179 lines
8.9 KiB
Markdown
179 lines
8.9 KiB
Markdown
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<!-- Begin breadcrumb -->
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<ul class="uk-breadcrumb">
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<li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials & Examples</a></li>
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<li><span>Stratigraphic Hex Mesh Tutorial</span></li>
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</ul>
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<!-- End breadcrumb -->
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<!-- Begin image -->
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<img data-src="{{ "/pages/tutorial/stratigraphy/images/02_hex_01_top_region.png" | relative_url }}" width="639" height="525" alt="" uk-img>
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<br/>
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<!-- End image -->
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<h2 id="psets" class="uk-h3 uk-margin-remove">2. Define Boundaries Using Point Sets</h2>
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In LaGriT, a pset (or *point-set*) is a collection of points (nodes) within a
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mesh object. Similarly, an eltset (*element-set*) 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.
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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.
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```
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# 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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```
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Capturing a `pset` is done through the command
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```
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pset / pset_name / select_type / select_type_options
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```
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where `pset_name` is an arbitrary variable name to store the pset into,
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`select_type` is the method of pset selection, and `select_type_options` are
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parameters specific to the chosen `select_type` for configuring the subset
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selection (see the [documentation](../../docs/commands/PSET.md) for more information).
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### 2.1 PSet Definitions
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As the boundary will live only in the top layer, nodes belonging to the top
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layer will be identified first.
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```
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pset / p_top / attribute / zic / 1 0 0 / ge / Z1
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```
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Here, a pset named `p_top` is created. This pset contains all nodes
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(stride = `1 0 0`) where the node's Z value (`zic`) is greater than or equal to
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(`ge`) the top of the mesh (`Z1`). Remember that we defined `Z1` above for the
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initial creation of the mesh - and that by simply changing `Z1` and re-running
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the script, this pset capture will still be valid for any value of `Z1`
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(where `Z1 > Z0`).
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Now that the top is defined, we will move to defining three cylindrical
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objects.
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This is done through the command
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```
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pset / pset_name / geom / rtz / ifirst,ilast,istride / r1,t1,z1 / r2,t2,z2 / xcen,ycen,zcen
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```
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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.
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```
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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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```
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Above, any points within a full circle (theta = `360`) of radius `1100.` and
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within `Z={-1.0,1.e4}` are captured. Three different cylinders are created,
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where only the centroids change.
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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 `p_region`:
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```
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pset / p_region / inter / p_top p_circle1 p_circle2 p_circle3
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```
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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.
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### 2.2 Map PSets to an Attribute
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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.
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First, create an attribute using the `cmo / addatt` command:
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```
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cmo / addatt / MONAME / id_top_region / vint / scalar / nnodes
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```
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Here, an attribute named `id_top_region` is created within the mesh `MONAME`,
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and has type integer (`vint`), is of scalar dimensions, and is a node-based
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attribute (`nnodes`).
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The attribute can be progressively filled in with different values based on
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the psets:
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```
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# 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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```
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Finally, release the psets from memory:
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```
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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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```
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Cutting through the mesh in ParaView, we can visualize `id_top_region` and
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validate that the mesh is being constructed as expected:
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<!-- Lightbox image -->
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<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
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<div>
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<a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/ch2_transparent_cbar.png" | relative_url }}" data-caption="Visualization of id_top_region">
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<img src="{{ "/pages/tutorial/stratigraphy/images/ch2_transparent_cbar.png" | relative_url }}" alt="">
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</a>
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</div>
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</div>
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<!-- Next / Prev -->
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<ul class="uk-pagination">
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<li><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
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<li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
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</ul>
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<!-- Sidebar -->
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<div class="tm-sidebar-right uk-visible@l">
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<div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
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<ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">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" | relative_url }}">3. Constructing Stratigraphy</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
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<li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
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<li class="uk-nav-divider"></li>
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<!---->
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<li><a href="{{ "/pages/tutorial/stratigraphy/images/gallery.html" | relative_url }}" target="_blank"><span uk-icon="icon: image" class="uk-margin-small-right uk-icon"></span> <span class="uk-text-middle">Image Gallery</span></a></li>
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<li><a href="https://github.com/lanl/LaGriT/issues" target="_blank"><span uk-icon="icon: warning" class="uk-margin-small-right uk-icon"><svg width="20" height="20" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg" data-svg="warning"><circle cx="10" cy="14" r="1"></circle><circle fill="none" stroke="#000" stroke-width="1.1" cx="10" cy="10" r="9"></circle><path d="M10.97,7.72 C10.85,9.54 10.56,11.29 10.56,11.29 C10.51,11.87 10.27,12 9.99,12 C9.69,12 9.49,11.87 9.43,11.29 C9.43,11.29 9.16,9.54 9.03,7.72 C8.96,6.54 9.03,6 9.03,6 C9.03,5.45 9.46,5.02 9.99,5 C10.53,5.01 10.97,5.44 10.97,6 C10.97,6 11.04,6.54 10.97,7.72 L10.97,7.72 Z"></path></svg></span> <span class="uk-text-middle">Report issue</span></a></li>
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<li><a href="mailto:lagrit-dev@lanl.gov" target="_blank"><span uk-icon="icon: commenting" class="uk-margin-small-right uk-icon"><svg width="20" height="20" viewBox="0 0 20 20" xmlns="http://www.w3.org/2000/svg" data-svg="commenting"><polygon fill="none" stroke="#000" points="1.5,1.5 18.5,1.5 18.5,13.5 10.5,13.5 6.5,17.5 6.5,13.5 1.5,13.5"></polygon><circle cx="10" cy="8" r="1"></circle><circle cx="6" cy="8" r="1"></circle><circle cx="14" cy="8" r="1"></circle></svg></span> <span class="uk-text-middle">Get help</span></a></li>
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</ul>
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</div>
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</div>
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