Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bespoke clean up #77

Merged
merged 4 commits into from
Oct 21, 2021
Merged

Bespoke clean up #77

merged 4 commits into from
Oct 21, 2021

Conversation

jthorton
Copy link
Contributor

@jthorton jthorton commented Oct 13, 2021

Description

This PR fixes some small issues in the bespokefit pipeline and simplifies some of the models.

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Remove the bespoke workflow factory smirks argument as this is included in the parameter hyper parameters field
  • add the option to keep fitting files
  • Remove the optimisation schema and re-use the qcsubmit object
  • Fix default geometric settings in torsion drives
  • Make sure we try and select heavy atoms in torsiondrives where possible
  • Fix the initial values for bespoke torsion parameters
  • Fix initial_parameter_values to return all of the fitting attributes per parameter

Questions

  • How should we expose the keep files option? as a workflow factory setting?

Status

  • Ready to go

…e torsions. Correct TD base settings in line with torsiondrive, use qcsubmit optimisation spec.
@codecov
Copy link

codecov bot commented Oct 13, 2021

Codecov Report

Merging #77 (931bb66) into master (dffb29e) will increase coverage by 0.07%.
The diff coverage is 97.29%.

Copy link
Contributor

@SimonBoothroyd SimonBoothroyd left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

A few minor suggestions but otherwise LGTM! Thanks for these fixes / improvements!

openff/bespokefit/utilities/smirnoff.py Outdated Show resolved Hide resolved
openff/bespokefit/workflows/bespoke.py Show resolved Hide resolved
openff/bespokefit/utilities/smirks.py Outdated Show resolved Hide resolved
openff/bespokefit/schema/tasks.py Outdated Show resolved Hide resolved
openff/bespokefit/schema/tasks.py Show resolved Hide resolved
Comment on lines +16 to +18
program: str = Field(..., description="The program to use to evaluate the model.")
model: Model = Field(..., description=str(Model.__doc__))

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Did you want to replace these with the QCSpec model at some point?

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes I think the validation in the QCSpec model should help avoid a lot of errors Ill swap these fields out for a qc_spec field.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is done in df5a6bf but this means that the qc cache now depends on arbitrary fields like the spec name and spec description, maybe the QCSpec object should be split in qcsubmit to offer a version without these fields but which still offers the validation?

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ahh true... yeah I think splitting would be good! Would it be worth revisiting openforcefield/openff-qcsubmit#152 at the same time?

openff/bespokefit/executor/services/qcgenerator/worker.py Outdated Show resolved Hide resolved
@SimonBoothroyd
Copy link
Contributor

How should we expose the keep files option? as a workflow factory setting?

We could also expose it as a setting of the service itself: https://github.com/openforcefield/bespoke-fit/blob/master/openff/bespokefit/executor/services/settings.py

@lgtm-com
Copy link

lgtm-com bot commented Oct 14, 2021

This pull request introduces 1 alert when merging df5a6bf into dffb29e - view on LGTM.com

new alerts:

  • 1 for Unused import

@jthorton jthorton merged commit 8688820 into master Oct 21, 2021
@jthorton jthorton deleted the bespoke_clean branch October 21, 2021 11:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants