fix markdown bold formatting

Author: cdarve245

documentation/flowsolver/creating_data/readme.md

@@ -33,6 +33,7 @@ In addition to the five standard files (geombc.dat.1, restart.0.1, numstart.dat,
 This will required an executable that implements a lumped parameter network model for the patient circulation. This will be covered in a later version of this tutorial. Stay tuned!
 
 <br>
+
 **HINT**: In both files geombc.data.1 and restart.0.1, the number “.1” refers to the **partition number** of the file. Remember **svSolver** has the ability of running a problem _in parallel_ (i.e., using multiple processors or computing cores), using MPI (message-passing interface). When we run a job using multiple processors, the first thing that happens is the “splitting” of these two files into as many processors we are going to use in our analysis, so the calculations can be performed faster. For example, if we use $4$ processors later in svSolver, these files will be split as follows:
 
 ```

documentation/genbc/intro/readme.md

@@ -4,40 +4,39 @@ This tutorial demonstrates how to use the General Boundary Conditions (GenBC) fr
 
 ## What is GenBC?
 
-GenBC provides a framework to programmatically define custom inflow and outflow boundary conditions for a CFD simulation. The framework 
-allows users to create an arbitrary lumped parameter network (LPN) layout suitable for their application. Some common examples include a 
-lumped parameter heart model that models contraction of the heart chambers to use as an inlet boundary condition, sophisticated models of 
-the downstream circulation for various areas of the body such as the legs and upper body, or a closed-loop formulation where all outflow 
+GenBC provides a framework to programmatically define custom inflow and outflow boundary conditions for a CFD simulation. The framework
+allows users to create an arbitrary lumped parameter network (LPN) layout suitable for their application. Some common examples include a
+lumped parameter heart model that models contraction of the heart chambers to use as an inlet boundary condition, sophisticated models of
+the downstream circulation for various areas of the body such as the legs and upper body, or a closed-loop formulation where all outflow
 of the SimVascular model returns back to the inflow after passing through the veins, heart, and pulmonary arteries.
 
-The GenBC framework is implemented as a Fortran program called by the SimVascular flow solver svSolver. Users must derive the governing 
-ordinary differential equations for the lumped parameter layout and implement them in Fortran inside the GenBC program. The Fortan program 
-is then compiled to produce a GenBC executable program. This executable is called by svSolver during execution to provide values for 
+The GenBC framework is implemented as a Fortran program called by the SimVascular flow solver svSolver. Users must derive the governing
+ordinary differential equations for the lumped parameter layout and implement them in Fortran inside the GenBC program. The Fortan program
+is then compiled to produce a GenBC executable program. This executable is called by svSolver during execution to provide values for
 custom boundary conditions.
 
 SimVascular does not currently provide functionality to define GenBC boundary conditions using the GUI. The GUI is used
 to generate simulation files for built-in boundary conditions. These files are then manually edited to incorporate the commands
-needed to define data for the boundary conditions and to tell svSolver to use the GenBC framework. 
-
+needed to define data for the boundary conditions and to tell svSolver to use the GenBC framework.
 
 ## Cylinder RCR example
 
-This tutorial demonstrates how to use GenBC to define inflow and RCR boundary conditions for flow in a cylinder. Although these 
-boundary conditions can be defined using the built-in features in SimVascular they are used here as a simple example of all the 
-steps needed to implement GenBC boundary conditions. A graphical representation of the boundary conditions for the cylinder example 
-is shown in the figure below. 
+This tutorial demonstrates how to use GenBC to define inflow and RCR boundary conditions for flow in a cylinder. Although these
+boundary conditions can be defined using the built-in features in SimVascular they are used here as a simple example of all the
+steps needed to implement GenBC boundary conditions. A graphical representation of the boundary conditions for the cylinder example
+is shown in the figure below.
 
 <figure>
   <img class="svImg svImgMd" src="/documentation/genbc/imgs/rcr_cylinder.jpeg">
   <figcaption class="svCaption" >Cylinder with sinusoidal inflow and RCR outflow.</figcaption>
 </figure>
 
-The SimVascular project for the cylinder example can be downloaded using the **Cylinder Example Project** link in the menu on the 
-left-hand side of this page. The project contains all of the data (image, model, and mesh) needed for the tutorial. You will need 
+The SimVascular project for the cylinder example can be downloaded using the **Cylinder Example Project** link in the menu on the
+left-hand side of this page. The project contains all of the data (image, model, and mesh) needed for the tutorial. You will need
 to manually load the mesh by selecting **Meshes->cylinder_mesh->Load/Unload Mesh** from the **SV Data Manager** menu. The project
 has two additional folders
 
-    1) GenBC-program - Contains the Fortran code implementing the GenBC framework 
-    2) flow-file - Contains the **inlet.flow** file used to to define the flow rate for Direchlet boundary conditions.
-
-
+```
+1. GenBC-program - Contains the Fortran code implementing the GenBC framework
+2. flow-file - Contains the **inlet.flow** file used to to define the flow rate for Direchlet boundary conditions.
+```

documentation/modeling/3D_seg/readme.md

@@ -84,8 +84,8 @@ Close the panel before creating or opening a SimVascular project.
 </div>
 
 <br>
-The **3D Level Set Tool** creates a **level-set** node under the SV Data Manager <i>Images</i> node. The **level-set** node
-itself has four sub-nodes used to store and display geometry created by each of the panels
+
+The **3D Level Set Tool** creates a **level-set** node under the SV Data Manager <i>Images</i> node. The **level-set** node itself has four sub-nodes used to store and display geometry created by each of the panels
 
 <ul style="list-style-type:none;">
   <li> <b>seed-points</b> - Seed points, displayed as green or red spheres. </li>
@@ -261,8 +261,7 @@ Create a SimVascular project and read in the demo-image.vti image data file from
 <br>
 <b>Step 2 - Open the 3D Level Set Tool</b> <br>
 Select the
-<img src="/documentation/modeling/imgs/3d-level-set/level-set-icon.png" width="20" height="20"> icon located at the top of the
-SimVascular toolbar to open the **3D Level Set Tool** panel. Select the <i>Seeds</i> sub-panel.
+<img src="/documentation/modeling/imgs/3d-level-set/level-set-icon.png" width="20" height="20"> icon located at the top of the SimVascular toolbar to open the <strong>3D Level Set Tool</strong> panel. Select the <i>Seeds</i> sub-panel.
 <figure>
 <img class="svImg svImgXl" src="/documentation/modeling/imgs/3d-level-set/example-1/fig-2.png">
 </figure>

documentation/modeling/level_set/readme.md

@@ -65,7 +65,7 @@ Now a new contour is created and added to the group.
 
 In general, you should go with the normal approach above: making more segmentations than you will need and then selecting a subset to define the vessel. However, in the following exercise, we will try to gain some intuition that makes batch level set segmentation possible and efficient.
 
-<font color="red">**HELPFUL HINT:**</font> Finding suitable level set parameters based on a few cross sections and then doing batch segmentation can dramatically speed up model building. Make sure the seed fits within the lumen of the vessel for all the positions we’d like to segment in the batch.
+<font color="red"><strong>HELPFUL HINT:</strong></font> Finding suitable level set parameters based on a few cross sections and then doing batch segmentation can dramatically speed up model building. Make sure the seed fits within the lumen of the vessel for all the positions we’d like to segment in the batch.
 
 Now let's try to create contours in batch model using levelset.
 
@@ -106,4 +106,4 @@ Secondly, you want to check to make sure that the segmentation does not include
   <figcaption class="svCaption" ></figcaption>
 </figure>
 
-<font color="red">**HELPFUL HINT:** </font> You want the spacing between locations to be sufficient to capture the curvature and other changes in the vessel. If the vessel is relatively straight, as is the case in this the abdominal aorta for this dataset, you can space the segmentations relatively far apart.
+<font color="red"><strong>HELPFUL HINT:</strong></font> You want the spacing between locations to be sufficient to capture the curvature and other changes in the vessel. If the vessel is relatively straight, as is the case in this the abdominal aorta for this dataset, you can space the segmentations relatively far apart.

documentation/python_interface/intro/python_shell/readme.md

@@ -16,6 +16,7 @@ where <em>DATE</em> is the SimVascular install date (e.g. 2020-04-06). In the fo
 the SimVascular launch script.
 
 <br>
+
 The SimVascular Python interpreter, the application that executes Python programs, is invoked in interactive mode using the **---python** flag.
 That means you can enter Python statements or expressions interactively and have them executed or evaluated while you wait.
 The **Python Shell** behaves like the standard Python interpreter and therefore supports automatic indentation to mark blocks of code.
@@ -38,6 +39,7 @@ Hello
 </pre>
 
 <br>
+
 The **Python Shell** is terminated using
 
 <pre>
@@ -47,7 +49,8 @@ Windows: exit() or hold the Ctrl key down while you enter a Z, then hit the “E
 </pre>
 
 <br>
-Python scripts are read in and executed using a double-dash **---** before the script name. The **Python Shell** passes the script to the 
+
+Python scripts are read in and executed using a double-dash **---** before the script name. The **Python Shell** passes the script to the
 Python interpreter for execution and then exits.
 
 <pre>

documentation/python_interface/modules/function_arguments/readme.md

@@ -10,8 +10,9 @@ the meaning of the data passed to the **Circle** class constructor
 </pre>
 
 <br>
+
 All data passed to a function is checked against the type expected by the function. A type mismatch generates an error.
-General type errors are detected by Python. For example, using a string for the <i>radius</i> argument which expects a 
+General type errors are detected by Python. For example, using a string for the <i>radius</i> argument which expects a
 float generates a Python **TypeError**
 
 <pre>
@@ -20,9 +21,10 @@ TypeError: CircleSegmentation() argument 1 must be float, not str
 </pre>
 
 <br>
+
 Errors associated with data needed by the C++ functions called from the SimVascular API are detected within the API C++
-implementation. For example, passing in a list of two instead of three floats for the **Circle** class constructor 
-<i>normal</i> argument generates a **segmentation** module error
+implementation. For example, passing in a list of two instead of three floats for the **Circle** class constructor
+<i>normal</i> argument generates a <b>segmentation</b> module error
 
 <pre>
 >>> seg = sv.segmentation.Circle(radius=1.0, center=[1.0,0.0,0.0], normal=[1.0])

documentation/python_interface/modules/help/readme.md

@@ -8,6 +8,7 @@ Typing <b>help(sv)</b> prints information about the **sv** package.
 </div>
 
 <br>
+
 Typing <b>help(sv.MODLENAME)</b> prints information about the **MODULENAME** module
 
 <ul>

documentation/python_interface/modules/sv_module/readme.md

@@ -17,9 +17,9 @@ The **sv** package defines the following modules
 
 <br>
 Modules are accessed using <b>sv.<i>MODULENAME</i></b>. The <b>sv</b> package can also be imported into Python using the 
-<b>from sv import \*</b> statement. This makes all of the module names accessible without the **sv** prefix. A single <b>sv</b> 
+<b>from sv import \*</b> statement. This makes all of the module names accessible without the <b>sv</b> prefix. A single <b>sv</b> 
 module can be imported using <b>from sv import <i>MODULENAME</i></b>. The difference between the these statements is seen using 
-the **dir()** function which shows imported modules
+the <b>dir()</b> function which shows imported modules
 
 <pre>
 <div style="font-size:10px; height: auto; overflow: visible;">

documentation/rom_simulation/1d-solver/input_file/readme.md

@@ -385,7 +385,7 @@ Output formats
 VTK export options
 
   <ul style="list-style-type:none;">
-    <li>0 - Output multiple files (default). A separate file is written for each saved increment. A **pvd** file is also provided which contains the time information of the sequence. This is the best option to create animations. </li><br>
+    <li>0 - Output multiple files (default). A separate file is written for each saved increment. A <b>pvd</b> file is also provided which contains the time information of the sequence. This is the best option to create animations. </li><br>
     <li>1 - The results for all time steps are plotted to a single XML VTK file. </li><br>
   </ul>
 
@@ -433,8 +433,8 @@ Arguments
     <li><i>id</i> (integer) - Segment ID. </li><br>
     <li><i>length</i> (double - Segment length. </li><br>
     <li><i>nelems</i> (integer) - Total finite elements in segment. </li><br>
-    <li><i>inode</i> (integer) - Segment inlet **Node**. </li><br>
-    <li><i>onode</i> (integer) - Segment outlet **Node**. </li><br>
+    <li><i>inode</i> (integer) - Segment inlet <b>Node</b>. </li><br>
+    <li><i>onode</i> (integer) - Segment outlet <b>Node</b>. </li><br>
     <li><i>iarea</i> (double - Segment inlet area. </li><br>
     <li><i>oarea</i> (double - Segment outlet area. </li><br>
     <li><i>iflow</i> (double - Segment initial flow. </li><br>

documentation/rom_simulation/1d-solver/theory/readme.md

@@ -99,8 +99,9 @@ where the initial condition is given by $\mathbf{U}^0(z) = \left[S^0(z),Q^0(z)\r
 The boundary conditions are not specified at this point.
 
 <h2> Disjoint Decomposition </h2>
-We adopt the disjoint decomposition approach described in 2.3 to derive appropriate outflow boundary conditions. 
-First, we divide our spatial domain $\Omega=[0,L]$ into an upstream **numerical** domain $\Omega^{n}: z\in(0,B)$, 
+
+We adopt the disjoint decomposition approach described in 2.3 to derive appropriate outflow boundary conditions.
+First, we divide our spatial domain $\Omega=[0,L]$ into an upstream **numerical** domain $\Omega^{n}: z\in(0,B)$,
 and a downstream **analytic** domain $\Omega^{a}: z\in(B,L)$.
 
 The boundary that separates these domains is defined as $\Gamma\_{B} : z = B$. We define a disjoint decomposition of