docs(docs): updated docs for version v0.2.0

Doxyfile

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 <code>#include &lt;iostream&gt;</code><br />
 <code>#include &lt;memory&gt;</code><br />
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 Configuration File</h2>
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 <div class="fragment"><div class="line">[main]</div>
-<div class="line">core_steepness = 1.0</div>
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+<div class="line">r_star = 5.0</div>
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 <div class="line">r_instability = 1e-14</div>
-<div class="line">r_star = 5.0</div>
+<div class="line">core_steepness = 1.0</div>
-<div class="line">refinement_levels = 4</div>
+<div class="line">surface_bdr_id = 1</div>
+<div class="line">inf_bdr_id = 2</div>
+<div class="line">core_id = 1</div>
+<div class="line">envelope_id = 2</div>
+<div class="line">vacuum_id = 3</div>
 </div><!-- fragment --><table class="markdownTable">
 <tr class="markdownTableHead">
 <th class="markdownTableHeadNone">Parameter   </th><th class="markdownTableHeadNone">Description   </th><th class="markdownTableHeadNone">Default    </th></tr>
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 <tr class="markdownTableRowOdd">
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+<td class="markdownTableBodyNone">include_external_domain   </td><td class="markdownTableBodyNone">Whether to include an external domain extending to r_infinity   </td><td class="markdownTableBodyNone">true    </td></tr>
 <tr class="markdownTableRowEven">
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@@ -179,7 +184,17 @@ Configuration File</h2>
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+<td class="markdownTableBodyNone">core_steepness   </td><td class="markdownTableBodyNone">The steepness of the transition between the core and envelope regions of the star   </td><td class="markdownTableBodyNone">1.0    </td></tr>
+<tr class="markdownTableRowEven">
+<td class="markdownTableBodyNone">surface_bdr_id   </td><td class="markdownTableBodyNone">The boundary ID to assign to the surface of the star   </td><td class="markdownTableBodyNone">1    </td></tr>
+<tr class="markdownTableRowOdd">
+<td class="markdownTableBodyNone">inf_bdr_id   </td><td class="markdownTableBodyNone">The boundary ID to assign to the outer boundary of the external domain (if included)   </td><td class="markdownTableBodyNone">2    </td></tr>
+<tr class="markdownTableRowEven">
+<td class="markdownTableBodyNone">core_id   </td><td class="markdownTableBodyNone">The material ID to assign to the core region of the star   </td><td class="markdownTableBodyNone">1    </td></tr>
+<tr class="markdownTableRowOdd">
+<td class="markdownTableBodyNone">envelope_id   </td><td class="markdownTableBodyNone">The material ID to assign to the envelope region of the star   </td><td class="markdownTableBodyNone">2    </td></tr>
+<tr class="markdownTableRowEven">
+<td class="markdownTableBodyNone">vacuum_id   </td><td class="markdownTableBodyNone">The material ID to assign to the vacuum region of the star (if included)   </td><td class="markdownTableBodyNone">3   </td></tr>
 </table>
 <p>If no configuration file is provided, stroid will use the default parameters listed above. Further, configuration files need only include parameters that differ from the defaults, any parameters not specified will use the default values.</p>
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+<tr class="memdesc:affad4638b0ae7b710f2b2db992f6f584"><td class="mdescLeft">&#160;</td><td class="mdescRight">Flattening factor for spheroidal shaping (0 = spherical, &gt;0 = oblate).  <br /></td></tr>
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+<tr class="memdesc:ac7546899ebbfe191ea3a8bf2403b31eb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Outer radius of the external domain when enabled.  <br /></td></tr>
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+<tr class="memdesc:a4da6d99ff7ba24d2f917e1fd98ddd877"><td class="mdescLeft">&#160;</td><td class="mdescRight">Radius inside which transformations are skipped to avoid singularities.  <br /></td></tr>
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+<tr class="memdesc:aed32864839b149c94842801b6413d94d"><td class="mdescLeft">&#160;</td><td class="mdescRight">Controls the smoothness/steepness of the core-to-envelope transition.  <br /></td></tr>
 <tr class="separator:aed32864839b149c94842801b6413d94d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a33f25ff277aa8834065e04ccb9cdbdda" id="r_a33f25ff277aa8834065e04ccb9cdbdda"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a33f25ff277aa8834065e04ccb9cdbdda">surface_bdr_id</a> = 1</td></tr>
+<tr class="memdesc:a33f25ff277aa8834065e04ccb9cdbdda"><td class="mdescLeft">&#160;</td><td class="mdescRight">Boundary attribute id for stellar surface.  <br /></td></tr>
+<tr class="separator:a33f25ff277aa8834065e04ccb9cdbdda"><td class="memSeparator" colspan="2">&#160;</td></tr>
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+<tr class="memdesc:a64cb00c8cba27267279a52207a4b5be0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Boundary attribute id for infinity in kelvin mapping.  <br /></td></tr>
+<tr class="separator:a64cb00c8cba27267279a52207a4b5be0"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a2faa5aa1fef84ebbda30590d3fb2799b" id="r_a2faa5aa1fef84ebbda30590d3fb2799b"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a2faa5aa1fef84ebbda30590d3fb2799b">core_id</a> = 1</td></tr>
+<tr class="memdesc:a2faa5aa1fef84ebbda30590d3fb2799b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Material attribute id for the core region.  <br /></td></tr>
+<tr class="separator:a2faa5aa1fef84ebbda30590d3fb2799b"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ac99aa48fe3e71e2ef57b09d48cacfef8" id="r_ac99aa48fe3e71e2ef57b09d48cacfef8"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#ac99aa48fe3e71e2ef57b09d48cacfef8">envelope_id</a> = 2</td></tr>
+<tr class="memdesc:ac99aa48fe3e71e2ef57b09d48cacfef8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Material attribute id for the envelope region.  <br /></td></tr>
+<tr class="separator:ac99aa48fe3e71e2ef57b09d48cacfef8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a36c7b05405691393d381086a27ea36ad" id="r_a36c7b05405691393d381086a27ea36ad"><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a36c7b05405691393d381086a27ea36ad">vacuum_id</a> = 3</td></tr>
+<tr class="memdesc:a36c7b05405691393d381086a27ea36ad"><td class="mdescLeft">&#160;</td><td class="mdescRight">Material attribute id for the external domain (if enabled)  <br /></td></tr>
+<tr class="separator:a36c7b05405691393d381086a27ea36ad"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Configuration parameters for stroid mesh generation. </p>
 <p>These values are typically loaded via <code>fourdst::config::Config&lt;<a class="el" href="structstroid_1_1config_1_1_mesh_config.html" title="Configuration parameters for stroid mesh generation.">stroid::config::MeshConfig</a>&gt;</code> from a TOML file. The README shows the expected TOML layout under the <code>[main]</code> table. Unspecified keys use the defaults defined here. </p>
 </div><h2 class="groupheader">Member Data Documentation</h2>
+<a id="a2faa5aa1fef84ebbda30590d3fb2799b" name="a2faa5aa1fef84ebbda30590d3fb2799b"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a2faa5aa1fef84ebbda30590d3fb2799b">&#9670;&#160;</a></span>core_id</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t stroid::config::MeshConfig::core_id = 1</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Material attribute id for the core region. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].core_id </li>
+</ul>
+
+</div>
+</div>
 <a id="aed32864839b149c94842801b6413d94d" name="aed32864839b149c94842801b6413d94d"></a>
 <h2 class="memtitle"><span class="permalink"><a href="#aed32864839b149c94842801b6413d94d">&#9670;&#160;</a></span>core_steepness</h2>
 
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       </table>
 </div><div class="memdoc">
 
-<p>Controls the smoothness/steepness of the core-to-envelope transition. @toml [main].core_steepness. </p>
+<p>Controls the smoothness/steepness of the core-to-envelope transition. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].core_steepness </li>
+</ul>
+
+</div>
+</div>
+<a id="ac99aa48fe3e71e2ef57b09d48cacfef8" name="ac99aa48fe3e71e2ef57b09d48cacfef8"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ac99aa48fe3e71e2ef57b09d48cacfef8">&#9670;&#160;</a></span>envelope_id</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t stroid::config::MeshConfig::envelope_id = 2</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Material attribute id for the envelope region. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].envelope_id </li>
+</ul>
 
 </div>
 </div>
@@ -175,7 +237,12 @@ Public Attributes</h2></td></tr>
       </table>
 </div><div class="memdoc">
 
-<p>Flattening factor for spheroidal shaping (0 = spherical, &gt;0 = oblate). @toml [main].flattening. </p>
+<p>Flattening factor for spheroidal shaping (0 = spherical, &gt;0 = oblate). </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].flattening </li>
+</ul>
 
 </div>
 </div>
@@ -186,13 +253,38 @@ Public Attributes</h2></td></tr>
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">bool stroid::config::MeshConfig::include_external_domain = false</td>
+          <td class="memname">bool stroid::config::MeshConfig::include_external_domain = true</td>
         </tr>
       </table>
 </div><div class="memdoc">
 
 <p>Whether to include an external domain extending to <code>r_infinity</code>. </p>
-<p>Currently this flag does not affect mesh generation. @toml [main].include_external_domain </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].include_external_domain </li>
+</ul>
+
+</div>
+</div>
+<a id="a64cb00c8cba27267279a52207a4b5be0" name="a64cb00c8cba27267279a52207a4b5be0"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a64cb00c8cba27267279a52207a4b5be0">&#9670;&#160;</a></span>inf_bdr_id</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t stroid::config::MeshConfig::inf_bdr_id = 2</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Boundary attribute id for infinity in kelvin mapping. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].inf_bdr_id </li>
+</ul>
 
 </div>
 </div>
@@ -208,7 +300,12 @@ Public Attributes</h2></td></tr>
       </table>
 </div><div class="memdoc">
 
-<p>Polynomial order for high-order elements. @toml [main].order. </p>
+<p>Polynomial order for high-order elements. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].order </li>
+</ul>
 
 </div>
 </div>
@@ -224,7 +321,12 @@ Public Attributes</h2></td></tr>
       </table>
 </div><div class="memdoc">
 
-<p>Radius of the stellar core region. @toml [main].r_core. </p>
+<p>Radius of the stellar core region. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].r_core </li>
+</ul>
 
 </div>
 </div>
@@ -240,7 +342,12 @@ Public Attributes</h2></td></tr>
       </table>
 </div><div class="memdoc">
 
-<p>Outer radius of the external domain when enabled. @toml [main].r_infinity. </p>
+<p>Outer radius of the external domain when enabled. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].r_infinity </li>
+</ul>
 
 </div>
 </div>
@@ -256,7 +363,12 @@ Public Attributes</h2></td></tr>
       </table>
 </div><div class="memdoc">
 
-<p>Radius inside which transformations are skipped to avoid singularities. @toml [main].r_instability. </p>
+<p>Radius inside which transformations are skipped to avoid singularities. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].r_instability </li>
+</ul>
 
 </div>
 </div>
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       </table>
 </div><div class="memdoc">
 
-<p>Radius of the stellar surface. @toml [main].r_star. </p>
+<p>Radius of the stellar surface. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].r_star </li>
+</ul>
 
 </div>
 </div>
@@ -288,7 +405,54 @@ Public Attributes</h2></td></tr>
       </table>
 </div><div class="memdoc">
 
-<p>Number of uniform refinement passes applied after topology creation. @toml [main].refinement_levels. </p>
+<p>Number of uniform refinement passes applied after topology creation. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].refinement_levels </li>
+</ul>
+
+</div>
+</div>
+<a id="a33f25ff277aa8834065e04ccb9cdbdda" name="a33f25ff277aa8834065e04ccb9cdbdda"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a33f25ff277aa8834065e04ccb9cdbdda">&#9670;&#160;</a></span>surface_bdr_id</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t stroid::config::MeshConfig::surface_bdr_id = 1</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Boundary attribute id for stellar surface. </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].surface_bdr_id </li>
+</ul>
+
+</div>
+</div>
+<a id="a36c7b05405691393d381086a27ea36ad" name="a36c7b05405691393d381086a27ea36ad"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a36c7b05405691393d381086a27ea36ad">&#9670;&#160;</a></span>vacuum_id</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">size_t stroid::config::MeshConfig::vacuum_id = 3</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Material attribute id for the external domain (if enabled) </p>
+<h1><a class="anchor" id="toml"></a>
+toml</h1>
+<ul>
+<li>[main].vacuum_id </li>
+</ul>
 
 </div>
 </div>

docs/html/structstroid_1_1config_1_1_mesh_config.js

@@ -1,12 +1,17 @@
 var structstroid_1_1config_1_1_mesh_config =
 [
+    [ "core_id", "structstroid_1_1config_1_1_mesh_config.html#a2faa5aa1fef84ebbda30590d3fb2799b", null ],
     [ "core_steepness", "structstroid_1_1config_1_1_mesh_config.html#aed32864839b149c94842801b6413d94d", null ],
+    [ "envelope_id", "structstroid_1_1config_1_1_mesh_config.html#ac99aa48fe3e71e2ef57b09d48cacfef8", null ],
     [ "flattening", "structstroid_1_1config_1_1_mesh_config.html#affad4638b0ae7b710f2b2db992f6f584", null ],
     [ "include_external_domain", "structstroid_1_1config_1_1_mesh_config.html#a062652781f4f3ea0b7ca8764362a7368", null ],
+    [ "inf_bdr_id", "structstroid_1_1config_1_1_mesh_config.html#a64cb00c8cba27267279a52207a4b5be0", null ],
     [ "order", "structstroid_1_1config_1_1_mesh_config.html#a860e78f1906acb0c3aa08d55f94de3fd", null ],
     [ "r_core", "structstroid_1_1config_1_1_mesh_config.html#a5c68a895f73dc82a38a8daac22a83ad7", null ],
     [ "r_infinity", "structstroid_1_1config_1_1_mesh_config.html#ac7546899ebbfe191ea3a8bf2403b31eb", null ],
     [ "r_instability", "structstroid_1_1config_1_1_mesh_config.html#a4da6d99ff7ba24d2f917e1fd98ddd877", null ],
     [ "r_star", "structstroid_1_1config_1_1_mesh_config.html#a3fe80a30990d484dcc39b6f9a0befc05", null ],
-    [ "refinement_levels", "structstroid_1_1config_1_1_mesh_config.html#a8cafcbebf64ae251517118eb152de981", null ]
+    [ "refinement_levels", "structstroid_1_1config_1_1_mesh_config.html#a8cafcbebf64ae251517118eb152de981", null ],
+    [ "surface_bdr_id", "structstroid_1_1config_1_1_mesh_config.html#a33f25ff277aa8834065e04ccb9cdbdda", null ],
+    [ "vacuum_id", "structstroid_1_1config_1_1_mesh_config.html#a36c7b05405691393d381086a27ea36ad", null ]
 ];

docs/html/topology_8cpp.html

@@ -31,7 +31,7 @@
  <tr id="projectrow">
   <td id="projectlogo"><img alt="Logo" src="Logo.png"/></td>
   <td id="projectalign">
-   <div id="projectname">stroid<span id="projectnumber">&#160;v0.1.0</span>
+   <div id="projectname">stroid<span id="projectnumber">&#160;v0.2.0</span>
    </div>
    <div id="projectbrief">Multi-block curvilinear mesh generation</div>
   </td>

docs/html/topology_8h.html

@@ -31,7 +31,7 @@
  <tr id="projectrow">
   <td id="projectlogo"><img alt="Logo" src="Logo.png"/></td>
   <td id="projectalign">
-   <div id="projectname">stroid<span id="projectnumber">&#160;v0.1.0</span>
+   <div id="projectname">stroid<span id="projectnumber">&#160;v0.2.0</span>
    </div>
    <div id="projectbrief">Multi-block curvilinear mesh generation</div>
   </td>

docs/static/mainpage.md

@@ -77,15 +77,20 @@ file is found below
 
 ```toml
 [main]
-core_steepness = 1.0
+refinement_levels = 2
-flattening = 0.0
-include_external_domain = false
 order = 3
+include_external_domain = true
 r_core = 1.5
+r_star = 5.0
+flattening = 0.08
 r_infinity = 6.0
 r_instability = 1e-14
-r_star = 5.0
+core_steepness = 1.0
-refinement_levels = 4
+surface_bdr_id = 1
+inf_bdr_id = 2
+core_id = 1
+envelope_id = 2
+vacuum_id = 3
 ```
 
 <!-- Table of what these parameters do -->
@@ -93,13 +98,18 @@ refinement_levels = 4
 |-------------------------|-----------------------------------------------------------------------------------------------------|---------|
 | refinement_levels       | Number of uniform refinement levels to apply to the mesh after generation                           | 4       |
 | order                   | The polynomial order of the finite elements in the mesh                                             | 3       |
-| include_external_domain | Whether to include an external domain extending to r_infinity                                       | false   |
+| include_external_domain | Whether to include an external domain extending to r_infinity                                       | true    |
 | r_core                  | The radius of the core region of the star                                                           | 1.5     |
 | r_star                  | The radius of the star                                                                              | 5.0     |
 | flattening              | The flattening factor of the star (0 for spherical, >0 for oblate)                                  | 0       |
 | r_infinity              | The outer radius of the external domain (if included)                                               | 6.0     |
 | r_instability           | The radius at which no transformations are applied to the initial topology (to avoid singularities) | 1e-14   |
 | core_steepness          | The steepness of the transition between the core and envelope regions of the star                   | 1.0     |
+| surface_bdr_id          | The boundary ID to assign to the surface of the star                                                | 1       |
+| inf_bdr_id              | The boundary ID to assign to the outer boundary of the external domain (if included)                | 2       |
+| core_id                 | The material ID to assign to the core region of the star                                            | 1       |
+| envelope_id             | The material ID to assign to the envelope region of the star                                        | 2       |
+| vacuum_id               | The material ID to assign to the vacuum region of the star (if included)                            | 3       |
 
 
 If no configuration file is provided, stroid will use the default parameters listed above. Further, configuration files

readme.md

@@ -78,15 +78,20 @@ file is found below
 
 ```toml
 [main]
-core_steepness = 1.0
+refinement_levels = 2
-flattening = 0.0
-include_external_domain = false
 order = 3
+include_external_domain = true
 r_core = 1.5
+r_star = 5.0
+flattening = 0.08
 r_infinity = 6.0
 r_instability = 1e-14
-r_star = 5.0
+core_steepness = 1.0
-refinement_levels = 4
+surface_bdr_id = 1
+inf_bdr_id = 2
+core_id = 1
+envelope_id = 2
+vacuum_id = 3
 ```
 
 <!-- Table of what these parameters do -->
@@ -94,13 +99,18 @@ refinement_levels = 4
 |-------------------------|-----------------------------------------------------------------------------------------------------|---------|
 | refinement_levels       | Number of uniform refinement levels to apply to the mesh after generation                           | 4       |
 | order                   | The polynomial order of the finite elements in the mesh                                             | 3       |
-| include_external_domain | Whether to include an external domain extending to r_infinity                                       | false   |
+| include_external_domain | Whether to include an external domain extending to r_infinity                                       | true    |
 | r_core                  | The radius of the core region of the star                                                           | 1.5     |
 | r_star                  | The radius of the star                                                                              | 5.0     |
 | flattening              | The flattening factor of the star (0 for spherical, >0 for oblate)                                  | 0       |
 | r_infinity              | The outer radius of the external domain (if included)                                               | 6.0     |
 | r_instability           | The radius at which no transformations are applied to the initial topology (to avoid singularities) | 1e-14   |
 | core_steepness          | The steepness of the transition between the core and envelope regions of the star                   | 1.0     |
+| surface_bdr_id          | The boundary ID to assign to the surface of the star                                                | 1       |
+| inf_bdr_id              | The boundary ID to assign to the outer boundary of the external domain (if included)                | 2       |
+| core_id                 | The material ID to assign to the core region of the star                                            | 1       |
+| envelope_id             | The material ID to assign to the envelope region of the star                                        | 2       |
+| vacuum_id               | The material ID to assign to the vacuum region of the star (if included)                            | 3       |
 
 
 If no configuration file is provided, stroid will use the default parameters listed above. Further, configuration files