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Implement DHS and DHS-GS methods #272

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merged 42 commits into from
Jun 5, 2023
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shoubhikraj
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@shoubhikraj shoubhikraj commented Apr 21, 2023

Implements Dewar-Healy-Stewart method and the hybrid DHS-GS (growing string) method. Optionally run CI-NEB from the end points of converged DHS and DHS-GS method. Also added the base classes for other bracketing methods that could be implemented in future.

Minor changes:

  1. Added feature for plotting the energies from a DHS/DHS-GS/other bracketing methods
  2. Return a copy instead of new_species from NEB/CI-NEB so that the energy can be read

Checklist

  • The changes include an associated explanation of how/why
  • Test pass
  • Documentation has been updated
  • Changelog has been updated

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codecov bot commented Apr 21, 2023

Codecov Report

Merging #272 (c5f47a3) into v1.4.0 (6210a14) will increase coverage by 0.08%.
The diff coverage is 98.52%.

@@            Coverage Diff             @@
##           v1.4.0     #272      +/-   ##
==========================================
+ Coverage   97.24%   97.32%   +0.08%     
==========================================
  Files         197      203       +6     
  Lines       21013    22055    +1042     
==========================================
+ Hits        20434    21466    +1032     
- Misses        579      589      +10     
Flag Coverage Δ
unittests 97.32% <98.52%> (+0.08%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
autode/opt/optimisers/base.py 97.94% <81.25%> (-0.26%) ⬇️
autode/bracket/base.py 95.65% <95.65%> (ø)
autode/bracket/dhs.py 98.34% <98.34%> (ø)
autode/bracket/imagepair.py 98.78% <98.78%> (ø)
tests/test_bracket/test_imagepair.py 99.53% <99.53%> (ø)
autode/bracket/__init__.py 100.00% <100.00%> (ø)
autode/plotting.py 96.44% <100.00%> (+0.39%) ⬆️
tests/test_bracket/test_dhs.py 100.00% <100.00%> (ø)

... and 7 files with indirect coverage changes

@shoubhikraj shoubhikraj changed the base branch from master to v1.4.0 April 21, 2023 20:43
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Looks awesome so far – thanks
(paused for the moment. hopefully I'll come back to this this evening 🌙 )

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No description provided.

@shoubhikraj shoubhikraj requested a review from t-young31 May 3, 2023 09:02
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🚀

@shoubhikraj
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shoubhikraj commented Jun 1, 2023

@t-young31 I decided to revert the changes to NEB peak_species, and instead put that part of the code in image pair class directly. Pls check the code once more if you want, otherwise feel free to merge the PR. Edit: The tests are failing due to one of the ones that randomly fail. The last commit was only doc change, no other changed.

@shoubhikraj shoubhikraj changed the title DHS and DHS-GS methods Implement DHS and DHS-GS methods Jun 3, 2023
@t-young31 t-young31 merged commit c8aa7e0 into duartegroup:v1.4.0 Jun 5, 2023
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2 participants