Remove things related to Penning trap project

README.md

@@ -1 +1,129 @@
-# Ising model
+# Ising Model
+
+[Repo](https://github.uio.no/FYS3150-G2-2023/Project-4)
+
+[Documentation](https://pages.github.uio.no/FYS3150-G2-2023/Project-4/)
+
+## Requirements
+
+### Operating systems
+
+- Linux
+    - Has been tested on [Fedora 38](https://fedoraproject.org/)
+    - Will most likely work on other Linux distributions
+- MacOS
+    - Might work, but hasn't been tested
+- Windows
+    - Will most likely not work
+
+### Tools
+
+- Profiling
+    - [gprof](https://ftp.gnu.org/old-gnu/Manuals/gprof-2.9.1/html_mono/gprof.html)
+    - [scalasca](https://www.scalasca.org/)
+    - [score-p](https://www.vi-hps.org/projects/score-p)
+
+### Libraries
+
+- Python
+    - [matplotlib](https://matplotlib.org/)
+    - [numpy](https://numpy.org/)
+
+- C++
+    - [Openmp](https://www.openmp.org/)
+    - [OpenMPI](https://www.open-mpi.org/)
+    - [Armadillo](https://arma.sourceforge.net/)
+
+
+## Compiling
+
+Compiling is as easy as running this command while being inside the src directory:
+
+```shell
+    make
+```
+
+## Running programs
+
+### C++ binaries
+
+To run **main** or **test_suite**, just run this command while being inside src:
+
+```shell
+    ./<program-name>
+```
+
+### Python scripts
+
+#### Install libraries
+
+Before running the scripts, make sure that all libraries are installed.
+Using pip, you can install all requirements like this:
+
+```shell
+    pip install -r requirements.txt
+```
+
+This recursively install all the packages that are listed in **requirements.txt**.
+
+#### Running scripts
+
+For the Python scripts, run them from the src directory like this:
+
+```shell
+    python scripts/<script-name>
+```
+
+If you have any problems running the scripts, you might have to run this instead:
+
+```shell
+    python3 scripts/<script-name>
+```
+
+### Batch system
+
+For the **phase_transition_mpi** program, there are scripts in the **src/jobs**
+directory that come along with it. This is to be able to run it on a
+batch system using Slurm if you have access to one. 
+This is the recommended way to use this program as it takes approximately 90 
+minutes to complete when using 8 processes where each process has 10 threads.
+
+If you happen to have such a system available to you, then you should clone
+this repo on that system, then compile it by running:
+
+```shell
+    make phase_transition_mpi
+```
+
+You might have to load the Armadillo library using the **module** system before compiling.
+
+After compiling, you can schedule it by running:
+
+```shell
+    sbatch jobs/<script-name>
+```
+
+## Performance
+
+This section aims to give an idea to the time it takes for the program to
+run so that you know a bit what to expect if you decide to run it for
+yourself.
+
+### CPU
+
+The times mentioned here are times achieved on a computer with these 
+specifications:
+
+- CPU model
+    - Intel i7-9850H
+- Threads
+    - 12
+- Clock speed
+    - 4.6GHz
+
+### Times
+
+## Credits
+
+The Doxygen theme used here is 
+[doxygen-awesome-css](https://github.com/jothepro/doxygen-awesome-css).