Update README.md

Author: yingyue2030699

README.md

@@ -41,17 +41,21 @@ To build serial NERDSS, you need:
     - For Ubuntu, install via apt
 3. To compile using make:
     - Navigate to the main directory
-    - Run *make serial*
-    - The executable will be placed in the *./bin* directory
+    - Run `make serial`
+    - The executable will be placed in the `./bin` directory
 
 To build parallel NERDSS, you need to checkout to the `mpi` branch:
 
+```
+git checkout mpi
+```
+
 1. MPI:
-    - For macOS, install OpenMPI with Homebrew: *brew install open-mpi*
-    - For Ubuntu, install OpenMPI through apt: *sudo apt install openmpi-bin libopenmpi-dev*
+    - For macOS, install OpenMPI with Homebrew: `brew install open-mpi`
+    - For Ubuntu, install OpenMPI through apt: `sudo apt install openmpi-bin libopenmpi-dev`
 2. To compile using make:
     - Navigate to the main directory
-    - Run *make mpi* (with profiling support: *make mpi ENABLE_PROFILING=1*)
+    - Run `make mpi` (with profiling support: *make mpi ENABLE_PROFILING=1*)
     - The executable will be placed in the ./bin directory
 
 ### Run Simulations
@@ -62,27 +66,23 @@ Click the following link to make a copy of the iPython notebook in your Google C
 
 [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/mjohn218/nerdss_development/blob/master/docs/Run_NERDSS_colab.ipynb?copy=true)
 
-#### Run a quick trial with our server
-
-Go to the [NERDSS server](http://18.188.233.206:5000/).
-
 #### Compile and run NERDSS on your local machine
 
-1. Example input files are located in the subdirectories within the *sample_inputs* folder. They can also be generated using the [python GUI program](./gui.py), which is also included in the ioNERDSS tool.
+1. Example input files are located in the subdirectories within the `sample_inputs` folder.
 
-2. To start the serial simulation, use the command *./nerdss -f parms.inp*.
+2. To start the serial simulation, use the command `./nerdss -f parms.inp`.
 
-3. To start the parallel simulation, use the command *mpirun -np $nprocs  ./nerdss_mpi -f parms.inp*.
+3. To start the parallel simulation, use the command `mpirun -np $nprocs  ./nerdss_mpi -f parms.inp`.
 
-4. To debug the parallel code, use the command *mpirun -np 2 xterm -e gdb --ex 'b error' --ex r --args ./nerdss_mpi -f parms.inp -s 123*.
+4. To debug the parallel code, use the command `mpirun -np 2 xterm -e gdb --ex 'b error' --ex r --args ./nerdss_mpi -f parms.inp -s 123`.
 
 ### Analyzing Results
 
 1. Use the ioNERDSS PyPi library for visualizing simulation results.
 2. Install ioNERDSS with *pip install ioNERDSS*.
 3. Refer to the [ionerdss repository](https://github.com/JohnsonBiophysicsLab/ionerdss) for more details.
 
-### Best Practices for Developers
+### Style Guides for Developers
 
-1. Choose meaningful names for variables, functions, and classes. Comment on complex logic, and maintain consistent indentation and formatting. Use CamelCase for variables, snake_case for functions, and PascalCase for classes. Avoid global variables.
-2. Follow the Google C++ Style Guide and the C++ Core Guidelines. Prefer using the C++ Standard Library and modern C++ features. Provide comments and documentation to explain complex or non-obvious code sections. Write unit tests to ensure code quality.
+1. We use the Google C++ Style Guide and the C++ Core Guidelines and prefer the C++ Standard Library and modern C++ features.
+2. Provide comments and documentation to explain complex or non-obvious code sections. Write unit tests to ensure code quality.