AMICI
v0.17.0
About
About AMICI
Availability
License conditions
How to cite AMICI
References
Background
Changelog
Glossary
Contributing
Python
Installation
Examples
Usage
FAQ
API reference
C++
Installation
Usage
API reference
MATLAB
Installation
Usage
FAQ
API reference
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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J
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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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W
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X
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Y
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Z
_
__init__() (amici.add_path method)
(amici.amici.CpuTimer 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.AmiciVersionError method)
(amici.de_export.DEExporter method)
(amici.de_export.DEModel method)
(amici.de_export.TemplateAmici method)
(amici.de_model.AlgebraicEquation method)
(amici.de_model.AlgebraicState method)
(amici.de_model.ConservationLaw method)
(amici.de_model.Constant method)
(amici.de_model.DifferentialState method)
(amici.de_model.Event method)
(amici.de_model.EventObservable method)
(amici.de_model.Expression method)
(amici.de_model.LogLikelihoodRZ method)
(amici.de_model.LogLikelihoodY method)
(amici.de_model.LogLikelihoodZ method)
(amici.de_model.ModelQuantity method)
(amici.de_model.Observable method)
(amici.de_model.Parameter method)
(amici.de_model.SigmaY method)
(amici.de_model.SigmaZ method)
(amici.de_model.State method)
(amici.import_utils.CircularDependencyError method)
(amici.import_utils.SBMLException method)
(amici.ModelModule method)
(amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView 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
adams (amici.amici.LinearMultistepMethod attribute)
add_component() (amici.de_export.DEModel method)
add_conservation_law() (amici.de_export.DEModel 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)
adjoint (amici.amici.SensitivityMethod attribute)
aggregate_sllh() (in module amici.petab_objective)
algebraic_states() (amici.de_export.DEModel method)
AlgebraicEquation (class in amici.de_model)
AlgebraicState (class in amici.de_model)
amici
module
amici.amici
module
amici.bngl_import
module
amici.conserved_quantities_demartino
module
amici.conserved_quantities_rref
module
amici.de_export
module
amici.de_model
module
amici.gradient_check
module
amici.import_utils
module
amici.logging
module
amici.numpy
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_FIRST_RHSFUNC_ERR (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_NOT_RUN (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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[2]
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[3]
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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)
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[1]
amici::AmiVector::end (C++ function)
amici::AmiVector::getLength (C++ function)
amici::AmiVector::getNVector (C++ function)
,
[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)
,
[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::CpuTimer (C++ class)
amici::CpuTimer::CpuTimer (C++ function)
amici::CpuTimer::elapsed_milliseconds (C++ function)
amici::CpuTimer::elapsed_seconds (C++ function)
amici::CpuTimer::reset (C++ function)
amici::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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[2]
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[3]
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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)
,
[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)
,
[1]
amici::hdf5::writeReturnDataDiagnosis (C++ function)
amici::hdf5::writeSimulationExpData (C++ function)
amici::hdf5::writeSolverSettingsToHDF5 (C++ function)
,
[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::fdxdotdp_explicit (C++ function)
amici::Model_DAE::fdxdotdp_explicit_colptrs (C++ function)
amici::Model_DAE::fdxdotdp_explicit_rowvals (C++ function)
amici::Model_DAE::fdxdotdw (C++ function)
,
[1]
amici::Model_DAE::fdxdotdw_colptrs (C++ function)
amici::Model_DAE::fdxdotdw_rowvals (C++ function)
amici::Model_DAE::fdxdotdx_explicit (C++ function)
amici::Model_DAE::fdxdotdx_explicit_colptrs (C++ function)
amici::Model_DAE::fdxdotdx_explicit_rowvals (C++ function)
amici::Model_DAE::fJ (C++ function)
,
[1]
amici::Model_DAE::fJB (C++ function)
,
[1]
amici::Model_DAE::fJDiag (C++ function)
amici::Model_DAE::fJSparse (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fJSparseB (C++ function)
,
[1]
amici::Model_DAE::fJSparseB_ss (C++ function)
amici::Model_DAE::fJv (C++ function)
,
[1]
amici::Model_DAE::fJvB (C++ function)
amici::Model_DAE::fM (C++ function)
,
[1]
amici::Model_DAE::fqBdot (C++ function)
amici::Model_DAE::fqBdot_ss (C++ function)
amici::Model_DAE::froot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fsxdot (C++ function)
,
[1]
amici::Model_DAE::fxBdot (C++ function)
amici::Model_DAE::fxBdot_ss (C++ function)
,
[1]
amici::Model_DAE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::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::dfdx_ (C++ member)
amici::ModelStateDerived::dJrzdsigma_ (C++ member)
amici::ModelStateDerived::dJrzdz_ (C++ member)
amici::ModelStateDerived::dJydp_ (C++ member)
amici::ModelStateDerived::dJydsigma_ (C++ member)
amici::ModelStateDerived::dJydx_ (C++ member)
amici::ModelStateDerived::dJydy_ (C++ member)
amici::ModelStateDerived::dJydy_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::MSparse_ (C++ member)
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::sy_ (C++ member)
amici::ModelStateDerived::w_ (C++ member)
amici::ModelStateDerived::x_pos_tmp_ (C++ member)
amici::ModelStateDerived::x_rdata_ (C++ member)
amici::ModelStateDerived::y_ (C++ member)
amici::ModelStateDerived::z_ (C++ member)
amici::N_VGetArrayPointerConst (C++ function)
amici::NewtonDampingFactorMode (C++ enum)
amici::NewtonDampingFactorMode::off (C++ enumerator)
amici::NewtonDampingFactorMode::on (C++ enumerator)
amici::NewtonFailure (C++ class)
amici::NewtonFailure::error_code (C++ member)
amici::NewtonFailure::NewtonFailure (C++ function)
amici::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)
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[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)
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[1]
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[2]
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[3]
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[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)
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[1]
amici::Solver::getNumNonlinSolvConvFailsB (C++ function)
amici::Solver::getNumRhsEvals (C++ function)
,
[1]
amici::Solver::getNumRhsEvalsB (C++ function)
amici::Solver::getNumSteps (C++ function)
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[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)
,
[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::simulation_timer_ (C++ member)
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::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_path (in module amici)
amici_to_petab_scale() (in module amici.parameter_mapping)
AMICI_VERSION (C macro)
amiciModulePath (in module amici)
amiciSrcPath (in module amici)
amiciSwigPath (in module amici)
AmiciVersionError
amievent (built-in class)
amifun (built-in class)
append() (amici.parameter_mapping.ParameterMapping method)
apply_template() (in module amici.de_export)
args (amici.AmiciVersionError attribute)
(amici.import_utils.CircularDependencyError attribute)
(amici.import_utils.SBMLException attribute)
assignmentRules2observables() (in module amici.sbml_import)
B
band (amici.amici.LinearSolver attribute)
BDF (amici.amici.LinearMultistepMethod attribute)
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]
braceidpattern (amici.de_export.TemplateAmici attribute)
by_id() (amici.numpy.ReturnDataView method)
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)
chi2 (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
CircularDependencyError
clone() (amici.amici.Model method)
(amici.amici.Solver method)
colptrs() (amici.de_export.DEModel method)
compile_model() (amici.de_export.DEExporter 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.de_export.DEModel method)
conservation_laws() (amici.de_export.DEModel method)
ConservationLaw (class in amici.de_model)
Constant (class in amici.de_model)
constants() (amici.de_export.DEModel method)
count() (amici.parameter_mapping.ParameterMapping method)
cpu_time (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
cpu_time_total (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
cpu_timeB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
CpuTimer (class in amici.amici)
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
DEExporter (class in amici.de_export)
delimiter (amici.de_export.TemplateAmici attribute)
DEModel (class in amici.de_export)
dense (amici.amici.LinearSolver attribute)
diag (amici.amici.LinearSolver attribute)
differential_states() (amici.de_export.DEModel method)
DifferentialState (class in amici.de_model)
directional (amici.amici.SecondOrderMode attribute)
DoubleVector (class in amici.amici)
dx (amici.amici.SimulationState property)
E
elapsed_milliseconds() (amici.amici.CpuTimer method)
elapsed_seconds() (amici.amici.CpuTimer method)
element_is_state() (in module amici.petab_import)
enum() (in module amici.amici)
eq() (amici.de_export.DEModel method)
Event (class in amici.de_model)
event_observables() (amici.de_export.DEModel method)
EventObservable (class in amici.de_model)
events() (amici.de_export.DEModel method)
ExpData (class in amici.amici)
ExpDataPtr (class in amici.amici)
ExpDataPtrVector (class in amici.amici)
ExpDataView (class in amici.numpy)
Expression (class in amici.de_model)
expressions() (amici.de_export.DEModel method)
extract_monomers() (in module amici.pysb_import)
F
failed (amici.amici.SteadyStateStatus attribute)
failed_convergence (amici.amici.SteadyStateStatus attribute)
failed_damping (amici.amici.SteadyStateStatus attribute)
failed_factorization (amici.amici.SteadyStateStatus attribute)
failed_too_long_simulation (amici.amici.SteadyStateStatus attribute)
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)
FIM (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
first (amici.amici.SensitivityOrder attribute)
fixed parameters
FixedParameterContext (class in amici.amici)
fixedParameters (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedParametersPreequilibration (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedParametersPresimulation (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedpoint (amici.amici.NonlinearSolverIteration attribute)
flags (amici.de_export.TemplateAmici attribute)
forward (amici.amici.SensitivityMethod attribute)
free_symbols (amici.parameter_mapping.ParameterMapping property)
(amici.parameter_mapping.ParameterMappingForCondition property)
free_symbols() (amici.de_export.DEModel 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)
full (amici.amici.RDataReporting attribute)
(amici.amici.SecondOrderMode attribute)
functional (amici.amici.NonlinearSolverIteration attribute)
G
generate_basic_variables() (amici.de_export.DEModel method)
generate_flux_symbol() (in module amici.import_utils)
generate_measurement_symbol() (in module amici.import_utils)
generate_model_code() (amici.de_export.DEExporter method)
generate_regularization_symbol() (in module amici.import_utils)
get() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
get_appearance_counts() (amici.de_export.DEModel method)
get_conservation_laws() (amici.de_export.DEModel method)
get_dt() (amici.de_model.DifferentialState method)
get_dx_rdata_dx_solver() (amici.de_model.AlgebraicState method)
(amici.de_model.DifferentialState method)
(amici.de_model.State method)
get_event() (amici.de_model.EventObservable method)
get_expressions_as_dataframe() (in module amici.pandas)
get_fixed_parameters() (in module amici.petab_import)
get_free_symbols() (amici.de_model.AlgebraicEquation method)
(amici.de_model.AlgebraicState method)
(amici.de_model.DifferentialState method)
get_function_extern_declaration() (in module amici.de_export)
get_id() (amici.de_model.AlgebraicEquation method)
(amici.de_model.AlgebraicState method)
(amici.de_model.ConservationLaw method)
(amici.de_model.Constant method)
(amici.de_model.DifferentialState method)
(amici.de_model.Event method)
(amici.de_model.EventObservable method)
(amici.de_model.Expression method)
(amici.de_model.LogLikelihoodRZ method)
(amici.de_model.LogLikelihoodY method)
(amici.de_model.LogLikelihoodZ method)
(amici.de_model.ModelQuantity method)
(amici.de_model.Observable method)
(amici.de_model.Parameter method)
(amici.de_model.SigmaY method)
(amici.de_model.SigmaZ method)
(amici.de_model.State method)
get_initial_value() (amici.de_model.Event method)
get_lb() (amici.petab_import_pysb.PysbPetabProblem method)
get_logger() (in module amici.logging)
get_measurement_symbol() (amici.de_model.EventObservable method)
(amici.de_model.Observable method)
get_model() (amici.ModelModule method)
get_model_override_implementation() (in module amici.de_export)
get_model_parameters() (amici.petab_import_pysb.PysbPetabProblem method)
get_name() (amici.de_model.AlgebraicEquation method)
(amici.de_model.AlgebraicState method)
(amici.de_model.ConservationLaw method)
(amici.de_model.Constant method)
(amici.de_model.DifferentialState method)
(amici.de_model.Event method)
(amici.de_model.EventObservable method)
(amici.de_model.Expression method)
(amici.de_model.LogLikelihoodRZ method)
(amici.de_model.LogLikelihoodY method)
(amici.de_model.LogLikelihoodZ method)
(amici.de_model.ModelQuantity method)
(amici.de_model.Observable method)
(amici.de_model.Parameter method)
(amici.de_model.SigmaY method)
(amici.de_model.SigmaZ method)
(amici.de_model.State method)
get_ncoeff() (amici.de_model.ConservationLaw method)
get_observable_ids() (amici.petab_import_pysb.PysbPetabProblem method)
get_observable_transformations() (amici.de_export.DEModel 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.de_model.EventObservable method)
(amici.de_model.Observable method)
get_simulation_conditions_from_measurement_df() (amici.petab_import_pysb.PysbPetabProblem method)
get_solver_indices() (amici.de_export.DEModel method)
get_species_initial() (in module amici.sbml_import)
get_sunindex_extern_declaration() (in module amici.de_export)
get_sunindex_override_implementation() (in module amici.de_export)
get_ub() (amici.petab_import_pysb.PysbPetabProblem method)
get_val() (amici.de_model.AlgebraicEquation method)
(amici.de_model.AlgebraicState method)
(amici.de_model.ConservationLaw method)
(amici.de_model.Constant method)
(amici.de_model.DifferentialState method)
(amici.de_model.Event method)
(amici.de_model.EventObservable method)
(amici.de_model.Expression method)
(amici.de_model.LogLikelihoodRZ method)
(amici.de_model.LogLikelihoodY method)
(amici.de_model.LogLikelihoodZ method)
(amici.de_model.ModelQuantity method)
(amici.de_model.Observable method)
(amici.de_model.Parameter method)
(amici.de_model.SigmaY method)
(amici.de_model.SigmaZ method)
(amici.de_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.de_model.AlgebraicState method)
(amici.de_model.ConservationLaw method)
(amici.de_model.DifferentialState method)
(amici.de_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.de_model.AlgebraicState method)
(amici.de_model.DifferentialState method)
(amici.de_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)
hdf5_enabled (in module amici)
hermite (amici.amici.InterpolationType attribute)
I
id (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
IDAS
identifier (amici.amici.LogItem property)
idlist (amici.amici.Model property)
(amici.amici.ModelPtr property)
idpattern (amici.de_export.TemplateAmici attribute)
import_from_sbml_importer() (amici.de_export.DEModel 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)
integrateIfNewtonFails (amici.amici.SteadyStateSensitivityMode attribute)
integrationOnly (amici.amici.SteadyStateSensitivityMode attribute)
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_ode() (amici.de_export.DEModel method)
is_rate_rule_target() (amici.sbml_import.SbmlImporter method)
is_valid_identifier() (in module amici.de_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)
items (amici.amici.Logger property)
items() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
J
J (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
K
k() (amici.amici.Model method)
keys() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
KLU (amici.amici.LinearSolver attribute)
L
LAPACKBand (amici.amici.LinearSolver attribute)
LAPACKDense (amici.amici.LinearSolver attribute)
lb (amici.petab_import_pysb.PysbPetabProblem property)
lb_scaled (amici.petab_import_pysb.PysbPetabProblem property)
lbw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
likelihood (amici.amici.RDataReporting attribute)
lin (amici.amici.ObservableScaling attribute)
LIN (amici.import_utils.ObservableTransformation attribute)
LinearMultistepMethod (class in amici.amici)
LinearSolver (class in amici.amici)
llh (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ln (amici.amici.ParameterScaling attribute)
log (amici.amici.ObservableScaling attribute)
LOG (amici.import_utils.ObservableTransformation attribute)
log() (amici.amici.Logger method)
log10 (amici.amici.ObservableScaling attribute)
(amici.amici.ParameterScaling attribute)
LOG10 (amici.import_utils.ObservableTransformation attribute)
log_execution_time() (in module amici.logging)
log_likelihood_rzs() (amici.de_export.DEModel method)
log_likelihood_ys() (amici.de_export.DEModel method)
log_likelihood_zs() (amici.de_export.DEModel method)
logger (amici.amici.Model property)
(amici.amici.ModelPtr property)
(amici.amici.Solver property)
(amici.amici.SolverPtr property)
Logger (class in amici.amici)
LogItem (class in amici.amici)
LogItemVector (class in amici.amici)
LogLikelihoodRZ (class in amici.de_model)
LogLikelihoodY (class in amici.de_model)
LogLikelihoodZ (class in amici.de_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)
message (amici.amici.LogItem property)
messages (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
Model (class in amici.amici)
ModelDimensions (class in amici.amici)
ModelModule (class in amici)
ModelPtr (class in amici.amici)
ModelQuantity (class in amici.de_model)
module
amici
amici.amici
amici.bngl_import
amici.conserved_quantities_demartino
amici.conserved_quantities_rref
amici.de_export
amici.de_model
amici.gradient_check
amici.import_utils
amici.logging
amici.numpy
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.de_export.DEModel method)
ncl() (amici.amici.Model method)
ndJydy (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndtotal_cldx_rdata (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndwdp (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndwdw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndwdx (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxdotdw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxrdatadtcl (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxrdatadxsolver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ne (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
newton (amici.amici.NonlinearSolverIteration attribute)
newton_maxsteps (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
NewtonDampingFactorMode (class in amici.amici)
newtonOnly (amici.amici.SteadyStateSensitivityMode attribute)
nJ (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nk (amici.amici.ModelDimensions property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nk() (amici.amici.Model method)
nmaxevent (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nmaxevent() (amici.amici.ExpData method)
nMaxEvent() (amici.amici.Model method)
nnz (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
noise_distribution_to_cost_function() (in module amici.import_utils)
noise_distribution_to_observable_transformation() (in module amici.import_utils)
none (amici.amici.ParameterScaling attribute)
(amici.amici.SecondOrderMode attribute)
(amici.amici.SensitivityMethod attribute)
(amici.amici.SensitivityOrder attribute)
NonlinearSolverIteration (class in amici.amici)
NonlinearSolverIteration_fixedpoint (in module amici.amici)
not_run (amici.amici.SteadyStateStatus attribute)
np (amici.amici.ModelDimensions property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
np() (amici.amici.Model method)
nplist (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nplist() (amici.amici.Model method)
(amici.amici.Solver method)
nquad() (amici.amici.Solver method)
nt (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nt() (amici.amici.ExpData method)
(amici.amici.Model method)
nullspace_by_rref() (in module amici.conserved_quantities_rref)
num_cons_law() (amici.de_export.DEModel method)
num_const() (amici.de_export.DEModel method)
num_eventobs() (amici.de_export.DEModel method)
num_events() (amici.de_export.DEModel method)
num_expr() (amici.de_export.DEModel method)
num_obs() (amici.de_export.DEModel method)
num_par() (amici.de_export.DEModel method)
num_state_reinits() (amici.de_export.DEModel method)
num_states_rdata() (amici.de_export.DEModel method)
num_states_solver() (amici.de_export.DEModel method)
numerrtestfails (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numerrtestfailsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numnonlinsolvconvfails (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numnonlinsolvconvfailsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numrhsevals (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numrhsevalsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numsteps (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numstepsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx() (amici.amici.Solver method)
nx_rdata (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx_reinit() (amici.amici.Model method)
nx_solver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx_solver_reinit (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue_rdata (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue_solver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ny (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nytrue (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nytrue() (amici.amici.ExpData method)
nz (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nztrue (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nztrue() (amici.amici.ExpData method)
O
o2mode (amici.amici.Model property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
Observable (class in amici.de_model)
observables() (amici.de_export.DEModel method)
ObservableScaling (class in amici.amici)
ObservableTransformation (class in amici.import_utils)
ODE
ode_model_from_pysb_importer() (in module amici.pysb_import)
off (amici.amici.NewtonDampingFactorMode attribute)
on (amici.amici.NewtonDampingFactorMode attribute)
order (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
P
Parameter (class in amici.de_model)
ParameterMapping (class in amici.parameter_mapping)
ParameterMappingForCondition (class in amici.parameter_mapping)
parameters (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
parameters() (amici.de_export.DEModel method)
ParameterScaling (class in amici.amici)
parameterScalingFromIntVector() (in module amici.amici)
ParameterScalingVector (class in amici.amici)
parse_events() (amici.de_export.DEModel method)
pattern (amici.de_export.TemplateAmici attribute)
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.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
plist() (amici.amici.Model method)
plot_jacobian() (in module amici.plotting)
plot_observable_trajectories() (in module amici.plotting)
plot_state_trajectories() (in module amici.plotting)
plotObservableTrajectories() (in module amici.plotting)
plotStateTrajectories() (in module amici.plotting)
polynomial (amici.amici.InterpolationType attribute)
posteq_cpu_time (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
posteq_cpu_timeB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
posteq_numsteps (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
posteq_numstepsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
posteq_status (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
posteq_t (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
posteq_wrms (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_cpu_time (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_cpu_timeB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_numsteps (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_numstepsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_status (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_t (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preeq_wrms (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
preequilibration
(amici.amici.FixedParameterContext attribute)
presimulation
(amici.amici.FixedParameterContext attribute)
process_conservation_laws() (amici.sbml_import.SbmlImporter method)
pscale (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationParameters property)
PySB
pysb2amici() (in module amici.pysb_import)
pysb_model_from_path() (in module amici.pysb_import)
PysbPetabProblem (class in amici.petab_import_pysb)
pythonGenerated (amici.amici.Model property)
(amici.amici.ModelPtr property)
R
rdata_reporting (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
RDataReporting (class in amici.amici)
rdatas_to_measurement_df() (in module amici.petab_objective)
rdatas_to_simulation_df() (in module amici.petab_objective)
reinitialization_state_idxs_presim (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
reinitialization_state_idxs_sim (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
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)
reinitializeFixedParameterInitialStates (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
remove_argument_types() (in module amici.de_export)
remove_working_dir() (amici.petab_simulate.PetabSimulator method)
replace_logx() (in module amici.sbml_import)
requireSensitivitiesForAllParameters() (amici.amici.Model method)
res (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
rescale_sensitivity() (in module amici.petab_objective)
reset() (amici.amici.CpuTimer method)
residuals (amici.amici.RDataReporting attribute)
ReturnData (class in amici.amici)
ReturnDataPtr (class in amici.amici)
ReturnDataView (class in amici.numpy)
rowvals() (amici.de_export.DEModel method)
rref() (in module amici.conserved_quantities_rref)
runAmiciSimulation() (in module amici.amici)
runAmiciSimulations() (in module amici.amici)
rz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
S
s2llh (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
s2rz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
safe_substitute() (amici.de_export.TemplateAmici method)
sample_parameter_startpoints() (amici.petab_import_pysb.PysbPetabProblem method)
SBML
sbml2amici() (amici.sbml_import.SbmlImporter method)
SBMLException
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)
second (amici.amici.SensitivityOrder attribute)
SecondOrderMode (class in amici.amici)
sensi (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sensi_meth (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SensitivityMethod (class in amici.amici)
SensitivityMethod_adjoint (in module amici.amici)
SensitivityMethod_forward (in module amici.amici)
SensitivityMethod_none (in module amici.amici)
SensitivityOrder (class in amici.amici)
SensitivityOrder_first (in module amici.amici)
SensitivityOrder_none (in module amici.amici)
SensitivityOrder_second (in module amici.amici)
set_conservation_law() (amici.de_model.DifferentialState method)
set_dt() (amici.de_model.DifferentialState method)
set_log_level() (in module amici.logging)
set_name() (amici.de_export.DEExporter method)
set_paths() (amici.de_export.DEExporter method)
set_val() (amici.de_model.AlgebraicEquation method)
(amici.de_model.AlgebraicState method)
(amici.de_model.ConservationLaw method)
(amici.de_model.Constant method)
(amici.de_model.DifferentialState method)
(amici.de_model.Event method)
(amici.de_model.EventObservable method)
(amici.de_model.Expression method)
(amici.de_model.LogLikelihoodRZ method)
(amici.de_model.LogLikelihoodY method)
(amici.de_model.LogLikelihoodZ method)
(amici.de_model.ModelQuantity method)
(amici.de_model.Observable method)
(amici.de_model.Parameter method)
(amici.de_model.SigmaY method)
(amici.de_model.SigmaZ method)
(amici.de_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)
severity (amici.amici.LogItem property)
show_model_info() (in module amici.petab_import)
sigma_res (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sigma_ys() (amici.de_export.DEModel method)
sigma_zs() (amici.de_export.DEModel method)
sigmay (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SigmaY (class in amici.de_model)
sigmaz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SigmaZ (class in amici.de_model)
simulate() (amici.petab_simulate.PetabSimulator method)
simulate_petab() (in module amici.petab_objective)
simulate_without_noise() (amici.petab_simulate.PetabSimulator method)
simulation (amici.amici.FixedParameterContext attribute)
simulation_status_to_str() (in module amici.amici)
SimulationParameters (class in amici.amici)
SimulationState (class in amici.amici)
simultaneous (amici.amici.InternalSensitivityMethod attribute)
sllh (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
smart_is_zero_matrix() (in module amici.de_export)
smart_jacobian() (in module amici.de_export)
smart_multiply() (in module amici.de_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.de_export.DEModel method)
sparsesym() (amici.de_export.DEModel method)
SPBCG (amici.amici.LinearSolver attribute)
species_to_parameters() (in module amici.petab_import)
SPGMR (amici.amici.LinearSolver attribute)
SPTFQMR (amici.amici.LinearSolver attribute)
sres (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
srz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ssigmay (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ssigmaz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
staggered (amici.amici.InternalSensitivityMethod attribute)
staggered1 (amici.amici.InternalSensitivityMethod attribute)
startTimer() (amici.amici.Solver method)
state (amici.amici.SimulationState property)
State (class in amici.de_model)
state_has_conservation_law() (amici.de_export.DEModel method)
state_has_fixed_parameter_initial_condition() (amici.de_export.DEModel method)
state_is_constant() (amici.de_export.DEModel method)
states() (amici.de_export.DEModel method)
status (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
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)
substitute() (amici.de_export.TemplateAmici method)
success (amici.amici.SteadyStateStatus attribute)
SUNDIALS
SuperLUMT (amici.amici.LinearSolver attribute)
SWIG
SwigPtrView (class in amici.numpy)
switchForwardSensisOff() (amici.amici.Solver method)
sx (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationState property)
sx0 (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationParameters property)
sx_ss (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sy (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sym() (amici.de_export.DEModel method)
sym_names() (amici.de_export.DEModel method)
sym_or_eq() (amici.de_export.DEModel method)
symbol_with_assumptions() (in module amici.import_utils)
sz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
T
t (amici.amici.SimulationState property)
t0() (amici.amici.Model method)
t_presim (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
TemplateAmici (class in amici.de_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)
ts (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ts_ (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
tstart_ (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
U
ub (amici.petab_import_pysb.PysbPetabProblem property)
ub_scaled (amici.petab_import_pysb.PysbPetabProblem property)
ubw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
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.de_export.DEModel method)
values() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
var_in_function_signature() (in module amici.de_export)
W
w (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
with_traceback() (amici.AmiciVersionError method)
(amici.import_utils.CircularDependencyError method)
(amici.import_utils.SBMLException method)
X
x (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationState property)
x0 (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationParameters property)
x_fixed_ids (amici.petab_import_pysb.PysbPetabProblem property)
x_fixed_indices (amici.petab_import_pysb.PysbPetabProblem property)
x_free_ids (amici.petab_import_pysb.PysbPetabProblem property)
x_free_indices (amici.petab_import_pysb.PysbPetabProblem property)
x_ids (amici.petab_import_pysb.PysbPetabProblem property)
x_nominal (amici.petab_import_pysb.PysbPetabProblem property)
x_nominal_fixed (amici.petab_import_pysb.PysbPetabProblem property)
x_nominal_fixed_scaled (amici.petab_import_pysb.PysbPetabProblem property)
x_nominal_free (amici.petab_import_pysb.PysbPetabProblem property)
x_nominal_free_scaled (amici.petab_import_pysb.PysbPetabProblem property)
x_nominal_scaled (amici.petab_import_pysb.PysbPetabProblem property)
x_ss (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
xdot (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
Y
y (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
Z
z (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
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