- c -

• calcColumnIndices() : Nbnxm::Grid
• calcConvolvedBias() : gmx::Bias , gmx::BiasState
• calcConvolvedForce() : gmx::BiasState
• calcForceAndUpdateBias() : gmx::Bias
• calculate() : gmx::test::anonymous_namespace{virtualsites.cpp}::VirtualSiteTest::VirtualSite , ListedForces , gmx::SurfaceAreaCalculator
• calculateForces() : gmx::DensityFittingForceProvider , gmx::anonymous_namespace{electricfield.cpp}::ElectricField , gmx::QMMMForceProvider , gmx::IForceProvider , gmx::ForceProviders , gmx::RestraintForceProvider
• calculateIntegral() : gmx::NoseHooverGroup
• calculateIntegralIfNeeded() : gmx::MttkData
• calcUmbrellaForceAndPotential() : gmx::BiasState
• callbackAfterReduction() : gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber
• callbackWhenBufferAvailable() : gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber
• callGrompp() : gmx::test::SimulationRunner
• callGromppOnThisRank() : gmx::test::SimulationRunner
• callMdrun() : gmx::test::SimulationRunner
• callNmeig() : gmx::test::SimulationRunner
• capacity() : gmx::ArrayRef< typename >
• cast() : gmx::Any
• castRef() : gmx::Any
• cellOffset() : Nbnxm::Grid
• cells() : Nbnxm::GridSet
• centerOfMass() : gmx::Site
• changePairlistRadii() : nonbonded_verlet_t , PairlistSets
• changeReferenceTemperatureCallback() : gmx::ModularSimulatorAlgorithmBuilderHelper
• changeTprNsteps() : gmx::test::SimulationRunner
• charge() : gmx::SelectionPosition
• charges() : gmx::Selection
• checkAbilityDependencies() : gmx::IOutputAdapter , gmx::OutputSelector , gmx::SetAtoms , gmx::SetBox , gmx::SetForces , gmx::SetPrecision , gmx::SetStartTime , gmx::SetTimeStep , gmx::SetVelocities
• checkAny() : gmx::test::TestReferenceChecker
• checkBlocka() : anonymous_namespace{indexutil.cpp}::IndexBlockTest
• checkBoolean() : gmx::test::TestReferenceChecker
• checkCOMCoordinates() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest
• checkCompound() : gmx::test::TestReferenceChecker
• checkCOMVelocity() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest
• checkConstrainsDirection() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest
• checkConstrainsLength() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest
• checkConstrainsSatisfied() : gmx::test::anonymous_namespace{settle.cpp}::SettleTest
• checkDouble() : gmx::test::TestReferenceChecker
• checkEdrFile() : gmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTest
• checkEmptySequence() : gmx::test::TestReferenceChecker
• checkEnergies() : gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest
• checkEnergyCaluclationFrequency() : gmx::DensityFittingOptions
• checkEntry() : gmx::test::TestReferenceChecker::Impl
• checker() : gmx::test::StringTestBase
• checkFile() : gmx::test::IFileMatcher
• checkFileContents() : gmx::test::StringTestBase
• checkFinalPositions() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest , gmx::test::anonymous_namespace{settle.cpp}::SettleTest
• checkFinalVelocities() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest , gmx::test::anonymous_namespace{settle.cpp}::SettleTest
• checkFloat() : gmx::test::TestReferenceChecker
• checkIndexGroup() : gmx::SelectionTreeElement
• checkInt32() : gmx::test::TestReferenceChecker
• checkInt64() : gmx::test::TestReferenceChecker
• checkInteger() : gmx::test::TestReferenceChecker
• checkKeyValueTreeObject() : gmx::test::TestReferenceChecker
• checkKeyValueTreeValue() : gmx::test::TestReferenceChecker
• checkMdrun() : gmx::test::DensityFittingTest , gmx::test::BondedInteractionsTest
• checkModuleProperties() : gmx::AnalysisDataModuleManager::Impl
• checkModuleProperty() : gmx::AnalysisDataModuleManager::Impl
• checkOutputFiles() : gmx::test::CommandLineTestHelper , gmx::test::CommandLineTestBase
• checkpointData() : gmx::ReadCheckpointDataHolder , gmx::WriteCheckpointDataHolder
• CheckpointError() : gmx::CheckpointError
• CheckpointHandler() : gmx::CheckpointHandler
• CheckpointHelper() : gmx::CheckpointHelper
• CheckpointHelperBuilder() : gmx::CheckpointHelperBuilder
• checkpointID() : gmx::FreeEnergyPerturbationData , gmx::StatePropagatorData
• checkPresent() : gmx::test::TestReferenceChecker
• checkReal() : gmx::test::TestReferenceChecker
• checkRealFromString() : gmx::test::TestReferenceChecker
• checkRedirectedFiles() : gmx::test::TestFileOutputRedirector
• checkRedirectedOutput() : gmx::test::CommandLineModuleManagerTestBase
• checkReferencePoints() : gmx::test::MockAnalysisDataModule::Impl
• checkRerun() : gmx::test::MimicTest
• checkSequence() : gmx::test::TestReferenceChecker
• checkSequenceArray() : gmx::test::TestReferenceChecker
• checkSequenceCompound() : gmx::test::TestReferenceChecker
• checkSession() : gmx::test::InteractiveTestHelper
• checkStream() : gmx::test::anonymous_namespace{msd.cpp}::MsdMatcher , gmx::test::ITextBlockMatcher
• checkString() : gmx::test::TestReferenceChecker
• checkText() : gmx::test::StringTestBase
• checkTextBlock() : gmx::test::TestReferenceChecker
• checkUChar() : gmx::test::TestReferenceChecker
• checkUInt32() : gmx::test::TestReferenceChecker
• checkUInt64() : gmx::test::TestReferenceChecker
• checkUnsortedAtoms() : gmx::SelectionTreeElement
• checkUnusedEntries() : gmx::test::TestReferenceChecker
• checkValue() : gmx::test::TestReferenceChecker
• checkVector() : gmx::test::TestReferenceChecker
• checkVirial() : gmx::test::anonymous_namespace{settle.cpp}::SettleTest
• checkVirialSymmetric() : gmx::test::anonymous_namespace{settle.cpp}::SettleTest
• checkVirialTensor() : gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest
• child() : gmx::anonymous_namespace{exceptions.cpp}::ErrorMessage
• clear() : gmx::AnalysisDataValue , gmx::AnalysisDataFrameLocalDataSetHandle< ValueType > , gmx::AnalysisDataFrameLocalDataHandle< ValueType > , gmx_ga2la_t , gmx::HashedMap< T > , gmx::PaddedVector< T, Allocator > , gmx::UpdateGroupsCog , gmx::TextTableFormatter , gmx::internal::EnumIndexStore< EnumType > , gmx::IOptionValueStore< T > , gmx::OptionValueStoreNull< T > , gmx::RestraintManager::Impl , gmx::RestraintManager , gmx::RangePartitioning , gmx::FixedCapacityVector< typename, size_t > , gmx::FlagsTemplate< FlagType > , gmx::MessageStringCollector , gmx::ListOfLists< typename >
• clearAll() : gmx::FlagsTemplate< FlagType >
• clearAndResizeHashTable() : gmx::HashedMap< T >
• clearEnergies() : gmx::ListedForcesGpu::Impl
• clearFlag() : gmx::AbstractOption , gmx::AbstractOptionStorage
• clearForcesAndEnergies() : gmx::ThreadForceBuffer< ForceBufferElementType >
• clearFrame() : gmx::internal::AnalysisDataStorageFrameData
• clearIfNeeded() : ChainIdFiller
• clearSet() : gmx::AbstractOptionStorage , gmx::OptionStorageTemplate< T >
• clearSymbolTable() : gmx::SelectionCollection::Impl
• ClfftInitializer() : gmx::ClfftInitializer
• ClHandle() : gmx::ClHandle< cl_type >
• clientID() : gmx::EnergyData::Element , gmx::ExpandedEnsembleElement , gmx::FirstOrderPressureCoupling , gmx::FreeEnergyPerturbationData::Element , gmx::ICheckpointHelperClient , gmx::MttkData , gmx::NoseHooverChainsData , gmx::ParrinelloRahmanBarostat , gmx::PullElement , gmx::StatePropagatorData::Element , gmx::VelocityScalingTemperatureCoupling
• clone() : gmx::AbstractAverageHistogram , gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityInnerProduct , gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityRelativeEntropy , gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityCrossCorrelation
• cloneOnSpawnedThread() : gmx::Mdrunner
• close() : gmx::StandardInputStream , gmx::TextInputFile , gmx::TextOutputFile , gmx::StringOutputStream , gmx::StringInputStream , gmx::TextReader , gmx::TextInputStream , gmx::TextOutputStream , gmx::TextWriter
• closeAfterForceComputationCpu() : DDBalanceRegionHandler
• closeAfterForceComputationGpu() : DDBalanceRegionHandler
• closeTimingRegion() : GpuRegionTimerWrapper< GpuRegionTimerImpl > , GpuRegionTimerImpl
• clusterFlags() : Nbnxm::Grid
• clusterIsPerturbed() : Nbnxm::Grid
• CMainCommandLineModule() : gmx::anonymous_namespace{cmdlinemodulemanager.cpp}::CMainCommandLineModule
• cog() : gmx::UpdateGroupsCog
• cogForAtom() : gmx::UpdateGroupsCog
• cogIndex() : gmx::UpdateGroupsCog
• collectiveIndex() : gmx::LocalAtomSet
• columnCount() : gmx::AnalysisDataStorageFrame , gmx::AbstractAnalysisData , gmx::AnalysisDataPointSetRef , gmx::AnalysisDataFrameAverager , gmx::test::AnalysisDataTestInput
• columnData() : gmx::TextTableFormatter::Impl
• ColumnData() : gmx::TextTableFormatter::Impl::ColumnData
• columnData() : gmx::TextTableFormatter::Impl
• CommandLine() : gmx::test::CommandLine
• commandLine() : gmx::CommandLineProgramContext , gmx::anonymous_namespace{programcontext.cpp}::DefaultProgramContext , gmx::IProgramContext , gmx::test::CommandLineTestBase , gmx::test::anonymous_namespace{testinit.cpp}::TestProgramContext
• CommandLineHelpContext() : gmx::CommandLineHelpContext
• CommandLineHelpModule() : gmx::CommandLineHelpModule
• CommandLineHelpWriter() : gmx::CommandLineHelpWriter
• CommandLineModuleGroup() : gmx::CommandLineModuleGroup
• CommandLineModuleGroupData() : gmx::CommandLineModuleGroupData
• CommandLineModuleManager() : gmx::CommandLineModuleManager
• CommandLineParser() : gmx::CommandLineParser
• CommandLineProgramContext() : gmx::CommandLineProgramContext
• CommandLineTestHelper() : gmx::test::CommandLineTestHelper
• CommandsHelpTopic() : gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::CommandsHelpTopic
• commitValues() : gmx::OptionStorageTemplate< T >
• communicateHaloCoordinates() : gmx::GpuHaloExchange
• communicateHaloForces() : gmx::GpuHaloExchange
• communicationBuffer() : gmx::ObservablesReducer
• compareAllFramePairs() : gmx::test::anonymous_namespace{exactcontinuation.cpp}::ContinuationFramePairManager< FrameReader > , gmx::test::FramePairManager< FrameReader >
• compareAllFrames() : gmx::test::MaxNumFrames
• compareFiles() : gmx::test::anonymous_namespace{extract_cluster.cpp}::ExtractClusterModuleTest
• compareSimd4RealEq() : gmx::test::Simd4Test
• compareSimd4RealUlp() : gmx::test::Simd4Test
• compareSimdEq() : gmx::test::SimdTest
• compareSimdRealUlp() : gmx::test::SimdTest
• compareVectorEq() : gmx::test::SimdBaseTest
• compareVectorRealUlp() : gmx::test::SimdBaseTest
• compile() : gmx::SelectionCollection
• completeDefaultFileName() : gmx::FileNameOptionManager
• completeFileName() : gmx::FileNameOptionManager
• CompositeSimulatorElement() : gmx::CompositeSimulatorElement
• computeAverageCoveredFraction() : gmx::internal::SelectionData
• ComputeGlobalsElement() : gmx::ComputeGlobalsElement< algorithm >
• computeStorageLocation() : gmx::internal::AnalysisDataStorageImpl
• computeVirial() : gmx::ForceWithShiftForces
• conditionSatisfied() : gmx::test::anonymous_namespace{threadaffinity_mpi.cpp}::RequireEvenRankCountWithAtLeastFourRanks , gmx::test::RequireRankCount< requiredNumRanks > , gmx::test::RequireMinimumRankCount< minimumNumRanks > , gmx::test::AllowAnyRankCount
• connectWithMatchingPropagator() : gmx::VelocityScalingTemperatureCoupling , gmx::ParrinelloRahmanBarostat
• connectWithPropagator() : gmx::NoseHooverChainsElement , gmx::NoseHooverTemperatureCoupling , gmx::VRescaleTemperatureCoupling , gmx::ITemperatureCouplingImpl , gmx::BerendsenTemperatureCoupling
• consoleOptionsFormatter() : gmx::HelpWriterContext::Impl::SharedState
• constArrayRefFromArray() : gmx::ArrayRef< typename >
• constArrayRefWithPadding() : gmx::PaddedVector< T, Allocator > , gmx::ArrayRefWithPadding< typename >
• constBox() : gmx::StatePropagatorData
• constForcesView() : gmx::StatePropagatorData
• constLambdaView() : gmx::FreeEnergyPerturbationData
• constPositionsView() : gmx::StatePropagatorData
• constPreviousBox() : gmx::StatePropagatorData
• constPreviousPositionsView() : gmx::StatePropagatorData
• ConstraintsElement() : gmx::ConstraintsElement< variable >
• ConstraintsParam() : gmx::ConstraintsParam
• constraintVirial() : gmx::EnergyData
• construct() : gmx::VirtualSitesHandler::Impl , PairlistSets , gmx::DefaultInitializationAllocator< T, A > , gmx::VirtualSitesHandler
• constructLocalAtomSet() : gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting
• constructPairlist() : nonbonded_verlet_t
• constructPairlists() : PairlistSet
• constVelocitiesView() : gmx::StatePropagatorData
• constView() : gmx::GaussTransform3D , gmx::MrcDensityMapOfFloatReader
• consume() : GpuEventSynchronizer
• contains() : gmx::test::CommandLine
• containsGroupName() : gmx::IndexGroupsAndNames
• context() : gmx::DeviceStreamManager
• ContinuationFramePairManager() : gmx::test::anonymous_namespace{exactcontinuation.cpp}::ContinuationFramePairManager< FrameReader >
• convert() : gmx::OptionValueConverterSimple< OutType >
• convertCoordinates() : nonbonded_verlet_t
• convertCoordinatesGpu() : nonbonded_verlet_t
• convertOptionValue() : gmx::SelectionOptionManager
• convertValue() : gmx::AbstractOptionStorage , anonymous_namespace{abstractoptionstorage.cpp}::MockOptionStorage , gmx::OptionStorageTemplate< T >
• coordData() : gmx::CorrelationBlockData
• CoordData() : gmx::CorrelationBlockData::CoordData
• coordinates() : gmx::Selection
• coordState() : gmx::BiasState
• CoordState() : gmx::CoordState
• coordValue() : gmx::CoordState
• copyAtoms() : gmx::TopologyInformation
• copyContents() : gmx::AbstractAnalysisArrayData
• copyright() : gmx::BinaryInformationSettings
• copyToLegacySymtab() : StringTable
• copyToMDForces() : gmx::ImdSession::Impl
• copyTot_atomtypes() : PreprocessingAtomTypes
• copyValues() : gmx::anonymous_namespace{pargs.cpp}::OptionsAdapter
• correctVirial() : DispersionCorrection::Correction
• CorrelationBlockData() : gmx::CorrelationBlockData
• CorrelationGrid() : gmx::CorrelationGrid
• correlationIntegral() : gmx::CorrelationBlockData
• CorrelationTensor() : gmx::CorrelationTensor
• count() : gmx_ana_pos_t , nbnxn_cycle_t , gmx::SelectionOptionManager::Impl::SelectionRequest
• countRestraints() : gmx::RestraintManager
• coveredFraction() : gmx::Selection
• coverRadius() : gmx::BiasParams
• covers() : gmx::BiasGrid
• cpuLimit() : gmx::HardwareTopology
• cpuLists() : PairlistSet
• create() : gmx::SelectionParserParameter , gmx::ConvertTprInfo , gmx::DensityFittingModuleInfo , gmx::Any , gmx::QMMMModuleInfo , gmx::SelectionParserParameter , gmx::Any , gmx::SelectionParserParameter , gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::DefaultExecutableEnvironment , gmx::NonbondedBenchmarkInfo , gmx::RestraintMDModule
• createArray() : gmx::KeyValueTreeValueBuilder
• createCalculation() : gmx::PositionCalculationCollection::Impl , gmx::PositionCalculationCollection
• createCalculationFromEnum() : gmx::PositionCalculationCollection
• createEmpty() : gmx::SelectionLocation
• createEntry() : gmx::test::TestReferenceChecker::Impl
• createExpr() : gmx::SelectionParserValue
• createFileMatcher() : gmx::test::IFileMatcherSettings , gmx::test::NoContentsMatch , gmx::test::TextFileMatch
• createFromExpression() : gmx::SelectionParserParameter
• createInteger() : gmx::SelectionParserValue
• createIntegerRange() : gmx::SelectionParserValue
• createList() : gmx::SelectionParserParameter , gmx::SelectionParserValue
• createMatcher() : gmx::test::ExactTextMatch , gmx::test::ITextBlockMatcherSettings , gmx::test::XvgMatch , gmx::test::FilteringExactTextMatch , gmx::test::NoTextMatch , gmx::test::ConfMatch
• createModule() : gmx::ICommandLineOptionsModule , gmx::test::TrajectoryAnalysisModuleTestFixture< ModuleInfo > , gmx::TrajectoryAnalysisCommandLineRunner , gmx::test::AbstractTrajectoryAnalysisModuleTestFixture , gmx::test::anonymous_namespace{extract_cluster.cpp}::ExtractClusterModuleTest
• createModuleHelpTopic() : gmx::CommandLineHelpModule
• createObject() : gmx::KeyValueTreeValueBuilder
• createPosition() : gmx::SelectionParserValue
• createReal() : gmx::SelectionParserValue
• createRealRange() : gmx::SelectionParserValue
• createStorage() : gmx::AbstractOptionSection , gmx::AbstractOption
• createString() : gmx::SelectionParserValue
• CreationHelper() : gmx::Constraints::CreationHelper
• cross() : gmx::BasicVector< ValueType >
• CrossCorrelationGradientAtVoxel() : gmx::anonymous_namespace{densityfit.cpp}::CrossCorrelationGradientAtVoxel
• CubicSplineTable() : gmx::CubicSplineTable
• currentFEPState() : gmx::FreeEnergyPerturbationData
• currentFrame() : gmx::AnalysisDataStorage
• currentPosition() : gmx::analysismodules::anonymous_namespace{angle.cpp}::AnglePositionIterator
• currentSection() : gmx::OptionsAssigner::Impl
• currentSelection() : gmx::analysismodules::anonymous_namespace{angle.cpp}::AnglePositionIterator
• currentTopic() : gmx::HelpManager::Impl
• currentTopicAsString() : gmx::HelpManager::Impl
• currentValuesSelected() : gmx::analysismodules::anonymous_namespace{angle.cpp}::AnglePositionIterator
• cxy_ind() : Nbnxm::Grid
• cxy_na() : Nbnxm::Grid