README.md

CG_cages

This repository contains code to simulate the packing of cages based off of the paper Coarse-grained modelling to predict the packing of porous organic cages

Before running the code you will need to make sure you are using HOOMD v2.9.6 specifically with jit installed.

This code assumes there is a folder in the working directory named output where your output files (a log file and a gsd file) are written to.

To run the code you will need to specify the patch width, $\sigma_{ang}$, for both the window-to-window patches and window-to-arene, as well as the interaction strength, $J$, for each interaction type. For example, for simulations where the window-to-window(arene) interactions have a patch width where $\sigma_{ang}=0.3(0.4)$ and $J=30(50)$ the simulation would be run as

python patchy_temp_decrease.py 0.3 0.4 30 50

An example of output files for some simulations are given in the output directory. The titles are labelled as phase_1.00_0.60_0.50_0.30_0_50_temp.log/gsd where $\sigma_{tor}$(window-to-window)=1.00, $\sigma_{tor}$(window-to-arene)=0.60, $\sigma_{ang}$(window-to-window)=0.50, $\sigma_{ang}$(window-to-arene)=0.30, $J$(window-to-window)=0, and $J$(window-to-arene)=50.