Merge pull request #40 from ktbolt/add-missing-solver-input-file-descriptions_39

Add missing solver input file descriptions 39

Author: ktbolt

documentation/multi_physics.html

@@ -189,6 +189,8 @@ <h4 class="skipTo solver-input-file"> Solver Input File </h4>
           <div>
             <p class="skipTo general_parameters "> General Simulation Parameters </p>
             <p class="skipTo mesh_parameters "> Mesh Section </p>
+            <p class="skipTo contact_section"> Contact Section </p>
+            <p class="skipTo precomputed_solution_section"> Precomputed Solution Section </p>
             <p class="skipTo projection_section"> Projection Section </p>
             <p class="skipTo equation_section"> Equation Section </p>
             <div>
@@ -357,6 +359,14 @@ <h4 class="skipTo appendix"> Appendix </h4>
         <zero-md src="multi_physics/solver-input-file/mesh_parameters/readme.md" no-shadow></zero-md>
       </span>
 
+      <span id="contact_section">
+        <zero-md src="multi_physics/solver-input-file/contact_parameters/readme.md" no-shadow></zero-md>
+      </span>
+
+      <span id="precomputed_solution_section">
+        <zero-md src="multi_physics/solver-input-file/precomputed_solution_parameters/readme.md" no-shadow></zero-md>
+      </span>
+
       <span id="projection_section">
         <zero-md src="multi_physics/solver-input-file/projection_parameters/readme.md" no-shadow></zero-md>
       </span>

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/boundary_condition_parameters/readme.md

@@ -78,6 +78,17 @@ in a text file.
 </nobr><br>
 Load a file used to set the spatial and temporal values for a boundary condition. The file can be a VTK VTP-format file or a text file. 
 <br>
+<strong>&lt;CST_shell_bc_type&gt;</strong> <i>string</i> [<i>none</i>]  <nobr> 
+<strong>&lt;/CST_shell_bc_type&gt;</strong>
+</nobr><br>
+Constrain the degrees of freedom of a Constant Strain Triangle (CST) of a triangular shell element. 
+condition. Permissible values are:
+<ul style="list-style-type:disc;">
+  <li> fixed - Fix the edge </li>
+  <li> hinged - Allow rotation about an edge </li>
+  <li> free - Allow free motion about an edge </li>
+</ul>
+<strong>&lt;Impose_on_state_variable_integral&gt;</strong> <i>boolean</i> [<i>false</i>]  <nobr> 
 <strong>&lt;Impose_flux&gt;</strong> <i>boolean</i> [<i>false</i>]  <nobr> 
 <strong>&lt;/Impose_flux&gt;</strong>
 </nobr><br>
@@ -279,5 +290,10 @@ If <i>true</i> then when the Robin BC is applied along the normal direction the
 <strong>&lt;/Damping&gt;</strong>
 </nobr><br>
 The damping constant for the spring-mass-damper force used to implement a Robin boundary condition.
+<br>
+<strong>&lt;Stiffness>&gt;</strong> <i>real [1.0]</i> <nobr> 
+<strong>&lt;/Stiffness&gt;</strong>
+</nobr><br>
+The stiffness constant for the spring-mass-damper force used to implement a Robin boundary condition.
 </div>
 

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

@@ -0,0 +1,45 @@
+<!-- =============================================================== -->
+<!-- ========================= Contact Section ===================== -->
+<!-- =============================================================== -->
+
+<h2 id="contact_section"> Contact Section </h2>
+The <i>Contact Section</i> of the solver parameters input file is used to define the parameters controlling the contact computations
+that prevents the geometric interpenetration of element domains.
+
+A <i>Contact Section</i> is organized as follows 
+<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 1px solid #d0d0d0">
+&lt;<strong>Contact</strong> model=<i>contact_model</i>&gt; 
+<br>
+[ <a href="#contact_parameters"> Contact Parameters </a> ]
+<br>
+&lt;<strong>/Contact</strong>&gt;
+</div>
+
+The <strong>Contact</strong> keyword is used to define the parameters used in a contact computation. The <strong>model</strong> attribute 
+<i>contact_model</i> is the name of a method used for the contact computation. The <strong>"penalty"</strong> model is currently the
+only model supported.
+
+<h3 id= "contact_parameters"> Contact Parameters </h3>
+<div class="bc_param_div">
+<strong>&lt;Closest_gap_to_activate_penalty></strong> <i>real</i> [1.0] <nobr>
+<strong>&lt;/Closest_gap_to_activate_penalty&gt;</strong>
+</nobr><br>
+The maximum depth of penetration between elements in contact.
+<br>
+<strong>&lt;Desired_separation></strong> <i>real</i> [0.05] <nobr>
+<strong>&lt;/Desired_separation&gt;</strong>
+</nobr><br>
+The minimum depth of penetration between elements in contact.
+<br>
+<strong>&lt;Min_norm_of_face_normals></strong> <i>real</i> [0.05] <nobr>
+<strong>&lt;/Min_norm_of_face_normals&gt;</strong>
+</nobr><br>
+The minimum norm of face normals in contact.
+<br>
+<strong>&lt;Penalty_constant></strong> <i>real</i> [1e5] <nobr>
+<strong>&lt;/Penalty_constant&gt;</strong>
+</nobr><br>
+The penalty constant used to prevent element interpenetration. 
+<br>
+</div>
+