Package Reference

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