mirror of
https://github.com/openmc-dev/openmc.git
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Merge branch 'develop' into photon-alund
This commit is contained in:
Paul Romano
commit
460452d4f7
746 changed files with 17707 additions and 10855 deletions
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@ -151,8 +151,8 @@ and `Volume II`_. You may also find it helpful to review the following terms:
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.. _git: http://git-scm.com/
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.. _git tutorials: http://git-scm.com/documentation
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.. _Reactor Concepts Manual: http://www.tayloredge.com/periodic/trivia/ReactorConcepts.pdf
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.. _Volume I: http://energy.gov/sites/prod/files/2013/06/f2/h1019v1.pdf
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.. _Volume II: http://energy.gov/sites/prod/files/2013/06/f2/h1019v2.pdf
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.. _Volume I: https://www.standards.doe.gov/standards-documents/1000/1019-bhdbk-1993-v1
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.. _Volume II: https://www.standards.doe.gov/standards-documents/1000/1019-bhdbk-1993-v2
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.. _OpenMC source code: https://github.com/mit-crpg/openmc
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.. _GitHub: https://github.com/
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.. _bug reports: https://github.com/mit-crpg/openmc/issues
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@ -222,6 +222,13 @@ named ``njoy`` available on your path. If you want to explicitly name the
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executable, the ``njoy_exec`` optional argument can be used. Additionally, the
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``stdout`` argument can be used to show the progress of the NJOY run.
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To generate a thermal scattering file, you need to specify both an ENDF incident
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neutron sub-library file as well as a thermal neutron scattering sub-library
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file; for example::
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light_water = openmc.data.ThermalScattering.from_njoy(
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'neutrons/n-001_H_001.endf', 'thermal_scatt/tsl-HinH2O.endf')
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Once you have instances of :class:`IncidentNeutron` and
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:class:`ThermalScattering`, a library can be created by using the
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``export_to_hdf5()`` methods and the :class:`DataLibrary` class as described in
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@ -6,17 +6,18 @@ Installation and Configuration
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.. currentmodule:: openmc
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.. _install_conda:
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----------------------------------------
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Installing on Linux/Mac with conda-forge
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----------------------------------------
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`Conda <http://conda.pydata.org/docs/>`_ is an open source package management
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system and environment management system for installing multiple versions of
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software packages and their dependencies and switching easily between
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them. `conda-forge <https://conda-forge.github.io/>`_ is a community-led conda
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channel of installable packages. For instructions on installing conda, please
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consult their `documentation
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<http://conda.pydata.org/docs/install/quick.html>`_.
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Conda_ is an open source package management system and environment management
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system for installing multiple versions of software packages and their
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dependencies and switching easily between them. `conda-forge
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<https://conda-forge.github.io/>`_ is a community-led conda channel of
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installable packages. For instructions on installing conda, please consult their
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`documentation <http://conda.pydata.org/docs/install/quick.html>`_.
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Once you have `conda` installed on your system, add the `conda-forge` channel to
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your configuration with:
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@ -38,6 +39,8 @@ It is possible to list all of the versions of OpenMC available on your platform
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conda search openmc --channel conda-forge
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.. _install_ppa:
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-----------------------------
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Installing on Ubuntu with PPA
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-----------------------------
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@ -68,9 +71,11 @@ are no longer supported.
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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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--------------------
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Building from Source
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--------------------
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.. _install_source:
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----------------------
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Installing from Source
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----------------------
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.. _prerequisites:
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@ -95,10 +100,10 @@ Prerequisites
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* A C/C++ compiler such as gcc_
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OpenMC includes two libraries written in C and C++, respectively. These
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libraries have been tested to work with a wide variety of compilers. If
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you are using a Debian-based distribution, you can install the g++
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compiler using the following command::
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OpenMC includes various source files written in C and C++,
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respectively. These source files have been tested to work with a wide
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variety of compilers. If you are using a Debian-based distribution, you
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can install the g++ compiler using the following command::
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sudo apt install g++
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@ -113,34 +118,38 @@ Prerequisites
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* HDF5_ Library for portable binary output format
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OpenMC uses HDF5 for binary output files. As such, you will need to have
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HDF5 installed on your computer. The installed version will need to have
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been compiled with the same compiler you intend to compile OpenMC with. If
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you are using HDF5 in conjunction with MPI, we recommend that your HDF5
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installation be built with parallel I/O features. An example of
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configuring HDF5_ is listed below::
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OpenMC uses HDF5 for many input/output files. As such, you will need to
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have HDF5 installed on your computer. The installed version will need to
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have been compiled with the same compiler you intend to compile OpenMC
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with. If compiling with gcc from the APT repositories, users of Debian
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derivatives can install HDF5 and/or parallel HDF5 through the package
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manager::
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FC=/opt/mpich/3.1/bin/mpif90 CC=/opt/mpich/3.1/bin/mpicc \
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./configure --prefix=/opt/hdf5/1.8.12 --enable-fortran \
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--enable-fortran2003 --enable-parallel
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sudo apt install libhdf5-dev
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Parallel versions of the HDF5 library called `libhdf5-mpich-dev` and
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`libhdf5-openmpi-dev` exist which are built against MPICH and OpenMPI,
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respectively. To link against a parallel HDF5 library, make sure to set
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the HDF5_PREFER_PARALLEL CMake option, e.g.::
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FC=mpifort.mpich cmake -DHDF5_PREFER_PARALLEL=on ..
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Note that the exact package names may vary depending on your particular
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distribution and version.
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If you are using building HDF5 from source in conjunction with MPI, we
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recommend that your HDF5 installation be built with parallel I/O
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features. An example of configuring HDF5_ is listed below::
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FC=mpifort ./configure --enable-fortran --enable-parallel
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You may omit ``--enable-parallel`` if you want to compile HDF5_ in serial.
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.. important::
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OpenMC uses various parts of the HDF5 Fortran 2003 API; as such you
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must include ``--enable-fortran2003`` or else OpenMC will not be able
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to compile.
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On Debian derivatives, HDF5 and/or parallel HDF5 can be installed through
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the APT package manager:
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.. code-block:: sh
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sudo apt install libhdf5-dev hdf5-helpers
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Note that the exact package names may vary depending on your particular
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distribution and version.
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If you are building HDF5 version 1.8.x or earlier, you must include
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``--enable-fortran2003`` when configuring HDF5 or else OpenMC will not
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be able to compile.
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.. admonition:: Optional
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:class: note
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@ -163,7 +172,7 @@ Prerequisites
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.. _CMake: http://www.cmake.org
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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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.. _HDF5: https://www.hdfgroup.org/solutions/hdf5/
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Obtaining the Source
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--------------------
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@ -187,8 +196,8 @@ switch to the source of the latest stable release, run the following commands::
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git checkout master
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.. _GitHub: https://github.com/mit-crpg/openmc
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.. _git: http://git-scm.com
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.. _ssh: http://en.wikipedia.org/wiki/Secure_Shell
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.. _git: https://git-scm.com
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.. _ssh: https://en.wikipedia.org/wiki/Secure_Shell
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.. _usersguide_build:
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@ -254,14 +263,15 @@ should be used:
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Compiling with MPI
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++++++++++++++++++
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To compile with MPI, set the :envvar:`FC` and :envvar:`CC` environment variables
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to the path to the MPI Fortran and C wrappers, respectively. For example, in a
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bash shell:
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To compile with MPI, set the :envvar:`FC`, :envvar:`CC`, and :envvar:`CXX`
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environment variables to the path to the MPI Fortran, C, and C++ wrappers,
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respectively. For example, in a bash shell:
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.. code-block:: sh
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export FC=mpif90
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export FC=mpifort
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export CC=mpicc
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export CXX=mpicxx
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cmake /path/to/openmc
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Note that in many shells, environment variables can be set for a single command,
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@ -269,7 +279,7 @@ i.e.
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.. code-block:: sh
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FC=mpif90 CC=mpicc cmake /path/to/openmc
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FC=mpifort CC=mpicc CXX=mpicxx cmake /path/to/openmc
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Selecting HDF5 Installation
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+++++++++++++++++++++++++++
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@ -345,7 +355,7 @@ follows:
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.. code-block:: sh
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mkdir build && cd build
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FC=ifort CC=icc FFLAGS=-mmic cmake -Dopenmp=on ..
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FC=ifort CC=icc CXX=icpc FFLAGS=-mmic cmake -Dopenmp=on ..
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make
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Note that unless an HDF5 build for the Intel Xeon Phi (Knights Corner) is
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@ -358,45 +368,59 @@ workarounds.
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Testing Build
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-------------
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If you have ENDF/B-VII.1 cross sections from NNDC_ you can test your build.
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Make sure the **OPENMC_CROSS_SECTIONS** environmental variable is set to the
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*cross_sections.xml* file in the *data/nndc* directory.
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There are two ways to run tests. The first is to use the Makefile present in
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the source directory and run the following:
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To run the test suite, you will first need to download a pre-generated cross
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section library along with windowed multipole data. Please refer to our
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:ref:`devguide_tests` documentation for further details.
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---------------------
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Installing Python API
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---------------------
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If you installed OpenMC using :ref:`Conda <install_conda>` or :ref:`PPA
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<install_ppa>`, no further steps are necessary in order to use OpenMC's
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:ref:`Python API <pythonapi>`. However, if you are :ref:`installing from source
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<install_source>`, the Python API is not installed by default when ``make
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install`` is run because in many situations it doesn't make sense to install a
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Python package in the same location as the ``openmc`` executable (for example,
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if you are installing the package into a `virtual environment
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<https://docs.python.org/3/tutorial/venv.html>`_). The easiest way to install
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the :mod:`openmc` Python package is to use pip_, which is included by default in
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Python 3.4+. From the root directory of the OpenMC distribution/repository, run:
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.. code-block:: sh
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make test
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pip install .
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If you want more options for testing you can use ctest_ command. For example,
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if we wanted to run only the plot tests with 4 processors, we run:
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pip will first check that all :ref:`required third-party packages
|
||||
<usersguide_python_prereqs>` have been installed, and if they are not present,
|
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they will be installed by downloading the appropriate packages from the Python
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Package Index (`PyPI <https://pypi.org/>`_). However, do note that since pip
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runs the ``setup.py`` script which requires NumPy, you will have to first
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install NumPy:
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.. code-block:: sh
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cd build
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ctest -j 4 -R plot
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pip install numpy
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If you want to run the full test suite with different build options please
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refer to our :ref:`test suite` documentation.
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Installing in "Development" Mode
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||||
--------------------------------
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||||
|
||||
--------------------
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||||
Python Prerequisites
|
||||
--------------------
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||||
If you are primarily doing development with OpenMC, it is strongly recommended
|
||||
to install the Python package in :ref:`"editable" mode <devguide_editable>`.
|
||||
|
||||
OpenMC's :ref:`Python API <pythonapi>` works with either Python 2.7 or Python
|
||||
3.2+. In addition to Python itself, the API relies on a number of third-party
|
||||
packages. All prerequisites can be installed using `conda
|
||||
<http://conda.pydata.org/docs/>`_ (recommended), `pip
|
||||
<https://pip.pypa.io/en/stable/>`_, or through the package manager in most Linux
|
||||
.. _usersguide_python_prereqs:
|
||||
|
||||
Prerequisites
|
||||
-------------
|
||||
|
||||
The Python API works with Python 3.4+. In addition to Python itself, the API
|
||||
relies on a number of third-party packages. All prerequisites can be installed
|
||||
using Conda_ (recommended), pip_, or through the package manager in most Linux
|
||||
distributions.
|
||||
|
||||
.. admonition:: Required
|
||||
:class: error
|
||||
|
||||
`six <https://pythonhosted.org/six/>`_
|
||||
The Python API works with both Python 2.7+ and 3.2+. To do so, the six
|
||||
compatibility library is used.
|
||||
|
||||
`NumPy <http://www.numpy.org/>`_
|
||||
NumPy is used extensively within the Python API for its powerful
|
||||
N-dimensional array.
|
||||
|
|
@ -428,6 +452,11 @@ distributions.
|
|||
.. admonition:: Optional
|
||||
:class: note
|
||||
|
||||
`mpi4py <http://mpi4py.scipy.org/>`_
|
||||
mpi4py provides Python bindings to MPI for running distributed-memory
|
||||
parallel runs. This package is needed if you plan on running depletion
|
||||
simulations in parallel using MPI.
|
||||
|
||||
`Cython <http://cython.org/>`_
|
||||
Cython is used for resonance reconstruction for ENDF data converted to
|
||||
:class:`openmc.data.IncidentNeutron`.
|
||||
|
|
@ -470,3 +499,5 @@ schemas.xml file in your own OpenMC source directory.
|
|||
.. _RELAX NG: http://relaxng.org/
|
||||
.. _NNDC: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
|
||||
.. _ctest: http://www.cmake.org/cmake/help/v2.8.12/ctest.html
|
||||
.. _Conda: https://conda.io/docs/
|
||||
.. _pip: https://pip.pypa.io/en/stable/
|
||||
|
|
|
|||
|
|
@ -168,8 +168,8 @@ ENDF/B-VII.1. It has the following optional arguments:
|
|||
|
||||
This script downloads `ENDF/B-VII.1 ACE data
|
||||
<http://www.nndc.bnl.gov/endf/b7.1/acefiles.html>`_ from NNDC and converts it to
|
||||
an HDF5 library for use with OpenMC. This data is used for OpenMC's regression
|
||||
test suite. This script has the following optional arguments:
|
||||
an HDF5 library for use with OpenMC. This script has the following optional
|
||||
arguments:
|
||||
|
||||
-b, --batch Suppress standard in
|
||||
|
||||
|
|
|
|||
|
|
@ -39,7 +39,7 @@ be specified:
|
|||
'plot'
|
||||
Generates slice or voxel plots (see :ref:`usersguide_plots`).
|
||||
|
||||
'particle_restart'
|
||||
'particle restart'
|
||||
Simulate a single source particle using a particle restart file.
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue