search

nlesc-nano / auto-FOX

A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
GNU Lesser General Public License v3.0
9 stars 8 forks source link

ENH: Add a recipe for calculating the similarity between 2 MD trajectories #207

Closed BvB93 closed 3 years ago

BvB93 commented 3 years ago

Closes https://github.com/nlesc-nano/auto-FOX/issues/206.

TODO

Generated Docs

https://auto-fox--207.org.readthedocs.build/en/207/7_recipes.html#module-FOX.recipes.similarity

codecov[bot] commented 3 years ago

Codecov Report

Merging #207 (eea560b) into master (755b92c) will decrease coverage by 0.14%. The diff coverage is 67.85%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #207      +/-   ##
==========================================
- Coverage   76.22%   76.08%   -0.15%     
==========================================
  Files          59       60       +1     
  Lines        6146     6221      +75     
  Branches     1026     1047      +21     
==========================================
+ Hits         4685     4733      +48     
- Misses       1201     1222      +21     
- Partials      260      266       +6
Impacted Files Coverage Δ
FOX/functions/rdf.py 62.50% <13.33%> (-29.81%) :arrow_down:
FOX/classes/multi_mol_magic.py 89.94% <60.00%> (-0.92%) :arrow_down:
FOX/classes/multi_mol.py 73.10% <65.71%> (-0.55%) :arrow_down:
FOX/recipes/__init__.py 100.00% <100.00%> (ø)
FOX/recipes/similarity.py 100.00% <100.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update cca2f82...eea560b. Read the comment docs.

BvB93 commented 3 years ago

As a comment on https://github.com/nlesc-nano/auto-FOX/pull/207/commits/7b6afbbdd30fbdd2302a060c12aeed91c25bc478: ase.Atoms internally seems to store most of its properties as arrays, which is excellent because FOX.MultiMolecule does the same. As a consequence, interconversion between the two is quite fast.