improved docs

Author: Malmahrouqi3

README.md

@@ -84,9 +84,9 @@ And here is a high amplitude acoustic wave reflecting and emerging through a cir
 
 
 ## Getting started
-For a quick start, open a GitHub Codespace to load a pre-configured docker container to get familiar with MFC commands. Click <kbd> <> Code</kbd> (green button at top right) → <kbd>Codespaces</kbd> (right tab) → <kbd>+</kbd> (create a codespace).
+For a quick start, open a GitHub Codespace to load a pre-configured Docker container to get familiar with MFC commands. Click <kbd> <> Code</kbd> (green button at top right) → <kbd>Codespaces</kbd> (right tab) → <kbd>+</kbd> (create a codespace).
 
-****Notes:**** Codespaces is a free service with a monthly quota of compute time and storage usage. It is commended for testing commands, troubleshooting, and running simple case files without the need to install dependencies and build MFC on your device. Remember to save any important files locally before closing your codespace. To learn more, read through [how docker & containers work](https://mflowcode.github.io/documentation/docker.html).
+****Notes:**** Codespaces is a free service with a monthly quota of compute time and storage usage. It is recommended for testing commands, troubleshooting, and running simple case files without the need to install dependencies and build MFC on your device. Remember to save any important files locally before closing your codespace. To learn more, read through [how Docker & Containers work](https://mflowcode.github.io/documentation/docker.html).
 
 Otherwise, you can navigate [to this webpage](https://mflowcode.github.io/documentation/md_getting-started.html) to get started using MFC!
 It's rather straightforward.

docs/documentation/docker.md

@@ -30,6 +30,13 @@ docker run -it --rm --entrypoint bash --platform linux/amd64 sbryngelson/mfc:lat
 ```
 <br>
 
+**What is Next:** 
+
+After starting a container, the primary working directory is `/opt/MFC`, where all necessary files are located. Read through [Example Cases](https://mflowcode.github.io/documentation/md_examples.html) to get familiar with running cases, then review [Case Files](https://mflowcode.github.io/documentation/md_case.html) to write a custom case file.
+
+
+<br>
+
 ## Running Containers
 
 Start a CPU container.
@@ -40,7 +47,7 @@ Start a GPU container.
 ```bash
 docker run -it --rm --gpus all --entrypoint bash sbryngelson/mfc:latest-gpu
 ```
-**Note:** `--gpus all` exposes the container to available GPUs, and only Nvidia GPUs are currently supported. Make sure your device's CUDA version is at least 12.3 to avoid backward compatibility issues.
+**Note:** `--gpus all` exposes the container to available GPUs, and only NVIDIA GPUs are currently supported. Make sure your device's CUDA version is at least 12.3 to avoid backward compatibility issues.
 
 <br>
 <br>
@@ -55,7 +62,7 @@ docker run -it --rm --entrypoint bash -v "$PWD":/mnt sbryngelson/mfc:latest-cpu
 
 **Shared Memory:** 
 
-Increase the shared memory size to prevent MPI memory binding errors which may fail some tests and cases. Otherwise, you can disable MPI inside the container (`--no-mpi`). 
+When encountering MPI memory binding errors resulting in failed tests and cases, increase the shared memory size or disable MPI inside the container (`./mfc.sh --no-mpi`).
 ```bash
 docker run -it --rm --entrypoint bash --shm-size=<e.g., 4gb> sbryngelson/mfc:latest-cpu
 ```
@@ -91,6 +98,7 @@ or
 ```bash
 apptainer exec --nv --fakeroot --writable-tmpfs --bind "$PWD":/mnt  docker://sbryngelson/mfc:latest-gpu bash -c "cd /opt/MFC && bash"
 ```
+**Note:** To run MFC on CPU cores, omit `--nv` and use `mfc:latest-cpu` container image.
 
 ### **For Portability,**
 On the source machine,
@@ -107,6 +115,7 @@ apptainer shell --nv --fakeroot --writable-tmpfs --bind "$PWD":/mnt mfc:latest-g
 
 
 ### Slurm Job
+Below is a slurm job template. Refer to your HPC user guide for instructions on properly loading and using apptainer.
 ```bash
 #!/bin/bash
 #SBATCH --job-name=mfc-sim
@@ -117,9 +126,6 @@ apptainer shell --nv --fakeroot --writable-tmpfs --bind "$PWD":/mnt mfc:latest-g
 #SBATCH --output=mfc-sim-%j.out
 #SBATCH --error=mfc-sim-%j.err
 
-# Load required modules
-module load apptainer
-
 cd $SLURM_SUBMIT_DIR
 
 # Define container image
@@ -135,7 +141,7 @@ Where,
 `/sim` directory should all the simulation files, including the case setup (`case.py`).
 
 `--nv --fakeroot --writable-tmpfs`, these flags are critical to:
-- Grant access to the host system's Nvidia GPU and its CUDA libraries.
+- Grant access to the host system's NVIDIA GPUs and its CUDA libraries.
 - Enable root-like permissions inside the container without actual root access.
 - Allow temporary write access to the container filesystem.
 

docs/documentation/getting-started.md

@@ -146,7 +146,7 @@ Examples:
 - Build MFC's `simulation` code in Debug mode with MPI and GPU support: `./mfc.sh build --debug --gpu -t simulation`.
 
 ## Using Containers
-As an alternative to building MFC from scratch, use containers to quickly access pre-built MFC with all its dependencies.
+Instead of building MFC from scratch, use containers to quickly access pre-built MFC along with its dependencies.
 
 Run the latest MFC container.
 ```bash