Calculate sites data from materials input

[stefsmeets]

This issue tracks processing the 'known materials' data and calculating sites data.

Features

• Read known materials from standard crystallographic input (wyckhof symbol, cif file, or otherwise?) -> Add methods to load a material from a CIF file #18

Variables

• Add implementation for calculating site transitions #19

  • transitions
  • all_transitions
  • succes
  • occupancy
  • occupancy_parts
  • atoms (atom_sites)

• Calculate occupancy per site #36

  • sites_occupancy
  • sites_occupancy_parts
  • atom_locations
  • atom_locations_parts

• Calculate jump rates and activation energy #43

  • jump_names
  • nr_jumps
  • rates
  • e_act

• Add implementation for calculating collective jumps #56

  • collective
  • collective_jumps
  • collective_matrix
  • multi_collective
  • solo_jumps
  • solo_frac

• Calculate jump diffusivity #48

  • jump_diffusivity
  • correlation_factor

[stefsmeets]

EDIT: solved by #18

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One of the issues I'm running into is a mismatch between the known materials and data in the simulation.

In our sample data, for argyrodite, the reported space group symmetry is $F\overline{4}3m$ (cubic). The sites in known materials are for 48h, which only exist in the cubic space group. The lattice in the simulation is triclinic (a=19.87, b=9.92, c=9.92, al=90.21, be=90.86, ga=89.95). These don't match.

This makes it difficult to define the sites in a standard crystallographic format.

[stefsmeets]

I think we got everything now, this issue can be closed! 🚀