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Will Boyd
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64
docs/source/devguide/docbuild.rst
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64
docs/source/devguide/docbuild.rst
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.. _devguide_docbuild:
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=============================
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Building Sphinx Documentation
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=============================
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In order to build the documentation in the ``docs`` directory, you will need to
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have the Sphinx_ third-party Python package. The easiest way to install Sphinx
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is via pip:
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.. code-block:: sh
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sudo pip install sphinx
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Additionally, you will also need two Sphinx extensions for TikZ support and
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numbering figures. The sphinxcontrib-tikz_ package should be installed directly
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from the git repository as such:
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.. code-block:: sh
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git clone https://bitbucket.org/philexander/tikz.git
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cd tikz
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sudo python setup.py install
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The Numfig_ package can be installed directly with pip:
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.. code-block:: sh
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sudo pip install sphinx-numfig
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-----------------------------------
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Building Documentation as a Webpage
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-----------------------------------
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To build the documentation as a webpage (what appears at
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http://mit-crpg.github.io/openmc), simply go to the ``docs`` directory and run:
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.. code-block:: sh
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make html
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-------------------------------
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Building Documentation as a PDF
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-------------------------------
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To build PDF documentation, you will need to have a LaTeX distribution installed
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on your computer as well as Inkscape_, which is used to convert .svg files to
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.pdf files. Inkscape can be installed in a Debian-derivative with:
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.. code-block:: sh
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sudo apt-get install inkscape
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One the pre-requisites are installed, simply go to the ``docs`` directory and
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run:
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.. code-block:: sh
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make latexpdf
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.. _Sphinx: http://sphinx-doc.org
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.. _sphinxcontrib-tikz: https://bitbucket.org/philexander/tikz
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.. _Numfig: https://pypi.python.org/pypi/sphinx_numfig
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.. _Inkscape: https://inkscape.org
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@ -18,3 +18,4 @@ as debugging.
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xml-parsing
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statepoint
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voxel
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docbuild
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@ -153,10 +153,6 @@ variables should be set if the default paths are incorrect:
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* Default - */opt/phdf5/1.8.14-gnu*
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* **PETSC_DIR** - The path to the PETSc directory.
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* Default - */opt/petsc/3.5.2-gnu*
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To run the full test suite, the following command can be executed in the
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tests directory:
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@ -22,14 +22,13 @@ package manager`_. Simply enter the following commands into the terminal:
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sudo apt-get update
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sudo apt-get install openmc
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Currently, the binary package does not allow for parallel simulations, HDF5_, or
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CMFD acceleration through PETSc_. Users who need such capabilities should build
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OpenMC from source as is described in :ref:`usersguide_install`.
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Currently, the binary package does not allow for parallel simulations or use of
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HDF5_. Users who need such capabilities should build OpenMC from source as is
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described in :ref:`usersguide_install`.
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.. _Personal Package Archive: https://launchpad.net/~paulromano/+archive/staging
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.. _APT package manager: https://help.ubuntu.com/community/AptGet/Howto
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.. _HDF5: http://www.hdfgroup.org/HDF5/
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.. _PETSc: http://www.mcs.anl.gov/petsc/
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-------------------------------------------
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Installing from Source on Linux or Mac OS X
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@ -1061,7 +1061,7 @@ Here is an example of a properly defined 2d hexagonal lattice:
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<pitch> 1.0 </pitch>
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<universes>
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202
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202 202
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202 202
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202 202 202
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202 202
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202 101 202
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@ -1718,20 +1718,10 @@ It can be turned on with "true" and off with "false".
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The ``<gauss_seidel_tolerance>`` element specifies two parameters. The first is
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the absolute inner tolerance for Gauss-Seidel iterations when performing CMFD
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and the second is the relative inner tolerance for Gauss-Seidel iterations
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for CMFD calculations. It is only used in the standalone CMFD power iteration
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solver and not when PETSc is active.
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for CMFD calculations.
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*Default*: 1.e-10 1.e-5
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``<ksp_monitor>`` Element
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-------------------------
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The ``<ksp_monitor>`` element is used to view the convergence of linear GMRES
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iterations in PETSc. This option can be turned on with "true" and turned off
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with "false".
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*Default*: false
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``<ktol>`` Element
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--------------------
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@ -1820,26 +1810,16 @@ iteration. This option can be turned on with "true" and turned off with "false".
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-------------------------
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The ``<run_adjoint>`` element can be turned on with "true" to have an adjoint
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calculation be performed on the last batch when CMFD is active. OpenMC should be
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compiled with PETSc when using this option.
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calculation be performed on the last batch when CMFD is active.
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*Default*: false
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``<solver>`` Element
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--------------------
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The ``<solver>`` element controls whether the CMFD eigenproblem is solved with
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standard power iteration or nonlinear Jacobian-free Newton Krylov (JFNK).
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By setting "power", power iteration is used and by setting "jfnk", JFNK is used.
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*Default*: power
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``<shift>`` Element
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--------------------
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The ``<shfit>`` element specifies an optional Wielandt shift parameter for
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accelerating power iterations. It can only be used when PETSc is not active.
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It is by default very large so the impact of the shift is effectively zero.
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The ``<shift>`` element specifies an optional Wielandt shift parameter for
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accelerating power iterations. It is by default very large so the impact of the
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shift is effectively zero.
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*Default*: 1e6
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@ -1848,10 +1828,9 @@ It is by default very large so the impact of the shift is effectively zero.
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The ``<spectral>`` element specifies an optional spectral radius that can be set to
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accelerate the convergence of Gauss-Seidel iterations during CMFD power iteration
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solve. Note this is only used in the standalone CMFD solver and does not affect
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the calculation when PETSc is active.
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solve.
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*Default*: power
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*Default*: 0.0
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``<stol>`` Element
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------------------
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@ -1872,10 +1851,9 @@ should be reset.
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``<write_matrices>`` Element
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----------------------------
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The ``<write_matrices>`` element is used to view the PETSc sparse matrices
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created when solving CMFD equations. These binary output files can be imported
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into MATLAB using PETSc-MATLAB utilities. This option can be
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turned on with "true" and off with "false".
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The ``<write_matrices>`` element is used to write the sparse matrices created
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when solving CMFD equations. This option can be turned on with "true" and off
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with "false".
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*Default*: false
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@ -86,21 +86,6 @@ Prerequisites
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You may omit ``--enable-parallel`` if you want to compile HDF5_ in serial.
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* PETSc_ for CMFD acceleration
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To enable some features of CMFD acceleration, you will need to have
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PETSc_ (3.4.2 or higher) installed on your computer. The installed version
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will need to have been compiled with the same compiler you intend to
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compile OpenMC with. OpenMC requires PETSc_ to be configured with Fortran
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datatypes. An example of configuring PETSc_ is listed below::
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./configure --prefix=/opt/petsc/3.4.4 --download-f-blas-lapack \
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--with-mpi-dir=/opt/mpich/3.1 --with-shared-libraries \
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--with-fortran-datatypes
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The BLAS/LAPACK library is not required to be downloaded and can be linked
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explicitly (e.g., Intel MKL library).
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* git_ version control software for obtaining source code
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.. _gfortran: http://gcc.gnu.org/wiki/GFortran
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@ -108,7 +93,6 @@ Prerequisites
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.. _OpenMPI: http://www.open-mpi.org
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.. _MPICH: http://www.mpich.org
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.. _HDF5: http://www.hdfgroup.org/HDF5/
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.. _PETSc: http://www.mcs.anl.gov/petsc/
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Obtaining the Source
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--------------------
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@ -139,10 +123,10 @@ Build Configuration
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-------------------
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Compiling OpenMC with CMake is carried out in two steps. First, ``cmake`` is run
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to determine the compiler, whether optional packages (MPI, HDF5, PETSc) are
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available, to generate a list of dependencies between source files so that they
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may be compiled in the correct order, and to generate a normal Makefile. The
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Makefile is then used by ``make`` to actually carry out the compile and linking
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to determine the compiler, whether optional packages (MPI, HDF5) are available,
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to generate a list of dependencies between source files so that they may be
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compiled in the correct order, and to generate a normal Makefile. The Makefile
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is then used by ``make`` to actually carry out the compile and linking
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commands. A typical out-of-source build would thus look something like the
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following
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@ -177,10 +161,6 @@ openmp
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Enables shared-memory parallelism using the OpenMP API. The Fortran compiler
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being used must support OpenMP.
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petsc
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Enables PETSc for use in CMFD acceleration. The PETSC_DIR variable should be
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set to the base directory of the PETSc installation.
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To set any of these options (e.g. turning on debug mode), the following form
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should be used:
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|
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