Release sage 2.0.0 opt/torsion #419

jaclark5 · 2024-12-18T20:07:45Z

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 · 2024-12-18T22:47:31Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,H ,P ,C ,S ,I ,Cl ,Br ,O ,F
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

lilyminium

Largely LGTM, just a few minor nitpicks!

...024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/generate-combined-dataset.py

submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/README.md

submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/ds_info.json

openff-dangerbot · 2024-12-19T14:25:14Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,P ,H ,I ,C ,Br ,S ,O ,F ,Cl
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

openff-dangerbot · 2024-12-19T14:31:02Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,P ,H ,I ,C ,Br ,S ,O ,F ,Cl
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

openff-dangerbot · 2024-12-19T15:32:39Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,P ,H ,I ,C ,Br ,S ,O ,F ,Cl
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

openff-dangerbot · 2024-12-19T15:37:11Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,P ,H ,I ,C ,Br ,S ,O ,F ,Cl
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

…g-Dataset-v1.0/generate-combined-dataset.py Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>

openff-dangerbot · 2024-12-19T17:14:31Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,P ,H ,I ,C ,Br ,S ,O ,F ,Cl
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

openff-dangerbot · 2024-12-20T14:49:16Z

QCSubmit Validation Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/dataset.json.bz2
Dataset Name	OpenFF Sage 2.0.0 Torsion Drive Training Dataset v1.0
Dataset Type	TorsionDriveDataset
Elements	N ,P ,H ,I ,C ,Br ,S ,O ,F ,Cl
Valid Cmiles	🔥
Connected Dihedrals	🔥
No Linear Torsions	🔥
No Molecular Complexes	🔥
Valid Constraints	🔥
Complete Metatdata	🔥

QC Specification Report

	submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-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	0.16.7
basis_set_exchange	0.10
qcelemental	0.28.0
rdkit	2024.09.3

…-submision

jaclark5 · 2025-04-29T16:00:57Z

@lilyminium Because of how this works, I can't generate the statistics until I make the dataset. If everything that is here now looks good then I'll run this before merging so that if I need any tweaks I can record them without a PR.

lilyminium · 2025-04-30T20:36:25Z

To do (from live discussion):

I'll check the metadata
JC runs the code once approved
JC will merge the PR after checking results

lilyminium

Largely LGTM Jen, I added some nitpicky comments to the description and the version number should be updated :-)

submissions/2025-02-10-OpenFF-Sage-2.0.0-Optimization-Training-Dataset-v1.1/README.md

submissions/2025-02-10-OpenFF-Sage-2.0.0-Optimization-Training-Dataset-v1.1/ds_info.json

submissions/2025-02-10-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/README.md

submissions/2025-02-10-OpenFF-Sage-2.0.0-Torsion-Drive-Training-Dataset-v1.0/ds_info.json

submissions/2025-05-01-OpenFF-Sage-2.0.0-Optimization-Training-Dataset-v1.1/README.md

lilyminium · 2025-05-05T14:51:13Z

Otherwise LGTM -- thanks @jaclark5! Feel free to run :-)

jaclark5 · 2025-05-05T17:49:44Z

Blocked: Copying the torsion drive records resulted in 115 of 713 records being duplicated, despite a DeepDiff showing only the record id and date of creation are changed. This PR is blocked until this is resolved.

jaclark5 added 3 commits December 18, 2024 14:22

Mostly fix dataset creation

61ba04b

Final output

2b0acda

Update files

75050c3

jaclark5 added the tracking label Dec 18, 2024

jaclark5 requested a review from lilyminium December 18, 2024 23:03

lilyminium requested changes Dec 19, 2024

View reviewed changes

Updated dataset description

1e80a61

jaclark5 added 2 commits December 19, 2024 09:25

Merge branch 'master' into release_sage_2.0.0_torsion

f773c3f

Update repo README table

02d699a

Add current conda env

9beae14

Format README

aa650b5

Update submissions/2024-12-17-OpenFF-Sage-2.0.0-Torsion-Drive-Trainin…

b236125

…g-Dataset-v1.0/generate-combined-dataset.py Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>

jaclark5 requested a review from lilyminium December 19, 2024 19:01

jaclark5 added 2 commits December 20, 2024 09:47

Update Generator field 2.0.0 Opt

87f8edd

Update docs

e4938d4

lilyminium assigned lilyminium and jaclark5 Jan 13, 2025

jaclark5 unassigned lilyminium Jan 15, 2025

jaclark5 marked this pull request as draft January 27, 2025 19:21

jaclark5 changed the title ~~Release sage 2.0.0 torsion~~ Release sage 2.0.0 opt/torsion Feb 11, 2025

Remove unneeded files, initial draft of attempt to bypass qca-dataset…

774d8a5

…-submision

lilyminium removed the tracking label Apr 14, 2025

Update process to directly copy records

0f7763f

jameseastwood assigned lilyminium and unassigned jaclark5 Apr 29, 2025

lilyminium approved these changes Apr 30, 2025

View reviewed changes

jameseastwood assigned jaclark5 and unassigned lilyminium May 1, 2025

jaclark5 added 3 commits May 1, 2025 12:38

Update metadata

029aa14

Merge branch 'master' into release_sage_2.0.0_torsion

6922e09

Update scaffold

e04175d

jaclark5 added the validation-off label May 1, 2025

jaclark5 marked this pull request as ready for review May 1, 2025 16:49

lilyminium reviewed May 5, 2025

View reviewed changes

submissions/2025-05-01-OpenFF-Sage-2.0.0-Optimization-Training-Dataset-v1.1/README.md Outdated Show resolved Hide resolved

jaclark5 added 2 commits May 5, 2025 10:52

Added opt dataset

ad3d605

Update torsiondrive dataset

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Release sage 2.0.0 opt/torsion #419

Release sage 2.0.0 opt/torsion #419

jaclark5 commented Dec 18, 2024 •

edited

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jaclark5 commented May 5, 2025

Release sage 2.0.0 opt/torsion #419

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Release sage 2.0.0 opt/torsion #419

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jaclark5 commented Dec 18, 2024 • edited Loading

New Submission Checklist

openff-dangerbot commented Dec 18, 2024

QCSubmit Validation Report

QC Specification Report

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openff-dangerbot commented Dec 19, 2024

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Dec 19, 2024

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Dec 19, 2024

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Dec 19, 2024

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Dec 19, 2024

QCSubmit Validation Report

QC Specification Report

openff-dangerbot commented Dec 20, 2024

QCSubmit Validation Report

QC Specification Report

jaclark5 commented Apr 29, 2025

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jaclark5 commented Dec 18, 2024 •

edited

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