Gromacs
5.1.3
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A
CommandLineModuleManager
(
gmx
)
gmx_sel_evaluate_t
MdrunTestFixture
(
gmx::test
)
SelectionTreeElement
(
gmx
)
CommandLineModuleManagerTestBase
(
gmx::test
)
gmx_sel_lexer_t
MdrunTestFixtureBase
(
gmx::test
)
SelelemTemporaryValueAssigner
(
anonymous_namespace{evaluate.cpp}
)
AbstractAnalysisArrayData
(
gmx
)
CommandLineModuleSettings
(
gmx
)
gmx_sel_mempool_block_t
MempoolGroupReserver
(
anonymous_namespace{evaluate.cpp}
)
ShakeTest
(
anonymous_namespace{shake.cpp}
)
AbstractAnalysisData
(
gmx
)
CommandLineOptionsModuleInterface
(
gmx
)
gmx_sel_mempool_t
MempoolSelelemReserver
(
anonymous_namespace{evaluate.cpp}
)
HelpWriterContext::Impl::SharedState
(
gmx
)
AbstractAverageHistogram
(
gmx
)
CommandLineParser
(
gmx
)
gmx_signalling_t
MessageStringCollector
(
gmx
)
Simd4Test
(
gmx::test
)
AbstractCompositeHelpTopic
(
gmx
)
CommandLineProgramContext
(
gmx
)
gmx_simd_dbool_t
MessageStringContext
(
gmx
)
SimdBaseTest
(
gmx::test
)
AbstractOption
(
gmx
)
CommandLineTestBase
(
gmx::test
)
gmx_simd_dibool_t
MessageWriterFileNoThrow
(
gmx::anonymous_namespace{exceptions.cpp}
)
SimdTest
(
gmx::test
)
AbstractOptionStorage
(
gmx
)
CommandLineTestHelper
(
gmx::test
)
gmx_simd_dint32_t
MessageWriterInterface
(
gmx::anonymous_namespace{exceptions.cpp}
)
SimpleHelpTopic
(
gmx
)
AbstractPlotModule
(
gmx
)
CommandsHelpTopic
(
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}
)
gmx_simd_double_t
MessageWriterString
(
gmx::anonymous_namespace{exceptions.cpp}
)
SimulationInstabilityError
(
gmx
)
AbstractSimpleHelpTopic
(
gmx
)
CompositeHelpTopic
(
gmx
)
gmx_simd_fbool_t
MindistAction
(
gmx::anonymous_namespace{nbsearch.cpp}
)
SimulationRunner
(
gmx::test
)
AbstractTrajectoryAnalysisModuleTestFixture
(
gmx::test
)
CompressedXOutputTest
(
anonymous_namespace{compressed_x_output.cpp}
)
gmx_simd_fibool_t
MockAverageHistogram
(
anonymous_namespace{histogram.cpp}
)
StaticAverageHistogram
(
gmx::anonymous_namespace{histogram.cpp}
)
AnalysisArrayData
(
gmx
)
ConstArrayRef
(
gmx
)
gmx_simd_fint32_t
MockModule
(
gmx::test
)
StaticDataFrameHeaderChecker
(
gmx::test::anonymous_namespace{mock_datamodule.cpp}
)
AnalysisData
(
gmx
)
cu_atomdata
gmx_simd_float_t
MockOption
(
anonymous_namespace{abstractoptionstorage.cpp}
)
StaticDataPointsChecker
(
gmx::test::anonymous_namespace{mock_datamodule.cpp}
)
AnalysisDataAverageModule
(
gmx
)
cu_nbparam
gmx_sparsematrix
MockOptionsModule
(
gmx::test
)
StaticDataPointsStorageChecker
(
gmx::test::anonymous_namespace{mock_datamodule.cpp}
)
AnalysisDataBinAverageModule
(
gmx
)
cu_plist
gmx_unique_ptr
(
gmx
)
MockOptionStorage
(
anonymous_namespace{abstractoptionstorage.cpp}
)
StringFormatter
(
gmx
)
AnalysisDataDisplacementModule
(
gmx
)
cu_timers
gmx_wallclock_gpu_t
ModuleHelpTopic
(
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}
)
StringKeywordMatchItem
(
anonymous_namespace{sm_keywords.cpp}
)
AnalysisDataFrameAverageModule
(
gmx
)
D
gmx_walltime_accounting
AnalysisDataModuleManager::Impl::ModuleInfo
(
gmx
)
StringOption
(
gmx
)
AnalysisDataFrameAverager
(
gmx
)
GromacsException
(
gmx
)
N
StringOptionInfo
(
gmx
)
AnalysisDataFrameHeader
(
gmx
)
DataFileFinder
(
gmx
)
GromppTest
(
anonymous_namespace{grompp.cpp}
)
StringOptionStorage
(
gmx
)
AnalysisDataFrameLocalData
(
gmx
)
DataFileInfo
(
gmx
)
H
nb_staging
StringTestBase
(
gmx::test
)
AnalysisDataFrameLocalDataHandle
(
gmx
)
DataFileOptions
(
gmx
)
NotImplementedError
(
gmx
)
SurfaceAreaCalculator
(
gmx
)
AnalysisDataFrameLocalDataSetHandle
(
gmx
)
DataStorageRequester
(
gmx::test::anonymous_namespace{mock_datamodule.cpp}
)
HelpExportCompletion
(
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}
)
O
swap_compartment
AnalysisDataFrameRef
(
gmx
)
DefaultExecutableEnvironment
(
gmx::anonymous_namespace{cmdlineprogramcontext.cpp}
)
HelpExportInterface
(
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}
)
swap_group
AnalysisDataHandle
(
gmx
)
DefaultInputRedirector
(
gmx::anonymous_namespace{fileredirector.cpp}
)
HelpExportReStructuredText
(
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}
)
ObsoleteToolModule
(
anonymous_namespace{legacymodules.cpp}
)
SynopsisFormatter
(
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}
)
AnalysisDataHandleImpl
(
gmx::internal
)
DefaultOutputRedirector
(
gmx::anonymous_namespace{fileredirector.cpp}
)
HelpLinks
(
gmx
)
ocl_gpu_id_t
T
AnalysisDataLifetimeModule
(
gmx
)
DefaultProgramContext
(
gmx::anonymous_namespace{programcontext.cpp}
)
HelpManager
(
gmx
)
omp_module_nthreads_t
AnalysisDataModuleInterface
(
gmx
)
DirectoryEnumerator
(
gmx
)
HelpTopicInterface
(
gmx
)
OptionInfo
(
gmx
)
t_compare_value
AnalysisDataModuleManager
(
gmx
)
DomainDecompositionSpecialCasesTest
(
anonymous_namespace{domain_decomposition.cpp}
)
HelpWriterContext
(
gmx
)
OptionManagerContainer
(
gmx
)
t_compiler_data
AnalysisDataModuleParallel
(
gmx
)
DoubleOption
(
gmx
)
I
OptionManagerInterface
(
gmx
)
t_conect
(
gmx::analysismodules::anonymous_namespace{sasa.cpp}
)
AnalysisDataModuleSerial
(
gmx
)
DoubleOptionInfo
(
gmx
)
Options
(
gmx
)
t_groupselection
AnalysisDataParallelOptions
(
gmx
)
DoubleOptionStorage
(
gmx
)
IdentityFormatter
(
gmx
)
OptionsAdapter
(
gmx::anonymous_namespace{pargs.cpp}
)
t_methoddata_compare
AnalysisDataPlotModule
(
gmx
)
E
ilist_data_t
OptionsAssigner
(
gmx
)
t_methoddata_distance
AnalysisDataPlotSettings
(
gmx
)
IMDEnergyBlock
OptionsFilter
(
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}
)
t_methoddata_insolidangle
AnalysisDataPointSetRef
(
gmx
)
eligible_gpu_ids
IMDHeader
OptionsFormatterInterface
(
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}
)
t_methoddata_kweval
AnalysisDataProxy
(
gmx
)
EmptyArrayRef
(
gmx
)
IMDSocket
OptionsIterator
(
gmx
)
t_methoddata_kwint
AnalysisDataSimpleHistogramModule
(
gmx
)
ErrorMessage
(
gmx::anonymous_namespace{exceptions.cpp}
)
TrajectoryAnalysisSettings::Impl
(
gmx
)
OptionsListFormatter
(
gmx::anonymous_namespace{cmdlinehelpwriter.cpp}
)
t_methoddata_kwreal
AnalysisDataStorage
(
gmx
)
ExceptionInitializer
(
gmx
)
TrajectoryAnalysisModuleData::Impl
(
gmx
)
OptionsModifyingIterator
(
gmx
)
t_methoddata_kwstr
(
anonymous_namespace{sm_keywords.cpp}
)
AnalysisDataStorageFrame
(
gmx
)
ExecutableEnvironmentInterface
(
gmx
)
TrajectoryAnalysisModule::Impl
(
gmx
)
OptionsModifyingTypeVisitor
(
gmx
)
t_methoddata_merge
AnalysisDataStorageFrameData
(
gmx::internal
)
F
TextTableFormatter::Impl
(
gmx
)
OptionsModifyingVisitor
(
gmx
)
t_methoddata_permute
AnalysisDataStorageImpl
(
gmx::internal
)
TestReferenceData::Impl
(
gmx::test
)
OptionStorageTemplate
(
gmx
)
t_methoddata_pos
AnalysisDataTestFixture
(
gmx::test
)
File
(
gmx
)
TestReferenceChecker::Impl
(
gmx::test
)
OptionsTypeVisitor
(
gmx
)
t_methoddata_same
AnalysisDataTestInput
(
gmx::test
)
FileInitializer
(
gmx
)
TestFileManager::Impl
(
gmx::test
)
OptionsVisitor
(
gmx
)
t_pargs
AnalysisDataTestInputFrame
(
gmx::test
)
FileInputRedirectorInterface
(
gmx
)
MockAnalysisDataModule::Impl
(
gmx::test
)
OptionTemplate
(
gmx
)
t_partition
AnalysisDataTestInputPointSet
(
gmx::test
)
FileIOError
(
gmx
)
SelectionParserSymbolTable::Impl
(
gmx
)
P
t_partition_item
AnalysisDataValue
(
gmx
)
FileNameOption
(
gmx
)
SelectionParserSymbolIterator::Impl
(
gmx
)
t_register_method
AnalysisDataVectorPlotModule
(
gmx
)
FileNameOptionInfo
(
gmx
)
SelectionParserSymbol::Impl
(
gmx
)
PairDistance
(
gmx::analysismodules::anonymous_namespace{pairdist.cpp}
)
t_spheresurfacebin
AnalysisDataWeightedHistogramModule
(
gmx
)
FileNameOptionManager
(
gmx
)
SelectionOptionManager::Impl
(
gmx
)
PairDistanceModuleData
(
gmx::analysismodules::anonymous_namespace{pairdist.cpp}
)
t_swap
AnalysisHistogramSettings
(
gmx
)
FileNameOptionStorage
(
gmx
)
SelectionCollection::Impl
(
gmx
)
ParameterizedMdrunTestFixture
(
gmx::test
)
t_UmbrellaHeader
AnalysisHistogramSettingsInitializer
(
gmx
)
FileOutputRedirectorInterface
(
gmx
)
PositionCalculationCollection::Impl
(
gmx
)
pme_setup_t
t_UmbrellaOptions
AnalysisNeighborhood
(
gmx
)
FileTypeHandler
(
gmx::anonymous_namespace{filenameoption.cpp}
)
OptionsAssigner::Impl
(
gmx
)
PositionCalculationCollection
(
gmx
)
t_UmbrellaWindow
AnalysisNeighborhoodPair
(
gmx
)
FileTypeMapping
(
gmx::anonymous_namespace{filenameoption.cpp}
)
Options::Impl
(
gmx
)
PrivateImplPointer
(
gmx
)
TestException
(
gmx::test
)
AnalysisNeighborhoodPairSearch
(
gmx
)
FlagsTemplate
(
gmx
)
HelpWriterContext::Impl
(
gmx
)
ProgramContextInterface
(
gmx
)
TestFileInputRedirector
(
gmx::test
)
AnalysisNeighborhoodPositions
(
gmx
)
FloatingPointDifference
(
gmx::test
)
HelpManager::Impl
(
gmx
)
R
TestFileManager
(
gmx::test
)
AnalysisNeighborhoodSearch
(
gmx
)
FloatingPointTolerance
(
gmx::test
)
HelpLinks::Impl
(
gmx
)
TestFileOutputRedirector
(
gmx::test
)
AnalysisTemplate
FloatOption
(
gmx
)
FileNameOptionManager::Impl
(
gmx
)
Rdf
(
gmx::analysismodules::anonymous_namespace{rdf.cpp}
)
TestOptionsProvider
(
gmx::test
)
AnglePositionIterator
(
gmx::analysismodules::anonymous_namespace{angle.cpp}
)
FloatOptionInfo
(
gmx
)
File::Impl
(
gmx
)
RdfModuleData
(
gmx::analysismodules::anonymous_namespace{rdf.cpp}
)
TestOptionsRegistry
(
gmx::test::anonymous_namespace{testoptions.cpp}
)
APIError
(
gmx
)
FloatOptionStorage
(
gmx
)
CommandLineParser::Impl
(
gmx
)
Regex
(
gmx
)
TestProgramContext
(
gmx::test::anonymous_namespace{testinit.cpp}
)
ArrayRef
(
gmx
)
FreeVolume
(
gmx::analysismodules::anonymous_namespace{freevolume.cpp}
)
CommandLineModuleManager::Impl
(
gmx
)
SelectionOptionManager::Impl::RequestsClearer
(
gmx
)
TestReferenceChecker
(
gmx::test
)
B
G
CommandLineHelpWriter::Impl
(
gmx
)
RootHelpTopic
(
gmx::anonymous_namespace{cmdlinehelpmodule.cpp}
)
TestReferenceData
(
gmx::test
)
CommandLineHelpContext::Impl
(
gmx
)
RstParagraphIterator
(
gmx
)
TestReferenceDataEnvironment
(
anonymous_namespace{refdata.cpp}
)
BasicAverageHistogramModule
(
gmx::internal
)
GlobalCommandLineHelpContext
(
gmx
)
AnalysisDataWeightedHistogramModule::Impl
(
gmx
)
TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
(
gmx
)
TextLineWrapper
(
gmx
)
BasicHistogramImpl
(
gmx::internal
)
gmx_ana_index_t
AnalysisDataSimpleHistogramModule::Impl
(
gmx
)
S
TextLineWrapperSettings
(
gmx
)
BasicVector
(
gmx
)
gmx_ana_indexgrps_t
AnalysisDataModuleManager::Impl
(
gmx
)
TextTableFormatter
(
gmx
)
BinaryInformationSettings
(
gmx
)
gmx_ana_indexmap_t
AnalysisDataLifetimeModule::Impl
(
gmx
)
Sasa
(
gmx::analysismodules::anonymous_namespace{sasa.cpp}
)
thread_work_t
BondedInteractionsTest
(
gmx::test
)
gmx_ana_pos_t
AnalysisDataDisplacementModule::Impl
(
gmx
)
SasaModuleData
(
gmx::analysismodules::anonymous_namespace{sasa.cpp}
)
TimeOptionScaler
(
gmx::anonymous_namespace{timeunitmanager.cpp}
)
BooleanOption
(
gmx
)
gmx_ana_poscalc_t
AnalysisData::Impl
(
gmx
)
scoped_cptr
(
gmx
)
TimeUnitManager
(
gmx
)
BooleanOptionInfo
(
gmx
)
gmx_ana_selcollection_t
AbstractCompositeHelpTopic::Impl
(
gmx
)
Selection
(
gmx
)
TopologyInformation
(
gmx
)
BooleanOptionStorage
(
gmx
)
gmx_ana_selmethod_help_t
AbstractAnalysisData::Impl
(
gmx
)
SelectionCollection
(
gmx
)
TrajectoryAnalysisCommandLineRunner
(
gmx
)
C
gmx_ana_selmethod_t
InconsistentInputError
(
gmx
)
SelectionCompiler
(
gmx
)
TrajectoryAnalysisModule
(
gmx
)
gmx_ana_selparam_t
IndexFileWriterModule
(
gmx::analysismodules::anonymous_namespace{select.cpp}
)
SelectionData
(
gmx::internal
)
TrajectoryAnalysisModuleData
(
gmx
)
cl_atomdata
gmx_ana_selvalue_t
InstallationPrefixInfo
(
gmx
)
SelectionEvaluator
(
gmx
)
TrajectoryAnalysisModuleDataBasic
(
gmx::anonymous_namespace{analysismodule.cpp}
)
cl_nb_staging
gmx_device_info_t
Int64Option
(
gmx
)
SelectionFileOption
(
gmx
)
TrajectoryAnalysisModuleTestFixture
(
gmx::test
)
cl_nbparam
gmx_domdec_constraints
Int64OptionInfo
(
gmx
)
SelectionFileOptionInfo
(
gmx
)
TrajectoryAnalysisRunnerCommon
(
gmx
)
cl_nbparam_params
gmx_domdec_specat_comm
Int64OptionStorage
(
gmx
)
SelectionFileOptionStorage
(
gmx
)
TrajectoryAnalysisSettings
(
gmx
)
cl_plist
gmx_fft_fftpack
IntegerOption
(
gmx
)
SelectionLocation
(
gmx
)
U
cl_timers
gmx_fft_fftw3
IntegerOptionInfo
(
gmx
)
SelectionOption
(
gmx
)
CMainCommandLineModule
(
gmx::anonymous_namespace{cmdlinemodulemanager.cpp}
)
gmx_fft_mkl
IntegerOptionStorage
(
gmx
)
SelectionOptionInfo
(
gmx
)
UserInputError
(
gmx
)
TextTableFormatter::Impl::ColumnData
(
gmx
)
gmx_help_make_index_group
IntegrationTestFixture
(
gmx::test
)
SelectionOptionManager
(
gmx
)
W
CommandLine
(
gmx::test
)
gmx_IMD
InternalError
(
gmx
)
SelectionOptionStorage
(
gmx
)
CommandLineCommonOptionsHolder
(
gmx
)
gmx_nbnxn_cuda_t
InvalidInputError
(
gmx
)
SelectionParserParameter
(
gmx
)
WrapperInterface
(
gmx::anonymous_namespace{helpwritercontext.cpp}
)
CommandLineHelpContext
(
gmx
)
gmx_nbnxn_kernel_timing_data_t
K
SelectionParserSymbol
(
gmx
)
WrapperToString
(
gmx::anonymous_namespace{helpwritercontext.cpp}
)
CommandLineHelpModule
(
gmx
)
gmx_nbnxn_ocl_t
SelectionParserSymbolIterator
(
gmx
)
WrapperToVector
(
gmx::anonymous_namespace{helpwritercontext.cpp}
)
CommandLineHelpWriter
(
gmx
)
gmx_pme_comm_n_box
KeywordDetailsHelpTopic
(
gmx::anonymous_namespace{selhelp.cpp}
)
SelectionParserSymbolTable
(
gmx
)
CommandLineModuleGroup
(
gmx
)
gmx_pme_comm_vir_ene_t
KeywordsHelpTopic
(
gmx::anonymous_namespace{selhelp.cpp}
)
SelectionParserValue
(
gmx
)
CommandLineModuleGroupData
(
gmx
)
gmx_pme_pp
M
SelectionPosition
(
gmx
)
CommandLineModuleInterface
(
gmx
)
gmx_reverse_top
SelectionOptionManager::Impl::SelectionRequest
(
gmx
)
MdrunRerun
(
anonymous_namespace{rerun.cpp}
)
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