rearrage docs, add link in theory

Author: menon-karthik

documentation/rom_simulation/0d-solver/solver/readme.md

@@ -16,15 +16,6 @@ interactively select nodes to view simulation results.
 drawing the network on an easy-to-use GUI. This provides an alternative to manually
 creating files and is useful for users without access to a 3D model.
 
-The main categories of blocks implemented in svZeroDSolver are:
-<ul>
-  <li>Blood vessels</li>
-  <li>Junctions</li>
-  <li>Boundary conditions</li>
-  <li>Heart chambers</li>
-  <li>Heart valves</li>
-</ul>
-
 ## Installation
 
 svZeroDSolver can be installed in two different ways. For using the Python API, an installation via pip is recommended.
@@ -67,6 +58,15 @@ cmake --build .
 
 The modular architecture of svZeroDSolver relies on "blocks", such as blood vessels, junctions, valves, boundary conditions, etc. Users can assemble and connect these blocks together in a variety of ways to create extensive and customizable 0D circulation models.   
 
+The main categories of blocks implemented in svZeroDSolver are:
+<ul>
+  <li>Blood vessels</li>
+  <li>Junctions</li>
+  <li>Boundary conditions</li>
+  <li>Heart chambers</li>
+  <li>Heart valves</li>
+</ul>
+
 An overview of all currently implemented blocks can be found [here](https://simvascular.github.io/svZeroDSolver/class_block.html). This collection of building blocks allows to model extensive and complex vascular networks. Many examples of vascular networks can be found [here](https://github.com/simvascular/svZeroDSolver/tree/master/tests/cases). The assembly of these blocks is specified in the `.json` configuration file. The user guide below provides details.
 
 We are always interested in adding new blocks to expand the funcitonality of svZeroDSolver. For developers interested in contributing, please read the [Developer Guide](https://simvascular.github.io/svZeroDSolver/developer_guide.html). 

documentation/rom_simulation/0d-solver/theory/readme.md

@@ -2,7 +2,7 @@
 
 Flow rate, pressure, and other hemodynamic quantities in 0D models of vascular anatomies are governed by a system of nonlinear differential-algebraic equations (DAEs). In svZeroDSolver, the governing equations for a full 0D model are based on the governing equations for the individual blocks that make up the model.
 
-### Governing equations
+### Governing Equations
 
 For each block, with $N_d^e$ degrees-of-freedom and $N_e^e$ governing equations, we represent its governing equations as the following DAE: 
 $$\mathbf{E}^e(\boldsymbol{\alpha}^e) \cdot \dot{\mathbf{y}}^e + \mathbf{F}^e(\boldsymbol{\alpha}^e) \cdot \mathbf{y}^e + \mathbf{c}^e(\mathbf{y}^e,\dot{\mathbf{y}}^e, t) = \mathbf{0},$$
@@ -23,7 +23,7 @@ The global governing equation is given by:
 $$\mathbf{r}(\boldsymbol{\alpha}, \mathbf{y},\dot{\mathbf{y}}, t) = \mathbf{E}(\boldsymbol{\alpha}) \cdot \dot{\mathbf{y}} + \mathbf{F}(\boldsymbol{\alpha}) \cdot \mathbf{y} + \mathbf{c}(\mathbf{y},\dot{\mathbf{y}}, t) = \mathbf{0}, $$
 where $\mathbf{r},\mathbf{y},\mathbf{c} \in \mathbb{R}^{N}$ and $\textbf{E},\textbf{F} \in \mathbb{R}^{N \times N}$. Here, $\mathbf{r}$ is the residual, $\mathbf{y}$ is the vector of solution quantities and $\dot{\mathbf{y}}$ is its time derivative. Note that the solution quantities are generally the pressure and flow at each node between blocks, as well as state variables internal to each block. $N$ is the total number of equations and the total number of global unknowns. 
 
-The DAE system is solved implicitly using the generalized-$\alpha$ method (<a href="#0d-Jansen2000">Jansen, et al., 2000</a>). A description of this is provided in the "Time integration" section of this documentation. We then use the Newton-Raphson method to iteratively solve
+The DAE system is solved implicitly using the generalized-$\alpha$ method (<a href="#0d-Jansen2000">Jansen, et al., 2000</a>). A description of this is provided in the <a href="#time-integration">Time Integration</a> section of this documentation. We then use the Newton-Raphson method to iteratively solve
 $$\mathbf{K}^{i} \cdot \Delta\dot{\mathbf{y}}^{i} = - \mathbf{r}^{i}$$
 with solution increment $\Delta\dot{\mathbf{y}}^{i}$ in iteration $i$. The linearization of the time-discretized system is
 $$\mathbf{K} =\frac{\partial \mathbf{r}}{\partial \mathbf{y}} = c_{\dot{\mathbf{y}}} \left( \mathbf{E} + \frac{\partial \mathbf{c}}{\partial
@@ -32,7 +32,8 @@ with time factors $c_{\dot{\mathbf{y}}}=\alpha_m$ and $c_{\mathbf{y}}=\alpha_f\g
 
 The implementation of the global governing equations is in the [SparseSystem class](https://simvascular.github.io/svZeroDSolver/class_sparse_system.html). 
 
-### Time integration
+<h3 id="time-integration">Time Integration</h3>
+<!--### Time integration-->
 
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