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Fix issues #49 and #50 #51

Merged
merged 7 commits into from May 12, 2023
Merged

Fix issues #49 and #50 #51

merged 7 commits into from May 12, 2023

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lohedges
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This pull request closes #49 and closes #50.

For #49 we now add a small bias when performing the triclinic lattice reduction to avoid issues with numerical precision due to the fixed-width format of box lattice vectors and angles in molecular input files. I've added a test to confirm that the resulting box is stable, i.e. it no longer oscillates about two sets of angles. The box is stable regardless of the way in which the triclinic box is instantiated, i.e. from box vectors, or magnitudes and angles.

For #50 I've added an appropriately pinned run_constrained entry for rdkit, so that a compatible version of rdkit will be installed alongside Sire, which currently isn't the case. This is currently entered directly in the conda recipe. It may be desirable to add this to a requirements file to be consistent with the other entries, or if we have other optional requirements that also need constraining. (That said, I'm not sure how the logic would be expressed.)

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

@lohedges lohedges added bug Something isn't working exscientia Related to work with Exscientia labels May 12, 2023
@lohedges lohedges temporarily deployed to sire-build May 12, 2023 13:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to sire-build May 12, 2023 13:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to sire-build May 12, 2023 13:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to sire-build May 12, 2023 13:20 — with GitHub Actions Inactive
@lohedges lohedges temporarily deployed to sire-build May 12, 2023 13:20 — with GitHub Actions Inactive
@lohedges lohedges merged commit 2a85e93 into devel May 12, 2023
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@lohedges lohedges deleted the fix_49_50 branch May 12, 2023 18:18
lohedges added a commit that referenced this pull request May 12, 2023
lohedges added a commit that referenced this pull request May 15, 2023
Backport fixes from PR #51 into main
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