Merge pull request #235 from openforcefield/resppol-v1.1

OpenFF RESP Polarizability Optimizations v1.1

README.md

@@ -140,6 +140,7 @@ These are currently used to find a minimum energy conformation of a molecule.
 | `OpenFF Theory Benchmarking Constrained Optimization Set MP2 heavy-aug-cc-pVTZ v1.1` | [2020-11-25-theory-bm-set-mp2-heavy-aug-cc-pvtz](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2020-11-25-theory-bm-set-mp2-heavy-aug-cc-pvtz) | This is a Constrained Optimization dataset for benchmarking MP2/heavy-aug-cc-pVTZ. |  | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange) |
 | `OpenFF Industry Benchmark Season 1 - MM v1.1` | [2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-07-28-OpenFF-Industry-Benchmark-Season-1-MM-v1.1) | The combination of all publicly chosen compound sets by industry partners from the OpenFF season 1 industry benchmark; MM computations starting from QM-optimized geometries. | N, F, Cl, C, H, O, Br, P, S | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange) |
 | `OpenFF RESP Polarizability Optimizations v1.0` | [2021-10-01-OpenFF-resppol-mp2-single-point](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-10-01-OpenFF-resppol-mp2-single-point) | A data set used for training ESP-fitting based typed atomic polarizabilities with a direct approximation. | N, C, H, O | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange) |
+| `OpenFF RESP Polarizability Optimizations v1.1` | [2021-10-01-OpenFF-resppol-mp2-single-point](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-10-01-OpenFF-resppol-mp2-single-point) | A data set used for training ESP-fitting based typed atomic polarizabilities with a direct approximation. | N, C, H, O | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange) |
 
 
 # TorsionDrive Datasets

submissions/2021-10-01-OpenFF-resppol-mp2-single-point/README.md

@@ -10,14 +10,16 @@ One positively charged and one negatively charged molecule are fitted simultaneo
 
 The initial data set is limited to only molecules composed of C, O, H, and N to enable an element-based and relatively fast test.
 
+The v1.1 version of this dataset fixes incorrect values for the `PERTURB_DIPOLE` keyword; these are meant to be a list of floats, not a string.
+
 
 ### General Information
 
-- Date: 2021.10.05
+- Date: 2021.10.14
 - Class: OpenFF Optimization Dataset
 - Purpose: C,H,O,N training data for training ESP-fitting based atomic polarizabilities and partial charges
 - Collection: OptimizationDataset
-- Name: OpenFF RESP Polarizability Optimizations v1.0 
+- Name: OpenFF RESP Polarizability Optimizations v1.1 
 - Number of unique molecules        39
 - Number of filtered molecules      0
 - Number of conformers              105
@@ -34,6 +36,7 @@ The initial data set is limited to only molecules composed of C, O, H, and N to
 ### QCSubmit generation pipeline
 
 - `generate-dataset.ipynb`: A notebook which shows how the dataset was prepared from the input files.
+- `generate-dataset-v1.1.ipynb`: A notebook which shows how the dataset was prepared from the input files, for v1.1
 - `molecules.smi`: A text file which includes the SMILES strings of input molecules.
 
 ### QCSubmit Manifest
@@ -42,14 +45,16 @@ The initial data set is limited to only molecules composed of C, O, H, and N to
 - `dataset.json.bz2`: The basic dataset ready for submission.
 - `dataset.pdf`: A pdf file containing molecule 2D structures.
 - `dataset.smi`: SMILES for every molecule in the submission.
+
+Corresponding files for v1.1 also included.
 
 ### Metadata
 
 ```
 {'collection_type': 'OptimizationDataset',
- 'creation_date': datetime.date(2021, 10, 5),
- 'dataset_name': 'OpenFF RESP Polarizability Optimizations v1.0',
- 'elements': {'H', 'C', 'O', 'N'},
+ 'creation_date': datetime.date(2021, 10, 14),
+ 'dataset_name': 'OpenFF RESP Polarizability Optimizations v1.1',
+ 'elements': {'O', 'C', 'N', 'H'},
  'long_description': 'A data set used for training typed polarizabilities '
                      'using direct polarization.\n'
                      'This data set only includes element C, H, N, and O.',
@@ -66,7 +71,7 @@ Spec: MP2/aug-cc-pVTZ/X-
 {'basis': 'aug-cc-pVTZ',
  'implicit_solvent': None,
  'keywords': {'E_CONVERGENCE': '1.0e-8',
-              'PERTURB_DIPOLE': '[-0.01, 0.0, 0.0]',
+              'PERTURB_DIPOLE': [-0.01, 0.0, 0.0],
               'PERTURB_H': True,
               'PERTURB_WITH': 'DIPOLE',
               'mp2_type': 'df',
@@ -86,7 +91,7 @@ Spec: MP2/aug-cc-pVTZ/X+
 {'basis': 'aug-cc-pVTZ',
  'implicit_solvent': None,
  'keywords': {'E_CONVERGENCE': '1.0e-8',
-              'PERTURB_DIPOLE': '[0.01, 0.0, 0.0]',
+              'PERTURB_DIPOLE': [0.01, 0.0, 0.0],
               'PERTURB_H': True,
               'PERTURB_WITH': 'DIPOLE',
               'mp2_type': 'df',
@@ -106,7 +111,7 @@ Spec: MP2/aug-cc-pVTZ/Y-
 {'basis': 'aug-cc-pVTZ',
  'implicit_solvent': None,
  'keywords': {'E_CONVERGENCE': '1.0e-8',
-              'PERTURB_DIPOLE': '[0.0, -0.01, 0.0]',
+              'PERTURB_DIPOLE': [0.0, -0.01, 0.0],
               'PERTURB_H': True,
               'PERTURB_WITH': 'DIPOLE',
               'mp2_type': 'df',
@@ -126,7 +131,7 @@ Spec: MP2/aug-cc-pVTZ/Y+
 {'basis': 'aug-cc-pVTZ',
  'implicit_solvent': None,
  'keywords': {'E_CONVERGENCE': '1.0e-8',
-              'PERTURB_DIPOLE': '[0.0, 0.01, 0.0]',
+              'PERTURB_DIPOLE': [0.0, 0.01, 0.0],
               'PERTURB_H': True,
               'PERTURB_WITH': 'DIPOLE',
               'mp2_type': 'df',
@@ -146,7 +151,7 @@ Spec: MP2/aug-cc-pVTZ/Z-
 {'basis': 'aug-cc-pVTZ',
  'implicit_solvent': None,
  'keywords': {'E_CONVERGENCE': '1.0e-8',
-              'PERTURB_DIPOLE': '[0.0, 0.0, -0.01]',
+              'PERTURB_DIPOLE': [0.0, 0.0, -0.01],
               'PERTURB_H': True,
               'PERTURB_WITH': 'DIPOLE',
               'mp2_type': 'df',
@@ -166,7 +171,7 @@ Spec: MP2/aug-cc-pVTZ/Z+
 {'basis': 'aug-cc-pVTZ',
  'implicit_solvent': None,
  'keywords': {'E_CONVERGENCE': '1.0e-8',
-              'PERTURB_DIPOLE': '[0.0, 0.0, 0.01]',
+              'PERTURB_DIPOLE': [0.0, 0.0, 0.01],
               'PERTURB_H': True,
               'PERTURB_WITH': 'DIPOLE',
               'mp2_type': 'df',

submissions/2021-10-01-OpenFF-resppol-mp2-single-point/dataset-v1.1.smi

@@ -0,0 +1,39 @@
+CCCC(CCC)CCC
+O=C1CCCO1
+C=C(C)C(=O)OC
+Oc1ccccc1
+OC1CCCCC1
+C=CCCCC
+CCCC[NH3+]
+CC(=O)C(C)C
+CCCCCC(=O)OC
+CCOCC
+NC1CCCCC1
+CCCO
+CCCC(=O)OC
+CC=O
+CCCCCC(=O)[O-]
+OCCCCO
+NC(=O)CCC(N)=O
+CCCCCCO
+C1CCCCCC1
+COC=O
+CCCCCCCO
+C
+CCCCC(=O)OC
+C1=CC=CCC=C1
+c1cncnc1
+c1cnccn1
+C1=CCCCC1
+C=CC(OC)OC
+C1CCCCC1
+CC(C)=O
+O
+C1CCCCCCC1
+CC(=O)CO
+c1ccc(-c2ccccc2)cc1
+O=C1C=CCO1
+c1ccncc1
+O=C1CCCCC1
+CCCCCCCC(=O)OC
+c1cc[nH]c1