0.3.0 tasks (md update)

[wolearyc]

This update brings molecular-dynamics-derived Raman spectra to ramannoodle.

New features

• Trajectory class for storing molecular dynamics trajectories. a3e4508
• MDRamanSpectrum for manipulating MD-derived Raman spectra. a3e4508
• New IO functionality
  • Read/write support for VASP XDATCAR ea00e68
  • Read support for vasprun.xml 6974243
  • Trajectory reading for VASP OUTCAR bef82ce

API changes

• PolarizabilityModel.get_polarizability -> PolarizabilityModel.calc_polarizabilities 0b9bde9 ef5c6b1
  • calc_polarizability takes fractional positions instead of Cartesian displacements 50fc9ff
  • calc_polarizability takes a batch of fractional positions ef5c6b1
• calculate_displacement -> calc_displacement 7d596d5
• Phonons includes reference positions and represents vibrations as fractional displacements, not Cartesian displacements 50fc9ff
• InterpolationModel.equilibrium_polarizability --> InterpolationModel.ref_polarizability 70fe3f8
• file_paths --> filepaths 4a4b030
• get_num_nonequivalent_atoms -> num_nonequivalent_atoms property. 77e4ca7

Minor enhancements and bugfixes

• calc_displacement computes displacement relative to first argument 2391109
• dependabot integration abc661d
• Renamed "*_file" args in IO functions to simply "file" a613713
• convolve_spectrum uses better default wavenumbers 8419de1
• Dependency management
  • Specify minimum dependencies c6e76d8
  • Github action to check minimum dependencies c6e76d8
  • tabulate is now a listed dependency c6e76d8
• Action runners for macos, windows

Documentation updates

• Molecular dynamics tutorial 88242fe
• Update readme to highlight MD features
• Extensive improvements to tutorials and documentation