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2
_sources/developers.txt
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@ -13,8 +13,10 @@ Advisors to the project include:
* `Benoit Forget`_
* `Kord Smith`_
* `Andrew Siegel`_
.. _Paul Romano: mailto:romano7@mit.edu
.. _Bryan Herman: mailto:bherman@mit.edu
.. _Benoit Forget: mailto:bforget@mit.edu
.. _Kord Smith: mailto:kord@mit.edu
.. _Andrew Siegel: mailto:siegela@mcs.anl.gov

46
_sources/install.txt
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@ -4,6 +4,24 @@
Installation
============
--------------------
Obtaining the Source
--------------------
All OpenMC source code is hosted on GitHub_. This means that you will need to
have git_ installed on your computer in order to get source code and updates
directly from the repository. GitHub has a good set of `instructions
<http://help.github.com/set-up-git-redirect>`_ for how to set up git to work
with GitHub since this involves setting up ssh_ keys. With git installed and
setup, the following command will download the full source code from the GitHub
repository::
git clone git@github.com:mit-crpg/openmc.git
.. _GitHub: http://github.com
.. _git: http://git-scm.com
.. _ssh: http://en.wikipedia.org/wiki/Secure_Shell
-------------
Prerequisites
-------------
@ -18,11 +36,6 @@ the gfortran compiler using the following command::
sudo apt-get install gfortran
.. warning:: The runtime preformance with the Intel Fortran compiler and PGI
Fortran compiler will likely exceed that of the gfortran compiler. Compiling
with high optimization on the gfortran compiler may make up for some of the
performance difference
To compile with support for parallel runs on a distributed-memory architecture,
you will need to have a valid implementation of MPI installed on your
machine. The code has been tested and is known to work with the latest versions
@ -33,9 +46,14 @@ with::
sudo apt-get install mpich2
sudo apt-get install openmpi-bin
To compile with support for HDF5_ output (highly recommended), you will need to
have HDF5 installed on your computer. The installed version will need to have
been compiled with the same compiler you intend to compile OpenMC with.
.. _gfortran: http://gcc.gnu.org/wiki/GFortran
.. _OpenMPI: http://www.open-mpi.org
.. _MPICH2: http://www.mcs.anl.gov/mpi/mpich/
.. _HDF5: http://www.hdfgroup.org/HDF5/
-------------
Configuration
@ -65,18 +83,18 @@ OPTIMIZE
interprocedural optimization.
USE_MPI
Enables parallel runs using the Message Passing Interface. Users should
also set the MPI root directory by setting the MPI variable further down in
the Makefile.
Enables parallel runs using the Message Passing Interface. Users should also
set the MPI_ROOT directory further down in the Makefile.
USE_OPENMP
Enables parallel runs on shared-memory architecture using OpenMP threading.
USE_HDF5
Enables HDF5 output in addition to normal screen and text file output. Users
should also set the HDF5_ROOT directory further down in the Makefile.
USE_COARRAY
Enables parallel runs using Fortran 2008 coarrays.
It is also possible to change these options from the command line itself. For
example, if you want to compile with DEBUG turned on without actually change the
Makefile, you can enter the following from a terminal::
.. note:: OpenMC does not yet support parallelism using OpenMP or Fortran 2008
coarrays.
make DEBUG=yes
---------
Compiling

62
_sources/usersguide/input.txt
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@ -117,9 +117,10 @@ Each ``surface`` element can have the following attributes or sub-elements:
*Default*: None
:boundary:
The boundary condition for the surface. This can be ``vacuum`` or ``reflective``.
The boundary condition for the surface. This can be ``transmission``,
``vacuum``, or ``reflective``.
*Default*: ``reflective``
*Default*: ``transmission``
The following quadratic surfaces can be modeled:
@ -205,9 +206,8 @@ universe. A ``lattice`` accepts the following attributes or sub-elements:
:id:
A unique integer that can be used to identify the surface.
:type:
A string indicating the arrangement of lattice cells. Accepted options are
"rectangular" and "hexagonal".
:type: A string indicating the arrangement of lattice cells. Currently, the
only accepted option is "rectangular".
*Default*: rectangular
@ -266,8 +266,8 @@ Each ``material`` element can have the following attributes or sub-elements:
weight percent of that nuclide within the material, respectively. One
example would be as follows::
<nuclide name="H-1" xs="03c" ao="2.0" />
<nuclide name="O-16" xs="03c" ao="1.0" />
<nuclide name="H-1" xs="70c" ao="2.0" />
<nuclide name="O-16" xs="70c" ao="1.0" />
.. note:: If one nuclide is specified in atom percent, all others must also
be given in atom percent. The same applies for weight percentages.
@ -342,6 +342,27 @@ below which particles undergo Russian roulette.
*Default*: 0.25
``entropy_box`` Element
-----------------------
This element describes the lower-left and upper-right corners of a box to be
used for calculting Shannon entropy. This box should cover all possible
fissionable materials in the problem. The values given after this element should
be six numbers, the first of which are the Cartesian coordinates of the
lower-left corner of the box and the last three of which are the Cartesian
coordinates of the upper-right corner of the box.
*Default*: None
``ptables`` Element
-------------------
The ``ptables`` element determines whether probability tables should be used in
the unresolved resonance range if available. This element has no attributes or
sub-elements and can be set to either "off" or "on".
*Default*: on
``source`` Element
------------------
@ -367,6 +388,15 @@ survival biasing, otherwise known as implicit capture or absorption.
*Default*: off
``trace`` Element
-----------------
The ``trace`` element can be used to print out detailed information about a
single particle during a simulation. This element should be followed by two
integers, the cycle and one for the particle number.
*Default*: None
``verbosity`` Element
---------------------
@ -503,6 +533,20 @@ attributes/sub-elements:
:width:
The width of mesh cells in each direction.
``assume_separate`` Element
---------------------------
In cases where the user needs to specify many different tallies each of which
are spatially separate, this tag can be used to cut down on some of the tally
overhead. The effect of assuming all tallies are spatially separate is that once
one tally is scored to, the same event is assumed not to score to any other
tallies. This element should be followed by "yes" or "no"
.. warning:: If used incorrectly, the assumption that all tallies are spatially
separate can lead to incorrect results.
*Default*: no
-------------------------------------------
Geometry Plotting Specification -- plot.xml
-------------------------------------------
@ -532,9 +576,7 @@ the plot in each of the basis directions.
-----------------
The ``basis`` element has no attributes/sub-elements and indicates the specified
basis for plotting.
.. note:: The only accepted option currently is "xy"
basis for plotting. The only option option currently accepted is "xy".
*Default*: xy

1
developers.html
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@ -59,6 +59,7 @@
<ul class="simple">
<li><a class="reference external" href="mailto:bforget&#37;&#52;&#48;mit&#46;edu">Benoit Forget</a></li>
<li><a class="reference external" href="mailto:kord&#37;&#52;&#48;mit&#46;edu">Kord Smith</a></li>
<li><a class="reference external" href="mailto:siegela&#37;&#52;&#48;mcs&#46;anl&#46;gov">Andrew Siegel</a></li>
</ul>
</div>

41
install.html
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@ -53,6 +53,17 @@
<div class="section" id="installation">
<span id="install"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1>
<div class="section" id="obtaining-the-source">
<h2>Obtaining the Source<a class="headerlink" href="#obtaining-the-source" title="Permalink to this headline"></a></h2>
<p>All OpenMC source code is hosted on <a class="reference external" href="http://github.com">GitHub</a>. This means that you will need to
have <a class="reference external" href="http://git-scm.com">git</a> installed on your computer in order to get source code and updates
directly from the repository. GitHub has a good set of <a class="reference external" href="http://help.github.com/set-up-git-redirect">instructions</a> for how to set up git to work
with GitHub since this involves setting up <a class="reference external" href="http://en.wikipedia.org/wiki/Secure_Shell">ssh</a> keys. With git installed and
setup, the following command will download the full source code from the GitHub
repository:</p>
<div class="highlight-python"><pre>git clone git@github.com:mit-crpg/openmc.git</pre>
</div>
</div>
<div class="section" id="prerequisites">
<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline"></a></h2>
<p>In order to compile OpenMC, you will need to have a Fortran compiler installed
@ -63,13 +74,6 @@ choose. For <a class="reference external" href="http://gcc.gnu.org/wiki/GFortran
the gfortran compiler using the following command:</p>
<div class="highlight-python"><pre>sudo apt-get install gfortran</pre>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The runtime preformance with the Intel Fortran compiler and PGI
Fortran compiler will likely exceed that of the gfortran compiler. Compiling
with high optimization on the gfortran compiler may make up for some of the
performance difference</p>
</div>
<p>To compile with support for parallel runs on a distributed-memory architecture,
you will need to have a valid implementation of MPI installed on your
machine. The code has been tested and is known to work with the latest versions
@ -79,6 +83,9 @@ with:</p>
<div class="highlight-python"><pre>sudo apt-get install mpich2
sudo apt-get install openmpi-bin</pre>
</div>
<p>To compile with support for <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> output (highly recommended), you will need to
have HDF5 installed on your computer. The installed version will need to have
been compiled with the same compiler you intend to compile OpenMC with.</p>
</div>
<div class="section" id="configuration">
<h2>Configuration<a class="headerlink" href="#configuration" title="Permalink to this headline"></a></h2>
@ -102,18 +109,16 @@ compiler is used.</dd>
this compiles with -O3. For Intel Fortran, this compiles with -O3 as well as
interprocedural optimization.</dd>
<dt>USE_MPI</dt>
<dd>Enables parallel runs using the Message Passing Interface. Users should
also set the MPI root directory by setting the MPI variable further down in
the Makefile.</dd>
<dt>USE_OPENMP</dt>
<dd>Enables parallel runs on shared-memory architecture using OpenMP threading.</dd>
<dt>USE_COARRAY</dt>
<dd>Enables parallel runs using Fortran 2008 coarrays.</dd>
<dd>Enables parallel runs using the Message Passing Interface. Users should also
set the MPI_ROOT directory further down in the Makefile.</dd>
<dt>USE_HDF5</dt>
<dd>Enables HDF5 output in addition to normal screen and text file output. Users
should also set the HDF5_ROOT directory further down in the Makefile.</dd>
</dl>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">OpenMC does not yet support parallelism using OpenMP or Fortran 2008
coarrays.</p>
<p>It is also possible to change these options from the command line itself. For
example, if you want to compile with DEBUG turned on without actually change the
Makefile, you can enter the following from a terminal:</p>
<div class="highlight-python"><pre>make DEBUG=yes</pre>
</div>
</div>
<div class="section" id="compiling">

2
searchindex.js
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65
usersguide/input.html
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@ -154,8 +154,9 @@ a list a what coefficients to specify for a given surface</p>
<p><em>Default</em>: None</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">boundary:</th><td class="field-body"><p class="first">The boundary condition for the surface. This can be <tt class="docutils literal"><span class="pre">vacuum</span></tt> or <tt class="docutils literal"><span class="pre">reflective</span></tt>.</p>
<p class="last"><em>Default</em>: <tt class="docutils literal"><span class="pre">reflective</span></tt></p>
<tr class="field-even field"><th class="field-name">boundary:</th><td class="field-body"><p class="first">The boundary condition for the surface. This can be <tt class="docutils literal"><span class="pre">transmission</span></tt>,
<tt class="docutils literal"><span class="pre">vacuum</span></tt>, or <tt class="docutils literal"><span class="pre">reflective</span></tt>.</p>
<p class="last"><em>Default</em>: <tt class="docutils literal"><span class="pre">transmission</span></tt></p>
</td>
</tr>
</tbody>
@ -254,8 +255,8 @@ universe. A <tt class="docutils literal"><span class="pre">lattice</span></tt> a
<tr class="field-odd field"><th class="field-name">id:</th><td class="field-body"><p class="first">A unique integer that can be used to identify the surface.</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">type:</th><td class="field-body"><p class="first">A string indicating the arrangement of lattice cells. Accepted options are
&#8220;rectangular&#8221; and &#8220;hexagonal&#8221;.</p>
<tr class="field-even field"><th class="field-name">type:</th><td class="field-body"><p class="first">A string indicating the arrangement of lattice cells. Currently, the
only accepted option is &#8220;rectangular&#8221;.</p>
<p><em>Default</em>: rectangular</p>
</td>
</tr>
@ -309,8 +310,8 @@ desired nuclide while the <tt class="docutils literal"><span class="pre">xs</spa
identifier. Finally, the <tt class="docutils literal"><span class="pre">ao</span></tt> and <tt class="docutils literal"><span class="pre">wo</span></tt> attributes specify the atom or
weight percent of that nuclide within the material, respectively. One
example would be as follows:</p>
<div class="highlight-python"><pre>&lt;nuclide name="H-1" xs="03c" ao="2.0" /&gt;
&lt;nuclide name="O-16" xs="03c" ao="1.0" /&gt;</pre>
<div class="highlight-python"><pre>&lt;nuclide name="H-1" xs="70c" ao="2.0" /&gt;
&lt;nuclide name="O-16" xs="70c" ao="1.0" /&gt;</pre>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
@ -390,6 +391,25 @@ below which particles undergo Russian roulette.</p>
<blockquote>
<div><em>Default</em>: 0.25</div></blockquote>
</div>
<div class="section" id="entropy-box-element">
<h3><tt class="docutils literal"><span class="pre">entropy_box</span></tt> Element<a class="headerlink" href="#entropy-box-element" title="Permalink to this headline"></a></h3>
<p>This element describes the lower-left and upper-right corners of a box to be
used for calculting Shannon entropy. This box should cover all possible
fissionable materials in the problem. The values given after this element should
be six numbers, the first of which are the Cartesian coordinates of the
lower-left corner of the box and the last three of which are the Cartesian
coordinates of the upper-right corner of the box.</p>
<blockquote>
<div><em>Default</em>: None</div></blockquote>
</div>
<div class="section" id="ptables-element">
<h3><tt class="docutils literal"><span class="pre">ptables</span></tt> Element<a class="headerlink" href="#ptables-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">ptables</span></tt> element determines whether probability tables should be used in
the unresolved resonance range if available. This element has no attributes or
sub-elements and can be set to either &#8220;off&#8221; or &#8220;on&#8221;.</p>
<blockquote>
<div><em>Default</em>: on</div></blockquote>
</div>
<div class="section" id="source-element">
<h3><tt class="docutils literal"><span class="pre">source</span></tt> Element<a class="headerlink" href="#source-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">source</span></tt> element gives information on an initial source guess for
@ -419,6 +439,14 @@ survival biasing, otherwise known as implicit capture or absorption.</p>
<blockquote>
<div><em>Default</em>: off</div></blockquote>
</div>
<div class="section" id="trace-element">
<h3><tt class="docutils literal"><span class="pre">trace</span></tt> Element<a class="headerlink" href="#trace-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">trace</span></tt> element can be used to print out detailed information about a
single particle during a simulation. This element should be followed by two
integers, the cycle and one for the particle number.</p>
<blockquote>
<div><em>Default</em>: None</div></blockquote>
</div>
<div class="section" id="verbosity-element">
<h3><tt class="docutils literal"><span class="pre">verbosity</span></tt> Element<a class="headerlink" href="#verbosity-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">verbosity</span></tt> element tells the code how much information to display to the
@ -561,6 +589,22 @@ given, it is assumed that the mesh is an x-y mesh.</td>
</table>
</div></blockquote>
</div>
<div class="section" id="assume-separate-element">
<h3><tt class="docutils literal"><span class="pre">assume_separate</span></tt> Element<a class="headerlink" href="#assume-separate-element" title="Permalink to this headline"></a></h3>
<p>In cases where the user needs to specify many different tallies each of which
are spatially separate, this tag can be used to cut down on some of the tally
overhead. The effect of assuming all tallies are spatially separate is that once
one tally is scored to, the same event is assumed not to score to any other
tallies. This element should be followed by &#8220;yes&#8221; or &#8220;no&#8221;</p>
<blockquote>
<div><div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If used incorrectly, the assumption that all tallies are spatially
separate can lead to incorrect results.</p>
</div>
<p><em>Default</em>: no</p>
</div></blockquote>
</div>
</div>
<div class="section" id="geometry-plotting-specification-plot-xml">
<h2>Geometry Plotting Specification &#8211; plot.xml<a class="headerlink" href="#geometry-plotting-specification-plot-xml" title="Permalink to this headline"></a></h2>
@ -585,14 +629,9 @@ the plot in each of the basis directions.</p>
<div class="section" id="basis-element">
<h3><tt class="docutils literal"><span class="pre">basis</span></tt> Element<a class="headerlink" href="#basis-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">basis</span></tt> element has no attributes/sub-elements and indicates the specified
basis for plotting.</p>
basis for plotting. The only option option currently accepted is &#8220;xy&#8221;.</p>
<blockquote>
<div><div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The only accepted option currently is &#8220;xy&#8221;</p>
</div>
<p><em>Default</em>: xy</p>
</div></blockquote>
<div><em>Default</em>: xy</div></blockquote>
</div>
<div class="section" id="pixel-element">
<h3><tt class="docutils literal"><span class="pre">pixel</span></tt> Element<a class="headerlink" href="#pixel-element" title="Permalink to this headline"></a></h3>