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Remove xs conversion scripts and update documentation
This commit is contained in:
Paul Romano
parent
cf65d9ed2e
commit
90568ba96c
10 changed files with 60 additions and 905 deletions
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@ -10,15 +10,16 @@ or multi-group mode.
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In continuous-energy mode, OpenMC uses a native `HDF5
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<https://support.hdfgroup.org/HDF5/>`_ format (see :ref:`io_nuclear_data`) to
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store all nuclear data. If you have ACE format data that was produced with
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NJOY_, such as that distributed with MCNP_ or Serpent_, it can be converted to
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the HDF5 format using the :ref:`scripts_ace` script (or :ref:`using the Python
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API <create_xs_library>`). Several sources provide openly available ACE data as
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described below and can be easily converted using the provided scripts. The
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TALYS-based evaluated nuclear data library, TENDL_, is also available in ACE
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format. In addition to tabulated cross sections in the HDF5 files, OpenMC relies
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on :ref:`windowed multipole <windowed_multipole>` data to perform on-the-fly
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Doppler broadening.
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store all nuclear data. Pregenerated HDF5 libraries can be found at
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https://openmc.mcs.anl.gov; unless you have specific data needs, it is highly
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recommended to use one of the pregenerated libraries. Alternatively, if you have
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ACE format data that was produced with NJOY_, such as that distributed with
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MCNP_ or Serpent_, it can be converted to the HDF5 format using the :ref:`using
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the Python API <create_xs_library>`. Several sources provide openly available
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ACE data including the `ENDF/B`_, JEFF_, and TENDL_
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libraries. In addition to tabulated cross sections in the HDF5 files, OpenMC
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relies on :ref:`windowed multipole <windowed_multipole>` data to perform
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on-the-fly Doppler broadening.
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In multi-group mode, OpenMC utilizes an HDF5-based library format which can be
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used to describe nuclide- or material-specific quantities.
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@ -56,85 +57,16 @@ profile (``.profile`` or ``.bashrc`` in bash_).
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Continuous-Energy Cross Sections
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--------------------------------
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Using ENDF/B-VII.1 Cross Sections from NNDC
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-------------------------------------------
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Using Pregenerated Libraries
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----------------------------
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The NNDC_ provides ACE data from the ENDF/B-VII.1 neutron and thermal scattering
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sublibraries at room temperature processed using NJOY_. To use this data with
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OpenMC, the :ref:`scripts_nndc` script can be used to automatically download and
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extract the ACE data, fix any deficiencies, and create an HDF5 library:
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.. code-block:: sh
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openmc-get-nndc-data
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At this point, you should set the :envvar:`OPENMC_CROSS_SECTIONS` environment
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variable to the absolute path of the file ``nndc_hdf5/cross_sections.xml``. This
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cross section set is used by the test suite.
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Using JEFF Cross Sections from OECD/NEA
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---------------------------------------
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The NEA_ provides processed ACE data from the JEFF_ library. To use this data
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with OpenMC, the :ref:`scripts_jeff` script can be used to automatically
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download and extract the ACE data, fix any deficiencies, and create an HDF5
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library.
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.. code-block:: sh
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openmc-get-jeff-data
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At this point, you should set the :envvar:`OPENMC_CROSS_SECTIONS` environment
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variable to the absolute path of the file ``jeff-3.2-hdf5/cross_sections.xml``.
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Using Cross Sections from MCNP
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------------------------------
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OpenMC provides two scripts (:ref:`scripts_mcnp70` and :ref:`scripts_mcnp71`)
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that will automatically convert ENDF/B-VII.0 and ENDF/B-VII.1 ACE data that is
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provided with MCNP5 or MCNP6. To convert the ENDF/B-VII.0 ACE files
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(``endf70[a-k]`` and ``endf70sab``) into the native HDF5 format, run the
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following:
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.. code-block:: sh
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openmc-convert-mcnp70-data /path/to/mcnpdata/
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where ``/path/to/mcnpdata`` is the directory containing the ``endf70[a-k]``
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files.
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To convert the ENDF/B-VII.1 ACE files (the endf71x and ENDF71SaB libraries), use
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the following script:
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.. code-block:: sh
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openmc-convert-mcnp71-data /path/to/mcnpdata
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where ``/path/to/mcnpdata`` is the directory containing the ``endf71x`` and
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``ENDF71SaB`` directories.
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.. _other_cross_sections:
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Using Other Cross Sections
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--------------------------
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If you have a library of ACE format cross sections other than those listed above
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that you need to convert to OpenMC's HDF5 format, the :ref:`scripts_ace` script
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can be used. There are four different ways you can specify ACE libraries that
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are to be converted:
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1. List each ACE library as a positional argument. This is very useful in
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conjunction with the usual shell utilities (ls, find, etc.).
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2. Use the ``--xml`` option to specify a pre-v0.9 cross_sections.xml file.
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3. Use the ``--xsdir`` option to specify a MCNP xsdir file.
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4. Use the ``--xsdata`` option to specify a Serpent xsdata file.
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The script does not use any extra information from cross_sections.xml/ xsdir/
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xsdata files to determine whether the nuclide is metastable. Instead, the
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``--metastable`` argument can be used to specify whether the ZAID naming
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convention follows the NNDC data convention (1000*Z + A + 300 + 100*m), or the
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MCNP data convention (essentially the same as NNDC, except that the first
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metastable state of Am242 is 95242 and the ground state is 95642).
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Various evaluated nuclear data libraries have been processed into the HDF5
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format required by OpenMC and can be found at https://openmc.mcs.anl.gov. You
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can find both libraries generated by the OpenMC development team as well as
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libraries based on ACE files distributed elsewhere. To use these libraries,
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download the archive file, unpack it, and then set your
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:envvar:`OPENMC_CROSS_SECTIONS` environment variable to the absolute path of
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the ``cross_sections.xml`` file contained in the unpacked directory.
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.. _create_xs_library:
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@ -201,7 +133,7 @@ If you need to create a nuclear data library and you do not already have
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suitable ACE files or you need to further customize the data (for example,
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adding more temperatures), the :meth:`IncidentNeutron.from_njoy` and
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:meth:`ThermalScattering.from_njoy` methods can be used to create data instances
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by directly running NJOY. Both methods require that you pass the name of ENDF
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by directly running NJOY_. Both methods require that you pass the name of ENDF
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file(s) that are passed on to NJOY. For example, to generate data for Zr-92::
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zr92 = openmc.data.IncidentNeutron.from_njoy('n-040_Zr_092.endf')
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@ -235,8 +167,10 @@ Enabling Resonance Scattering Treatments
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In order for OpenMC to correctly treat elastic scattering in heavy nuclides
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where low-lying resonances might be present (see
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:ref:`energy_dependent_xs_model`), the elastic scattering cross section at 0 K
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must be present. To add the 0 K elastic scattering cross section to existing
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:class:`IncidentNeutron` instance, you can use the
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must be present. If the data you are using was generated via
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:meth:`IncidentNeutron.from_njoy`, you will already have 0 K elastic scattering
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cross sections available. Otherwise, to add 0 K elastic scattering cross
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sections to an existing :class:`IncidentNeutron` instance, you can use the
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:meth:`IncidentNeutron.add_elastic_0K_from_endf` method which requires an ENDF
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file for the nuclide you are modifying::
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@ -260,21 +194,15 @@ Photon interaction data is needed to run OpenMC with photon transport enabled.
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Some of this data, namely bremsstrahlung cross sections from `Seltzer and
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Berger`_, stopping powers from the `NIST ESTAR database`_, and Compton profiles
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calculated by `Biggs et al.`_ and available in the Geant4 G4EMLOW data file, is
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distributed with OpenMC. The rest is available from the NNDC, which provides
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distributed with OpenMC. The rest is available from the NNDC_, which provides
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ENDF data from the photo-atomic and atomic relaxation sublibraries of the
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ENDF/B-VII.1 library. By default, the :ref:`scripts_nndc` script will download
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the ENDF data in addition to the neutron and thermal scattering data, extract
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it, combine it with the data from other sources, and convert it to an HDF5
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library. Alternatively, the :ref:`scripts_photon` script can be used to
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download the photon data on its own and create the HDF5 library:
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ENDF/B-VII.1 library.
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.. code-block:: sh
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openmc-get-photon-data
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As with neutrons and thermal scattering, it is possible to use the Python API
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directly to convert photon interaction data from an ENDF or ACE file to an HDF5
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file. The :class:`openmc.data.IncidentPhoton` class contains an
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Most of the pregenerated HDF5 libraries available at https://openmc.mcs.anl.gov
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already have photon interaction data included. If you are building a data
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library yourself, it is possible to use the Python API directly to convert
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photon interaction data from an ENDF or ACE file to an HDF5 file. The
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:class:`openmc.data.IncidentPhoton` class contains an
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:meth:`IncidentPhoton.from_ace` method that will generate photon data from an
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ACE table and an :meth:`IncidentPhoton.export_to_hdf5` method that writes the
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data to an HDF5 file:
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@ -285,7 +213,7 @@ data to an HDF5 file:
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u.export_to_hdf5('U.h5')
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Similarly, the :meth:`IncidentPhoton.from_endf` method can be used to read
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photon data from an ENDF file. In the case, both the photo-atomic and atomic
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photon data from an ENDF file. In this case, both the photo-atomic and atomic
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relaxation sublibrary files are required:
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::
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@ -308,6 +236,11 @@ and unpack an archive (.zip or .tag.gz) from GitHub. Once unpacked, you can use
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the :class:`openmc.data.DataLibrary` class to register the .h5 files as
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described in :ref:`create_xs_library`.
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The `official ENDF/B-VII.1 HDF5 library
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<https://openmc.mcs.anl.gov/official-data-libraries/>`_ includes the windowed
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multipole library, so if you are using this library, the windowed multipole data
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will already be available to you.
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--------------------------
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Multi-Group Cross Sections
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--------------------------
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@ -322,13 +255,13 @@ to the absolute path of the file library expected to used most frequently.
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For an example of how to create a multi-group library, see
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:ref:`notebook_mg_mode_part_i`.
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.. _NJOY: https://njoy.github.io/NJOY2016/
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.. _NNDC: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
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.. _NEA: http://www.oecd-nea.org
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.. _JEFF: https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_32/
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.. _MCNP: http://mcnp.lanl.gov
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.. _NJOY: http://www.njoy21.io/
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.. _NNDC: https://www.nndc.bnl.gov/endf
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.. _MCNP: https://mcnp.lanl.gov
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.. _Serpent: http://montecarlo.vtt.fi
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.. _TENDL: https://tendl.web.psi.ch/tendl_2015/tendl2015.html
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.. _Seltzer and Berger: https://www.sciencedirect.com/science/article/pii/0092640X86900148?via%3Dihub
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.. _ENDF/B: https://www.nndc.bnl.gov/endf/b7.1/acefiles.html
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.. _JEFF: http://www.oecd-nea.org/dbdata/jeff/jeff33/
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.. _TENDL: https://tendl.web.psi.ch/tendl_2017/tendl2017.html
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.. _Seltzer and Berger: https://doi.org/10.1016/0092-640X(86)90014-8
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.. _NIST ESTAR database: https://physics.nist.gov/PhysRefData/Star/Text/ESTAR.html
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.. _Biggs et al.: https://www.sciencedirect.com/science/article/pii/0092640X75900303
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.. _Biggs et al.: https://doi.org/10.1016/0092-640X(75)90030-3
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@ -167,7 +167,7 @@ Prerequisites
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<https://svalinn.github.io/DAGMC/install/dag_multiple.html>`_). For use in
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OpenMC, only the ``MOAB_DIR`` and ``BUILD_TALLY`` variables need to be
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specified in the CMake configuration step.
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* git_ version control software for obtaining source code
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@ -478,10 +478,6 @@ as for OpenMC.
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The Python VTK bindings are needed to convert voxel and track files to VTK
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format.
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`silomesh <https://github.com/nhorelik/silomesh>`_
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The silomesh package is needed to convert voxel and track files to SILO
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format.
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`pytest <https://docs.pytest.org>`_
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The pytest framework is used for unit testing the Python API.
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@ -125,10 +125,10 @@ can subsequently be converted into a standard mesh format that can be viewed in
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`ParaView <http://www.paraview.org/>`_, `VisIt
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<https://wci.llnl.gov/simulation/computer-codes/visit>`_, etc. This typically
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will compress the size of the file significantly. The provided
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:ref:`scripts_voxel` script can convert the HDF5 voxel file to VTK or SILO
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formats. Once processed into a standard 3D file format, colors and masks can be
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defined using the stored ID numbers to better explore the geometry. The process
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for doing this will depend on the 3D viewer, but should be straightforward.
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:ref:`scripts_voxel` script can convert the HDF5 voxel file to VTK formats. Once
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processed into a standard 3D file format, colors and masks can be defined using
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the stored ID numbers to better explore the geometry. The process for doing this
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will depend on the 3D viewer, but should be straightforward.
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.. note:: 3D voxel plotting can be very computer intensive for the viewing
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program (Visit, ParaView, etc.) if the number of voxels is large (>10
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@ -95,94 +95,6 @@ otherwise.
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--fission_energy_release FISSION_ENERGY_RELEASE
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HDF5 file containing fission energy release data
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.. _scripts_mcnp70:
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------------------------------
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``openmc-convert-mcnp70-data``
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------------------------------
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This script converts ENDF/B-VII.0 ACE data from the MCNP5/6 distribution into an
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HDF5 library that can be used by OpenMC. This assumes that you have a directory
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containing files named endf70a, endf70b, ..., endf70k, and endf70sab. The path
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to the directory containing these files should be given as a positional
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argument. The following optional arguments are available:
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-d DESTINATION, --destination DESTINATION
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Directory to create new library in (Default: mcnp_endfb70)
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.. _scripts_mcnp71:
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------------------------------
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``openmc-convert-mcnp71-data``
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------------------------------
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This script converts ENDF/B-VII.1 ACE data from the MCNP6 distribution into an
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HDF5 library that can be used by OpenMC. This assumes that you have a directory
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containing subdirectories 'endf71x' and 'ENDF71SaB'. The path to the directory
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containing these subdirectories should be given as a positional argument. The
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following optional arguments are available:
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-d DESTINATION, --destination DESTINATION
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Directory to create new library in (Default: mcnp_endfb71)
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-f FER, --fission_energy_release FER
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HDF5 file containing fission energy release data
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.. _scripts_jeff:
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------------------------
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``openmc-get-jeff-data``
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------------------------
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This script downloads `JEFF 3.2 ACE data
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<https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_32/>`_ from OECD/NEA
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and converts it to a multi-temperature HDF5 library for use with OpenMC. It has
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the following optional arguments:
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-b, --batch
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Suppress standard in
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-d DESTINATION, --destination DESTINATION
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Directory to create new library in (default: jeff-3.2-hdf5)
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.. warning:: This script will download approximately 9 GB of data. Extracting
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and processing the data may require as much as 40 GB of additional
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free disk space.
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.. _scripts_nndc:
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------------------------
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``openmc-get-nndc-data``
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------------------------
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This script downloads `ENDF/B-VII.1
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<http://www.nndc.bnl.gov/endf/b7.1/acefiles.html>`_ incident neutron ACE data
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and incident photon ENDF data from NNDC and converts it to an HDF5 library for
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use with OpenMC. This script has the following optional arguments:
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-b, --batch
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Suppress standard in
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-n, --neutron_only
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Whether to exclude photon interaction/atomic data
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.. _scripts_photon:
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--------------------------
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``openmc-get-photon-data``
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--------------------------
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This script downloads `ENDF data <http://www.nndc.bnl.gov/endf/b7.1/zips/>`_
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from NNDC for photo-atomic and atomic relaxation sublibraries and converts it
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to an HDF5 library for use with photon transport in OpenMC. This script has the
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following optional arguments:
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-b, --batch
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Suppress standard in
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-c, --cross-sections
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cross_sections.xml file to append libraries to
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.. _scripts_compton:
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-----------------------
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@ -294,24 +206,21 @@ Message Description
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.. _scripts_voxel:
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---------------------------
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``openmc-voxel-to-silovtk``
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``openmc-voxel-to-vtk``
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---------------------------
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When OpenMC generates :ref:`voxel plots <usersguide_voxel>`, they are in an
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:ref:`HDF5 format <io_voxel>` that is not terribly useful by itself. The
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``openmc-voxel-to-silovtk`` script converts a voxel HDF5 file to `VTK
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<http://www.vtk.org/>`_ or `SILO
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<https://wci.llnl.gov/simulation/computer-codes/silo>`_ file. For VTK, you need
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to have the VTK Python bindings installed. For SILO, you need to have `silomesh
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<https://github.com/nhorelik/silomesh>`_ installed. To convert a voxel file,
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simply provide the path to the file:
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``openmc-voxel-to-vtk`` script converts a voxel HDF5 file to a `VTK
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<http://www.vtk.org/>`_ file. To run this script, you will need to have the VTK
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Python bindings installed. To convert a voxel file, simply provide the path to
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the file:
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.. code-block:: sh
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openmc-voxel-to-silovtk voxel_1.h5
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openmc-voxel-to-vtk voxel_1.h5
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The ``openmc-voxel-to-silovtk`` script also takes the following optional
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The ``openmc-voxel-to-vtk`` script also takes the following optional
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command-line arguments:
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-o, --output Path to output VTK or SILO file
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-s, --silo Flag to convert to SILO instead of VTK
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-o, --output Path to output VTK file
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