AMICI C++ API

AMICI C++ library functions

Class Hierarchy

• • Namespace amici
    • Enum LogSeverity
    • Enum NewtonDampingFactorMode
    • Enum NonlinearSolverIteration
    • Enum SensitivityMethod
    • Enum SplineExtrapolation
    • Enum SteadyStateContext
    • Struct LogItem
    • Struct ModelDimensions
    • Struct ModelState
    • Struct ModelStateDerived
    • Struct SimulationState
    • Class AbstractModel
    • Class AbstractSpline
    • Class AmiException
    • Class AmiVector
    • Class AmiVectorArray
    • Class BackwardProblem
    • Class ConditionContext
    • Class ContextManager
    • Class CpuTimer
    • Class CvodeException
    • Class CVodeSolver
    • 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 NewtonSolver
    • Class ReturnData
    • Class SetupFailure
    • Class SimulationParameters
    • Class Solver
    • 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
    • Enum BLASLayout
    • Enum BLASTranspose
    • Enum Constraint
    • Enum FixedParameterContext
    • Enum InternalSensitivityMethod
    • Enum InterpolationType
    • Enum LinearMultistepMethod
    • Enum LinearSolver
    • Enum ModelQuantity
    • Enum ObservableScaling
    • Enum ParameterScaling
    • Enum RDataReporting
    • Enum SecondOrderMode
    • Enum SensitivityOrder
    • Enum SplineBoundaryCondition
    • 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 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 LogItem
  • Struct Documentation
    • amici::LogItem
      • LogItem()
      • LogItem()
      • severity
      • identifier
      • message

• Struct ModelDimensions
  • Inheritance Relationships
    • Derived Types
  • Struct Documentation
    • amici::ModelDimensions
      • ModelDimensions()
      • ModelDimensions()
      • 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
      • pythonGenerated
      • ndxdotdp_explicit
      • ndxdotdx_explicit
      • w_recursion_depth

• Struct ModelState
  • Struct Documentation
    • amici::ModelState
      • ModelState()
      • ModelState()
      • h
      • total_cl
      • stotal_cl
      • unscaledParameters
      • fixedParameters
      • plist

• Struct ModelStateDerived
  • Struct Documentation
    • amici::ModelStateDerived
      • ModelStateDerived()
      • ModelStateDerived()
      • ModelStateDerived()
      • sunctx_
      • J_
      • JB_
      • dxdotdw_
      • dwdx_
      • dwdp_
      • M_
      • MSparse_
      • dfdx_
      • dxdotdp_full
      • dxdotdp_explicit
      • dxdotdp_implicit
      • dxdotdx_explicit
      • dxdotdx_implicit
      • dx_rdatadx_solver
      • dx_rdatadtcl
      • dtotal_cldx_rdata
      • dxdotdp
      • dJydy_
      • dJydy_matlab_
      • 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 SimulationState
  • Struct Documentation
    • amici::SimulationState
      • t
      • x
      • dx
      • sx
      • state

• Class AbstractModel
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • amici::AbstractModel
      • ~AbstractModel()
      • getSolver()
      • froot()
      • fxdot()
      • fsxdot()
      • fxBdot_ss()
      • fJSparseB_ss()
      • writeSteadystateJB()
      • fJ()
      • fJB()
      • fJSparse()
      • fJSparseB()
      • fJDiag()
      • fdxdotdp()
      • fJv()
      • getAmiciVersion()
      • getAmiciCommit()
      • fx0()
      • isFixedParameterStateReinitializationAllowed()
      • fx0_fixedParameters()
      • fsx0_fixedParameters()
      • fsx0()
      • fdx0()
      • fstau()
      • fy()
      • fdydp()
      • 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()

• 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()
      • operator=()
      • operator*=()
      • operator/=()
      • begin()
      • end()
      • data()
      • data()
      • getNVector()
      • getNVector()
      • getVector()
      • getLength()
      • zero()
      • minus()
      • set()
      • 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()
      • getNVectorArray()
      • getNVector()
      • getNVector()
      • operator[]()
      • operator[]()
      • getLength()
      • zero()
      • flatten_to_vector()
      • copy()
      • set_ctx()

• Class BackwardProblem
  • Class Documentation
    • amici::BackwardProblem
      • BackwardProblem()
      • workBackwardProblem()
      • gett()
      • getwhich()
      • getwhichptr()
      • getdJydx()
      • getAdjointState()
      • getAdjointQuadrature()

• Class ConditionContext
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ConditionContext
      • ConditionContext()
      • operator=()
      • ~ConditionContext()
      • applyCondition()
      • 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()
      • reInit()
      • sensReInit()
      • sensToggleOff()
      • reInitB()
      • quadReInitB()
      • solve()
      • solveF()
      • solveB()
      • getDky()
      • getSensDky()
      • getQuadDkyB()
      • getDkyB()
      • getRootInfo()
      • setStopTime()
      • turnOffRootFinding()
      • getModel()
      • setLinearSolver()
      • setLinearSolverB()
      • setNonLinearSolver()
      • setNonLinearSolverSens()
      • setNonLinearSolverB()
      • Solver()
      • Solver()
      • calcIC()
      • calcICB()
      • getB()
      • getSens()
      • getQuadB()
      • getQuad()
      • getQuadDky()
      • reInitPostProcessF()
      • reInitPostProcessB()
      • reInitPostProcess()
      • allocateSolver()
      • setSStolerances()
      • setSensSStolerances()
      • setSensErrCon()
      • setQuadErrConB()
      • setQuadErrCon()
      • setUserData()
      • setUserDataB()
      • setMaxNumSteps()
      • setStabLimDet()
      • setStabLimDetB()
      • setId()
      • setSuppressAlg()
      • resetState()
      • setSensParams()
      • adjInit()
      • quadInit()
      • allocateSolverB()
      • setSStolerancesB()
      • quadSStolerancesB()
      • quadSStolerances()
      • setMaxNumStepsB()
      • diag()
      • diagB()
      • getNumSteps()
      • getNumRhsEvals()
      • getNumErrTestFails()
      • getNumNonlinSolvConvFails()
      • getLastOrder()
      • getAdjBmem()
      • init()
      • initSteadystate()
      • sensInit1()
      • binit()
      • qbinit()
      • rootInit()
      • setDenseJacFn()
      • setSparseJacFn()
      • setBandJacFn()
      • setJacTimesVecFn()
      • setDenseJacFnB()
      • setSparseJacFnB()
      • setBandJacFnB()
      • setJacTimesVecFnB()
      • setSparseJacFn_ss()
      • apply_max_nonlin_iters()
      • apply_max_conv_fails()
      • apply_constraints()
      • apply_max_step_size()
      • boost::serialization::serialize
      • operator==

• Class ExpData
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ExpData
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ExpData()
      • ~ExpData()
      • nytrue()
      • nztrue()
      • nmaxevent()
      • nt()
      • setTimepoints()
      • getTimepoints()
      • getTimepoint()
      • setObservedData()
      • setObservedData()
      • isSetObservedData()
      • getObservedData()
      • getObservedDataPtr()
      • setObservedDataStdDev()
      • setObservedDataStdDev()
      • setObservedDataStdDev()
      • setObservedDataStdDev()
      • isSetObservedDataStdDev()
      • getObservedDataStdDev()
      • getObservedDataStdDevPtr()
      • setObservedEvents()
      • setObservedEvents()
      • isSetObservedEvents()
      • getObservedEvents()
      • getObservedEventsPtr()
      • setObservedEventsStdDev()
      • setObservedEventsStdDev()
      • setObservedEventsStdDev()
      • setObservedEventsStdDev()
      • isSetObservedEventsStdDev()
      • getObservedEventsStdDev()
      • getObservedEventsStdDevPtr()
      • clear_observations()
      • id
      • applyDimensions()
      • applyDataDimension()
      • applyEventDimension()
      • checkDataDimension()
      • checkEventsDimension()
      • 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()
      • workForwardProblem()
      • getAdjointUpdates()
      • getTime()
      • getState()
      • getStateDerivative()
      • getStateSensitivity()
      • getStatesAtDiscontinuities()
      • getRHSAtDiscontinuities()
      • getRHSBeforeDiscontinuities()
      • getNumberOfRoots()
      • getDiscontinuities()
      • getRootIndexes()
      • getDJydx()
      • getDJzdx()
      • getStatePointer()
      • getStateDerivativePointer()
      • getStateSensitivityPointer()
      • getStateDerivativeSensitivityPointer()
      • getCurrentTimeIteration()
      • getFinalTime()
      • getEventCounter()
      • getRootCounter()
      • getSimulationStateTimepoint()
      • getSimulationStateEvent()
      • getInitialSimulationState()
      • getFinalSimulationState()
      • 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()
      • reInitPostProcessF()
      • reInitPostProcessB()
      • reInit()
      • sensReInit()
      • sensToggleOff()
      • reInitB()
      • quadReInitB()
      • quadSStolerancesB()
      • quadSStolerances()
      • solve()
      • solveF()
      • solveB()
      • getRootInfo()
      • getDky()
      • getSens()
      • getSensDky()
      • getB()
      • getDkyB()
      • getQuadB()
      • getQuadDkyB()
      • getQuad()
      • getQuadDky()
      • calcIC()
      • calcICB()
      • setStopTime()
      • turnOffRootFinding()
      • getModel()
      • setLinearSolver()
      • setLinearSolverB()
      • setNonLinearSolver()
      • setNonLinearSolverSens()
      • setNonLinearSolverB()
      • Solver()
      • Solver()
      • reInitPostProcess()
      • allocateSolver()
      • setSStolerances()
      • setSensSStolerances()
      • setSensErrCon()
      • setQuadErrConB()
      • setQuadErrCon()
      • setUserData()
      • setUserDataB()
      • setMaxNumSteps()
      • setStabLimDet()
      • setStabLimDetB()
      • setId()
      • setSuppressAlg()
      • resetState()
      • setSensParams()
      • adjInit()
      • quadInit()
      • allocateSolverB()
      • setMaxNumStepsB()
      • setSStolerancesB()
      • diag()
      • diagB()
      • getNumSteps()
      • getNumRhsEvals()
      • getNumErrTestFails()
      • getNumNonlinSolvConvFails()
      • getLastOrder()
      • getAdjBmem()
      • init()
      • initSteadystate()
      • sensInit1()
      • binit()
      • qbinit()
      • rootInit()
      • setDenseJacFn()
      • setSparseJacFn()
      • setBandJacFn()
      • setJacTimesVecFn()
      • setDenseJacFnB()
      • setSparseJacFnB()
      • setBandJacFnB()
      • setJacTimesVecFnB()
      • setSparseJacFn_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()
      • initializeB()
      • initializeStates()
      • initializeStateSensitivities()
      • initializeSplines()
      • initializeSplineSensitivities()
      • initEvents()
      • nplist()
      • np()
      • nk()
      • ncl()
      • nx_reinit()
      • k()
      • nMaxEvent()
      • setNMaxEvent()
      • nt()
      • getParameterScale()
      • setParameterScale()
      • setParameterScale()
      • getUnscaledParameters()
      • getParameters()
      • getParameterById()
      • getParameterByName()
      • setParameters()
      • setParameterById()
      • setParameterById()
      • setParametersByIdRegex()
      • setParameterByName()
      • setParameterByName()
      • setParametersByNameRegex()
      • getFixedParameters()
      • getFixedParameterById()
      • getFixedParameterByName()
      • setFixedParameters()
      • setFixedParameterById()
      • setFixedParametersByIdRegex()
      • setFixedParameterByName()
      • setFixedParametersByNameRegex()
      • getName()
      • hasParameterNames()
      • getParameterNames()
      • hasStateNames()
      • getStateNames()
      • getStateNamesSolver()
      • hasFixedParameterNames()
      • getFixedParameterNames()
      • hasObservableNames()
      • getObservableNames()
      • hasExpressionNames()
      • getExpressionNames()
      • hasParameterIds()
      • getParameterIds()
      • hasStateIds()
      • getStateIds()
      • getStateIdsSolver()
      • hasFixedParameterIds()
      • getFixedParameterIds()
      • hasObservableIds()
      • getObservableIds()
      • hasExpressionIds()
      • getExpressionIds()
      • hasQuadraticLLH()
      • getTimepoints()
      • getTimepoint()
      • setTimepoints()
      • t0()
      • setT0()
      • getStateIsNonNegative()
      • setStateIsNonNegative()
      • setAllStatesNonNegative()
      • getModelState()
      • setModelState()
      • setMinimumSigmaResiduals()
      • getMinimumSigmaResiduals()
      • setAddSigmaResiduals()
      • getAddSigmaResiduals()
      • getParameterList()
      • plist()
      • setParameterList()
      • getInitialStates()
      • setInitialStates()
      • hasCustomInitialStates()
      • getInitialStateSensitivities()
      • setInitialStateSensitivities()
      • hasCustomInitialStateSensitivities()
      • setUnscaledInitialStateSensitivities()
      • setSteadyStateComputationMode()
      • getSteadyStateComputationMode()
      • setSteadyStateSensitivityMode()
      • getSteadyStateSensitivityMode()
      • setReinitializeFixedParameterInitialStates()
      • getReinitializeFixedParameterInitialStates()
      • requireSensitivitiesForAllParameters()
      • getExpression()
      • getObservable()
      • getObservableScaling()
      • getObservableSensitivity()
      • getObservableSigma()
      • getObservableSigmaSensitivity()
      • addObservableObjective()
      • addObservableObjectiveSensitivity()
      • addPartialObservableObjectiveSensitivity()
      • getAdjointStateObservableUpdate()
      • getEvent()
      • getEventSensitivity()
      • getUnobservedEventSensitivity()
      • getEventRegularization()
      • getEventRegularizationSensitivity()
      • getEventSigma()
      • getEventSigmaSensitivity()
      • addEventObjective()
      • addEventObjectiveRegularization()
      • addEventObjectiveSensitivity()
      • addPartialEventObjectiveSensitivity()
      • getAdjointStateEventUpdate()
      • getEventTimeSensitivity()
      • addStateEventUpdate()
      • addStateSensitivityEventUpdate()
      • addAdjointStateEventUpdate()
      • addAdjointQuadratureEventUpdate()
      • updateHeaviside()
      • updateHeavisideB()
      • checkFinite()
      • checkFinite()
      • checkFinite()
      • setAlwaysCheckFinite()
      • getAlwaysCheckFinite()
      • fx0()
      • fx0_fixedParameters()
      • fsx0()
      • fsx0_fixedParameters()
      • fsdx0()
      • fx_rdata()
      • fsx_rdata()
      • setReinitializationStateIdxs()
      • getReinitializationStateIdxs()
      • get_dxdotdp()
      • get_dxdotdp_full()
      • get_trigger_timepoints()
      • get_steadystate_mask()
      • set_steadystate_mask()
      • 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()
      • fdydp()
      • fdydx()
      • fdzdp()
      • fdzdx()
      • fJrz()
      • fJy()
      • fJz()
      • frz()
      • fsigmay()
      • fsigmaz()
      • fsrz()
      • fstau()
      • fsx0()
      • fsx0_fixedParameters()
      • fsz()
      • fw()
      • fx0()
      • fx0_fixedParameters()
      • fy()
      • fz()
      • o2mode
      • idlist
      • logger
      • state_independent_events_
      • writeSliceEvent()
      • writeSensitivitySliceEvent()
      • writeLLHSensitivitySlice()
      • checkLLHBufferSize()
      • initializeVectors()
      • fy()
      • fdydp()
      • fdydx()
      • fsigmay()
      • fdsigmaydp()
      • fdsigmaydy()
      • fJy()
      • fdJydy()
      • fdJydsigma()
      • fdJydp()
      • fdJydx()
      • fz()
      • fdzdp()
      • fdzdx()
      • frz()
      • fdrzdp()
      • fdrzdx()
      • fsigmaz()
      • fdsigmazdp()
      • fJz()
      • fdJzdz()
      • fdJzdsigma()
      • fdJzdp()
      • fdJzdx()
      • fJrz()
      • fdJrzdz()
      • fdJrzdsigma()
      • fspl()
      • fsspl()
      • fw()
      • fdwdp()
      • fdwdx()
      • fdwdw()
      • fx_rdata()
      • fsx_rdata()
      • fx_solver()
      • fsx_solver()
      • ftotal_cl()
      • fstotal_cl()
      • computeX_pos()
      • computeX_pos()
      • state_
      • derived_state_
      • splines_
      • z2event_
      • x0data_
      • sx0data_
      • state_is_non_negative_
      • root_initial_values_
      • 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()
      • getSolver()
      • 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()
      • getSolver()
      • fJSparse()
      • fJSparse()
      • fJSparse_colptrs()
      • fJSparse_rowvals()
      • 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()
      • 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 NewtonSolver
  • Class Documentation
    • amici::NewtonSolver
      • NewtonSolver()
      • NewtonSolver()
      • operator=()
      • getStep()
      • computeNewtonSensis()
      • prepareLinearSystem()
      • prepareLinearSystemB()
      • solveLinearSystem()
      • reinitialize()
      • is_singular()

• Class ReturnData
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::ReturnData
      • ReturnData()
      • ReturnData()
      • ReturnData()
      • ~ReturnData()
      • processSimulationObjects()
      • id
      • ts
      • xdot
      • J
      • w
      • z
      • sigmaz
      • sz
      • ssigmaz
      • rz
      • srz
      • s2rz
      • x
      • sx
      • y
      • sigmay
      • sy
      • ssigmay
      • res
      • sres
      • FIM
      • numsteps
      • numstepsB
      • numrhsevals
      • numrhsevalsB
      • numerrtestfails
      • numerrtestfailsB
      • numnonlinsolvconvfails
      • numnonlinsolvconvfailsB
      • order
      • cpu_time
      • cpu_timeB
      • cpu_time_total
      • preeq_status
      • preeq_cpu_time
      • preeq_cpu_timeB
      • posteq_status
      • posteq_cpu_time
      • posteq_cpu_timeB
      • preeq_numsteps
      • preeq_numstepsB
      • posteq_numsteps
      • posteq_numstepsB
      • preeq_t
      • preeq_wrms
      • posteq_t
      • posteq_wrms
      • x0
      • x_ss
      • sx0
      • sx_ss
      • llh
      • chi2
      • sllh
      • s2llh
      • status
      • nx
      • nxtrue
      • nplist
      • nmaxevent
      • nt
      • newton_maxsteps
      • pscale
      • o2mode
      • sensi
      • sensi_meth
      • rdata_reporting
      • sigma_res
      • messages
      • t_last
      • initializeLikelihoodReporting()
      • initializeObservablesLikelihoodReporting()
      • initializeResidualReporting()
      • initializeFullReporting()
      • initializeObjectiveFunction()
      • processPreEquilibration()
      • processPostEquilibration()
      • processForwardProblem()
      • processBackwardProblem()
      • processSolver()
      • storeJacobianAndDerivativeInReturnData()
      • fres()
      • fchi2()
      • fsres()
      • fFIM()
      • invalidate()
      • invalidateLLH()
      • invalidateSLLH()
      • applyChainRuleFactorToSimulationResults()
      • computingFSA()
      • getDataOutput()
      • getDataSensisFSA()
      • getEventOutput()
      • getEventSensisFSA()
      • handleSx0Backward()
      • handleSx0Forward()
      • 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()
      • reinitializeAllFixedParameterDependentInitialStatesForPresimulation()
      • reinitializeAllFixedParameterDependentInitialStatesForSimulation()
      • reinitializeAllFixedParameterDependentInitialStates()
      • fixedParameters
      • fixedParametersPreequilibration
      • fixedParametersPresimulation
      • parameters
      • x0
      • sx0
      • pscale
      • plist
      • tstart_
      • t_presim
      • ts_
      • reinitializeFixedParameterInitialStates
      • 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()
      • getSunContext()
      • run()
      • step()
      • runB()
      • setup()
      • setupB()
      • setupSteadystate()
      • updateAndReinitStatesAndSensitivities()
      • getRootInfo()
      • calcIC()
      • calcICB()
      • solveB()
      • turnOffRootFinding()
      • getSensitivityMethod()
      • setSensitivityMethod()
      • getSensitivityMethodPreequilibration()
      • setSensitivityMethodPreequilibration()
      • switchForwardSensisOff()
      • getNewtonMaxSteps()
      • setNewtonMaxSteps()
      • getNewtonDampingFactorMode()
      • setNewtonDampingFactorMode()
      • getNewtonDampingFactorLowerBound()
      • setNewtonDampingFactorLowerBound()
      • getSensitivityOrder()
      • setSensitivityOrder()
      • getRelativeTolerance()
      • setRelativeTolerance()
      • getAbsoluteTolerance()
      • setAbsoluteTolerance()
      • getRelativeToleranceFSA()
      • setRelativeToleranceFSA()
      • getAbsoluteToleranceFSA()
      • setAbsoluteToleranceFSA()
      • getRelativeToleranceB()
      • setRelativeToleranceB()
      • getAbsoluteToleranceB()
      • setAbsoluteToleranceB()
      • getRelativeToleranceQuadratures()
      • setRelativeToleranceQuadratures()
      • getAbsoluteToleranceQuadratures()
      • setAbsoluteToleranceQuadratures()
      • getSteadyStateToleranceFactor()
      • setSteadyStateToleranceFactor()
      • getRelativeToleranceSteadyState()
      • setRelativeToleranceSteadyState()
      • getAbsoluteToleranceSteadyState()
      • setAbsoluteToleranceSteadyState()
      • getSteadyStateSensiToleranceFactor()
      • setSteadyStateSensiToleranceFactor()
      • getRelativeToleranceSteadyStateSensi()
      • setRelativeToleranceSteadyStateSensi()
      • getAbsoluteToleranceSteadyStateSensi()
      • setAbsoluteToleranceSteadyStateSensi()
      • getMaxSteps()
      • setMaxSteps()
      • getMaxTime()
      • setMaxTime()
      • startTimer()
      • timeExceeded()
      • getMaxStepsBackwardProblem()
      • setMaxStepsBackwardProblem()
      • getLinearMultistepMethod()
      • setLinearMultistepMethod()
      • getNonlinearSolverIteration()
      • setNonlinearSolverIteration()
      • getInterpolationType()
      • setInterpolationType()
      • getStateOrdering()
      • setStateOrdering()
      • getStabilityLimitFlag()
      • setStabilityLimitFlag()
      • getLinearSolver()
      • setLinearSolver()
      • getInternalSensitivityMethod()
      • setInternalSensitivityMethod()
      • getReturnDataReportingMode()
      • setReturnDataReportingMode()
      • writeSolution()
      • writeSolutionB()
      • getState()
      • getDerivativeState()
      • getStateSensitivity()
      • getAdjointState()
      • getAdjointDerivativeState()
      • getAdjointQuadrature()
      • getQuadrature()
      • reInit()
      • sensReInit()
      • sensToggleOff()
      • reInitB()
      • quadReInitB()
      • gett()
      • getCpuTime()
      • getCpuTimeB()
      • nx()
      • nplist()
      • nquad()
      • computingFSA()
      • computingASA()
      • resetDiagnosis()
      • storeDiagnosis()
      • storeDiagnosisB()
      • getNumSteps()
      • getNumStepsB()
      • getNumRhsEvals()
      • getNumRhsEvalsB()
      • getNumErrTestFails()
      • getNumErrTestFailsB()
      • getNumNonlinSolvConvFails()
      • getNumNonlinSolvConvFailsB()
      • getLastOrder()
      • getNewtonStepSteadyStateCheck()
      • getSensiSteadyStateCheck()
      • setNewtonStepSteadyStateCheck()
      • setSensiSteadyStateCheck()
      • setMaxNonlinIters()
      • getMaxNonlinIters()
      • setMaxConvFails()
      • getMaxConvFails()
      • setConstraints()
      • getConstraints()
      • setMaxStepSize()
      • getMaxStepSize()
      • logger
      • setStopTime()
      • solve()
      • solveF()
      • reInitPostProcessF()
      • reInitPostProcessB()
      • getSens()
      • getB()
      • getQuadB()
      • getQuad()
      • init()
      • initSteadystate()
      • sensInit1()
      • binit()
      • qbinit()
      • rootInit()
      • initializeNonLinearSolverSens()
      • setDenseJacFn()
      • setSparseJacFn()
      • setBandJacFn()
      • setJacTimesVecFn()
      • setDenseJacFnB()
      • setSparseJacFnB()
      • setBandJacFnB()
      • setJacTimesVecFnB()
      • setSparseJacFn_ss()
      • allocateSolver()
      • setSStolerances()
      • setSensSStolerances()
      • setSensErrCon()
      • setQuadErrConB()
      • setQuadErrCon()
      • setErrHandlerFn()
      • setUserData()
      • setUserDataB()
      • setMaxNumSteps()
      • setMaxNumStepsB()
      • setStabLimDet()
      • setStabLimDetB()
      • setId()
      • setSuppressAlg()
      • setSensParams()
      • getDky()
      • getDkyB()
      • getSensDky()
      • getQuadDkyB()
      • getQuadDky()
      • adjInit()
      • quadInit()
      • allocateSolverB()
      • setSStolerancesB()
      • quadSStolerancesB()
      • quadSStolerances()
      • getNumSteps()
      • getNumRhsEvals()
      • getNumErrTestFails()
      • getNumNonlinSolvConvFails()
      • getLastOrder()
      • initializeLinearSolver()
      • initializeNonLinearSolver()
      • setLinearSolver()
      • setLinearSolverB()
      • setNonLinearSolver()
      • setNonLinearSolverB()
      • setNonLinearSolverSens()
      • initializeLinearSolverB()
      • initializeNonLinearSolverB()
      • getModel()
      • getInitDone()
      • getSensInitDone()
      • getAdjInitDone()
      • getInitDoneB()
      • getQuadInitDoneB()
      • getQuadInitDone()
      • diag()
      • diagB()
      • resetMutableMemory()
      • getAdjBmem()
      • applyTolerances()
      • applyTolerancesFSA()
      • applyTolerancesASA()
      • applyQuadTolerancesASA()
      • applyQuadTolerances()
      • applySensitivityTolerances()
      • apply_constraints()
      • setInitDone()
      • setSensInitDone()
      • setSensInitOff()
      • setAdjInitDone()
      • setInitDoneB()
      • setQuadInitDoneB()
      • setQuadInitDone()
      • checkSensitivityMethod()
      • 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 SteadystateProblem
  • Class Documentation
    • amici::SteadystateProblem
      • SteadystateProblem()
      • workSteadyStateProblem()
      • workSteadyStateBackwardProblem()
      • getFinalSimulationState()
      • getEquilibrationQuadratures()
      • getState()
      • getStateSensitivity()
      • getDJydx()
      • getCPUTime()
      • getCPUTimeB()
      • getSteadyStateStatus()
      • getSteadyStateTime()
      • getResidualNorm()
      • getNumSteps()
      • getNumStepsB()
      • getAdjointUpdates()
      • getAdjointState()
      • getAdjointQuadrature()
      • hasQuadrature()
      • checkSteadyStateSuccess()

• 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()
      • setOrdering()
      • is_singular()

• Class SUNLinSolPCG
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolPCG
      • SUNLinSolPCG()
      • setATimes()
      • setPreconditioner()
      • setScalingVectors()
      • getNumIters()
      • getResNorm()
      • getResid()

• Class SUNLinSolSPBCGS
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPBCGS
      • SUNLinSolSPBCGS()
      • SUNLinSolSPBCGS()
      • setATimes()
      • setPreconditioner()
      • setScalingVectors()
      • getNumIters()
      • getResNorm()
      • getResid()

• Class SUNLinSolSPFGMR
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPFGMR
      • SUNLinSolSPFGMR()
      • setATimes()
      • setPreconditioner()
      • setScalingVectors()
      • getNumIters()
      • getResNorm()
      • getResid()

• Class SUNLinSolSPGMR
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPGMR
      • SUNLinSolSPGMR()
      • setATimes()
      • setPreconditioner()
      • setScalingVectors()
      • getNumIters()
      • getResNorm()
      • getResid()

• Class SUNLinSolSPTFQMR
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • amici::SUNLinSolSPTFQMR
      • SUNLinSolSPTFQMR()
      • SUNLinSolSPTFQMR()
      • setATimes()
      • setPreconditioner()
      • setScalingVectors()
      • getNumIters()
      • getResNorm()
      • getResid()

• Class SUNLinSolWrapper
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • amici::SUNLinSolWrapper
      • SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • ~SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • SUNLinSolWrapper()
      • operator=()
      • operator=()
      • get()
      • getType()
      • setup()
      • solve()
      • getLastFlag()
      • 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()
      • getSysFn()

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

• Class SUNNonLinSolWrapper
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • amici::SUNNonLinSolWrapper
      • SUNNonLinSolWrapper()
      • ~SUNNonLinSolWrapper()
      • SUNNonLinSolWrapper()
      • SUNNonLinSolWrapper()
      • operator=()
      • operator=()
      • get()
      • getType()
      • setup()
      • Solve()
      • setSysFn()
      • setLSetupFn()
      • setLSolveFn()
      • setConvTestFn()
      • setMaxIters()
      • getNumIters()
      • getCurIter()
      • getNumConvFails()
      • initialize()
      • solver

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
      • dJydy_matlab
      • 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
      • functional
      • 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 SteadyStateContext
  • Enum Documentation
    • SteadyStateContext
      • newtonSensi
      • sensiStorage
      • solverCreation

• 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::addSlice(gsl::span<T const> const, gsl::span<T>)
  • Function Documentation
    • addSlice()

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

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

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

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

• Function amici::backtraceString
  • Function Documentation
    • backtraceString()

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

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

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

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

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

• Function amici::dotProd
  • Function Documentation
    • dotProd()

• Function amici::getScaledParameter
  • Function Documentation
    • getScaledParameter()

• Function amici::getUnscaledParameter
  • Function Documentation
    • getUnscaledParameter()

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

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

• Function amici::hdf5::createAndWriteDouble1DDataset
  • Function Documentation
    • createAndWriteDouble1DDataset()

• Function amici::hdf5::createAndWriteDouble2DDataset
  • Function Documentation
    • createAndWriteDouble2DDataset()

• Function amici::hdf5::createAndWriteDouble3DDataset
  • Function Documentation
    • createAndWriteDouble3DDataset()

• Function amici::hdf5::createAndWriteInt1DDataset
  • Function Documentation
    • createAndWriteInt1DDataset()

• Function amici::hdf5::createAndWriteInt2DDataset
  • Function Documentation
    • createAndWriteInt2DDataset()

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

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

• Function amici::hdf5::getDoubleDataset1D
  • Function Documentation
    • getDoubleDataset1D()

• Function amici::hdf5::getDoubleDataset2D
  • Function Documentation
    • getDoubleDataset2D()

• Function amici::hdf5::getDoubleDataset3D
  • Function Documentation
    • getDoubleDataset3D()

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

• Function amici::hdf5::getIntDataset1D
  • Function Documentation
    • getIntDataset1D()

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

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

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

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

• Function amici::hdf5::readModelDataFromHDF5(std::string const&, Model&, std::string const&)
  • Function Documentation
    • readModelDataFromHDF5()

• Function amici::hdf5::readModelDataFromHDF5(H5::H5File const&, Model&, std::string const&)
  • Function Documentation
    • readModelDataFromHDF5()

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

• Function amici::hdf5::readSolverSettingsFromHDF5(const H5::H5File&, Solver&, std::string const&)
  • Function Documentation
    • readSolverSettingsFromHDF5()

• Function amici::hdf5::readSolverSettingsFromHDF5(std::string const&, Solver&, std::string const&)
  • Function Documentation
    • readSolverSettingsFromHDF5()

• Function amici::hdf5::writeLogItemsToHDF5
  • Function Documentation
    • writeLogItemsToHDF5()

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

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

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

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

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

• Function amici::hdf5::writeSolverSettingsToHDF5(Solver const&, std::string const&, std::string const&)
  • Function Documentation
    • writeSolverSettingsToHDF5()

• Function amici::hdf5::writeSolverSettingsToHDF5(Solver const&, H5::H5File const&, std::string const&)
  • Function Documentation
    • writeSolverSettingsToHDF5()

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

• Function amici::linearSum
  • Function Documentation
    • linearSum()

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

• 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::printfToString
  • Function Documentation
    • printfToString()

• Function amici::regexErrorToString
  • Function Documentation
    • regexErrorToString()

• Function amici::runAmiciSimulation
  • Function Documentation
    • runAmiciSimulation()

• Function amici::runAmiciSimulations
  • Function Documentation
    • runAmiciSimulations()

• Function amici::scaleParameters
  • Function Documentation
    • scaleParameters()

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

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

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

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

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

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

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

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

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

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

• 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)
  • 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_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_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