Fixed merge conflicts with develop

docs/source/conf.py

@@ -17,13 +17,18 @@ import sys, os
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('../sphinxext'))
+sys.path.insert(0, os.path.abspath('../..'))
 
 
 # -- General configuration -----------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.pngmath', 'sphinxcontrib.tikz', 'sphinx_numfig']
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.napoleon',
+              'sphinx.ext.pngmath',
+              'sphinxcontrib.tikz',
+              'sphinx_numfig']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/source/devguide/docbuild.rst

@@ -18,9 +18,7 @@ from the git repository as such:
 
 .. code-block:: sh
 
-   git clone https://bitbucket.org/philexander/tikz.git
-   cd tikz
-   sudo python setup.py install
+   sudo pip install https://bitbucket.org/philexander/tikz/get/HEAD.tar.gz
 
 The Numfig_ package can be installed directly with pip:
 

docs/source/devguide/styleguide.rst

@@ -125,8 +125,16 @@ program, subroutine, function, if, associate, etc. Emacs users should set the
 variables f90-if-indent, f90-do-indent, f90-continuation-indent,
 f90-type-indent, f90-associate-indent, and f90-program indent to 2.
 
-Continuation lines should be indented by an extra 5 spaces. This is the default
-value of f90-continuation-indent in Emacs.
+Continuation lines should be indented by at least 5 spaces. They may be indented
+more in order to make the content match the context.  For example, either of
+these are valid continuation indentations:
+
+.. code-block:: fortran
+
+    local_xyz(1) = xyz(1) - (this % lower_left(1) + &
+         (i_xyz(1) - HALF)*this % pitch(1))
+    call which_data(scatt_type, get_scatt, get_nuscatt, get_chi_t, get_chi_p, &
+                    get_chi_d, scatt_order)
 
 Whitespace in Expressions
 -------------------------

docs/source/index.rst

@@ -32,6 +32,7 @@ free to send a message to the User's Group `mailing list`_.
     methods/index
     usersguide/index
     devguide/index
+    pythonapi/index
     publications
     license
     developers

docs/source/publications.rst

@@ -10,9 +10,8 @@ Overviews
 
 - Paul K. Romano, Nicholas E. Horelik, Bryan R. Herman, Adam G. Nelson, Benoit
   Forget, and Kord Smith, "OpenMC: A State-of-the-Art Monte Carlo Code for
-  Research and Development," *Proc. Joint International Conference on
-  Supercomputing in Nuclear Applications and Monte Carlo*, Paris, France,
-  Oct. 27--31 (2013). `<http://dx.doi.org/10.1051/snamc/201406016>`_
+  Research and Development," *Ann. Nucl. Energy*, **82**, 90--97
+  (2015). `<http://dx.doi.org/10.1016/j.anucene.2014.07.048>`_
 
 - Paul K. Romano, Bryan R. Herman, Nicholas E. Horelik, Benoit Forget, Kord
   Smith, and Andrew R. Siegel, "Progress and Status of the OpenMC Monte Carlo

docs/source/pythonapi/ace.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_ace:
+
+==========
+ACE Format
+==========
+
+.. automodule:: openmc.ace
+    :members:

docs/source/pythonapi/cmfd.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_cmfd:
+
+====
+CMFD
+====
+
+.. automodule:: openmc.cmfd
+    :members:

docs/source/pythonapi/element.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_element:
+
+=======
+Element
+=======
+
+.. automodule:: openmc.element
+    :members:

docs/source/pythonapi/executor.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_executor:
+
+========
+Executor
+========
+
+.. automodule:: openmc.executor
+    :members:

docs/source/pythonapi/filter.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_filter:
+
+======
+Filter
+======
+
+.. automodule:: openmc.filter
+    :members:

docs/source/pythonapi/geometry.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_geometry:
+
+========
+Geometry
+========
+
+.. automodule:: openmc.geometry
+    :members:

docs/source/pythonapi/index.rst

@@ -0,0 +1,32 @@
+.. _pythonapi:
+
+==========
+Python API
+==========
+
+--------
+Contents
+--------
+
+.. toctree::
+    :maxdepth: 1
+
+    ace
+    cmfd
+    element
+    executor
+    filter
+    geometry
+    material
+    mesh
+    nuclide
+    opencg_compatible
+    particle_restart
+    plots
+    settings
+    statepoint
+    summary
+    surface
+    tallies
+    trigger
+    universe

docs/source/pythonapi/material.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_material:
+
+=========
+Materials
+=========
+
+.. automodule:: openmc.material
+    :members:

docs/source/pythonapi/mesh.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_mesh:
+
+====
+Mesh
+====
+
+.. automodule:: openmc.mesh
+    :members:

docs/source/pythonapi/nuclide.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_nuclide:
+
+=======
+Nuclide
+=======
+
+.. automodule:: openmc.nuclide
+    :members:

docs/source/pythonapi/opencg_compatible.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_opencg_compatible:
+
+====================
+OpenCG Compatibility
+====================
+
+.. automodule:: openmc.opencg_compatible
+    :members:

docs/source/pythonapi/particle_restart.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_particle_restart:
+
+================
+Particle Restart
+================
+
+.. automodule:: openmc.particle_restart
+    :members:

docs/source/pythonapi/plots.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_plots:
+
+=====
+Plots
+=====
+
+.. automodule:: openmc.plots
+    :members:

docs/source/pythonapi/settings.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_settings:
+
+========
+Settings
+========
+
+.. automodule:: openmc.settings
+    :members:

docs/source/pythonapi/statepoint.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_statepoint:
+
+==========
+Statepoint
+==========
+
+.. automodule:: openmc.statepoint
+    :members:

docs/source/pythonapi/summary.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_summary:
+
+=======
+Summary
+=======
+
+.. automodule:: openmc.summary
+    :members:

docs/source/pythonapi/surface.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_surface:
+
+=======
+Surface
+=======
+
+.. automodule:: openmc.surface
+    :members:

docs/source/pythonapi/tallies.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_tallies:
+
+=======
+Tallies
+=======
+
+.. automodule:: openmc.tallies
+    :members:

docs/source/pythonapi/trigger.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_trigger:
+
+=======
+Trigger
+=======
+
+.. automodule:: openmc.trigger
+    :members:

docs/source/pythonapi/universe.rst

@@ -0,0 +1,8 @@
+.. _pythonapi_universe:
+
+========
+Universe
+========
+
+.. automodule:: openmc.universe
+    :members:

docs/source/usersguide/input.rst

@@ -441,24 +441,22 @@ attributes/sub-elements:
     has the following attributes:
 
     :type:
-      The type of spatial distribution. Valid options are "box" and "point". A
-      "box" spatial distribution has coordinates sampled uniformly in a
-      parallelepiped. A "point" spatial distribution has coordinates specified
-      by a triplet.
+
+      The type of spatial distribution. Valid options are "box", "fission", and
+      "point". A "box" spatial distribution has coordinates sampled uniformly in
+      a parallelepiped. A "fission" spatial distribution samples locations from
+      a "box" distribution but only locations in fissionable materials are
+      accepted. A "point" spatial distribution has coordinates specified by a
+      triplet.
 
       *Default*: None
 
     :parameters:
-      For a "box" spatial distribution, ``parameters`` should be given as six
-      real numbers, the first three of which specify the lower-left corner of a
-      parallelepiped and the last three of which specify the upper-right
-      corner. Source sites are sampled uniformly through that parallelepiped.
-
-      To filter a "box" spatial distribution by fissionable material, specify
-      "fission" tag instead of "box". The ``parameters`` should be given as six
-      real numbers, the first three of which specify the lower-left corner of a
-      parallelepiped and the last three of which specify the upper-right
-      corner. Source sites are sampled uniformly through that parallelepiped.
+      For a "box" or "fission" spatial distribution, ``parameters`` should be
+      given as six real numbers, the first three of which specify the lower-left
+      corner of a parallelepiped and the last three of which specify the
+      upper-right corner. Source sites are sampled uniformly through that
+      parallelepiped.
 
       For a "point" spatial distribution, ``parameters`` should be given as
       three real numbers which specify the (x,y,z) location of an isotropic
@@ -481,7 +479,7 @@ attributes/sub-elements:
 
     :parameters:
       For an "isotropic" angular distribution, ``parameters`` should not be
-      specified
+      specified.
 
       For a "monodirectional" angular distribution, ``parameters`` should be
       given as three real numbers which specify the angular cosines with respect
@@ -499,7 +497,7 @@ attributes/sub-elements:
       "watt", and "maxwell". The "monoenergetic" option produces source sites at
       a single energy. The "watt" option produces source sites whose energy is
       sampled from a Watt fission spectrum. The "maxwell" option produce source
-      sites whose energy is sampled from a Maxwell fission spectrum
+      sites whose energy is sampled from a Maxwell fission spectrum.
 
       *Default*: watt
 
@@ -605,8 +603,6 @@ survival biasing, otherwise known as implicit capture or absorption.
 
   *Default*: false
 
-.. _trace:
-
 ``<threads>`` Element
 ---------------------
 
@@ -615,6 +611,8 @@ a simulation. It has no attributes and accepts a positive integer value.
 
   *Default*: None (Determined by environment variable :envvar:`OMP_NUM_THREADS`)
 
+.. _trace:
+
 ``<trace>`` Element
 -------------------
 
@@ -631,9 +629,9 @@ integers: the batch number, generation number, and particle number.
 
 The ``<track>`` element specifies particles for which OpenMC will output binary
 files describing particle position at every step of its transport. This element
-should be followed by triplets of integers.  Each triplet describes one particle
-. The integers in each triplet specify the batch number, generation number, and
-particle number, respectively.
+should be followed by triplets of integers.  Each triplet describes one
+particle. The integers in each triplet specify the batch number, generation
+number, and particle number, respectively.
 
   *Default*: None
 
@@ -1224,8 +1222,8 @@ The ``<tally>`` element accepts the following sub-elements:
     The ``filter`` element has the following attributes/sub-elements:
 
       :type:
-        The type of the filter. Accepted options are "cell", "cellborn", 
-        "material", "universe", "energy", "energyout", "mesh", and 
+        The type of the filter. Accepted options are "cell", "cellborn",
+        "material", "universe", "energy", "energyout", "mesh", and
         "distribcell".
 
       :bins:
@@ -1307,24 +1305,25 @@ The ``<tally>`` element accepts the following sub-elements:
     physical quantities:
 
     :flux:
-      Total flux
+      Total flux in particle-cm per source particle.
 
     :total:
-      Total reaction rate
+      Total reaction rate in reactions per source particle.
 
     :scatter:
       Total scattering rate. Can also be identified with the ``scatter-0``
-      response type.
+      response type. Units are reactions per source particle.
 
     :absorption:
       Total absorption rate. This accounts for all reactions which do not
-      produce secondary neutrons.
+      produce secondary neutrons. Units are reactions per source particle.
 
     :fission:
-      Total fission rate
+      Total fission rate in reactions per source particle.
 
     :nu-fission:
-      Total production of neutrons due to fission
+      Total production of neutrons due to fission. Units are neutrons produced
+      per source neutron.
 
     :kappa-fission:
       The recoverable energy production rate due to fission. The recoverable
@@ -1333,51 +1332,55 @@ The ``<tally>`` element accepts the following sub-elements:
       total energies, and the total energy released by the delayed :math:`\beta`
       particles. The neutrino energy does not contribute to this response. The
       prompt and delayed :math:`\gamma`-rays are assumed to deposit their energy
-      locally.
+      locally. Units are MeV per source particle.
 
     :scatter-N:
       Tally the N\ :sup:`th` \ scattering moment, where N is the Legendre
       expansion order of the change in particle angle :math:`\left(\mu\right)`.
-      N must be between 0 and 10. As an example, tallying the
-      2\ :sup:`nd` \ scattering moment would be specified as
-      ``<scores> scatter-2 </scores>``.
+      N must be between 0 and 10. As an example, tallying the 2\ :sup:`nd` \
+      scattering moment would be specified as ``<scores> scatter-2
+      </scores>``. Units are reactions per source particle.
 
     :scatter-PN:
       Tally all of the scattering moments from order 0 to N, where N is the
       Legendre expansion order of the change in particle angle
       :math:`\left(\mu\right)`. That is, ``scatter-P1`` is equivalent to
       requesting tallies of ``scatter-0`` and ``scatter-1``.  Like for
-      ``scatter-N``, N must be between 0 and 10. As an example, tallying up
-      to the 2\ :sup:`nd` \ scattering moment would be specified as
-      ``<scores> scatter-P2 </scores>``.
+      ``scatter-N``, N must be between 0 and 10. As an example, tallying up to
+      the 2\ :sup:`nd` \ scattering moment would be specified as ``<scores>
+      scatter-P2 </scores>``. Units are reactions per source particle.
 
     :scatter-YN:
-      ``scatter-YN`` is similar to ``scatter-PN`` except an additional
-      expansion is performed for the incoming particle direction
+      ``scatter-YN`` is similar to ``scatter-PN`` except an additional expansion
+      is performed for the incoming particle direction
       :math:`\left(\Omega\right)` using the real spherical harmonics.  This is
       useful for performing angular flux moment weighting of the scattering
-      moments. Like ``scatter-PN``, ``scatter-YN`` will tally all of the
-      moments from order 0 to N; N again must be between 0 and 10.
+      moments. Like ``scatter-PN``, ``scatter-YN`` will tally all of the moments
+      from order 0 to N; N again must be between 0 and 10. Units are reactions
+      per source particle.
 
     :nu-scatter, nu-scatter-N, nu-scatter-PN, nu-scatter-YN:
       These scores are similar in functionality to their ``scatter*``
-      equivalents except the total production of neutrons due to
-      scattering is scored vice simply the scattering rate. This accounts for
-      multiplicity from (n,2n), (n,3n), and (n,4n) reactions.
+      equivalents except the total production of neutrons due to scattering is
+      scored vice simply the scattering rate. This accounts for multiplicity
+      from (n,2n), (n,3n), and (n,4n) reactions. Units are neutrons produced per
+      source particle.
 
     :flux-YN:
       Spherical harmonic expansion of the direction of motion
-      :math:`\left(\Omega\right)` of the total flux.  This score will tally
-      all of the harmonic moments of order 0 to N.  N must be between 0 and 10.
+      :math:`\left(\Omega\right)` of the total flux.  This score will tally all
+      of the harmonic moments of order 0 to N.  N must be between 0
+      and 10. Units are particle-cm per source particle.
 
     :total-YN:
       The total reaction rate expanded via spherical harmonics about the
       direction of motion of the neutron, :math:`\Omega`.
       This score will tally all of the harmonic moments of order 0 to N.  N must
-      be between 0 and 10.
+      be between 0 and 10. Units are reactions per source particle.
 
     :current:
-      Partial currents on the boundaries of each cell in a mesh.
+      Partial currents on the boundaries of each cell in a mesh. Units are
+      particles per source particle.
 
       .. note::
           This score can only be used if a mesh filter has been
@@ -1385,7 +1388,7 @@ The ``<tally>`` element accepts the following sub-elements:
           other score.
 
     :events:
-      Number of scoring events
+      Number of scoring events. Units are events per source particle.
 
   :trigger:
     Precision trigger applied to all filter bins and nuclides for this tally.
@@ -1675,6 +1678,15 @@ The ``<begin>`` element controls what batch CMFD calculations should begin.
 
   *Default*: 1
 
+``<dhat_reset>`` Element
+------------------------
+
+The ``<dhat_reset>`` element controls whether :math:`\widehat{D}` nonlinear
+CMFD parameters should be reset to zero before solving CMFD eigenproblem.
+It can be turned on with "true" and off with "false".
+
+  *Default*: false
+
 ``<display>`` Element
 ---------------------
 
@@ -1691,15 +1703,6 @@ The ``<display>`` element sets one additional CMFD output column. Options are:
 
   *Default*: balance
 
-``<dhat_reset>`` Element
-------------------------
-
-The ``<dhat_reset>`` element controls whether :math:`\widehat{D}` nonlinear
-CMFD parameters should be reset to zero before solving CMFD eigenproblem.
-It can be turned on with "true" and off with "false".
-
-  *Default*: false
-
 ``<downscatter>`` Element
 -------------------------
 
@@ -1743,11 +1746,11 @@ The CMFD mesh is a structured Cartesian mesh. This element has the following
 attributes/sub-elements:
 
   :lower_left:
-    The lower-left corner of the structured mesh. If only two coordinate are
+    The lower-left corner of the structured mesh. If only two coordinates are
     given, it is assumed that the mesh is an x-y mesh.
 
   :upper_right:
-    The upper-right corner of the structrued mesh. If only two coordinate are
+    The upper-right corner of the structrued mesh. If only two coordinates are
     given, it is assumed that the mesh is an x-y mesh.
 
   :dimension:
@@ -1770,7 +1773,7 @@ attributes/sub-elements:
 
   :map:
     An optional acceleration map can be specified to overlay on the coarse
-    mesh spatial grid. If this option is used a ``1`` is used for a
+    mesh spatial grid. If this option is used, a ``1`` is used for a
     non-accelerated region and a ``2`` is used for an accelerated region.
     For a simple 4x4 coarse mesh with a 2x2 fuel lattice surrounded by
     reflector, the map is:

docs/source/usersguide/install.rst

@@ -160,6 +160,13 @@ openmp
   Enables shared-memory parallelism using the OpenMP API. The Fortran compiler
   being used must support OpenMP.
 
+coverage
+  Compile and link code instrumented for coverage analysis. This is typically
+  used in conjunction with gcov_.
+
+maxcoord
+  Maximum number of nested coordinate levels in geometry. Defaults to 10.
+
 To set any of these options (e.g. turning on debug mode), the following form
 should be used:
 
@@ -167,6 +174,8 @@ should be used:
 
     cmake -Ddebug=on /path/to/openmc
 
+.. _gcov: https://gcc.gnu.org/onlinedocs/gcc/Gcov.html
+
 Compiling with MPI
 ++++++++++++++++++