parPE C++ API

parPE C++ library functions

Class Hierarchy

• • Namespace parpe
    • Struct JobData
    • Class AmiciSimulationRunner
      • Struct AmiciSimulationRunner::AmiciResultPackageSimple
      • Struct AmiciSimulationRunner::AmiciWorkPackageSimple
    • Class AmiciSummedGradientFunction
    • Class AnalyticalParameterHdf5Reader
    • Class AnalyticalParameterProvider
    • Class AnalyticalParameterProviderDefault
    • Class CostFunction
    • Class CpuTimer
    • Class GradientFunction
    • Class HDF5Exception
    • Class HierarchicalOptimizationProblemWrapper
    • Class HierarchicalOptimizationReporter
    • Class HierarchicalOptimizationWrapper
    • Template Class InverseUniqueLock
    • Class LearningRateUpdater
    • Class LinearModel
    • Class LinearModelMSE
    • Class LoadBalancerWorker
    • Class LocalOptimizationIpoptTNLP
    • Class Logger
    • Class MeanSquaredError
    • Template Class MinibatchOptimizationProblem
    • Template Class MinibatchOptimizer
    • Template Class Model
    • Class MultiConditionDataProvider
    • Class MultiConditionDataProviderDefault
    • Class MultiConditionDataProviderHDF5
    • Class MultiConditionProblem
    • Class MultiConditionProblemMultiStartOptimizationProblem
    • Class MultiStartOptimization
    • Class MultiStartOptimizationProblem
    • Class OptimizationApplication
    • Class OptimizationOptions
    • Class OptimizationProblem
    • Class OptimizationProblemImpl
    • Class OptimizationReporter
    • Class OptimizationResultWriter
    • Class Optimizer
    • Class OptimizerCeres
    • Class OptimizerDlibLineSearch
    • Class OptimizerFides
    • Class OptimizerFsqp
    • Class OptimizerIpOpt
    • Class OptimizerToms611TrustRegionSumsl
    • Class ParameterUpdater
    • Class ParameterUpdaterAdam
    • Class ParameterUpdaterAdamClassic
    • Class ParameterUpdaterMomentum
    • Class ParameterUpdaterRmsProp
    • Class ParameterUpdaterVanilla
    • Class ParPEException
    • Class SimulationResultWriter
    • Class StandaloneSimulator
    • Template Class SummedGradientFunction
    • Template Class SummedGradientFunctionGradientFunctionAdapter
    • Class WallTimer
    • Enum ErrorModel
    • Enum FunctionEvaluationStatus
    • Enum interceptType
    • Enum learningRateInterp
    • Enum loglevel
    • Enum minibatchExitStatus
    • Enum optimizerName

File Hierarchy

• • Directory include
    • Directory parpeamici
      • File amiciMisc.h
      • File amiciSimulationRunner.h
      • File hierarchicalOptimization.h
      • File hierarchicalOptimizationAnalyticalParameterProvider.h
      • File multiConditionDataProvider.h
      • File multiConditionProblem.h
      • File optimizationApplication.h
      • File simulationResultWriter.h
      • File standaloneSimulator.h
    • Directory parpecommon
      • File costFunction.h
      • File functions.h
      • File hdf5Misc.h
      • File logging.h
      • File misc.h
      • File model.h
      • File parpeException.h
    • Directory parpeloadbalancer
      • File loadBalancerMaster.h
      • File loadBalancerWorker.h
    • Directory parpeoptimization
      • File localOptimizationCeres.h
      • File localOptimizationDlib.h
      • File localOptimizationFides.h
      • File localOptimizationFsqp.h
      • File localOptimizationIpopt.h
      • File localOptimizationIpoptTNLP.h
      • File localOptimizationToms611.h
      • File minibatchOptimization.h
      • File multiStartOptimization.h
      • File optimizationOptions.h
      • File optimizationProblem.h
      • File optimizationResultWriter.h
      • File optimizer.h

Full API

Namespaces

• Namespace boost
  • Namespaces

• Namespace boost::serialization
  • Functions

• Namespace Ipopt

• Namespace parpe
  • Classes
  • Enums
  • Functions
  • Typedefs
  • Variables

• Namespace std
  • Functions

Classes and Structs

• Struct AmiciSimulationRunner::AmiciResultPackageSimple
  • Nested Relationships
  • Struct Documentation
    • AmiciResultPackageSimple
      • AmiciResultPackageSimple::AmiciResultPackageSimple()
      • AmiciResultPackageSimple::llh
      • AmiciResultPackageSimple::simulationTimeSeconds
      • AmiciResultPackageSimple::gradient
      • AmiciResultPackageSimple::modelOutput
      • AmiciResultPackageSimple::modelSigmas
      • AmiciResultPackageSimple::modelStates
      • AmiciResultPackageSimple::status

• Struct AmiciSimulationRunner::AmiciWorkPackageSimple
  • Nested Relationships
  • Struct Documentation
    • AmiciWorkPackageSimple
      • AmiciWorkPackageSimple::AmiciWorkPackageSimple()
      • AmiciWorkPackageSimple::optimizationParameters
      • AmiciWorkPackageSimple::sensitivityOrder
      • AmiciWorkPackageSimple::conditionIndices
      • AmiciWorkPackageSimple::logPrefix

• Struct JobData
  • Struct Documentation
    • JobData
      • JobData::JobData()
      • JobData::JobData()
      • JobData::jobId
      • JobData::sendBuffer
      • JobData::recvBuffer
      • JobData::jobDone
      • JobData::jobDoneChangedCondition
      • JobData::jobDoneChangedMutex
      • JobData::callbackJobFinished

• Class AmiciSimulationRunner
  • Nested Relationships
    • Nested Types
  • Class Documentation
    • AmiciSimulationRunner
      • AmiciSimulationRunner::messageHandlerFunc
      • AmiciSimulationRunner::callbackJobFinishedType
      • AmiciSimulationRunner::callbackAllFinishedType
      • AmiciSimulationRunner::AmiciSimulationRunner()
      • AmiciSimulationRunner::AmiciSimulationRunner()
      • AmiciSimulationRunner::runSharedMemory()
      • AmiciSimulationRunner::AmiciResultPackageSimple
        • AmiciSimulationRunner::AmiciResultPackageSimple::AmiciResultPackageSimple()
        • AmiciSimulationRunner::AmiciResultPackageSimple::llh
        • AmiciSimulationRunner::AmiciResultPackageSimple::simulationTimeSeconds
        • AmiciSimulationRunner::AmiciResultPackageSimple::gradient
        • AmiciSimulationRunner::AmiciResultPackageSimple::modelOutput
        • AmiciSimulationRunner::AmiciResultPackageSimple::modelSigmas
        • AmiciSimulationRunner::AmiciResultPackageSimple::modelStates
        • AmiciSimulationRunner::AmiciResultPackageSimple::status
      • AmiciSimulationRunner::AmiciWorkPackageSimple
        • AmiciSimulationRunner::AmiciWorkPackageSimple::AmiciWorkPackageSimple()
        • AmiciSimulationRunner::AmiciWorkPackageSimple::optimizationParameters
        • AmiciSimulationRunner::AmiciWorkPackageSimple::sensitivityOrder
        • AmiciSimulationRunner::AmiciWorkPackageSimple::conditionIndices
        • AmiciSimulationRunner::AmiciWorkPackageSimple::logPrefix

• Class AmiciSummedGradientFunction
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • AmiciSummedGradientFunction
      • AmiciSummedGradientFunction::WorkPackage
      • AmiciSummedGradientFunction::ResultPackage
      • AmiciSummedGradientFunction::ResultMap
      • AmiciSummedGradientFunction::AmiciSummedGradientFunction()
      • AmiciSummedGradientFunction::~AmiciSummedGradientFunction()
      • AmiciSummedGradientFunction::evaluate()
      • AmiciSummedGradientFunction::evaluate()
      • AmiciSummedGradientFunction::numParameters()
      • AmiciSummedGradientFunction::getParameterIds()
      • AmiciSummedGradientFunction::getModelOutputsAndSigmas()
      • AmiciSummedGradientFunction::getAllMeasurements()
      • AmiciSummedGradientFunction::messageHandler()
      • AmiciSummedGradientFunction::getParameterScaling()
      • AmiciSummedGradientFunction::sendStates
      • AmiciSummedGradientFunction::AmiciSummedGradientFunction()
      • AmiciSummedGradientFunction::runSimulations()
      • AmiciSummedGradientFunction::aggregateLikelihood()
      • AmiciSummedGradientFunction::addSimulationGradientToObjectiveFunctionGradient()
      • AmiciSummedGradientFunction::setSensitivityOptions()

• Class AnalyticalParameterHdf5Reader
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • AnalyticalParameterHdf5Reader
      • AnalyticalParameterHdf5Reader::AnalyticalParameterHdf5Reader()
      • AnalyticalParameterHdf5Reader::AnalyticalParameterHdf5Reader()
      • AnalyticalParameterHdf5Reader::AnalyticalParameterHdf5Reader()
      • AnalyticalParameterHdf5Reader::getConditionsForParameter()
      • AnalyticalParameterHdf5Reader::getObservablesForParameter()
      • AnalyticalParameterHdf5Reader::getOptimizationParameterIndices()
      • AnalyticalParameterHdf5Reader::~AnalyticalParameterHdf5Reader()

• Class AnalyticalParameterProvider
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • AnalyticalParameterProvider
      • AnalyticalParameterProvider::~AnalyticalParameterProvider()
      • AnalyticalParameterProvider::getConditionsForParameter()
      • AnalyticalParameterProvider::getObservablesForParameter()
      • AnalyticalParameterProvider::getOptimizationParameterIndices()

• Class AnalyticalParameterProviderDefault
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • AnalyticalParameterProviderDefault
      • AnalyticalParameterProviderDefault::AnalyticalParameterProviderDefault()
      • AnalyticalParameterProviderDefault::getConditionsForParameter()
      • AnalyticalParameterProviderDefault::getObservablesForParameter()
      • AnalyticalParameterProviderDefault::getOptimizationParameterIndices()
      • AnalyticalParameterProviderDefault::conditionsForParameter
      • AnalyticalParameterProviderDefault::optimizationParameterIndices
      • AnalyticalParameterProviderDefault::mapping

• Class CostFunction
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • CostFunction
      • CostFunction::~CostFunction()
      • CostFunction::evaluate()
      • CostFunction::evaluate()

• Class CpuTimer
  • Class Documentation
    • CpuTimer
      • CpuTimer::CpuTimer()
      • CpuTimer::reset()
      • CpuTimer::getRound()
      • CpuTimer::getTotal()

• Class GradientFunction
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • GradientFunction
      • GradientFunction::evaluate()
      • GradientFunction::evaluate()
      • GradientFunction::numParameters()
      • GradientFunction::getParameterIds()
      • GradientFunction::~GradientFunction()

• Class HDF5Exception
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • HDF5Exception
      • HDF5Exception::HDF5Exception()
      • HDF5Exception::HDF5Exception()
      • HDF5Exception::what()
      • HDF5Exception::msg
      • HDF5Exception::stackTrace

• Class HierarchicalOptimizationProblemWrapper
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • HierarchicalOptimizationProblemWrapper
      • HierarchicalOptimizationProblemWrapper::HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper::HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper::HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper::HierarchicalOptimizationProblemWrapper()
      • HierarchicalOptimizationProblemWrapper::fillInitialParameters()
      • HierarchicalOptimizationProblemWrapper::fillParametersMin()
      • HierarchicalOptimizationProblemWrapper::fillParametersMax()
      • HierarchicalOptimizationProblemWrapper::fillFilteredParams()
      • HierarchicalOptimizationProblemWrapper::getOptimizationOptions()
      • HierarchicalOptimizationProblemWrapper::setOptimizationOptions()
      • HierarchicalOptimizationProblemWrapper::getReporter()

• Class HierarchicalOptimizationReporter
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • HierarchicalOptimizationReporter
      • HierarchicalOptimizationReporter::HierarchicalOptimizationReporter()
      • HierarchicalOptimizationReporter::evaluate()
      • HierarchicalOptimizationReporter::iterationFinished()
      • HierarchicalOptimizationReporter::afterCostFunctionCall()
      • HierarchicalOptimizationReporter::finished()
      • HierarchicalOptimizationReporter::getFinalParameters()
      • HierarchicalOptimizationReporter::evaluate()
      • HierarchicalOptimizationReporter::hierarchical_wrapper_
      • HierarchicalOptimizationReporter::cached_full_parameters_
      • HierarchicalOptimizationReporter::cached_full_gradient_

• Class HierarchicalOptimizationWrapper
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • HierarchicalOptimizationWrapper
      • HierarchicalOptimizationWrapper::HierarchicalOptimizationWrapper()
      • HierarchicalOptimizationWrapper::HierarchicalOptimizationWrapper()
      • HierarchicalOptimizationWrapper::HierarchicalOptimizationWrapper()
      • HierarchicalOptimizationWrapper::evaluate()
      • HierarchicalOptimizationWrapper::evaluate()
      • HierarchicalOptimizationWrapper::getDefaultScalingFactors()
      • HierarchicalOptimizationWrapper::getDefaultOffsetParameters()
      • HierarchicalOptimizationWrapper::getDefaultSigmaParameters()
      • HierarchicalOptimizationWrapper::getUnscaledModelOutputsAndSigmas()
      • HierarchicalOptimizationWrapper::computeAnalyticalScalings()
      • HierarchicalOptimizationWrapper::applyOptimalScalings()
      • HierarchicalOptimizationWrapper::computeAnalyticalOffsets()
      • HierarchicalOptimizationWrapper::computeAnalyticalSigmas()
      • HierarchicalOptimizationWrapper::applyOptimalOffsets()
      • HierarchicalOptimizationWrapper::fillInAnalyticalSigmas()
      • HierarchicalOptimizationWrapper::evaluateWithOptimalParameters()
      • HierarchicalOptimizationWrapper::numParameters()
      • HierarchicalOptimizationWrapper::numProportionalityFactors()
      • HierarchicalOptimizationWrapper::getProportionalityFactorIndices()
      • HierarchicalOptimizationWrapper::numOffsetParameters()
      • HierarchicalOptimizationWrapper::numSigmaParameters()
      • HierarchicalOptimizationWrapper::getOffsetParameterIndices()
      • HierarchicalOptimizationWrapper::getSigmaParameterIndices()
      • HierarchicalOptimizationWrapper::getAnalyticalParameterIndices()
      • HierarchicalOptimizationWrapper::getWrappedFunction()
      • HierarchicalOptimizationWrapper::getParameterIds()
      • HierarchicalOptimizationWrapper::evaluate()

• Template Class InverseUniqueLock
  • Class Documentation
    • InverseUniqueLock
      • InverseUniqueLock::InverseUniqueLock()
      • InverseUniqueLock::InverseUniqueLock()
      • InverseUniqueLock::operator=()
      • InverseUniqueLock::InverseUniqueLock()
      • InverseUniqueLock::operator=()
      • InverseUniqueLock::~InverseUniqueLock()

• Class LearningRateUpdater
  • Class Documentation
    • LearningRateUpdater
      • LearningRateUpdater::LearningRateUpdater()
      • LearningRateUpdater::updateLearningRate()
      • LearningRateUpdater::reduceLearningRate()
      • LearningRateUpdater::increaseLearningRate()
      • LearningRateUpdater::getCurrentLearningRate()
      • LearningRateUpdater::setReductionFactor()
      • LearningRateUpdater::setMaxEpochs()
      • LearningRateUpdater::setStartLearningRate()
      • LearningRateUpdater::setEndLearningRate()

• Class LinearModel
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • LinearModel
      • LinearModel::LinearModel()
      • LinearModel::evaluate()
      • LinearModel::evaluate()
      • LinearModel::evaluate()

• Class LinearModelMSE
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • LinearModelMSE
      • LinearModelMSE::LinearModelMSE()
      • LinearModelMSE::evaluate()
      • LinearModelMSE::evaluate()
      • LinearModelMSE::numParameters()
      • LinearModelMSE::getParameterIds()
      • LinearModelMSE::numParameters_
      • LinearModelMSE::datasets
      • LinearModelMSE::labels
      • LinearModelMSE::lm

• Class LoadBalancerWorker
  • Class Documentation
    • LoadBalancerWorker
      • LoadBalancerWorker::messageHandlerFunc
      • LoadBalancerWorker::LoadBalancerWorker()
      • LoadBalancerWorker::run()

• Class LocalOptimizationIpoptTNLP
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • LocalOptimizationIpoptTNLP
      • LocalOptimizationIpoptTNLP::LocalOptimizationIpoptTNLP()
      • LocalOptimizationIpoptTNLP::~LocalOptimizationIpoptTNLP()
      • LocalOptimizationIpoptTNLP::get_nlp_info()
      • LocalOptimizationIpoptTNLP::get_bounds_info()
      • LocalOptimizationIpoptTNLP::get_starting_point()
      • LocalOptimizationIpoptTNLP::eval_f()
      • LocalOptimizationIpoptTNLP::eval_grad_f()
      • LocalOptimizationIpoptTNLP::eval_g()
      • LocalOptimizationIpoptTNLP::eval_jac_g()
      • LocalOptimizationIpoptTNLP::intermediate_callback()
      • LocalOptimizationIpoptTNLP::finalize_solution()

• Class Logger
  • Class Documentation
    • Logger
      • Logger::Logger()
      • Logger::Logger()
      • Logger::getChild()
      • Logger::logmessage()
      • Logger::logmessage()
      • Logger::logmessage()
      • Logger::setPrefix()
      • Logger::getPrefix()

• Class MeanSquaredError
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • MeanSquaredError
      • MeanSquaredError::evaluate()
      • MeanSquaredError::evaluate()

• Template Class MinibatchOptimizationProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • MinibatchOptimizationProblem
      • MinibatchOptimizationProblem::MinibatchOptimizationProblem()
      • MinibatchOptimizationProblem::MinibatchOptimizationProblem()
      • MinibatchOptimizationProblem::MinibatchOptimizationProblem()
      • MinibatchOptimizationProblem::~MinibatchOptimizationProblem()
      • MinibatchOptimizationProblem::getTrainingData()
      • MinibatchOptimizationProblem::getGradientFunction()

• Template Class MinibatchOptimizer
  • Class Documentation
    • MinibatchOptimizer
      • MinibatchOptimizer::optimize()
      • MinibatchOptimizer::evaluate()
      • MinibatchOptimizer::finish()
      • MinibatchOptimizer::rescueInterceptor()
      • MinibatchOptimizer::handleStep()
      • MinibatchOptimizer::performLineSearch()
      • MinibatchOptimizer::parameterUpdater
      • MinibatchOptimizer::interceptor
      • MinibatchOptimizer::lineSearchSteps
      • MinibatchOptimizer::batchSize
      • MinibatchOptimizer::maxEpochs
      • MinibatchOptimizer::gradientNormThreshold
      • MinibatchOptimizer::learningRate
      • MinibatchOptimizer::learningRateUpdater

• Template Class Model
  • Class Documentation
    • Model
      • Model::~Model()
      • Model::evaluate()
      • Model::evaluate()

• Class MultiConditionDataProvider
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • MultiConditionDataProvider
      • MultiConditionDataProvider::~MultiConditionDataProvider()
      • MultiConditionDataProvider::getNumberOfSimulationConditions()
      • MultiConditionDataProvider::getSimulationToOptimizationParameterMapping()
      • MultiConditionDataProvider::mapSimulationToOptimizationGradientAddMultiply()
      • MultiConditionDataProvider::mapAndSetOptimizationToSimulationVariables()
      • MultiConditionDataProvider::getParameterScaleOpt()
      • MultiConditionDataProvider::getParameterScaleOpt()
      • MultiConditionDataProvider::getParameterScaleSim()
      • MultiConditionDataProvider::getParameterScaleSim()
      • MultiConditionDataProvider::updateSimulationParametersAndScale()
      • MultiConditionDataProvider::getExperimentalDataForCondition()
      • MultiConditionDataProvider::getAllMeasurements()
      • MultiConditionDataProvider::getAllSigmas()
      • MultiConditionDataProvider::getNumOptimizationParameters()
      • MultiConditionDataProvider::getProblemParameterIds()
      • MultiConditionDataProvider::getModel()
      • MultiConditionDataProvider::getSolver()

• Class MultiConditionDataProviderDefault
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • MultiConditionDataProviderDefault
      • MultiConditionDataProviderDefault::MultiConditionDataProviderDefault()
      • MultiConditionDataProviderDefault::~MultiConditionDataProviderDefault()
      • MultiConditionDataProviderDefault::getNumberOfSimulationConditions()
      • MultiConditionDataProviderDefault::getSimulationToOptimizationParameterMapping()
      • MultiConditionDataProviderDefault::mapSimulationToOptimizationGradientAddMultiply()
      • MultiConditionDataProviderDefault::mapAndSetOptimizationToSimulationVariables()
      • MultiConditionDataProviderDefault::getParameterScaleOpt()
      • MultiConditionDataProviderDefault::getParameterScaleOpt()
      • MultiConditionDataProviderDefault::getParameterScaleSim()
      • MultiConditionDataProviderDefault::getParameterScaleSim()
      • MultiConditionDataProviderDefault::updateSimulationParametersAndScale()
      • MultiConditionDataProviderDefault::getExperimentalDataForCondition()
      • MultiConditionDataProviderDefault::getAllMeasurements()
      • MultiConditionDataProviderDefault::getAllSigmas()
      • MultiConditionDataProviderDefault::getNumOptimizationParameters()
      • MultiConditionDataProviderDefault::getModel()
      • MultiConditionDataProviderDefault::getSolver()
      • MultiConditionDataProviderDefault::getProblemParameterIds()
      • MultiConditionDataProviderDefault::edata_

• Class MultiConditionDataProviderHDF5
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • MultiConditionDataProviderHDF5
      • MultiConditionDataProviderHDF5::MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5::MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5::MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5::MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5::~MultiConditionDataProviderHDF5()
      • MultiConditionDataProviderHDF5::getNumberOfSimulationConditions()
      • MultiConditionDataProviderHDF5::getSimulationToOptimizationParameterMapping()
      • MultiConditionDataProviderHDF5::mapSimulationToOptimizationGradientAddMultiply()
      • MultiConditionDataProviderHDF5::mapAndSetOptimizationToSimulationVariables()
      • MultiConditionDataProviderHDF5::getParameterScaleOpt()
      • MultiConditionDataProviderHDF5::getParameterScaleOpt()
      • MultiConditionDataProviderHDF5::getParameterScaleSim()
      • MultiConditionDataProviderHDF5::getParameterScaleSim()
      • MultiConditionDataProviderHDF5::checkDataIntegrity()
      • MultiConditionDataProviderHDF5::readFixedSimulationParameters()
      • MultiConditionDataProviderHDF5::getExperimentalDataForCondition()
      • MultiConditionDataProviderHDF5::getSensitivityParameterList()
      • MultiConditionDataProviderHDF5::getAllMeasurements()
      • MultiConditionDataProviderHDF5::getAllSigmas()
      • MultiConditionDataProviderHDF5::getSigmaForSimulationIndex()
      • MultiConditionDataProviderHDF5::getMeasurementForSimulationIndex()
      • MultiConditionDataProviderHDF5::getOptimizationParametersLowerBounds()
      • MultiConditionDataProviderHDF5::getOptimizationParametersUpperBounds()
      • MultiConditionDataProviderHDF5::getNumOptimizationParameters()
      • MultiConditionDataProviderHDF5::getModel()
      • MultiConditionDataProviderHDF5::getSolver()
      • MultiConditionDataProviderHDF5::updateSimulationParametersAndScale()
      • MultiConditionDataProviderHDF5::copyInputData()
      • MultiConditionDataProviderHDF5::getSimAndPreeqConditions()
      • MultiConditionDataProviderHDF5::getReinitializationIndices()
      • MultiConditionDataProviderHDF5::getHdf5File()
      • MultiConditionDataProviderHDF5::setModel()
      • MultiConditionDataProviderHDF5::getProblemParameterIds()
      • MultiConditionDataProviderHDF5::updateFixedSimulationParameters()

• Class MultiConditionProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • MultiConditionProblem
      • MultiConditionProblem::MultiConditionProblem()
      • MultiConditionProblem::MultiConditionProblem()
      • MultiConditionProblem::MultiConditionProblem()
      • MultiConditionProblem::~MultiConditionProblem()
      • MultiConditionProblem::earlyStopping()
      • MultiConditionProblem::getDataProvider()
      • MultiConditionProblem::getResultWriter()
      • MultiConditionProblem::setInitialParameters()
      • MultiConditionProblem::setParametersMin()
      • MultiConditionProblem::setParametersMax()
      • MultiConditionProblem::fillParametersMin()
      • MultiConditionProblem::fillParametersMax()
      • MultiConditionProblem::fillInitialParameters()
      • MultiConditionProblem::getReporter()
      • MultiConditionProblem::getTrainingData()

• Class MultiConditionProblemMultiStartOptimizationProblem
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • MultiConditionProblemMultiStartOptimizationProblem
      • MultiConditionProblemMultiStartOptimizationProblem::MultiConditionProblemMultiStartOptimizationProblem()
      • MultiConditionProblemMultiStartOptimizationProblem::getNumberOfStarts()
      • MultiConditionProblemMultiStartOptimizationProblem::restartOnFailure()
      • MultiConditionProblemMultiStartOptimizationProblem::getLocalProblem()

• Class MultiStartOptimization
  • Class Documentation
    • MultiStartOptimization
      • MultiStartOptimization::MultiStartOptimization()
      • MultiStartOptimization::~MultiStartOptimization()
      • MultiStartOptimization::run()
      • MultiStartOptimization::runMultiThreaded()
      • MultiStartOptimization::runSingleThreaded()
      • MultiStartOptimization::setRunParallel()

• Class MultiStartOptimizationProblem
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • MultiStartOptimizationProblem
      • MultiStartOptimizationProblem::getNumberOfStarts()
      • MultiStartOptimizationProblem::restartOnFailure()
      • MultiStartOptimizationProblem::getLocalProblem()
      • MultiStartOptimizationProblem::~MultiStartOptimizationProblem()

• Class OptimizationApplication
  • Class Documentation
    • OptimizationApplication
      • OptimizationApplication::OptimizationApplication()
      • OptimizationApplication::~OptimizationApplication()
      • OptimizationApplication::initProblem()
      • OptimizationApplication::run()
      • OptimizationApplication::runMaster()
      • OptimizationApplication::runSingleProcess()
      • OptimizationApplication::OperationType
        • OptimizationApplication::OperationType::parameterEstimation
        • OptimizationApplication::OperationType::gradientCheck
      • OptimizationApplication::finalizeTiming()
      • OptimizationApplication::processResultFilenameCommandLineArgument()
      • OptimizationApplication::isMaster()
      • OptimizationApplication::isWorker()
      • OptimizationApplication::parseCliOptionsPreMpiInit()
      • OptimizationApplication::parseCliOptionsPostMpiInit()
      • OptimizationApplication::printUsage()
      • OptimizationApplication::logParPEVersion()
      • OptimizationApplication::shortOptions
      • OptimizationApplication::longOptions
      • OptimizationApplication::dataFileName
      • OptimizationApplication::resultFileName
      • OptimizationApplication::first_start_idx
      • OptimizationApplication::multiStartOptimizationProblem
      • OptimizationApplication::problem
      • OptimizationApplication::h5File
      • OptimizationApplication::operationType
      • OptimizationApplication::loadBalancer
      • OptimizationApplication::withMPI
      • OptimizationApplication::initMPI()

• Class OptimizationOptions
  • Class Documentation
    • OptimizationOptions
      • OptimizationOptions::OptimizationOptions()
      • OptimizationOptions::createOptimizer()
      • OptimizationOptions::toString()
      • OptimizationOptions::getIntOption()
      • OptimizationOptions::getDoubleOption()
      • OptimizationOptions::getStringOption()
      • OptimizationOptions::setOption()
      • OptimizationOptions::setOption()
      • OptimizationOptions::setOption()
      • OptimizationOptions::for_each()
      • OptimizationOptions::optimizer
      • OptimizationOptions::logFile
      • OptimizationOptions::printToStdout
      • OptimizationOptions::maxOptimizerIterations
      • OptimizationOptions::numStarts
      • OptimizationOptions::retryOptimization
      • OptimizationOptions::hierarchicalOptimization
      • OptimizationOptions::multistartsInParallel
      • OptimizationOptions::fromHDF5()
      • OptimizationOptions::fromHDF5()
      • OptimizationOptions::getStartingPoint()

• Class OptimizationProblem
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • OptimizationProblem
      • OptimizationProblem::OptimizationProblem()
      • OptimizationProblem::OptimizationProblem()
      • OptimizationProblem::OptimizationProblem()
      • OptimizationProblem::~OptimizationProblem()
      • OptimizationProblem::fillInitialParameters()
      • OptimizationProblem::fillParametersMin()
      • OptimizationProblem::fillParametersMax()
      • OptimizationProblem::getOptimizationOptions()
      • OptimizationProblem::setOptimizationOptions()
      • OptimizationProblem::getReporter()
      • OptimizationProblem::cost_fun_
      • OptimizationProblem::logger_

• Class OptimizationProblemImpl
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizationProblemImpl
      • OptimizationProblemImpl::fillParametersMin()
      • OptimizationProblemImpl::fillParametersMax()
      • OptimizationProblemImpl::setParametersMin()
      • OptimizationProblemImpl::setParametersMax()
      • OptimizationProblemImpl::setInitialParameters()
      • OptimizationProblemImpl::fillInitialParameters()
      • OptimizationProblemImpl::OptimizationProblem()
      • OptimizationProblemImpl::OptimizationProblem()
      • OptimizationProblemImpl::OptimizationProblem()

• Class OptimizationReporter
  • Inheritance Relationships
    • Base Type
    • Derived Type
  • Class Documentation
    • OptimizationReporter
      • OptimizationReporter::OptimizationReporter()
      • OptimizationReporter::OptimizationReporter()
      • OptimizationReporter::evaluate()
      • OptimizationReporter::numParameters()
      • OptimizationReporter::starting()
      • OptimizationReporter::iterationFinished()
      • OptimizationReporter::beforeCostFunctionCall()
      • OptimizationReporter::afterCostFunctionCall()
      • OptimizationReporter::finished()
      • OptimizationReporter::getFinalCost()
      • OptimizationReporter::getFinalParameters()
      • OptimizationReporter::setGradientFunction()
      • OptimizationReporter::getParameterIds()
      • OptimizationReporter::result_writer_
      • OptimizationReporter::cpu_time_total_sec_
      • OptimizationReporter::cpu_time_iteration_sec_
      • OptimizationReporter::logger_
      • OptimizationReporter::printObjectiveFunctionFailureMessage()
      • OptimizationReporter::wall_timer_
      • OptimizationReporter::num_function_calls_
      • OptimizationReporter::num_iterations_
      • OptimizationReporter::num_parameters_
      • OptimizationReporter::started_
      • OptimizationReporter::grad_fun_
      • OptimizationReporter::have_cached_cost_
      • OptimizationReporter::have_cached_gradient_
      • OptimizationReporter::cached_gradient_
      • OptimizationReporter::cached_cost_
      • OptimizationReporter::cached_status_
      • OptimizationReporter::final_cost_
      • OptimizationReporter::cached_parameters_
      • OptimizationReporter::default_logger_prefix_

• Class OptimizationResultWriter
  • Class Documentation
    • OptimizationResultWriter
      • OptimizationResultWriter::OptimizationResultWriter()
      • OptimizationResultWriter::OptimizationResultWriter()
      • OptimizationResultWriter::operator=()
      • OptimizationResultWriter::OptimizationResultWriter()
      • OptimizationResultWriter::~OptimizationResultWriter()
      • OptimizationResultWriter::logObjectiveFunctionEvaluation()
      • OptimizationResultWriter::logOptimizerIteration()
      • OptimizationResultWriter::setLoggingEachIteration()
      • OptimizationResultWriter::setLoggingEachFunctionEvaluation()
      • OptimizationResultWriter::starting()
      • OptimizationResultWriter::saveOptimizerResults()
      • OptimizationResultWriter::getH5File()
      • OptimizationResultWriter::getRootPath()
      • OptimizationResultWriter::setRootPath()
      • OptimizationResultWriter::logParametersEachFunctionEvaluation
      • OptimizationResultWriter::logGradientEachFunctionEvaluation
      • OptimizationResultWriter::logGradientEachIteration
      • OptimizationResultWriter::flushResultWriter()

• Class Optimizer
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • Optimizer
      • Optimizer::optimize()
      • Optimizer::~Optimizer()

• Class OptimizerCeres
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizerCeres
      • OptimizerCeres::OptimizerCeres()
      • OptimizerCeres::optimize()

• Class OptimizerDlibLineSearch
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizerDlibLineSearch
      • OptimizerDlibLineSearch::OptimizerDlibLineSearch()
      • OptimizerDlibLineSearch::optimize()

• Class OptimizerFides
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizerFides
      • OptimizerFides::OptimizerFides()
      • OptimizerFides::optimize()

• Class OptimizerFsqp
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizerFsqp
      • OptimizerFsqp::OptimizerFsqp()
      • OptimizerFsqp::optimize()

• Class OptimizerIpOpt
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizerIpOpt
      • OptimizerIpOpt::OptimizerIpOpt()
      • OptimizerIpOpt::optimize()

• Class OptimizerToms611TrustRegionSumsl
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • OptimizerToms611TrustRegionSumsl
      • OptimizerToms611TrustRegionSumsl::OptimizerToms611TrustRegionSumsl()
      • OptimizerToms611TrustRegionSumsl::optimize()

• Class ParameterUpdater
  • Inheritance Relationships
    • Derived Types
  • Class Documentation
    • ParameterUpdater
      • ParameterUpdater::updateParameters()
      • ParameterUpdater::undoLastStep()
      • ParameterUpdater::clearCache()
      • ParameterUpdater::initialize()
      • ParameterUpdater::~ParameterUpdater()

• Class ParameterUpdaterAdam
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ParameterUpdaterAdam
      • ParameterUpdaterAdam::ParameterUpdaterAdam()
      • ParameterUpdaterAdam::updateParameters()
      • ParameterUpdaterAdam::undoLastStep()
      • ParameterUpdaterAdam::clearCache()
      • ParameterUpdaterAdam::initialize()

• Class ParameterUpdaterAdamClassic
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ParameterUpdaterAdamClassic
      • ParameterUpdaterAdamClassic::ParameterUpdaterAdamClassic()
      • ParameterUpdaterAdamClassic::updateParameters()
      • ParameterUpdaterAdamClassic::undoLastStep()
      • ParameterUpdaterAdamClassic::clearCache()
      • ParameterUpdaterAdamClassic::initialize()

• Class ParameterUpdaterMomentum
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ParameterUpdaterMomentum
      • ParameterUpdaterMomentum::ParameterUpdaterMomentum()
      • ParameterUpdaterMomentum::updateParameters()
      • ParameterUpdaterMomentum::undoLastStep()
      • ParameterUpdaterMomentum::clearCache()
      • ParameterUpdaterMomentum::initialize()

• Class ParameterUpdaterRmsProp
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ParameterUpdaterRmsProp
      • ParameterUpdaterRmsProp::ParameterUpdaterRmsProp()
      • ParameterUpdaterRmsProp::updateParameters()
      • ParameterUpdaterRmsProp::undoLastStep()
      • ParameterUpdaterRmsProp::clearCache()
      • ParameterUpdaterRmsProp::initialize()

• Class ParameterUpdaterVanilla
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ParameterUpdaterVanilla
      • ParameterUpdaterVanilla::ParameterUpdaterVanilla()
      • ParameterUpdaterVanilla::updateParameters()
      • ParameterUpdaterVanilla::undoLastStep()
      • ParameterUpdaterVanilla::clearCache()
      • ParameterUpdaterVanilla::initialize()

• Class ParPEException
  • Inheritance Relationships
    • Base Type
  • Class Documentation
    • ParPEException
      • ParPEException::ParPEException()
      • ParPEException::ParPEException()
      • ParPEException::~ParPEException()
      • ParPEException::what()

• Class SimulationResultWriter
  • Class Documentation
    • SimulationResultWriter
      • SimulationResultWriter::SimulationResultWriter()
      • SimulationResultWriter::SimulationResultWriter()
      • SimulationResultWriter::SimulationResultWriter()
      • SimulationResultWriter::SimulationResultWriter()
      • SimulationResultWriter::~SimulationResultWriter()
      • SimulationResultWriter::createDatasets()
      • SimulationResultWriter::createDatasets()
      • SimulationResultWriter::saveSimulationResults()
      • SimulationResultWriter::saveTimepoints()
      • SimulationResultWriter::saveMeasurements()
      • SimulationResultWriter::saveModelOutputs()
      • SimulationResultWriter::saveStates()
      • SimulationResultWriter::saveParameters()
      • SimulationResultWriter::saveLikelihood()
      • SimulationResultWriter::reopenFile()
      • SimulationResultWriter::saveX
      • SimulationResultWriter::saveLlh
      • SimulationResultWriter::saveYSim
      • SimulationResultWriter::saveYMes
      • SimulationResultWriter::save_parameters_
      • SimulationResultWriter::yMesPath
      • SimulationResultWriter::ySimPath
      • SimulationResultWriter::xPath
      • SimulationResultWriter::llhPath
      • SimulationResultWriter::timePath
      • SimulationResultWriter::parametersPath

• Class StandaloneSimulator
  • Class Documentation
    • StandaloneSimulator
      • StandaloneSimulator::StandaloneSimulator()
      • StandaloneSimulator::run()
      • StandaloneSimulator::messageHandler()

• Template Class SummedGradientFunction
  • Inheritance Relationships
    • Derived Type
  • Class Documentation
    • SummedGradientFunction
      • SummedGradientFunction::evaluate()
      • SummedGradientFunction::evaluate()
      • SummedGradientFunction::numParameters()
      • SummedGradientFunction::getParameterIds()
      • SummedGradientFunction::~SummedGradientFunction()

• Template Class SummedGradientFunctionGradientFunctionAdapter
  • Inheritance Relationships
    • Base Types
  • Class Documentation
    • SummedGradientFunctionGradientFunctionAdapter
      • SummedGradientFunctionGradientFunctionAdapter::SummedGradientFunctionGradientFunctionAdapter()
      • SummedGradientFunctionGradientFunctionAdapter::evaluate()
      • SummedGradientFunctionGradientFunctionAdapter::evaluate()
      • SummedGradientFunctionGradientFunctionAdapter::evaluate()
      • SummedGradientFunctionGradientFunctionAdapter::numParameters()
      • SummedGradientFunctionGradientFunctionAdapter::getParameterIds()
      • SummedGradientFunctionGradientFunctionAdapter::getWrappedFunction()

• Class WallTimer
  • Class Documentation
    • WallTimer
      • WallTimer::WallTimer()
      • WallTimer::reset()
      • WallTimer::getRound()
      • WallTimer::getTotal()

Enums

• Enum ErrorModel
  • Enum Documentation
    • ErrorModel
      • ErrorModel::normal

• Enum FunctionEvaluationStatus
  • Enum Documentation
    • FunctionEvaluationStatus
      • FunctionEvaluationStatus::functionEvaluationSuccess
      • FunctionEvaluationStatus::functionEvaluationFailure

• Enum interceptType
  • Enum Documentation
    • interceptType
      • interceptType::none
      • interceptType::reduceStep
      • interceptType::reduceStepAndRestart

• Enum learningRateInterp
  • Enum Documentation
    • learningRateInterp
      • learningRateInterp::linear
      • learningRateInterp::inverseLinear
      • learningRateInterp::logarithmic

• Enum loglevel
  • Enum Documentation
    • loglevel
      • loglevel::critical
      • loglevel::error
      • loglevel::warning
      • loglevel::info
      • loglevel::debug

• Enum minibatchExitStatus
  • Enum Documentation
    • minibatchExitStatus
      • minibatchExitStatus::gradientNormConvergence
      • minibatchExitStatus::maxEpochsExceeded
      • minibatchExitStatus::invalidNumber

• Enum optimizerName
  • Enum Documentation
    • optimizerName
      • optimizerName::OPTIMIZER_IPOPT
      • optimizerName::OPTIMIZER_CERES
      • optimizerName::OPTIMIZER_DLIB
      • optimizerName::OPTIMIZER_TOMS611
      • optimizerName::OPTIMIZER_FSQP
      • optimizerName::OPTIMIZER_FIDES
      • optimizerName::OPTIMIZER_MINIBATCH_1

Functions

• Template Function boost::serialization::serialize(Archive&, parpe::AmiciSimulationRunner::AmiciWorkPackageSimple&, const unsigned int)
  • Function Documentation
    • serialize()

• Template Function boost::serialization::serialize(Archive&, parpe::AmiciSimulationRunner::AmiciResultPackageSimple&, const unsigned int)
  • Function Documentation
    • serialize()

• Template Function operator<<(std::ostream&, std::vector<T> const&)
  • Function Documentation
    • operator<<()

• Template Function operator<<(std::ostream&, gsl::span<T> const&)
  • Function Documentation
    • operator<<()

• Function parpe::almostEqual
  • Function Documentation
    • almostEqual()

• Function parpe::applyChainRule
  • Function Documentation
    • applyChainRule()

• Function parpe::applyOptimalOffset
  • Function Documentation
    • applyOptimalOffset()

• Function parpe::applyOptimalScaling
  • Function Documentation
    • applyOptimalScaling()

• Function parpe::checkGradientForAnalyticalParameters
  • Function Documentation
    • checkGradientForAnalyticalParameters()

• Template Function parpe::clipToBounds
  • Function Documentation
    • clipToBounds()

• Function parpe::computeAnalyticalOffsets
  • Function Documentation
    • computeAnalyticalOffsets()

• Function parpe::computeAnalyticalScalings
  • Function Documentation
    • computeAnalyticalScalings()

• Function parpe::computeAnalyticalSigmas
  • Function Documentation
    • computeAnalyticalSigmas()

• Function parpe::computeNegLogLikelihood(std::vector<std::vector<double>> const&, std::vector<std::vector<double>> const&, const std::vector<std::vector<double>>&)
  • Function Documentation
    • computeNegLogLikelihood()

• Function parpe::computeNegLogLikelihood(std::vector<double> const&, std::vector<double> const&, const std::vector<double>&)
  • Function Documentation
    • computeNegLogLikelihood()

• Function parpe::fillArrayRandomDoubleIndividualInterval
  • Function Documentation
    • fillArrayRandomDoubleIndividualInterval()

• Function parpe::fillArrayRandomDoubleSameInterval
  • Function Documentation
    • fillArrayRandomDoubleSameInterval()

• Function parpe::fillFilteredParams
  • Function Documentation
    • fillFilteredParams()

• Function parpe::finalizeMpiIfNeeded
  • Function Documentation
    • finalizeMpiIfNeeded()

• Function parpe::getBacktrace
  • Function Documentation
    • getBacktrace()

• Template Function parpe::getBatches
  • Function Documentation
    • getBatches()

• Function parpe::getDefaultOffsetParameter
  • Function Documentation
    • getDefaultOffsetParameter()

• Function parpe::getDefaultScalingFactor
  • Function Documentation
    • getDefaultScalingFactor()

• Function parpe::getFinalParameters
  • Function Documentation
    • getFinalParameters()

• Function parpe::getFunctionEvaluationWithMinimalCost
  • Function Documentation
    • getFunctionEvaluationWithMinimalCost()

• Function parpe::getLocalOptimum
  • Function Documentation
    • getLocalOptimum()

• Template Function parpe::getMinibatchOptimizer
  • Function Documentation
    • getMinibatchOptimizer()

• Function parpe::getModelOutputsAndSigmas
  • Function Documentation
    • getModelOutputsAndSigmas()

• Function parpe::getMpiActive
  • Function Documentation
    • getMpiActive()

• Function parpe::getMpiCommSize
  • Function Documentation
    • getMpiCommSize()

• Function parpe::getMpiRank
  • Function Documentation
    • getMpiRank()

• Function parpe::getNumStarts
  • Function Documentation
    • getNumStarts()

• Function parpe::getOuterParameters
  • Function Documentation
    • getOuterParameters()

• Function parpe::getParameterTrajectory
  • Function Documentation
    • getParameterTrajectory()

• Function parpe::getVectorDifference
  • Function Documentation
    • getVectorDifference()

• Function parpe::getVectorNorm
  • Function Documentation
    • getVectorNorm()

• Function parpe::hdf5AttributeExists
  • Function Documentation
    • hdf5AttributeExists()

• Function parpe::hdf5CreateExtendableDouble2DArray
  • Function Documentation
    • hdf5CreateExtendableDouble2DArray()

• Function parpe::hdf5CreateExtendableDouble3DArray
  • Function Documentation
    • hdf5CreateExtendableDouble3DArray()

• Function parpe::hdf5CreateExtendableInt2DArray
  • Function Documentation
    • hdf5CreateExtendableInt2DArray()

• Function parpe::hdf5CreateExtendableString1DArray
  • Function Documentation
    • hdf5CreateExtendableString1DArray()

• Function parpe::hdf5CreateFile
  • Function Documentation
    • hdf5CreateFile()

• Function parpe::hdf5CreateGroup
  • Function Documentation
    • hdf5CreateGroup()

• Function parpe::hdf5CreateOrExtendAndWriteToDouble2DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToDouble2DArray()

• Function parpe::hdf5CreateOrExtendAndWriteToDouble3DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToDouble3DArray()

• Function parpe::hdf5CreateOrExtendAndWriteToInt2DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToInt2DArray()

• Function parpe::hdf5CreateOrExtendAndWriteToString1DArray
  • Function Documentation
    • hdf5CreateOrExtendAndWriteToString1DArray()

• Function parpe::hdf5EnsureGroupExists
  • Function Documentation
    • hdf5EnsureGroupExists()

• Function parpe::hdf5ErrorStackWalker_cb
  • Function Documentation
    • hdf5ErrorStackWalker_cb()

• Function parpe::hdf5Extend2ndDimensionAndWriteToDouble2DArray
  • Function Documentation
    • hdf5Extend2ndDimensionAndWriteToDouble2DArray()

• Function parpe::hdf5Extend2ndDimensionAndWriteToInt2DArray
  • Function Documentation
    • hdf5Extend2ndDimensionAndWriteToInt2DArray()

• Function parpe::hdf5Extend3rdDimensionAndWriteToDouble3DArray
  • Function Documentation
    • hdf5Extend3rdDimensionAndWriteToDouble3DArray()

• Function parpe::hdf5ExtendAndWriteToString1DArray
  • Function Documentation
    • hdf5ExtendAndWriteToString1DArray()

• Function parpe::hdf5Get3DDoubleHyperslab
  • Function Documentation
    • hdf5Get3DDoubleHyperslab()

• Function parpe::hdf5GetDatasetDimensions
  • Function Documentation
    • hdf5GetDatasetDimensions()

• Function parpe::hdf5GroupExists
  • Function Documentation
    • hdf5GroupExists()

• Function parpe::hdf5MutexGetLock
  • Function Documentation
    • hdf5MutexGetLock()

• Function parpe::hdf5OpenForAppending
  • Function Documentation
    • hdf5OpenForAppending()

• Function parpe::hdf5OpenForReading
  • Function Documentation
    • hdf5OpenForReading()

• Function parpe::hdf5Read1DIntegerHyperslab
  • Function Documentation
    • hdf5Read1DIntegerHyperslab()

• Function parpe::hdf5Read1dStringDataset
  • Function Documentation
    • hdf5Read1dStringDataset()

• Function parpe::hdf5Read2DDoubleHyperslab
  • Function Documentation
    • hdf5Read2DDoubleHyperslab()

• Function parpe::hdf5Read2DIntegerHyperslab
  • Function Documentation
    • hdf5Read2DIntegerHyperslab()

• Function parpe::hdf5Read3DDoubleHyperslab
  • Function Documentation
    • hdf5Read3DDoubleHyperslab()

• Function parpe::hdf5Write1dStringDataset
  • Function Documentation
    • hdf5Write1dStringDataset()

• Function parpe::hdf5WriteStringAttribute
  • Function Documentation
    • hdf5WriteStringAttribute()

• Function parpe::initHDF5Mutex
  • Function Documentation
    • initHDF5Mutex()

• Function parpe::ipOptGetLock
  • Function Documentation
    • ipOptGetLock()

• Function parpe::ipOptReleaseLock
  • Function Documentation
    • ipOptReleaseLock()

• Function parpe::logmessage(loglevel, std::string const&)
  • Function Documentation
    • logmessage()

• Function parpe::logmessage(loglevel, const char *, …)
  • Function Documentation
    • logmessage()

• Function parpe::logmessage(loglevel, const char *, va_list)
  • Function Documentation
    • logmessage()

• Function parpe::logProcessStats
  • Function Documentation
    • logProcessStats()

• Function parpe::messageHandler
  • Function Documentation
    • messageHandler()

• Function parpe::operator==
  • Function Documentation
    • operator==()

• Function parpe::optimizationProblemGradientCheck(OptimizationProblem *, int, double)
  • Function Documentation
    • optimizationProblemGradientCheck()

• Function parpe::optimizationProblemGradientCheck(OptimizationProblem *, gsl::span<const int>, double)
  • Function Documentation
    • optimizationProblemGradientCheck()

• Function parpe::optimizationProblemGradientCheckMultiEps(OptimizationProblem *, int)
  • Function Documentation
    • optimizationProblemGradientCheckMultiEps()

• Function parpe::optimizationProblemGradientCheckMultiEps(OptimizationProblem *, gsl::span<const int>, gsl::span<double>)
  • Function Documentation
    • optimizationProblemGradientCheckMultiEps()

• Function parpe::optimizerFactory
  • Function Documentation
    • optimizerFactory()

• Function parpe::printAvailableOptimizers
  • Function Documentation
    • printAvailableOptimizers()

• Function parpe::printBacktrace
  • Function Documentation
    • printBacktrace()

• Function parpe::printDebugInfoAndWait
  • Function Documentation
    • printDebugInfoAndWait()

• Function parpe::printfToString
  • Function Documentation
    • printfToString()

• Function parpe::printMPIInfo
  • Function Documentation
    • printMPIInfo()

• Function parpe::randDouble
  • Function Documentation
    • randDouble()

• Template Function parpe::removeInnerParameters
  • Function Documentation
    • removeInnerParameters()

• Function parpe::run_amici_simulation
  • Function Documentation
    • run_amici_simulation()

• Function parpe::runAlongTrajectory
  • Function Documentation
    • runAlongTrajectory()

• Function parpe::runAndLogSimulation
  • Function Documentation
    • runAndLogSimulation()

• Function parpe::runFinalParameters
  • Function Documentation
    • runFinalParameters()

• Function parpe::runMinibatchOptimization
  • Function Documentation
    • runMinibatchOptimization()

• Function parpe::runSimulator
  • Function Documentation
    • runSimulator()

• Function parpe::saveSimulation
  • Function Documentation
    • saveSimulation()

• Function parpe::saveTotalCpuTime
  • Function Documentation
    • saveTotalCpuTime()

• Function parpe::setIpOptOption
  • Function Documentation
    • setIpOptOption()

• Function parpe::setMinibatchOption
  • Function Documentation
    • setMinibatchOption()

• Function parpe::spliceParameters
  • Function Documentation
    • spliceParameters()

• Function parpe::strFormatCurrentLocaltime
  • Function Documentation
    • strFormatCurrentLocaltime()

• Function parpe::swap
  • Function Documentation
    • swap()

• Template Function parpe::withinBounds
  • Function Documentation
    • withinBounds()

• Template Function std::make_unique
  • Function Documentation
    • make_unique()

Variables

• Variable MPI_TAG_EXIT_SIGNAL
  • Variable Documentation
    • MPI_TAG_EXIT_SIGNAL

• Variable parpe::ANSI_COLOR_BLUE
  • Variable Documentation
    • ANSI_COLOR_BLUE

• Variable parpe::ANSI_COLOR_CYAN
  • Variable Documentation
    • ANSI_COLOR_CYAN

• Variable parpe::ANSI_COLOR_GREEN
  • Variable Documentation
    • ANSI_COLOR_GREEN

• Variable parpe::ANSI_COLOR_MAGENTA
  • Variable Documentation
    • ANSI_COLOR_MAGENTA

• Variable parpe::ANSI_COLOR_RED
  • Variable Documentation
    • ANSI_COLOR_RED

• Variable parpe::ANSI_COLOR_RESET
  • Variable Documentation
    • ANSI_COLOR_RESET

• Variable parpe::ANSI_COLOR_YELLOW
  • Variable Documentation
    • ANSI_COLOR_YELLOW

• Variable parpe::minimumLogLevel
  • Variable Documentation
    • minimumLogLevel

• Variable parpe::mutexIpOpt
  • Variable Documentation
    • mutexIpOpt

Defines

• Define H5_RESTORE_ERROR_HANDLER
  • Define Documentation

• Define H5_SAVE_ERROR_HANDLER
  • Define Documentation

• Define HAVE_CSTDDEF
  • Define Documentation

• Define RELEASE_ASSERT
  • Define Documentation

Typedefs

• Typedef parpe::LoadBalancerMaster
  • Typedef Documentation
    • LoadBalancerMaster

• Typedef parpe::LoadBalancerWorker
  • Typedef Documentation
    • LoadBalancerWorker

• Typedef parpe::mutexHdfType
  • Typedef Documentation
    • mutexHdfType

• Typedef parpe::mutexIpOptType
  • Typedef Documentation
    • mutexIpOptType