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QMDAnalysis

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.

Installation

  • 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

Modules

Trajectories:

  • Initialise trajectories from xyz files
  • Calculate internal coordinates
  • Calculate RMSD over time wrt a reference structure

Scattering:

  • Calculate rotationally averaged scattering signals
  • Non-resonant x-ray scattering
  • Electron scattering

Frequencies:

  • 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

Coordinate Transforms:

  • Transform from cartesian to normal mode coordinates and back
  • Transform from cartesian to internal coordinates

Potential Generation:

  • Generate grids that can be used in an electronic structure code
  • Normal mode coordinates
  • Cartesian coordinates
  • Internal coordinates

DVR:

  • TBD

Generating documentation

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

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