Rewrite the Simulation docs.

Author: ktbolt

documentation/cfd_simulation.html

@@ -170,8 +170,20 @@ <h4 class="skipTo introduction">Introduction</h4>
         <h4 class="skipTo simulation_input_data">Simulation Input Data</h4>
       </div>
       <div>
-        <h4 class="skipTo bcphysics">Boundary Conditions</h4>
+        <h4 class="skipTo boundary_conditions">Boundary Conditions</h4>
       </div>
+
+      <!-- ==================== CFD Simulation Tool ==================== -->
+      <div>
+        <h4 class="skipTo cfd_simulation_tool"> CFD Simulation Tool </h4>
+        <div>
+          <p class="skipTo basic_parameters_panel"> Basic Parameters panel </p>
+          <p class="skipTo inlet_outlet_bcs_panel"> Inlet and Outlet BCs panel </p>
+          <p class="skipTo solver_parameters_panel"> Solver parameters panel </p>
+          <p class="skipTo create_files_and_run_simulation_panel"> Create Files and Run Simulation panel </p>
+        <div>
+      </div>
+
     </section>
 
     <!-- The following code defines the place where the markdown files are rendered -->
@@ -189,10 +201,31 @@ <h4 class="skipTo bcphysics">Boundary Conditions</h4>
       <span id="simulation_input_data">
         <zero-md  src="cfd_simulation/simulation_input_data/readme.md" no-shadow></zero-md>
       </span>
-      <span id="bcphysics">
+      <span id="boundary_conditions">
         <zero-md src="cfd_simulation/boundary_conditions/readme.md" no-shadow></zero-md>
       </span>
 
+      <!-- ==================== CFD Simulation Tool ==================== -->
+      <span id="cfd_simulation_tool">
+        <zero-md src="cfd_simulation/cfd_simulation_tool/readme.md" no-shadow></zero-md>
+      </span>
+
+      <span id="basic_parameters_panel">
+        <zero-md src="cfd_simulation/cfd_simulation_tool/basic_parameters_panel/readme.md" no-shadow></zero-md>
+      </span>
+
+      <span id="inlet_outlet_bcs_panel">
+        <zero-md src="cfd_simulation/cfd_simulation_tool/inlet_outlet_bcs_panel/readme.md" no-shadow></zero-md>
+      </span>
+
+      <span id="solver_parameters_panel">
+        <zero-md src="cfd_simulation/cfd_simulation_tool/solver_parameters_panel/readme.md" no-shadow></zero-md>
+      </span>
+
+      <span id="create_files_and_run_simulation_panel">
+        <zero-md src="cfd_simulation/cfd_simulation_tool/create_files_and_run_simulation_panel/readme.md" no-shadow></zero-md>
+      </span>
+
     </section>
   </section>
   <section class="skipToTopSection">

documentation/cfd_simulation/appendix/readme.md

@@ -17,16 +17,16 @@ Boundary conditions are applied to the finite element mesh walls and inlet/outle
 The boundaries of a computational domain $\Omega$ are classified as (Fig. 1)
 
 <ol>
- <li> <strong>inflow</strong> boundary $\Gamma_g$ - Surfaces where a volumetric flow rate of fluid entering the domain is prescribed. It is used to derive a Dirichlet velocity boundary condition applied in the direction normal to the surface.
+ <li> <strong>inlet</strong> boundary $\Gamma_g$ - Surfaces where a volumetric flow rate of fluid entering the domain is prescribed. It is used to derive a Dirichlet velocity boundary condition applied in the direction normal to the surface.
  <li> <strong>wall</strong> boundary $\Gamma_s$ - This boundary represents the interface between the fluid domain and the vessel wall. Blood flow simulations typically assume a <strong>rigid wall assumption</strong> where a zero velocity condition is applied to vessel surfaces. 
 </li>
  <li> <strong>outflow</strong> boundary $\Gamma_h$ - Surfaces where a uniform pressure value is prescribed. 
 </ol>
 
 <br> <br>
 <figure>
-  <img class="svImg svImgMd" src="/documentation/cfd_simulation/imgs/Fig_15.png">
-  <figcaption class="svCaption" >Fig. 1 &nbsp Boundaries of a fluid domain: inflow ($\Gamma_g$), wall ($\Gamma_s$), and outlet ($\Gamma_h$). </figcaption>
+  <img class="svImg svImgMd" src="/documentation/cfd_simulation/images/Fig_1.png">
+  <figcaption class="svCaption" >Fig. 1 &nbsp Boundaries of a fluid domain: inlet ($\Gamma_g$), wall ($\Gamma_s$), and outlet ($\Gamma_h$). </figcaption>
 </figure>
 
 
@@ -46,7 +46,7 @@ There are several boundary conditions that can be used to represent the pressure
 
 <br><br>
 <figure>
-  <img class="svImg svImgMd" src="/documentation/cfd_simulation/imgs/Fig_18.png">
+  <img class="svImg svImgMd" src="/documentation/cfd_simulation/images/Fig_2.png">
   <figcaption class="svCaption" >Fig. 2 &nbsp An RCR 3-element lumped parameter network </figcaption>
 </figure>
 

documentation/cfd_simulation/basic/readme.md

@@ -0,0 +1,20 @@
+<br>
+
+<h2 id="basic_parameters_panel" style="text-align:center;"> Basic Parameters Panel </h2>
+
+The <strong>Basic Parameters Panel</strong> is used to set the physical properties of the fluid used in the simulation
+
+<figure>
+<img class="svImg svImgSm" src="/documentation/cfd_simulation/cfd_simulation_tool/images/basic_params_panel.png">
+<figcaption class="svCaption"> The <strong>Basic Parameters </strong> panel.
+</figcaption>
+</figure>
+
+The panel contains two <i>TextBox</i>s used to set property values 
+
+<ul style="list-style-type:disc;">
+  <li> <strong>Fluid Density</strong> The fluid density. Default value 1.0 g/cm³  </li>
+  <li> <strong>Fluid Viscosity</strong> The fluid viscosity. Default value 0.04 poise [g · cm<sup>-1</sup> · s<sup>-1</sup>]  </li>
+</ul>
+
+

documentation/cfd_simulation/bct_file/readme.md

@@ -0,0 +1,20 @@
+<br>
+
+<h2 id="create_files_and_run_simulation_panel" style="text-align:center;"> Create Files and Run Simulation Panel </h2>
+
+The <strong>Create Files and Run Simulation Panel</strong> is used to execute the svMultiPhysics solver for the fluid simulation.
+
+<figure>
+<img class="svImg svImgSm" src="/documentation/cfd_simulation/cfd_simulation_tool/images/create_and_run_panel.png">
+<figcaption class="svCaption"> The <strong>Files and Run Simulation</strong> panel.
+</figcaption>
+</figure>
+
+<ul style="list-style-type:disc;">
+  <li> <strong>Choose Mesh</strong> - A <i>ComboBox</> used to select the mesh for the simulation. </li>
+  <li> <strong>Create Data Files for Simulation</strong> When selected the mesh files and solver XML files are created. </li> 
+  <li> <strong>Number of Processors</strong> The number of processors (cores) used by MPI to run the simulation. </li> 
+  <li> <strong>Run Simualtion</strong> When selected the simulation will be run. </li> 
+</ul>
+
+