Update README.md

Author: drdrjacobs

README.md

@@ -14,3 +14,40 @@ Reactive Deposition of Brownian Particles. [arXiv:2204.01173 [cond-mat]](https:/
 | <img src="https://raw.githubusercontent.com/drdrjacobs/reactive_deposition_sim/master/images/dendritic_transition.png" width="600" height="803"> | 
 |:--:| 
 | The compact-to-dendritic transition in the reactive deposition of Brownian particles at $\log_{10} \mathrm{Da} = -2.12$. Color schemes vary depending on the panel, as indicated in the descriptions. Panels (a) and (b) depict two-dimensional deposition. The $N$ particles in these panels are rendered with a radius twice that of the actual radius for clarity. The $i$-th band of color moving outwards from the center corresponds to the structure after $i N / 5$ particles have been deposited. (a) Initially, the cluster displays a compact morphology. (b) However, upon reaching a critical radius, it spontaneously forms dendritic branches. (c) Main Panel: During three-dimensional deposition, a similar dendritic morphology emerges at large length scales. Particles are colored based on their distance from the origin. Inset: A two-dimensional slice through the initial compact 3D cluster, $N = 1 \times 10^{6}$. The color scheme follows a continuous gradient based on the deposition order. |
+
+# Dependencies
+
+- [Boost](https://www.boost.org/)
+- [Eigen](https://eigen.tuxfamily.org/index.php?title=Main_Page): Template library for linear algebra.
+
+# Usage
+
+### Config File
+
+First generate a config file for Make starting from `example_config.mk`:
+
+```cp example_config.mk config.mk```
+
+Change `BOOST_PATH` and `EIGEN_INC_PATH` in `config.mk` to point to your installations of Boost and Eigen.
+
+### Compile
+
+Create the build directories:
+
+```mkdir obj2d obj3d bin```
+
+And compile with:
+
+```make```
+
+This will generete two executables, `bin/ga_simulation_2d` for running two-dimensional simulations and `bin/ga_simulation_3d` for running three-dimensional simulations.
+
+### Run
+
+Finally, modify the `params.txt` file to specify physical system you would like to simulate. You can now run with:
+
+```./bin/ga_simulation_2d```
+
+After, the simulation finishes, it will output a `frame_NNN.xyz` file (where `NNN` is the number of particles) that lists the positions off all the particles in the cluster. This file can be vizualized with [Ovito](https://www.ovito.org/).
+
+