Update mesh paramters and add a bit more detail to data file formats.

Author: ktbolt

documentation/multi_physics/data-file-formats/data_file_formats_fiber_direction/readme.md

@@ -3,7 +3,7 @@
 A fiber and sheet direction data file is used to define a local orthonormal coordinate system 
 for each element in a finite element volume mesh representing cardiac muscle.
 The data file is a <a href="#appendix_vtk_file_format"> VTK VTU </a> format file containing a CellData 
-array named </strong>FIB_DIR</strong>.
+array of three-component vecors named <strong>FIB_DIR</strong>.
 
 The data file is set using the solver input file 
 <a href="#mesh_params_Fiber_direction_file_path"> Fiber_direction_file_path </a> keyword.

documentation/multi_physics/data-file-formats/data_file_formats_initial_condition/readme.md

@@ -1,14 +1,16 @@
 
 <h2 id="data_file_formats_initial_condition"> Initial Condition Data</h2>
-The data file is used to initialize values on a finite element volume mesh. It is a 
+Initial condition data for a finite element volume mesh can be initialized from values contained in a 
 <a href="#appendix_vtk_file_format"> VTK VTU </a> format file containing PointData arrays.
 
-<h3> Velocity and Pressue Data</h3>
-Velocity and pressure data is initialized using <a href="#appendix_vtk_file_format"> VTK VTU </a> 
-format file containing PointData arrays named <strong>Velocity</strong> and <strong>Pressure</strong>.
+<h3> Displacement, Pressure, Stress, and Velocity Data</h3>
+Displacement, pressure, stress, and velocity data can be initialized using <a href="#appendix_vtk_file_format"> VTK VTU </a> 
+format file containing PointData arrays named <strong>Displacement</strong>, <strong>Pressure</strong>, <strong>Stress</strong>, and <strong>Velocity</strong>. 
 
 The data files are set using the solver input file 
-<a href="#bc_mesh_params_Initial_pressures_file_path"> Initial_pressures_file_path</a> and 
+<a href="#mesh_params_Initial_displacements_file_path"> Initial_displacements_file_path</a>, 
+<a href="#mesh_params_Initial_pressures_file_path"> Initial_pressures_file_path</a> and 
+<a href="#mesh_params_Prestress_file_path"> Prestress_file_path </a> and 
 <a href="#mesh_params_Initial_velocities_file_path"> Initial_velocities_file_path</a> keywords.
 
 <h3> State Variables </h3>

documentation/multi_physics/solver-input-file/mesh_parameters/readme.md

@@ -28,7 +28,9 @@ A <i>Mesh Section</i> is organized as follows
 &lt;<strong>Add_face</strong>&gt; 
 <br>
 
-[Mesh Parameters]
+<a href="#mesh_parameters">
+
+[<a href="#mesh_parameters"> Mesh Parameters </a> ]
 
 &lt;<strong>/Add_mesh</strong> &gt;
 </div>
@@ -73,40 +75,42 @@ The value used to scale mesh nodal coordinates.
 <strong>&lt;Initial_pressures_file_path&gt;</strong> <i>string [none] </i> <nobr>
 <strong>&lt;/Initial_pressures_file_path&gt;</strong>
 </nobr><br>
-The name of the file used to 
+The name of the VTK VTU file used to initialize simulation pressure values on a fluid domain. See <a href="#data_file_formats_initial_condition"> Initial Condition Data</a>.
 <br>
 <section id="mesh_params_Initial_velocities_file_path">
 <strong>&lt;Initial_velocities_file_path&gt;</strong> <i>string [none] </i> <nobr>
 <strong>&lt;/Initial_velocities_file_path&gt;</strong>
 </nobr><br>
-The name of the file used to 
+The name of the VTK VTU file used to initialize simulation velocity values on a fluid domain. See <a href="#data_file_formats_initial_condition"> Initial Condition Data</a>.
 <br>
 <section id="mesh_params_Initial_displacements_file_path">
 <strong>&lt;Initial_displacements_file_path&gt;</strong> <i>string [none] </i> <nobr>
 <strong>&lt;/Initial_displacements_file_path&gt;</strong>
 </nobr><br>
-The name of the file used to 
+The name of the VTK VTU file used to initialize simulation displacement values on a solid domain. See <a href="#data_file_formats_initial_condition"> Initial Condition Data</a>.
 <br>
+<section id="mesh_params_Prestress_file_path">
 <strong>&lt;Prestress_file_path&gt;</strong> <i>string [none] </i> <nobr>
 <strong>&lt;/Prestress_file_path&gt;</strong>
 </nobr><br>
-The name of the file used to 
+The name of the VTK VTU file used to initialize simulation stress values on a solid domain. See <a href="#data_file_formats_initial_condition"> Initial Condition Data</a>.
 <br>
 <section id="mesh_params_Fiber_direction_file_path">
 <strong>&lt;Fiber_direction_file_path&gt;</strong> <i>string [none] </i> <nobr>
 <strong>&lt;/Fiber_direction_file_path&gt;</strong>
 </nobr><br>
-The name of the file used to 
+The name of the VTK VTU file used to define the fiber directions for a solid domain. See <a href="#data_file_formats_fiber_direction"> Fiber and Sheet Direction Data</a>.
 <br>
 <strong>&lt;Set_mesh_as_fibers&gt;</strong> <i>boolean [false] </i> <nobr>
 <strong>&lt;/Set_mesh_as_fibers&gt;</strong>
 </nobr><br>
-The name of the file used to 
+If <i>true</i> then the mesh given in the <strong>Mesh_file_path</strong> keywork is treated as a mesh of one-dimensional elements in 3D.
+The mesh typically defines a network of Purkinje fibers used in cardiac electrophysiology simulations.
 <br>
 <strong>&lt;Set_mesh_as_shell&gt;</strong> <i>boolean [false] </i> <nobr>
 <strong>&lt;/Set_mesh_as_shell&gt;</strong>
 </nobr><br>
-The name of the file used to 
+If <i>true</i> then the mesh given in the <strong>Mesh_file_path</strong> keywork is treated as a mesh of shell elements. The mesh can then be used for solving the <strong>shell</strong> equation type. A shell mesh is also needed for initializing a <strong>CMM</strong> equation using a prestress or displacements.
 <br>
 </div>
 

documentation/multi_physics/solver-input-file/readme.md

@@ -20,7 +20,7 @@ There are two types of tag
 An XML element is everything from (including) the element's start tag to (including) the element's end tag. 
 
 <pre>
-&lt;Tolerance> 0.001 &lt;/Tolerance>;
+&lt;Tolerance> 0.001 &lt;/Tolerance>
 </pre>
 
 There are three types of elements