Index

_

_database (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute)

_dtype (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute)

A

activate_experiments() (mdsuite.project.Project method) (mdsuite.project.project.Project method) active (mdsuite.database.experiment_database.ExperimentDatabase property) (mdsuite.database.scheme.Experiment attribute) active_experiments (mdsuite.project.Project property) (mdsuite.project.project.Project property) add_data() (mdsuite.database.simulation_database.Database method) (mdsuite.database.simulation_database.TrajectoryChunkData method) (mdsuite.experiment.Experiment method) (mdsuite.experiment.experiment.Experiment method) (mdsuite.project.Project method) (mdsuite.project.project.Project method) add_dataset() (mdsuite.database.simulation_database.Database method) add_experiment() (mdsuite.project.Project method) (mdsuite.project.project.Project method) AdjacencyMatrix (class in mdsuite.graph_modules.adjacency_matrix) amount (mdsuite.utils.molecule.Molecule attribute), [1] analysis_name (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity attribute) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity attribute) (mdsuite.calculators.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboIonicConductivity attribute) (mdsuite.calculators.GreenKuboThermalConductivity attribute) (mdsuite.calculators.GreenKuboViscosity attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute) angle_between() (in module mdsuite.utils.linalg) angular_velocity_non_spherical (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute)

angular_velocity_spherical (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) AngularDistributionFunction (class in mdsuite.calculators) (class in mdsuite.calculators.angular_distribution_function) (mdsuite.experiment.run.RunComputation property) apply_minimum_image() (in module mdsuite.utils.linalg) apply_savgol_filter() (in module mdsuite.utils.meta_functions), [1] apply_system_cutoff() (in module mdsuite.utils.linalg) Args (class in mdsuite.calculators.angular_distribution_function) (class in mdsuite.calculators.coordination_number_calculation) (class in mdsuite.calculators.einstein_diffusion_coefficients) (class in mdsuite.calculators.einstein_distinct_diffusion_coefficients) (class in mdsuite.calculators.einstein_helfand_ionic_conductivity) (class in mdsuite.calculators.einstein_helfand_thermal_conductivity) (class in mdsuite.calculators.einstein_helfand_thermal_kinaci) (class in mdsuite.calculators.green_kubo_distinct_diffusion_coefficients) (class in mdsuite.calculators.green_kubo_ionic_conductivity) (class in mdsuite.calculators.green_kubo_self_diffusion_coefficients) (class in mdsuite.calculators.green_kubo_thermal_conductivity) (class in mdsuite.calculators.green_kubo_viscosity) (class in mdsuite.calculators.green_kubo_viscosity_flux) (class in mdsuite.calculators.kirkwood_buff_integrals) (class in mdsuite.calculators.potential_of_mean_force) (class in mdsuite.calculators.radial_distribution_function) (class in mdsuite.calculators.spatial_distribution_function) (class in mdsuite.database.calculator_database) assert_species_list_consistent() (in module mdsuite.file_io.file_read) assertDeepAlmostEqual() (in module mdsuite.utils.testing) atom_selection (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_helfand_ionic_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.Args attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.Args attribute) (mdsuite.calculators.green_kubo_viscosity.Args attribute) (mdsuite.calculators.green_kubo_viscosity_flux.Args attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.calculators.spatial_distribution_function.Args attribute) attach_file_logger() (mdsuite.project.Project method) (mdsuite.project.project.Project method) avogadro (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute)

B

base (mdsuite.database.database_base.DatabaseBase property) batch_generator() (mdsuite.database.data_manager.DataManager method) batch_size (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.AngularDistributionFunction attribute) (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations attribute) bin_minibatch() (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction static method) (mdsuite.calculators.RadialDistributionFunction static method) bins (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.AngularDistributionFunction attribute)

bokeh_sizing_mode (mdsuite.utils.config.Config attribute), [1] boltzmann (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) box_array (mdsuite.database.experiment_database.ExperimentDatabase property) box_images (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) box_l (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] box_length (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute), [1] build_configuration_graph() (mdsuite.graph_modules.molecular_graph.MolecularGraph method) build_database() (mdsuite.database.database_base.DatabaseBase method) build_smiles_graph() (in module mdsuite.graph_modules.molecular_graph)

C

Calculator (class in mdsuite.calculators) (class in mdsuite.calculators.calculator) CalculatorDatabase (class in mdsuite.database.calculator_database) call() (in module mdsuite.calculators.calculator) (mdsuite.utils.tensor_flow.layers.NLLayer method) CannotFindPropertyError CannotFindTransformationError CannotPerformThisAnalysis cartesian_to_spherical_coordinates() (in module mdsuite.utils.linalg) change_key_names() (mdsuite.database.simulation_database.Database method) charge (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) (mdsuite.database.simulation_database.SpeciesInfo attribute) check_a_in_b() (in module mdsuite.utils.meta_functions), [1] check_existence() (mdsuite.database.simulation_database.Database method) check_input() (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction method) (mdsuite.calculators.AngularDistributionFunction method) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients method) (mdsuite.calculators.einstein_helfand_ionic_conductivity.EinsteinHelfandIonicConductivity method) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity method) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci method) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients method) (mdsuite.calculators.EinsteinHelfandIonicConductivity method) (mdsuite.calculators.EinsteinHelfandThermalConductivity method) (mdsuite.calculators.EinsteinHelfandThermalKinaci method) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity method) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity method) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity method) (mdsuite.calculators.green_kubo_viscosity_flux.GreenKuboViscosityFlux method) (mdsuite.calculators.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.GreenKuboIonicConductivity method) (mdsuite.calculators.GreenKuboThermalConductivity method) (mdsuite.calculators.GreenKuboViscosity method) (mdsuite.calculators.GreenKuboViscosityFlux method) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction method) (mdsuite.calculators.RadialDistributionFunction method) closest_point() (in module mdsuite.utils.meta_functions), [1] cls_transformation_run() (mdsuite.experiment.Experiment method) (mdsuite.experiment.experiment.Experiment method) coerce() (mdsuite.database.types.MutableDict class method) Colour (class in mdsuite.utils) combine_dictionaries() (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction static method) (mdsuite.calculators.RadialDistributionFunction static method) Computation (class in mdsuite.database.scheme) computation (mdsuite.database.scheme.ComputationAttribute attribute) (mdsuite.database.scheme.ComputationResult attribute)

computation_attributes (mdsuite.database.scheme.Computation attribute) computation_id (mdsuite.database.scheme.ComputationAttribute attribute) (mdsuite.database.scheme.ComputationResult attribute) computation_parameter (mdsuite.database.scheme.Computation property) computation_result (mdsuite.database.scheme.ExperimentSpecies attribute) (mdsuite.database.scheme.SpeciesAssociation attribute) computation_results (mdsuite.database.scheme.Computation attribute) computation_results_id (mdsuite.database.scheme.SpeciesAssociation attribute) ComputationAttribute (class in mdsuite.database.scheme) ComputationResult (class in mdsuite.database.scheme) ComputationResults (class in mdsuite.database.calculator_database) computations (mdsuite.database.scheme.Experiment attribute) compute_species_values() (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction method) (mdsuite.calculators.RadialDistributionFunction method) Config (class in mdsuite.utils.config) construct_plot() (mdsuite.visualizer.d2_data_visualization.DataVisualizer2D method) conv_to_db() (in module mdsuite.database.calculator_database) CoordinateUnwrapper (class in mdsuite.transformations) (class in mdsuite.transformations.unwrap_coordinates), [1] (mdsuite.experiment.run.RunComputation property) CoordinateWrapper (class in mdsuite.transformations) (class in mdsuite.transformations.wrap_coordinates) (mdsuite.experiment.run.RunComputation property) CoordinationNumbers (class in mdsuite.calculators) (class in mdsuite.calculators.coordination_number_calculation), [1] (mdsuite.experiment.run.RunComputation property) correlate() (in module mdsuite.utils.calculator_helper_methods) correlation_time (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_helfand_ionic_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.Args attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.Args attribute) (mdsuite.calculators.green_kubo_viscosity.Args attribute) (mdsuite.calculators.green_kubo_viscosity_flux.Args attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.calculators.spatial_distribution_function.Args attribute) count (mdsuite.database.scheme.SpeciesAssociation attribute) cutoff (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.coordination_number_calculation.Args attribute) (mdsuite.calculators.kirkwood_buff_integrals.Args attribute) (mdsuite.calculators.potential_of_mean_force.Args attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.utils.molecule.Molecule attribute), [1]

D

data (mdsuite.database.calculator_database.ComputationResults attribute) (mdsuite.database.scheme.ComputationAttribute attribute) (mdsuite.database.scheme.ComputationResult attribute) (mdsuite.database.scheme.ExperimentAttribute attribute) (mdsuite.database.scheme.ExperimentSpecies attribute) (mdsuite.time_series.base.TimeSeries property) data_dict (mdsuite.database.scheme.Computation property) data_files (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) data_manager (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations attribute) data_path (mdsuite.memory_management.memory_manager.MemoryManager attribute) (mdsuite.memory_management.MemoryManager attribute) data_range (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_helfand_ionic_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.Args attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.Args attribute) (mdsuite.calculators.green_kubo_viscosity.Args attribute) (mdsuite.calculators.green_kubo_viscosity_flux.Args attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute) (mdsuite.calculators.spatial_distribution_function.Args attribute) (mdsuite.database.scheme.Computation property)

data_resolution (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) Database (class in mdsuite.database.simulation_database) database (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator property) (mdsuite.memory_management.memory_manager.MemoryManager attribute) (mdsuite.memory_management.MemoryManager attribute) (mdsuite.time_series.base.TimeSeries property) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.Transformations property) (mdsuite.transformations.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations property) database_exists() (mdsuite.database.simulation_database.Database method) DatabaseBase (class in mdsuite.database.database_base) DatabaseDoesNotExist DataManager (class in mdsuite.database.data_manager) DatasetExists DataVisualizer2D (class in mdsuite.visualizer.d2_data_visualization) DataVisualizer3D (class in mdsuite.visualizer.d3_data_visualizer) db_computation (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute) db_experiments (mdsuite.database.project_database.ProjectDatabase property) dependency (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) description (mdsuite.database.project_database.ProjectDatabase property) (mdsuite.database.scheme.Project attribute) (mdsuite.project.Project attribute) (mdsuite.project.project.Project attribute) dipole_orientation_magnitude (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) disable_experiments() (mdsuite.project.Project method) (mdsuite.project.project.Project method) dtype (mdsuite.calculators.Calculator property) (mdsuite.calculators.calculator.Calculator property)

E

EinsteinDiffusionCoefficients (class in mdsuite.calculators) (class in mdsuite.calculators.einstein_diffusion_coefficients) (mdsuite.experiment.run.RunComputation property) EinsteinDistinctDiffusionCoefficients (class in mdsuite.calculators) (class in mdsuite.calculators.einstein_distinct_diffusion_coefficients) (mdsuite.experiment.run.RunComputation property) EinsteinHelfandIonicConductivity (class in mdsuite.calculators) (class in mdsuite.calculators.einstein_helfand_ionic_conductivity) (mdsuite.experiment.run.RunComputation property) EinsteinHelfandThermalConductivity (class in mdsuite.calculators) (class in mdsuite.calculators.einstein_helfand_thermal_conductivity) (mdsuite.experiment.run.RunComputation property) EinsteinHelfandThermalKinaci (class in mdsuite.calculators) (class in mdsuite.calculators.einstein_helfand_thermal_kinaci) (mdsuite.experiment.run.RunComputation property) elementary_charge (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) ElementMassAssignedZero Energies (class in mdsuite.time_series.energies) energy (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) engine (mdsuite.database.database_base.DatabaseBase property) ensemble_generator() (mdsuite.database.data_manager.DataManager method) ensemble_operation() (mdsuite.calculators.einstein_diffusion_coefficients.EinsteinDiffusionCoefficients method) (mdsuite.calculators.einstein_helfand_ionic_conductivity.EinsteinHelfandIonicConductivity method) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity method) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci method) (mdsuite.calculators.EinsteinDiffusionCoefficients method) (mdsuite.calculators.EinsteinHelfandIonicConductivity method) (mdsuite.calculators.EinsteinHelfandThermalConductivity method) (mdsuite.calculators.EinsteinHelfandThermalKinaci method) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity method) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity method) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity method) (mdsuite.calculators.green_kubo_viscosity_flux.GreenKuboViscosityFlux method) (mdsuite.calculators.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.GreenKuboIonicConductivity method) (mdsuite.calculators.GreenKuboThermalConductivity method) (mdsuite.calculators.GreenKuboViscosity method) (mdsuite.calculators.GreenKuboViscosityFlux method) exception (mdsuite.utils.testing.MDSuiteProcess property) exp_wrapper() (mdsuite.experiment.run.RunComputation method) Experiment (class in mdsuite.database.scheme) (class in mdsuite.experiment) (class in mdsuite.experiment.experiment) experiment (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1], [2] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity attribute) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity attribute) (mdsuite.calculators.green_kubo_viscosity_flux.GreenKuboViscosityFlux attribute) (mdsuite.calculators.GreenKuboIonicConductivity attribute) (mdsuite.calculators.GreenKuboThermalConductivity attribute) (mdsuite.calculators.GreenKuboViscosity attribute) (mdsuite.calculators.GreenKuboViscosityFlux attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute) (mdsuite.database.scheme.Computation attribute) (mdsuite.database.scheme.ExperimentAttribute attribute) (mdsuite.database.scheme.ExperimentSpecies attribute) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.Transformations property) (mdsuite.transformations.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations property)

experiment_attributes (mdsuite.database.scheme.Experiment attribute) experiment_id (mdsuite.database.scheme.Computation attribute) (mdsuite.database.scheme.ExperimentAttribute attribute) (mdsuite.database.scheme.ExperimentSpecies attribute) experiment_species_id (mdsuite.database.scheme.SpeciesAssociation attribute) experimental (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) ExperimentAttribute (class in mdsuite.database.scheme) ExperimentDatabase (class in mdsuite.database.experiment_database) experiments (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute) (mdsuite.database.scheme.Project attribute) (mdsuite.project.Project attribute) (mdsuite.project.Project property) (mdsuite.project.project.Project attribute) (mdsuite.project.project.Project property) ExperimentSpecies (class in mdsuite.database.scheme) export_property_data() (mdsuite.database.experiment_database.ExperimentDatabase method) extract_properties_from_header() (in module mdsuite.file_io.lammps_trajectory_files) EXTXYZFile (class in mdsuite.file_io.extxyz_files)

F

file_to_study (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) FileProcessor (class in mdsuite.file_io.file_read), [1] find_item() (in module mdsuite.utils.meta_functions), [1] find_property_per_config() (mdsuite.transformations.Transformations method) (mdsuite.transformations.transformations.Transformations method)

find_property_single_val() (mdsuite.transformations.Transformations method) (mdsuite.transformations.transformations.Transformations method) fit_diff_coeff() (mdsuite.calculators.einstein_diffusion_coefficients.EinsteinDiffusionCoefficients method) (mdsuite.calculators.EinsteinDiffusionCoefficients method) fit_einstein_curve() (in module mdsuite.utils.calculator_helper_methods) fit_range (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_helfand_ionic_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.Args attribute) forces (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute)

G

get2dHistogram() (in module mdsuite.utils.linalg) get_angles() (in module mdsuite.utils.linalg) get_batch_dataset() (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator method) get_batch_size() (mdsuite.memory_management.memory_manager.MemoryManager method) (mdsuite.memory_management.MemoryManager method) get_computation_data() (mdsuite.database.calculator_database.CalculatorDatabase method) get_configurations_generator() (mdsuite.file_io.file_read.FileProcessor method), [1] (mdsuite.file_io.tabular_text_files.TabularTextFileProcessor method) get_data() (mdsuite.database.simulation_database.TrajectoryChunkData method) get_data_size() (mdsuite.database.simulation_database.Database method) get_database_summary() (mdsuite.database.simulation_database.Database method) get_db() (mdsuite.database.experiment_database.ExperimentDatabase method) get_dij() (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction static method) (mdsuite.calculators.RadialDistributionFunction static method) get_dimensionality() (in module mdsuite.utils.meta_functions), [1] get_ensemble_dataset() (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator method) get_ensemble_loop() (mdsuite.memory_management.memory_manager.MemoryManager method) (mdsuite.memory_management.MemoryManager method) get_generator_type_spec_and_const_data() (mdsuite.transformations.Transformations method) (mdsuite.transformations.transformations.Transformations method) get_load_time() (mdsuite.database.simulation_database.Database method) get_machine_properties() (in module mdsuite.utils.meta_functions), [1] get_memory_information() (mdsuite.database.simulation_database.Database method) get_molecules() (mdsuite.database.scheme.Experiment method) get_nearest_divisor() (in module mdsuite.utils.meta_functions), [1] get_neighbour_list() (in module mdsuite.graph_modules.molecular_graph) (in module mdsuite.utils.neighbour_list) get_or_create() (in module mdsuite.utils.database) get_partial_triu_indices() (in module mdsuite.utils.linalg) get_pomf_peaks() (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce method) (mdsuite.calculators.PotentialOfMeanForce method)

get_prop_through_transformation() (mdsuite.transformations.Transformations method) (mdsuite.transformations.transformations.Transformations method) get_species() (mdsuite.database.scheme.Experiment method) get_species_list_from_tabular_text_reader_data() (in module mdsuite.file_io.tabular_text_files) get_triplets() (in module mdsuite.utils.neighbour_list) get_triu_indicies() (in module mdsuite.utils.neighbour_list) golden_section_search() (in module mdsuite.utils.meta_functions), [1] gpu (mdsuite.memory_management.memory_manager.MemoryManager attribute) (mdsuite.memory_management.MemoryManager attribute) gpu_available() (in module mdsuite.utils.meta_functions), [1] GreenKuboDiffusionCoefficients (class in mdsuite.calculators) (class in mdsuite.calculators.green_kubo_self_diffusion_coefficients) (mdsuite.experiment.run.RunComputation property) GreenKuboDistinctDiffusionCoefficients (class in mdsuite.calculators) (class in mdsuite.calculators.green_kubo_distinct_diffusion_coefficients) (mdsuite.experiment.run.RunComputation property) GreenKuboIonicConductivity (class in mdsuite.calculators) (class in mdsuite.calculators.green_kubo_ionic_conductivity) (mdsuite.experiment.run.RunComputation property) GreenKuboThermalConductivity (class in mdsuite.calculators) (class in mdsuite.calculators.green_kubo_thermal_conductivity) (mdsuite.experiment.run.RunComputation property) GreenKuboViscosity (class in mdsuite.calculators) (class in mdsuite.calculators.green_kubo_viscosity) (mdsuite.experiment.run.RunComputation property) GreenKuboViscosityFlux (class in mdsuite.calculators) (class in mdsuite.calculators.green_kubo_viscosity_flux) (mdsuite.experiment.run.RunComputation property) grid_show() (mdsuite.visualizer.d2_data_visualization.DataVisualizer2D method) groups (mdsuite.database.simulation_database.MoleculeInfo attribute), [1]

H

hdf5_load_time() (mdsuite.memory_management.memory_manager.MemoryManager static method) (mdsuite.memory_management.MemoryManager static method)

header_lines_for_each_config (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1]

I

id (mdsuite.database.scheme.Computation attribute) (mdsuite.database.scheme.ComputationAttribute attribute) (mdsuite.database.scheme.ComputationResult attribute) (mdsuite.database.scheme.Experiment attribute) (mdsuite.database.scheme.ExperimentAttribute attribute), [1] (mdsuite.database.scheme.ExperimentSpecies attribute) (mdsuite.database.scheme.Project attribute) ideal_correction (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction property) (mdsuite.calculators.RadialDistributionFunction property) impl (mdsuite.database.types.JSONEncodedDict attribute) indices (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) initialize_database() (mdsuite.database.simulation_database.Database method) integral_data (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute)

integrated_heat_current (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) IntegratedHeatCurrent (class in mdsuite.transformations) (class in mdsuite.transformations.integrated_heat_current) (mdsuite.experiment.run.RunComputation property) integration_range (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.Args attribute) (mdsuite.calculators.green_kubo_viscosity.Args attribute) (mdsuite.calculators.green_kubo_viscosity_flux.Args attribute) ionic_current (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) IonicCurrent (class in mdsuite.transformations) (class in mdsuite.transformations.ionic_current) (mdsuite.experiment.run.RunComputation property) is_jsonable() (in module mdsuite.utils.meta_functions), [1]

J

join_path() (in module mdsuite.utils.meta_functions), [1]

JSONEncodedDict (class in mdsuite.database.types) jupyter (mdsuite.utils.config.Config attribute), [1]

K

keys() (mdsuite.database.scheme.Computation method) kinaci_heat_current (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) KinaciIntegratedHeatCurrent (class in mdsuite.transformations) (class in mdsuite.transformations.kinaci_integrated_heat_current) (mdsuite.experiment.run.RunComputation property)

kinetic_energy (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) KirkwoodBuffIntegral (class in mdsuite.calculators) (class in mdsuite.calculators.kirkwood_buff_integrals) (mdsuite.experiment.run.RunComputation property)

L

LAMMPSTrajectoryFile (class in mdsuite.file_io.lammps_trajectory_files), [1] LazyProperty (class in mdsuite.database.experiment_database) length (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) line_counter() (in module mdsuite.utils.meta_functions), [1] linear_fitting_function() (in module mdsuite.utils.meta_functions), [1] linear_scale_function() (in module mdsuite.utils.scale_functions) linearithmic_scale_function() (in module mdsuite.utils.scale_functions) load_data() (mdsuite.database.simulation_database.Database method) load_experiments() (mdsuite.project.Project method) (mdsuite.project.project.Project method) load_matrix() (mdsuite.experiment.Experiment method) (mdsuite.experiment.experiment.Experiment method) loaded_property (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity attribute) (mdsuite.calculators.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboIonicConductivity attribute) (mdsuite.calculators.GreenKuboViscosity attribute) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute) (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute)

M

mass (mdsuite.database.simulation_database.SpeciesInfo attribute) mdsuite.calculators module mdsuite.calculators.angular_distribution_function module mdsuite.calculators.calculator module mdsuite.calculators.coordination_number_calculation module mdsuite.calculators.einstein_diffusion_coefficients module mdsuite.calculators.einstein_distinct_diffusion_coefficients module mdsuite.calculators.einstein_helfand_ionic_conductivity module mdsuite.calculators.einstein_helfand_thermal_conductivity module mdsuite.calculators.einstein_helfand_thermal_kinaci module mdsuite.calculators.green_kubo_distinct_diffusion_coefficients module mdsuite.calculators.green_kubo_ionic_conductivity module mdsuite.calculators.green_kubo_self_diffusion_coefficients module mdsuite.calculators.green_kubo_thermal_conductivity module mdsuite.calculators.green_kubo_viscosity module mdsuite.calculators.green_kubo_viscosity_flux module mdsuite.calculators.kirkwood_buff_integrals module mdsuite.calculators.nernst_einstein_ionic_conductivity module mdsuite.calculators.potential_of_mean_force module mdsuite.calculators.radial_distribution_function module mdsuite.calculators.spatial_distribution_function module mdsuite.calculators.trajectory_calculator module mdsuite.calculators.transformations_reference module mdsuite.database module mdsuite.database.calculator_database module mdsuite.database.data_manager module mdsuite.database.database_base module mdsuite.database.experiment_database module mdsuite.database.mdsuite_properties module mdsuite.database.project_database module mdsuite.database.scheme module mdsuite.database.simulation_database module mdsuite.database.types module mdsuite.experiment module mdsuite.experiment.experiment module mdsuite.experiment.run module mdsuite.experiment.run_module module mdsuite.file_io module mdsuite.file_io.extxyz_files module mdsuite.file_io.file_read module mdsuite.file_io.lammps_trajectory_files module mdsuite.file_io.tabular_text_files module mdsuite.graph_modules module mdsuite.graph_modules.adjacency_matrix module mdsuite.graph_modules.molecular_graph module mdsuite.memory_management module mdsuite.memory_management.memory_manager module mdsuite.project module mdsuite.project.project module mdsuite.time_series module mdsuite.time_series.base module mdsuite.time_series.energies module mdsuite.transformations module mdsuite.transformations.integrated_heat_current module mdsuite.transformations.ionic_current module mdsuite.transformations.kinaci_integrated_heat_current module mdsuite.transformations.map_molecules module mdsuite.transformations.momentum_flux module mdsuite.transformations.scale_coordinates module mdsuite.transformations.test_trafos module mdsuite.transformations.thermal_flux module mdsuite.transformations.transformation_dict module mdsuite.transformations.transformations module mdsuite.transformations.translational_dipole_moment module mdsuite.transformations.unwrap_coordinates module mdsuite.transformations.unwrap_via_indices module mdsuite.transformations.velocity_from_positions module mdsuite.transformations.wrap_coordinates module mdsuite.utils module mdsuite.utils.calculator_helper_methods module mdsuite.utils.config module mdsuite.utils.constants module mdsuite.utils.database module mdsuite.utils.exceptions module mdsuite.utils.helpers module mdsuite.utils.linalg module mdsuite.utils.meta_functions module, [1] mdsuite.utils.molecule module

mdsuite.utils.neighbour_list module mdsuite.utils.report_computer_characteristics module mdsuite.utils.scale_functions module mdsuite.utils.tensor_flow module mdsuite.utils.tensor_flow.helpers module mdsuite.utils.tensor_flow.layers module mdsuite.utils.testing module mdsuite.utils.units module mdsuite.visualizer module mdsuite.visualizer.d2_data_visualization module mdsuite.visualizer.d3_data_visualizer module MDSuiteProcess (class in mdsuite.utils.testing) MDSuiteProperties (class in mdsuite.database.mdsuite_properties) memory_fraction (mdsuite.memory_management.memory_manager.MemoryManager attribute) (mdsuite.memory_management.MemoryManager attribute) (mdsuite.utils.config.Config attribute), [1] memory_manager (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations attribute) MemoryManager (class in mdsuite.memory_management) (class in mdsuite.memory_management.memory_manager) metadata (mdsuite.file_io.file_read.FileProcessor property) minibatch (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute) (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) module mdsuite.calculators mdsuite.calculators.angular_distribution_function mdsuite.calculators.calculator mdsuite.calculators.coordination_number_calculation mdsuite.calculators.einstein_diffusion_coefficients mdsuite.calculators.einstein_distinct_diffusion_coefficients mdsuite.calculators.einstein_helfand_ionic_conductivity mdsuite.calculators.einstein_helfand_thermal_conductivity mdsuite.calculators.einstein_helfand_thermal_kinaci mdsuite.calculators.green_kubo_distinct_diffusion_coefficients mdsuite.calculators.green_kubo_ionic_conductivity mdsuite.calculators.green_kubo_self_diffusion_coefficients mdsuite.calculators.green_kubo_thermal_conductivity mdsuite.calculators.green_kubo_viscosity mdsuite.calculators.green_kubo_viscosity_flux mdsuite.calculators.kirkwood_buff_integrals mdsuite.calculators.nernst_einstein_ionic_conductivity mdsuite.calculators.potential_of_mean_force mdsuite.calculators.radial_distribution_function mdsuite.calculators.spatial_distribution_function mdsuite.calculators.trajectory_calculator mdsuite.calculators.transformations_reference mdsuite.database mdsuite.database.calculator_database mdsuite.database.data_manager mdsuite.database.database_base mdsuite.database.experiment_database mdsuite.database.mdsuite_properties mdsuite.database.project_database mdsuite.database.scheme mdsuite.database.simulation_database mdsuite.database.types mdsuite.experiment mdsuite.experiment.experiment mdsuite.experiment.run mdsuite.experiment.run_module mdsuite.file_io mdsuite.file_io.extxyz_files mdsuite.file_io.file_read mdsuite.file_io.lammps_trajectory_files mdsuite.file_io.tabular_text_files mdsuite.graph_modules mdsuite.graph_modules.adjacency_matrix mdsuite.graph_modules.molecular_graph mdsuite.memory_management mdsuite.memory_management.memory_manager mdsuite.project mdsuite.project.project mdsuite.time_series mdsuite.time_series.base mdsuite.time_series.energies mdsuite.transformations mdsuite.transformations.integrated_heat_current mdsuite.transformations.ionic_current mdsuite.transformations.kinaci_integrated_heat_current mdsuite.transformations.map_molecules mdsuite.transformations.momentum_flux mdsuite.transformations.scale_coordinates mdsuite.transformations.test_trafos mdsuite.transformations.thermal_flux mdsuite.transformations.transformation_dict mdsuite.transformations.transformations mdsuite.transformations.translational_dipole_moment mdsuite.transformations.unwrap_coordinates mdsuite.transformations.unwrap_via_indices mdsuite.transformations.velocity_from_positions mdsuite.transformations.wrap_coordinates mdsuite.utils mdsuite.utils.calculator_helper_methods mdsuite.utils.config mdsuite.utils.constants mdsuite.utils.database mdsuite.utils.exceptions mdsuite.utils.helpers mdsuite.utils.linalg mdsuite.utils.meta_functions, [1] mdsuite.utils.molecule mdsuite.utils.neighbour_list mdsuite.utils.report_computer_characteristics mdsuite.utils.scale_functions mdsuite.utils.tensor_flow mdsuite.utils.tensor_flow.helpers mdsuite.utils.tensor_flow.layers mdsuite.utils.testing mdsuite.utils.units mdsuite.visualizer mdsuite.visualizer.d2_data_visualization mdsuite.visualizer.d3_data_visualizer mol_pbc (mdsuite.utils.molecule.Molecule attribute), [1] molecular_groups (mdsuite.graph_modules.molecular_graph.MolecularGraph attribute) molecular_mass (mdsuite.graph_modules.molecular_graph.MolecularGraph attribute) MolecularGraph (class in mdsuite.graph_modules.molecular_graph) MolecularMap (class in mdsuite.transformations) (class in mdsuite.transformations.map_molecules) (mdsuite.experiment.run.RunComputation property) Molecule (class in mdsuite.utils.molecule) molecule (mdsuite.database.scheme.ExperimentSpecies attribute) MoleculeInfo (class in mdsuite.database.simulation_database) molecules (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.calculators.spatial_distribution_function.Args attribute) (mdsuite.database.experiment_database.ExperimentDatabase property) (mdsuite.transformations.map_molecules.MolecularMap attribute) (mdsuite.transformations.MolecularMap attribute) momenta (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) momentum_flux (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) MomentumFlux (class in mdsuite.transformations) (class in mdsuite.transformations.momentum_flux) (mdsuite.experiment.run.RunComputation property) msd_array (mdsuite.calculators.einstein_diffusion_coefficients.EinsteinDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinDiffusionCoefficients attribute) msd_operation() (in module mdsuite.utils.calculator_helper_methods) MULBERRY (mdsuite.utils.Colour attribute) MultiSpeciesTrafo (class in mdsuite.transformations.transformations) MutableDict (class in mdsuite.database.types)

N

n_batches (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations attribute) n_bins (mdsuite.calculators.spatial_distribution_function.Args attribute) n_configs (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1] n_configurations (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] n_confs (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.AngularDistributionFunction attribute) n_dims (mdsuite.database.simulation_database.PropertyInfo attribute), [1] n_header_lines (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1] n_minibatches (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.AngularDistributionFunction attribute) n_particles (mdsuite.database.simulation_database.SpeciesInfo attribute), [1] (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1] name (mdsuite.database.scheme.Computation attribute) (mdsuite.database.scheme.ComputationAttribute attribute) (mdsuite.database.scheme.Experiment attribute) (mdsuite.database.scheme.ExperimentAttribute attribute), [1] (mdsuite.database.scheme.ExperimentSpecies attribute) (mdsuite.database.scheme.SpeciesAssociation property) (mdsuite.database.simulation_database.PropertyInfo attribute), [1] (mdsuite.database.simulation_database.SpeciesInfo attribute), [1] (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute) (mdsuite.project.Project attribute) (mdsuite.project.project.Project attribute) (mdsuite.utils.molecule.Molecule attribute), [1] NernstEinsteinIonicConductivity (class in mdsuite.calculators) (class in mdsuite.calculators.nernst_einstein_ionic_conductivity) (mdsuite.experiment.run.RunComputation property)

NkTV2p (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) NLLayer (class in mdsuite.utils.tensor_flow.layers) NoElementInDump NoGPUInSystem NoneType (class in mdsuite.utils.helpers) norm_power (mdsuite.calculators.angular_distribution_function.Args attribute) NotApplicableToAnalysis NoTempInData NotInDataFile number_of_atoms (mdsuite.database.experiment_database.ExperimentDatabase attribute) (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute) number_of_bins (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.coordination_number_calculation.Args attribute) (mdsuite.calculators.kirkwood_buff_integrals.Args attribute) (mdsuite.calculators.potential_of_mean_force.Args attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) number_of_configurations (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.coordination_number_calculation.Args attribute) (mdsuite.calculators.kirkwood_buff_integrals.Args attribute) (mdsuite.calculators.potential_of_mean_force.Args attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.calculators.spatial_distribution_function.Args attribute) (mdsuite.database.experiment_database.ExperimentDatabase attribute) number_of_shells (mdsuite.calculators.coordination_number_calculation.Args attribute) (mdsuite.calculators.potential_of_mean_force.Args attribute)

O

optimize_batch_size() (in module mdsuite.utils.meta_functions), [1]

ORANGE (mdsuite.utils.Colour attribute)

P

parallel (mdsuite.memory_management.memory_manager.MemoryManager attribute) (mdsuite.memory_management.MemoryManager attribute) particles_list (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction property) (mdsuite.calculators.RadialDistributionFunction property) path (mdsuite.database.simulation_database.Database attribute) PAUA (mdsuite.utils.Colour attribute) plot (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) plot() (mdsuite.time_series.base.TimeSeries method) (mdsuite.visualizer.d3_data_visualizer.DataVisualizer3D method) plot_array (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) plot_data() (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction method) (mdsuite.calculators.AngularDistributionFunction method) (mdsuite.calculators.Calculator method) (mdsuite.calculators.calculator.Calculator method) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers method), [1] (mdsuite.calculators.CoordinationNumbers method) (mdsuite.calculators.einstein_diffusion_coefficients.EinsteinDiffusionCoefficients method) (mdsuite.calculators.EinsteinDiffusionCoefficients method) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity method) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.GreenKuboIonicConductivity method) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral method) (mdsuite.calculators.KirkwoodBuffIntegral method) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce method) (mdsuite.calculators.PotentialOfMeanForce method) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction method) (mdsuite.calculators.RadialDistributionFunction method) plotter (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute)

polynomial_scale_function() (in module mdsuite.utils.scale_functions) positions (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) postprocessing() (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.GreenKuboDiffusionCoefficients method) potential_energy (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) PotentialOfMeanForce (class in mdsuite.calculators) (class in mdsuite.calculators.potential_of_mean_force) (mdsuite.experiment.run.RunComputation property) prefactor (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) prepare_computation() (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction method) (mdsuite.calculators.AngularDistributionFunction method) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction method) (mdsuite.calculators.RadialDistributionFunction method) prepare_db_entry() (mdsuite.database.calculator_database.CalculatorDatabase method) preprocess_data (mdsuite.time_series.base.TimeSeries property) pressure (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) process_bind_param() (mdsuite.database.types.JSONEncodedDict method) process_result_value() (mdsuite.database.types.JSONEncodedDict method) Project (class in mdsuite.database.scheme) (class in mdsuite.project) (class in mdsuite.project.project) project (mdsuite.database.scheme.Experiment attribute) project_id (mdsuite.database.project_database.ProjectDatabase property) (mdsuite.database.scheme.Experiment attribute) ProjectDatabase (class in mdsuite.database.project_database) properties (mdsuite.database.simulation_database.SpeciesInfo attribute), [1] property_groups (mdsuite.database.experiment_database.ExperimentDatabase attribute) property_to_column_idx_dict (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1] PropertyInfo (class in mdsuite.database.simulation_database) PRUSSIAN_BLUE (mdsuite.utils.Colour attribute)

Q

quadratic_scale_function() (in module mdsuite.utils.scale_functions)

queue_data() (mdsuite.database.calculator_database.CalculatorDatabase method)

R

r_cut (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.AngularDistributionFunction attribute) r_ij_to_bins() (mdsuite.calculators.spatial_distribution_function.SpatialDistributionFunction method) r_max (mdsuite.calculators.spatial_distribution_function.Args attribute) r_min (mdsuite.calculators.spatial_distribution_function.Args attribute) RadialDistributionFunction (class in mdsuite.calculators) (class in mdsuite.calculators.radial_distribution_function) (mdsuite.experiment.run.RunComputation property) RangeExceeded rdf_data (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1], [2] (mdsuite.calculators.CoordinationNumbers attribute), [1] read_files (mdsuite.database.experiment_database.ExperimentDatabase property) read_n_lines() (in module mdsuite.file_io.tabular_text_files) reference_configuration_idx (mdsuite.utils.molecule.Molecule attribute), [1] reference_property (mdsuite.graph_modules.molecular_graph.MolecularGraph attribute) remainder (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) (mdsuite.transformations.Transformations attribute) (mdsuite.transformations.transformations.Transformations attribute) Report (class in mdsuite.utils.report_computer_characteristics) resize_datasets() (mdsuite.database.simulation_database.Database method) result_keys (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) result_series_keys (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) run (mdsuite.experiment.Experiment property) (mdsuite.experiment.experiment.Experiment property) (mdsuite.project.Project property) (mdsuite.project.project.Project property) run() (mdsuite.utils.testing.MDSuiteProcess method) run_analysis() (mdsuite.calculators.Calculator method) (mdsuite.calculators.calculator.Calculator method) run_calculator() (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction method) (mdsuite.calculators.AngularDistributionFunction method) (mdsuite.calculators.Calculator method) (mdsuite.calculators.calculator.Calculator method) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers method), [1] (mdsuite.calculators.CoordinationNumbers method) (mdsuite.calculators.einstein_diffusion_coefficients.EinsteinDiffusionCoefficients method) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients method) (mdsuite.calculators.einstein_helfand_ionic_conductivity.EinsteinHelfandIonicConductivity method) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity method) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci method) (mdsuite.calculators.EinsteinDiffusionCoefficients method) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients method) (mdsuite.calculators.EinsteinHelfandIonicConductivity method) (mdsuite.calculators.EinsteinHelfandThermalConductivity method) (mdsuite.calculators.EinsteinHelfandThermalKinaci method) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity method) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity method) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity method) (mdsuite.calculators.green_kubo_viscosity_flux.GreenKuboViscosityFlux method) (mdsuite.calculators.GreenKuboDiffusionCoefficients method) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients method) (mdsuite.calculators.GreenKuboIonicConductivity method) (mdsuite.calculators.GreenKuboThermalConductivity method) (mdsuite.calculators.GreenKuboViscosity method) (mdsuite.calculators.GreenKuboViscosityFlux method) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral method) (mdsuite.calculators.KirkwoodBuffIntegral method) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce method) (mdsuite.calculators.PotentialOfMeanForce method) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction method) (mdsuite.calculators.RadialDistributionFunction method) (mdsuite.calculators.spatial_distribution_function.SpatialDistributionFunction method)

run_minibatch_loop() (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction method) (mdsuite.calculators.RadialDistributionFunction method) run_post_generation_analysis() (mdsuite.calculators.nernst_einstein_ionic_conductivity.NernstEinsteinIonicConductivity method) (mdsuite.calculators.NernstEinsteinIonicConductivity method) run_transformation() (mdsuite.transformations.map_molecules.MolecularMap method) (mdsuite.transformations.MolecularMap method) (mdsuite.transformations.Transformations method) (mdsuite.transformations.transformations.MultiSpeciesTrafo method) (mdsuite.transformations.transformations.SingleSpeciesTrafo method) (mdsuite.transformations.transformations.Transformations method) run_visualization() (mdsuite.calculators.Calculator method) (mdsuite.calculators.calculator.Calculator method) (mdsuite.experiment.Experiment method) (mdsuite.experiment.experiment.Experiment method) RunComputation (class in mdsuite.experiment.run) RunModule (class in mdsuite.experiment.run_module) running_mean() (in module mdsuite.time_series.base)

S

sample_rate (mdsuite.database.experiment_database.ExperimentDatabase attribute) (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute), [1] (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] sample_step (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] save_computation_args() (mdsuite.database.calculator_database.CalculatorDatabase method) save_db_data() (mdsuite.database.calculator_database.CalculatorDatabase method) savgol_order (mdsuite.calculators.coordination_number_calculation.Args attribute) (mdsuite.calculators.kirkwood_buff_integrals.Args attribute) (mdsuite.calculators.potential_of_mean_force.Args attribute) savgol_window_length (mdsuite.calculators.coordination_number_calculation.Args attribute) (mdsuite.calculators.kirkwood_buff_integrals.Args attribute) (mdsuite.calculators.potential_of_mean_force.Args attribute) scale_function (mdsuite.calculators.trajectory_calculator.TrajectoryCalculator attribute) (mdsuite.memory_management.memory_manager.MemoryManager attribute) (mdsuite.memory_management.MemoryManager attribute) (mdsuite.transformations.map_molecules.MolecularMap attribute) (mdsuite.transformations.MolecularMap attribute) ScaleCoordinates (class in mdsuite.transformations) (class in mdsuite.transformations.scale_coordinates) (mdsuite.experiment.run.RunComputation property) scaled_positions (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute), [1] scaled_unwrapped_positions (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) selected_species (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) session (mdsuite.database.database_base.DatabaseBase property) set_charge() (mdsuite.experiment.Experiment method) (mdsuite.experiment.experiment.Experiment method) set_db() (mdsuite.database.experiment_database.ExperimentDatabase method) set_mass() (mdsuite.experiment.Experiment method) (mdsuite.experiment.experiment.Experiment method) simple_file_read() (in module mdsuite.utils.meta_functions), [1] simulation_data (mdsuite.database.experiment_database.ExperimentDatabase property) (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] SingleSpeciesTrafo (class in mdsuite.transformations.transformations) skip_n_lines() (in module mdsuite.file_io.tabular_text_files) smiles (mdsuite.utils.molecule.Molecule attribute), [1] sort_array_by_column() (in module mdsuite.utils.meta_functions) sort_by_column_idx (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1] SpatialDistributionFunction (class in mdsuite.calculators.spatial_distribution_function) species (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) (mdsuite.calculators.spatial_distribution_function.Args attribute) (mdsuite.database.experiment_database.ExperimentDatabase property) (mdsuite.database.scheme.ComputationResult attribute) (mdsuite.database.scheme.Experiment attribute) (mdsuite.database.scheme.SpeciesAssociation attribute) (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute)

species_dict (mdsuite.utils.molecule.Molecule attribute), [1] species_list (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] species_name_to_line_idx_dict (mdsuite.file_io.tabular_text_files.TabularTextFileReaderMData attribute), [1] species_tuple (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) SpeciesAssociation (class in mdsuite.database.scheme) SpeciesInfo (class in mdsuite.database.simulation_database) spherical_to_cartesian_coordinates() (in module mdsuite.utils.linalg) split_array() (in module mdsuite.utils.meta_functions), [1] start (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.AngularDistributionFunction attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) stop (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.angular_distribution_function.Args attribute) (mdsuite.calculators.AngularDistributionFunction attribute) (mdsuite.calculators.radial_distribution_function.Args attribute) storage_path (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute) (mdsuite.project.Project attribute) (mdsuite.project.project.Project attribute) str_value (mdsuite.database.scheme.ExperimentAttribute attribute) stress (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) stress_viscosity (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) subjects (mdsuite.database.calculator_database.ComputationResults attribute) (mdsuite.database.scheme.Computation property) system_property (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute)

T

tabular_text_reader_data (mdsuite.file_io.tabular_text_files.TabularTextFileProcessor property) TabularTextFileProcessor (class in mdsuite.file_io.tabular_text_files) TabularTextFileReaderMData (class in mdsuite.file_io.tabular_text_files) tau_values (mdsuite.calculators.einstein_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.einstein_helfand_ionic_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.Args attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.Args attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.Args attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.Args attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.Args attribute) (mdsuite.calculators.green_kubo_viscosity.Args attribute) (mdsuite.calculators.green_kubo_viscosity_flux.Args attribute) temperature (mdsuite.database.experiment_database.ExperimentDatabase attribute) (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) (mdsuite.database.simulation_database.TrajectoryMetadata attribute), [1] (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute) (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) TestMultispecies (class in mdsuite.transformations.test_trafos) TestSingleSpecies (class in mdsuite.transformations.test_trafos) thermal_flux (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) ThermalFlux (class in mdsuite.transformations) (class in mdsuite.transformations.thermal_flux) (mdsuite.experiment.run.RunComputation property) time (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) (mdsuite.utils.Units attribute) (mdsuite.utils.units.Units attribute) time_step (mdsuite.database.experiment_database.ExperimentDatabase attribute) (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute), [1] (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute) timeit() (in module mdsuite.utils.meta_functions), [1] TimeSeries (class in mdsuite.time_series.base) torque (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute)

TrajectoryCalculator (class in mdsuite.calculators.trajectory_calculator) TrajectoryChunkData (class in mdsuite.database.simulation_database) TrajectoryMetadata (class in mdsuite.database.simulation_database) transform_batch() (mdsuite.transformations.CoordinateUnwrapper method) (mdsuite.transformations.CoordinateWrapper method) (mdsuite.transformations.integrated_heat_current.IntegratedHeatCurrent method) (mdsuite.transformations.IntegratedHeatCurrent method) (mdsuite.transformations.ionic_current.IonicCurrent method) (mdsuite.transformations.IonicCurrent method) (mdsuite.transformations.kinaci_integrated_heat_current.KinaciIntegratedHeatCurrent method) (mdsuite.transformations.KinaciIntegratedHeatCurrent method) (mdsuite.transformations.momentum_flux.MomentumFlux method) (mdsuite.transformations.MomentumFlux method) (mdsuite.transformations.scale_coordinates.ScaleCoordinates method) (mdsuite.transformations.ScaleCoordinates method) (mdsuite.transformations.test_trafos.TestMultispecies method) (mdsuite.transformations.test_trafos.TestSingleSpecies method) (mdsuite.transformations.thermal_flux.ThermalFlux method) (mdsuite.transformations.ThermalFlux method) (mdsuite.transformations.transformations.MultiSpeciesTrafo method) (mdsuite.transformations.transformations.SingleSpeciesTrafo method) (mdsuite.transformations.translational_dipole_moment.TranslationalDipoleMoment method) (mdsuite.transformations.TranslationalDipoleMoment method) (mdsuite.transformations.unwrap_coordinates.CoordinateUnwrapper method), [1] (mdsuite.transformations.unwrap_via_indices.UnwrapViaIndices method) (mdsuite.transformations.UnwrapViaIndices method) (mdsuite.transformations.velocity_from_positions.VelocityFromPositions method) (mdsuite.transformations.VelocityFromPositions method) (mdsuite.transformations.wrap_coordinates.CoordinateWrapper method) transformation_wrapper() (mdsuite.experiment.run.RunComputation method) Transformations (class in mdsuite.transformations) (class in mdsuite.transformations.transformations) translational_dipole_moment (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) TranslationalDipoleMoment (class in mdsuite.transformations) (class in mdsuite.transformations.translational_dipole_moment) (mdsuite.experiment.run.RunComputation property) triu_indices() (in module mdsuite.utils.tensor_flow.helpers) triu_mask() (in module mdsuite.utils.tensor_flow.helpers) truth_table (mdsuite.calculators.nernst_einstein_ionic_conductivity.NernstEinsteinIonicConductivity property) (mdsuite.calculators.NernstEinsteinIonicConductivity property)

U

unit_vector() (in module mdsuite.utils.linalg) Units (class in mdsuite.utils) (class in mdsuite.utils.units) units (mdsuite.database.experiment_database.ExperimentDatabase property) units_to_si() (mdsuite.experiment.Experiment static method) (mdsuite.experiment.experiment.Experiment static method) unwrapped_positions (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute)

UnwrapViaIndices (class in mdsuite.transformations) (class in mdsuite.transformations.unwrap_via_indices) (mdsuite.experiment.run.RunComputation property) update_database() (mdsuite.database.calculator_database.CalculatorDatabase method) update_species_attributes_with_pubchempy() (in module mdsuite.experiment.experiment) use_tf_function (mdsuite.calculators.angular_distribution_function.AngularDistributionFunction attribute) (mdsuite.calculators.AngularDistributionFunction attribute)

V

value (mdsuite.database.scheme.ExperimentAttribute attribute) velocities (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) velocities_from_positions (mdsuite.database.mdsuite_properties.MDSuiteProperties attribute) VelocityFromPositions (class in mdsuite.transformations) (class in mdsuite.transformations.velocity_from_positions) (mdsuite.experiment.run.RunComputation property)

version (mdsuite.database.experiment_database.ExperimentDatabase property) volume (mdsuite.database.experiment_database.ExperimentDatabase property) (mdsuite.experiment.Experiment attribute) (mdsuite.experiment.experiment.Experiment attribute) (mdsuite.utils.Units property) (mdsuite.utils.units.Units property)

X

x_label (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity attribute) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity attribute) (mdsuite.calculators.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboIonicConductivity attribute) (mdsuite.calculators.GreenKuboThermalConductivity attribute) (mdsuite.calculators.GreenKuboViscosity attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute)

Y

y_label (mdsuite.calculators.Calculator attribute) (mdsuite.calculators.calculator.Calculator attribute) (mdsuite.calculators.coordination_number_calculation.CoordinationNumbers attribute), [1] (mdsuite.calculators.CoordinationNumbers attribute) (mdsuite.calculators.einstein_distinct_diffusion_coefficients.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.einstein_helfand_thermal_conductivity.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.einstein_helfand_thermal_kinaci.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.EinsteinDistinctDiffusionCoefficients attribute) (mdsuite.calculators.EinsteinHelfandThermalConductivity attribute) (mdsuite.calculators.EinsteinHelfandThermalKinaci attribute) (mdsuite.calculators.green_kubo_distinct_diffusion_coefficients.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_ionic_conductivity.GreenKuboIonicConductivity attribute) (mdsuite.calculators.green_kubo_self_diffusion_coefficients.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.green_kubo_thermal_conductivity.GreenKuboThermalConductivity attribute) (mdsuite.calculators.green_kubo_viscosity.GreenKuboViscosity attribute) (mdsuite.calculators.GreenKuboDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboDistinctDiffusionCoefficients attribute) (mdsuite.calculators.GreenKuboIonicConductivity attribute) (mdsuite.calculators.GreenKuboThermalConductivity attribute) (mdsuite.calculators.GreenKuboViscosity attribute) (mdsuite.calculators.kirkwood_buff_integrals.KirkwoodBuffIntegral attribute) (mdsuite.calculators.KirkwoodBuffIntegral attribute) (mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce attribute) (mdsuite.calculators.PotentialOfMeanForce attribute) (mdsuite.calculators.radial_distribution_function.RadialDistributionFunction attribute) (mdsuite.calculators.RadialDistributionFunction attribute)