initial upload

docs/pages/tutorial/stratigraphy/images/gallery.md

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+# Image Gallery 
+
+Gallery written: Fri Aug  9 16:26:43 2019
+
+Image Directory: /project/meshing/demos/Tutorial\_Hex\_Mesh/images 
+
+
+|  |  |   | 
+| :---: | :---: | :---:  | 
+|  |  |   | 
+|  **01\_hex\_01** |  **02\_hex\_01\_top\_region** |  **03\_hex\_01\_2surfs**  | 
+| ![](gallery/01_hex_01.png)| ![](gallery/02_hex_01_top_region.png)| ![](gallery/03_hex_01_2surfs.png) | 
+|  **03\_hex\_01\_2surfs\_b** |  **03\_hex\_01\_set\_imt\_itetclr** |  **03\_hex\_01\_set\_imt\_itetclr\_threshold\_remove\_material3**  | 
+| ![](gallery/03_hex_01_2surfs_b.png)| ![](gallery/03_hex_01_set_imt_itetclr.png)| ![](gallery/03_hex_01_set_imt_itetclr_threshold_remove_material3.png) | 
+|  **05\_hex\_01\_fault\_imt\_itetclr** |  **06\_boundary\_truncate** |  **07\_boundary\_truncate\_fence**  | 
+| ![](gallery/05_hex_01_fault_imt_itetclr.png)| ![](gallery/06_boundary_truncate.png)| ![](gallery/07_boundary_truncate_fence.png) | 
+|  **08\_truncate\_set\_id** |  **09\_truncate\_set\_id\_close\_up** |  **10\_hex\_01\_truncate\_close\_up**  | 
+| ![](gallery/08_truncate_set_id.png)| ![](gallery/09_truncate_set_id_close_up.png)| ![](gallery/10_hex_01_truncate_close_up.png) | 
+|  **11\_hex\_01\_truncate** |  **12\_hex\_01\_truncate\_w\_grid** |  **13\_hex\_01\_fault\_refine**  | 
+| ![](gallery/11_hex_01_truncate.png)| ![](gallery/12_hex_01_truncate_w_grid.png)| ![](gallery/13_hex_01_fault_refine.png) | 
+|  **14\_hex\_01\_fault\_refine\_close\_up** |  **15\_hex\_01\_insert\_wells** |  **16\_hex\_01\_insert\_wells\_close\_up**  | 
+| ![](gallery/14_hex_01_fault_refine_close_up.png)| ![](gallery/15_hex_01_insert_wells.png)| ![](gallery/16_hex_01_insert_wells_close_up.png) | 
+|  **17\_hex\_01\_insert\_wells\_outline** |  **18\_hex\_01\_insert\_wells\_dfield\_wells** |  **19\_hex\_01\_to\_tet**  | 
+| ![](gallery/17_hex_01_insert_wells_outline.png)| ![](gallery/18_hex_01_insert_wells_dfield_wells.png)| ![](gallery/19_hex_01_to_tet.png) | 
+|  **21\_tet\_01\_exo\_blocks** |  **21\_tet\_01\_exo\_blocks\_ex** |  **21\_tet\_01\_exo\_bndry\_faces**  | 
+| ![](gallery/21_tet_01_exo_blocks.png)| ![](gallery/21_tet_01_exo_blocks_ex.png)| ![](gallery/21_tet_01_exo_bndry_faces.png) | 
+|  **21\_tet\_01\_fehm\_node\_zone\_rad16** |  **21\_tet\_01\_fehm\_node\_zone\_top** |  **21\_tet\_01\_fehm\_nodes**  | 
+| ![](gallery/21_tet_01_fehm_node_zone_rad16.png)| ![](gallery/21_tet_01_fehm_node_zone_top.png)| ![](gallery/21_tet_01_fehm_nodes.png) | 
+|  **21\_tet\_01\_fehm\_tet\_a** |  **21\_tet\_01\_fehm\_vor\_a** |  **21\_tet\_01\_fehm\_vor\_tet\_a**  | 
+| ![](gallery/21_tet_01_fehm_tet_a.png)| ![](gallery/21_tet_01_fehm_vor_a.png)| ![](gallery/21_tet_01_fehm_vor_tet_a.png) | 
+|  **21\_tet\_01\_fehm\_voronoi** |  **21\_tet\_01\_fehm\_voronoi\_a**  | 
+| ![](gallery/21_tet_01_fehm_voronoi.png)| ![](gallery/21_tet_01_fehm_voronoi_a.png) | 
+
+
+End Gallery

docs/pages/tutorial/stratigraphy/index.md

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+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+
+<div class="uk-inline">
+    <img src="{{ "/pages/tutorial/stratigraphy/images/19_hex_01_to_tet.png" | relative_url }}" alt="">
+    <div class="uk-overlay uk-light uk-position-bottom">
+        <h2 id="strat-index" class="uk-h3 uk-margin-remove">Stratigraphic Hex Mesh Tutorial</h2>
+    </div>
+</div>
+
+<a href="{{ "/pages/tutorial/stratigraphy/Tutorial_Hex_Mesh.zip" | relative_url }}" class="uk-button uk-button-primary tm-button-default uk-icon">
+    Download Resources (7.5 MB)
+    <span uk-icon="download"></span>
+</a>
+
+<div uk-alert>
+    In this tutorial, we will be constructing a complex geostratigraphic mesh with a fault, distinct subsurface layering and multiple wells.
+    The goal of this tutorial is to introduce the reader to intermediate and advanced LaGriT topics, including refinement, truncation, point-sets, element-sets and more.
+</div>
+
+<ul class="uk-pagination">
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class="uk-active"><a href="#strat-index">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Well</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_01.md

@@ -0,0 +1,105 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image -->
+<img data-src="{{ "/pages/tutorial/stratigraphy/images/01_hex_01.png" | relative_url }}" width="639" height="525" alt="" uk-img>
+<br/>
+<!-- End image -->
+
+<h2 id="build-hex" class="uk-h3 uk-margin-remove">1. Building a Hex Mesh</h2>
+
+First, we are going to construct a structured hex mesh. The hex mesh will span
+from 0 meters to 4000 m, 4000 m, and 3000 m, for the x/y/z coordinates
+respectively.
+
+For both consistency and rapid parameter manipulation, these can be stored in
+variables. In LaGriT, variables are assigned using the `define` keyword. 
+
+```
+define / X0 / 0.
+define / X1 / 4000.
+define / Y0 / 0.
+define / Y1 / 4000.
+define / Z0 / 0.
+define / Z1 / 3000.
+
+define / NX / 51
+define / NY / 51
+define / NZ / 26
+
+define / MONAME / mohex
+```
+
+Above, the spatial domain (`X0,X1,Y0,...`), element density (`NX/NY/NZ`), and
+mesh name (`MONAME`) have been defined.
+
+Next, we will create an empty mesh object, with element type `hex`, using the
+[`cmo / create`](../../docs/commands/cmo/cmo_create.md) command:
+
+```
+cmo / create / MONAME / / / hex
+```
+
+Due to the variable assignment of `MONAME <- mohex` above, this command is
+translated internally as:
+
+```
+cmo / create / mohex / / / hex
+```
+
+This empty object can then be populated with nodes and elements. 
+The [`createpts / brick`](../../docs/commands/createpts/CRTPTBRICK.md) command will generate a defined number of
+hex elements across a defined domain. 
+
+```
+createpts / brick / xyz / NX NY NZ / X0 Y0 Z0 / X1 Y1 Z1 / 1 1 1
+```
+
+`NX` number of hex elements, along with their corresponding vertices, have been
+created in the spatial domain spanning `X0->X1`, along with `NY` elements in
+the Y domain and `NZ` elements in the Z domain.
+
+Optionally, [save the mesh object](../../docs/commands/DUMP2.md):
+
+```
+dump / avs / tmp_hex_01.inp / MONAME
+```
+
+This file can be rendered in certain scientific 3D visualization applications,
+such as [ParaView](https://www.paraview.org).
+
+<!-- Page left / right -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class="uk-active"><a href="#build-hex">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_02.md

@@ -0,0 +1,179 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image -->
+<img data-src="{{ "/pages/tutorial/stratigraphy/images/02_hex_01_top_region.png" | relative_url }}" width="639" height="525" alt="" uk-img>
+<br/>
+<!-- End image -->
+
+<h2 id="psets" class="uk-h3 uk-margin-remove">2. Define Boundaries Using Point Sets</h2>
+
+In LaGriT, a pset (or *point-set*) is a collection of points (nodes) within a 
+mesh object. Similarly, an eltset (*element-set*) is a collection of mesh
+elements. By capturing points and elements, discrete manipulations can be
+performed on them, such as translation, removal, or attribute functions. 
+
+In this example, point sets are used to create a boundary on the top surface of 
+the created hex mesh. The boundary will be the intersection of three circles on
+the top layer of the mesh.
+
+```
+# Set vertices (imt) and cells (itetlcr) to 1
+cmo / setatt / mohex / imt / 1 0 0 / 1
+cmo / setatt / mohex / itetclr / 1 0 0 / 1
+
+resetpts / itp
+```
+
+Capturing a `pset` is done through the command
+
+```
+pset / pset_name / select_type / select_type_options
+```
+
+where `pset_name` is an arbitrary variable name to store the pset into, 
+`select_type` is the method of pset selection, and `select_type_options` are
+parameters specific to the chosen `select_type` for configuring the subset
+selection (see the [documentation](../../docs/commands/PSET.md) for more information).
+
+### 2.1 PSet Definitions
+
+As the boundary will live only in the top layer, nodes belonging to the top 
+layer will be identified first.
+
+```
+pset / p_top / attribute / zic / 1 0 0 / ge / Z1
+```
+
+Here, a pset named `p_top` is created. This pset contains all nodes 
+(stride = `1 0 0`) where the node's Z value (`zic`) is greater than or equal to
+(`ge`) the top of the mesh (`Z1`). Remember that we defined `Z1` above for the
+initial creation of the mesh - and that by simply changing `Z1` and re-running
+the script, this pset capture will still be valid for any value of `Z1`
+(where `Z1 > Z0`).
+
+Now that the top is defined, we will move to defining three cylindrical
+objects.
+
+This is done through the command
+
+```
+pset / pset_name / geom / rtz / ifirst,ilast,istride / r1,t1,z1 / r2,t2,z2 / xcen,ycen,zcen
+```
+
+which forms a pset of nodes within the cylinder or cylindrical shell given by 
+radius r1 to r2, angle theta t1 to t2 and height z1 to z2.
+
+```
+pset / p_circle1 / geom / rtz / 1 0 0 / 0. 0. -1.0 / &
+       1100. 360. 1.e4 / 1500. 1500. 0.
+pset / p_circle2 / geom / rtz / 1 0 0 / 0. 0. -1.0 / &
+       1100. 360. 1.e4 / 2500. 2500. 0.
+pset / p_circle3 / geom / rtz / 1 0 0 / 0. 0. -1.0 / &
+       1100. 360. 1.e4 / 2500. 1500. 0.
+```
+
+Above, any points within a full circle (theta = `360`) of radius `1100.` and 
+within `Z={-1.0,1.e4}` are captured. Three different cylinders are created,
+where only the centroids change.
+
+Finally, all four psets are intersected such that all points belonging to the
+union of all given sets are preserved into the point seet `p_region`:
+
+```
+pset / p_region / inter / p_top p_circle1 p_circle2 p_circle3
+```
+
+This creates a point-set where all points (i) live on the top layer, and (ii)
+live within the intersection of the three cylinders.
+
+### 2.2 Map PSets to an Attribute
+
+As a simple sanity check during meshing, it can be helpful to map mesh
+operations to an attribute. These can be visualized at intermediate steps in
+the meshing process to provide a form of verification or debugging.
+
+First, create an attribute using the `cmo / addatt` command:
+
+```
+cmo / addatt / MONAME / id_top_region / vint / scalar / nnodes
+```
+
+Here, an attribute named `id_top_region` is created within the mesh `MONAME`,
+and has type integer (`vint`), is of scalar dimensions, and is a node-based
+attribute (`nnodes`).
+
+The attribute can be progressively filled in with different values based on
+the psets:
+
+```
+# Fill the entire attribute with 1
+cmo / setatt / MONAME / id_top_region / 1 0 0 / 1
+
+# Color all nodes in the pset p_circle1 with the value 2
+cmo / setatt / MONAME / id_top_region / pset get p_circle1 / 2
+
+# Color all nodes in the pset p_circle2 with the value 2
+cmo / setatt / MONAME / id_top_region / pset get p_circle2 / 3
+
+# And so on...
+cmo / setatt / MONAME / id_top_region / pset get p_circle3 / 4
+cmo / setatt / MONAME / id_top_region / pset get p_region / 5
+```
+
+Finally, release the psets from memory:
+
+```
+pset / p_top / release
+pset / p_circle1 / release
+pset / p_circle2 / release
+pset / p_circle3 / release
+pset / p_region / release
+```
+
+Cutting through the mesh in ParaView, we can visualize `id_top_region` and
+validate that the mesh is being constructed as expected:
+
+<!-- Lightbox image -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/ch2_transparent_cbar.png" | relative_url }}" data-caption="Visualization of id_top_region">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/ch2_transparent_cbar.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <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>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class="uk-active"><a href="#psets">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_03.md

@@ -0,0 +1,94 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image -->
+<img data-src="{{ "/pages/tutorial/stratigraphy/images/03_hex_01_2surfs_b.png" | relative_url }}" width="639" height="525" alt="" uk-img>
+<br/>
+<!-- End image -->
+
+<h2 id="const-stratigraphy" class="uk-h3 uk-margin-remove">3. Constructing Stratigraphy</h2>
+
+In the next step of this tutorial, we will build some surfaces to define
+stratigraphy.
+In a real model, the surfaces would come from some geologic framework model
+and would define geologic or hydro-geologic horizons and topography.
+
+These surfaces will be planar quad meshes that cut through a defined section of
+the hex mesh. Later, we will map the intersections of the surfaces to the hex
+mesh.
+
+#### Create the top surface:
+
+```
+cmo / create / mosurf1
+cmo / select / mosurf1
+
+define / X0S /  -20.0
+define / X1S / 4020.0
+define / Y0S /  -20.0
+define / Y1S / 4020.0
+
+define / Z1 / 1000.
+define / Z2 / 1500.
+define / Z3 / 2500.
+define / Z4 /  500.
+
+quadxy / NX NY /X0S Y0S Z1/X1S Y0S Z2/X1S Y1S Z3/X0S Y1S Z4
+createpts/brick/xyz/ NX NY 1 /1,0,0/connect
+```
+
+Note that the X and Y domains of the quad mesh exceed that of the hex mesh.
+This serves two purposes. First, it serves as a helpful visualization aid,
+allowing one to easily see how the surfaces cut the hex mesh without adjusting
+opacity. Second, and more importantly, it ensures that all elements cut by the
+surfaces will be properly recognized as such. Rounding errors may affect
+elements at the perimeter of the cutting planes from being properly labeled.
+
+#### Create the bottom surface:
+
+```
+cmo / create / mosurf2
+cmo / select / mosurf2
+
+define / Z1 / 1800.
+define / Z2 / 2100.
+define / Z3 / 2800.
+define / Z4 /  800.
+quadxy / NX NY /X0S Y0S Z1/X1S Y0S Z2/X1S Y1S Z3/X0S Y1S Z4
+createpts/brick/xyz/ NX NY 1 /1,0,0/connect
+```
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class="uk-active"><a href="#const-stratigraphy">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_04.md

@@ -0,0 +1,162 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image slideshow -->
+<div class="uk-position-relative uk-visible-toggle uk-light" tabindex="-1" uk-slideshow>
+    <ul class="uk-slideshow-items">
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/03_hex_01_set_imt_itetclr.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/03_hex_01_set_imt_itetclr_threshold_remove_material3.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+    </ul>
+    <a class="uk-position-center-left uk-position-small uk-hidden-hover" href="#" uk-slidenav-previous uk-slideshow-item="previous"></a>
+    <a class="uk-position-center-right uk-position-small uk-hidden-hover" href="#" uk-slidenav-next uk-slideshow-item="next"></a>
+</div>
+<!-- End image slideshow -->
+<br/>
+
+<h2 id="map-surfaces-to-mesh" class="uk-h3 uk-margin-remove">4. Map Surfaces to Mesh</h2>
+
+Now that the straitipgrahy has been modeled and we are comfortable with our
+results, we will map their spanning domain to the parent mesh. As done with the
+psets above, this process will be driven via attributes.
+
+We now have two planes spanning the X,Y domain of the mesh. These planes can be
+leveraged to create different material IDs at different regions of the
+subsurface.
+
+For example,
+
+* For all nodes/cells above plane 1, set their material ID to 1
+* For all nodes/cells between plane 1 and plane 2, set their material ID to 2
+* For all nodes/cells below plane 2, set their material ID to 3
+
+This process can be accomplished by:
+
+1. Defining the above regions using the `region` keyword
+2. Capturing the relevant nodes and elements that fall within the defined regions
+3. Setting the node and element material IDs based on the `psets` and `eltsets`
+
+### 4.1 Defining Regions
+
+The syntax for `region` is:
+
+     region / region_name / region_definition
+
+where `region_definition` is a string composed of boolean operators and 
+instantiated `surface` objects.
+
+Recall that we have defined two planes, `mosurf1` and `mosurf2`. We would like
+to generate the `region` objects from these planes, but the arguments for
+`region` require `surface` objects.
+
+Fortunately, we can map the planes to a `surface` very easily. The syntax for
+generating a `surface` object from a quad or triangle mesh is:
+
+     surface / surface_name / reflect / sheet / input_mesh
+
+The two planes can then be mapped to surface objects:
+
+```
+surface / s_1 / reflect / sheet / mosurf1
+surface / s_2 / reflect / sheet / mosurf2
+```
+
+And finally, we can remove the plane meshes and define regions:
+
+```
+cmo / delete / mosurf1
+cmo / delete / mosurf2
+cmo / select / MONAME
+
+region / r_1 / le s_1
+region / r_2 / gt s_1 and le s_2
+region / r_3 / gt s_2
+```
+
+### 4.2 Creating Eltsets and PSets from Regions
+
+Point sets and element sets can easily be created through region objects.
+The syntax is:
+
+     pset / pset_name / region / region_object / 1,0,0
+     eltset / eltset_name / region / region_object
+
+Applying this to our `region` objects yields:
+
+```
+pset   / p_r_1 / region / r_1 / 1 0 0
+pset   / p_r_2 / region / r_2 / 1 0 0
+pset   / p_r_3 / region / r_3 / 1 0 0
+
+eltset / e_r_1 / region / r_1
+eltset / e_r_2 / region / r_2
+eltset / e_r_3 / region / r_3
+```
+
+### 4.3 Setting Attributes from Eltsets and PSets
+
+Recall that the node attribute `imt` holds the 'node colors' of the mesh, and
+cell attribute `itetclr` stores the 'cell colors' (or material ID).
+
+Let's use the defined `pset`s and `eltset`s to change these:
+
+```
+cmo / setatt / MONAME / imt     / pset   get p_r_1 / 1
+cmo / setatt / MONAME / imt     / pset   get p_r_2 / 2
+cmo / setatt / MONAME / imt     / pset   get p_r_3 / 3
+
+cmo / setatt / MONAME / itetclr / eltset get e_r_1 / 1
+cmo / setatt / MONAME / itetclr / eltset get e_r_2 / 2
+cmo / setatt / MONAME / itetclr / eltset get e_r_3 / 3
+```
+
+Our mesh's cells and nodes now store information about their intersections
+with the cut-planes. Visualizing `itetclr`, we can see that this has behaved
+as expected:
+
+<!-- Lightbox image -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/ch4.png" | relative_url }}" data-caption="Visualization of materialID">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/ch4.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class="uk-active"><a href="#map-surfaces-to-mesh">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_05.md

@@ -0,0 +1,186 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image slideshow -->
+<div class="uk-position-relative uk-visible-toggle uk-light" tabindex="-1" uk-slideshow>
+    <ul class="uk-slideshow-items">
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/05_hex_01_fault_imt_itetclr.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+    </ul>
+</div>
+<!-- End image slideshow -->
+<br/>
+
+<h2 id="constructing-a-fault" class="uk-h3 uk-margin-remove">5. Constructing a Fault and Layers</h2>
+
+### 5.1 Creating a Fault and Subsurface Layers
+
+Next, we are going to map a fault and surfaces to our mesh. The objects created
+will be:
+
+
+<!-- Lightbox image -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/05_fault_objects.png" | relative_url }}" data-caption="Fault and layer surfaces">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/05_fault_objects.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+
+For all five of these surfaces, we will:
+
+1. Define the X,Y,Z extent
+2. Use `quadxy` to generate the point distribution
+3. Connect the points into a quad mesh using `createpts/brick`.
+
+For the main fault mesh, this process looks like:
+
+```
+cmo / create / mosurf_fault
+cmo / select / mosurf_fault
+
+define / X0S /  -20.0
+define / X1S / 4020.0
+
+define / Y0S /  -20.0
+define / Y1S / 4020.0
+
+define / Z1 / -1.e4
+define / Z2 / -1.e4
+define / Z3 /  1.e4
+define / Z4 /  1.e4
+
+quadxy / NX NY /X0S Y0S Z1/X1S Y0S Z2/X1S Y1S Z3/X0S Y1S Z4
+createpts/brick/xyz/ NX NY 1 /1,0,0/connect
+cmo / printatt / mosurf / -xyz- / minmax
+```
+
+For the remaining four surfaces this process is repeated, with `Z1,Z2,Z3,Z4`
+altered independently.
+
+The created surfaces have the names `mosurf1_fminus`, `mosurf2_fminus`,
+`mosurf1_fplus`, `mosurf2_fplus`, and `mosurf_fault`.
+
+### 5.2 Define Geometry of Hydrostratigraphic Model
+
+Recall in step 4 how we used two surface meshes to alter `imt` and `itetclr`
+values: first, by defining `surfaces` from the planar meshes; second, using the
+`surface` objects to define `region` objects; third, creating `psets` and
+`eltsets` from the `regions`; and finally, by modifying `itetclr` and `imt`
+through the defined `psets` and `eltsets`.
+
+This process is replicated here. First, by creating the `surfaces`:
+
+```
+surface / s_1_fm / reflect / sheet / mosurf1_fminus
+surface / s_2_fm / reflect / sheet / mosurf2_fminus
+surface / s_1_fp / reflect / sheet / mosurf1_fplus
+surface / s_2_fp / reflect / sheet / mosurf2_fplus
+surface / s_f    / reflect / sheet / mosurf_fault
+```
+
+Then, by mapping the surfaces to regions (and deleting the planar meshes to
+free up memory):
+
+```
+region / r_1_fm / le s_1_fm and               le s_f
+region / r_2_fm / gt s_1_fm and le s_2_fm and le s_f
+region / r_3_fm / gt s_2_fm and               le s_f
+region / r_1_fp / le s_1_fp and               gt s_f
+region / r_2_fp / gt s_1_fp and le s_2_fp and gt s_f
+region / r_3_fp / gt s_2_fp and               gt s_f
+
+cmo / delete / mosurf1_fminus
+cmo / delete / mosurf2_fminus
+cmo / delete / mosurf1_fplus
+cmo / delete / mosurf2_fplus
+cmo / delete / mosurf_fault
+```
+
+And finally, by creating `psets` and `eltsets` and using them to modify material
+attributes of the parent mesh:
+
+```
+pset   / p_r_1_fm / region / r_1_fm / 1 0 0
+pset   / p_r_2_fm / region / r_2_fm / 1 0 0
+pset   / p_r_3_fm / region / r_3_fm / 1 0 0
+pset   / p_r_1_fp / region / r_1_fp / 1 0 0
+pset   / p_r_2_fp / region / r_2_fp / 1 0 0
+pset   / p_r_3_fp / region / r_3_fp / 1 0 0
+
+eltset / e_r_1_fm / region / r_1_fm
+eltset / e_r_2_fm / region / r_2_fm
+eltset / e_r_3_fm / region / r_3_fm
+eltset / e_r_1_fp / region / r_1_fp
+eltset / e_r_2_fp / region / r_2_fp
+eltset / e_r_3_fp / region / r_3_fp
+
+cmo / setatt / MONAME / imt / 1 0 0 / 7
+cmo / setatt / MONAME / itetclr / 1 0 0 / 7
+
+cmo / setatt / MONAME / imt     / pset   get p_r_1_fm / 1
+cmo / setatt / MONAME / imt     / pset   get p_r_2_fm / 2
+cmo / setatt / MONAME / imt     / pset   get p_r_3_fm / 3
+cmo / setatt / MONAME / imt     / pset   get p_r_1_fp / 4
+cmo / setatt / MONAME / imt     / pset   get p_r_2_fp / 5
+cmo / setatt / MONAME / imt     / pset   get p_r_3_fp / 6
+
+cmo / setatt / MONAME / itetclr / eltset get e_r_1_fm / 1
+cmo / setatt / MONAME / itetclr / eltset get e_r_2_fm / 2
+cmo / setatt / MONAME / itetclr / eltset get e_r_3_fm / 3
+cmo / setatt / MONAME / itetclr / eltset get e_r_1_fp / 4
+cmo / setatt / MONAME / itetclr / eltset get e_r_2_fp / 5
+cmo / setatt / MONAME / itetclr / eltset get e_r_3_fp / 6
+```
+
+The six distinct regions can now be seen by viewing `itetclr` on the
+parent mesh:
+
+
+<!-- Lightbox image -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/05_hex_01_fault_imt_itetclr.png" | relative_url }}" data-caption="Visualizing the fault in relation to subsurface layers">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/05_hex_01_fault_imt_itetclr.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class="uk-active"><a href="#constructing-a-fault">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_06.md

@@ -0,0 +1,176 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image slideshow -->
+<div class="uk-position-relative uk-visible-toggle uk-light" tabindex="-1" uk-slideshow>
+    <ul class="uk-slideshow-items">
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/06_truncate_set_id.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+    </ul>
+</div>
+<!-- End image slideshow -->
+<br/>
+
+<h2 id="truncate-with-polyline" class="uk-h3 uk-margin-remove">6. Truncate with Polyline</h2>
+
+### 6.1 Create boundary surface
+
+We now have a mesh with complex stratigraphy encoded in its material ID. 
+However, the domain of this mesh is a rather boring cuboid and doesn't
+accurately reflect the geospatial domain that we are trying to model.
+
+By importing a polyline, the exterior boundary of the mesh can be truncated.
+As in previous steps, we will use a mesh to define a `region` that will be used
+for element-wise operations.
+
+However, the boundary is a line object. In order to use it as a surface/region,
+it must be a surface. A polyline can be turned into a vertical surface by
+'extruding' it in the vertical (0,0,1) direction:
+
+```
+read / avs / basin_bnd_ply_rescale.inp / mo_bndry
+extrude / mo_fence / mo_bndry / const / 3200. / volume / 0. 0. -1.
+```
+
+We will also translate the extrusion so that it covers the vertical extent
+of the hex mesh:
+
+```
+trans / 1 0 0 / 0. 0. -3200. / 0. 0. 0.
+```
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/06_boundary_truncate.png" | relative_url }}" data-caption="Polyline boundary">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/06_boundary_truncate.png" | relative_url }}" alt="">
+        </a>
+    </div>
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/06_boundary_truncate_fence.png" | relative_url }}" data-caption="Polyline boundary extruded">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/06_boundary_truncate_fence.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+### 6.2 Truncate mesh
+
+Next, we use the boundary to truncate (remove) cells outside the boundary.
+
+There are three ways to define 'outside':
+
+1. Only remove a cell if ALL vertices are outside
+2. Remove a cell if the centroid (average of all vertices) is outside
+3. Remove a cell if one or more vertices are outside
+
+```
+cmo / select / MONAME
+surface / s_bndry / reflect / sheet / mo_fence
+cmo / select / MONAME
+region / r_bndry / ge s_bndry
+pset / p_bndry / region r_bndry
+```
+**Method 1:**
+
+    eltset / e_delete1 / exclusive / pset get p_bndry
+
+**Method 2:**
+
+    eltset / e_delete2 / region r_bndry
+
+**Method 3:**
+
+    eltset / e_delete3 / inclusive / pset get p_bndry
+
+Next, add the integer cell attribute `id_in_out_bndry`:
+
+    cmo / addatt / MONAME / id_in_out_bndry / vint / scalar / nelements
+
+and 'color' it based on the three element sets created above:
+
+```
+cmo / setatt / MONAME / id_in_out_bndry / 1 0 0 / 4
+cmo / setatt / MONAME / id_in_out_bndry / eltset get e_delete3 / 3
+cmo / setatt / MONAME / id_in_out_bndry / eltset get e_delete2 / 2
+cmo / setatt / MONAME / id_in_out_bndry / eltset get e_delete1 / 1
+```
+
+All elements colored 4 (the default value for `id_in_out_bndry`) are elements
+who evaluate false for all of the above `eltsets`.
+
+Create an element set for all `id_in_out_bndry(cell_i) == 4`:
+
+```
+eltset / e_delete4 /    id_in_out_bndry / eq / 4
+eltset / e_delete3 /    id_in_out_bndry / eq / 3
+eltset / e_delete2 /    id_in_out_bndry / eq / 2
+eltset / e_delete1 /    id_in_out_bndry / eq / 1
+```
+
+Finally, remove all elements 'colored' by method 3 and all elements *not* colored by any of methods 1, 2, or 3:
+
+```
+rmpoint / element / eltset get e_delete4
+rmpoint / element / eltset get e_delete3
+rmpoint / compress
+resetpts / itp
+```
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/06_truncate_set_id_close_up.png" | relative_url }}" data-caption="Boundary fence intersection with hex mesh">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/06_truncate_set_id_close_up.png" | relative_url }}" alt="">
+        </a>
+    </div>
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/06_hex_01_truncate_w_grid.png" | relative_url }}" data-caption="Hex mesh truncated with boundary fence">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/06_hex_01_truncate_w_grid.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class="uk-active"><a href="#truncate-with-polyline">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_07.md

@@ -0,0 +1,128 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image slideshow -->
+<div class="uk-position-relative uk-visible-toggle uk-light" tabindex="-1" uk-slideshow>
+    <ul class="uk-slideshow-items">
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/07_hex_01_fault_refine.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/07_hex_01_fault_refine_close_up.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+    </ul>
+    <a class="uk-position-center-left uk-position-small uk-hidden-hover" href="#" uk-slidenav-previous uk-slideshow-item="previous"></a>
+    <a class="uk-position-center-right uk-position-small uk-hidden-hover" href="#" uk-slidenav-next uk-slideshow-item="next"></a>
+</div>
+<!-- End image slideshow -->
+<br/>
+
+<h2 id="refine-fault" class="uk-h3 uk-margin-remove">7. Refine Fault</h2>
+
+In step 5, we defined a fault surface (named `s_f`) intersecting the mesh. In 
+this section, we are going to refine the mesh where the fault intersects it.
+
+The LaGriT command `intersect_elements` takes two meshes and creates an
+element-based attribute in mesh1 that contains the number of elements in mesh2
+that intersected the respective element in mesh1.
+
+Performing the intersection between the mesh `MONAME` and fault `s_f`, storing
+the intersection count in attribute `if_inter`:
+
+```
+cmo / select / MONAME
+intersect_elements / MONAME / s_f / if_inter
+```
+
+The attribute `if_inter` will be non-zero everywhere there is an intersection,
+and zero where there was not intersection. Taking advantage of this fact,
+we can create an eltset to refine:
+
+```
+eltset / e_refine / if_inter / gt / 0
+refine / eltset / eltset get e_refine
+cmo / DELATT / MONAME / if_inter
+```
+
+The element density has now increased where the mesh intersects `s_f`.
+We can then run this step *again*, further refining elements along that intersection:
+
+```
+intersect_elements / MONAME / s_f / if_inter
+eltset / e_refine / if_inter / gt / 0
+refine/ eltset / eltset get e_refine
+cmo / setatt / MONAME / if_inter / 1 0 0 / 0
+```
+
+And finally, remove the attribute `if_inter`, as it is no longer needed:
+
+```
+cmo / DELATT / MONAME / if_inter
+```
+
+At this point, many different mesh objects and surfaces still exist in memory from previous steps. Let's deallocate them and verify with the `memory` command:
+
+```
+cmo / status / brief
+cmo / status / MONAME
+memory / verify
+memory / print
+
+cmo / delete / s_bndry
+cmo / delete / mo_fence
+cmo / delete / mo_bndry
+cmo / delete / s_f
+cmo / delete / s_2_fp
+cmo / delete / s_1_fp
+cmo / delete / s_2_fm
+cmo / delete / s_1_fm
+cmo / delete / s_2
+cmo / delete / s_1
+
+memory / verify
+memory / print
+```
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/07_hex_01_fault_refine_close_up.png" | relative_url }}" data-caption="Boundary fence intersection with hex mesh">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/07_hex_01_fault_refine_close_up.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class="uk-active"><a href="#refine-fault">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_08.md

@@ -0,0 +1,250 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image slideshow -->
+<div class="uk-position-relative uk-visible-toggle uk-light" tabindex="-1" uk-slideshow>
+    <ul class="uk-slideshow-items">
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/08_hex_01_insert_wells.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/08_hex_01_insert_wells_close_up.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/08_hex_01_insert_wells_dfield_wells.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+    </ul>
+    <a class="uk-position-center-left uk-position-small uk-hidden-hover" href="#" uk-slidenav-previous uk-slideshow-item="previous"></a>
+    <a class="uk-position-center-right uk-position-small uk-hidden-hover" href="#" uk-slidenav-next uk-slideshow-item="next"></a>
+</div>
+<!-- End image slideshow -->
+<br/>
+
+<h2 id="insert-well" class="uk-h3 uk-margin-remove">8. Insert Wells</h2>
+
+In this step, we will generate two cylindrical 'wells', refine the mesh
+`MONAME` around them, and identify a line of nodes that will be the well
+source/sink for boundary conditions (ultimately writing these nodes
+to `zone` files).
+
+### 8.1 Generating Cylindrical Tetrahedral Wells
+
+First, we define variables for the well's position (`XWELL`,`YWELL`), radius (`RADIUS_WELL`), and number of nodes across the cylindrical radius
+(`NRADIUS`):
+
+```
+define / XWELL1 / 1234.56
+define / YWELL1 / 1987.65
+
+define / XWELL2 / 2243.21
+define / YWELL2 / 1212.34
+
+define / RADIUS_WELL / 25.0
+define / NRADIUS / 2
+```
+
+Now, we create a cylindrical point cloud defining the first well using
+`createpts / rtz`:
+
+```
+cmo / create / mo_well1 / / / tet
+createpts / rtz / NRADIUS 9 NZ / 0. 0. 3100. / RADIUS_WELL 360. 1500. / 1 1 1
+```
+
+This creates a point cloud centered around (0,0,0) with a radius of `RADIUS_WELL`, an angular component spanning a full 360 degrees (`φ = {0., 360.}`), and a Z range of `{3100.,1500.}`.
+
+Run `filter`, `rmpoint / compress`, and set `imt` to 1 for the well:
+
+```
+filter / 1 0 0
+rmpoint / compress
+cmo / setatt / mo_well1 / imt / 1 0 0 / 1
+```
+
+Next, connect the point cloud into a tetrahedral mesh and translate the
+X and Y origin to `{XWELL1,YWELL1}`:
+
+```
+connect
+resetpts / itp
+cmo / printatt / mo_well1 / -xyz- / minmax
+trans / 1 0 0 / 0. 0. 0. / XWELL1 YWELL1 0.0
+cmo / printatt / mo_well1 / -xyz- / minmax
+```
+
+The first 'well' mesh object has been generated. Repeat this process with different parameters to create the second well:
+
+```
+cmo / create / mo_well2 / / / tet
+createpts / rtz / NRADIUS 9 NZ / 0. 0. 3100. / RADIUS_WELL 360. 2200. / 1 1 1
+filter / 1 0 0
+rmpoint / compress
+cmo / setatt / mo_well1 / imt / 1 0 0 / 1
+connect
+resetpts / itp
+cmo / printatt / mo_well2 / -xyz- / minmax
+trans / 1 0 0 / 0. 0. 0. / XWELL2 YWELL2 0.0
+cmo / printatt / mo_well2 / -xyz- / minmax
+```
+
+Finally, join the two distinct wells into a single mesh object with `addmesh / merge`:
+
+```
+addmesh / merge / mo_wells / mo_well1 mo_well2
+```
+
+### 8.2 Refining `MONAME` around the wells
+
+As we did for the fault in step 7, we refine the main mesh `MONAME` around the wells:
+
+```
+# First pass refinement
+cmo / select / MONAME
+intersect_elements / MONAME / mo_wells / if_inter
+eltset / e_refine / if_inter / gt / 0
+refine/ eltset / eltset get e_refine
+cmo / setatt / MONAME / if_inter / 1 0 0 / 0
+eltset / e_refine / delete
+
+# Second pass refinement
+cmo / select / MONAME
+intersect_elements / MONAME / mo_wells / if_inter
+eltset / e_refine / if_inter / gt / 0
+refine/ eltset / eltset get e_refine
+cmo / setatt / MONAME / if_inter / 1 0 0 / 0
+eltset / e_refine / delete
+
+# Third pass refinement
+cmo / select / MONAME
+intersect_elements / MONAME / mo_wells / if_inter
+eltset / e_refine / if_inter / gt / 0
+refine/ eltset / eltset get e_refine
+cmo / setatt / MONAME / if_inter / 1 0 0 / 0
+eltset / e_refine / delete
+```
+
+The refinement process returns a octree grid object, which stores information about parent-children relationships, among other properties. It's important, as the prepare to finalize the mesh for exporting, to strip this information and convert the octree grid object to a standard mesh object.
+
+This conversion is done through the `grid2grid / tree_to_fe` command:
+
+```
+grid2grid / tree_to_fe / mohex_octree /  mohex
+define / MONAME / mohex_octree
+```
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/08_hex_01_insert_wells_dfield_wells.png" | relative_url }}" data-caption="Node Euclidean distances to wells">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/08_hex_01_insert_wells_dfield_wells.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+### 8.3 Writing `zone` files based on well distances
+
+The `zone` files are lists of node numbers in [FEHM](https://fehm.lanl.gov) file format and used to identify materials, well source/sinks, and boundary conditions.
+
+In this subsection, we will generate `zone` files describing all nodes within 32, 16, 8, 4, 2 and 1 meters of the wells.
+
+To begin, we will compute the well point cloud again, as we did above. First, for well 1:
+
+```
+cmo / create / mo_pts1
+createpts / rtz / 2 2 1000 / 0. 0. 3100. / 0.0 360. 2200. / 1 1 1
+trans / 1 0 0 / 0. 0. 0. / XWELL1 YWELL1 0.0
+```
+
+Then for well 2:
+
+```
+cmo / create / mo_pts2
+createpts / rtz / 2 2 1000 / 0. 0. 3100. / 0.0 360. 2200. / 1 1 1
+trans / 1 0 0 / 0. 0. 0. / XWELL2 YWELL2 0.0
+```
+
+and joining them into a single mesh object, `mo_pts`:
+
+```
+addmesh / merge / mo_pts / mo_pts1 / mo_pts2
+cmo / select / mo_pts
+filter / 1 0 0
+rmpoint / compress
+```
+
+Next, we will compute a distance field attribute, `dfield_well`, which is a node-based attribute storing the Euclidean distance from `node_i` in one mesh to the closest node in another mesh. In other words, all nodes in `MONAME` store their distance to the closest well (`mo_pts`) node.
+
+```
+compute / distance_field / MONAME / mo_pts / dfield_well
+```
+
+Clean up unneeded mesh objects:
+
+```
+cmo / delete / mo_pts1
+cmo / delete / mo_pts2
+cmo / delete / mo_pts
+cmo / delete / mo_wells
+cmo / delete / mo_well1
+cmo / delete / mo_well2
+```
+
+And finally, for each mesh-to-well distance in {32,16,8,4,2,1} (which is stored in `dfield_well`), (i) create a pset object
+containing all nodes within that distance, and (ii) write those nodes to a `zone` file:
+
+```
+cmo / select / MONAME
+
+pset / pwell / attribute / dfield_well / 1 0 0 / le / 1.0
+pset / pwell / zone / zone_radius_01.0.zone
+
+pset / pwell / attribute / dfield_well / 1 0 0 / le / 2.0
+pset / pwell / zone / zone_radius_02.0.zone
+
+pset / pwell / attribute / dfield_well / 1 0 0 / le / 4.0
+pset / pwell / zone / zone_radius_04.0.zone
+
+pset / pwell / attribute / dfield_well / 1 0 0 / le / 8.0
+pset / pwell / zone / zone_radius_08.0.zone
+
+pset / pwell / attribute / dfield_well / 1 0 0 / le / 16.0
+pset / pwell / zone / zone_radius_16.0.zone
+
+pset / pwell / attribute / dfield_well / 1 0 0 / le / 32.0
+pset / pwell / zone / zone_radius_32.0.zone
+```
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class="uk-active"><a href="#insert-well">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_09.md

@@ -0,0 +1,130 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image slideshow -->
+<div class="uk-position-relative uk-visible-toggle uk-light" tabindex="-1" uk-slideshow>
+    <ul class="uk-slideshow-items">
+        <li>
+            <img data-src="{{ "/pages/tutorial/stratigraphy/images/19_hex_01_to_tet.png" | relative_url }}" width="1800" height="1200" alt="" uk-cover uk-img="target: !.uk-slideshow-items">
+        </li>
+    </ul>
+</div>
+<!-- End image slideshow -->
+<br/>
+
+<h2 id="convert-hex-mesh-to-tet" class="uk-h3 uk-margin-remove">9. Convert Hex Mesh to Tet</h2>
+
+In this final step, we will convert our mesh from hexahedral to tetrahedral
+elements.
+
+Create an empty mesh object, `motet`, and copy all nodes from `MONAME`
+(or, `mohex_octree`) to `motet`:
+
+```
+cmo / create / motet
+
+copypts / motet / mohex_octree
+```
+
+Next, reset the `imt` and `itp` variables and connect the nodes into
+tetrahedral elements:
+
+```
+cmo / setatt / motet / imt / 1 0 0 / 1
+cmo / setatt / motet / itp / 1 0 0 / 0
+connect
+resetpts / itp
+```
+
+Interpolate the node and cell 'colors' over the tetrahedral mesh, using
+`interpolate / voronoi` for node-to-node interpolations, and 
+`interpolate / map` for cell-to-cell interpolations:
+
+```
+interpolate / voronoi / motet / imt / 1 0 0 / mohex_octree / imt
+interpolate / map / motet / itetclr / 1 0 0 / mohex_octree / itetclr
+```
+
+Recall in step 5 that we set `imt` and `itetclr` to the value 7 for all
+nodes and elements that weren't captured by the surface-created element sets. 
+We can use the command `rmmat / 7` to remove all nodes and elements with
+`imt` and `itetclr` values of 7:
+
+```
+rmmat / 7
+rmpoint / compress
+resetpts / itp
+```
+
+Check the mesh that it has all positive element volumes and no bad aspect ratios.
+Use the `quality` command for a report on these mesh quantities.
+
+```
+quality
+
+epsilonl, epsilonaspect:   1.3230281E-09  2.3158330E-27                         
+--------------------------------------------                                    
+elements with aspect ratio < .01:                    0                          
+elements with aspect ratio b/w .01 and .02:          0                          
+elements with aspect ratio b/w .02 and .05:          0                          
+elements with aspect ratio b/w .05 and .1 :          0                          
+elements with aspect ratio b/w .1  and .2 :         18                          
+elements with aspect ratio b/w .2  and .5 :      20538                          
+elements with aspect ratio b/w .5  and 1. :     631394                          
+min aspect ratio =  0.1613E+00  max aspect ratio =  0.9377E+00                  
+ 
+epsilonvol:   8.8249408E-03                                                     
+---------------------------------------                                         
+element volumes b/w  0.2500E+03 and  0.8706E+03:     43109                      
+element volumes b/w  0.8706E+03 and  0.3031E+04:    273639                      
+element volumes b/w  0.3031E+04 and  0.1056E+05:     98379                      
+element volumes b/w  0.1056E+05 and  0.3676E+05:     63075                      
+element volumes b/w  0.3676E+05 and  0.1280E+06:    173748                      
+min volume =   2.5000000E+02  max volume =   1.2800000E+05                      
+-----------------------------------------------------------                     
+    651950 total elements evaluated.                                        
+```
+
+Finally, write the mesh object to AVS UCD file format and signal the EOF
+`finish` command:
+
+```
+dump/avs/tet_mesh.inp/motet                                                     
+
+finish
+```
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class="uk-active"><a href="#convert-hex-mesh-to-tet">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_10_exo.md

@@ -0,0 +1,154 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image -->
+<img data-src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_exo_blocks.png" | relative_url }}" width="639" height="525" alt="" uk-img>
+<br/>
+<!-- End image -->
+
+<h2 id="dump-exo" class="uk-h3 uk-margin-remove">10.2 Write ExodusII Files</h2>
+
+Write the tet mesh in Exodus II format. This format defines materials as blocks
+and is element based.
+The node properties will be ignored. The below image shows the Exodus mesh
+(read with GMV or ParaView) with material blocks shown in 'exploded' view.
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_exo_blocks_ex.png" | relative_url }}" data-caption="Exodus cells 'exploded' by material blocks">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_exo_blocks_ex.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+We can define the boundary faces for this mesh by extracting the 2D external
+surface and writing the element and face id for each. These can be written as
+sets based on element selection.
+
+In this example we use `settets/normal` to assign values 1-6 to the faces
+based on normal directions where `1=bot`, `2=top`, `3=right`, `4=back`, `5=left`,
+`6=front`. Define element sets for top, bottom, and lump sides
+all together for set 3. Write the faceset relation for each element set.
+
+```
+define / FILENAME / ss3_sides.faceset
+define / SS_ID / 3
+  cmo / copy / mo_tmp / mo_surf
+  cmo / select / mo_tmp
+  eltset / e_keep / itetclr / eq / SS_ID
+  eltset / e_delete / not / e_keep
+  rmpoint / element / eltset get e_delete
+  rmpoint / compress
+  dump / avs2 / FILENAME / mo_tmp / 0 0 0 2
+  cmo / delete / mo_tmp
+
+
+define / FILENAME / ss1_bottom.faceset
+define / SS_ID / 1
+  cmo / copy / mo_tmp / mo_surf
+  cmo / select / mo_tmp
+  eltset / e_keep / itetclr / eq / SS_ID
+  eltset / e_delete / not / e_keep
+  rmpoint / element / eltset get e_delete
+  rmpoint / compress
+  dump / avs2 / FILENAME / mo_tmp / 0 0 0 2
+  cmo / delete / mo_tmp
+
+
+define / FILENAME / ss2_top.faceset
+define / SS_ID / 2
+  cmo / copy / mo_tmp / mo_surf
+  cmo / select / mo_tmp
+  eltset / e_keep / itetclr / eq / SS_ID
+  eltset / e_delete / not / e_keep
+  rmpoint / element / eltset get e_delete
+  rmpoint / compress
+  dump / avs2 / FILENAME / mo_tmp / 0 0 0 2
+  cmo / delete / mo_tmp
+```
+
+Write the Exodus II mesh with the faceset files. This mesh and associated
+face sets can be viewed with GMV or ParaView.
+
+```
+dump/exo/ mesh_fs.exo / MO_MESH / / / facesets &
+    ss1_bottom.faceset, ss2_top.faceset,  ss3_sides.faceset
+```
+
+Check the summary report to see that mesh quantities are as expected.
+The report shows 6 element blocks (materials) and 3 side sets with appropriate face counts.
+
+```
+Title: LAGRIT TO EXODUSII                                                       
+number of dimension:               3                                            
+number of nodes:              115547                                            
+number of elements:           651950                                            
+number of edges:                   0                                            
+number of edge blocks:             0                                            
+number of element blocks:          6                                            
+number of face blocks:             0                                            
+number of node sets:               0                                            
+number of edge sets:               0                                            
+number of element sets:            0                                            
+number of side sets:               3                                            
+number of face sets:               0                                            
+number of node maps:               0                                            
+number of edge maps:               0                                            
+number of face maps:               0                                            
+number of element maps:            0                                            
+ 
+ 
+------------------------------------------                                      
+EXPSS loop:                                                                     
+        1 Side Set tag:             1 Faces:          4098                      
+        2 Side Set tag:             2 Faces:          4640                      
+        3 Side Set tag:             3 Faces:         11812                      
+------------------------------------------                                      
+Done ExodusII Side Sets Total:       3                                   
+```
+
+Image show the Exodus face sets (side sets) with bottom (blue), top (red), and sides (light blue).
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_exo_bndry_faces.png" | relative_url }}" data-caption="Exodus side sets: bottom (blue), top (red), and sides (light blue).">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_exo_bndry_faces.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_fehm.html" | relative_url }}">10.1 Write FEHM Files</a></li>
+            <li class="uk-active"><a href="#dump-exo">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>

docs/pages/tutorial/stratigraphy/step_10_fehm.md

@@ -0,0 +1,158 @@
+<!-- Begin breadcrumb -->
+<ul class="uk-breadcrumb">
+    <li><a href="{{ "/pages/tutorial/index.html" | relative_url }}">Tutorials &amp; Examples</a></li>
+    <li><span>Stratigraphic Hex Mesh Tutorial</span></li>
+</ul>
+<!-- End breadcrumb -->
+
+<!-- Begin image -->
+<img data-src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_voronoi.png" | relative_url }}" width="639" height="525" alt="" uk-img>
+<br/>
+<!-- End image -->
+
+<h2 id="dump-fehm" class="uk-h3 uk-margin-remove">10. Write FEHM Files</h2>
+
+Write out a series of files for the FEHM flow and transport code. 
+FEHM uses the control volume finite element method (CVFE) with node materials
+and properties assigned to the mesh nodes.
+
+The image shows the tetrahedral mesh colored by the 6 node `imt` (materials)
+values and showing the voronoi cell edges.
+
+These two close-up images show the relationship between the Delaunay tet mesh
+edges and the voronoi volumes, the latter of which are used by FEHM.
+The mesh nodes are the vertices of the tetrahedral elements and are the center
+of each voronoi volume.
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_tet_a.png" | relative_url }}" data-caption="Close-up view of mesh with Delaunay tetrahedral cells">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_tet_a.png" | relative_url }}" alt="">
+        </a>
+    </div>
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_vor_a.png" | relative_url }}" data-caption="Close-up view of mesh with Voronoi cells">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_vor_a.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+We prepare the tet mesh for FEHM with the following commands. These ensure
+that there are no duplicate nodes and sets the elements to a single material.
+We also make sure nodes are not doubly defined and parent-child chains are
+removed.
+
+```
+cmo/select/motet                                                               
+resetpts/parent                                                                 
+filter/1,0,0     
+rmpoint/compress
+```
+
+LaGriT can write a full set of FEHM model files with a single command.
+The `keepatt` option will save attributes tagging nodes on the outside boundaries.
+These can be used to define additional point sets and zones for FEHM.
+
+The following files are written:
+
+* `.fehm` - mesh coordinates and geometry 
+* `_material.zone` - node imt (material) zone lists 
+* `_outside.zone` - node external boundary zone lists 
+* `_outside_vor.area` - node external boundary area lists 
+* `_interface.zone` - zone lists for nodes along material interfaces
+* `_multi_mat.zone` - lists of node pairs connected across material interfaces
+* `.stor` - FEHM format file giving the voronoi (control volume) associated with each node and the sparce matrix structure
+
+```
+dump / fehm / mesh / motet / keepatt
+```
+
+Review the report written to the screen and the output file (`lagrit.out`) for
+mesh quantities.
+These are usful summaries and will help in finding problems in the mesh design.
+Check that material node counts are as expected.
+
+```
+*** Write FEHMN GEOM AND ZONE FILES ***                                         
+*********dump_material_lists********                                            
+Minimum material ID value =      1                                              
+Maximum material ID value =      6                                              
+Total possible materials  =      6                                              
+Material           1 has     23944 nodes. #nodes/nnodes is   0.207223027945     
+Material           2 has      6867 nodes. #nodes/nnodes is   0.594303607941E-01 
+Material           3 has     16072 nodes. #nodes/nnodes is   0.139094918966     
+Material           4 has     33192 nodes. #nodes/nnodes is   0.287259727716     
+Material           5 has     12871 nodes. #nodes/nnodes is   0.111391901970     
+Material           6 has     22601 nodes. #nodes/nnodes is   0.195600062609   
+```
+
+Check that the Sparse Matrix volumes are positive.
+Negative coefficient values can result from poorly formed tetrahedra.
+These usually occur on non-convex boundaries.
+FEHM will still run but accuracy may be impacted.
+
+```
+*** Construct and Compress Sparse Matrix:3D ***                                 
+   *** Compress Area Coefficient Values ***                                     
+ 
+AMatbld3d_stor: Matrix compress_eps:  0.1000000E-07                             
+AMatbld3d_stor: Local epsilon:  0.1000000E-14                                   
+AMatbld3d_stor: *****Zero Negative Coefficients ******                          
+AMatbld3d_stor: Number of 'zero' (< compress_eps) coefs         0               
+AMatbld3d_stor: npoints =   115547  ncoefs =     964637                         
+AMatbld3d_stor: Number of unique coefs =       313                              
+AMatbld3d_stor: Maximum num. connections to a node =         25                 
+AMatbld3d_stor: Volume min =   7.4999999E+02                                    
+AMatbld3d_stor: Volume max =   7.6800000E+05                                    
+AMatbld3d_stor: Total Volume:   2.3846400E+10                                   
+AMatbld3d_stor: abs(Aij/xij) min =   0.0000000E+00                              
+AMatbld3d_stor: abs(Aij/xij) max =   1.3500000E+02                              
+AMatbld3d_stor: (Aij/xij) max =   0.0000000E+00                                 
+AMatbld3d_stor: (Aij/xij) min =  -1.3500000E+02                                 
+AMatbld3d_stor Matrix coefficient values stored as scalar area/distance         
+AMatbld3d_stor Matrix compression used for graph and coefficient values         
+ascii STOR file written with name mesh.stor   
+```                            
+
+Visually inspect the mesh for the assignment of boundary zones such as top nodes.
+
+<!-- Lightbox -->
+<div class="uk-child-width-1-2@m" uk-grid uk-lightbox="animation: slide">
+    <div>
+        <a class="uk-inline" href="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_node_zone_top.png" | relative_url }}" data-caption="GMV visualization of mesh nodes, with top nodes colored red">
+            <img src="{{ "/pages/tutorial/stratigraphy/images/21_tet_01_fehm_node_zone_top.png" | relative_url }}" alt="">
+        </a>
+    </div>
+</div>
+
+<!-- Next / Prev -->
+<ul class="uk-pagination">
+    <li><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}"><span class="uk-margin-small-right" uk-pagination-previous></span> Previous</a></li>
+    <li class="uk-margin-auto-left"><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">Next <span class="uk-margin-small-left" uk-pagination-next></span></a></li>
+</ul>
+
+<!-- Sidebar -->
+<div class="tm-sidebar-right uk-visible@l">
+    <div uk-sticky="offset: 160" class="uk-sticky uk-active uk-sticky-fixed" style="position: fixed; top: 160px; width: 200px;">
+        <ul uk-scrollspy-nav="closest: li; scroll: true; offset: 100" class="uk-nav uk-nav-default tm-nav uk-nav-parent-icon">
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/index.html" | relative_url }}">Index</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_01.html" | relative_url }}">1. Building a Hex Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_02.html" | relative_url }}">2. Define Boundaries Using Point Sets</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_03.html" | relative_url }}">3. Constructing Stratigraphy</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_04.html" | relative_url }}">4. Map Surfaces to Mesh</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_05.html" | relative_url }}">5. Constructing a Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_06.html" | relative_url }}">6. Truncate with Polyline</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_07.html" | relative_url }}">7. Refine Fault</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_08.html" | relative_url }}">8. Insert Wells</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_09.html" | relative_url }}">9. Convert Hex Mesh to Tet</a></li>
+            <li class="uk-active"><a href="#dump-fehm">10.1 Write FEHM Files</a></li>
+            <li class=""><a href="{{ "/pages/tutorial/stratigraphy/step_10_exo.html" | relative_url }}">10.2 Write ExodusII Files</a></li>
+            <li class="uk-nav-divider"></li>
+            <!---->
+            <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>
+            <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>
+            <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>
+        </ul>
+    </div>
+</div>