Scripts and data for the paper "Topological data analysis for revealing structural origin of density anomalies in silica glass"
conda create --name TDA python=3.8.11
conda activate TDA
conda install pip
pip install -r requirements.txt
PD_compute.py is a python script to compute PDs using atomic configurations obtained from MD simulations (MDs/quench_atoms_list.pickle). Here, quench_atoms_list.pickle is a pickled file containing the atomic configurations as ASE atoms instances.
Warning: PD calculations for the -O-O- and -Si-O- networks need a large amount of memory. One should try the -Si-Si- network first.
TDA_analysys.ipynb is a jupyter notebook implementing the TDA workflow. The steps of the workflow are consistent with Fig. 1 in the paper.