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- c -
calcColumnIndices() :
Nbnxm::Grid
calcConvolvedBias() :
gmx::Bias
,
gmx::BiasState
calcConvolvedForce() :
gmx::BiasState
calcForceAndUpdateBias() :
gmx::Bias
calculate() :
ListedForces
,
gmx::SurfaceAreaCalculator
calculateForces() :
gmx::DensityFittingForceProvider
,
gmx::anonymous_namespace{electricfield.cpp}::ElectricField
,
gmx::IForceProvider
,
gmx::ForceProviders
,
gmx::RestraintForceProvider
calcUmbrellaForceAndPotential() :
gmx::BiasState
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
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
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{settle.cpp}::SettleTest
checkFinalVelocities() :
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
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
checkResults() :
gmx::test::anonymous_namespace{mutex.cpp}::DifferentTasksTest
checkSequence() :
gmx::test::TestReferenceChecker
checkSequenceArray() :
gmx::test::TestReferenceChecker
checkSequenceCompound() :
gmx::test::TestReferenceChecker
checkSession() :
gmx::test::InteractiveTestHelper
checkStream() :
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< T, capacity >
,
gmx::FlagsTemplate< FlagType >
,
gmx::ListOfLists< typename >
,
gmx::MessageStringCollector
clearAll() :
gmx::FlagsTemplate< FlagType >
clearEnergies() :
gmx::GpuBonded::Impl
clearFlag() :
gmx::AbstractOption
,
gmx::AbstractOptionStorage
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::FreeEnergyPerturbationData::Element
,
gmx::ICheckpointHelperClient
,
gmx::ParrinelloRahmanBarostat
,
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::AbstractAnalysisData
,
gmx::AnalysisDataPointSetRef
,
gmx::AnalysisDataStorageFrame
,
gmx::AnalysisDataFrameAverager
,
gmx::test::AnalysisDataTestInput
ColumnData() :
gmx::TextTableFormatter::Impl::ColumnData
columnData() :
gmx::TextTableFormatter::Impl
commandLine() :
gmx::anonymous_namespace{programcontext.cpp}::DefaultProgramContext
CommandLine() :
gmx::test::CommandLine
commandLine() :
gmx::CommandLineProgramContext
,
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
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
connectWithPropagator() :
gmx::ITemperatureCouplingImpl
,
gmx::ParrinelloRahmanBarostat
,
gmx::VRescaleTemperatureCoupling
,
gmx::BerendsenTemperatureCoupling
,
gmx::VelocityScalingTemperatureCoupling
conservedEnergyContribution() :
gmx::VelocityScalingTemperatureCoupling
,
gmx::ParrinelloRahmanBarostat
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() :
PairlistSets
,
gmx::DefaultInitializationAllocator< T, A >
,
gmx::VirtualSitesHandler
,
gmx::VirtualSitesHandler::Impl
,
gmx::DefaultInitializationAllocator< T, A >
constructLocalAtomSet() :
gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting
constructPairlist() :
nonbonded_verlet_t
constructPairlists() :
PairlistSet
constVelocitiesView() :
gmx::StatePropagatorData
constView() :
gmx::GaussTransform3D
,
gmx::MrcDensityMapOfFloatReader
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
,
gmx::OptionStorageTemplate< T >
,
anonymous_namespace{abstractoptionstorage.cpp}::MockOptionStorage
CoordData() :
gmx::CorrelationBlockData::CoordData
coordData() :
gmx::CorrelationBlockData
coordinates() :
gmx::Selection
CoordState() :
gmx::CoordState
coordState() :
gmx::BiasState
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() :
nbnxn_cycle_t
,
gmx::SelectionOptionManager::Impl::SelectionRequest
,
gmx_ana_pos_t
countRestraints() :
gmx::RestraintManager
coveredFraction() :
gmx::Selection
coverRadius() :
gmx::BiasParams
covers() :
gmx::BiasGrid
cpuLists() :
PairlistSet
create() :
gmx::SelectionParserParameter
,
gmx::Any
,
gmx::ConvertTprInfo
,
gmx::NonbondedBenchmarkInfo
,
gmx::RestraintMDModule
,
gmx::SelectionParserParameter
,
gmx::DensityFittingModuleInfo
,
gmx::Any
,
gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::DefaultExecutableEnvironment
,
gmx::SelectionParserParameter
createArray() :
gmx::KeyValueTreeValueBuilder
createCalculation() :
gmx::PositionCalculationCollection
,
gmx::PositionCalculationCollection::Impl
createCalculationFromEnum() :
gmx::PositionCalculationCollection
createEmpty() :
gmx::SelectionLocation
createEntry() :
gmx::test::TestReferenceChecker::Impl
createExpr() :
gmx::SelectionParserValue
createFileMatcher() :
gmx::test::TextFileMatch
,
gmx::test::IFileMatcherSettings
,
gmx::test::NoContentsMatch
createFromExpression() :
gmx::SelectionParserParameter
createInteger() :
gmx::SelectionParserValue
createIntegerRange() :
gmx::SelectionParserValue
createList() :
gmx::SelectionParserValue
,
gmx::SelectionParserParameter
createMatcher() :
gmx::test::XvgMatch
,
gmx::test::ConfMatch
,
gmx::test::FilteringExactTextMatch
,
gmx::test::NoTextMatch
,
gmx::test::ExactTextMatch
,
gmx::test::ITextBlockMatcherSettings
createModule() :
gmx::ICommandLineOptionsModule
,
gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
,
gmx::TrajectoryAnalysisCommandLineRunner
,
gmx::test::TrajectoryAnalysisModuleTestFixture< ModuleInfo >
,
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
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