chemcoord icon indicating copy to clipboard operation
chemcoord copied to clipboard

Added B matrix functionality

Open nwhel opened this issue 1 year ago • 2 comments

Added support for primitive internal coordinates, Wilson B matrices, and generating trajectories using these.

nwhel avatar Jan 14 '25 19:01 nwhel

Codecov Report

Attention: Patch coverage is 0% with 161 lines in your changes missing coverage. Please review.

Project coverage is 0.00%. Comparing base (6bf9e98) to head (b474b14). Report is 7 commits behind head on master.

Files with missing lines Patch % Lines
...rd/_cartesian_coordinates/_cartesian_class_bmat.py 0.00% 144 Missing :warning:
src/chemcoord/_utilities/typing.py 0.00% 15 Missing :warning:
...ord/_cartesian_coordinates/cartesian_class_main.py 0.00% 2 Missing :warning:
Additional details and impacted files
@@           Coverage Diff           @@
##           master    #122    +/-   ##
=======================================
  Coverage    0.00%   0.00%            
=======================================
  Files          29      31     +2     
  Lines        2761    2921   +160     
=======================================
- Misses       2761    2921   +160     

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

codecov[bot] avatar Jan 14 '25 21:01 codecov[bot]

  • [x] tests tests tests
  • [x] no mutable default arguments
  • [ ] break into functions
  • [ ] smaller helper function for doing a step and then backwards interpolation
  • [x] decorator wrapper for mypy and numba.njit, passing on __annotation__
  • [x] ensuring that stuff stays array and/or list when it is array and/or list
  • [x] pass in cartesian coordinates + lookup table instead of pos_arr
  • [ ] more descriptive names
  • [ ] fragment-based code
  • [x] pure internal movement (?) (get_inertia and get_barycenter might be useful)

perhaps (could be done for another MR)

  • [x] profiling

mcocdawc avatar Jan 15 '25 22:01 mcocdawc