Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | X | Y | Z A activation_map() (in module simcardems.postprocess) ActiveModel (class in simcardems.models.explicit_ORdmm_Land) (in module simcardems.models.fully_coupled_ORdmm_Land) as_dict() (simcardems.Config method) (simcardems.config.Config method) assign() (simcardems.datacollector.Assigners method) assign_ep() (simcardems.datacollector.Assigners method) assign_item_is_None() (in module simcardems.datacollector) assign_mechanics() (simcardems.datacollector.Assigners method) assign_pre() (simcardems.datacollector.Assigners method) assign_pre_ep() (simcardems.datacollector.Assigners method) assign_pre_mechanics() (simcardems.datacollector.Assigners method) Assigners (class in simcardems.datacollector) assigners (simcardems.models.em_model.BaseEMCoupling property) (simcardems.models.explicit_ORdmm_Land.EMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) (simcardems.models.pureEP_ORdmm_Land.EMCoupling property) average() (simcardems.value_extractor.ValueExtractor method) B BaseEMCoupling (class in simcardems.models.em_model) BaseGeometry (class in simcardems.geometry) bnd_rigid (simcardems.Config attribute) (simcardems.config.Config attribute) boundaries (simcardems.value_extractor.SlabBoundary property) Boundary (class in simcardems.value_extractor) C cell_init_file (simcardems.Config attribute) (simcardems.config.Config attribute) cell_params() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) CellModel (in module simcardems.models.explicit_ORdmm_Land) (in module simcardems.models.fully_coupled_ORdmm_Land) (in module simcardems.models.pureEP_ORdmm_Land) center (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute) center_func() (in module simcardems.value_extractor) check_file_exists() (in module simcardems.save_load_functions) check_overloads_called() (simcardems.MechanicsNewtonSolver method) (simcardems.newton_solver.MechanicsNewtonSolver method) cleanup() (simcardems.datacollector.DataLoader method) (simcardems.DataLoader method) close_h5file() (in module simcardems.datacollector) close_h5pyfile() (in module simcardems.datacollector) comm() (simcardems.geometry.BaseGeometry method) compute_norm() (in module simcardems.utils) compute_pre_norm() (simcardems.datacollector.Assigners method) Config (class in simcardems) (class in simcardems.config) ContinuationBasedMechanicsProblem (class in simcardems.mechanics_model) converged() (simcardems.MechanicsNewtonSolver method) (simcardems.newton_solver.MechanicsNewtonSolver method) coupling_to_ep() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) coupling_to_mechanics() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) coupling_type (simcardems.Config attribute) (simcardems.config.Config attribute) (simcardems.models.em_model.BaseEMCoupling property) (simcardems.models.explicit_ORdmm_Land.EMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) (simcardems.models.pureEP_ORdmm_Land.EMCoupling property) create_boxmesh() (in module simcardems.slabgeometry) create_problem() (in module simcardems.mechanics_model) create_progressbar() (in module simcardems.runner) create_slab_facet_function() (in module simcardems.slabgeometry) create_slab_microstructure() (in module simcardems.slabgeometry) D DataCollector (class in simcardems) (class in simcardems.datacollector) DataGroups (class in simcardems.datacollector) DataLoader (class in simcardems) (class in simcardems.datacollector) debug_mode (simcardems.Config attribute) (simcardems.config.Config attribute) decode() (in module simcardems.save_load_functions) default_conductivities() (in module simcardems.ep_model) default_markers() (simcardems.geometry.BaseGeometry static method) (simcardems.lvgeometry.LeftVentricularGeometry static method) (simcardems.slabgeometry.SlabGeometry static method) default_parameters() (in module simcardems) (in module simcardems.config) (simcardems.geometry.BaseGeometry static method) (simcardems.lvgeometry.LeftVentricularGeometry static method) (simcardems.slabgeometry.SlabGeometry static method) default_schema() (simcardems.geometry.BaseGeometry static method) default_solver_parameters() (simcardems.MechanicsNewtonSolver static method) (simcardems.newton_solver.MechanicsNewtonSolver static method) default_stimulus_domain() (simcardems.geometry.BaseGeometry static method) define_conductivity_tensor() (in module simcardems.ep_model) dict_to_h5() (in module simcardems.save_load_functions) disease_state (simcardems.Config attribute) (simcardems.config.Config attribute) dLambda_ep (simcardems.models.explicit_ORdmm_Land.EMCoupling property) domain (simcardems.geometry.StimulusDomain attribute) drug_factors_file (simcardems.Config attribute) (simcardems.config.Config attribute) ds (simcardems.geometry.BaseGeometry property) dt (simcardems.Config attribute) (simcardems.config.Config attribute) (simcardems.TimeStepper property) dt_mech (simcardems.Config attribute) (simcardems.config.Config attribute) dt_mechanics (simcardems.models.em_model.BaseEMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) dump() (simcardems.geometry.BaseGeometry method) dx (simcardems.geometry.BaseGeometry property) E ecg() (in module simcardems.postprocess) ecg_recovery() (in module simcardems.postprocess) EMCoupling (class in simcardems.models.explicit_ORdmm_Land) (class in simcardems.models.fully_coupled_ORdmm_Land) (class in simcardems.models.pureEP_ORdmm_Land) enum2str() (in module simcardems.utils) ep (simcardems.datacollector.DataGroups attribute) ep_mesh (simcardems.datacollector.DataLoader property) (simcardems.DataLoader property) (simcardems.geometry.BaseGeometry property) (simcardems.models.explicit_ORdmm_Land.EMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) (simcardems.models.pureEP_ORdmm_Land.EMCoupling property) ep_ode_scheme (simcardems.Config attribute) (simcardems.config.Config attribute) ep_preconditioner (simcardems.Config attribute) (simcardems.config.Config attribute) ep_theta (simcardems.Config attribute) (simcardems.config.Config attribute) ep_to_coupling() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) eval() (simcardems.value_extractor.ValueExtractor method) eval_at_node() (simcardems.value_extractor.ValueExtractor method) extract_biomarkers() (in module simcardems.postprocess) extract_last_beat() (in module simcardems.postprocess) extract_number_from_h5py() (in module simcardems.datacollector) extract_sub_results() (in module simcardems.postprocess) extract_traces() (in module simcardems.postprocess) extract_value() (simcardems.datacollector.DataLoader method) (simcardems.DataLoader method) F f0 (simcardems.geometry.BaseGeometry property) f0_ep (simcardems.geometry.BaseGeometry property) facet_normal (simcardems.geometry.BaseGeometry property) ffun (simcardems.geometry.BaseGeometry property) ffun_ep (simcardems.geometry.BaseGeometry property) file_exist() (in module simcardems.ep_model) filter() (simcardems.utils.MPIFilt method) find_decaytime() (in module simcardems.postprocess) find_duration() (in module simcardems.postprocess) find_ttp() (in module simcardems.postprocess) fix_right_plane (simcardems.Config attribute) (simcardems.config.Config attribute) float_to_constant() (in module simcardems.utils) from_files() (simcardems.geometry.BaseGeometry class method) from_geometry() (simcardems.geometry.BaseGeometry class method) from_models() (simcardems.Runner class method) (simcardems.runner.Runner class method) from_state() (simcardems.models.em_model.BaseEMCoupling static method) (simcardems.models.explicit_ORdmm_Land.EMCoupling class method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling class method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling class method) function_names (simcardems.DataCollector property) (simcardems.datacollector.DataCollector property) (simcardems.datacollector.DataLoader property) (simcardems.DataLoader property) G geometry_path (simcardems.Config attribute) (simcardems.config.Config attribute) geometry_schema_path (simcardems.Config attribute) (simcardems.config.Config attribute) get() (simcardems.datacollector.DataLoader method) (simcardems.DataLoader method) get_biomarkers() (in module simcardems.postprocess) getLogger() (in module simcardems.utils) group_in_file() (in module simcardems.save_load_functions) H h5_to_dict() (in module simcardems.save_load_functions) h5pyfile() (in module simcardems.save_load_functions) handle_cell_inits() (in module simcardems.ep_model) handle_cell_params() (in module simcardems.ep_model) I interpolate() (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) InvalidReductionError J json_serial() (in module simcardems.postprocess) L LeftVentricularGeometry (class in simcardems.lvgeometry) linear_mechanics_solver (simcardems.Config attribute) (simcardems.config.Config attribute) lmbda_mech (simcardems.models.explicit_ORdmm_Land.EMCoupling property) lmbda_mech_func (simcardems.models.explicit_ORdmm_Land.EMCoupling property) load_geometry() (in module simcardems.geometry) load_initial_conditions_from_h5() (in module simcardems.save_load_functions) load_json() (in module simcardems.ep_model) load_state (simcardems.Config attribute) (simcardems.config.Config attribute) load_state() (in module simcardems.save_load_functions) local_project() (in module simcardems.utils) loglevel (simcardems.Config attribute) (simcardems.config.Config attribute) LVBoundary (class in simcardems.value_extractor) M main() (in module simcardems.cli) make_xdmffiles() (in module simcardems.postprocess) marker (simcardems.geometry.StimulusDomain attribute) marker_functions (simcardems.geometry.BaseGeometry property) mech_heart_to_bnd_cond() (in module simcardems.save_load_functions) mech_mesh (simcardems.datacollector.DataLoader property) (simcardems.DataLoader property) (simcardems.models.explicit_ORdmm_Land.EMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) mech_state (simcardems.models.explicit_ORdmm_Land.EMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) mech_threshold (simcardems.Config attribute) (simcardems.config.Config attribute) mechanics (simcardems.datacollector.DataGroups attribute) mechanics_mesh (simcardems.geometry.BaseGeometry property) mechanics_solve_strategy (simcardems.Config attribute) (simcardems.config.Config attribute) mechanics_to_coupling() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) mechanics_use_continuation (simcardems.Config attribute) (simcardems.config.Config attribute) mechanics_use_custom_newton_solver (simcardems.Config attribute) (simcardems.config.Config attribute) MechanicsNewtonSolver (class in simcardems) (class in simcardems.newton_solver) MechanicsNewtonSolver_ODE (class in simcardems) (class in simcardems.newton_solver) MechanicsProblem (class in simcardems) (class in simcardems.mechanics_model) mesh (simcardems.geometry.BaseGeometry property) microstructure (simcardems.geometry.BaseGeometry property) microstructure_ep (simcardems.geometry.BaseGeometry property) module simcardems simcardems.cli simcardems.config simcardems.datacollector simcardems.ep_model simcardems.geometry simcardems.lvgeometry simcardems.mechanics_model simcardems.models.em_model simcardems.models.explicit_ORdmm_Land simcardems.models.fully_coupled_ORdmm_Land simcardems.models.pureEP_ORdmm_Land simcardems.newton_solver simcardems.postprocess simcardems.runner simcardems.save_load_functions simcardems.slabgeometry simcardems.utils simcardems.value_extractor simcardems.version MPIFilt (class in simcardems.utils) ms2ns() (simcardems.TimeStepper static method) N n0 (simcardems.geometry.BaseGeometry property) n0_ep (simcardems.geometry.BaseGeometry property) names (simcardems.DataCollector property) (simcardems.datacollector.DataCollector property) nodes() (simcardems.value_extractor.Boundary static method) (simcardems.value_extractor.LVBoundary static method) (simcardems.value_extractor.SlabBoundary static method) ns2ms() (simcardems.TimeStepper static method) num_refinements (simcardems.Config attribute) (simcardems.config.Config attribute) (simcardems.geometry.BaseGeometry property) numpyfy() (in module simcardems.postprocess) O outdir (simcardems.Config attribute) (simcardems.config.Config attribute) (simcardems.geometry.BaseGeometry property) (simcardems.Runner property) (simcardems.runner.Runner property) outfilename (simcardems.Config attribute) (simcardems.config.Config attribute) P PCL (simcardems.Config attribute) (simcardems.config.Config attribute) plot_peaks() (in module simcardems.postprocess) plot_population() (in module simcardems.postprocess) plot_state_traces() (in module simcardems.postprocess) popu_factors_file (simcardems.Config attribute) (simcardems.config.Config attribute) pre_stretch (simcardems.Config attribute) (simcardems.config.Config attribute) print_ep_info() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) print_mechanics_info() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) print_mesh_info() (in module simcardems.utils) project() (simcardems.utils.Projector method) Projector (class in simcardems.utils) R refine_mesh() (in module simcardems.geometry) register() (simcardems.DataCollector method) (simcardems.datacollector.DataCollector method) register_datacollector() (simcardems.MechanicsNewtonSolver method) (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.newton_solver.MechanicsNewtonSolver method) register_ep_model() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) register_mech_model() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) register_subfunction() (simcardems.datacollector.Assigners method) register_time_stepper() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) remove_file() (in module simcardems.utils) reset() (simcardems.TimeStepper method) residual (simcardems.datacollector.DataLoader property) (simcardems.DataLoader property) resolve_boundary_conditions() (in module simcardems.mechanics_model) results_file (simcardems.DataCollector property) (simcardems.datacollector.DataCollector property) rigid_motion_term() (simcardems.mechanics_model.RigidMotionProblem method) (simcardems.RigidMotionProblem method) RigidMotionProblem (class in simcardems) (class in simcardems.mechanics_model) Runner (class in simcardems) (class in simcardems.runner) S s0 (simcardems.geometry.BaseGeometry property) s0_ep (simcardems.geometry.BaseGeometry property) save_freq (simcardems.Config attribute) (simcardems.config.Config attribute) save_popu_json() (in module simcardems.postprocess) save_residual() (simcardems.DataCollector method) (simcardems.datacollector.DataCollector method) save_residuals() (simcardems.MechanicsNewtonSolver method) (simcardems.newton_solver.MechanicsNewtonSolver method) save_state() (in module simcardems.save_load_functions) (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) (simcardems.Runner method) (simcardems.runner.Runner method) serialize_dict() (in module simcardems.save_load_functions) set_material (simcardems.Config attribute) (simcardems.config.Config attribute) setup_assigner() (in module simcardems.utils) setup_assigners() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) setup_cell_model() (in module simcardems.ep_model) setup_EM_model() (in module simcardems.models.em_model) setup_EM_model_from_config() (in module simcardems.models.em_model) setup_model() (in module simcardems.ep_model) setup_solver() (in module simcardems.ep_model) (in module simcardems.mechanics_model) setup_splitting_solver_parameters() (in module simcardems.ep_model) show_progress_bar (simcardems.Config attribute) (simcardems.config.Config attribute) simcardems module simcardems.cli module simcardems.config module simcardems.datacollector module simcardems.ep_model module simcardems.geometry module simcardems.lvgeometry module simcardems.mechanics_model module simcardems.models.em_model module simcardems.models.explicit_ORdmm_Land module simcardems.models.fully_coupled_ORdmm_Land module simcardems.models.pureEP_ORdmm_Land module simcardems.newton_solver module simcardems.postprocess module simcardems.runner module simcardems.save_load_functions module simcardems.slabgeometry module simcardems.utils module simcardems.value_extractor module simcardems.version module size (simcardems.datacollector.DataLoader property) (simcardems.DataLoader property) SlabBoundary (class in simcardems.value_extractor) SlabBoundaryNodes (class in simcardems.value_extractor) SlabGeometry (class in simcardems.slabgeometry) solve() (simcardems.mechanics_model.ContinuationBasedMechanicsProblem method) (simcardems.mechanics_model.MechanicsProblem method) (simcardems.MechanicsNewtonSolver method) (simcardems.MechanicsProblem method) (simcardems.newton_solver.MechanicsNewtonSolver method) (simcardems.Runner method) (simcardems.runner.Runner method) solve_ep() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) solve_for_control() (simcardems.mechanics_model.ContinuationBasedMechanicsProblem method) solve_mechanics() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) solver_setup() (simcardems.MechanicsNewtonSolver method) (simcardems.newton_solver.MechanicsNewtonSolver method) spring (simcardems.Config attribute) (simcardems.config.Config attribute) state_params (simcardems.models.em_model.BaseEMCoupling property) state_path (simcardems.Runner property) (simcardems.runner.Runner property) stats() (in module simcardems.postprocess) StimulusDomain (class in simcardems.geometry) store() (simcardems.DataCollector method) (simcardems.datacollector.DataCollector method) (simcardems.Runner method) (simcardems.runner.Runner method) sub_function() (in module simcardems.utils) T T (simcardems.Config attribute) (simcardems.config.Config attribute) t (simcardems.Runner property) (simcardems.runner.Runner property) T (simcardems.TimeStepper property) t0 (simcardems.Runner property) (simcardems.runner.Runner property) TimeStepper (class in simcardems) total_steps (simcardems.TimeStepper property) traction (simcardems.Config attribute) (simcardems.config.Config attribute) U u_subspace_index (simcardems.mechanics_model.MechanicsProblem property) (simcardems.mechanics_model.RigidMotionProblem property) (simcardems.MechanicsProblem property) (simcardems.RigidMotionProblem property) update_prev_ep() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) (simcardems.models.pureEP_ORdmm_Land.EMCoupling method) update_prev_mechanics() (simcardems.models.em_model.BaseEMCoupling method) (simcardems.models.explicit_ORdmm_Land.EMCoupling method) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling method) update_solution() (simcardems.MechanicsNewtonSolver_ODE method) (simcardems.newton_solver.MechanicsNewtonSolver_ODE method) V valid_reductions (simcardems.DataCollector property) (simcardems.datacollector.DataCollector property) validate() (simcardems.geometry.BaseGeometry method) (simcardems.lvgeometry.LeftVentricularGeometry method) (simcardems.slabgeometry.SlabGeometry method) ValueExtractor (class in simcardems.value_extractor) vs (simcardems.models.explicit_ORdmm_Land.EMCoupling property) (simcardems.models.fully_coupled_ORdmm_Land.EMCoupling property) (simcardems.models.pureEP_ORdmm_Land.EMCoupling property) vs_functions_to_dict() (in module simcardems.save_load_functions) X xmax (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute) xmin (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute) Y ymax (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute) ymin (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute) Z zmax (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute) zmin (simcardems.value_extractor.SlabBoundary property) (simcardems.value_extractor.SlabBoundaryNodes attribute)
