From 855cc24d558ba5f20e84e1187632580e2c86bf29 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Mon, 8 Jul 2024 16:06:30 +0000
Subject: [PATCH] Update gh pages

---
 docs/_images/ConcurrentExample.png   | Bin 0 -> 52331 bytes
 docs/_images/CpuConfig.png           | Bin 0 -> 13589 bytes
 docs/_images/CpuGpuDataParallel.png  | Bin 0 -> 41688 bytes
 docs/_images/GpuConfig.png           | Bin 0 -> 23703 bytes
 docs/_sources/macroprocessor.rst.txt | 189 +++++++++++++++++++++++++++
 docs/_sources/milhoja.rst.txt        |  58 ++++++++
 docs/_sources/softwaresystem.rst.txt |  15 ---
 docs/macroprocessor.html             | 170 +++++++++++++++++++++++-
 docs/milhoja.html                    |  42 ++++++
 docs/objects.inv                     | Bin 3933 -> 3964 bytes
 docs/searchindex.js                  |   2 +-
 docs/softwaresystem.html             | 126 ------------------
 12 files changed, 458 insertions(+), 144 deletions(-)
 create mode 100644 docs/_images/ConcurrentExample.png
 create mode 100644 docs/_images/CpuConfig.png
 create mode 100644 docs/_images/CpuGpuDataParallel.png
 create mode 100644 docs/_images/GpuConfig.png
 delete mode 100644 docs/_sources/softwaresystem.rst.txt
 delete mode 100644 docs/softwaresystem.html

diff --git a/docs/_images/ConcurrentExample.png b/docs/_images/ConcurrentExample.png
new file mode 100644
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diff --git a/docs/_sources/macroprocessor.rst.txt b/docs/_sources/macroprocessor.rst.txt
index 2e9d3d3..36b0c29 100644
--- a/docs/_sources/macroprocessor.rst.txt
+++ b/docs/_sources/macroprocessor.rst.txt
@@ -105,5 +105,194 @@ present it any of its own ".ini" files. As with files, the definitions
 placed in the Simulation directory of the application override all
 definitions encountered earlier.
 
+We have defined several macros for convenience that are available in
+the file "macro_processors.ini" in the *bin* directory. The more
+commonly used ones are described below.
 
+.. container:: codeseg
+  
+   [loop_3d]
+   
+   args=limits
+   
+   definition =
+      do k=limits(LOW,KAXIS),limits(HIGH,KAXIS)
+         do j=limits(LOW,JAXIS),limits(HIGH,JAXIS)
+             do i=limits(LOW,IAXIS),limits(HIGH,IAXIS)
+
+Use as @M loop_3d(blkLimits)  results in the loop bounds for a triply
+nested loop in place of the macro name where every occurence of
+"limits" is replaced with "blkLimits"
+	     
+
+.. container:: codeseg
+	     
+  [bounds_3d]
+  
+  args=limits
+
+  definition =
+    limits(LOW,IAXIS):limits(HIGH,IAXIS),&
+    
+    limits(LOW,JAXIS):limits(HIGH,JAXIS),&
+    
+    limits(LOW,KAXIS):limits(HIGH,KAXIS)
+
+    usage in declaration as
+
+    real, dimension(@M bounds_3d(blkLimits)) :: arr
+
+will result in a 3D array being declared with bounds defined using the
+supplied two dimensional array blkLimits.
+
+
+.. container:: codeseg
+ 
+   [bounds_2d]
+   
+   args=x1,x2,limits
+   
+   definition =
+   
+    limits(LOW,x1AXIS):limits(HIGH,x1AXIS),&
+
+    limits(LOW,x2AXIS):limits(HIGH,x2AXIS)
+
+This macros is used for declaring 2D arrays when bounds are included
+in the supplied array to replace *limits*. This one has an additional
+feature, x1 and x2 can be "I", "J", or "K" to define which two
+directions are included in the array
+
+
+.. container:: codeseg
+	       
+    [tileDesc_get]
+    
+    args =lim1,lim2,lim3,del
+    
+    definition =
+    
+     lim1(:,:)=tileDesc%%limits
+     
+     lim2(:,:)=tileDesc%%blkLimitsGC
+     
+     lim3(:,:)=tileDesc%%grownLimits
+     
+     call tileDesc%%deltas(del)
+     
+     level=tileDesc%%level
+
+@M tileDesc_get(blkLimits,blkLimitsGC,grownLimits,deltas) fills the
+supplied arrays with the corresponding tile data. It assumes that all
+these variables have been declared in the code. The argument lim1 has
+bounds for the interior cells of the block where the solution is to be
+advanced and lim2 has bounds for all cells of the block including the
+guardcells. The third argument lim3 is needed for tiling, that is if a
+block is subdivided into tiles, the lim3 has bounds for the section of
+the block that is the part of the tile and also includes those
+interior cells that effectively become the guardcells for the cells
+that are to be advanced in this tile. The final argument is a real 1D
+array of size 3 in which deltax, deltay and delaz are returned. Note
+that the function returns valid values for 1:NDIM dimensions
+only. Also note that this macro fetches the value of the "level"
+assuming that it has been declared as is in the declaration section of
+the code. For convenience one
+can use the next macro, "tileDesc_declare" in the declaration section
+of the code to ensure that the variables are appropriately declared. Note
+that the first three arguments given to the two macros must be
+identical and identically ordered for correct behavior. 
+     
+
+.. container:: codeseg
+
+  [tileDesc_declare]
+  
+  args = lim1,lim2,lim3
+  
+  definition =
+  
+      integer :: level
+      
+      integer, dimension(LOW:HIGH,MDIM) :: lim1,lim2,lim3
+      
+      real,dimension(MDIM) :: deltas
+
+There are additional tile related macros that can be put in the "use"
+and declaration sections of the code, as well as used as arguments. It
+is not necessary to use any of these macros, however, users are
+strongly encouraged to use them wherever needed. If we need to change
+the tile class for any reason, it would be straightforward to make the
+code compatible everywhere by just making the change to the macro
+definition instead of writing scripts to do search and replace.
+
+The next few macros pertain to the use of iterators in the code. As
+with tiles there is one for the "use" section and one for the "declare"
+section. For starting the iterator two different macros are provided;
+one compatible with |amrex|'s prefered mode of operating on a level by
+level basis, and the other one compatible with |paramesh|'s preference
+of operating on all levels in the same loop. The arguments for the two
+
+
+.. container:: codeseg
+
+   [iter_all_begin]
+
+   args=x1,t1,lim1,lim2,del
+
+   definition =
+
+       call Grid_getTileIterator(itor, x1, tiling=t1) 
+  
+      do while(itor%%isValid())
+  
+         call itor%%currentTile(tileDesc)
+     
+        @M tileDesc_get(lim1,lim2,grownLimits,del)
+     
+        call tileDesc%%getDataPtr(Uin, CENTER)
+
+This is the macro for |paramesh| preferred iterators where x1 is the
+argument for the blocktype (usually LEAF} and t1 is either .true. if
+tiing is desired, and .false. if it is not. The arguments lim1 and
+lim2 are the usual blkLimits and blkLimitsGC. Note that the macros is
+assuming that grownLimits and Uin are declared as expected, they are
+not among the arguments. The next macro has an additional argument l1,
+where the value of level resides. 
+
+     
+.. container:: codeseg
+      
+     [iter_level_begin]
+
+     args=x1,t1,l1,lim1,lim2,del
+
+     definition=
+
+        call Grid_getTileIterator(itor,x1,level=l1,tiling=t1)
+
+	    do while(itor%%isValid())
+
+	         call itor%%currentTile(tileDesc)
+
+		 @M tileDesc_get(lim1,lim2,grownLimits,del)
+
+		 call tileDesc%%getDataPtr(Uin, CENTER)
+
+		 
+The next macro is to be used at the end of the iterator loop. It
+release the pointer Uin, and also the tile iterator.		 
+
+
+ .. container:: codeseg
+     
+      [iter_end]
+
+      definition =
+         call tileDesc%%releaseDataPtr(Uin,CENTER)
+	 
+         call itor%%next()
+	 
+      end do !!block loop
+      
+      call Grid_releaseTileIterator(itor)
 
diff --git a/docs/_sources/milhoja.rst.txt b/docs/_sources/milhoja.rst.txt
index 7ae236f..4d619f7 100644
--- a/docs/_sources/milhoja.rst.txt
+++ b/docs/_sources/milhoja.rst.txt
@@ -116,3 +116,61 @@ on any device without being aware of the specifics of the device so long as the
 required data is resident in the appropriate memory system.
 
 
+.. _`Sec:examples`:
+
+Runtime Examples
+-------------------
+
+Below are the examples of possible thread team configurations in
+increasing order of complexity. 
+
+.. container:: center
+
+   .. figure:: CpuConfig.png
+      :alt: cpuconfig
+      :name: Fig:cpuconfig
+      :width: 3.0in
+
+	      
+The figure above shows a configuration where computation is being done
+only on the CPU, while the next figure shows computation only on the
+GPU. Note that there are addiotional steps of data packing and
+unpacking and the data is moving back and forth between the host and
+the GPU.
+
+
+.. container:: center
+
+   .. figure:: GpuConfig.png
+      :alt: gpuconfig
+      :name: Fig:gpuconfig
+      :width: 3.5in
+
+The next figure shows a configuration with the next level of
+complexity where both CPU and GPU are applied to the same task. Two
+teams are in operation, the CPU team is given 3 thread and the GPU
+team is given 4 threads. These threads are used only for moving data,
+not for computation.
+
+.. container:: center
+
+   .. figure:: CpuGpuDataParallel.png
+      :alt: cpugpuparallel
+      :name: Fig:cpugpuparallel
+      :width: 4.0in
+
+
+The final figure shows an example of how we envision |milhoja| being
+used. Here concurrent computations are proceeding on the two devices
+but they are allotted different tasks at first. The data from GPU is
+sent back to the CPU once its computation is done, and yet another
+task is performed on the CPU. 
+
+
+.. container:: center
+
+   .. figure:: ConcurrentExample.png
+      :alt: concurrentl
+      :name: Fig:concurrent
+      :width: 5.0in
+>>>>>>> main
diff --git a/docs/_sources/softwaresystem.rst.txt b/docs/_sources/softwaresystem.rst.txt
deleted file mode 100644
index 4b6ab51..0000000
--- a/docs/_sources/softwaresystem.rst.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-.. include:: defs.h
-
-The Configuration Toolchain
-===========================
-
-This section covers the structure of |flashx| configuration toolchain.
-
-
-.. toctree::
-    :maxdepth: 1
-    :caption: Contents
-
-    setup
-    macroprocessor
-    
diff --git a/docs/macroprocessor.html b/docs/macroprocessor.html
index 57bbf35..b88d21c 100644
--- a/docs/macroprocessor.html
+++ b/docs/macroprocessor.html
@@ -45,12 +45,22 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
-<ul>
+<ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="disclaimers.html">Current Status and Disclaimers</a></li>
 <li class="toctree-l1"><a class="reference internal" href="intro.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="quickstart.html">Quick Start</a></li>
 <li class="toctree-l1"><a class="reference internal" href="arch.html">Overview of Flash-X architecture</a></li>
-<li class="toctree-l1"><a class="reference internal" href="orcha.html">The Performance Portability System</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="orcha.html">The Performance Portability System</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="orcha_overview.html">Overview of ORCHA</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cgkit.html">Code Generation Toolkit</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Macroprocessor</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#using-macros">Using Macros</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="milhoja.html">Milhoja</a></li>
+<li class="toctree-l2"><a class="reference internal" href="application_use.html">Application’s Use of Orcha</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="setup.html">The Flash-X configuration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="timeadvance.html">TimeAdvance</a></li>
 <li class="toctree-l1"><a class="reference internal" href="infrastructure.html">Infrastructure</a></li>
@@ -172,6 +182,162 @@
 present it any of its own “.ini” files. As with files, the definitions
 placed in the Simulation directory of the application override all
 definitions encountered earlier.</p>
+<p>We have defined several macros for convenience that are available in
+the file “macro_processors.ini” in the <em>bin</em> directory. The more
+commonly used ones are described below.</p>
+<div class="codeseg docutils container">
+<p>[loop_3d]</p>
+<p>args=limits</p>
+<dl class="simple">
+<dt>definition =</dt><dd><dl class="simple">
+<dt>do k=limits(LOW,KAXIS),limits(HIGH,KAXIS)</dt><dd><dl class="simple">
+<dt>do j=limits(LOW,JAXIS),limits(HIGH,JAXIS)</dt><dd><p>do i=limits(LOW,IAXIS),limits(HIGH,IAXIS)</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd>
+</dl>
+</div>
+<p>Use as &#64;M loop_3d(blkLimits)  results in the loop bounds for a triply
+nested loop in place of the macro name where every occurence of
+“limits” is replaced with “blkLimits”</p>
+<div class="codeseg docutils container">
+<p>[bounds_3d]</p>
+<p>args=limits</p>
+<dl>
+<dt>definition =</dt><dd><p>limits(LOW,IAXIS):limits(HIGH,IAXIS),&amp;</p>
+<p>limits(LOW,JAXIS):limits(HIGH,JAXIS),&amp;</p>
+<p>limits(LOW,KAXIS):limits(HIGH,KAXIS)</p>
+<p>usage in declaration as</p>
+<p>real, dimension(&#64;M bounds_3d(blkLimits)) :: arr</p>
+</dd>
+</dl>
+</div>
+<p>will result in a 3D array being declared with bounds defined using the
+supplied two dimensional array blkLimits.</p>
+<div class="codeseg docutils container">
+<p>[bounds_2d]</p>
+<p>args=x1,x2,limits</p>
+<p>definition =</p>
+<blockquote>
+<div><p>limits(LOW,x1AXIS):limits(HIGH,x1AXIS),&amp;</p>
+<p>limits(LOW,x2AXIS):limits(HIGH,x2AXIS)</p>
+</div></blockquote>
+</div>
+<p>This macros is used for declaring 2D arrays when bounds are included
+in the supplied array to replace <em>limits</em>. This one has an additional
+feature, x1 and x2 can be “I”, “J”, or “K” to define which two
+directions are included in the array</p>
+<div class="codeseg docutils container">
+<p>[tileDesc_get]</p>
+<p>args =lim1,lim2,lim3,del</p>
+<p>definition =</p>
+<blockquote>
+<div><p>lim1(:,:)=tileDesc%%limits</p>
+<p>lim2(:,:)=tileDesc%%blkLimitsGC</p>
+<p>lim3(:,:)=tileDesc%%grownLimits</p>
+<p>call tileDesc%%deltas(del)</p>
+<p>level=tileDesc%%level</p>
+</div></blockquote>
+</div>
+<p>&#64;M tileDesc_get(blkLimits,blkLimitsGC,grownLimits,deltas) fills the
+supplied arrays with the corresponding tile data. It assumes that all
+these variables have been declared in the code. The argument lim1 has
+bounds for the interior cells of the block where the solution is to be
+advanced and lim2 has bounds for all cells of the block including the
+guardcells. The third argument lim3 is needed for tiling, that is if a
+block is subdivided into tiles, the lim3 has bounds for the section of
+the block that is the part of the tile and also includes those
+interior cells that effectively become the guardcells for the cells
+that are to be advanced in this tile. The final argument is a real 1D
+array of size 3 in which deltax, deltay and delaz are returned. Note
+that the function returns valid values for 1:NDIM dimensions
+only. Also note that this macro fetches the value of the “level”
+assuming that it has been declared as is in the declaration section of
+the code. For convenience one
+can use the next macro, “tileDesc_declare” in the declaration section
+of the code to ensure that the variables are appropriately declared. Note
+that the first three arguments given to the two macros must be
+identical and identically ordered for correct behavior.</p>
+<div class="codeseg docutils container">
+<p>[tileDesc_declare]</p>
+<p>args = lim1,lim2,lim3</p>
+<p>definition =</p>
+<blockquote>
+<div><p>integer :: level</p>
+<p>integer, dimension(LOW:HIGH,MDIM) :: lim1,lim2,lim3</p>
+<p>real,dimension(MDIM) :: deltas</p>
+</div></blockquote>
+</div>
+<p>There are additional tile related macros that can be put in the “use”
+and declaration sections of the code, as well as used as arguments. It
+is not necessary to use any of these macros, however, users are
+strongly encouraged to use them wherever needed. If we need to change
+the tile class for any reason, it would be straightforward to make the
+code compatible everywhere by just making the change to the macro
+definition instead of writing scripts to do search and replace.</p>
+<p>The next few macros pertain to the use of iterators in the code. As
+with tiles there is one for the “use” section and one for the “declare”
+section. For starting the iterator two different macros are provided;
+one compatible with AMReX’s prefered mode of operating on a level by
+level basis, and the other one compatible with Paramesh’s preference
+of operating on all levels in the same loop. The arguments for the two</p>
+<div class="codeseg docutils container">
+<p>[iter_all_begin]</p>
+<p>args=x1,t1,lim1,lim2,del</p>
+<p>definition =</p>
+<blockquote>
+<div><blockquote>
+<div><p>call Grid_getTileIterator(itor, x1, tiling=t1)</p>
+</div></blockquote>
+<p>do while(itor%%isValid())</p>
+<blockquote>
+<div><blockquote>
+<div><p>call itor%%currentTile(tileDesc)</p>
+</div></blockquote>
+<p>&#64;M tileDesc_get(lim1,lim2,grownLimits,del)</p>
+<p>call tileDesc%%getDataPtr(Uin, CENTER)</p>
+</div></blockquote>
+</div></blockquote>
+</div>
+<p>This is the macro for Paramesh preferred iterators where x1 is the
+argument for the blocktype (usually LEAF} and t1 is either .true. if
+tiing is desired, and .false. if it is not. The arguments lim1 and
+lim2 are the usual blkLimits and blkLimitsGC. Note that the macros is
+assuming that grownLimits and Uin are declared as expected, they are
+not among the arguments. The next macro has an additional argument l1,
+where the value of level resides.</p>
+<div class="codeseg docutils container">
+<p>[iter_level_begin]</p>
+<p>args=x1,t1,l1,lim1,lim2,del</p>
+<p>definition=</p>
+<blockquote>
+<div><p>call Grid_getTileIterator(itor,x1,level=l1,tiling=t1)</p>
+<blockquote>
+<div><p>do while(itor%%isValid())</p>
+<blockquote>
+<div><p>call itor%%currentTile(tileDesc)</p>
+<p>&#64;M tileDesc_get(lim1,lim2,grownLimits,del)</p>
+<p>call tileDesc%%getDataPtr(Uin, CENTER)</p>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div>
+<p>The next macro is to be used at the end of the iterator loop. It
+release the pointer Uin, and also the tile iterator.</p>
+<blockquote>
+<div><div class="codeseg docutils container">
+<p>[iter_end]</p>
+<dl>
+<dt>definition =</dt><dd><p>call tileDesc%%releaseDataPtr(Uin,CENTER)</p>
+<p>call itor%%next()</p>
+</dd>
+</dl>
+<p>end do !!block loop</p>
+<p>call Grid_releaseTileIterator(itor)</p>
+</div>
+</div></blockquote>
 </section>
 </section>
 
diff --git a/docs/milhoja.html b/docs/milhoja.html
index b165570..cd3c85f 100644
--- a/docs/milhoja.html
+++ b/docs/milhoja.html
@@ -58,6 +58,7 @@
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Milhoja</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#milhoja-design-features">Milhoja Design Features</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#runtime-elements">Runtime Elements</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#runtime-examples">Runtime Examples</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="application_use.html">Application’s Use of Orcha</a></li>
@@ -194,6 +195,47 @@
 on any device without being aware of the specifics of the device so long as the
 required data is resident in the appropriate memory system.</p>
 </section>
+<section id="runtime-examples">
+<span id="sec-examples"></span><h2>Runtime Examples<a class="headerlink" href="#runtime-examples" title="Link to this heading"></a></h2>
+<p>Below are the examples of possible thread team configurations in
+increasing order of complexity.</p>
+<div class="center docutils container">
+<figure class="align-default" id="fig-cpuconfig">
+<a class="reference internal image-reference" href="_images/CpuConfig.png"><img alt="cpuconfig" src="_images/CpuConfig.png" style="width: 3.0in;" /></a>
+</figure>
+</div>
+<p>The figure above shows a configuration where computation is being done
+only on the CPU, while the next figure shows computation only on the
+GPU. Note that there are addiotional steps of data packing and
+unpacking and the data is moving back and forth between the host and
+the GPU.</p>
+<div class="center docutils container">
+<figure class="align-default" id="fig-gpuconfig">
+<a class="reference internal image-reference" href="_images/GpuConfig.png"><img alt="gpuconfig" src="_images/GpuConfig.png" style="width: 3.5in;" /></a>
+</figure>
+</div>
+<p>The next figure shows a configuration with the next level of
+complexity where both CPU and GPU are applied to the same task. Two
+teams are in operation, the CPU team is given 3 thread and the GPU
+team is given 4 threads. These threads are used only for moving data,
+not for computation.</p>
+<div class="center docutils container">
+<figure class="align-default" id="fig-cpugpuparallel">
+<a class="reference internal image-reference" href="_images/CpuGpuDataParallel.png"><img alt="cpugpuparallel" src="_images/CpuGpuDataParallel.png" style="width: 4.0in;" /></a>
+</figure>
+</div>
+<p>The final figure shows an example of how we envision Milhoja being
+used. Here concurrent computations are proceeding on the two devices
+but they are allotted different tasks at first. The data from GPU is
+sent back to the CPU once its computation is done, and yet another
+task is performed on the CPU.</p>
+<div class="center docutils container">
+<figure class="align-default" id="fig-concurrent">
+<a class="reference internal image-reference" href="_images/ConcurrentExample.png"><img alt="concurrentl" src="_images/ConcurrentExample.png" style="width: 5.0in;" /></a>
+</figure>
+</div>
+<p>&gt;&gt;&gt;&gt;&gt;&gt;&gt; main</p>
+</section>
 </section>
 
 
diff --git a/docs/objects.inv b/docs/objects.inv
index d13c3bb8f8b22c2e3e53326222f521b005d2739c..a7e3a7dde3cdea4934f4b99f4067ef43ae72fc25 100644
GIT binary patch
delta 3828
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diff --git a/docs/searchindex.js b/docs/searchindex.js
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@@ -1 +1 @@
-Search.setIndex({"alltitles": {"AMR Algorithm": [[4, "amr-algorithm"]], "Accessor Functions and Timestep Data": [[8, "accessor-functions-and-timestep-data"]], "Adaptive Mesh Refinement (AMR) Grid": [[4, "adaptive-mesh-refinement-amr-grid"]], "Algorithms": [[35, "algorithms"]], "Alternative Method for Defining Species": [[9, "alternative-method-for-defining-species"]], "Applicable Runtime Parameters": [[11, "applicable-runtime-parameters"]], "Application Programming Interface (API)": [[0, "application-programming-interface-api"]], "Application\u2019s Use of Orcha": [[14, "application-s-use-of-orcha"]], "Available Constants and Units": [[11, "available-constants-and-units"]], "Available Geometries": [[4, "available-geometries"]], "Available Physical Constants": [[11, "id1"]], "Available Units for Conversion of Physical Constants": [[11, "id2"]], "Boundary Condition Types": [[4, "boundary-condition-types"]], "Boundary Conditions": [[4, "boundary-conditions"]], "Boundary Conditions at 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FLASH to Flash-X": [[2, "converting-from-flash-to-flash-x"]], "Coupling Gravity with Hydrodynamics": [[3, "coupling-gravity-with-hydrodynamics"]], "Creating a Site-specific Makefile": [[32, "creating-a-site-specific-makefile"]], "Current Status and Disclaimers": [[18, "current-status-and-disclaimers"]], "Customization": [[15, "customization"]], "Cylindrical geometry": [[4, "cylindrical-geometry"]], "Defining Runtime Parameters": [[13, "defining-runtime-parameters"]], "Defining Species": [[9, "defining-species"]], "Derived data type I/O": [[6, "derived-data-type-i-o"]], "Detecting shocks": [[35, "detecting-shocks"]], "Developer\u2019s Guide": [[17, "developer-s-guide"]], "Direct IO": [[6, "direct-io"]], "Direct and Wrapped Calls": [[1, "direct-and-wrapped-calls"]], "Directional Move": [[4, "directional-move"]], "Driver Routines": [[19, "driver-routines"]], "Driver Unit": [[19, "driver-unit"]], "Driver accessor functions": [[19, "driver-accessor-functions"]], "Driver_finalizeAll": [[19, "driver-finalizeall"]], "Driver_initAll": [[19, "driver-initall"]], "Energy generation rates and reaction rates": [[35, "energy-generation-rates-and-reaction-rates"]], "Equation of State Unit": [[1, "equation-of-state-unit"]], "Example": [[16, "example"]], "Example Usage": [[8, "example-usage"], [9, "example-usage"], [13, "example-usage"]], "Extensive Quantities in Reduced Dimensionality": [[4, "extensive-quantities-in-reduced-dimensionality"]], "Externally Applied Fields": [[3, "externally-applied-fields"]], "FIXEDBLOCKSIZE Mode": [[4, "fixedblocksize-mode"]], "Face-Centered Data": [[6, "face-centered-data"]], "Files Created During the setup Process": [[32, "files-created-during-the-setup-process"]], "Flash-X Inheritance": [[15, "flashx-inheritance"]], "Flash-X Testing Framework (FlashXTest)": [[20, "flash-x-testing-framework-flashxtest"]], "Gamma Law": [[1, "gamma-law"]], "Gas hydrodynamics": [[5, "gas-hydrodynamics"]], "General Runtime Parameters": [[6, "general-runtime-parameters"]], "Generic time step limiting for positive definiteness": [[19, "generic-time-step-limiting-for-positive-definiteness"]], "Getting Geometry Information in Program Code": [[4, "getting-geometry-information-in-program-code"]], "Good Practices for Maintenance": [[0, "good-practices-for-maintenance"]], "Gravitational Field of a Point Mass": [[3, "gravitational-field-of-a-point-mass"]], "Gravity Unit": [[3, "gravity-unit"]], "Grid Geometry": [[4, "grid-geometry"]], "Grid Interpolation (and Averaging)": [[4, "grid-interpolation-and-averaging"]], "Grid Unit": [[4, "grid-unit"]], "GridMain Data Structures": [[4, "gridmain-data-structures"]], "GridMain Usage": [[4, "gridmain-usage"]], "GridParticles": [[4, "gridparticles"]], "GridParticlesMove": [[4, "gridparticlesmove"]], "GridSolvers": [[4, "gridsolvers"]], "HDF5": [[6, "hdf5"]], "HDF5 Data Format": [[6, "hdf5-data-format"]], "HYPRE": [[4, "hypre"]], "Helmholtz": [[1, "helmholtz"]], "Hydrodynamics Units": [[5, "hydrodynamics-units"]], "IO Implementations": [[6, "io-implementations"]], "IO Unit": [[6, "io-unit"]], "Identifying Valid Runtime Parameters": [[13, "identifying-valid-runtime-parameters"]], "Implementing Boundary Conditions": [[4, "implementing-boundary-conditions"]], "Incompressible Navier-Stokes Unit": [[7, "incompressible-navier-stokes-unit"]], "Indices and tables": [[21, "indices-and-tables"]], "Informational files": [[32, "informational-files"]], "Infrastructure": [[22, "infrastructure"]], "Initialization": [[1, "initialization"]], "Initializing Species Information in Simulation_initSpecies": [[9, "initializing-species-information-in-simulation-initspecies"]], "Integrated Grid Quantities \u2013 flash.dat": [[6, "integrated-grid-quantities-flash-dat"]], "Interpolation for mass-specific solution variables": [[4, "interpolation-for-mass-specific-solution-variables"]], "Introduction": [[1, "introduction"], [3, "introduction"], [23, "introduction"]], "Local Source Terms": [[35, "local-source-terms"]], "Logfile Unit": [[8, "logfile-unit"]], "MPINative": [[12, "mpinative"]], "Machine Compatibility": [[6, "machine-compatibility"]], "Macroprocessor": [[24, "mp"]], "Makefiles generated by setup": [[32, "makefiles-generated-by-setup"]], "Mesh/Particle Mapping": [[10, "mesh-particle-mapping"]], "Meta Data": [[8, "meta-data"]], "Milhoja": [[25, "milhoja"]], "Milhoja Design Features": [[25, "milhoja-design-features"]], "Monitor Units": [[26, "monitor-units"]], "Multigrid": [[4, "multigrid"]], "Multipole Poisson solver": [[4, "multipole-poisson-solver"]], "Multispecies Unit": [[9, "multispecies-unit"]], "NONFIXEDBLOCKSIZE mode": [[4, "nonfixedblocksize-mode"]], "Naming Conventions": [[27, "naming-conventions"]], "Obtaining and configuring Flash-X for quick start": [[31, "obtaining-and-configuring-flashx-for-quick-start"]], "Output Filenames": [[6, "output-filenames"]], "Output Files": [[6, "output-files"]], "Output Formats": [[6, "output-formats"]], "Output Scalars": 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"plane-parallel-gravitational-field"]], "Plotfile IO parameters (continued).": [[6, "id10"]], "Plotfiles": [[6, "plotfiles"]], "Poisson equation": [[4, "poisson-equation"]], "Polar geometry": [[4, "polar-geometry"]], "Profiler": [[12, "profiler"]], "Properties available through the Multispecies unit.": [[9, "id1"]], "Quadratic Mesh Mapping": [[10, "quadratic-mesh-mapping"]], "Quick Start": [[31, "quick-start"]], "Reaction networks": [[35, "reaction-networks"]], "Refinement": [[4, "refinement"]], "Refinement Criteria": [[4, "refinement-criteria"]], "Refinement Processing": [[4, "refinement-processing"]], "Restarts and Runtime Parameters": [[6, "restarts-and-runtime-parameters"]], "Routine Descriptions": [[9, "routine-descriptions"], [11, "routine-descriptions"], [13, "routine-descriptions"]], "Running Flash-X": [[31, "running-flashx"]], "Runtime Elements": [[25, "runtime-elements"]], "Runtime Parameters": [[1, "runtime-parameters"], [19, "runtime-parameters"]], "Runtime Parameters Unit": [[13, "runtime-parameters-unit"]], "Runtime Parameters, Physical Constants, and Multispecies Data": [[8, "runtime-parameters-physical-constants-and-multispecies-data"]], "Self-gravity": [[3, "self-gravity"]], "Serial Flash-X Output Comparison Utility (sfocu)": [[33, "serial-flashx-output-comparison-utility-sfocu"]], "Setup Arguments": [[32, "setup-arguments"]], "Setup Variables and Preprocessing Config Files": [[32, "setup-variables-and-preprocessing-config-files"]], "Setup a hybrid MPI+|openmp| Flash-X application": [[32, "setup-a-hybrid-mpi-openmp-flashx-application"]], "Shortcuts for often-used options": [[32, "id25"]], "Specialized Refinement Routines": [[4, "specialized-refinement-routines"]], "Specifying Constituent Elements of a Species": [[9, "specifying-constituent-elements-of-a-species"]], "Spherical geometry": [[4, "spherical-geometry"]], "Split File IO": [[6, "split-file-io"]], "Structure of a Unit": [[0, "structure-of-a-unit"]], "System requirements": [[31, "system-requirements"]], "Tau": [[12, "tau"]], "Temperature-based timestep limiting": [[35, "temperature-based-timestep-limiting"]], "The Configuration Toolchain": [[34, "the-configuration-toolchain"]], "The Flash-X configuration": [[32, "the-flashx-configuration"]], "The Performance Portability System": [[28, "the-performance-portability-system"]], "The Setup Tool": [[32, "the-setup-tool"]], "The unsplit hydro solver": [[5, "the-unsplit-hydro-solver"]], "Time Integration": [[10, "time-integration"]], "Time Step Limiting": [[19, "time-step-limiting"]], "TimeAdvance": [[36, "timeadvance"]], "Timer and Profiler Units": [[12, "timer-and-profiler-units"]], "Timers": [[12, "timers"]], "Timers parameters (continued).": [[12, "id1"]], "Tools": [[37, "tools"]], "Tree Gravity": [[3, "tree-gravity"]], "Tree Gravity Unit Usage": [[3, "tree-gravity-unit-usage"]], "Two time integration methods": [[35, "two-time-integration-methods"]], "Understanding 1D, 2D, and Curvilinear Coordinates": [[4, 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19, 20, 32], "adapt": [5, 7, 8, 15, 23, 25, 31, 32], "add": [0, 3, 4, 6, 7, 8, 10, 11, 12, 14, 20, 23, 32, 33], "add_fluid_to_db": 9, "addit": [0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 14, 19, 24, 25, 27, 32, 33, 35, 36], "addition": [1, 6, 10, 15, 18, 23, 31], "address": [1, 4, 15, 24, 29], "adhruv": 18, "adiabat": [1, 5], "adjac": 4, "adjust": 4, "admiss": 32, "adopt": [0, 5], "adubei": 18, "adv": 10, "advanc": [2, 4, 6, 10, 14, 19, 31, 32, 35, 36], "advantag": [4, 6, 14, 29, 33], "advect": [3, 5, 9, 19, 32, 35], "advent": 24, "advers": 33, "advis": [6, 10, 31, 35], "advmethod": [10, 32], "aelem": 9, "aelems_": 9, "affect": [0, 5, 6, 10, 13, 32, 33], "after": [0, 1, 4, 6, 8, 10, 12, 13, 14, 20, 31, 32, 35], "afterward": 1, "again": [4, 5, 6, 25], "against": 20, "aggreg": 6, "agnost": [4, 15], "agre": 4, "aid": 16, "air": [9, 32], "air_spec": 9, "aix": 33, "aka": 5, "akash": 18, "al": [1, 4, 6, 7, 11, 35], "aldfnameaccv42": 3, "aldfnamepotv42": 3, "alert": 32, "algebra": [4, 8, 10, 23, 35], "algorithm": [1, 3, 5, 10, 16, 19, 24, 29, 31, 32], "align": [3, 4, 5, 10, 35], "all": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25, 27, 29, 31, 32, 33, 35], "alloc": [0, 4, 6, 10, 14, 16, 29, 32], "allow": [1, 3, 4, 6, 7, 9, 10, 15, 19, 24, 25, 31, 32, 33, 35], "alon": 4, "along": [1, 3, 4, 8, 10, 12, 16, 25, 31, 32, 35], "alpha": [3, 4, 35], "alphabet": [8, 13], "alreadi": [6, 9, 10, 12, 20, 24, 31, 32], "also": [0, 1, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 23, 24, 25, 29, 31, 32, 33, 35], "alter": [8, 25, 29], "altern": [0, 4, 5, 6, 10, 11, 12, 15, 19, 24, 32, 36], "although": [4, 6, 12, 32, 33, 35], "alwai": [0, 4, 6, 9, 10, 32, 35], "alwayscomputeuservar": 6, "alwaysgener": 3, "alwaysrestrictcheckpoint": 6, "am": 6, "ambigu": 2, "amen": 32, "among": [0, 4, 6, 10, 14, 32], "amount": [3, 4, 5, 6, 10, 18, 32, 35], "amr": [0, 7, 31, 32], "amr_refine_derefin": 8, "amrex": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37], "amsmath": 4, "amu": 11, "an": [0, 1, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 23, 24, 25, 27, 29, 31, 32, 33, 35], "analog": 4, "analysi": [1, 5, 6, 25, 31, 35], "analyt": [1, 3, 9, 35], "analyz": [4, 31], "ancestor": 15, "angl": 4, "angular": [3, 4], "ani": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 13, 14, 15, 16, 19, 24, 25, 27, 31, 32, 33, 35], "anl": [6, 18], "ann": 3, "annot": [0, 14, 25], "annulu": 4, "anomali": 12, "anoth": [1, 4, 5, 6, 10, 12, 15, 16, 24, 25, 27, 32, 33, 35], "anshu": 18, "answer": 35, "anyth": 32, "anywher": [4, 24, 32], "ap": 3, "aparicio": 1, "apart": 32, "api": [1, 2, 3, 4, 6, 8, 9, 12, 13, 15, 17, 19, 25, 27, 32, 35], "appear": [2, 7, 8, 31, 32, 35], "append": [6, 8, 9, 32, 35], "appli": [0, 1, 4, 6, 10, 16, 19, 25, 32, 35], "applic": [1, 3, 4, 6, 9, 10, 15, 16, 17, 21, 23, 24, 25, 28, 29, 31], "approach": [3, 4, 5, 9, 10, 24, 29, 35], "appropri": [1, 3, 4, 6, 10, 14, 25, 29, 31, 32, 35], "approx": 4, "approxim": [1, 3, 4, 5, 10, 35], "approxpartialerr": 3, "apriori": 25, "aprox13": 35, "aprox19": 35, "ar": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 23, 24, 25, 27, 29, 31, 32, 33, 35], "ar36": 8, "arbitr": [15, 24, 32], "arbitrari": [0, 1, 3, 6, 8, 10, 15, 24, 25, 32], "arbitrarili": [4, 10, 32], "arc": 4, "architect": 23, "architectur": [0, 3, 6, 13, 21, 32], "area": [4, 14], "aren": 11, "arg": [20, 32], "arg1": 32, "arg2": 32, "arguement": 1, "argument": [1, 2, 3, 4, 6, 9, 11, 13, 14, 24, 25, 31], "aris": 35, "arithmet": [16, 24, 29], "armfield": 7, "arnett": 1, "around": [4, 10, 12, 16], "arrai": [1, 2, 4, 9, 10, 24, 32, 33], "arrang": [4, 7], "arriv": 4, "artifici": [5, 35], "asc": 6, "asci": 6, "ascii": 1, "asign": 4, "ask": 13, "aspect": [4, 10, 15, 35], "assembl": [15, 25, 32], "assembli": 4, "assign": [4, 10, 12, 13, 15, 25, 32], "associ": [4, 10, 13, 25, 32, 35], "assum": [0, 1, 3, 4, 10, 14, 16, 31, 32], "assume_format": 6, "assumpt": [1, 3, 4, 6, 16, 29], "ast": 16, "astronom": 11, "astrophys": [1, 4, 6, 23, 35], "asymptot": 35, "asynchron": [4, 25], "ath": 12, "atom": [1, 4, 9, 11], "attempt": [5, 10, 29, 31, 32], "attend": 19, "attribut": [4, 6, 32, 33], "au": 11, "augment": 32, "aument": 32, "austin": 18, "author": 32, "auto": [1, 4, 6, 10, 20, 31, 32], "autom": [25, 33], "automat": [3, 4, 5, 9, 10, 12, 32], "avaiabl": 27, "avail": [0, 1, 3, 5, 6, 10, 15, 19, 20, 23, 24, 31, 32, 33], "averag": [1, 3, 9, 10, 35], "avg": [8, 12], "avogadro": [1, 11, 35], "avoid": [0, 1, 2, 3, 4, 5, 8, 10, 15, 19, 24, 25, 29, 32, 35], "awai": [3, 4], "awar": [1, 10, 25, 32], "ax": [3, 4, 5, 10], "axi": [1, 3, 4], "axial": 4, "axisymmetr": 4, "azimuth": 4, "b": [4, 10, 33, 35], "b_2": 3, "b_3": 3, "b_i": 35, "b_n": 3, "back": [1, 3, 4, 5, 10, 18, 25, 32], "backsubstitut": 35, "backward": 1, "bad": 33, "bader": 35, "balanc": 35, "balara": 7, "bar": [1, 4, 9, 32], "base": [1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 15, 19, 20, 23, 24, 25, 31, 32], "basenam": 6, "basename_s0000_": 6, "basenm": [6, 8, 31], "bashrc": 20, "basi": [4, 12, 16, 35], "basic": [2, 4, 5, 6, 8, 19, 33, 35], "baz": 32, "bd": 35, "bdat": 1, "becaus": [0, 1, 3, 4, 5, 6, 8, 9, 10, 12, 13, 14, 15, 18, 19, 23, 25, 32, 33, 35], "becom": [4, 5, 10, 18, 19, 24, 27, 35], "been": [1, 2, 4, 5, 6, 8, 10, 13, 18, 19, 23, 25, 29, 31, 32, 33, 35], "befor": [0, 1, 4, 5, 6, 8, 9, 10, 11, 16, 31, 32], "begin": [0, 3, 4, 5, 6, 8, 10, 12, 13, 14, 15, 16, 24, 27, 31, 32, 35], "begin_orchestr": 14, "behav": 10, "behavior": [4, 6, 10, 31, 32, 35], "being": [0, 1, 3, 4, 6, 10, 14, 15, 19, 25, 29, 32, 35], "believ": 25, "belong": [4, 32], "below": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 12, 14, 15, 16, 18, 24, 25, 32, 35], "beneath": 0, "benefit": 6, "berger": 4, "besid": 6, "best": [1, 2, 3, 4, 6, 35], "beta": 1, "better": [3, 4, 6, 32], "between": [0, 1, 3, 4, 5, 6, 9, 10, 15, 19, 23, 25, 29, 32, 33, 35, 36], "beyond": [4, 10], "bf": [3, 4, 5, 10, 35], "bgpm": 12, "bgsy": 12, "bhewaldnrefv42": 3, "bhewaldseriesn": 3, "bhextrnpotfil": 3, "bhextrnpottyp": 3, "bhtree": 3, "bhtreeacc": 3, "bhtreeewaldv42": 3, "bhuserelaccerr": 3, "bi": 1, "bias": 5, "big": 6, "bigger": 6, "biggest": 2, "bin": [4, 20, 32], "binari": [1, 35], "bind": [8, 9], "bindenergi": 9, "bipcgstab": 7, "bit": [4, 29], "bitmap": 4, "bittre": 4, "blackbodi": 1, "blank": 31, "bless": 0, "blk": 8, "blklimit": [2, 14], "blklimitsgc": [2, 9], "block": [1, 2, 3, 4, 6, 8, 10, 12, 14, 16, 23, 24, 25, 32, 33, 35], "block_id": 2, "blockcount": 2, "blockid": 2, "blocklist": 2, "blocksiz": [4, 6], "bndpriorityon": 8, "bndprioritythre": 8, "bodi": [4, 10, 35], "boltzman": 11, "boltzmann": [1, 11], "book": 2, "boolean": [3, 6, 8, 31, 32], "border": 4, "both": [0, 1, 3, 4, 5, 6, 7, 10, 12, 14, 15, 19, 23, 24, 25, 29, 32, 33], "bottleneck": 6, "bound": [1, 2, 4, 5, 6, 9, 14, 33], "boundai": 4, "boundari": [2, 3, 7, 10, 15, 31, 32], "box": [4, 6, 33], "bracket": 4, "branch": [0, 4], "break": 20, "breakup": 20, "brief": [10, 31], "briefli": 9, "bring": [3, 4, 6], "broadcast": 1, "broken": 6, "brought": 0, "buffer": [4, 6, 8], "bug": [6, 20], "build": [2, 3, 16, 23, 31, 32], "buildup": [4, 35], "built": [4, 24, 25, 31, 32, 35], "bulk": [4, 15], "bundl": 4, "burger": 35, "burn": [1, 4, 9, 18], "burn_computedt": 35, "burn_init": 35, "burner": 35, "byte": 6, "bytepack": 8, "c": [1, 3, 4, 6, 10, 11, 19, 23, 24, 31, 32, 35], "c12": 8, "c_": 35, "c_1": 10, "c_2": 10, "c_3": 10, "c_4": 10, "ca40": 8, "cal": [3, 9], "calcul": [1, 3, 4, 5, 6, 9, 10, 32, 35], "call": [0, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 19, 21, 24, 31, 33, 35], "caller": 1, "callpath": 12, "can": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25, 29, 31, 32, 33, 35], "cancel": 4, "cannot": [0, 1, 4, 8, 10, 24, 32], "capabl": [1, 4, 5, 6, 24], "capac": 9, "capbl": 4, "capila": 27, "capit": [0, 27], "captur": 5, "carbon": 35, "care": [1, 4, 6, 9, 15, 31, 35], "carefulli": 35, "carri": [4, 10, 35], "carriag": 31, "cartesian": [8, 10, 32, 35], "case": [0, 1, 3, 4, 5, 6, 7, 9, 10, 12, 15, 19, 31, 32, 35], "cast": 24, "catch": 32, "categori": [0, 32], "caughlan": 35, "caught": 8, "caus": [1, 2, 6, 8, 19, 32], "caveat": 4, "ccc": 10, "cccccc": 10, "ccccccc": 10, "cd": 31, "cdefin": 33, "cdot": [3, 4, 5, 10, 35], "cel": 6, "cell": [1, 3, 4, 5, 6, 14, 16, 19, 32, 35], "cellular": 8, "cellular_": 8, "cen": 4, "center": [2, 3, 4, 5, 10, 32], "centimet": 11, "central": 6, "certain": [0, 1, 4, 6, 9, 10, 12, 19, 32, 33, 35], "cfl": [5, 8, 13, 19, 35], "cflag": 32, "cflags_debug": 32, "cflags_opt": 32, "cflags_test": 32, "cg": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37], "chain": [14, 29, 35], "challeng": [10, 18, 24], "chandrasekhar": 1, "chang": [0, 1, 2, 4, 5, 6, 8, 9, 10, 13, 14, 15, 16, 24, 32, 33, 35], "chapman": 35, "chapter": [0, 4, 6, 10, 17, 22, 26, 28, 30, 31, 32, 37], "charact": [6, 11, 13, 32], "characterist": [3, 5, 24, 32], "charg": [1, 11], "charlimit": 5, "cheaper": 3, "check": [2, 6, 18, 19, 31, 32, 35], "checkp": 6, "checkpoin": 6, "checkpoint": [2, 4, 8, 10, 19, 31, 33], "checkpointfi": 6, "checkpointfileintervalstep": 13, "checkpointfileintervaltim": [8, 13, 31], "checkpointfilenumb": [6, 13], "chemic": [1, 5], "chicago": 23, "child": [4, 15, 27], "child1": 32, "child2": 32, "childord": [0, 32], "children": [4, 32], "chkguardcel": 8, "chkguardcellsinput": 6, "chkguardcellsoutput": 6, "choic": [0, 3, 4, 5, 10, 32, 35], "choos": [5, 6, 9, 10, 19, 32, 35], "chose": 10, "chosen": [3, 4, 9, 10, 13, 19, 25, 31, 35], "chp": 32, "cic": 10, "circular": 4, "circumst": [0, 4, 5], "circumv": 32, "cite": 35, "ck": 5, "clariti": [0, 6, 31, 32], "classic": 35, "clean": [6, 31], "cleanup": 19, "clear": 15, "clearli": [13, 25, 32], "cli": 20, "client": 4, "clock": 6, "clone": [20, 31], "close": [1, 4, 6, 8, 32], "closur": 35, "cluster": [0, 6, 10], "cm": [1, 4, 8, 11], "cno": 35, "cnt": 6, "co": [4, 5, 10], "coars": [2, 4, 32], "coarser": 4, "code": [2, 3, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 31, 33, 35], "coeffici": [3, 5, 10, 35], "coke": 35, "cold": 9, "colella": [1, 4, 5], "collabor": [4, 31], "collect": [1, 2, 4, 8, 9, 10, 15, 23, 24, 32], "collis": [4, 10], "coloumb": 11, "column": [3, 4, 33], "com": [20, 31], "comb": 10, "combin": [3, 4, 5, 6, 10, 15, 23, 24, 25, 29, 32, 35], "combinatori": 24, "come": [0, 1, 6, 10, 25, 31, 32, 35], "comm": 35, "comma": 32, "command": [0, 1, 3, 4, 6, 9, 10, 20, 31, 32, 33], "commandlin": 32, "comment": [0, 9, 13, 14, 25, 31, 32], "common": [0, 1, 4, 9, 11, 14, 25, 31, 33], "commonli": [2, 4, 6, 19, 32], "commun": [4, 6, 16, 19, 23, 32], "communit": 4, "compact": 35, "compar": [3, 4, 5, 10, 33, 35], "comparison": [21, 37], "compat": [0, 1, 23, 31, 32], "compen": 32, "compens": 35, "compet": 35, "compil": [2, 3, 4, 6, 8, 10, 12, 16, 31, 32, 33], "complet": [1, 3, 4, 6, 8, 9, 31], "complex": [1, 4, 9, 10, 15, 18, 24, 25, 29], "compliant": 32, "complic": [4, 32], "compoment": 32, "compon": [1, 2, 3, 4, 5, 15, 18, 23, 24, 29, 32], "componentnam": 32, "compos": [3, 16, 24, 25], "composit": [1, 25, 27, 35], "comprehens": [31, 32], "compress": [1, 5, 23, 35], "compris": 9, "comput": [0, 1, 3, 5, 6, 9, 10, 14, 15, 16, 23, 25, 29, 32, 35], "computation": [1, 4, 5], "con": 7, "concaten": 32, "concentr": 4, "concept": [15, 25], "conceptu": 29, "concern": [4, 10, 15, 25, 29, 35], "concurr": 16, "cond": 32, "condit": [1, 3, 5, 7, 10, 15, 16, 31, 32], "condition": 32, "confid": 1, "config": [0, 3, 4, 5, 6, 8, 9, 10, 13, 15, 20, 21], "configpars": 24, "configur": [3, 4, 6, 9, 10, 13, 14, 15, 20, 21, 23, 24, 25, 29], "conflict": [0, 4, 32], "conform": 32, "confus": [4, 15], "conquer": 29, "consecut": 4, "consequ": [4, 6], "consequentlywith": 4, "conserv": [3, 4, 5, 29, 32, 35], "conserved_var": 4, "consid": [1, 4, 5, 6, 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\ No newline at end of file
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