A python module for analysis of mixed quantum-classical trajectory simulations, calculation of scattering observables, frequencey calculations, coordinate transforms, and the generation of potential energy surfaces.
- git clone this repo
- run
pip install -e .in the root directory of the repo for development - otherwise run
pip install .in the root directory
- Initialise trajectories from xyz files
- Calculate internal coordinates
- Calculate RMSD over time wrt a reference structure
- Calculate rotationally averaged scattering signals
- Non-resonant x-ray scattering
- Electron scattering
- Calculate vibrational frequencies and normal modes from a Hessian file
- Compute the Hessian of a structure through a wrapper to pyscf (dft, mp2, ccsd, scf)
- Displace a reference structure along selected normal modes
- Transform from cartesian to normal mode coordinates and back
- Transform from cartesian to internal coordinates
- Generate grids that can be used in an electronic structure code
- Normal mode coordinates
- Cartesian coordinates
- Internal coordinates
- TBD
install pdoc3 if not installed:
pip install pdoc3
to generate a local server to view documentation of the modules run the following command in the root directory of the repo
pdoc3 --http localhost:8080 QMDAnalysis
go to:
http://localhost:8080