# Source code for propertyestimator.properties.density

    """
    A collection of density physical property definitions.
    """
    from propertyestimator import unit
    from propertyestimator.datasets.plugins import register_thermoml_property
    from propertyestimator.properties import PhysicalProperty, PropertyPhase
    from propertyestimator.properties.plugins import register_estimable_property
    from propertyestimator.protocols import analysis, reweighting, miscellaneous
    from propertyestimator.protocols.utils import generate_base_simulation_protocols, generate_base_reweighting_protocols, \
        generate_gradient_protocol_group
    from propertyestimator.storage import StoredSimulationData
    from propertyestimator.utils.quantities import EstimatedQuantity
    from propertyestimator.utils.statistics import ObservableType
    from propertyestimator.workflow import WorkflowOptions
    from propertyestimator.workflow.schemas import WorkflowSchema, ProtocolReplicator
    from propertyestimator.workflow.utils import ProtocolPath, ReplicatorValue

    @register_estimable_property()
    @register_thermoml_property(thermoml_string='Mass density, kg/m3', supported_phases=PropertyPhase.Liquid)
    class Density(PhysicalProperty):
        """A class representation of a density property"""

        @property
        def multi_component_property(self):
            return False

        @property
        def required_data_class(self):
            return StoredSimulationData

        @staticmethod
        def get_default_workflow_schema(calculation_layer, options=None):

            if calculation_layer == 'SimulationLayer':
                return Density.get_default_simulation_workflow_schema(options)
            elif calculation_layer == 'ReweightingLayer':
                return Density.get_default_reweighting_workflow_schema(options)

            return None

        @staticmethod
        def get_default_simulation_workflow_schema(options=None):
            """Returns the default workflow to use when estimating this property
            from direct simulations.

            Parameters
            ----------
            options: WorkflowOptions
                The default options to use when setting up the estimation workflow.

            Returns
            -------
            WorkflowSchema
                The schema to follow when estimating this property.
            """

            # Define the protocol which will extract the average density from
            # the results of a simulation.
            extract_density = analysis.ExtractAverageStatistic('extract_density')
            extract_density.statistics_type = ObservableType.Density

            # Define the protocols which will run the simulation itself.
            protocols, value_source, output_to_store = generate_base_simulation_protocols(extract_density,
                                                                                          options)

            # Set up the gradient calculations
            reweight_density_template = reweighting.ReweightStatistics('')
            reweight_density_template.statistics_type = ObservableType.Density
            reweight_density_template.statistics_paths = [ProtocolPath('statistics_file_path',
                                                                       protocols.converge_uncertainty.id,
                                                                       protocols.production_simulation.id)]

            coordinate_source = ProtocolPath('output_coordinate_file', protocols.equilibration_simulation.id)
            trajectory_source = ProtocolPath('trajectory_file_path', protocols.converge_uncertainty.id,
                                             protocols.production_simulation.id)
            statistics_source = ProtocolPath('statistics_file_path', protocols.converge_uncertainty.id,
                                             protocols.production_simulation.id)

            gradient_group, gradient_replicator, gradient_source = \
                generate_gradient_protocol_group(reweight_density_template,
                                                 [ProtocolPath('force_field_path', 'global')],
                                                 ProtocolPath('force_field_path', 'global'),
                                                 coordinate_source,
                                                 trajectory_source,
                                                 statistics_source)

            # Build the workflow schema.
            schema = WorkflowSchema(property_type=Density.__name__)
            schema.id = '{}{}'.format(Density.__name__, 'Schema')

            schema.protocols = {
                protocols.build_coordinates.id: protocols.build_coordinates.schema,
                protocols.assign_parameters.id: protocols.assign_parameters.schema,
                protocols.energy_minimisation.id: protocols.energy_minimisation.schema,
                protocols.equilibration_simulation.id: protocols.equilibration_simulation.schema,
                protocols.converge_uncertainty.id: protocols.converge_uncertainty.schema,
                protocols.extract_uncorrelated_trajectory.id: protocols.extract_uncorrelated_trajectory.schema,
                protocols.extract_uncorrelated_statistics.id: protocols.extract_uncorrelated_statistics.schema,
                gradient_group.id: gradient_group.schema
            }

            schema.replicators = [gradient_replicator]

            schema.outputs_to_store = {'full_system': output_to_store}

            schema.gradients_sources = [gradient_source]
            schema.final_value_source = value_source

            return schema

        @staticmethod
        def get_default_reweighting_workflow_schema(options):
            """Returns the default workflow to use when estimating this property
            by reweighting existing data.

            Parameters
            ----------
            options: WorkflowOptions
                The default options to use when setting up the estimation workflow.

            Returns
            -------
            WorkflowSchema
                The schema to follow when estimating this property.
            """

            data_replicator_id = 'data_replicator'

            # The protocol which will be used to calculate the densities from
            # the existing data.
            density_calculation = analysis.ExtractAverageStatistic(f'calc_density_$({data_replicator_id})')
            density_calculation.statistics_type = ObservableType.Density

            reweight_density = reweighting.ReweightStatistics(f'reweight_density')
            reweight_density.statistics_type = ObservableType.Density

            reweighting_protocols, data_replicator = generate_base_reweighting_protocols(density_calculation,
                                                                                         reweight_density,
                                                                                         options,
                                                                                         data_replicator_id)

            # Set up the gradient calculations
            coordinate_path = ProtocolPath('output_coordinate_path', reweighting_protocols.concatenate_trajectories.id)
            trajectory_path = ProtocolPath('output_trajectory_path', reweighting_protocols.concatenate_trajectories.id)

            reweight_density_template = reweighting.ReweightStatistics('')
            reweight_density_template.statistics_type = ObservableType.Density
            reweight_density_template.statistics_paths = ProtocolPath('output_statistics_path',
                                                                      reweighting_protocols.decorrelate_statistics.id)

            gradient_group, gradient_replicator, gradient_source = \
                generate_gradient_protocol_group(reweight_density_template,
                                                 ProtocolPath('force_field_path',
                                                              reweighting_protocols.unpack_stored_data.id),
                                                 ProtocolPath('force_field_path', 'global'),
                                                 coordinate_path,
                                                 trajectory_path,
                                                 replicator_id='grad',
                                                 use_subset_of_force_field=False,
                                                 effective_sample_indices=ProtocolPath('effective_sample_indices',
                                                                                       reweighting_protocols.
                                                                                       mbar_protocol.id))

            schema = WorkflowSchema(property_type=Density.__name__)
            schema.id = '{}{}'.format(Density.__name__, 'Schema')

            schema.protocols = {protocol.id: protocol.schema for protocol in reweighting_protocols}
            schema.protocols[gradient_group.id] = gradient_group.schema

            schema.replicators = [data_replicator, gradient_replicator]

            schema.gradients_sources = [gradient_source]
            schema.final_value_source = ProtocolPath('value', reweighting_protocols.mbar_protocol.id)

            return schema

    @register_estimable_property()
    @register_thermoml_property('Excess molar volume, m3/mol', supported_phases=PropertyPhase.Liquid)
    class ExcessMolarVolume(PhysicalProperty):
        """A class representation of an excess molar volume property"""

        @property
        def multi_component_property(self):
            return True

        @property
        def required_data_class(self):
            return StoredSimulationData

        @staticmethod
        def get_default_workflow_schema(calculation_layer, options=None):

            if calculation_layer == 'SimulationLayer':
                return ExcessMolarVolume.get_default_simulation_workflow_schema(options)
            elif calculation_layer == 'ReweightingLayer':
                return ExcessMolarVolume.get_default_reweighting_workflow_schema(options)

            return None

        @staticmethod
        def _get_simulation_protocols(id_suffix, gradient_replicator_id, replicator_id=None, weight_by_mole_fraction=False,
                                      component_substance_reference=None, full_substance_reference=None, options=None):

            """Returns the set of protocols which when combined in a workflow
            will yield the molar volume of a substance.

            Parameters
            ----------
            id_suffix: str
                A suffix to append to the id of each of the returned protocols.
            gradient_replicator_id: str
                The id of the replicator which will clone those protocols which will
                estimate the gradient of the molar volume with respect to a given parameter.
            replicator_id: str, optional
                The id of the replicator which will be used to clone these protocols.
                This will be appended to the id of each of the returned protocols if
                set.
            weight_by_mole_fraction: bool
                If true, an extra protocol will be added to weight the calculated
                molar volume by the mole fraction of the component.
            component_substance_reference: ProtocolPath or PlaceholderInput, optional
                An optional protocol path (or replicator reference) to the component substance
                whose enthalpy is being estimated.
            full_substance_reference: ProtocolPath or PlaceholderInput, optional
                An optional protocol path (or replicator reference) to the full substance
                whose enthalpy of mixing is being estimated. This cannot be `None` if
                `weight_by_mole_fraction` is `True`.
            options: WorkflowOptions
                The options to use when setting up the workflows.

            Returns
            -------
            BaseSimulationProtocols
                The protocols used to estimate the molar volume of a substance.
            DivideValue
                The protocol used to calculate the number of molar molecules in
                the system.
            ProtocolPath
                A reference to the estimated molar volume.
            WorkflowSimulationDataToStore
                An object which describes the default data from a simulation to store,
                such as the uncorrelated statistics and configurations.
            ProtocolGroup
                The group of protocols which will calculate the gradient of the reduced potential
                with respect to a given property.
            ProtocolReplicator
                The protocol which will replicate the gradient group for every gradient to
                estimate.
            ProtocolPath
                A reference to the value of the gradient.
            """

            if replicator_id is not None:
                id_suffix = f'{id_suffix}_$({replicator_id})'

            if component_substance_reference is None:
                component_substance_reference = ProtocolPath('substance', 'global')

            if weight_by_mole_fraction is True and full_substance_reference is None:

                raise ValueError('The full substance reference must be set when weighting by'
                                 'the mole fraction')

            # Define the protocol which will extract the average molar volume from
            # the results of a simulation.
            extract_volume = analysis.ExtractAverageStatistic(f'extract_volume{id_suffix}')
            extract_volume.statistics_type = ObservableType.Volume

            # Define the protocols which will run the simulation itself.
            simulation_protocols, value_source, output_to_store = generate_base_simulation_protocols(extract_volume,
                                                                                                     options,
                                                                                                     id_suffix)

            # Divide the volume by the number of molecules in the system
            number_of_molecules = ProtocolPath('output_number_of_molecules', simulation_protocols.build_coordinates.id)
            built_substance = ProtocolPath('output_substance', simulation_protocols.build_coordinates.id)

            number_of_molar_molecules = miscellaneous.DivideValue(f'number_of_molar_molecules{id_suffix}')
            number_of_molar_molecules.value = number_of_molecules
            number_of_molar_molecules.divisor = (1.0 * unit.avogadro_number).to('mole**-1')

            extract_volume.divisor = ProtocolPath('result', number_of_molar_molecules.id)

            # Use the correct substance.
            simulation_protocols.build_coordinates.substance = component_substance_reference
            simulation_protocols.assign_parameters.substance = built_substance
            output_to_store.substance = built_substance

            conditional_group = simulation_protocols.converge_uncertainty

            if weight_by_mole_fraction:
                # The component workflows need an extra step to multiply their molar volumes by their
                # relative mole fraction.
                weight_by_mole_fraction = miscellaneous.WeightByMoleFraction(f'weight_by_mole_fraction{id_suffix}')
                weight_by_mole_fraction.value = ProtocolPath('value', extract_volume.id)
                weight_by_mole_fraction.full_substance = full_substance_reference
                weight_by_mole_fraction.component = component_substance_reference

                conditional_group.add_protocols(weight_by_mole_fraction)

                value_source = ProtocolPath('weighted_value', conditional_group.id, weight_by_mole_fraction.id)

            if options.convergence_mode != WorkflowOptions.ConvergenceMode.NoChecks:

                # Make sure the convergence criteria is set to use the per component
                # uncertainty target.
                conditional_group.conditions[0].right_hand_value = ProtocolPath('per_component_uncertainty', 'global')

                if weight_by_mole_fraction:
                    # Make sure the weighted uncertainty is being used in the conditional comparison.
                    conditional_group.conditions[0].left_hand_value = ProtocolPath('weighted_value.uncertainty',
                                                                                   conditional_group.id,
                                                                                   weight_by_mole_fraction.id)

            # Set up the gradient calculations
            reweight_molar_volume_template = reweighting.ReweightStatistics('')
            reweight_molar_volume_template.statistics_type = ObservableType.Volume
            reweight_molar_volume_template.statistics_paths = [ProtocolPath('statistics_file_path',
                                                                            conditional_group.id,
                                                                            simulation_protocols.production_simulation.id)]

            coordinate_source = ProtocolPath('output_coordinate_file', simulation_protocols.equilibration_simulation.id)
            trajectory_source = ProtocolPath('trajectory_file_path', simulation_protocols.converge_uncertainty.id,
                                             simulation_protocols.production_simulation.id)
            statistics_source = ProtocolPath('statistics_file_path', simulation_protocols.converge_uncertainty.id,
                                             simulation_protocols.production_simulation.id)

            gradient_group, gradient_replicator, gradient_source = \
                generate_gradient_protocol_group(reweight_molar_volume_template,
                                                 [ProtocolPath('force_field_path', 'global')],
                                                 ProtocolPath('force_field_path', 'global'),
                                                 coordinate_source,
                                                 trajectory_source,
                                                 statistics_source,
                                                 replicator_id=gradient_replicator_id,
                                                 substance_source=built_substance,
                                                 id_suffix=id_suffix)

            # Remove the group id from the path.
            gradient_source.pop_next_in_path()

            if weight_by_mole_fraction:
                # The component workflows need an extra step to multiply their gradients by their
                # relative mole fraction.
                weight_gradient = miscellaneous.WeightByMoleFraction(f'weight_gradient_by_mole_fraction{id_suffix}')
                weight_gradient.value = gradient_source
                weight_gradient.full_substance = full_substance_reference
                weight_gradient.component = component_substance_reference

                gradient_group.add_protocols(weight_gradient)
                gradient_source = ProtocolPath('weighted_value', weight_gradient.id)

            scale_gradient = miscellaneous.DivideValue(f'scale_gradient{id_suffix}')
            scale_gradient.value = gradient_source
            scale_gradient.divisor = ProtocolPath('result', number_of_molar_molecules.id)

            gradient_group.add_protocols(scale_gradient)
            gradient_source = ProtocolPath('result', gradient_group.id, scale_gradient.id)

            return (simulation_protocols, number_of_molar_molecules, value_source, output_to_store,
                    gradient_group, gradient_replicator, gradient_source)

        @staticmethod
        def _get_reweighting_protocols(id_suffix, gradient_replicator_id, data_replicator_id, replicator_id=None,
                                       weight_by_mole_fraction=False, substance_reference=None, options=None):

            """Returns the set of protocols which when combined in a workflow
            will yield the molar volume of a substance by reweighting cached data.

            Parameters
            ----------
            id_suffix: str
                A suffix to append to the id of each of the returned protocols.
            gradient_replicator_id: str
                The id of the replicator which will clone those protocols which will
                estimate the gradient of the molar volume with respect to a given parameter.
            data_replicator_id: str
                The id of the replicator which will be used to clone these protocols
                for each cached simulation data.
            replicator_id: str, optional
                The optional id of the replicator which will be used to clone these
                protocols, e.g. for each component in the system.
            weight_by_mole_fraction: bool
                If true, an extra protocol will be added to weight the calculated
                molar volume by the mole fraction of the component.
            substance_reference: ProtocolPath or PlaceholderInput, optional
                An optional protocol path (or replicator reference) to the substance
                whose molar volume is being estimated.
            options: WorkflowOptions
                The options to use when setting up the workflows.

            Returns
            -------
            BaseReweightingProtocols
                The protocols used to estimate the molar volume of a substance.
            ProtocolPath
                A reference to the estimated molar volume.
            ProtocolReplicator
                The replicator which will replicate each protocol for each
                cached simulation datum.
            ProtocolGroup
                The group of protocols which will calculate the gradient of the reduced potential
                with respect to a given property.
            ProtocolPath
                A reference to the value of the gradient.
            """

            if replicator_id is not None:
                id_suffix = f'{id_suffix}_$({replicator_id})'

            full_id_suffix = id_suffix

            if data_replicator_id is not None:
                full_id_suffix = f'{id_suffix}_$({data_replicator_id})'

            if substance_reference is None:
                substance_reference = ProtocolPath('substance', 'global')

            extract_volume = analysis.ExtractAverageStatistic(f'extract_volume{full_id_suffix}')
            extract_volume.statistics_type = ObservableType.Volume
            reweight_volume = reweighting.ReweightStatistics(f'reweight_volume{id_suffix}')
            reweight_volume.statistics_type = ObservableType.Volume

            (protocols,
             data_replicator) = generate_base_reweighting_protocols(analysis_protocol=extract_volume,
                                                                    mbar_protocol=reweight_volume,
                                                                    workflow_options=options,
                                                                    replicator_id=data_replicator_id,
                                                                    id_suffix=id_suffix)

            # Make sure to use the correct substance.
            protocols.build_target_system.substance = substance_reference

            value_source = ProtocolPath('value', protocols.mbar_protocol.id)

            # Set up the protocols which will be responsible for adding together
            # the component molar volumes, and subtracting these from the full system volume.
            weight_volume = None

            if weight_by_mole_fraction is True:
                weight_volume = miscellaneous.WeightByMoleFraction(f'weight_volume{id_suffix}')
                weight_volume.value = ProtocolPath('value', protocols.mbar_protocol.id)
                weight_volume.full_substance = ProtocolPath('substance', 'global')
                weight_volume.component = substance_reference

                value_source = ProtocolPath('weighted_value', weight_volume.id)

            # Divide by the component molar volumes by the number of molecules in the system
            number_of_molecules = ProtocolPath('total_number_of_molecules', protocols.
                                               unpack_stored_data.id.replace(f'$({data_replicator_id})', '0'))

            number_of_molar_molecules = miscellaneous.MultiplyValue(f'number_of_molar_molecules{id_suffix}')
            number_of_molar_molecules.value = EstimatedQuantity((1.0 / unit.avogadro_number).to(unit.mole),
                                                                (0.0 / unit.avogadro_number).to(unit.mole), '')
            number_of_molar_molecules.multiplier = number_of_molecules

            divide_by_molecules = miscellaneous.DivideValue(f'divide_by_molecules{id_suffix}')
            divide_by_molecules.value = value_source
            divide_by_molecules.divisor = ProtocolPath('result.value', number_of_molar_molecules.id)

            value_source = ProtocolPath('result', divide_by_molecules.id)

            # Set up the gradient calculations.
            reweight_volume_template = reweighting.ReweightStatistics('')
            reweight_volume_template.statistics_type = ObservableType.Volume
            reweight_volume_template.statistics_paths = ProtocolPath('output_statistics_path',
                                                                     protocols.decorrelate_statistics.id)

            coordinate_path = ProtocolPath('output_coordinate_path', protocols.concatenate_trajectories.id)
            trajectory_path = ProtocolPath('output_trajectory_path', protocols.concatenate_trajectories.id)

            gradient_group, _, gradient_source = \
                generate_gradient_protocol_group(reweight_volume_template,
                                                 ProtocolPath('force_field_path', protocols.unpack_stored_data.id),
                                                 ProtocolPath('force_field_path', 'global'),
                                                 coordinate_path,
                                                 trajectory_path,
                                                 replicator_id=gradient_replicator_id,
                                                 id_suffix=id_suffix,
                                                 substance_source=substance_reference,
                                                 use_subset_of_force_field=False,
                                                 effective_sample_indices=ProtocolPath('effective_sample_indices',
                                                                                       protocols.mbar_protocol.id))

            # Remove the group id from the path.
            gradient_source.pop_next_in_path()

            if weight_by_mole_fraction is True:
                # The component workflows need an extra step to multiply their gradients by their
                # relative mole fraction.
                weight_gradient = miscellaneous.WeightByMoleFraction(f'weight_gradient_$({gradient_replicator_id})_'
                                                                     f'by_mole_fraction{id_suffix}')
                weight_gradient.value = gradient_source
                weight_gradient.full_substance = ProtocolPath('substance', 'global')
                weight_gradient.component = substance_reference

                gradient_group.add_protocols(weight_gradient)
                gradient_source = ProtocolPath('weighted_value', weight_gradient.id)

            scale_gradient = miscellaneous.DivideValue(f'scale_gradient_$({gradient_replicator_id}){id_suffix}')
            scale_gradient.value = gradient_source
            scale_gradient.divisor = ProtocolPath('result.value', number_of_molar_molecules.id)

            gradient_group.add_protocols(scale_gradient)
            gradient_source = ProtocolPath('result', gradient_group.id, scale_gradient.id)

            all_protocols = (*protocols, number_of_molar_molecules, divide_by_molecules)

            if weight_volume is not None:
                all_protocols = (*all_protocols, weight_volume)

            return all_protocols, value_source, data_replicator, gradient_group, gradient_source

        @staticmethod
        def get_default_simulation_workflow_schema(options=None):
            """Returns the default workflow to use when estimating this property
            from direct simulations.

            Parameters
            ----------
            options: WorkflowOptions
                The default options to use when setting up the estimation workflow.

            Returns
            -------
            WorkflowSchema
                The schema to follow when estimating this property.
            """

            # Define the id of the replicator which will clone the gradient protocols
            # for each gradient key to be estimated.
            gradient_replicator_id = 'gradient_replicator'

            # Set up a workflow to calculate the molar volume of the full, mixed system.
            (full_system_protocols,
             full_system_molar_molecules,
             full_system_volume,
             full_output,
             full_system_gradient_group,
             full_system_gradient_replicator,
             full_system_gradient) = ExcessMolarVolume._get_simulation_protocols('_full',
                                                                                 gradient_replicator_id,
                                                                                 options=options)

            # Set up a general workflow for calculating the molar volume of one of the system components.
            component_replicator_id = 'component_replicator'
            component_substance = ReplicatorValue(component_replicator_id)

            # Make sure to weight by the mole fractions of the actual full system as these may be slightly
            # different to the mole fractions of the measure property due to rounding.
            full_substance = ProtocolPath('output_substance', full_system_protocols.build_coordinates.id)

            (component_protocols,
             component_molar_molecules,
             component_volumes,
             component_output,
             component_gradient_group,
             component_gradient_replicator,
             component_gradient) = ExcessMolarVolume._get_simulation_protocols('_component',
                                                                               gradient_replicator_id,
                                                                               replicator_id=component_replicator_id,
                                                                               weight_by_mole_fraction=True,
                                                                               component_substance_reference=
                                                                                       component_substance,
                                                                               full_substance_reference=full_substance,
                                                                               options=options)

            # Finally, set up the protocols which will be responsible for adding together
            # the component molar volumes, and subtracting these from the mixed system molar volume.
            add_component_molar_volumes = miscellaneous.AddValues('add_component_molar_volumes')
            add_component_molar_volumes.values = component_volumes

            calculate_excess_volume = miscellaneous.SubtractValues('calculate_excess_volume')
            calculate_excess_volume.value_b = full_system_volume
            calculate_excess_volume.value_a = ProtocolPath('result', add_component_molar_volumes.id)

            # Create the replicator object which defines how the pure component
            # molar volume estimation protocols will be replicated for each component.
            component_replicator = ProtocolReplicator(replicator_id=component_replicator_id)
            component_replicator.template_values = ProtocolPath('components', 'global')

            # Combine the gradients.
            add_component_gradients = miscellaneous.AddValues(f'add_component_gradients'
                                                              f'_$({gradient_replicator_id})')
            add_component_gradients.values = component_gradient

            combine_gradients = miscellaneous.SubtractValues(f'combine_gradients_$({gradient_replicator_id})')
            combine_gradients.value_b = full_system_gradient
            combine_gradients.value_a = ProtocolPath('result', add_component_gradients.id)

            # Combine the gradient replicators.
            gradient_replicator = ProtocolReplicator(replicator_id=gradient_replicator_id)
            gradient_replicator.template_values = ProtocolPath('parameter_gradient_keys', 'global')

            # Build the final workflow schema
            schema = WorkflowSchema(property_type=ExcessMolarVolume.__name__)
            schema.id = '{}{}'.format(ExcessMolarVolume.__name__, 'Schema')

            schema.protocols = {
                component_protocols.build_coordinates.id: component_protocols.build_coordinates.schema,
                component_protocols.assign_parameters.id: component_protocols.assign_parameters.schema,
                component_protocols.energy_minimisation.id: component_protocols.energy_minimisation.schema,
                component_protocols.equilibration_simulation.id: component_protocols.equilibration_simulation.schema,
                component_protocols.converge_uncertainty.id: component_protocols.converge_uncertainty.schema,
                component_molar_molecules.id: component_molar_molecules.schema,

                full_system_protocols.build_coordinates.id: full_system_protocols.build_coordinates.schema,
                full_system_protocols.assign_parameters.id: full_system_protocols.assign_parameters.schema,
                full_system_protocols.energy_minimisation.id: full_system_protocols.energy_minimisation.schema,
                full_system_protocols.equilibration_simulation.id: full_system_protocols.equilibration_simulation.schema,
                full_system_protocols.converge_uncertainty.id: full_system_protocols.converge_uncertainty.schema,
                full_system_molar_molecules.id: full_system_molar_molecules.schema,

                component_protocols.extract_uncorrelated_trajectory.id:
                    component_protocols.extract_uncorrelated_trajectory.schema,
                component_protocols.extract_uncorrelated_statistics.id:
                    component_protocols.extract_uncorrelated_statistics.schema,

                full_system_protocols.extract_uncorrelated_trajectory.id:
                    full_system_protocols.extract_uncorrelated_trajectory.schema,
                full_system_protocols.extract_uncorrelated_statistics.id:
                    full_system_protocols.extract_uncorrelated_statistics.schema,

                add_component_molar_volumes.id: add_component_molar_volumes.schema,
                calculate_excess_volume.id: calculate_excess_volume.schema,

                component_gradient_group.id: component_gradient_group.schema,
                full_system_gradient_group.id: full_system_gradient_group.schema,
                add_component_gradients.id: add_component_gradients.schema,
                combine_gradients.id: combine_gradients.schema
            }

            schema.replicators = [gradient_replicator, component_replicator]

            # Finally, tell the schemas where to look for its final values.
            schema.gradients_sources = [ProtocolPath('result', combine_gradients.id)]
            schema.final_value_source = ProtocolPath('result', calculate_excess_volume.id)

            schema.outputs_to_store = {
                'full_system': full_output,
                f'component_$({component_replicator_id})': component_output
            }

            return schema

        @staticmethod
        def get_default_reweighting_workflow_schema(options=None):
            """Returns the default workflow to use when estimating this property
            by reweighting existing data.

            Parameters
            ----------
            options: WorkflowOptions
                The default options to use when setting up the estimation workflow.

            Returns
            -------
            WorkflowSchema
                The schema to follow when estimating this property.
            """

            # Set up a replicator that will re-run the component reweighting workflow for each
            # component in the system.
            component_replicator = ProtocolReplicator(replicator_id='component_replicator')
            component_replicator.template_values = ProtocolPath('components', 'global')

            gradient_replicator = ProtocolReplicator('gradient')
            gradient_replicator.template_values = ProtocolPath('parameter_gradient_keys', 'global')

            # Set up the protocols which will reweight data for the full system.
            full_data_replicator_id = 'full_data_replicator'

            (full_protocols,
             full_volume,
             full_data_replicator,
             full_gradient_group,
             full_gradient_source) = ExcessMolarVolume._get_reweighting_protocols('_full',
                                                                                  gradient_replicator.id,
                                                                                  full_data_replicator_id,
                                                                                  options=options)

            # Set up the protocols which will reweight data for each component.
            component_data_replicator_id = f'component_{component_replicator.placeholder_id}_data_replicator'

            (component_protocols,
             component_volumes,
             component_data_replicator,
             component_gradient_group,
             component_gradient_source) = ExcessMolarVolume._get_reweighting_protocols('_component',
                                                                                       gradient_replicator.id,
                                                                                       component_data_replicator_id,
                                                                                       replicator_id=component_replicator.id,
                                                                                       weight_by_mole_fraction=True,
                                                                                       substance_reference=ReplicatorValue(
                                                                                           component_replicator.id),
                                                                                       options=options)

            # Make sure the replicator is only replicating over component data.
            component_data_replicator.template_values = ProtocolPath(f'component_data[$({component_replicator.id})]',
                                                                     'global')

            add_component_molar_volumes = miscellaneous.AddValues('add_component_molar_volumes')
            add_component_molar_volumes.values = component_volumes

            calculate_excess_volume = miscellaneous.SubtractValues('calculate_excess_potential')
            calculate_excess_volume.value_b = full_volume
            calculate_excess_volume.value_a = ProtocolPath('result', add_component_molar_volumes.id)

            # Combine the gradients.
            add_component_gradients = miscellaneous.AddValues(f'add_component_gradients'
                                                              f'_{gradient_replicator.placeholder_id}')
            add_component_gradients.values = component_gradient_source

            combine_gradients = miscellaneous.SubtractValues(f'combine_gradients_{gradient_replicator.placeholder_id}')
            combine_gradients.value_b = full_gradient_source
            combine_gradients.value_a = ProtocolPath('result', add_component_gradients.id)

            # Build the final workflow schema.
            schema = WorkflowSchema(property_type=ExcessMolarVolume.__name__)
            schema.id = '{}{}'.format(ExcessMolarVolume.__name__, 'Schema')

            schema.protocols = dict()

            schema.protocols.update({protocol.id: protocol.schema for protocol in full_protocols})
            schema.protocols.update({protocol.id: protocol.schema for protocol in component_protocols})

            schema.protocols[add_component_molar_volumes.id] = add_component_molar_volumes.schema
            schema.protocols[calculate_excess_volume.id] = calculate_excess_volume.schema

            schema.protocols[full_gradient_group.id] = full_gradient_group.schema
            schema.protocols[component_gradient_group.id] = component_gradient_group.schema
            schema.protocols[add_component_gradients.id] = add_component_gradients.schema
            schema.protocols[combine_gradients.id] = combine_gradients.schema

            schema.replicators = [
                full_data_replicator,
                component_replicator,
                component_data_replicator,
                gradient_replicator
            ]

            schema.gradients_sources = [ProtocolPath('result', combine_gradients.id)]
            schema.final_value_source = ProtocolPath('result', calculate_excess_volume.id)

            return schema