Functions for Metadynamics analysis

[jcwang587]

Several scripts are currently available for analyzing metadynamics results:

1. fmtd01_xdc2xtc.py: Converts from the XDATCAR format to the .xtc trajectory, a compressed trajectory format from Gromacs.
2. fmtd02_hillspot2hills.py: Converts from the VASP-supported hillspot/penaltypot format to the PLUMED-supported hills format.
3. fmtd03_report_loader.py: Implements a loader function that reads and extracts CV information from VASP-supported report files. It currently supports multiple dimensions of CVs.

The expected functions for metadynamics:

• Calculate 1D and 2D free energy profiles.
• Track the time evolution of CVs (supports multiple dimensions) using extracted information from hills or report files.
• Calculate the 3D free energy profiles, now taking into account the .cube output. This output should be compatible with various visualization software, such as VESTA.