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Fix SOMD #124#403

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lohedges merged 5 commits intodevelfrom
fix_somd_124
Mar 6, 2026
Merged

Fix SOMD #124#403
lohedges merged 5 commits intodevelfrom
fix_somd_124

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@lohedges lohedges commented Mar 5, 2026

This PR provides a convenience method on the sire.mol.dynamics object to fix a performance bug in somd2 that arises from accessing the entire (growing) energy trajectory at the end of each repex cycle. Instead, we store the current energy records each time they are computed and provide a method to return the current values. The values are sorted in ascending lambda order by default when input is provided by somd2, but the convenience function also has a sort kwarg to allow a user to ensure sorted order if the lambda window array that is passed in is unsorted.

  • 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 added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

@akalpokas

@lohedges lohedges merged commit 208c15f into devel Mar 6, 2026
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@lohedges lohedges deleted the fix_somd_124 branch March 6, 2026 14:36
lohedges added a commit that referenced this pull request Mar 6, 2026
lohedges added a commit that referenced this pull request Mar 6, 2026
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