Datasets:
License:
| license: cc0-1.0 | |
| tags: | |
| - ANI-1x | |
| - MACE | |
| - molecular dynamics | |
| - HDF5 | |
| - extxyz | |
| - machine learning potential | |
| language: | |
| - en | |
| - zh | |
| <p align="center"> | |
| <strong> | |
| <span style="font-size: 30px;">ANI-1x</span> | |
| </strong> | |
| </p> | |
| ## Dataset Description | |
| The ANI-1x dataset is a molecular-configuration dataset for training and evaluation. The data package contains training, validation, and test HDF5 shards, along with a statistics JSON file and auxiliary extxyz files. Its fields are consistent with the energy and force fields in the MACE ANI-1x configuration, making it a standard benchmark dataset for learning and validating machine-learning interatomic potentials with MACE. | |
| The element set consists of H, C, N, and O. The original ANI-1x data comes from [ANI-1x datasets (FigShare)](https://springernature.figshare.com/collections/The_ANI-1ccx_and_ANI-1x_data_sets_coupled-cluster_and_density_functional_theory_properties_for_molecules/4712477); this repository is the companion data package for OneScience MACE training and evaluation examples. | |
| The current data package contains approximately 30 files. | |
| ## Supported Tasks | |
| This standardized data repository provides the complete data package for the ANI-1x example, including training, validation, and test sets. It can be used for: | |
| - Training and validation of potential-energy-surface models for molecular configurations | |
| - Potential-energy-surface fitting for molecular dynamics simulations | |
| - Functional testing and benchmark evaluation of the MACE framework | |
| ## Dataset Format and Structure | |
| The data files are located in the `data/ani1x/` directory: | |
| | File Path | Format | shape / Content | Description | | |
| |---|---|---|---| | |
| | `ani1x/ANI1x_cc_DFT_rc5_train/train_*.h5` | HDF5 | `[N_frames, N_atoms]` | Training set, with 8 shards in total | | |
| | `ani1x/ANI1x_cc_DFT_rc5_val/val_*.h5` | HDF5 | `[N_frames, N_atoms]` | Validation set, with 8 shards in total | | |
| | `ani1x/ANI1x_cc_DFT_rc5_test/Default__*.h5` | HDF5 | `[N_frames, N_atoms]` | Test set, with 8 shards in total | | |
| | `ani1x/ANI1x_cc_DFT_rc5_statistics.json` | JSON | Statistical information | Contains `atomic_energies`, `avg_num_neighbors`, `mean`, `std`, `atomic_numbers`, and `r_max` | | |
| | `ani1x/ani1x_train.xyz` | extxyz | `[N_frames, N_atoms]` | Auxiliary training-set file | | |
| | `ani1x/ani1x_test.xyz` | extxyz | `[N_frames, N_atoms]` | Auxiliary test-set file | | |
| | `ani1x/ani1x_cc_dft.xyz` | extxyz | `[N_frames, N_atoms]` | Auxiliary file for the full dataset | | |
| | `metadata/sha256_manifest.txt` | SHA256 | Checksum manifest | File-integrity verification | | |
| ### HDF5 Data Format | |
| The HDF5 file structure is `config_batch_*/config_*`. Each configuration contains: | |
| | Path | dtype | shape | Description | | |
| |---|---|---|---| | |
| | `atomic_numbers` | `int64` | `[N_atoms]` | Atomic numbers | | |
| | `positions` | `float64` | `[N_atoms, 3]` | Atomic coordinates, in Å | | |
| | `cell` | `float64` | `[3, 3]` | Periodic cell matrix | | |
| | `pbc` | `bool` | `[3]` | Periodic boundary conditions | | |
| | `properties/energy` | `float64` | Scalar | Total configuration energy, in eV | | |
| | `properties/forces` | `float64` | `[N_atoms, 3]` | Atomic forces, in eV/Å | | |
| ## How to Use the Dataset | |
| Download the dataset: | |
| ```bash | |
| hf download --dataset OneScience-Sugon/ani1x --local-dir ./data | |
| ``` | |
| ## Official OneScience Information | |
| | Platform | OneScience Main Repository | Skills Repository | | |
| |---|---|---| | |
| | Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills | | |
| | GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills | | |
| ## Limitations and License | |
| This dataset is the example data for MACE ANI-1x; it does not contain any newly generated samples or alter the original data. The original data comes from ANI-1x datasets (FigShare), with calculations performed at the wB97X/6-31G(d) level. | |
| - **Original Source**: https://springernature.figshare.com/collections/The_ANI-1ccx_and_ANI-1x_data_sets_coupled-cluster_and_density_functional_theory_properties_for_molecules/4712477 | |
| - **GitHub Repository**: https://github.com/aiqm/ANI1x_datasets | |
| - **License**: CC0 1.0 Universal (public domain dedication) | |
| When using the ANI-1x dataset, please cite: | |
| - Smith, J. S.; Nebgen, B.; Lubbers, N.; Isayev, O.; Roitberg, A. E. Less Is More: Sampling Chemical Space with Active Learning. *J. Chem. Phys.* **2018**, *148* (24), 241733. https://doi.org/10.1063/1.5023802 | |
| - Smith, J. S.; Zubatyuk, R.; Nebgen, B.; Lubbers, N.; Barros, K.; Roitberg, A. E.; Isayev, O.; Tretiak, S. The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules. *Sci. Data* **2020**, *7*, 134. https://doi.org/10.1038/s41597-020-0473-z | |