mirror of
https://github.com/openmc-dev/openmc.git
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Merge branch 'develop' into new-scatt-mat
This commit is contained in:
Will Boyd
commit
e640146f8f
64 changed files with 15896 additions and 1606 deletions
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@ -4,7 +4,8 @@
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Development Team
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================
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Active development of the OpenMC Monte Carlo code is currently led by:
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The following people have contributed to development of the OpenMC Monte Carlo
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code:
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* `Paul Romano <https://github.com/paulromano>`_
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* `Bryan Herman <https://github.com/bhermanmit>`_
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@ -14,6 +15,9 @@ Active development of the OpenMC Monte Carlo code is currently led by:
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* `Sterling Harper <https://github.com/smharper>`_
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* `Will Boyd <https://github.com/wbinventor>`_
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* `Samuel Shaner <https://github.com/samuelshaner>`_
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* `Jingang Liang <https://github.com/liangjg>`_
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* `Colin Josey <https://github.com/cjosey>`_
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* `Amanda Lund <https://github.com/amandalund>`_
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* `Benoit Forget <http://web.mit.edu/nse/people/faculty/forget.html>`_
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* `Kord Smith <http://web.mit.edu/nse/people/faculty/smith.html>`_
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* `Andrew Siegel <http://www.mcs.anl.gov/person/andrew-siegel>`_
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@ -15,5 +15,5 @@ as debugging.
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structures
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styleguide
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workflow
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xml-parsing
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user-input
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docbuild
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73
docs/source/devguide/user-input.rst
Normal file
73
docs/source/devguide/user-input.rst
Normal file
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@ -0,0 +1,73 @@
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.. _devguide_user_input:
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=========================
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Making User Input Changes
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=========================
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Users are encouraged to use OpenMC's :ref:`pythonapi` to build XML files that
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the OpenMC solver then reads during the initialization phase. Thus, to modify,
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add, or remove user input options, changes must be made both within the Python
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API and the Fortran source that reads XML files produced by the Python API. The
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following steps should be followed to make changes to user input:
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1. Determine the Python class you need to change. For example, if you are adding
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a new setting, you probably want to change the :class:`openmc.Settings`
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class. If you are adding a new surface type, you would need to create a
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subclass of :class:`openmc.Surface`.
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2. To add a new option, the class will need a `property attribute`_. For
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example, if you wanted to add a "fast_mode" setting, you would need two
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methods that look like:
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.. code-block:: python
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@property
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def fast_mode(self):
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...
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@fast_mode.setter
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def fast_mode(self, fast_mode):
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...
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3. Make sure that when an instance of the class is exported to XML (usually
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through a ``export_to_xml()`` or ``to_xml_element()`` method), a new element
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is written to the appropriate file. OpenMC uses the
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:mod:`xml.etree.ElementTree` API, so refer to the documentation of that
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module for guidance on creating elements/attributes.
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4. Make sure that your input can be categorized as one of the datatypes from
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`XML Schema Part 2`_ and that parsing of the data appropriately reflects
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this. For example, for a boolean_ value, true can be represented either by
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"true" or by "1".
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5. Now that you're done with the Python side, you need to make modifications to
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the Fortran codebase. Make appropriate changes in the `input_xml module`_ to
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read your new user input. You should use procedures and types defined by the
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`xml_interface module`_.
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6. If you've made changes in the geometry or materials, make sure they are
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written out to the statepoint or summary files and that the
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:class:`openmc.StatePoint` and :class:`openmc.Summary` classes read them in.
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7. Finally, a set of `RELAX NG`_ schemas exists that enables validation of input
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files. You should modify the RELAX NG schema for the file you changed. The
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easiest way to do this is to change the `compact syntax`_ file
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(e.g. ``src/relaxng/geometry.rnc``) and then convert it to regular XML syntax
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using trang_::
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trang geometry.rnc geometry.rng
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For most user input additions and changes, it is simple enough to follow a
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"monkey see, monkey do" approach. When in doubt, contact your nearest OpenMC
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developer or send a message to the `developers mailing list`_.
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.. _property attribute: https://docs.python.org/3.6/library/functions.html#property
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.. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
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.. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
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.. _xml_interface module: https://github.com/mit-crpg/openmc/blob/develop/src/xml_interface.F90
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.. _input_xml module: https://github.com/mit-crpg/openmc/blob/develop/src/input_xml.F90
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.. _RELAX NG: http://relaxng.org/
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.. _compact syntax: http://relaxng.org/compact-tutorial-20030326.html
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.. _trang: http://www.thaiopensource.com/relaxng/trang.html
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.. _developers mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-dev
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@ -1,118 +0,0 @@
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.. _devguide_xml-parsing:
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=================
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XML Input Parsing
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=================
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OpenMC relies on the FoX_ Fortran XML library for reading and intrepreting the
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XML input files for geometry, materials, settings, tallies, etc. The use of an
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XML format makes writing input files considerably more flexible than would
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otherwise be possible.
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With the FoX library, extending the user input files to include new tags is
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fairly straightforward. The steps for modifying/adding input are as follows:
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1. Add appropriate calls to procedures from the `xml_interface module`_, such as
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``check_for_node``, ``get_node_value``, and ``get_node_array``. All input
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reading is performed in the `input_xml module`_.
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2. Make sure that your input can be categorized as one of the datatypes from
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`XML Schema Part 2`_ and that parsing of the data appropriately reflects
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this. For example, for a boolean_ value, true can be represented either by
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"true" or by "1".
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3. Add code to check the variable for any possible errors.
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A set of `RELAX NG`_ schemata exists that enables real-time validation of input
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files when using the GNU Emacs text editor. You should also modify the RELAX NG
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schema for the file you changed (e.g. src/relaxng/geometry.rnc) so that
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those who use Emacs can confirm whether their input is valid before they
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run. You will need to be familiar with RELAX NG `compact syntax`_.
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Working with the FoX Submodule
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==============================
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The FoX_ library is included as a submodule_ in OpenMC. This means that for a
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given commit in OpenMC, there is an associated commit id that links to FoX.
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The actual FoX source code is maintained at mit-crpg/fox, branch openmc. When
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cloning the OpenMC repo for the first time, you will notice that the directory
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*src/xml/fox* is empty. To fetch the submodule source code, you can manually
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enter the following from the root directory of OpenMC:
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.. code-block:: sh
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git submodule init
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git submodule update
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It should be noted that if the submodule is not initialized and updated, *cmake*
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will automatically perform these commands if it cannot file the FoX source code.
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If you navigate into the FoX source code in OpenMC, src/xml/fox, and check git
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information, you will notice that you are in a completely different repo. Actually,
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you are in a clone of mit-crpg/fox. If you have write access to this repo, you can
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make changes to the FoX source code, commit and push just like any other repo.
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Just because you make changes to the FoX source code in OpenMC or in a standalone
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repo, this does not mean that OpenMC will automatically fetch these changes. The
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way submodules work is that they are just stored as a commit id. To save FoX xml
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source changes to your OpenMC branch, do the following:
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1. Go into src/xml/fox and check out the appropriate source code state
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2. Navigate back out of fox subdirectory and type:
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.. code-block:: sh
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git status
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3. Make sure you see that git recognized that the state of FoX changed:
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::
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# On branch fox_submodule
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# Changes not staged for commit:
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# (use "git add <file>..." to update what will be committed)
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# (use "git checkout -- <file>..." to discard changes in working directory)
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#
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# modified: fox (new commits)
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4. Commit and push this change
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Editing FoX on Personal Fork
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============================
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If you don't have write access to mit-crpg/fox and thus can't make a branch off of the openmc
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branch there, you will need to fork mit-crpg/fox to your personal account. You need to then
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link your branch in your OpenMC repo, to the *openmc* branch on your own personal FoX fork.
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To do this, edit the *.gitmodules* file in the root folder of the repo. It contains the
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following information:
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::
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[submodule "src/xml/fox"]
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path = src/xml/fox
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url = git@github.com:mit-crpg/fox
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Change the url remote to your own fork. The commit id should stay constant until you start
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making modification to FoX yourself. Once you have made changes to your FoX fork and linked
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the new commit id to your OpenMC branch, you can pull request your changes in by peforming
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the following steps:
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1. Create a pull request from your fork of FoX to mit-crpg/fox and wait until it
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is merged into the openmc branch.
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2. In your OpenMC repo, change your *.gitmodules* file back to point at mit-crpg/fox.
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3. Submit a pull request to mit-crpg/openmc
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.. warning:: If you make changes to your FoX submodule inside of an OpenMC repo and do not
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commit, do **not** run *git submodule update*. This may throw away any changes that
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were not committed.
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.. _FoX: https://github.com/mit-crpg/fox
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.. _xml_interface module: https://github.com/mit-crpg/openmc/blob/develop/src/xml_interface.F90
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.. _input_xml module: https://github.com/mit-crpg/openmc/blob/develop/src/input_xml.F90
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.. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
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.. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
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.. _RELAX NG: http://relaxng.org/
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.. _compact syntax: http://relaxng.org/compact-tutorial-20030326.html
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.. _submodule: http://git-scm.com/book/en/Git-Tools-Submodules
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File diff suppressed because one or more lines are too long
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@ -839,17 +839,27 @@ problem. It has the following attributes/sub-elements:
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*Default*: None
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.. _verbosity:
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``<verbosity>`` Element
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-----------------------
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The ``<verbosity>`` element tells the code how much information to display to
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the standard output. A higher verbosity corresponds to more information being
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displayed. This element takes the following attributes:
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displayed. The text of this element should be an integer between between 1
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and 10. The verbosity levels are defined as follows:
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:value:
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The specified verbosity between 1 and 10.
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:1: don't display any output
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:2: only show OpenMC logo
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:3: all of the above + headers
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:4: all of the above + results
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:5: all of the above + file I/O
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:6: all of the above + timing statistics and initialization messages
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:7: all of the above + :math:`k` by generation
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:9: all of the above + indicate when each particle starts
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:10: all of the above + event information
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*Default*: 5
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*Default*: 7
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``<create_fission_neutrons>`` Element
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-------------------------------------
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|
|
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@ -58,7 +58,7 @@ Now OpenMC should be recognized within the repository and can be installed:
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.. code-block:: sh
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sudo apt-get install openmc
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sudo apt install openmc
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Binary packages from this PPA may exist for earlier versions of Ubuntu, but they
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are no longer supported.
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@ -88,7 +88,16 @@ Prerequisites
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If you are using Debian or a Debian derivative such as Ubuntu, you can
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install the gfortran compiler using the following command::
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sudo apt-get install gfortran
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sudo apt install gfortran
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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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sudo apt install g++
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* CMake_ cross-platform build system
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@ -97,7 +106,7 @@ Prerequisites
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|||
derivative such as Ubuntu, you can install CMake using the following
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command::
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sudo apt-get install cmake
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sudo apt install cmake
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||||
* HDF5_ Library for portable binary output format
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@ -125,7 +134,7 @@ Prerequisites
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|||
|
||||
.. code-block:: sh
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||||
sudo apt-get install libhdf5-8 libhdf5-dev hdf5-helpers
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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
|
||||
distribution and version.
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|
@ -140,12 +149,13 @@ Prerequisites
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|||
with the latest versions of both OpenMPI_ and MPICH_. OpenMPI and/or MPICH
|
||||
can be installed on Debian derivatives with::
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||||
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||||
sudo apt-get install mpich libmpich-dev
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||||
sudo apt-get install openmpi-bin libopenmpi1.6 libopenmpi-dev
|
||||
sudo apt install mpich libmpich-dev
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||||
sudo apt install openmpi-bin libopenmpi-dev
|
||||
|
||||
* git_ version control software for obtaining source code
|
||||
|
||||
.. _gfortran: http://gcc.gnu.org/wiki/GFortran
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.. _gcc: https://gcc.gnu.org/
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||||
.. _CMake: http://www.cmake.org
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||||
.. _OpenMPI: http://www.open-mpi.org
|
||||
.. _MPICH: http://www.mpich.org
|
||||
|
|
|
|||
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