Read the Docs Documentation

.gitignore

@@ -16,4 +16,6 @@ build
 
 #ignore pyne amalgamation
 src/pyne/pyne.cpp
-src/pyne/pyne.h
+src/pyne/pyne.h
+docs/Doxyfile
+docs/_build

CMakeLists.txt

@@ -68,6 +68,7 @@ if (BUILD_TESTS)
   enable_testing()
 endif ()
 
+add_subdirectory(docs)
 add_subdirectory(src)
 
 dagmc_make_configure_files()

doc/CHANGELOG.rst

@@ -16,6 +16,7 @@ Next version
   * Simplify Housekeeping Process for DAGMC (#943)
   * Allow Double Down v1.1.0 Installation in Dockerfile (#929 #944 #949)
   * Inline documentation improvements (#945)
+  * RTD documentation site (#950)
   * Streamline dependencies of docker CI images (#951 #952)
 
 v3.2.3

doc/usersguide/codes/index.rst

@@ -1,6 +1,8 @@
 Monte Carlo code-specific steps
 ===============================
 
+.. _code-specific-steps:
+
 ..  toctree::
     :maxdepth: 1
 

doc/usersguide/cubit_basics.rst

@@ -59,6 +59,8 @@ geometries (on the order of 100 volumes) the process is rather quick.
 Grouping volumes and surfaces
 -----------------------------
 
+.. note:: Metadata assignment in this section applies to the UW DAGMC plugin, not the native DAGMC exporter provivded in Coreform Cubit (>= version 2023.8).
+
 A DAGMC-based analysis allows a number of attributes of the geometry to be
 defined within the geometry file. These characteristics generally relate to the
 physical behavior of the volume, for example its material definition or boundary
@@ -91,10 +93,39 @@ Due to the importance of using the ``group`` command reading the
 `CUBIT manual <CUBIT_manual_>`_
 section on its full usage is highly recommended.
 
+.. _coreform_metadata:
+
+Assinging Metadata to Volumes and Surfaces: Coreform Cubit
+----------------------------------------------------------
+
+
+Please refer to Coreform's `DAGMC Tutorial
+<https://coreform.com/products/coreform-cubit/tutorials/dagmc/tutorial_1/>`_ for
+more inform on how to apply DAGMC metadata for the integrated DAGMC export
+capability provided in Coreform Cubit (>= version 2023.8).
+
+.. _coreform_export:
+
+Production of the DAGMC Geometry: Coreform Native Export
+--------------------------------------------------------
+
+As of version 2023.8, Coreform Cubit has a native DAGMC export capability. This
+requires that the model is meshed either with the tetmesh or trimesh schemes
+(i.e. that surfaces of the model have triangles associated with them to be
+exported.) Faceting/meshing parameters are absent from this command as they are
+supplied to the meshing schemes mentioned previously. The export command is as
+follows:
+
+::
+
+    CUBIT> export cf_dagmc <filename> [overwrite]
+
+**This export option is also available as an export file format** `File -> Export... -> DAGMC (\*.h5m)`.
+
 .. _geom_production:
 
-Production of the DAGMC geometry
---------------------------------
+Production of the DAGMC geometry: DAGMC Plugin
+----------------------------------------------
 
 Now that the geometry is ready for DAGMC we must export it. Using the
 Cubit plugin make this very straightforward, assuming that the user has

doc/usersguide/cubit_workflow.rst

@@ -1,5 +1,5 @@
 Producing solid models for DAGMC using Cubit
-===================================================
+============================================
 
 The general workflow for the production of models for analysis using DAGMC
 looks like that shown in the Figure below.
@@ -56,20 +56,55 @@ The general workflow for the production of DAGMC models is the following:
     - inspect volumes in pre-imprint model with significant change in volume
     - re-check for small areas, curves, volumes
     - any problems in these steps repair volumes in pre-imprint model and go back to step 3
+
+
+
 7.  Facet model
     ::
 
         CUBIT> export dagmc "geom.h5m" faceting_tolerance 1.0e-4
 
-8.  Seal model if possible (use `make_watertight <tools.html#make-watertight>`_)
+8.  Ensure the model is sealed with the :ref:`check_watertight` tool. If not, attempt to
+    seal the model if possible using the :ref:`make_watertight` tool.
+
+
 9.  Flood and/or transport particles in model
+
 10. If lost particles or leaky:
 
     - examine lost locations (use `mklostvis.pl <tools.html#mklostvis>`_)
     - examine "leaks"/tunneling (can use a mesh tally to locate)
     - repair the pre-imprint/merge model (go to step 2)
 11. If no lost particles or leaks, then the model is ready for transport
 
+.. _coreform_export:
+
+Using the Coreform Cubit plugin
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If using the Coreform Cubit plugin to generate DAGMC models (`export cf_dagmc`)
+available since the 2023.8 release, steps 1-6 remain the same.
+
+7. At this point, the model is meshed using either the tetmesher or trimesher.
+   These models are inherently watertight thanks to the meshing algorithms
+   applied in Coreform.
+
+8. Export the model using the `export cf_dagmc` command
+   ::
+
+       CUBIT> export cf_dagmc "geom.h5m"
+
+Steps 9-11 remain the same as well.
+
+In contrast to the `export dagmc` command, this pathway allows for visualization
+of the faceting in Cubit before export and for singe-surface modifications to be
+made for fine-tuning the resulting DAGMC model.
+
+Additionally, if a tetmesh is used, the model can be exported as a DAGMC model
+with surfaces that are conformal to the boundaries of the tetmesh, which can be
+advantageous when preparing a model for multiphysics or for unstructured mesh
+tallies in the Monte Carlo simulation.
+
 Preparing solid models
 ~~~~~~~~~~~~~~~~~~~~~~
 

docs/CMakeLists.txt

@@ -0,0 +1,18 @@
+
+
+# Configure the documentation file
+
+find_package(Doxygen)
+
+set(DAGMC_SOURCE_DIR ${PROJECT_SOURCE_DIR})
+
+if (DOXYGEN_FOUND)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Makefile ${CMAKE_CURRENT_BINARY_DIR}/Makefile COPYONLY)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/index.rst ${CMAKE_CURRENT_BINARY_DIR}/index.rst COPYONLY)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/conf.py ${CMAKE_CURRENT_BINARY_DIR}/conf.py COPYONLY)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/requirements.txt ${CMAKE_CURRENT_BINARY_DIR}/requirements.txt COPYONLY)
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/make.bat ${CMAKE_CURRENT_BINARY_DIR}/make.bat COPYONLY)
+else()
+  message(WARNING "Doxygen is required to build the documentation for DAGMC.")
+endif()