Namespace parpe

Classes

• Struct AmiciSimulationRunner::AmiciResultPackageSimple

• Struct AmiciSimulationRunner::AmiciWorkPackageSimple

• Struct JobData

• Class AmiciSimulationRunner

• 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

Enums

• Enum ErrorModel

• Enum FunctionEvaluationStatus

• Enum interceptType

• Enum learningRateInterp

• Enum loglevel

• Enum minibatchExitStatus

• Enum optimizerName

Functions

• Function parpe::almostEqual

• Function parpe::applyChainRule

• Function parpe::applyOptimalOffset

• Function parpe::applyOptimalScaling

• Function parpe::checkGradientForAnalyticalParameters

• Template Function parpe::clipToBounds

• Function parpe::computeAnalyticalOffsets

• Function parpe::computeAnalyticalScalings

• Function parpe::computeAnalyticalSigmas

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

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

• Function parpe::fillArrayRandomDoubleIndividualInterval

• Function parpe::fillArrayRandomDoubleSameInterval

• Function parpe::fillFilteredParams

• Function parpe::finalizeMpiIfNeeded

• Function parpe::getBacktrace

• Template Function parpe::getBatches

• Function parpe::getDefaultOffsetParameter

• Function parpe::getDefaultScalingFactor

• Function parpe::getFinalParameters

• Function parpe::getFunctionEvaluationWithMinimalCost

• Function parpe::getLocalOptimum

• Template Function parpe::getMinibatchOptimizer

• Function parpe::getModelOutputsAndSigmas

• Function parpe::getMpiActive

• Function parpe::getMpiCommSize

• Function parpe::getMpiRank

• Function parpe::getNumStarts

• Function parpe::getOuterParameters

• Function parpe::getParameterTrajectory

• Function parpe::getVectorDifference

• Function parpe::getVectorNorm

• Function parpe::hdf5AttributeExists

• Function parpe::hdf5CreateExtendableDouble2DArray

• Function parpe::hdf5CreateExtendableDouble3DArray

• Function parpe::hdf5CreateExtendableInt2DArray

• Function parpe::hdf5CreateExtendableString1DArray

• Function parpe::hdf5CreateFile

• Function parpe::hdf5CreateGroup

• Function parpe::hdf5CreateOrExtendAndWriteToDouble2DArray

• Function parpe::hdf5CreateOrExtendAndWriteToDouble3DArray

• Function parpe::hdf5CreateOrExtendAndWriteToInt2DArray

• Function parpe::hdf5CreateOrExtendAndWriteToString1DArray

• Function parpe::hdf5EnsureGroupExists

• Function parpe::hdf5ErrorStackWalker_cb

• Function parpe::hdf5Extend2ndDimensionAndWriteToDouble2DArray

• Function parpe::hdf5Extend2ndDimensionAndWriteToInt2DArray

• Function parpe::hdf5Extend3rdDimensionAndWriteToDouble3DArray

• Function parpe::hdf5ExtendAndWriteToString1DArray

• Function parpe::hdf5Get3DDoubleHyperslab

• Function parpe::hdf5GetDatasetDimensions

• Function parpe::hdf5GroupExists

• Function parpe::hdf5MutexGetLock

• Function parpe::hdf5OpenForAppending

• Function parpe::hdf5OpenForReading

• Function parpe::hdf5Read1DIntegerHyperslab

• Function parpe::hdf5Read1dStringDataset

• Function parpe::hdf5Read2DDoubleHyperslab

• Function parpe::hdf5Read2DIntegerHyperslab

• Function parpe::hdf5Read3DDoubleHyperslab

• Function parpe::hdf5Write1dStringDataset

• Function parpe::hdf5WriteStringAttribute

• Function parpe::initHDF5Mutex

• Function parpe::ipOptGetLock

• Function parpe::ipOptReleaseLock

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

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

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

• Function parpe::logProcessStats

• Function parpe::messageHandler

• Function parpe::operator==

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

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

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

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

• Function parpe::optimizerFactory

• Function parpe::printAvailableOptimizers

• Function parpe::printBacktrace

• Function parpe::printDebugInfoAndWait

• Function parpe::printfToString

• Function parpe::printMPIInfo

• Function parpe::randDouble

• Template Function parpe::removeInnerParameters

• Function parpe::run_amici_simulation

• Function parpe::runAlongTrajectory

• Function parpe::runAndLogSimulation

• Function parpe::runFinalParameters

• Function parpe::runMinibatchOptimization

• Function parpe::runSimulator

• Function parpe::saveSimulation

• Function parpe::saveTotalCpuTime

• Function parpe::setIpOptOption

• Function parpe::setMinibatchOption

• Function parpe::spliceParameters

• Function parpe::strFormatCurrentLocaltime

• Function parpe::swap

• Template Function parpe::withinBounds

Typedefs

• Typedef parpe::LoadBalancerMaster

• Typedef parpe::LoadBalancerWorker

• Typedef parpe::mutexHdfType

• Typedef parpe::mutexIpOptType

Variables

• Variable parpe::ANSI_COLOR_BLUE

• Variable parpe::ANSI_COLOR_CYAN

• Variable parpe::ANSI_COLOR_GREEN

• Variable parpe::ANSI_COLOR_MAGENTA

• Variable parpe::ANSI_COLOR_RED

• Variable parpe::ANSI_COLOR_RESET

• Variable parpe::ANSI_COLOR_YELLOW

• Variable parpe::minimumLogLevel

• Variable parpe::mutexIpOpt