Index

_

__init__() (amici.importers.petab.PetabImporter method) (amici.importers.sbml.SbmlImporter method) (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) (amici.importers.sbml.splines.UniformGrid method) (amici.importers.utils.MeasurementChannel method) (amici.sim.jax.JAXModel method) (amici.sim.jax.JAXProblem method) (amici.sim.sundials.Constraint method) (amici.sim.sundials.CpuTimer method) (amici.sim.sundials.ExpData method) (amici.sim.sundials.ExpDataView method) (amici.sim.sundials.FixedParameterContext method) (amici.sim.sundials.InternalSensitivityMethod method) (amici.sim.sundials.InterpolationType method) (amici.sim.sundials.LinearMultistepMethod method) (amici.sim.sundials.LinearSolver method) (amici.sim.sundials.LogItem method) (amici.sim.sundials.LogSeverity method) (amici.sim.sundials.Model method) (amici.sim.sundials.ModelDimensions method) (amici.sim.sundials.ModelModule method) (amici.sim.sundials.NewtonDampingFactorMode method) (amici.sim.sundials.NonlinearSolverIteration method) (amici.sim.sundials.ObservableScaling method) (amici.sim.sundials.ParameterScaling method) (amici.sim.sundials.petab.ExperimentManager method) (amici.sim.sundials.petab.PetabSimulationResult method) (amici.sim.sundials.petab.PetabSimulator method) (amici.sim.sundials.petab.v1.PetabProblem method) (amici.sim.sundials.petab.v1.PetabSimulator method) (amici.sim.sundials.RDataReporting method) (amici.sim.sundials.ReturnData method) (amici.sim.sundials.ReturnDataView method) (amici.sim.sundials.SecondOrderMode method) (amici.sim.sundials.SensitivityMethod method) (amici.sim.sundials.SensitivityOrder method) (amici.sim.sundials.SimulationParameters method) (amici.sim.sundials.Solver method) (amici.sim.sundials.SteadyStateComputationMode method) (amici.sim.sundials.SteadyStateSensitivityMode method) (amici.sim.sundials.SteadyStateStatus method)

_USE_MATH_DEFINES (C macro)

A

AbstractSpline (class in amici.importers.sbml.splines) adams (amici.sim.sundials.LinearMultistepMethod attribute) add_noise() (amici.sim.sundials.petab.v1.PetabSimulator method) add_to_sbml_model() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) adjoint (amici.sim.sundials.SensitivityMethod attribute) amici module amici.adapters.fiddy module amici.importers.antimony module amici.importers.bngl module amici.importers.petab module amici.importers.petab.v1 module amici.importers.pysb module amici.importers.sbml module amici.importers.sbml.splines module amici.importers.utils module amici.sim.jax module amici.sim.sundials module amici.sim.sundials.gradient_check module amici.sim.sundials.petab module amici.sim.sundials.petab.v1 module amici.sim.sundials.plotting module amici::AbstractModel (C++ class) amici::AbstractModel::create_solver (C++ function) amici::AbstractModel::fcreate_splines (C++ function) amici::AbstractModel::fdeltaqB (C++ function) amici::AbstractModel::fdeltasx (C++ function) amici::AbstractModel::fdeltax (C++ function) amici::AbstractModel::fdeltaxB (C++ function) amici::AbstractModel::fdJrzdsigma (C++ function) amici::AbstractModel::fdJrzdz (C++ function) amici::AbstractModel::fdJydsigma (C++ function) amici::AbstractModel::fdJydy (C++ function) amici::AbstractModel::fdJydy_colptrs (C++ function) amici::AbstractModel::fdJydy_rowvals (C++ function) amici::AbstractModel::fdJzdsigma (C++ function) amici::AbstractModel::fdJzdz (C++ function) amici::AbstractModel::fdrzdp (C++ function) amici::AbstractModel::fdrzdx (C++ function) amici::AbstractModel::fdsigmaydp (C++ function) amici::AbstractModel::fdsigmaydy (C++ function) amici::AbstractModel::fdsigmazdp (C++ function) amici::AbstractModel::fdspline_slopesdp (C++ function) amici::AbstractModel::fdspline_valuesdp (C++ function) amici::AbstractModel::fdtotal_cldp (C++ function) amici::AbstractModel::fdtotal_cldx_rdata (C++ function) amici::AbstractModel::fdtotal_cldx_rdata_colptrs (C++ function) amici::AbstractModel::fdtotal_cldx_rdata_rowvals (C++ function) amici::AbstractModel::fdwdp (C++ function) amici::AbstractModel::fdwdp_colptrs (C++ function) amici::AbstractModel::fdwdp_rowvals (C++ function) amici::AbstractModel::fdwdw (C++ function) amici::AbstractModel::fdwdw_colptrs (C++ function) amici::AbstractModel::fdwdw_rowvals (C++ function) amici::AbstractModel::fdwdx (C++ function) amici::AbstractModel::fdwdx_colptrs (C++ function) amici::AbstractModel::fdwdx_rowvals (C++ function) amici::AbstractModel::fdx0 (C++ function) amici::AbstractModel::fdx_rdatadp (C++ function) amici::AbstractModel::fdx_rdatadtcl (C++ function) amici::AbstractModel::fdx_rdatadtcl_colptrs (C++ function) amici::AbstractModel::fdx_rdatadtcl_rowvals (C++ function) amici::AbstractModel::fdx_rdatadx_solver (C++ function) amici::AbstractModel::fdx_rdatadx_solver_colptrs (C++ function) amici::AbstractModel::fdx_rdatadx_solver_rowvals (C++ function) amici::AbstractModel::fdxdotdp (C++ function) amici::AbstractModel::fdydp (C++ function) amici::AbstractModel::fdydx (C++ function) amici::AbstractModel::fdzdp (C++ function) amici::AbstractModel::fdzdx (C++ function) amici::AbstractModel::fexplicit_roots (C++ function) amici::AbstractModel::fJ (C++ function) amici::AbstractModel::fJB (C++ function) amici::AbstractModel::fJDiag (C++ function) amici::AbstractModel::fJrz (C++ function) amici::AbstractModel::fJSparse (C++ function) amici::AbstractModel::fJSparseB (C++ function) amici::AbstractModel::fJSparseB_ss (C++ function) amici::AbstractModel::fJv (C++ function) amici::AbstractModel::fJy (C++ function) amici::AbstractModel::fJz (C++ function) amici::AbstractModel::froot (C++ function) amici::AbstractModel::frz (C++ function) amici::AbstractModel::fsigmay (C++ function) amici::AbstractModel::fsigmaz (C++ function) amici::AbstractModel::fsrz (C++ function) amici::AbstractModel::fstau (C++ function) amici::AbstractModel::fsx0 (C++ function) amici::AbstractModel::fsx0_fixedParameters (C++ function) amici::AbstractModel::fsxdot (C++ function) amici::AbstractModel::fsz (C++ function) amici::AbstractModel::fw (C++ function) amici::AbstractModel::fx0 (C++ function) amici::AbstractModel::fx0_fixedParameters (C++ function) amici::AbstractModel::fxBdot_ss (C++ function) amici::AbstractModel::fxdot (C++ function) amici::AbstractModel::fy (C++ function) amici::AbstractModel::fz (C++ function) amici::AbstractModel::get_amici_commit (C++ function) amici::AbstractModel::get_amici_version (C++ function) amici::AbstractModel::is_fixed_parameter_state_reinitialization_allowed (C++ function) amici::AbstractModel::write_steady_state_JB (C++ function) amici::AbstractModel::~AbstractModel (C++ function) amici::AbstractSpline (C++ class) amici::AbstractSpline::AbstractSpline (C++ function), [1] amici::AbstractSpline::coefficients (C++ member) amici::AbstractSpline::coefficients_extrapolate (C++ member) amici::AbstractSpline::coefficients_extrapolate_sensi (C++ member) amici::AbstractSpline::coefficients_sensi (C++ member) amici::AbstractSpline::compute_coefficients (C++ function) amici::AbstractSpline::compute_coefficients_sensi (C++ function) amici::AbstractSpline::compute_final_sensitivity (C++ function) amici::AbstractSpline::compute_final_value (C++ function) amici::AbstractSpline::get_equidistant_spacing (C++ function) amici::AbstractSpline::get_final_sensitivity (C++ function) amici::AbstractSpline::get_final_sensitivity_scaled (C++ function) amici::AbstractSpline::get_final_value (C++ function) amici::AbstractSpline::get_final_value_scaled (C++ function) amici::AbstractSpline::get_logarithmic_parametrization (C++ function) amici::AbstractSpline::get_node_value (C++ function) amici::AbstractSpline::get_node_value_scaled (C++ function) amici::AbstractSpline::get_sensitivity (C++ function), [1] amici::AbstractSpline::get_sensitivity_scaled (C++ function) amici::AbstractSpline::get_value (C++ function) amici::AbstractSpline::get_value_scaled (C++ function) amici::AbstractSpline::n_nodes (C++ function) amici::AbstractSpline::node_values_ (C++ member) amici::AbstractSpline::nodes_ (C++ member) amici::AbstractSpline::set_final_sensitivity_scaled (C++ function) amici::AbstractSpline::set_final_value_scaled (C++ function) amici::AbstractSpline::~AbstractSpline (C++ function) amici::add_slice (C++ function), [1] amici::AMICI_BAD_DKY (C++ member) amici::AMICI_BAD_T (C++ member) amici::AMICI_CONSTR_FAIL (C++ member) amici::AMICI_CONV_FAILURE (C++ member) amici::AMICI_CVODES_CONSTR_FAIL (C++ member) amici::AMICI_DAMPING_FACTOR_ERROR (C++ member) amici::AMICI_DATA_RETURN (C++ member) amici::amici_daxpy (C++ function) amici::amici_dgemm (C++ function) amici::amici_dgemv (C++ function) amici::AMICI_ERR_FAILURE (C++ member) amici::AMICI_ERROR (C++ member) amici::AMICI_FIRST_QRHSFUNC_ERR (C++ member) amici::AMICI_FIRST_RHSFUNC_ERR (C++ member) amici::AMICI_FIRST_SRHSFUNC_ERR (C++ member) amici::AMICI_IDAS_CONSTR_FAIL (C++ member) amici::AMICI_ILL_INPUT (C++ member) amici::AMICI_LINESEARCH_FAIL (C++ member) amici::AMICI_LSETUP_FAIL (C++ member) amici::AMICI_MAX_TIME_EXCEEDED (C++ member) amici::AMICI_NO_STEADY_STATE (C++ member) amici::AMICI_NORMAL (C++ member) amici::AMICI_NOT_IMPLEMENTED (C++ member) amici::AMICI_NOT_RUN (C++ member) amici::AMICI_ONE_STEP (C++ member) amici::AMICI_PREEQUILIBRATE (C++ member) amici::AMICI_RECOVERABLE_ERROR (C++ member) amici::AMICI_REPTD_SRHSFUNC_ERR (C++ member) amici::AMICI_RHSFUNC_FAIL (C++ member) amici::AMICI_ROOT_RETURN (C++ member) amici::AMICI_RTFUNC_FAIL (C++ member) amici::AMICI_SINGULAR_JACOBIAN (C++ member) amici::AMICI_SRHSFUNC_FAIL (C++ member) amici::AMICI_SUCCESS (C++ member) amici::AMICI_T_OVERFLOW (C++ member) amici::AMICI_TOO_MUCH_ACC (C++ member) amici::AMICI_TOO_MUCH_WORK (C++ member) amici::AMICI_UNREC_SRHSFUNC_ERR (C++ member) amici::AMICI_UNRECOVERABLE_ERROR (C++ member) amici::AMICI_WARNING (C++ member) amici::AmiException (C++ class) amici::AmiException::AmiException (C++ function), [1] amici::AmiException::getBacktrace (C++ function) amici::AmiException::storeBacktrace (C++ function) amici::AmiException::storeMessage (C++ function) amici::AmiException::what (C++ function) amici::AmiVector (C++ class) amici::AmiVector::abs (C++ function) amici::AmiVector::AmiVector (C++ function), [1], [2], [3], [4], [5], [6] amici::AmiVector::at (C++ function), [1] amici::AmiVector::begin (C++ function) amici::AmiVector::boost::serialization::serialize (C++ function) amici::AmiVector::copy (C++ function) amici::AmiVector::data (C++ function), [1] amici::AmiVector::end (C++ function) amici::AmiVector::get_ctx (C++ function) amici::AmiVector::get_nvector (C++ function), [1] amici::AmiVector::get_vector (C++ function) amici::AmiVector::minus (C++ function) amici::AmiVector::operator*= (C++ function) amici::AmiVector::operator/= (C++ function) amici::AmiVector::operator= (C++ function) amici::AmiVector::operator[] (C++ function), [1] amici::AmiVector::set (C++ function) amici::AmiVector::set_ctx (C++ function) amici::AmiVector::size (C++ function) amici::AmiVector::zero (C++ function) amici::AmiVector::~AmiVector (C++ function) amici::AmiVectorArray (C++ class) amici::AmiVectorArray::AmiVectorArray (C++ function), [1], [2] amici::AmiVectorArray::at (C++ function), [1] amici::AmiVectorArray::copy (C++ function) amici::AmiVectorArray::data (C++ function), [1] amici::AmiVectorArray::flatten_to_vector (C++ function) amici::AmiVectorArray::get_nvector (C++ function), [1] amici::AmiVectorArray::get_nvector_array (C++ function) amici::AmiVectorArray::operator= (C++ function) amici::AmiVectorArray::operator[] (C++ function), [1] amici::AmiVectorArray::set_ctx (C++ function) amici::AmiVectorArray::size (C++ function) amici::AmiVectorArray::zero (C++ function) amici::AmiVectorArray::~AmiVectorArray (C++ function) amici::BackwardProblem (C++ class) amici::BackwardProblem::BackwardProblem (C++ function) amici::BackwardProblem::get_adjoint_quadrature (C++ function) amici::BackwardProblem::get_adjoint_quadrature_pre_preeq (C++ function) amici::BackwardProblem::get_adjoint_state (C++ function) amici::BackwardProblem::get_adjoint_state_pre_preeq (C++ function) amici::BackwardProblem::get_posteq_bwd_problem (C++ function) amici::BackwardProblem::get_preeq_bwd_problem (C++ function) amici::BackwardProblem::workBackwardProblem (C++ function) amici::BLASLayout (C++ enum) amici::BLASLayout::colMajor (C++ enumerator) amici::BLASLayout::rowMajor (C++ enumerator) amici::BLASTranspose (C++ enum) amici::BLASTranspose::conjTrans (C++ enumerator) amici::BLASTranspose::noTrans (C++ enumerator) amici::BLASTranspose::trans (C++ enumerator) amici::BwdSimWorkspace (C++ struct) amici::BwdSimWorkspace::BwdSimWorkspace (C++ function) amici::BwdSimWorkspace::discs_ (C++ member) amici::BwdSimWorkspace::dxB_ (C++ member) amici::BwdSimWorkspace::model_ (C++ member) amici::BwdSimWorkspace::nroots_ (C++ member) amici::BwdSimWorkspace::which (C++ member) amici::BwdSimWorkspace::xB_ (C++ member) amici::BwdSimWorkspace::xQB_ (C++ member) amici::check_buffer_size (C++ function) amici::check_sigma_positivity (C++ function), [1] amici::compute_nroots (C++ function) amici::ConditionContext (C++ class) amici::ConditionContext::apply_condition (C++ function) amici::ConditionContext::ConditionContext (C++ function) amici::ConditionContext::operator= (C++ function) amici::ConditionContext::restore (C++ function) amici::ConditionContext::~ConditionContext (C++ function) amici::const_N_Vector (C++ type) amici::Constraint (C++ enum) amici::Constraint::negative (C++ enumerator) amici::Constraint::non_negative (C++ enumerator) amici::Constraint::non_positive (C++ enumerator) amici::Constraint::none (C++ enumerator) amici::Constraint::positive (C++ enumerator) amici::ContextManager (C++ class) amici::ContextManager::ContextManager (C++ function), [1], [2] amici::CpuTimer (C++ class) amici::CpuTimer::CpuTimer (C++ function) amici::CpuTimer::elapsed_milliseconds (C++ function) amici::CpuTimer::elapsed_seconds (C++ function) amici::CpuTimer::reset (C++ function) amici::CpuTimer::uses_thread_clock (C++ member) amici::CvodeException (C++ class) amici::CvodeException::CvodeException (C++ function) amici::CVodeSolver (C++ class) amici::CVodeSolver::adj_init (C++ function) amici::CVodeSolver::allocate_solver (C++ function) amici::CVodeSolver::allocate_solver_b (C++ function) amici::CVodeSolver::apply_constraints (C++ function) amici::CVodeSolver::apply_max_conv_fails (C++ function) amici::CVodeSolver::apply_max_nonlin_iters (C++ function) amici::CVodeSolver::apply_max_step_size (C++ function) amici::CVodeSolver::b_init (C++ function) amici::CVodeSolver::boost::serialization::serialize (C++ function) amici::CVodeSolver::calc_ic (C++ function) amici::CVodeSolver::calc_ic_b (C++ function) amici::CVodeSolver::clone (C++ function) amici::CVodeSolver::diag (C++ function) amici::CVodeSolver::diag_b (C++ function) amici::CVodeSolver::get_adj_b_mem (C++ function) amici::CVodeSolver::get_b (C++ function) amici::CVodeSolver::get_class_name (C++ function) amici::CVodeSolver::get_dky (C++ function) amici::CVodeSolver::get_dky_b (C++ function) amici::CVodeSolver::get_last_order (C++ function) amici::CVodeSolver::get_model (C++ function) amici::CVodeSolver::get_num_err_test_fails (C++ function) amici::CVodeSolver::get_num_non_lin_solv_conv_fails (C++ function) amici::CVodeSolver::get_num_rhs_evals (C++ function) amici::CVodeSolver::get_num_steps (C++ function) amici::CVodeSolver::get_quad (C++ function) amici::CVodeSolver::get_quad_b (C++ function) amici::CVodeSolver::get_quad_dky (C++ function) amici::CVodeSolver::get_quad_dky_b (C++ function) amici::CVodeSolver::get_root_info (C++ function) amici::CVodeSolver::get_sens (C++ function) amici::CVodeSolver::get_sens_dky (C++ function) amici::CVodeSolver::init (C++ function) amici::CVodeSolver::init_steady_state (C++ function) amici::CVodeSolver::operator== (C++ function) amici::CVodeSolver::qb_init (C++ function) amici::CVodeSolver::quad_init (C++ function) amici::CVodeSolver::quad_ss_tolerances (C++ function) amici::CVodeSolver::quad_ss_tolerances_b (C++ function) amici::CVodeSolver::reinit (C++ function) amici::CVodeSolver::reinit_b (C++ function) amici::CVodeSolver::reInit_post_process (C++ function) amici::CVodeSolver::reinit_post_process_b (C++ function) amici::CVodeSolver::reinit_post_process_f (C++ function) amici::CVodeSolver::reinit_quad_b (C++ function) amici::CVodeSolver::reset_state (C++ function) amici::CVodeSolver::root_init (C++ function) amici::CVodeSolver::sens_init_1 (C++ function) amici::CVodeSolver::sens_reinit (C++ function) amici::CVodeSolver::sens_toggle_off (C++ function) amici::CVodeSolver::set_band_jac_fn (C++ function) amici::CVodeSolver::set_band_jac_fn_b (C++ function) amici::CVodeSolver::set_dense_jac_fn (C++ function) amici::CVodeSolver::set_dense_jac_fn_b (C++ function) amici::CVodeSolver::set_id (C++ function) amici::CVodeSolver::set_jac_times_vec_fn (C++ function) amici::CVodeSolver::set_jac_times_vec_fn_b (C++ function) amici::CVodeSolver::set_linear_solver (C++ function) amici::CVodeSolver::set_linear_solver_b (C++ function) amici::CVodeSolver::set_max_num_steps (C++ function) amici::CVodeSolver::set_max_num_steps_b (C++ function) amici::CVodeSolver::set_non_linear_solver (C++ function) amici::CVodeSolver::set_non_linear_solver_b (C++ function) amici::CVodeSolver::set_non_linear_solver_sens (C++ function) amici::CVodeSolver::set_quad_err_con (C++ function) amici::CVodeSolver::set_quad_err_con_b (C++ function) amici::CVodeSolver::set_sens_err_con (C++ function) amici::CVodeSolver::set_sens_params (C++ function) amici::CVodeSolver::set_sens_ss_tolerances (C++ function) amici::CVodeSolver::set_sparse_jac_fn (C++ function) amici::CVodeSolver::set_sparse_jac_fn_b (C++ function) amici::CVodeSolver::set_sparse_jac_fn_ss (C++ function) amici::CVodeSolver::set_ss_tolerances (C++ function) amici::CVodeSolver::set_ss_tolerances_b (C++ function) amici::CVodeSolver::set_stab_lim_det (C++ function) amici::CVodeSolver::set_stab_lim_det_b (C++ function) amici::CVodeSolver::set_stop_time (C++ function) amici::CVodeSolver::set_suppress_alg (C++ function) amici::CVodeSolver::set_user_data (C++ function) amici::CVodeSolver::set_user_data_b (C++ function) amici::CVodeSolver::solve (C++ function) amici::CVodeSolver::solve_b (C++ function) amici::CVodeSolver::solve_f (C++ function) amici::CVodeSolver::Solver (C++ function), [1] amici::CVodeSolver::turn_off_root_finding (C++ function) amici::CVodeSolver::~CVodeSolver (C++ function) amici::deserialize_from_char (C++ function) amici::deserialize_from_string (C++ function) amici::DEStateView (C++ struct) amici::DEStateView::DEStateView (C++ function), [1] amici::DEStateView::dx (C++ member) amici::DEStateView::t (C++ member) amici::DEStateView::x (C++ member) amici::Discontinuity (C++ struct) amici::Discontinuity::Discontinuity (C++ function) amici::Discontinuity::dx_post (C++ member) amici::Discontinuity::h_pre (C++ member) amici::Discontinuity::root_info (C++ member) amici::Discontinuity::time (C++ member) amici::Discontinuity::total_cl_pre (C++ member) amici::Discontinuity::x_post (C++ member) amici::Discontinuity::x_pre (C++ member) amici::Discontinuity::xdot_post (C++ member) amici::Discontinuity::xdot_pre (C++ member) amici::dot_prod (C++ function) amici::Event (C++ class) amici::Event::Event (C++ function) amici::Event::get_id (C++ function) amici::Event::get_initial_value (C++ function) amici::Event::get_priority (C++ function) amici::Event::uses_values_from_trigger_time (C++ function) amici::EventHandlingBwdSimulator (C++ class) amici::EventHandlingBwdSimulator::EventHandlingBwdSimulator (C++ function) amici::EventHandlingBwdSimulator::run (C++ function) amici::EventHandlingSimulator (C++ class) amici::EventHandlingSimulator::EventHandlingSimulator (C++ function) amici::EventHandlingSimulator::get_event_counter (C++ function) amici::EventHandlingSimulator::get_root_counter (C++ function) amici::EventHandlingSimulator::get_simulation_state (C++ function) amici::EventHandlingSimulator::handle_events (C++ function) amici::EventHandlingSimulator::handle_initial_events (C++ function) amici::EventHandlingSimulator::it_ (C++ member) amici::EventHandlingSimulator::result (C++ member) amici::EventHandlingSimulator::run (C++ function) amici::EventHandlingSimulator::run_steady_state (C++ function) amici::EventQueue (C++ class) amici::EventQueue::empty (C++ function) amici::EventQueue::EventQueue (C++ function) amici::EventQueue::pop (C++ function) amici::EventQueue::push (C++ function) amici::ExpData (C++ class) amici::ExpData::apply_data_dimension (C++ function) amici::ExpData::apply_dimensions (C++ function) amici::ExpData::apply_event_dimension (C++ function) amici::ExpData::check_data_dimension (C++ function) amici::ExpData::check_events_dimension (C++ function) amici::ExpData::clear_observations (C++ function) amici::ExpData::event_measurements_ (C++ member) amici::ExpData::event_noise_scales_ (C++ member) amici::ExpData::ExpData (C++ function), [1], [2], [3], [4], [5], [6], [7], [8] amici::ExpData::get_event_measurements (C++ function) amici::ExpData::get_event_measurements_ptr (C++ function) amici::ExpData::get_event_noise_scales (C++ function) amici::ExpData::get_event_noise_scales_ptr (C++ function) amici::ExpData::get_measurements (C++ function) amici::ExpData::get_measurements_ptr (C++ function) amici::ExpData::get_noise_scales (C++ function) amici::ExpData::get_noise_scales_ptr (C++ function) amici::ExpData::get_timepoint (C++ function) amici::ExpData::get_timepoints (C++ function) amici::ExpData::id (C++ member) amici::ExpData::is_set_event_measurement (C++ function) amici::ExpData::is_set_event_noise_scale (C++ function) amici::ExpData::is_set_measurement (C++ function) amici::ExpData::is_set_noise_scale (C++ function) amici::ExpData::measurements_ (C++ member) amici::ExpData::nmaxevent (C++ function) amici::ExpData::nmaxevent_ (C++ member) amici::ExpData::noise_scales_ (C++ member) amici::ExpData::nt (C++ function) amici::ExpData::nytrue (C++ function) amici::ExpData::nytrue_ (C++ member) amici::ExpData::nztrue (C++ function) amici::ExpData::nztrue_ (C++ member) amici::ExpData::operator== (C++ function) amici::ExpData::set_event_measurements (C++ function), [1] amici::ExpData::set_event_noise_scales (C++ function), [1], [2], [3] amici::ExpData::set_measurements (C++ function), [1] amici::ExpData::set_noise_scales (C++ function), [1], [2], [3] amici::ExpData::set_timepoints (C++ function) amici::ExpData::~ExpData (C++ function) amici::FinalStateStorer (C++ class) amici::FinalStateStorer::FinalStateStorer (C++ function) amici::FinalStateStorer::operator= (C++ function) amici::FinalStateStorer::~FinalStateStorer (C++ function) amici::FixedParameterContext (C++ enum) amici::FixedParameterContext::preequilibration (C++ enumerator) amici::FixedParameterContext::presimulation (C++ enumerator) amici::FixedParameterContext::simulation (C++ enumerator) amici::ForwardProblem (C++ class) amici::ForwardProblem::edata (C++ member) amici::ForwardProblem::ForwardProblem (C++ function) amici::ForwardProblem::get_adjoint_updates (C++ function) amici::ForwardProblem::get_current_time_iteration (C++ function) amici::ForwardProblem::get_discontinuities (C++ function) amici::ForwardProblem::get_dJzdx (C++ function) amici::ForwardProblem::get_event_counter (C++ function) amici::ForwardProblem::get_final_simulation_state (C++ function) amici::ForwardProblem::get_final_time (C++ function) amici::ForwardProblem::get_initial_simulation_state (C++ function) amici::ForwardProblem::get_posteq_problem (C++ function), [1] amici::ForwardProblem::get_preeq_problem (C++ function), [1] amici::ForwardProblem::get_presimulation_result (C++ function) amici::ForwardProblem::get_simulation_state_event (C++ function) amici::ForwardProblem::get_simulation_state_timepoint (C++ function) amici::ForwardProblem::get_state_sensitivity (C++ function) amici::ForwardProblem::model (C++ member) amici::ForwardProblem::run (C++ function) amici::ForwardProblem::solver (C++ member) amici::ForwardProblem::was_preequilibrated (C++ function) amici::ForwardProblem::~ForwardProblem (C++ function) amici::FwdSimWorkspace (C++ struct) amici::FwdSimWorkspace::FwdSimWorkspace (C++ function) amici::FwdSimWorkspace::nroots (C++ member) amici::FwdSimWorkspace::pending_events (C++ member) amici::FwdSimWorkspace::roots_found (C++ member) amici::FwdSimWorkspace::rootvals (C++ member) amici::FwdSimWorkspace::rval_tmp (C++ member) amici::FwdSimWorkspace::sdx (C++ member) amici::FwdSimWorkspace::sol (C++ member) amici::FwdSimWorkspace::stau (C++ member) amici::FwdSimWorkspace::tlastroot (C++ member) amici::FwdSimWorkspace::x_old (C++ member) amici::FwdSimWorkspace::xdot (C++ member) amici::FwdSimWorkspace::xdot_old (C++ member) amici::get_backtrace_string (C++ function) amici::hdf5::attribute_exists (C++ function), [1] amici::hdf5::create_and_write_double_1d_dataset (C++ function) amici::hdf5::create_and_write_double_2d_dataset (C++ function) amici::hdf5::create_and_write_double_3d_dataset (C++ function) amici::hdf5::create_and_write_int_1d_dataset (C++ function) amici::hdf5::create_and_write_int_2d_dataset (C++ function) amici::hdf5::create_group (C++ function) amici::hdf5::create_or_open_for_writing (C++ function) amici::hdf5::get_double_1d_dataset (C++ function) amici::hdf5::get_double_2d_dataset (C++ function) amici::hdf5::get_double_3d_dataset (C++ function) amici::hdf5::get_double_scalar_attribute (C++ function) amici::hdf5::get_int_1d_dataset (C++ function) amici::hdf5::get_int_scalar_attribute (C++ function) amici::hdf5::get_string_attribute (C++ function) amici::hdf5::location_exists (C++ function), [1] amici::hdf5::read_exp_data_from_hdf5 (C++ function) amici::hdf5::read_model_data_from_hdf5 (C++ function), [1] amici::hdf5::read_solver_settings_from_hdf5 (C++ function), [1] amici::hdf5::write_exp_data_to_hdf5 (C++ function), [1] amici::hdf5::write_log_items_to_hdf5 (C++ function) amici::hdf5::write_return_data_diagnosis (C++ function) amici::hdf5::write_return_data_to_hdf5 (C++ function), [1] amici::hdf5::write_solver_settings_to_hdf5 (C++ function), [1] amici::heaviside_differs (C++ function) amici::HermiteSpline (C++ class) amici::HermiteSpline::compute_coefficients (C++ function) amici::HermiteSpline::compute_coefficients_sensi (C++ function) amici::HermiteSpline::compute_final_sensitivity (C++ function) amici::HermiteSpline::compute_final_value (C++ function) amici::HermiteSpline::get_node_derivative (C++ function) amici::HermiteSpline::get_node_derivative_by_fd (C++ function) amici::HermiteSpline::get_node_derivative_scaled (C++ function) amici::HermiteSpline::get_sensitivity_scaled (C++ function) amici::HermiteSpline::get_value_scaled (C++ function) amici::HermiteSpline::HermiteSpline (C++ function), [1] amici::IDAException (C++ class) amici::IDAException::IDAException (C++ function) amici::IDASolver (C++ class) amici::IDASolver::adj_init (C++ function) amici::IDASolver::allocate_solver (C++ function) amici::IDASolver::allocate_solver_b (C++ function) amici::IDASolver::apply_constraints (C++ function) amici::IDASolver::apply_max_conv_fails (C++ function) amici::IDASolver::apply_max_nonlin_iters (C++ function) amici::IDASolver::apply_max_step_size (C++ function) amici::IDASolver::b_init (C++ function) amici::IDASolver::calc_ic (C++ function) amici::IDASolver::calc_ic_b (C++ function) amici::IDASolver::clone (C++ function) amici::IDASolver::diag (C++ function) amici::IDASolver::diag_b (C++ function) amici::IDASolver::get_adj_b_mem (C++ function) amici::IDASolver::get_b (C++ function) amici::IDASolver::get_class_name (C++ function) amici::IDASolver::get_dky (C++ function) amici::IDASolver::get_dky_b (C++ function) amici::IDASolver::get_last_order (C++ function) amici::IDASolver::get_model (C++ function) amici::IDASolver::get_num_err_test_fails (C++ function) amici::IDASolver::get_num_non_lin_solv_conv_fails (C++ function) amici::IDASolver::get_num_rhs_evals (C++ function) amici::IDASolver::get_num_steps (C++ function) amici::IDASolver::get_quad (C++ function) amici::IDASolver::get_quad_b (C++ function) amici::IDASolver::get_quad_dky (C++ function) amici::IDASolver::get_quad_dky_b (C++ function) amici::IDASolver::get_root_info (C++ function) amici::IDASolver::get_sens (C++ function) amici::IDASolver::get_sens_dky (C++ function) amici::IDASolver::init (C++ function) amici::IDASolver::init_steady_state (C++ function) amici::IDASolver::qb_init (C++ function) amici::IDASolver::quad_init (C++ function) amici::IDASolver::quad_ss_tolerances (C++ function) amici::IDASolver::quad_ss_tolerances_b (C++ function) amici::IDASolver::reinit (C++ function) amici::IDASolver::reinit_b (C++ function) amici::IDASolver::reinit_post_process (C++ function) amici::IDASolver::reinit_post_process_b (C++ function) amici::IDASolver::reinit_post_process_f (C++ function) amici::IDASolver::reinit_quad_b (C++ function) amici::IDASolver::reset_state (C++ function) amici::IDASolver::root_init (C++ function) amici::IDASolver::sens_init_1 (C++ function) amici::IDASolver::sens_reinit (C++ function) amici::IDASolver::sens_toggle_off (C++ function) amici::IDASolver::set_band_jac_fn (C++ function) amici::IDASolver::set_band_jac_fn_b (C++ function) amici::IDASolver::set_dense_jac_fn (C++ function) amici::IDASolver::set_dense_jac_fn_b (C++ function) amici::IDASolver::set_id (C++ function) amici::IDASolver::set_jac_times_vec_fn (C++ function) amici::IDASolver::set_jac_times_vec_fn_b (C++ function) amici::IDASolver::set_linear_solver (C++ function) amici::IDASolver::set_linear_solver_b (C++ function) amici::IDASolver::set_max_num_steps (C++ function) amici::IDASolver::set_max_num_steps_b (C++ function) amici::IDASolver::set_non_linear_solver (C++ function) amici::IDASolver::set_non_linear_solver_b (C++ function) amici::IDASolver::set_non_linear_solver_sens (C++ function) amici::IDASolver::set_quad_err_con (C++ function) amici::IDASolver::set_quad_err_con_b (C++ function) amici::IDASolver::set_sens_err_con (C++ function) amici::IDASolver::set_sens_params (C++ function) amici::IDASolver::set_sens_ss_tolerances (C++ function) amici::IDASolver::set_sparse_jac_fn (C++ function) amici::IDASolver::set_sparse_jac_fn_b (C++ function) amici::IDASolver::set_sparse_jac_fn_ss (C++ function) amici::IDASolver::set_ss_tolerances (C++ function) amici::IDASolver::set_ss_tolerances_b (C++ function) amici::IDASolver::set_stab_lim_det (C++ function) amici::IDASolver::set_stab_lim_det_b (C++ function) amici::IDASolver::set_stop_time (C++ function) amici::IDASolver::set_suppress_alg (C++ function) amici::IDASolver::set_user_data (C++ function) amici::IDASolver::set_user_data_b (C++ function) amici::IDASolver::solve (C++ function) amici::IDASolver::solve_b (C++ function) amici::IDASolver::solve_f (C++ function) amici::IDASolver::Solver (C++ function), [1] amici::IDASolver::turn_off_root_finding (C++ function) amici::IDASolver::~IDASolver (C++ function) amici::IntegrationFailure (C++ class) amici::IntegrationFailure::error_code (C++ member) amici::IntegrationFailure::IntegrationFailure (C++ function) amici::IntegrationFailure::time (C++ member) amici::IntegrationFailureB (C++ class) amici::IntegrationFailureB::error_code (C++ member) amici::IntegrationFailureB::IntegrationFailureB (C++ function) amici::IntegrationFailureB::time (C++ member) amici::InternalSensitivityMethod (C++ enum) amici::InternalSensitivityMethod::simultaneous (C++ enumerator) amici::InternalSensitivityMethod::staggered (C++ enumerator) amici::InternalSensitivityMethod::staggered1 (C++ enumerator) amici::InterpolationType (C++ enum) amici::InterpolationType::hermite (C++ enumerator) amici::InterpolationType::polynomial (C++ enumerator) amici::is_equal (C++ function) amici::linear_sum (C++ function) amici::LinearMultistepMethod (C++ enum) amici::LinearMultistepMethod::adams (C++ enumerator) amici::LinearMultistepMethod::BDF (C++ enumerator) amici::LinearSolver (C++ enum) amici::LinearSolver::band (C++ enumerator) amici::LinearSolver::dense (C++ enumerator) amici::LinearSolver::diag (C++ enumerator) amici::LinearSolver::KLU (C++ enumerator) amici::LinearSolver::LAPACKBand (C++ enumerator) amici::LinearSolver::LAPACKDense (C++ enumerator) amici::LinearSolver::SPBCG (C++ enumerator) amici::LinearSolver::SPGMR (C++ enumerator) amici::LinearSolver::SPTFQMR (C++ enumerator) amici::LinearSolver::SuperLUMT (C++ enumerator) amici::Logger (C++ class) amici::Logger::items (C++ member) amici::Logger::log (C++ function), [1] amici::Logger::Logger (C++ function) amici::LogItem (C++ struct) amici::LogItem::identifier (C++ member) amici::LogItem::LogItem (C++ function), [1] amici::LogItem::message (C++ member) amici::LogItem::severity (C++ member) amici::LogSeverity (C++ enum) amici::LogSeverity::debug (C++ enumerator) amici::LogSeverity::error (C++ enumerator) amici::LogSeverity::warning (C++ enumerator) amici::Model (C++ class) amici::Model::add_adjoint_quadrature_event_update (C++ function) amici::Model::add_adjoint_state_event_update (C++ function) amici::Model::add_event_objective (C++ function) amici::Model::add_event_objective_regularization (C++ function) amici::Model::add_event_objective_sensitivity (C++ function) amici::Model::add_observable_objective (C++ function) amici::Model::add_observable_objective_sensitivity (C++ function) amici::Model::add_partial_event_objective_sensitivity (C++ function) amici::Model::add_partial_observable_objective_sensitivity (C++ function) amici::Model::add_state_event_update (C++ function) amici::Model::add_state_sensitivity_event_update (C++ function) amici::Model::always_check_finite_ (C++ member) amici::Model::any_state_non_negative_ (C++ member) amici::Model::boost::serialization::serialize (C++ function) amici::Model::check_finite (C++ function), [1], [2] amici::Model::check_llh_buffer_size (C++ function) amici::Model::clone (C++ function) amici::Model::compute_x_pos (C++ function), [1] amici::Model::derived_state_ (C++ member) amici::Model::fdeltaqB (C++ function) amici::Model::fdeltasx (C++ function) amici::Model::fdeltax (C++ function) amici::Model::fdeltaxB (C++ function) amici::Model::fdJrzdsigma (C++ function), [1] amici::Model::fdJrzdz (C++ function), [1] amici::Model::fdJydp (C++ function) amici::Model::fdJydsigma (C++ function), [1] amici::Model::fdJydx (C++ function) amici::Model::fdJydy (C++ function), [1] amici::Model::fdJydy_colptrs (C++ function) amici::Model::fdJydy_rowvals (C++ function) amici::Model::fdJzdp (C++ function) amici::Model::fdJzdsigma (C++ function), [1] amici::Model::fdJzdx (C++ function) amici::Model::fdJzdz (C++ function), [1] amici::Model::fdrzdp (C++ function), [1] amici::Model::fdrzdx (C++ function), [1] amici::Model::fdsigmaydp (C++ function), [1] amici::Model::fdsigmaydy (C++ function), [1] amici::Model::fdsigmazdp (C++ function), [1] amici::Model::fdtotal_cldp (C++ function) amici::Model::fdtotal_cldx_rdata (C++ function) amici::Model::fdtotal_cldx_rdata_colptrs (C++ function) amici::Model::fdtotal_cldx_rdata_rowvals (C++ function) amici::Model::fdwdp (C++ function), [1] amici::Model::fdwdp_colptrs (C++ function) amici::Model::fdwdp_rowvals (C++ function) amici::Model::fdwdw (C++ function), [1] amici::Model::fdwdw_colptrs (C++ function) amici::Model::fdwdw_rowvals (C++ function) amici::Model::fdwdx (C++ function), [1] amici::Model::fdwdx_colptrs (C++ function) amici::Model::fdwdx_rowvals (C++ function) amici::Model::fdx_rdatadp (C++ function) amici::Model::fdx_rdatadtcl (C++ function) amici::Model::fdx_rdatadtcl_colptrs (C++ function) amici::Model::fdx_rdatadtcl_rowvals (C++ function) amici::Model::fdx_rdatadx_solver (C++ function) amici::Model::fdx_rdatadx_solver_colptrs (C++ function) amici::Model::fdx_rdatadx_solver_rowvals (C++ function) amici::Model::fdydp (C++ function), [1] amici::Model::fdydx (C++ function), [1] amici::Model::fdzdp (C++ function), [1] amici::Model::fdzdx (C++ function), [1] amici::Model::fexplicit_roots (C++ function) amici::Model::fJrz (C++ function) amici::Model::fJy (C++ function) amici::Model::fJz (C++ function) amici::Model::frz (C++ function), [1] amici::Model::fsdx0 (C++ function) amici::Model::fsigmay (C++ function), [1] amici::Model::fsigmaz (C++ function), [1] amici::Model::fspl (C++ function) amici::Model::fsrz (C++ function) amici::Model::fsspl (C++ function) amici::Model::fstau (C++ function) amici::Model::fstotal_cl (C++ function) amici::Model::fsx0 (C++ function), [1] amici::Model::fsx0_fixedParameters (C++ function), [1] amici::Model::fsx_rdata (C++ function), [1] amici::Model::fsx_solver (C++ function) amici::Model::fsz (C++ function) amici::Model::ftotal_cl (C++ function) amici::Model::fw (C++ function), [1] amici::Model::fx0 (C++ function), [1] amici::Model::fx0_fixedParameters (C++ function), [1] amici::Model::fx_rdata (C++ function), [1] amici::Model::fx_solver (C++ function) amici::Model::fy (C++ function), [1] amici::Model::fz (C++ function), [1] amici::Model::get_add_sigma_residuals (C++ function) amici::Model::get_adjoint_state_event_update (C++ function) amici::Model::get_adjoint_state_observable_update (C++ function) amici::Model::get_always_check_finite (C++ function) amici::Model::get_any_state_nonnegative (C++ function) amici::Model::get_dxdotdp_full (C++ function) amici::Model::get_event (C++ function), [1] amici::Model::get_event_regularization (C++ function) amici::Model::get_event_regularization_sensitivity (C++ function) amici::Model::get_event_sensitivity (C++ function) amici::Model::get_event_sigma (C++ function) amici::Model::get_event_sigma_sensitivity (C++ function) amici::Model::get_event_time_sensitivity (C++ function) amici::Model::get_explicit_roots (C++ function) amici::Model::get_expression (C++ function) amici::Model::get_expression_ids (C++ function) amici::Model::get_expression_names (C++ function) amici::Model::get_fixed_parameter_by_id (C++ function) amici::Model::get_fixed_parameter_by_name (C++ function) amici::Model::get_fixed_parameter_ids (C++ function) amici::Model::get_fixed_parameter_names (C++ function) amici::Model::get_fixed_parameters (C++ function) amici::Model::get_free_parameter_by_id (C++ function) amici::Model::get_free_parameter_by_name (C++ function) amici::Model::get_free_parameter_ids (C++ function) amici::Model::get_free_parameter_names (C++ function) amici::Model::get_free_parameters (C++ function) amici::Model::get_id_list (C++ function) amici::Model::get_initial_state (C++ function), [1] amici::Model::get_initial_state_sensitivities (C++ function), [1] amici::Model::get_logger (C++ function) amici::Model::get_minimum_sigma_residuals (C++ function) amici::Model::get_model_state (C++ function) amici::Model::get_name (C++ function) amici::Model::get_observable (C++ function) amici::Model::get_observable_ids (C++ function) amici::Model::get_observable_names (C++ function) amici::Model::get_observable_scaling (C++ function) amici::Model::get_observable_sensitivity (C++ function) amici::Model::get_observable_sigma (C++ function) amici::Model::get_observable_sigma_sensitivity (C++ function) amici::Model::get_parameter_list (C++ function) amici::Model::get_parameter_scale (C++ function) amici::Model::get_reinitialization_state_idxs (C++ function) amici::Model::get_reinitialize_fixed_parameter_initial_states (C++ function) amici::Model::get_second_order_mode (C++ function) amici::Model::get_state_ids (C++ function) amici::Model::get_state_ids_solver (C++ function) amici::Model::get_state_is_non_negative (C++ function) amici::Model::get_state_names (C++ function) amici::Model::get_state_names_solver (C++ function) amici::Model::get_steady_state_computation_mode (C++ function) amici::Model::get_steady_state_sensitivity_mode (C++ function) amici::Model::get_steadystate_mask (C++ function) amici::Model::get_timepoint (C++ function) amici::Model::get_timepoints (C++ function) amici::Model::get_trigger_timepoints (C++ function) amici::Model::get_unobserved_event_sensitivity (C++ function) amici::Model::get_unscaled_parameters (C++ function) amici::Model::has_custom_initial_state (C++ function) amici::Model::has_custom_initial_state_sensitivities (C++ function) amici::Model::has_expression_ids (C++ function) amici::Model::has_expression_names (C++ function) amici::Model::has_fixed_parameter_ids (C++ function) amici::Model::has_fixed_parameter_names (C++ function) amici::Model::has_free_parameter_ids (C++ function) amici::Model::has_free_parameter_names (C++ function) amici::Model::has_observable_ids (C++ function) amici::Model::has_observable_names (C++ function) amici::Model::has_quadratic_llh (C++ function) amici::Model::has_state_ids (C++ function) amici::Model::has_state_names (C++ function) amici::Model::initialize (C++ function) amici::Model::initialize_b (C++ function) amici::Model::initialize_events (C++ function) amici::Model::initialize_spline_sensitivities (C++ function) amici::Model::initialize_splines (C++ function) amici::Model::initialize_state (C++ function) amici::Model::initialize_state_sensitivities (C++ function) amici::Model::initialize_vectors (C++ function) amici::Model::k (C++ function) amici::Model::min_sigma_ (C++ member) amici::Model::Model (C++ function), [1] amici::Model::n_max_event (C++ function) amici::Model::ncl (C++ function) amici::Model::nk (C++ function) amici::Model::nmaxevent_ (C++ member) amici::Model::np (C++ function) amici::Model::nplist (C++ function) amici::Model::nt (C++ function) amici::Model::nx_reinit (C++ function) amici::Model::operator= (C++ function) amici::Model::operator== (C++ function) amici::Model::plist (C++ function) amici::Model::reinit_events (C++ function) amici::Model::reinit_explicit_roots (C++ function) amici::Model::reinitialize (C++ function) amici::Model::require_sensitivities_for_all_parameters (C++ function) amici::Model::set_add_sigma_residuals (C++ function) amici::Model::set_all_states_non_negative (C++ function) amici::Model::set_always_check_finite (C++ function) amici::Model::set_fixed_parameter_by_id (C++ function) amici::Model::set_fixed_parameter_by_name (C++ function) amici::Model::set_fixed_parameters (C++ function) amici::Model::set_fixed_parameters_by_id_regex (C++ function) amici::Model::set_fixed_parameters_by_name_regex (C++ function) amici::Model::set_free_parameter_by_id (C++ function), [1] amici::Model::set_free_parameter_by_name (C++ function), [1] amici::Model::set_free_parameters (C++ function) amici::Model::set_free_parameters_by_id_regex (C++ function) amici::Model::set_free_parameters_by_name_regex (C++ function) amici::Model::set_initial_state (C++ function) amici::Model::set_initial_state_sensitivities (C++ function) amici::Model::set_logger (C++ function) amici::Model::set_minimum_sigma_residuals (C++ function) amici::Model::set_model_state (C++ function) amici::Model::set_n_max_event (C++ function) amici::Model::set_parameter_list (C++ function) amici::Model::set_parameter_scale (C++ function), [1] amici::Model::set_reinitialization_state_idxs (C++ function) amici::Model::set_reinitialize_fixed_parameter_initial_states (C++ function) amici::Model::set_state_is_non_negative (C++ function) amici::Model::set_steady_state_computation_mode (C++ function) amici::Model::set_steady_state_sensitivity_mode (C++ function) amici::Model::set_steadystate_mask (C++ function) amici::Model::set_t0 (C++ function) amici::Model::set_t0_preeq (C++ function) amici::Model::set_timepoints (C++ function) amici::Model::set_unscaled_initial_state_sensitivities (C++ function) amici::Model::sigma_res_ (C++ member) amici::Model::splines_ (C++ member) amici::Model::state_ (C++ member) amici::Model::state_is_non_negative_ (C++ member) amici::Model::steadystate_computation_mode_ (C++ member) amici::Model::steadystate_sensitivity_mode_ (C++ member) amici::Model::sx0data_ (C++ member) amici::Model::t0 (C++ function) amici::Model::t0_preeq (C++ function) amici::Model::update_heaviside (C++ function) amici::Model::write_llh_sensitivity_slice (C++ function) amici::Model::write_sensitivity_slice_event (C++ function)

amici::Model::write_slice_event (C++ function) amici::Model::x0data_ (C++ member) amici::Model::z2event_ (C++ member) amici::Model::~Model (C++ function) amici::Model_DAE (C++ class) amici::Model_DAE::create_solver (C++ function) amici::Model_DAE::fdxdotdp (C++ function), [1], [2] amici::Model_DAE::fdxdotdp_explicit (C++ function) amici::Model_DAE::fdxdotdp_explicit_colptrs (C++ function) amici::Model_DAE::fdxdotdp_explicit_rowvals (C++ function) amici::Model_DAE::fdxdotdw (C++ function), [1] amici::Model_DAE::fdxdotdw_colptrs (C++ function) amici::Model_DAE::fdxdotdw_rowvals (C++ function) amici::Model_DAE::fdxdotdx_explicit (C++ function) amici::Model_DAE::fdxdotdx_explicit_colptrs (C++ function) amici::Model_DAE::fdxdotdx_explicit_rowvals (C++ function) amici::Model_DAE::fJ (C++ function), [1] amici::Model_DAE::fJB (C++ function), [1] amici::Model_DAE::fJDiag (C++ function) amici::Model_DAE::fJSparse (C++ function), [1], [2] amici::Model_DAE::fJSparseB (C++ function), [1] amici::Model_DAE::fJSparseB_ss (C++ function) amici::Model_DAE::fJv (C++ function), [1] amici::Model_DAE::fJvB (C++ function) amici::Model_DAE::fM (C++ function), [1] amici::Model_DAE::fqBdot (C++ function) amici::Model_DAE::fqBdot_ss (C++ function) amici::Model_DAE::froot (C++ function), [1], [2] amici::Model_DAE::fsxdot (C++ function), [1] amici::Model_DAE::fxBdot (C++ function) amici::Model_DAE::fxBdot_ss (C++ function), [1] amici::Model_DAE::fxdot (C++ function), [1], [2] amici::Model_DAE::Model_DAE (C++ function), [1] amici::Model_DAE::write_steady_state_JB (C++ function) amici::Model_ODE (C++ class) amici::Model_ODE::create_solver (C++ function) amici::Model_ODE::fdxdotdp (C++ function), [1] amici::Model_ODE::fdxdotdp_explicit (C++ function) amici::Model_ODE::fdxdotdp_explicit_colptrs (C++ function) amici::Model_ODE::fdxdotdp_explicit_rowvals (C++ function) amici::Model_ODE::fdxdotdw (C++ function), [1] amici::Model_ODE::fdxdotdw_colptrs (C++ function) amici::Model_ODE::fdxdotdw_rowvals (C++ function) amici::Model_ODE::fdxdotdx_explicit (C++ function) amici::Model_ODE::fdxdotdx_explicit_colptrs (C++ function) amici::Model_ODE::fdxdotdx_explicit_rowvals (C++ function) amici::Model_ODE::fJ (C++ function), [1] amici::Model_ODE::fJB (C++ function), [1] amici::Model_ODE::fJDiag (C++ function), [1] amici::Model_ODE::fJSparse (C++ function), [1], [2] amici::Model_ODE::fJSparse_colptrs (C++ function) amici::Model_ODE::fJSparse_rowvals (C++ function) amici::Model_ODE::fJSparseB (C++ function), [1] amici::Model_ODE::fJSparseB_ss (C++ function) amici::Model_ODE::fJv (C++ function), [1] amici::Model_ODE::fJvB (C++ function) amici::Model_ODE::fqBdot (C++ function) amici::Model_ODE::fqBdot_ss (C++ function) amici::Model_ODE::froot (C++ function), [1], [2] amici::Model_ODE::fsxdot (C++ function), [1] amici::Model_ODE::fxBdot (C++ function) amici::Model_ODE::fxBdot_ss (C++ function), [1] amici::Model_ODE::fxdot (C++ function), [1], [2] amici::Model_ODE::Model_ODE (C++ function), [1] amici::Model_ODE::write_steady_state_JB (C++ function) amici::model_quantity_to_str (C++ member) amici::ModelContext (C++ class) amici::ModelContext::ModelContext (C++ function) amici::ModelContext::operator= (C++ function) amici::ModelContext::restore (C++ function) amici::ModelContext::~ModelContext (C++ function) amici::ModelDimensions (C++ struct) amici::ModelDimensions::lbw (C++ member) amici::ModelDimensions::ndJydy (C++ member) amici::ModelDimensions::ndtotal_cldx_rdata (C++ member) amici::ModelDimensions::ndwdp (C++ member) amici::ModelDimensions::ndwdw (C++ member) amici::ModelDimensions::ndwdx (C++ member) amici::ModelDimensions::ndxdotdp_explicit (C++ member) amici::ModelDimensions::ndxdotdw (C++ member) amici::ModelDimensions::ndxdotdx_explicit (C++ member) amici::ModelDimensions::ndxrdatadtcl (C++ member) amici::ModelDimensions::ndxrdatadxsolver (C++ member) amici::ModelDimensions::ne (C++ member) amici::ModelDimensions::ne_solver (C++ member) amici::ModelDimensions::nJ (C++ member) amici::ModelDimensions::nk (C++ member) amici::ModelDimensions::nnz (C++ member) amici::ModelDimensions::np (C++ member) amici::ModelDimensions::nspl (C++ member) amici::ModelDimensions::nw (C++ member) amici::ModelDimensions::nx_rdata (C++ member) amici::ModelDimensions::nx_solver (C++ member) amici::ModelDimensions::nx_solver_reinit (C++ member) amici::ModelDimensions::nxtrue_rdata (C++ member) amici::ModelDimensions::nxtrue_solver (C++ member) amici::ModelDimensions::ny (C++ member) amici::ModelDimensions::nytrue (C++ member) amici::ModelDimensions::nz (C++ member) amici::ModelDimensions::nztrue (C++ member) amici::ModelDimensions::ubw (C++ member) amici::ModelDimensions::validate (C++ function) amici::ModelDimensions::w_recursion_depth (C++ member) amici::ModelQuantity (C++ enum) amici::ModelQuantity::deltaqB (C++ enumerator) amici::ModelQuantity::deltasx (C++ enumerator) amici::ModelQuantity::deltax (C++ enumerator) amici::ModelQuantity::deltaxB (C++ enumerator) amici::ModelQuantity::dJrzdsigma (C++ enumerator) amici::ModelQuantity::dJrzdx (C++ enumerator) amici::ModelQuantity::dJrzdz (C++ enumerator) amici::ModelQuantity::dJydsigma (C++ enumerator) amici::ModelQuantity::dJydx (C++ enumerator) amici::ModelQuantity::dJydy (C++ enumerator) amici::ModelQuantity::dJzdsigma (C++ enumerator) amici::ModelQuantity::dJzdx (C++ enumerator) amici::ModelQuantity::dJzdz (C++ enumerator) amici::ModelQuantity::drzdp (C++ enumerator) amici::ModelQuantity::drzdx (C++ enumerator) amici::ModelQuantity::dsigmaydp (C++ enumerator) amici::ModelQuantity::dsigmaydy (C++ enumerator) amici::ModelQuantity::dsigmazdp (C++ enumerator) amici::ModelQuantity::dwdp (C++ enumerator) amici::ModelQuantity::dwdw (C++ enumerator) amici::ModelQuantity::dwdx (C++ enumerator) amici::ModelQuantity::dydp (C++ enumerator) amici::ModelQuantity::dydx (C++ enumerator) amici::ModelQuantity::dzdp (C++ enumerator) amici::ModelQuantity::dzdx (C++ enumerator) amici::ModelQuantity::J (C++ enumerator) amici::ModelQuantity::JB (C++ enumerator) amici::ModelQuantity::JDiag (C++ enumerator) amici::ModelQuantity::JSparseB_ss (C++ enumerator) amici::ModelQuantity::Jv (C++ enumerator) amici::ModelQuantity::JvB (C++ enumerator) amici::ModelQuantity::k (C++ enumerator) amici::ModelQuantity::p (C++ enumerator) amici::ModelQuantity::qBdot (C++ enumerator) amici::ModelQuantity::qBdot_ss (C++ enumerator) amici::ModelQuantity::root (C++ enumerator) amici::ModelQuantity::srz (C++ enumerator) amici::ModelQuantity::ssigmay (C++ enumerator) amici::ModelQuantity::ssigmaz (C++ enumerator) amici::ModelQuantity::sx (C++ enumerator) amici::ModelQuantity::sxdot (C++ enumerator) amici::ModelQuantity::sy (C++ enumerator) amici::ModelQuantity::sz (C++ enumerator) amici::ModelQuantity::ts (C++ enumerator) amici::ModelQuantity::w (C++ enumerator) amici::ModelQuantity::x (C++ enumerator) amici::ModelQuantity::x0 (C++ enumerator) amici::ModelQuantity::x0_rdata (C++ enumerator) amici::ModelQuantity::x_rdata (C++ enumerator) amici::ModelQuantity::xBdot (C++ enumerator) amici::ModelQuantity::xBdot_ss (C++ enumerator) amici::ModelQuantity::xdot (C++ enumerator) amici::ModelQuantity::y (C++ enumerator) amici::ModelState (C++ struct) amici::ModelState::fixed_parameters (C++ member) amici::ModelState::h (C++ member) amici::ModelState::ModelState (C++ function), [1] amici::ModelState::plist (C++ member) amici::ModelState::stotal_cl (C++ member) amici::ModelState::total_cl (C++ member) amici::ModelState::unscaled_parameters (C++ member) amici::ModelStateDerived (C++ struct) amici::ModelStateDerived::deltaqB_ (C++ member) amici::ModelStateDerived::deltasx_ (C++ member) amici::ModelStateDerived::deltax_ (C++ member) amici::ModelStateDerived::deltaxB_ (C++ member) amici::ModelStateDerived::dfdx_ (C++ member) amici::ModelStateDerived::dJrzdsigma_ (C++ member) amici::ModelStateDerived::dJrzdz_ (C++ member) amici::ModelStateDerived::dJydp_ (C++ member) amici::ModelStateDerived::dJydsigma_ (C++ member) amici::ModelStateDerived::dJydx_ (C++ member) amici::ModelStateDerived::dJydy_ (C++ member) amici::ModelStateDerived::dJydy_dense_ (C++ member) amici::ModelStateDerived::dJzdp_ (C++ member) amici::ModelStateDerived::dJzdsigma_ (C++ member) amici::ModelStateDerived::dJzdx_ (C++ member) amici::ModelStateDerived::dJzdz_ (C++ member) amici::ModelStateDerived::drzdp_ (C++ member) amici::ModelStateDerived::drzdx_ (C++ member) amici::ModelStateDerived::dsigmaydp_ (C++ member) amici::ModelStateDerived::dsigmaydy_ (C++ member) amici::ModelStateDerived::dsigmazdp_ (C++ member) amici::ModelStateDerived::dtotal_cldx_rdata (C++ member) amici::ModelStateDerived::dwdp_ (C++ member) amici::ModelStateDerived::dwdp_hierarchical_ (C++ member) amici::ModelStateDerived::dwdw_ (C++ member) amici::ModelStateDerived::dwdx_ (C++ member) amici::ModelStateDerived::dwdx_hierarchical_ (C++ member) amici::ModelStateDerived::dx_rdatadtcl (C++ member) amici::ModelStateDerived::dx_rdatadx_solver (C++ member) amici::ModelStateDerived::dxdotdp (C++ member) amici::ModelStateDerived::dxdotdp_explicit (C++ member) amici::ModelStateDerived::dxdotdp_full (C++ member) amici::ModelStateDerived::dxdotdp_implicit (C++ member) amici::ModelStateDerived::dxdotdw_ (C++ member) amici::ModelStateDerived::dxdotdx_explicit (C++ member) amici::ModelStateDerived::dxdotdx_implicit (C++ member) amici::ModelStateDerived::dydp_ (C++ member) amici::ModelStateDerived::dydx_ (C++ member) amici::ModelStateDerived::dzdp_ (C++ member) amici::ModelStateDerived::dzdx_ (C++ member) amici::ModelStateDerived::J_ (C++ member) amici::ModelStateDerived::JB_ (C++ member) amici::ModelStateDerived::ModelStateDerived (C++ function), [1], [2] amici::ModelStateDerived::MSparse_ (C++ member) amici::ModelStateDerived::rz_ (C++ member) amici::ModelStateDerived::sigmay_ (C++ member) amici::ModelStateDerived::sigmaz_ (C++ member) amici::ModelStateDerived::spl_ (C++ member) amici::ModelStateDerived::sspl_ (C++ member) amici::ModelStateDerived::sunctx_ (C++ member) amici::ModelStateDerived::sx_ (C++ member) amici::ModelStateDerived::sx_rdata_ (C++ member) amici::ModelStateDerived::sy_ (C++ member) amici::ModelStateDerived::w_ (C++ member) amici::ModelStateDerived::x_pos_tmp_ (C++ member) amici::ModelStateDerived::x_rdata_ (C++ member) amici::ModelStateDerived::y_ (C++ member) amici::ModelStateDerived::z_ (C++ member) amici::N_VGetArrayPointerConst (C++ function) amici::NewtonDampingFactorMode (C++ enum) amici::NewtonDampingFactorMode::off (C++ enumerator) amici::NewtonDampingFactorMode::on (C++ enumerator) amici::NewtonFailure (C++ class) amici::NewtonFailure::error_code (C++ member) amici::NewtonFailure::NewtonFailure (C++ function) amici::NewtonsMethod (C++ class) amici::NewtonsMethod::compute_step (C++ function) amici::NewtonsMethod::get_delta (C++ function) amici::NewtonsMethod::get_num_steps (C++ function) amici::NewtonsMethod::get_wrms (C++ function) amici::NewtonsMethod::NewtonsMethod (C++ function) amici::NewtonsMethod::run (C++ function) amici::NewtonSolver (C++ class) amici::NewtonSolver::compute_newton_sensis (C++ function) amici::NewtonSolver::get_step (C++ function) amici::NewtonSolver::is_singular (C++ function) amici::NewtonSolver::NewtonSolver (C++ function), [1] amici::NewtonSolver::operator= (C++ function) amici::NewtonSolver::prepare_linear_system (C++ function) amici::NewtonSolver::prepare_linear_system_b (C++ function) amici::NewtonSolver::reinitialize (C++ function) amici::NewtonSolver::solve_linear_system (C++ function) amici::NonlinearSolverIteration (C++ enum) amici::NonlinearSolverIteration::fixedpoint (C++ enumerator) amici::NonlinearSolverIteration::newton (C++ enumerator) amici::ObservableScaling (C++ enum) amici::ObservableScaling::lin (C++ enumerator) amici::ObservableScaling::log (C++ enumerator) amici::ObservableScaling::log10 (C++ enumerator) amici::operator<< (C++ function), [1], [2] amici::operator== (C++ function), [1], [2], [3], [4], [5] amici::ParameterScaling (C++ enum) amici::ParameterScaling::ln (C++ enumerator) amici::ParameterScaling::log10 (C++ enumerator) amici::ParameterScaling::none (C++ enumerator) amici::PendingEvent (C++ struct) amici::PendingEvent::event (C++ member) amici::PendingEvent::idx (C++ member) amici::PendingEvent::state_old (C++ member) amici::PeriodResult (C++ struct) amici::PeriodResult::discs (C++ member) amici::PeriodResult::event_states_ (C++ member) amici::PeriodResult::final_state_ (C++ member) amici::PeriodResult::initial_state_ (C++ member) amici::PeriodResult::timepoint_states_ (C++ member) amici::pi (C++ member) amici::printf_to_string (C++ function) amici::RDataReporting (C++ enum) amici::RDataReporting::full (C++ enumerator) amici::RDataReporting::likelihood (C++ enumerator) amici::RDataReporting::observables_likelihood (C++ enumerator) amici::RDataReporting::residuals (C++ enumerator) amici::realtype (C++ type) amici::regex_error_to_string (C++ function) amici::ReturnData (C++ class) amici::ReturnData::apply_chain_rule_factor_to_simulation_results (C++ function) amici::ReturnData::boost::serialization::serialize (C++ function) amici::ReturnData::chi2 (C++ member) amici::ReturnData::computing_fsa (C++ function) amici::ReturnData::cpu_time (C++ member) amici::ReturnData::cpu_time_b (C++ member) amici::ReturnData::cpu_time_total (C++ member) amici::ReturnData::expression_ids (C++ member) amici::ReturnData::expression_names (C++ member) amici::ReturnData::fchi2 (C++ function) amici::ReturnData::fFIM (C++ function) amici::ReturnData::FIM (C++ member) amici::ReturnData::fixed_parameter_ids (C++ member) amici::ReturnData::fixed_parameter_names (C++ member) amici::ReturnData::free_parameter_ids (C++ member) amici::ReturnData::free_parameter_names (C++ member) amici::ReturnData::fres (C++ function) amici::ReturnData::fsres (C++ function) amici::ReturnData::get_data_output (C++ function) amici::ReturnData::get_data_sensis_fsa (C++ function) amici::ReturnData::get_event_output (C++ function) amici::ReturnData::get_event_sensis_fsa (C++ function) amici::ReturnData::handle_sx0_backward (C++ function) amici::ReturnData::handle_sx0_forward (C++ function) amici::ReturnData::id (C++ member) amici::ReturnData::initialize_full_reporting (C++ function) amici::ReturnData::initialize_likelihood_reporting (C++ function) amici::ReturnData::initialize_objective_function (C++ function) amici::ReturnData::initialize_observables_likelihood_reporting (C++ function) amici::ReturnData::initialize_residual_reporting (C++ function) amici::ReturnData::invalidate (C++ function) amici::ReturnData::invalidate_llh (C++ function) amici::ReturnData::invalidate_sllh (C++ function) amici::ReturnData::J (C++ member) amici::ReturnData::llh (C++ member) amici::ReturnData::messages (C++ member) amici::ReturnData::newton_maxsteps (C++ member) amici::ReturnData::nmaxevent (C++ member) amici::ReturnData::nplist (C++ member) amici::ReturnData::nroots_ (C++ member) amici::ReturnData::nt (C++ member) amici::ReturnData::num_err_test_fails (C++ member) amici::ReturnData::num_err_test_fails_b (C++ member) amici::ReturnData::num_non_lin_solv_conv_fails (C++ member) amici::ReturnData::num_non_lin_solv_conv_fails_b (C++ member) amici::ReturnData::num_rhs_evals (C++ member) amici::ReturnData::num_rhs_evals_b (C++ member) amici::ReturnData::numsteps (C++ member) amici::ReturnData::numsteps_b (C++ member) amici::ReturnData::o2mode (C++ member) amici::ReturnData::observable_ids (C++ member) amici::ReturnData::observable_names (C++ member) amici::ReturnData::order (C++ member) amici::ReturnData::plist (C++ member) amici::ReturnData::posteq_cpu_time (C++ member) amici::ReturnData::posteq_cpu_time_b (C++ member) amici::ReturnData::posteq_numsteps (C++ member) amici::ReturnData::posteq_numsteps_b (C++ member) amici::ReturnData::posteq_status (C++ member) amici::ReturnData::posteq_t (C++ member) amici::ReturnData::posteq_wrms (C++ member) amici::ReturnData::preeq_cpu_time (C++ member) amici::ReturnData::preeq_cpu_time_b (C++ member) amici::ReturnData::preeq_numsteps (C++ member) amici::ReturnData::preeq_numsteps_b (C++ member) amici::ReturnData::preeq_status (C++ member) amici::ReturnData::preeq_t (C++ member) amici::ReturnData::preeq_wrms (C++ member) amici::ReturnData::process_backward_problem (C++ function) amici::ReturnData::process_forward_problem (C++ function) amici::ReturnData::process_post_equilibration (C++ function) amici::ReturnData::process_pre_equilibration (C++ function) amici::ReturnData::process_simulation_objects (C++ function) amici::ReturnData::process_solver (C++ function) amici::ReturnData::pscale (C++ member) amici::ReturnData::rdata_reporting (C++ member) amici::ReturnData::res (C++ member) amici::ReturnData::ReturnData (C++ function), [1], [2] amici::ReturnData::rz (C++ member) amici::ReturnData::s2llh (C++ member) amici::ReturnData::s2rz (C++ member) amici::ReturnData::sensi (C++ member) amici::ReturnData::sensi_meth (C++ member) amici::ReturnData::sigma_offset (C++ member) amici::ReturnData::sigma_res (C++ member) amici::ReturnData::sigmay (C++ member) amici::ReturnData::sigmaz (C++ member) amici::ReturnData::sllh (C++ member) amici::ReturnData::sres (C++ member) amici::ReturnData::srz (C++ member) amici::ReturnData::ssigmay (C++ member) amici::ReturnData::ssigmaz (C++ member) amici::ReturnData::state_ids (C++ member) amici::ReturnData::state_ids_solver (C++ member) amici::ReturnData::state_names (C++ member) amici::ReturnData::state_names_solver (C++ member) amici::ReturnData::status (C++ member) amici::ReturnData::store_jacobian_and_derivative (C++ function) amici::ReturnData::sx (C++ member) amici::ReturnData::sx0 (C++ member) amici::ReturnData::sx_ss (C++ member) amici::ReturnData::sy (C++ member) amici::ReturnData::sz (C++ member) amici::ReturnData::t_last (C++ member) amici::ReturnData::ts (C++ member) amici::ReturnData::w (C++ member) amici::ReturnData::x (C++ member) amici::ReturnData::x0 (C++ member) amici::ReturnData::x_ss (C++ member) amici::ReturnData::xdot (C++ member) amici::ReturnData::y (C++ member) amici::ReturnData::z (C++ member) amici::ReturnData::~ReturnData (C++ function) amici::run_simulation (C++ function) amici::run_simulations (C++ function) amici::scale_parameter (C++ function) amici::scale_parameters (C++ function) amici::SecondOrderMode (C++ enum) amici::SecondOrderMode::directional (C++ enumerator) amici::SecondOrderMode::full (C++ enumerator) amici::SecondOrderMode::none (C++ enumerator) amici::SensitivityMethod (C++ enum) amici::SensitivityMethod::adjoint (C++ enumerator) amici::SensitivityMethod::forward (C++ enumerator) amici::SensitivityMethod::none (C++ enumerator) amici::SensitivityOrder (C++ enum) amici::SensitivityOrder::first (C++ enumerator) amici::SensitivityOrder::none (C++ enumerator) amici::SensitivityOrder::second (C++ enumerator) amici::serialize_to_char (C++ function) amici::serialize_to_std_vec (C++ function) amici::serialize_to_string (C++ function) amici::SetupFailure (C++ class) amici::SetupFailure::SetupFailure (C++ function) amici::simulation_status_to_str (C++ function) amici::SimulationParameters (C++ class) amici::SimulationParameters::fixed_parameters (C++ member) amici::SimulationParameters::fixed_parameters_pre_equilibration (C++ member) amici::SimulationParameters::fixed_parameters_presimulation (C++ member) amici::SimulationParameters::free_parameters (C++ member) amici::SimulationParameters::plist (C++ member) amici::SimulationParameters::pscale (C++ member) amici::SimulationParameters::reinitialization_state_idxs_presim (C++ member) amici::SimulationParameters::reinitialization_state_idxs_sim (C++ member) amici::SimulationParameters::reinitialize_all_fixed_parameter_dependent_initial_states (C++ function) amici::SimulationParameters::reinitialize_all_fixed_parameter_dependent_initial_states_for_presimulation (C++ function) amici::SimulationParameters::reinitialize_all_fixed_parameter_dependent_initial_states_for_simulation (C++ function) amici::SimulationParameters::reinitialize_fixed_parameter_initial_states (C++ member) amici::SimulationParameters::SimulationParameters (C++ function), [1], [2], [3], [4] amici::SimulationParameters::sx0 (C++ member) amici::SimulationParameters::t_presim (C++ member) amici::SimulationParameters::t_start (C++ member) amici::SimulationParameters::t_start_preeq (C++ member) amici::SimulationParameters::timepoints (C++ member) amici::SimulationParameters::x0 (C++ member) amici::SimulationState (C++ struct) amici::SimulationState::mod (C++ member) amici::SimulationState::sol (C++ member) amici::slice (C++ function), [1] amici::SolutionState (C++ struct) amici::SolutionState::dx (C++ member) amici::SolutionState::SolutionState (C++ function), [1] amici::SolutionState::sx (C++ member) amici::SolutionState::t (C++ member) amici::SolutionState::x (C++ member) amici::Solver (C++ class) amici::Solver::adj_init (C++ function) amici::Solver::allocate_solver (C++ function) amici::Solver::allocate_solver_b (C++ function) amici::Solver::apply_constraints (C++ function) amici::Solver::apply_max_conv_fails (C++ function) amici::Solver::apply_max_nonlin_iters (C++ function) amici::Solver::apply_max_step_size (C++ function) amici::Solver::apply_quad_tolerances (C++ function) amici::Solver::apply_quad_tolerances_asa (C++ function) amici::Solver::apply_sensitivity_tolerances (C++ function) amici::Solver::apply_tolerances (C++ function) amici::Solver::apply_tolerances_asa (C++ function) amici::Solver::apply_tolerances_fsa (C++ function) amici::Solver::b_init (C++ function) amici::Solver::boost::serialization::serialize (C++ function) amici::Solver::calc_ic (C++ function) amici::Solver::calc_ic_b (C++ function) amici::Solver::check_sensitivity_method (C++ function) amici::Solver::clone (C++ function) amici::Solver::computing_asa (C++ function) amici::Solver::computing_fsa (C++ function) amici::Solver::constraints_ (C++ member) amici::Solver::diag (C++ function) amici::Solver::diag_b (C++ function) amici::Solver::dky_ (C++ member) amici::Solver::dx_ (C++ member) amici::Solver::dxB_ (C++ member) amici::Solver::force_reinit_postprocess_B_ (C++ member) amici::Solver::force_reinit_postprocess_F_ (C++ member) amici::Solver::free_solver_ptr (C++ type) amici::Solver::get_absolute_tolerance (C++ function) amici::Solver::get_absolute_tolerance_b (C++ function) amici::Solver::get_absolute_tolerance_fsa (C++ function) amici::Solver::get_absolute_tolerance_quadratures (C++ function) amici::Solver::get_absolute_tolerance_steady_state (C++ function) amici::Solver::get_absolute_tolerance_steady_state_sensi (C++ function) amici::Solver::get_adj_b_mem (C++ function) amici::Solver::get_adj_init_done (C++ function) amici::Solver::get_adjoint_derivative_state (C++ function) amici::Solver::get_adjoint_quadrature (C++ function) amici::Solver::get_adjoint_state (C++ function) amici::Solver::get_b (C++ function) amici::Solver::get_class_name (C++ function) amici::Solver::get_constraints (C++ function) amici::Solver::get_cpu_time (C++ function) amici::Solver::get_cpu_time_b (C++ function) amici::Solver::get_derivative_state (C++ function) amici::Solver::get_dky (C++ function) amici::Solver::get_dky_b (C++ function) amici::Solver::get_init_done (C++ function) amici::Solver::get_init_done_b (C++ function) amici::Solver::get_internal_sensitivity_method (C++ function) amici::Solver::get_interpolation_type (C++ function) amici::Solver::get_last_order (C++ function), [1] amici::Solver::get_linear_multistep_method (C++ function) amici::Solver::get_linear_solver (C++ function) amici::Solver::get_logger (C++ function) amici::Solver::get_max_conv_fails (C++ function) amici::Solver::get_max_nonlin_iters (C++ function) amici::Solver::get_max_step_size (C++ function) amici::Solver::get_max_steps (C++ function) amici::Solver::get_max_steps_backward_problem (C++ function) amici::Solver::get_max_time (C++ function) amici::Solver::get_model (C++ function) amici::Solver::get_newton_damping_factor_lower_bound (C++ function) amici::Solver::get_newton_damping_factor_mode (C++ function) amici::Solver::get_newton_max_steps (C++ function) amici::Solver::get_newton_step_steady_state_check (C++ function) amici::Solver::get_non_linear_solver_iteration (C++ function) amici::Solver::get_num_err_test_fails (C++ function), [1] amici::Solver::get_num_err_test_fails_b (C++ function) amici::Solver::get_num_non_lin_solv_conv_fails (C++ function), [1] amici::Solver::get_num_non_lin_solv_conv_fails_b (C++ function) amici::Solver::get_num_rhs_evals (C++ function), [1] amici::Solver::get_num_rhs_evals_b (C++ function) amici::Solver::get_num_steps (C++ function), [1] amici::Solver::get_num_steps_b (C++ function) amici::Solver::get_quad (C++ function) amici::Solver::get_quad_b (C++ function) amici::Solver::get_quad_dky (C++ function) amici::Solver::get_quad_dky_b (C++ function) amici::Solver::get_quad_init_done (C++ function) amici::Solver::get_quad_init_done_b (C++ function) amici::Solver::get_quadrature (C++ function) amici::Solver::get_relative_tolerance (C++ function) amici::Solver::get_relative_tolerance_b (C++ function) amici::Solver::get_relative_tolerance_fsa (C++ function) amici::Solver::get_relative_tolerance_quadratures (C++ function) amici::Solver::get_relative_tolerance_steady_state (C++ function) amici::Solver::get_relative_tolerance_steady_state_sensi (C++ function) amici::Solver::get_return_data_reporting_mode (C++ function) amici::Solver::get_root_info (C++ function) amici::Solver::get_sens (C++ function) amici::Solver::get_sens_dky (C++ function) amici::Solver::get_sens_init_done (C++ function) amici::Solver::get_sensi_steady_state_check (C++ function) amici::Solver::get_sensitivity_method (C++ function) amici::Solver::get_sensitivity_method_pre_equilibration (C++ function) amici::Solver::get_sensitivity_order (C++ function) amici::Solver::get_stability_limit_flag (C++ function) amici::Solver::get_state (C++ function) amici::Solver::get_state_ordering (C++ function) amici::Solver::get_state_sensitivity (C++ function) amici::Solver::get_steady_state_sensi_tolerance_factor (C++ function) amici::Solver::get_steady_state_tolerance_factor (C++ function) amici::Solver::get_sun_context (C++ function) amici::Solver::get_t (C++ function) amici::Solver::init (C++ function) amici::Solver::init_steady_state (C++ function) amici::Solver::initialize_linear_solver (C++ function) amici::Solver::initialize_linear_solver_b (C++ function) amici::Solver::initialize_non_linear_solver (C++ function) amici::Solver::initialize_non_linear_solver_b (C++ function) amici::Solver::initialize_non_linear_solver_sens (C++ function) amici::Solver::interp_type_ (C++ member) amici::Solver::ism_ (C++ member) amici::Solver::iter_ (C++ member) amici::Solver::linear_solver_ (C++ member) amici::Solver::linear_solver_B_ (C++ member) amici::Solver::lmm_ (C++ member) amici::Solver::maxsteps_ (C++ member) amici::Solver::maxtime_ (C++ member) amici::Solver::non_linear_solver_ (C++ member) amici::Solver::non_linear_solver_B_ (C++ member) amici::Solver::non_linear_solver_sens_ (C++ member) amici::Solver::nplist (C++ function) amici::Solver::nquad (C++ function) amici::Solver::nx (C++ function) amici::Solver::operator== (C++ function) amici::Solver::qb_init (C++ function) amici::Solver::quad_init (C++ function) amici::Solver::quad_ss_tolerances (C++ function) amici::Solver::quad_ss_tolerances_b (C++ function) amici::Solver::reinit (C++ function) amici::Solver::reinit_b (C++ function) amici::Solver::reinit_post_process_b (C++ function) amici::Solver::reinit_post_process_f (C++ function) amici::Solver::reinit_quad_b (C++ function) amici::Solver::reset_diagnosis (C++ function) amici::Solver::reset_mutable_memory (C++ function) amici::Solver::root_init (C++ function) amici::Solver::run (C++ function) amici::Solver::run_b (C++ function) amici::Solver::sdx_ (C++ member) amici::Solver::sens_init_1 (C++ function) amici::Solver::sens_initialized_ (C++ member) amici::Solver::sens_reinit (C++ function) amici::Solver::sens_toggle_off (C++ function) amici::Solver::set_absolute_tolerance (C++ function) amici::Solver::set_absolute_tolerance_b (C++ function) amici::Solver::set_absolute_tolerance_fsa (C++ function) amici::Solver::set_absolute_tolerance_quadratures (C++ function) amici::Solver::set_absolute_tolerance_steady_state (C++ function) amici::Solver::set_absolute_tolerance_steady_state_sensi (C++ function) amici::Solver::set_adj_init_done (C++ function) amici::Solver::set_band_jac_fn (C++ function) amici::Solver::set_band_jac_fn_b (C++ function) amici::Solver::set_constraints (C++ function) amici::Solver::set_dense_jac_fn (C++ function) amici::Solver::set_dense_jac_fn_b (C++ function) amici::Solver::set_err_handler_fn (C++ function) amici::Solver::set_id (C++ function) amici::Solver::set_init_done (C++ function) amici::Solver::set_init_done_b (C++ function) amici::Solver::set_internal_sensitivity_method (C++ function) amici::Solver::set_interpolation_type (C++ function) amici::Solver::set_jac_times_vec_fn (C++ function) amici::Solver::set_jac_times_vec_fn_b (C++ function) amici::Solver::set_linear_multistep_method (C++ function) amici::Solver::set_linear_solver (C++ function), [1] amici::Solver::set_linear_solver_b (C++ function) amici::Solver::set_logger (C++ function) amici::Solver::set_max_conv_fails (C++ function) amici::Solver::set_max_nonlin_iters (C++ function) amici::Solver::set_max_num_steps (C++ function) amici::Solver::set_max_num_steps_b (C++ function) amici::Solver::set_max_step_size (C++ function) amici::Solver::set_max_steps (C++ function) amici::Solver::set_max_steps_backward_problem (C++ function) amici::Solver::set_max_time (C++ function) amici::Solver::set_newton_damping_factor_lower_bound (C++ function) amici::Solver::set_newton_damping_factor_mode (C++ function) amici::Solver::set_newton_max_steps (C++ function) amici::Solver::set_newton_step_steady_state_check (C++ function) amici::Solver::set_non_linear_solver (C++ function) amici::Solver::set_non_linear_solver_b (C++ function) amici::Solver::set_non_linear_solver_iteration (C++ function) amici::Solver::set_non_linear_solver_sens (C++ function) amici::Solver::set_quad_err_con (C++ function) amici::Solver::set_quad_err_con_b (C++ function) amici::Solver::set_quad_init_done (C++ function) amici::Solver::set_quad_init_done_b (C++ function) amici::Solver::set_relative_tolerance (C++ function) amici::Solver::set_relative_tolerance_b (C++ function) amici::Solver::set_relative_tolerance_fsa (C++ function) amici::Solver::set_relative_tolerance_quadratures (C++ function) amici::Solver::set_relative_tolerance_steady_state (C++ function) amici::Solver::set_relative_tolerance_steady_state_sensi (C++ function) amici::Solver::set_return_data_reporting_mode (C++ function) amici::Solver::set_sens_err_con (C++ function) amici::Solver::set_sens_init_done (C++ function) amici::Solver::set_sens_params (C++ function) amici::Solver::set_sens_ss_tolerances (C++ function) amici::Solver::set_sensi_steady_state_check (C++ function) amici::Solver::set_sensitivity_method (C++ function) amici::Solver::set_sensitivity_method_pre_equilibration (C++ function) amici::Solver::set_sensitivity_order (C++ function) amici::Solver::set_sparse_jac_fn (C++ function) amici::Solver::set_sparse_jac_fn_b (C++ function) amici::Solver::set_sparse_jac_fn_ss (C++ function) amici::Solver::set_ss_tolerances (C++ function) amici::Solver::set_ss_tolerances_b (C++ function) amici::Solver::set_stab_lim_det (C++ function) amici::Solver::set_stab_lim_det_b (C++ function) amici::Solver::set_stability_limit_flag (C++ function) amici::Solver::set_state_ordering (C++ function) amici::Solver::set_steady_state_sensi_tolerance_factor (C++ function) amici::Solver::set_steady_state_tolerance_factor (C++ function) amici::Solver::set_stop_time (C++ function) amici::Solver::set_suppress_alg (C++ function) amici::Solver::set_user_data (C++ function) amici::Solver::set_user_data_b (C++ function) amici::Solver::setup (C++ function) amici::Solver::setup_b (C++ function) amici::Solver::setup_steady_state (C++ function) amici::Solver::simulation_timer_ (C++ member) amici::Solver::solve (C++ function) amici::Solver::solve_b (C++ function) amici::Solver::solve_f (C++ function) amici::Solver::Solver (C++ function), [1] amici::Solver::solver_memory_ (C++ member) amici::Solver::solver_memory_B_ (C++ member) amici::Solver::solver_was_called_B_ (C++ member) amici::Solver::solver_was_called_F_ (C++ member) amici::Solver::start_timer (C++ function) amici::Solver::step (C++ function) amici::Solver::store_diagnosis (C++ function) amici::Solver::store_diagnosis_b (C++ function) amici::Solver::sunctx_ (C++ member) amici::Solver::switch_forward_sensis_off (C++ function) amici::Solver::sx_ (C++ member) amici::Solver::t_ (C++ member) amici::Solver::time_exceeded (C++ function) amici::Solver::turn_off_root_finding (C++ function) amici::Solver::update_and_reinit_states_and_sensitivities (C++ function) amici::Solver::user_data_ (C++ member) amici::Solver::user_data_type (C++ type) amici::Solver::write_solution (C++ function), [1], [2], [3] amici::Solver::write_solution_b (C++ function) amici::Solver::x_ (C++ member) amici::Solver::xB_ (C++ member) amici::Solver::xQ_ (C++ member) amici::Solver::xQB_ (C++ member) amici::Solver::~Solver (C++ function) amici::SplineBoundaryCondition (C++ enum) amici::SplineBoundaryCondition::given (C++ enumerator) amici::SplineBoundaryCondition::natural (C++ enumerator) amici::SplineBoundaryCondition::naturalZeroDerivative (C++ enumerator) amici::SplineBoundaryCondition::periodic (C++ enumerator) amici::SplineBoundaryCondition::zeroDerivative (C++ enumerator) amici::SplineExtrapolation (C++ enum) amici::SplineExtrapolation::constant (C++ enumerator) amici::SplineExtrapolation::linear (C++ enumerator) amici::SplineExtrapolation::noExtrapolation (C++ enumerator) amici::SplineExtrapolation::periodic (C++ enumerator) amici::SplineExtrapolation::polynomial (C++ enumerator) amici::SteadyStateBackwardProblem (C++ class) amici::SteadyStateBackwardProblem::get_adjoint_quadrature (C++ function) amici::SteadyStateBackwardProblem::get_adjoint_state (C++ function) amici::SteadyStateBackwardProblem::get_cpu_time_b (C++ function) amici::SteadyStateBackwardProblem::get_num_steps_b (C++ function) amici::SteadyStateBackwardProblem::has_quadrature (C++ function) amici::SteadyStateBackwardProblem::run (C++ function) amici::SteadyStateBackwardProblem::SteadyStateBackwardProblem (C++ function) amici::SteadyStateComputationMode (C++ enum) amici::SteadyStateComputationMode::integrateIfNewtonFails (C++ enumerator) amici::SteadyStateComputationMode::integrationOnly (C++ enumerator) amici::SteadyStateComputationMode::newtonOnly (C++ enumerator) amici::SteadyStateProblem (C++ class) amici::SteadyStateProblem::check_steady_state_success (C++ function) amici::SteadyStateProblem::get_cpu_time (C++ function) amici::SteadyStateProblem::get_final_simulation_state (C++ function) amici::SteadyStateProblem::get_num_steps (C++ function) amici::SteadyStateProblem::get_residual_norm (C++ function) amici::SteadyStateProblem::get_result (C++ function) amici::SteadyStateProblem::get_solver (C++ function) amici::SteadyStateProblem::get_state (C++ function) amici::SteadyStateProblem::get_state_sensitivity (C++ function) amici::SteadyStateProblem::get_steady_state_status (C++ function) amici::SteadyStateProblem::get_steady_state_time (C++ function) amici::SteadyStateProblem::run (C++ function) amici::SteadyStateProblem::SteadyStateProblem (C++ function) amici::SteadyStateSensitivityMode (C++ enum) amici::SteadyStateSensitivityMode::integrateIfNewtonFails (C++ enumerator) amici::SteadyStateSensitivityMode::integrationOnly (C++ enumerator) amici::SteadyStateSensitivityMode::newtonOnly (C++ enumerator) amici::SteadyStateStatus (C++ enum) amici::SteadyStateStatus::failed (C++ enumerator) amici::SteadyStateStatus::failed_convergence (C++ enumerator) amici::SteadyStateStatus::failed_damping (C++ enumerator) amici::SteadyStateStatus::failed_factorization (C++ enumerator) amici::SteadyStateStatus::failed_too_long_simulation (C++ enumerator) amici::SteadyStateStatus::not_run (C++ enumerator) amici::SteadyStateStatus::success (C++ enumerator) amici::SUNLinSolBand (C++ class) amici::SUNLinSolBand::SUNLinSolBand (C++ function), [1] amici::SUNLinSolDense (C++ class) amici::SUNLinSolDense::SUNLinSolDense (C++ function) amici::SUNLinSolKLU (C++ class) amici::SUNLinSolKLU::is_singular (C++ function) amici::SUNLinSolKLU::reinit (C++ function) amici::SUNLinSolKLU::set_ordering (C++ function) amici::SUNLinSolKLU::StateOrdering (C++ enum) amici::SUNLinSolKLU::StateOrdering::AMD (C++ enumerator) amici::SUNLinSolKLU::StateOrdering::COLAMD (C++ enumerator) amici::SUNLinSolKLU::StateOrdering::natural (C++ enumerator) amici::SUNLinSolKLU::SUNLinSolKLU (C++ function), [1] amici::SUNLinSolPCG (C++ class) amici::SUNLinSolPCG::get_num_iters (C++ function) amici::SUNLinSolPCG::get_res_norm (C++ function) amici::SUNLinSolPCG::get_resid (C++ function) amici::SUNLinSolPCG::set_a_times (C++ function) amici::SUNLinSolPCG::set_preconditioner (C++ function) amici::SUNLinSolPCG::set_scaling_vectors (C++ function) amici::SUNLinSolPCG::SUNLinSolPCG (C++ function) amici::SUNLinSolSPBCGS (C++ class) amici::SUNLinSolSPBCGS::get_num_iters (C++ function) amici::SUNLinSolSPBCGS::get_res_norm (C++ function) amici::SUNLinSolSPBCGS::get_resid (C++ function) amici::SUNLinSolSPBCGS::set_a_times (C++ function) amici::SUNLinSolSPBCGS::set_preconditioner (C++ function) amici::SUNLinSolSPBCGS::set_scaling_vectors (C++ function) amici::SUNLinSolSPBCGS::SUNLinSolSPBCGS (C++ function), [1] amici::SUNLinSolSPFGMR (C++ class) amici::SUNLinSolSPFGMR::get_num_iters (C++ function) amici::SUNLinSolSPFGMR::get_res_norm (C++ function) amici::SUNLinSolSPFGMR::get_resid (C++ function) amici::SUNLinSolSPFGMR::set_a_times (C++ function) amici::SUNLinSolSPFGMR::set_preconditioner (C++ function) amici::SUNLinSolSPFGMR::set_scaling_vectors (C++ function) amici::SUNLinSolSPFGMR::SUNLinSolSPFGMR (C++ function) amici::SUNLinSolSPGMR (C++ class) amici::SUNLinSolSPGMR::get_num_iters (C++ function) amici::SUNLinSolSPGMR::get_res_norm (C++ function) amici::SUNLinSolSPGMR::get_resid (C++ function) amici::SUNLinSolSPGMR::set_a_times (C++ function) amici::SUNLinSolSPGMR::set_preconditioner (C++ function) amici::SUNLinSolSPGMR::set_scaling_vectors (C++ function) amici::SUNLinSolSPGMR::SUNLinSolSPGMR (C++ function) amici::SUNLinSolSPTFQMR (C++ class) amici::SUNLinSolSPTFQMR::get_num_iters (C++ function) amici::SUNLinSolSPTFQMR::get_res_norm (C++ function) amici::SUNLinSolSPTFQMR::get_resid (C++ function) amici::SUNLinSolSPTFQMR::set_a_times (C++ function) amici::SUNLinSolSPTFQMR::set_preconditioner (C++ function) amici::SUNLinSolSPTFQMR::set_scaling_vectors (C++ function) amici::SUNLinSolSPTFQMR::SUNLinSolSPTFQMR (C++ function), [1] amici::SUNLinSolWrapper (C++ class) amici::SUNLinSolWrapper::A_ (C++ member) amici::SUNLinSolWrapper::get (C++ function) amici::SUNLinSolWrapper::get_last_flag (C++ function) amici::SUNLinSolWrapper::get_type (C++ function) amici::SUNLinSolWrapper::getMatrix (C++ function) amici::SUNLinSolWrapper::initialize (C++ function) amici::SUNLinSolWrapper::operator= (C++ function), [1] amici::SUNLinSolWrapper::setup (C++ function) amici::SUNLinSolWrapper::solve (C++ function) amici::SUNLinSolWrapper::solver_ (C++ member) amici::SUNLinSolWrapper::space (C++ function) amici::SUNLinSolWrapper::SUNLinSolWrapper (C++ function), [1], [2], [3], [4] amici::SUNLinSolWrapper::~SUNLinSolWrapper (C++ function) amici::SUNMatrixWrapper (C++ class) amici::SUNMatrixWrapper::capacity (C++ function) amici::SUNMatrixWrapper::columns (C++ function) amici::SUNMatrixWrapper::data (C++ function), [1] amici::SUNMatrixWrapper::get (C++ function) amici::SUNMatrixWrapper::get_ctx (C++ function) amici::SUNMatrixWrapper::get_data (C++ function), [1] amici::SUNMatrixWrapper::get_indexptr (C++ function) amici::SUNMatrixWrapper::get_indexval (C++ function) amici::SUNMatrixWrapper::matrix_id (C++ function) amici::SUNMatrixWrapper::multiply (C++ function), [1], [2], [3], [4] amici::SUNMatrixWrapper::num_indexptrs (C++ function) amici::SUNMatrixWrapper::num_nonzeros (C++ function) amici::SUNMatrixWrapper::operator SUNMatrix (C++ function) amici::SUNMatrixWrapper::operator= (C++ function), [1] amici::SUNMatrixWrapper::realloc (C++ function) amici::SUNMatrixWrapper::reallocate (C++ function) amici::SUNMatrixWrapper::refresh (C++ function) amici::SUNMatrixWrapper::rows (C++ function) amici::SUNMatrixWrapper::scale (C++ function) amici::SUNMatrixWrapper::scatter (C++ function) amici::SUNMatrixWrapper::set_ctx (C++ function) amici::SUNMatrixWrapper::set_data (C++ function), [1] amici::SUNMatrixWrapper::set_indexptr (C++ function) amici::SUNMatrixWrapper::set_indexptrs (C++ function) amici::SUNMatrixWrapper::set_indexval (C++ function) amici::SUNMatrixWrapper::set_indexvals (C++ function) amici::SUNMatrixWrapper::sparse_add (C++ function) amici::SUNMatrixWrapper::sparse_multiply (C++ function) amici::SUNMatrixWrapper::sparse_sum (C++ function) amici::SUNMatrixWrapper::sparsetype (C++ function) amici::SUNMatrixWrapper::SUNMatrixWrapper (C++ function), [1], [2], [3], [4], [5], [6], [7] amici::SUNMatrixWrapper::to_dense (C++ function) amici::SUNMatrixWrapper::to_diag (C++ function) amici::SUNMatrixWrapper::transpose (C++ function) amici::SUNMatrixWrapper::zero (C++ function) amici::SUNMatrixWrapper::~SUNMatrixWrapper (C++ function) amici::SUNNonLinSolFixedPoint (C++ class) amici::SUNNonLinSolFixedPoint::get_sys_fn (C++ function) amici::SUNNonLinSolFixedPoint::SUNNonLinSolFixedPoint (C++ function), [1] amici::SUNNonLinSolNewton (C++ class) amici::SUNNonLinSolNewton::get_sys_fn (C++ function) amici::SUNNonLinSolNewton::SUNNonLinSolNewton (C++ function), [1] amici::SUNNonLinSolWrapper (C++ class) amici::SUNNonLinSolWrapper::get (C++ function) amici::SUNNonLinSolWrapper::get_cur_iter (C++ function) amici::SUNNonLinSolWrapper::get_num_conv_fails (C++ function) amici::SUNNonLinSolWrapper::get_num_iters (C++ function) amici::SUNNonLinSolWrapper::get_type (C++ function) amici::SUNNonLinSolWrapper::initialize (C++ function) amici::SUNNonLinSolWrapper::operator= (C++ function), [1] amici::SUNNonLinSolWrapper::set_conv_test_fn (C++ function) amici::SUNNonLinSolWrapper::set_l_setup_fn (C++ function) amici::SUNNonLinSolWrapper::set_l_solve_fn (C++ function) amici::SUNNonLinSolWrapper::set_max_iters (C++ function) amici::SUNNonLinSolWrapper::set_sys_fn (C++ function) amici::SUNNonLinSolWrapper::setup (C++ function) amici::SUNNonLinSolWrapper::solve (C++ function) amici::SUNNonLinSolWrapper::solver (C++ member) amici::SUNNonLinSolWrapper::SUNNonLinSolWrapper (C++ function), [1], [2] amici::SUNNonLinSolWrapper::~SUNNonLinSolWrapper (C++ function) amici::unravel_index (C++ function), [1] amici::unscale_parameter (C++ function) amici::unscale_parameters (C++ function) amici::write_slice (C++ function), [1], [2], [3] amici::WRMSComputer (C++ class) amici::WRMSComputer::wrms (C++ function) amici::WRMSComputer::WRMSComputer (C++ function) amici_annotation (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) AMICI_H5_RESTORE_ERROR_HANDLER (C macro) AMICI_H5_SAVE_ERROR_HANDLER (C macro) AMICI_VERSION (C macro) AmiciVersionError antimony2amici() (in module amici.importers.antimony) antimony2sbml() (in module amici.importers.antimony) api_version (amici.sim.jax.JAXModel attribute) apply_parameters() (amici.sim.sundials.petab.ExperimentManager method) assignment_rules_to_observables() (in module amici.importers.sbml)

B

band (amici.sim.sundials.LinearSolver attribute) bc (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) BDF (amici.sim.sundials.LinearMultistepMethod attribute) BNGL

bngl2amici() (in module amici.importers.bngl) BoolVector (class in amici.sim.sundials) boost::serialization::archive_vector (C++ function) boost::serialization::serialize (C++ function), [1], [2], [3], [4], [5] by_id() (amici.sim.sundials.ReturnDataView method)

C

check_finite_difference() (in module amici.sim.sundials.gradient_check) check_if_valid() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) chi2 (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) clear_observations() (amici.sim.sundials.ExpData method) clone() (amici.sim.sundials.Model method) (amici.sim.sundials.Solver method) compiled_with_openmp() (in module amici.sim.sundials) computing_asa() (amici.sim.sundials.Solver method) computing_fsa() (amici.sim.sundials.Solver method) Constraint (class in amici.sim.sundials) count() (amici.importers.sbml.splines.UniformGrid method) cpu_time (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

cpu_time_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) cpu_time_total (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) CpuTimer (class in amici.sim.sundials) create_edata() (amici.sim.sundials.petab.ExperimentManager method) create_edatas() (amici.sim.sundials.petab.ExperimentManager method) (in module amici.sim.sundials.petab.v1) create_model() (amici.importers.petab.PetabImporter method) create_parameterized_edatas() (in module amici.sim.sundials.petab.v1) create_simulator() (amici.importers.petab.PetabImporter method) create_solver() (amici.sim.sundials.Model method) CubicHermiteSpline (class in amici.importers.sbml.splines) CVODES

D

d_scaled() (amici.importers.sbml.splines.CubicHermiteSpline method) DAE debug (amici.sim.sundials.LogSeverity attribute) dense (amici.sim.sundials.LinearSolver attribute) derivative() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method)

derivatives_at_nodes (amici.importers.sbml.splines.CubicHermiteSpline property) derivatives_by_fd (amici.importers.sbml.splines.CubicHermiteSpline property) diag (amici.sim.sundials.LinearSolver attribute) directional (amici.sim.sundials.SecondOrderMode attribute) DoubleVector (class in amici.sim.sundials)

E

edatas (amici.sim.sundials.petab.PetabSimulationResult attribute) elapsed_milliseconds() (amici.sim.sundials.CpuTimer method) elapsed_seconds() (amici.sim.sundials.CpuTimer method) equilibration error (amici.sim.sundials.LogSeverity attribute) evaluate() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) (in module amici.sim.sundials) evaluate_at (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) exp_man (amici.sim.sundials.petab.PetabSimulator property) ExpData (class in amici.sim.sundials)

ExpDataPtr (class in amici.sim.sundials) ExpDataPtrVector (class in amici.sim.sundials) ExpDataView (class in amici.sim.sundials) ExperimentManager (class in amici.sim.sundials.petab) expression_ids (amici.sim.jax.JAXModel property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) expression_names (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) extrapolate (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) extrapolation_formulas (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property)

F

failed (amici.sim.sundials.SteadyStateStatus attribute) failed_convergence (amici.sim.sundials.SteadyStateStatus attribute) failed_damping (amici.sim.sundials.SteadyStateStatus attribute) failed_factorization (amici.sim.sundials.SteadyStateStatus attribute) failed_too_long_simulation (amici.sim.sundials.SteadyStateStatus attribute) fill_in_parameters() (in module amici.sim.sundials.petab.v1) FIM (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) first (amici.sim.sundials.SensitivityOrder attribute) fixed parameters fixed_parameter_ids (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) fixed_parameter_names (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) fixed_parameters (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) fixed_parameters_pre_equilibration (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property)

fixed_parameters_presimulation (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) FixedParameterContext (class in amici.sim.sundials) fixedpoint (amici.sim.sundials.NonlinearSolverIteration attribute) flatten_timepoint_specific_output_overrides() (in module amici.importers.petab) formula (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) forward (amici.sim.sundials.SensitivityMethod attribute) free parameters free_parameter_ids (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) free_parameter_names (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) free_parameters (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) from_annotation() (amici.importers.sbml.splines.AbstractSpline static method) (amici.importers.sbml.splines.CubicHermiteSpline static method) full (amici.sim.sundials.RDataReporting attribute) (amici.sim.sundials.SecondOrderMode attribute)

G

get() (amici.sim.sundials.ExpDataView method) (amici.sim.sundials.ReturnDataView method) get_absolute_tolerance() (amici.sim.sundials.Solver method) get_absolute_tolerance_b() (amici.sim.sundials.Solver method) get_absolute_tolerance_fsa() (amici.sim.sundials.Solver method) get_absolute_tolerance_quadratures() (amici.sim.sundials.Solver method) get_absolute_tolerance_steady_state() (amici.sim.sundials.Solver method) get_absolute_tolerance_steady_state_sensi() (amici.sim.sundials.Solver method) get_add_sigma_residuals() (amici.sim.sundials.Model method) get_all_simulation_conditions() (amici.sim.jax.JAXProblem method) get_always_check_finite() (amici.sim.sundials.Model method) get_amici_commit() (amici.sim.sundials.Model method) get_amici_version() (amici.sim.sundials.Model method) get_annotation() (amici.importers.sbml.splines.AbstractSpline static method) (amici.importers.sbml.splines.CubicHermiteSpline static method) get_any_state_nonnegative() (amici.sim.sundials.Model method) get_backtrace_string() (in module amici.sim.sundials) get_class_name() (amici.sim.sundials.Solver method) get_constraints() (amici.sim.sundials.Solver method) get_edata() (amici.sim.sundials.petab.v1.PetabProblem method) get_edatas() (amici.sim.sundials.petab.v1.PetabProblem method) get_event_measurements() (amici.sim.sundials.ExpData method) get_event_measurements_ptr() (amici.sim.sundials.ExpData method) get_event_noise_scales() (amici.sim.sundials.ExpData method) get_event_noise_scales_ptr() (amici.sim.sundials.ExpData method) get_expression_ids() (amici.sim.sundials.Model method) get_expression_names() (amici.sim.sundials.Model method) get_fixed_parameter_by_id() (amici.sim.sundials.Model method) get_fixed_parameter_by_name() (amici.sim.sundials.Model method) get_fixed_parameter_ids() (amici.sim.sundials.Model method) get_fixed_parameter_names() (amici.sim.sundials.Model method) get_fixed_parameters() (amici.sim.sundials.Model method) get_free_parameter_by_id() (amici.sim.sundials.Model method) get_free_parameter_by_name() (amici.sim.sundials.Model method) get_free_parameter_ids() (amici.sim.sundials.Model method) get_free_parameter_names() (amici.sim.sundials.Model method) get_free_parameters() (amici.sim.sundials.Model method) get_id_list() (amici.sim.sundials.Model method) get_initial_state() (amici.sim.sundials.Model method) get_initial_state_sensitivities() (amici.sim.sundials.Model method) get_internal_sensitivity_method() (amici.sim.sundials.Solver method) get_interpolation_type() (amici.sim.sundials.Solver method) get_linear_multistep_method() (amici.sim.sundials.Solver method) get_linear_solver() (amici.sim.sundials.Solver method) get_max_conv_fails() (amici.sim.sundials.Solver method) get_max_nonlin_iters() (amici.sim.sundials.Solver method) get_max_step_size() (amici.sim.sundials.Solver method) get_max_steps() (amici.sim.sundials.Solver method) get_max_steps_backward_problem() (amici.sim.sundials.Solver method) get_max_time() (amici.sim.sundials.Solver method) get_measurements() (amici.sim.sundials.ExpData method) get_minimum_sigma_residuals() (amici.sim.sundials.Model method)

get_model() (amici.sim.sundials.ModelModule method) get_model_dir() (in module amici) get_model_for_preeq() (in module amici.sim.sundials) get_model_root_dir() (in module amici) get_model_settings() (in module amici.sim.sundials) get_name() (amici.sim.sundials.Model method) get_newton_damping_factor_lower_bound() (amici.sim.sundials.Solver method) get_newton_damping_factor_mode() (amici.sim.sundials.Solver method) get_newton_max_steps() (amici.sim.sundials.Solver method) get_newton_step_steady_state_check() (amici.sim.sundials.Solver method) get_noise_scales() (amici.sim.sundials.ExpData method) get_non_linear_solver_iteration() (amici.sim.sundials.Solver method) get_observable_ids() (amici.sim.sundials.Model method) get_observable_names() (amici.sim.sundials.Model method) get_observable_scaling() (amici.sim.sundials.Model method) get_parameter_list() (amici.sim.sundials.Model method) get_parameter_scale() (amici.sim.sundials.Model method) get_petab_parameter_by_id() (amici.sim.jax.JAXProblem method) get_reinitialization_state_idxs() (amici.sim.sundials.Model method) get_reinitialize_fixed_parameter_initial_states() (amici.sim.sundials.Model method) get_relative_tolerance() (amici.sim.sundials.Solver method) get_relative_tolerance_b() (amici.sim.sundials.Solver method) get_relative_tolerance_fsa() (amici.sim.sundials.Solver method) get_relative_tolerance_quadratures() (amici.sim.sundials.Solver method) get_relative_tolerance_steady_state() (amici.sim.sundials.Solver method) get_relative_tolerance_steady_state_sensi() (amici.sim.sundials.Solver method) get_return_data_reporting_mode() (amici.sim.sundials.Solver method) get_second_order_mode() (amici.sim.sundials.Model method) get_sensi_steady_state_check() (amici.sim.sundials.Solver method) get_sensitivity_method() (amici.sim.sundials.Solver method) get_sensitivity_method_pre_equilibration() (amici.sim.sundials.Solver method) get_sensitivity_order() (amici.sim.sundials.Solver method) get_stability_limit_flag() (amici.sim.sundials.Solver method) get_state_ids() (amici.sim.sundials.Model method) get_state_ids_solver() (amici.sim.sundials.Model method) get_state_is_non_negative() (amici.sim.sundials.Model method) get_state_names() (amici.sim.sundials.Model method) get_state_names_solver() (amici.sim.sundials.Model method) get_state_ordering() (amici.sim.sundials.Solver method) get_steady_state_computation_mode() (amici.sim.sundials.Model method) get_steady_state_sensi_tolerance_factor() (amici.sim.sundials.Solver method) get_steady_state_sensitivity_mode() (amici.sim.sundials.Model method) get_steady_state_tolerance_factor() (amici.sim.sundials.Solver method) get_steadystate_mask() (amici.sim.sundials.Model method) get_t() (amici.sim.sundials.Solver method) get_timepoint() (amici.sim.sundials.ExpData method) (amici.sim.sundials.Model method) get_timepoints() (amici.sim.sundials.ExpData method) (amici.sim.sundials.Model method) get_trigger_timepoints() (amici.sim.sundials.Model method) get_unscaled_parameters() (amici.sim.sundials.Model method) gsl::make_span (C++ function), [1], [2]

H

has_custom_initial_state() (amici.sim.sundials.Model method) has_custom_initial_state_sensitivities() (amici.sim.sundials.Model method) has_expression_ids() (amici.sim.sundials.Model method) has_expression_names() (amici.sim.sundials.Model method) has_fixed_parameter_ids() (amici.sim.sundials.Model method) has_fixed_parameter_names() (amici.sim.sundials.Model method) has_free_parameter_ids() (amici.sim.sundials.Model method)

has_free_parameter_names() (amici.sim.sundials.Model method) has_observable_ids() (amici.sim.sundials.Model method) has_observable_names() (amici.sim.sundials.Model method) has_quadratic_llh() (amici.sim.sundials.Model method) has_state_ids() (amici.sim.sundials.Model method) has_state_names() (amici.sim.sundials.Model method) has_timepoint_specific_overrides() (in module amici.importers.petab) hermite (amici.sim.sundials.InterpolationType attribute)

I

id (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) IDAS identifier (amici.sim.sundials.LogItem property) import_model_module() (in module amici) (in module amici.sim.sundials) import_module() (amici.importers.petab.PetabImporter method) import_petab_problem() (in module amici.importers.petab.v1) index() (amici.importers.sbml.splines.UniformGrid method) integrate() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) integrateIfNewtonFails (amici.sim.sundials.SteadyStateComputationMode attribute) (amici.sim.sundials.SteadyStateSensitivityMode attribute)

integrationOnly (amici.sim.sundials.SteadyStateComputationMode attribute) (amici.sim.sundials.SteadyStateSensitivityMode attribute) InternalSensitivityMethod (class in amici.sim.sundials) InterpolationType (class in amici.sim.sundials) IntVector (class in amici.sim.sundials) is_event_resolved (amici.importers.utils.MeasurementChannel property) is_fixed_parameter_state_reinitialization_allowed() (amici.sim.sundials.Model method) is_set_event_measurement() (amici.sim.sundials.ExpData method) is_set_event_noise_scale() (amici.sim.sundials.ExpData method) is_set_measurement() (amici.sim.sundials.ExpData method) is_set_noise_scale() (amici.sim.sundials.ExpData method) is_spline() (amici.importers.sbml.splines.AbstractSpline static method) (amici.importers.sbml.splines.CubicHermiteSpline static method) is_time_resolved (amici.importers.utils.MeasurementChannel property) items() (amici.sim.sundials.ExpDataView method) (amici.sim.sundials.ReturnDataView method)

J

J (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

jax_py_file (amici.sim.jax.JAXModel attribute) JAXModel (class in amici.sim.jax) JAXProblem (class in amici.sim.jax)

K

k() (amici.sim.sundials.Model method) keys() (amici.sim.sundials.ExpDataView method) (amici.sim.sundials.ReturnDataView method)

KLU (amici.sim.sundials.LinearSolver attribute)

L

LAPACKBand (amici.sim.sundials.LinearSolver attribute) LAPACKDense (amici.sim.sundials.LinearSolver attribute) lbw (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) likelihood (amici.sim.sundials.RDataReporting attribute) lin (amici.sim.sundials.ObservableScaling attribute) LinearMultistepMethod (class in amici.sim.sundials) LinearSolver (class in amici.sim.sundials) llh (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.petab.PetabSimulationResult property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

ln (amici.sim.sundials.ParameterScaling attribute) load() (amici.sim.jax.JAXProblem class method) load_model_parameters() (amici.sim.jax.JAXProblem method) load_reinitialisation() (amici.sim.jax.JAXProblem method) log (amici.sim.sundials.ObservableScaling attribute) log10 (amici.sim.sundials.ObservableScaling attribute) (amici.sim.sundials.ParameterScaling attribute) logarithmic_parametrization (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) LogItem (class in amici.sim.sundials) LogItemVector (class in amici.sim.sundials) LogSeverity (class in amici.sim.sundials)

M

M_1_PI (C macro) M_2_PI (C macro) M_2_SQRTPI (C macro) M_E (C macro) M_LN10 (C macro) M_LN2 (C macro) M_LOG10E (C macro) M_LOG2E (C macro) M_PI (C macro) M_PI_2 (C macro) M_PI_4 (C macro) M_SQRT1_2 (C macro) M_SQRT2 (C macro) mathml_formula (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) MeasurementChannel (class in amici.importers.utils) message (amici.sim.sundials.LogItem property) messages (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) method (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) model (amici.sim.jax.JAXProblem attribute) (amici.sim.sundials.petab.ExperimentManager property) (amici.sim.sundials.petab.PetabSimulator property) (amici.sim.sundials.petab.v1.PetabProblem property)

Model (class in amici.sim.sundials) MODEL_API_VERSION (amici.sim.jax.JAXModel attribute) model_id (amici.importers.petab.PetabImporter property) ModelDimensions (class in amici.sim.sundials) ModelModule (class in amici.sim.sundials) ModelPtr (class in amici.sim.sundials) module amici amici.adapters.fiddy amici.importers.antimony amici.importers.bngl amici.importers.petab amici.importers.petab.v1 amici.importers.pysb amici.importers.sbml amici.importers.sbml.splines amici.importers.utils amici.sim.jax amici.sim.sundials amici.sim.sundials.gradient_check amici.sim.sundials.petab amici.sim.sundials.petab.v1 amici.sim.sundials.plotting

N

n_events (amici.sim.jax.JAXModel property) n_max_event() (amici.sim.sundials.Model method) ncl() (amici.sim.sundials.Model method) ndJydy (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndtotal_cldx_rdata (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndwdp (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndwdw (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndwdx (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndxdotdp_explicit (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndxdotdw (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndxdotdx_explicit (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndxrdatadtcl (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ndxrdatadxsolver (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ne (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ne_solver (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) negative (amici.sim.sundials.Constraint attribute) newton (amici.sim.sundials.NonlinearSolverIteration attribute) newton_maxsteps (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) NewtonDampingFactorMode (class in amici.sim.sundials) newtonOnly (amici.sim.sundials.SteadyStateComputationMode attribute) (amici.sim.sundials.SteadyStateSensitivityMode attribute) nJ (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nk (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nk() (amici.sim.sundials.Model method) nllhs (amici.sim.jax.ReturnValue attribute) nmaxevent (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nmaxevent() (amici.sim.sundials.ExpData method) nn_output_ids (amici.sim.jax.JAXProblem property) nns (amici.sim.jax.JAXModel attribute) nnz (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nodes (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) non_negative (amici.sim.sundials.Constraint attribute) non_positive (amici.sim.sundials.Constraint attribute) none (amici.sim.sundials.Constraint attribute) (amici.sim.sundials.ParameterScaling attribute) (amici.sim.sundials.SecondOrderMode attribute) (amici.sim.sundials.SensitivityMethod attribute) (amici.sim.sundials.SensitivityOrder attribute)

NonlinearSolverIteration (class in amici.sim.sundials) not_run (amici.sim.sundials.SteadyStateStatus attribute) np (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) np() (amici.sim.sundials.Model method) nplist (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nplist() (amici.sim.sundials.Model method) (amici.sim.sundials.Solver method) nquad() (amici.sim.sundials.Solver method) nspl (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nt (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nt() (amici.sim.sundials.ExpData method) (amici.sim.sundials.Model method) num_err_test_fails (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) num_err_test_fails_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) num_non_lin_solv_conv_fails (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) num_non_lin_solv_conv_fails_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) num_rhs_evals (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) num_rhs_evals_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) number_of_nodes (amici.importers.sbml.splines.UniformGrid property) numsteps (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) numsteps_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nw (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nx() (amici.sim.sundials.Solver method) nx_rdata (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nx_reinit() (amici.sim.sundials.Model method) nx_solver (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nx_solver_reinit (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nxtrue_rdata (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nxtrue_solver (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ny (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nytrue (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nytrue() (amici.sim.sundials.ExpData method) nz (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nztrue (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) nztrue() (amici.sim.sundials.ExpData method)

O

o2mode (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) observable_ids (amici.sim.jax.JAXModel property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) observable_names (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) observables_likelihood (amici.sim.sundials.RDataReporting attribute)

ObservableScaling (class in amici.sim.sundials) ODE ode_model_symbol() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) off (amici.sim.sundials.NewtonDampingFactorMode attribute) on (amici.sim.sundials.NewtonDampingFactorMode attribute) order (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) output_dir (amici.importers.petab.PetabImporter property)

P

parameter_ids (amici.sim.jax.JAXModel property) (amici.sim.jax.JAXProblem property) parameter_scaling_from_int_vector() (in module amici.sim.sundials) parameters (amici.sim.jax.JAXModel attribute) (amici.sim.jax.JAXProblem attribute) parameters() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) ParameterScaling (class in amici.sim.sundials) ParameterScalingVector (class in amici.sim.sundials) period (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) PEtab petab_problem (amici.sim.sundials.petab.ExperimentManager property) petab_simulate() (in module amici.sim.jax) PetabImporter (class in amici.importers.petab) PetabProblem (class in amici.sim.sundials.petab.v1) PetabSimulationResult (class in amici.sim.sundials.petab) PetabSimulator (class in amici.sim.sundials.petab) (class in amici.sim.sundials.petab.v1) plist (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) (amici.sim.sundials.SimulationParameters property) plist() (amici.sim.sundials.Model method) plot() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) plot_expressions() (in module amici.sim.sundials.plotting) plot_jacobian() (in module amici.sim.sundials.plotting) plot_observable_trajectories() (in module amici.sim.sundials.plotting) plot_state_trajectories() (in module amici.sim.sundials.plotting) poly() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) poly_variable() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) polynomial (amici.sim.sundials.InterpolationType attribute) positive (amici.sim.sundials.Constraint attribute) post-equilibration posteq_cpu_time (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

posteq_cpu_time_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) posteq_numsteps (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) posteq_numsteps_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) posteq_status (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) posteq_t (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) posteq_wrms (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) pre-equilibration pre-simulation preeq_cpu_time (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preeq_cpu_time_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preeq_numsteps (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preeq_numsteps_b (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preeq_status (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preeq_t (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preeq_wrms (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) preequilibrate_condition() (amici.sim.jax.JAXModel method) preequilibration (amici.sim.sundials.FixedParameterContext attribute) presimulation (amici.sim.sundials.FixedParameterContext attribute) pscale (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) (amici.sim.sundials.SimulationParameters property) PySB pysb2amici() (in module amici.importers.pysb) pysb2jax() (in module amici.importers.pysb) pysb_model_from_path() (in module amici.importers.pysb)

R

rdata_reporting (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) RDataReporting (class in amici.sim.sundials) rdatas (amici.sim.sundials.petab.PetabSimulationResult attribute) rdatas_to_measurement_df() (in module amici.importers.petab) (in module amici.sim.sundials.petab.v1) rdatas_to_simulation_df() (in module amici.importers.petab) (in module amici.sim.sundials.petab.v1) read_exp_data_from_hdf5() (in module amici.sim.sundials) read_model_data_from_hdf5() (in module amici.sim.sundials) read_solver_settings_from_hdf5() (in module amici.sim.sundials) reinitialization_state_idxs_presim (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) reinitialization_state_idxs_sim (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) reinitialize_all_fixed_parameter_dependent_initial_states() (amici.sim.sundials.ExpData method) (amici.sim.sundials.SimulationParameters method) reinitialize_all_fixed_parameter_dependent_initial_states_for_presimulation() (amici.sim.sundials.ExpData method) (amici.sim.sundials.SimulationParameters method) reinitialize_all_fixed_parameter_dependent_initial_states_for_simulation() (amici.sim.sundials.ExpData method) (amici.sim.sundials.SimulationParameters method) reinitialize_fixed_parameter_initial_states (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property)

remove_working_dir() (amici.sim.sundials.petab.v1.PetabSimulator method) require_sensitivities_for_all_parameters() (amici.sim.sundials.Model method) res (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) res() (amici.sim.sundials.petab.PetabSimulationResult method) reset() (amici.sim.sundials.CpuTimer method) residuals (amici.sim.sundials.RDataReporting attribute) ReturnData (class in amici.sim.sundials) ReturnDataPtr (class in amici.sim.sundials) ReturnDataView (class in amici.sim.sundials) ReturnValue (class in amici.sim.jax) run_preequilibration() (amici.sim.jax.JAXProblem method) run_preequilibrations() (amici.sim.jax.JAXProblem method) run_simulation() (amici.sim.jax.JAXProblem method) (in module amici.sim.sundials) run_simulation_to_cached_functions() (in module amici.adapters.fiddy) run_simulations() (amici.sim.jax.JAXProblem method) (in module amici.sim.jax) (in module amici.sim.sundials) rz (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

S

s2llh (amici.sim.sundials.petab.PetabSimulationResult attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) s2rz (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) save() (amici.sim.jax.JAXProblem method) SBML sbml2amici() (amici.importers.sbml.SbmlImporter method) sbml2jax() (amici.importers.sbml.SbmlImporter method) sbml_formula (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) sbml_id (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) sbml_model (amici.importers.sbml.SbmlImporter attribute) SBMLException SbmlImporter (class in amici.importers.sbml) scale_parameter() (in module amici.sim.sundials) second (amici.sim.sundials.SensitivityOrder attribute) second_derivative() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) SecondOrderMode (class in amici.sim.sundials) segment_formula() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) sensi (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) sensi_meth (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) SensitivityMethod (class in amici.sim.sundials) SensitivityOrder (class in amici.sim.sundials) set_absolute_tolerance() (amici.sim.sundials.Solver method) set_absolute_tolerance_b() (amici.sim.sundials.Solver method) set_absolute_tolerance_fsa() (amici.sim.sundials.Solver method) set_absolute_tolerance_quadratures() (amici.sim.sundials.Solver method) set_absolute_tolerance_steady_state() (amici.sim.sundials.Solver method) set_absolute_tolerance_steady_state_sensi() (amici.sim.sundials.Solver method) set_add_sigma_residuals() (amici.sim.sundials.Model method) set_all_states_non_negative() (amici.sim.sundials.Model method) set_always_check_finite() (amici.sim.sundials.Model method) set_constraints() (amici.sim.sundials.Solver method) set_event_measurements() (amici.sim.sundials.ExpData method) set_event_noise_scales() (amici.sim.sundials.ExpData method) set_fixed_parameter_by_id() (amici.sim.sundials.Model method) set_fixed_parameter_by_name() (amici.sim.sundials.Model method) set_fixed_parameters() (amici.sim.sundials.Model method) set_fixed_parameters_by_id_regex() (amici.sim.sundials.Model method) set_fixed_parameters_by_name_regex() (amici.sim.sundials.Model method) set_free_parameter_by_id() (amici.sim.sundials.Model method) set_free_parameter_by_name() (amici.sim.sundials.Model method) set_free_parameters() (amici.sim.sundials.Model method) set_free_parameters_by_id_regex() (amici.sim.sundials.Model method) set_free_parameters_by_name_regex() (amici.sim.sundials.Model method) set_initial_state() (amici.sim.sundials.Model method) set_initial_state_sensitivities() (amici.sim.sundials.Model method) set_internal_sensitivity_method() (amici.sim.sundials.Solver method) set_interpolation_type() (amici.sim.sundials.Solver method) set_linear_multistep_method() (amici.sim.sundials.Solver method) set_linear_solver() (amici.sim.sundials.Solver method) set_max_conv_fails() (amici.sim.sundials.Solver method) set_max_nonlin_iters() (amici.sim.sundials.Solver method) set_max_step_size() (amici.sim.sundials.Solver method) set_max_steps() (amici.sim.sundials.Solver method) set_max_steps_backward_problem() (amici.sim.sundials.Solver method) set_max_time() (amici.sim.sundials.Solver method) set_measurements() (amici.sim.sundials.ExpData method) set_minimum_sigma_residuals() (amici.sim.sundials.Model method) set_model_settings() (in module amici.sim.sundials) set_n_max_event() (amici.sim.sundials.Model method) set_newton_damping_factor_lower_bound() (amici.sim.sundials.Solver method) set_newton_damping_factor_mode() (amici.sim.sundials.Solver method) set_newton_max_steps() (amici.sim.sundials.Solver method) set_newton_step_steady_state_check() (amici.sim.sundials.Solver method) set_noise_scales() (amici.sim.sundials.ExpData method) set_non_linear_solver_iteration() (amici.sim.sundials.Solver method) set_parameter_list() (amici.sim.sundials.Model method) set_parameter_scale() (amici.sim.sundials.Model method) set_parameters() (amici.sim.sundials.petab.v1.PetabProblem method) set_reinitialization_state_idxs() (amici.sim.sundials.Model method) set_reinitialize_fixed_parameter_initial_states() (amici.sim.sundials.Model method) set_relative_tolerance() (amici.sim.sundials.Solver method) set_relative_tolerance_b() (amici.sim.sundials.Solver method) set_relative_tolerance_fsa() (amici.sim.sundials.Solver method) set_relative_tolerance_quadratures() (amici.sim.sundials.Solver method) set_relative_tolerance_steady_state() (amici.sim.sundials.Solver method) set_relative_tolerance_steady_state_sensi() (amici.sim.sundials.Solver method) set_return_data_reporting_mode() (amici.sim.sundials.Solver method) set_sensi_steady_state_check() (amici.sim.sundials.Solver method) set_sensitivity_method() (amici.sim.sundials.Solver method) set_sensitivity_method_pre_equilibration() (amici.sim.sundials.Solver method) set_sensitivity_order() (amici.sim.sundials.Solver method) set_stability_limit_flag() (amici.sim.sundials.Solver method) set_state_is_non_negative() (amici.sim.sundials.Model method) set_state_ordering() (amici.sim.sundials.Solver method) set_steady_state_computation_mode() (amici.sim.sundials.Model method) set_steady_state_sensi_tolerance_factor() (amici.sim.sundials.Solver method)

set_steady_state_sensitivity_mode() (amici.sim.sundials.Model method) set_steady_state_tolerance_factor() (amici.sim.sundials.Solver method) set_steadystate_mask() (amici.sim.sundials.Model method) set_t0() (amici.sim.sundials.Model method) set_t0_preeq() (amici.sim.sundials.Model method) set_timepoints() (amici.sim.sundials.ExpData method) (amici.sim.sundials.Model method) set_unscaled_initial_state_sensitivities() (amici.sim.sundials.Model method) severity (amici.sim.sundials.LogItem property) sigma_res (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) sigmay (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) sigmaz (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) simulate() (amici.sim.sundials.Model method) (amici.sim.sundials.petab.PetabSimulator method) (amici.sim.sundials.petab.v1.PetabSimulator method) simulate_condition() (amici.sim.jax.JAXModel method) simulate_condition_unjitted() (amici.sim.jax.JAXModel method) simulate_petab() (in module amici.sim.sundials.petab.v1) simulate_petab_to_cached_functions() (in module amici.adapters.fiddy) simulate_petab_v2_to_cached_functions() (in module amici.adapters.fiddy) simulate_without_noise() (amici.sim.sundials.petab.v1.PetabSimulator method) simulation (amici.sim.sundials.FixedParameterContext attribute) simulation periods simulation_conditions (amici.sim.jax.JAXProblem attribute) simulation_status_to_str() (in module amici.sim.sundials) SimulationParameters (class in amici.sim.sundials) simultaneous (amici.sim.sundials.InternalSensitivityMethod attribute) sllh (amici.sim.sundials.petab.PetabSimulationResult attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) smoothness (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property) solver (amici.sim.sundials.petab.PetabSimulator property) Solver (class in amici.sim.sundials) SolverPtr (class in amici.sim.sundials) SPBCG (amici.sim.sundials.LinearSolver attribute) SPGMR (amici.sim.sundials.LinearSolver attribute) SPTFQMR (amici.sim.sundials.LinearSolver attribute) squared_L2_norm_of_curvature() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method) sres (amici.sim.sundials.petab.PetabSimulationResult attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) srz (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ssigmay (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) ssigmaz (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) staggered (amici.sim.sundials.InternalSensitivityMethod attribute) staggered1 (amici.sim.sundials.InternalSensitivityMethod attribute) start (amici.importers.sbml.splines.UniformGrid property) start_timer() (amici.sim.sundials.Solver method) state_ids (amici.sim.jax.JAXModel property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) state_ids_solver (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) state_names (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) state_names_solver (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) status (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) steady state SteadyStateComputationMode (class in amici.sim.sundials) SteadyStateSensitivityMode (class in amici.sim.sundials) SteadyStateStatus (class in amici.sim.sundials) SteadyStateStatusVector (class in amici.sim.sundials) step (amici.importers.sbml.splines.UniformGrid property) stop (amici.importers.sbml.splines.UniformGrid property) StringDoubleMap (class in amici.sim.sundials) StringVector (class in amici.sim.sundials) success (amici.sim.sundials.SteadyStateStatus attribute) SUNDIALS SuperLUMT (amici.sim.sundials.LinearSolver attribute) SWIG switch_forward_sensis_off() (amici.sim.sundials.Solver method) sx (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) sx0 (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) (amici.sim.sundials.SimulationParameters property) sx_ss (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) sy (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) sz (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

T

t0() (amici.sim.sundials.Model method) t0_preeq() (amici.sim.sundials.Model method) t_last (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) t_presim (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) t_start (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property)

t_start_preeq (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) tcl (amici.sim.jax.ReturnValue attribute) time_exceeded() (amici.sim.sundials.Solver method) timepoints (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.SimulationParameters property) ts (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

U

ubw (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

unflatten_simulation_df() (in module amici.importers.petab) UniformGrid (class in amici.importers.sbml.splines) unscale_parameter() (in module amici.sim.sundials) update_parameters() (amici.sim.jax.JAXProblem method) uses_thread_clock (amici.sim.sundials.CpuTimer attribute)

V

validate() (amici.sim.sundials.Model method) (amici.sim.sundials.ModelDimensions method) (amici.sim.sundials.ReturnData method)

values() (amici.sim.sundials.ExpDataView method) (amici.sim.sundials.ReturnDataView method) values_at_nodes (amici.importers.sbml.splines.AbstractSpline property) (amici.importers.sbml.splines.CubicHermiteSpline property)

W

w (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) w_recursion_depth (amici.sim.sundials.Model property) (amici.sim.sundials.ModelDimensions property) (amici.sim.sundials.ModelPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

warning (amici.sim.sundials.LogSeverity attribute) write_exp_data_to_hdf5() (in module amici.sim.sundials) write_return_data_to_hdf5() (in module amici.sim.sundials) write_solver_settings_to_hdf5() (in module amici.sim.sundials)

X

x (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) x0 (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.ExpData property) (amici.sim.sundials.ExpDataPtr property) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) (amici.sim.sundials.SimulationParameters property)

x0_solver (amici.sim.jax.ReturnValue attribute) x_solver (amici.sim.jax.ReturnValue attribute) x_ss (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property) xdot (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

Y

y (amici.sim.jax.ReturnValue attribute) (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)

y_scaled() (amici.importers.sbml.splines.AbstractSpline method) (amici.importers.sbml.splines.CubicHermiteSpline method)

Z

z (amici.sim.sundials.ReturnData property) (amici.sim.sundials.ReturnDataPtr property)