Merge branch 'release-v0.5.4'

.gitignore

@@ -1,4 +1,5 @@
 # Compiled objects and modules
+*.a
 *.o
 *.mod
 *.log
@@ -18,6 +19,7 @@ src/openmc
 
 # Documentation builds
 docs/build
+docs/source/_images/*.pdf
 
 # xml-fortran reader
 src/xml-fortran/xmlreader
@@ -26,4 +28,7 @@ src/xml-fortran/xmlreader
 src/templates/*.f90
 
 # Test results error file
-results_error.dat
+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 @@
 
 # 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 @@
 
 # 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 @@
    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/index.rst

@@ -15,6 +15,6 @@ as debugging.
     structures
     styleguide
     workflow
-    xml-fortran
+    xml-parsing
     statepoint
     voxel