Updated documentation.

This commit is contained in:
Paul Romano 2012-08-26 13:52:08 -04:00
parent e21e92ccc5
commit 0a8fed139e
9 changed files with 123 additions and 60 deletions

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@ -118,7 +118,7 @@ in equation :eq:`unbiased-variance` is especially suitable for computation since
we do not need to store the values at every realization of the random variable
as the simulation proceeds. Instead, we can simply keep a running sum and sum of
squares of the values at each realization of the random variable and use that to
calulate the variance.
calculate the variance.
Variance of the Mean
--------------------

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@ -26,3 +26,7 @@ New Features
---------
Bug Fixes
---------
- 792eb3_: Fixed degrees of freedom for confidence intervals.
.. _792eb3: https://github.com/mit-crpg/openmc/commit/792eb3

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@ -191,6 +191,23 @@ tally data, this option can significantly improve the parallel efficiency.
*Default*: off
``<output>`` Element
--------------------
The ``<output>`` element determines what output files should be written to disk
during the run. This element has no attributes or sub-elements and should be set
to a list of strings separated by spaces. Valid options are "summary",
"cross-sections", and "tallies". For example, if you want the summary and cross
sections summary file to be written, this element should be given as:
.. code-block:: xml
<output>summary cross_sections</output>
.. note:: The tally results will be written to a binary/HDF5 state point file by
default.
*Default*: "tallies"
``<ptables>`` Element
---------------------
@ -298,6 +315,34 @@ attributes/sub-elements:
*Default*: 0.988 2.249
``<state_point>`` Element
-------------------------
The ``<state_point>`` element indicates at what batches a state point file
should be written. A state point file can be used to restart a run or to get
tally results at any batch. This element has the following
attributes/sub-elements:
:batches:
A list of integers separated by spaces indicating at what batches a state
point file should be written.
*Default*: Last batch only
:interval:
A single integer :math:`n` indicating that a state point should be written
every :math:`n` batches. This option can be given in lieu of listing
batches explicitly.
*Default*: None
:source_separate:
If this element is set to "on", a separate binary source file will be
written. Otherwise, the source sites will be written in the state point
directly.
*Default*: "off"
``<survival_biasing>`` Element
------------------------------
@ -355,28 +400,6 @@ displayed. This element takes the following attributes:
*Default*: 5
``<write_state_point>`` Element
-------------------------------
The ``<write_state_point>`` element is used to indicate batches at which the
user wishes to have a binary state point file written to disk. The state point
file can be used to restart a run or to get tally results at an intermediate
stage. This element has no attributes and should consist of a list of integers
corresponding to batches at which a binary state point file should be written to
disk.
*Default*: None
``<write_source>`` Element
--------------------------
The ``<write_source>`` element has no attributes and has an accepted value of
"on" or "off". If set to "on", a binary source file will be written to disk at
the end of the run that can be used as a starting source for another run.
*Default*: off
--------------------------------------
Geometry Specification -- geometry.xml
--------------------------------------

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@ -137,7 +137,7 @@ in equation <a href="#equation-unbiased-variance">(5)</a> is especially suitable
we do not need to store the values at every realization of the random variable
as the simulation proceeds. Instead, we can simply keep a running sum and sum of
squares of the values at each realization of the random variable and use that to
calulate the variance.</p>
calculate the variance.</p>
</div>
<div class="section" id="variance-of-the-mean">
<h3>3.3.3. Variance of the Mean<a class="headerlink" href="#variance-of-the-mean" title="Permalink to this headline"></a></h3>

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@ -74,6 +74,9 @@ the problem at hand (mostly on the number of nuclides in the problem).</p>
</div>
<div class="section" id="bug-fixes">
<h2>Bug Fixes<a class="headerlink" href="#bug-fixes" title="Permalink to this headline"></a></h2>
<ul class="simple">
<li><a class="reference external" href="https://github.com/mit-crpg/openmc/commit/792eb3">792eb3</a>: Fixed degrees of freedom for confidence intervals.</li>
</ul>
</div>
</div>

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@ -84,15 +84,15 @@ essential aspects of using OpenMC to perform neutronic simulations.</p>
<li class="toctree-l3"><a class="reference internal" href="input.html#entropy-element">3.2.6. <tt class="docutils literal"><span class="pre">&lt;entropy&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#fixed-source-element">3.2.7. <tt class="docutils literal"><span class="pre">&lt;fixed_source&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#no-reduce-element">3.2.8. <tt class="docutils literal"><span class="pre">&lt;no_reduce&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#ptables-element">3.2.9. <tt class="docutils literal"><span class="pre">&lt;ptables&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#seed-element">3.2.10. <tt class="docutils literal"><span class="pre">&lt;seed&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#source-element">3.2.11. <tt class="docutils literal"><span class="pre">&lt;source&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#survival-biasing-element">3.2.12. <tt class="docutils literal"><span class="pre">&lt;survival_biasing&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#trace-element">3.2.13. <tt class="docutils literal"><span class="pre">&lt;trace&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#uniform-fs-element">3.2.14. <tt class="docutils literal"><span class="pre">&lt;uniform_fs&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#verbosity-element">3.2.15. <tt class="docutils literal"><span class="pre">&lt;verbosity&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#write-state-point-element">3.2.16. <tt class="docutils literal"><span class="pre">&lt;write_state_point&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#write-source-element">3.2.17. <tt class="docutils literal"><span class="pre">&lt;write_source&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#output-element">3.2.9. <tt class="docutils literal"><span class="pre">&lt;output&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#ptables-element">3.2.10. <tt class="docutils literal"><span class="pre">&lt;ptables&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#seed-element">3.2.11. <tt class="docutils literal"><span class="pre">&lt;seed&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#source-element">3.2.12. <tt class="docutils literal"><span class="pre">&lt;source&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#state-point-element">3.2.13. <tt class="docutils literal"><span class="pre">&lt;state_point&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#survival-biasing-element">3.2.14. <tt class="docutils literal"><span class="pre">&lt;survival_biasing&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#trace-element">3.2.15. <tt class="docutils literal"><span class="pre">&lt;trace&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#uniform-fs-element">3.2.16. <tt class="docutils literal"><span class="pre">&lt;uniform_fs&gt;</span></tt> Element</a></li>
<li class="toctree-l3"><a class="reference internal" href="input.html#verbosity-element">3.2.17. <tt class="docutils literal"><span class="pre">&lt;verbosity&gt;</span></tt> Element</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="input.html#geometry-specification-geometry-xml">3.3. Geometry Specification &#8211; geometry.xml</a><ul>

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@ -245,8 +245,27 @@ tally data, this option can significantly improve the parallel efficiency.</p>
<blockquote>
<div><em>Default</em>: off</div></blockquote>
</div>
<div class="section" id="output-element">
<h3>3.2.9. <tt class="docutils literal"><span class="pre">&lt;output&gt;</span></tt> Element<a class="headerlink" href="#output-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">&lt;output&gt;</span></tt> element determines what output files should be written to disk
during the run. This element has no attributes or sub-elements and should be set
to a list of strings separated by spaces. Valid options are &#8220;summary&#8221;,
&#8220;cross-sections&#8221;, and &#8220;tallies&#8221;. For example, if you want the summary and cross
sections summary file to be written, this element should be given as:</p>
<blockquote>
<div><div class="highlight-xml"><div class="highlight"><pre><span class="nt">&lt;output&gt;</span>summary cross_sections<span class="nt">&lt;/output&gt;</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The tally results will be written to a binary/HDF5 state point file by
default.</p>
</div>
<p><em>Default</em>: &#8220;tallies&#8221;</p>
</div></blockquote>
</div>
<div class="section" id="ptables-element">
<h3>3.2.9. <tt class="docutils literal"><span class="pre">&lt;ptables&gt;</span></tt> Element<a class="headerlink" href="#ptables-element" title="Permalink to this headline"></a></h3>
<h3>3.2.10. <tt class="docutils literal"><span class="pre">&lt;ptables&gt;</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">&lt;ptables&gt;</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>
@ -254,14 +273,14 @@ or sub-elements and can be set to either &#8220;off&#8221; or &#8220;on&#8221;.<
<div><em>Default</em>: on</div></blockquote>
</div>
<div class="section" id="seed-element">
<h3>3.2.10. <tt class="docutils literal"><span class="pre">&lt;seed&gt;</span></tt> Element<a class="headerlink" href="#seed-element" title="Permalink to this headline"></a></h3>
<h3>3.2.11. <tt class="docutils literal"><span class="pre">&lt;seed&gt;</span></tt> Element<a class="headerlink" href="#seed-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">seed</span></tt> element is used to set the seed used for the linear congruential
pseudo-random number generator.</p>
<blockquote>
<div><em>Default</em>: 1</div></blockquote>
</div>
<div class="section" id="source-element">
<h3>3.2.11. <tt class="docutils literal"><span class="pre">&lt;source&gt;</span></tt> Element<a class="headerlink" href="#source-element" title="Permalink to this headline"></a></h3>
<h3>3.2.12. <tt class="docutils literal"><span class="pre">&lt;source&gt;</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 external source distribution to
be used either as the source for a fixed source calculation or the initial
source guess for criticality calculations. It takes the following
@ -362,8 +381,41 @@ c E e^{-E/a} dE"/>.</p>
</table>
</div></blockquote>
</div>
<div class="section" id="state-point-element">
<h3>3.2.13. <tt class="docutils literal"><span class="pre">&lt;state_point&gt;</span></tt> Element<a class="headerlink" href="#state-point-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">&lt;state_point&gt;</span></tt> element indicates at what batches a state point file
should be written. A state point file can be used to restart a run or to get
tally results at any batch. This element has the following
attributes/sub-elements:</p>
<blockquote>
<div><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">batches:</th><td class="field-body"><p class="first">A list of integers separated by spaces indicating at what batches a state
point file should be written.</p>
<p><em>Default</em>: Last batch only</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">interval:</th><td class="field-body"><p class="first">A single integer <img class="math" src="../_images/math/174fadd07fd54c9afe288e96558c92e0c1da733a.png" alt="n"/> indicating that a state point should be written
every <img class="math" src="../_images/math/174fadd07fd54c9afe288e96558c92e0c1da733a.png" alt="n"/> batches. This option can be given in lieu of listing
batches explicitly.</p>
<p><em>Default</em>: None</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name" colspan="2">source_separate:</th></tr>
<tr class="field-odd field"><td>&nbsp;</td><td class="field-body"><p class="first">If this element is set to &#8220;on&#8221;, a separate binary source file will be
written. Otherwise, the source sites will be written in the state point
directly.</p>
<p class="last"><em>Default</em>: &#8220;off&#8221;</p>
</td>
</tr>
</tbody>
</table>
</div></blockquote>
</div>
<div class="section" id="survival-biasing-element">
<h3>3.2.12. <tt class="docutils literal"><span class="pre">&lt;survival_biasing&gt;</span></tt> Element<a class="headerlink" href="#survival-biasing-element" title="Permalink to this headline"></a></h3>
<h3>3.2.14. <tt class="docutils literal"><span class="pre">&lt;survival_biasing&gt;</span></tt> Element<a class="headerlink" href="#survival-biasing-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">&lt;survival_biasing&gt;</span></tt> element has no attributes and has an accepted value
of &#8220;on&#8221; or &#8220;off&#8221;. If set to &#8220;on&#8221;, this option will enable the use of survival
biasing, otherwise known as implicit capture or absorption.</p>
@ -371,7 +423,7 @@ biasing, otherwise known as implicit capture or absorption.</p>
<div><em>Default</em>: off</div></blockquote>
</div>
<div class="section" id="trace-element">
<span id="trace"></span><h3>3.2.13. <tt class="docutils literal"><span class="pre">&lt;trace&gt;</span></tt> Element<a class="headerlink" href="#trace-element" title="Permalink to this headline"></a></h3>
<span id="trace"></span><h3>3.2.15. <tt class="docutils literal"><span class="pre">&lt;trace&gt;</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">&lt;trace&gt;</span></tt> element can be used to print out detailed information about a
single particle during a simulation. This element should be followed by three
integers: the batch number, generation number, and particle number.</p>
@ -379,7 +431,7 @@ integers: the batch number, generation number, and particle number.</p>
<div><em>Default</em>: None</div></blockquote>
</div>
<div class="section" id="uniform-fs-element">
<h3>3.2.14. <tt class="docutils literal"><span class="pre">&lt;uniform_fs&gt;</span></tt> Element<a class="headerlink" href="#uniform-fs-element" title="Permalink to this headline"></a></h3>
<h3>3.2.16. <tt class="docutils literal"><span class="pre">&lt;uniform_fs&gt;</span></tt> Element<a class="headerlink" href="#uniform-fs-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">&lt;uniform_fs&gt;</span></tt> element describes a mesh that is used for re-weighting
source sites at every generation based on the uniform fission site methodology
described in Kelly et al., &#8220;MC21 Analysis of the Nuclear Energy Agency Monte
@ -408,7 +460,7 @@ problem. It has the following attributes/sub-elements:</p>
</div></blockquote>
</div>
<div class="section" id="verbosity-element">
<h3>3.2.15. <tt class="docutils literal"><span class="pre">&lt;verbosity&gt;</span></tt> Element<a class="headerlink" href="#verbosity-element" title="Permalink to this headline"></a></h3>
<h3>3.2.17. <tt class="docutils literal"><span class="pre">&lt;verbosity&gt;</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">&lt;verbosity&gt;</span></tt> element tells the code how much information to display to
the standard output. A higher verbosity corresponds to more information being
displayed. This element takes the following attributes:</p>
@ -425,25 +477,6 @@ displayed. This element takes the following attributes:</p>
</table>
</div></blockquote>
</div>
<div class="section" id="write-state-point-element">
<h3>3.2.16. <tt class="docutils literal"><span class="pre">&lt;write_state_point&gt;</span></tt> Element<a class="headerlink" href="#write-state-point-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">&lt;write_state_point&gt;</span></tt> element is used to indicate batches at which the
user wishes to have a binary state point file written to disk. The state point
file can be used to restart a run or to get tally results at an intermediate
stage. This element has no attributes and should consist of a list of integers
corresponding to batches at which a binary state point file should be written to
disk.</p>
<blockquote>
<div><em>Default</em>: None</div></blockquote>
</div>
<div class="section" id="write-source-element">
<h3>3.2.17. <tt class="docutils literal"><span class="pre">&lt;write_source&gt;</span></tt> Element<a class="headerlink" href="#write-source-element" title="Permalink to this headline"></a></h3>
<p>The <tt class="docutils literal"><span class="pre">&lt;write_source&gt;</span></tt> element has no attributes and has an accepted value of
&#8220;on&#8221; or &#8220;off&#8221;. If set to &#8220;on&#8221;, a binary source file will be written to disk at
the end of the run that can be used as a starting source for another run.</p>
<blockquote>
<div><em>Default</em>: off</div></blockquote>
</div>
</div>
<div class="section" id="geometry-specification-geometry-xml">
<h2>3.3. Geometry Specification &#8211; geometry.xml<a class="headerlink" href="#geometry-specification-geometry-xml" title="Permalink to this headline"></a></h2>