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<li><a href="/pages/tutorial/index.html">Tutorials & Examples</a></li>
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<li><span>Stratigraphic Hex Mesh Tutorial</span></li>
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<p><img data-src="/pages/tutorial/stratigraphy/images/02_hex_01_top_region.png" width="639" height="525" alt="" uk-img="" />
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<br />
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<!-- End image --></p>
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<h2 id="psets" class="uk-h3 uk-margin-remove">2. Define Boundaries Using Point Sets</h2>
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<p>In LaGriT, a pset (or <em>point-set</em>) is a collection of points (nodes) within a
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mesh object. Similarly, an eltset (<em>element-set</em>) is a collection of mesh
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elements. By capturing points and elements, discrete manipulations can be
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performed on them, such as translation, removal, or attribute functions.</p>
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<p>In this example, point sets are used to create a boundary on the top surface of
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the created hex mesh. The boundary will be the intersection of three circles on
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the top layer of the mesh.</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code># Set vertices (imt) and cells (itetlcr) to 1
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cmo / setatt / mohex / imt / 1 0 0 / 1
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cmo / setatt / mohex / itetclr / 1 0 0 / 1
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resetpts / itp
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</code></pre></div></div>
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<p>Capturing a <code class="language-plaintext highlighter-rouge">pset</code> is done through the command</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pset / pset_name / select_type / select_type_options
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</code></pre></div></div>
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<p>where <code class="language-plaintext highlighter-rouge">pset_name</code> is an arbitrary variable name to store the pset into,
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<code class="language-plaintext highlighter-rouge">select_type</code> is the method of pset selection, and <code class="language-plaintext highlighter-rouge">select_type_options</code> are
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parameters specific to the chosen <code class="language-plaintext highlighter-rouge">select_type</code> for configuring the subset
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selection (see the <a href="/pages/docs/commands/PSET.html">documentation</a> for more information).</p>
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<h3 id="21-pset-definitions">2.1 PSet Definitions</h3>
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<p>As the boundary will live only in the top layer, nodes belonging to the top
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layer will be identified first.</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pset / p_top / attribute / zic / 1 0 0 / ge / Z1
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</code></pre></div></div>
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<p>Here, a pset named <code class="language-plaintext highlighter-rouge">p_top</code> is created. This pset contains all nodes
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(stride = <code class="language-plaintext highlighter-rouge">1 0 0</code>) where the node’s Z value (<code class="language-plaintext highlighter-rouge">zic</code>) is greater than or equal to
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(<code class="language-plaintext highlighter-rouge">ge</code>) the top of the mesh (<code class="language-plaintext highlighter-rouge">Z1</code>). Remember that we defined <code class="language-plaintext highlighter-rouge">Z1</code> above for the
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initial creation of the mesh - and that by simply changing <code class="language-plaintext highlighter-rouge">Z1</code> and re-running
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the script, this pset capture will still be valid for any value of <code class="language-plaintext highlighter-rouge">Z1</code>
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(where <code class="language-plaintext highlighter-rouge">Z1 > Z0</code>).</p>
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<p>Now that the top is defined, we will move to defining three cylindrical
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objects.</p>
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<p>This is done through the command</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pset / pset_name / geom / rtz / ifirst,ilast,istride / r1,t1,z1 / r2,t2,z2 / xcen,ycen,zcen
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</code></pre></div></div>
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<p>which forms a pset of nodes within the cylinder or cylindrical shell given by
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radius r1 to r2, angle theta t1 to t2 and height z1 to z2.</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pset / p_circle1 / geom / rtz / 1 0 0 / 0. 0. -1.0 / &
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1100. 360. 1.e4 / 1500. 1500. 0.
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pset / p_circle2 / geom / rtz / 1 0 0 / 0. 0. -1.0 / &
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1100. 360. 1.e4 / 2500. 2500. 0.
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pset / p_circle3 / geom / rtz / 1 0 0 / 0. 0. -1.0 / &
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1100. 360. 1.e4 / 2500. 1500. 0.
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</code></pre></div></div>
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<p>Above, any points within a full circle (theta = <code class="language-plaintext highlighter-rouge">360</code>) of radius <code class="language-plaintext highlighter-rouge">1100.</code> and
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within <code class="language-plaintext highlighter-rouge">Z={-1.0,1.e4}</code> are captured. Three different cylinders are created,
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where only the centroids change.</p>
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<p>Finally, all four psets are intersected such that all points belonging to the
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union of all given sets are preserved into the point seet <code class="language-plaintext highlighter-rouge">p_region</code>:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pset / p_region / inter / p_top p_circle1 p_circle2 p_circle3
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</code></pre></div></div>
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<p>This creates a point-set where all points (i) live on the top layer, and (ii)
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live within the intersection of the three cylinders.</p>
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<h3 id="22-map-psets-to-an-attribute">2.2 Map PSets to an Attribute</h3>
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<p>As a simple sanity check during meshing, it can be helpful to map mesh
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operations to an attribute. These can be visualized at intermediate steps in
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the meshing process to provide a form of verification or debugging.</p>
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<p>First, create an attribute using the <code class="language-plaintext highlighter-rouge">cmo / addatt</code> command:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cmo / addatt / MONAME / id_top_region / vint / scalar / nnodes
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</code></pre></div></div>
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<p>Here, an attribute named <code class="language-plaintext highlighter-rouge">id_top_region</code> is created within the mesh <code class="language-plaintext highlighter-rouge">MONAME</code>,
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and has type integer (<code class="language-plaintext highlighter-rouge">vint</code>), is of scalar dimensions, and is a node-based
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attribute (<code class="language-plaintext highlighter-rouge">nnodes</code>).</p>
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<p>The attribute can be progressively filled in with different values based on
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the psets:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code># Fill the entire attribute with 1
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cmo / setatt / MONAME / id_top_region / 1 0 0 / 1
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# Color all nodes in the pset p_circle1 with the value 2
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cmo / setatt / MONAME / id_top_region / pset get p_circle1 / 2
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# Color all nodes in the pset p_circle2 with the value 2
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cmo / setatt / MONAME / id_top_region / pset get p_circle2 / 3
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# And so on...
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cmo / setatt / MONAME / id_top_region / pset get p_circle3 / 4
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cmo / setatt / MONAME / id_top_region / pset get p_region / 5
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</code></pre></div></div>
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<p>Finally, release the psets from memory:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pset / p_top / release
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pset / p_circle1 / release
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pset / p_circle2 / release
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pset / p_circle3 / release
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pset / p_region / release
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</code></pre></div></div>
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<p>Cutting through the mesh in ParaView, we can visualize <code class="language-plaintext highlighter-rouge">id_top_region</code> and
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validate that the mesh is being constructed as expected:</p>
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<a class="uk-inline" href="/pages/tutorial/stratigraphy/images/ch2_transparent_cbar.png" data-caption="Visualization of id_top_region">
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<li class=""><a href="/pages/tutorial/stratigraphy/index.html">Index</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_01.html">1. Building a Hex Mesh</a></li>
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<li class="uk-active"><a href="#psets">2. Define Boundaries Using Point Sets</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_03.html">3. Constructing Stratigraphy</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_04.html">4. Map Surfaces to Mesh</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_05.html">5. Constructing a Fault</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_06.html">6. Truncate with Polyline</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_07.html">7. Refine Fault</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_08.html">8. Insert Wells</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_09.html">9. Convert Hex Mesh to Tet</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_10_fehm.html">10.1 Write FEHM Files</a></li>
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<li class=""><a href="/pages/tutorial/stratigraphy/step_10_exo.html">10.2 Write ExodusII Files</a></li>
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<p>© 2019 Los Alamos National Laboratory</p>
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