OpenFF Lipid Optimization Benchmark Supplement v1.0

[ntBre]

This is the benchmarking counterpart to #394, constructed from full molecules in the LIPID MAPS database. I think this is generally ready to go (besides updating the main README), but I'm leaving it as a draft because @j-wags and I discussed a bit about possibly partitioning datasets based on molecule size to make requesting compute resources of a certain size easier. We weren't sure exactly where to draw that cutoff, but this set ranges in size from 6 atoms to 106 atoms, so I thought it might be worth discussing. (Edit: the splitting stuff is resolved by the new tagging mechanism in #412, so this should be good to go).

New Submission Checklist

• Created a new folder in the submissions directory containing the dataset
• Added README.md describing the dataset see here for examples
• All files used to produce the dataset are included with a description
• Dataset follows the QCSubmit schema defined for Datasets, OptimizationDatasets and TorsionDriveDatasets
• Dataset filename matches pattern dataset*.json; may feature a compression extension, such as .bz2
• A PDF depicting the molecules is attached, in the case of torsiondrives this should include the highlighting of the central bond, this can be done automatically using qcsubmit.
• QCSubmit validation passed
• Made a new dataset entry in the mapping table in repository README.md
• Ready to submit!

[openff-dangerbot]

QCSubmit Validation Report

	submissions/2024-10-30-OpenFF-Lipid-Optimization-Benchmark-Supplement-v1.0/dataset.json.bz2
Dataset Name	OpenFF Lipid Optimization Benchmark Supplement v1.0
Dataset Type	OptimizationDataset
Elements	O ,H ,C ,Br ,P ,N ,Cl ,F ,S ,I
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-10-30-OpenFF-Lipid-Optimization-Benchmark-Supplement-v1.0/dataset.json.bz2/default
Specification Name	default
Method	B3LYP-D3BJ
Basis	DZVP
Wavefunction Protocol	none
Implicit Solvent
Keywords	{}
Validated	🔥
Valid SCF Properties	🔥
Full Basis Coverage	🔥

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.53.0
openff.toolkit	0.16.5
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.2

[openff-dangerbot]

QCSubmit Validation Report

	submissions/2024-10-30-OpenFF-Lipid-Optimization-Benchmark-Supplement-v1.0/dataset.json.bz2
Dataset Name	OpenFF Lipid Optimization Benchmark Supplement v1.0
Dataset Type	OptimizationDataset
Elements	O ,H ,C ,Br ,P ,N ,Cl ,F ,S ,I
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-10-30-OpenFF-Lipid-Optimization-Benchmark-Supplement-v1.0/dataset.json.bz2/default
Specification Name	default
Method	B3LYP-D3BJ
Basis	DZVP
Wavefunction Protocol	none
Implicit Solvent
Keywords	{}
Validated	🔥
Valid SCF Properties	🔥
Full Basis Coverage	🔥

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.54.0
openff.toolkit	0.16.6
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

[ntBre]

Marking this ready for review now that #412 is in, and we don't need to worry about splitting it.

[lilyminium]

Minor note about the threshold -- otherwise LGTM. Looking forward to see how the split workers go!

[openff-dangerbot]

QCSubmit Validation Report

	submissions/2024-10-30-OpenFF-Lipid-Optimization-Benchmark-Supplement-v1.0/dataset.json.bz2
Dataset Name	OpenFF Lipid Optimization Benchmark Supplement v1.0
Dataset Type	OptimizationDataset
Elements	O ,H ,C ,Br ,P ,N ,Cl ,F ,S ,I
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-10-30-OpenFF-Lipid-Optimization-Benchmark-Supplement-v1.0/dataset.json.bz2/default
Specification Name	default
Method	B3LYP-D3BJ
Basis	DZVP
Wavefunction Protocol	none
Implicit Solvent
Keywords	{}
Validated	🔥
Valid SCF Properties	🔥
Full Basis Coverage	🔥

QCSubmit version information(click to expand)

	version
openff.qcsubmit	0.54.0
openff.toolkit	0.16.6
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

[lilyminium]

LGTM thank you Brent! I'll let you merge so you can figure out compute tags?

[lilyminium]

  File "/home/runner/work/qca-dataset-submission/qca-dataset-submission/./management/lifecycle.py", line 16, in <module>
    from qcelemental.models import Molecule
ModuleNotFoundError: No module named 'qcelemental'

Ah oops -- probably from #412. Surprised it's not pulled in by qcportal!

Edit: actually it's the backlog environment and script, I'll open a PR to only import on type checking