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Add new opt-write sequence. #189

Merged
merged 18 commits into from
Nov 15, 2024
Merged

Add new opt-write sequence. #189

merged 18 commits into from
Nov 15, 2024

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andrewtarzia
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@andrewtarzia andrewtarzia commented Oct 27, 2024 •
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Related Issues: #176
Requested Reviewers: @lukasturcani

  • adds a new sequence optimiser that writes to file
  • fixes the docs
  • makes all code examples (except those requiring external paths, xtb, gulp macrmodel) testcode
  • some minor things
  • Set a numpy version requirement such that the order of install of dev environment and openmm infrastructure does not cause any issues (openmm seems to still require numpy < 2.0) -- a mixed conda/mamba install overrides, without clarity, the numpy and rdkit versions

@andrewtarzia andrewtarzia changed the title Check for dir. Add new opt-write sequence. Oct 28, 2024
@andrewtarzia andrewtarzia marked this pull request as ready for review October 29, 2024 12:19
lukasturcani
lukasturcani approved these changes Nov 5, 2024
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examples/optwrite_example.py Outdated Show resolved Hide resolved
src/stko/_internal/calculators/openmm_calculators.py Outdated Show resolved Hide resolved
src/stko/_internal/calculators/torsion_calculators.py Outdated Show resolved Hide resolved
src/stko/_internal/molecular/torsion/torsion.py Outdated Show resolved Hide resolved
src/stko/_internal/molecular/torsion/torsion_info.py Outdated Show resolved Hide resolved
src/stko/_internal/optimizers/openmm.py Outdated Show resolved Hide resolved
src/stko/_internal/optimizers/openmm.py Outdated Show resolved Hide resolved
src/stko/_internal/optimizers/optimizers.py Outdated Show resolved Hide resolved
@andrewtarzia andrewtarzia mentioned this pull request Nov 15, 2024
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@andrewtarzia andrewtarzia merged commit c39a56a into JelfsMaterialsGroup:master Nov 15, 2024
5 of 6 checks passed
@andrewtarzia andrewtarzia deleted the optwriter_sequence branch November 15, 2024 14:11
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@lukasturcani lukasturcani lukasturcani approved these changes

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@andrewtarzia @lukasturcani