Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Y A add_configs() (kliff.dataset.Dataset method) add_layers() (kliff.models.NeuralNetwork method) args (kliff.error.InputError attribute) (kliff.error.KeyNotFoundError attribute) (kliff.loss.LossError attribute) as_dict() (kliff.models.OptimizingParameters method) (kliff.models.Parameter method) assemble_forces() (in module kliff.neighbor) assemble_stress() (in module kliff.neighbor) autocorr() (in module kliff.uq) B Bispectrum (class in kliff.descriptors) builtin_samplers (kliff.uq.MCMC attribute) C Calculator (class in kliff.calculators) CalculatorTorch (class in kliff.calculators) cell (kliff.dataset.Configuration property) compute() (kliff.calculators.Calculator method) (kliff.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) ComputeArguments (class in kliff.models) Configuration (class in kliff.dataset) coords (kliff.dataset.Configuration property) (kliff.neighbor.NeighborList attribute) count_atoms_by_species() (kliff.dataset.Configuration method) create() (kliff.calculators.Calculator method) (kliff.calculators.CalculatorTorch method) create_a_kim_compute_argument() (kliff.models.KIMModel method) create_directory() (in module kliff.utils) create_neigh() (kliff.neighbor.NeighborList method) D Dataset (class in kliff.dataset) Descriptor (class in kliff.descriptors) descriptor (kliff.models.LinearRegression property) (kliff.models.ModelTorch property) (kliff.models.NeuralNetwork property) device (kliff.models.LinearRegression property) (kliff.models.ModelTorch property) (kliff.models.NeuralNetwork property) download_dataset() (in module kliff.utils) Dropout (class in kliff.nn) dtype (kliff.models.LinearRegression property) (kliff.models.ModelTorch property) (kliff.models.NeuralNetwork property) E echo_model_params() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) echo_opt_params() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.OptimizingParameters method) energy (kliff.dataset.Configuration property) energy_forces_residual() (in module kliff.loss) energy_residual() (in module kliff.loss) EnergyForcesRMSE (class in kliff.analyzers) F Fisher (class in kliff.analyzers) fit() (kliff.calculators.CalculatorTorch method) (kliff.models.LinearRegression method) (kliff.models.ModelTorch method) (kliff.models.NeuralNetwork method) fixed (kliff.models.Parameter property) forces (kliff.dataset.Configuration property) forces_residual() (in module kliff.loss) forward() (kliff.models.LinearRegression method) (kliff.models.ModelTorch method) (kliff.models.NeuralNetwork method) (kliff.nn.Dropout method) from_dict() (kliff.models.OptimizingParameters class method) (kliff.models.Parameter class method) from_file() (kliff.dataset.Configuration class method) G generate_fingerprints() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_compute_argument_class() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) get_compute_arguments() (kliff.calculators.Calculator method) (kliff.calculators.CalculatorTorch method) get_compute_flag() (kliff.models.ComputeArguments method) get_configs() (kliff.dataset.Dataset method) get_context() (in module kliff.parallel) get_coords() (kliff.neighbor.NeighborList method) get_cutoff() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_dtype() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_energy() (kliff.calculators.Calculator method) (kliff.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) get_forces() (kliff.calculators.Calculator method) (kliff.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) get_hyperparams() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_image() (kliff.neighbor.NeighborList method) get_influence_distance() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) get_kim_model_params() (kliff.models.KIMModel method) get_log_level() (in module kliff.log) get_mean() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_model_params() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) get_MPI_world_size() (in module kliff.parallel) get_neigh() (kliff.neighbor.NeighborList method) get_num_atoms() (kliff.dataset.Configuration method) get_num_atoms_by_species() (kliff.dataset.Configuration method) get_num_configs() (kliff.dataset.Dataset method) get_num_opt_params() (kliff.calculators.Calculator method) (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.OptimizingParameters method) get_numneigh_and_neighlist_1D() (kliff.neighbor.NeighborList method) get_opt_param_name_value_and_indices() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.OptimizingParameters method) get_opt_params() (kliff.calculators.Calculator method) (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.OptimizingParameters method) get_opt_params_bounds() (kliff.calculators.Calculator method) (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.OptimizingParameters method) get_padding_coords() (kliff.neighbor.NeighborList method) get_padding_image() (kliff.neighbor.NeighborList method) get_padding_species_code() (kliff.neighbor.NeighborList method) get_padding_speices() (kliff.neighbor.NeighborList method) get_prediction() (kliff.calculators.Calculator method) (kliff.models.ComputeArguments method) get_property() (kliff.models.ComputeArguments method) get_reference() (kliff.calculators.Calculator method) (kliff.models.ComputeArguments method) get_size() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_species() (kliff.neighbor.NeighborList method) get_species_code() (kliff.neighbor.NeighborList method) get_stdev() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) get_stress() (kliff.calculators.Calculator method) (kliff.calculators.CalculatorTorch method) (kliff.models.ComputeArguments method) get_supported_species() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) get_T0() (in module kliff.uq) get_volume() (kliff.dataset.Configuration method) H has_opt_params_bounds() (kliff.calculators.Calculator method) (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) (kliff.models.OptimizingParameters method) I identifier (kliff.dataset.Configuration property) image (kliff.neighbor.NeighborList attribute) implemented_property (kliff.calculators.CalculatorTorch attribute) (kliff.models.ComputeArguments attribute) index (kliff.models.Parameter property) init_influence_distance() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) init_model_params() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) init_supported_species() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) InputError K KeyNotFoundError KIMModel (class in kliff.models) kliff.analyzers module kliff.atomic_data module kliff.calculators module kliff.dataset module kliff.descriptors module kliff.error module kliff.log module kliff.loss module kliff.models module kliff.neighbor module kliff.nn module kliff.parallel module kliff.uq module kliff.utils module L length_equal() (in module kliff.utils) LennardJones (class in kliff.models) LinearRegression (class in kliff.models) load() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.LinearRegression method) (kliff.models.Model method) (kliff.models.ModelTorch method) (kliff.models.NeuralNetwork method) load_optimizer_state() (kliff.loss.LossNeuralNetworkModel method) load_state_dict() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) Loss (class in kliff.loss) LossError LossNeuralNetworkModel (class in kliff.loss) LossPhysicsMotivatedModel (class in kliff.loss) lower_bound (kliff.models.Parameter property) M MCMC (class in kliff.uq) mean (kliff.descriptors.Descriptor attribute) minimize() (kliff.loss.LossNeuralNetworkModel method) (kliff.loss.LossPhysicsMotivatedModel method) Model (class in kliff.models) model (kliff.calculators.CalculatorTorch property) ModelTorch (class in kliff.models) module kliff.analyzers kliff.atomic_data kliff.calculators kliff.dataset kliff.descriptors kliff.error kliff.log kliff.loss kliff.models kliff.neighbor kliff.nn kliff.parallel kliff.uq kliff.utils mser() (in module kliff.uq) N name (kliff.models.Parameter property) NeighborList (class in kliff.neighbor) NeuralNetwork (class in kliff.models) O OptimizingParameters (class in kliff.models) order_by_species() (kliff.dataset.Configuration method) P padding_coords (kliff.neighbor.NeighborList attribute) padding_image (kliff.neighbor.NeighborList attribute) padding_species (kliff.neighbor.NeighborList attribute) Parameter (class in kliff.models) parmap1() (in module kliff.parallel) parmap2() (in module kliff.parallel) path (kliff.dataset.Configuration property) PBC (kliff.dataset.Configuration property) pickle_dump() (in module kliff.utils) pickle_load() (in module kliff.utils) R read() (kliff.models.OptimizingParameters method) read_extxyz() (in module kliff.dataset) read_opt_params() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) REDIRECT (kliff.models.OptimizingParameters attribute) (kliff.models.Parameter attribute) report_import_error() (in module kliff.error) rhat() (in module kliff.uq) run() (kliff.analyzers.EnergyForcesRMSE method) (kliff.analyzers.Fisher method) S save() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.LinearRegression method) (kliff.models.Model method) (kliff.models.ModelTorch method) (kliff.models.NeuralNetwork method) save_frequency (kliff.models.LinearRegression property) (kliff.models.ModelTorch property) (kliff.models.NeuralNetwork property) save_model() (kliff.calculators.CalculatorTorch method) save_optimizer_state() (kliff.loss.LossNeuralNetworkModel method) save_prefix (kliff.models.LinearRegression property) (kliff.models.ModelTorch property) (kliff.models.NeuralNetwork property) save_start (kliff.models.LinearRegression property) (kliff.models.ModelTorch property) (kliff.models.NeuralNetwork property) scipy_least_squares_methods (kliff.loss.LossPhysicsMotivatedModel attribute) scipy_least_squares_methods_not_supported_args (kliff.loss.LossPhysicsMotivatedModel attribute) scipy_minimize_methods (kliff.loss.LossPhysicsMotivatedModel attribute) scipy_minimize_methods_not_supported_args (kliff.loss.LossPhysicsMotivatedModel attribute) seed_all() (in module kliff.utils) set() (kliff.models.OptimizingParameters method) set_fixed() (kliff.models.Parameter method) set_logger() (in module kliff.log) set_lower_bound() (kliff.models.Parameter method) set_one() (kliff.models.OptimizingParameters method) set_one_opt_param() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) set_opt_params() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) set_save_metadata() (kliff.models.LinearRegression method) (kliff.models.ModelTorch method) (kliff.models.NeuralNetwork method) set_upper_bound() (kliff.models.Parameter method) set_value() (kliff.models.Parameter method) size (kliff.descriptors.Descriptor attribute) species (kliff.dataset.Configuration property) (kliff.neighbor.NeighborList attribute) split_string() (in module kliff.utils) state_dict() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) stdev (kliff.descriptors.Descriptor attribute) stress (kliff.dataset.Configuration property) SymmetryFunction (class in kliff.descriptors) T to_file() (kliff.dataset.Configuration method) to_json() (kliff.models.OptimizingParameters method) (kliff.models.Parameter method) to_path() (in module kliff.utils) torch_available() (in module kliff.utils) torch_minimize_methods (kliff.loss.LossNeuralNetworkModel attribute) transform() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) U unsafe_hash() (kliff.models.OptimizingParameters method) (kliff.models.Parameter method) update_hyperparams() (kliff.descriptors.Bispectrum method) update_model_params() (kliff.calculators.Calculator method) (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.Model method) update_opt_params() (kliff.models.OptimizingParameters method) upper_bound (kliff.models.Parameter property) V validate_monty() (kliff.models.OptimizingParameters class method) (kliff.models.Parameter class method) value (kliff.models.Parameter property) W weight (kliff.dataset.Configuration property) with_traceback() (kliff.error.InputError method) (kliff.error.KeyNotFoundError method) (kliff.loss.LossError method) write_extxyz() (in module kliff.dataset) write_kim_model() (kliff.models.KIMModel method) (kliff.models.LennardJones method) (kliff.models.LinearRegression method) (kliff.models.Model method) (kliff.models.ModelTorch method) (kliff.models.NeuralNetwork method) write_kim_params() (kliff.descriptors.Bispectrum method) (kliff.descriptors.Descriptor method) (kliff.descriptors.SymmetryFunction method) Y yaml_dump() (in module kliff.utils) yaml_load() (in module kliff.utils)