fix simplex boundary #838
Merged
fix simplex boundary #838
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
The implementations of the degree one std and the bubble bases for the `SimplexTopology` incorrectly assume that the `simplices` array contains vertex in `range(nverts)` without holes, and use this array as is as dofs, thereby introducing zeros in the basis for every dof in `set(range(simplices.max() + 1)) - set(simplices.flat)`. The boundary of a `SimplexTopology`, however, simply returns a subset of the volume `simplices` array, without renumbering. This bug was introduced by 7e29a28, which removes `_renumber` as preprocessor for the `simplices` parameter of the `SimplexTopology` constructor. To fix this problem this patch adds a `contiguous_simplices` property and uses thses as dofs. The alternative, requiring constructing a `SimplexTopology` with contiguous `simplices`, was rejected because this puts a computational burden on every boundary of a `SimplexTopology`, even if we don't create a basis.
This patch adds the `connectivity` attribute to `EmptyTopology` for completeness.
This patch implements the `boundary` and `interfaces` attributes for the `EmptyTopology`, which is needed by a subsequent patch fixing empty boundaries of a `SimplexTopology`.
joostvanzwieten
force-pushed
the
fix-simplex-boundary
branch
from
900d569
to
70f5fc8
Compare
The constructor of `SimplexTopology` trips over
assert numpy.greater(self.simplices[:, 1:], self.simplices[:, :-1]).all()
if there are no simplices. This is triggered when taking the boundary of
a fully periodic mesh.
This patch fixes the problem by returning an `EmptyTopology` when the
boundary is empty. In addition this patch adds a slightly improved error
message when trying to create an empty `SimplexTopology.
joostvanzwieten
force-pushed
the
fix-simplex-boundary
branch
from
70f5fc8
to
41090cc
Compare
gertjanvanzwieten
approved these changes
Nov 28, 2023
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 PR fixes two issues with boundaries of the
SimplexTopology:SimplexTopologyis empty, an assertion error is raised.SimplexTopologytypically contains a large number of zeros.