Update README.md
Browse filesUpdating README with dataset features, subdirectories, citation, and contact. Fix links to preprint and github later.
README.md
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---
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license: apache-2.0
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---
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license: apache-2.0
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tags:
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- chemistry
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size_categories:
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- 10K<n<100K
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---
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# TrajCast Dataset arXiv 2025
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This dataset contains atomic configurations of molecular and condensed matter systems used to train, validate, and test the *TrajCast* framework for forecasting molecular dynamics (MD) trajectories using autoregressive equivariant message-passing networks.
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Each entry represents a snapshot from a MD trajectory, defined by the chemical elements, instantaneous positions, and velocities of all atoms, along with information about their state at a slightly later time interval Δt.
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## Subdirectories
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The dataset includes data for the models presented and benchmarked in our [preprint](https://arxiv.org/), with time intervals varying for each system.
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Additionally, we provide a small example dataset to help you get started with our [example notebooks](https://github.com/IBM).
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- **paracetamol**: Dataset for gas-phase paracetamol (20 atoms) using a time interval of 7 fs.
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- **quartz**: Data for crystalline quartz (162 atoms) using a time interval of 30 fs.
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- **water**: Data for liquid bulk water (192 atoms) using a time interval of 5 fs.
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- **example**: Subset of dataset for gas-phase paracetamol (20 atoms) using a time interval of 7 fs. About 5-10 % of the full dataset.
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## Dataset Features
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The data comes in `.extxyz` format and we follow the units of style `real` from [LAMMPS](https://docs.lammps.org/units.html). Each entry correspondgs to an atomic configuration and includes the following fields:
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- **species**: The type of atom (e.g., C for Carbon, O for Oxygen (O), ...).
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- **positions**: 3D atomic positions (in Angstroms).
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- **velocities**: 3D atomic velocities (in Angstroms per fs).
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- **displacements**: 3D atomic displacements to the new positions after time interval Δt (in Angstroms).
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- **update_velocities**: 3D atomic velocities at time interval Δt (in Angstroms per fs).
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- **timestep**: Time interval Δt (in femtoseconds).
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- **pbc**: Information about periodic boundary conditions (e.g., `T T T`).
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- **Lattice**: The lattice vectors of the simulation box.
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- **num_atoms**: The total number of atoms in the system (first line).
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## Citation
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If you decide to use this dataset, please consider citing our preprint
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```
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@misc{Thiemann2025Force-Free,
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title={Force-Free Molecular Dynamics Through Autoregressive Equivariant Networks},
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author={Thiemann, Fabian L and Reschützegger, Thiago, and Olarte-Plata, Juan D. and Taddese, Tseden and Esposito, Massimiliano, and Martelli, Fausto},
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year={2025},
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eprint={...},
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archivePrefix={arXiv},
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primaryClass={...},
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url={https://arxiv.org/...},
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}
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```
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## Contact
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For more information or if you like to contribute, please reach out to [email protected].
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