Comments (2)
I'm not convinced that the current hardcoded matrix (primitive to conventional) should be the default. It depends on the outcome lattice type, and this is not fixed.
I'd rather we used the pymatgen machinery here, e.g. pymatgen has Structure.to_primitive
/ Structure.to_conventional
, which uses SpacegroupAnalyzer.get_[primitive|conventional]_standard_structure
, which uses SpacegroupAnalyzer.get_conventional_to_primitive_transformation_matrix
.
from gemdat.
We can configure it so the user can specify the matrix.
from gemdat.
Related Issues (20)
- Orientations methods wrongly assume primitive-to-conventional transformation
- orientations function to return non-normalized cartesian vectors HOT 1
- autocorrelation should use unit vectors
- Orientations should return Trajectories instead of np.ndarrays HOT 2
- Streamline Orientations api HOT 1
- Rename 'mean squared angular displacement' to 'autocorrelation' everywhere HOT 2
- Add citation / zenodo link to readme
- Update captions to all plots HOT 2
- Revise shaded areas for plots
- More plotly plots HOT 1
- Return molecule trajectory from Orientations
- Tests are failing HOT 2
- Move legacy.py to scipts
- Add plotly plot for shape analysis
- Make backend for plots user configurable
- Approach to percolation with networkx graphs HOT 1
- Statistical average activation energy for edges in jump network
- MSD plot HOT 11
- example notebooks broken - plots backend option HOT 6
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from gemdat.