Toy dataset with pairs of molecules differing in total charge

<pre>On the inclusion of charge and spin states in Cartesian tensor neural network potentials. (2024)<br>Guillem Simeon, Antonio Mirarchi, Raul P. Pelaez, Raimondas Galvelis and Gianni De Fabritiis. Two toy datasets, Dataset A and Dataset B, each one comprising five members of five pairs of<br>unique molecular systems, each of the elements in the pair differing in total charge. <br><br>These pairs are indistinguishable to a neural network that does not account for total charge,<br>as they share identical atomic numbers and geometric configurations.<br><br>The datasets include total charges, Gasteiger partial charges computed with RDKit,<br>and calculated energies and atomic forces for 2000 conformers per molecule using GFN2-xTB.<br><br>Therefore, each dataset contains a total of 10k data points.<br><br>Conformers were generated by minimizing each molecule, displacing atomic positions with Gaussian<br>noise with a standard deviation of 0.2&Aring;, and filtering them such that maximum atomic forces are <br>&lt;100 eV/&Aring;. <br>Data Format and Availability:<br> Both datasets are available in HDF5 (Hierarchical Data Format version 5) format,<br>compatible with Ace dataset (layout version 2.0) in TorchMD-Net <br>(https://github.com/torchmd/torchmd-net/blob/main/torchmdnet/datasets/ace.py). Data Structure: Each molecule is assigned a unique integer identifier, consistent across both sub-datasets,<br>facilitating pairing between conformations. The HDF5 file is structured as follows:<br> Each top-level group corresponds to a unique molecule. Within each group, considering N is the number of atoms in the molecule and M is the number of<br>conformations, the following datasets are provided: - atomic_numbers: Atomic numbers of atoms in the molecule, with a shape of (N,); - formal_charges: Formal charges of atoms in the molecule, with a shape of (N,); - formation_energies: Formation energy of each conformation, with a shape of (M,),<br> expressed in units of eV;<br>- forces: Forces on atoms in each conformation, with a shape of (M, N, 3), expressed in eV/&Aring;. - partial_charges: Gasteiger partial charges of atoms in each conformation,<br> with a shape of (M, N), expressed in e; - positions: Cartesian coordinates of atoms in each conformation, with a shape of (M, N, 3),<br> expressed in &Aring;. </pre>