New update to document with v2.3 changes

version_changes.md

@@ -2,30 +2,34 @@
 
 Moderate update to 2.2, released in July 2021. The main changes are new applications, new postprocessing scripts, improvements in performance, big fixes and comparibility with the latest version of deal.II.
 
-Added Features:
+## Added Features:
 
-- New application: alloySolidification_uniform. This app simulates solidification of a binary alloy at uniform temperature. 
-- New application: corrosion_microgalvanic. This application simulates the evolution of the metal-electrolyte interface during free immersion due to the microgalvanic coupling between the anodic and cathodic metals. 
+- New applications: 
+  - [corrosion_microgalvanic](https://github.com/prisms-center/phaseField/tree/master/applications/corrosion_microgalvanic): Simulates the evolution of the metal-electrolyte interface during free immersion due to the microgalvanic coupling between anodic and cathodic metals.
+  - [alloySolidification_uniform](https://github.com/prisms-center/phaseField/tree/master/applications/alloySolidification_uniform): Simulates solidification of a binary alloy at uniform temperature.
+  - [allenCahn_conserved](https://github.com/prisms-center/phaseField/tree/master/applications/allenCahn_conserved): Simulates a system undergoing Allen-Cahn dynamics subject to global (as opposed to local) conservation.
 - New postprocessing scripts. The following Python scripts for suite post-processing suite were added:
   - plot_and_save.py - This script creates a pseudocolor (in 2D) or contour (in 3D) plot for each outputted time states and saves the serieas of plots as png images.
   - domain_stats.py - This script calculates the following quantities for each of the time states:
-    1. Number of domains, defined as the number or separate regions based on the values of field variable, "n". Each interconnected region for which n>0.5 is counted as a separate domain.
-    2. Average domain size (area in 2D and volume in 3D)
-    3. Standard deviation of the domain sizes
+    - Number of domains, defined as the number or separate regions based on the values of field variable, "n". Each interconnected region for which n>0.5 is counted as a separate domain.
+
+    - Average domain size (area in 2D and volume in 3D)
+
+    - Standard deviation of the domain sizes
   - splitvtufiles.py - This script splits the output .vtu files into several files, allowing for parallel visualization in VisIt or ParaView.
 - New options for nucleation were added: an option to set the time interval for then nucleation is allowed and an option to allow for microstructure evolution before the first nucleation event.
 - Improved the method for grain detection when reading data from a DREAM3D microstructure file.
 - Added depencency of element degree for time step used in initial smoothing after reading from a DREAM3D microstructure file. This avoids posible numerical instabilities.
 - Added Troubleshooting/FAQ page with the most common compilation/runtime errors and the way to fix them.
 
-Bug Fixes:
+## Bug Fixes:
 
 - Fixed incomplete loop to detect dirichlet boundary conditions in init.cc
 - The code now correctly updates time-dependent non-uniform Dirichlet boundary conditions.
 - Updated input file parameters.prm for grainGrowth_dream3d application
 - Fixed several typos and errors in the documentation of built-in applications
 
-Other Changes:
+## Other Changes:
 
 - Updated comparibility with deal.II version 9.5.x