Add cache to StructureStorage.get_elements #568
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
For multi million element storages this functions is quite slow ~1s, so cache it. We cannot use standard lib caches since arrays are mutable, instead invalidate the cache on each write access to the 'symbols' array.
pmrv
added
enhancement
Pull Request Test Coverage Report for Build 2003366645
💛 - Coveralls |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This method got quite slow when used on storages with millions of atoms, so I put a cache in front of it. The method is still slow, but iterating over large storages is usable now.
An alternative would be to save only element indices in the storage and translate them to chemical symbols.
np.uniqueshould be much faster on integers, but I haven't checked that and thought it's not necessary so far.