AMICI C++ API

AMICI C++ library functions

Class Hierarchy

• • Namespace amici
    • Struct BwdSimWorkspace
    • Struct DEStateView
    • Struct Discontinuity
    • Struct FwdSimWorkspace
    • Struct LogItem
    • Struct ModelDimensions
    • Struct ModelState
    • Struct ModelStateDerived
    • Struct PendingEvent
    • Struct PeriodResult
    • Struct SimulationState
    • Struct SolutionState
    • Class AbstractModel
    • Class AbstractSpline
    • Class AmiException
    • Class AmiVector
    • Class AmiVectorArray
    • Class BackwardProblem
    • Class ConditionContext
    • Class ContextManager
    • Class CpuTimer
    • Class CvodeException
    • Class CVodeSolver
    • Class Event
    • Class EventHandlingBwdSimulator
    • Class EventHandlingSimulator
    • Class EventQueue
    • Class ExpData
    • Class FinalStateStorer
    • Class ForwardProblem
    • Class HermiteSpline
    • Class IDAException
    • Class IDASolver
    • Class IntegrationFailure
    • Class IntegrationFailureB
    • Class Logger
    • Class Model
    • Class Model_DAE
    • Class Model_ODE
    • Class ModelContext
    • Class NewtonFailure
    • Class NewtonsMethod
    • Class NewtonSolver
    • Class ReturnData
    • Class SetupFailure
    • Class SimulationParameters
    • Class Solver
    • Class SteadyStateBackwardProblem
    • Class SteadyStateProblem
    • Class SUNLinSolBand
    • Class SUNLinSolDense
    • Class SUNLinSolKLU
    • Class SUNLinSolPCG
    • Class SUNLinSolSPBCGS
    • Class SUNLinSolSPFGMR
    • Class SUNLinSolSPGMR
    • Class SUNLinSolSPTFQMR
    • Class SUNLinSolWrapper
    • Class SUNMatrixWrapper
    • Class SUNNonLinSolFixedPoint
    • Class SUNNonLinSolNewton
    • Class SUNNonLinSolWrapper
    • Class WRMSComputer
    • Enum BLASLayout
    • Enum BLASTranspose
    • Enum Constraint
    • Enum FixedParameterContext
    • Enum InternalSensitivityMethod
    • Enum InterpolationType
    • Enum LinearMultistepMethod
    • Enum LinearSolver
    • Enum LogSeverity
    • Enum ModelQuantity
    • Enum NewtonDampingFactorMode
    • Enum NonlinearSolverIteration
    • Enum ObservableScaling
    • Enum ParameterScaling
    • Enum RDataReporting
    • Enum SecondOrderMode
    • Enum SensitivityMethod
    • Enum SensitivityOrder
    • Enum SplineBoundaryCondition
    • Enum SplineExtrapolation
    • Enum SteadyStateComputationMode
    • Enum SteadyStateSensitivityMode
    • Enum SteadyStateStatus

File Hierarchy

• • Directory include
    • Directory amici
      • File abstract_model.h
      • File amici.h
      • File backwardproblem.h
      • File cblas.h
      • File defines.h
      • File edata.h
      • File event.h
      • File exception.h
      • File forwardproblem.h
      • File hdf5.h
      • File logging.h
      • File misc.h
      • File model.h
      • File model_dae.h
      • File model_dimensions.h
      • File model_ode.h
      • File model_state.h
      • File newton_solver.h
      • File rdata.h
      • File serialization.h
      • File simulation_parameters.h
      • File solver.h
      • File solver_cvodes.h
      • File solver_idas.h
      • File splinefunctions.h
      • File steadystateproblem.h
      • File sundials_linsol_wrapper.h
      • File sundials_matrix_wrapper.h
      • File vector.h
      • File version.in.h

Full API

Namespaces

• Namespace amici
  • Namespaces
  • Classes
  • Enums
  • Functions
  • Typedefs
  • Variables

• Namespace amici::hdf5
  • Functions

• Namespace boost
  • Namespaces

• Namespace boost::serialization
  • Functions

• Namespace gsl
  • Functions

• Namespace std

Classes and Structs

• Struct BwdSimWorkspace
  • Struct Documentation
    • amici::BwdSimWorkspace
      • BwdSimWorkspace()
      • model_
      • xB_
      • dxB_
      • xQB_
      • nroots_
      • discs_
      • which

• Struct DEStateView
  • Struct Documentation
    • amici::DEStateView
      • DEStateView()
      • DEStateView()
      • t
      • x
      • dx

• Struct Discontinuity
  • Struct Documentation
    • amici::Discontinuity
      • Discontinuity()
      • time
      • x_post
      • x_pre
      • xdot_post
      • xdot_pre
      • root_info
      • h_pre
      • dx_post
      • total_cl_pre

• Struct FwdSimWorkspace
  • Struct Documentation
    • amici::FwdSimWorkspace
      • FwdSimWorkspace()
      • sol
      • x_old
      • xdot
      • xdot_old
      • sdx
      • stau
      • roots_found
      • tlastroot
      • pending_events
      • rval_tmp
      • nroots
      • rootvals

• Struct LogItem
  • Struct Documentation
    • amici::LogItem
      • LogItem()
      • LogItem()
      • severity
      • identifier
      • message

• Struct ModelDimensions
  • Inheritance Relationships
    • Derived Types
  • Struct Documentation
    • amici::ModelDimensions
      • validate()
      • nx_rdata
      • nxtrue_rdata
      • nx_solver
      • nxtrue_solver
      • nx_solver_reinit
      • np
      • nk
      • ny
      • nytrue
      • nz
      • nztrue
      • ne
      • ne_solver
      • nspl
      • nw
      • ndwdx
      • ndwdp
      • ndwdw
      • ndxdotdw
      • ndJydy
      • ndxrdatadxsolver
      • ndxrdatadtcl
      • ndtotal_cldx_rdata
      • nnz
      • nJ
      • ubw
      • lbw
      • ndxdotdp_explicit
      • ndxdotdx_explicit
      • w_recursion_depth

• Struct ModelState
  • Struct Documentation
    • amici::ModelState
      • ModelState()
      • ModelState()
      • h
      • total_cl
      • stotal_cl
      • unscaled_parameters
      • fixed_parameters
      • plist

• Struct ModelStateDerived
  • Struct Documentation
    • amici::ModelStateDerived
      • ModelStateDerived()
      • ModelStateDerived()
      • ModelStateDerived()
      • sunctx_
      • J_
      • JB_
      • dxdotdw_
      • dwdx_
      • dwdp_
      • MSparse_
      • dfdx_
      • dxdotdp_full
      • dxdotdp_explicit
      • dxdotdp_implicit
      • dxdotdx_explicit
      • dxdotdx_implicit
      • dx_rdatadx_solver
      • dx_rdatadtcl
      • dtotal_cldx_rdata
      • dxdotdp
      • dJydy_
      • dJydsigma_
      • dJydx_
      • dJydp_
      • dJzdz_
      • dJzdsigma_
      • dJrzdz_
      • dJrzdsigma_
      • dJzdx_
      • dJzdp_
      • dzdx_
      • dzdp_
      • drzdx_
      • drzdp_
      • dydp_
      • dydx_
      • w_
      • sx_
      • sy_
      • x_rdata_
      • sx_rdata_
      • y_
      • sigmay_
      • dsigmaydp_
      • dsigmaydy_
      • z_
      • rz_
      • sigmaz_
      • dsigmazdp_
      • deltax_
      • deltasx_
      • deltaxB_
      • deltaqB_
      • sspl_
      • x_pos_tmp_
      • spl_
      • dwdp_hierarchical_
      • dwdw_
      • dwdx_hierarchical_
      • dJydy_dense_

• Struct PendingEvent
  • Struct Documentation
    • amici::PendingEvent
      • event
      • idx
      • state_old

• Struct PeriodResult
  • Struct Documentation
    • amici::PeriodResult
      • discs
      • timepoint_states_
      • event_states_
      • initial_state_
      • final_state_

• Struct SimulationState
  • Struct Documentation
    • amici::SimulationState
      • sol
      • mod

• Struct SolutionState
  • Struct Documentation
    • amici::SolutionState
      • SolutionState()
      • SolutionState()
      • t
      • x
      • dx
      • sx

• Class AbstractModel
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • amici::AbstractModel
      • ~AbstractModel()
      • create_solver()
      • froot()
      • fxdot()
      • fsxdot()
      • fxBdot_ss()
      • fJSparseB_ss()
      • writeSteadystateJB()
      • fJ()
      • fJB()
      • fJSparse()
      • fJSparseB()
      • fJDiag()
      • fdxdotdp()
      • fJv()
      • get_amici_version()
      • get_amici_commit()
      • fx0()
      • is_fixed_parameter_state_reinitialization_allowed()
      • fx0_fixedParameters()
      • fsx0_fixedParameters()
      • fsx0()
      • fdx0()
      • fstau()
      • fy()
      • fdydp()
      • fdydx()
      • fz()
      • fsz()
      • frz()
      • fsrz()
      • fdzdp()
      • fdzdx()
      • fdrzdp()
      • fdrzdx()
      • fdeltax()
      • fdeltasx()
      • fdeltaxB()
      • fdeltaqB()
      • fsigmay()
      • fdsigmaydp()
      • fdsigmaydy()
      • fsigmaz()
      • fdsigmazdp()
      • fJy()
      • fJz()
      • fJrz()
      • fdJydy()
      • fdJydy_colptrs()
      • fdJydy_rowvals()
      • fdJydsigma()
      • fdJzdz()
      • fdJzdsigma()
      • fdJrzdz()
      • fdJrzdsigma()
      • fw()
      • fdwdp()
      • fdwdp_colptrs()
      • fdwdp_rowvals()
      • fdwdx()
      • fdwdx_colptrs()
      • fdwdx_rowvals()
      • fdwdw()
      • fdwdw_colptrs()
      • fdwdw_rowvals()
      • fdx_rdatadx_solver()
      • fdx_rdatadx_solver_colptrs()
      • fdx_rdatadx_solver_rowvals()
      • fdx_rdatadp()
      • fdx_rdatadtcl()
      • fdx_rdatadtcl_colptrs()
      • fdx_rdatadtcl_rowvals()
      • fdtotal_cldp()
      • fdtotal_cldx_rdata()
      • fdtotal_cldx_rdata_colptrs()
      • fdtotal_cldx_rdata_rowvals()
      • fcreate_splines()
      • fdspline_valuesdp()
      • fdspline_slopesdp()
      • fexplicit_roots()

• Class AbstractSpline
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • amici::AbstractSpline
      • AbstractSpline()
      • AbstractSpline()
      • ~AbstractSpline()
      • compute_coefficients()
      • compute_coefficients_sensi()
      • get_value()
      • get_value_scaled()
      • get_node_value()
      • get_node_value_scaled()
      • get_sensitivity()
      • get_sensitivity()
      • get_sensitivity_scaled()
      • compute_final_value()
      • compute_final_sensitivity()
      • get_final_value()
      • get_final_value_scaled()
      • get_final_sensitivity()
      • get_final_sensitivity_scaled()
      • get_equidistant_spacing()
      • get_logarithmic_parametrization()
      • n_nodes()
      • set_final_value_scaled()
      • set_final_sensitivity_scaled()
      • nodes_
      • node_values_
      • coefficients
      • coefficients_extrapolate
      • coefficients_sensi
      • coefficients_extrapolate_sensi

• Class AmiException
  • Inheritance Relationships
    • Base Type
    • Derived Types
  • Class Documentation
    • amici::AmiException
      • AmiException()
      • AmiException()
      • what()
      • getBacktrace()
      • storeBacktrace()
      • storeMessage()

• Class AmiVector
  • Class Documentation
    • amici::AmiVector
      • AmiVector()
      • AmiVector()
      • AmiVector()
      • AmiVector()
      • AmiVector()
      • AmiVector()
      • AmiVector()
      • ~AmiVector()
      • operator=()
      • operator*=()
      • operator/=()
      • begin()
      • end()
      • data()
      • data()
      • get_nvector()
      • get_nvector()
      • get_vector()
      • size()
      • zero()
      • minus()
      • set()
      • operator[]()
      • operator[]()
      • at()
      • at()
      • copy()
      • abs()
      • get_ctx()
      • set_ctx()
      • boost::serialization::serialize

• Class AmiVectorArray
  • Class Documentation
    • amici::AmiVectorArray
      • AmiVectorArray()
      • AmiVectorArray()
      • AmiVectorArray()
      • ~AmiVectorArray()
      • operator=()
      • data()
      • data()
      • at()
      • at()
      • get_nvector_array()
      • get_nvector()
      • get_nvector()
      • operator[]()
      • operator[]()
      • size()
      • zero()
      • flatten_to_vector()
      • copy()
      • set_ctx()

• Class BackwardProblem
  • Class Documentation
    • amici::BackwardProblem
      • BackwardProblem()
      • workBackwardProblem()
      • get_adjoint_state_pre_preeq()
      • get_adjoint_quadrature_pre_preeq()
      • get_adjoint_state()
      • get_adjoint_quadrature()
      • get_posteq_bwd_problem()
      • get_preeq_bwd_problem()

• Class ConditionContext
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ConditionContext
      • ConditionContext()
      • operator=()
      • ~ConditionContext()
      • apply_condition()
      • restore()

• Class ContextManager
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • amici::ContextManager
      • ContextManager()
      • ContextManager()
      • ContextManager()

• Class CpuTimer
  • Class Documentation
    • amici::CpuTimer
      • CpuTimer()
      • reset()
      • elapsed_seconds()
      • elapsed_milliseconds()
      • uses_thread_clock

• Class CvodeException
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::CvodeException
      • CvodeException()

• Class CVodeSolver
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::CVodeSolver
      • ~CVodeSolver()
      • clone()
      • get_class_name()
      • reinit()
      • sens_reinit()
      • sens_toggle_off()
      • reinit_b()
      • reinit_quad_b()
      • solve()
      • solve_f()
      • solve_b()
      • get_dky()
      • get_sens_dky()
      • get_quad_dky_b()
      • get_dky_b()
      • get_root_info()
      • set_stop_time()
      • turn_off_root_finding()
      • get_model()
      • set_linear_solver()
      • set_linear_solver_b()
      • set_non_linear_solver()
      • set_non_linear_solver_sens()
      • set_non_linear_solver_b()
      • Solver()
      • Solver()
      • calc_ic()
      • calc_ic_b()
      • get_b()
      • get_sens()
      • get_quad_b()
      • get_quad()
      • get_quad_dky()
      • reinit_post_process_f()
      • reinit_post_process_b()
      • reInit_post_process()
      • allocate_solver()
      • set_ss_tolerances()
      • set_sens_ss_tolerances()
      • set_sens_err_con()
      • set_quad_err_con_b()
      • set_quad_err_con()
      • set_user_data()
      • set_user_data_b()
      • set_max_num_steps()
      • set_stab_lim_det()
      • set_stab_lim_det_b()
      • set_id()
      • set_suppress_alg()
      • reset_state()
      • set_sens_params()
      • adj_init()
      • quad_init()
      • allocate_solver_b()
      • set_ss_tolerances_b()
      • quad_ss_tolerances_b()
      • quad_ss_tolerances()
      • set_max_num_steps_b()
      • diag()
      • diag_b()
      • get_num_steps()
      • get_num_rhs_evals()
      • get_num_err_test_fails()
      • get_num_non_lin_solv_conv_fails()
      • get_last_order()
      • get_adj_b_mem()
      • init()
      • init_steady_state()
      • sens_init_1()
      • b_init()
      • qb_init()
      • root_init()
      • set_dense_jac_fn()
      • set_sparse_jac_fn()
      • set_band_jac_fn()
      • set_jac_times_vec_fn()
      • set_dense_jac_fn_b()
      • set_sparse_jac_fn_b()
      • set_band_jac_fn_b()
      • set_jac_times_vec_fn_b()
      • set_sparse_jac_fn_ss()
      • apply_max_nonlin_iters()
      • apply_max_conv_fails()
      • apply_constraints()
      • apply_max_step_size()
      • boost::serialization::serialize
      • operator==

• Class Event
  • Class Documentation
    • amici::Event
      • Event()
      • get_id()
      • get_initial_value()
      • get_priority()
      • uses_values_from_trigger_time()

• Class EventHandlingBwdSimulator
  • Class Documentation
    • amici::EventHandlingBwdSimulator
      • EventHandlingBwdSimulator()
      • run()

• Class EventHandlingSimulator
  • Class Documentation
    • amici::EventHandlingSimulator
      • EventHandlingSimulator()
      • run()
      • run_steady_state()
      • get_root_counter()
      • get_event_counter()
      • get_simulation_state()
      • handle_events()
      • handle_initial_events()
      • result
      • it_

• Class EventQueue
  • Class Documentation
    • amici::EventQueue
      • EventQueue()
      • empty()
      • push()
      • pop()

• Class ExpData
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ExpData
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ~ExpData()
      • nytrue()
      • nztrue()
      • nmaxevent()
      • nt()
      • set_timepoints()
      • get_timepoints()
      • get_timepoint()
      • set_observed_data()
      • set_observed_data()
      • is_set_observed_data()
      • get_observed_data()
      • get_observed_data_ptr()
      • set_observed_data_std_dev()
      • set_observed_data_std_dev()
      • set_observed_data_std_dev()
      • set_observed_data_std_dev()
      • is_set_observed_data_std_dev()
      • get_observed_data_std_dev()
      • get_observed_data_std_dev_ptr()
      • set_observed_events()
      • set_observed_events()
      • is_set_observed_events()
      • get_observed_events()
      • get_observed_events_ptr()
      • set_observed_events_std_dev()
      • set_observed_events_std_dev()
      • set_observed_events_std_dev()
      • set_observed_events_std_dev()
      • is_set_observed_events_std_dev()
      • get_observed_events_std_dev()
      • get_observed_events_std_dev_ptr()
      • clear_observations()
      • id
      • apply_dimensions()
      • apply_data_dimension()
      • apply_event_dimension()
      • check_data_dimension()
      • check_events_dimension()
      • nytrue_
      • nztrue_
      • nmaxevent_
      • observed_data_
      • observed_data_std_dev_
      • observed_events_
      • observed_events_std_dev_
      • operator==

• Class FinalStateStorer
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::FinalStateStorer
      • FinalStateStorer()
      • operator=()
      • ~FinalStateStorer()

• Class ForwardProblem
  • Class Documentation
    • amici::ForwardProblem
      • ForwardProblem()
      • ~ForwardProblem()
      • run()
      • get_adjoint_updates()
      • get_state_sensitivity()
      • get_discontinuities()
      • get_dJzdx()
      • get_current_time_iteration()
      • get_final_time()
      • get_event_counter()
      • get_simulation_state_timepoint()
      • get_simulation_state_event()
      • get_initial_simulation_state()
      • get_final_simulation_state()
      • get_preeq_problem()
      • get_preeq_problem()
      • get_posteq_problem()
      • get_posteq_problem()
      • get_presimulation_result()
      • was_preequilibrated()
      • model
      • solver
      • edata

• Class HermiteSpline
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::HermiteSpline
      • HermiteSpline()
      • HermiteSpline()
      • compute_coefficients()
      • compute_coefficients_sensi()
      • compute_final_value()
      • compute_final_sensitivity()
      • get_value_scaled()
      • get_node_derivative()
      • get_node_derivative_scaled()
      • get_sensitivity_scaled()
      • get_node_derivative_by_fd()

• Class IDAException
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::IDAException
      • IDAException()

• Class IDASolver
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::IDASolver
      • ~IDASolver()
      • clone()
      • get_class_name()
      • reinit_post_process_f()
      • reinit_post_process_b()
      • reinit()
      • sens_reinit()
      • sens_toggle_off()
      • reinit_b()
      • reinit_quad_b()
      • quad_ss_tolerances_b()
      • quad_ss_tolerances()
      • solve()
      • solve_f()
      • solve_b()
      • get_root_info()
      • get_dky()
      • get_sens()
      • get_sens_dky()
      • get_b()
      • get_dky_b()
      • get_quad_b()
      • get_quad_dky_b()
      • get_quad()
      • get_quad_dky()
      • calc_ic()
      • calc_ic_b()
      • set_stop_time()
      • turn_off_root_finding()
      • get_model()
      • set_linear_solver()
      • set_linear_solver_b()
      • set_non_linear_solver()
      • set_non_linear_solver_sens()
      • set_non_linear_solver_b()
      • Solver()
      • Solver()
      • reinit_post_process()
      • allocate_solver()
      • set_ss_tolerances()
      • set_sens_ss_tolerances()
      • set_sens_err_con()
      • set_quad_err_con_b()
      • set_quad_err_con()
      • set_user_data()
      • set_user_data_b()
      • set_max_num_steps()
      • set_stab_lim_det()
      • set_stab_lim_det_b()
      • set_id()
      • set_suppress_alg()
      • reset_state()
      • set_sens_params()
      • adj_init()
      • quad_init()
      • allocate_solver_b()
      • set_max_num_steps_b()
      • set_ss_tolerances_b()
      • diag()
      • diag_b()
      • get_num_steps()
      • get_num_rhs_evals()
      • get_num_err_test_fails()
      • get_num_non_lin_solv_conv_fails()
      • get_last_order()
      • get_adj_b_mem()
      • init()
      • init_steady_state()
      • sens_init_1()
      • b_init()
      • qb_init()
      • root_init()
      • set_dense_jac_fn()
      • set_sparse_jac_fn()
      • set_band_jac_fn()
      • set_jac_times_vec_fn()
      • set_dense_jac_fn_b()
      • set_sparse_jac_fn_b()
      • set_band_jac_fn_b()
      • set_jac_times_vec_fn_b()
      • set_sparse_jac_fn_ss()
      • apply_max_nonlin_iters()
      • apply_max_conv_fails()
      • apply_constraints()
      • apply_max_step_size()

• Class IntegrationFailure
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::IntegrationFailure
      • IntegrationFailure()
      • error_code
      • time

• Class IntegrationFailureB
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::IntegrationFailureB
      • IntegrationFailureB()
      • error_code
      • time

• Class Logger
  • Class Documentation
    • amici::Logger
      • Logger()
      • log()
      • log()
      • items

• Class Model
  • Inheritance Relationships
    • Base Types
    • Derived Types
  • Class Documentation
    • amici::Model
      • Model()
      • Model()
      • ~Model()
      • operator=()
      • clone()
      • initialize()
      • reinitialize()
      • initialize_b()
      • initialize_state()
      • initialize_state_sensitivities()
      • initialize_splines()
      • initialize_spline_sensitivities()
      • initialize_events()
      • reinit_events()
      • reinit_explicit_roots()
      • nplist()
      • np()
      • nk()
      • ncl()
      • nx_reinit()
      • k()
      • n_max_event()
      • set_n_max_event()
      • nt()
      • get_parameter_scale()
      • set_parameter_scale()
      • set_parameter_scale()
      • get_unscaled_parameters()
      • get_parameters()
      • get_parameter_by_id()
      • get_parameter_by_name()
      • set_parameters()
      • set_parameter_by_id()
      • set_parameter_by_id()
      • set_parameters_by_id_regex()
      • set_parameter_by_name()
      • set_parameter_by_name()
      • set_parameters_by_name_regex()
      • get_fixed_parameters()
      • get_fixed_parameter_by_id()
      • get_fixed_parameter_by_name()
      • set_fixed_parameters()
      • set_fixed_parameter_by_id()
      • set_fixed_parameters_by_id_regex()
      • set_fixed_parameter_by_name()
      • set_fixed_parameters_by_name_regex()
      • get_name()
      • has_parameter_names()
      • get_parameter_names()
      • has_state_names()
      • get_state_names()
      • get_state_names_solver()
      • has_fixed_parameter_names()
      • get_fixed_parameter_names()
      • has_observable_names()
      • get_observable_names()
      • has_expression_names()
      • get_expression_names()
      • has_parameter_ids()
      • get_parameter_ids()
      • has_state_ids()
      • get_state_ids()
      • get_state_ids_solver()
      • has_fixed_parameter_ids()
      • get_fixed_parameter_ids()
      • has_observable_ids()
      • get_observable_ids()
      • has_expression_ids()
      • get_expression_ids()
      • has_quadratic_llh()
      • get_timepoints()
      • get_timepoint()
      • set_timepoints()
      • t0()
      • set_t0()
      • t0_preeq()
      • set_t0_preeq()
      • get_state_is_non_negative()
      • set_state_is_non_negative()
      • set_all_states_non_negative()
      • get_model_state()
      • set_model_state()
      • set_minimum_sigma_residuals()
      • get_minimum_sigma_residuals()
      • set_add_sigma_residuals()
      • get_add_sigma_residuals()
      • get_parameter_list()
      • plist()
      • set_parameter_list()
      • get_initial_state()
      • get_initial_state()
      • set_initial_state()
      • has_custom_initial_state()
      • get_initial_state_sensitivities()
      • get_initial_state_sensitivities()
      • set_initial_state_sensitivities()
      • has_custom_initial_state_sensitivities()
      • set_unscaled_initial_state_sensitivities()
      • set_steady_state_computation_mode()
      • get_steady_state_computation_mode()
      • set_steady_state_sensitivity_mode()
      • get_steady_state_sensitivity_mode()
      • set_reinitialize_fixed_parameter_initial_states()
      • get_reinitialize_fixed_parameter_initial_states()
      • require_sensitivities_for_all_parameters()
      • get_expression()
      • get_observable()
      • get_observable_scaling()
      • get_observable_sensitivity()
      • get_observable_sigma()
      • get_observable_sigma_sensitivity()
      • add_observable_objective()
      • add_observable_objective_sensitivity()
      • add_partial_observable_objective_sensitivity()
      • get_adjoint_state_observable_update()
      • get_event()
      • get_event_sensitivity()
      • get_unobserved_event_sensitivity()
      • get_event_regularization()
      • get_event_regularization_sensitivity()
      • get_event_sigma()
      • get_event_sigma_sensitivity()
      • add_event_objective()
      • add_event_objective_regularization()
      • add_event_objective_sensitivity()
      • add_partial_event_objective_sensitivity()
      • get_adjoint_state_event_update()
      • get_event_time_sensitivity()
      • add_state_event_update()
      • add_state_sensitivity_event_update()
      • add_adjoint_state_event_update()
      • add_adjoint_quadrature_event_update()
      • update_heaviside()
      • check_finite()
      • check_finite()
      • check_finite()
      • set_always_check_finite()
      • get_always_check_finite()
      • fx0()
      • fx0_fixedParameters()
      • fsx0()
      • fsx0_fixedParameters()
      • fsdx0()
      • fx_rdata()
      • fsx_rdata()
      • set_reinitialization_state_idxs()
      • get_reinitialization_state_idxs()
      • get_dxdotdp_full()
      • get_trigger_timepoints()
      • get_steadystate_mask()
      • set_steadystate_mask()
      • get_event()
      • get_any_state_nonnegative()
      • fexplicit_roots()
      • get_id_list()
      • get_second_order_mode()
      • get_logger()
      • set_logger()
      • get_explicit_roots()
      • fdeltaqB()
      • fdeltasx()
      • fdeltax()
      • fdeltaxB()
      • fdJrzdsigma()
      • fdJrzdz()
      • fdJydsigma()
      • fdJydy()
      • fdJydy_colptrs()
      • fdJydy_rowvals()
      • fdJzdsigma()
      • fdJzdz()
      • fdrzdp()
      • fdrzdx()
      • fdsigmaydp()
      • fdsigmaydy()
      • fdsigmazdp()
      • fdtotal_cldp()
      • fdtotal_cldx_rdata()
      • fdtotal_cldx_rdata_colptrs()
      • fdtotal_cldx_rdata_rowvals()
      • fdwdp()
      • fdwdp_colptrs()
      • fdwdp_rowvals()
      • fdwdw()
      • fdwdw_colptrs()
      • fdwdw_rowvals()
      • fdwdx()
      • fdwdx_colptrs()
      • fdwdx_rowvals()
      • fdx_rdatadp()
      • fdx_rdatadtcl()
      • fdx_rdatadtcl_colptrs()
      • fdx_rdatadtcl_rowvals()
      • fdx_rdatadx_solver()
      • fdx_rdatadx_solver_colptrs()
      • fdx_rdatadx_solver_rowvals()
      • fdydp()
      • fdydx()
      • fdzdp()
      • fdzdx()
      • fJrz()
      • fJy()
      • fJz()
      • frz()
      • fsigmay()
      • fsigmaz()
      • fsrz()
      • fstau()
      • fsx0()
      • fsx0_fixedParameters()
      • fsz()
      • fw()
      • fx0()
      • fx0_fixedParameters()
      • fy()
      • fz()
      • write_slice_event()
      • write_sensitivity_slice_event()
      • write_llh_sensitivity_slice()
      • check_llh_buffer_size()
      • initialize_vectors()
      • fy()
      • fdydp()
      • fdydx()
      • fsigmay()
      • fdsigmaydp()
      • fdsigmaydy()
      • fdJydy()
      • fdJydsigma()
      • fdJydp()
      • fdJydx()
      • fz()
      • fdzdp()
      • fdzdx()
      • frz()
      • fdrzdp()
      • fdrzdx()
      • fsigmaz()
      • fdsigmazdp()
      • fdJzdz()
      • fdJzdsigma()
      • fdJzdp()
      • fdJzdx()
      • fdJrzdz()
      • fdJrzdsigma()
      • fspl()
      • fsspl()
      • fw()
      • fdwdp()
      • fdwdx()
      • fdwdw()
      • fx_rdata()
      • fsx_rdata()
      • fx_solver()
      • fsx_solver()
      • ftotal_cl()
      • fstotal_cl()
      • compute_x_pos()
      • compute_x_pos()
      • state_
      • derived_state_
      • splines_
      • z2event_
      • x0data_
      • sx0data_
      • state_is_non_negative_
      • any_state_non_negative_
      • nmaxevent_
      • steadystate_computation_mode_
      • steadystate_sensitivity_mode_
      • always_check_finite_
      • sigma_res_
      • min_sigma_
      • boost::serialization::serialize
      • operator==

• Class Model_DAE
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::Model_DAE
      • Model_DAE()
      • Model_DAE()
      • fJ()
      • fJ()
      • fJB()
      • fJB()
      • fJSparse()
      • fJSparse()
      • fJSparseB()
      • fJSparseB()
      • fJDiag()
      • fJv()
      • fJv()
      • fJvB()
      • froot()
      • froot()
      • fxdot()
      • fxdot()
      • fxBdot()
      • fqBdot()
      • fxBdot_ss()
      • fxBdot_ss()
      • fqBdot_ss()
      • fJSparseB_ss()
      • writeSteadystateJB()
      • fdxdotdp()
      • fdxdotdp()
      • fsxdot()
      • fsxdot()
      • fM()
      • create_solver()
      • fJSparse()
      • froot()
      • fxdot()
      • fdxdotdp()
      • fdxdotdp_explicit()
      • fdxdotdp_explicit_colptrs()
      • fdxdotdp_explicit_rowvals()
      • fdxdotdx_explicit()
      • fdxdotdx_explicit_colptrs()
      • fdxdotdx_explicit_rowvals()
      • fdxdotdw()
      • fdxdotdw_colptrs()
      • fdxdotdw_rowvals()
      • fdxdotdw()
      • fM()

• Class Model_ODE
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::Model_ODE
      • Model_ODE()
      • Model_ODE()
      • fJ()
      • fJ()
      • fJB()
      • fJB()
      • fJSparse()
      • fJSparse()
      • fJSparseB()
      • fJSparseB()
      • fJDiag()
      • fJDiag()
      • fJv()
      • fJv()
      • fJvB()
      • froot()
      • froot()
      • fxdot()
      • fxdot()
      • fxBdot()
      • fqBdot()
      • fxBdot_ss()
      • fxBdot_ss()
      • fqBdot_ss()
      • fJSparseB_ss()
      • writeSteadystateJB()
      • fsxdot()
      • fsxdot()
      • create_solver()
      • fJSparse()
      • fJSparse_colptrs()
      • fJSparse_rowvals()
      • froot()
      • fxdot()
      • fdxdotdp_explicit()
      • fdxdotdp_explicit_colptrs()
      • fdxdotdp_explicit_rowvals()
      • fdxdotdx_explicit()
      • fdxdotdx_explicit_colptrs()
      • fdxdotdx_explicit_rowvals()
      • fdxdotdw()
      • fdxdotdw_colptrs()
      • fdxdotdw_rowvals()
      • fdxdotdw()
      • fdxdotdp()
      • fdxdotdp()

• Class ModelContext
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ModelContext
      • ModelContext()
      • operator=()
      • ~ModelContext()
      • restore()

• Class NewtonFailure
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::NewtonFailure
      • NewtonFailure()
      • error_code

• Class NewtonsMethod
  • Class Documentation
    • amici::NewtonsMethod
      • NewtonsMethod()
      • run()
      • compute_step()
      • get_delta()
      • get_num_steps()
      • get_wrms()

• Class NewtonSolver
  • Class Documentation
    • amici::NewtonSolver
      • NewtonSolver()
      • NewtonSolver()
      • operator=()
      • get_step()
      • compute_newton_sensis()
      • prepare_linear_system()
      • prepare_linear_system_b()
      • solve_linear_system()
      • reinitialize()
      • is_singular()

• Class ReturnData
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ReturnData
      • ReturnData()
      • ReturnData()
      • ReturnData()
      • ~ReturnData()
      • process_simulation_objects()
      • id
      • ts
      • xdot
      • J
      • w
      • z
      • sigmaz
      • sz
      • ssigmaz
      • rz
      • srz
      • s2rz
      • x
      • sx
      • y
      • sigmay
      • sy
      • ssigmay
      • res
      • sres
      • FIM
      • numsteps
      • numsteps_b
      • num_rhs_evals
      • num_rhs_evals_b
      • num_err_test_fails
      • num_err_test_fails_b
      • num_non_lin_solv_conv_fails
      • num_non_lin_solv_conv_fails_b
      • order
      • cpu_time
      • cpu_time_b
      • cpu_time_total
      • preeq_status
      • preeq_cpu_time
      • preeq_cpu_time_b
      • posteq_status
      • posteq_cpu_time
      • posteq_cpu_time_b
      • preeq_numsteps
      • preeq_numsteps_b
      • posteq_numsteps
      • posteq_numsteps_b
      • preeq_t
      • preeq_wrms
      • posteq_t
      • posteq_wrms
      • x0
      • x_ss
      • sx0
      • sx_ss
      • llh
      • chi2
      • sllh
      • s2llh
      • status
      • nplist
      • nmaxevent
      • nt
      • newton_maxsteps
      • pscale
      • o2mode
      • sensi
      • sensi_meth
      • rdata_reporting
      • sigma_res
      • messages
      • t_last
      • plist
      • initialize_likelihood_reporting()
      • initializeObservablesLikelihoodReporting()
      • initialize_residual_reporting()
      • initialize_full_reporting()
      • initialize_objective_function()
      • process_pre_equilibration()
      • process_post_equilibration()
      • process_forward_problem()
      • process_backward_problem()
      • process_solver()
      • store_jacobian_and_derivative()
      • fres()
      • fchi2()
      • fsres()
      • fFIM()
      • invalidate()
      • invalidate_llh()
      • invalidate_sllh()
      • apply_chain_rule_factor_to_simulation_results()
      • computing_fsa()
      • get_data_output()
      • get_data_sensis_fsa()
      • get_event_output()
      • get_event_sensis_fsa()
      • handle_sx0_backward()
      • handle_sx0_forward()
      • sigma_offset
      • nroots_
      • boost::serialization::serialize

• Class SetupFailure
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SetupFailure
      • SetupFailure()

• Class SimulationParameters
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • amici::SimulationParameters
      • SimulationParameters()
      • SimulationParameters()
      • SimulationParameters()
      • SimulationParameters()
      • SimulationParameters()
      • reinitialize_all_fixed_parameter_dependent_initial_states_for_presimulation()
      • reinitialize_all_fixed_parameter_dependent_initial_states_for_simulation()
      • reinitialize_all_fixed_parameter_dependent_initial_states()
      • fixed_parameters
      • fixed_parameters_pre_equilibration
      • fixed_parameters_presimulation
      • parameters
      • x0
      • sx0
      • pscale
      • plist
      • t_start_preeq
      • t_start
      • t_presim
      • timepoints
      • reinitialize_fixed_parameter_initial_states
      • reinitialization_state_idxs_presim
      • reinitialization_state_idxs_sim

• Class Solver
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • amici::Solver
      • user_data_type
      • free_solver_ptr
      • Solver()
      • Solver()
      • ~Solver()
      • clone()
      • get_sun_context()
      • get_class_name()
      • run()
      • step()
      • run_b()
      • setup()
      • setup_b()
      • setup_steady_state()
      • update_and_reinit_states_and_sensitivities()
      • get_root_info()
      • calc_ic()
      • calc_ic_b()
      • solve_b()
      • turn_off_root_finding()
      • get_sensitivity_method()
      • set_sensitivity_method()
      • get_sensitivity_method_pre_equilibration()
      • set_sensitivity_method_pre_equilibration()
      • switch_forward_sensis_off()
      • get_newton_max_steps()
      • set_newton_max_steps()
      • get_newton_damping_factor_mode()
      • set_newton_damping_factor_mode()
      • get_newton_damping_factor_lower_bound()
      • set_newton_damping_factor_lower_bound()
      • get_sensitivity_order()
      • set_sensitivity_order()
      • get_relative_tolerance()
      • set_relative_tolerance()
      • get_absolute_tolerance()
      • set_absolute_tolerance()
      • get_relative_tolerance_fsa()
      • set_relative_tolerance_fsa()
      • get_absolute_tolerance_fsa()
      • set_absolute_tolerance_fsa()
      • get_relative_tolerance_b()
      • set_relative_tolerance_b()
      • get_absolute_tolerance_b()
      • set_absolute_tolerance_b()
      • get_relative_tolerance_quadratures()
      • set_relative_tolerance_quadratures()
      • get_absolute_tolerance_quadratures()
      • set_absolute_tolerance_quadratures()
      • get_steady_state_tolerance_factor()
      • set_steady_state_tolerance_factor()
      • get_relative_tolerance_steady_state()
      • set_relative_tolerance_steady_state()
      • get_absolute_tolerance_steady_state()
      • set_absolute_tolerance_steady_state()
      • get_steady_state_sensi_tolerance_factor()
      • set_steady_state_sensi_tolerance_factor()
      • get_relative_tolerance_steady_state_sensi()
      • set_relative_tolerance_steady_state_sensi()
      • get_absolute_tolerance_steady_state_sensi()
      • set_absolute_tolerance_steady_state_sensi()
      • get_max_steps()
      • set_max_steps()
      • get_max_time()
      • set_max_time()
      • start_timer()
      • time_exceeded()
      • get_max_steps_backward_problem()
      • set_max_steps_backward_problem()
      • get_linear_multistep_method()
      • set_linear_multistep_method()
      • get_non_linear_solver_iteration()
      • set_non_linear_solver_iteration()
      • get_interpolation_type()
      • set_interpolation_type()
      • get_state_ordering()
      • set_state_ordering()
      • get_stability_limit_flag()
      • set_stability_limit_flag()
      • get_linear_solver()
      • set_linear_solver()
      • get_internal_sensitivity_method()
      • set_internal_sensitivity_method()
      • get_return_data_reporting_mode()
      • set_return_data_reporting_mode()
      • write_solution()
      • write_solution()
      • write_solution()
      • write_solution()
      • write_solution_b()
      • get_state()
      • get_derivative_state()
      • get_state_sensitivity()
      • get_adjoint_state()
      • get_adjoint_derivative_state()
      • get_adjoint_quadrature()
      • get_quadrature()
      • reinit()
      • sens_reinit()
      • sens_toggle_off()
      • reinit_b()
      • reinit_quad_b()
      • get_t()
      • get_cpu_time()
      • get_cpu_time_b()
      • nx()
      • nplist()
      • nquad()
      • computing_fsa()
      • computing_asa()
      • reset_diagnosis()
      • store_diagnosis()
      • store_diagnosis_b()
      • get_num_steps()
      • get_num_steps_b()
      • get_num_rhs_evals()
      • get_num_rhs_evals_b()
      • get_num_err_test_fails()
      • get_num_err_test_fails_b()
      • get_num_non_lin_solv_conv_fails()
      • get_num_non_lin_solv_conv_fails_b()
      • get_last_order()
      • get_newton_step_steady_state_check()
      • get_sensi_steady_state_check()
      • set_newton_step_steady_state_check()
      • set_sensi_steady_state_check()
      • set_max_nonlin_iters()
      • get_max_nonlin_iters()
      • set_max_conv_fails()
      • get_max_conv_fails()
      • set_constraints()
      • get_constraints()
      • set_max_step_size()
      • get_max_step_size()
      • get_logger()
      • set_logger()
      • set_stop_time()
      • solve()
      • solve_f()
      • reinit_post_process_f()
      • reinit_post_process_b()
      • get_sens()
      • get_b()
      • get_quad_b()
      • get_quad()
      • init()
      • init_steady_state()
      • sens_init_1()
      • b_init()
      • qb_init()
      • root_init()
      • initialize_non_linear_solver_sens()
      • set_dense_jac_fn()
      • set_sparse_jac_fn()
      • set_band_jac_fn()
      • set_jac_times_vec_fn()
      • set_dense_jac_fn_b()
      • set_sparse_jac_fn_b()
      • set_band_jac_fn_b()
      • set_jac_times_vec_fn_b()
      • set_sparse_jac_fn_ss()
      • allocate_solver()
      • set_ss_tolerances()
      • set_sens_ss_tolerances()
      • set_sens_err_con()
      • set_quad_err_con_b()
      • set_quad_err_con()
      • set_err_handler_fn()
      • set_user_data()
      • set_user_data_b()
      • set_max_num_steps()
      • set_max_num_steps_b()
      • set_stab_lim_det()
      • set_stab_lim_det_b()
      • set_id()
      • set_suppress_alg()
      • set_sens_params()
      • get_dky()
      • get_dky_b()
      • get_sens_dky()
      • get_quad_dky_b()
      • get_quad_dky()
      • adj_init()
      • quad_init()
      • allocate_solver_b()
      • set_ss_tolerances_b()
      • quad_ss_tolerances_b()
      • quad_ss_tolerances()
      • get_num_steps()
      • get_num_rhs_evals()
      • get_num_err_test_fails()
      • get_num_non_lin_solv_conv_fails()
      • get_last_order()
      • initialize_linear_solver()
      • initialize_non_linear_solver()
      • set_linear_solver()
      • set_linear_solver_b()
      • set_non_linear_solver()
      • set_non_linear_solver_b()
      • set_non_linear_solver_sens()
      • initialize_linear_solver_b()
      • initialize_non_linear_solver_b()
      • get_model()
      • get_init_done()
      • get_sens_init_done()
      • get_adj_init_done()
      • get_init_done_b()
      • get_quad_init_done_b()
      • get_quad_init_done()
      • diag()
      • diag_b()
      • reset_mutable_memory()
      • get_adj_b_mem()
      • apply_tolerances()
      • apply_tolerances_fsa()
      • apply_tolerances_asa()
      • apply_quad_tolerances_asa()
      • apply_quad_tolerances()
      • apply_sensitivity_tolerances()
      • apply_constraints()
      • set_init_done()
      • set_sens_init_done()
      • set_adj_init_done()
      • set_init_done_b()
      • set_quad_init_done_b()
      • set_quad_init_done()
      • check_sensitivity_method()
      • apply_max_nonlin_iters()
      • apply_max_conv_fails()
      • apply_max_step_size()
      • sunctx_
      • solver_memory_
      • solver_memory_B_
      • user_data_
      • ism_
      • lmm_
      • iter_
      • interp_type_
      • maxsteps_
      • maxtime_
      • simulation_timer_
      • linear_solver_
      • linear_solver_B_
      • non_linear_solver_
      • non_linear_solver_B_
      • non_linear_solver_sens_
      • solver_was_called_F_
      • solver_was_called_B_
      • x_
      • dky_
      • dx_
      • sx_
      • sdx_
      • xB_
      • dxB_
      • xQB_
      • xQ_
      • t_
      • force_reinit_postprocess_F_
      • force_reinit_postprocess_B_
      • sens_initialized_
      • constraints_
      • boost::serialization::serialize
      • operator==

• Class SteadyStateBackwardProblem
  • Class Documentation
    • amici::SteadyStateBackwardProblem
      • SteadyStateBackwardProblem()
      • run()
      • get_cpu_time_b()
      • get_num_steps_b()
      • get_adjoint_state()
      • get_adjoint_quadrature()
      • has_quadrature()

• Class SteadyStateProblem
  • Class Documentation
    • amici::SteadyStateProblem
      • SteadyStateProblem()
      • run()
      • get_final_simulation_state()
      • get_state()
      • get_state_sensitivity()
      • get_cpu_time()
      • get_steady_state_status()
      • get_steady_state_time()
      • get_residual_norm()
      • get_num_steps()
      • check_steady_state_success()
      • get_solver()
      • get_result()

• Class SUNLinSolBand
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolBand
      • SUNLinSolBand()
      • SUNLinSolBand()

• Class SUNLinSolDense
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolDense
      • SUNLinSolDense()

• Class SUNLinSolKLU
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolKLU
      • StateOrdering
        • AMD
        • COLAMD
        • natural
      • SUNLinSolKLU()
      • SUNLinSolKLU()
      • reinit()
      • set_ordering()
      • is_singular()

• Class SUNLinSolPCG
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolPCG
      • SUNLinSolPCG()
      • set_a_times()
      • set_preconditioner()
      • set_scaling_vectors()
      • get_num_iters()
      • get_res_norm()
      • get_resid()

• Class SUNLinSolSPBCGS
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPBCGS
      • SUNLinSolSPBCGS()
      • SUNLinSolSPBCGS()
      • set_a_times()
      • set_preconditioner()
      • set_scaling_vectors()
      • get_num_iters()
      • get_res_norm()
      • get_resid()

• Class SUNLinSolSPFGMR
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPFGMR
      • SUNLinSolSPFGMR()
      • set_a_times()
      • set_preconditioner()
      • set_scaling_vectors()
      • get_num_iters()
      • get_res_norm()
      • get_resid()

• Class SUNLinSolSPGMR
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPGMR
      • SUNLinSolSPGMR()
      • set_a_times()
      • set_preconditioner()
      • set_scaling_vectors()
      • get_num_iters()
      • get_res_norm()
      • get_resid()

• Class SUNLinSolSPTFQMR
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPTFQMR
      • SUNLinSolSPTFQMR()
      • SUNLinSolSPTFQMR()
      • set_a_times()
      • set_preconditioner()
      • set_scaling_vectors()
      • get_num_iters()
      • get_res_norm()
      • get_resid()

• Class SUNLinSolWrapper
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • amici::SUNLinSolWrapper
      • SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • ~SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • operator=()
      • operator=()
      • get()
      • get_type()
      • setup()
      • solve()
      • get_last_flag()
      • space()
      • getMatrix()
      • initialize()
      • solver_
      • A_

• Class SUNMatrixWrapper
  • Class Documentation
    • amici::SUNMatrixWrapper
      • SUNMatrixWrapper()
      • SUNMatrixWrapper()
      • SUNMatrixWrapper()
      • SUNMatrixWrapper()
      • SUNMatrixWrapper()
      • SUNMatrixWrapper()
      • ~SUNMatrixWrapper()
      • operator SUNMatrix()
      • SUNMatrixWrapper()
      • SUNMatrixWrapper()
      • operator=()
      • operator=()
      • reallocate()
      • realloc()
      • get()
      • rows()
      • columns()
      • num_nonzeros()
      • num_indexptrs()
      • capacity()
      • data()
      • data()
      • get_data()
      • get_data()
      • set_data()
      • set_data()
      • get_indexval()
      • set_indexval()
      • set_indexvals()
      • get_indexptr()
      • set_indexptr()
      • set_indexptrs()
      • sparsetype()
      • scale()
      • multiply()
      • multiply()
      • multiply()
      • multiply()
      • multiply()
      • sparse_multiply()
      • sparse_add()
      • sparse_sum()
      • scatter()
      • transpose()
      • to_dense()
      • to_diag()
      • zero()
      • matrix_id()
      • refresh()
      • get_ctx()
      • set_ctx()

• Class SUNNonLinSolFixedPoint
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNNonLinSolFixedPoint
      • SUNNonLinSolFixedPoint()
      • SUNNonLinSolFixedPoint()
      • get_sys_fn()

• Class SUNNonLinSolNewton
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNNonLinSolNewton
      • SUNNonLinSolNewton()
      • SUNNonLinSolNewton()
      • get_sys_fn()

• Class SUNNonLinSolWrapper
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • amici::SUNNonLinSolWrapper
      • SUNNonLinSolWrapper()
      • ~SUNNonLinSolWrapper()
      • SUNNonLinSolWrapper()
      • SUNNonLinSolWrapper()
      • operator=()
      • operator=()
      • get()
      • get_type()
      • setup()
      • solve()
      • set_sys_fn()
      • set_l_setup_fn()
      • set_l_solve_fn()
      • set_conv_test_fn()
      • set_max_iters()
      • get_num_iters()
      • get_cur_iter()
      • get_num_conv_fails()
      • initialize()
      • solver

• Class WRMSComputer
  • Class Documentation
    • amici::WRMSComputer
      • WRMSComputer()
      • wrms()

Enums

• Enum BLASLayout
  • Enum Documentation
    • BLASLayout
      • rowMajor
      • colMajor

• Enum BLASTranspose
  • Enum Documentation
    • BLASTranspose
      • noTrans
      • trans
      • conjTrans

• Enum Constraint
  • Enum Documentation
    • Constraint
      • none
      • non_negative
      • non_positive
      • positive
      • negative

• Enum FixedParameterContext
  • Enum Documentation
    • FixedParameterContext
      • simulation
      • preequilibration
      • presimulation

• Enum InternalSensitivityMethod
  • Enum Documentation
    • InternalSensitivityMethod
      • simultaneous
      • staggered
      • staggered1

• Enum InterpolationType
  • Enum Documentation
    • InterpolationType
      • hermite
      • polynomial

• Enum LinearMultistepMethod
  • Enum Documentation
    • LinearMultistepMethod
      • adams
      • BDF

• Enum LinearSolver
  • Enum Documentation
    • LinearSolver
      • dense
      • band
      • LAPACKDense
      • LAPACKBand
      • diag
      • SPGMR
      • SPBCG
      • SPTFQMR
      • KLU
      • SuperLUMT

• Enum LogSeverity
  • Enum Documentation
    • LogSeverity
      • error
      • warning
      • debug

• Enum ModelQuantity
  • Enum Documentation
    • ModelQuantity
      • J
      • JB
      • Jv
      • JvB
      • JDiag
      • sx
      • sy
      • sz
      • srz
      • ssigmay
      • ssigmaz
      • xdot
      • sxdot
      • xBdot
      • x0_rdata
      • x0
      • x_rdata
      • x
      • dwdw
      • dwdx
      • dwdp
      • y
      • dydp
      • dydx
      • w
      • root
      • qBdot
      • qBdot_ss
      • xBdot_ss
      • JSparseB_ss
      • deltax
      • deltasx
      • deltaxB
      • k
      • p
      • ts
      • dJydy
      • deltaqB
      • dsigmaydp
      • dsigmaydy
      • dsigmazdp
      • dJydsigma
      • dJydx
      • dzdx
      • dzdp
      • dJrzdsigma
      • dJrzdz
      • dJrzdx
      • dJzdsigma
      • dJzdz
      • dJzdx
      • drzdp
      • drzdx

• Enum NewtonDampingFactorMode
  • Enum Documentation
    • NewtonDampingFactorMode
      • off
      • on

• Enum NonlinearSolverIteration
  • Enum Documentation
    • NonlinearSolverIteration
      • fixedpoint
      • newton

• Enum ObservableScaling
  • Enum Documentation
    • ObservableScaling
      • lin
      • log
      • log10

• Enum ParameterScaling
  • Enum Documentation
    • ParameterScaling
      • none
      • ln
      • log10

• Enum RDataReporting
  • Enum Documentation
    • RDataReporting
      • full
      • residuals
      • likelihood
      • observables_likelihood

• Enum SecondOrderMode
  • Enum Documentation
    • SecondOrderMode
      • none
      • full
      • directional

• Enum SensitivityMethod
  • Enum Documentation
    • SensitivityMethod
      • none
      • forward
      • adjoint

• Enum SensitivityOrder
  • Enum Documentation
    • SensitivityOrder
      • none
      • first
      • second

• Enum SplineBoundaryCondition
  • Enum Documentation
    • SplineBoundaryCondition
      • given
      • zeroDerivative
      • natural
      • naturalZeroDerivative
      • periodic

• Enum SplineExtrapolation
  • Enum Documentation
    • SplineExtrapolation
      • noExtrapolation
      • constant
      • linear
      • polynomial
      • periodic

• Enum SteadyStateComputationMode
  • Enum Documentation
    • SteadyStateComputationMode
      • newtonOnly
      • integrationOnly
      • integrateIfNewtonFails

• Enum SteadyStateSensitivityMode
  • Enum Documentation
    • SteadyStateSensitivityMode
      • newtonOnly
      • integrationOnly
      • integrateIfNewtonFails

• Enum SteadyStateStatus
  • Enum Documentation
    • SteadyStateStatus
      • failed_too_long_simulation
      • failed_damping
      • failed_factorization
      • failed_convergence
      • failed
      • not_run
      • success

Functions

• Template Function amici::add_slice(gsl::span<T const> const, gsl::span<T>)
  • Function Documentation
    • add_slice()

• Template Function amici::add_slice(std::vector<T> const&, gsl::span<T>)
  • Function Documentation
    • add_slice()

• Function amici::amici_daxpy
  • Function Documentation
    • amici_daxpy()

• Function amici::amici_dgemm
  • Function Documentation
    • amici_dgemm()

• Function amici::amici_dgemv
  • Function Documentation
    • amici_dgemv()

• Template Function amici::check_buffer_size
  • Function Documentation
    • check_buffer_size()

• Function amici::checkSigmaPositivity(std::vector<realtype> const&, char const *)
  • Function Documentation
    • checkSigmaPositivity()

• Function amici::checkSigmaPositivity(realtype, char const *)
  • Function Documentation
    • checkSigmaPositivity()

• Function amici::compute_nroots
  • Function Documentation
    • compute_nroots()

• Template Function amici::deserialize_from_char
  • Function Documentation
    • deserialize_from_char()

• Template Function amici::deserialize_from_string
  • Function Documentation
    • deserialize_from_string()

• Function amici::dot_prod
  • Function Documentation
    • dot_prod()

• Function amici::get_backtrace_string
  • Function Documentation
    • get_backtrace_string()

• Function amici::hdf5::attribute_exists(H5::H5File const&, std::string const&, std::string const&)
  • Function Documentation
    • attribute_exists()

• Function amici::hdf5::attribute_exists(H5::H5Object const&, std::string const&)
  • Function Documentation
    • attribute_exists()

• Function amici::hdf5::create_and_write_double_1d_dataset
  • Function Documentation
    • create_and_write_double_1d_dataset()

• Function amici::hdf5::create_and_write_double_2d_dataset
  • Function Documentation
    • create_and_write_double_2d_dataset()

• Function amici::hdf5::create_and_write_double_3d_dataset
  • Function Documentation
    • create_and_write_double_3d_dataset()

• Function amici::hdf5::create_and_write_int_1d_dataset
  • Function Documentation
    • create_and_write_int_1d_dataset()

• Function amici::hdf5::create_and_write_int_2d_dataset
  • Function Documentation
    • create_and_write_int_2d_dataset()

• Function amici::hdf5::create_group
  • Function Documentation
    • create_group()

• Function amici::hdf5::create_or_open_for_writing
  • Function Documentation
    • create_or_open_for_writing()

• Function amici::hdf5::get_double_1d_dataset
  • Function Documentation
    • get_double_1d_dataset()

• Function amici::hdf5::get_double_2d_dataset
  • Function Documentation
    • get_double_2d_dataset()

• Function amici::hdf5::get_double_3d_dataset
  • Function Documentation
    • get_double_3d_dataset()

• Function amici::hdf5::get_double_scalar_attribute
  • Function Documentation
    • get_double_scalar_attribute()

• Function amici::hdf5::get_int_1d_dataset
  • Function Documentation
    • get_int_1d_dataset()

• Function amici::hdf5::get_int_scalar_attribute
  • Function Documentation
    • get_int_scalar_attribute()

• Function amici::hdf5::get_string_attribute
  • Function Documentation
    • get_string_attribute()

• Function amici::hdf5::location_exists(std::string const&, std::string const&)
  • Function Documentation
    • location_exists()

• Function amici::hdf5::location_exists(H5::H5File const&, std::string const&)
  • Function Documentation
    • location_exists()

• Function amici::hdf5::read_exp_data_from_hdf5
  • Function Documentation
    • read_exp_data_from_hdf5()

• Function amici::hdf5::read_model_data_from_hdf5(std::string const&, Model&, std::string const&)
  • Function Documentation
    • read_model_data_from_hdf5()

• Function amici::hdf5::read_model_data_from_hdf5(H5::H5File const&, Model&, std::string const&)
  • Function Documentation
    • read_model_data_from_hdf5()

• Function amici::hdf5::read_solver_settings_from_hdf5(const H5::H5File&, Solver&, std::string const&)
  • Function Documentation
    • read_solver_settings_from_hdf5()

• Function amici::hdf5::read_solver_settings_from_hdf5(std::string const&, Solver&, std::string const&)
  • Function Documentation
    • read_solver_settings_from_hdf5()

• Function amici::hdf5::write_exp_data_to_hdf5(ExpData const&, H5::H5File const&, std::string const&)
  • Function Documentation
    • write_exp_data_to_hdf5()

• Function amici::hdf5::write_exp_data_to_hdf5(ExpData const&, std::string const&, std::string const&)
  • Function Documentation
    • write_exp_data_to_hdf5()

• Function amici::hdf5::write_log_items_to_hdf5
  • Function Documentation
    • write_log_items_to_hdf5()

• Function amici::hdf5::write_return_data_diagnosis
  • Function Documentation
    • write_return_data_diagnosis()

• Function amici::hdf5::write_return_data_to_hdf5(ReturnData const&, H5::H5File const&, std::string const&)
  • Function Documentation
    • write_return_data_to_hdf5()

• Function amici::hdf5::write_return_data_to_hdf5(ReturnData const&, std::string const&, std::string const&)
  • Function Documentation
    • write_return_data_to_hdf5()

• Function amici::hdf5::write_solver_settings_to_hdf5(Solver const&, std::string const&, std::string const&)
  • Function Documentation
    • write_solver_settings_to_hdf5()

• Function amici::hdf5::write_solver_settings_to_hdf5(Solver const&, H5::H5File const&, std::string const&)
  • Function Documentation
    • write_solver_settings_to_hdf5()

• Template Function amici::heaviside_differs
  • Function Documentation
    • heaviside_differs()

• Template Function amici::is_equal
  • Function Documentation
    • is_equal()

• Function amici::linear_sum
  • Function Documentation
    • linear_sum()

• Function amici::N_VGetArrayPointerConst
  • Function Documentation
    • N_VGetArrayPointerConst()

• Function amici::operator<<(std::ostream&, SUNMatrixWrapper const&)
  • Function Documentation
    • operator<<()

• Function amici::operator<<(std::ostream&, AmiVector const&)
  • Function Documentation
    • operator<<()

• Function amici::operator<<(std::ostream&, AmiVectorArray const&)
  • Function Documentation
    • operator<<()

• Function amici::operator==(ExpData const&, ExpData const&)
  • Function Documentation
    • operator==()

• Function amici::operator==(Model const&, Model const&)
  • Function Documentation
    • operator==()

• Function amici::operator==(ModelDimensions const&, ModelDimensions const&)
  • Function Documentation
    • operator==()

• Function amici::operator==(ModelState const&, ModelState const&)
  • Function Documentation
    • operator==()

• Function amici::operator==(SimulationParameters const&, SimulationParameters const&)
  • Function Documentation
    • operator==()

• Function amici::operator==(Solver const&, Solver const&)
  • Function Documentation
    • operator==()

• Function amici::printf_to_string
  • Function Documentation
    • printf_to_string()

• Function amici::regex_error_to_string
  • Function Documentation
    • regex_error_to_string()

• Function amici::run_simulation
  • Function Documentation
    • run_simulation()

• Function amici::run_simulations
  • Function Documentation
    • run_simulations()

• Function amici::scale_parameter
  • Function Documentation
    • scale_parameter()

• Function amici::scale_parameters
  • Function Documentation
    • scale_parameters()

• Template Function amici::serialize_to_char
  • Function Documentation
    • serialize_to_char()

• Template Function amici::serialize_to_std_vec
  • Function Documentation
    • serialize_to_std_vec()

• Template Function amici::serialize_to_string
  • Function Documentation
    • serialize_to_string()

• Function amici::simulation_status_to_str
  • Function Documentation
    • simulation_status_to_str()

• Template Function amici::slice(std::vector<T>&, int const, unsigned const)
  • Function Documentation
    • slice()

• Template Function amici::slice(std::vector<T> const&, int, unsigned)
  • Function Documentation
    • slice()

• Function amici::unravel_index(size_t, size_t)
  • Function Documentation
    • unravel_index()

• Function amici::unravel_index(sunindextype, SUNMatrix)
  • Function Documentation
    • unravel_index()

• Function amici::unscale_parameter
  • Function Documentation
    • unscale_parameter()

• Function amici::unscale_parameters
  • Function Documentation
    • unscale_parameters()

• Template Function amici::write_slice(gsl::span<T const> const, gsl::span<T>)
  • Function Documentation
    • write_slice()

• Template Function amici::write_slice(std::vector<T> const&, std::vector<T>&)
  • Function Documentation
    • write_slice()

• Template Function amici::write_slice(std::vector<T> const&, gsl::span<T>)
  • Function Documentation
    • write_slice()

• Function amici::write_slice(AmiVector const&, gsl::span<realtype>)
  • Function Documentation
    • write_slice()

• Template Function boost::serialization::archive_vector
  • Function Documentation
    • archive_vector()

• Template Function boost::serialization::serialize(Archive&, amici::Model&, unsigned int)
  • Function Documentation
    • serialize()

• Template Function boost::serialization::serialize(Archive&, amici::ReturnData&, unsigned int)
  • Function Documentation
    • serialize()

• Template Function boost::serialization::serialize(Archive&, amici::Solver&, unsigned int)
  • Function Documentation
    • serialize()

• Template Function boost::serialization::serialize(Archive&, amici::CVodeSolver&, unsigned int)
  • Function Documentation
    • serialize()

• Template Function boost::serialization::serialize(Archive&, amici::IDASolver&, unsigned int)
  • Function Documentation
    • serialize()

• Template Function boost::serialization::serialize(Archive&, amici::AmiVector&, unsigned int)
  • Function Documentation
    • serialize()

• Function gsl::make_span(SUNMatrix const)
  • Function Documentation
    • make_span()

• Function gsl::make_span(N_Vector)
  • Function Documentation
    • make_span()

• Function gsl::make_span(amici::AmiVector const&)
  • Function Documentation
    • make_span()

Variables

• Variable amici::AMICI_BAD_DKY
  • Variable Documentation
    • AMICI_BAD_DKY

• Variable amici::AMICI_BAD_T
  • Variable Documentation
    • AMICI_BAD_T

• Variable amici::AMICI_CONSTR_FAIL
  • Variable Documentation
    • AMICI_CONSTR_FAIL

• Variable amici::AMICI_CONV_FAILURE
  • Variable Documentation
    • AMICI_CONV_FAILURE

• Variable amici::AMICI_CVODES_CONSTR_FAIL
  • Variable Documentation
    • AMICI_CVODES_CONSTR_FAIL

• Variable amici::AMICI_DAMPING_FACTOR_ERROR
  • Variable Documentation
    • AMICI_DAMPING_FACTOR_ERROR

• Variable amici::AMICI_DATA_RETURN
  • Variable Documentation
    • AMICI_DATA_RETURN

• Variable amici::AMICI_ERR_FAILURE
  • Variable Documentation
    • AMICI_ERR_FAILURE

• Variable amici::AMICI_ERROR
  • Variable Documentation
    • AMICI_ERROR

• Variable amici::AMICI_FIRST_QRHSFUNC_ERR
  • Variable Documentation
    • AMICI_FIRST_QRHSFUNC_ERR

• Variable amici::AMICI_FIRST_RHSFUNC_ERR
  • Variable Documentation
    • AMICI_FIRST_RHSFUNC_ERR

• Variable amici::AMICI_FIRST_SRHSFUNC_ERR
  • Variable Documentation
    • AMICI_FIRST_SRHSFUNC_ERR

• Variable amici::AMICI_IDAS_CONSTR_FAIL
  • Variable Documentation
    • AMICI_IDAS_CONSTR_FAIL

• Variable amici::AMICI_ILL_INPUT
  • Variable Documentation
    • AMICI_ILL_INPUT

• Variable amici::AMICI_LINESEARCH_FAIL
  • Variable Documentation
    • AMICI_LINESEARCH_FAIL

• Variable amici::AMICI_LSETUP_FAIL
  • Variable Documentation
    • AMICI_LSETUP_FAIL

• Variable amici::AMICI_MAX_TIME_EXCEEDED
  • Variable Documentation
    • AMICI_MAX_TIME_EXCEEDED

• Variable amici::AMICI_NO_STEADY_STATE
  • Variable Documentation
    • AMICI_NO_STEADY_STATE

• Variable amici::AMICI_NORMAL
  • Variable Documentation
    • AMICI_NORMAL

• Variable amici::AMICI_NOT_IMPLEMENTED
  • Variable Documentation
    • AMICI_NOT_IMPLEMENTED

• Variable amici::AMICI_NOT_RUN
  • Variable Documentation
    • AMICI_NOT_RUN

• Variable amici::AMICI_ONE_STEP
  • Variable Documentation
    • AMICI_ONE_STEP

• Variable amici::AMICI_PREEQUILIBRATE
  • Variable Documentation
    • AMICI_PREEQUILIBRATE

• Variable amici::AMICI_RECOVERABLE_ERROR
  • Variable Documentation
    • AMICI_RECOVERABLE_ERROR

• Variable amici::AMICI_REPTD_SRHSFUNC_ERR
  • Variable Documentation
    • AMICI_REPTD_SRHSFUNC_ERR

• Variable amici::AMICI_RHSFUNC_FAIL
  • Variable Documentation
    • AMICI_RHSFUNC_FAIL

• Variable amici::AMICI_ROOT_RETURN
  • Variable Documentation
    • AMICI_ROOT_RETURN

• Variable amici::AMICI_RTFUNC_FAIL
  • Variable Documentation
    • AMICI_RTFUNC_FAIL

• Variable amici::AMICI_SINGULAR_JACOBIAN
  • Variable Documentation
    • AMICI_SINGULAR_JACOBIAN

• Variable amici::AMICI_SRHSFUNC_FAIL
  • Variable Documentation
    • AMICI_SRHSFUNC_FAIL

• Variable amici::AMICI_SUCCESS
  • Variable Documentation
    • AMICI_SUCCESS

• Variable amici::AMICI_TOO_MUCH_ACC
  • Variable Documentation
    • AMICI_TOO_MUCH_ACC

• Variable amici::AMICI_TOO_MUCH_WORK
  • Variable Documentation
    • AMICI_TOO_MUCH_WORK

• Variable amici::AMICI_UNREC_SRHSFUNC_ERR
  • Variable Documentation
    • AMICI_UNREC_SRHSFUNC_ERR

• Variable amici::AMICI_UNRECOVERABLE_ERROR
  • Variable Documentation
    • AMICI_UNRECOVERABLE_ERROR

• Variable amici::AMICI_WARNING
  • Variable Documentation
    • AMICI_WARNING

• Variable amici::model_quantity_to_str
  • Variable Documentation
    • model_quantity_to_str

• Variable amici::pi
  • Variable Documentation
    • pi

Defines

• Define _USE_MATH_DEFINES
  • Define Documentation
    • _USE_MATH_DEFINES

• Define AMICI_H5_RESTORE_ERROR_HANDLER
  • Define Documentation
    • AMICI_H5_RESTORE_ERROR_HANDLER

• Define AMICI_H5_SAVE_ERROR_HANDLER
  • Define Documentation
    • AMICI_H5_SAVE_ERROR_HANDLER

• Define AMICI_VERSION
  • Define Documentation
    • AMICI_VERSION

• Define M_1_PI
  • Define Documentation
    • M_1_PI

• Define M_2_PI
  • Define Documentation
    • M_2_PI

• Define M_2_SQRTPI
  • Define Documentation
    • M_2_SQRTPI

• Define M_E
  • Define Documentation
    • M_E

• Define M_LN10
  • Define Documentation
    • M_LN10

• Define M_LN2
  • Define Documentation
    • M_LN2

• Define M_LOG10E
  • Define Documentation
    • M_LOG10E

• Define M_LOG2E
  • Define Documentation
    • M_LOG2E

• Define M_PI
  • Define Documentation
    • M_PI

• Define M_PI_2
  • Define Documentation
    • M_PI_2

• Define M_PI_4
  • Define Documentation
    • M_PI_4

• Define M_SQRT1_2
  • Define Documentation
    • M_SQRT1_2

• Define M_SQRT2
  • Define Documentation
    • M_SQRT2

Typedefs

• Typedef amici::const_N_Vector
  • Typedef Documentation
    • const_N_Vector

• Typedef amici::realtype
  • Typedef Documentation
    • realtype