Does anyone know of a good way to calculate the covariance matrix from LAMMPS data? Is there a way to do this in LAMMPS? If not, what open source tools do people use to do this?
I’m trying to do principal component analysis (PCA, also known as quasi-harmonic analysis), and need to calculate the fluctuation matrix / covariance matrix.
Any help pointing me to good open source solutions to this problem would be appreciated.
Thank you very much for taking the time to read this.
Stressed-out Ph.D student.