AMICI
v0.15.0
About
About AMICI
Availability
License conditions
How to cite AMICI
References
Background
Changelog
Glossary
Contributing
User's guide
Python interface
C++ interface
Matlab interface
Developer's guide
AMICI developer’s guide
Handling of Discontinuities
AMICI
Index
Edit on GitHub
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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__init__() (amici.add_path method)
(amici.amici.ExpData method)
(amici.amici.Logger method)
(amici.amici.LogItem method)
(amici.amici.Model method)
(amici.amici.ModelDimensions method)
(amici.amici.ReturnData method)
(amici.amici.SimulationParameters method)
(amici.amici.SimulationState method)
(amici.amici.Solver method)
(amici.ModelModule method)
(amici.ode_export.ODEExporter method)
(amici.ode_export.ODEModel method)
(amici.ode_export.TemplateAmici method)
(amici.ode_model.ConservationLaw method)
(amici.ode_model.Constant method)
(amici.ode_model.Event method)
(amici.ode_model.EventObservable method)
(amici.ode_model.Expression method)
(amici.ode_model.LogLikelihood method)
(amici.ode_model.LogLikelihoodRZ method)
(amici.ode_model.LogLikelihoodY method)
(amici.ode_model.LogLikelihoodZ method)
(amici.ode_model.ModelQuantity method)
(amici.ode_model.Observable method)
(amici.ode_model.Parameter method)
(amici.ode_model.Sigma method)
(amici.ode_model.SigmaY method)
(amici.ode_model.SigmaZ method)
(amici.ode_model.State method)
(amici.parameter_mapping.ParameterMapping method)
(amici.parameter_mapping.ParameterMappingForCondition method)
(amici.petab_import_pysb.PysbPetabProblem method)
(amici.petab_simulate.PetabSimulator method)
(amici.sbml_import.SbmlImporter method)
_USE_MATH_DEFINES (C macro)
A
add_component() (amici.ode_export.ODEModel method)
add_conservation_law() (amici.ode_export.ODEModel method)
add_d_dt() (amici.sbml_import.SbmlImporter method)
add_local_symbol() (amici.sbml_import.SbmlImporter method)
add_noise() (amici.petab_simulate.PetabSimulator method)
add_path (class in amici)
amici
module
amici.amici
module
amici.bngl_import
module
amici.conserved_quantities_demartino
module
amici.conserved_quantities_rref
module
amici.gradient_check
module
amici.import_utils
module
amici.logging
module
amici.ode_export
module
amici.ode_model
module
amici.pandas
module
amici.parameter_mapping
module
amici.petab_import
module
amici.petab_import_pysb
module
amici.petab_objective
module
amici.petab_simulate
module
amici.plotting
module
amici.pysb_import
module
amici.sbml_import
module
amici::AbstractModel (C++ class)
amici::AbstractModel::fdeltaqB (C++ function)
amici::AbstractModel::fdeltasx (C++ function)
amici::AbstractModel::fdeltax (C++ function)
amici::AbstractModel::fdeltaxB (C++ function)
amici::AbstractModel::fdJrzdsigma (C++ function)
amici::AbstractModel::fdJrzdz (C++ function)
amici::AbstractModel::fdJydsigma (C++ function)
amici::AbstractModel::fdJydy (C++ function)
amici::AbstractModel::fdJydy_colptrs (C++ function)
amici::AbstractModel::fdJydy_rowvals (C++ function)
amici::AbstractModel::fdJzdsigma (C++ function)
amici::AbstractModel::fdJzdz (C++ function)
amici::AbstractModel::fdrzdp (C++ function)
amici::AbstractModel::fdrzdx (C++ function)
amici::AbstractModel::fdsigmaydp (C++ function)
amici::AbstractModel::fdsigmaydy (C++ function)
amici::AbstractModel::fdsigmazdp (C++ function)
amici::AbstractModel::fdtotal_cldp (C++ function)
amici::AbstractModel::fdtotal_cldx_rdata (C++ function)
amici::AbstractModel::fdtotal_cldx_rdata_colptrs (C++ function)
amici::AbstractModel::fdtotal_cldx_rdata_rowvals (C++ function)
amici::AbstractModel::fdwdp (C++ function)
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[1]
amici::AbstractModel::fdwdp_colptrs (C++ function)
amici::AbstractModel::fdwdp_rowvals (C++ function)
amici::AbstractModel::fdwdw (C++ function)
amici::AbstractModel::fdwdw_colptrs (C++ function)
amici::AbstractModel::fdwdw_rowvals (C++ function)
amici::AbstractModel::fdwdx (C++ function)
amici::AbstractModel::fdwdx_colptrs (C++ function)
amici::AbstractModel::fdwdx_rowvals (C++ function)
amici::AbstractModel::fdx0 (C++ function)
amici::AbstractModel::fdx_rdatadp (C++ function)
amici::AbstractModel::fdx_rdatadtcl (C++ function)
amici::AbstractModel::fdx_rdatadtcl_colptrs (C++ function)
amici::AbstractModel::fdx_rdatadtcl_rowvals (C++ function)
amici::AbstractModel::fdx_rdatadx_solver (C++ function)
amici::AbstractModel::fdx_rdatadx_solver_colptrs (C++ function)
amici::AbstractModel::fdx_rdatadx_solver_rowvals (C++ function)
amici::AbstractModel::fdxdotdp (C++ function)
amici::AbstractModel::fdydp (C++ function)
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[1]
amici::AbstractModel::fdydx (C++ function)
amici::AbstractModel::fdzdp (C++ function)
amici::AbstractModel::fdzdx (C++ function)
amici::AbstractModel::fJ (C++ function)
amici::AbstractModel::fJB (C++ function)
amici::AbstractModel::fJDiag (C++ function)
amici::AbstractModel::fJrz (C++ function)
amici::AbstractModel::fJSparse (C++ function)
amici::AbstractModel::fJSparseB (C++ function)
amici::AbstractModel::fJSparseB_ss (C++ function)
amici::AbstractModel::fJv (C++ function)
amici::AbstractModel::fJy (C++ function)
amici::AbstractModel::fJz (C++ function)
amici::AbstractModel::froot (C++ function)
amici::AbstractModel::frz (C++ function)
amici::AbstractModel::fsigmay (C++ function)
amici::AbstractModel::fsigmaz (C++ function)
amici::AbstractModel::fsrz (C++ function)
amici::AbstractModel::fstau (C++ function)
amici::AbstractModel::fsx0 (C++ function)
amici::AbstractModel::fsx0_fixedParameters (C++ function)
amici::AbstractModel::fsxdot (C++ function)
amici::AbstractModel::fsz (C++ function)
amici::AbstractModel::fw (C++ function)
amici::AbstractModel::fx0 (C++ function)
amici::AbstractModel::fx0_fixedParameters (C++ function)
amici::AbstractModel::fxBdot_ss (C++ function)
amici::AbstractModel::fxdot (C++ function)
amici::AbstractModel::fy (C++ function)
amici::AbstractModel::fz (C++ function)
amici::AbstractModel::getAmiciCommit (C++ function)
amici::AbstractModel::getAmiciVersion (C++ function)
amici::AbstractModel::getSolver (C++ function)
amici::AbstractModel::isFixedParameterStateReinitializationAllowed (C++ function)
amici::AbstractModel::writeSteadystateJB (C++ function)
amici::AbstractModel::~AbstractModel (C++ function)
amici::addSlice (C++ function)
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[1]
amici::AMICI_CONV_FAILURE (C++ member)
amici::AMICI_DAMPING_FACTOR_ERROR (C++ member)
amici::AMICI_DATA_RETURN (C++ member)
amici::amici_daxpy (C++ function)
amici::amici_dgemm (C++ function)
amici::amici_dgemv (C++ function)
amici::AMICI_ERR_FAILURE (C++ member)
amici::AMICI_ERROR (C++ member)
amici::AMICI_ILL_INPUT (C++ member)
amici::AMICI_MAX_TIME_EXCEEDED (C++ member)
amici::AMICI_NO_STEADY_STATE (C++ member)
amici::AMICI_NORMAL (C++ member)
amici::AMICI_NOT_IMPLEMENTED (C++ member)
amici::AMICI_ONE_STEP (C++ member)
amici::AMICI_ONEOUTPUT (C++ member)
amici::AMICI_PREEQUILIBRATE (C++ member)
amici::AMICI_RECOVERABLE_ERROR (C++ member)
amici::AMICI_RHSFUNC_FAIL (C++ member)
amici::AMICI_ROOT_RETURN (C++ member)
amici::AMICI_SINGULAR_JACOBIAN (C++ member)
amici::AMICI_SUCCESS (C++ member)
amici::AMICI_TOO_MUCH_ACC (C++ member)
amici::AMICI_TOO_MUCH_WORK (C++ member)
amici::AMICI_UNRECOVERABLE_ERROR (C++ member)
amici::AmiException (C++ class)
amici::AmiException::AmiException (C++ function)
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[1]
amici::AmiException::getBacktrace (C++ function)
amici::AmiException::storeBacktrace (C++ function)
amici::AmiException::storeMessage (C++ function)
amici::AmiException::what (C++ function)
amici::AmiVector (C++ class)
amici::AmiVector::abs (C++ function)
amici::AmiVector::AmiVector (C++ function)
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[1]
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[4]
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[5]
amici::AmiVector::at (C++ function)
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[1]
amici::AmiVector::begin (C++ function)
amici::AmiVector::copy (C++ function)
amici::AmiVector::data (C++ function)
,
[1]
amici::AmiVector::end (C++ function)
amici::AmiVector::getLength (C++ function)
amici::AmiVector::getNVector (C++ function)
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[1]
amici::AmiVector::getVector (C++ function)
amici::AmiVector::minus (C++ function)
amici::AmiVector::operator*= (C++ function)
amici::AmiVector::operator/= (C++ function)
amici::AmiVector::operator= (C++ function)
amici::AmiVector::operator[] (C++ function)
amici::AmiVector::set (C++ function)
amici::AmiVector::zero (C++ function)
amici::AmiVector::~AmiVector (C++ function)
amici::AmiVectorArray (C++ class)
amici::AmiVectorArray::AmiVectorArray (C++ function)
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[1]
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[2]
amici::AmiVectorArray::at (C++ function)
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[1]
amici::AmiVectorArray::copy (C++ function)
amici::AmiVectorArray::data (C++ function)
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[1]
amici::AmiVectorArray::flatten_to_vector (C++ function)
amici::AmiVectorArray::getLength (C++ function)
amici::AmiVectorArray::getNVector (C++ function)
,
[1]
amici::AmiVectorArray::getNVectorArray (C++ function)
amici::AmiVectorArray::operator= (C++ function)
amici::AmiVectorArray::operator[] (C++ function)
,
[1]
amici::AmiVectorArray::zero (C++ function)
amici::AmiVectorArray::~AmiVectorArray (C++ function)
amici::backtraceString (C++ function)
amici::BackwardProblem (C++ class)
amici::BackwardProblem::BackwardProblem (C++ function)
amici::BackwardProblem::getAdjointQuadrature (C++ function)
amici::BackwardProblem::getAdjointState (C++ function)
amici::BackwardProblem::getdJydx (C++ function)
amici::BackwardProblem::gett (C++ function)
amici::BackwardProblem::getwhich (C++ function)
amici::BackwardProblem::getwhichptr (C++ function)
amici::BackwardProblem::workBackwardProblem (C++ function)
amici::BLASLayout (C++ enum)
amici::BLASLayout::colMajor (C++ enumerator)
amici::BLASLayout::rowMajor (C++ enumerator)
amici::BLASTranspose (C++ enum)
amici::BLASTranspose::conjTrans (C++ enumerator)
amici::BLASTranspose::noTrans (C++ enumerator)
amici::BLASTranspose::trans (C++ enumerator)
amici::checkBufferSize (C++ function)
amici::checkSigmaPositivity (C++ function)
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[1]
amici::ConditionContext (C++ class)
amici::ConditionContext::applyCondition (C++ function)
amici::ConditionContext::ConditionContext (C++ function)
amici::ConditionContext::operator= (C++ function)
amici::ConditionContext::restore (C++ function)
amici::ConditionContext::~ConditionContext (C++ function)
amici::const_N_Vector (C++ type)
amici::ContextManager (C++ class)
amici::ContextManager::ContextManager (C++ function)
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[1]
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[2]
amici::CvodeException (C++ class)
amici::CvodeException::CvodeException (C++ function)
amici::CVodeSolver (C++ class)
amici::CVodeSolver::adjInit (C++ function)
amici::CVodeSolver::allocateSolver (C++ function)
amici::CVodeSolver::allocateSolverB (C++ function)
amici::CVodeSolver::binit (C++ function)
amici::CVodeSolver::boost::serialization::serialize (C++ function)
amici::CVodeSolver::calcIC (C++ function)
amici::CVodeSolver::calcICB (C++ function)
amici::CVodeSolver::clone (C++ function)
amici::CVodeSolver::diag (C++ function)
amici::CVodeSolver::diagB (C++ function)
amici::CVodeSolver::getAdjBmem (C++ function)
amici::CVodeSolver::getB (C++ function)
amici::CVodeSolver::getDky (C++ function)
amici::CVodeSolver::getDkyB (C++ function)
amici::CVodeSolver::getLastOrder (C++ function)
amici::CVodeSolver::getModel (C++ function)
amici::CVodeSolver::getNumErrTestFails (C++ function)
amici::CVodeSolver::getNumNonlinSolvConvFails (C++ function)
amici::CVodeSolver::getNumRhsEvals (C++ function)
amici::CVodeSolver::getNumSteps (C++ function)
amici::CVodeSolver::getQuad (C++ function)
amici::CVodeSolver::getQuadB (C++ function)
amici::CVodeSolver::getQuadDky (C++ function)
amici::CVodeSolver::getQuadDkyB (C++ function)
amici::CVodeSolver::getRootInfo (C++ function)
amici::CVodeSolver::getSens (C++ function)
amici::CVodeSolver::getSensDky (C++ function)
amici::CVodeSolver::init (C++ function)
amici::CVodeSolver::initSteadystate (C++ function)
amici::CVodeSolver::operator== (C++ function)
amici::CVodeSolver::qbinit (C++ function)
amici::CVodeSolver::quadInit (C++ function)
amici::CVodeSolver::quadReInitB (C++ function)
amici::CVodeSolver::quadSStolerances (C++ function)
amici::CVodeSolver::quadSStolerancesB (C++ function)
amici::CVodeSolver::reInit (C++ function)
amici::CVodeSolver::reInitB (C++ function)
amici::CVodeSolver::reInitPostProcess (C++ function)
amici::CVodeSolver::reInitPostProcessB (C++ function)
amici::CVodeSolver::reInitPostProcessF (C++ function)
amici::CVodeSolver::resetState (C++ function)
amici::CVodeSolver::rootInit (C++ function)
amici::CVodeSolver::sensInit1 (C++ function)
amici::CVodeSolver::sensReInit (C++ function)
amici::CVodeSolver::sensToggleOff (C++ function)
amici::CVodeSolver::setBandJacFn (C++ function)
amici::CVodeSolver::setBandJacFnB (C++ function)
amici::CVodeSolver::setDenseJacFn (C++ function)
amici::CVodeSolver::setDenseJacFnB (C++ function)
amici::CVodeSolver::setErrHandlerFn (C++ function)
amici::CVodeSolver::setId (C++ function)
amici::CVodeSolver::setJacTimesVecFn (C++ function)
amici::CVodeSolver::setJacTimesVecFnB (C++ function)
amici::CVodeSolver::setLinearSolver (C++ function)
amici::CVodeSolver::setLinearSolverB (C++ function)
amici::CVodeSolver::setMaxNumSteps (C++ function)
amici::CVodeSolver::setMaxNumStepsB (C++ function)
amici::CVodeSolver::setNonLinearSolver (C++ function)
amici::CVodeSolver::setNonLinearSolverB (C++ function)
amici::CVodeSolver::setNonLinearSolverSens (C++ function)
amici::CVodeSolver::setQuadErrCon (C++ function)
amici::CVodeSolver::setQuadErrConB (C++ function)
amici::CVodeSolver::setSensErrCon (C++ function)
amici::CVodeSolver::setSensParams (C++ function)
amici::CVodeSolver::setSensSStolerances (C++ function)
amici::CVodeSolver::setSparseJacFn (C++ function)
amici::CVodeSolver::setSparseJacFn_ss (C++ function)
amici::CVodeSolver::setSparseJacFnB (C++ function)
amici::CVodeSolver::setSStolerances (C++ function)
amici::CVodeSolver::setSStolerancesB (C++ function)
amici::CVodeSolver::setStabLimDet (C++ function)
amici::CVodeSolver::setStabLimDetB (C++ function)
amici::CVodeSolver::setStopTime (C++ function)
amici::CVodeSolver::setSuppressAlg (C++ function)
amici::CVodeSolver::setUserData (C++ function)
amici::CVodeSolver::setUserDataB (C++ function)
amici::CVodeSolver::solve (C++ function)
amici::CVodeSolver::solveB (C++ function)
amici::CVodeSolver::solveF (C++ function)
amici::CVodeSolver::Solver (C++ function)
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[1]
amici::CVodeSolver::turnOffRootFinding (C++ function)
amici::CVodeSolver::~CVodeSolver (C++ function)
amici::deserializeFromChar (C++ function)
amici::deserializeFromString (C++ function)
amici::dotProd (C++ function)
amici::ExpData (C++ class)
amici::ExpData::applyDataDimension (C++ function)
amici::ExpData::applyDimensions (C++ function)
amici::ExpData::applyEventDimension (C++ function)
amici::ExpData::checkDataDimension (C++ function)
amici::ExpData::checkEventsDimension (C++ function)
amici::ExpData::ExpData (C++ function)
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[1]
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[4]
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[5]
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[6]
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[7]
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[8]
amici::ExpData::getObservedData (C++ function)
amici::ExpData::getObservedDataPtr (C++ function)
amici::ExpData::getObservedDataStdDev (C++ function)
amici::ExpData::getObservedDataStdDevPtr (C++ function)
amici::ExpData::getObservedEvents (C++ function)
amici::ExpData::getObservedEventsPtr (C++ function)
amici::ExpData::getObservedEventsStdDev (C++ function)
amici::ExpData::getObservedEventsStdDevPtr (C++ function)
amici::ExpData::getTimepoint (C++ function)
amici::ExpData::getTimepoints (C++ function)
amici::ExpData::id (C++ member)
amici::ExpData::isSetObservedData (C++ function)
amici::ExpData::isSetObservedDataStdDev (C++ function)
amici::ExpData::isSetObservedEvents (C++ function)
amici::ExpData::isSetObservedEventsStdDev (C++ function)
amici::ExpData::nmaxevent (C++ function)
amici::ExpData::nmaxevent_ (C++ member)
amici::ExpData::nt (C++ function)
amici::ExpData::nytrue (C++ function)
amici::ExpData::nytrue_ (C++ member)
amici::ExpData::nztrue (C++ function)
amici::ExpData::nztrue_ (C++ member)
amici::ExpData::observed_data_ (C++ member)
amici::ExpData::observed_data_std_dev_ (C++ member)
amici::ExpData::observed_events_ (C++ member)
amici::ExpData::observed_events_std_dev_ (C++ member)
amici::ExpData::operator== (C++ function)
amici::ExpData::setObservedData (C++ function)
,
[1]
amici::ExpData::setObservedDataStdDev (C++ function)
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[1]
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[2]
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[3]
amici::ExpData::setObservedEvents (C++ function)
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[1]
amici::ExpData::setObservedEventsStdDev (C++ function)
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[1]
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[2]
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[3]
amici::ExpData::setTimepoints (C++ function)
amici::ExpData::~ExpData (C++ function)
amici::FinalStateStorer (C++ class)
amici::FinalStateStorer::FinalStateStorer (C++ function)
amici::FinalStateStorer::operator= (C++ function)
amici::FinalStateStorer::~FinalStateStorer (C++ function)
amici::FixedParameterContext (C++ enum)
amici::FixedParameterContext::preequilibration (C++ enumerator)
amici::FixedParameterContext::presimulation (C++ enumerator)
amici::FixedParameterContext::simulation (C++ enumerator)
amici::ForwardProblem (C++ class)
amici::ForwardProblem::edata (C++ member)
amici::ForwardProblem::ForwardProblem (C++ function)
amici::ForwardProblem::getAdjointUpdates (C++ function)
amici::ForwardProblem::getCurrentTimeIteration (C++ function)
amici::ForwardProblem::getDiscontinuities (C++ function)
amici::ForwardProblem::getDJydx (C++ function)
amici::ForwardProblem::getDJzdx (C++ function)
amici::ForwardProblem::getEventCounter (C++ function)
amici::ForwardProblem::getFinalSimulationState (C++ function)
amici::ForwardProblem::getFinalTime (C++ function)
amici::ForwardProblem::getInitialSimulationState (C++ function)
amici::ForwardProblem::getNumberOfRoots (C++ function)
amici::ForwardProblem::getRHSAtDiscontinuities (C++ function)
amici::ForwardProblem::getRHSBeforeDiscontinuities (C++ function)
amici::ForwardProblem::getRootCounter (C++ function)
amici::ForwardProblem::getRootIndexes (C++ function)
amici::ForwardProblem::getSimulationStateEvent (C++ function)
amici::ForwardProblem::getSimulationStateTimepoint (C++ function)
amici::ForwardProblem::getState (C++ function)
amici::ForwardProblem::getStateDerivative (C++ function)
amici::ForwardProblem::getStateDerivativePointer (C++ function)
amici::ForwardProblem::getStateDerivativeSensitivityPointer (C++ function)
amici::ForwardProblem::getStatePointer (C++ function)
amici::ForwardProblem::getStatesAtDiscontinuities (C++ function)
amici::ForwardProblem::getStateSensitivity (C++ function)
amici::ForwardProblem::getStateSensitivityPointer (C++ function)
amici::ForwardProblem::getTime (C++ function)
amici::ForwardProblem::model (C++ member)
amici::ForwardProblem::solver (C++ member)
amici::ForwardProblem::workForwardProblem (C++ function)
amici::ForwardProblem::~ForwardProblem (C++ function)
amici::getScaledParameter (C++ function)
amici::getUnscaledParameter (C++ function)
amici::hdf5::attributeExists (C++ function)
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[1]
amici::hdf5::createAndWriteDouble1DDataset (C++ function)
amici::hdf5::createAndWriteDouble2DDataset (C++ function)
amici::hdf5::createAndWriteDouble3DDataset (C++ function)
amici::hdf5::createAndWriteInt1DDataset (C++ function)
amici::hdf5::createAndWriteInt2DDataset (C++ function)
amici::hdf5::createGroup (C++ function)
amici::hdf5::createOrOpenForWriting (C++ function)
amici::hdf5::getDoubleDataset1D (C++ function)
amici::hdf5::getDoubleDataset2D (C++ function)
amici::hdf5::getDoubleDataset3D (C++ function)
amici::hdf5::getDoubleScalarAttribute (C++ function)
amici::hdf5::getIntDataset1D (C++ function)
amici::hdf5::getIntScalarAttribute (C++ function)
amici::hdf5::getStringAttribute (C++ function)
amici::hdf5::locationExists (C++ function)
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[1]
amici::hdf5::readModelDataFromHDF5 (C++ function)
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[1]
amici::hdf5::readSimulationExpData (C++ function)
amici::hdf5::readSolverSettingsFromHDF5 (C++ function)
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[1]
amici::hdf5::writeReturnData (C++ function)
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[1]
amici::hdf5::writeReturnDataDiagnosis (C++ function)
amici::hdf5::writeSimulationExpData (C++ function)
amici::hdf5::writeSolverSettingsToHDF5 (C++ function)
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[1]
amici::IDAException (C++ class)
amici::IDAException::IDAException (C++ function)
amici::IDASolver (C++ class)
amici::IDASolver::adjInit (C++ function)
amici::IDASolver::allocateSolver (C++ function)
amici::IDASolver::allocateSolverB (C++ function)
amici::IDASolver::binit (C++ function)
amici::IDASolver::calcIC (C++ function)
amici::IDASolver::calcICB (C++ function)
amici::IDASolver::clone (C++ function)
amici::IDASolver::diag (C++ function)
amici::IDASolver::diagB (C++ function)
amici::IDASolver::getAdjBmem (C++ function)
amici::IDASolver::getB (C++ function)
amici::IDASolver::getDky (C++ function)
amici::IDASolver::getDkyB (C++ function)
amici::IDASolver::getLastOrder (C++ function)
amici::IDASolver::getModel (C++ function)
amici::IDASolver::getNumErrTestFails (C++ function)
amici::IDASolver::getNumNonlinSolvConvFails (C++ function)
amici::IDASolver::getNumRhsEvals (C++ function)
amici::IDASolver::getNumSteps (C++ function)
amici::IDASolver::getQuad (C++ function)
amici::IDASolver::getQuadB (C++ function)
amici::IDASolver::getQuadDky (C++ function)
amici::IDASolver::getQuadDkyB (C++ function)
amici::IDASolver::getRootInfo (C++ function)
amici::IDASolver::getSens (C++ function)
amici::IDASolver::getSensDky (C++ function)
amici::IDASolver::init (C++ function)
amici::IDASolver::initSteadystate (C++ function)
amici::IDASolver::qbinit (C++ function)
amici::IDASolver::quadInit (C++ function)
amici::IDASolver::quadReInitB (C++ function)
amici::IDASolver::quadSStolerances (C++ function)
amici::IDASolver::quadSStolerancesB (C++ function)
amici::IDASolver::reInit (C++ function)
amici::IDASolver::reInitB (C++ function)
amici::IDASolver::reInitPostProcess (C++ function)
amici::IDASolver::reInitPostProcessB (C++ function)
amici::IDASolver::reInitPostProcessF (C++ function)
amici::IDASolver::resetState (C++ function)
amici::IDASolver::rootInit (C++ function)
amici::IDASolver::sensInit1 (C++ function)
amici::IDASolver::sensReInit (C++ function)
amici::IDASolver::sensToggleOff (C++ function)
amici::IDASolver::setBandJacFn (C++ function)
amici::IDASolver::setBandJacFnB (C++ function)
amici::IDASolver::setDenseJacFn (C++ function)
amici::IDASolver::setDenseJacFnB (C++ function)
amici::IDASolver::setErrHandlerFn (C++ function)
amici::IDASolver::setId (C++ function)
amici::IDASolver::setJacTimesVecFn (C++ function)
amici::IDASolver::setJacTimesVecFnB (C++ function)
amici::IDASolver::setLinearSolver (C++ function)
amici::IDASolver::setLinearSolverB (C++ function)
amici::IDASolver::setMaxNumSteps (C++ function)
amici::IDASolver::setMaxNumStepsB (C++ function)
amici::IDASolver::setNonLinearSolver (C++ function)
amici::IDASolver::setNonLinearSolverB (C++ function)
amici::IDASolver::setNonLinearSolverSens (C++ function)
amici::IDASolver::setQuadErrCon (C++ function)
amici::IDASolver::setQuadErrConB (C++ function)
amici::IDASolver::setSensErrCon (C++ function)
amici::IDASolver::setSensParams (C++ function)
amici::IDASolver::setSensSStolerances (C++ function)
amici::IDASolver::setSparseJacFn (C++ function)
amici::IDASolver::setSparseJacFn_ss (C++ function)
amici::IDASolver::setSparseJacFnB (C++ function)
amici::IDASolver::setSStolerances (C++ function)
amici::IDASolver::setSStolerancesB (C++ function)
amici::IDASolver::setStabLimDet (C++ function)
amici::IDASolver::setStabLimDetB (C++ function)
amici::IDASolver::setStopTime (C++ function)
amici::IDASolver::setSuppressAlg (C++ function)
amici::IDASolver::setUserData (C++ function)
amici::IDASolver::setUserDataB (C++ function)
amici::IDASolver::solve (C++ function)
amici::IDASolver::solveB (C++ function)
amici::IDASolver::solveF (C++ function)
amici::IDASolver::Solver (C++ function)
,
[1]
amici::IDASolver::turnOffRootFinding (C++ function)
amici::IDASolver::~IDASolver (C++ function)
amici::IntegrationFailure (C++ class)
amici::IntegrationFailure::error_code (C++ member)
amici::IntegrationFailure::IntegrationFailure (C++ function)
amici::IntegrationFailure::time (C++ member)
amici::IntegrationFailureB (C++ class)
amici::IntegrationFailureB::error_code (C++ member)
amici::IntegrationFailureB::IntegrationFailureB (C++ function)
amici::IntegrationFailureB::time (C++ member)
amici::InternalSensitivityMethod (C++ enum)
amici::InternalSensitivityMethod::simultaneous (C++ enumerator)
amici::InternalSensitivityMethod::staggered (C++ enumerator)
amici::InternalSensitivityMethod::staggered1 (C++ enumerator)
amici::InterpolationType (C++ enum)
amici::InterpolationType::hermite (C++ enumerator)
amici::InterpolationType::polynomial (C++ enumerator)
amici::is_equal (C++ function)
amici::LinearMultistepMethod (C++ enum)
amici::LinearMultistepMethod::adams (C++ enumerator)
amici::LinearMultistepMethod::BDF (C++ enumerator)
amici::LinearSolver (C++ enum)
amici::LinearSolver::band (C++ enumerator)
amici::LinearSolver::dense (C++ enumerator)
amici::LinearSolver::diag (C++ enumerator)
amici::LinearSolver::KLU (C++ enumerator)
amici::LinearSolver::LAPACKBand (C++ enumerator)
amici::LinearSolver::LAPACKDense (C++ enumerator)
amici::LinearSolver::SPBCG (C++ enumerator)
amici::LinearSolver::SPGMR (C++ enumerator)
amici::LinearSolver::SPTFQMR (C++ enumerator)
amici::LinearSolver::SuperLUMT (C++ enumerator)
amici::linearSum (C++ function)
amici::Logger (C++ class)
amici::Logger::items (C++ member)
amici::Logger::log (C++ function)
,
[1]
amici::Logger::Logger (C++ function)
amici::LogItem (C++ struct)
amici::LogItem::identifier (C++ member)
amici::LogItem::LogItem (C++ function)
,
[1]
amici::LogItem::message (C++ member)
amici::LogItem::severity (C++ member)
amici::LogSeverity (C++ enum)
amici::LogSeverity::debug (C++ enumerator)
amici::LogSeverity::error (C++ enumerator)
amici::LogSeverity::warning (C++ enumerator)
amici::Model (C++ class)
amici::Model::addAdjointQuadratureEventUpdate (C++ function)
amici::Model::addAdjointStateEventUpdate (C++ function)
amici::Model::addEventObjective (C++ function)
amici::Model::addEventObjectiveRegularization (C++ function)
amici::Model::addEventObjectiveSensitivity (C++ function)
amici::Model::addObservableObjective (C++ function)
amici::Model::addObservableObjectiveSensitivity (C++ function)
amici::Model::addPartialEventObjectiveSensitivity (C++ function)
amici::Model::addPartialObservableObjectiveSensitivity (C++ function)
amici::Model::addStateEventUpdate (C++ function)
amici::Model::addStateSensitivityEventUpdate (C++ function)
amici::Model::always_check_finite_ (C++ member)
amici::Model::any_state_non_negative_ (C++ member)
amici::Model::boost::serialization::serialize (C++ function)
amici::Model::checkFinite (C++ function)
,
[1]
,
[2]
amici::Model::checkLLHBufferSize (C++ function)
amici::Model::clone (C++ function)
amici::Model::computeX_pos (C++ function)
,
[1]
amici::Model::derived_state_ (C++ member)
amici::Model::fdeltaqB (C++ function)
amici::Model::fdeltasx (C++ function)
amici::Model::fdeltax (C++ function)
amici::Model::fdeltaxB (C++ function)
amici::Model::fdJrzdsigma (C++ function)
,
[1]
amici::Model::fdJrzdz (C++ function)
,
[1]
amici::Model::fdJydp (C++ function)
amici::Model::fdJydsigma (C++ function)
,
[1]
amici::Model::fdJydx (C++ function)
amici::Model::fdJydy (C++ function)
,
[1]
amici::Model::fdJydy_colptrs (C++ function)
amici::Model::fdJydy_rowvals (C++ function)
amici::Model::fdJzdp (C++ function)
amici::Model::fdJzdsigma (C++ function)
,
[1]
amici::Model::fdJzdx (C++ function)
amici::Model::fdJzdz (C++ function)
,
[1]
amici::Model::fdrzdp (C++ function)
,
[1]
amici::Model::fdrzdx (C++ function)
,
[1]
amici::Model::fdsigmaydp (C++ function)
,
[1]
amici::Model::fdsigmaydy (C++ function)
,
[1]
amici::Model::fdsigmazdp (C++ function)
,
[1]
amici::Model::fdtotal_cldp (C++ function)
amici::Model::fdtotal_cldx_rdata (C++ function)
amici::Model::fdtotal_cldx_rdata_colptrs (C++ function)
amici::Model::fdtotal_cldx_rdata_rowvals (C++ function)
amici::Model::fdwdp (C++ function)
,
[1]
,
[2]
amici::Model::fdwdp_colptrs (C++ function)
amici::Model::fdwdp_rowvals (C++ function)
amici::Model::fdwdw (C++ function)
,
[1]
amici::Model::fdwdw_colptrs (C++ function)
amici::Model::fdwdw_rowvals (C++ function)
amici::Model::fdwdx (C++ function)
,
[1]
amici::Model::fdwdx_colptrs (C++ function)
amici::Model::fdwdx_rowvals (C++ function)
amici::Model::fdx_rdatadp (C++ function)
amici::Model::fdx_rdatadtcl (C++ function)
amici::Model::fdx_rdatadtcl_colptrs (C++ function)
amici::Model::fdx_rdatadtcl_rowvals (C++ function)
amici::Model::fdx_rdatadx_solver (C++ function)
amici::Model::fdx_rdatadx_solver_colptrs (C++ function)
amici::Model::fdx_rdatadx_solver_rowvals (C++ function)
amici::Model::fdydp (C++ function)
,
[1]
,
[2]
amici::Model::fdydx (C++ function)
,
[1]
amici::Model::fdzdp (C++ function)
,
[1]
amici::Model::fdzdx (C++ function)
,
[1]
amici::Model::fJrz (C++ function)
,
[1]
amici::Model::fJy (C++ function)
,
[1]
amici::Model::fJz (C++ function)
,
[1]
amici::Model::frz (C++ function)
,
[1]
amici::Model::fsdx0 (C++ function)
amici::Model::fsigmay (C++ function)
,
[1]
amici::Model::fsigmaz (C++ function)
,
[1]
amici::Model::fsrz (C++ function)
amici::Model::fstau (C++ function)
amici::Model::fstotal_cl (C++ function)
amici::Model::fsx0 (C++ function)
,
[1]
amici::Model::fsx0_fixedParameters (C++ function)
,
[1]
amici::Model::fsx_rdata (C++ function)
,
[1]
amici::Model::fsx_solver (C++ function)
amici::Model::fsz (C++ function)
amici::Model::ftotal_cl (C++ function)
amici::Model::fw (C++ function)
,
[1]
amici::Model::fx0 (C++ function)
,
[1]
amici::Model::fx0_fixedParameters (C++ function)
,
[1]
amici::Model::fx_rdata (C++ function)
,
[1]
amici::Model::fx_solver (C++ function)
amici::Model::fy (C++ function)
,
[1]
amici::Model::fz (C++ function)
,
[1]
amici::Model::get_dxdotdp (C++ function)
amici::Model::get_dxdotdp_full (C++ function)
amici::Model::getAddSigmaResiduals (C++ function)
amici::Model::getAdjointStateEventUpdate (C++ function)
amici::Model::getAdjointStateObservableUpdate (C++ function)
amici::Model::getAlwaysCheckFinite (C++ function)
amici::Model::getEvent (C++ function)
amici::Model::getEventRegularization (C++ function)
amici::Model::getEventRegularizationSensitivity (C++ function)
amici::Model::getEventSensitivity (C++ function)
amici::Model::getEventSigma (C++ function)
amici::Model::getEventSigmaSensitivity (C++ function)
amici::Model::getEventTimeSensitivity (C++ function)
amici::Model::getExpression (C++ function)
amici::Model::getExpressionIds (C++ function)
amici::Model::getExpressionNames (C++ function)
amici::Model::getFixedParameterById (C++ function)
amici::Model::getFixedParameterByName (C++ function)
amici::Model::getFixedParameterIds (C++ function)
amici::Model::getFixedParameterNames (C++ function)
amici::Model::getFixedParameters (C++ function)
amici::Model::getInitialStates (C++ function)
amici::Model::getInitialStateSensitivities (C++ function)
amici::Model::getMinimumSigmaResiduals (C++ function)
amici::Model::getModelState (C++ function)
amici::Model::getName (C++ function)
amici::Model::getObservable (C++ function)
amici::Model::getObservableIds (C++ function)
amici::Model::getObservableNames (C++ function)
amici::Model::getObservableScaling (C++ function)
amici::Model::getObservableSensitivity (C++ function)
amici::Model::getObservableSigma (C++ function)
amici::Model::getObservableSigmaSensitivity (C++ function)
amici::Model::getParameterById (C++ function)
amici::Model::getParameterByName (C++ function)
amici::Model::getParameterIds (C++ function)
amici::Model::getParameterList (C++ function)
amici::Model::getParameterNames (C++ function)
amici::Model::getParameters (C++ function)
amici::Model::getParameterScale (C++ function)
amici::Model::getReinitializationStateIdxs (C++ function)
amici::Model::getReinitializeFixedParameterInitialStates (C++ function)
amici::Model::getStateIds (C++ function)
amici::Model::getStateIdsSolver (C++ function)
amici::Model::getStateIsNonNegative (C++ function)
amici::Model::getStateNames (C++ function)
amici::Model::getStateNamesSolver (C++ function)
amici::Model::getSteadyStateSensitivityMode (C++ function)
amici::Model::getTimepoint (C++ function)
amici::Model::getTimepoints (C++ function)
amici::Model::getUnobservedEventSensitivity (C++ function)
amici::Model::getUnscaledParameters (C++ function)
amici::Model::hasCustomInitialStates (C++ function)
amici::Model::hasCustomInitialStateSensitivities (C++ function)
amici::Model::hasExpressionIds (C++ function)
amici::Model::hasExpressionNames (C++ function)
amici::Model::hasFixedParameterIds (C++ function)
amici::Model::hasFixedParameterNames (C++ function)
amici::Model::hasObservableIds (C++ function)
amici::Model::hasObservableNames (C++ function)
amici::Model::hasParameterIds (C++ function)
amici::Model::hasParameterNames (C++ function)
amici::Model::hasQuadraticLLH (C++ function)
amici::Model::hasStateIds (C++ function)
amici::Model::hasStateNames (C++ function)
amici::Model::idlist (C++ member)
amici::Model::initEvents (C++ function)
amici::Model::initialize (C++ function)
amici::Model::initializeB (C++ function)
amici::Model::initializeStates (C++ function)
amici::Model::initializeStateSensitivities (C++ function)
amici::Model::initializeVectors (C++ function)
amici::Model::k (C++ function)
amici::Model::logger (C++ member)
amici::Model::min_sigma_ (C++ member)
amici::Model::Model (C++ function)
,
[1]
amici::Model::ncl (C++ function)
amici::Model::nk (C++ function)
amici::Model::nMaxEvent (C++ function)
amici::Model::nmaxevent_ (C++ member)
amici::Model::np (C++ function)
amici::Model::nplist (C++ function)
amici::Model::nt (C++ function)
amici::Model::nx_reinit (C++ function)
amici::Model::o2mode (C++ member)
amici::Model::operator= (C++ function)
amici::Model::operator== (C++ function)
amici::Model::plist (C++ function)
amici::Model::pythonGenerated (C++ member)
amici::Model::requireSensitivitiesForAllParameters (C++ function)
amici::Model::root_initial_values_ (C++ member)
amici::Model::setAddSigmaResiduals (C++ function)
amici::Model::setAllStatesNonNegative (C++ function)
amici::Model::setAlwaysCheckFinite (C++ function)
amici::Model::setFixedParameterById (C++ function)
amici::Model::setFixedParameterByName (C++ function)
amici::Model::setFixedParameters (C++ function)
amici::Model::setFixedParametersByIdRegex (C++ function)
amici::Model::setFixedParametersByNameRegex (C++ function)
amici::Model::setInitialStates (C++ function)
amici::Model::setInitialStateSensitivities (C++ function)
amici::Model::setMinimumSigmaResiduals (C++ function)
amici::Model::setModelState (C++ function)
amici::Model::setNMaxEvent (C++ function)
amici::Model::setParameterById (C++ function)
,
[1]
amici::Model::setParameterByName (C++ function)
,
[1]
amici::Model::setParameterList (C++ function)
amici::Model::setParameters (C++ function)
amici::Model::setParametersByIdRegex (C++ function)
amici::Model::setParametersByNameRegex (C++ function)
amici::Model::setParameterScale (C++ function)
,
[1]
amici::Model::setReinitializationStateIdxs (C++ function)
amici::Model::setReinitializeFixedParameterInitialStates (C++ function)
amici::Model::setStateIsNonNegative (C++ function)
amici::Model::setSteadyStateSensitivityMode (C++ function)
amici::Model::setT0 (C++ function)
amici::Model::setTimepoints (C++ function)
amici::Model::setUnscaledInitialStateSensitivities (C++ function)
amici::Model::sigma_res_ (C++ member)
amici::Model::state_ (C++ member)
amici::Model::state_is_non_negative_ (C++ member)
amici::Model::steadystate_sensitivity_mode_ (C++ member)
amici::Model::sx0data_ (C++ member)
amici::Model::t0 (C++ function)
amici::Model::updateHeaviside (C++ function)
amici::Model::updateHeavisideB (C++ function)
amici::Model::writeLLHSensitivitySlice (C++ function)
amici::Model::writeSensitivitySliceEvent (C++ function)
amici::Model::writeSliceEvent (C++ function)
amici::Model::x0data_ (C++ member)
amici::Model::z2event_ (C++ member)
amici::Model::~Model (C++ function)
amici::Model_DAE (C++ class)
amici::Model_DAE::fdxdotdp (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fJ (C++ function)
,
[1]
amici::Model_DAE::fJB (C++ function)
,
[1]
amici::Model_DAE::fJDiag (C++ function)
amici::Model_DAE::fJSparse (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fJSparseB (C++ function)
,
[1]
amici::Model_DAE::fJSparseB_ss (C++ function)
amici::Model_DAE::fJv (C++ function)
,
[1]
amici::Model_DAE::fJvB (C++ function)
amici::Model_DAE::fM (C++ function)
,
[1]
amici::Model_DAE::fqBdot (C++ function)
amici::Model_DAE::fqBdot_ss (C++ function)
amici::Model_DAE::froot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fsxdot (C++ function)
,
[1]
amici::Model_DAE::fxBdot (C++ function)
amici::Model_DAE::fxBdot_ss (C++ function)
,
[1]
amici::Model_DAE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::getSolver (C++ function)
amici::Model_DAE::Model_DAE (C++ function)
,
[1]
amici::Model_DAE::writeSteadystateJB (C++ function)
amici::Model_ODE (C++ class)
amici::Model_ODE::fdxdotdp (C++ function)
,
[1]
,
[2]
amici::Model_ODE::fdxdotdp_explicit (C++ function)
amici::Model_ODE::fdxdotdp_explicit_colptrs (C++ function)
amici::Model_ODE::fdxdotdp_explicit_rowvals (C++ function)
amici::Model_ODE::fdxdotdw (C++ function)
,
[1]
amici::Model_ODE::fdxdotdw_colptrs (C++ function)
amici::Model_ODE::fdxdotdw_rowvals (C++ function)
amici::Model_ODE::fdxdotdx_explicit (C++ function)
amici::Model_ODE::fdxdotdx_explicit_colptrs (C++ function)
amici::Model_ODE::fdxdotdx_explicit_rowvals (C++ function)
amici::Model_ODE::fJ (C++ function)
,
[1]
amici::Model_ODE::fJB (C++ function)
,
[1]
amici::Model_ODE::fJDiag (C++ function)
,
[1]
amici::Model_ODE::fJSparse (C++ function)
,
[1]
,
[2]
,
[3]
amici::Model_ODE::fJSparse_colptrs (C++ function)
amici::Model_ODE::fJSparse_rowvals (C++ function)
amici::Model_ODE::fJSparseB (C++ function)
,
[1]
amici::Model_ODE::fJSparseB_ss (C++ function)
amici::Model_ODE::fJv (C++ function)
,
[1]
amici::Model_ODE::fJvB (C++ function)
amici::Model_ODE::fqBdot (C++ function)
amici::Model_ODE::fqBdot_ss (C++ function)
amici::Model_ODE::froot (C++ function)
,
[1]
,
[2]
amici::Model_ODE::fsxdot (C++ function)
,
[1]
amici::Model_ODE::fxBdot (C++ function)
amici::Model_ODE::fxBdot_ss (C++ function)
,
[1]
amici::Model_ODE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_ODE::getSolver (C++ function)
amici::Model_ODE::Model_ODE (C++ function)
,
[1]
amici::Model_ODE::writeSteadystateJB (C++ function)
amici::model_quantity_to_str (C++ member)
amici::ModelContext (C++ class)
amici::ModelContext::ModelContext (C++ function)
amici::ModelContext::operator= (C++ function)
amici::ModelContext::restore (C++ function)
amici::ModelContext::~ModelContext (C++ function)
amici::ModelDimensions (C++ struct)
amici::ModelDimensions::lbw (C++ member)
amici::ModelDimensions::ModelDimensions (C++ function)
,
[1]
amici::ModelDimensions::ndJydy (C++ member)
amici::ModelDimensions::ndtotal_cldx_rdata (C++ member)
amici::ModelDimensions::ndwdp (C++ member)
amici::ModelDimensions::ndwdw (C++ member)
amici::ModelDimensions::ndwdx (C++ member)
amici::ModelDimensions::ndxdotdw (C++ member)
amici::ModelDimensions::ndxrdatadtcl (C++ member)
amici::ModelDimensions::ndxrdatadxsolver (C++ member)
amici::ModelDimensions::ne (C++ member)
amici::ModelDimensions::nJ (C++ member)
amici::ModelDimensions::nk (C++ member)
amici::ModelDimensions::nnz (C++ member)
amici::ModelDimensions::np (C++ member)
amici::ModelDimensions::nw (C++ member)
amici::ModelDimensions::nx_rdata (C++ member)
amici::ModelDimensions::nx_solver (C++ member)
amici::ModelDimensions::nx_solver_reinit (C++ member)
amici::ModelDimensions::nxtrue_rdata (C++ member)
amici::ModelDimensions::nxtrue_solver (C++ member)
amici::ModelDimensions::ny (C++ member)
amici::ModelDimensions::nytrue (C++ member)
amici::ModelDimensions::nz (C++ member)
amici::ModelDimensions::nztrue (C++ member)
amici::ModelDimensions::ubw (C++ member)
amici::ModelQuantity (C++ enum)
amici::ModelQuantity::deltaqB (C++ enumerator)
amici::ModelQuantity::deltasx (C++ enumerator)
amici::ModelQuantity::deltax (C++ enumerator)
amici::ModelQuantity::deltaxB (C++ enumerator)
amici::ModelQuantity::dJrzdsigma (C++ enumerator)
amici::ModelQuantity::dJrzdx (C++ enumerator)
amici::ModelQuantity::dJrzdz (C++ enumerator)
amici::ModelQuantity::dJydsigma (C++ enumerator)
amici::ModelQuantity::dJydx (C++ enumerator)
amici::ModelQuantity::dJydy (C++ enumerator)
amici::ModelQuantity::dJydy_matlab (C++ enumerator)
amici::ModelQuantity::dJzdsigma (C++ enumerator)
amici::ModelQuantity::dJzdx (C++ enumerator)
amici::ModelQuantity::dJzdz (C++ enumerator)
amici::ModelQuantity::drzdp (C++ enumerator)
amici::ModelQuantity::drzdx (C++ enumerator)
amici::ModelQuantity::dsigmaydp (C++ enumerator)
amici::ModelQuantity::dsigmaydy (C++ enumerator)
amici::ModelQuantity::dsigmazdp (C++ enumerator)
amici::ModelQuantity::dwdp (C++ enumerator)
amici::ModelQuantity::dwdw (C++ enumerator)
amici::ModelQuantity::dwdx (C++ enumerator)
amici::ModelQuantity::dydp (C++ enumerator)
amici::ModelQuantity::dydx (C++ enumerator)
amici::ModelQuantity::dzdp (C++ enumerator)
amici::ModelQuantity::dzdx (C++ enumerator)
amici::ModelQuantity::J (C++ enumerator)
amici::ModelQuantity::JB (C++ enumerator)
amici::ModelQuantity::JDiag (C++ enumerator)
amici::ModelQuantity::JSparseB_ss (C++ enumerator)
amici::ModelQuantity::Jv (C++ enumerator)
amici::ModelQuantity::JvB (C++ enumerator)
amici::ModelQuantity::k (C++ enumerator)
amici::ModelQuantity::p (C++ enumerator)
amici::ModelQuantity::qBdot (C++ enumerator)
amici::ModelQuantity::qBdot_ss (C++ enumerator)
amici::ModelQuantity::root (C++ enumerator)
amici::ModelQuantity::srz (C++ enumerator)
amici::ModelQuantity::ssigmay (C++ enumerator)
amici::ModelQuantity::ssigmaz (C++ enumerator)
amici::ModelQuantity::sx (C++ enumerator)
amici::ModelQuantity::sxdot (C++ enumerator)
amici::ModelQuantity::sy (C++ enumerator)
amici::ModelQuantity::sz (C++ enumerator)
amici::ModelQuantity::ts (C++ enumerator)
amici::ModelQuantity::w (C++ enumerator)
amici::ModelQuantity::x (C++ enumerator)
amici::ModelQuantity::x0 (C++ enumerator)
amici::ModelQuantity::x0_rdata (C++ enumerator)
amici::ModelQuantity::x_rdata (C++ enumerator)
amici::ModelQuantity::xBdot (C++ enumerator)
amici::ModelQuantity::xBdot_ss (C++ enumerator)
amici::ModelQuantity::xdot (C++ enumerator)
amici::ModelQuantity::y (C++ enumerator)
amici::ModelState (C++ struct)
amici::ModelState::fixedParameters (C++ member)
amici::ModelState::h (C++ member)
amici::ModelState::plist (C++ member)
amici::ModelState::stotal_cl (C++ member)
amici::ModelState::total_cl (C++ member)
amici::ModelState::unscaledParameters (C++ member)
amici::ModelStateDerived (C++ struct)
amici::ModelStateDerived::deltaqB_ (C++ member)
amici::ModelStateDerived::deltasx_ (C++ member)
amici::ModelStateDerived::deltax_ (C++ member)
amici::ModelStateDerived::deltaxB_ (C++ member)
amici::ModelStateDerived::dJrzdsigma_ (C++ member)
amici::ModelStateDerived::dJrzdz_ (C++ member)
amici::ModelStateDerived::dJydp_ (C++ member)
amici::ModelStateDerived::dJydsigma_ (C++ member)
amici::ModelStateDerived::dJydx_ (C++ member)
amici::ModelStateDerived::dJydy_ (C++ member)
amici::ModelStateDerived::dJydy_matlab_ (C++ member)
amici::ModelStateDerived::dJzdp_ (C++ member)
amici::ModelStateDerived::dJzdsigma_ (C++ member)
amici::ModelStateDerived::dJzdx_ (C++ member)
amici::ModelStateDerived::dJzdz_ (C++ member)
amici::ModelStateDerived::drzdp_ (C++ member)
amici::ModelStateDerived::drzdx_ (C++ member)
amici::ModelStateDerived::dsigmaydp_ (C++ member)
amici::ModelStateDerived::dsigmaydy_ (C++ member)
amici::ModelStateDerived::dsigmazdp_ (C++ member)
amici::ModelStateDerived::dtotal_cldx_rdata (C++ member)
amici::ModelStateDerived::dwdp_ (C++ member)
amici::ModelStateDerived::dwdx_ (C++ member)
amici::ModelStateDerived::dx_rdatadtcl (C++ member)
amici::ModelStateDerived::dx_rdatadx_solver (C++ member)
amici::ModelStateDerived::dxdotdp (C++ member)
amici::ModelStateDerived::dxdotdp_explicit (C++ member)
amici::ModelStateDerived::dxdotdp_full (C++ member)
amici::ModelStateDerived::dxdotdp_implicit (C++ member)
amici::ModelStateDerived::dxdotdw_ (C++ member)
amici::ModelStateDerived::dxdotdx_explicit (C++ member)
amici::ModelStateDerived::dxdotdx_implicit (C++ member)
amici::ModelStateDerived::dydp_ (C++ member)
amici::ModelStateDerived::dydx_ (C++ member)
amici::ModelStateDerived::dzdp_ (C++ member)
amici::ModelStateDerived::dzdx_ (C++ member)
amici::ModelStateDerived::J_ (C++ member)
amici::ModelStateDerived::JB_ (C++ member)
amici::ModelStateDerived::M_ (C++ member)
amici::ModelStateDerived::ModelStateDerived (C++ function)
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[1]
amici::ModelStateDerived::rz_ (C++ member)
amici::ModelStateDerived::sigmay_ (C++ member)
amici::ModelStateDerived::sigmaz_ (C++ member)
amici::ModelStateDerived::sx_ (C++ member)
amici::ModelStateDerived::sx_rdata_ (C++ member)
amici::ModelStateDerived::w_ (C++ member)
amici::ModelStateDerived::x_pos_tmp_ (C++ member)
amici::ModelStateDerived::x_rdata_ (C++ member)
amici::ModelStateDerived::y_ (C++ member)
amici::ModelStateDerived::z_ (C++ member)
amici::N_VGetArrayPointerConst (C++ function)
amici::NewtonDampingFactorMode (C++ enum)
amici::NewtonDampingFactorMode::off (C++ enumerator)
amici::NewtonDampingFactorMode::on (C++ enumerator)
amici::NewtonFailure (C++ class)
amici::NewtonFailure::error_code (C++ member)
amici::NewtonFailure::NewtonFailure (C++ function)
amici::NewtonSolver (C++ class)
amici::NewtonSolver::computeNewtonSensis (C++ function)
amici::NewtonSolver::dxB_ (C++ member)
amici::NewtonSolver::getSolver (C++ function)
amici::NewtonSolver::getStep (C++ function)
amici::NewtonSolver::is_singular (C++ function)
amici::NewtonSolver::NewtonSolver (C++ function)
amici::NewtonSolver::prepareLinearSystem (C++ function)
amici::NewtonSolver::prepareLinearSystemB (C++ function)
amici::NewtonSolver::reinitialize (C++ function)
amici::NewtonSolver::solveLinearSystem (C++ function)
amici::NewtonSolver::x_ (C++ member)
amici::NewtonSolver::xB_ (C++ member)
amici::NewtonSolver::xdot_ (C++ member)
amici::NewtonSolver::~NewtonSolver (C++ function)
amici::NewtonSolverDense (C++ class)
amici::NewtonSolverDense::is_singular (C++ function)
amici::NewtonSolverDense::NewtonSolverDense (C++ function)
,
[1]
amici::NewtonSolverDense::operator= (C++ function)
amici::NewtonSolverDense::prepareLinearSystem (C++ function)
amici::NewtonSolverDense::prepareLinearSystemB (C++ function)
amici::NewtonSolverDense::reinitialize (C++ function)
amici::NewtonSolverDense::solveLinearSystem (C++ function)
amici::NewtonSolverDense::~NewtonSolverDense (C++ function)
amici::NewtonSolverSparse (C++ class)
amici::NewtonSolverSparse::is_singular (C++ function)
amici::NewtonSolverSparse::NewtonSolverSparse (C++ function)
,
[1]
amici::NewtonSolverSparse::operator= (C++ function)
amici::NewtonSolverSparse::prepareLinearSystem (C++ function)
amici::NewtonSolverSparse::prepareLinearSystemB (C++ function)
amici::NewtonSolverSparse::reinitialize (C++ function)
amici::NewtonSolverSparse::solveLinearSystem (C++ function)
amici::NewtonSolverSparse::~NewtonSolverSparse (C++ function)
amici::NonlinearSolverIteration (C++ enum)
amici::NonlinearSolverIteration::fixedpoint (C++ enumerator)
amici::NonlinearSolverIteration::functional (C++ enumerator)
amici::NonlinearSolverIteration::newton (C++ enumerator)
amici::ObservableScaling (C++ enum)
amici::ObservableScaling::lin (C++ enumerator)
amici::ObservableScaling::log (C++ enumerator)
amici::ObservableScaling::log10 (C++ enumerator)
amici::operator== (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
amici::ParameterScaling (C++ enum)
amici::ParameterScaling::ln (C++ enumerator)
amici::ParameterScaling::log10 (C++ enumerator)
amici::ParameterScaling::none (C++ enumerator)
amici::pi (C++ member)
amici::printfToString (C++ function)
amici::RDataReporting (C++ enum)
amici::RDataReporting::full (C++ enumerator)
amici::RDataReporting::likelihood (C++ enumerator)
amici::RDataReporting::residuals (C++ enumerator)
amici::realtype (C++ type)
amici::regexErrorToString (C++ function)
amici::ReturnData (C++ class)
amici::ReturnData::applyChainRuleFactorToSimulationResults (C++ function)
amici::ReturnData::boost::serialization::serialize (C++ function)
amici::ReturnData::chi2 (C++ member)
amici::ReturnData::computingFSA (C++ function)
amici::ReturnData::cpu_time (C++ member)
amici::ReturnData::cpu_time_total (C++ member)
amici::ReturnData::cpu_timeB (C++ member)
amici::ReturnData::dx_solver_ (C++ member)
amici::ReturnData::fchi2 (C++ function)
amici::ReturnData::fFIM (C++ function)
amici::ReturnData::FIM (C++ member)
amici::ReturnData::fres (C++ function)
amici::ReturnData::fsres (C++ function)
amici::ReturnData::getDataOutput (C++ function)
amici::ReturnData::getDataSensisFSA (C++ function)
amici::ReturnData::getEventOutput (C++ function)
amici::ReturnData::getEventSensisFSA (C++ function)
amici::ReturnData::handleSx0Backward (C++ function)
amici::ReturnData::handleSx0Forward (C++ function)
amici::ReturnData::id (C++ member)
amici::ReturnData::initializeFullReporting (C++ function)
amici::ReturnData::initializeLikelihoodReporting (C++ function)
amici::ReturnData::initializeObjectiveFunction (C++ function)
amici::ReturnData::initializeResidualReporting (C++ function)
amici::ReturnData::invalidate (C++ function)
amici::ReturnData::invalidateLLH (C++ function)
amici::ReturnData::invalidateSLLH (C++ function)
amici::ReturnData::J (C++ member)
amici::ReturnData::llh (C++ member)
amici::ReturnData::messages (C++ member)
amici::ReturnData::newton_maxsteps (C++ member)
amici::ReturnData::nmaxevent (C++ member)
amici::ReturnData::nplist (C++ member)
amici::ReturnData::nroots_ (C++ member)
amici::ReturnData::nt (C++ member)
amici::ReturnData::numerrtestfails (C++ member)
amici::ReturnData::numerrtestfailsB (C++ member)
amici::ReturnData::numnonlinsolvconvfails (C++ member)
amici::ReturnData::numnonlinsolvconvfailsB (C++ member)
amici::ReturnData::numrhsevals (C++ member)
amici::ReturnData::numrhsevalsB (C++ member)
amici::ReturnData::numsteps (C++ member)
amici::ReturnData::numstepsB (C++ member)
amici::ReturnData::nx (C++ member)
amici::ReturnData::nxtrue (C++ member)
amici::ReturnData::o2mode (C++ member)
amici::ReturnData::order (C++ member)
amici::ReturnData::posteq_cpu_time (C++ member)
amici::ReturnData::posteq_cpu_timeB (C++ member)
amici::ReturnData::posteq_numsteps (C++ member)
amici::ReturnData::posteq_numstepsB (C++ member)
amici::ReturnData::posteq_status (C++ member)
amici::ReturnData::posteq_t (C++ member)
amici::ReturnData::posteq_wrms (C++ member)
amici::ReturnData::preeq_cpu_time (C++ member)
amici::ReturnData::preeq_cpu_timeB (C++ member)
amici::ReturnData::preeq_numsteps (C++ member)
amici::ReturnData::preeq_numstepsB (C++ member)
amici::ReturnData::preeq_status (C++ member)
amici::ReturnData::preeq_t (C++ member)
amici::ReturnData::preeq_wrms (C++ member)
amici::ReturnData::processBackwardProblem (C++ function)
amici::ReturnData::processForwardProblem (C++ function)
amici::ReturnData::processPostEquilibration (C++ function)
amici::ReturnData::processPreEquilibration (C++ function)
amici::ReturnData::processSimulationObjects (C++ function)
amici::ReturnData::processSolver (C++ function)
amici::ReturnData::pscale (C++ member)
amici::ReturnData::rdata_reporting (C++ member)
amici::ReturnData::readSimulationState (C++ function)
amici::ReturnData::res (C++ member)
amici::ReturnData::ReturnData (C++ function)
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[1]
,
[2]
amici::ReturnData::rz (C++ member)
amici::ReturnData::s2llh (C++ member)
amici::ReturnData::s2rz (C++ member)
amici::ReturnData::sensi (C++ member)
amici::ReturnData::sensi_meth (C++ member)
amici::ReturnData::sigma_offset (C++ member)
amici::ReturnData::sigma_res (C++ member)
amici::ReturnData::sigmay (C++ member)
amici::ReturnData::sigmaz (C++ member)
amici::ReturnData::sllh (C++ member)
amici::ReturnData::sres (C++ member)
amici::ReturnData::srz (C++ member)
amici::ReturnData::ssigmay (C++ member)
amici::ReturnData::ssigmaz (C++ member)
amici::ReturnData::status (C++ member)
amici::ReturnData::storeJacobianAndDerivativeInReturnData (C++ function)
amici::ReturnData::sx (C++ member)
amici::ReturnData::sx0 (C++ member)
amici::ReturnData::sx_rdata_ (C++ member)
amici::ReturnData::sx_solver_ (C++ member)
amici::ReturnData::sx_ss (C++ member)
amici::ReturnData::sy (C++ member)
amici::ReturnData::sz (C++ member)
amici::ReturnData::t_ (C++ member)
amici::ReturnData::ts (C++ member)
amici::ReturnData::w (C++ member)
amici::ReturnData::x (C++ member)
amici::ReturnData::x0 (C++ member)
amici::ReturnData::x_rdata_ (C++ member)
amici::ReturnData::x_solver_ (C++ member)
amici::ReturnData::x_ss (C++ member)
amici::ReturnData::xdot (C++ member)
amici::ReturnData::y (C++ member)
amici::ReturnData::z (C++ member)
amici::ReturnData::~ReturnData (C++ function)
amici::runAmiciSimulation (C++ function)
amici::runAmiciSimulations (C++ function)
amici::scaleParameters (C++ function)
amici::SecondOrderMode (C++ enum)
amici::SecondOrderMode::directional (C++ enumerator)
amici::SecondOrderMode::full (C++ enumerator)
amici::SecondOrderMode::none (C++ enumerator)
amici::SensitivityMethod (C++ enum)
amici::SensitivityMethod::adjoint (C++ enumerator)
amici::SensitivityMethod::forward (C++ enumerator)
amici::SensitivityMethod::none (C++ enumerator)
amici::SensitivityOrder (C++ enum)
amici::SensitivityOrder::first (C++ enumerator)
amici::SensitivityOrder::none (C++ enumerator)
amici::SensitivityOrder::second (C++ enumerator)
amici::serializeToChar (C++ function)
amici::serializeToStdVec (C++ function)
amici::serializeToString (C++ function)
amici::SetupFailure (C++ class)
amici::SetupFailure::SetupFailure (C++ function)
amici::simulation_status_to_str (C++ function)
amici::SimulationParameters (C++ class)
amici::SimulationParameters::fixedParameters (C++ member)
amici::SimulationParameters::fixedParametersPreequilibration (C++ member)
amici::SimulationParameters::fixedParametersPresimulation (C++ member)
amici::SimulationParameters::parameters (C++ member)
amici::SimulationParameters::plist (C++ member)
amici::SimulationParameters::pscale (C++ member)
amici::SimulationParameters::reinitialization_state_idxs_presim (C++ member)
amici::SimulationParameters::reinitialization_state_idxs_sim (C++ member)
amici::SimulationParameters::reinitializeAllFixedParameterDependentInitialStates (C++ function)
amici::SimulationParameters::reinitializeAllFixedParameterDependentInitialStatesForPresimulation (C++ function)
amici::SimulationParameters::reinitializeAllFixedParameterDependentInitialStatesForSimulation (C++ function)
amici::SimulationParameters::reinitializeFixedParameterInitialStates (C++ member)
amici::SimulationParameters::SimulationParameters (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
amici::SimulationParameters::sx0 (C++ member)
amici::SimulationParameters::t_presim (C++ member)
amici::SimulationParameters::ts_ (C++ member)
amici::SimulationParameters::tstart_ (C++ member)
amici::SimulationParameters::x0 (C++ member)
amici::SimulationState (C++ struct)
amici::SimulationState::dx (C++ member)
amici::SimulationState::state (C++ member)
amici::SimulationState::sx (C++ member)
amici::SimulationState::t (C++ member)
amici::SimulationState::x (C++ member)
amici::slice (C++ function)
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[1]
amici::Solver (C++ class)
amici::Solver::adjInit (C++ function)
amici::Solver::allocateSolver (C++ function)
amici::Solver::allocateSolverB (C++ function)
amici::Solver::applyQuadTolerances (C++ function)
amici::Solver::applyQuadTolerancesASA (C++ function)
amici::Solver::applySensitivityTolerances (C++ function)
amici::Solver::applyTolerances (C++ function)
amici::Solver::applyTolerancesASA (C++ function)
amici::Solver::applyTolerancesFSA (C++ function)
amici::Solver::binit (C++ function)
amici::Solver::boost::serialization::serialize (C++ function)
amici::Solver::calcIC (C++ function)
amici::Solver::calcICB (C++ function)
amici::Solver::checkSensitivityMethod (C++ function)
amici::Solver::clone (C++ function)
amici::Solver::computingASA (C++ function)
amici::Solver::computingFSA (C++ function)
amici::Solver::diag (C++ function)
amici::Solver::diagB (C++ function)
amici::Solver::dky_ (C++ member)
amici::Solver::dx_ (C++ member)
amici::Solver::dxB_ (C++ member)
amici::Solver::force_reinit_postprocess_B_ (C++ member)
amici::Solver::force_reinit_postprocess_F_ (C++ member)
amici::Solver::getAbsoluteTolerance (C++ function)
amici::Solver::getAbsoluteToleranceB (C++ function)
amici::Solver::getAbsoluteToleranceFSA (C++ function)
amici::Solver::getAbsoluteToleranceQuadratures (C++ function)
amici::Solver::getAbsoluteToleranceSteadyState (C++ function)
amici::Solver::getAbsoluteToleranceSteadyStateSensi (C++ function)
amici::Solver::getAdjBmem (C++ function)
amici::Solver::getAdjInitDone (C++ function)
amici::Solver::getAdjointDerivativeState (C++ function)
amici::Solver::getAdjointQuadrature (C++ function)
amici::Solver::getAdjointState (C++ function)
amici::Solver::getB (C++ function)
amici::Solver::getCpuTime (C++ function)
amici::Solver::getCpuTimeB (C++ function)
amici::Solver::getDerivativeState (C++ function)
amici::Solver::getDky (C++ function)
amici::Solver::getDkyB (C++ function)
amici::Solver::getInitDone (C++ function)
amici::Solver::getInitDoneB (C++ function)
amici::Solver::getInternalSensitivityMethod (C++ function)
amici::Solver::getInterpolationType (C++ function)
amici::Solver::getLastOrder (C++ function)
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[1]
amici::Solver::getLinearMultistepMethod (C++ function)
amici::Solver::getLinearSolver (C++ function)
amici::Solver::getMaxSteps (C++ function)
amici::Solver::getMaxStepsBackwardProblem (C++ function)
amici::Solver::getMaxTime (C++ function)
amici::Solver::getModel (C++ function)
amici::Solver::getNewtonDampingFactorLowerBound (C++ function)
amici::Solver::getNewtonDampingFactorMode (C++ function)
amici::Solver::getNewtonMaxSteps (C++ function)
amici::Solver::getNewtonStepSteadyStateCheck (C++ function)
amici::Solver::getNonlinearSolverIteration (C++ function)
amici::Solver::getNumErrTestFails (C++ function)
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[1]
amici::Solver::getNumErrTestFailsB (C++ function)
amici::Solver::getNumNonlinSolvConvFails (C++ function)
,
[1]
amici::Solver::getNumNonlinSolvConvFailsB (C++ function)
amici::Solver::getNumRhsEvals (C++ function)
,
[1]
amici::Solver::getNumRhsEvalsB (C++ function)
amici::Solver::getNumSteps (C++ function)
,
[1]
amici::Solver::getNumStepsB (C++ function)
amici::Solver::getQuad (C++ function)
amici::Solver::getQuadB (C++ function)
amici::Solver::getQuadDky (C++ function)
amici::Solver::getQuadDkyB (C++ function)
amici::Solver::getQuadInitDone (C++ function)
amici::Solver::getQuadInitDoneB (C++ function)
amici::Solver::getQuadrature (C++ function)
amici::Solver::getRelativeTolerance (C++ function)
amici::Solver::getRelativeToleranceB (C++ function)
amici::Solver::getRelativeToleranceFSA (C++ function)
amici::Solver::getRelativeToleranceQuadratures (C++ function)
amici::Solver::getRelativeToleranceSteadyState (C++ function)
amici::Solver::getRelativeToleranceSteadyStateSensi (C++ function)
amici::Solver::getReturnDataReportingMode (C++ function)
amici::Solver::getRootInfo (C++ function)
amici::Solver::getSens (C++ function)
amici::Solver::getSensDky (C++ function)
amici::Solver::getSensInitDone (C++ function)
amici::Solver::getSensiSteadyStateCheck (C++ function)
amici::Solver::getSensitivityMethod (C++ function)
amici::Solver::getSensitivityMethodPreequilibration (C++ function)
amici::Solver::getSensitivityOrder (C++ function)
amici::Solver::getStabilityLimitFlag (C++ function)
amici::Solver::getState (C++ function)
amici::Solver::getStateOrdering (C++ function)
amici::Solver::getStateSensitivity (C++ function)
amici::Solver::getSteadyStateSensiToleranceFactor (C++ function)
amici::Solver::getSteadyStateToleranceFactor (C++ function)
amici::Solver::gett (C++ function)
amici::Solver::init (C++ function)
amici::Solver::initializeLinearSolver (C++ function)
amici::Solver::initializeLinearSolverB (C++ function)
amici::Solver::initializeNonLinearSolver (C++ function)
amici::Solver::initializeNonLinearSolverB (C++ function)
amici::Solver::initializeNonLinearSolverSens (C++ function)
amici::Solver::initSteadystate (C++ function)
amici::Solver::interp_type_ (C++ member)
amici::Solver::ism_ (C++ member)
amici::Solver::iter_ (C++ member)
amici::Solver::linear_solver_ (C++ member)
amici::Solver::linear_solver_B_ (C++ member)
amici::Solver::lmm_ (C++ member)
amici::Solver::logger (C++ member)
amici::Solver::maxsteps_ (C++ member)
amici::Solver::maxtime_ (C++ member)
amici::Solver::non_linear_solver_ (C++ member)
amici::Solver::non_linear_solver_B_ (C++ member)
amici::Solver::non_linear_solver_sens_ (C++ member)
amici::Solver::nplist (C++ function)
amici::Solver::nquad (C++ function)
amici::Solver::nx (C++ function)
amici::Solver::operator== (C++ function)
amici::Solver::qbinit (C++ function)
amici::Solver::quadInit (C++ function)
amici::Solver::quadReInitB (C++ function)
amici::Solver::quadSStolerances (C++ function)
amici::Solver::quadSStolerancesB (C++ function)
amici::Solver::reInit (C++ function)
amici::Solver::reInitB (C++ function)
amici::Solver::reInitPostProcessB (C++ function)
amici::Solver::reInitPostProcessF (C++ function)
amici::Solver::resetDiagnosis (C++ function)
amici::Solver::resetMutableMemory (C++ function)
amici::Solver::rootInit (C++ function)
amici::Solver::run (C++ function)
amici::Solver::runB (C++ function)
amici::Solver::sdx_ (C++ member)
amici::Solver::sens_initialized_ (C++ member)
amici::Solver::sensInit1 (C++ function)
amici::Solver::sensReInit (C++ function)
amici::Solver::sensToggleOff (C++ function)
amici::Solver::setAbsoluteTolerance (C++ function)
amici::Solver::setAbsoluteToleranceB (C++ function)
amici::Solver::setAbsoluteToleranceFSA (C++ function)
amici::Solver::setAbsoluteToleranceQuadratures (C++ function)
amici::Solver::setAbsoluteToleranceSteadyState (C++ function)
amici::Solver::setAbsoluteToleranceSteadyStateSensi (C++ function)
amici::Solver::setAdjInitDone (C++ function)
amici::Solver::setBandJacFn (C++ function)
amici::Solver::setBandJacFnB (C++ function)
amici::Solver::setDenseJacFn (C++ function)
amici::Solver::setDenseJacFnB (C++ function)
amici::Solver::setErrHandlerFn (C++ function)
amici::Solver::setId (C++ function)
amici::Solver::setInitDone (C++ function)
amici::Solver::setInitDoneB (C++ function)
amici::Solver::setInternalSensitivityMethod (C++ function)
amici::Solver::setInterpolationType (C++ function)
amici::Solver::setJacTimesVecFn (C++ function)
amici::Solver::setJacTimesVecFnB (C++ function)
amici::Solver::setLinearMultistepMethod (C++ function)
amici::Solver::setLinearSolver (C++ function)
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[1]
amici::Solver::setLinearSolverB (C++ function)
amici::Solver::setMaxNumSteps (C++ function)
amici::Solver::setMaxNumStepsB (C++ function)
amici::Solver::setMaxSteps (C++ function)
amici::Solver::setMaxStepsBackwardProblem (C++ function)
amici::Solver::setMaxTime (C++ function)
amici::Solver::setNewtonDampingFactorLowerBound (C++ function)
amici::Solver::setNewtonDampingFactorMode (C++ function)
amici::Solver::setNewtonMaxSteps (C++ function)
amici::Solver::setNewtonStepSteadyStateCheck (C++ function)
amici::Solver::setNonLinearSolver (C++ function)
amici::Solver::setNonLinearSolverB (C++ function)
amici::Solver::setNonlinearSolverIteration (C++ function)
amici::Solver::setNonLinearSolverSens (C++ function)
amici::Solver::setQuadErrCon (C++ function)
amici::Solver::setQuadErrConB (C++ function)
amici::Solver::setQuadInitDone (C++ function)
amici::Solver::setQuadInitDoneB (C++ function)
amici::Solver::setRelativeTolerance (C++ function)
amici::Solver::setRelativeToleranceB (C++ function)
amici::Solver::setRelativeToleranceFSA (C++ function)
amici::Solver::setRelativeToleranceQuadratures (C++ function)
amici::Solver::setRelativeToleranceSteadyState (C++ function)
amici::Solver::setRelativeToleranceSteadyStateSensi (C++ function)
amici::Solver::setReturnDataReportingMode (C++ function)
amici::Solver::setSensErrCon (C++ function)
amici::Solver::setSensInitDone (C++ function)
amici::Solver::setSensInitOff (C++ function)
amici::Solver::setSensiSteadyStateCheck (C++ function)
amici::Solver::setSensitivityMethod (C++ function)
amici::Solver::setSensitivityMethodPreequilibration (C++ function)
amici::Solver::setSensitivityOrder (C++ function)
amici::Solver::setSensParams (C++ function)
amici::Solver::setSensSStolerances (C++ function)
amici::Solver::setSparseJacFn (C++ function)
amici::Solver::setSparseJacFn_ss (C++ function)
amici::Solver::setSparseJacFnB (C++ function)
amici::Solver::setSStolerances (C++ function)
amici::Solver::setSStolerancesB (C++ function)
amici::Solver::setStabilityLimitFlag (C++ function)
amici::Solver::setStabLimDet (C++ function)
amici::Solver::setStabLimDetB (C++ function)
amici::Solver::setStateOrdering (C++ function)
amici::Solver::setSteadyStateSensiToleranceFactor (C++ function)
amici::Solver::setSteadyStateToleranceFactor (C++ function)
amici::Solver::setStopTime (C++ function)
amici::Solver::setSuppressAlg (C++ function)
amici::Solver::setup (C++ function)
amici::Solver::setupB (C++ function)
amici::Solver::setupSteadystate (C++ function)
amici::Solver::setUserData (C++ function)
amici::Solver::setUserDataB (C++ function)
amici::Solver::solve (C++ function)
amici::Solver::solveB (C++ function)
amici::Solver::solveF (C++ function)
amici::Solver::Solver (C++ function)
,
[1]
amici::Solver::solver_memory_ (C++ member)
amici::Solver::solver_memory_B_ (C++ member)
amici::Solver::solver_was_called_B_ (C++ member)
amici::Solver::solver_was_called_F_ (C++ member)
amici::Solver::starttime_ (C++ member)
amici::Solver::startTimer (C++ function)
amici::Solver::step (C++ function)
amici::Solver::storeDiagnosis (C++ function)
amici::Solver::storeDiagnosisB (C++ function)
amici::Solver::switchForwardSensisOff (C++ function)
amici::Solver::sx_ (C++ member)
amici::Solver::t_ (C++ member)
amici::Solver::timeExceeded (C++ function)
amici::Solver::turnOffRootFinding (C++ function)
amici::Solver::updateAndReinitStatesAndSensitivities (C++ function)
amici::Solver::user_data (C++ member)
amici::Solver::user_data_type (C++ type)
amici::Solver::writeSolution (C++ function)
amici::Solver::writeSolutionB (C++ function)
amici::Solver::x_ (C++ member)
amici::Solver::xB_ (C++ member)
amici::Solver::xQ_ (C++ member)
amici::Solver::xQB_ (C++ member)
amici::Solver::~Solver (C++ function)
amici::SteadyStateContext (C++ enum)
amici::SteadyStateContext::newtonSensi (C++ enumerator)
amici::SteadyStateContext::sensiStorage (C++ enumerator)
amici::SteadyStateContext::solverCreation (C++ enumerator)
amici::SteadystateProblem (C++ class)
amici::SteadystateProblem::checkSteadyStateSuccess (C++ function)
amici::SteadystateProblem::getAdjointQuadrature (C++ function)
amici::SteadystateProblem::getAdjointState (C++ function)
amici::SteadystateProblem::getAdjointUpdates (C++ function)
amici::SteadystateProblem::getCPUTime (C++ function)
amici::SteadystateProblem::getCPUTimeB (C++ function)
amici::SteadystateProblem::getDJydx (C++ function)
amici::SteadystateProblem::getEquilibrationQuadratures (C++ function)
amici::SteadystateProblem::getFinalSimulationState (C++ function)
amici::SteadystateProblem::getNumSteps (C++ function)
amici::SteadystateProblem::getNumStepsB (C++ function)
amici::SteadystateProblem::getResidualNorm (C++ function)
amici::SteadystateProblem::getState (C++ function)
amici::SteadystateProblem::getStateSensitivity (C++ function)
amici::SteadystateProblem::getSteadyStateStatus (C++ function)
amici::SteadystateProblem::getSteadyStateTime (C++ function)
amici::SteadystateProblem::hasQuadrature (C++ function)
amici::SteadystateProblem::SteadystateProblem (C++ function)
amici::SteadystateProblem::workSteadyStateBackwardProblem (C++ function)
amici::SteadystateProblem::workSteadyStateProblem (C++ function)
amici::SteadyStateSensitivityMode (C++ enum)
amici::SteadyStateSensitivityMode::integrateIfNewtonFails (C++ enumerator)
amici::SteadyStateSensitivityMode::integrationOnly (C++ enumerator)
amici::SteadyStateSensitivityMode::newtonOnly (C++ enumerator)
amici::SteadyStateStatus (C++ enum)
amici::SteadyStateStatus::failed (C++ enumerator)
amici::SteadyStateStatus::failed_convergence (C++ enumerator)
amici::SteadyStateStatus::failed_damping (C++ enumerator)
amici::SteadyStateStatus::failed_factorization (C++ enumerator)
amici::SteadyStateStatus::failed_too_long_simulation (C++ enumerator)
amici::SteadyStateStatus::not_run (C++ enumerator)
amici::SteadyStateStatus::success (C++ enumerator)
amici::SUNLinSolBand (C++ class)
amici::SUNLinSolBand::getMatrix (C++ function)
amici::SUNLinSolBand::SUNLinSolBand (C++ function)
,
[1]
amici::SUNLinSolDense (C++ class)
amici::SUNLinSolDense::getMatrix (C++ function)
amici::SUNLinSolDense::SUNLinSolDense (C++ function)
amici::SUNLinSolKLU (C++ class)
amici::SUNLinSolKLU::getMatrix (C++ function)
amici::SUNLinSolKLU::reInit (C++ function)
amici::SUNLinSolKLU::setOrdering (C++ function)
amici::SUNLinSolKLU::StateOrdering (C++ enum)
amici::SUNLinSolKLU::StateOrdering::AMD (C++ enumerator)
amici::SUNLinSolKLU::StateOrdering::COLAMD (C++ enumerator)
amici::SUNLinSolKLU::StateOrdering::natural (C++ enumerator)
amici::SUNLinSolKLU::SUNLinSolKLU (C++ function)
,
[1]
amici::SUNLinSolPCG (C++ class)
amici::SUNLinSolPCG::getNumIters (C++ function)
amici::SUNLinSolPCG::getResid (C++ function)
amici::SUNLinSolPCG::getResNorm (C++ function)
amici::SUNLinSolPCG::setATimes (C++ function)
amici::SUNLinSolPCG::setPreconditioner (C++ function)
amici::SUNLinSolPCG::setScalingVectors (C++ function)
amici::SUNLinSolPCG::SUNLinSolPCG (C++ function)
amici::SUNLinSolSPBCGS (C++ class)
amici::SUNLinSolSPBCGS::getNumIters (C++ function)
amici::SUNLinSolSPBCGS::getResid (C++ function)
amici::SUNLinSolSPBCGS::getResNorm (C++ function)
amici::SUNLinSolSPBCGS::setATimes (C++ function)
amici::SUNLinSolSPBCGS::setPreconditioner (C++ function)
amici::SUNLinSolSPBCGS::setScalingVectors (C++ function)
amici::SUNLinSolSPBCGS::SUNLinSolSPBCGS (C++ function)
,
[1]
amici::SUNLinSolSPFGMR (C++ class)
amici::SUNLinSolSPFGMR::getNumIters (C++ function)
amici::SUNLinSolSPFGMR::getResid (C++ function)
amici::SUNLinSolSPFGMR::getResNorm (C++ function)
amici::SUNLinSolSPFGMR::setATimes (C++ function)
amici::SUNLinSolSPFGMR::setPreconditioner (C++ function)
amici::SUNLinSolSPFGMR::setScalingVectors (C++ function)
amici::SUNLinSolSPFGMR::SUNLinSolSPFGMR (C++ function)
amici::SUNLinSolSPGMR (C++ class)
amici::SUNLinSolSPGMR::getNumIters (C++ function)
amici::SUNLinSolSPGMR::getResid (C++ function)
amici::SUNLinSolSPGMR::getResNorm (C++ function)
amici::SUNLinSolSPGMR::setATimes (C++ function)
amici::SUNLinSolSPGMR::setPreconditioner (C++ function)
amici::SUNLinSolSPGMR::setScalingVectors (C++ function)
amici::SUNLinSolSPGMR::SUNLinSolSPGMR (C++ function)
amici::SUNLinSolSPTFQMR (C++ class)
amici::SUNLinSolSPTFQMR::getNumIters (C++ function)
amici::SUNLinSolSPTFQMR::getResid (C++ function)
amici::SUNLinSolSPTFQMR::getResNorm (C++ function)
amici::SUNLinSolSPTFQMR::setATimes (C++ function)
amici::SUNLinSolSPTFQMR::setPreconditioner (C++ function)
amici::SUNLinSolSPTFQMR::setScalingVectors (C++ function)
amici::SUNLinSolSPTFQMR::SUNLinSolSPTFQMR (C++ function)
,
[1]
amici::SUNLinSolWrapper (C++ class)
amici::SUNLinSolWrapper::get (C++ function)
amici::SUNLinSolWrapper::getLastFlag (C++ function)
amici::SUNLinSolWrapper::getMatrix (C++ function)
amici::SUNLinSolWrapper::getType (C++ function)
amici::SUNLinSolWrapper::initialize (C++ function)
amici::SUNLinSolWrapper::operator= (C++ function)
,
[1]
amici::SUNLinSolWrapper::setup (C++ function)
,
[1]
amici::SUNLinSolWrapper::Solve (C++ function)
amici::SUNLinSolWrapper::solver_ (C++ member)
amici::SUNLinSolWrapper::space (C++ function)
amici::SUNLinSolWrapper::SUNLinSolWrapper (C++ function)
,
[1]
,
[2]
,
[3]
amici::SUNLinSolWrapper::~SUNLinSolWrapper (C++ function)
amici::SUNMatrixWrapper (C++ class)
amici::SUNMatrixWrapper::capacity (C++ function)
amici::SUNMatrixWrapper::columns (C++ function)
amici::SUNMatrixWrapper::data (C++ function)
,
[1]
amici::SUNMatrixWrapper::get (C++ function)
amici::SUNMatrixWrapper::get_data (C++ function)
,
[1]
amici::SUNMatrixWrapper::get_indexptr (C++ function)
amici::SUNMatrixWrapper::get_indexval (C++ function)
amici::SUNMatrixWrapper::matrix_id (C++ function)
amici::SUNMatrixWrapper::multiply (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
amici::SUNMatrixWrapper::num_indexptrs (C++ function)
amici::SUNMatrixWrapper::num_nonzeros (C++ function)
amici::SUNMatrixWrapper::operator= (C++ function)
,
[1]
amici::SUNMatrixWrapper::realloc (C++ function)
amici::SUNMatrixWrapper::reallocate (C++ function)
amici::SUNMatrixWrapper::refresh (C++ function)
amici::SUNMatrixWrapper::rows (C++ function)
amici::SUNMatrixWrapper::scale (C++ function)
amici::SUNMatrixWrapper::scatter (C++ function)
amici::SUNMatrixWrapper::set_data (C++ function)
,
[1]
amici::SUNMatrixWrapper::set_indexptr (C++ function)
amici::SUNMatrixWrapper::set_indexptrs (C++ function)
amici::SUNMatrixWrapper::set_indexval (C++ function)
amici::SUNMatrixWrapper::set_indexvals (C++ function)
amici::SUNMatrixWrapper::sparse_add (C++ function)
amici::SUNMatrixWrapper::sparse_multiply (C++ function)
amici::SUNMatrixWrapper::sparse_sum (C++ function)
amici::SUNMatrixWrapper::sparsetype (C++ function)
amici::SUNMatrixWrapper::SUNMatrixWrapper (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
amici::SUNMatrixWrapper::to_dense (C++ function)
amici::SUNMatrixWrapper::to_diag (C++ function)
amici::SUNMatrixWrapper::transpose (C++ function)
amici::SUNMatrixWrapper::zero (C++ function)
amici::SUNMatrixWrapper::~SUNMatrixWrapper (C++ function)
amici::SUNNonLinSolFixedPoint (C++ class)
amici::SUNNonLinSolFixedPoint::getSysFn (C++ function)
amici::SUNNonLinSolFixedPoint::SUNNonLinSolFixedPoint (C++ function)
,
[1]
amici::SUNNonLinSolNewton (C++ class)
amici::SUNNonLinSolNewton::getSysFn (C++ function)
amici::SUNNonLinSolNewton::SUNNonLinSolNewton (C++ function)
,
[1]
amici::SUNNonLinSolWrapper (C++ class)
amici::SUNNonLinSolWrapper::get (C++ function)
amici::SUNNonLinSolWrapper::getCurIter (C++ function)
amici::SUNNonLinSolWrapper::getNumConvFails (C++ function)
amici::SUNNonLinSolWrapper::getNumIters (C++ function)
amici::SUNNonLinSolWrapper::getType (C++ function)
amici::SUNNonLinSolWrapper::initialize (C++ function)
amici::SUNNonLinSolWrapper::operator= (C++ function)
,
[1]
amici::SUNNonLinSolWrapper::setConvTestFn (C++ function)
amici::SUNNonLinSolWrapper::setLSetupFn (C++ function)
amici::SUNNonLinSolWrapper::setLSolveFn (C++ function)
amici::SUNNonLinSolWrapper::setMaxIters (C++ function)
amici::SUNNonLinSolWrapper::setSysFn (C++ function)
amici::SUNNonLinSolWrapper::setup (C++ function)
amici::SUNNonLinSolWrapper::Solve (C++ function)
amici::SUNNonLinSolWrapper::solver (C++ member)
amici::SUNNonLinSolWrapper::SUNNonLinSolWrapper (C++ function)
,
[1]
,
[2]
amici::SUNNonLinSolWrapper::~SUNNonLinSolWrapper (C++ function)
amici::unravel_index (C++ function)
,
[1]
amici::unscaleParameters (C++ function)
amici::wrapErrHandlerFn (C++ function)
amici::writeSlice (C++ function)
,
[1]
,
[2]
,
[3]
AMICI_H5_RESTORE_ERROR_HANDLER (C macro)
AMICI_H5_SAVE_ERROR_HANDLER (C macro)
amici_to_petab_scale() (in module amici.parameter_mapping)
AMICI_VERSION (C macro)
amievent (built-in class)
amifun (built-in class)
append() (amici.parameter_mapping.ParameterMapping method)
apply_template() (in module amici.ode_export)
assignmentRules2observables() (in module amici.sbml_import)
B
backtraceString() (in module amici.amici)
BNGL
bngl2amici() (in module amici.bngl_import)
BoolVector (class in amici.amici)
boost::serialization::archiveVector (C++ function)
boost::serialization::serialize (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
C
cast_to_sym() (in module amici.import_utils)
check_derivatives() (in module amici.gradient_check)
check_event_support() (amici.sbml_import.SbmlImporter method)
check_finite_difference() (in module amici.gradient_check)
check_model() (in module amici.petab_import)
check_support() (amici.sbml_import.SbmlImporter method)
clone() (amici.amici.Model method)
(amici.amici.Solver method)
colptrs() (amici.ode_export.ODEModel method)
compile_model() (amici.ode_export.ODEExporter method)
compiledWithOpenMP() (in module amici.amici)
compute_moiety_conservation_laws() (in module amici.conserved_quantities_demartino)
computingASA() (amici.amici.Solver method)
computingFSA() (amici.amici.Solver method)
conservation_law_has_multispecies() (amici.ode_export.ODEModel method)
ConservationLaw (class in amici.ode_model)
Constant (class in amici.ode_model)
constructEdataFromDataFrame() (in module amici.pandas)
count() (amici.parameter_mapping.ParameterMapping method)
create_dummy_sbml() (in module amici.petab_import_pysb)
create_edata_for_condition() (in module amici.petab_objective)
create_edatas() (in module amici.petab_objective)
create_parameter_df() (amici.petab_import_pysb.PysbPetabProblem method)
create_parameter_mapping() (in module amici.petab_objective)
create_parameter_mapping_for_condition() (in module amici.petab_objective)
create_parameterized_edatas() (in module amici.petab_objective)
CVODES
D
DAE
DoubleVector (class in amici.amici)
E
element_is_state() (in module amici.petab_import)
enum() (in module amici.amici)
eq() (amici.ode_export.ODEModel method)
Event (class in amici.ode_model)
EventObservable (class in amici.ode_model)
ExpData (class in amici.amici)
ExpDataPtr (class in amici.amici)
ExpDataPtrVector (class in amici.amici)
Expression (class in amici.ode_model)
extract_monomers() (in module amici.pysb_import)
F
fdsigmaydy() (amici.amici.Model method)
fdtotal_cldp() (amici.amici.Model method)
fdtotal_cldx_rdata() (amici.amici.Model method)
fdx_rdatadp() (amici.amici.Model method)
fdx_rdatadtcl() (amici.amici.Model method)
fdx_rdatadx_solver() (amici.amici.Model method)
fill_in_parameters() (in module amici.parameter_mapping)
fill_in_parameters_for_condition() (in module amici.parameter_mapping)
fixed parameters
FixedParameterContext (class in amici.amici)
free_symbols() (amici.ode_export.ODEModel method)
from_combine() (amici.petab_import_pysb.PysbPetabProblem static method)
from_files() (amici.petab_import_pysb.PysbPetabProblem static method)
from_yaml() (amici.petab_import_pysb.PysbPetabProblem static method)
G
generate_basic_variables() (amici.ode_export.ODEModel method)
generate_flux_symbol() (in module amici.import_utils)
generate_measurement_symbol() (in module amici.import_utils)
generate_model_code() (amici.ode_export.ODEExporter method)
generate_regularization_symbol() (in module amici.import_utils)
get_appearance_counts() (amici.ode_export.ODEModel method)
get_conservation_laws() (amici.ode_export.ODEModel method)
get_dt() (amici.ode_model.State method)
get_dx_rdata_dx_solver() (amici.ode_model.State method)
get_event() (amici.ode_model.EventObservable method)
get_expressions_as_dataframe() (in module amici.pandas)
get_fixed_parameters() (in module amici.petab_import)
get_free_symbols() (amici.ode_model.State method)
get_function_extern_declaration() (in module amici.ode_export)
get_id() (amici.ode_model.ConservationLaw method)
(amici.ode_model.Constant method)
(amici.ode_model.Event method)
(amici.ode_model.EventObservable method)
(amici.ode_model.Expression method)
(amici.ode_model.LogLikelihood method)
(amici.ode_model.LogLikelihoodRZ method)
(amici.ode_model.LogLikelihoodY method)
(amici.ode_model.LogLikelihoodZ method)
(amici.ode_model.ModelQuantity method)
(amici.ode_model.Observable method)
(amici.ode_model.Parameter method)
(amici.ode_model.Sigma method)
(amici.ode_model.SigmaY method)
(amici.ode_model.SigmaZ method)
(amici.ode_model.State method)
get_initial_value() (amici.ode_model.Event method)
get_lb() (amici.petab_import_pysb.PysbPetabProblem method)
get_logger() (in module amici.logging)
get_measurement_symbol() (amici.ode_model.EventObservable method)
(amici.ode_model.Observable method)
get_model_override_implementation() (in module amici.ode_export)
get_model_parameters() (amici.petab_import_pysb.PysbPetabProblem method)
get_name() (amici.ode_model.ConservationLaw method)
(amici.ode_model.Constant method)
(amici.ode_model.Event method)
(amici.ode_model.EventObservable method)
(amici.ode_model.Expression method)
(amici.ode_model.LogLikelihood method)
(amici.ode_model.LogLikelihoodRZ method)
(amici.ode_model.LogLikelihoodY method)
(amici.ode_model.LogLikelihoodZ method)
(amici.ode_model.ModelQuantity method)
(amici.ode_model.Observable method)
(amici.ode_model.Parameter method)
(amici.ode_model.Sigma method)
(amici.ode_model.SigmaY method)
(amici.ode_model.SigmaZ method)
(amici.ode_model.State method)
get_ncoeff() (amici.ode_model.ConservationLaw method)
get_observable_ids() (amici.petab_import_pysb.PysbPetabProblem method)
get_observable_transformations() (amici.ode_export.ODEModel method)
get_observation_model() (in module amici.petab_import)
get_optimization_parameter_scales() (amici.petab_import_pysb.PysbPetabProblem method)
get_optimization_parameters() (amici.petab_import_pysb.PysbPetabProblem method)
get_optimization_to_simulation_parameter_mapping() (amici.petab_import_pysb.PysbPetabProblem method)
get_regularization_symbol() (amici.ode_model.EventObservable method)
(amici.ode_model.Observable method)
get_simulation_conditions_from_measurement_df() (amici.petab_import_pysb.PysbPetabProblem method)
get_solver_indices() (amici.ode_export.ODEModel method)
get_species_initial() (in module amici.sbml_import)
get_sunindex_extern_declaration() (in module amici.ode_export)
get_sunindex_override_implementation() (in module amici.ode_export)
get_ub() (amici.petab_import_pysb.PysbPetabProblem method)
get_val() (amici.ode_model.ConservationLaw method)
(amici.ode_model.Constant method)
(amici.ode_model.Event method)
(amici.ode_model.EventObservable method)
(amici.ode_model.Expression method)
(amici.ode_model.LogLikelihood method)
(amici.ode_model.LogLikelihoodRZ method)
(amici.ode_model.LogLikelihoodY method)
(amici.ode_model.LogLikelihoodZ method)
(amici.ode_model.ModelQuantity method)
(amici.ode_model.Observable method)
(amici.ode_model.Parameter method)
(amici.ode_model.Sigma method)
(amici.ode_model.SigmaY method)
(amici.ode_model.SigmaZ method)
(amici.ode_model.State method)
get_x_ids() (amici.petab_import_pysb.PysbPetabProblem method)
get_x_nominal() (amici.petab_import_pysb.PysbPetabProblem method)
get_x_rdata() (amici.ode_model.ConservationLaw method)
(amici.ode_model.State method)
getAbsoluteTolerance() (amici.amici.Solver method)
getAbsoluteToleranceB() (amici.amici.Solver method)
getAbsoluteToleranceFSA() (amici.amici.Solver method)
getAbsoluteToleranceQuadratures() (amici.amici.Solver method)
getAbsoluteToleranceSteadyState() (amici.amici.Solver method)
getAbsoluteToleranceSteadyStateSensi() (amici.amici.Solver method)
getAddSigmaResiduals() (amici.amici.Model method)
getAlwaysCheckFinite() (amici.amici.Model method)
getAmiciCommit() (amici.amici.Model method)
getAmiciVersion() (amici.amici.Model method)
getCpuTime() (amici.amici.Solver method)
getCpuTimeB() (amici.amici.Solver method)
getDataObservablesAsDataFrame() (in module amici.pandas)
getEdataFromDataFrame() (in module amici.pandas)
getExpressionIds() (amici.amici.Model method)
getExpressionNames() (amici.amici.Model method)
getFixedParameterById() (amici.amici.Model method)
getFixedParameterByName() (amici.amici.Model method)
getFixedParameterIds() (amici.amici.Model method)
getFixedParameterNames() (amici.amici.Model method)
getFixedParameters() (amici.amici.Model method)
getInitialStates() (amici.amici.Model method)
getInitialStateSensitivities() (amici.amici.Model method)
getInternalSensitivityMethod() (amici.amici.Solver method)
getInterpolationType() (amici.amici.Solver method)
getLastOrder() (amici.amici.Solver method)
getLinearMultistepMethod() (amici.amici.Solver method)
getLinearSolver() (amici.amici.Solver method)
getMaxSteps() (amici.amici.Solver method)
getMaxStepsBackwardProblem() (amici.amici.Solver method)
getMaxTime() (amici.amici.Solver method)
getMinimumSigmaResiduals() (amici.amici.Model method)
getModel() (amici.ModelModule method)
getName() (amici.amici.Model method)
getNewtonDampingFactorLowerBound() (amici.amici.Solver method)
getNewtonDampingFactorMode() (amici.amici.Solver method)
getNewtonMaxSteps() (amici.amici.Solver method)
getNewtonStepSteadyStateCheck() (amici.amici.Solver method)
getNonlinearSolverIteration() (amici.amici.Solver method)
getNumErrTestFails() (amici.amici.Solver method)
getNumErrTestFailsB() (amici.amici.Solver method)
getNumNonlinSolvConvFails() (amici.amici.Solver method)
getNumNonlinSolvConvFailsB() (amici.amici.Solver method)
getNumRhsEvals() (amici.amici.Solver method)
getNumRhsEvalsB() (amici.amici.Solver method)
getNumSteps() (amici.amici.Solver method)
getNumStepsB() (amici.amici.Solver method)
getObservableIds() (amici.amici.Model method)
getObservableNames() (amici.amici.Model method)
getObservableScaling() (amici.amici.Model method)
getObservedData() (amici.amici.ExpData method)
getObservedDataPtr() (amici.amici.ExpData method)
getObservedDataStdDev() (amici.amici.ExpData method)
getObservedDataStdDevPtr() (amici.amici.ExpData method)
getObservedEvents() (amici.amici.ExpData method)
getObservedEventsPtr() (amici.amici.ExpData method)
getObservedEventsStdDev() (amici.amici.ExpData method)
getObservedEventsStdDevPtr() (amici.amici.ExpData method)
getParameterById() (amici.amici.Model method)
getParameterByName() (amici.amici.Model method)
getParameterIds() (amici.amici.Model method)
getParameterList() (amici.amici.Model method)
getParameterNames() (amici.amici.Model method)
getParameters() (amici.amici.Model method)
getParameterScale() (amici.amici.Model method)
getReinitializationStateIdxs() (amici.amici.Model method)
getReinitializeFixedParameterInitialStates() (amici.amici.Model method)
getRelativeTolerance() (amici.amici.Solver method)
getRelativeToleranceB() (amici.amici.Solver method)
getRelativeToleranceFSA() (amici.amici.Solver method)
getRelativeToleranceQuadratures() (amici.amici.Solver method)
getRelativeToleranceSteadyState() (amici.amici.Solver method)
getRelativeToleranceSteadyStateSensi() (amici.amici.Solver method)
getResidualsAsDataFrame() (in module amici.pandas)
getReturnDataReportingMode() (amici.amici.Solver method)
getScaledParameter() (in module amici.amici)
getSensiSteadyStateCheck() (amici.amici.Solver method)
getSensitivityMethod() (amici.amici.Solver method)
getSensitivityMethodPreequilibration() (amici.amici.Solver method)
getSensitivityOrder() (amici.amici.Solver method)
getSimulationObservablesAsDataFrame() (in module amici.pandas)
getSimulationStatesAsDataFrame() (in module amici.pandas)
getSolver() (amici.amici.Model method)
getStabilityLimitFlag() (amici.amici.Solver method)
getStateIds() (amici.amici.Model method)
getStateIdsSolver() (amici.amici.Model method)
getStateIsNonNegative() (amici.amici.Model method)
getStateNames() (amici.amici.Model method)
getStateNamesSolver() (amici.amici.Model method)
getStateOrdering() (amici.amici.Solver method)
getSteadyStateSensitivityMode() (amici.amici.Model method)
getSteadyStateSensiToleranceFactor() (amici.amici.Solver method)
getSteadyStateToleranceFactor() (amici.amici.Solver method)
gett() (amici.amici.Solver method)
getTimepoint() (amici.amici.ExpData method)
(amici.amici.Model method)
getTimepoints() (amici.amici.ExpData method)
(amici.amici.Model method)
getUnscaledParameter() (in module amici.amici)
getUnscaledParameters() (amici.amici.Model method)
grouper() (in module amici.import_utils)
gsl::make_span (C++ function)
,
[1]
H
has_conservation_law() (amici.ode_model.State method)
has_fixed_parameter_ic() (in module amici.pysb_import)
hasCustomInitialStates() (amici.amici.Model method)
hasCustomInitialStateSensitivities() (amici.amici.Model method)
hasExpressionIds() (amici.amici.Model method)
hasExpressionNames() (amici.amici.Model method)
hasFixedParameterIds() (amici.amici.Model method)
hasFixedParameterNames() (amici.amici.Model method)
hasObservableIds() (amici.amici.Model method)
hasObservableNames() (amici.amici.Model method)
hasParameterIds() (amici.amici.Model method)
hasParameterNames() (amici.amici.Model method)
hasQuadraticLLH() (amici.amici.Model method)
hasStateIds() (amici.amici.Model method)
hasStateNames() (amici.amici.Model method)
I
IDAS
import_from_sbml_importer() (amici.ode_export.ODEModel method)
import_model() (in module amici.petab_import)
import_model_module() (in module amici)
import_model_pysb() (in module amici.petab_import_pysb)
import_model_sbml() (in module amici.petab_import)
import_petab_problem() (in module amici.petab_import)
index() (amici.parameter_mapping.ParameterMapping method)
InternalSensitivityMethod (class in amici.amici)
InterpolationType (class in amici.amici)
IntVector (class in amici.amici)
is_assignment_rule_target() (amici.sbml_import.SbmlImporter method)
is_rate_rule_target() (amici.sbml_import.SbmlImporter method)
is_valid_identifier() (in module amici.ode_export)
isFixedParameterStateReinitializationAllowed() (amici.amici.Model method)
isSetObservedData() (amici.amici.ExpData method)
isSetObservedDataStdDev() (amici.amici.ExpData method)
isSetObservedEvents() (amici.amici.ExpData method)
isSetObservedEventsStdDev() (amici.amici.ExpData method)
K
k() (amici.amici.Model method)
L
LinearMultistepMethod (class in amici.amici)
LinearSolver (class in amici.amici)
log() (amici.amici.Logger method)
log_execution_time() (in module amici.logging)
Logger (class in amici.amici)
LogItem (class in amici.amici)
LogItemVector (class in amici.amici)
LogLikelihood (class in amici.ode_model)
LogLikelihoodRZ (class in amici.ode_model)
LogLikelihoodY (class in amici.ode_model)
LogLikelihoodZ (class in amici.ode_model)
M
M_1_PI (C macro)
M_2_PI (C macro)
M_2_SQRTPI (C macro)
M_E (C macro)
M_LN10 (C macro)
M_LN2 (C macro)
M_LOG10E (C macro)
M_LOG2E (C macro)
M_PI (C macro)
M_PI_2 (C macro)
M_PI_4 (C macro)
M_SQRT1_2 (C macro)
M_SQRT2 (C macro)
main() (in module amici.petab_import)
Model (class in amici.amici)
ModelDimensions (class in amici.amici)
ModelModule (class in amici)
ModelPtr (class in amici.amici)
ModelQuantity (class in amici.ode_model)
module
amici
amici.amici
amici.bngl_import
amici.conserved_quantities_demartino
amici.conserved_quantities_rref
amici.gradient_check
amici.import_utils
amici.logging
amici.ode_export
amici.ode_model
amici.pandas
amici.parameter_mapping
amici.petab_import
amici.petab_import_pysb
amici.petab_objective
amici.petab_simulate
amici.plotting
amici.pysb_import
amici.sbml_import
N
name() (amici.ode_export.ODEModel method)
ncl() (amici.amici.Model method)
NewtonDampingFactorMode (class in amici.amici)
nk() (amici.amici.Model method)
nmaxevent() (amici.amici.ExpData method)
nMaxEvent() (amici.amici.Model method)
noise_distribution_to_cost_function() (in module amici.import_utils)
noise_distribution_to_observable_transformation() (in module amici.import_utils)
NonlinearSolverIteration (class in amici.amici)
np() (amici.amici.Model method)
nplist() (amici.amici.Model method)
(amici.amici.Solver method)
nquad() (amici.amici.Solver method)
nt() (amici.amici.ExpData method)
(amici.amici.Model method)
nullspace_by_rref() (in module amici.conserved_quantities_rref)
num_cons_law() (amici.ode_export.ODEModel method)
num_const() (amici.ode_export.ODEModel method)
num_eventobs() (amici.ode_export.ODEModel method)
num_events() (amici.ode_export.ODEModel method)
num_expr() (amici.ode_export.ODEModel method)
num_obs() (amici.ode_export.ODEModel method)
num_par() (amici.ode_export.ODEModel method)
num_state_reinits() (amici.ode_export.ODEModel method)
num_states_rdata() (amici.ode_export.ODEModel method)
num_states_solver() (amici.ode_export.ODEModel method)
nx() (amici.amici.Solver method)
nx_reinit() (amici.amici.Model method)
nytrue() (amici.amici.ExpData method)
nztrue() (amici.amici.ExpData method)
O
Observable (class in amici.ode_model)
ObservableScaling (class in amici.amici)
ObservableTransformation (class in amici.import_utils)
ODE
ode_model_from_pysb_importer() (in module amici.pysb_import)
ODEExporter (class in amici.ode_export)
ODEModel (class in amici.ode_export)
P
Parameter (class in amici.ode_model)
ParameterMapping (class in amici.parameter_mapping)
ParameterMappingForCondition (class in amici.parameter_mapping)
ParameterScaling (class in amici.amici)
parameterScalingFromIntVector() (in module amici.amici)
ParameterScalingVector (class in amici.amici)
parse_events() (amici.ode_export.ODEModel method)
PEtab
petab_noise_distributions_to_amici() (in module amici.petab_import)
petab_scale_to_amici_scale() (in module amici.petab_import)
petab_to_amici_scale() (in module amici.parameter_mapping)
PetabSimulator (class in amici.petab_simulate)
pivots() (in module amici.conserved_quantities_rref)
plist() (amici.amici.Model method)
plotObservableTrajectories() (in module amici.plotting)
plotStateTrajectories() (in module amici.plotting)
preequilibration
presimulation
process_conservation_laws() (amici.sbml_import.SbmlImporter method)
PySB
pysb2amici() (in module amici.pysb_import)
pysb_model_from_path() (in module amici.pysb_import)
PysbPetabProblem (class in amici.petab_import_pysb)
R
RDataReporting (class in amici.amici)
rdatas_to_measurement_df() (in module amici.petab_objective)
rdatas_to_simulation_df() (in module amici.petab_objective)
reinitializeAllFixedParameterDependentInitialStates() (amici.amici.ExpData method)
(amici.amici.SimulationParameters method)
reinitializeAllFixedParameterDependentInitialStatesForPresimulation() (amici.amici.ExpData method)
(amici.amici.SimulationParameters method)
reinitializeAllFixedParameterDependentInitialStatesForSimulation() (amici.amici.ExpData method)
(amici.amici.SimulationParameters method)
remove_argument_types() (in module amici.ode_export)
remove_working_dir() (amici.petab_simulate.PetabSimulator method)
replace_logx() (in module amici.sbml_import)
requireSensitivitiesForAllParameters() (amici.amici.Model method)
ReturnData (class in amici.amici)
ReturnDataPtr (class in amici.amici)
rowvals() (amici.ode_export.ODEModel method)
rref() (in module amici.conserved_quantities_rref)
runAmiciSimulation() (in module amici.amici)
runAmiciSimulations() (in module amici.amici)
S
safe_substitute() (amici.ode_export.TemplateAmici method)
sample_parameter_startpoints() (amici.petab_import_pysb.PysbPetabProblem method)
SBML
sbml2amici() (amici.sbml_import.SbmlImporter method)
SbmlImporter (class in amici.sbml_import)
scale_parameter() (in module amici.parameter_mapping)
scale_parameters() (amici.petab_import_pysb.PysbPetabProblem method)
scale_parameters_dict() (in module amici.parameter_mapping)
scaleParameters() (in module amici.amici)
SecondOrderMode (class in amici.amici)
SensitivityMethod (class in amici.amici)
SensitivityOrder (class in amici.amici)
set_conservation_law() (amici.ode_model.State method)
set_dt() (amici.ode_model.State method)
set_log_level() (in module amici.logging)
set_name() (amici.ode_export.ODEExporter method)
set_paths() (amici.ode_export.ODEExporter method)
set_val() (amici.ode_model.ConservationLaw method)
(amici.ode_model.Constant method)
(amici.ode_model.Event method)
(amici.ode_model.EventObservable method)
(amici.ode_model.Expression method)
(amici.ode_model.LogLikelihood method)
(amici.ode_model.LogLikelihoodRZ method)
(amici.ode_model.LogLikelihoodY method)
(amici.ode_model.LogLikelihoodZ method)
(amici.ode_model.ModelQuantity method)
(amici.ode_model.Observable method)
(amici.ode_model.Parameter method)
(amici.ode_model.Sigma method)
(amici.ode_model.SigmaY method)
(amici.ode_model.SigmaZ method)
(amici.ode_model.State method)
setAbsoluteTolerance() (amici.amici.Solver method)
setAbsoluteToleranceB() (amici.amici.Solver method)
setAbsoluteToleranceFSA() (amici.amici.Solver method)
setAbsoluteToleranceQuadratures() (amici.amici.Solver method)
setAbsoluteToleranceSteadyState() (amici.amici.Solver method)
setAbsoluteToleranceSteadyStateSensi() (amici.amici.Solver method)
setAddSigmaResiduals() (amici.amici.Model method)
setAllStatesNonNegative() (amici.amici.Model method)
setAlwaysCheckFinite() (amici.amici.Model method)
setFixedParameterById() (amici.amici.Model method)
setFixedParameterByName() (amici.amici.Model method)
setFixedParameters() (amici.amici.Model method)
setFixedParametersByIdRegex() (amici.amici.Model method)
setFixedParametersByNameRegex() (amici.amici.Model method)
setInitialStates() (amici.amici.Model method)
setInitialStateSensitivities() (amici.amici.Model method)
setInternalSensitivityMethod() (amici.amici.Solver method)
setInterpolationType() (amici.amici.Solver method)
setLinearMultistepMethod() (amici.amici.Solver method)
setLinearSolver() (amici.amici.Solver method)
setMaxSteps() (amici.amici.Solver method)
setMaxStepsBackwardProblem() (amici.amici.Solver method)
setMaxTime() (amici.amici.Solver method)
setMinimumSigmaResiduals() (amici.amici.Model method)
setNewtonDampingFactorLowerBound() (amici.amici.Solver method)
setNewtonDampingFactorMode() (amici.amici.Solver method)
setNewtonMaxSteps() (amici.amici.Solver method)
setNewtonStepSteadyStateCheck() (amici.amici.Solver method)
setNMaxEvent() (amici.amici.Model method)
setNonlinearSolverIteration() (amici.amici.Solver method)
setObservedData() (amici.amici.ExpData method)
setObservedDataStdDev() (amici.amici.ExpData method)
setObservedEvents() (amici.amici.ExpData method)
setObservedEventsStdDev() (amici.amici.ExpData method)
setParameterById() (amici.amici.Model method)
setParameterByName() (amici.amici.Model method)
setParameterList() (amici.amici.Model method)
setParameters() (amici.amici.Model method)
setParametersByIdRegex() (amici.amici.Model method)
setParametersByNameRegex() (amici.amici.Model method)
setParameterScale() (amici.amici.Model method)
setReinitializationStateIdxs() (amici.amici.Model method)
setReinitializeFixedParameterInitialStates() (amici.amici.Model method)
setRelativeTolerance() (amici.amici.Solver method)
setRelativeToleranceB() (amici.amici.Solver method)
setRelativeToleranceFSA() (amici.amici.Solver method)
setRelativeToleranceQuadratures() (amici.amici.Solver method)
setRelativeToleranceSteadyState() (amici.amici.Solver method)
setRelativeToleranceSteadyStateSensi() (amici.amici.Solver method)
setReturnDataReportingMode() (amici.amici.Solver method)
setSensiSteadyStateCheck() (amici.amici.Solver method)
setSensitivityMethod() (amici.amici.Solver method)
setSensitivityMethodPreequilibration() (amici.amici.Solver method)
setSensitivityOrder() (amici.amici.Solver method)
setStabilityLimitFlag() (amici.amici.Solver method)
setStateIsNonNegative() (amici.amici.Model method)
setStateOrdering() (amici.amici.Solver method)
setSteadyStateSensitivityMode() (amici.amici.Model method)
setSteadyStateSensiToleranceFactor() (amici.amici.Solver method)
setSteadyStateToleranceFactor() (amici.amici.Solver method)
setT0() (amici.amici.Model method)
setTimepoints() (amici.amici.ExpData method)
(amici.amici.Model method)
setUnscaledInitialStateSensitivities() (amici.amici.Model method)
show_model_info() (in module amici.petab_import)
Sigma (class in amici.ode_model)
SigmaY (class in amici.ode_model)
SigmaZ (class in amici.ode_model)
simulate() (amici.petab_simulate.PetabSimulator method)
simulate_petab() (in module amici.petab_objective)
simulate_without_noise() (amici.petab_simulate.PetabSimulator method)
simulation_status_to_str() (in module amici.amici)
SimulationParameters (class in amici.amici)
SimulationState (class in amici.amici)
smart_is_zero_matrix() (in module amici.ode_export)
smart_jacobian() (in module amici.ode_export)
smart_multiply() (in module amici.ode_export)
smart_subs() (in module amici.import_utils)
smart_subs_dict() (in module amici.import_utils)
Solver (class in amici.amici)
SolverPtr (class in amici.amici)
sparseeq() (amici.ode_export.ODEModel method)
sparsesym() (amici.ode_export.ODEModel method)
species_to_parameters() (in module amici.petab_import)
startTimer() (amici.amici.Solver method)
State (class in amici.ode_model)
state_has_conservation_law() (amici.ode_export.ODEModel method)
state_has_fixed_parameter_initial_condition() (amici.ode_export.ODEModel method)
state_is_constant() (amici.ode_export.ODEModel method)
SteadyStateSensitivityMode (class in amici.amici)
SteadyStateStatus (class in amici.amici)
SteadyStateStatusVector (class in amici.amici)
StringDoubleMap (class in amici.amici)
StringVector (class in amici.amici)
strip_pysb() (in module amici.import_utils)
subset_call() (in module amici.petab_simulate)
subset_dict() (in module amici.petab_objective)
substitute() (amici.ode_export.TemplateAmici method)
SUNDIALS
SWIG
switchForwardSensisOff() (amici.amici.Solver method)
sym() (amici.ode_export.ODEModel method)
sym_names() (amici.ode_export.ODEModel method)
sym_or_eq() (amici.ode_export.ODEModel method)
symbol_with_assumptions() (in module amici.import_utils)
T
t0() (amici.amici.Model method)
TemplateAmici (class in amici.ode_export)
timeExceeded() (amici.amici.Solver method)
to_files() (amici.petab_import_pysb.PysbPetabProblem method)
to_files_generic() (amici.petab_import_pysb.PysbPetabProblem method)
toposort_symbols() (in module amici.import_utils)
U
unscale_parameter() (in module amici.parameter_mapping)
unscale_parameters() (amici.petab_import_pysb.PysbPetabProblem method)
unscale_parameters_dict() (in module amici.parameter_mapping)
unscaleParameters() (in module amici.amici)
V
val() (amici.ode_export.ODEModel method)
var_in_function_signature() (in module amici.ode_export)
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