Added README, and files option in json

Author: Shaunak

Basic/README.md

@@ -87,7 +87,11 @@ def import_from_file(file_name):
             Config.run_name = os.path.splitext(file_name)[0]
 
             if not Config.ada:
-                Config.files = "../../runs"
+                if 'files' in data:
+                    Config.files = data['files']
+                else:
+                    Config.files = "../../runs"
+
 
             if 'primary_replica' in data:
                 Config.primary_replica = data['primary_replica']

Basic/src/config.py

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Shaunak Badani
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

LICENSE.txt

@@ -0,0 +1,160 @@
+<br />
+<div align="center">
+    <img src="./images/RENS.png" alt="Logo" width="200" height="80">
+  
+
+<h3 align="center">Replica Exchange With Non-Equilibrium Switches</h3>
+
+  <p align="center">
+    An enhanced-sampling algorithm that increases acceptance probability by perfomring non-equilibrium work simulations.
+    <br />
+  </p>
+</div>
+
+
+
+<!-- TABLE OF CONTENTS -->
+<details>
+  <summary>Table of Contents</summary>
+  <ol>
+    <li>
+      <a href="#about-the-project">About The Project</a>
+    </li>
+    <li>
+      <a href="#getting-started">Getting Started</a>
+    </li>
+    <li><a href="#systems">Systems</a></li>
+    <li><a href="#roadmap">Roadmap</a></li>
+    <li><a href="#license">License</a></li>
+    <li><a href="#contact">Contact</a></li>
+    <li><a href="#acknowledgments">Acknowledgments</a></li>
+  </ol>
+</details>
+
+
+
+<!-- ABOUT THE PROJECT -->
+## About The Project
+
+This repository was made with the intention of implementing a Molecular Dynamics algorithm written in 2009 by Prof. Jarzynski and Mr. Andrew Ballard, titled ["Replica Exchange with Non-Equilibrium Switches"](https://www.pnas.org/content/106/30/12224). It eventually became a module which not only did that, but also as a framework for attempting molecular dynamics simulations on any toy system.
+
+<p align="right">(<a href="#top">back to top</a>)</p>
+
+
+
+<!-- GETTING STARTED -->
+## Getting Started
+
+* Clone the repository : 
+    ```
+    git clone https://github.com/shaunak-badani/1D_MD.git
+    ```
+* Install [anaconda](https://docs.anaconda.com/anaconda/install/index.html) or [miniconda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html) to manage the packages required to run this code.
+
+* Use the `MD.yml` environment file to create an environment `MD` which contains all the packages required to run this module, and activate it. Some of the packages in the environment may not be required, like `openmm`, so you can manually remove them if there are space constraints.
+    ```
+    conda env create -f MD.yml
+    conda activate MD
+    ```
+
+* Copy the following into a file `nve.json` : 
+    ```
+    {
+        "num_particles": 10,
+        "num_steps": 10000,
+        "run_type": "nve",
+        "files" : "."
+    }
+    ```
+* Run the code with the json file, in the `Basic` directory : 
+    ```
+    cd Basic
+    python3 main.py -c nve.json
+    ```
+
+* This creates a folder in the directory `Basic/`, by the name of the json file, `nve`.
+
+* The folder contains the following files : 
+
+    ```tree
+    nve
+    ├── end.rst
+    ├── p.txt
+    ├── scalars.txt
+    └── v.txt
+    ```
+
+* The above mentioned folder contains data about the simulation that was just performed. More details on it are given below. Furthermore, analysis of the simulation can be performed using the following command : 
+  ```
+  cd Basic
+  python3 analyze.py -c nve.json
+  ```
+
+* This creates a bunch of plots in `analysis_plots` folder, which help in analyzing the simulation. For the NVE run, it is sufficient to see the `energies` plot and check whether the total energy remained constant or not.
+
+* Further options for the json file are given in the README in `Basic`.
+
+
+## Systems 
+
+The module implements a couple of interesting toy systems on which MD is performed. 
+
+
+
+###  1-Dimensional Leach
+
+This system contains a single particle moving in 1 direction, along the x-axis. It is a continuous version of the potential function as described in chapter 13 of Leach. Its potential, at any given point, is calculated using the graph below : 
+
+ <img src="./images/U.png" alt="1D_U" width="400" height="300">
+
+This graph has three local minima, transitions between which are of great interest in studying Molecular Dynamics Algorithms.
+
+If a system were to include multiple particles at once, they would be considered non-interacting particles, and the potential energy of the system would be the sum of potential energies of all particles on the surface.
+
+### 2-Dimensional Muller Brown Potential
+
+The Muller Brown potential is a combination of multiple gaussians in the 2-D plane. Its potential energy surface, or PES, looks like the following : 
+
+
+<img src="./images/2D_U.png" alt="2D_U" width="400" height="350">
+
+There are two valleys separated by an energy barrier, which again makes this system of great interest.
+
+
+
+<!-- ROADMAP -->
+## Roadmap
+
+- [] Implement Analysis objects for 2-D brown muller potential
+- [] Benchmarking for RENS runs.
+
+
+
+<!-- CONTRIBUTING -->
+## Contributing
+
+Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.
+
+If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
+Don't forget to give the project a star! Thanks again!
+
+1. Fork the Project
+2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)
+3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)
+4. Push to the Branch (`git push origin feature/AmazingFeature`)
+5. Open a Pull Request
+
+
+<!-- LICENSE -->
+## License
+
+Distributed under the MIT License. See `LICENSE.txt` for more information.
+
+
+
+<!-- ACKNOWLEDGMENTS -->
+## Acknowledgments
+
+* `snsinfu's` [Replica Exchange implementation](https://github.com/snsinfu/f95-replica-exchange) which gave inspiration to the REMD implementation in this module.
+* sandeshkalantre, for his [Jarzynski repo](https://github.com/sandeshkalantre/jarzynski) which contains computational examples on proving Jarzynski's equality.
+