AMICI C++ API

AMICI C++ library functions

Class Hierarchy

• • Namespace amici
    • 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 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 SteadyStateContext
    • 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
    • LogItem
      • LogItem::LogItem()
      • LogItem::LogItem()
      • LogItem::severity
      • LogItem::identifier
      • LogItem::message

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

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

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

• Struct SimulationState
  • Struct Documentation
    • SimulationState
      • SimulationState::t
      • SimulationState::x
      • SimulationState::dx
      • SimulationState::sx
      • SimulationState::state

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

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

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

• Class AmiVector
  • Class Documentation
    • AmiVector
      • AmiVector::AmiVector()
      • AmiVector::AmiVector()
      • AmiVector::AmiVector()
      • AmiVector::AmiVector()
      • AmiVector::AmiVector()
      • AmiVector::AmiVector()
      • AmiVector::~AmiVector()
      • AmiVector::operator=()
      • AmiVector::operator*=()
      • AmiVector::operator/=()
      • AmiVector::begin()
      • AmiVector::end()
      • AmiVector::data()
      • AmiVector::data()
      • AmiVector::getNVector()
      • AmiVector::getNVector()
      • AmiVector::getVector()
      • AmiVector::getLength()
      • AmiVector::zero()
      • AmiVector::minus()
      • AmiVector::set()
      • AmiVector::operator[]()
      • AmiVector::at()
      • AmiVector::at()
      • AmiVector::copy()
      • AmiVector::abs()
      • AmiVector::get_ctx()
      • AmiVector::set_ctx()
      • AmiVector::serialize()

• Class AmiVectorArray
  • Class Documentation
    • AmiVectorArray
      • AmiVectorArray::AmiVectorArray()
      • AmiVectorArray::AmiVectorArray()
      • AmiVectorArray::AmiVectorArray()
      • AmiVectorArray::~AmiVectorArray()
      • AmiVectorArray::operator=()
      • AmiVectorArray::data()
      • AmiVectorArray::data()
      • AmiVectorArray::at()
      • AmiVectorArray::at()
      • AmiVectorArray::getNVectorArray()
      • AmiVectorArray::getNVector()
      • AmiVectorArray::getNVector()
      • AmiVectorArray::operator[]()
      • AmiVectorArray::operator[]()
      • AmiVectorArray::getLength()
      • AmiVectorArray::zero()
      • AmiVectorArray::flatten_to_vector()
      • AmiVectorArray::copy()
      • AmiVectorArray::set_ctx()

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

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

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

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

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

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

• Class ExpData
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ExpData
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::ExpData()
      • ExpData::~ExpData()
      • ExpData::nytrue()
      • ExpData::nztrue()
      • ExpData::nmaxevent()
      • ExpData::nt()
      • ExpData::setTimepoints()
      • ExpData::getTimepoints()
      • ExpData::getTimepoint()
      • ExpData::setObservedData()
      • ExpData::setObservedData()
      • ExpData::isSetObservedData()
      • ExpData::getObservedData()
      • ExpData::getObservedDataPtr()
      • ExpData::setObservedDataStdDev()
      • ExpData::setObservedDataStdDev()
      • ExpData::setObservedDataStdDev()
      • ExpData::setObservedDataStdDev()
      • ExpData::isSetObservedDataStdDev()
      • ExpData::getObservedDataStdDev()
      • ExpData::getObservedDataStdDevPtr()
      • ExpData::setObservedEvents()
      • ExpData::setObservedEvents()
      • ExpData::isSetObservedEvents()
      • ExpData::getObservedEvents()
      • ExpData::getObservedEventsPtr()
      • ExpData::setObservedEventsStdDev()
      • ExpData::setObservedEventsStdDev()
      • ExpData::setObservedEventsStdDev()
      • ExpData::setObservedEventsStdDev()
      • ExpData::isSetObservedEventsStdDev()
      • ExpData::getObservedEventsStdDev()
      • ExpData::getObservedEventsStdDevPtr()
      • ExpData::clear_observations()
      • ExpData::id
      • ExpData::applyDimensions()
      • ExpData::applyDataDimension()
      • ExpData::applyEventDimension()
      • ExpData::checkDataDimension()
      • ExpData::checkEventsDimension()
      • ExpData::nytrue_
      • ExpData::nztrue_
      • ExpData::nmaxevent_
      • ExpData::observed_data_
      • ExpData::observed_data_std_dev_
      • ExpData::observed_events_
      • ExpData::observed_events_std_dev_
      • ExpData::operator==()

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

• Class ForwardProblem
  • Class Documentation
    • ForwardProblem
      • ForwardProblem::ForwardProblem()
      • ForwardProblem::~ForwardProblem()
      • ForwardProblem::workForwardProblem()
      • ForwardProblem::getAdjointUpdates()
      • ForwardProblem::getTime()
      • ForwardProblem::getState()
      • ForwardProblem::getStateDerivative()
      • ForwardProblem::getStateSensitivity()
      • ForwardProblem::getStatesAtDiscontinuities()
      • ForwardProblem::getRHSAtDiscontinuities()
      • ForwardProblem::getRHSBeforeDiscontinuities()
      • ForwardProblem::getNumberOfRoots()
      • ForwardProblem::getDiscontinuities()
      • ForwardProblem::getRootIndexes()
      • ForwardProblem::getDJydx()
      • ForwardProblem::getDJzdx()
      • ForwardProblem::getStatePointer()
      • ForwardProblem::getStateDerivativePointer()
      • ForwardProblem::getStateSensitivityPointer()
      • ForwardProblem::getStateDerivativeSensitivityPointer()
      • ForwardProblem::getCurrentTimeIteration()
      • ForwardProblem::getFinalTime()
      • ForwardProblem::getEventCounter()
      • ForwardProblem::getRootCounter()
      • ForwardProblem::getSimulationStateTimepoint()
      • ForwardProblem::getSimulationStateEvent()
      • ForwardProblem::getInitialSimulationState()
      • ForwardProblem::getFinalSimulationState()
      • ForwardProblem::model
      • ForwardProblem::solver
      • ForwardProblem::edata

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

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

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

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

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

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

• Class Model
  • Inheritance Relationships
    • Base Types
    • Derived Types
  • Class Documentation
    • Model
      • Model::Model()
      • Model::Model()
      • Model::~Model()
      • Model::operator=()
      • Model::clone()
      • Model::initialize()
      • Model::reinitialize()
      • Model::initializeB()
      • Model::initializeStates()
      • Model::initializeStateSensitivities()
      • Model::initializeSplines()
      • Model::initializeSplineSensitivities()
      • Model::initEvents()
      • Model::nplist()
      • Model::np()
      • Model::nk()
      • Model::ncl()
      • Model::nx_reinit()
      • Model::k()
      • Model::nMaxEvent()
      • Model::setNMaxEvent()
      • Model::nt()
      • Model::getParameterScale()
      • Model::setParameterScale()
      • Model::setParameterScale()
      • Model::getUnscaledParameters()
      • Model::getParameters()
      • Model::getParameterById()
      • Model::getParameterByName()
      • Model::setParameters()
      • Model::setParameterById()
      • Model::setParameterById()
      • Model::setParametersByIdRegex()
      • Model::setParameterByName()
      • Model::setParameterByName()
      • Model::setParametersByNameRegex()
      • Model::getFixedParameters()
      • Model::getFixedParameterById()
      • Model::getFixedParameterByName()
      • Model::setFixedParameters()
      • Model::setFixedParameterById()
      • Model::setFixedParametersByIdRegex()
      • Model::setFixedParameterByName()
      • Model::setFixedParametersByNameRegex()
      • Model::getName()
      • Model::hasParameterNames()
      • Model::getParameterNames()
      • Model::hasStateNames()
      • Model::getStateNames()
      • Model::getStateNamesSolver()
      • Model::hasFixedParameterNames()
      • Model::getFixedParameterNames()
      • Model::hasObservableNames()
      • Model::getObservableNames()
      • Model::hasExpressionNames()
      • Model::getExpressionNames()
      • Model::hasParameterIds()
      • Model::getParameterIds()
      • Model::hasStateIds()
      • Model::getStateIds()
      • Model::getStateIdsSolver()
      • Model::hasFixedParameterIds()
      • Model::getFixedParameterIds()
      • Model::hasObservableIds()
      • Model::getObservableIds()
      • Model::hasExpressionIds()
      • Model::getExpressionIds()
      • Model::hasQuadraticLLH()
      • Model::getTimepoints()
      • Model::getTimepoint()
      • Model::setTimepoints()
      • Model::t0()
      • Model::setT0()
      • Model::getStateIsNonNegative()
      • Model::setStateIsNonNegative()
      • Model::setAllStatesNonNegative()
      • Model::getModelState()
      • Model::setModelState()
      • Model::setMinimumSigmaResiduals()
      • Model::getMinimumSigmaResiduals()
      • Model::setAddSigmaResiduals()
      • Model::getAddSigmaResiduals()
      • Model::getParameterList()
      • Model::plist()
      • Model::setParameterList()
      • Model::getInitialStates()
      • Model::setInitialStates()
      • Model::hasCustomInitialStates()
      • Model::getInitialStateSensitivities()
      • Model::setInitialStateSensitivities()
      • Model::hasCustomInitialStateSensitivities()
      • Model::setUnscaledInitialStateSensitivities()
      • Model::setSteadyStateComputationMode()
      • Model::getSteadyStateComputationMode()
      • Model::setSteadyStateSensitivityMode()
      • Model::getSteadyStateSensitivityMode()
      • Model::setReinitializeFixedParameterInitialStates()
      • Model::getReinitializeFixedParameterInitialStates()
      • Model::requireSensitivitiesForAllParameters()
      • Model::getExpression()
      • Model::getObservable()
      • Model::getObservableScaling()
      • Model::getObservableSensitivity()
      • Model::getObservableSigma()
      • Model::getObservableSigmaSensitivity()
      • Model::addObservableObjective()
      • Model::addObservableObjectiveSensitivity()
      • Model::addPartialObservableObjectiveSensitivity()
      • Model::getAdjointStateObservableUpdate()
      • Model::getEvent()
      • Model::getEventSensitivity()
      • Model::getUnobservedEventSensitivity()
      • Model::getEventRegularization()
      • Model::getEventRegularizationSensitivity()
      • Model::getEventSigma()
      • Model::getEventSigmaSensitivity()
      • Model::addEventObjective()
      • Model::addEventObjectiveRegularization()
      • Model::addEventObjectiveSensitivity()
      • Model::addPartialEventObjectiveSensitivity()
      • Model::getAdjointStateEventUpdate()
      • Model::getEventTimeSensitivity()
      • Model::addStateEventUpdate()
      • Model::addStateSensitivityEventUpdate()
      • Model::addAdjointStateEventUpdate()
      • Model::addAdjointQuadratureEventUpdate()
      • Model::updateHeaviside()
      • Model::updateHeavisideB()
      • Model::checkFinite()
      • Model::checkFinite()
      • Model::checkFinite()
      • Model::setAlwaysCheckFinite()
      • Model::getAlwaysCheckFinite()
      • Model::fx0()
      • Model::fx0_fixedParameters()
      • Model::fsx0()
      • Model::fsx0_fixedParameters()
      • Model::fsdx0()
      • Model::fx_rdata()
      • Model::fsx_rdata()
      • Model::setReinitializationStateIdxs()
      • Model::getReinitializationStateIdxs()
      • Model::get_dxdotdp()
      • Model::get_dxdotdp_full()
      • Model::get_trigger_timepoints()
      • Model::get_steadystate_mask()
      • Model::set_steadystate_mask()
      • Model::fdeltaqB()
      • Model::fdeltasx()
      • Model::fdeltax()
      • Model::fdeltaxB()
      • Model::fdJrzdsigma()
      • Model::fdJrzdz()
      • Model::fdJydsigma()
      • Model::fdJydy()
      • Model::fdJydy_colptrs()
      • Model::fdJydy_rowvals()
      • Model::fdJzdsigma()
      • Model::fdJzdz()
      • Model::fdrzdp()
      • Model::fdrzdx()
      • Model::fdsigmaydp()
      • Model::fdsigmaydy()
      • Model::fdsigmazdp()
      • Model::fdtotal_cldp()
      • Model::fdtotal_cldx_rdata()
      • Model::fdtotal_cldx_rdata_colptrs()
      • Model::fdtotal_cldx_rdata_rowvals()
      • Model::fdwdp()
      • Model::fdwdp_colptrs()
      • Model::fdwdp_rowvals()
      • Model::fdwdw()
      • Model::fdwdw_colptrs()
      • Model::fdwdw_rowvals()
      • Model::fdwdx()
      • Model::fdwdx_colptrs()
      • Model::fdwdx_rowvals()
      • Model::fdx_rdatadp()
      • Model::fdx_rdatadtcl()
      • Model::fdx_rdatadtcl_colptrs()
      • Model::fdx_rdatadtcl_rowvals()
      • Model::fdx_rdatadx_solver()
      • Model::fdx_rdatadx_solver_colptrs()
      • Model::fdx_rdatadx_solver_rowvals()
      • Model::fdydp()
      • Model::fdydp()
      • Model::fdydx()
      • Model::fdzdp()
      • Model::fdzdx()
      • Model::fJrz()
      • Model::fJy()
      • Model::fJz()
      • Model::frz()
      • Model::fsigmay()
      • Model::fsigmaz()
      • Model::fsrz()
      • Model::fstau()
      • Model::fsx0()
      • Model::fsx0_fixedParameters()
      • Model::fsz()
      • Model::fw()
      • Model::fx0()
      • Model::fx0_fixedParameters()
      • Model::fy()
      • Model::fz()
      • Model::o2mode
      • Model::idlist
      • Model::logger
      • Model::state_independent_events_
      • Model::writeSliceEvent()
      • Model::writeSensitivitySliceEvent()
      • Model::writeLLHSensitivitySlice()
      • Model::checkLLHBufferSize()
      • Model::initializeVectors()
      • Model::fy()
      • Model::fdydp()
      • Model::fdydx()
      • Model::fsigmay()
      • Model::fdsigmaydp()
      • Model::fdsigmaydy()
      • Model::fJy()
      • Model::fdJydy()
      • Model::fdJydsigma()
      • Model::fdJydp()
      • Model::fdJydx()
      • Model::fz()
      • Model::fdzdp()
      • Model::fdzdx()
      • Model::frz()
      • Model::fdrzdp()
      • Model::fdrzdx()
      • Model::fsigmaz()
      • Model::fdsigmazdp()
      • Model::fJz()
      • Model::fdJzdz()
      • Model::fdJzdsigma()
      • Model::fdJzdp()
      • Model::fdJzdx()
      • Model::fJrz()
      • Model::fdJrzdz()
      • Model::fdJrzdsigma()
      • Model::fspl()
      • Model::fsspl()
      • Model::fw()
      • Model::fdwdp()
      • Model::fdwdx()
      • Model::fdwdw()
      • Model::fx_rdata()
      • Model::fsx_rdata()
      • Model::fx_solver()
      • Model::fsx_solver()
      • Model::ftotal_cl()
      • Model::fstotal_cl()
      • Model::computeX_pos()
      • Model::computeX_pos()
      • Model::state_
      • Model::derived_state_
      • Model::splines_
      • Model::z2event_
      • Model::x0data_
      • Model::sx0data_
      • Model::state_is_non_negative_
      • Model::root_initial_values_
      • Model::any_state_non_negative_
      • Model::nmaxevent_
      • Model::steadystate_computation_mode_
      • Model::steadystate_sensitivity_mode_
      • Model::always_check_finite_
      • Model::sigma_res_
      • Model::min_sigma_
      • Model::serialize()
      • Model::operator==()

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

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

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

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

• Class NewtonSolver
  • Class Documentation
    • NewtonSolver
      • NewtonSolver::NewtonSolver()
      • NewtonSolver::NewtonSolver()
      • NewtonSolver::operator=()
      • NewtonSolver::getStep()
      • NewtonSolver::computeNewtonSensis()
      • NewtonSolver::prepareLinearSystem()
      • NewtonSolver::prepareLinearSystemB()
      • NewtonSolver::solveLinearSystem()
      • NewtonSolver::reinitialize()
      • NewtonSolver::is_singular()

• Class ReturnData
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ReturnData
      • ReturnData::ReturnData()
      • ReturnData::ReturnData()
      • ReturnData::ReturnData()
      • ReturnData::~ReturnData()
      • ReturnData::processSimulationObjects()
      • ReturnData::id
      • ReturnData::ts
      • ReturnData::xdot
      • ReturnData::J
      • ReturnData::w
      • ReturnData::z
      • ReturnData::sigmaz
      • ReturnData::sz
      • ReturnData::ssigmaz
      • ReturnData::rz
      • ReturnData::srz
      • ReturnData::s2rz
      • ReturnData::x
      • ReturnData::sx
      • ReturnData::y
      • ReturnData::sigmay
      • ReturnData::sy
      • ReturnData::ssigmay
      • ReturnData::res
      • ReturnData::sres
      • ReturnData::FIM
      • ReturnData::numsteps
      • ReturnData::numstepsB
      • ReturnData::numrhsevals
      • ReturnData::numrhsevalsB
      • ReturnData::numerrtestfails
      • ReturnData::numerrtestfailsB
      • ReturnData::numnonlinsolvconvfails
      • ReturnData::numnonlinsolvconvfailsB
      • ReturnData::order
      • ReturnData::cpu_time
      • ReturnData::cpu_timeB
      • ReturnData::cpu_time_total
      • ReturnData::preeq_status
      • ReturnData::preeq_cpu_time
      • ReturnData::preeq_cpu_timeB
      • ReturnData::posteq_status
      • ReturnData::posteq_cpu_time
      • ReturnData::posteq_cpu_timeB
      • ReturnData::preeq_numsteps
      • ReturnData::preeq_numstepsB
      • ReturnData::posteq_numsteps
      • ReturnData::posteq_numstepsB
      • ReturnData::preeq_t
      • ReturnData::preeq_wrms
      • ReturnData::posteq_t
      • ReturnData::posteq_wrms
      • ReturnData::x0
      • ReturnData::x_ss
      • ReturnData::sx0
      • ReturnData::sx_ss
      • ReturnData::llh
      • ReturnData::chi2
      • ReturnData::sllh
      • ReturnData::s2llh
      • ReturnData::status
      • ReturnData::nx
      • ReturnData::nxtrue
      • ReturnData::nplist
      • ReturnData::nmaxevent
      • ReturnData::nt
      • ReturnData::newton_maxsteps
      • ReturnData::pscale
      • ReturnData::o2mode
      • ReturnData::sensi
      • ReturnData::sensi_meth
      • ReturnData::rdata_reporting
      • ReturnData::sigma_res
      • ReturnData::messages
      • ReturnData::t_last
      • ReturnData::initializeLikelihoodReporting()
      • ReturnData::initializeObservablesLikelihoodReporting()
      • ReturnData::initializeResidualReporting()
      • ReturnData::initializeFullReporting()
      • ReturnData::initializeObjectiveFunction()
      • ReturnData::processPreEquilibration()
      • ReturnData::processPostEquilibration()
      • ReturnData::processForwardProblem()
      • ReturnData::processBackwardProblem()
      • ReturnData::processSolver()
      • ReturnData::storeJacobianAndDerivativeInReturnData()
      • ReturnData::fres()
      • ReturnData::fchi2()
      • ReturnData::fsres()
      • ReturnData::fFIM()
      • ReturnData::invalidate()
      • ReturnData::invalidateLLH()
      • ReturnData::invalidateSLLH()
      • ReturnData::applyChainRuleFactorToSimulationResults()
      • ReturnData::computingFSA()
      • ReturnData::getDataOutput()
      • ReturnData::getDataSensisFSA()
      • ReturnData::getEventOutput()
      • ReturnData::getEventSensisFSA()
      • ReturnData::handleSx0Backward()
      • ReturnData::handleSx0Forward()
      • ReturnData::sigma_offset
      • ReturnData::nroots_
      • ReturnData::serialize()

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

• Class SimulationParameters
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • SimulationParameters
      • SimulationParameters::SimulationParameters()
      • SimulationParameters::SimulationParameters()
      • SimulationParameters::SimulationParameters()
      • SimulationParameters::SimulationParameters()
      • SimulationParameters::SimulationParameters()
      • SimulationParameters::reinitializeAllFixedParameterDependentInitialStatesForPresimulation()
      • SimulationParameters::reinitializeAllFixedParameterDependentInitialStatesForSimulation()
      • SimulationParameters::reinitializeAllFixedParameterDependentInitialStates()
      • SimulationParameters::fixedParameters
      • SimulationParameters::fixedParametersPreequilibration
      • SimulationParameters::fixedParametersPresimulation
      • SimulationParameters::parameters
      • SimulationParameters::x0
      • SimulationParameters::sx0
      • SimulationParameters::pscale
      • SimulationParameters::plist
      • SimulationParameters::tstart_
      • SimulationParameters::t_presim
      • SimulationParameters::ts_
      • SimulationParameters::reinitializeFixedParameterInitialStates
      • SimulationParameters::reinitialization_state_idxs_presim
      • SimulationParameters::reinitialization_state_idxs_sim

• Class Solver
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • Solver
      • Solver::user_data_type
      • Solver::free_solver_ptr
      • Solver::Solver()
      • Solver::Solver()
      • Solver::~Solver()
      • Solver::clone()
      • Solver::getSunContext()
      • Solver::run()
      • Solver::step()
      • Solver::runB()
      • Solver::setup()
      • Solver::setupB()
      • Solver::setupSteadystate()
      • Solver::updateAndReinitStatesAndSensitivities()
      • Solver::getRootInfo()
      • Solver::calcIC()
      • Solver::calcICB()
      • Solver::solveB()
      • Solver::turnOffRootFinding()
      • Solver::getSensitivityMethod()
      • Solver::setSensitivityMethod()
      • Solver::getSensitivityMethodPreequilibration()
      • Solver::setSensitivityMethodPreequilibration()
      • Solver::switchForwardSensisOff()
      • Solver::getNewtonMaxSteps()
      • Solver::setNewtonMaxSteps()
      • Solver::getNewtonDampingFactorMode()
      • Solver::setNewtonDampingFactorMode()
      • Solver::getNewtonDampingFactorLowerBound()
      • Solver::setNewtonDampingFactorLowerBound()
      • Solver::getSensitivityOrder()
      • Solver::setSensitivityOrder()
      • Solver::getRelativeTolerance()
      • Solver::setRelativeTolerance()
      • Solver::getAbsoluteTolerance()
      • Solver::setAbsoluteTolerance()
      • Solver::getRelativeToleranceFSA()
      • Solver::setRelativeToleranceFSA()
      • Solver::getAbsoluteToleranceFSA()
      • Solver::setAbsoluteToleranceFSA()
      • Solver::getRelativeToleranceB()
      • Solver::setRelativeToleranceB()
      • Solver::getAbsoluteToleranceB()
      • Solver::setAbsoluteToleranceB()
      • Solver::getRelativeToleranceQuadratures()
      • Solver::setRelativeToleranceQuadratures()
      • Solver::getAbsoluteToleranceQuadratures()
      • Solver::setAbsoluteToleranceQuadratures()
      • Solver::getSteadyStateToleranceFactor()
      • Solver::setSteadyStateToleranceFactor()
      • Solver::getRelativeToleranceSteadyState()
      • Solver::setRelativeToleranceSteadyState()
      • Solver::getAbsoluteToleranceSteadyState()
      • Solver::setAbsoluteToleranceSteadyState()
      • Solver::getSteadyStateSensiToleranceFactor()
      • Solver::setSteadyStateSensiToleranceFactor()
      • Solver::getRelativeToleranceSteadyStateSensi()
      • Solver::setRelativeToleranceSteadyStateSensi()
      • Solver::getAbsoluteToleranceSteadyStateSensi()
      • Solver::setAbsoluteToleranceSteadyStateSensi()
      • Solver::getMaxSteps()
      • Solver::setMaxSteps()
      • Solver::getMaxTime()
      • Solver::setMaxTime()
      • Solver::startTimer()
      • Solver::timeExceeded()
      • Solver::getMaxStepsBackwardProblem()
      • Solver::setMaxStepsBackwardProblem()
      • Solver::getLinearMultistepMethod()
      • Solver::setLinearMultistepMethod()
      • Solver::getNonlinearSolverIteration()
      • Solver::setNonlinearSolverIteration()
      • Solver::getInterpolationType()
      • Solver::setInterpolationType()
      • Solver::getStateOrdering()
      • Solver::setStateOrdering()
      • Solver::getStabilityLimitFlag()
      • Solver::setStabilityLimitFlag()
      • Solver::getLinearSolver()
      • Solver::setLinearSolver()
      • Solver::getInternalSensitivityMethod()
      • Solver::setInternalSensitivityMethod()
      • Solver::getReturnDataReportingMode()
      • Solver::setReturnDataReportingMode()
      • Solver::writeSolution()
      • Solver::writeSolutionB()
      • Solver::getState()
      • Solver::getDerivativeState()
      • Solver::getStateSensitivity()
      • Solver::getAdjointState()
      • Solver::getAdjointDerivativeState()
      • Solver::getAdjointQuadrature()
      • Solver::getQuadrature()
      • Solver::reInit()
      • Solver::sensReInit()
      • Solver::sensToggleOff()
      • Solver::reInitB()
      • Solver::quadReInitB()
      • Solver::gett()
      • Solver::getCpuTime()
      • Solver::getCpuTimeB()
      • Solver::nx()
      • Solver::nplist()
      • Solver::nquad()
      • Solver::computingFSA()
      • Solver::computingASA()
      • Solver::resetDiagnosis()
      • Solver::storeDiagnosis()
      • Solver::storeDiagnosisB()
      • Solver::getNumSteps()
      • Solver::getNumStepsB()
      • Solver::getNumRhsEvals()
      • Solver::getNumRhsEvalsB()
      • Solver::getNumErrTestFails()
      • Solver::getNumErrTestFailsB()
      • Solver::getNumNonlinSolvConvFails()
      • Solver::getNumNonlinSolvConvFailsB()
      • Solver::getLastOrder()
      • Solver::getNewtonStepSteadyStateCheck()
      • Solver::getSensiSteadyStateCheck()
      • Solver::setNewtonStepSteadyStateCheck()
      • Solver::setSensiSteadyStateCheck()
      • Solver::setMaxNonlinIters()
      • Solver::getMaxNonlinIters()
      • Solver::setMaxConvFails()
      • Solver::getMaxConvFails()
      • Solver::setConstraints()
      • Solver::getConstraints()
      • Solver::setMaxStepSize()
      • Solver::getMaxStepSize()
      • Solver::logger
      • Solver::setStopTime()
      • Solver::solve()
      • Solver::solveF()
      • Solver::reInitPostProcessF()
      • Solver::reInitPostProcessB()
      • Solver::getSens()
      • Solver::getB()
      • Solver::getQuadB()
      • Solver::getQuad()
      • Solver::init()
      • Solver::initSteadystate()
      • Solver::sensInit1()
      • Solver::binit()
      • Solver::qbinit()
      • Solver::rootInit()
      • Solver::initializeNonLinearSolverSens()
      • Solver::setDenseJacFn()
      • Solver::setSparseJacFn()
      • Solver::setBandJacFn()
      • Solver::setJacTimesVecFn()
      • Solver::setDenseJacFnB()
      • Solver::setSparseJacFnB()
      • Solver::setBandJacFnB()
      • Solver::setJacTimesVecFnB()
      • Solver::setSparseJacFn_ss()
      • Solver::allocateSolver()
      • Solver::setSStolerances()
      • Solver::setSensSStolerances()
      • Solver::setSensErrCon()
      • Solver::setQuadErrConB()
      • Solver::setQuadErrCon()
      • Solver::setErrHandlerFn()
      • Solver::setUserData()
      • Solver::setUserDataB()
      • Solver::setMaxNumSteps()
      • Solver::setMaxNumStepsB()
      • Solver::setStabLimDet()
      • Solver::setStabLimDetB()
      • Solver::setId()
      • Solver::setSuppressAlg()
      • Solver::setSensParams()
      • Solver::getDky()
      • Solver::getDkyB()
      • Solver::getSensDky()
      • Solver::getQuadDkyB()
      • Solver::getQuadDky()
      • Solver::adjInit()
      • Solver::quadInit()
      • Solver::allocateSolverB()
      • Solver::setSStolerancesB()
      • Solver::quadSStolerancesB()
      • Solver::quadSStolerances()
      • Solver::getNumSteps()
      • Solver::getNumRhsEvals()
      • Solver::getNumErrTestFails()
      • Solver::getNumNonlinSolvConvFails()
      • Solver::getLastOrder()
      • Solver::initializeLinearSolver()
      • Solver::initializeNonLinearSolver()
      • Solver::setLinearSolver()
      • Solver::setLinearSolverB()
      • Solver::setNonLinearSolver()
      • Solver::setNonLinearSolverB()
      • Solver::setNonLinearSolverSens()
      • Solver::initializeLinearSolverB()
      • Solver::initializeNonLinearSolverB()
      • Solver::getModel()
      • Solver::getInitDone()
      • Solver::getSensInitDone()
      • Solver::getAdjInitDone()
      • Solver::getInitDoneB()
      • Solver::getQuadInitDoneB()
      • Solver::getQuadInitDone()
      • Solver::diag()
      • Solver::diagB()
      • Solver::resetMutableMemory()
      • Solver::getAdjBmem()
      • Solver::applyTolerances()
      • Solver::applyTolerancesFSA()
      • Solver::applyTolerancesASA()
      • Solver::applyQuadTolerancesASA()
      • Solver::applyQuadTolerances()
      • Solver::applySensitivityTolerances()
      • Solver::apply_constraints()
      • Solver::setInitDone()
      • Solver::setSensInitDone()
      • Solver::setSensInitOff()
      • Solver::setAdjInitDone()
      • Solver::setInitDoneB()
      • Solver::setQuadInitDoneB()
      • Solver::setQuadInitDone()
      • Solver::checkSensitivityMethod()
      • Solver::apply_max_nonlin_iters()
      • Solver::apply_max_conv_fails()
      • Solver::apply_max_step_size()
      • Solver::sunctx_
      • Solver::solver_memory_
      • Solver::solver_memory_B_
      • Solver::user_data
      • Solver::ism_
      • Solver::lmm_
      • Solver::iter_
      • Solver::interp_type_
      • Solver::maxsteps_
      • Solver::maxtime_
      • Solver::simulation_timer_
      • Solver::linear_solver_
      • Solver::linear_solver_B_
      • Solver::non_linear_solver_
      • Solver::non_linear_solver_B_
      • Solver::non_linear_solver_sens_
      • Solver::solver_was_called_F_
      • Solver::solver_was_called_B_
      • Solver::x_
      • Solver::dky_
      • Solver::dx_
      • Solver::sx_
      • Solver::sdx_
      • Solver::xB_
      • Solver::dxB_
      • Solver::xQB_
      • Solver::xQ_
      • Solver::t_
      • Solver::force_reinit_postprocess_F_
      • Solver::force_reinit_postprocess_B_
      • Solver::sens_initialized_
      • Solver::constraints_
      • Solver::serialize()
      • Solver::operator==()

• Class SteadystateProblem
  • Class Documentation
    • SteadystateProblem
      • SteadystateProblem::SteadystateProblem()
      • SteadystateProblem::workSteadyStateProblem()
      • SteadystateProblem::workSteadyStateBackwardProblem()
      • SteadystateProblem::getFinalSimulationState()
      • SteadystateProblem::getEquilibrationQuadratures()
      • SteadystateProblem::getState()
      • SteadystateProblem::getStateSensitivity()
      • SteadystateProblem::getDJydx()
      • SteadystateProblem::getCPUTime()
      • SteadystateProblem::getCPUTimeB()
      • SteadystateProblem::getSteadyStateStatus()
      • SteadystateProblem::getSteadyStateTime()
      • SteadystateProblem::getResidualNorm()
      • SteadystateProblem::getNumSteps()
      • SteadystateProblem::getNumStepsB()
      • SteadystateProblem::getAdjointUpdates()
      • SteadystateProblem::getAdjointState()
      • SteadystateProblem::getAdjointQuadrature()
      • SteadystateProblem::hasQuadrature()
      • SteadystateProblem::checkSteadyStateSuccess()

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

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

• Class SUNLinSolKLU
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • SUNLinSolKLU
      • SUNLinSolKLU::StateOrdering
        • SUNLinSolKLU::StateOrdering::AMD
        • SUNLinSolKLU::StateOrdering::COLAMD
        • SUNLinSolKLU::StateOrdering::natural
      • SUNLinSolKLU::SUNLinSolKLU()
      • SUNLinSolKLU::SUNLinSolKLU()
      • SUNLinSolKLU::reInit()
      • SUNLinSolKLU::setOrdering()
      • SUNLinSolKLU::is_singular()

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

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

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

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

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

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

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

• Class SUNNonLinSolFixedPoint
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • SUNNonLinSolFixedPoint
      • SUNNonLinSolFixedPoint::SUNNonLinSolFixedPoint()
      • SUNNonLinSolFixedPoint::SUNNonLinSolFixedPoint()
      • SUNNonLinSolFixedPoint::getSysFn()

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

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

Enums

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

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

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

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

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

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

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

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

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

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

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

• Enum NonlinearSolverIteration
  • Enum Documentation
    • NonlinearSolverIteration
      • NonlinearSolverIteration::functional
      • NonlinearSolverIteration::fixedpoint
      • NonlinearSolverIteration::newton

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

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

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

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

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

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

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

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

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

• Enum SteadyStateContext
  • Enum Documentation
    • SteadyStateContext
      • SteadyStateContext::newtonSensi
      • SteadyStateContext::sensiStorage
      • SteadyStateContext::solverCreation

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

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

• Define AMICI_H5_RESTORE_ERROR_HANDLER
  • Define Documentation

• Define AMICI_H5_SAVE_ERROR_HANDLER
  • Define Documentation

• Define AMICI_VERSION
  • Define Documentation

• Define M_1_PI
  • Define Documentation

• Define M_2_PI
  • Define Documentation

• Define M_2_SQRTPI
  • Define Documentation

• Define M_E
  • Define Documentation

• Define M_LN10
  • Define Documentation

• Define M_LN2
  • Define Documentation

• Define M_LOG10E
  • Define Documentation

• Define M_LOG2E
  • Define Documentation

• Define M_PI
  • Define Documentation

• Define M_PI_2
  • Define Documentation

• Define M_PI_4
  • Define Documentation

• Define M_SQRT1_2
  • Define Documentation

• Define M_SQRT2
  • Define Documentation

Typedefs

• Typedef amici::const_N_Vector
  • Typedef Documentation
    • const_N_Vector

• Typedef amici::realtype
  • Typedef Documentation
    • realtype