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<section id="amrclaw-description-and-detailed-contents">
<span id="amrclaw"></span><h1>AMRClaw Description and Detailed Contents<a class="headerlink" href="#amrclaw-description-and-detailed-contents" title="Permalink to this heading">¶</a></h1>
<p>The AMRClaw version of Clawpack provides Adaptive Mesh Refinement (AMR)
capabilities in 2 and 3 space dimensions. (The two-dimensional code can
also be used for 1-dimensional problems, see <a class="reference internal" href="amrclaw1d.html#amrclaw-1d"><span class="std std-ref">AMRClaw for 1d problems</span></a>.)</p>
<p><strong>See also:</strong></p>
<ul class="simple">
<li><p><a class="reference internal" href="amr_algorithm.html#amr-algorithm"><span class="std std-ref">Adaptive mesh refinement (AMR) algorithms</span></a></p></li>
<li><p><a class="reference internal" href="refinement.html#refinement"><span class="std std-ref">AMR refinement criteria</span></a></p></li>
<li><p><a class="reference internal" href="amrclaw_doxygen.html#amrclaw-doxygen"><span class="std std-ref">Doxygen documentation of AMRClaw</span></a></p></li>
<li><p><a class="reference internal" href="amrclaw_flowcharts.html#amrclaw-flowcharts"><span class="std std-ref">AMRClaw Flowcharts</span></a></p></li>
</ul>
<p>Block-structured AMR is implemented, in which rectangular patches of the
grid at level <cite>L</cite> are refined to level <cite>L+1</cite>.
See <a class="reference internal" href="setrun_amrclaw.html#setrun-amrclaw"><span class="std std-ref">Specifying AMRClaw run-time parameters in setrun.py</span></a> for a list of the input parameters that can be
specified to help control how refinement is done.
The general algorithms are described in <a class="reference internal" href="biblio.html#bergerleveque98" id="id1"><span>[BergerLeVeque98]</span></a>.</p>
<p>See <a class="reference internal" href="ClawPlotItem.html#clawplotitem"><span class="std std-ref">ClawPlotItem</span></a> for a list of 2d plot types that can be used to
create a <cite>setplot</cite> function to control plotting of two-dimensional results.
Some of the attribute names start with the string <cite>amr_</cite>, indicating that a
list of different values can be specified for each AMR level.
See <a class="reference internal" href="plotting.html#plotting"><span class="std std-ref">Plotting with Visclaw</span></a> and <a class="reference internal" href="setplot.html#setplot"><span class="std std-ref">Using setplot.py to specify the desired plots</span></a> for more about plotting.</p>
<p>Python plotting tools for 3d are still under development. For now, the
Matlab tools from Clawpack 4.3 can still be used, see
<a class="reference internal" href="matlab_plotting.html#matlabplots"><span class="std std-ref">Plotting using Matlab</span></a>.</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="amrclaw1d.html">AMRClaw for 1d problems</a><ul>
<li class="toctree-l2"><a class="reference internal" href="amrclaw1d.html#old-approach-deprecated">Old approach, deprecated:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="setrun_amrclaw.html">Specifying AMRClaw run-time parameters in <cite>setrun.py</cite></a><ul>
<li class="toctree-l2"><a class="reference internal" href="setrun_amrclaw.html#input">Input</a></li>
<li class="toctree-l2"><a class="reference internal" href="setrun_amrclaw.html#output">Output</a></li>
<li class="toctree-l2"><a class="reference internal" href="setrun_amrclaw.html#run-time-parameters">Run-time parameters</a></li>
<li class="toctree-l2"><a class="reference internal" href="setrun_amrclaw.html#special-amr-parameters">Special AMR parameters</a></li>
<li class="toctree-l2"><a class="reference internal" href="setrun_amrclaw.html#debugging-flags-for-additional-printing">Debugging flags for additional printing</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="setrun_amrclaw_sample.html">Sample <cite>setrun.py</cite> module for AMRClaw</a></li>
<li class="toctree-l1"><a class="reference internal" href="amr_algorithm.html">Adaptive mesh refinement (AMR) algorithms</a><ul>
<li class="toctree-l2"><a class="reference internal" href="amr_algorithm.html#ghost-cells-and-boundary-conditions-for-amr">Ghost cells and boundary conditions for AMR</a></li>
<li class="toctree-l2"><a class="reference internal" href="amr_algorithm.html#choosing-and-initializing-finer-grids">Choosing and initializing finer grids</a></li>
<li class="toctree-l2"><a class="reference internal" href="amr_algorithm.html#flagging-cells-for-refinement">Flagging cells for refinement</a></li>
<li class="toctree-l2"><a class="reference internal" href="amr_algorithm.html#for-more-details">For more details</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="refinement.html">AMR refinement criteria</a><ul>
<li class="toctree-l2"><a class="reference internal" href="refinement.html#flagging-criteria">Flagging criteria</a><ul>
<li class="toctree-l3"><a class="reference internal" href="refinement.html#flag2refine">flag2refine</a></li>
<li class="toctree-l3"><a class="reference internal" href="refinement.html#richardson-extrapolation">Richardson extrapolation</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="refinement.html#specifying-amr-regions">Specifying AMR regions</a></li>
<li class="toctree-l2"><a class="reference internal" href="refinement.html#implementation">Implementation</a></li>
<li class="toctree-l2"><a class="reference internal" href="refinement.html#flagging-criteria-in-geoclaw">Flagging criteria in GeoClaw</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="flagregions.html">Specifying flagregions for adaptive refinement</a><ul>
<li class="toctree-l2"><a class="reference internal" href="flagregions.html#using-ruled-rectangles-as-flagregions">Using ruled rectangles as flagregions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="ruled_rectangles.html">Ruled Rectangles</a><ul>
<li class="toctree-l2"><a class="reference internal" href="ruled_rectangles.html#contents">Contents</a></li>
<li class="toctree-l2"><a class="reference internal" href="ruled_rectangles.html#examples">Examples</a></li>
<li class="toctree-l2"><a class="reference internal" href="ruled_rectangles.html#relation-to-convex-polygons">Relation to convex polygons</a></li>
<li class="toctree-l2"><a class="reference internal" href="ruled_rectangles.html#other-attributes-and-methods">Other attributes and methods</a><ul>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#ds"><cite>ds</cite></a></li>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#slu"><cite>slu</cite></a></li>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#bounding-box"><cite>bounding_box</cite></a></li>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#mask-outside"><cite>mask_outside</cite></a></li>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#read-and-write-and-instantiating-from-a-file">read and write, and instantiating from a file</a></li>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#make-kml"><cite>make_kml</cite></a></li>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#a-geoclaw-amr-flag-region">A GeoClaw AMR flag region</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="ruled_rectangles.html#a-simple-rectangle">A simple rectangle</a></li>
<li class="toctree-l2"><a class="reference internal" href="ruled_rectangles.html#defining-a-ruled-rectangle-covering-selected-cells">Defining a Ruled Rectangle covering selected cells</a><ul>
<li class="toctree-l3"><a class="reference internal" href="ruled_rectangles.html#example-covering-the-continental-shelf">Example covering the continental shelf</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adjoint.html">Guiding AMR with adjoint flagging</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adjoint.html#using-adjoint-flagging-in-geoclaw">Using adjoint flagging in GeoClaw</a></li>
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<li class="toctree-l2"><a class="reference internal" href="gauges.html#gauge-parameters-in-setrun">Gauge parameters in setrun</a></li>
<li class="toctree-l2"><a class="reference internal" href="gauges.html#plotting-tools">Plotting tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="gauges.html#plotting-gauge-locations">Plotting gauge locations</a></li>
<li class="toctree-l2"><a class="reference internal" href="gauges.html#examples">Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="amrclaw_doxygen.html">Doxygen documentation of AMRClaw</a></li>
<li class="toctree-l1"><a class="reference internal" href="amrclaw_flowcharts.html">AMRClaw Flowcharts</a></li>
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