Conventions
Glossary
Some common terms used in the codebase are presented as follows.
config: the
.yamlfile that is used to configure the training, validation, and/or testing run
Data Format Conventions
Cells vectors are given in ASE style as the rows of the cell matrix
The first index in an edge tuple (
edge_index[0]) is the center atom, and the second (edge_index[1]) is the neighbor
Pressure / stress / virials
nequip always expresses stress in the “consistent” units of energy / length³, which are not the typical physical units used by many codes for stress. For example, consider data where the cell and atomic positions are provided in Å and the energy labels are in eV but the stress is given in GPa or kbar. The user would then need to convert the stress to eV/ų before providing the data to nequip.
Warning
Training labels for stress in the original dataset must be pre-processed by the user to be in consistent units.
Stress also includes an arbitrary sign convention, for which we adopt the choice that virial = -stress x volume <=> stress = (-1/volume) * virial. This is the most common sign convention in the literature (e.g. adopted by ASE), but notably differs from that used by VASP (see here). In the sign convention used by nequip, stress is defined as the derivative of the energy \(E\) with respect to the strain tensor \(\eta_{ji}\):
such that a positive in the diagonals implies the system is under tensile strain and wants to compress, while a negative value implies the system is under compressive strain and wants to expand. When VASP results are parsed by ASE, the sign is flipped to match the nequip convention.
Warning
Training labels for stress in the original dataset must be pre-processed by the user to be in this sign convention, which they may or may not already be depending on their origin.
Users that have data with virials but seek to train on stress can use the data transform nequip.data.transforms.VirialToStressTransform.