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OpenFF Sulfur Hessian Training Coverage Supplement v1.0 (#384)
* OpenFF Sulfur Hessian Training Coverage Supplement v1.0 * update main readme * add connectivity filter, which removed no records --------- Co-authored-by: Lily Wang <[email protected]>
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‎README.md‎

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|`MLPepper RECAP Optimized Fragments v1.0`| [2024-07-26-MLPepper-RECAP-Optimized-Fragments-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-07-26-MLPepper-RECAP-Optimized-Fragments-v1.0) | Single point property calculations for charge models | P ,B ,Cl ,Br ,C ,H ,I ,F ,O ,N ,Si ,S | |
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|`OpenFF NAGL2 ESP Timing Benchmark v1.0` | [2024-09-06-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-06-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.0) | Single point ESP calculations for timing/memory benchmarking | 'P', 'S', 'N', 'C', 'Cl', 'F', 'Br', 'O', 'H', 'I' | |
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|`OpenFF NAGL2 ESP Timing Benchmark v1.1` | [2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-18-OpenFF-NAGL2-ESP-Timing-Benchmark-v1.1) | Single point ESP calculations for timing/memory benchmarking | 'P', 'S', 'N', 'C', 'Cl', 'F', 'Br', 'O', 'H', 'I' | |
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|`OpenFF Sulfur Hessian Training Coverage Supplement v1.0` | [2024-09-18-OpenFF-Sulfur-Hessian-Training-Coverage-Supplement-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-18-OpenFF-Sulfur-Hessian-Training-Coverage-Supplement-v1.0) | Additional Hessian training data for Sage sulfur and phosphorus parameters (from 'OpenFF Sulfur Optimization Training Coverage Supplement v1.0') | O, S, C, Cl, P, N, F, Br, H | |
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# Optimization Datasets

‎submissions/2024-09-18-OpenFF-Sulfur-Hessian-Training-Coverage-Supplement-v1.0/README.md‎

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# OpenFF Sulfur Hessian Training Coverage Supplement v1.0
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## Description
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A basic data set created to improve the training coverage of sulfonic and
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phosphonic acids, sulfone, sulfonate, sulfinyl, sulfoximine, sulfonamides,
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thioether, and 1,3-thiazole groups. The structures in this data set are the
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optimized geometries from `OpenFF Sulfur Optimization Training Coverage
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Supplement v1.0`.
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## General Information
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* Date: 2024-09-18
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* Class: OpenFF Optimization Dataset
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* Purpose: Improve coverage in Sage
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* Name: OpenFF Sulfur Hessian Training Coverage Supplement v1.0
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* Number of unique molecules: 129
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* Number of filtered molecules: 0
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* Number of conformers: 899
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* Number of conformers per molecule (min, mean, max): 1, 6.97, 10
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* Mean molecular weight: 218.80
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* Max molecular weight: 493.37
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* Charges: [-2.0, -1.0, 0.0]
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* Dataset submitter: Brent Westbrook
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* Dataset generator: Brent Westbrook
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## QCSubmit Generation Pipeline
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* `generate-dataset.py`: This script shows how the dataset was prepared.
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## QCSubmit Manifest
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* `generate-dataset.py`: Script describing dataset generation and submission
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* `input-environment.yaml`: Environment file used to create the Python environment for the script
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* `full-environment.yaml`: Fully-resolved environment used to execute the script
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* `opt.toml`: Experimental [qcaide](https://github.com/ntBre/qcaide) input file for defining
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variables used throughout the QCA submission process
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* `dataset.json.bz2`: Compressed dataset ready for submission
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* `dataset.pdf`: Visualization of dataset molecules
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* `dataset.smi`: SMILES strings for dataset molecules
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## Metadata
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* Elements: {O, S, C, Cl, P, N, F, Br, H}
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* Spec: default
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* basis: DZVP
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* implicit_solvent: None
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* keywords: {}
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* maxiter: 200
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* method: B3LYP-D3BJ
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* program: psi4
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* SCF properties:
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* dipole
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* quadrupole
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* wiberg_lowdin_indices
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* mayer_indices

‎submissions/2024-09-18-OpenFF-Sulfur-Hessian-Training-Coverage-Supplement-v1.0/dataset.json.bz2‎

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‎submissions/2024-09-18-OpenFF-Sulfur-Hessian-Training-Coverage-Supplement-v1.0/dataset.pdf‎

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‎submissions/2024-09-18-OpenFF-Sulfur-Hessian-Training-Coverage-Supplement-v1.0/full-environment.yaml‎

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- soupsieve=2.5=pyhd8ed1ab_1
250+
- sqlalchemy=2.0.25=py311h459d7ec_0
251+
- sqlite=3.46.0=h6d4b2fc_0
252+
- stack_data=0.6.2=pyhd8ed1ab_0
253+
- tabulate=0.9.0=pyhd8ed1ab_1
254+
- terminado=0.18.0=pyh0d859eb_0
255+
- tinycss2=1.2.1=pyhd8ed1ab_0
256+
- tk=8.6.13=noxft_h4845f30_101
257+
- tomli=2.0.1=pyhd8ed1ab_0
258+
- tornado=6.3.3=py311h459d7ec_1
259+
- tqdm=4.66.1=pyhd8ed1ab_0
260+
- traitlets=5.14.1=pyhd8ed1ab_0
261+
- types-python-dateutil=2.8.19.20240106=pyhd8ed1ab_0
262+
- typing-extensions=4.9.0=hd8ed1ab_0
263+
- typing_extensions=4.9.0=pyha770c72_0
264+
- typing_utils=0.1.0=pyhd8ed1ab_0
265+
- tzdata=2023d=h0c530f3_0
266+
- unidecode=1.3.8=pyhd8ed1ab_0
267+
- uri-template=1.3.0=pyhd8ed1ab_0
268+
- urllib3=2.2.0=pyhd8ed1ab_0
269+
- wcwidth=0.2.13=pyhd8ed1ab_0
270+
- webcolors=1.13=pyhd8ed1ab_0
271+
- webencodings=0.5.1=pyhd8ed1ab_2
272+
- websocket-client=1.7.0=pyhd8ed1ab_0
273+
- wheel=0.42.0=pyhd8ed1ab_0
274+
- widgetsnbextension=4.0.9=pyhd8ed1ab_0
275+
- xmltodict=0.13.0=pyhd8ed1ab_0
276+
- xorg-kbproto=1.0.7=h7f98852_1002
277+
- xorg-libice=1.1.1=hd590300_0
278+
- xorg-libsm=1.2.4=h7391055_0
279+
- xorg-libx11=1.8.7=h8ee46fc_0
280+
- xorg-libxau=1.0.11=hd590300_0
281+
- xorg-libxdmcp=1.1.3=h7f98852_0
282+
- xorg-libxext=1.3.4=h0b41bf4_2
283+
- xorg-libxrender=0.9.11=hd590300_0
284+
- xorg-libxt=1.3.0=hd590300_1
285+
- xorg-renderproto=0.11.1=h7f98852_1002
286+
- xorg-xextproto=7.3.0=h0b41bf4_1003
287+
- xorg-xproto=7.0.31=h7f98852_1007
288+
- xz=5.2.6=h166bdaf_0
289+
- yaml=0.2.5=h7f98852_2
290+
- zeromq=4.3.5=h59595ed_0
291+
- zipp=3.17.0=pyhd8ed1ab_0
292+
- zlib=1.2.13=hd590300_5
293+
- zlib-ng=2.0.7=h0b41bf4_0
294+
- zstandard=0.22.0=py311haa97af0_0
295+
- zstd=1.5.5=hfc55251_0
296+
- pip:
297+
- amberutils==21.0
298+
- edgembar==0.2
299+
- mmpbsa-py==16.0
300+
- packmol-memgen==2023.2.24
301+
- pdb4amber==22.0
302+
- pymsmt==22.0
303+
- pytraj==2.0.6
304+
- sander==22.0
305+
prefix: /home/brent/mambaforge/envs/qcarchive-user-submit

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