/chiral-symmetry-breaking

Analysis scripts and input files to reproduce simulations of manuscript "Critical behavior in a chiral molecular model" by Piaggi, Car, Stillinger, and Debenedetti. Output files are available at https://doi.org/10.34770/aby7-r955

Primary LanguageJupyter Notebook

Critical behavior in a chiral molecular model

Authors: Pablo M. Piaggi, Roberto Car, Frank H. Stillinger, Pablo G. Debenedetti

DataSpace

Analysis scripts and input files to reproduce simulations of manuscript "Critical behavior in a chiral molecular model" by Piaggi, Car, Stillinger, and Debenedetti. Output files are available at this link.

Description of folder contents:

  • SystemSize<N>tetramers: Input and output files of molecular dynamics simulations for a system with molecules. Inside each folder there are subfolders T-<temp> where is the temperature. In each subfolder, the following files can be found:
    • in.lammps: LAMMPS input file
    • in.restart.lammps: LAMMPS input file for restarts
    • initialconfig.dat: Initial configuration in LAMMPS data format
    • forcefield-base.dat: Force field parameters
    • job.sh: Slurm submission script
  • Clustering: Clustering script and results:
    • cluster.py: Python script to perform clustering
  • Analysis.ipynb: Jupyter notebook with scripts to generate figures

Simulations were performed using the following code:

The jupyter notebook and the python script were tested with the following packages:

  • Python 3.8.8 [GCC 7.3.0]
  • Matplotlib 3.3.4
  • Numpy 1.24.2
  • Scipy 1.9.1
  • Freud 2.8.0
  • Ase 3.20.1

Please e-mail me if you have trouble reproducing the results.