mxene project

Analyzing how entropy-driven aggregation drives phase separation in mxene-polymer systems

⚙️ Installation

Run the following in your terminal:

bash/zsh

git clone [email protected]:eridanirojas/mxene.git

then navigate into mxene

cd mxene

Create the conda environment

conda env create -f environment.yml

Activate the environment

conda activate mxene

If GPU compatible version required of hoomd, run

conda install -c conda-forge "hoomd=*=gpu*"

Launch Jupyter, run

jupyter notebook

Then, in order to run a small scale simulation, navigate to the sims/ directory:

• clean_sim.ipynb = current working simulation you should use, shrink step is included allowing system to be packed loosely then shrunk to be dense, causing more interactions to occur
• clean_sim_with_randomwalk.ipynb = a future notebook, has a shrink step but also manipulates the geometry of the chains is randomly set so that we may set a dihedral to be something other than zero

To analyze results, navigate to working_example/:

• clustering_plots.ipynb = we use this to determine the magnitude of clustering over time in a simulation. this means both size and amount of clusters, also using independent samples
• TPSvsN.ipynb = a notebook to graph TPS v. N

In order to run a large scale simulation, navigate to signac/:

• submit.sh = running sbatch submit.sh will run sim_with_shrink.py as it currently is, with the configurations present in this file.
• sim_with_shrink.py = simulation file specifically made for running on cluster