mhellstr/packmol with current structure #181
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
…cks tightly in non-orthorhombic cells, but may fail for very skewed cells. SO--
dormrod
reviewed
Dec 4, 2024
mhellstr
changed the title
|
Once merged I'll update the regression nightly test output |
dormrod
reviewed
Dec 13, 2024
| return my_packed | ||
|
|
||
|
|
||
| @requires_optional_package("scm.libbase") |
There was a problem hiding this comment.
This is bold, are we sure we want to limit this in such a way at the moment? None of the other packmol methods have such a restriction, and as libbase can't currently be installed outside amspython, we are limiting its usage to there currently?
| trafo = np.linalg.inv(original_ucs.lattice.vectors) @ np.array(target_lattice) | ||
| trafo = np.sign(trafo) * np.ceil(np.abs(trafo)) | ||
| trafo = np.int_(trafo) | ||
| supercell.supercell_trafo(trafo) |
There was a problem hiding this comment.
Also for example the UCS public interface is not yet stable... although I agree it is easier to do this in UCS.
If we don't have UCS available should there always be a fallback to the plams molecule?
Comment on lines
+984
to
+985
| out_ucs = original_ucs.copy() | ||
| out_ucs.add_other(distorted) |
There was a problem hiding this comment.
(could be out_ucs = original_ucs + distorted)
dormrod
approved these changes
Dec 16, 2024
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Outdated suggestions cannot be applied.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.
@dormrod one existing issue with this branch (for example if you run examples/PackMo.py) is that it leaves a plams_workdir folder on disk.
Do you know how to safely delete this if it only contains this kind of packmol job, but definitely not delete it if it contains user jobs (or if user jobs are run after the packmol job)?
See SCMSUITE-10086 and SCMSUITE-7478 for details.