AMICI
About
About AMICI
Availability
License conditions
How to cite AMICI
References
Background
Changelog
Versioning policy
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
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
|
L
|
M
|
N
|
O
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P
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R
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S
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T
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U
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V
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W
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X
|
Y
|
Z
_
__init__() (amici.add_path method)
(amici.amici.Constraint method)
(amici.amici.CpuTimer method)
(amici.amici.ExpData method)
(amici.amici.FixedParameterContext method)
(amici.amici.InternalSensitivityMethod method)
(amici.amici.InterpolationType method)
(amici.amici.LinearMultistepMethod method)
(amici.amici.LinearSolver method)
(amici.amici.LogItem method)
(amici.amici.Model method)
(amici.amici.ModelDimensions method)
(amici.amici.NewtonDampingFactorMode method)
(amici.amici.NonlinearSolverIteration method)
(amici.amici.ObservableScaling method)
(amici.amici.ParameterScaling method)
(amici.amici.RDataReporting method)
(amici.amici.ReturnData method)
(amici.amici.SecondOrderMode method)
(amici.amici.SensitivityMethod method)
(amici.amici.SensitivityOrder method)
(amici.amici.SimulationParameters method)
(amici.amici.Solver method)
(amici.amici.SteadyStateComputationMode method)
(amici.amici.SteadyStateSensitivityMode method)
(amici.amici.SteadyStateStatus method)
(amici.de_export.DEExporter method)
(amici.de_model.DEModel method)
(amici.de_model_components.AlgebraicEquation method)
(amici.de_model_components.AlgebraicState method)
(amici.de_model_components.ConservationLaw method)
(amici.de_model_components.Constant method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.Event method)
(amici.de_model_components.EventObservable method)
(amici.de_model_components.Expression method)
(amici.de_model_components.LogLikelihoodRZ method)
(amici.de_model_components.LogLikelihoodY method)
(amici.de_model_components.LogLikelihoodZ method)
(amici.de_model_components.ModelQuantity method)
(amici.de_model_components.Observable method)
(amici.de_model_components.Parameter method)
(amici.de_model_components.SigmaY method)
(amici.de_model_components.SigmaZ method)
(amici.de_model_components.State method)
(amici.import_utils.CircularDependencyError method)
(amici.import_utils.ObservableTransformation method)
(amici.ModelModule method)
(amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
(amici.parameter_mapping.ParameterMapping method)
(amici.parameter_mapping.ParameterMappingForCondition method)
(amici.petab.parameter_mapping.ParameterMapping method)
(amici.petab.parameter_mapping.ParameterMappingForCondition method)
(amici.petab.simulator.PetabSimulator method)
(amici.petab_simulate.PetabSimulator method)
(amici.sbml_import.SbmlImporter method)
(amici.sbml_utils.MathMLSbmlPrinter method)
(amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
(amici.splines.UniformGrid method)
_USE_MATH_DEFINES (C macro)
A
AbstractSpline (class in amici.splines)
adams (amici.amici.LinearMultistepMethod attribute)
add_assignment_rule() (in module amici.sbml_utils)
add_compartment() (in module amici.sbml_utils)
add_component() (amici.de_model.DEModel method)
add_conservation_law() (amici.de_model.DEModel method)
add_d_dt() (amici.sbml_import.SbmlImporter method)
add_inflow() (in module amici.sbml_utils)
add_local_symbol() (amici.sbml_import.SbmlImporter method)
add_noise() (amici.petab.simulator.PetabSimulator method)
(amici.petab_simulate.PetabSimulator method)
add_parameter() (in module amici.sbml_utils)
add_path (class in amici)
add_rate_rule() (in module amici.sbml_utils)
add_species() (in module amici.sbml_utils)
add_spline() (amici.de_model.DEModel method)
add_to_sbml_model() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
adjoint (amici.amici.SensitivityMethod attribute)
aggregate_sllh() (in module amici.petab_objective)
algebraic_states() (amici.de_model.DEModel method)
AlgebraicEquation (class in amici.de_model_components)
AlgebraicState (class in amici.de_model_components)
amici
module
amici.amici
module
amici.bngl_import
module
amici.conserved_quantities_demartino
module
amici.conserved_quantities_rref
module
amici.de_export
module
amici.de_model
module
amici.de_model_components
module
amici.gradient_check
module
amici.import_utils
module
amici.logging
module
amici.numpy
module
amici.pandas
module
amici.parameter_mapping
module
amici.petab
module
amici.petab.conditions
module
amici.petab.import_helpers
module
amici.petab.parameter_mapping
module
amici.petab.petab_import
module
amici.petab.pysb_import
module
amici.petab.sbml_import
module
amici.petab.simulations
module
amici.petab.simulator
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.sbml_utils
module
amici.splines
module
amici::AbstractModel (C++ class)
amici::AbstractModel::fcreate_splines (C++ function)
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::fdspline_slopesdp (C++ function)
amici::AbstractModel::fdspline_valuesdp (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)
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)
,
[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::AbstractSpline (C++ class)
amici::AbstractSpline::AbstractSpline (C++ function)
,
[1]
amici::AbstractSpline::coefficients (C++ member)
amici::AbstractSpline::coefficients_extrapolate (C++ member)
amici::AbstractSpline::coefficients_extrapolate_sensi (C++ member)
amici::AbstractSpline::coefficients_sensi (C++ member)
amici::AbstractSpline::compute_coefficients (C++ function)
amici::AbstractSpline::compute_coefficients_sensi (C++ function)
amici::AbstractSpline::compute_final_sensitivity (C++ function)
amici::AbstractSpline::compute_final_value (C++ function)
amici::AbstractSpline::get_equidistant_spacing (C++ function)
amici::AbstractSpline::get_final_sensitivity (C++ function)
amici::AbstractSpline::get_final_sensitivity_scaled (C++ function)
amici::AbstractSpline::get_final_value (C++ function)
amici::AbstractSpline::get_final_value_scaled (C++ function)
amici::AbstractSpline::get_logarithmic_parametrization (C++ function)
amici::AbstractSpline::get_node_value (C++ function)
amici::AbstractSpline::get_node_value_scaled (C++ function)
amici::AbstractSpline::get_sensitivity (C++ function)
,
[1]
amici::AbstractSpline::get_sensitivity_scaled (C++ function)
amici::AbstractSpline::get_value (C++ function)
amici::AbstractSpline::get_value_scaled (C++ function)
amici::AbstractSpline::n_nodes (C++ function)
amici::AbstractSpline::node_values_ (C++ member)
amici::AbstractSpline::nodes_ (C++ member)
amici::AbstractSpline::set_final_sensitivity_scaled (C++ function)
amici::AbstractSpline::set_final_value_scaled (C++ function)
amici::AbstractSpline::~AbstractSpline (C++ function)
amici::addSlice (C++ function)
,
[1]
amici::AMICI_BAD_DKY (C++ member)
amici::AMICI_BAD_T (C++ member)
amici::AMICI_CONSTR_FAIL (C++ member)
amici::AMICI_CONV_FAILURE (C++ member)
amici::AMICI_CVODES_CONSTR_FAIL (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_QRHSFUNC_ERR (C++ member)
amici::AMICI_FIRST_RHSFUNC_ERR (C++ member)
amici::AMICI_FIRST_SRHSFUNC_ERR (C++ member)
amici::AMICI_IDAS_CONSTR_FAIL (C++ member)
amici::AMICI_ILL_INPUT (C++ member)
amici::AMICI_LSETUP_FAIL (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_PREEQUILIBRATE (C++ member)
amici::AMICI_RECOVERABLE_ERROR (C++ member)
amici::AMICI_REPTD_SRHSFUNC_ERR (C++ member)
amici::AMICI_RHSFUNC_FAIL (C++ member)
amici::AMICI_ROOT_RETURN (C++ member)
amici::AMICI_SINGULAR_JACOBIAN (C++ member)
amici::AMICI_SRHSFUNC_FAIL (C++ member)
amici::AMICI_SUCCESS (C++ member)
amici::AMICI_TOO_MUCH_ACC (C++ member)
amici::AMICI_TOO_MUCH_WORK (C++ member)
amici::AMICI_UNREC_SRHSFUNC_ERR (C++ member)
amici::AMICI_UNRECOVERABLE_ERROR (C++ member)
amici::AMICI_WARNING (C++ member)
amici::AmiException (C++ class)
amici::AmiException::AmiException (C++ function)
,
[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)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
amici::AmiVector::at (C++ function)
,
[1]
amici::AmiVector::begin (C++ function)
amici::AmiVector::boost::serialization::serialize (C++ function)
amici::AmiVector::copy (C++ function)
amici::AmiVector::data (C++ function)
,
[1]
amici::AmiVector::end (C++ function)
amici::AmiVector::get_ctx (C++ function)
amici::AmiVector::getLength (C++ function)
amici::AmiVector::getNVector (C++ function)
,
[1]
amici::AmiVector::getVector (C++ function)
amici::AmiVector::minus (C++ function)
amici::AmiVector::operator*= (C++ function)
amici::AmiVector::operator/= (C++ function)
amici::AmiVector::operator= (C++ function)
amici::AmiVector::operator[] (C++ function)
amici::AmiVector::set (C++ function)
amici::AmiVector::set_ctx (C++ function)
amici::AmiVector::zero (C++ function)
amici::AmiVector::~AmiVector (C++ function)
amici::AmiVectorArray (C++ class)
amici::AmiVectorArray::AmiVectorArray (C++ function)
,
[1]
,
[2]
amici::AmiVectorArray::at (C++ function)
,
[1]
amici::AmiVectorArray::copy (C++ function)
amici::AmiVectorArray::data (C++ function)
,
[1]
amici::AmiVectorArray::flatten_to_vector (C++ function)
amici::AmiVectorArray::getLength (C++ function)
amici::AmiVectorArray::getNVector (C++ function)
,
[1]
amici::AmiVectorArray::getNVectorArray (C++ function)
amici::AmiVectorArray::operator= (C++ function)
amici::AmiVectorArray::operator[] (C++ function)
,
[1]
amici::AmiVectorArray::set_ctx (C++ function)
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)
,
[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::Constraint (C++ enum)
amici::Constraint::negative (C++ enumerator)
amici::Constraint::non_negative (C++ enumerator)
amici::Constraint::non_positive (C++ enumerator)
amici::Constraint::none (C++ enumerator)
amici::Constraint::positive (C++ enumerator)
amici::ContextManager (C++ class)
amici::ContextManager::ContextManager (C++ function)
,
[1]
,
[2]
amici::CpuTimer (C++ class)
amici::CpuTimer::CpuTimer (C++ function)
amici::CpuTimer::elapsed_milliseconds (C++ function)
amici::CpuTimer::elapsed_seconds (C++ function)
amici::CpuTimer::reset (C++ function)
amici::CpuTimer::uses_thread_clock (C++ member)
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::apply_constraints (C++ function)
amici::CVodeSolver::apply_max_conv_fails (C++ function)
amici::CVodeSolver::apply_max_nonlin_iters (C++ function)
amici::CVodeSolver::apply_max_step_size (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::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)
,
[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::clear_observations (C++ function)
amici::ExpData::ExpData (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
,
[8]
amici::ExpData::getObservedData (C++ function)
amici::ExpData::getObservedDataPtr (C++ function)
amici::ExpData::getObservedDataStdDev (C++ function)
amici::ExpData::getObservedDataStdDevPtr (C++ function)
amici::ExpData::getObservedEvents (C++ function)
amici::ExpData::getObservedEventsPtr (C++ function)
amici::ExpData::getObservedEventsStdDev (C++ function)
amici::ExpData::getObservedEventsStdDevPtr (C++ function)
amici::ExpData::getTimepoint (C++ function)
amici::ExpData::getTimepoints (C++ function)
amici::ExpData::id (C++ member)
amici::ExpData::isSetObservedData (C++ function)
amici::ExpData::isSetObservedDataStdDev (C++ function)
amici::ExpData::isSetObservedEvents (C++ function)
amici::ExpData::isSetObservedEventsStdDev (C++ function)
amici::ExpData::nmaxevent (C++ function)
amici::ExpData::nmaxevent_ (C++ member)
amici::ExpData::nt (C++ function)
amici::ExpData::nytrue (C++ function)
amici::ExpData::nytrue_ (C++ member)
amici::ExpData::nztrue (C++ function)
amici::ExpData::nztrue_ (C++ member)
amici::ExpData::observed_data_ (C++ member)
amici::ExpData::observed_data_std_dev_ (C++ member)
amici::ExpData::observed_events_ (C++ member)
amici::ExpData::observed_events_std_dev_ (C++ member)
amici::ExpData::operator== (C++ function)
amici::ExpData::setObservedData (C++ function)
,
[1]
amici::ExpData::setObservedDataStdDev (C++ function)
,
[1]
,
[2]
,
[3]
amici::ExpData::setObservedEvents (C++ function)
,
[1]
amici::ExpData::setObservedEventsStdDev (C++ function)
,
[1]
,
[2]
,
[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)
,
[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)
,
[1]
amici::hdf5::readModelDataFromHDF5 (C++ function)
,
[1]
amici::hdf5::readSimulationExpData (C++ function)
amici::hdf5::readSolverSettingsFromHDF5 (C++ function)
,
[1]
amici::hdf5::writeReturnData (C++ function)
,
[1]
amici::hdf5::writeReturnDataDiagnosis (C++ function)
amici::hdf5::writeSimulationExpData (C++ function)
amici::hdf5::writeSolverSettingsToHDF5 (C++ function)
,
[1]
amici::HermiteSpline (C++ class)
amici::HermiteSpline::compute_coefficients (C++ function)
amici::HermiteSpline::compute_coefficients_sensi (C++ function)
amici::HermiteSpline::compute_final_sensitivity (C++ function)
amici::HermiteSpline::compute_final_value (C++ function)
amici::HermiteSpline::get_node_derivative (C++ function)
amici::HermiteSpline::get_node_derivative_by_fd (C++ function)
amici::HermiteSpline::get_node_derivative_scaled (C++ function)
amici::HermiteSpline::get_sensitivity_scaled (C++ function)
amici::HermiteSpline::get_value_scaled (C++ function)
amici::HermiteSpline::HermiteSpline (C++ function)
,
[1]
amici::IDAException (C++ class)
amici::IDAException::IDAException (C++ function)
amici::IDASolver (C++ class)
amici::IDASolver::adjInit (C++ function)
amici::IDASolver::allocateSolver (C++ function)
amici::IDASolver::allocateSolverB (C++ function)
amici::IDASolver::apply_constraints (C++ function)
amici::IDASolver::apply_max_conv_fails (C++ function)
amici::IDASolver::apply_max_nonlin_iters (C++ function)
amici::IDASolver::apply_max_step_size (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::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]
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::fspl (C++ function)
amici::Model::fsrz (C++ function)
amici::Model::fsspl (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::get_steadystate_mask (C++ function)
amici::Model::get_trigger_timepoints (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::getSteadyStateComputationMode (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::initializeSplines (C++ function)
amici::Model::initializeSplineSensitivities (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::reinitialize (C++ function)
amici::Model::requireSensitivitiesForAllParameters (C++ function)
amici::Model::root_initial_values_ (C++ member)
amici::Model::set_steadystate_mask (C++ function)
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::setSteadyStateComputationMode (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::splines_ (C++ member)
amici::Model::state_ (C++ member)
amici::Model::state_independent_events_ (C++ member)
amici::Model::state_is_non_negative_ (C++ member)
amici::Model::steadystate_computation_mode_ (C++ member)
amici::Model::steadystate_sensitivity_mode_ (C++ member)
amici::Model::sx0data_ (C++ member)
amici::Model::t0 (C++ function)
amici::Model::updateHeaviside (C++ function)
amici::Model::updateHeavisideB (C++ function)
amici::Model::writeLLHSensitivitySlice (C++ function)
amici::Model::writeSensitivitySliceEvent (C++ function)
amici::Model::writeSliceEvent (C++ function)
amici::Model::x0data_ (C++ member)
amici::Model::z2event_ (C++ member)
amici::Model::~Model (C++ function)
amici::Model_DAE (C++ class)
amici::Model_DAE::fdxdotdp (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fdxdotdp_explicit (C++ function)
amici::Model_DAE::fdxdotdp_explicit_colptrs (C++ function)
amici::Model_DAE::fdxdotdp_explicit_rowvals (C++ function)
amici::Model_DAE::fdxdotdw (C++ function)
,
[1]
amici::Model_DAE::fdxdotdw_colptrs (C++ function)
amici::Model_DAE::fdxdotdw_rowvals (C++ function)
amici::Model_DAE::fdxdotdx_explicit (C++ function)
amici::Model_DAE::fdxdotdx_explicit_colptrs (C++ function)
amici::Model_DAE::fdxdotdx_explicit_rowvals (C++ function)
amici::Model_DAE::fJ (C++ function)
,
[1]
amici::Model_DAE::fJB (C++ function)
,
[1]
amici::Model_DAE::fJDiag (C++ function)
amici::Model_DAE::fJSparse (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fJSparseB (C++ function)
,
[1]
amici::Model_DAE::fJSparseB_ss (C++ function)
amici::Model_DAE::fJv (C++ function)
,
[1]
amici::Model_DAE::fJvB (C++ function)
amici::Model_DAE::fM (C++ function)
,
[1]
amici::Model_DAE::fqBdot (C++ function)
amici::Model_DAE::fqBdot_ss (C++ function)
amici::Model_DAE::froot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::fsxdot (C++ function)
,
[1]
amici::Model_DAE::fxBdot (C++ function)
amici::Model_DAE::fxBdot_ss (C++ function)
,
[1]
amici::Model_DAE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_DAE::getSolver (C++ function)
amici::Model_DAE::Model_DAE (C++ function)
,
[1]
amici::Model_DAE::writeSteadystateJB (C++ function)
amici::Model_ODE (C++ class)
amici::Model_ODE::fdxdotdp (C++ function)
,
[1]
,
[2]
amici::Model_ODE::fdxdotdp_explicit (C++ function)
amici::Model_ODE::fdxdotdp_explicit_colptrs (C++ function)
amici::Model_ODE::fdxdotdp_explicit_rowvals (C++ function)
amici::Model_ODE::fdxdotdw (C++ function)
,
[1]
amici::Model_ODE::fdxdotdw_colptrs (C++ function)
amici::Model_ODE::fdxdotdw_rowvals (C++ function)
amici::Model_ODE::fdxdotdx_explicit (C++ function)
amici::Model_ODE::fdxdotdx_explicit_colptrs (C++ function)
amici::Model_ODE::fdxdotdx_explicit_rowvals (C++ function)
amici::Model_ODE::fJ (C++ function)
,
[1]
amici::Model_ODE::fJB (C++ function)
,
[1]
amici::Model_ODE::fJDiag (C++ function)
,
[1]
amici::Model_ODE::fJSparse (C++ function)
,
[1]
,
[2]
,
[3]
amici::Model_ODE::fJSparse_colptrs (C++ function)
amici::Model_ODE::fJSparse_rowvals (C++ function)
amici::Model_ODE::fJSparseB (C++ function)
,
[1]
amici::Model_ODE::fJSparseB_ss (C++ function)
amici::Model_ODE::fJv (C++ function)
,
[1]
amici::Model_ODE::fJvB (C++ function)
amici::Model_ODE::fqBdot (C++ function)
amici::Model_ODE::fqBdot_ss (C++ function)
amici::Model_ODE::froot (C++ function)
,
[1]
,
[2]
amici::Model_ODE::fsxdot (C++ function)
,
[1]
amici::Model_ODE::fxBdot (C++ function)
amici::Model_ODE::fxBdot_ss (C++ function)
,
[1]
amici::Model_ODE::fxdot (C++ function)
,
[1]
,
[2]
amici::Model_ODE::getSolver (C++ function)
amici::Model_ODE::Model_ODE (C++ function)
,
[1]
amici::Model_ODE::writeSteadystateJB (C++ function)
amici::model_quantity_to_str (C++ member)
amici::ModelContext (C++ class)
amici::ModelContext::ModelContext (C++ function)
amici::ModelContext::operator= (C++ function)
amici::ModelContext::restore (C++ function)
amici::ModelContext::~ModelContext (C++ function)
amici::ModelDimensions (C++ struct)
amici::ModelDimensions::lbw (C++ member)
amici::ModelDimensions::ModelDimensions (C++ function)
,
[1]
amici::ModelDimensions::ndJydy (C++ member)
amici::ModelDimensions::ndtotal_cldx_rdata (C++ member)
amici::ModelDimensions::ndwdp (C++ member)
amici::ModelDimensions::ndwdw (C++ member)
amici::ModelDimensions::ndwdx (C++ member)
amici::ModelDimensions::ndxdotdp_explicit (C++ member)
amici::ModelDimensions::ndxdotdw (C++ member)
amici::ModelDimensions::ndxdotdx_explicit (C++ member)
amici::ModelDimensions::ndxrdatadtcl (C++ member)
amici::ModelDimensions::ndxrdatadxsolver (C++ member)
amici::ModelDimensions::ne (C++ member)
amici::ModelDimensions::ne_solver (C++ member)
amici::ModelDimensions::nJ (C++ member)
amici::ModelDimensions::nk (C++ member)
amici::ModelDimensions::nnz (C++ member)
amici::ModelDimensions::np (C++ member)
amici::ModelDimensions::nspl (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::pythonGenerated (C++ member)
amici::ModelDimensions::ubw (C++ member)
amici::ModelDimensions::w_recursion_depth (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::ModelState (C++ function)
,
[1]
amici::ModelState::plist (C++ member)
amici::ModelState::stotal_cl (C++ member)
amici::ModelState::total_cl (C++ member)
amici::ModelState::unscaledParameters (C++ member)
amici::ModelStateDerived (C++ struct)
amici::ModelStateDerived::deltaqB_ (C++ member)
amici::ModelStateDerived::deltasx_ (C++ member)
amici::ModelStateDerived::deltax_ (C++ member)
amici::ModelStateDerived::deltaxB_ (C++ member)
amici::ModelStateDerived::dfdx_ (C++ member)
amici::ModelStateDerived::dJrzdsigma_ (C++ member)
amici::ModelStateDerived::dJrzdz_ (C++ member)
amici::ModelStateDerived::dJydp_ (C++ member)
amici::ModelStateDerived::dJydsigma_ (C++ member)
amici::ModelStateDerived::dJydx_ (C++ member)
amici::ModelStateDerived::dJydy_ (C++ member)
amici::ModelStateDerived::dJydy_dense_ (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::dwdp_hierarchical_ (C++ member)
amici::ModelStateDerived::dwdw_ (C++ member)
amici::ModelStateDerived::dwdx_ (C++ member)
amici::ModelStateDerived::dwdx_hierarchical_ (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)
,
[1]
,
[2]
amici::ModelStateDerived::MSparse_ (C++ member)
amici::ModelStateDerived::rz_ (C++ member)
amici::ModelStateDerived::sigmay_ (C++ member)
amici::ModelStateDerived::sigmaz_ (C++ member)
amici::ModelStateDerived::spl_ (C++ member)
amici::ModelStateDerived::sspl_ (C++ member)
amici::ModelStateDerived::sunctx_ (C++ member)
amici::ModelStateDerived::sx_ (C++ member)
amici::ModelStateDerived::sx_rdata_ (C++ member)
amici::ModelStateDerived::sy_ (C++ member)
amici::ModelStateDerived::w_ (C++ member)
amici::ModelStateDerived::x_pos_tmp_ (C++ member)
amici::ModelStateDerived::x_rdata_ (C++ member)
amici::ModelStateDerived::y_ (C++ member)
amici::ModelStateDerived::z_ (C++ member)
amici::N_VGetArrayPointerConst (C++ function)
amici::NewtonDampingFactorMode (C++ enum)
amici::NewtonDampingFactorMode::off (C++ enumerator)
amici::NewtonDampingFactorMode::on (C++ enumerator)
amici::NewtonFailure (C++ class)
amici::NewtonFailure::error_code (C++ member)
amici::NewtonFailure::NewtonFailure (C++ function)
amici::NewtonSolver (C++ class)
amici::NewtonSolver::computeNewtonSensis (C++ function)
amici::NewtonSolver::getStep (C++ function)
amici::NewtonSolver::is_singular (C++ function)
amici::NewtonSolver::NewtonSolver (C++ function)
,
[1]
amici::NewtonSolver::operator= (C++ function)
amici::NewtonSolver::prepareLinearSystem (C++ function)
amici::NewtonSolver::prepareLinearSystemB (C++ function)
amici::NewtonSolver::reinitialize (C++ function)
amici::NewtonSolver::solveLinearSystem (C++ function)
amici::NonlinearSolverIteration (C++ enum)
amici::NonlinearSolverIteration::fixedpoint (C++ enumerator)
amici::NonlinearSolverIteration::functional (C++ enumerator)
amici::NonlinearSolverIteration::newton (C++ enumerator)
amici::ObservableScaling (C++ enum)
amici::ObservableScaling::lin (C++ enumerator)
amici::ObservableScaling::log (C++ enumerator)
amici::ObservableScaling::log10 (C++ enumerator)
amici::operator== (C++ function)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
amici::ParameterScaling (C++ enum)
amici::ParameterScaling::ln (C++ enumerator)
amici::ParameterScaling::log10 (C++ enumerator)
amici::ParameterScaling::none (C++ enumerator)
amici::pi (C++ member)
amici::printfToString (C++ function)
amici::RDataReporting (C++ enum)
amici::RDataReporting::full (C++ enumerator)
amici::RDataReporting::likelihood (C++ enumerator)
amici::RDataReporting::residuals (C++ enumerator)
amici::realtype (C++ type)
amici::regexErrorToString (C++ function)
amici::ReturnData (C++ class)
amici::ReturnData::applyChainRuleFactorToSimulationResults (C++ function)
amici::ReturnData::boost::serialization::serialize (C++ function)
amici::ReturnData::chi2 (C++ member)
amici::ReturnData::computingFSA (C++ function)
amici::ReturnData::cpu_time (C++ member)
amici::ReturnData::cpu_time_total (C++ member)
amici::ReturnData::cpu_timeB (C++ member)
amici::ReturnData::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::res (C++ member)
amici::ReturnData::ReturnData (C++ function)
,
[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_ss (C++ member)
amici::ReturnData::sy (C++ member)
amici::ReturnData::sz (C++ member)
amici::ReturnData::t_last (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_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)
,
[1]
amici::Solver (C++ class)
amici::Solver::adjInit (C++ function)
amici::Solver::allocateSolver (C++ function)
amici::Solver::allocateSolverB (C++ function)
amici::Solver::apply_constraints (C++ function)
amici::Solver::apply_max_conv_fails (C++ function)
amici::Solver::apply_max_nonlin_iters (C++ function)
amici::Solver::apply_max_step_size (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::constraints_ (C++ member)
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::free_solver_ptr (C++ type)
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::getConstraints (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::getMaxConvFails (C++ function)
amici::Solver::getMaxNonlinIters (C++ function)
amici::Solver::getMaxSteps (C++ function)
amici::Solver::getMaxStepsBackwardProblem (C++ function)
amici::Solver::getMaxStepSize (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)
,
[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::getSunContext (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::setConstraints (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::setMaxConvFails (C++ function)
amici::Solver::setMaxNonlinIters (C++ function)
amici::Solver::setMaxNumSteps (C++ function)
amici::Solver::setMaxNumStepsB (C++ function)
amici::Solver::setMaxSteps (C++ function)
amici::Solver::setMaxStepsBackwardProblem (C++ function)
amici::Solver::setMaxStepSize (C++ function)
amici::Solver::setMaxTime (C++ function)
amici::Solver::setNewtonDampingFactorLowerBound (C++ function)
amici::Solver::setNewtonDampingFactorMode (C++ function)
amici::Solver::setNewtonMaxSteps (C++ function)
amici::Solver::setNewtonStepSteadyStateCheck (C++ function)
amici::Solver::setNonLinearSolver (C++ function)
amici::Solver::setNonLinearSolverB (C++ function)
amici::Solver::setNonlinearSolverIteration (C++ function)
amici::Solver::setNonLinearSolverSens (C++ function)
amici::Solver::setQuadErrCon (C++ function)
amici::Solver::setQuadErrConB (C++ function)
amici::Solver::setQuadInitDone (C++ function)
amici::Solver::setQuadInitDoneB (C++ function)
amici::Solver::setRelativeTolerance (C++ function)
amici::Solver::setRelativeToleranceB (C++ function)
amici::Solver::setRelativeToleranceFSA (C++ function)
amici::Solver::setRelativeToleranceQuadratures (C++ function)
amici::Solver::setRelativeToleranceSteadyState (C++ function)
amici::Solver::setRelativeToleranceSteadyStateSensi (C++ function)
amici::Solver::setReturnDataReportingMode (C++ function)
amici::Solver::setSensErrCon (C++ function)
amici::Solver::setSensInitDone (C++ function)
amici::Solver::setSensInitOff (C++ function)
amici::Solver::setSensiSteadyStateCheck (C++ function)
amici::Solver::setSensitivityMethod (C++ function)
amici::Solver::setSensitivityMethodPreequilibration (C++ function)
amici::Solver::setSensitivityOrder (C++ function)
amici::Solver::setSensParams (C++ function)
amici::Solver::setSensSStolerances (C++ function)
amici::Solver::setSparseJacFn (C++ function)
amici::Solver::setSparseJacFn_ss (C++ function)
amici::Solver::setSparseJacFnB (C++ function)
amici::Solver::setSStolerances (C++ function)
amici::Solver::setSStolerancesB (C++ function)
amici::Solver::setStabilityLimitFlag (C++ function)
amici::Solver::setStabLimDet (C++ function)
amici::Solver::setStabLimDetB (C++ function)
amici::Solver::setStateOrdering (C++ function)
amici::Solver::setSteadyStateSensiToleranceFactor (C++ function)
amici::Solver::setSteadyStateToleranceFactor (C++ function)
amici::Solver::setStopTime (C++ function)
amici::Solver::setSuppressAlg (C++ function)
amici::Solver::setup (C++ function)
amici::Solver::setupB (C++ function)
amici::Solver::setupSteadystate (C++ function)
amici::Solver::setUserData (C++ function)
amici::Solver::setUserDataB (C++ function)
amici::Solver::simulation_timer_ (C++ member)
amici::Solver::solve (C++ function)
amici::Solver::solveB (C++ function)
amici::Solver::solveF (C++ function)
amici::Solver::Solver (C++ function)
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[1]
amici::Solver::solver_memory_ (C++ member)
amici::Solver::solver_memory_B_ (C++ member)
amici::Solver::solver_was_called_B_ (C++ member)
amici::Solver::solver_was_called_F_ (C++ member)
amici::Solver::startTimer (C++ function)
amici::Solver::step (C++ function)
amici::Solver::storeDiagnosis (C++ function)
amici::Solver::storeDiagnosisB (C++ function)
amici::Solver::sunctx_ (C++ member)
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::SplineBoundaryCondition (C++ enum)
amici::SplineBoundaryCondition::given (C++ enumerator)
amici::SplineBoundaryCondition::natural (C++ enumerator)
amici::SplineBoundaryCondition::naturalZeroDerivative (C++ enumerator)
amici::SplineBoundaryCondition::periodic (C++ enumerator)
amici::SplineBoundaryCondition::zeroDerivative (C++ enumerator)
amici::SplineExtrapolation (C++ enum)
amici::SplineExtrapolation::constant (C++ enumerator)
amici::SplineExtrapolation::linear (C++ enumerator)
amici::SplineExtrapolation::noExtrapolation (C++ enumerator)
amici::SplineExtrapolation::periodic (C++ enumerator)
amici::SplineExtrapolation::polynomial (C++ enumerator)
amici::SteadyStateComputationMode (C++ enum)
amici::SteadyStateComputationMode::integrateIfNewtonFails (C++ enumerator)
amici::SteadyStateComputationMode::integrationOnly (C++ enumerator)
amici::SteadyStateComputationMode::newtonOnly (C++ enumerator)
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::SUNLinSolBand (C++ function)
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[1]
amici::SUNLinSolDense (C++ class)
amici::SUNLinSolDense::SUNLinSolDense (C++ function)
amici::SUNLinSolKLU (C++ class)
amici::SUNLinSolKLU::is_singular (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)
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[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)
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[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)
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[1]
amici::SUNLinSolWrapper (C++ class)
amici::SUNLinSolWrapper::A_ (C++ member)
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)
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[1]
amici::SUNLinSolWrapper::setup (C++ function)
amici::SUNLinSolWrapper::solve (C++ function)
amici::SUNLinSolWrapper::solver_ (C++ member)
amici::SUNLinSolWrapper::space (C++ function)
amici::SUNLinSolWrapper::SUNLinSolWrapper (C++ function)
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[1]
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[2]
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[3]
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[4]
amici::SUNLinSolWrapper::~SUNLinSolWrapper (C++ function)
amici::SUNMatrixWrapper (C++ class)
amici::SUNMatrixWrapper::capacity (C++ function)
amici::SUNMatrixWrapper::columns (C++ function)
amici::SUNMatrixWrapper::data (C++ function)
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[1]
amici::SUNMatrixWrapper::get (C++ function)
amici::SUNMatrixWrapper::get_ctx (C++ function)
amici::SUNMatrixWrapper::get_data (C++ function)
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[1]
amici::SUNMatrixWrapper::get_indexptr (C++ function)
amici::SUNMatrixWrapper::get_indexval (C++ function)
amici::SUNMatrixWrapper::matrix_id (C++ function)
amici::SUNMatrixWrapper::multiply (C++ function)
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[1]
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[2]
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[3]
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[4]
amici::SUNMatrixWrapper::num_indexptrs (C++ function)
amici::SUNMatrixWrapper::num_nonzeros (C++ function)
amici::SUNMatrixWrapper::operator SUNMatrix (C++ function)
amici::SUNMatrixWrapper::operator= (C++ function)
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[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_ctx (C++ function)
amici::SUNMatrixWrapper::set_data (C++ function)
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[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)
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[1]
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[2]
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[3]
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[4]
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[5]
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[6]
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[7]
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)
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[1]
amici::SUNNonLinSolNewton (C++ class)
amici::SUNNonLinSolNewton::getSysFn (C++ function)
amici::SUNNonLinSolNewton::SUNNonLinSolNewton (C++ function)
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[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)
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[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)
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[1]
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[2]
amici::SUNNonLinSolWrapper::~SUNNonLinSolWrapper (C++ function)
amici::unravel_index (C++ function)
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[1]
amici::unscaleParameters (C++ function)
amici::writeSlice (C++ function)
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[1]
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[2]
,
[3]
amici_annotation (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
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)
(in module amici.petab.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)
(amici.petab.parameter_mapping.ParameterMapping method)
assignmentRules2observables() (in module amici.sbml_import)
B
band (amici.amici.LinearSolver attribute)
bc (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
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]
,
[5]
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_if_valid() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
check_model() (in module amici.petab.import_helpers)
(in module amici.petab_import)
check_support() (amici.sbml_import.SbmlImporter method)
chi2 (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
CircularDependencyError
clear_observations() (amici.amici.ExpData method)
clone() (amici.amici.Model method)
(amici.amici.Solver method)
colptrs() (amici.de_model.DEModel method)
compile_model() (amici.de_export.DEExporter method)
compiledWithOpenMP() (in module amici.amici)
compute_moiety_conservation_laws() (in module amici.conserved_quantities_demartino)
computingASA() (amici.amici.Solver method)
computingFSA() (amici.amici.Solver method)
conservation_law_has_multispecies() (amici.de_model.DEModel method)
conservation_laws() (amici.de_model.DEModel method)
ConservationLaw (class in amici.de_model_components)
Constant (class in amici.de_model_components)
constants() (amici.de_model.DEModel method)
Constraint (class in amici.amici)
count() (amici.parameter_mapping.ParameterMapping method)
(amici.petab.parameter_mapping.ParameterMapping method)
(amici.splines.UniformGrid method)
cpu_time (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
cpu_time_total (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
cpu_timeB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
CpuTimer (class in amici.amici)
create_edata_for_condition() (in module amici.petab.conditions)
create_edatas() (in module amici.petab.conditions)
(in module amici.petab_objective)
create_parameter_mapping() (in module amici.petab.parameter_mapping)
(in module amici.petab_objective)
create_parameter_mapping_for_condition() (in module amici.petab.parameter_mapping)
create_parameterized_edatas() (in module amici.petab.conditions)
create_sbml_model() (in module amici.sbml_utils)
CubicHermiteSpline (class in amici.splines)
CUSTOM_FUNCTIONS (in module amici.de_export)
CVODES
D
d_scaled() (amici.splines.CubicHermiteSpline method)
DAE
DEExporter (class in amici.de_export)
DEModel (class in amici.de_model)
dense (amici.amici.LinearSolver attribute)
derivative() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
derivatives_at_nodes (amici.splines.CubicHermiteSpline property)
derivatives_by_fd (amici.splines.CubicHermiteSpline property)
diag (amici.amici.LinearSolver attribute)
differential_states() (amici.de_model.DEModel method)
DifferentialState (class in amici.de_model_components)
directional (amici.amici.SecondOrderMode attribute)
doprint() (amici.sbml_utils.MathMLSbmlPrinter method)
DoubleVector (class in amici.amici)
dynamic_indices() (amici.de_model.DEModel method)
E
elapsed_milliseconds() (amici.amici.CpuTimer method)
elapsed_seconds() (amici.amici.CpuTimer method)
emptyPrinter() (amici.sbml_utils.MathMLSbmlPrinter method)
eq() (amici.de_model.DEModel method)
evaluate() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
(in module amici.numpy)
evaluate_at (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
Event (class in amici.de_model_components)
event_observables() (amici.de_model.DEModel method)
EventObservable (class in amici.de_model_components)
events() (amici.de_model.DEModel method)
ExpData (class in amici.amici)
ExpDataPtr (class in amici.amici)
ExpDataPtrVector (class in amici.amici)
ExpDataView (class in amici.numpy)
Expression (class in amici.de_model_components)
expressions() (amici.de_model.DEModel method)
extract_monomers() (in module amici.pysb_import)
extrapolate (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
extrapolation_formulas (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
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)
fdspline_slopesdp() (amici.amici.Model method)
fdspline_valuesdp() (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)
(in module amici.petab.conditions)
(in module amici.petab_objective)
fill_in_parameters_for_condition() (in module amici.parameter_mapping)
(in module amici.petab.conditions)
FIM (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
first (amici.amici.SensitivityOrder attribute)
fixed parameters
FixedParameterContext (class in amici.amici)
fixedParameters (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedParametersPreequilibration (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedParametersPresimulation (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
fixedpoint (amici.amici.NonlinearSolverIteration attribute)
formula (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
forward (amici.amici.SensitivityMethod attribute)
free_symbols (amici.parameter_mapping.ParameterMapping property)
(amici.parameter_mapping.ParameterMappingForCondition property)
(amici.petab.parameter_mapping.ParameterMapping property)
(amici.petab.parameter_mapping.ParameterMappingForCondition property)
free_symbols() (amici.de_model.DEModel method)
from_annotation() (amici.splines.AbstractSpline static method)
(amici.splines.CubicHermiteSpline static method)
full (amici.amici.RDataReporting attribute)
(amici.amici.SecondOrderMode attribute)
functional (amici.amici.NonlinearSolverIteration attribute)
G
generate_basic_variables() (amici.de_model.DEModel method)
generate_flux_symbol() (in module amici.import_utils)
generate_measurement_symbol() (in module amici.import_utils)
generate_model_code() (amici.de_export.DEExporter method)
generate_regularization_symbol() (in module amici.import_utils)
get() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
get_annotation() (amici.splines.AbstractSpline static method)
(amici.splines.CubicHermiteSpline static method)
get_appearance_counts() (amici.de_model.DEModel method)
get_conservation_laws() (amici.de_model.DEModel method)
get_dt() (amici.de_model_components.DifferentialState method)
get_dx_rdata_dx_solver() (amici.de_model_components.AlgebraicState method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.State method)
get_event() (amici.de_model_components.EventObservable method)
get_expressions_as_dataframe() (in module amici.pandas)
get_fixed_parameters() (in module amici.petab.import_helpers)
(in module amici.petab_import)
get_free_symbols() (amici.de_model_components.AlgebraicEquation method)
(amici.de_model_components.AlgebraicState method)
(amici.de_model_components.DifferentialState method)
get_id() (amici.de_model_components.AlgebraicEquation method)
(amici.de_model_components.AlgebraicState method)
(amici.de_model_components.ConservationLaw method)
(amici.de_model_components.Constant method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.Event method)
(amici.de_model_components.EventObservable method)
(amici.de_model_components.Expression method)
(amici.de_model_components.LogLikelihoodRZ method)
(amici.de_model_components.LogLikelihoodY method)
(amici.de_model_components.LogLikelihoodZ method)
(amici.de_model_components.ModelQuantity method)
(amici.de_model_components.Observable method)
(amici.de_model_components.Parameter method)
(amici.de_model_components.SigmaY method)
(amici.de_model_components.SigmaZ method)
(amici.de_model_components.State method)
get_initial_value() (amici.de_model_components.Event method)
get_logger() (in module amici.logging)
get_measurement_symbol() (amici.de_model_components.EventObservable method)
(amici.de_model_components.Observable method)
get_model() (amici.ModelModule method)
get_name() (amici.de_model_components.AlgebraicEquation method)
(amici.de_model_components.AlgebraicState method)
(amici.de_model_components.ConservationLaw method)
(amici.de_model_components.Constant method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.Event method)
(amici.de_model_components.EventObservable method)
(amici.de_model_components.Expression method)
(amici.de_model_components.LogLikelihoodRZ method)
(amici.de_model_components.LogLikelihoodY method)
(amici.de_model_components.LogLikelihoodZ method)
(amici.de_model_components.ModelQuantity method)
(amici.de_model_components.Observable method)
(amici.de_model_components.Parameter method)
(amici.de_model_components.SigmaY method)
(amici.de_model_components.SigmaZ method)
(amici.de_model_components.State method)
get_ncoeff() (amici.de_model_components.ConservationLaw method)
get_observable_transformations() (amici.de_model.DEModel method)
get_observation_model() (in module amici.petab.import_helpers)
(in module amici.petab_import)
get_regularization_symbol() (amici.de_model_components.EventObservable method)
(amici.de_model_components.Observable method)
get_sbml_units() (in module amici.sbml_utils)
get_solver_indices() (amici.de_model.DEModel method)
get_species_initial() (in module amici.sbml_import)
get_steadystate_mask() (amici.amici.Model method)
get_trigger_time() (amici.de_model_components.Event method)
get_trigger_timepoints() (amici.amici.Model method)
get_val() (amici.de_model_components.AlgebraicEquation method)
(amici.de_model_components.AlgebraicState method)
(amici.de_model_components.ConservationLaw method)
(amici.de_model_components.Constant method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.Event method)
(amici.de_model_components.EventObservable method)
(amici.de_model_components.Expression method)
(amici.de_model_components.LogLikelihoodRZ method)
(amici.de_model_components.LogLikelihoodY method)
(amici.de_model_components.LogLikelihoodZ method)
(amici.de_model_components.ModelQuantity method)
(amici.de_model_components.Observable method)
(amici.de_model_components.Parameter method)
(amici.de_model_components.SigmaY method)
(amici.de_model_components.SigmaZ method)
(amici.de_model_components.State method)
get_x_rdata() (amici.de_model_components.AlgebraicState method)
(amici.de_model_components.ConservationLaw method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.State method)
getAbsoluteTolerance() (amici.amici.Solver method)
getAbsoluteToleranceB() (amici.amici.Solver method)
getAbsoluteToleranceFSA() (amici.amici.Solver method)
getAbsoluteToleranceQuadratures() (amici.amici.Solver method)
getAbsoluteToleranceSteadyState() (amici.amici.Solver method)
getAbsoluteToleranceSteadyStateSensi() (amici.amici.Solver method)
getAddSigmaResiduals() (amici.amici.Model method)
getAlwaysCheckFinite() (amici.amici.Model method)
getAmiciCommit() (amici.amici.Model method)
getAmiciVersion() (amici.amici.Model method)
getConstraints() (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)
getLinearMultistepMethod() (amici.amici.Solver method)
getLinearSolver() (amici.amici.Solver method)
getMaxConvFails() (amici.amici.Solver method)
getMaxNonlinIters() (amici.amici.Solver method)
getMaxSteps() (amici.amici.Solver method)
getMaxStepsBackwardProblem() (amici.amici.Solver method)
getMaxStepSize() (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)
getObservableIds() (amici.amici.Model method)
getObservableNames() (amici.amici.Model method)
getObservableScaling() (amici.amici.Model method)
getObservedData() (amici.amici.ExpData method)
getObservedDataPtr() (amici.amici.ExpData method)
getObservedDataStdDev() (amici.amici.ExpData method)
getObservedDataStdDevPtr() (amici.amici.ExpData method)
getObservedEvents() (amici.amici.ExpData method)
getObservedEventsPtr() (amici.amici.ExpData method)
getObservedEventsStdDev() (amici.amici.ExpData method)
getObservedEventsStdDevPtr() (amici.amici.ExpData method)
getParameterById() (amici.amici.Model method)
getParameterByName() (amici.amici.Model method)
getParameterIds() (amici.amici.Model method)
getParameterList() (amici.amici.Model method)
getParameterNames() (amici.amici.Model method)
getParameters() (amici.amici.Model method)
getParameterScale() (amici.amici.Model method)
getReinitializationStateIdxs() (amici.amici.Model method)
getReinitializeFixedParameterInitialStates() (amici.amici.Model method)
getRelativeTolerance() (amici.amici.Solver method)
getRelativeToleranceB() (amici.amici.Solver method)
getRelativeToleranceFSA() (amici.amici.Solver method)
getRelativeToleranceQuadratures() (amici.amici.Solver method)
getRelativeToleranceSteadyState() (amici.amici.Solver method)
getRelativeToleranceSteadyStateSensi() (amici.amici.Solver method)
getResidualsAsDataFrame() (in module amici.pandas)
getReturnDataReportingMode() (amici.amici.Solver method)
getScaledParameter() (in module amici.amici)
getSensiSteadyStateCheck() (amici.amici.Solver method)
getSensitivityMethod() (amici.amici.Solver method)
getSensitivityMethodPreequilibration() (amici.amici.Solver method)
getSensitivityOrder() (amici.amici.Solver method)
getSimulationObservablesAsDataFrame() (in module amici.pandas)
getSimulationStatesAsDataFrame() (in module amici.pandas)
getSolver() (amici.amici.Model method)
getStabilityLimitFlag() (amici.amici.Solver method)
getStateIds() (amici.amici.Model method)
getStateIdsSolver() (amici.amici.Model method)
getStateIsNonNegative() (amici.amici.Model method)
getStateNames() (amici.amici.Model method)
getStateNamesSolver() (amici.amici.Model method)
getStateOrdering() (amici.amici.Solver method)
getSteadyStateComputationMode() (amici.amici.Model method)
getSteadyStateSensitivityMode() (amici.amici.Model method)
getSteadyStateSensiToleranceFactor() (amici.amici.Solver method)
getSteadyStateToleranceFactor() (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]
,
[2]
H
has_conservation_law() (amici.de_model_components.AlgebraicState method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.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_model() (in module amici.petab_import)
import_model_module() (in module amici)
import_model_pysb() (in module amici.petab.pysb_import)
(in module amici.petab_import_pysb)
import_model_sbml() (in module amici.petab.sbml_import)
(in module amici.petab_import)
import_petab_problem() (in module amici.petab)
(in module amici.petab.petab_import)
(in module amici.petab_import)
index() (amici.parameter_mapping.ParameterMapping method)
(amici.petab.parameter_mapping.ParameterMapping method)
(amici.splines.UniformGrid method)
initializeSplines() (amici.amici.Model method)
initializeSplineSensitivities() (amici.amici.Model method)
integrate() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
integrateIfNewtonFails (amici.amici.SteadyStateComputationMode attribute)
(amici.amici.SteadyStateSensitivityMode attribute)
integrationOnly (amici.amici.SteadyStateComputationMode attribute)
(amici.amici.SteadyStateSensitivityMode attribute)
InternalSensitivityMethod (class in amici.amici)
InterpolationType (class in amici.amici)
IntVector (class in amici.amici)
is_assignment_rule_target() (amici.sbml_import.SbmlImporter method)
is_ode() (amici.de_model.DEModel method)
is_rate_rule_target() (amici.sbml_import.SbmlImporter method)
is_spline() (amici.splines.AbstractSpline static method)
(amici.splines.CubicHermiteSpline static method)
is_valid_identifier() (in module amici.de_export)
isFixedParameterStateReinitializationAllowed() (amici.amici.Model method)
isSetObservedData() (amici.amici.ExpData method)
isSetObservedDataStdDev() (amici.amici.ExpData method)
isSetObservedEvents() (amici.amici.ExpData method)
isSetObservedEventsStdDev() (amici.amici.ExpData method)
items() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
J
J (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
K
k() (amici.amici.Model method)
keys() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
KLU (amici.amici.LinearSolver attribute)
L
LAPACKBand (amici.amici.LinearSolver attribute)
LAPACKDense (amici.amici.LinearSolver attribute)
lbw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
likelihood (amici.amici.RDataReporting attribute)
lin (amici.amici.ObservableScaling attribute)
LIN (amici.import_utils.ObservableTransformation attribute)
LinearMultistepMethod (class in amici.amici)
LinearSolver (class in amici.amici)
llh (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ln (amici.amici.ParameterScaling attribute)
log (amici.amici.ObservableScaling attribute)
LOG (amici.import_utils.ObservableTransformation attribute)
log10 (amici.amici.ObservableScaling attribute)
(amici.amici.ParameterScaling attribute)
LOG10 (amici.import_utils.ObservableTransformation attribute)
log_execution_time() (in module amici.logging)
log_likelihood_rzs() (amici.de_model.DEModel method)
log_likelihood_ys() (amici.de_model.DEModel method)
log_likelihood_zs() (amici.de_model.DEModel method)
logarithmic_parametrization (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
logger (amici.amici.Model property)
(amici.amici.ModelPtr property)
(amici.amici.Solver property)
(amici.amici.SolverPtr property)
(in module amici.de_export)
LogItem (class in amici.amici)
LogItemVector (class in amici.amici)
LogLikelihoodRZ (class in amici.de_model_components)
LogLikelihoodY (class in amici.de_model_components)
LogLikelihoodZ (class in amici.de_model_components)
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)
maketrans() (amici.import_utils.ObservableTransformation static method)
mathml2sympy() (in module amici.sbml_utils)
mathml_formula (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
mathml_tag() (amici.sbml_utils.MathMLSbmlPrinter method)
MathMLSbmlPrinter (class in amici.sbml_utils)
message (amici.amici.LogItem property)
messages (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
method (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
Model (class in amici.amici)
ModelDimensions (class in amici.amici)
ModelModule (class in amici)
ModelPtr (class in amici.amici)
ModelQuantity (class in amici.de_model_components)
module
amici
amici.amici
amici.bngl_import
amici.conserved_quantities_demartino
amici.conserved_quantities_rref
amici.de_export
amici.de_model
amici.de_model_components
amici.gradient_check
amici.import_utils
amici.logging
amici.numpy
amici.pandas
amici.parameter_mapping
amici.petab
amici.petab.conditions
amici.petab.import_helpers
amici.petab.parameter_mapping
amici.petab.petab_import
amici.petab.pysb_import
amici.petab.sbml_import
amici.petab.simulations
amici.petab.simulator
amici.petab_import
amici.petab_import_pysb
amici.petab_objective
amici.petab_simulate
amici.plotting
amici.pysb_import
amici.sbml_import
amici.sbml_utils
amici.splines
N
name() (amici.de_model.DEModel method)
ncl() (amici.amici.Model method)
ndJydy (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndtotal_cldx_rdata (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndwdp (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndwdw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndwdx (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxdotdp_explicit (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxdotdw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxdotdx_explicit (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxrdatadtcl (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ndxrdatadxsolver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ne (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ne_solver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
negative (amici.amici.Constraint attribute)
newton (amici.amici.NonlinearSolverIteration attribute)
newton_maxsteps (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
NewtonDampingFactorMode (class in amici.amici)
newtonOnly (amici.amici.SteadyStateComputationMode attribute)
(amici.amici.SteadyStateSensitivityMode attribute)
nJ (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nk (amici.amici.ModelDimensions property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nk() (amici.amici.Model method)
nmaxevent (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nmaxevent() (amici.amici.ExpData method)
nMaxEvent() (amici.amici.Model method)
nnz (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nodes (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
noise_distribution_to_cost_function() (in module amici.import_utils)
noise_distribution_to_observable_transformation() (in module amici.import_utils)
non_negative (amici.amici.Constraint attribute)
non_positive (amici.amici.Constraint attribute)
non_unique_id_symbols (in module amici.de_export)
none (amici.amici.Constraint attribute)
(amici.amici.ParameterScaling attribute)
(amici.amici.SecondOrderMode attribute)
(amici.amici.SensitivityMethod attribute)
(amici.amici.SensitivityOrder attribute)
NonlinearSolverIteration (class in amici.amici)
NonlinearSolverIteration_fixedpoint (in module amici.amici)
not_run (amici.amici.SteadyStateStatus attribute)
np (amici.amici.ModelDimensions property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
np() (amici.amici.Model method)
nplist (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nplist() (amici.amici.Model method)
(amici.amici.Solver method)
nquad() (amici.amici.Solver method)
nspl (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nt (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nt() (amici.amici.ExpData method)
(amici.amici.Model method)
nullspace_by_rref() (in module amici.conserved_quantities_rref)
num_cons_law() (amici.de_model.DEModel method)
num_const() (amici.de_model.DEModel method)
num_eventobs() (amici.de_model.DEModel method)
num_events() (amici.de_model.DEModel method)
num_events_solver() (amici.de_model.DEModel method)
num_expr() (amici.de_model.DEModel method)
num_obs() (amici.de_model.DEModel method)
num_par() (amici.de_model.DEModel method)
num_state_reinits() (amici.de_model.DEModel method)
num_states_rdata() (amici.de_model.DEModel method)
num_states_solver() (amici.de_model.DEModel method)
number_of_nodes (amici.splines.UniformGrid property)
numerrtestfails (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numerrtestfailsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numnonlinsolvconvfails (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numnonlinsolvconvfailsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numrhsevals (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numrhsevalsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numsteps (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
numstepsB (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx() (amici.amici.Solver method)
nx_rdata (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx_reinit() (amici.amici.Model method)
nx_solver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nx_solver_reinit (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue_rdata (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nxtrue_solver (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ny (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nytrue (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nytrue() (amici.amici.ExpData method)
nz (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nztrue (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
nztrue() (amici.amici.ExpData method)
O
o2mode (amici.amici.Model property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
Observable (class in amici.de_model_components)
observables() (amici.de_model.DEModel method)
ObservableScaling (class in amici.amici)
ObservableTransformation (class in amici.import_utils)
ODE
ode_model_from_pysb_importer() (in module amici.pysb_import)
ode_model_symbol() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
off (amici.amici.NewtonDampingFactorMode attribute)
on (amici.amici.NewtonDampingFactorMode attribute)
order (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.sbml_utils.MathMLSbmlPrinter property)
P
Parameter (class in amici.de_model_components)
ParameterMapping (class in amici.parameter_mapping)
(class in amici.petab.parameter_mapping)
ParameterMappingForCondition (class in amici.parameter_mapping)
(class in amici.petab.parameter_mapping)
parameters (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
parameters() (amici.de_model.DEModel method)
(amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
ParameterScaling (class in amici.amici)
parameterScalingFromIntVector() (in module amici.amici)
ParameterScalingVector (class in amici.amici)
parse_events() (amici.de_model.DEModel method)
period (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
PEtab
petab_noise_distributions_to_amici() (in module amici.petab.import_helpers)
(in module amici.petab_import)
petab_scale_to_amici_scale() (in module amici.petab.import_helpers)
(in module amici.petab_import)
petab_to_amici_scale() (in module amici.parameter_mapping)
(in module amici.petab.parameter_mapping)
PetabSimulator (class in amici.petab.simulator)
(class in amici.petab_simulate)
pivots() (in module amici.conserved_quantities_rref)
plist (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
plist() (amici.amici.Model method)
plot() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
plot_expressions() (in module amici.plotting)
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)
poly() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
poly_variable() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
polynomial (amici.amici.InterpolationType attribute)
positive (amici.amici.Constraint 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)
pretty_xml() (in module amici.sbml_utils)
printmethod (amici.sbml_utils.MathMLSbmlPrinter attribute)
pscale (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationParameters property)
PySB
pysb2amici() (in module amici.pysb_import)
pysb_model_from_path() (in module amici.pysb_import)
pythonGenerated (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr 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)
(in module amici.petab_objective)
rdatas_to_simulation_df() (in module amici.petab)
(in module amici.petab_objective)
reinitialization_state_idxs_presim (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
reinitialization_state_idxs_sim (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
reinitializeAllFixedParameterDependentInitialStates() (amici.amici.ExpData method)
(amici.amici.SimulationParameters method)
reinitializeAllFixedParameterDependentInitialStatesForPresimulation() (amici.amici.ExpData method)
(amici.amici.SimulationParameters method)
reinitializeAllFixedParameterDependentInitialStatesForSimulation() (amici.amici.ExpData method)
(amici.amici.SimulationParameters method)
reinitializeFixedParameterInitialStates (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
remove_working_dir() (amici.petab.simulator.PetabSimulator method)
(amici.petab_simulate.PetabSimulator method)
replace_logx() (in module amici.sbml_import)
requireSensitivitiesForAllParameters() (amici.amici.Model method)
res (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
rescale_sensitivity() (in module amici.petab_objective)
reset() (amici.amici.CpuTimer method)
residuals (amici.amici.RDataReporting attribute)
ReturnData (class in amici.amici)
ReturnDataPtr (class in amici.amici)
ReturnDataView (class in amici.numpy)
rowvals() (amici.de_model.DEModel method)
rref() (in module amici.conserved_quantities_rref)
runAmiciSimulation() (in module amici.amici)
runAmiciSimulations() (in module amici.amici)
rz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
S
s2llh (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
s2rz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SBML
sbml2amici() (amici.sbml_import.SbmlImporter method)
sbml_formula (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
sbml_id (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
sbml_math_ast() (in module amici.sbml_utils)
sbml_mathml() (in module amici.sbml_utils)
SbmlAnnotationError
SbmlDuplicateComponentIdError
SBMLException
SbmlImporter (class in amici.sbml_import)
SbmlInvalidIdSyntax
SbmlMathError
SbmlMissingComponentIdError
scale_parameter() (in module amici.parameter_mapping)
(in module amici.petab.parameter_mapping)
scale_parameters_dict() (in module amici.parameter_mapping)
(in module amici.petab.parameter_mapping)
second (amici.amici.SensitivityOrder attribute)
second_derivative() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
SecondOrderMode (class in amici.amici)
segment_formula() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
sensi (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sensi_meth (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SensitivityMethod (class in amici.amici)
SensitivityMethod_adjoint (in module amici.amici)
SensitivityMethod_forward (in module amici.amici)
SensitivityMethod_none (in module amici.amici)
SensitivityOrder (class in amici.amici)
SensitivityOrder_first (in module amici.amici)
SensitivityOrder_none (in module amici.amici)
SensitivityOrder_second (in module amici.amici)
set_conservation_law() (amici.de_model_components.DifferentialState method)
set_dt() (amici.de_model_components.DifferentialState method)
set_global_settings() (amici.sbml_utils.MathMLSbmlPrinter class method)
set_log_level() (in module amici.logging)
set_name() (amici.de_export.DEExporter method)
set_paths() (amici.de_export.DEExporter method)
set_sbml_math() (in module amici.sbml_utils)
set_steadystate_mask() (amici.amici.Model method)
set_val() (amici.de_model_components.AlgebraicEquation method)
(amici.de_model_components.AlgebraicState method)
(amici.de_model_components.ConservationLaw method)
(amici.de_model_components.Constant method)
(amici.de_model_components.DifferentialState method)
(amici.de_model_components.Event method)
(amici.de_model_components.EventObservable method)
(amici.de_model_components.Expression method)
(amici.de_model_components.LogLikelihoodRZ method)
(amici.de_model_components.LogLikelihoodY method)
(amici.de_model_components.LogLikelihoodZ method)
(amici.de_model_components.ModelQuantity method)
(amici.de_model_components.Observable method)
(amici.de_model_components.Parameter method)
(amici.de_model_components.SigmaY method)
(amici.de_model_components.SigmaZ method)
(amici.de_model_components.State method)
setAbsoluteTolerance() (amici.amici.Solver method)
setAbsoluteToleranceB() (amici.amici.Solver method)
setAbsoluteToleranceFSA() (amici.amici.Solver method)
setAbsoluteToleranceQuadratures() (amici.amici.Solver method)
setAbsoluteToleranceSteadyState() (amici.amici.Solver method)
setAbsoluteToleranceSteadyStateSensi() (amici.amici.Solver method)
setAddSigmaResiduals() (amici.amici.Model method)
setAllStatesNonNegative() (amici.amici.Model method)
setAlwaysCheckFinite() (amici.amici.Model method)
setConstraints() (amici.amici.Solver 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)
setMaxConvFails() (amici.amici.Solver method)
setMaxNonlinIters() (amici.amici.Solver method)
setMaxSteps() (amici.amici.Solver method)
setMaxStepsBackwardProblem() (amici.amici.Solver method)
setMaxStepSize() (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)
setSteadyStateComputationMode() (amici.amici.Model 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.sbml_import)
sigma_res (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sigma_ys() (amici.de_model.DEModel method)
sigma_zs() (amici.de_model.DEModel method)
sigmay (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SigmaY (class in amici.de_model_components)
sigmaz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SigmaZ (class in amici.de_model_components)
simulate() (amici.petab.simulator.PetabSimulator method)
(amici.petab_simulate.PetabSimulator method)
simulate_petab() (in module amici.petab)
(in module amici.petab.simulations)
(in module amici.petab_objective)
simulate_without_noise() (amici.petab.simulator.PetabSimulator method)
(amici.petab_simulate.PetabSimulator method)
simulation (amici.amici.FixedParameterContext attribute)
simulation_status_to_str() (in module amici.amici)
SimulationParameters (class in amici.amici)
simultaneous (amici.amici.InternalSensitivityMethod attribute)
sllh (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
smart_subs() (in module amici.import_utils)
smart_subs_dict() (in module amici.import_utils)
smoothness (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
Solver (class in amici.amici)
SolverPtr (class in amici.amici)
sparseeq() (amici.de_model.DEModel method)
sparsesym() (amici.de_model.DEModel method)
SPBCG (amici.amici.LinearSolver attribute)
species_to_parameters() (in module amici.petab.sbml_import)
(in module amici.petab_import)
SPGMR (amici.amici.LinearSolver attribute)
spline_user_functions() (in module amici.splines)
SPTFQMR (amici.amici.LinearSolver attribute)
squared_L2_norm_of_curvature() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
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)
start (amici.splines.UniformGrid property)
State (class in amici.de_model_components)
state_has_conservation_law() (amici.de_model.DEModel method)
state_has_fixed_parameter_initial_condition() (amici.de_model.DEModel method)
state_independent_events_ (amici.amici.Model property)
(amici.amici.ModelPtr property)
state_is_constant() (amici.de_model.DEModel method)
states() (amici.de_model.DEModel method)
static_indices() (amici.de_model.DEModel method)
status (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
SteadyStateComputationMode (class in amici.amici)
SteadyStateSensitivityMode (class in amici.amici)
SteadyStateStatus (class in amici.amici)
SteadyStateStatusVector (class in amici.amici)
step (amici.splines.UniformGrid property)
stop (amici.splines.UniformGrid property)
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)
sx (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sx0 (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
(amici.amici.SimulationParameters property)
sx_ss (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sy (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
sym() (amici.de_model.DEModel method)
sym_names() (amici.de_model.DEModel method)
sym_or_eq() (amici.de_model.DEModel method)
symbol_with_assumptions() (in module amici.import_utils)
sympify_noeval() (in module amici.splines)
sz (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
T
t0() (amici.amici.Model method)
t_last (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
t_presim (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
toposort_symbols() (in module amici.import_utils)
triggers_at_fixed_timepoint() (amici.de_model_components.Event method)
ts (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
ts_ (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
tstart_ (amici.amici.ExpData property)
(amici.amici.ExpDataPtr property)
(amici.amici.SimulationParameters property)
U
ubw (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
UniformGrid (class in amici.splines)
unique_preserve_order() (in module amici.import_utils)
unscale_parameter() (in module amici.parameter_mapping)
(in module amici.petab.parameter_mapping)
unscale_parameters_dict() (in module amici.parameter_mapping)
(in module amici.petab.parameter_mapping)
uses_thread_clock (amici.amici.CpuTimer attribute)
V
val() (amici.de_model.DEModel method)
values() (amici.numpy.ExpDataView method)
(amici.numpy.ReturnDataView method)
(amici.numpy.SwigPtrView method)
values_at_nodes (amici.splines.AbstractSpline property)
(amici.splines.CubicHermiteSpline property)
W
w (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
w_recursion_depth (amici.amici.Model property)
(amici.amici.ModelDimensions property)
(amici.amici.ModelPtr property)
(amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
X
x (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)
x0 (amici.amici.ExpData property)
(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)
y_scaled() (amici.splines.AbstractSpline method)
(amici.splines.CubicHermiteSpline method)
Z
z (amici.amici.ReturnData property)
(amici.amici.ReturnDataPtr property)