Add missing parameters and a couple of new sections.

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/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>
+

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

@@ -81,6 +81,7 @@ The following sections list the parameters associated with a domain for a specif
 <a href="#domain_Force_x"> Force_x <a>
 <a href="#domain_Force_y"> Force_y <a>
 <a href="#domain_Force_z"> Force_z <a>
+<a href="#domain_Inverse_darcy_permeability"> Inverse_darcy_permeability <a>
 </pre>
 
 <!-- ---------- fluid-solid-interactio domain Parameters ---------- -->
@@ -108,7 +109,7 @@ linear elasticity, structural or structural velocity pressure parameters.
 <a href="#domain_Poisson_ratio"> Poisson_ratio <a>
 </pre>
 
-<!-- ---------- shel domain Parameters ---------- -->
+<!-- ---------- shell domain Parameters ---------- -->
 
 <h5 id="shell_domain_parameters"> Shell Domain Parameters </h5>
 <pre>
@@ -291,6 +292,12 @@ The maximal rapid delayed rectifier sodium current used in the TenTusscher-Panfi
 </nobr><br>
 The maximal transient outward current conductance used in the TenTusscher-Panfilov Ventricular Myocyte Model.
 <br>
+<section id="domain_Inverse_darcy_permeability">
+<strong>&lt;Inverse_darcy_permeability&gt;</strong> <i>real</i> [0.0] <nobr>
+<strong>&lt;/Inverse_darcy_permeability&gt;</strong>
+</nobr><br>
+Sets the inverse darcy permeability constant.
+<br>
 <strong>&lt;Isotropic_conductivity&gt;</strong> <i>real</i> [0.0] <nobr>
 <strong>&lt;/Isotropic_conductivity&gt;</strong>
 </nobr><br>

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

@@ -13,7 +13,7 @@ The <i>Equation Section</i> is organized as follows
 <div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 1px solid #d0d0d0">
 &lt;<strong>Add_equation</strong> type=<i>equation_type</i>&gt;
 <br><br>
-[<a href="#equation_parameters"> Equation Parameters </a> ]
+[<a href="#equation_parameters_section"> Equation Parameters </a> ]
 <br> <br>
 
 &lt;<strong>Domain</strong> id=<i>domain_id</i>&gt;
@@ -22,6 +22,17 @@ The <i>Equation Section</i> is organized as follows
 <br>
 &lt;<strong>/Domain</strong>&gt;
 
+&lt;<strong>ECGLeads</strong>&gt;
+<br>
+[<a href="#ECGLeads_subsection"> ECG Leads Subsection </a> ]
+<br>
+&lt;<strong>/ECGLeads</strong>&gt;
+
+&lt;<strong>Variable_wall_properties</strong> mesh_name=<i>mesh_name</i>&gt;<br>
+[<a href="#Variable_wall_properties_subsection"> Variable wall properties Subsection </a> ]
+<br>
+&lt;<strong>Viscosity</strong>&gt;
+
 &lt;<strong>Viscosity</strong> model=<i>viscosity_model</i>&gt;<br>
 [<a href="#viscosity_parameters"> Viscosity Subsection </a> ]
 <br>
@@ -66,7 +77,7 @@ The value of <i>equation_type</i> is a <i>string</i> identifying the equation ty
 <!-- ---------- Equation Parameters ---------- -->
 <!-- ----------------------------------------- -->
 
-<h3 id="equation_parameters"> Equation Parameters </h3>
+<h3 id="equation_parameters_section"> Equation Parameters </h3>
 <div class="bc_param_div">
 <strong>&lt;Coupled&gt;</strong> <i>boolean [true]</i> <nobr>
 <strong>&lt;/Coupled&gt;</strong>
@@ -114,6 +125,73 @@ If <i>true</i> then use a Taylor-Hood element pair for increased stability.
 <br>
 </div>
 
+<!-- ============================================================== -->
+<!-- ====================== ECGLeads Subsection =================== -->
+<!-- ============================================================== -->
+<h4 id="ECGLeads_subsection"> ECG Leads Subsection </h4>
+The <i>ECG Leads Subsection</i> of the <i>Equation Section</i> or <i>Domain Subsection</i> contains 
+the parameters used to define ECG leads. 
+
+The <i>ECG Leads  Subsection</i> is organized as follows
+<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 1px solid #d0d0d0">
+&lt;<strong>ECGLeads</strong>&gt;
+<br><br>
+[ <a href="#ECGLeads_parameters"> ECG Leads Parameters </a> ]
+<br> <br>
+&lt;<strong>/ECGLeads</strong>&gt;
+</div>
+
+The <strong>ECGLeads</strong> keyword defines a subsection for ECG Leads parameters.
+
+<h5 id="ECGLeads_parameters"> ECG Leads Parameters</h5>
+<div class="bc_param_div">
+<strong>&lt;X_coords_file_path&gt;</strong> <i>string</i> [none] <nobr>
+<strong>&lt;/X_coords_file_path&gt;</strong>
+</nobr><br>
+The path to the text file containing the x-coordinates for the ECG leads. 
+<br>
+<strong>&lt;Y_coords_file_path&gt;</strong> <i>string</i> [none] <nobr>
+<strong>&lt;/Y_coords_file_path&gt;</strong>
+</nobr><br>
+The path to the text file containing the y-coordinates for the ECG leads. 
+<br>
+<strong>&lt;Z_coords_file_path&gt;</strong> <i>string</i> [none] <nobr>
+<strong>&lt;/Z_coords_file_path&gt;</strong>
+</nobr><br>
+The path to the text file containing the z-coordinates for the ECG leads. 
+<br>
+</div>
+
+
+<!-- ============================================================== -->
+<!-- =============== Variable wall properties Subsection ========= -->
+<!-- ============================================================== -->
+<h4 id="Variable_wall_properties_subsection"> Variable wall properties Subsection </h4>
+The <i>Variable wall properties Subsection</i> of the <i>Equation Section</i> or <i>Domain Subsection</i> defines
+the parameters used to define the node-based material properties used in a CMM equation.
+
+The <i>Variable wall properties Subsection</i> is organized as follows
+<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 1px solid #d0d0d0">
+&lt;<strong>Variable_wall_properties</strong> mesh_name=<i>mesh_name</i>&gt;
+<br><br>
+[ <a href="#Variable_wall_properties_parameters"> Variable wall properties Parameters </a> ]
+<br> <br>
+&lt;<strong>/Variable_wall_properties</strong>&gt;
+</div>
+
+The <strong>Variable_wall_properties</strong> keyword defines a subsection for variable wall properties parameters.
+The <i>mesh_name</i> attribute is the mesh name to assign the variable wall properties. 
+
+<h5 id="Variable_wall_properties_parameters"> Variable wall properties Parameters</h5>
+<div class="bc_param_div">
+<strong>&lt;Wall_properties_file_path&gt;</strong> <i>string</i> [none] <nobr>
+<strong>&lt;/Wall_properties_file_path&gt;</strong>
+</nobr><br>
+The path to the VTK VTP-format file used to set the node-wise elasticity modulus and shell thickness properties. 
+<br>
+</div>
+
+
 <!-- ============================================================== -->
 <!-- ==================== Viscosity Subsection ==================== -->
 <!-- ============================================================== -->

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

@@ -37,6 +37,11 @@ The number of time steps to run the simulation.
 </nobr><br>
 The value use to increment the simulation time.
 <br>
+<strong>&lt;Starting_time_step&gt;</strong> <i>int</i> [0] <nobr>
+<strong>&lt;/Starting_time_step&gt;</strong>
+</nobr><br>
+The starting time step used for the simulation. 
+<br>
 <strong>&lt;Spectral_radius_of_infinite_time_step&gt;</strong> <i>real</i>  [0.5] <nobr>
 <strong>&lt;/Spectral_radius_of_infinite_time_step&gt;</strong>
 </nobr><br>
@@ -83,6 +88,11 @@ Save simulation results after the given time step.
 If <i>true</i> then compute time-averaged results from the entire simulation. The averaging is 
 performed after the last time step of the simulation using VTU files written during the simulation.
 <br>
+<strong>&lt;Start_averaging_from_zero&gt;</strong> <i>boolean [false]</i> <nobr>
+<strong>&lt;/Start_averaging_from_zero&gt;</strong>
+</nobr><br>
+If <i>true</i> then start everging results from time zero. 
+<br>
 <section id="gen_Increment_in_saving_restart_files">
 <strong>&lt;Increment_in_saving_restart_files&gt;</strong> <i>integer</i> [10] <nobr>
 <strong>&lt;/Increment_in_saving_restart_files&gt;</strong>
@@ -95,6 +105,12 @@ Indicates how often to save restart files.
 </nobr><br>
 Name of the file used to store simulation state data. This file is used for restarting simulations.
 <br>
+<section id="gen_Overwrite_restart_file">
+<strong>&lt;Overwrite_restart_file&gt;</strong> <i>bool</i> [<i>false</i>] <nobr>
+<strong>&lt;/Overwrite_restart_file&gt;</strong>
+</nobr><br>
+If <i>true</i> then the simulation results restart file is overwritten.
+<br>
 <section id="general_params_Simulation_initialization_file_path">
 <strong>&lt;Simulation_initialization_file_path&gt;</strong> <i>string [none] </i> <nobr>
 <strong>&lt;/Simulation_initialization_file_path&gt;</strong>

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

@@ -112,6 +112,11 @@ The mesh typically defines a network of Purkinje fibers used in cardiac electrop
 </nobr><br>
 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>
+<strong>&lt;quadrature_modifier_TET4&gt;</strong> <i>real</i> [0.5854] <nobr>
+<strong>&lt;/quadrature_modifier_TET4&gt;</strong>
+</nobr><br>
+The quadrature used for tetrahedral elements.
+<br>
 </div>
 
 <!-- ------------------------------------- -->
@@ -125,6 +130,12 @@ If <i>true</i> then the mesh given in the <strong>Mesh_file_path</strong> keywor
 <strong>&lt;/Face_file_path&gt;</strong>
 </nobr><br>
 The path to a VTK VTP file defining a finite element surface mesh for a face in the simulation.
+<br>
+<strong>&lt;Quadrature_modifier_TRI3&gt;</strong> <i>real</i> [0.6666] <nobr>
+<strong>&lt;/Quadrature_modifier_TRI3&gt;</strong>
+</nobr><br>
+The quadrature used for triangle elements.
+<br>
 <strong>&lt;/Add_face&gt;</strong>
 </div>
 

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

@@ -0,0 +1,43 @@
+<!-- =============================================================== -->
+<!-- ============== Precomputed Solution Section =================== -->
+<!-- =============================================================== -->
+
+<h2 id="precomputed_solution_section"> Precomputed Solution Section </h2>
+The <i>Precomputed Solution Section</i> of the solver parameters input file is used to define the parameters 
+used to read in the data from a precomputed solution for the simulation state.
+
+A <i>Precomputed Solution Section</i> is organized as follows 
+<div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 1px solid #d0d0d0">
+&lt;<strong>Precomputed_solution</strong>&gt; 
+<br>
+[ <a href="#precomputed_solution_parameters"> Precomputed Solution Parameters </a> ]
+<br>
+&lt;<strong>/Precomputed_solution</strong>&gt;
+</div>
+
+The <strong>Precomputed_solution</strong> keyword is used to define the parameters to for reading in a precomputed solution data and using it in a simulation. 
+
+<h3 id= "precomputed_solution_parameters"> Precomputed Solution Parameters </h3>
+<div class="bc_param_div">
+<strong>&lt;Use_precomputed_solution></strong> <i>bool</i> [<i>false</i>] <nobr>
+<strong>&lt;/Use_precomputed_solution&gt;</strong>
+</nobr><br>
+If <i>true</i> then use a precomputed solution for a simulation.
+<br>
+<strong>&lt;Precomputed_solution_field_name></strong> <i>string</i> [none] <nobr>
+<strong>&lt;/Precomputed_solution_field_name&gt;</strong>
+</nobr><br>
+The name of the precomputed solution data field in the VTK VTU file.
+<br>
+<strong>&lt;Precomputed_solution_file_path></strong> <i>string</i> [none] <nobr>
+<strong>&lt;/Precomputed_solution_file_path&gt;</strong>
+</nobr><br>
+The path to the VTK VTU file containing the precomputed solution data.
+<br>
+<strong>&lt;Precomputed_time_step_size></strong> <i>real</i> [0.05] <nobr>
+<strong>&lt;/Precomputed_time_step_size&gt;</strong>
+</nobr><br>
+The time step used to compute the precomputed solution data.
+<br>
+</div>
+

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

@@ -9,22 +9,25 @@ A <i>Projection Section</i> is organized as follows
 <div style="background-color: #F0F0F0; padding: 10px; border: 1px solid #d0d0d0; border-left: 1px solid #d0d0d0">
 &lt;<strong>Projection</strong> name=<i>project_to_face_name</i>&gt; 
 <br>
-&lt;<strong>Project_from_face</strong>&gt; <i>string</i>
-&lt;<strong>/Project_from_face</strong>&gt;
+[ <a href="#projection_parameters"> Projection Parameters </a> ]
 <br>
 &lt;<strong>/Projection</strong>&gt;
 </div>
 
 The <strong>Projection</strong> keyword is used to create a projection. The <strong>name</strong> attribute 
 <i>project_from_face_name</i> is the name of a face defined in the <i>Mesh Section</i>.
 
-<h3> Projection Parameters </h3>
+<h3 id="projection_parameters"> Projection Parameters </h3>
 <div class="bc_param_div">
 <strong>&lt;Project_from_face></strong> <i>string</i><nobr>
 <strong>&lt;/Project_from_face&gt;</strong>
 </nobr><br>
 The name of a face defined in the <i>Mesh Section</i> that is to be coupled to the <i>project_from_face_name</i> face.
 <br>
+<strong>&lt;Projection_tolerance></strong> <i>real</i> [0.0] <nobr>
+<strong>&lt;/Projection_tolerance&gt;</strong>
+</nobr><br>
+Face node distances within this tolerance will be treated as equal. 
 </div>