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.
SystemSize<N>tetramers
: Input and output files of molecular dynamics simulations for a system with molecules. Inside each folder there are subfoldersT-<temp>
where is the temperature. In each subfolder, the following files can be found:in.lammps
: LAMMPS input filein.restart.lammps
: LAMMPS input file for restartsinitialconfig.dat
: Initial configuration in LAMMPS data formatforcefield-base.dat
: Force field parametersjob.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:
- Modified version of LAMMPS available at this GitHub repository.
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.