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README.md

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----
-license: cc-by-nc-4.0
----
+---
+license: cc-by-nc-4.0
+language:
+- en
+pretty_name: THEMol
+size_categories:
+- 1B<n<10B
+tags:
+- chemistry
+- molecular-dynamics
+- density-functional-theory
+- medicine
+- electrolytes
+configs:
+- config_name: hessian
+  data_files:
+  - split: full
+    path: "Hessian/hessian_dataset.csv"
+- config_name: hessianrelax
+  data_files:
+  - split: full
+    path: "HessianRelax/relax_dataset.csv"
+- config_name: torsionscan
+  data_files:
+  - split: full
+    path: "TorsionScan/torsion_dataset.csv"
+- config_name: torsionscanrelax
+  data_files:
+  - split: full
+    path: "TorsionScanRelax/torsion_relax_dataset.csv"
+- config_name: mbis
+  data_files:
+  - split: full
+    path: "MBIS/mbis_dataset.csv"
+---
+
+# THEMol: Torsion, Hessian, Energy of Molecules
+
+## Dataset Summary
+
+THEMol is an open-source collection of quantum mechanical properties tailored for organic molecules. It provides large-scale density functional theory (DFT) data for exploring intramolecular potential energy surfaces, including optimized geometries, structural relaxation trajectories, torsion scans, constrained torsion relaxation trajectories, Hessian matrices, and MBIS-derived atomic properties.
+
+The dataset contains five tailored subsets and over three billion DFT calculations for molecules with up to 50 non-hydrogen atoms. Its chemical space spans twelve essential elements and diverse molecular architectures relevant to drug discovery, electrolytes, ionic liquids, and broader molecular modeling applications.
+
+See the [paper](https://arxiv.org/abs/XXXX.XXXXX) and [GitHub repository](https://github.com/ByteDance-Seed/THEMol) for more details. The GitHub repository provides data readers, validation utilities, and statistical scripts.
+
+## Dataset Details
+
+### Dataset Description
+
+- **Repository**: [https://github.com/ByteDance-Seed/THEMol](https://github.com/ByteDance-Seed/THEMol)
+- **Paper**: [https://arxiv.org/abs/XXXX.XXXXX](https://arxiv.org/abs/XXXX.XXXXX)
+- **Data format**: CSV index files plus HDF5 data files.
+- **Computation scale**: more than three billion DFT calculations across five subsets.
+- **Molecular scope**: organic molecules with up to 50 non-hydrogen atoms.
+- **Element coverage**: H, C, N, O, S, F, Cl, Br, Si, B, P, and I.
+
+### Subsets
+
+| Subset | Level of Theory | Entries | Supplementary Metrics | Description |
+| :--- | :--- | ---: | :--- | :--- |
+| Hessian | B3LYP-D3(BJ)/DZVP | 3,102,537 | - | Optimized molecular geometries and corresponding Hessian matrices. |
+| Hessian Relax | B3LYP-D3(BJ)/DZVP | 4,811,722 | 281,123,880 relaxation steps | Complete structural relaxation trajectories for the Hessian subset. |
+| TorsionScan | B3LYP-D3(BJ)/DZVP | 4,192,791 | 2,436,985 molecules; 93,994,576 constraints | Comprehensive in-ring and non-ring torsional scans after constrained optimization. |
+| TorsionScan Relax | B3LYP-D3(BJ)/DZVP | 4,914,677 | 3,090,560 molecules; 110,235,160 constraints; 2,993,685,868 steps | Complete constrained structural relaxation trajectories for the TorsionScan subset. |
+| MBIS | PBE0/def2-TZVPD, or DZVP for I atoms | 3,082,151 | - | Atomic properties and model parameters from Minimal Basis Iterative Stockholder (MBIS) partitioning. |
+
+## Dataset Structure
+
+The dataset is organized by subset. Each subset contains one CSV index file and HDF5 files referenced by the `h5_file` column.
+
+```text
+/
+├── Hessian/
+│   ├── hessian_dataset.csv
+│   └── *.h5
+├── HessianRelax/
+│   ├── relax_dataset.csv
+│   └── *.h5
+├── TorsionScan/
+│   ├── torsion_dataset.csv
+│   └── *.h5
+├── TorsionScanRelax/
+│   ├── torsion_relax_dataset.csv
+│   └── *.h5
+└── MBIS/
+    ├── mbis_dataset.csv
+    └── *.h5
+```
+
+### Data Fields
+
+All HDF5 files are keyed by `uuid`. The CSV index files contain the UUID, mapped SMILES strings, and the HDF5 file location needed to retrieve each molecular record.
+
+#### Hessian
+
+**CSV columns**: `uuid`, `mapped_nonisomeric_smiles`, `mapped_isomeric_smiles`, `h5_file`
+
+**HDF5 structure**:
+
+```text
+/<uuid>/
+  mapped_nonisomeric_smiles  utf-8 string
+  mapped_isomeric_smiles     utf-8 string
+  atomic_numbers             (N, 1) int32
+  coords                     (N, 3) float64
+  hessian                    (3N, 3N) float64
+```
+
+#### Hessian Relax
+
+**CSV columns**: `uuid`, `mapped_nonisomeric_smiles`, `mapped_isomeric_smiles`, `num_steps`, `h5_file`
+
+**HDF5 structure**:
+
+```text
+/<uuid>/
+  mapped_nonisomeric_smiles  utf-8 string
+  mapped_isomeric_smiles     utf-8 string
+  atomic_numbers             (N, 1) int32
+  step 0/
+    energy                   scalar float64
+    coords                   (N, 3) float64
+    forces                   (N, 3) float64
+  ...
+  step k/
+    energy                   scalar float64
+    coords                   (N, 3) float64
+    forces                   (N, 3) float64
+```
+
+#### TorsionScan
+
+**CSV columns**: `uuid`, `mapped_nonisomeric_smiles`, `mapped_isomeric_smiles`, `torsion_indices`, `h5_file`, `num_constraints`
+
+**HDF5 structure**:
+
+```text
+/<uuid>/
+  mapped_nonisomeric_smiles  utf-8 string
+  mapped_isomeric_smiles     utf-8 string
+  atomic_numbers             (N, 1) int32
+  torsion_atom_indices       (4,) int32
+  constraint 0/
+    energy                   scalar float64
+    coords                   (N, 3) float64
+    forces                   (N, 3) float64
+  constraint 1/
+    ...
+```
+
+#### TorsionScan Relax
+
+**CSV columns**: `uuid`, `mapped_nonisomeric_smiles`, `mapped_isomeric_smiles`, `torsion_indices`, `h5_file`, `num_constraints`, `num_total_steps`
+
+**HDF5 structure**:
+
+```text
+/<uuid>/
+  mapped_nonisomeric_smiles  utf-8 string
+  mapped_isomeric_smiles     utf-8 string
+  atomic_numbers             (N, 1) int32
+  torsion_atom_indices       (4,) int32
+  constraint 0/
+    energy                   (M,) float64
+    coords                   (M, N, 3) float64
+    forces                   (M, N, 3) float64
+  constraint 1/
+    ...
+```
+Here `M` is the number of steps.
+
+#### MBIS
+
+**CSV columns**: `uuid`, `mapped_nonisomeric_smiles`, `mapped_isomeric_smiles`, `h5_file`
+
+**HDF5 structure**:
+
+```text
+/<uuid>/
+  mapped_nonisomeric_smiles  utf-8 string
+  mapped_isomeric_smiles     utf-8 string
+  atomic_numbers             (N, 1) int32
+  coords                     (N, 3) float64
+  mbis_info/
+    atomic_volumes           (N, 1) float64
+    atomic_charge            (N, 1) float64
+    atomic_dipole            (N, 3) float64
+    atomic_quadrupole        (N, 3, 3) float64
+  parameters                 (M, 3) float64
+```
+Here `M` is the number of MBIS Slater functions.
+
+For `parameters`, each row contains the 0-based parent atom index, the Slater-function charge population `N_i`, and the inverse width `1/sigma_i`.
+
+### Units
+
+| Quantity | Unit |
+| :--- | :--- |
+| Coordinates | Å |
+| Energy | kcal mol^-1 |
+| Force | kcal mol^-1 Å^-1 |
+| Hessian | kcal mol^-1 Å^-2 |
+| Charge | e |
+| Dipole | e Å |
+| Quadrupole | e Å^2 |
+| Volume | Å^3 |
+| 1/sigma_i | Å^-1 |
+
+## Licenses
+
+[Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)](https://creativecommons.org/licenses/by-nc/4.0/).
+
+## Citation
+
+If you use THEMol in your research or applications, please cite:
+
+```bibtex
+@article{THEMol,
+      title={THEMol: Torsion, Hessian, Energy of Molecules},
+      author={Author1 and Author2},
+      year={2026},
+      eprint={XXXX.XXXXX},
+      archivePrefix={arXiv},
+      primaryClass={cs.XX}
+}
+```