and fission bank
   type(Bank), allocatable, target :: source_bank(:)
   type(Bank), allocatable, target :: fission_bank(:)
-#ifdef OPENMP
+#ifdef _OPENMP
   type(Bank), allocatable, target :: master_fission_bank(:)
 #endif
   integer(8) :: n_bank       ! # of sites in fission bank
@@ -189,6 +189,7 @@ module global
   ! Write source at end of simulation
   logical :: source_separate = .false.
   logical :: source_write = .true.
+  logical :: source_latest = .false.
 
   ! ============================================================================
   ! PARALLEL PROCESSING VARIABLES
@@ -205,7 +206,7 @@ module global
   integer :: MPI_BANK              ! MPI datatype for fission bank
   integer :: MPI_TALLYRESULT       ! MPI datatype for TallyResult
 
-#ifdef OPENMP
+#ifdef _OPENMP
   integer :: n_threads = NONE      ! number of OpenMP threads
   integer :: thread_id             ! ID of a given thread
 #endif
@@ -260,6 +261,7 @@ module global
   character(MAX_FILE_LEN) :: path_cross_sections   ! Path to cross_sections.xml
   character(MAX_FILE_LEN) :: path_source = ''      ! Path to binary source
   character(MAX_FILE_LEN) :: path_state_point      ! Path to binary state point
+  character(MAX_FILE_LEN) :: path_source_point     ! Path to binary source point
   character(MAX_FILE_LEN) :: path_particle_restart ! Path to particle restart
   character(MAX_FILE_LEN) :: path_output = ''      ! Path to output directory
 
@@ -363,6 +365,10 @@ module global
   integer :: n_state_points = 0
   type(SetInt) :: statepoint_batch
 
+  ! Information about source points to be written
+  integer :: n_source_points = 0
+  type(SetInt) :: sourcepoint_batch
+
   ! Various output options
   logical :: output_summary = .false.
   logical :: output_xs      = .false.
@@ -450,7 +456,7 @@ contains
 !$omp parallel
     if (allocated(fission_bank)) deallocate(fission_bank)
 !$omp end parallel
-#ifdef OPENMP
+#ifdef _OPENMP
     if (allocated(master_fission_bank)) deallocate(master_fission_bank)
 #endif
     if (allocated(source_bank)) deallocate(source_bank)

src/hdf5_summary.F90

@@ -100,6 +100,7 @@ contains
 
     integer          :: i, j, k, m
     integer          :: n_x, n_y, n_z
+    integer          :: length(3)
     integer, allocatable :: lattice_universes(:,:,:)
     type(Cell),     pointer :: c => null()
     type(Surface),  pointer :: s => null()
@@ -312,8 +313,8 @@ contains
           end do
         end do
       end do
-      call su % write_data(lattice_universes, "universes", &
-           length=(/n_x, n_y, n_z/), &
+      length = [n_x, n_y, n_z]
+      call su % write_data(lattice_universes, "universes", length=length, &
            group="geometry/lattices/lattice " // trim(to_str(lat % id)))
       deallocate(lattice_universes)
 

src/initialize.F90

@@ -26,7 +26,7 @@ module initialize
   use mpi
 #endif
 
-#ifdef OPENMP
+#ifdef _OPENMP
   use omp_lib
 #endif
 
@@ -363,8 +363,50 @@ contains
           case (FILETYPE_PARTICLE_RESTART)
             path_particle_restart = argv(i)
             particle_restart_run = .true.
+          case default
+            message = "Unrecognized file after restart flag."
+            call fatal_error()
           end select
 
+          ! If its a restart run check for additional source file
+          if (restart_run .and. i + 1 <= argc) then
+
+            ! Increment arg
+            i = i + 1
+
+            ! Check if it has extension we can read
+            if ((ends_with(argv(i), '.binary') .or. &
+                 ends_with(argv(i), '.h5'))) then
+
+              ! Check file type is a source file
+              call sp % file_open(argv(i), 'r', serial = .false.)
+              call sp % read_data(filetype, 'filetype')
+              call sp % file_close()
+              if (filetype /= FILETYPE_SOURCE) then
+                message = "Second file after restart flag must be a source file"
+                call fatal_error()
+              end if
+
+              ! It is a source file
+              path_source_point = argv(i)
+
+            else ! Different option is specified not a source file
+
+              ! Source is in statepoint file
+              path_source_point = path_state_point
+
+              ! Set argument back
+              i = i - 1
+
+            end if
+
+          else ! No command line arg after statepoint
+
+            ! Source is assumed to be in statepoint file
+            path_source_point = path_state_point
+
+          end if
+
         case ('-g', '-geometry-debug', '--geometry-debug')
           check_overlaps = .true.
 
@@ -372,7 +414,7 @@ contains
           ! Read number of threads
           i = i + 1
 
-#ifdef OPENMP          
+#ifdef _OPENMP          
           ! Read and set number of OpenMP threads
           n_threads = str_to_int(argv(i))
           if (n_threads < 1) then
@@ -830,14 +872,15 @@ contains
       call fatal_error()
     end if
 
-#ifdef OPENMP
+#ifdef _OPENMP
     ! If OpenMP is being used, each thread needs its own private fission
     ! bank. Since the private fission banks need to be combined at the end of a
     ! generation, there is also a 'master_fission_bank' that is used to collect
     ! the sites from each thread.
 
+    n_threads = omp_get_max_threads()
+
 !$omp parallel
-    n_threads = omp_get_num_threads()
     thread_id = omp_get_thread_num()
 
     if (thread_id == 0) then

src/input_xml.F90

@@ -231,7 +231,7 @@ contains
 
     ! Number of OpenMP threads
     if (check_for_node(doc, "threads")) then
-#ifdef OPENMP
+#ifdef _OPENMP
       if (n_threads == NONE) then
         call get_node_value(doc, "threads", n_threads)
         if (n_threads < 1) then
@@ -628,20 +628,6 @@ contains
         n_state_points = 1
         call statepoint_batch % add(n_batches)
       end if
-
-      ! Check if the user has specified to write binary source file
-      if (check_for_node(node_sp, "source_separate")) then
-        call get_node_value(node_sp, "source_separate", temp_str)
-        call lower_case(temp_str)
-        if (trim(temp_str) == 'true' .or. &
-             trim(temp_str) == '1') source_separate = .true.
-      end if
-      if (check_for_node(node_sp, "source_write")) then
-        call get_node_value(node_sp, "source_write", temp_str)
-        call lower_case(temp_str)
-        if (trim(temp_str) == 'false' .or. &
-             trim(temp_str) == '0') source_write = .false.
-      end if
     else
       ! If no <state_point> tag was present, by default write state point at
       ! last batch only
@@ -649,6 +635,85 @@ contains
       call statepoint_batch % add(n_batches)
     end if
 
+    ! Check if the user has specified to write source points
+    if (check_for_node(doc, "source_point")) then
+
+      ! Get pointer to source_point node
+      call get_node_ptr(doc, "source_point", node_sp)
+
+      ! Determine number of batches at which to store source points
+      if (check_for_node(node_sp, "batches")) then
+        n_source_points = get_arraysize_integer(node_sp, "batches") 
+      else
+        n_source_points = 0
+      end if
+
+      if (n_source_points > 0) then
+        ! User gave specific batches to write source points
+        allocate(temp_int_array(n_source_points))
+        call get_node_array(node_sp, "batches", temp_int_array)
+        do i = 1, n_source_points
+          call sourcepoint_batch % add(temp_int_array(i))
+        end do
+        deallocate(temp_int_array)
+      elseif (check_for_node(node_sp, "interval")) then
+        ! User gave an interval for writing source points
+        call get_node_value(node_sp, "interval", temp_int)
+        n_source_points = n_batches / temp_int
+        do i = 1, n_source_points
+          call sourcepoint_batch % add(temp_int * i)
+        end do
+      else
+        ! If neither were specified, write source points with state points
+        n_source_points = n_state_points
+        do i = 1, n_state_points
+          call sourcepoint_batch % add(statepoint_batch % get_item(i))
+        end do
+      end if
+
+      ! Check if the user has specified to write binary source file
+      if (check_for_node(node_sp, "separate")) then
+        call get_node_value(node_sp, "separate", temp_str)
+        call lower_case(temp_str)
+        if (trim(temp_str) == 'true' .or. &
+             trim(temp_str) == '1') source_separate = .true.
+      end if
+      if (check_for_node(node_sp, "write")) then
+        call get_node_value(node_sp, "write", temp_str)
+        call lower_case(temp_str)
+        if (trim(temp_str) == 'false' .or. &
+             trim(temp_str) == '0') source_write = .false.
+      end if
+      if (check_for_node(node_sp, "overwrite_latest")) then
+        call get_node_value(node_sp, "overwrite_latest", temp_str)
+        call lower_case(temp_str)
+        if (trim(temp_str) == 'true' .or. &
+             trim(temp_str) == '1') source_latest = .true.
+      end if
+    else
+      ! If no <source_point> tag was present, by default we keep source bank in
+      ! statepoint file and write it out at statepoints intervals 
+      source_separate = .false.
+      n_source_points = n_state_points
+      do i = 1, n_state_points
+        call sourcepoint_batch % add(statepoint_batch % get_item(i))
+      end do
+    end if
+
+    ! If source is not seperate and is to be written out in the statepoint file,
+    ! make sure that the sourcepoint batch numbers are contained in the
+    ! statepoint list
+    if (.not. source_separate) then
+      do i = 1, n_source_points
+        if (.not. statepoint_batch % contains(sourcepoint_batch % &
+            get_item(i))) then
+          message = 'Sourcepoint batches are not a subset&
+                    & of statepoint batches.'
+          call fatal_error()
+        end if
+      end do
+    end if
+
     ! Check if the user has specified to not reduce tallies at the end of every
     ! batch
     if (check_for_node(doc, "no_reduce")) then

src/output.F90

@@ -31,6 +31,10 @@ contains
 
   subroutine title()
 
+#ifdef _OPENMP
+    use omp_lib
+#endif
+
     write(UNIT=OUTPUT_UNIT, FMT='(/11(A/))') &
          '       .d88888b.                             888b     d888  .d8888b.', &
          '      d88P" "Y88b                            8888b   d8888 d88P  Y88b', &
@@ -46,25 +50,31 @@ contains
 
     ! Write version information
     write(UNIT=OUTPUT_UNIT, FMT=*) &
-         '     Copyright:     2011-2013 Massachusetts Institute of Technology'
+         '     Copyright:      2011-2014 Massachusetts Institute of Technology'
     write(UNIT=OUTPUT_UNIT, FMT=*) &
-         '     License:       http://mit-crpg.github.io/openmc/license.html'
-    write(UNIT=OUTPUT_UNIT, FMT='(6X,"Version:",7X,I1,".",I1,".",I1)') &
+         '     License:        http://mit-crpg.github.io/openmc/license.html'
+    write(UNIT=OUTPUT_UNIT, FMT='(6X,"Version:",8X,I1,".",I1,".",I1)') &
          VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE
 #ifdef GIT_SHA1
-    write(UNIT=OUTPUT_UNIT, FMT='(6X,"Git SHA1:",6X,A)') GIT_SHA1
+    write(UNIT=OUTPUT_UNIT, FMT='(6X,"Git SHA1:",7X,A)') GIT_SHA1
 #endif
 
     ! Write the date and time
-    write(UNIT=OUTPUT_UNIT, FMT='(6X,"Date/Time:",5X,A)') &
+    write(UNIT=OUTPUT_UNIT, FMT='(6X,"Date/Time:",6X,A)') &
          time_stamp()
 
 #ifdef MPI
     ! Write number of processors
-    write(UNIT=OUTPUT_UNIT, FMT='(6X,"MPI Processes:",1X,A)') &
+    write(UNIT=OUTPUT_UNIT, FMT='(6X,"MPI Processes:",2X,A)') &
          trim(to_str(n_procs))
 #endif
 
+#ifdef _OPENMP
+    ! Write number of OpenMP threads
+    write(UNIT=OUTPUT_UNIT, FMT='(6X,"OpenMP Threads:",1X,A)') &
+         trim(to_str(omp_get_max_threads()))
+#endif
+
   end subroutine title
 
 !===============================================================================

src/random_lcg.F90

@@ -5,8 +5,13 @@ module random_lcg
   private
   save
 
+  ! Random number streams
+  integer, parameter :: N_STREAMS = 2
+  integer, parameter :: STREAM_TRACKING = 1
+  integer, parameter :: STREAM_TALLIES  = 2
+
   integer(8) :: prn_seed0  ! original seed
-  integer(8) :: prn_seed   ! current seed
+  integer(8) :: prn_seed(N_STREAMS) ! current seed
   integer(8) :: prn_mult   ! multiplication factor, g
   integer(8) :: prn_add    ! additive factor, c
   integer    :: prn_bits   ! number of bits, M
@@ -14,6 +19,7 @@ module random_lcg
   integer(8) :: prn_mask   ! 2^M - 1
   integer(8) :: prn_stride ! stride between particles
   real(8)    :: prn_norm   ! 2^(-M)
+  integer    :: stream     ! current RNG stream
 
 !$omp threadprivate(prn_seed)
 
@@ -21,6 +27,8 @@ module random_lcg
   public :: initialize_prng
   public :: set_particle_seed
   public :: prn_skip
+  public :: prn_set_stream
+  public :: STREAM_TRACKING, STREAM_TALLIES
 
 contains
 
@@ -35,12 +43,12 @@ contains
     ! This algorithm uses bit-masking to find the next integer(8) value to be
     ! used to calculate the random number
 
-    prn_seed = iand(prn_mult*prn_seed + prn_add, prn_mask)
+    prn_seed(stream) = iand(prn_mult*prn_seed(stream) + prn_add, prn_mask)
 
     ! Once the integer is calculated, we just need to divide by 2**m,
     ! represented here as multiplying by a pre-calculated factor
 
-    pseudo_rn = prn_seed * prn_norm
+    pseudo_rn = prn_seed(stream) * prn_norm
 
   end function prn
 
@@ -53,8 +61,13 @@ contains
 
     use global, only: seed
 
+    integer :: i
+
+    stream     = STREAM_TRACKING
     prn_seed0  = seed
-    prn_seed   = prn_seed
+    do i = 1, N_STREAMS
+      prn_seed(i) = prn_seed0 + i - 1
+    end do
     prn_mult   = 2806196910506780709_8
     prn_add    = 1_8
     prn_bits   = 63
@@ -74,7 +87,11 @@ contains
 
     integer(8), intent(in) :: id
 
-    prn_seed = prn_skip_ahead(id*prn_stride, prn_seed0)
+    integer :: i
+
+    do i = 1, N_STREAMS
+      prn_seed(i) = prn_skip_ahead(id*prn_stride, prn_seed0 + i - 1)
+    end do
 
   end subroutine set_particle_seed
     
@@ -86,7 +103,7 @@ contains
 
     integer(8), intent(in) :: n ! number of seeds to skip
 
-    prn_seed = prn_skip_ahead(n, prn_seed)
+    prn_seed(stream) = prn_skip_ahead(n, prn_seed(stream))
 
   end subroutine prn_skip
 
@@ -151,4 +168,18 @@ contains
 
   end function prn_skip_ahead
 
+!===============================================================================
+! PRN_SET_STREAM changes the random number stream. If random numbers are needed
+! in routines not used directly for tracking (e.g. physics), this allows the
+! numbers to be generated without affecting reproducibility of the physics.
+!===============================================================================
+
+  subroutine prn_set_stream(i)
+
+    integer, intent(in) :: i
+
+    stream = i
+
+  end subroutine prn_set_stream
+
 end module random_lcg

src/relaxng/settings.rnc

@@ -92,11 +92,22 @@ element settings {
         attribute batches { list { xsd:positiveInteger+ } }) |
       (element interval { xsd:positiveInteger } | 
         attribute interval { xsd:positiveInteger })
-    ) &
-    (element source_separate { xsd:boolean } | 
-      attribute source_separate { xsd:boolean })? &
-    (element source_write { xsd:boolean } | 
-      attribute source_write { xsd:boolean })?
+    )
+  }? &
+
+  element source_point {
+    (
+      (element batches { list { xsd:positiveInteger+ } } |
+        attribute batches { list { xsd:positiveInteger+ } }) |
+      (element interval { xsd:positiveInteger } | 
+        attribute interval { xsd:positiveInteger })
+    )? &
+    (element separate { xsd:boolean } | 
+      attribute separate { xsd:boolean })? &
+    (element write { xsd:boolean } | 
+      attribute write { xsd:boolean })? &
+    (element overwrite_latest { xsd:boolean} |
+      attribute overwrite_latest {xsd:boolean})?
   }? &
 
   element survival_biasing { xsd:boolean }? &

src/source.F90

@@ -1,16 +1,17 @@
 module source
 
-  use bank_header,     only: Bank
+  use bank_header,      only: Bank
   use constants
-  use error,           only: fatal_error
-  use geometry,        only: find_cell
-  use geometry_header, only: BASE_UNIVERSE
+  use error,            only: fatal_error
+  use geometry,         only: find_cell
+  use geometry_header,  only: BASE_UNIVERSE
   use global
-  use math,            only: maxwell_spectrum, watt_spectrum
-  use output,          only: write_message
-  use particle_header, only: Particle
-  use random_lcg,      only: prn, set_particle_seed
-  use string,          only: to_str
+  use math,             only: maxwell_spectrum, watt_spectrum
+  use output,           only: write_message
+  use output_interface, only: BinaryOutput
+  use particle_header,  only: Particle
+  use random_lcg,       only: prn, set_particle_seed
+  use string,           only: to_str
 
 #ifdef MPI
   use mpi
@@ -28,8 +29,9 @@ contains
 
     integer(8) :: i          ! loop index over bank sites
     integer(8) :: id         ! particle id
-
+    integer(4) :: itmp       ! temporary integer
     type(Bank), pointer :: src => null() ! source bank site
+    type(BinaryOutput) :: sp ! statepoint/source binary file
 
     message = "Initializing source particles..."
     call write_message(6)
@@ -38,8 +40,26 @@ contains
       ! Read the source from a binary file instead of sampling from some
       ! assumed source distribution
 
-      message = 'This feature is currently disabled and will be added back in.'
-      call fatal_error()
+      message = 'Reading source file from ' // trim(path_source) // '...'
+      call write_message(6)
+
+      ! Open the binary file
+      call sp % file_open(path_source, 'r', serial = .false.)
+
+      ! Read the file type
+      call sp % read_data(itmp, "filetype")
+
+      ! Check to make sure this is a source file
+      if (itmp /= FILETYPE_SOURCE) then
+        message = "Specified starting source file not a source file type."
+        call fatal_error()
+      end if
+
+      ! Read in the source bank
+      call sp % read_source_bank()
+
+      ! Close file
+      call sp % file_close()
 
     else
       ! Generation source sites from specified distribution in user input

src/state_point.F90

@@ -232,6 +232,13 @@ contains
 
     end if
 
+    ! Indicate where source bank is stored in statepoint
+    if (source_separate) then
+      call sp % write_data(0, "source_present")
+    else
+      call sp % write_data(1, "source_present")
+    end if
+
     ! Check for the no-tally-reduction method
     if (.not. reduce_tallies) then
       ! If using the no-tally-reduction method, we need to collect tally
@@ -280,14 +287,45 @@ contains
 
     end if
 
-    ! Check for eigenvalue calculation
-    if (run_mode == MODE_EIGENVALUE .and. source_write) then
+  end subroutine write_state_point
 
-      ! Check for writing source out separately
+!===============================================================================
+! WRITE_SOURCE_POINT
+!===============================================================================
+
+  subroutine write_source_point()
+
+    type(BinaryOutput) :: sp
+    character(MAX_FILE_LEN) :: filename
+
+    ! Check to write out source for a specified batch
+    if (sourcepoint_batch % contains(current_batch)) then
+
+      ! Create or open up file
       if (source_separate) then
 
-        ! Set filename for source
-        filename = trim(path_output) // 'source.' // &
+        ! Set filename
+        filename = trim(path_output) // 'source.' // trim(to_str(current_batch))
+#ifdef HDF5
+        filename = trim(filename) // '.h5'
+#else
+        filename = trim(filename) // '.binary'
+#endif
+
+        ! Write message for new file creation
+        message = "Creating source file " // trim(filename) // "..."
+        call write_message(1)
+
+        ! Create separate source file
+        call sp % file_create(filename, serial = .false.)
+
+        ! Write file type
+        call sp % write_data(FILETYPE_SOURCE, "filetype")
+
+      else
+
+        ! Set filename for state point
+        filename = trim(path_output) // 'statepoint.' // &
                    trim(to_str(current_batch))
 #ifdef HDF5
         filename = trim(filename) // '.h5'
@@ -295,16 +333,7 @@ contains
         filename = trim(filename) // '.binary'
 #endif
 
-        ! Write message
-        message = "Creating source file " // trim(filename) // "..."
-        call write_message(1)
-
-        ! Create source file 
-        call sp % file_create(filename, serial = .false.)
-
-      else
-
-        ! Reopen state point file in parallel
+        ! Reopen statepoint file in parallel
         call sp % file_open(filename, 'w', serial = .false.)
 
       end if
@@ -317,7 +346,36 @@ contains
 
     end if
 
-  end subroutine write_state_point
+    ! Also check to write source separately in overwritten file
+    if (source_latest) then
+
+      ! Set filename
+      filename = trim(path_output) // 'source'
+#ifdef HDF5
+      filename = trim(filename) // '.h5'
+#else
+      filename = trim(filename) // '.binary'
+#endif
+
+      ! Write message for new file creation
+      message = "Creating source file " // trim(filename) // "..."
+      call write_message(1)
+
+      ! Always create this file because it will be overwritten
+      call sp % file_create(filename, serial = .false.)
+
+      ! Write file type
+      call sp % write_data(FILETYPE_SOURCE, "filetype")
+
+      ! Write out source
+      call sp % write_source_bank()
+
+      ! Close file
+      call sp % file_close()
+
+    end if
+
+  end subroutine write_source_point
 
 !===============================================================================
 ! WRITE_TALLY_RESULTS_NR
@@ -464,8 +522,10 @@ contains
     character(19)           :: current_time
     integer                 :: i
     integer                 :: j
+    integer                 :: length(4)
     integer                 :: int_array(3)
     integer, allocatable    :: temp_array(:)
+    logical                 :: source_present
     real(8)                 :: real_array(3) 
     type(TallyObject), pointer :: t => null()
 
@@ -542,10 +602,9 @@ contains
         call sp % read_data(cmfd % indices, "indicies", length=4, group="cmfd")
         call sp % read_data(cmfd % k_cmfd, "k_cmfd", length=restart_batch, &
              group="cmfd")
+        length = cmfd % indices([4,1,2,3])
         call sp % read_data(cmfd % cmfd_src, "cmfd_src", &
-             length=(/cmfd % indices(4), cmfd % indices(1), &
-             cmfd % indices(2), cmfd % indices(3)/), &
-             group="cmfd")
+             length=length, group="cmfd")
         call sp % read_data(cmfd % entropy, "cmfd_entropy", &
                        length=restart_batch, group="cmfd")
         call sp % read_data(cmfd % balance, "cmfd_balance", &
@@ -671,6 +730,20 @@ contains
 
     end do TALLY_METADATA
 
+    ! Check for source in statepoint if needed
+    call sp % read_data(int_array(1), "source_present")
+    if (int_array(1) == 1) then
+      source_present = .true.
+    else
+      source_present = .false.
+    end if
+
+    ! Check to make sure source bank is present
+    if (path_source_point == path_state_point .and. .not. source_present) then
+      message = "Source bank must be contained in statepoint restart file"
+      call fatal_error()
+    end if 
+
     ! Read tallies to master
     if (master) then
 
@@ -711,26 +784,20 @@ contains
     if (run_mode == MODE_EIGENVALUE) then
 
       ! Check if source was written out separately
-      if (source_separate) then
+      if (.not. source_present) then
 
         ! Close statepoint file 
         call sp % file_close()
 
-        ! Set filename for source
-        filename = trim(path_output) // 'source.' // &
-                   trim(to_str(restart_batch))
-#ifdef HDF5
-        filename = trim(filename) // '.h5'
-#else
-        filename = trim(filename) // '.binary'
-#endif
-
         ! Write message
         message = "Loading source file " // trim(filename) // "..."
         call write_message(1)
 
         ! Open source file 
-        call sp % file_open(filename, 'r', serial = .false.)
+        call sp % file_open(path_source_point, 'r', serial = .false.)
+
+        ! Read file type
+        call sp % read_data(int_array(1), "filetype")
 
       end if
 

src/track_output.F90

@@ -56,6 +56,7 @@ contains
   subroutine finalize_particle_track(p)
     type(Particle), intent(in)  :: p
 
+    integer                  :: length(2)
     character(MAX_FILE_LEN)  :: fname
     type(BinaryOutput)       :: binout
 
@@ -69,7 +70,8 @@ contains
          // '.binary'
 #endif
     call binout % file_create(fname)
-    call binout % write_data(coords, 'coordinates', length=(/3, n_tracks/))
+    length = [3, n_tracks]
+    call binout % write_data(coords, 'coordinates', length=length)
     call binout % file_close()
     deallocate(coords)
   end subroutine finalize_particle_track

src/utils/convert_xsdir.py

@@ -35,8 +35,12 @@ class Xsdir(object):
         words = line.split()
         if words:
             if words[0].lower().startswith('datapath'):
-                index = line.index('=')
-                self.datapath = line[index+1:].strip()
+                if '=' in words[0]:
+                    index = line.index('=')
+                    self.datapath = line[index+1:].strip()
+                else:
+                    if len(line.strip()) > 8:
+                        self.datapath = line[8:].strip()
             else:
                 self.f.seek(0)
 

src/utils/plot_mesh_tally.py

@@ -1,262 +1,279 @@
 #!/usr/bin/env python2
 
-'''Python script to plot tally data generated by OpenMC.'''
+"""Python script to plot tally data generated by OpenMC."""
 
+import os
 import sys
-from statepoint import *
 
-# Color intensity dependent on individual score?
-
-from PyQt4.QtCore import *
-from PyQt4.QtGui import *
-import matplotlib.pyplot as plt
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
+from matplotlib.backends.backend_tkagg import NavigationToolbar2TkAgg
 from matplotlib.figure import Figure
-from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar
+import matplotlib.pyplot as plt
 import numpy as np
 
-class AppForm(QMainWindow):
-    def __init__(self, parent=None):
-        QMainWindow.__init__(self, parent)
+from statepoint import *
+
+if sys.version_info[0] < 3:
+    import Tkinter as tk
+else:
+    import tkinter as tk
+import tkFileDialog
+import tkFont
+import tkMessageBox
+import ttk
+
+
+class MeshPlotter(tk.Frame):
+    def __init__(self, parent, filename):
+        tk.Frame.__init__(self, parent)
+
+        self.labels = {'cell': 'Cell:', 'cellborn': 'Cell born:',
+                       'surface': 'Surface:', 'material': 'Material:',
+                       'universe': 'Universe:', 'energyin': 'Energy in:',
+                       'energyout': 'Energy out:'}
+
+        self.filterBoxes = {}
 
         # Read data from source or leakage fraction file
-        self.get_file_data()
-        self.main_frame = QWidget() 
-        self.setCentralWidget(self.main_frame)
-       
-        # Create the Figure, Canvas, and Axes
+        self.get_file_data(filename)
+
+        # Set up top-level window
+        top = self.winfo_toplevel()
+        top.title('Mesh Tally Plotter: ' + filename)
+        top.rowconfigure(0, weight=1)
+        top.columnconfigure(0, weight=1)
+        self.grid(sticky=tk.W+tk.N)
+
+        # Create widgets and draw to screen
+        self.create_widgets()
+        self.update()
+
+    def create_widgets(self):
+        figureFrame = tk.Frame(self)
+        figureFrame.grid(row=0, column=0)
+
+        # Create the Figure and Canvas
         self.dpi = 100
-        self.fig = Figure((5.0, 15.0), dpi=self.dpi)
-        self.canvas = FigureCanvas(self.fig)
-        self.canvas.setParent(self.main_frame)
-        self.axes = self.fig.add_subplot(111)
-        
+        self.fig = Figure((5.0, 5.0), dpi=self.dpi)
+        self.canvas = FigureCanvasTkAgg(self.fig, master=figureFrame)
+        self.canvas.get_tk_widget().pack(side=tk.TOP, fill=tk.BOTH, expand=1)
+
         # Create the navigation toolbar, tied to the canvas
-        self.mpl_toolbar = NavigationToolbar(self.canvas, self.main_frame)
+        self.mpl_toolbar = NavigationToolbar2TkAgg(self.canvas, figureFrame)
+        self.mpl_toolbar.update()
+        self.canvas._tkcanvas.pack(side=tk.TOP, fill=tk.BOTH, expand=1)
 
-        # Grid layout at bottom
-        self.grid = QGridLayout()
+        # Create frame for comboboxes
+        self.selectFrame = tk.Frame(self)
+        self.selectFrame.grid(row=1, column=0, sticky=tk.W+tk.E)
 
-        # Overall layout
-        self.vbox = QVBoxLayout()
-        self.vbox.addWidget(self.canvas)
-        self.vbox.addWidget(self.mpl_toolbar)
-        self.vbox.addLayout(self.grid)
-        self.main_frame.setLayout(self.vbox)
+        # Tally selection
+        labelTally = tk.Label(self.selectFrame, text='Tally:')
+        labelTally.grid(row=0, column=0, sticky=tk.W)
+        self.tallyBox = ttk.Combobox(self.selectFrame, state='readonly')
+        self.tallyBox['values'] = [self.datafile.tallies[i].id
+                                   for i in self.meshTallies]
+        self.tallyBox.current(0)
+        self.tallyBox.grid(row=0, column=1, sticky=tk.W+tk.E)
+        self.tallyBox.bind('<<ComboboxSelected>>', self.update)
 
-        # Tally selections
-        label_tally = QLabel("Tally:")
-        self.tally = QComboBox()
-        self.tally.addItems([(str(i + 1)) for i in range(self.n_tallies)])
-        self.connect(self.tally, SIGNAL('activated(int)'),
-                     self._update)
-        self.connect(self.tally, SIGNAL('activated(int)'),
-                     self.populate_boxes)
-        self.connect(self.tally, SIGNAL('activated(int)'),
-                     self.on_draw)
+        # Planar basis selection
+        labelBasis = tk.Label(self.selectFrame, text='Basis:')
+        labelBasis.grid(row=1, column=0, sticky=tk.W)
+        self.basisBox = ttk.Combobox(self.selectFrame, state='readonly')
+        self.basisBox['values'] = ('xy', 'yz', 'xz')
+        self.basisBox.current(0)
+        self.basisBox.grid(row=1, column=1, sticky=tk.W+tk.E)
+        self.basisBox.bind('<<ComboboxSelected>>', self.update)
 
-        # Planar basis
-        label_basis = QLabel("Basis:")
-        self.basis = QComboBox()
-        self.basis.addItems(['xy', 'yz', 'xz'])
+        # Axial level
+        labelAxial = tk.Label(self.selectFrame, text='Axial level:')
+        labelAxial.grid(row=2, column=0, sticky=tk.W)
+        self.axialBox = ttk.Combobox(self.selectFrame, state='readonly')
+        self.axialBox.grid(row=2, column=1, sticky=tk.W+tk.E)
+        self.axialBox.bind('<<ComboboxSelected>>', self.redraw)
 
-        # Update window when 'Basis' selection is changed
-        self.connect(self.basis, SIGNAL('activated(int)'),
-                     self._update)
-        self.connect(self.basis, SIGNAL('activated(int)'),
-                     self.populate_boxes)
-        self.connect(self.basis, SIGNAL('activated(int)'),
-                     self.on_draw)
+        # Option for mean/uncertainty
+        labelMean = tk.Label(self.selectFrame, text='Mean/Uncertainty:')
+        labelMean.grid(row=3, column=0, sticky=tk.W)
+        self.meanBox = ttk.Combobox(self.selectFrame, state='readonly')
+        self.meanBox['values'] = ('Mean', 'Absolute uncertainty',
+                                  'Relative uncertainty')
+        self.meanBox.current(0)
+        self.meanBox.grid(row=3, column=1, sticky=tk.W+tk.E)
+        self.meanBox.bind('<<ComboboxSelected>>', self.update)
 
-        # Axial level within selected basis
-        label_axial_level = QLabel("Axial Level:")
-        self.axial_level = QComboBox()
-        self.connect(self.axial_level, SIGNAL('activated(int)'),
-                     self.on_draw)
-                     
-        # Add Option to plot mean or uncertainty
-        label_mean = QLabel("Mean or Uncertainty:")
-        self.mean = QComboBox()
-        self.mean.addItems(['Mean','Absolute Uncertainty', 
-                            'Relative Uncertainty'])
-        
-        # Update window when mean selection is changed
-        self.connect(self.mean, SIGNAL('activated(int)'),
-                     self.on_draw)
-        
+        # Scores
+        labelScore = tk.Label(self.selectFrame, text='Score:')
+        labelScore.grid(row=4, column=0, sticky=tk.W)
+        self.scoreBox = ttk.Combobox(self.selectFrame, state='readonly')
+        self.scoreBox.grid(row=4, column=1, sticky=tk.W+tk.E)
+        self.scoreBox.bind('<<ComboboxSelected>>', self.redraw)
 
-        self.label_filters = QLabel("Filter options:")
+        # Filter label
+        font = tkFont.Font(weight='bold')
+        labelFilters = tk.Label(self.selectFrame, text='Filters:', font=font)
+        labelFilters.grid(row=5, column=0, sticky=tk.W)
 
-        # Labels for all possible filters
-        self.labels = {'cell': 'Cell: ', 'cellborn': 'Cell born: ',
-                       'surface': 'Surface: ', 'material': 'Material',
-                       'universe': 'Universe: ', 'energyin': 'Energy in: ',
-                       'energyout': 'Energy out: '}
+    def update(self, event=None):
+        if not event:
+            widget = None
+        else:
+            widget = event.widget
 
-        # Empty reusable labels
-        self.qlabels = {}
-        for j in range(8):
-            self.nextLabel = QLabel
-            self.qlabels[j] = self.nextLabel
+        tally_id = self.meshTallies[self.tallyBox.current()]
+        selectedTally = self.datafile.tallies[tally_id]
 
-        # Reusable comboboxes labelled with filter names
-        self.boxes = {}
-        for key in self.labels.keys():
-            self.nextBox = QComboBox()
-            self.connect(self.nextBox, SIGNAL('activated(int)'),
-                         self.on_draw)
-            self.boxes[key] = self.nextBox
+        # Get mesh for selected tally
+        self.mesh = self.datafile.meshes[
+            selectedTally.filters['mesh'].bins[0] - 1]
 
-        # Combobox to select among scores
-        self.score_label = QLabel("Score:")
-        self.scoreBox = QComboBox()
-        for item in self.tally_scores[0]:
-            self.scoreBox.addItems(str(item))
-        self.connect(self.scoreBox, SIGNAL('activated(int)'),
-                     self.on_draw)
+        # Get mesh dimensions
+        self.nx, self.ny, self.nz = self.mesh.dimension
 
-        # Fill layout
-        self.grid.addWidget(label_tally, 0, 0)
-        self.grid.addWidget(self.tally, 0, 1)
-        self.grid.addWidget(label_basis, 1, 0)
-        self.grid.addWidget(self.basis, 1, 1)
-        self.grid.addWidget(label_axial_level, 2, 0)
-        self.grid.addWidget(self.axial_level, 2, 1)
-        self.grid.addWidget(label_mean, 3, 0)
-        self.grid.addWidget(self.mean, 3, 1)
-        self.grid.addWidget(self.label_filters, 4, 0)
+        # Repopulate comboboxes baesd on current basis selection
+        text = self.basisBox['values'][self.basisBox.current()]
+        if text == 'xy':
+            self.axialBox['values'] = [str(i+1) for i in range(self.nz)]
+        elif text == 'yz':
+            self.axialBox['values'] = [str(i+1) for i in range(self.nx)]
+        else:
+            self.axialBox['values'] = [str(i+1) for i in range(self.ny)]
+        self.axialBox.current(0)
 
-        self._update()
-        self.populate_boxes() 
-        self.on_draw()
+        # If update() was called by a change in the basis combobox, we don't
+        # need to repopulate the filters
+        if widget == self.basisBox:
+            self.redraw()
+            return
 
-    def get_file_data(self):
-        # Get data file name from "open file" browser
-        filename = QFileDialog.getOpenFileName(self, 'Select statepoint file', '.')
+        # Update scores
+        self.scoreBox['values'] = selectedTally.scores
+        self.scoreBox.current(0)
 
-        # Create StatePoint object and read in data
-        self.datafile = StatePoint(str(filename))
-        self.datafile.read_results()
-        self.datafile.generate_stdev()
+        # Remove any filter labels/comboboxes that exist
+        for row in range(6, self.selectFrame.grid_size()[1]):
+            for w in self.selectFrame.grid_slaves(row=row):
+                w.grid_forget()
+                w.destroy()
 
-        self.setWindowTitle('Core Map Tool : ' + str(self.datafile.path))
+        # create a label/combobox for each filter in selected tally
+        count = 0
+        for filterType in selectedTally.filters:
+            if filterType == 'mesh':
+                continue
+            count += 1
 
-        # Set maximum colorbar value by maximum tally data value
-        self.maxvalue = self.datafile.tallies[0].results.max()
+            # Create label and combobox for this filter
+            label = tk.Label(self.selectFrame, text=self.labels[filterType])
+            label.grid(row=count+6, column=0, sticky=tk.W)
+            combobox = ttk.Combobox(self.selectFrame, state='readonly')
+            self.filterBoxes[filterType] = combobox
 
-        self.labelList = []
+            # Set combobox items
+            f = selectedTally.filters[filterType]
+            if filterType in ['energyin', 'energyout']:
+                combobox['values'] = ['{0} to {1}'.format(*f.bins[i:i+2])
+                                      for i in range(f.length)]
+            else:
+                combobox['values'] = [str(i) for i in f.bins]
 
-        # Read mesh dimensions
-#        for mesh in self.datafile.meshes:
-#            self.nx, self.ny, self.nz = mesh.dimension
+            combobox.current(0)
+            combobox.grid(row=count+6, column=1, sticky=tk.W+tk.E)
+            combobox.bind('<<ComboboxSelected>>', self.redraw)
 
-        # Read filter types from statepoint file
-        self.n_tallies = len(self.datafile.tallies)
-        self.tally_list = []
-        for tally in self.datafile.tallies:
-            self.filter_types = []
-            for f in tally.filters:
-                self.filter_types.append(f)
-            self.tally_list.append(self.filter_types)
+        # If There are no filters, leave a 'None available' message
+        if count == 0:
+            count += 1
+            label = tk.Label(self.selectFrame, text="None Available")
+            label.grid(row=count+6, column=0, sticky=tk.W)
 
-        # Read score types from statepoint file
-        self.tally_scores = []
-        for tally in self.datafile.tallies:
-            self.score_types = []
-            for s in tally.scores:
-                self.score_types.append(s)
-            self.tally_scores.append(self.score_types)
-#        print 'self.tally_scores = ', self.tally_scores
+        self.redraw()
 
-    def on_draw(self):
-        """ Redraws the figure
-        """
+    def redraw(self, event=None):
+        basis = self.basisBox.current() + 1
+        axial_level = self.axialBox.current() + 1
+        is_mean = self.meanBox.current()
 
-#        print 'Calling on_draw...'
-        # Get selected basis, axial_level and stage
-        basis = self.basis.currentIndex() + 1
-        axial_level = self.axial_level.currentIndex() + 1
-        is_mean = self.mean.currentIndex()
+        # Get selected tally
+        tally_id = self.meshTallies[self.tallyBox.current()]
+        selectedTally = self.datafile.tallies[tally_id]
 
         # Create spec_list
         spec_list = []
-        for tally in self.datafile.tallies[self.tally.currentIndex()].filters.values():
-            if tally.type == 'mesh':
+        for f in selectedTally.filters.values():
+            if f.type == 'mesh':
                 continue
-            index = self.boxes[tally.type].currentIndex()
-            spec_list.append((tally.type, index))
-        
+            index = self.filterBoxes[f.type].current()
+            spec_list.append((f.type, index))
+
         # Take is_mean and convert it to an index of the score
         score_loc = is_mean
         if score_loc > 1:
             score_loc = 1
-        
-        if self.basis.currentText() == 'xy':
+
+        text = self.basisBox['values'][self.basisBox.current()]
+        if text == 'xy':
             matrix = np.zeros((self.nx, self.ny))
             for i in range(self.nx):
                 for j in range(self.ny):
-                    matrix[i,j] = self.datafile.get_value(self.tally.currentIndex(), 
-                        spec_list + [('mesh', (i, j, axial_level))], 
-                        self.scoreBox.currentIndex())[score_loc]
-                    # Calculate relative uncertainty from absolute, if
-                    # requested
+                    matrix[i, j] = self.datafile.get_value(tally_id,
+                        spec_list + [('mesh', (i + 1, j + 1, axial_level))],
+                        self.scoreBox.current())[score_loc]
+                    # Calculate relative uncertainty from absolute, if requested
                     if is_mean == 2:
                         # Take care to handle zero means when normalizing
-                        mean_val = self.datafile.get_value(self.tally.currentIndex(), 
-                            spec_list + [('mesh', (i, j, axial_level))], 
-                            self.scoreBox.currentIndex())[0]
+                        mean_val = self.datafile.get_value(tally_id,
+                            spec_list + [('mesh', (i + 1, j + 1, axial_level))],
+                            self.scoreBox.current())[0]
                         if mean_val > 0.0:
-                            matrix[i,j] = matrix[i,j] / mean_val
+                            matrix[i, j] = matrix[i, j] / mean_val
                         else:
-                            matrix[i,j] = 0.0
-                        
-        elif self.basis.currentText() == 'yz':
+                            matrix[i, j] = 0.0
+
+        elif text == 'yz':
             matrix = np.zeros((self.ny, self.nz))
             for i in range(self.ny):
                 for j in range(self.nz):
-                    matrix[i,j] = self.datafile.get_value(self.tally.currentIndex(), 
-                        spec_list + [('mesh', (axial_level, i, j))], 
-                        self.scoreBox.currentIndex())[score_loc]
-                    # Calculate relative uncertainty from absolute, if
-                    # requested
+                    matrix[i, j] = self.datafile.get_value(tally_id,
+                        spec_list + [('mesh', (axial_level, i + 1, j + 1))],
+                        self.scoreBox.current())[score_loc]
+                    # Calculate relative uncertainty from absolute, if requested
                     if is_mean == 2:
                         # Take care to handle zero means when normalizing
-                        mean_val = self.datafile.get_value(self.tally.currentIndex(), 
-                            spec_list + [('mesh', (axial_level, i, j))], 
-                            self.scoreBox.currentIndex())[0]
+                        mean_val = self.datafile.get_value(tally_id,
+                            spec_list + [('mesh', (axial_level, i + 1, j + 1))],
+                            self.scoreBox.current())[0]
                         if mean_val > 0.0:
-                            matrix[i,j] = matrix[i,j] / mean_val
+                            matrix[i, j] = matrix[i, j] / mean_val
                         else:
-                            matrix[i,j] = 0.0
-                   
+                            matrix[i, j] = 0.0
+
         else:
             matrix = np.zeros((self.nx, self.nz))
             for i in range(self.nx):
                 for j in range(self.nz):
-                    matrix[i,j] = self.datafile.get_value(self.tally.currentIndex(), 
-                        spec_list + [('mesh', (i, axial_level, j))], 
-                        self.scoreBox.currentIndex())[score_loc]
-                    # Calculate relative uncertainty from absolute, if
-                    # requested
+                    matrix[i, j] = self.datafile.get_value(tally_id,
+                        spec_list + [('mesh', (i + 1, axial_level, j + 1))],
+                        self.scoreBox.current())[score_loc]
+                    # Calculate relative uncertainty from absolute, if requested
                     if is_mean == 2:
                         # Take care to handle zero means when normalizing
-                        mean_val = self.datafile.get_value(self.tally.currentIndex(), 
-                            spec_list + [('mesh', (i, axial_level, j))], 
-                            self.scoreBox.currentIndex())[0]
+                        mean_val = self.datafile.get_value(tally_id,
+                            spec_list + [('mesh', (i + 1, axial_level, j + 1))],
+                            self.scoreBox.current())[0]
                         if mean_val > 0.0:
-                            matrix[i,j] = matrix[i,j] / mean_val
+                            matrix[i, j] = matrix[i, j] / mean_val
                         else:
-                            matrix[i,j] = 0.0
-
-#        print spec_list
+                            matrix[i, j] = 0.0
 
         # Clear the figure
         self.fig.clear()
 
         # Make figure, set up color bar
         self.axes = self.fig.add_subplot(111)
-        cax = self.axes.imshow(matrix, vmin=0.0, vmax=matrix.max(), 
-          interpolation="nearest")
+        cax = self.axes.imshow(matrix.transpose(), vmin=0.0, vmax=matrix.max(),
+                               interpolation='none', origin='lower')
         self.fig.colorbar(cax)
 
         self.axes.set_xticks([])
@@ -266,95 +283,43 @@ class AppForm(QMainWindow):
         # Draw canvas
         self.canvas.draw()
 
-    def _update(self):
-        '''Updates widget to display new relevant comboboxes and figure data
-        '''
-#        print 'Calling _update...'
+    def get_file_data(self, filename):
+        # Create StatePoint object and read in data
+        self.datafile = StatePoint(filename)
+        self.datafile.read_results()
+        self.datafile.generate_stdev()
 
-        self.mesh = self.datafile.meshes[
-          self.datafile.tallies[
-          self.tally.currentIndex()].filters['mesh'].bins[0] - 1]
+        # Find which tallies are mesh tallies
+        self.meshTallies = []
+        for itally, tally in enumerate(self.datafile.tallies):
+            if 'mesh' in tally.filters:
+                self.meshTallies.append(itally)
 
-        self.nx, self.ny, self.nz = self.mesh.dimension
-
-        # Clear axial level combobox
-        self.axial_level.clear()
-
-        # Repopulate axial level combobox based on current basis selection
-        if (self.basis.currentText() == 'xy'):
-            self.axial_level.addItems([str(i+1) for i in range(self.nz)])
-        elif (self.basis.currentText() == 'yz'):
-            self.axial_level.addItems([str(i+1) for i in range(self.nx)])
-        else:
-            self.axial_level.addItems([str(i+1) for i in range(self.ny)])
-
-        # Determine maximum value from current tally data set
-        self.maxvalue = self.datafile.tallies[
-          self.tally.currentIndex()].results.max()
-#        print self.maxvalue
-
-        # Clear and hide old filter labels
-        for item in self.labelList:
-            item.clear()
-
-        # Clear and hide old filter boxes
-        for j in self.labels:
-            self.boxes[j].clear()
-            self.boxes[j].setParent(None)
-
-        self.update()
-
-    def populate_boxes(self):
-#        print 'Calling populate_boxes...'
-
-        n = 5
-        labels = {'cell': 'Cell : ',
-                       'cellborn': 'Cell born: ',
-                       'surface': 'Surface: ',
-                       'material': 'Material: ',
-                       'universe': 'Universe: '}
-
-        # For each filter in newly-selected tally, name a label and fill the
-        # relevant combobox with options
-        for element in self.tally_list[self.tally.currentIndex()]:
-            nextFilter = self.datafile.tallies[
-              self.tally.currentIndex()].filters[element]
-            if element == 'mesh':
-                continue
-
-            label = QLabel(self.labels[element])
-            self.labelList.append(label)
-            combobox = self.boxes[element]
-            self.grid.addWidget(label, n, 0)
-            self.grid.addWidget(combobox, n, 1)
-            n += 1
-
-#            print element
-            if element in ['cell', 'cellborn', 'surface', 'material', 'universe']:
-                combobox.addItems([str(i) for i in nextFilter.bins])
-#                for i in nextFilter.bins:
-#                    print i
-
-            elif element == 'energyin' or element == 'energyout':
-                for i in range(nextFilter.length):
-                    text = (str(nextFilter.bins[i]) + ' to ' + 
-                      str(nextFilter.bins[i+1]))
-                    combobox.addItem(text)
-
-        self.scoreBox.clear()
-        for item in self.tally_scores[self.tally.currentIndex()]:
-            self.scoreBox.addItem(str(item))
-        self.grid.addWidget(self.score_label, n, 0)
-        self.grid.addWidget(self.scoreBox, n, 1)
+        if not self.meshTallies:
+            tkMessageBox.showerror("Invalid StatePoint File",
+                                   "File does not contain mesh tallies!")
+            sys.exit(1)
 
 
+if __name__ == '__main__':
+    # Hide root window
+    root = tk.Tk()
+    root.withdraw()
 
-def main():
-    app = QApplication(sys.argv)
-    form = AppForm()
-    form.show()
-    app.exec_()
+    # If no filename given as command-line argument, open file dialog
+    if len(sys.argv) < 2:
+        filename = tkFileDialog.askopenfilename(title='Select statepoint file',
+                                                initialdir='.')
+    else:
+        filename = sys.argv[1]
 
+    if filename:
+        # Check to make sure file exists
+        if not os.path.isfile(filename):
+            tkMessageBox.showerror("File not found",
+                                   "Could not find regular file: " + filename)
+            sys.exit(1)
 
-if __name__ == "__main__":
-    main()
+        app = MeshPlotter(root, filename)
+        root.deiconify()
+        root.mainloop()

src/utils/statepoint.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python2
 
 import struct
-from math import sqrt
 from collections import OrderedDict
 
 import numpy as np
@@ -10,10 +9,10 @@ import scipy.stats
 filter_types = {1: 'universe', 2: 'material', 3: 'cell', 4: 'cellborn',
                 5: 'surface', 6: 'mesh', 7: 'energyin', 8: 'energyout'}
 
-score_types = {-1: 'flux', 
+score_types = {-1: 'flux',
                 -2: 'total',
                 -3: 'scatter',
-                -4: 'nu-scatter', 
+                -4: 'nu-scatter',
                 -5: 'scatter-n',
                 -6: 'scatter-pn',
                 -7: 'transport',
@@ -152,7 +151,7 @@ class StatePoint(object):
 
         # Read statepoint revision
         self.revision = self._get_int(path='revision')[0]
-        if self.revision != 10:
+        if self.revision != 11:
           raise Exception('Statepoint Revision is not consistent.')
 
         # Read OpenMC version
@@ -276,7 +275,7 @@ class StatePoint(object):
                     f.bins = self._get_int(path=base+'bins')
                 else:
                     f.bins = self._get_int(f.length, path=base+'bins')
-            
+
             base = 'tallies/tally' + str(i+1) + '/'
 
             # Read nuclide bins
@@ -299,6 +298,13 @@ class StatePoint(object):
                 f.stride = stride
                 stride *= f.length
 
+        # Source bank present
+        source_present = self._get_int(path='source_present')[0]
+        if source_present == 1:
+            self.source_present = True       
+        else:
+            self.source_present = False
+
         # Set flag indicating metadata has already been read
         self._metadata = True
 
@@ -343,6 +349,11 @@ class StatePoint(object):
         if not self._results:
             self.read_results()
 
+        # Check if source bank is in statepoint
+        if not self.source_present:
+            print('Source not in statepoint file.')
+            return
+
         # For HDF5 state points, copy entire bank
         if self._hdf5:
             source_sites = self._f['source_bank'].value
@@ -379,7 +390,7 @@ class StatePoint(object):
         Calculates the sample mean and standard deviation of the mean for each
         tally bin.
         """
-        
+
         # Determine number of realizations
         n = self.n_realizations
 
@@ -387,14 +398,14 @@ class StatePoint(object):
         for i in range(len(self.global_tallies)):
             # Get sum and sum of squares
             s, s2 = self.global_tallies[i]
-                    
+
             # Calculate sample mean and replace value
             s /= n
             self.global_tallies[i,0] = s
 
             # Calculate standard deviation
             if s != 0.0:
-                self.global_tallies[i,1] = t_value*sqrt((s2/n - s*s)/(n-1))
+                self.global_tallies[i,1] = t_value*np.sqrt((s2/n - s*s)/(n-1))
 
         # Regular tallies
         for t in self.tallies:
@@ -402,14 +413,14 @@ class StatePoint(object):
                 for j in range(t.results.shape[1]):
                     # Get sum and sum of squares
                     s, s2 = t.results[i,j]
-                    
+
                     # Calculate sample mean and replace value
                     s /= n
                     t.results[i,j,0] = s
 
                     # Calculate standard deviation
                     if s != 0.0:
-                        t.results[i,j,1] = t_value*sqrt((s2/n - s*s)/(n-1))
+                        t.results[i,j,1] = t_value*np.sqrt((s2/n - s*s)/(n-1))
 
     def get_value(self, tally_index, spec_list, score_index):
         """Returns a tally score given a list of filters to satisfy.
@@ -458,7 +469,7 @@ class StatePoint(object):
                 filter_index += value*t.filters[f_type].stride
             else:
                 filter_index += f_index*t.filters[f_type].stride
-        
+
         # Return the desired result from Tally.results. This could be the sum and
         # sum of squares, or it could be mean and stdev if self.generate_stdev()
         # has been called already.
@@ -531,7 +542,7 @@ class StatePoint(object):
         for i in range(n_filters):
 
             # compute indices for filter combination
-            filters[:,n_filters - i - 1] = np.floor((np.arange(n_bins) % 
+            filters[:,n_filters - i - 1] = np.floor((np.arange(n_bins) %
                    np.prod(filtmax[0:i+2]))/(np.prod(filtmax[0:i+1]))) + 1
 
             # append in dictionary bin with filter
@@ -544,14 +555,14 @@ class StatePoint(object):
                 dims.reverse()
                 dims = np.asarray(dims)
                 if score_str == 'current':
-                    dims += 1 
-                meshmax[1:4] = dims 
+                    dims += 1
+                meshmax[1:4] = dims
                 mesh_bins = np.zeros((n_bins,3))
-                mesh_bins[:,2] = np.floor(((filters[:,n_filters - i - 1] - 1) % 
+                mesh_bins[:,2] = np.floor(((filters[:,n_filters - i - 1] - 1) %
                             np.prod(meshmax[0:2]))/(np.prod(meshmax[0:1]))) + 1
-                mesh_bins[:,1] = np.floor(((filters[:,n_filters - i - 1] - 1) % 
+                mesh_bins[:,1] = np.floor(((filters[:,n_filters - i - 1] - 1) %
                             np.prod(meshmax[0:3]))/(np.prod(meshmax[0:2]))) + 1
-                mesh_bins[:,0] = np.floor(((filters[:,n_filters - i - 1] - 1) % 
+                mesh_bins[:,0] = np.floor(((filters[:,n_filters - i - 1] - 1) %
                             np.prod(meshmax[0:4]))/(np.prod(meshmax[0:3]))) + 1
                 data.update({'mesh':zip(mesh_bins[:,0],mesh_bins[:,1],
                             mesh_bins[:,2])})
@@ -576,7 +587,7 @@ class StatePoint(object):
     def _get_data(self, n, typeCode, size):
         return list(struct.unpack('={0}{1}'.format(n,typeCode),
                                   self._f.read(n*size)))
-    
+
     def _get_int(self, n=1, path=None):
         if self._hdf5:
             return [int(v) for v in self._f[path].value]

src/xml/dom/FoX_dom.F90

@@ -74,6 +74,7 @@ module FoX_dom
   public :: createAttribute
   public :: createEntityReference
   public :: getElementsByTagName
+  public :: getChildrenByTagName
   public :: getElementById
 
   public :: importNode

src/xml/dom/m_dom_dom.F90

@@ -349,6 +349,7 @@ module m_dom_dom
   public :: createEntityReference
   public :: createEmptyEntityReference
   public :: getElementsByTagName
+  public :: getChildrenByTagName
   public :: importNode
   public :: createElementNS
   public :: createAttributeNS
@@ -6908,6 +6909,166 @@ endif
 
   end function getElementsByTagName
 
+  function getChildrenByTagName(doc, tagName, name, ex)result(list) 
+    type(DOMException), intent(out), optional :: ex
+    type(Node), pointer :: doc
+    character(len=*), intent(in), optional :: tagName, name
+    type(NodeList), pointer :: list
+
+    type(NodeListPtr), pointer :: nll(:), temp_nll(:)
+    type(Node), pointer :: arg, this, treeroot
+    logical :: doneChildren, doneAttributes, allElements
+    integer :: i, i_tree
+
+    if (.not.associated(doc)) then
+      if (getFoX_checks().or.FoX_NODE_IS_NULL<200) then
+  call throw_exception(FoX_NODE_IS_NULL, "getElementsByTagName", ex)
+  if (present(ex)) then
+    if (inException(ex)) then
+       return
+    endif
+  endif
+endif
+
+    endif
+
+    if (doc%nodeType==DOCUMENT_NODE) then
+      if (present(name).or..not.present(tagName)) then
+        if (getFoX_checks().or.FoX_INVALID_NODE<200) then
+  call throw_exception(FoX_INVALID_NODE, "getElementsByTagName", ex)
+  if (present(ex)) then
+    if (inException(ex)) then
+       return
+    endif
+  endif
+endif
+
+      endif
+    elseif (doc%nodeType==ELEMENT_NODE) then
+      if (present(name).or..not.present(tagName)) then
+        if (getFoX_checks().or.FoX_INVALID_NODE<200) then
+  call throw_exception(FoX_INVALID_NODE, "getElementsByTagName", ex)
+  if (present(ex)) then
+    if (inException(ex)) then
+       return
+    endif
+  endif
+endif
+
+      endif
+    else      
+      if (getFoX_checks().or.FoX_INVALID_NODE<200) then
+  call throw_exception(FoX_INVALID_NODE, "getElementsByTagName", ex)
+  if (present(ex)) then
+    if (inException(ex)) then
+       return
+    endif
+  endif
+endif
+
+    endif
+
+    if (doc%nodeType==DOCUMENT_NODE) then
+      arg => getDocumentElement(doc)
+    else
+      arg => doc
+    endif
+
+    allocate(list)
+    allocate(list%nodes(0))
+    list%element => doc
+    if (present(name)) list%nodeName => vs_str_alloc(name)
+    if (present(tagName)) list%nodeName => vs_str_alloc(tagName)
+
+    allElements = (str_vs(list%nodeName)=="*")
+
+    if (doc%nodeType==DOCUMENT_NODE) then
+      nll => doc%docExtras%nodelists
+    elseif (doc%nodeType==ELEMENT_NODE) then
+      nll => doc%ownerDocument%docExtras%nodelists
+    endif
+    allocate(temp_nll(size(nll)+1))
+    do i = 1, size(nll)
+      temp_nll(i)%this => nll(i)%this
+    enddo
+    temp_nll(i)%this => list
+    deallocate(nll)
+    if (doc%nodeType==DOCUMENT_NODE) then
+      doc%docExtras%nodelists => temp_nll
+    elseif (doc%nodeType==ELEMENT_NODE) then
+      doc%ownerDocument%docExtras%nodelists => temp_nll
+    endif
+
+    treeroot => arg
+
+    i_tree = 0
+    doneChildren = .false.
+    doneAttributes = .false.
+    this => treeroot
+    do
+      if (.not.doneChildren.and..not.(getNodeType(this)==ELEMENT_NODE.and.doneAttributes)) then
+        if (this%nodeType==ELEMENT_NODE) then
+          if ((allElements .or. str_vs(this%nodeName)==tagName) &
+            .and..not.(getNodeType(doc)==ELEMENT_NODE.and.associated(this, arg))) &
+            call append(list, this)
+          doneAttributes = .true.
+        endif
+
+      else
+        if (getNodeType(this)==ELEMENT_NODE.and..not.doneChildren) then
+          doneAttributes = .true.
+        else
+
+        endif
+      endif
+
+
+      if (.not.doneChildren) then
+        if (getNodeType(this)==ELEMENT_NODE.and..not.doneAttributes) then
+          if (getLength(getAttributes(this))>0) then
+            this => item(getAttributes(this), 0)
+          else
+            doneAttributes = .true.
+          endif
+        elseif (hasChildNodes(this) .and. .not. associated(getParentNode(this), treeroot)) then
+          this => getFirstChild(this)
+          doneChildren = .false.
+          doneAttributes = .false.
+        else
+          doneChildren = .true.
+          doneAttributes = .false.
+        endif
+
+      else ! if doneChildren
+
+        if (associated(this, treeroot)) exit
+        if (getNodeType(this)==ATTRIBUTE_NODE) then
+          if (i_tree<getLength(getAttributes(getOwnerElement(this)))-1) then
+            i_tree= i_tree+ 1
+            this => item(getAttributes(getOwnerElement(this)), i_tree)
+            doneChildren = .false.
+          else
+            i_tree= 0
+            this => getOwnerElement(this)
+            doneAttributes = .true.
+            doneChildren = .false.
+          endif
+        elseif (associated(getNextSibling(this))) then
+
+          this => getNextSibling(this)
+          doneChildren = .false.
+          doneAttributes = .false.
+        else
+          this => getParentNode(this)
+        endif
+      endif
+
+    enddo
+
+
+
+  end function getChildrenByTagName
+
   function importNode(doc , arg, deep , ex)result(np) 
     type(DOMException), intent(out), optional :: ex
     type(Node), pointer :: doc

src/xml_interface.F90

@@ -72,7 +72,7 @@ contains
 ! node name. This should only be used for checking a single occurance of a
 ! sub-element node. To check for sub-element nodes that repeat, use
 ! get_node_list and get_list_size. This is to minimize number of calls
-! to getElementsByTagName.
+! to getChildrenByTagName.
 !===============================================================================
 
   function check_for_node(ptr, node_name) result(found)
@@ -94,7 +94,7 @@ contains
     if (associated(temp_ptr)) return
 
     ! Check for a sub-element 
-    elem_list => getElementsByTagName(ptr, trim(node_name))
+    elem_list => getChildrenByTagName(ptr, trim(node_name))
 
     ! Get the length of the list
     if (getLength(elem_list) == 0) then
@@ -124,7 +124,7 @@ contains
     found_ = .false.
 
     ! Check for a sub-element 
-    elem_list => getElementsByTagName(in_ptr, trim(node_name))
+    elem_list => getChildrenByTagName(in_ptr, trim(node_name))
 
     ! Get the length of the list
     if (getLength(elem_list) == 0) return
@@ -149,7 +149,7 @@ contains
     type(NodeList), pointer, intent(out) :: out_ptr
 
     ! Check for a sub-element 
-    out_ptr => getElementsByTagName(in_ptr, trim(node_name))
+    out_ptr => getChildrenByTagName(in_ptr, trim(node_name))
 
   end subroutine get_node_list
 
@@ -525,7 +525,7 @@ contains
     if (associated(out_ptr)) return
 
     ! Check for a sub-element 
-    elem_list => getElementsByTagName(in_ptr, trim(node_name))
+    elem_list => getChildrenByTagName(in_ptr, trim(node_name))
 
     ! Get the length of the list
     if (getLength(elem_list) == 0) then

tests/cleanup

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# 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.
+find . \( -name "*.binary" -o -name "*.h5" \) -exec rm -f {} \;

tests/run_tests.py

@@ -117,6 +117,8 @@ if len(sys.argv) > 1:
                     if j.rfind(suffix) != -1:
                         if suffix == 'omp' and j == 'compile':
                             continue
+                        if j == 'compile':
+                            continue 
                         tests__.append(j)
         else:
             tests__.append(i)  # append specific test (e.g., mpi-debug)

tests/test_source_file/geometry.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Sphere with radius 10 -->
+  <surface id="1" type="sphere" coeffs="0 0 0 10" boundary="vacuum"/>
+  <cell id="1" material="1" surfaces="-1" />
+    
+</geometry>

tests/test_source_file/materials.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<materials>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" xs="70c" ao="1.0" />
+  </material>
+
+</materials>

tests/test_source_file/results.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+import sys
+
+# import statepoint
+sys.path.append('../../src/utils')
+import statepoint
+
+# read in statepoint file
+if len(sys.argv) > 1:
+    sp = statepoint.StatePoint(sys.argv[1])
+else:
+    sp = statepoint.StatePoint('statepoint.10.binary')
+sp.read_results()
+
+# set up output string
+outstr = ''
+ 
+# write out k-combined
+outstr += 'k-combined:\n'
+outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
+
+# write results to file
+with open('results_test.dat','w') as fh:
+    fh.write(outstr)

tests/test_source_file/results_true.dat

@@ -0,0 +1,2 @@
+k-combined:
+2.977307E-01 2.848670E-03

tests/test_source_file/settings.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<settings>
+
+  <state_point batches="10" />
+  <source_point separate="true" />
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>

tests/test_source_file/test_source_file.py

@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+import os
+from subprocess import Popen, STDOUT, PIPE, call
+import filecmp
+from nose_mpi import NoseMPI
+import glob
+
+pwd = os.path.dirname(__file__)
+
+settings1="""<?xml version="1.0"?>
+<settings>
+
+  <state_point batches="10" />
+  <source_point separate="true" />
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>
+"""
+
+settings2 = """<?xml version="1.0"?>
+<settings>
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <file> source.10.{0} </file>
+  </source>
+
+</settings>
+"""
+
+def setup(): 
+    os.putenv('PWD', pwd)
+    os.chdir(pwd)
+
+def test_run1():
+    openmc_path = pwd + '/../../src/openmc'
+    if int(NoseMPI.mpi_np) > 0:
+        proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([openmc_path], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0
+
+def test_statepoint_exists():
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
+    assert len(statepoint) == 1
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+    source = glob.glob(pwd + '/source.10.*')
+    assert len(statepoint) == 1
+    assert source[0].endswith('binary') or source[0].endswith('h5')
+
+def test_run2():
+    openmc_path = pwd + '/../../src/openmc'
+    source = glob.glob(pwd + '/source.10.*')
+    with open('settings.xml','w') as fh:
+        fh.write(settings2.format(source[0].split('.')[2]))
+    if int(NoseMPI.mpi_np) > 0:
+        proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([openmc_path], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0
+
+def test_results():
+    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
+
+def teardown():
+    with open('settings.xml','w') as fh:
+        fh.write(settings1)
+    output = glob.glob(pwd + '/statepoint.10.*')
+    output += glob.glob(pwd + '/source.10.*')
+    output.append(pwd + '/results_test.dat')
+    for f in output:
+        if os.path.exists(f):
+            os.remove(f)

tests/test_sourcepoint_batch/geometry.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Sphere with radius 10 -->
+  <surface id="1" type="sphere" coeffs="0 0 0 10" boundary="vacuum"/>
+  <cell id="1" material="1" surfaces="-1" />
+    
+</geometry>

tests/test_sourcepoint_batch/materials.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<materials>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" xs="70c" ao="1.0" />
+  </material>
+
+</materials>

tests/test_sourcepoint_batch/results.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+import sys
+
+# import statepoint
+sys.path.append('../../src/utils')
+import statepoint
+
+# read in statepoint file
+if len(sys.argv) > 1:
+    sp = statepoint.StatePoint(sys.argv[1])
+else:
+    sp = statepoint.StatePoint('statepoint.8.binary')
+sp.read_results()
+sp.read_source()
+
+# set up output string
+outstr = ''
+ 
+# write out k-combined
+outstr += 'k-combined:\n'
+outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
+
+# write out xyz
+xyz = sp.source[0].xyz
+for i in xyz:
+    outstr += "{0:12.6E} ".format(i)
+outstr += "\n"
+
+# write results to file
+with open('results_test.dat','w') as fh:
+    fh.write(outstr)

tests/test_sourcepoint_batch/results_true.dat

@@ -0,0 +1,3 @@
+k-combined:
+0.000000E+00 0.000000E+00
+-9.438655E-02 -4.436810E+00 -2.416825E+00 

tests/test_sourcepoint_batch/settings.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<settings>
+
+  <state_point batches="2 3 4 5 8"/>
+  <source_point batches="2 5 8"/>
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>

tests/test_sourcepoint_batch/test_sourcepoint_batch.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import os
+from subprocess import Popen, STDOUT, PIPE, call
+import filecmp
+from nose_mpi import NoseMPI
+import glob
+
+pwd = os.path.dirname(__file__)
+
+def setup(): 
+    os.putenv('PWD', pwd)
+    os.chdir(pwd)
+
+def test_run():
+    openmc_path = pwd + '/../../src/openmc'
+    if int(NoseMPI.mpi_np) > 0:
+        proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([openmc_path], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0
+
+def test_statepoint_exists():
+    statepoint = glob.glob(pwd + '/statepoint.*')
+    assert len(statepoint) == 5
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+
+def test_results():
+    statepoint = glob.glob(pwd + '/statepoint.8.*')
+    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
+
+def teardown():
+    output = glob.glob(pwd + '/statepoint.*')
+    output.append(pwd + '/results_test.dat')
+    for f in output:
+        if os.path.exists(f):
+            os.remove(f)

tests/test_sourcepoint_interval/geometry.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Sphere with radius 10 -->
+  <surface id="1" type="sphere" coeffs="0 0 0 10" boundary="vacuum"/>
+  <cell id="1" material="1" surfaces="-1" />
+    
+</geometry>

tests/test_sourcepoint_interval/materials.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<materials>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" xs="70c" ao="1.0" />
+  </material>
+
+</materials>

tests/test_sourcepoint_interval/results.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+import sys
+
+# import statepoint
+sys.path.append('../../src/utils')
+import statepoint
+
+# read in statepoint file
+if len(sys.argv) > 1:
+    sp = statepoint.StatePoint(sys.argv[1])
+else:
+    sp = statepoint.StatePoint('statepoint.8.binary')
+sp.read_results()
+sp.read_source()
+
+# set up output string
+outstr = ''
+ 
+# write out k-combined
+outstr += 'k-combined:\n'
+outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
+
+# write out xyz
+xyz = sp.source[0].xyz
+for i in xyz:
+    outstr += "{0:12.6E} ".format(i)
+outstr += "\n"
+
+# write results to file
+with open('results_test.dat','w') as fh:
+    fh.write(outstr)

tests/test_sourcepoint_interval/results_true.dat

@@ -0,0 +1,3 @@
+k-combined:
+0.000000E+00 0.000000E+00
+-9.438655E-02 -4.436810E+00 -2.416825E+00 

tests/test_sourcepoint_interval/settings.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<settings>
+
+  <state_point interval="2"/>
+  <source_point interval="4"/>
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>

tests/test_sourcepoint_interval/test_sourcepoint_interval.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import os
+from subprocess import Popen, STDOUT, PIPE, call
+import filecmp
+from nose_mpi import NoseMPI
+import glob
+
+pwd = os.path.dirname(__file__)
+
+def setup(): 
+    os.putenv('PWD', pwd)
+    os.chdir(pwd)
+
+def test_run():
+    openmc_path = pwd + '/../../src/openmc'
+    if int(NoseMPI.mpi_np) > 0:
+        proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([openmc_path], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0
+
+def test_statepoint_exists():
+    statepoint = glob.glob(pwd + '/statepoint.*')
+    assert len(statepoint) == 5
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+
+def test_results():
+    statepoint = glob.glob(pwd + '/statepoint.8.*')
+    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
+
+def teardown():
+    output = glob.glob(pwd + '/statepoint.*')
+    output.append(pwd + '/results_test.dat')
+    for f in output:
+        if os.path.exists(f):
+            os.remove(f)

tests/test_sourcepoint_latest/geometry.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Sphere with radius 10 -->
+  <surface id="1" type="sphere" coeffs="0 0 0 10" boundary="vacuum"/>
+  <cell id="1" material="1" surfaces="-1" />
+    
+</geometry>

tests/test_sourcepoint_latest/materials.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<materials>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" xs="70c" ao="1.0" />
+  </material>
+
+</materials>

tests/test_sourcepoint_latest/results.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+import sys
+
+# import statepoint
+sys.path.append('../../src/utils')
+import statepoint
+
+# read in statepoint file
+if len(sys.argv) > 1:
+    sp = statepoint.StatePoint(sys.argv[1])
+else:
+    sp = statepoint.StatePoint('statepoint.10.binary')
+sp.read_results()
+
+# set up output string
+outstr = ''
+ 
+# write out k-combined
+outstr += 'k-combined:\n'
+outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
+
+# write results to file
+with open('results_test.dat','w') as fh:
+    fh.write(outstr)

tests/test_sourcepoint_latest/results_true.dat

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

tests/test_sourcepoint_latest/settings.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<settings>
+
+  <source_point batches="0" separate="true" overwrite_latest="true"/>
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>

tests/test_sourcepoint_latest/test_sourcepoint_latest.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+import os
+from subprocess import Popen, STDOUT, PIPE, call
+import filecmp
+from nose_mpi import NoseMPI
+import glob
+
+pwd = os.path.dirname(__file__)
+
+def setup(): 
+    os.putenv('PWD', pwd)
+    os.chdir(pwd)
+
+def test_run():
+    openmc_path = pwd + '/../../src/openmc'
+    if int(NoseMPI.mpi_np) > 0:
+        proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([openmc_path], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0
+
+def test_statepoint_exists():
+    statepoint = glob.glob(pwd + '/statepoint.10.*')
+    assert len(statepoint) == 1
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+    source = glob.glob(pwd + '/source.*')
+    assert len(source) == 1
+    assert source[0].endswith('binary') or source[0].endswith('h5')
+
+def test_results():
+    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
+
+def teardown():
+    output = glob.glob(pwd + '/statepoint.10.*')
+    output += glob.glob(pwd + '/source.*')
+    output.append(pwd + '/results_test.dat')
+    for f in output:
+        if os.path.exists(f):
+            os.remove(f)

tests/test_sourcepoint_restart/geometry.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<geometry>
+
+  <!-- Sphere with radius 10 -->
+  <surface id="1" type="sphere" coeffs="0 0 0 10" boundary="vacuum"/>
+  <cell id="1" material="1" surfaces="-1" />
+    
+</geometry>

tests/test_sourcepoint_restart/materials.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<materials>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" xs="70c" ao="1.0" />
+  </material>
+
+</materials>

tests/test_sourcepoint_restart/results.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import sys
+import numpy as np
+
+# import statepoint
+sys.path.append('../../src/utils')
+import statepoint
+
+# read in statepoint file
+if len(sys.argv) > 1:
+    sp = statepoint.StatePoint(sys.argv[1])
+else:
+    sp = statepoint.StatePoint('statepoint.10.binary')
+sp.read_results()
+
+# extract tally results and convert to vector
+results1 = sp.tallies[0].results
+shape1 = results1.shape
+size1 = (np.product(shape1))
+results1 = np.reshape(results1, size1)
+results2 = sp.tallies[1].results
+shape2 = results2.shape
+size2 = (np.product(shape2))
+results2 = np.reshape(results2, size2)
+
+# set up output string
+outstr = ''
+ 
+# write out k-combined
+outstr += 'k-combined:\n'
+outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
+
+# write out tally results
+outstr += 'tally 1:\n'
+for item in results1:
+  outstr += "{0:12.6E}\n".format(item)
+outstr += 'tally 2:\n'
+for item in results2:
+  outstr += "{0:12.6E}\n".format(item)
+
+# write results to file
+with open('results_test.dat','w') as fh:
+    fh.write(outstr)

tests/test_sourcepoint_restart/settings.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<settings>
+
+  <state_point batches="7 10" />
+  <source_point batches="7" separate="true" />
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>

tests/test_sourcepoint_restart/tallies.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tallies>
+
+  <mesh id="1">
+    <type>rectangular</type>
+    <dimension>5 3 4</dimension>
+    <lower_left>-10. -5. 0.</lower_left>
+    <upper_right>10. 4. 9.</upper_right>
+  </mesh>
+
+  <tally id="10">
+    <filter type="mesh" bins="1" />
+    <filter type="energy" bins="0.0 5.0 10.0" />
+    <filter type="energyout" bins="0.0 5.0 10.0" />
+    <scores>scatter-P3 nu-fission</scores>
+  </tally>
+
+  <tally id="5">
+    <filter type="cell" bins="1" />
+    <scores>fission absorption total flux</scores>
+  </tally>
+
+</tallies>

tests/test_sourcepoint_restart/test_sourcepoint_restart.py

@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+
+import os
+from subprocess import Popen, STDOUT, PIPE, call
+import filecmp
+from nose_mpi import NoseMPI
+import glob
+
+pwd = os.path.dirname(__file__)
+
+def setup(): 
+    os.putenv('PWD', pwd)
+    os.chdir(pwd)
+
+def test_run():
+    openmc_path = pwd + '/../../src/openmc'
+    if int(NoseMPI.mpi_np) > 0:
+        proc = Popen([NoseMPI.mpi_exec, '-np', NoseMPI.mpi_np, openmc_path],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([openmc_path], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0
+
+def test_created_statepoint():
+    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.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], sourcepoint[0]],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        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.10.*')
+    assert len(statepoint) == 1
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+
+def test_results_form1():
+    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.*')
+    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, 
+                      '--restart', statepoint[0], sourcepoint[0]],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        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.10.*')
+    assert len(statepoint) == 1
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+
+def test_results_form2():
+    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], 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.10.*')
+    assert len(statepoint) == 1
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5')
+
+def test_results_serial():
+    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
+
+def teardown():
+    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):
+            os.remove(f)

tests/test_statepoint_sourcesep/settings.xml

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