AMICI
v0.16.1
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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P
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R
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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
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_USE_MATH_DEFINES (C macro)
A
adams (amici.amici.LinearMultistepMethod attribute)
add_component() (amici.ode_export.ODEModel method)
add_conservation_law() (amici.ode_export.ODEModel method)
add_d_dt() (amici.sbml_import.SbmlImporter method)
add_local_symbol() (amici.sbml_import.SbmlImporter method)
add_path (class in amici)
adjoint (amici.amici.SensitivityMethod attribute)
amici
module
amici.amici
module
amici.bngl_import
module
amici.conserved_quantities_demartino
module
amici.conserved_quantities_rref
module
amici.gradient_check
module
amici.import_utils
module
amici.logging
module
amici.numpy
module
amici.ode_export
module
amici.ode_model
module
amici.pandas
module
amici.parameter_mapping
module
amici.petab_import
module
amici.petab_import_pysb
module
amici.petab_objective
module
amici.petab_simulate
module
amici.plotting
module
amici.pysb_import
module
amici.sbml_import
module
amici::AbstractModel (C++ class)
amici::AbstractModel::fdeltaqB (C++ function)
amici::AbstractModel::fdeltasx (C++ function)
amici::AbstractModel::fdeltax (C++ function)
amici::AbstractModel::fdeltaxB (C++ function)
amici::AbstractModel::fdJrzdsigma (C++ function)
amici::AbstractModel::fdJrzdz (C++ function)
amici::AbstractModel::fdJydsigma (C++ function)
amici::AbstractModel::fdJydy (C++ function)
amici::AbstractModel::fdJydy_colptrs (C++ function)
amici::AbstractModel::fdJydy_rowvals (C++ function)
amici::AbstractModel::fdJzdsigma (C++ function)
amici::AbstractModel::fdJzdz (C++ function)
amici::AbstractModel::fdrzdp (C++ function)
amici::AbstractModel::fdrzdx (C++ function)
amici::AbstractModel::fdsigmaydp (C++ function)
amici::AbstractModel::fdsigmaydy (C++ function)
amici::AbstractModel::fdsigmazdp (C++ function)
amici::AbstractModel::fdtotal_cldp (C++ function)
amici::AbstractModel::fdtotal_cldx_rdata (C++ function)
amici::AbstractModel::fdtotal_cldx_rdata_colptrs (C++ function)
amici::AbstractModel::fdtotal_cldx_rdata_rowvals (C++ function)
amici::AbstractModel::fdwdp (C++ function)
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[1]
amici::AbstractModel::fdwdp_colptrs (C++ function)
amici::AbstractModel::fdwdp_rowvals (C++ function)
amici::AbstractModel::fdwdw (C++ function)
amici::AbstractModel::fdwdw_colptrs (C++ function)
amici::AbstractModel::fdwdw_rowvals (C++ function)
amici::AbstractModel::fdwdx (C++ function)
amici::AbstractModel::fdwdx_colptrs (C++ function)
amici::AbstractModel::fdwdx_rowvals (C++ function)
amici::AbstractModel::fdx0 (C++ function)
amici::AbstractModel::fdx_rdatadp (C++ function)
amici::AbstractModel::fdx_rdatadtcl (C++ function)
amici::AbstractModel::fdx_rdatadtcl_colptrs (C++ function)
amici::AbstractModel::fdx_rdatadtcl_rowvals (C++ function)
amici::AbstractModel::fdx_rdatadx_solver (C++ function)
amici::AbstractModel::fdx_rdatadx_solver_colptrs (C++ function)
amici::AbstractModel::fdx_rdatadx_solver_rowvals (C++ function)
amici::AbstractModel::fdxdotdp (C++ function)
amici::AbstractModel::fdydp (C++ function)
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[1]
amici::AbstractModel::fdydx (C++ function)
amici::AbstractModel::fdzdp (C++ function)
amici::AbstractModel::fdzdx (C++ function)
amici::AbstractModel::fJ (C++ function)
amici::AbstractModel::fJB (C++ function)
amici::AbstractModel::fJDiag (C++ function)
amici::AbstractModel::fJrz (C++ function)
amici::AbstractModel::fJSparse (C++ function)
amici::AbstractModel::fJSparseB (C++ function)
amici::AbstractModel::fJSparseB_ss (C++ function)
amici::AbstractModel::fJv (C++ function)
amici::AbstractModel::fJy (C++ function)
amici::AbstractModel::fJz (C++ function)
amici::AbstractModel::froot (C++ function)
amici::AbstractModel::frz (C++ function)
amici::AbstractModel::fsigmay (C++ function)
amici::AbstractModel::fsigmaz (C++ function)
amici::AbstractModel::fsrz (C++ function)
amici::AbstractModel::fstau (C++ function)
amici::AbstractModel::fsx0 (C++ function)
amici::AbstractModel::fsx0_fixedParameters (C++ function)
amici::AbstractModel::fsxdot (C++ function)
amici::AbstractModel::fsz (C++ function)
amici::AbstractModel::fw (C++ function)
amici::AbstractModel::fx0 (C++ function)
amici::AbstractModel::fx0_fixedParameters (C++ function)
amici::AbstractModel::fxBdot_ss (C++ function)
amici::AbstractModel::fxdot (C++ function)
amici::AbstractModel::fy (C++ function)
amici::AbstractModel::fz (C++ function)
amici::AbstractModel::getAmiciCommit (C++ function)
amici::AbstractModel::getAmiciVersion (C++ function)
amici::AbstractModel::getSolver (C++ function)
amici::AbstractModel::isFixedParameterStateReinitializationAllowed (C++ function)
amici::AbstractModel::writeSteadystateJB (C++ function)
amici::AbstractModel::~AbstractModel (C++ function)
amici::addSlice (C++ function)
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[1]
amici::AMICI_CONV_FAILURE (C++ member)
amici::AMICI_DAMPING_FACTOR_ERROR (C++ member)
amici::AMICI_DATA_RETURN (C++ member)
amici::amici_daxpy (C++ function)
amici::amici_dgemm (C++ function)
amici::amici_dgemv (C++ function)
amici::AMICI_ERR_FAILURE (C++ member)
amici::AMICI_ERROR (C++ member)
amici::AMICI_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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[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)
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[1]
amici::AmiVector::getVector (C++ function)
amici::AmiVector::minus (C++ function)
amici::AmiVector::operator*= (C++ function)
amici::AmiVector::operator/= (C++ function)
amici::AmiVector::operator= (C++ function)
amici::AmiVector::operator[] (C++ function)
amici::AmiVector::set (C++ function)
amici::AmiVector::zero (C++ function)
amici::AmiVector::~AmiVector (C++ function)
amici::AmiVectorArray (C++ class)
amici::AmiVectorArray::AmiVectorArray (C++ function)
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[1]
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[2]
amici::AmiVectorArray::at (C++ function)
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[1]
amici::AmiVectorArray::copy (C++ function)
amici::AmiVectorArray::data (C++ function)
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[1]
amici::AmiVectorArray::flatten_to_vector (C++ function)
amici::AmiVectorArray::getLength (C++ function)
amici::AmiVectorArray::getNVector (C++ function)
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[1]
amici::AmiVectorArray::getNVectorArray (C++ function)
amici::AmiVectorArray::operator= (C++ function)
amici::AmiVectorArray::operator[] (C++ function)
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[1]
amici::AmiVectorArray::zero (C++ function)
amici::AmiVectorArray::~AmiVectorArray (C++ function)
amici::backtraceString (C++ function)
amici::BackwardProblem (C++ class)
amici::BackwardProblem::BackwardProblem (C++ function)
amici::BackwardProblem::getAdjointQuadrature (C++ function)
amici::BackwardProblem::getAdjointState (C++ function)
amici::BackwardProblem::getdJydx (C++ function)
amici::BackwardProblem::gett (C++ function)
amici::BackwardProblem::getwhich (C++ function)
amici::BackwardProblem::getwhichptr (C++ function)
amici::BackwardProblem::workBackwardProblem (C++ function)
amici::BLASLayout (C++ enum)
amici::BLASLayout::colMajor (C++ enumerator)
amici::BLASLayout::rowMajor (C++ enumerator)
amici::BLASTranspose (C++ enum)
amici::BLASTranspose::conjTrans (C++ enumerator)
amici::BLASTranspose::noTrans (C++ enumerator)
amici::BLASTranspose::trans (C++ enumerator)
amici::checkBufferSize (C++ function)
amici::checkSigmaPositivity (C++ function)
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[1]
amici::ConditionContext (C++ class)
amici::ConditionContext::applyCondition (C++ function)
amici::ConditionContext::ConditionContext (C++ function)
amici::ConditionContext::operator= (C++ function)
amici::ConditionContext::restore (C++ function)
amici::ConditionContext::~ConditionContext (C++ function)
amici::const_N_Vector (C++ type)
amici::ContextManager (C++ class)
amici::ContextManager::ContextManager (C++ function)
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[1]
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[2]
amici::CvodeException (C++ class)
amici::CvodeException::CvodeException (C++ function)
amici::CVodeSolver (C++ class)
amici::CVodeSolver::adjInit (C++ function)
amici::CVodeSolver::allocateSolver (C++ function)
amici::CVodeSolver::allocateSolverB (C++ function)
amici::CVodeSolver::binit (C++ function)
amici::CVodeSolver::boost::serialization::serialize (C++ function)
amici::CVodeSolver::calcIC (C++ function)
amici::CVodeSolver::calcICB (C++ function)
amici::CVodeSolver::clone (C++ function)
amici::CVodeSolver::diag (C++ function)
amici::CVodeSolver::diagB (C++ function)
amici::CVodeSolver::getAdjBmem (C++ function)
amici::CVodeSolver::getB (C++ function)
amici::CVodeSolver::getDky (C++ function)
amici::CVodeSolver::getDkyB (C++ function)
amici::CVodeSolver::getLastOrder (C++ function)
amici::CVodeSolver::getModel (C++ function)
amici::CVodeSolver::getNumErrTestFails (C++ function)
amici::CVodeSolver::getNumNonlinSolvConvFails (C++ function)
amici::CVodeSolver::getNumRhsEvals (C++ function)
amici::CVodeSolver::getNumSteps (C++ function)
amici::CVodeSolver::getQuad (C++ function)
amici::CVodeSolver::getQuadB (C++ function)
amici::CVodeSolver::getQuadDky (C++ function)
amici::CVodeSolver::getQuadDkyB (C++ function)
amici::CVodeSolver::getRootInfo (C++ function)
amici::CVodeSolver::getSens (C++ function)
amici::CVodeSolver::getSensDky (C++ function)
amici::CVodeSolver::init (C++ function)
amici::CVodeSolver::initSteadystate (C++ function)
amici::CVodeSolver::operator== (C++ function)
amici::CVodeSolver::qbinit (C++ function)
amici::CVodeSolver::quadInit (C++ function)
amici::CVodeSolver::quadReInitB (C++ function)
amici::CVodeSolver::quadSStolerances (C++ function)
amici::CVodeSolver::quadSStolerancesB (C++ function)
amici::CVodeSolver::reInit (C++ function)
amici::CVodeSolver::reInitB (C++ function)
amici::CVodeSolver::reInitPostProcess (C++ function)
amici::CVodeSolver::reInitPostProcessB (C++ function)
amici::CVodeSolver::reInitPostProcessF (C++ function)
amici::CVodeSolver::resetState (C++ function)
amici::CVodeSolver::rootInit (C++ function)
amici::CVodeSolver::sensInit1 (C++ function)
amici::CVodeSolver::sensReInit (C++ function)
amici::CVodeSolver::sensToggleOff (C++ function)
amici::CVodeSolver::setBandJacFn (C++ function)
amici::CVodeSolver::setBandJacFnB (C++ function)
amici::CVodeSolver::setDenseJacFn (C++ function)
amici::CVodeSolver::setDenseJacFnB (C++ function)
amici::CVodeSolver::setErrHandlerFn (C++ function)
amici::CVodeSolver::setId (C++ function)
amici::CVodeSolver::setJacTimesVecFn (C++ function)
amici::CVodeSolver::setJacTimesVecFnB (C++ function)
amici::CVodeSolver::setLinearSolver (C++ function)
amici::CVodeSolver::setLinearSolverB (C++ function)
amici::CVodeSolver::setMaxNumSteps (C++ function)
amici::CVodeSolver::setMaxNumStepsB (C++ function)
amici::CVodeSolver::setNonLinearSolver (C++ function)
amici::CVodeSolver::setNonLinearSolverB (C++ function)
amici::CVodeSolver::setNonLinearSolverSens (C++ function)
amici::CVodeSolver::setQuadErrCon (C++ function)
amici::CVodeSolver::setQuadErrConB (C++ function)
amici::CVodeSolver::setSensErrCon (C++ function)
amici::CVodeSolver::setSensParams (C++ function)
amici::CVodeSolver::setSensSStolerances (C++ function)
amici::CVodeSolver::setSparseJacFn (C++ function)
amici::CVodeSolver::setSparseJacFn_ss (C++ function)
amici::CVodeSolver::setSparseJacFnB (C++ function)
amici::CVodeSolver::setSStolerances (C++ function)
amici::CVodeSolver::setSStolerancesB (C++ function)
amici::CVodeSolver::setStabLimDet (C++ function)
amici::CVodeSolver::setStabLimDetB (C++ function)
amici::CVodeSolver::setStopTime (C++ function)
amici::CVodeSolver::setSuppressAlg (C++ function)
amici::CVodeSolver::setUserData (C++ function)
amici::CVodeSolver::setUserDataB (C++ function)
amici::CVodeSolver::solve (C++ function)
amici::CVodeSolver::solveB (C++ function)
amici::CVodeSolver::solveF (C++ function)
amici::CVodeSolver::Solver (C++ function)
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[1]
amici::CVodeSolver::turnOffRootFinding (C++ function)
amici::CVodeSolver::~CVodeSolver (C++ function)
amici::deserializeFromChar (C++ function)
amici::deserializeFromString (C++ function)
amici::dotProd (C++ function)
amici::ExpData (C++ class)
amici::ExpData::applyDataDimension (C++ function)
amici::ExpData::applyDimensions (C++ function)
amici::ExpData::applyEventDimension (C++ function)
amici::ExpData::checkDataDimension (C++ function)
amici::ExpData::checkEventsDimension (C++ function)
amici::ExpData::ExpData (C++ function)
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[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)
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[1]
amici::ExpData::setObservedDataStdDev (C++ function)
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[1]
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[2]
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[3]
amici::ExpData::setObservedEvents (C++ function)
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[1]
amici::ExpData::setObservedEventsStdDev (C++ function)
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[1]
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[2]
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[3]
amici::ExpData::setTimepoints (C++ function)
amici::ExpData::~ExpData (C++ function)
amici::FinalStateStorer (C++ class)
amici::FinalStateStorer::FinalStateStorer (C++ function)
amici::FinalStateStorer::operator= (C++ function)
amici::FinalStateStorer::~FinalStateStorer (C++ function)
amici::FixedParameterContext (C++ enum)
amici::FixedParameterContext::preequilibration (C++ enumerator)
amici::FixedParameterContext::presimulation (C++ enumerator)
amici::FixedParameterContext::simulation (C++ enumerator)
amici::ForwardProblem (C++ class)
amici::ForwardProblem::edata (C++ member)
amici::ForwardProblem::ForwardProblem (C++ function)
amici::ForwardProblem::getAdjointUpdates (C++ function)
amici::ForwardProblem::getCurrentTimeIteration (C++ function)
amici::ForwardProblem::getDiscontinuities (C++ function)
amici::ForwardProblem::getDJydx (C++ function)
amici::ForwardProblem::getDJzdx (C++ function)
amici::ForwardProblem::getEventCounter (C++ function)
amici::ForwardProblem::getFinalSimulationState (C++ function)
amici::ForwardProblem::getFinalTime (C++ function)
amici::ForwardProblem::getInitialSimulationState (C++ function)
amici::ForwardProblem::getNumberOfRoots (C++ function)
amici::ForwardProblem::getRHSAtDiscontinuities (C++ function)
amici::ForwardProblem::getRHSBeforeDiscontinuities (C++ function)
amici::ForwardProblem::getRootCounter (C++ function)
amici::ForwardProblem::getRootIndexes (C++ function)
amici::ForwardProblem::getSimulationStateEvent (C++ function)
amici::ForwardProblem::getSimulationStateTimepoint (C++ function)
amici::ForwardProblem::getState (C++ function)
amici::ForwardProblem::getStateDerivative (C++ function)
amici::ForwardProblem::getStateDerivativePointer (C++ function)
amici::ForwardProblem::getStateDerivativeSensitivityPointer (C++ function)
amici::ForwardProblem::getStatePointer (C++ function)
amici::ForwardProblem::getStatesAtDiscontinuities (C++ function)
amici::ForwardProblem::getStateSensitivity (C++ function)
amici::ForwardProblem::getStateSensitivityPointer (C++ function)
amici::ForwardProblem::getTime (C++ function)
amici::ForwardProblem::model (C++ member)
amici::ForwardProblem::solver (C++ member)
amici::ForwardProblem::workForwardProblem (C++ function)
amici::ForwardProblem::~ForwardProblem (C++ function)
amici::getScaledParameter (C++ function)
amici::getUnscaledParameter (C++ function)
amici::hdf5::attributeExists (C++ function)
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[1]
amici::hdf5::createAndWriteDouble1DDataset (C++ function)
amici::hdf5::createAndWriteDouble2DDataset (C++ function)
amici::hdf5::createAndWriteDouble3DDataset (C++ function)
amici::hdf5::createAndWriteInt1DDataset (C++ function)
amici::hdf5::createAndWriteInt2DDataset (C++ function)
amici::hdf5::createGroup (C++ function)
amici::hdf5::createOrOpenForWriting (C++ function)
amici::hdf5::getDoubleDataset1D (C++ function)
amici::hdf5::getDoubleDataset2D (C++ function)
amici::hdf5::getDoubleDataset3D (C++ function)
amici::hdf5::getDoubleScalarAttribute (C++ function)
amici::hdf5::getIntDataset1D (C++ function)
amici::hdf5::getIntScalarAttribute (C++ function)
amici::hdf5::getStringAttribute (C++ function)
amici::hdf5::locationExists (C++ function)
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[1]
amici::hdf5::readModelDataFromHDF5 (C++ function)
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[1]
amici::hdf5::readSimulationExpData (C++ function)
amici::hdf5::readSolverSettingsFromHDF5 (C++ function)
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[1]
amici::hdf5::writeReturnData (C++ function)
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amici::hdf5::writeReturnDataDiagnosis (C++ function)
amici::hdf5::writeSimulationExpData (C++ function)
amici::hdf5::writeSolverSettingsToHDF5 (C++ function)
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[1]
amici::IDAException (C++ class)
amici::IDAException::IDAException (C++ function)
amici::IDASolver (C++ class)
amici::IDASolver::adjInit (C++ function)
amici::IDASolver::allocateSolver (C++ function)
amici::IDASolver::allocateSolverB (C++ function)
amici::IDASolver::binit (C++ function)
amici::IDASolver::calcIC (C++ function)
amici::IDASolver::calcICB (C++ function)
amici::IDASolver::clone (C++ function)
amici::IDASolver::diag (C++ function)
amici::IDASolver::diagB (C++ function)
amici::IDASolver::getAdjBmem (C++ function)
amici::IDASolver::getB (C++ function)
amici::IDASolver::getDky (C++ function)
amici::IDASolver::getDkyB (C++ function)
amici::IDASolver::getLastOrder (C++ function)
amici::IDASolver::getModel (C++ function)
amici::IDASolver::getNumErrTestFails (C++ function)
amici::IDASolver::getNumNonlinSolvConvFails (C++ function)
amici::IDASolver::getNumRhsEvals (C++ function)
amici::IDASolver::getNumSteps (C++ function)
amici::IDASolver::getQuad (C++ function)
amici::IDASolver::getQuadB (C++ function)
amici::IDASolver::getQuadDky (C++ function)
amici::IDASolver::getQuadDkyB (C++ function)
amici::IDASolver::getRootInfo (C++ function)
amici::IDASolver::getSens (C++ function)
amici::IDASolver::getSensDky (C++ function)
amici::IDASolver::init (C++ function)
amici::IDASolver::initSteadystate (C++ function)
amici::IDASolver::qbinit (C++ function)
amici::IDASolver::quadInit (C++ function)
amici::IDASolver::quadReInitB (C++ function)
amici::IDASolver::quadSStolerances (C++ function)
amici::IDASolver::quadSStolerancesB (C++ function)
amici::IDASolver::reInit (C++ function)
amici::IDASolver::reInitB (C++ function)
amici::IDASolver::reInitPostProcess (C++ function)
amici::IDASolver::reInitPostProcessB (C++ function)
amici::IDASolver::reInitPostProcessF (C++ function)
amici::IDASolver::resetState (C++ function)
amici::IDASolver::rootInit (C++ function)
amici::IDASolver::sensInit1 (C++ function)
amici::IDASolver::sensReInit (C++ function)
amici::IDASolver::sensToggleOff (C++ function)
amici::IDASolver::setBandJacFn (C++ function)
amici::IDASolver::setBandJacFnB (C++ function)
amici::IDASolver::setDenseJacFn (C++ function)
amici::IDASolver::setDenseJacFnB (C++ function)
amici::IDASolver::setErrHandlerFn (C++ function)
amici::IDASolver::setId (C++ function)
amici::IDASolver::setJacTimesVecFn (C++ function)
amici::IDASolver::setJacTimesVecFnB (C++ function)
amici::IDASolver::setLinearSolver (C++ function)
amici::IDASolver::setLinearSolverB (C++ function)
amici::IDASolver::setMaxNumSteps (C++ function)
amici::IDASolver::setMaxNumStepsB (C++ function)
amici::IDASolver::setNonLinearSolver (C++ function)
amici::IDASolver::setNonLinearSolverB (C++ function)
amici::IDASolver::setNonLinearSolverSens (C++ function)
amici::IDASolver::setQuadErrCon (C++ function)
amici::IDASolver::setQuadErrConB (C++ function)
amici::IDASolver::setSensErrCon (C++ function)
amici::IDASolver::setSensParams (C++ function)
amici::IDASolver::setSensSStolerances (C++ function)
amici::IDASolver::setSparseJacFn (C++ function)
amici::IDASolver::setSparseJacFn_ss (C++ function)
amici::IDASolver::setSparseJacFnB (C++ function)
amici::IDASolver::setSStolerances (C++ function)
amici::IDASolver::setSStolerancesB (C++ function)
amici::IDASolver::setStabLimDet (C++ function)
amici::IDASolver::setStabLimDetB (C++ function)
amici::IDASolver::setStopTime (C++ function)
amici::IDASolver::setSuppressAlg (C++ function)
amici::IDASolver::setUserData (C++ function)
amici::IDASolver::setUserDataB (C++ function)
amici::IDASolver::solve (C++ function)
amici::IDASolver::solveB (C++ function)
amici::IDASolver::solveF (C++ function)
amici::IDASolver::Solver (C++ function)
,
[1]
amici::IDASolver::turnOffRootFinding (C++ function)
amici::IDASolver::~IDASolver (C++ function)
amici::IntegrationFailure (C++ class)
amici::IntegrationFailure::error_code (C++ member)
amici::IntegrationFailure::IntegrationFailure (C++ function)
amici::IntegrationFailure::time (C++ member)
amici::IntegrationFailureB (C++ class)
amici::IntegrationFailureB::error_code (C++ member)
amici::IntegrationFailureB::IntegrationFailureB (C++ function)
amici::IntegrationFailureB::time (C++ member)
amici::InternalSensitivityMethod (C++ enum)
amici::InternalSensitivityMethod::simultaneous (C++ enumerator)
amici::InternalSensitivityMethod::staggered (C++ enumerator)
amici::InternalSensitivityMethod::staggered1 (C++ enumerator)
amici::InterpolationType (C++ enum)
amici::InterpolationType::hermite (C++ enumerator)
amici::InterpolationType::polynomial (C++ enumerator)
amici::is_equal (C++ function)
amici::LinearMultistepMethod (C++ enum)
amici::LinearMultistepMethod::adams (C++ enumerator)
amici::LinearMultistepMethod::BDF (C++ enumerator)
amici::LinearSolver (C++ enum)
amici::LinearSolver::band (C++ enumerator)
amici::LinearSolver::dense (C++ enumerator)
amici::LinearSolver::diag (C++ enumerator)
amici::LinearSolver::KLU (C++ enumerator)
amici::LinearSolver::LAPACKBand (C++ enumerator)
amici::LinearSolver::LAPACKDense (C++ enumerator)
amici::LinearSolver::SPBCG (C++ enumerator)
amici::LinearSolver::SPGMR (C++ enumerator)
amici::LinearSolver::SPTFQMR (C++ enumerator)
amici::LinearSolver::SuperLUMT (C++ enumerator)
amici::linearSum (C++ function)
amici::Logger (C++ class)
amici::Logger::items (C++ member)
amici::Logger::log (C++ function)
,
[1]
amici::Logger::Logger (C++ function)
amici::LogItem (C++ struct)
amici::LogItem::identifier (C++ member)
amici::LogItem::LogItem (C++ function)
,
[1]
amici::LogItem::message (C++ member)
amici::LogItem::severity (C++ member)
amici::LogSeverity (C++ enum)
amici::LogSeverity::debug (C++ enumerator)
amici::LogSeverity::error (C++ enumerator)
amici::LogSeverity::warning (C++ enumerator)
amici::Model (C++ class)
amici::Model::addAdjointQuadratureEventUpdate (C++ function)
amici::Model::addAdjointStateEventUpdate (C++ function)
amici::Model::addEventObjective (C++ function)
amici::Model::addEventObjectiveRegularization (C++ function)
amici::Model::addEventObjectiveSensitivity (C++ function)
amici::Model::addObservableObjective (C++ function)
amici::Model::addObservableObjectiveSensitivity (C++ function)
amici::Model::addPartialEventObjectiveSensitivity (C++ function)
amici::Model::addPartialObservableObjectiveSensitivity (C++ function)
amici::Model::addStateEventUpdate (C++ function)
amici::Model::addStateSensitivityEventUpdate (C++ function)
amici::Model::always_check_finite_ (C++ member)
amici::Model::any_state_non_negative_ (C++ member)
amici::Model::boost::serialization::serialize (C++ function)
amici::Model::checkFinite (C++ function)
,
[1]
,
[2]
amici::Model::checkLLHBufferSize (C++ function)
amici::Model::clone (C++ function)
amici::Model::computeX_pos (C++ function)
,
[1]
amici::Model::derived_state_ (C++ member)
amici::Model::fdeltaqB (C++ function)
amici::Model::fdeltasx (C++ function)
amici::Model::fdeltax (C++ function)
amici::Model::fdeltaxB (C++ function)
amici::Model::fdJrzdsigma (C++ function)
,
[1]
amici::Model::fdJrzdz (C++ function)
,
[1]
amici::Model::fdJydp (C++ function)
amici::Model::fdJydsigma (C++ function)
,
[1]
amici::Model::fdJydx (C++ function)
amici::Model::fdJydy (C++ function)
,
[1]
amici::Model::fdJydy_colptrs (C++ function)
amici::Model::fdJydy_rowvals (C++ function)
amici::Model::fdJzdp (C++ function)
amici::Model::fdJzdsigma (C++ function)
,
[1]
amici::Model::fdJzdx (C++ function)
amici::Model::fdJzdz (C++ function)
,
[1]
amici::Model::fdrzdp (C++ function)
,
[1]
amici::Model::fdrzdx (C++ function)
,
[1]
amici::Model::fdsigmaydp (C++ function)
,
[1]
amici::Model::fdsigmaydy (C++ function)
,
[1]
amici::Model::fdsigmazdp (C++ function)
,
[1]
amici::Model::fdtotal_cldp (C++ function)
amici::Model::fdtotal_cldx_rdata (C++ function)
amici::Model::fdtotal_cldx_rdata_colptrs (C++ function)
amici::Model::fdtotal_cldx_rdata_rowvals (C++ function)
amici::Model::fdwdp (C++ function)
,
[1]
,
[2]
amici::Model::fdwdp_colptrs (C++ function)
amici::Model::fdwdp_rowvals (C++ function)
amici::Model::fdwdw (C++ function)
,
[1]
amici::Model::fdwdw_colptrs (C++ function)
amici::Model::fdwdw_rowvals (C++ function)
amici::Model::fdwdx (C++ function)
,
[1]
amici::Model::fdwdx_colptrs (C++ function)
amici::Model::fdwdx_rowvals (C++ function)
amici::Model::fdx_rdatadp (C++ function)
amici::Model::fdx_rdatadtcl (C++ function)
amici::Model::fdx_rdatadtcl_colptrs (C++ function)
amici::Model::fdx_rdatadtcl_rowvals (C++ function)
amici::Model::fdx_rdatadx_solver (C++ function)
amici::Model::fdx_rdatadx_solver_colptrs (C++ function)
amici::Model::fdx_rdatadx_solver_rowvals (C++ function)
amici::Model::fdydp (C++ function)
,
[1]
,
[2]
amici::Model::fdydx (C++ function)
,
[1]
amici::Model::fdzdp (C++ function)
,
[1]
amici::Model::fdzdx (C++ function)
,
[1]
amici::Model::fJrz (C++ function)
,
[1]
amici::Model::fJy (C++ function)
,
[1]
amici::Model::fJz (C++ function)
,
[1]
amici::Model::frz (C++ function)
,
[1]
amici::Model::fsdx0 (C++ function)
amici::Model::fsigmay (C++ function)
,
[1]
amici::Model::fsigmaz (C++ function)
,
[1]
amici::Model::fsrz (C++ function)
amici::Model::fstau (C++ function)
amici::Model::fstotal_cl (C++ function)
amici::Model::fsx0 (C++ function)
,
[1]
amici::Model::fsx0_fixedParameters (C++ function)
,
[1]
amici::Model::fsx_rdata (C++ function)
,
[1]
amici::Model::fsx_solver (C++ function)
amici::Model::fsz (C++ function)
amici::Model::ftotal_cl (C++ function)
amici::Model::fw (C++ function)
,
[1]
amici::Model::fx0 (C++ function)
,
[1]
amici::Model::fx0_fixedParameters (C++ function)
,
[1]
amici::Model::fx_rdata (C++ function)
,
[1]
amici::Model::fx_solver (C++ function)
amici::Model::fy (C++ function)
,
[1]
amici::Model::fz (C++ function)
,
[1]
amici::Model::get_dxdotdp (C++ function)
amici::Model::get_dxdotdp_full (C++ function)
amici::Model::getAddSigmaResiduals (C++ function)
amici::Model::getAdjointStateEventUpdate (C++ function)
amici::Model::getAdjointStateObservableUpdate (C++ function)
amici::Model::getAlwaysCheckFinite (C++ function)
amici::Model::getEvent (C++ function)
amici::Model::getEventRegularization (C++ function)
amici::Model::getEventRegularizationSensitivity (C++ function)
amici::Model::getEventSensitivity (C++ function)
amici::Model::getEventSigma (C++ function)
amici::Model::getEventSigmaSensitivity (C++ function)
amici::Model::getEventTimeSensitivity (C++ function)
amici::Model::getExpression (C++ function)
amici::Model::getExpressionIds (C++ function)
amici::Model::getExpressionNames (C++ function)
amici::Model::getFixedParameterById (C++ function)
amici::Model::getFixedParameterByName (C++ function)
amici::Model::getFixedParameterIds (C++ function)
amici::Model::getFixedParameterNames (C++ function)
amici::Model::getFixedParameters (C++ function)
amici::Model::getInitialStates (C++ function)
amici::Model::getInitialStateSensitivities (C++ function)
amici::Model::getMinimumSigmaResiduals (C++ function)
amici::Model::getModelState (C++ function)
amici::Model::getName (C++ function)
amici::Model::getObservable (C++ function)
amici::Model::getObservableIds (C++ function)
amici::Model::getObservableNames (C++ function)
amici::Model::getObservableScaling (C++ function)
amici::Model::getObservableSensitivity (C++ function)
amici::Model::getObservableSigma (C++ function)
amici::Model::getObservableSigmaSensitivity (C++ function)
amici::Model::getParameterById (C++ function)
amici::Model::getParameterByName (C++ function)
amici::Model::getParameterIds (C++ function)
amici::Model::getParameterList (C++ function)
amici::Model::getParameterNames (C++ function)
amici::Model::getParameters (C++ function)
amici::Model::getParameterScale (C++ function)
amici::Model::getReinitializationStateIdxs (C++ function)
amici::Model::getReinitializeFixedParameterInitialStates (C++ function)
amici::Model::getStateIds (C++ function)
amici::Model::getStateIdsSolver (C++ function)
amici::Model::getStateIsNonNegative (C++ function)
amici::Model::getStateNames (C++ function)
amici::Model::getStateNamesSolver (C++ function)
amici::Model::getSteadyStateSensitivityMode (C++ function)
amici::Model::getTimepoint (C++ function)
amici::Model::getTimepoints (C++ function)
amici::Model::getUnobservedEventSensitivity (C++ function)
amici::Model::getUnscaledParameters (C++ function)
amici::Model::hasCustomInitialStates (C++ function)
amici::Model::hasCustomInitialStateSensitivities (C++ function)
amici::Model::hasExpressionIds (C++ function)
amici::Model::hasExpressionNames (C++ function)
amici::Model::hasFixedParameterIds (C++ function)
amici::Model::hasFixedParameterNames (C++ function)
amici::Model::hasObservableIds (C++ function)
amici::Model::hasObservableNames (C++ function)
amici::Model::hasParameterIds (C++ function)
amici::Model::hasParameterNames (C++ function)
amici::Model::hasQuadraticLLH (C++ function)
amici::Model::hasStateIds (C++ function)
amici::Model::hasStateNames (C++ function)
amici::Model::idlist (C++ member)
amici::Model::initEvents (C++ function)
amici::Model::initialize (C++ function)
amici::Model::initializeB (C++ function)
amici::Model::initializeStates (C++ function)
amici::Model::initializeStateSensitivities (C++ function)
amici::Model::initializeVectors (C++ function)
amici::Model::k (C++ function)
amici::Model::logger (C++ member)
amici::Model::min_sigma_ (C++ member)
amici::Model::Model (C++ function)
,
[1]
amici::Model::ncl (C++ function)
amici::Model::nk (C++ function)
amici::Model::nMaxEvent (C++ function)
amici::Model::nmaxevent_ (C++ member)
amici::Model::np (C++ function)
amici::Model::nplist (C++ function)
amici::Model::nt (C++ function)
amici::Model::nx_reinit (C++ function)
amici::Model::o2mode (C++ member)
amici::Model::operator= (C++ function)
amici::Model::operator== (C++ function)
amici::Model::plist (C++ function)
amici::Model::pythonGenerated (C++ member)
amici::Model::requireSensitivitiesForAllParameters (C++ function)
amici::Model::root_initial_values_ (C++ member)
amici::Model::setAddSigmaResiduals (C++ function)
amici::Model::setAllStatesNonNegative (C++ function)
amici::Model::setAlwaysCheckFinite (C++ function)
amici::Model::setFixedParameterById (C++ function)
amici::Model::setFixedParameterByName (C++ function)
amici::Model::setFixedParameters (C++ function)
amici::Model::setFixedParametersByIdRegex (C++ function)
amici::Model::setFixedParametersByNameRegex (C++ function)
amici::Model::setInitialStates (C++ function)
amici::Model::setInitialStateSensitivities (C++ function)
amici::Model::setMinimumSigmaResiduals (C++ function)
amici::Model::setModelState (C++ function)
amici::Model::setNMaxEvent (C++ function)
amici::Model::setParameterById (C++ function)
,
[1]
amici::Model::setParameterByName (C++ function)
,
[1]
amici::Model::setParameterList (C++ function)
amici::Model::setParameters (C++ function)
amici::Model::setParametersByIdRegex (C++ function)
amici::Model::setParametersByNameRegex (C++ function)
amici::Model::setParameterScale (C++ function)
,
[1]
amici::Model::setReinitializationStateIdxs (C++ function)
amici::Model::setReinitializeFixedParameterInitialStates (C++ function)
amici::Model::setStateIsNonNegative (C++ function)
amici::Model::setSteadyStateSensitivityMode (C++ function)
amici::Model::setT0 (C++ function)
amici::Model::setTimepoints (C++ function)
amici::Model::setUnscaledInitialStateSensitivities (C++ function)
amici::Model::sigma_res_ (C++ member)
amici::Model::state_ (C++ member)
amici::Model::state_is_non_negative_ (C++ member)
amici::Model::steadystate_sensitivity_mode_ (C++ member)
amici::Model::sx0data_ (C++ member)
amici::Model::t0 (C++ function)
amici::Model::updateHeaviside (C++ function)
amici::Model::updateHeavisideB (C++ function)
amici::Model::writeLLHSensitivitySlice (C++ function)
amici::Model::writeSensitivitySliceEvent (C++ function)
amici::Model::writeSliceEvent (C++ function)
amici::Model::x0data_ (C++ member)
amici::Model::z2event_ (C++ member)
amici::Model::~Model (C++ function)
amici::Model_DAE (C++ class)
amici::Model_DAE::fdxdotdp (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fJ (C++ function)
,
[1]
amici::Model_DAE::fJB (C++ function)
,
[1]
amici::Model_DAE::fJDiag (C++ function)
amici::Model_DAE::fJSparse (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fJSparseB (C++ function)
,
[1]
amici::Model_DAE::fJSparseB_ss (C++ function)
amici::Model_DAE::fJv (C++ function)
,
[1]
amici::Model_DAE::fJvB (C++ function)
amici::Model_DAE::fM (C++ function)
,
[1]
amici::Model_DAE::fqBdot (C++ function)
amici::Model_DAE::fqBdot_ss (C++ function)
amici::Model_DAE::froot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fsxdot (C++ function)
,
[1]
amici::Model_DAE::fxBdot (C++ function)
amici::Model_DAE::fxBdot_ss (C++ function)
,
[1]
amici::Model_DAE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::getSolver (C++ function)
amici::Model_DAE::Model_DAE (C++ function)
,
[1]
amici::Model_DAE::writeSteadystateJB (C++ function)
amici::Model_ODE (C++ class)
amici::Model_ODE::fdxdotdp (C++ function)
,
[1]
,
[2]
amici::Model_ODE::fdxdotdp_explicit (C++ function)
amici::Model_ODE::fdxdotdp_explicit_colptrs (C++ function)
amici::Model_ODE::fdxdotdp_explicit_rowvals (C++ function)
amici::Model_ODE::fdxdotdw (C++ function)
,
[1]
amici::Model_ODE::fdxdotdw_colptrs (C++ function)
amici::Model_ODE::fdxdotdw_rowvals (C++ function)
amici::Model_ODE::fdxdotdx_explicit (C++ function)
amici::Model_ODE::fdxdotdx_explicit_colptrs (C++ function)
amici::Model_ODE::fdxdotdx_explicit_rowvals (C++ function)
amici::Model_ODE::fJ (C++ function)
,
[1]
amici::Model_ODE::fJB (C++ function)
,
[1]
amici::Model_ODE::fJDiag (C++ function)
,
[1]
amici::Model_ODE::fJSparse (C++ function)
,
[1]
,
[2]
,
[3]
amici::Model_ODE::fJSparse_colptrs (C++ function)
amici::Model_ODE::fJSparse_rowvals (C++ function)
amici::Model_ODE::fJSparseB (C++ function)
,
[1]
amici::Model_ODE::fJSparseB_ss (C++ function)
amici::Model_ODE::fJv (C++ function)
,
[1]
amici::Model_ODE::fJvB (C++ function)
amici::Model_ODE::fqBdot (C++ function)
amici::Model_ODE::fqBdot_ss (C++ function)
amici::Model_ODE::froot (C++ function)
,
[1]
,
[2]
amici::Model_ODE::fsxdot (C++ function)
,
[1]
amici::Model_ODE::fxBdot (C++ function)
amici::Model_ODE::fxBdot_ss (C++ function)
,
[1]
amici::Model_ODE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_ODE::getSolver (C++ function)
amici::Model_ODE::Model_ODE (C++ function)
,
[1]
amici::Model_ODE::writeSteadystateJB (C++ function)
amici::model_quantity_to_str (C++ member)
amici::ModelContext (C++ class)
amici::ModelContext::ModelContext (C++ function)
amici::ModelContext::operator= (C++ function)
amici::ModelContext::restore (C++ function)
amici::ModelContext::~ModelContext (C++ function)
amici::ModelDimensions (C++ struct)
amici::ModelDimensions::lbw (C++ member)
amici::ModelDimensions::ModelDimensions (C++ function)
,
[1]
amici::ModelDimensions::ndJydy (C++ member)
amici::ModelDimensions::ndtotal_cldx_rdata (C++ member)
amici::ModelDimensions::ndwdp (C++ member)
amici::ModelDimensions::ndwdw (C++ member)
amici::ModelDimensions::ndwdx (C++ member)
amici::ModelDimensions::ndxdotdw (C++ member)
amici::ModelDimensions::ndxrdatadtcl (C++ member)
amici::ModelDimensions::ndxrdatadxsolver (C++ member)
amici::ModelDimensions::ne (C++ member)
amici::ModelDimensions::nJ (C++ member)
amici::ModelDimensions::nk (C++ member)
amici::ModelDimensions::nnz (C++ member)
amici::ModelDimensions::np (C++ member)
amici::ModelDimensions::nw (C++ member)
amici::ModelDimensions::nx_rdata (C++ member)
amici::ModelDimensions::nx_solver (C++ member)
amici::ModelDimensions::nx_solver_reinit (C++ member)
amici::ModelDimensions::nxtrue_rdata (C++ member)
amici::ModelDimensions::nxtrue_solver (C++ member)
amici::ModelDimensions::ny (C++ member)
amici::ModelDimensions::nytrue (C++ member)
amici::ModelDimensions::nz (C++ member)
amici::ModelDimensions::nztrue (C++ member)
amici::ModelDimensions::ubw (C++ member)
amici::ModelQuantity (C++ enum)
amici::ModelQuantity::deltaqB (C++ enumerator)
amici::ModelQuantity::deltasx (C++ enumerator)
amici::ModelQuantity::deltax (C++ enumerator)
amici::ModelQuantity::deltaxB (C++ enumerator)
amici::ModelQuantity::dJrzdsigma (C++ enumerator)
amici::ModelQuantity::dJrzdx (C++ enumerator)
amici::ModelQuantity::dJrzdz (C++ enumerator)
amici::ModelQuantity::dJydsigma (C++ enumerator)
amici::ModelQuantity::dJydx (C++ enumerator)
amici::ModelQuantity::dJydy (C++ enumerator)
amici::ModelQuantity::dJydy_matlab (C++ enumerator)
amici::ModelQuantity::dJzdsigma (C++ enumerator)
amici::ModelQuantity::dJzdx (C++ enumerator)
amici::ModelQuantity::dJzdz (C++ enumerator)
amici::ModelQuantity::drzdp (C++ enumerator)
amici::ModelQuantity::drzdx (C++ enumerator)
amici::ModelQuantity::dsigmaydp (C++ enumerator)
amici::ModelQuantity::dsigmaydy (C++ enumerator)
amici::ModelQuantity::dsigmazdp (C++ enumerator)
amici::ModelQuantity::dwdp (C++ enumerator)
amici::ModelQuantity::dwdw (C++ enumerator)
amici::ModelQuantity::dwdx (C++ enumerator)
amici::ModelQuantity::dydp (C++ enumerator)
amici::ModelQuantity::dydx (C++ enumerator)
amici::ModelQuantity::dzdp (C++ enumerator)
amici::ModelQuantity::dzdx (C++ enumerator)
amici::ModelQuantity::J (C++ enumerator)
amici::ModelQuantity::JB (C++ enumerator)
amici::ModelQuantity::JDiag (C++ enumerator)
amici::ModelQuantity::JSparseB_ss (C++ enumerator)
amici::ModelQuantity::Jv (C++ enumerator)
amici::ModelQuantity::JvB (C++ enumerator)
amici::ModelQuantity::k (C++ enumerator)
amici::ModelQuantity::p (C++ enumerator)
amici::ModelQuantity::qBdot (C++ enumerator)
amici::ModelQuantity::qBdot_ss (C++ enumerator)
amici::ModelQuantity::root (C++ enumerator)
amici::ModelQuantity::srz (C++ enumerator)
amici::ModelQuantity::ssigmay (C++ enumerator)
amici::ModelQuantity::ssigmaz (C++ enumerator)
amici::ModelQuantity::sx (C++ enumerator)
amici::ModelQuantity::sxdot (C++ enumerator)
amici::ModelQuantity::sy (C++ enumerator)
amici::ModelQuantity::sz (C++ enumerator)
amici::ModelQuantity::ts (C++ enumerator)
amici::ModelQuantity::w (C++ enumerator)
amici::ModelQuantity::x (C++ enumerator)
amici::ModelQuantity::x0 (C++ enumerator)
amici::ModelQuantity::x0_rdata (C++ enumerator)
amici::ModelQuantity::x_rdata (C++ enumerator)
amici::ModelQuantity::xBdot (C++ enumerator)
amici::ModelQuantity::xBdot_ss (C++ enumerator)
amici::ModelQuantity::xdot (C++ enumerator)
amici::ModelQuantity::y (C++ enumerator)
amici::ModelState (C++ struct)
amici::ModelState::fixedParameters (C++ member)
amici::ModelState::h (C++ member)
amici::ModelState::plist (C++ member)
amici::ModelState::stotal_cl (C++ member)
amici::ModelState::total_cl (C++ member)
amici::ModelState::unscaledParameters (C++ member)
amici::ModelStateDerived (C++ struct)
amici::ModelStateDerived::deltaqB_ (C++ member)
amici::ModelStateDerived::deltasx_ (C++ member)
amici::ModelStateDerived::deltax_ (C++ member)
amici::ModelStateDerived::deltaxB_ (C++ member)
amici::ModelStateDerived::dJrzdsigma_ (C++ member)
amici::ModelStateDerived::dJrzdz_ (C++ member)
amici::ModelStateDerived::dJydp_ (C++ member)
amici::ModelStateDerived::dJydsigma_ (C++ member)
amici::ModelStateDerived::dJydx_ (C++ member)
amici::ModelStateDerived::dJydy_ (C++ member)
amici::ModelStateDerived::dJydy_matlab_ (C++ member)
amici::ModelStateDerived::dJzdp_ (C++ member)
amici::ModelStateDerived::dJzdsigma_ (C++ member)
amici::ModelStateDerived::dJzdx_ (C++ member)
amici::ModelStateDerived::dJzdz_ (C++ member)
amici::ModelStateDerived::drzdp_ (C++ member)
amici::ModelStateDerived::drzdx_ (C++ member)
amici::ModelStateDerived::dsigmaydp_ (C++ member)
amici::ModelStateDerived::dsigmaydy_ (C++ member)
amici::ModelStateDerived::dsigmazdp_ (C++ member)
amici::ModelStateDerived::dtotal_cldx_rdata (C++ member)
amici::ModelStateDerived::dwdp_ (C++ member)
amici::ModelStateDerived::dwdx_ (C++ member)
amici::ModelStateDerived::dx_rdatadtcl (C++ member)
amici::ModelStateDerived::dx_rdatadx_solver (C++ member)
amici::ModelStateDerived::dxdotdp (C++ member)
amici::ModelStateDerived::dxdotdp_explicit (C++ member)
amici::ModelStateDerived::dxdotdp_full (C++ member)
amici::ModelStateDerived::dxdotdp_implicit (C++ member)
amici::ModelStateDerived::dxdotdw_ (C++ member)
amici::ModelStateDerived::dxdotdx_explicit (C++ member)
amici::ModelStateDerived::dxdotdx_implicit (C++ member)
amici::ModelStateDerived::dydp_ (C++ member)
amici::ModelStateDerived::dydx_ (C++ member)
amici::ModelStateDerived::dzdp_ (C++ member)
amici::ModelStateDerived::dzdx_ (C++ member)
amici::ModelStateDerived::J_ (C++ member)
amici::ModelStateDerived::JB_ (C++ member)
amici::ModelStateDerived::M_ (C++ member)
amici::ModelStateDerived::ModelStateDerived (C++ function)
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[1]
amici::ModelStateDerived::rz_ (C++ member)
amici::ModelStateDerived::sigmay_ (C++ member)
amici::ModelStateDerived::sigmaz_ (C++ member)
amici::ModelStateDerived::sx_ (C++ member)
amici::ModelStateDerived::sx_rdata_ (C++ member)
amici::ModelStateDerived::w_ (C++ member)
amici::ModelStateDerived::x_pos_tmp_ (C++ member)
amici::ModelStateDerived::x_rdata_ (C++ member)
amici::ModelStateDerived::y_ (C++ member)
amici::ModelStateDerived::z_ (C++ member)
amici::N_VGetArrayPointerConst (C++ function)
amici::NewtonDampingFactorMode (C++ enum)
amici::NewtonDampingFactorMode::off (C++ enumerator)
amici::NewtonDampingFactorMode::on (C++ enumerator)
amici::NewtonFailure (C++ class)
amici::NewtonFailure::error_code (C++ member)
amici::NewtonFailure::NewtonFailure (C++ function)
amici::NewtonSolver (C++ class)
amici::NewtonSolver::computeNewtonSensis (C++ function)
amici::NewtonSolver::dxB_ (C++ member)
amici::NewtonSolver::getSolver (C++ function)
amici::NewtonSolver::getStep (C++ function)
amici::NewtonSolver::is_singular (C++ function)
amici::NewtonSolver::NewtonSolver (C++ function)
amici::NewtonSolver::prepareLinearSystem (C++ function)
amici::NewtonSolver::prepareLinearSystemB (C++ function)
amici::NewtonSolver::reinitialize (C++ function)
amici::NewtonSolver::solveLinearSystem (C++ function)
amici::NewtonSolver::x_ (C++ member)
amici::NewtonSolver::xB_ (C++ member)
amici::NewtonSolver::xdot_ (C++ member)
amici::NewtonSolver::~NewtonSolver (C++ function)
amici::NewtonSolverDense (C++ class)
amici::NewtonSolverDense::is_singular (C++ function)
amici::NewtonSolverDense::NewtonSolverDense (C++ function)
,
[1]
amici::NewtonSolverDense::operator= (C++ function)
amici::NewtonSolverDense::prepareLinearSystem (C++ function)
amici::NewtonSolverDense::prepareLinearSystemB (C++ function)
amici::NewtonSolverDense::reinitialize (C++ function)
amici::NewtonSolverDense::solveLinearSystem (C++ function)
amici::NewtonSolverDense::~NewtonSolverDense (C++ function)
amici::NewtonSolverSparse (C++ class)
amici::NewtonSolverSparse::is_singular (C++ function)
amici::NewtonSolverSparse::NewtonSolverSparse (C++ function)
,
[1]
amici::NewtonSolverSparse::operator= (C++ function)
amici::NewtonSolverSparse::prepareLinearSystem (C++ function)
amici::NewtonSolverSparse::prepareLinearSystemB (C++ function)
amici::NewtonSolverSparse::reinitialize (C++ function)
amici::NewtonSolverSparse::solveLinearSystem (C++ function)
amici::NewtonSolverSparse::~NewtonSolverSparse (C++ function)
amici::NonlinearSolverIteration (C++ enum)
amici::NonlinearSolverIteration::fixedpoint (C++ enumerator)
amici::NonlinearSolverIteration::functional (C++ enumerator)
amici::NonlinearSolverIteration::newton (C++ enumerator)
amici::ObservableScaling (C++ enum)
amici::ObservableScaling::lin (C++ enumerator)
amici::ObservableScaling::log (C++ enumerator)
amici::ObservableScaling::log10 (C++ enumerator)
amici::operator== (C++ function)
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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]
,
[2]
,
[3]
,
[4]
amici::SimulationParameters::sx0 (C++ member)
amici::SimulationParameters::t_presim (C++ member)
amici::SimulationParameters::ts_ (C++ member)
amici::SimulationParameters::tstart_ (C++ member)
amici::SimulationParameters::x0 (C++ member)
amici::SimulationState (C++ struct)
amici::SimulationState::dx (C++ member)
amici::SimulationState::state (C++ member)
amici::SimulationState::sx (C++ member)
amici::SimulationState::t (C++ member)
amici::SimulationState::x (C++ member)
amici::slice (C++ function)
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[1]
amici::Solver (C++ class)
amici::Solver::adjInit (C++ function)
amici::Solver::allocateSolver (C++ function)
amici::Solver::allocateSolverB (C++ function)
amici::Solver::applyQuadTolerances (C++ function)
amici::Solver::applyQuadTolerancesASA (C++ function)
amici::Solver::applySensitivityTolerances (C++ function)
amici::Solver::applyTolerances (C++ function)
amici::Solver::applyTolerancesASA (C++ function)
amici::Solver::applyTolerancesFSA (C++ function)
amici::Solver::binit (C++ function)
amici::Solver::boost::serialization::serialize (C++ function)
amici::Solver::calcIC (C++ function)
amici::Solver::calcICB (C++ function)
amici::Solver::checkSensitivityMethod (C++ function)
amici::Solver::clone (C++ function)
amici::Solver::computingASA (C++ function)
amici::Solver::computingFSA (C++ function)
amici::Solver::diag (C++ function)
amici::Solver::diagB (C++ function)
amici::Solver::dky_ (C++ member)
amici::Solver::dx_ (C++ member)
amici::Solver::dxB_ (C++ member)
amici::Solver::force_reinit_postprocess_B_ (C++ member)
amici::Solver::force_reinit_postprocess_F_ (C++ member)
amici::Solver::getAbsoluteTolerance (C++ function)
amici::Solver::getAbsoluteToleranceB (C++ function)
amici::Solver::getAbsoluteToleranceFSA (C++ function)
amici::Solver::getAbsoluteToleranceQuadratures (C++ function)
amici::Solver::getAbsoluteToleranceSteadyState (C++ function)
amici::Solver::getAbsoluteToleranceSteadyStateSensi (C++ function)
amici::Solver::getAdjBmem (C++ function)
amici::Solver::getAdjInitDone (C++ function)
amici::Solver::getAdjointDerivativeState (C++ function)
amici::Solver::getAdjointQuadrature (C++ function)
amici::Solver::getAdjointState (C++ function)
amici::Solver::getB (C++ function)
amici::Solver::getCpuTime (C++ function)
amici::Solver::getCpuTimeB (C++ function)
amici::Solver::getDerivativeState (C++ function)
amici::Solver::getDky (C++ function)
amici::Solver::getDkyB (C++ function)
amici::Solver::getInitDone (C++ function)
amici::Solver::getInitDoneB (C++ function)
amici::Solver::getInternalSensitivityMethod (C++ function)
amici::Solver::getInterpolationType (C++ function)
amici::Solver::getLastOrder (C++ function)
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[1]
amici::Solver::getLinearMultistepMethod (C++ function)
amici::Solver::getLinearSolver (C++ function)
amici::Solver::getMaxSteps (C++ function)
amici::Solver::getMaxStepsBackwardProblem (C++ function)
amici::Solver::getMaxTime (C++ function)
amici::Solver::getModel (C++ function)
amici::Solver::getNewtonDampingFactorLowerBound (C++ function)
amici::Solver::getNewtonDampingFactorMode (C++ function)
amici::Solver::getNewtonMaxSteps (C++ function)
amici::Solver::getNewtonStepSteadyStateCheck (C++ function)
amici::Solver::getNonlinearSolverIteration (C++ function)
amici::Solver::getNumErrTestFails (C++ function)
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[1]
amici::Solver::getNumErrTestFailsB (C++ function)
amici::Solver::getNumNonlinSolvConvFails (C++ function)
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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)
,
[1]
amici::Solver::getNumStepsB (C++ function)
amici::Solver::getQuad (C++ function)
amici::Solver::getQuadB (C++ function)
amici::Solver::getQuadDky (C++ function)
amici::Solver::getQuadDkyB (C++ function)
amici::Solver::getQuadInitDone (C++ function)
amici::Solver::getQuadInitDoneB (C++ function)
amici::Solver::getQuadrature (C++ function)
amici::Solver::getRelativeTolerance (C++ function)
amici::Solver::getRelativeToleranceB (C++ function)
amici::Solver::getRelativeToleranceFSA (C++ function)
amici::Solver::getRelativeToleranceQuadratures (C++ function)
amici::Solver::getRelativeToleranceSteadyState (C++ function)
amici::Solver::getRelativeToleranceSteadyStateSensi (C++ function)
amici::Solver::getReturnDataReportingMode (C++ function)
amici::Solver::getRootInfo (C++ function)
amici::Solver::getSens (C++ function)
amici::Solver::getSensDky (C++ function)
amici::Solver::getSensInitDone (C++ function)
amici::Solver::getSensiSteadyStateCheck (C++ function)
amici::Solver::getSensitivityMethod (C++ function)
amici::Solver::getSensitivityMethodPreequilibration (C++ function)
amici::Solver::getSensitivityOrder (C++ function)
amici::Solver::getStabilityLimitFlag (C++ function)
amici::Solver::getState (C++ function)
amici::Solver::getStateOrdering (C++ function)
amici::Solver::getStateSensitivity (C++ function)
amici::Solver::getSteadyStateSensiToleranceFactor (C++ function)
amici::Solver::getSteadyStateToleranceFactor (C++ function)
amici::Solver::gett (C++ function)
amici::Solver::init (C++ function)
amici::Solver::initializeLinearSolver (C++ function)
amici::Solver::initializeLinearSolverB (C++ function)
amici::Solver::initializeNonLinearSolver (C++ function)
amici::Solver::initializeNonLinearSolverB (C++ function)
amici::Solver::initializeNonLinearSolverSens (C++ function)
amici::Solver::initSteadystate (C++ function)
amici::Solver::interp_type_ (C++ member)
amici::Solver::ism_ (C++ member)
amici::Solver::iter_ (C++ member)
amici::Solver::linear_solver_ (C++ member)
amici::Solver::linear_solver_B_ (C++ member)
amici::Solver::lmm_ (C++ member)
amici::Solver::logger (C++ member)
amici::Solver::maxsteps_ (C++ member)
amici::Solver::maxtime_ (C++ member)
amici::Solver::non_linear_solver_ (C++ member)
amici::Solver::non_linear_solver_B_ (C++ member)
amici::Solver::non_linear_solver_sens_ (C++ member)
amici::Solver::nplist (C++ function)
amici::Solver::nquad (C++ function)
amici::Solver::nx (C++ function)
amici::Solver::operator== (C++ function)
amici::Solver::qbinit (C++ function)
amici::Solver::quadInit (C++ function)
amici::Solver::quadReInitB (C++ function)
amici::Solver::quadSStolerances (C++ function)
amici::Solver::quadSStolerancesB (C++ function)
amici::Solver::reInit (C++ function)
amici::Solver::reInitB (C++ function)
amici::Solver::reInitPostProcessB (C++ function)
amici::Solver::reInitPostProcessF (C++ function)
amici::Solver::resetDiagnosis (C++ function)
amici::Solver::resetMutableMemory (C++ function)
amici::Solver::rootInit (C++ function)
amici::Solver::run (C++ function)
amici::Solver::runB (C++ function)
amici::Solver::sdx_ (C++ member)
amici::Solver::sens_initialized_ (C++ member)
amici::Solver::sensInit1 (C++ function)
amici::Solver::sensReInit (C++ function)
amici::Solver::sensToggleOff (C++ function)
amici::Solver::setAbsoluteTolerance (C++ function)
amici::Solver::setAbsoluteToleranceB (C++ function)
amici::Solver::setAbsoluteToleranceFSA (C++ function)
amici::Solver::setAbsoluteToleranceQuadratures (C++ function)
amici::Solver::setAbsoluteToleranceSteadyState (C++ function)
amici::Solver::setAbsoluteToleranceSteadyStateSensi (C++ function)
amici::Solver::setAdjInitDone (C++ function)
amici::Solver::setBandJacFn (C++ function)
amici::Solver::setBandJacFnB (C++ function)
amici::Solver::setDenseJacFn (C++ function)
amici::Solver::setDenseJacFnB (C++ function)
amici::Solver::setErrHandlerFn (C++ function)
amici::Solver::setId (C++ function)
amici::Solver::setInitDone (C++ function)
amici::Solver::setInitDoneB (C++ function)
amici::Solver::setInternalSensitivityMethod (C++ function)
amici::Solver::setInterpolationType (C++ function)
amici::Solver::setJacTimesVecFn (C++ function)
amici::Solver::setJacTimesVecFnB (C++ function)
amici::Solver::setLinearMultistepMethod (C++ function)
amici::Solver::setLinearSolver (C++ function)
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[1]
amici::Solver::setLinearSolverB (C++ function)
amici::Solver::setMaxNumSteps (C++ function)
amici::Solver::setMaxNumStepsB (C++ function)
amici::Solver::setMaxSteps (C++ function)
amici::Solver::setMaxStepsBackwardProblem (C++ function)
amici::Solver::setMaxTime (C++ function)
amici::Solver::setNewtonDampingFactorLowerBound (C++ function)
amici::Solver::setNewtonDampingFactorMode (C++ function)
amici::Solver::setNewtonMaxSteps (C++ function)
amici::Solver::setNewtonStepSteadyStateCheck (C++ function)
amici::Solver::setNonLinearSolver (C++ function)
amici::Solver::setNonLinearSolverB (C++ function)
amici::Solver::setNonlinearSolverIteration (C++ function)
amici::Solver::setNonLinearSolverSens (C++ function)
amici::Solver::setQuadErrCon (C++ function)
amici::Solver::setQuadErrConB (C++ function)
amici::Solver::setQuadInitDone (C++ function)
amici::Solver::setQuadInitDoneB (C++ function)
amici::Solver::setRelativeTolerance (C++ function)
amici::Solver::setRelativeToleranceB (C++ function)
amici::Solver::setRelativeToleranceFSA (C++ function)
amici::Solver::setRelativeToleranceQuadratures (C++ function)
amici::Solver::setRelativeToleranceSteadyState (C++ function)
amici::Solver::setRelativeToleranceSteadyStateSensi (C++ function)
amici::Solver::setReturnDataReportingMode (C++ function)
amici::Solver::setSensErrCon (C++ function)
amici::Solver::setSensInitDone (C++ function)
amici::Solver::setSensInitOff (C++ function)
amici::Solver::setSensiSteadyStateCheck (C++ function)
amici::Solver::setSensitivityMethod (C++ function)
amici::Solver::setSensitivityMethodPreequilibration (C++ function)
amici::Solver::setSensitivityOrder (C++ function)
amici::Solver::setSensParams (C++ function)
amici::Solver::setSensSStolerances (C++ function)
amici::Solver::setSparseJacFn (C++ function)
amici::Solver::setSparseJacFn_ss (C++ function)
amici::Solver::setSparseJacFnB (C++ function)
amici::Solver::setSStolerances (C++ function)
amici::Solver::setSStolerancesB (C++ function)
amici::Solver::setStabilityLimitFlag (C++ function)
amici::Solver::setStabLimDet (C++ function)
amici::Solver::setStabLimDetB (C++ function)
amici::Solver::setStateOrdering (C++ function)
amici::Solver::setSteadyStateSensiToleranceFactor (C++ function)
amici::Solver::setSteadyStateToleranceFactor (C++ function)
amici::Solver::setStopTime (C++ function)
amici::Solver::setSuppressAlg (C++ function)
amici::Solver::setup (C++ function)
amici::Solver::setupB (C++ function)
amici::Solver::setupSteadystate (C++ function)
amici::Solver::setUserData (C++ function)
amici::Solver::setUserDataB (C++ function)
amici::Solver::solve (C++ function)
amici::Solver::solveB (C++ function)
amici::Solver::solveF (C++ function)
amici::Solver::Solver (C++ function)
,
[1]
amici::Solver::solver_memory_ (C++ member)
amici::Solver::solver_memory_B_ (C++ member)
amici::Solver::solver_was_called_B_ (C++ member)
amici::Solver::solver_was_called_F_ (C++ member)
amici::Solver::starttime_ (C++ member)
amici::Solver::startTimer (C++ function)
amici::Solver::step (C++ function)
amici::Solver::storeDiagnosis (C++ function)
amici::Solver::storeDiagnosisB (C++ function)
amici::Solver::switchForwardSensisOff (C++ function)
amici::Solver::sx_ (C++ member)
amici::Solver::t_ (C++ member)
amici::Solver::timeExceeded (C++ function)
amici::Solver::turnOffRootFinding (C++ function)
amici::Solver::updateAndReinitStatesAndSensitivities (C++ function)
amici::Solver::user_data (C++ member)
amici::Solver::user_data_type (C++ type)
amici::Solver::writeSolution (C++ function)
amici::Solver::writeSolutionB (C++ function)
amici::Solver::x_ (C++ member)
amici::Solver::xB_ (C++ member)
amici::Solver::xQ_ (C++ member)
amici::Solver::xQB_ (C++ member)
amici::Solver::~Solver (C++ function)
amici::SteadyStateContext (C++ enum)
amici::SteadyStateContext::newtonSensi (C++ enumerator)
amici::SteadyStateContext::sensiStorage (C++ enumerator)
amici::SteadyStateContext::solverCreation (C++ enumerator)
amici::SteadystateProblem (C++ class)
amici::SteadystateProblem::checkSteadyStateSuccess (C++ function)
amici::SteadystateProblem::getAdjointQuadrature (C++ function)
amici::SteadystateProblem::getAdjointState (C++ function)
amici::SteadystateProblem::getAdjointUpdates (C++ function)
amici::SteadystateProblem::getCPUTime (C++ function)
amici::SteadystateProblem::getCPUTimeB (C++ function)
amici::SteadystateProblem::getDJydx (C++ function)
amici::SteadystateProblem::getEquilibrationQuadratures (C++ function)
amici::SteadystateProblem::getFinalSimulationState (C++ function)
amici::SteadystateProblem::getNumSteps (C++ function)
amici::SteadystateProblem::getNumStepsB (C++ function)
amici::SteadystateProblem::getResidualNorm (C++ function)
amici::SteadystateProblem::getState (C++ function)
amici::SteadystateProblem::getStateSensitivity (C++ function)
amici::SteadystateProblem::getSteadyStateStatus (C++ function)
amici::SteadystateProblem::getSteadyStateTime (C++ function)
amici::SteadystateProblem::hasQuadrature (C++ function)
amici::SteadystateProblem::SteadystateProblem (C++ function)
amici::SteadystateProblem::workSteadyStateBackwardProblem (C++ function)
amici::SteadystateProblem::workSteadyStateProblem (C++ function)
amici::SteadyStateSensitivityMode (C++ enum)
amici::SteadyStateSensitivityMode::integrateIfNewtonFails (C++ enumerator)
amici::SteadyStateSensitivityMode::integrationOnly (C++ enumerator)
amici::SteadyStateSensitivityMode::newtonOnly (C++ enumerator)
amici::SteadyStateStatus (C++ enum)
amici::SteadyStateStatus::failed (C++ enumerator)
amici::SteadyStateStatus::failed_convergence (C++ enumerator)
amici::SteadyStateStatus::failed_damping (C++ enumerator)
amici::SteadyStateStatus::failed_factorization (C++ enumerator)
amici::SteadyStateStatus::failed_too_long_simulation (C++ enumerator)
amici::SteadyStateStatus::not_run (C++ enumerator)
amici::SteadyStateStatus::success (C++ enumerator)
amici::SUNLinSolBand (C++ class)
amici::SUNLinSolBand::getMatrix (C++ function)
amici::SUNLinSolBand::SUNLinSolBand (C++ function)
,
[1]
amici::SUNLinSolDense (C++ class)
amici::SUNLinSolDense::getMatrix (C++ function)
amici::SUNLinSolDense::SUNLinSolDense (C++ function)
amici::SUNLinSolKLU (C++ class)
amici::SUNLinSolKLU::getMatrix (C++ function)
amici::SUNLinSolKLU::reInit (C++ function)
amici::SUNLinSolKLU::setOrdering (C++ function)
amici::SUNLinSolKLU::StateOrdering (C++ enum)
amici::SUNLinSolKLU::StateOrdering::AMD (C++ enumerator)
amici::SUNLinSolKLU::StateOrdering::COLAMD (C++ enumerator)
amici::SUNLinSolKLU::StateOrdering::natural (C++ enumerator)
amici::SUNLinSolKLU::SUNLinSolKLU (C++ function)
,
[1]
amici::SUNLinSolPCG (C++ class)
amici::SUNLinSolPCG::getNumIters (C++ function)
amici::SUNLinSolPCG::getResid (C++ function)
amici::SUNLinSolPCG::getResNorm (C++ function)
amici::SUNLinSolPCG::setATimes (C++ function)
amici::SUNLinSolPCG::setPreconditioner (C++ function)
amici::SUNLinSolPCG::setScalingVectors (C++ function)
amici::SUNLinSolPCG::SUNLinSolPCG (C++ function)
amici::SUNLinSolSPBCGS (C++ class)
amici::SUNLinSolSPBCGS::getNumIters (C++ function)
amici::SUNLinSolSPBCGS::getResid (C++ function)
amici::SUNLinSolSPBCGS::getResNorm (C++ function)
amici::SUNLinSolSPBCGS::setATimes (C++ function)
amici::SUNLinSolSPBCGS::setPreconditioner (C++ function)
amici::SUNLinSolSPBCGS::setScalingVectors (C++ function)
amici::SUNLinSolSPBCGS::SUNLinSolSPBCGS (C++ function)
,
[1]
amici::SUNLinSolSPFGMR (C++ class)
amici::SUNLinSolSPFGMR::getNumIters (C++ function)
amici::SUNLinSolSPFGMR::getResid (C++ function)
amici::SUNLinSolSPFGMR::getResNorm (C++ function)
amici::SUNLinSolSPFGMR::setATimes (C++ function)
amici::SUNLinSolSPFGMR::setPreconditioner (C++ function)
amici::SUNLinSolSPFGMR::setScalingVectors (C++ function)
amici::SUNLinSolSPFGMR::SUNLinSolSPFGMR (C++ function)
amici::SUNLinSolSPGMR (C++ class)
amici::SUNLinSolSPGMR::getNumIters (C++ function)
amici::SUNLinSolSPGMR::getResid (C++ function)
amici::SUNLinSolSPGMR::getResNorm (C++ function)
amici::SUNLinSolSPGMR::setATimes (C++ function)
amici::SUNLinSolSPGMR::setPreconditioner (C++ function)
amici::SUNLinSolSPGMR::setScalingVectors (C++ function)
amici::SUNLinSolSPGMR::SUNLinSolSPGMR (C++ function)
amici::SUNLinSolSPTFQMR (C++ class)
amici::SUNLinSolSPTFQMR::getNumIters (C++ function)
amici::SUNLinSolSPTFQMR::getResid (C++ function)
amici::SUNLinSolSPTFQMR::getResNorm (C++ function)
amici::SUNLinSolSPTFQMR::setATimes (C++ function)
amici::SUNLinSolSPTFQMR::setPreconditioner (C++ function)
amici::SUNLinSolSPTFQMR::setScalingVectors (C++ function)
amici::SUNLinSolSPTFQMR::SUNLinSolSPTFQMR (C++ function)
,
[1]
amici::SUNLinSolWrapper (C++ class)
amici::SUNLinSolWrapper::get (C++ function)
amici::SUNLinSolWrapper::getLastFlag (C++ function)
amici::SUNLinSolWrapper::getMatrix (C++ function)
amici::SUNLinSolWrapper::getType (C++ function)
amici::SUNLinSolWrapper::initialize (C++ function)
amici::SUNLinSolWrapper::operator= (C++ function)
,
[1]
amici::SUNLinSolWrapper::setup (C++ function)
,
[1]
amici::SUNLinSolWrapper::Solve (C++ function)
amici::SUNLinSolWrapper::solver_ (C++ member)
amici::SUNLinSolWrapper::space (C++ function)
amici::SUNLinSolWrapper::SUNLinSolWrapper (C++ function)
,
[1]
,
[2]
,
[3]
amici::SUNLinSolWrapper::~SUNLinSolWrapper (C++ function)
amici::SUNMatrixWrapper (C++ class)
amici::SUNMatrixWrapper::capacity (C++ function)
amici::SUNMatrixWrapper::columns (C++ function)
amici::SUNMatrixWrapper::data (C++ function)
,
[1]
amici::SUNMatrixWrapper::get (C++ function)
amici::SUNMatrixWrapper::get_data (C++ function)
,
[1]
amici::SUNMatrixWrapper::get_indexptr (C++ function)
amici::SUNMatrixWrapper::get_indexval (C++ function)
amici::SUNMatrixWrapper::matrix_id (C++ function)
amici::SUNMatrixWrapper::multiply (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
amici::SUNMatrixWrapper::num_indexptrs (C++ function)
amici::SUNMatrixWrapper::num_nonzeros (C++ function)
amici::SUNMatrixWrapper::operator= (C++ function)
,
[1]
amici::SUNMatrixWrapper::realloc (C++ function)
amici::SUNMatrixWrapper::reallocate (C++ function)
amici::SUNMatrixWrapper::refresh (C++ function)
amici::SUNMatrixWrapper::rows (C++ function)
amici::SUNMatrixWrapper::scale (C++ function)
amici::SUNMatrixWrapper::scatter (C++ function)
amici::SUNMatrixWrapper::set_data (C++ function)
,
[1]
amici::SUNMatrixWrapper::set_indexptr (C++ function)
amici::SUNMatrixWrapper::set_indexptrs (C++ function)
amici::SUNMatrixWrapper::set_indexval (C++ function)
amici::SUNMatrixWrapper::set_indexvals (C++ function)
amici::SUNMatrixWrapper::sparse_add (C++ function)
amici::SUNMatrixWrapper::sparse_multiply (C++ function)
amici::SUNMatrixWrapper::sparse_sum (C++ function)
amici::SUNMatrixWrapper::sparsetype (C++ function)
amici::SUNMatrixWrapper::SUNMatrixWrapper (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
amici::SUNMatrixWrapper::to_dense (C++ function)
amici::SUNMatrixWrapper::to_diag (C++ function)
amici::SUNMatrixWrapper::transpose (C++ function)
amici::SUNMatrixWrapper::zero (C++ function)
amici::SUNMatrixWrapper::~SUNMatrixWrapper (C++ function)
amici::SUNNonLinSolFixedPoint (C++ class)
amici::SUNNonLinSolFixedPoint::getSysFn (C++ function)
amici::SUNNonLinSolFixedPoint::SUNNonLinSolFixedPoint (C++ function)
,
[1]
amici::SUNNonLinSolNewton (C++ class)
amici::SUNNonLinSolNewton::getSysFn (C++ function)
amici::SUNNonLinSolNewton::SUNNonLinSolNewton (C++ function)
,
[1]
amici::SUNNonLinSolWrapper (C++ class)
amici::SUNNonLinSolWrapper::get (C++ function)
amici::SUNNonLinSolWrapper::getCurIter (C++ function)
amici::SUNNonLinSolWrapper::getNumConvFails (C++ function)
amici::SUNNonLinSolWrapper::getNumIters (C++ function)
amici::SUNNonLinSolWrapper::getType (C++ function)
amici::SUNNonLinSolWrapper::initialize (C++ function)
amici::SUNNonLinSolWrapper::operator= (C++ function)
,
[1]
amici::SUNNonLinSolWrapper::setConvTestFn (C++ function)
amici::SUNNonLinSolWrapper::setLSetupFn (C++ function)
amici::SUNNonLinSolWrapper::setLSolveFn (C++ function)
amici::SUNNonLinSolWrapper::setMaxIters (C++ function)
amici::SUNNonLinSolWrapper::setSysFn (C++ function)
amici::SUNNonLinSolWrapper::setup (C++ function)
amici::SUNNonLinSolWrapper::Solve (C++ function)
amici::SUNNonLinSolWrapper::solver (C++ member)
amici::SUNNonLinSolWrapper::SUNNonLinSolWrapper (C++ function)
,
[1]
,
[2]
amici::SUNNonLinSolWrapper::~SUNNonLinSolWrapper (C++ function)
amici::unravel_index (C++ function)
,
[1]
amici::unscaleParameters (C++ function)
amici::wrapErrHandlerFn (C++ function)
amici::writeSlice (C++ function)
,
[1]
,
[2]
,
[3]
AMICI_H5_RESTORE_ERROR_HANDLER (C macro)
AMICI_H5_SAVE_ERROR_HANDLER (C macro)
amici_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.ode_export)
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]
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.ode_export.ODEModel method)
compile_model() (amici.ode_export.ODEExporter method)
compiledWithOpenMP() (in module amici.amici)
compute_moiety_conservation_laws() (in module amici.conserved_quantities_demartino)
computingASA() (amici.amici.Solver method)
computingFSA() (amici.amici.Solver method)
conservation_law_has_multispecies() (amici.ode_export.ODEModel method)
ConservationLaw (class in amici.ode_model)
Constant (class in amici.ode_model)
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)
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_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
delimiter (amici.ode_export.TemplateAmici attribute)
dense (amici.amici.LinearSolver attribute)
diag (amici.amici.LinearSolver attribute)
directional (amici.amici.SecondOrderMode attribute)
DoubleVector (class in amici.amici)
dx (amici.amici.SimulationState property)
E
element_is_state() (in module amici.petab_import)
enum() (in module amici.amici)
eq() (amici.ode_export.ODEModel method)
Event (class in amici.ode_model)
EventObservable (class in amici.ode_model)
ExpData (class in amici.amici)
ExpDataPtr (class in amici.amici)
ExpDataPtrVector (class in amici.amici)
ExpDataView (class in amici.numpy)
Expression (class in amici.ode_model)
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.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedParametersPreequilibration (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedParametersPresimulation (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedpoint (amici.amici.NonlinearSolverIteration attribute)
forward (amici.amici.SensitivityMethod attribute)
free_symbols (amici.parameter_mapping.ParameterMapping property)
(amici.parameter_mapping.ParameterMappingForCondition property)
free_symbols() (amici.ode_export.ODEModel 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.ode_export.ODEModel method)
generate_flux_symbol() (in module amici.import_utils)
generate_measurement_symbol() (in module amici.import_utils)
generate_model_code() (amici.ode_export.ODEExporter method)
generate_regularization_symbol() (in module amici.import_utils)
get_appearance_counts() (amici.ode_export.ODEModel method)
get_conservation_laws() (amici.ode_export.ODEModel method)
get_dt() (amici.ode_model.State method)
get_dx_rdata_dx_solver() (amici.ode_model.State method)
get_event() (amici.ode_model.EventObservable method)
get_expressions_as_dataframe() (in module amici.pandas)
get_fixed_parameters() (in module amici.petab_import)
get_free_symbols() (amici.ode_model.State method)
get_function_extern_declaration() (in module amici.ode_export)
get_id() (amici.ode_model.ModelQuantity method)
get_initial_value() (amici.ode_model.Event method)
get_logger() (in module amici.logging)
get_measurement_symbol() (amici.ode_model.Observable method)
get_model() (amici.ModelModule method)
get_model_override_implementation() (in module amici.ode_export)
get_name() (amici.ode_model.ModelQuantity method)
get_ncoeff() (amici.ode_model.ConservationLaw method)
get_observable_transformations() (amici.ode_export.ODEModel method)
get_observation_model() (in module amici.petab_import)
get_regularization_symbol() (amici.ode_model.Observable method)
get_solver_indices() (amici.ode_export.ODEModel method)
get_species_initial() (in module amici.sbml_import)
get_sunindex_extern_declaration() (in module amici.ode_export)
get_sunindex_override_implementation() (in module amici.ode_export)
get_val() (amici.ode_model.ModelQuantity method)
get_x_rdata() (amici.ode_model.ConservationLaw method)
(amici.ode_model.State method)
getAbsoluteTolerance() (amici.amici.Solver method)
getAbsoluteToleranceB() (amici.amici.Solver method)
getAbsoluteToleranceFSA() (amici.amici.Solver method)
getAbsoluteToleranceQuadratures() (amici.amici.Solver method)
getAbsoluteToleranceSteadyState() (amici.amici.Solver method)
getAbsoluteToleranceSteadyStateSensi() (amici.amici.Solver method)
getAddSigmaResiduals() (amici.amici.Model method)
getAlwaysCheckFinite() (amici.amici.Model method)
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)
getStabilityLimitFlag() (amici.amici.Solver method)
getStateIds() (amici.amici.Model method)
getStateIdsSolver() (amici.amici.Model method)
getStateIsNonNegative() (amici.amici.Model method)
getStateNames() (amici.amici.Model method)
getStateNamesSolver() (amici.amici.Model method)
getStateOrdering() (amici.amici.Solver method)
getSteadyStateSensitivityMode() (amici.amici.Model method)
getSteadyStateSensiToleranceFactor() (amici.amici.Solver method)
getSteadyStateToleranceFactor() (amici.amici.Solver method)
gett() (amici.amici.Solver method)
getTimepoint() (amici.amici.ExpData method)
(amici.amici.Model method)
getTimepoints() (amici.amici.ExpData method)
(amici.amici.Model method)
getUnscaledParameter() (in module amici.amici)
getUnscaledParameters() (amici.amici.Model method)
grouper() (in module amici.import_utils)
gsl::make_span (C++ function)
,
[1]
H
has_conservation_law() (amici.ode_model.State method)
has_fixed_parameter_ic() (in module amici.pysb_import)
hasCustomInitialStates() (amici.amici.Model method)
hasCustomInitialStateSensitivities() (amici.amici.Model method)
hasExpressionIds() (amici.amici.Model method)
hasExpressionNames() (amici.amici.Model method)
hasFixedParameterIds() (amici.amici.Model method)
hasFixedParameterNames() (amici.amici.Model method)
hasObservableIds() (amici.amici.Model method)
hasObservableNames() (amici.amici.Model method)
hasParameterIds() (amici.amici.Model method)
hasParameterNames() (amici.amici.Model method)
hasQuadraticLLH() (amici.amici.Model method)
hasStateIds() (amici.amici.Model method)
hasStateNames() (amici.amici.Model method)
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)
import_from_sbml_importer() (amici.ode_export.ODEModel method)
import_model() (in module amici.petab_import)
import_model_module() (in module amici)
import_model_pysb() (in module amici.petab_import_pysb)
import_model_sbml() (in module amici.petab_import)
import_petab_problem() (in module amici.petab_import)
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_rate_rule_target() (amici.sbml_import.SbmlImporter method)
is_valid_identifier() (in module amici.ode_export)
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)
J
J (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
K
k() (amici.amici.Model method)
KLU (amici.amici.LinearSolver attribute)
L
LAPACKBand (amici.amici.LinearSolver attribute)
LAPACKDense (amici.amici.LinearSolver attribute)
lbw (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr 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)
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.ode_model)
LogLikelihoodY (class in amici.ode_model)
LogLikelihoodZ (class in amici.ode_model)
M
M_1_PI (C macro)
M_2_PI (C macro)
M_2_SQRTPI (C macro)
M_E (C macro)
M_LN10 (C macro)
M_LN2 (C macro)
M_LOG10E (C macro)
M_LOG2E (C macro)
M_PI (C macro)
M_PI_2 (C macro)
M_PI_4 (C macro)
M_SQRT1_2 (C macro)
M_SQRT2 (C macro)
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.ode_model)
module
amici
amici.amici
amici.bngl_import
amici.conserved_quantities_demartino
amici.conserved_quantities_rref
amici.gradient_check
amici.import_utils
amici.logging
amici.numpy
amici.ode_export
amici.ode_model
amici.pandas
amici.parameter_mapping
amici.petab_import
amici.petab_import_pysb
amici.petab_objective
amici.petab_simulate
amici.plotting
amici.pysb_import
amici.sbml_import
N
name() (amici.ode_export.ODEModel method)
ncl() (amici.amici.Model method)
ndJydy (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndtotal_cldx_rdata (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndwdp (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndwdw (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndwdx (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndxdotdw (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndxrdatadtcl (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ndxrdatadxsolver (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ne (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr 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.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nk (amici.amici.ModelDimensions 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.ModelDimensions property)
(amici.amici.ModelPtr 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.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.ode_export.ODEModel method)
num_const() (amici.ode_export.ODEModel method)
num_eventobs() (amici.ode_export.ODEModel method)
num_events() (amici.ode_export.ODEModel method)
num_expr() (amici.ode_export.ODEModel method)
num_obs() (amici.ode_export.ODEModel method)
num_par() (amici.ode_export.ODEModel method)
num_state_reinits() (amici.ode_export.ODEModel method)
num_states_rdata() (amici.ode_export.ODEModel method)
num_states_solver() (amici.ode_export.ODEModel method)
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.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nx (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx() (amici.amici.Solver method)
nx_rdata (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nx_reinit() (amici.amici.Model method)
nx_solver (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nx_solver_reinit (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nxtrue (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue_rdata (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nxtrue_solver (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
ny (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nytrue (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nytrue() (amici.amici.ExpData method)
nz (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
nztrue (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr 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.ode_model)
ObservableScaling (class in amici.amici)
ObservableTransformation (class in amici.import_utils)
ODE
ode_model_from_pysb_importer() (in module amici.pysb_import)
ODEExporter (class in amici.ode_export)
ODEModel (class in amici.ode_export)
off (amici.amici.NewtonDampingFactorMode attribute)
on (amici.amici.NewtonDampingFactorMode attribute)
order (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
P
Parameter (class in amici.ode_model)
ParameterMapping (class in amici.parameter_mapping)
ParameterMappingForCondition (class in amici.parameter_mapping)
parameters (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
ParameterScaling (class in amici.amici)
parameterScalingFromIntVector() (in module amici.amici)
ParameterScalingVector (class in amici.amici)
parse_events() (amici.ode_export.ODEModel method)
pattern (amici.ode_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.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.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.ExpDataPtr property)
(amici.amici.SimulationParameters property)
reinitialization_state_idxs_sim (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
reinitializeAllFixedParameterDependentInitialStates() (amici.amici.SimulationParameters method)
reinitializeAllFixedParameterDependentInitialStatesForPresimulation() (amici.amici.SimulationParameters method)
reinitializeAllFixedParameterDependentInitialStatesForSimulation() (amici.amici.SimulationParameters method)
reinitializeFixedParameterInitialStates (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
remove_argument_types() (in module amici.ode_export)
replace_logx() (in module amici.sbml_import)
requireSensitivitiesForAllParameters() (amici.amici.Model method)
res (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
residuals (amici.amici.RDataReporting attribute)
ReturnData (class in amici.amici)
ReturnDataPtr (class in amici.amici)
ReturnDataView (class in amici.numpy)
rowvals() (amici.ode_export.ODEModel 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)
SBML
sbml2amici() (amici.sbml_import.SbmlImporter method)
SBMLException
SbmlImporter (class in amici.sbml_import)
scale_parameter() (in module amici.parameter_mapping)
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.ode_model.State method)
set_dt() (amici.ode_model.State method)
set_log_level() (in module amici.logging)
set_name() (amici.ode_export.ODEExporter method)
set_paths() (amici.ode_export.ODEExporter method)
set_val() (amici.ode_model.ModelQuantity 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)
sigmay (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SigmaY (class in amici.ode_model)
sigmaz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SigmaZ (class in amici.ode_model)
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.ode_export)
smart_jacobian() (in module amici.ode_export)
smart_multiply() (in module amici.ode_export)
smart_subs() (in module amici.import_utils)
smart_subs_dict() (in module amici.import_utils)
Solver (class in amici.amici)
SolverPtr (class in amici.amici)
sparseeq() (amici.ode_export.ODEModel method)
sparsesym() (amici.ode_export.ODEModel method)
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.ode_model)
state_has_conservation_law() (amici.ode_export.ODEModel method)
state_has_fixed_parameter_initial_condition() (amici.ode_export.ODEModel method)
state_is_constant() (amici.ode_export.ODEModel method)
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)
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.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.ode_export.ODEModel method)
sym_names() (amici.ode_export.ODEModel method)
sym_or_eq() (amici.ode_export.ODEModel method)
symbol_with_assumptions() (in module amici.import_utils)
sz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
T
t (amici.amici.SimulationState property)
t0() (amici.amici.Model method)
t_presim (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
TemplateAmici (class in amici.ode_export)
timeExceeded() (amici.amici.Solver method)
toposort_symbols() (in module amici.import_utils)
ts (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ts_ (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
tstart_ (amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
U
ubw (amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnDataPtr property)
unscale_parameter() (in module amici.parameter_mapping)
unscale_parameters_dict() (in module amici.parameter_mapping)
unscaleParameters() (in module amici.amici)
V
val() (amici.ode_export.ODEModel method)
var_in_function_signature() (in module amici.ode_export)
W
w (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
X
x (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationState property)
x0 (amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationParameters 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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