Index

A

AbstractBaseOperators (class in physioblocks.base.operators) AbstractFunction (class in physioblocks.simulation.functions) AbstractSimulation (class in physioblocks.simulation.runtime) AbstractSolver (class in physioblocks.simulation.solvers) accel (VelocityLawHHTModelComponent attribute) activation (ActiveLawMacroscopicHuxleyTwoMoment attribute) active_energy_sqrt (ActiveLawMacroscopicHuxleyTwoMoment attribute) active_law_residual() (ActiveLawMacroscopicHuxleyTwoMoment method) active_law_residual_dactive_energy_sqrt() (ActiveLawMacroscopicHuxleyTwoMoment method) active_law_residual_dactive_stiffness() (ActiveLawMacroscopicHuxleyTwoMoment method) active_law_residual_dactive_tension() (ActiveLawMacroscopicHuxleyTwoMoment method) active_law_residual_dfib_deform() (ActiveLawMacroscopicHuxleyTwoMoment method) active_stiffness (ActiveLawMacroscopicHuxleyTwoMoment attribute) active_tension_discr (ActiveLawMacroscopicHuxleyTwoMoment attribute) (RheologyFiberAdditiveModelComponent attribute)

ActiveLawMacroscopicHuxleyTwoMoment (class in physioblocks.library.model_components.active_law) add (Sum attribute) add_alias() (in module physioblocks.configuration.aliases) add_block() (Net method) add_boundary_condition() (Node method) add_dof() (Node method) add_node() (Net method) add_node_local() (Node method) add_submodel() (ModelComponentDescription method) add_system_part() (EqSystem method) add_variable() (State method) alpha (RescaleTwoPhasesFunction attribute) amplitude (SinusOffset attribute) amplitudes (FirstOrder attribute)

B

backward_conductance (ValveRLBlock attribute) baseline_value (FirstOrder attribute) BaseTypes (in module physioblocks.configuration.functions) Block (class in physioblocks.computing.models) BlockDescription (class in physioblocks.description.blocks) BlockMetaClass (class in physioblocks.computing.models) blocks (Net property)

boundary_conditions (Net property) (Node property) BoundaryCondition (class in physioblocks.description.nets) build_blocks() (in module physioblocks.simulation.setup) build_eq_system() (in module physioblocks.simulation.setup) build_parameters() (in module physioblocks.simulation.setup) build_saved_quantities() (in module physioblocks.simulation.setup) build_state() (in module physioblocks.simulation.setup)

C

capacitance (CBlock attribute) (RCBlock attribute) (RCRBlock attribute) cavity_flux() (SphericalCavityBlock method) CBlock (class in physioblocks.library.blocks.capacitances) check_key_value_type() (in module physioblocks.base.registers) compute_gradient() (EqSystem method) compute_residual() (EqSystem method) compute_volume_stored() (RCRBlock method) condition_id (BoundaryCondition attribute) condition_type (BoundaryCondition attribute) conductance (ValveRLBlock attribute) Configuration (class in physioblocks.configuration.base)

configuration_items (Configuration attribute) ConfigurationAlias (in module physioblocks.configuration.aliases) ConfigurationError contractility (ActiveLawMacroscopicHuxleyTwoMoment attribute) converged (Solution attribute) ConvergenceError copy() (Configuration method) create_models() (in module physioblocks.simulation.setup) create_simulation() (SimulationFactory method) create_uncaught_exception_logger_handler() (in module physioblocks.utils.exceptions_utils) crossbridge_stiffness (ActiveLawMacroscopicHuxleyTwoMoment attribute) current (Quantity property) current_step_size (TimeManager property)

D

damping_coef (SphericalDynamicsModelComponent attribute) damping_parallel (RheologyFiberAdditiveModelComponent attribute) dcavity_flux_ddisp() (SphericalCavityBlock method) declares_flux_expression() (BlockMetaClass method) declares_internal_expression() (ModelComponentMetaClass method) declares_saved_quantity_expression() (ModelComponentMetaClass method) described_type (BlockDescription property) (ModelComponentDescription property) destruction_rate (ActiveLawMacroscopicHuxleyTwoMoment attribute) dfib_deform_equation_dactive_tension_discr() (RheologyFiberAdditiveModelComponent method) dfib_deform_equation_ddisp() (RheologyFiberAdditiveModelComponent method) dfib_deform_equation_dfib_deform() (RheologyFiberAdditiveModelComponent method) dflux_1_dflux() (ValveRLBlock method) dflux_1_dp_1() (RCRBlock method) dflux_1_dp_mid() (RCRBlock method) dflux_1_dpressure_1() (RCBlock method) dflux_1_dpressure_2() (RCBlock method) dflux_2_dflux() (ValveRLBlock method) dflux_2_dp_2() (RCRBlock method) dflux_2_dp_mid() (RCRBlock method)

dflux_2_dpressure_1() (RCBlock method) dflux_2_dpressure_2() (RCBlock method) dflux_dpressure() (CBlock method) diff() (in module physioblocks.computing.quantities) disp (RheologyFiberAdditiveModelComponent attribute) (SphericalCavityBlock attribute) (SphericalDynamicsModelComponent attribute) (VelocityLawHHTModelComponent attribute) Dof (class in physioblocks.description.flux) dof_flux_couples (FluxDofTypesRegister property) dof_id (Dof attribute) dof_type (Dof attribute) dofs (Node property) dt (Time property) duration (TimeManager property) dynamics_residual() (SphericalDynamicsModelComponent method) dynamics_residual_ddisp() (SphericalDynamicsModelComponent method) dynamics_residual_dfib_deform() (SphericalDynamicsModelComponent method) dynamics_residual_dpressure() (SphericalDynamicsModelComponent method) dynamics_residual_dpressure_external() (SphericalDynamicsModelComponent method) dynamics_residual_dvel() (SphericalDynamicsModelComponent method)

E

elements (SumBlocksQuantity attribute) end (TimeManager property) ended (TimeManager property) EqSystem (class in physioblocks.computing.assembling) eval() (AbstractFunction method) (FirstOrder method) (PiecewiseLinear method) (PiecewiseLinearPeriodic method) (Product method) (RescaleTwoPhasesFunction method) (SinusOffset method) (Sum method) (SumBlocksQuantity method) (WatchQuantity method)

ExceptionHandlerFunction (in module physioblocks.utils.exceptions_utils) exp_diff() (in module physioblocks.utils.math_utils) expr_func (Expression attribute) expr_gradients (Expression attribute) Expression (class in physioblocks.computing.models) expression (ExpressionDefinition attribute) ExpressionDefinition (class in physioblocks.computing.models) ExpressionsCollection (in module physioblocks.computing.models) external_variables_ids (BlockMetaClass property)

F

factors (Product attribute) fib_deform (ActiveLawMacroscopicHuxleyTwoMoment attribute) (RheologyFiberAdditiveModelComponent attribute) (SphericalDynamicsModelComponent attribute) fib_deform_equation() (RheologyFiberAdditiveModelComponent method) FirstOrder (class in physioblocks.library.functions.first_order) fluid_volume_current() (SphericalCavityBlock method) fluid_volume_new() (SphericalCavityBlock method) flux (ValveRLBlock attribute) flux() (CBlock method) flux_1() (RCBlock method) (RCRBlock method) (ValveRLBlock method)

flux_2() (RCBlock method) (RCRBlock method) (ValveRLBlock method) flux_dof_couples (FluxDofTypesRegister property) flux_residual() (ValveRLBlock method) flux_residual_dflux() (ValveRLBlock method) flux_residual_dp1() (ValveRLBlock method) flux_residual_dp2() (ValveRLBlock method) flux_type (BlockDescription property) FluxDofTypesRegister (class in physioblocks.description.flux) fluxes (BlockDescription property) fluxes_expressions (BlockMetaClass property) ForwardSimulation (class in physioblocks.simulation.runtime) frequency (SinusOffset attribute)

G

get() (State method) get_alias() (in module physioblocks.configuration.aliases) get_dof() (Node method) get_errors_gradient() (in module physioblocks.utils.gradient_test_utils) get_flux_dof() (Node method) get_flux_dof_register() (in module physioblocks.description.flux) get_internal_variable_expression() (ModelComponentMetaClass method) get_load_function() (in module physioblocks.registers.load_function_register) get_registered_type() (in module physioblocks.registers.type_register) get_registered_type_id() (in module physioblocks.registers.type_register) get_save_function() (in module physioblocks.registers.save_function_register)

get_saved_quantity_expression() (ModelComponentMetaClass method) get_term() (ExpressionDefinition method) get_variable_id() (State method) get_variable_index() (State method) get_variable_size() (State method) global_ids (ModelComponentDescription property) gradient_test() (in module physioblocks.utils.gradient_test_utils) gradient_test_from_expression() (in module physioblocks.utils.gradient_test_utils) gradient_test_from_file() (in module physioblocks.utils.gradient_test_utils) gradient_test_from_model() (in module physioblocks.utils.gradient_test_utils) GradientError

H

has_alias() (in module physioblocks.configuration.aliases) has_flux_type() (Node method) has_internal_variable() (ModelComponentMetaClass method)

has_node_local() (Node method) has_save_function() (in module physioblocks.registers.save_function_register) has_saved_quantity() (ModelComponentMetaClass method) hyperelastic_cst (SphericalDynamicsModelComponent attribute)

I

import_libraries() (in module physioblocks.utils.dynamic_import_utils) index (TermDefinition attribute) indexes (State property) inductance (ValveRLBlock attribute) initialize() (ModelComponent method) (Quantity method) (RheologyFiberAdditiveModelComponent method) (SphericalCavityBlock method) (SphericalDynamicsModelComponent method) (Time method) (TimeManager method) (ValveRLBlock method)

intermediate_results (SimulationError attribute) internal_expressions (ModelComponentDescription property) (ModelComponentMetaClass property) internal_variables (ModelComponentDescription property) (ModelComponentMetaClass property) inv_dt (Time property) inverses (Product attribute) is_boundary (Node property) is_registered() (in module physioblocks.registers.type_register) is_state_function() (in module physioblocks.simulation.functions) is_time_function() (in module physioblocks.simulation.functions) items() (Configuration method) iteration_max (AbstractSolver attribute)

K

keys() (Configuration method)

L

label (Configuration attribute) left_value (PiecewiseLinear attribute) load() (in module physioblocks.configuration.functions) load_aliases() (in module physioblocks.io.aliases) load_configuration() (in module physioblocks.configuration.functions) load_dict() (in module physioblocks.configuration.functions)

load_list() (in module physioblocks.configuration.functions) loads() (in module physioblocks.registers.load_function_register) local_ids (ModelComponentMetaClass property) local_nodes (Node property) local_to_global_node_id() (Net method) log_exception() (in module physioblocks.utils.exceptions_utils)

M

mid_alpha() (in module physioblocks.computing.quantities) mid_point() (in module physioblocks.computing.quantities) min_step (TimeManager property) ModelComponent (class in physioblocks.computing.models) ModelComponentDescription (class in physioblocks.description.blocks) ModelComponentMetaClass (class in physioblocks.computing.models) module physioblocks.base physioblocks.base.operators physioblocks.base.registers physioblocks.computing.assembling physioblocks.computing.models physioblocks.computing.quantities physioblocks.configuration.aliases physioblocks.configuration.base physioblocks.configuration.functions physioblocks.description.blocks physioblocks.description.flux physioblocks.description.nets physioblocks.io physioblocks.io.aliases physioblocks.io.configuration physioblocks.library.blocks.capacitances physioblocks.library.blocks.cavity physioblocks.library.blocks.valves physioblocks.library.functions.base_operations physioblocks.library.functions.first_order physioblocks.library.functions.piecewise physioblocks.library.functions.trigonometric physioblocks.library.functions.watchers physioblocks.library.model_components.active_law physioblocks.library.model_components.dynamics physioblocks.library.model_components.rheology physioblocks.library.model_components.velocity_law physioblocks.registers.load_function_register physioblocks.registers.save_function_register physioblocks.registers.type_register physioblocks.simulation.functions physioblocks.simulation.runtime physioblocks.simulation.saved_quantities physioblocks.simulation.setup physioblocks.simulation.solvers physioblocks.simulation.state physioblocks.simulation.time_manager physioblocks.utils physioblocks.utils.dynamic_import_utils physioblocks.utils.exceptions_utils physioblocks.utils.gradient_test_utils physioblocks.utils.math_utils

N

name (ModelComponentDescription property) (Node property) Net (class in physioblocks.description.nets) new (Quantity property)

NewtonSolver (class in physioblocks.simulation.solvers) Node (class in physioblocks.description.nets) nodes (BlockMetaClass property) (Net property)

O

offset_value (SinusOffset attribute) operation_value (AbstractBaseOperators property) (Product property) (Quantity property) (Sum property) (SumBlocksQuantity property) (WatchQuantity property)

outputs_functions (AbstractSimulation property)

P

Parameters (in module physioblocks.simulation.runtime) period (PiecewiseLinearPeriodic attribute) phase_shift (SinusOffset attribute) phases (RescaleTwoPhasesFunction attribute) physioblocks.base module physioblocks.base.operators module physioblocks.base.registers module physioblocks.computing.assembling module physioblocks.computing.models module physioblocks.computing.quantities module physioblocks.configuration.aliases module physioblocks.configuration.base module physioblocks.configuration.functions module physioblocks.description.blocks module physioblocks.description.flux module physioblocks.description.nets module physioblocks.io module physioblocks.io.aliases module physioblocks.io.configuration module physioblocks.library.blocks.capacitances module physioblocks.library.blocks.cavity module physioblocks.library.blocks.valves module physioblocks.library.functions.base_operations module physioblocks.library.functions.first_order module physioblocks.library.functions.piecewise module physioblocks.library.functions.trigonometric module physioblocks.library.functions.watchers module physioblocks.library.model_components.active_law module physioblocks.library.model_components.dynamics module physioblocks.library.model_components.rheology module

physioblocks.library.model_components.velocity_law module physioblocks.registers.load_function_register module physioblocks.registers.save_function_register module physioblocks.registers.type_register module physioblocks.simulation.functions module physioblocks.simulation.runtime module physioblocks.simulation.saved_quantities module physioblocks.simulation.setup module physioblocks.simulation.solvers module physioblocks.simulation.state module physioblocks.simulation.time_manager module physioblocks.utils module physioblocks.utils.dynamic_import_utils module physioblocks.utils.exceptions_utils module physioblocks.utils.gradient_test_utils module physioblocks.utils.math_utils module PiecewiseLinear (class in physioblocks.library.functions.piecewise) PiecewiseLinearPeriodic (class in physioblocks.library.functions.piecewise) points_abscissas (PiecewiseLinear attribute) (PiecewiseLinearPeriodic attribute) points_ordinates (PiecewiseLinear attribute) (PiecewiseLinearPeriodic attribute) power_diff() (in module physioblocks.utils.math_utils) pressure (CBlock attribute) (SphericalDynamicsModelComponent attribute) pressure_1 (RCBlock attribute) (RCRBlock attribute) (ValveRLBlock attribute) pressure_2 (RCBlock attribute) (RCRBlock attribute) (ValveRLBlock attribute) pressure_external (SphericalDynamicsModelComponent attribute) pressure_mid (RCRBlock attribute) pressure_mid_residual() (RCRBlock method) pressure_mid_residual_dp_1() (RCRBlock method) pressure_mid_residual_dp_2() (RCRBlock method) pressure_mid_residual_dp_mid() (RCRBlock method) Product (class in physioblocks.library.functions.base_operations)

Q

quantities (AbstractSimulation property) Quantity (class in physioblocks.computing.quantities)

quantity (WatchQuantity attribute) quantity_id (SumBlocksQuantity attribute)

R

radius (RheologyFiberAdditiveModelComponent attribute) (SphericalCavityBlock attribute) (SphericalDynamicsModelComponent attribute) RCBlock (class in physioblocks.library.blocks.capacitances) RCRBlock (class in physioblocks.library.blocks.capacitances) read_json() (in module physioblocks.io.configuration) reference_function (RescaleTwoPhasesFunction attribute) register() (in module physioblocks.base.registers) (SavedQuantities method) register_flux_dof_couple() (FluxDofTypesRegister method) register_output_function() (AbstractSimulation method) register_timed_parameter_update() (AbstractSimulation method) register_type() (in module physioblocks.registers.type_register) RegisterError remove_alias() (in module physioblocks.configuration.aliases) remove_block() (Net method) remove_boundary() (Net method) remove_boundary_condition() (Node method)

remove_dof() (Node method) remove_node() (Net method) remove_node_local() (Node method) remove_submodel() (ModelComponentDescription method) remove_variable() (State method) rename_global_id() (ModelComponentDescription method) rescaled_period (RescaleTwoPhasesFunction attribute) RescaleTwoPhasesFunction (class in physioblocks.library.functions.piecewise) reset_state_vector() (State method) resistance (RCBlock attribute) resistance_1 (RCRBlock attribute) resistance_2 (RCRBlock attribute) Result (in module physioblocks.simulation.runtime) Results (in module physioblocks.simulation.runtime) RheologyFiberAdditiveModelComponent (class in physioblocks.library.model_components.rheology) right_value (PiecewiseLinear attribute) run() (AbstractSimulation method) (ForwardSimulation method)

S

save() (in module physioblocks.configuration.functions) saved_quantities (ModelComponentDescription property) (ModelComponentMetaClass property) saved_quantities_expressions (ModelComponentDescription property) (ModelComponentMetaClass property) SavedQuantities (class in physioblocks.simulation.saved_quantities) saves() (in module physioblocks.registers.save_function_register) scheme_ts_flux (ValveRLBlock attribute) scheme_ts_hht (VelocityLawHHTModelComponent attribute) series_stiffness (RheologyFiberAdditiveModelComponent attribute) (SphericalDynamicsModelComponent attribute) set_boundary() (Net method) set_state_vector() (State method) sign() (in module physioblocks.computing.quantities) SimulationError SimulationFactory (class in physioblocks.simulation.setup) SinusOffset (class in physioblocks.library.functions.trigonometric) size (Expression attribute) (Quantity property) (State property) (TermDefinition attribute)

Solution (class in physioblocks.simulation.solvers) solve() (AbstractSolver method) (NewtonSolver method) SphericalCavityBlock (class in physioblocks.library.blocks.cavity) SphericalDynamicsModelComponent (class in physioblocks.library.model_components.dynamics) starling_abscissas (ActiveLawMacroscopicHuxleyTwoMoment attribute) starling_ordinates (ActiveLawMacroscopicHuxleyTwoMoment attribute) start (TimeManager attribute) State (class in physioblocks.simulation.state) state_vector (State property) step_size (TimeManager property) submodels (ModelComponentDescription property) subtract (Sum attribute) Sum (class in physioblocks.library.functions.base_operations) SumBlocksQuantity (class in physioblocks.library.functions.watchers) system_size (EqSystem property) SystemExpressions (in module physioblocks.simulation.setup) SystemFunction (in module physioblocks.computing.models)

T

term_id (TermDefinition attribute) TermDefinition (class in physioblocks.computing.models) terms (ExpressionDefinition attribute) thickness (SphericalCavityBlock attribute) (SphericalDynamicsModelComponent attribute) time (ActiveLawMacroscopicHuxleyTwoMoment attribute) (CBlock attribute) Time (class in physioblocks.simulation.time_manager) time (RCBlock attribute) (RCRBlock attribute) (RheologyFiberAdditiveModelComponent attribute) (SphericalCavityBlock attribute) (SphericalDynamicsModelComponent attribute) (TimeManager property) (ValveRLBlock attribute) (VelocityLawHHTModelComponent attribute)

time_constants (FirstOrder attribute) TimeManager (class in physioblocks.simulation.time_manager) times_start (FirstOrder attribute) tolerance (AbstractSolver attribute)

U

unregister() (SavedQuantities method) unregister_flux_dof_couple() (FluxDofTypesRegister method) unregister_output_function() (AbstractSimulation method) unregister_timed_parameter_update() (AbstractSimulation method) unwrap_aliases() (in module physioblocks.configuration.aliases) update() (Quantity method) (SavedQuantities method) (State method) (Time method)

update_functions (AbstractSimulation property) update_state_vector() (State method) update_time() (TimeManager method)

V

valid (ExpressionDefinition property) values() (Configuration method) ValveRLBlock (class in physioblocks.library.blocks.valves) variables (State property) vel (SphericalDynamicsModelComponent attribute) (VelocityLawHHTModelComponent attribute)

velocity_law_residual() (VelocityLawHHTModelComponent method) velocity_law_residual_daccel() (VelocityLawHHTModelComponent method) velocity_law_residual_ddisp() (VelocityLawHHTModelComponent method) velocity_law_residual_dvel() (VelocityLawHHTModelComponent method) VelocityLawHHTModelComponent (class in physioblocks.library.model_components.velocity_law) vol_mass (SphericalDynamicsModelComponent attribute)

W

WatchQuantity (class in physioblocks.library.functions.watchers)

write_json() (in module physioblocks.io.configuration)

X

x (Solution attribute)