Index

_

__init__()

A

add_bounds_model_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) add_bounds_param_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) add_from_ase() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) add_from_colabfit() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) add_from_huggingface() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) add_from_lmdb() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) add_from_path() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) add_layers() (kliff.models.neural_network.NeuralNetwork method) (kliff.models.NeuralNetwork method)

add_metadata() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) add_opt_mask() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) add_transform() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) (kliff.trainer.utils.dataloaders.DescriptorDataset method) add_weights() (kliff.dataset.Dataset static method) (kliff.dataset.dataset.Dataset static method) AnalyzerError (class in kliff.analyzers.rmse) as_dict() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) autocorr() (in module kliff.uq) (in module kliff.uq.mcmc_utils) AvailableDescriptors() (in module kliff.transforms.configuration_transforms.descriptors)

B

bispectrum_default() (in module kliff.transforms.configuration_transforms.default_hyperparams) Bootstrap (class in kliff.uq) (class in kliff.uq.bootstrap) bootstrap_cas_generator_empirical() (in module kliff.uq.bootstrap) bootstrap_cas_generator_neuralnetwork() (in module kliff.uq.bootstrap) BootstrapEmpiricalModel (class in kliff.uq) (class in kliff.uq.bootstrap) BootstrapError

BootstrapNeuralNetworkModel (class in kliff.uq) (class in kliff.uq.bootstrap) bounds (kliff.models.Parameter attribute), [1] (kliff.models.parameter.Parameter attribute), [1] builtin_samplers (kliff.uq.MCMC attribute) (kliff.uq.mcmc.MCMC attribute) bulk() (kliff.dataset.Configuration class method) (kliff.dataset.configuration.Configuration class method)

C

calc_phi() (kliff.models.lennard_jones.LJComputeArguments static method) calc_phi_dphi() (kliff.models.lennard_jones.LJComputeArguments static method) Calculator (class in kliff.legacy.calculators) (class in kliff.legacy.calculators.calculator) CalculatorError CalculatorTorch (class in kliff.legacy.calculators) (class in kliff.legacy.calculators.calculator_torch) CalculatorTorchError CalculatorTorchSeparateSpecies (class in kliff.legacy.calculators.calculator_torch) cell (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) check_properties_consistency() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) checkpoint() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) collate() (kliff.trainer.utils.dataloaders.DescriptorDataset method) collate_fn() (kliff.transforms.configuration_transforms.configuration_transform.ConfigurationTransform method) (kliff.transforms.configuration_transforms.ConfigurationTransform method) compute() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.calculator_torch.CalculatorTorchSeparateSpecies method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) (kliff.models.kim.KIMComputeArguments method) (kliff.models.lennard_jones.LJComputeArguments method) (kliff.models.model.ComputeArguments method) compute_weight() (kliff.dataset.weight.MagnitudeInverseWeight method), [1] (kliff.dataset.weight.Weight method), [1]

ComputeArguments (class in kliff.models) (class in kliff.models.model) config_to_dict() (kliff.trainer.base_trainer.Trainer method) config_weight (kliff.dataset.weight.Weight property), [1] Configuration (class in kliff.dataset) (class in kliff.dataset.configuration) ConfigurationError ConfigurationTransform (class in kliff.transforms.configuration_transforms) (class in kliff.transforms.configuration_transforms.configuration_transform) coords (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) copy_at_param_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) copy_from_model_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) copy_from_param_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) copy_to_config (kliff.transforms.configuration_transforms.configuration_transform.ConfigurationTransform property) (kliff.transforms.configuration_transforms.ConfigurationTransform property) count_atoms_by_species() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) create() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) create_a_kim_compute_argument() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) create_directory() (in module kliff.utils)

D

Dataset (class in kliff.dataset) (class in kliff.dataset.dataset) DatasetError default_callback() (in module kliff.uq.bootstrap) default_weight_params (kliff.dataset.weight.MagnitudeInverseWeight attribute), [1] Descriptor (class in kliff.legacy.descriptors) (class in kliff.legacy.descriptors.descriptor) descriptor (kliff.models.model_torch.ModelTorch property) (kliff.models.ModelTorch property) Descriptor() (in module kliff.transforms.configuration_transforms) (in module kliff.transforms.configuration_transforms.descriptors)

DescriptorDataset (class in kliff.trainer.utils.dataloaders) DescriptorError DescriptorsError device (kliff.models.model_torch.ModelTorch property) (kliff.models.ModelTorch property) DNNTrainer (class in kliff.trainer.torch_trainer) download_dataset() (in module kliff.utils) Dropout (class in kliff.legacy.nn) dtype (kliff.models.model_torch.ModelTorch property) (kliff.models.ModelTorch property)

E

echo_model_params() (kliff.models.Model method) (kliff.models.model.Model method) echo_opt_params() (kliff.models.Model method) (kliff.models.model.Model method) energy (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) energy_forces_residual() (in module kliff.legacy.loss)

energy_residual() (in module kliff.legacy.loss) energy_weight (kliff.dataset.weight.Weight property), [1] EnergyForcesRMSE (class in kliff.analyzers) (class in kliff.analyzers.rmse), [1] export_kim_model() (kliff.transforms.configuration_transforms.configuration_transform.ConfigurationTransform method) (kliff.transforms.configuration_transforms.ConfigurationTransform method) (kliff.transforms.configuration_transforms.graphs.generate_graph.RadialGraph method) (kliff.transforms.configuration_transforms.graphs.RadialGraph method) (kliff.transforms.configuration_transforms.RadialGraph method)

F

fingerprint (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) fingerprints_collate_fn() (in module kliff.dataset.dataset_torch) FingerprintsDataset (class in kliff.dataset.dataset_torch) Fisher (class in kliff.analyzers) (class in kliff.analyzers.fisher), [1] fit() (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.linear_regression.LinearRegression method) (kliff.models.LinearRegression method) (kliff.models.model_torch.ModelTorch method) (kliff.models.ModelTorch method) forces (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) forces_residual() (in module kliff.legacy.loss) forces_weight (kliff.dataset.weight.Weight property), [1] forward() (kliff.legacy.nn.Dropout method) (kliff.models.linear_regression.LinearRegression method) (kliff.models.LinearRegression method) (kliff.models.model_torch.ModelTorch method) (kliff.models.ModelTorch method) (kliff.models.neural_network.NeuralNetwork method) (kliff.models.NeuralNetwork method) (kliff.transforms.configuration_transforms.configuration_transform.ConfigurationTransform method) (kliff.transforms.configuration_transforms.ConfigurationTransform method) (kliff.transforms.configuration_transforms.graphs.generate_graph.RadialGraph method) (kliff.transforms.configuration_transforms.graphs.RadialGraph method) (kliff.transforms.configuration_transforms.RadialGraph method)

from_ase() (kliff.dataset.Dataset class method) (kliff.dataset.dataset.Dataset class method) from_ase_atoms() (kliff.dataset.Configuration class method) (kliff.dataset.configuration.Configuration class method) from_colabfit() (kliff.dataset.Configuration class method) (kliff.dataset.configuration.Configuration class method) (kliff.dataset.Dataset class method) (kliff.dataset.dataset.Dataset class method) from_dict() (kliff.models.Parameter class method) (kliff.models.parameter.Parameter class method) (kliff.transforms.configuration_transforms.graphs.generate_graph.PyGGraph class method) (kliff.transforms.configuration_transforms.graphs.PyGGraph class method) (kliff.transforms.configuration_transforms.PyGGraph class method) from_file() (kliff.dataset.Configuration class method) (kliff.dataset.configuration.Configuration class method) (kliff.trainer.base_trainer.Trainer class method) from_huggingface() (kliff.dataset.Dataset class method) (kliff.dataset.dataset.Dataset class method) from_lmdb() (kliff.dataset.Dataset class method) (kliff.dataset.dataset.Dataset class method) from_path() (kliff.dataset.Dataset class method) (kliff.dataset.dataset.Dataset class method)

G

generate_bootstrap_compute_arguments() (kliff.uq.bootstrap.BootstrapEmpiricalModel method) (kliff.uq.bootstrap.BootstrapNeuralNetworkModel method) (kliff.uq.BootstrapEmpiricalModel method) (kliff.uq.BootstrapNeuralNetworkModel method) generate_fingerprints() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) generate_full_cutoff() (in module kliff.legacy.descriptors.descriptor) generate_species_code() (in module kliff.legacy.descriptors.descriptor) generate_unique_cutoff_pairs() (in module kliff.legacy.descriptors.descriptor) get() (kliff.trainer.utils.dataloaders.GraphDataset method) get_bounds_model_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) get_bounds_param_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) get_bs_size() (in module kliff.transforms.configuration_transforms.utils) get_compute_argument_class() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.lennard_jones.LennardJones method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.model.Model method) get_compute_arguments() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) get_compute_flag() (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_configs() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) get_configuration_list() (kliff.transforms.property_transforms.PropertyTransform static method) get_context() (in module kliff.parallel) get_cutoff() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) get_dataset_from_manifest() (kliff.dataset.Dataset static method) (kliff.dataset.dataset.Dataset static method) get_dtype() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) get_energy() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_fingerprints() (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) get_forces() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_formatted_param_bounds() (kliff.models.Model method) (kliff.models.model.Model method) get_hyperparams() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) get_identifiers_from_compute_arguments() (in module kliff.uq.bootstrap) get_identifiers_from_fingerprints() (in module kliff.uq.bootstrap) get_influence_distance() (kliff.models.Model method) (kliff.models.model.Model method) get_kim_model_params() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) get_last_checkpoint() (kliff.trainer.torch_trainer.DNNTrainer method) get_log_level() (in module kliff.log) get_manifest_checksum() (kliff.dataset.Dataset static method) (kliff.dataset.dataset.Dataset static method) get_mean() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) get_metadata() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) get_model_driver_name() (kliff.models.kim.KIMModel static method) (kliff.models.KIMModel static method)

get_model_from_manifest() (kliff.models.kim.KIMModel static method) (kliff.models.KIMModel static method) get_model_params() (kliff.models.Model method) (kliff.models.model.Model method) get_MPI_world_size() (in module kliff.parallel) get_n_configs_in_xyz() (in module kliff.utils) get_num_atoms() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) get_num_atoms_by_species() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) get_num_opt_params() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.Model method) (kliff.models.model.Model method) get_numpy_array_model_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) get_numpy_array_param_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) get_opt_numpy_array_param_space() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) get_opt_param_name_value_and_indices() (kliff.models.Model method) (kliff.models.model.Model method) (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) get_opt_params() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.Model method) (kliff.models.model.Model method) get_opt_params_bounds() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) get_optimizer() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) get_prediction() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_property() (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_reference() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_size() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) get_size_opt_params() (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) get_soap_size() (in module kliff.transforms.configuration_transforms.utils) get_stdev() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) get_stress() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) (kliff.models.model.ComputeArguments method) get_supercell() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) get_supported_species() (kliff.models.Model method) (kliff.models.model.Model method) get_T0() (in module kliff.uq) (in module kliff.uq.mcmc) get_trainer_hash() (kliff.trainer.base_trainer.Trainer method) get_volume() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) GraphDataset (class in kliff.trainer.utils.dataloaders)

H

has_bounds() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method)

I

identifier (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) implemented_property (kliff.legacy.calculators.calculator_torch.CalculatorTorch attribute) (kliff.legacy.calculators.CalculatorTorch attribute) (kliff.models.ComputeArguments attribute) (kliff.models.kim.KIMComputeArguments attribute) (kliff.models.lennard_jones.LJComputeArguments attribute) (kliff.models.model.ComputeArguments attribute) index (kliff.models.Parameter attribute), [1] (kliff.models.parameter.Parameter attribute), [1] init_influence_distance() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.lennard_jones.LennardJones method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.model.Model method) init_model_params() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.lennard_jones.LennardJones method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.model.Model method) init_supported_species() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.lennard_jones.LennardJones method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.model.Model method)

initialize() (kliff.trainer.base_trainer.Trainer method) initialize_bispectrum_functions() (in module kliff.transforms.configuration_transforms.descriptor_initializers) initialize_symmetry_functions() (in module kliff.transforms.configuration_transforms.descriptor_initializers) InputError (class in kliff.error) install_kim_model() (in module kliff.utils) inverse() (kliff.transforms.configuration_transforms.configuration_transform.ConfigurationTransform method) (kliff.transforms.configuration_transforms.ConfigurationTransform method) (kliff.transforms.property_transforms.NormalizedPropertyTransform method) (kliff.transforms.property_transforms.PropertyTransform method) (kliff.transforms.property_transforms.RMSMagnitudeNormalizePropertyTransform method) (kliff.transforms.property_transforms.RMSNormalizePropertyTransform method) inverse_transform() (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) (kliff.transforms.parameter_transforms.LogParameterTransform method), [1] (kliff.transforms.parameter_transforms.ParameterTransform method), [1] is_kim_model_installed() (in module kliff.utils) is_mutable (kliff.models.Parameter property) (kliff.models.parameter.Parameter property)

K

keep_original (kliff.transforms.property_transforms.PropertyTransform attribute) (kliff.transforms.property_transforms.PropertyTransform property) KeyNotFoundError (class in kliff.error) KIMComputeArguments (class in kliff.models.kim) KIMModel (class in kliff.models) (class in kliff.models.kim) KIMModelError KIMTrainer (class in kliff.trainer.kim_trainer) kliff.analyzers module kliff.analyzers.fisher module kliff.analyzers.rmse module kliff.atomic_data module kliff.dataset module kliff.dataset.configuration module kliff.dataset.dataset module kliff.dataset.dataset_torch module kliff.dataset.extxyz module kliff.dataset.weight module kliff.error module kliff.legacy module kliff.legacy.calculators module kliff.legacy.calculators.calculator module kliff.legacy.calculators.calculator_torch module kliff.legacy.descriptors module kliff.legacy.descriptors.bispectrum module kliff.legacy.descriptors.bispectrum.bispectrum module kliff.legacy.descriptors.descriptor module kliff.legacy.descriptors.symmetry_function module kliff.legacy.descriptors.symmetry_function.sym_fn module kliff.legacy.loss module kliff.legacy.nn module kliff.log module kliff.models module kliff.models.kim module kliff.models.lennard_jones module

kliff.models.linear_regression module kliff.models.model module kliff.models.model_torch module kliff.models.neural_network module kliff.models.parameter module kliff.neighbor module kliff.neighbor.neighbor module kliff.parallel module kliff.trainer module kliff.trainer.base_trainer module kliff.trainer.kim_trainer module kliff.trainer.torch_trainer module kliff.trainer.utils module kliff.trainer.utils.dataloaders module kliff.trainer.utils.lightning_utils module kliff.trainer.utils.losses module kliff.transforms module kliff.transforms.configuration_transforms module kliff.transforms.configuration_transforms.configuration_transform module kliff.transforms.configuration_transforms.default_hyperparams module kliff.transforms.configuration_transforms.descriptor_initializers module kliff.transforms.configuration_transforms.descriptors module kliff.transforms.configuration_transforms.graphs module kliff.transforms.configuration_transforms.graphs.generate_graph module kliff.transforms.configuration_transforms.utils module kliff.transforms.parameter_transforms module kliff.transforms.property_transforms module kliff.uq module kliff.uq.bootstrap module kliff.uq.mcmc module kliff.uq.mcmc_utils module kliff.utils module

L

len() (kliff.trainer.utils.dataloaders.GraphDataset method) length_equal() (in module kliff.utils) LennardJones (class in kliff.models) (class in kliff.models.lennard_jones) LinearRegression (class in kliff.models) (class in kliff.models.linear_regression) LinearRegressionError LJComputeArguments (class in kliff.models.lennard_jones) load() (kliff.models.Model method) (kliff.models.model.Model method) (kliff.models.model_torch.ModelTorch method) (kliff.models.ModelTorch method) (kliff.models.Parameter class method) (kliff.models.parameter.Parameter class method) load_bootstrap_compute_arguments() (kliff.uq.bootstrap.BootstrapEmpiricalModel method) (kliff.uq.bootstrap.BootstrapNeuralNetworkModel method) (kliff.uq.BootstrapEmpiricalModel method) (kliff.uq.BootstrapNeuralNetworkModel method)

load_checkpoint() (kliff.trainer.torch_trainer.DNNTrainer method) load_fingerprints() (in module kliff.legacy.descriptors.descriptor) load_optimizer_state() (kliff.legacy.loss.LossNeuralNetworkModel method) load_state_dict() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) log_per_atom_outputs() (kliff.trainer.base_trainer.Trainer method) LogParameterTransform (class in kliff.transforms.parameter_transforms), [1] logprior_uniform() (in module kliff.uq.mcmc) Loss (class in kliff.legacy.loss) loss() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) LossError LossNeuralNetworkModel (class in kliff.legacy.loss) LossPhysicsMotivatedModel (class in kliff.legacy.loss) lower_bound (kliff.models.Parameter property) (kliff.models.parameter.Parameter property)

M

MAE_loss() (in module kliff.trainer.utils.losses) MagnitudeInverseWeight (class in kliff.dataset.weight), [1] MCMC (class in kliff.uq) (class in kliff.uq.mcmc) MCMCError mean (kliff.legacy.descriptors.Descriptor attribute) (kliff.legacy.descriptors.descriptor.Descriptor attribute) metadata (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) (kliff.dataset.Dataset property) (kliff.dataset.dataset.Dataset property) minimize() (kliff.legacy.loss.LossNeuralNetworkModel method) (kliff.legacy.loss.LossPhysicsMotivatedModel method) Model (class in kliff.models) (class in kliff.models.model) model (kliff.legacy.calculators.calculator_torch.CalculatorTorch property) (kliff.legacy.calculators.calculator_torch.CalculatorTorchSeparateSpecies property) (kliff.legacy.calculators.CalculatorTorch property) ModelError ModelTorch (class in kliff.models) (class in kliff.models.model_torch) ModelTorchError module kliff.analyzers kliff.analyzers.fisher kliff.analyzers.rmse kliff.atomic_data kliff.dataset kliff.dataset.configuration kliff.dataset.dataset kliff.dataset.dataset_torch kliff.dataset.extxyz kliff.dataset.weight kliff.error kliff.legacy kliff.legacy.calculators kliff.legacy.calculators.calculator kliff.legacy.calculators.calculator_torch kliff.legacy.descriptors kliff.legacy.descriptors.bispectrum kliff.legacy.descriptors.bispectrum.bispectrum kliff.legacy.descriptors.descriptor kliff.legacy.descriptors.symmetry_function kliff.legacy.descriptors.symmetry_function.sym_fn kliff.legacy.loss kliff.legacy.nn kliff.log kliff.models kliff.models.kim kliff.models.lennard_jones kliff.models.linear_regression kliff.models.model kliff.models.model_torch kliff.models.neural_network kliff.models.parameter kliff.neighbor kliff.neighbor.neighbor kliff.parallel kliff.trainer kliff.trainer.base_trainer kliff.trainer.kim_trainer kliff.trainer.torch_trainer kliff.trainer.utils kliff.trainer.utils.dataloaders kliff.trainer.utils.lightning_utils kliff.trainer.utils.losses kliff.transforms kliff.transforms.configuration_transforms kliff.transforms.configuration_transforms.configuration_transform kliff.transforms.configuration_transforms.default_hyperparams kliff.transforms.configuration_transforms.descriptor_initializers kliff.transforms.configuration_transforms.descriptors kliff.transforms.configuration_transforms.graphs kliff.transforms.configuration_transforms.graphs.generate_graph kliff.transforms.configuration_transforms.utils kliff.transforms.parameter_transforms kliff.transforms.property_transforms kliff.uq kliff.uq.bootstrap kliff.uq.mcmc kliff.uq.mcmc_utils kliff.utils

MSE_loss() (in module kliff.trainer.utils.losses) mser() (in module kliff.uq) (in module kliff.uq.mcmc_utils)

N

name (kliff.models.Parameter attribute), [1] (kliff.models.parameter.Parameter attribute), [1] named_parameters() (kliff.models.Model method) (kliff.models.model.Model method)

NeighborListDataset (class in kliff.trainer.utils.dataloaders) NeuralNetwork (class in kliff.models) (class in kliff.models.neural_network) NeuralNetworkError NormalizedPropertyTransform (class in kliff.transforms.property_transforms)

O

on_train_batch_end() (kliff.trainer.utils.lightning_utils.SavePerAtomPredictions method) on_validation_batch_end() (kliff.trainer.utils.lightning_utils.SavePerAtomPredictions method) on_validation_epoch_end() (kliff.trainer.utils.lightning_utils.SaveModelCallback method) opt_mask (kliff.models.Parameter attribute), [1] (kliff.models.parameter.Parameter attribute), [1] opt_params_has_bounds() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.models.Model method) (kliff.models.model.Model method)

order_by_species() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) original_values (kliff.transforms.property_transforms.PropertyTransform attribute)

P

Parameter (class in kliff.models) (class in kliff.models.parameter) ParameterError parameters() (kliff.models.Model method) (kliff.models.model.Model method) ParameterTransform (class in kliff.transforms.parameter_transforms), [1] parmap1() (in module kliff.parallel) parmap2() (in module kliff.parallel) parse_manifest() (kliff.trainer.base_trainer.Trainer method) path (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property)

PBC (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) pickle_dump() (in module kliff.utils) pickle_load() (in module kliff.utils) property_key (kliff.transforms.property_transforms.PropertyTransform attribute) PropertyTransform (class in kliff.transforms.property_transforms) PropertyTransformError PyGGraph (class in kliff.transforms.configuration_transforms) (class in kliff.transforms.configuration_transforms.graphs) (class in kliff.transforms.configuration_transforms.graphs.generate_graph)

R

RadialGraph (class in kliff.transforms.configuration_transforms) (class in kliff.transforms.configuration_transforms.graphs) (class in kliff.transforms.configuration_transforms.graphs.generate_graph) read_extxyz() (in module kliff.dataset) (in module kliff.dataset.extxyz) read_opt_params() (kliff.models.Model method) (kliff.models.model.Model method) report_import_error() (in module kliff.error) restore_loss() (kliff.uq.bootstrap.BootstrapEmpiricalModel method) (kliff.uq.bootstrap.BootstrapNeuralNetworkModel method) (kliff.uq.BootstrapEmpiricalModel method) (kliff.uq.BootstrapNeuralNetworkModel method)

rhat() (in module kliff.uq) (in module kliff.uq.mcmc_utils) RMSMagnitudeNormalizePropertyTransform (class in kliff.transforms.property_transforms) RMSNormalizePropertyTransform (class in kliff.transforms.property_transforms) run() (kliff.analyzers.EnergyForcesRMSE method) (kliff.analyzers.Fisher method) (kliff.analyzers.fisher.Fisher method), [1] (kliff.analyzers.rmse.EnergyForcesRMSE method), [1] (kliff.uq.bootstrap.BootstrapEmpiricalModel method) (kliff.uq.bootstrap.BootstrapNeuralNetworkModel method) (kliff.uq.BootstrapEmpiricalModel method) (kliff.uq.BootstrapNeuralNetworkModel method)

S

save() (kliff.models.Model method) (kliff.models.model.Model method) (kliff.models.model_torch.ModelTorch method) (kliff.models.ModelTorch method) (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) save_bootstrap_compute_arguments() (kliff.uq.bootstrap.BootstrapEmpiricalModel method) (kliff.uq.bootstrap.BootstrapNeuralNetworkModel method) (kliff.uq.BootstrapEmpiricalModel method) (kliff.uq.BootstrapNeuralNetworkModel method) save_config() (kliff.trainer.base_trainer.Trainer method) save_frequency (kliff.models.model_torch.ModelTorch property) (kliff.models.ModelTorch property) save_kim_model() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) save_model() (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.calculator_torch.CalculatorTorchSeparateSpecies method) (kliff.legacy.calculators.CalculatorTorch method) save_optimizer_state() (kliff.legacy.loss.LossNeuralNetworkModel method) save_prefix (kliff.models.model_torch.ModelTorch property) (kliff.models.ModelTorch property) save_start (kliff.models.model_torch.ModelTorch property) (kliff.models.ModelTorch property) save_weights() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) SaveModelCallback (class in kliff.trainer.utils.lightning_utils) SavePerAtomPredictions (class in kliff.trainer.utils.lightning_utils) scipy_least_squares_methods (kliff.legacy.loss.LossPhysicsMotivatedModel attribute) scipy_least_squares_methods_not_supported_args (kliff.legacy.loss.LossPhysicsMotivatedModel attribute) scipy_minimize_methods (kliff.legacy.loss.LossPhysicsMotivatedModel attribute) scipy_minimize_methods_not_supported_args (kliff.legacy.loss.LossPhysicsMotivatedModel attribute) seed_all() (in module kliff.utils) (kliff.trainer.base_trainer.Trainer method) set_fingerprints() (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) set_logger() (in module kliff.log) set_one_opt_param() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.Model method) (kliff.models.model.Model method)

set_opt_params() (kliff.models.Model method) (kliff.models.model.Model method) set_params_mutable() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.Model method) (kliff.models.model.Model method) set_save_metadata() (kliff.models.model_torch.ModelTorch method) (kliff.models.ModelTorch method) setup_dataloaders() (kliff.trainer.torch_trainer.DNNTrainer method) setup_dataset() (kliff.trainer.base_trainer.Trainer method) setup_dataset_split() (kliff.trainer.base_trainer.Trainer method) setup_dataset_transforms() (kliff.trainer.base_trainer.Trainer method) setup_model() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) setup_optimizer() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) setup_parameter_transforms() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.torch_trainer.DNNTrainer method) setup_workspace() (kliff.trainer.base_trainer.Trainer method) show_available_descriptors() (in module kliff.transforms.configuration_transforms) (in module kliff.transforms.configuration_transforms.descriptors) size (kliff.legacy.descriptors.Descriptor attribute) (kliff.legacy.descriptors.descriptor.Descriptor attribute) soap_default() (in module kliff.transforms.configuration_transforms.default_hyperparams) species (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) split_string() (in module kliff.utils) state_dict() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) stdev (kliff.legacy.descriptors.Descriptor attribute) (kliff.legacy.descriptors.descriptor.Descriptor attribute) str_to_numpy() (in module kliff.utils) stress (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) stress_to_tensor() (in module kliff.utils) stress_to_voigt() (in module kliff.utils) stress_weight (kliff.dataset.weight.Weight property), [1] symmetry_functions_set30() (in module kliff.transforms.configuration_transforms.default_hyperparams) symmetry_functions_set51() (in module kliff.transforms.configuration_transforms.default_hyperparams)

T

to_ase() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) to_ase_atoms() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) to_ase_list() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) to_colabfit() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) to_dict() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) (kliff.dataset.weight.Weight method), [1] (kliff.transforms.configuration_transforms.graphs.generate_graph.PyGGraph method) (kliff.transforms.configuration_transforms.graphs.PyGGraph method) (kliff.transforms.configuration_transforms.PyGGraph method) to_file() (kliff.dataset.Configuration method) (kliff.dataset.configuration.Configuration method) to_lmdb() (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) to_path() (in module kliff.utils) (kliff.dataset.Dataset method) (kliff.dataset.dataset.Dataset method) to_py_graph() (kliff.transforms.configuration_transforms.graphs.generate_graph.RadialGraph static method) (kliff.transforms.configuration_transforms.graphs.RadialGraph static method) (kliff.transforms.configuration_transforms.RadialGraph static method)

torch_available() (in module kliff.utils) torch_geometric_available() (in module kliff.utils) torch_minimize_methods (kliff.legacy.loss.LossNeuralNetworkModel attribute) train() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) train_step() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method) Trainer (class in kliff.trainer.base_trainer) TrainerError transform() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) (kliff.models.Parameter method) (kliff.models.parameter.Parameter method) (kliff.transforms.configuration_transforms.configuration_transform.ConfigurationTransform method) (kliff.transforms.configuration_transforms.ConfigurationTransform method) (kliff.transforms.parameter_transforms.LogParameterTransform method), [1] (kliff.transforms.parameter_transforms.ParameterTransform method), [1] (kliff.transforms.property_transforms.NormalizedPropertyTransform method) (kliff.transforms.property_transforms.PropertyTransform method) (kliff.transforms.property_transforms.RMSMagnitudeNormalizePropertyTransform method) (kliff.transforms.property_transforms.RMSNormalizePropertyTransform method) transform_function (kliff.models.Parameter attribute), [1] (kliff.models.parameter.Parameter attribute), [1]

U

update_model_params() (kliff.legacy.calculators.Calculator method) (kliff.legacy.calculators.calculator.Calculator method) (kliff.legacy.calculators.calculator_torch.CalculatorTorch method) (kliff.legacy.calculators.CalculatorTorch method) (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.Model method) (kliff.models.model.Model method)

upper_bound (kliff.models.Parameter property) (kliff.models.parameter.Parameter property)

V

validation_step() (kliff.trainer.base_trainer.Trainer method) (kliff.trainer.kim_trainer.KIMTrainer method) (kliff.trainer.torch_trainer.DNNTrainer method)

W

Weight (class in kliff.dataset.weight), [1] weight (kliff.dataset.Configuration property) (kliff.dataset.configuration.Configuration property) WeightError (class in kliff.dataset.weight) write_extxyz() (in module kliff.dataset) (in module kliff.dataset.extxyz) write_kim_model() (kliff.models.kim.KIMModel method) (kliff.models.KIMModel method) (kliff.models.Model method) (kliff.models.model.Model method) (kliff.models.model_torch.ModelTorch method) (kliff.models.ModelTorch method) (kliff.models.neural_network.NeuralNetwork method) (kliff.models.NeuralNetwork method)

write_kim_params() (kliff.legacy.descriptors.Descriptor method) (kliff.legacy.descriptors.descriptor.Descriptor method) write_training_env_edn() (kliff.trainer.base_trainer.Trainer method)

Y

yaml_dump() (in module kliff.utils)

yaml_load() (in module kliff.utils)