0.6.0

[Linux-cpp-lisp]

[0.6.0] - 2024-5-10

Added

• add Tensorboard as logger option
• [Breaking] Refactor overall model logic into GraphModel top-level module
• [Breaking] Added model_dtype
• BATCH_PTR_KEY in AtomicDataDict
• AtomicInMemoryDataset.rdf() and examples/rdf.py
• type_to_chemical_symbol
• Pair potential terms
• nequip-evaluate --output-fields-from-original-dataset
• Error (or warn) on unused options in YAML that likely indicate typos
• dataset_*_absmax statistics option
• HDF5Dataset (Created HDF5 based dataset #227)
• include_file_as_baseline_config for simple modifications of existing configs
• nequip-deploy --using-dataset to support data-dependent deployment steps
• Support for Gaussian Mixture Model uncertainty quantification (https://doi.org/10.1063/5.0136574)
• start_of_epoch_callbacks
• nequip.train.callbacks.loss_schedule.SimpleLossSchedule for changing the loss coefficients at specified epochs
• nequip-deploy build --checkpoint and --override to avoid many largely duplicated YAML files
• matscipy neighborlist support enabled with NEQUIP_MATSCIPY_NL environment variable

Changed

• Always require explicit seed
• [Breaking] Set dataset_seed to seed if it is not explicitly provided
• Don't log as often by default
• [Breaking] Default nonlinearities are silu (e) and tanh (o)
• Will not reproduce previous versions' data shuffling order (for all practical purposes this does not matter, the shuffle option is unchanged)
• [Breaking] default_dtype defaults to float64 (model_dtype default float32, allow_tf32: true by default--- see https://arxiv.org/abs/2304.10061)
• nequip-benchmark now only uses --n-data frames to build the model
• [Breaking] By default models now use StressForceOutput, not ForceOutput
• Added edge_energy to ALL_ENERGY_KEYS subjecting it to global rescale

Fixed

• Work with wandb>=0.13.8
• Better error for standard deviation with too few data
• load_model_state GPU -> CPU
• No negative volumes in rare cases

Removed

• [Breaking] fixed_fields machinery (npz_fixed_field_keys is still supported, but through a more straightforward implementation)
• Default run name/WandB project name of NequIP, they must now always be provided explicitly
• [Breaking] Removed _params as an allowable subconfiguration suffix (i.e. instead of optimizer_params now only optimizer_kwargs is valid, not both)
• [Breaking] Removed per_species_rescale_arguments_in_dataset_units