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Published 20 hours ago • verified publisher icon MolSSI

[WIP] [draft] Add a TS search module

Open alongd opened this issue 5 years ago • 4 comments

Description

This PR enhances fractal with reaction transition state search capabilities. Methods which will be implemented are: AutoTST, DE-GSM, brute-force heuristics, KinBot, ML, NEB via ASE, NEB via TeraChem, and STQN QST2 via Gaussian.

Changelog description

Added the ts_search module under interface.models Added RMG-Py as a dependency (three of the above methods require identification of the reaction family, heuristics also require atom labelling by RMG)

This is a draft PR. Todo list:

  • [x] Conda package zmats
  • [ ] Add zmats as a dependency
  • [ ] Implement AutoTST
  • [ ] Implement DE-GSM
  • [ ] Implement KinBot
  • [ ] Implement NEB-ASE
  • [ ] Implement NEB-TeraChem
  • [ ] Implement QST2
  • [ ] Complete H Abstraction heuristics implementation
  • [ ] Implement heuristics for additional reaction families
  • [ ] Add tests for all modules

Status

  • [ ] Code base linted
  • [ ] Ready to go

alongd avatar Feb 06 '20 02:02 alongd

This pull request introduces 11 alerts when merging e625dfa324abc53291a48eeb8571901ae941101d into f40dd1a9efa0e0fa44746e8db6dba28967ac0202 - view on LGTM.com

new alerts:

  • 7 for Unused import
  • 4 for Module imports itself

lgtm-com[bot] avatar Feb 06 '20 02:02 lgtm-com[bot]

This pull request introduces 13 alerts when merging 81f1e00a6802f6814db4c3cceae93acd18989a1f into 123c89f1cea4cbc962d366e9d520ce618b91b97e - view on LGTM.com

new alerts:

  • 7 for Module imports itself
  • 5 for Unused import
  • 1 for Variable defined multiple times

lgtm-com[bot] avatar Feb 12 '20 04:02 lgtm-com[bot]

This pull request introduces 13 alerts when merging 50bfa2d069b6a29247b2b3c47ce05100bc8c7853 into 137cb91d4409a1395273239a9df668a314a1914b - view on LGTM.com

new alerts:

  • 7 for Module imports itself
  • 5 for Unused import
  • 1 for Variable defined multiple times

lgtm-com[bot] avatar Feb 18 '20 16:02 lgtm-com[bot]

This pull request introduces 14 alerts when merging 99b8e49b00cb34f3734e023aeca185393516c46d into 137cb91d4409a1395273239a9df668a314a1914b - view on LGTM.com

new alerts:

  • 7 for Module imports itself
  • 5 for Unused import
  • 1 for Implicit string concatenation in a list
  • 1 for Variable defined multiple times

lgtm-com[bot] avatar Feb 18 '20 19:02 lgtm-com[bot]

I am certainly interested in adding a TS feature/calculation type. This PR is outdated, though, and no longer applies to v0.50.

bennybp avatar Sep 14 '23 15:09 bennybp