Index

B

boost::serialization::serialize (C++ function), [1]

H

H5_RESTORE_ERROR_HANDLER (C macro)

H5_SAVE_ERROR_HANDLER (C macro) HAVE_CSTDDEF (C macro)

M

MPI_TAG_EXIT_SIGNAL (C++ member)

O

operator<< (C++ function), [1]

P

parpe::almostEqual (C++ function) parpe::AmiciSimulationRunner (C++ class) parpe::AmiciSimulationRunner::AmiciResultPackageSimple (C++ struct), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::AmiciResultPackageSimple (C++ function), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::gradient (C++ member), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::llh (C++ member), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::modelOutput (C++ member), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::modelSigmas (C++ member), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::modelStates (C++ member), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::simulationTimeSeconds (C++ member), [1] parpe::AmiciSimulationRunner::AmiciResultPackageSimple::status (C++ member), [1] parpe::AmiciSimulationRunner::AmiciSimulationRunner (C++ function), [1] parpe::AmiciSimulationRunner::AmiciWorkPackageSimple (C++ struct), [1] parpe::AmiciSimulationRunner::AmiciWorkPackageSimple::AmiciWorkPackageSimple (C++ function), [1] parpe::AmiciSimulationRunner::AmiciWorkPackageSimple::conditionIndices (C++ member), [1] parpe::AmiciSimulationRunner::AmiciWorkPackageSimple::logPrefix (C++ member), [1] parpe::AmiciSimulationRunner::AmiciWorkPackageSimple::optimizationParameters (C++ member), [1] parpe::AmiciSimulationRunner::AmiciWorkPackageSimple::sensitivityOrder (C++ member), [1] parpe::AmiciSimulationRunner::callbackAllFinishedType (C++ type) parpe::AmiciSimulationRunner::callbackJobFinishedType (C++ type) parpe::AmiciSimulationRunner::messageHandlerFunc (C++ type) parpe::AmiciSimulationRunner::runSharedMemory (C++ function) parpe::AmiciSummedGradientFunction (C++ class) parpe::AmiciSummedGradientFunction::addSimulationGradientToObjectiveFunctionGradient (C++ function) parpe::AmiciSummedGradientFunction::aggregateLikelihood (C++ function) parpe::AmiciSummedGradientFunction::AmiciSummedGradientFunction (C++ function), [1] parpe::AmiciSummedGradientFunction::evaluate (C++ function), [1] parpe::AmiciSummedGradientFunction::getAllMeasurements (C++ function) parpe::AmiciSummedGradientFunction::getModelOutputsAndSigmas (C++ function) parpe::AmiciSummedGradientFunction::getParameterIds (C++ function) parpe::AmiciSummedGradientFunction::getParameterScaling (C++ function) parpe::AmiciSummedGradientFunction::messageHandler (C++ function) parpe::AmiciSummedGradientFunction::numParameters (C++ function) parpe::AmiciSummedGradientFunction::ResultMap (C++ type) parpe::AmiciSummedGradientFunction::ResultPackage (C++ type) parpe::AmiciSummedGradientFunction::runSimulations (C++ function) parpe::AmiciSummedGradientFunction::sendStates (C++ member) parpe::AmiciSummedGradientFunction::setSensitivityOptions (C++ function) parpe::AmiciSummedGradientFunction::WorkPackage (C++ type) parpe::AmiciSummedGradientFunction::~AmiciSummedGradientFunction (C++ function) parpe::AnalyticalParameterHdf5Reader (C++ class) parpe::AnalyticalParameterHdf5Reader::AnalyticalParameterHdf5Reader (C++ function), [1], [2] parpe::AnalyticalParameterHdf5Reader::getConditionsForParameter (C++ function) parpe::AnalyticalParameterHdf5Reader::getObservablesForParameter (C++ function) parpe::AnalyticalParameterHdf5Reader::getOptimizationParameterIndices (C++ function) parpe::AnalyticalParameterHdf5Reader::~AnalyticalParameterHdf5Reader (C++ function) parpe::AnalyticalParameterProvider (C++ class) parpe::AnalyticalParameterProvider::getConditionsForParameter (C++ function) parpe::AnalyticalParameterProvider::getObservablesForParameter (C++ function) parpe::AnalyticalParameterProvider::getOptimizationParameterIndices (C++ function) parpe::AnalyticalParameterProvider::~AnalyticalParameterProvider (C++ function) parpe::AnalyticalParameterProviderDefault (C++ class) parpe::AnalyticalParameterProviderDefault::AnalyticalParameterProviderDefault (C++ function) parpe::AnalyticalParameterProviderDefault::conditionsForParameter (C++ member) parpe::AnalyticalParameterProviderDefault::getConditionsForParameter (C++ function) parpe::AnalyticalParameterProviderDefault::getObservablesForParameter (C++ function) parpe::AnalyticalParameterProviderDefault::getOptimizationParameterIndices (C++ function) parpe::AnalyticalParameterProviderDefault::mapping (C++ member) parpe::AnalyticalParameterProviderDefault::optimizationParameterIndices (C++ member) parpe::ANSI_COLOR_BLUE (C++ member) parpe::ANSI_COLOR_CYAN (C++ member) parpe::ANSI_COLOR_GREEN (C++ member) parpe::ANSI_COLOR_MAGENTA (C++ member) parpe::ANSI_COLOR_RED (C++ member) parpe::ANSI_COLOR_RESET (C++ member) parpe::ANSI_COLOR_YELLOW (C++ member) parpe::applyChainRule (C++ function) parpe::applyOptimalOffset (C++ function) parpe::applyOptimalScaling (C++ function) parpe::checkGradientForAnalyticalParameters (C++ function) parpe::clipToBounds (C++ function) parpe::computeAnalyticalOffsets (C++ function) parpe::computeAnalyticalScalings (C++ function) parpe::computeAnalyticalSigmas (C++ function) parpe::computeNegLogLikelihood (C++ function), [1] parpe::CostFunction (C++ class) parpe::CostFunction::evaluate (C++ function), [1] parpe::CostFunction::~CostFunction (C++ function) parpe::CpuTimer (C++ class) parpe::CpuTimer::CpuTimer (C++ function) parpe::CpuTimer::getRound (C++ function) parpe::CpuTimer::getTotal (C++ function) parpe::CpuTimer::reset (C++ function) parpe::ErrorModel (C++ enum) parpe::ErrorModel::normal (C++ enumerator) parpe::fillArrayRandomDoubleIndividualInterval (C++ function) parpe::fillArrayRandomDoubleSameInterval (C++ function) parpe::fillFilteredParams (C++ function) parpe::finalizeMpiIfNeeded (C++ function) parpe::FunctionEvaluationStatus (C++ enum) parpe::FunctionEvaluationStatus::functionEvaluationFailure (C++ enumerator) parpe::FunctionEvaluationStatus::functionEvaluationSuccess (C++ enumerator) parpe::getBacktrace (C++ function) parpe::getBatches (C++ function) parpe::getDefaultOffsetParameter (C++ function) parpe::getDefaultScalingFactor (C++ function) parpe::getFinalParameters (C++ function) parpe::getFunctionEvaluationWithMinimalCost (C++ function) parpe::getLocalOptimum (C++ function) parpe::getMinibatchOptimizer (C++ function) parpe::getModelOutputsAndSigmas (C++ function) parpe::getMpiActive (C++ function) parpe::getMpiCommSize (C++ function) parpe::getMpiRank (C++ function) parpe::getNumStarts (C++ function) parpe::getOuterParameters (C++ function) parpe::getParameterTrajectory (C++ function) parpe::getVectorDifference (C++ function) parpe::getVectorNorm (C++ function) parpe::GradientFunction (C++ class) parpe::GradientFunction::evaluate (C++ function), [1] parpe::GradientFunction::getParameterIds (C++ function) parpe::GradientFunction::numParameters (C++ function) parpe::GradientFunction::~GradientFunction (C++ function) parpe::hdf5AttributeExists (C++ function) parpe::hdf5CreateExtendableDouble2DArray (C++ function) parpe::hdf5CreateExtendableDouble3DArray (C++ function) parpe::hdf5CreateExtendableInt2DArray (C++ function) parpe::hdf5CreateExtendableString1DArray (C++ function) parpe::hdf5CreateFile (C++ function) parpe::hdf5CreateGroup (C++ function) parpe::hdf5CreateOrExtendAndWriteToDouble2DArray (C++ function) parpe::hdf5CreateOrExtendAndWriteToDouble3DArray (C++ function) parpe::hdf5CreateOrExtendAndWriteToInt2DArray (C++ function) parpe::hdf5CreateOrExtendAndWriteToString1DArray (C++ function) parpe::hdf5EnsureGroupExists (C++ function) parpe::hdf5ErrorStackWalker_cb (C++ function) parpe::HDF5Exception (C++ class) parpe::HDF5Exception::HDF5Exception (C++ function), [1] parpe::HDF5Exception::msg (C++ member) parpe::HDF5Exception::stackTrace (C++ member) parpe::HDF5Exception::what (C++ function) parpe::hdf5Extend2ndDimensionAndWriteToDouble2DArray (C++ function) parpe::hdf5Extend2ndDimensionAndWriteToInt2DArray (C++ function) parpe::hdf5Extend3rdDimensionAndWriteToDouble3DArray (C++ function) parpe::hdf5ExtendAndWriteToString1DArray (C++ function) parpe::hdf5Get3DDoubleHyperslab (C++ function) parpe::hdf5GetDatasetDimensions (C++ function) parpe::hdf5GroupExists (C++ function) parpe::hdf5MutexGetLock (C++ function) parpe::hdf5OpenForAppending (C++ function) parpe::hdf5OpenForReading (C++ function) parpe::hdf5Read1DIntegerHyperslab (C++ function) parpe::hdf5Read1dStringDataset (C++ function) parpe::hdf5Read2DDoubleHyperslab (C++ function) parpe::hdf5Read2DIntegerHyperslab (C++ function) parpe::hdf5Read3DDoubleHyperslab (C++ function) parpe::hdf5Write1dStringDataset (C++ function) parpe::hdf5WriteStringAttribute (C++ function) parpe::HierarchicalOptimizationProblemWrapper (C++ class) parpe::HierarchicalOptimizationProblemWrapper::fillFilteredParams (C++ function) parpe::HierarchicalOptimizationProblemWrapper::fillInitialParameters (C++ function) parpe::HierarchicalOptimizationProblemWrapper::fillParametersMax (C++ function) parpe::HierarchicalOptimizationProblemWrapper::fillParametersMin (C++ function) parpe::HierarchicalOptimizationProblemWrapper::getOptimizationOptions (C++ function) parpe::HierarchicalOptimizationProblemWrapper::getReporter (C++ function) parpe::HierarchicalOptimizationProblemWrapper::HierarchicalOptimizationProblemWrapper (C++ function), [1], [2], [3] parpe::HierarchicalOptimizationProblemWrapper::setOptimizationOptions (C++ function) parpe::HierarchicalOptimizationReporter (C++ class) parpe::HierarchicalOptimizationReporter::afterCostFunctionCall (C++ function) parpe::HierarchicalOptimizationReporter::cached_full_gradient_ (C++ member) parpe::HierarchicalOptimizationReporter::cached_full_parameters_ (C++ member) parpe::HierarchicalOptimizationReporter::evaluate (C++ function), [1], [2] parpe::HierarchicalOptimizationReporter::finished (C++ function) parpe::HierarchicalOptimizationReporter::getFinalParameters (C++ function) parpe::HierarchicalOptimizationReporter::hierarchical_wrapper_ (C++ member) parpe::HierarchicalOptimizationReporter::HierarchicalOptimizationReporter (C++ function) parpe::HierarchicalOptimizationReporter::iterationFinished (C++ function) parpe::HierarchicalOptimizationWrapper (C++ class) parpe::HierarchicalOptimizationWrapper::applyOptimalOffsets (C++ function) parpe::HierarchicalOptimizationWrapper::applyOptimalScalings (C++ function) parpe::HierarchicalOptimizationWrapper::computeAnalyticalOffsets (C++ function) parpe::HierarchicalOptimizationWrapper::computeAnalyticalScalings (C++ function) parpe::HierarchicalOptimizationWrapper::computeAnalyticalSigmas (C++ function) parpe::HierarchicalOptimizationWrapper::evaluate (C++ function), [1], [2], [3] parpe::HierarchicalOptimizationWrapper::evaluateWithOptimalParameters (C++ function) parpe::HierarchicalOptimizationWrapper::fillInAnalyticalSigmas (C++ function) parpe::HierarchicalOptimizationWrapper::getAnalyticalParameterIndices (C++ function) parpe::HierarchicalOptimizationWrapper::getDefaultOffsetParameters (C++ function) parpe::HierarchicalOptimizationWrapper::getDefaultScalingFactors (C++ function) parpe::HierarchicalOptimizationWrapper::getDefaultSigmaParameters (C++ function) parpe::HierarchicalOptimizationWrapper::getOffsetParameterIndices (C++ function) parpe::HierarchicalOptimizationWrapper::getParameterIds (C++ function) parpe::HierarchicalOptimizationWrapper::getProportionalityFactorIndices (C++ function) parpe::HierarchicalOptimizationWrapper::getSigmaParameterIndices (C++ function) parpe::HierarchicalOptimizationWrapper::getUnscaledModelOutputsAndSigmas (C++ function) parpe::HierarchicalOptimizationWrapper::getWrappedFunction (C++ function) parpe::HierarchicalOptimizationWrapper::HierarchicalOptimizationWrapper (C++ function), [1], [2] parpe::HierarchicalOptimizationWrapper::numOffsetParameters (C++ function) parpe::HierarchicalOptimizationWrapper::numParameters (C++ function) parpe::HierarchicalOptimizationWrapper::numProportionalityFactors (C++ function) parpe::HierarchicalOptimizationWrapper::numSigmaParameters (C++ function) parpe::initHDF5Mutex (C++ function) parpe::interceptType (C++ enum) parpe::interceptType::none (C++ enumerator) parpe::interceptType::reduceStep (C++ enumerator) parpe::interceptType::reduceStepAndRestart (C++ enumerator) parpe::InverseUniqueLock (C++ class) parpe::InverseUniqueLock::InverseUniqueLock (C++ function), [1], [2] parpe::InverseUniqueLock::operator= (C++ function), [1] parpe::InverseUniqueLock::~InverseUniqueLock (C++ function) parpe::ipOptGetLock (C++ function) parpe::ipOptReleaseLock (C++ function) parpe::JobData (C++ struct) parpe::JobData::callbackJobFinished (C++ member) parpe::JobData::JobData (C++ function), [1] parpe::JobData::jobDone (C++ member) parpe::JobData::jobDoneChangedCondition (C++ member) parpe::JobData::jobDoneChangedMutex (C++ member) parpe::JobData::jobId (C++ member) parpe::JobData::recvBuffer (C++ member) parpe::JobData::sendBuffer (C++ member) parpe::learningRateInterp (C++ enum) parpe::learningRateInterp::inverseLinear (C++ enumerator) parpe::learningRateInterp::linear (C++ enumerator) parpe::learningRateInterp::logarithmic (C++ enumerator) parpe::LearningRateUpdater (C++ class) parpe::LearningRateUpdater::getCurrentLearningRate (C++ function) parpe::LearningRateUpdater::increaseLearningRate (C++ function) parpe::LearningRateUpdater::LearningRateUpdater (C++ function) parpe::LearningRateUpdater::reduceLearningRate (C++ function) parpe::LearningRateUpdater::setEndLearningRate (C++ function) parpe::LearningRateUpdater::setMaxEpochs (C++ function) parpe::LearningRateUpdater::setReductionFactor (C++ function) parpe::LearningRateUpdater::setStartLearningRate (C++ function) parpe::LearningRateUpdater::updateLearningRate (C++ function) parpe::LinearModel (C++ class) parpe::LinearModel::evaluate (C++ function), [1], [2] parpe::LinearModel::LinearModel (C++ function) parpe::LinearModelMSE (C++ class) parpe::LinearModelMSE::datasets (C++ member) parpe::LinearModelMSE::evaluate (C++ function), [1] parpe::LinearModelMSE::getParameterIds (C++ function) parpe::LinearModelMSE::labels (C++ member) parpe::LinearModelMSE::LinearModelMSE (C++ function) parpe::LinearModelMSE::lm (C++ member) parpe::LinearModelMSE::numParameters (C++ function) parpe::LinearModelMSE::numParameters_ (C++ member) parpe::LoadBalancerMaster (C++ type) parpe::LoadBalancerWorker (C++ class) (C++ type) parpe::LoadBalancerWorker::LoadBalancerWorker (C++ function) parpe::LoadBalancerWorker::messageHandlerFunc (C++ type) parpe::LoadBalancerWorker::run (C++ function) parpe::LocalOptimizationIpoptTNLP (C++ class) parpe::LocalOptimizationIpoptTNLP::eval_f (C++ function) parpe::LocalOptimizationIpoptTNLP::eval_g (C++ function) parpe::LocalOptimizationIpoptTNLP::eval_grad_f (C++ function) parpe::LocalOptimizationIpoptTNLP::eval_jac_g (C++ function) parpe::LocalOptimizationIpoptTNLP::finalize_solution (C++ function) parpe::LocalOptimizationIpoptTNLP::get_bounds_info (C++ function) parpe::LocalOptimizationIpoptTNLP::get_nlp_info (C++ function) parpe::LocalOptimizationIpoptTNLP::get_starting_point (C++ function) parpe::LocalOptimizationIpoptTNLP::intermediate_callback (C++ function) parpe::LocalOptimizationIpoptTNLP::LocalOptimizationIpoptTNLP (C++ function) parpe::LocalOptimizationIpoptTNLP::~LocalOptimizationIpoptTNLP (C++ function) parpe::Logger (C++ class) parpe::Logger::getChild (C++ function) parpe::Logger::getPrefix (C++ function) parpe::Logger::Logger (C++ function), [1] parpe::Logger::logmessage (C++ function), [1], [2] parpe::Logger::setPrefix (C++ function) parpe::loglevel (C++ enum) parpe::loglevel::critical (C++ enumerator) parpe::loglevel::debug (C++ enumerator) parpe::loglevel::error (C++ enumerator) parpe::loglevel::info (C++ enumerator) parpe::loglevel::warning (C++ enumerator) parpe::logmessage (C++ function), [1], [2] parpe::logProcessStats (C++ function) parpe::MeanSquaredError (C++ class) parpe::MeanSquaredError::evaluate (C++ function), [1], [2] parpe::messageHandler (C++ function) parpe::minibatchExitStatus (C++ enum) parpe::minibatchExitStatus::gradientNormConvergence (C++ enumerator) parpe::minibatchExitStatus::invalidNumber (C++ enumerator) parpe::minibatchExitStatus::maxEpochsExceeded (C++ enumerator) parpe::MinibatchOptimizationProblem (C++ class) parpe::MinibatchOptimizationProblem::getGradientFunction (C++ function) parpe::MinibatchOptimizationProblem::getTrainingData (C++ function) parpe::MinibatchOptimizationProblem::MinibatchOptimizationProblem (C++ function), [1], [2] parpe::MinibatchOptimizationProblem::~MinibatchOptimizationProblem (C++ function) parpe::MinibatchOptimizer (C++ class) parpe::MinibatchOptimizer::batchSize (C++ member) parpe::MinibatchOptimizer::evaluate (C++ function) parpe::MinibatchOptimizer::finish (C++ function) parpe::MinibatchOptimizer::gradientNormThreshold (C++ member) parpe::MinibatchOptimizer::handleStep (C++ function) parpe::MinibatchOptimizer::interceptor (C++ member) parpe::MinibatchOptimizer::learningRate (C++ member) parpe::MinibatchOptimizer::learningRateUpdater (C++ member) parpe::MinibatchOptimizer::lineSearchSteps (C++ member) parpe::MinibatchOptimizer::maxEpochs (C++ member) parpe::MinibatchOptimizer::optimize (C++ function) parpe::MinibatchOptimizer::parameterUpdater (C++ member) parpe::MinibatchOptimizer::performLineSearch (C++ function) parpe::MinibatchOptimizer::rescueInterceptor (C++ function) parpe::minimumLogLevel (C++ member) parpe::Model (C++ class) parpe::Model::evaluate (C++ function), [1] parpe::Model::~Model (C++ function) parpe::MultiConditionDataProvider (C++ class) parpe::MultiConditionDataProvider::getAllMeasurements (C++ function) parpe::MultiConditionDataProvider::getAllSigmas (C++ function) parpe::MultiConditionDataProvider::getExperimentalDataForCondition (C++ function) parpe::MultiConditionDataProvider::getModel (C++ function) parpe::MultiConditionDataProvider::getNumberOfSimulationConditions (C++ function) parpe::MultiConditionDataProvider::getNumOptimizationParameters (C++ function) parpe::MultiConditionDataProvider::getParameterScaleOpt (C++ function), [1] parpe::MultiConditionDataProvider::getParameterScaleSim (C++ function), [1] parpe::MultiConditionDataProvider::getProblemParameterIds (C++ function) parpe::MultiConditionDataProvider::getSimulationToOptimizationParameterMapping (C++ function) parpe::MultiConditionDataProvider::getSolver (C++ function) parpe::MultiConditionDataProvider::mapAndSetOptimizationToSimulationVariables (C++ function) parpe::MultiConditionDataProvider::mapSimulationToOptimizationGradientAddMultiply (C++ function) parpe::MultiConditionDataProvider::updateSimulationParametersAndScale (C++ function) parpe::MultiConditionDataProvider::~MultiConditionDataProvider (C++ function) parpe::MultiConditionDataProviderDefault (C++ class) parpe::MultiConditionDataProviderDefault::edata_ (C++ member) parpe::MultiConditionDataProviderDefault::getAllMeasurements (C++ function) parpe::MultiConditionDataProviderDefault::getAllSigmas (C++ function) parpe::MultiConditionDataProviderDefault::getExperimentalDataForCondition (C++ function) parpe::MultiConditionDataProviderDefault::getModel (C++ function) parpe::MultiConditionDataProviderDefault::getNumberOfSimulationConditions (C++ function) parpe::MultiConditionDataProviderDefault::getNumOptimizationParameters (C++ function) parpe::MultiConditionDataProviderDefault::getParameterScaleOpt (C++ function), [1]

parpe::MultiConditionDataProviderDefault::getParameterScaleSim (C++ function), [1] parpe::MultiConditionDataProviderDefault::getProblemParameterIds (C++ function) parpe::MultiConditionDataProviderDefault::getSimulationToOptimizationParameterMapping (C++ function) parpe::MultiConditionDataProviderDefault::getSolver (C++ function) parpe::MultiConditionDataProviderDefault::mapAndSetOptimizationToSimulationVariables (C++ function) parpe::MultiConditionDataProviderDefault::mapSimulationToOptimizationGradientAddMultiply (C++ function) parpe::MultiConditionDataProviderDefault::MultiConditionDataProviderDefault (C++ function) parpe::MultiConditionDataProviderDefault::updateSimulationParametersAndScale (C++ function) parpe::MultiConditionDataProviderDefault::~MultiConditionDataProviderDefault (C++ function) parpe::MultiConditionDataProviderHDF5 (C++ class) parpe::MultiConditionDataProviderHDF5::checkDataIntegrity (C++ function) parpe::MultiConditionDataProviderHDF5::copyInputData (C++ function) parpe::MultiConditionDataProviderHDF5::getAllMeasurements (C++ function) parpe::MultiConditionDataProviderHDF5::getAllSigmas (C++ function) parpe::MultiConditionDataProviderHDF5::getExperimentalDataForCondition (C++ function) parpe::MultiConditionDataProviderHDF5::getHdf5File (C++ function) parpe::MultiConditionDataProviderHDF5::getMeasurementForSimulationIndex (C++ function) parpe::MultiConditionDataProviderHDF5::getModel (C++ function) parpe::MultiConditionDataProviderHDF5::getNumberOfSimulationConditions (C++ function) parpe::MultiConditionDataProviderHDF5::getNumOptimizationParameters (C++ function) parpe::MultiConditionDataProviderHDF5::getOptimizationParametersLowerBounds (C++ function) parpe::MultiConditionDataProviderHDF5::getOptimizationParametersUpperBounds (C++ function) parpe::MultiConditionDataProviderHDF5::getParameterScaleOpt (C++ function), [1] parpe::MultiConditionDataProviderHDF5::getParameterScaleSim (C++ function), [1] parpe::MultiConditionDataProviderHDF5::getProblemParameterIds (C++ function) parpe::MultiConditionDataProviderHDF5::getReinitializationIndices (C++ function) parpe::MultiConditionDataProviderHDF5::getSensitivityParameterList (C++ function) parpe::MultiConditionDataProviderHDF5::getSigmaForSimulationIndex (C++ function) parpe::MultiConditionDataProviderHDF5::getSimAndPreeqConditions (C++ function) parpe::MultiConditionDataProviderHDF5::getSimulationToOptimizationParameterMapping (C++ function) parpe::MultiConditionDataProviderHDF5::getSolver (C++ function) parpe::MultiConditionDataProviderHDF5::mapAndSetOptimizationToSimulationVariables (C++ function) parpe::MultiConditionDataProviderHDF5::mapSimulationToOptimizationGradientAddMultiply (C++ function) parpe::MultiConditionDataProviderHDF5::MultiConditionDataProviderHDF5 (C++ function), [1], [2], [3] parpe::MultiConditionDataProviderHDF5::readFixedSimulationParameters (C++ function) parpe::MultiConditionDataProviderHDF5::setModel (C++ function) parpe::MultiConditionDataProviderHDF5::updateFixedSimulationParameters (C++ function) parpe::MultiConditionDataProviderHDF5::updateSimulationParametersAndScale (C++ function) parpe::MultiConditionDataProviderHDF5::~MultiConditionDataProviderHDF5 (C++ function) parpe::MultiConditionProblem (C++ class) parpe::MultiConditionProblem::earlyStopping (C++ function) parpe::MultiConditionProblem::fillInitialParameters (C++ function) parpe::MultiConditionProblem::fillParametersMax (C++ function) parpe::MultiConditionProblem::fillParametersMin (C++ function) parpe::MultiConditionProblem::getDataProvider (C++ function) parpe::MultiConditionProblem::getReporter (C++ function) parpe::MultiConditionProblem::getResultWriter (C++ function) parpe::MultiConditionProblem::getTrainingData (C++ function) parpe::MultiConditionProblem::MultiConditionProblem (C++ function), [1], [2] parpe::MultiConditionProblem::setInitialParameters (C++ function) parpe::MultiConditionProblem::setParametersMax (C++ function) parpe::MultiConditionProblem::setParametersMin (C++ function) parpe::MultiConditionProblem::~MultiConditionProblem (C++ function) parpe::MultiConditionProblemMultiStartOptimizationProblem (C++ class) parpe::MultiConditionProblemMultiStartOptimizationProblem::getLocalProblem (C++ function) parpe::MultiConditionProblemMultiStartOptimizationProblem::getNumberOfStarts (C++ function) parpe::MultiConditionProblemMultiStartOptimizationProblem::MultiConditionProblemMultiStartOptimizationProblem (C++ function) parpe::MultiConditionProblemMultiStartOptimizationProblem::restartOnFailure (C++ function) parpe::MultiStartOptimization (C++ class) parpe::MultiStartOptimization::MultiStartOptimization (C++ function) parpe::MultiStartOptimization::run (C++ function) parpe::MultiStartOptimization::runMultiThreaded (C++ function) parpe::MultiStartOptimization::runSingleThreaded (C++ function) parpe::MultiStartOptimization::setRunParallel (C++ function) parpe::MultiStartOptimization::~MultiStartOptimization (C++ function) parpe::MultiStartOptimizationProblem (C++ class) parpe::MultiStartOptimizationProblem::getLocalProblem (C++ function) parpe::MultiStartOptimizationProblem::getNumberOfStarts (C++ function) parpe::MultiStartOptimizationProblem::restartOnFailure (C++ function) parpe::MultiStartOptimizationProblem::~MultiStartOptimizationProblem (C++ function) parpe::mutexHdfType (C++ type) parpe::mutexIpOpt (C++ member) parpe::mutexIpOptType (C++ type) parpe::operator== (C++ function) parpe::OptimizationApplication (C++ class) parpe::OptimizationApplication::dataFileName (C++ member) parpe::OptimizationApplication::finalizeTiming (C++ function) parpe::OptimizationApplication::first_start_idx (C++ member) parpe::OptimizationApplication::h5File (C++ member) parpe::OptimizationApplication::initMPI (C++ function) parpe::OptimizationApplication::initProblem (C++ function) parpe::OptimizationApplication::isMaster (C++ function) parpe::OptimizationApplication::isWorker (C++ function) parpe::OptimizationApplication::loadBalancer (C++ member) parpe::OptimizationApplication::logParPEVersion (C++ function) parpe::OptimizationApplication::longOptions (C++ member) parpe::OptimizationApplication::multiStartOptimizationProblem (C++ member) parpe::OptimizationApplication::OperationType (C++ enum) parpe::OptimizationApplication::operationType (C++ member) parpe::OptimizationApplication::OperationType::gradientCheck (C++ enumerator) parpe::OptimizationApplication::OperationType::parameterEstimation (C++ enumerator) parpe::OptimizationApplication::OptimizationApplication (C++ function) parpe::OptimizationApplication::parseCliOptionsPostMpiInit (C++ function) parpe::OptimizationApplication::parseCliOptionsPreMpiInit (C++ function) parpe::OptimizationApplication::printUsage (C++ function) parpe::OptimizationApplication::problem (C++ member) parpe::OptimizationApplication::processResultFilenameCommandLineArgument (C++ function) parpe::OptimizationApplication::resultFileName (C++ member) parpe::OptimizationApplication::run (C++ function) parpe::OptimizationApplication::runMaster (C++ function) parpe::OptimizationApplication::runSingleProcess (C++ function) parpe::OptimizationApplication::shortOptions (C++ member) parpe::OptimizationApplication::withMPI (C++ member) parpe::OptimizationApplication::~OptimizationApplication (C++ function) parpe::OptimizationOptions (C++ class) parpe::OptimizationOptions::createOptimizer (C++ function) parpe::OptimizationOptions::for_each (C++ function) parpe::OptimizationOptions::fromHDF5 (C++ function), [1] parpe::OptimizationOptions::getDoubleOption (C++ function) parpe::OptimizationOptions::getIntOption (C++ function) parpe::OptimizationOptions::getStartingPoint (C++ function) parpe::OptimizationOptions::getStringOption (C++ function) parpe::OptimizationOptions::hierarchicalOptimization (C++ member) parpe::OptimizationOptions::logFile (C++ member) parpe::OptimizationOptions::maxOptimizerIterations (C++ member) parpe::OptimizationOptions::multistartsInParallel (C++ member) parpe::OptimizationOptions::numStarts (C++ member) parpe::OptimizationOptions::OptimizationOptions (C++ function) parpe::OptimizationOptions::optimizer (C++ member) parpe::OptimizationOptions::printToStdout (C++ member) parpe::OptimizationOptions::retryOptimization (C++ member) parpe::OptimizationOptions::setOption (C++ function), [1], [2] parpe::OptimizationOptions::toString (C++ function) parpe::OptimizationProblem (C++ class) parpe::OptimizationProblem::cost_fun_ (C++ member) parpe::OptimizationProblem::fillInitialParameters (C++ function) parpe::OptimizationProblem::fillParametersMax (C++ function) parpe::OptimizationProblem::fillParametersMin (C++ function) parpe::OptimizationProblem::getOptimizationOptions (C++ function) parpe::OptimizationProblem::getReporter (C++ function) parpe::OptimizationProblem::logger_ (C++ member) parpe::OptimizationProblem::OptimizationProblem (C++ function), [1], [2] parpe::OptimizationProblem::setOptimizationOptions (C++ function) parpe::OptimizationProblem::~OptimizationProblem (C++ function) parpe::optimizationProblemGradientCheck (C++ function), [1] parpe::optimizationProblemGradientCheckMultiEps (C++ function), [1] parpe::OptimizationProblemImpl (C++ class) parpe::OptimizationProblemImpl::fillInitialParameters (C++ function) parpe::OptimizationProblemImpl::fillParametersMax (C++ function) parpe::OptimizationProblemImpl::fillParametersMin (C++ function) parpe::OptimizationProblemImpl::OptimizationProblem (C++ function), [1], [2] parpe::OptimizationProblemImpl::setInitialParameters (C++ function) parpe::OptimizationProblemImpl::setParametersMax (C++ function) parpe::OptimizationProblemImpl::setParametersMin (C++ function) parpe::OptimizationReporter (C++ class) parpe::OptimizationReporter::afterCostFunctionCall (C++ function) parpe::OptimizationReporter::beforeCostFunctionCall (C++ function) parpe::OptimizationReporter::cached_cost_ (C++ member) parpe::OptimizationReporter::cached_gradient_ (C++ member) parpe::OptimizationReporter::cached_parameters_ (C++ member) parpe::OptimizationReporter::cached_status_ (C++ member) parpe::OptimizationReporter::cpu_time_iteration_sec_ (C++ member) parpe::OptimizationReporter::cpu_time_total_sec_ (C++ member) parpe::OptimizationReporter::default_logger_prefix_ (C++ member) parpe::OptimizationReporter::evaluate (C++ function) parpe::OptimizationReporter::final_cost_ (C++ member) parpe::OptimizationReporter::finished (C++ function) parpe::OptimizationReporter::getFinalCost (C++ function) parpe::OptimizationReporter::getFinalParameters (C++ function) parpe::OptimizationReporter::getParameterIds (C++ function) parpe::OptimizationReporter::grad_fun_ (C++ member) parpe::OptimizationReporter::have_cached_cost_ (C++ member) parpe::OptimizationReporter::have_cached_gradient_ (C++ member) parpe::OptimizationReporter::iterationFinished (C++ function) parpe::OptimizationReporter::logger_ (C++ member) parpe::OptimizationReporter::num_function_calls_ (C++ member) parpe::OptimizationReporter::num_iterations_ (C++ member) parpe::OptimizationReporter::num_parameters_ (C++ member) parpe::OptimizationReporter::numParameters (C++ function) parpe::OptimizationReporter::OptimizationReporter (C++ function), [1] parpe::OptimizationReporter::printObjectiveFunctionFailureMessage (C++ function) parpe::OptimizationReporter::result_writer_ (C++ member) parpe::OptimizationReporter::setGradientFunction (C++ function) parpe::OptimizationReporter::started_ (C++ member) parpe::OptimizationReporter::starting (C++ function) parpe::OptimizationReporter::wall_timer_ (C++ member) parpe::OptimizationResultWriter (C++ class) parpe::OptimizationResultWriter::flushResultWriter (C++ function) parpe::OptimizationResultWriter::getH5File (C++ function) parpe::OptimizationResultWriter::getRootPath (C++ function) parpe::OptimizationResultWriter::logGradientEachFunctionEvaluation (C++ member) parpe::OptimizationResultWriter::logGradientEachIteration (C++ member) parpe::OptimizationResultWriter::logObjectiveFunctionEvaluation (C++ function) parpe::OptimizationResultWriter::logOptimizerIteration (C++ function) parpe::OptimizationResultWriter::logParametersEachFunctionEvaluation (C++ member) parpe::OptimizationResultWriter::operator= (C++ function) parpe::OptimizationResultWriter::OptimizationResultWriter (C++ function), [1], [2] parpe::OptimizationResultWriter::saveOptimizerResults (C++ function) parpe::OptimizationResultWriter::setLoggingEachFunctionEvaluation (C++ function) parpe::OptimizationResultWriter::setLoggingEachIteration (C++ function) parpe::OptimizationResultWriter::setRootPath (C++ function) parpe::OptimizationResultWriter::starting (C++ function) parpe::OptimizationResultWriter::~OptimizationResultWriter (C++ function) parpe::Optimizer (C++ class) parpe::Optimizer::optimize (C++ function) parpe::Optimizer::~Optimizer (C++ function) parpe::OptimizerCeres (C++ class) parpe::OptimizerCeres::optimize (C++ function) parpe::OptimizerCeres::OptimizerCeres (C++ function) parpe::OptimizerDlibLineSearch (C++ class) parpe::OptimizerDlibLineSearch::optimize (C++ function) parpe::OptimizerDlibLineSearch::OptimizerDlibLineSearch (C++ function) parpe::optimizerFactory (C++ function) parpe::OptimizerFides (C++ class) parpe::OptimizerFides::optimize (C++ function) parpe::OptimizerFides::OptimizerFides (C++ function) parpe::OptimizerFsqp (C++ class) parpe::OptimizerFsqp::optimize (C++ function) parpe::OptimizerFsqp::OptimizerFsqp (C++ function) parpe::OptimizerIpOpt (C++ class) parpe::OptimizerIpOpt::optimize (C++ function) parpe::OptimizerIpOpt::OptimizerIpOpt (C++ function) parpe::optimizerName (C++ enum) parpe::optimizerName::OPTIMIZER_CERES (C++ enumerator) parpe::optimizerName::OPTIMIZER_DLIB (C++ enumerator) parpe::optimizerName::OPTIMIZER_FIDES (C++ enumerator) parpe::optimizerName::OPTIMIZER_FSQP (C++ enumerator) parpe::optimizerName::OPTIMIZER_IPOPT (C++ enumerator) parpe::optimizerName::OPTIMIZER_MINIBATCH_1 (C++ enumerator) parpe::optimizerName::OPTIMIZER_TOMS611 (C++ enumerator) parpe::OptimizerToms611TrustRegionSumsl (C++ class) parpe::OptimizerToms611TrustRegionSumsl::optimize (C++ function) parpe::OptimizerToms611TrustRegionSumsl::OptimizerToms611TrustRegionSumsl (C++ function) parpe::ParameterUpdater (C++ class) parpe::ParameterUpdater::clearCache (C++ function) parpe::ParameterUpdater::initialize (C++ function) parpe::ParameterUpdater::undoLastStep (C++ function) parpe::ParameterUpdater::updateParameters (C++ function) parpe::ParameterUpdater::~ParameterUpdater (C++ function) parpe::ParameterUpdaterAdam (C++ class) parpe::ParameterUpdaterAdam::clearCache (C++ function) parpe::ParameterUpdaterAdam::initialize (C++ function) parpe::ParameterUpdaterAdam::ParameterUpdaterAdam (C++ function) parpe::ParameterUpdaterAdam::undoLastStep (C++ function) parpe::ParameterUpdaterAdam::updateParameters (C++ function) parpe::ParameterUpdaterAdamClassic (C++ class) parpe::ParameterUpdaterAdamClassic::clearCache (C++ function) parpe::ParameterUpdaterAdamClassic::initialize (C++ function) parpe::ParameterUpdaterAdamClassic::ParameterUpdaterAdamClassic (C++ function) parpe::ParameterUpdaterAdamClassic::undoLastStep (C++ function) parpe::ParameterUpdaterAdamClassic::updateParameters (C++ function) parpe::ParameterUpdaterMomentum (C++ class) parpe::ParameterUpdaterMomentum::clearCache (C++ function) parpe::ParameterUpdaterMomentum::initialize (C++ function) parpe::ParameterUpdaterMomentum::ParameterUpdaterMomentum (C++ function) parpe::ParameterUpdaterMomentum::undoLastStep (C++ function) parpe::ParameterUpdaterMomentum::updateParameters (C++ function) parpe::ParameterUpdaterRmsProp (C++ class) parpe::ParameterUpdaterRmsProp::clearCache (C++ function) parpe::ParameterUpdaterRmsProp::initialize (C++ function) parpe::ParameterUpdaterRmsProp::ParameterUpdaterRmsProp (C++ function) parpe::ParameterUpdaterRmsProp::undoLastStep (C++ function) parpe::ParameterUpdaterRmsProp::updateParameters (C++ function) parpe::ParameterUpdaterVanilla (C++ class) parpe::ParameterUpdaterVanilla::clearCache (C++ function) parpe::ParameterUpdaterVanilla::initialize (C++ function) parpe::ParameterUpdaterVanilla::ParameterUpdaterVanilla (C++ function) parpe::ParameterUpdaterVanilla::undoLastStep (C++ function) parpe::ParameterUpdaterVanilla::updateParameters (C++ function) parpe::ParPEException (C++ class) parpe::ParPEException::ParPEException (C++ function), [1] parpe::ParPEException::what (C++ function) parpe::ParPEException::~ParPEException (C++ function) parpe::printAvailableOptimizers (C++ function) parpe::printBacktrace (C++ function) parpe::printDebugInfoAndWait (C++ function) parpe::printfToString (C++ function) parpe::printMPIInfo (C++ function) parpe::randDouble (C++ function) parpe::removeInnerParameters (C++ function) parpe::run_amici_simulation (C++ function) parpe::runAlongTrajectory (C++ function) parpe::runAndLogSimulation (C++ function) parpe::runFinalParameters (C++ function) parpe::runMinibatchOptimization (C++ function) parpe::runSimulator (C++ function) parpe::saveSimulation (C++ function) parpe::saveTotalCpuTime (C++ function) parpe::setIpOptOption (C++ function) parpe::setMinibatchOption (C++ function) parpe::SimulationResultWriter (C++ class) parpe::SimulationResultWriter::createDatasets (C++ function), [1] parpe::SimulationResultWriter::llhPath (C++ member) parpe::SimulationResultWriter::parametersPath (C++ member) parpe::SimulationResultWriter::reopenFile (C++ function) parpe::SimulationResultWriter::save_parameters_ (C++ member) parpe::SimulationResultWriter::saveLikelihood (C++ function) parpe::SimulationResultWriter::saveLlh (C++ member) parpe::SimulationResultWriter::saveMeasurements (C++ function) parpe::SimulationResultWriter::saveModelOutputs (C++ function) parpe::SimulationResultWriter::saveParameters (C++ function) parpe::SimulationResultWriter::saveSimulationResults (C++ function) parpe::SimulationResultWriter::saveStates (C++ function) parpe::SimulationResultWriter::saveTimepoints (C++ function) parpe::SimulationResultWriter::saveX (C++ member) parpe::SimulationResultWriter::saveYMes (C++ member) parpe::SimulationResultWriter::saveYSim (C++ member) parpe::SimulationResultWriter::SimulationResultWriter (C++ function), [1], [2], [3] parpe::SimulationResultWriter::timePath (C++ member) parpe::SimulationResultWriter::xPath (C++ member) parpe::SimulationResultWriter::yMesPath (C++ member) parpe::SimulationResultWriter::ySimPath (C++ member) parpe::SimulationResultWriter::~SimulationResultWriter (C++ function) parpe::spliceParameters (C++ function) parpe::StandaloneSimulator (C++ class) parpe::StandaloneSimulator::messageHandler (C++ function) parpe::StandaloneSimulator::run (C++ function) parpe::StandaloneSimulator::StandaloneSimulator (C++ function) parpe::strFormatCurrentLocaltime (C++ function) parpe::SummedGradientFunction (C++ class) parpe::SummedGradientFunction::evaluate (C++ function), [1] parpe::SummedGradientFunction::getParameterIds (C++ function) parpe::SummedGradientFunction::numParameters (C++ function) parpe::SummedGradientFunction::~SummedGradientFunction (C++ function) parpe::SummedGradientFunctionGradientFunctionAdapter (C++ class) parpe::SummedGradientFunctionGradientFunctionAdapter::evaluate (C++ function), [1], [2] parpe::SummedGradientFunctionGradientFunctionAdapter::getParameterIds (C++ function) parpe::SummedGradientFunctionGradientFunctionAdapter::getWrappedFunction (C++ function) parpe::SummedGradientFunctionGradientFunctionAdapter::numParameters (C++ function) parpe::SummedGradientFunctionGradientFunctionAdapter::SummedGradientFunctionGradientFunctionAdapter (C++ function) parpe::swap (C++ function) parpe::WallTimer (C++ class) parpe::WallTimer::getRound (C++ function) parpe::WallTimer::getTotal (C++ function) parpe::WallTimer::reset (C++ function) parpe::WallTimer::WallTimer (C++ function) parpe::withinBounds (C++ function)

R

RELEASE_ASSERT (C macro)

S

std::make_unique (C++ function)