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Class Hierarchy

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This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCgmx::accessor_basic< float >
oCgmx::accessor_basic< value_type >
oCgmx::ArrayRef< BoundingBox >
oCgmx::ArrayRef< const AnalysisDataValue >
oCgmx::ArrayRef< const char *const >
oCgmx::ArrayRef< const char >
oCgmx::ArrayRef< const double >
oCgmx::ArrayRef< const float >
oCgmx::ArrayRef< const gmx::BasicVector >
oCgmx::ArrayRef< const int >
oCgmx::ArrayRef< const InteractionList >
oCgmx::ArrayRef< const real >
oCgmx::ArrayRef< const t_filenm >
oCgmx::ArrayRef< const t_iparams >
oCgmx::ArrayRef< gmx::BasicVector >
oCgmx::ArrayRef< gmx::gmx::BasicVector >
oCgmx::ArrayRef< gmx::RVec >
oCgmx::ArrayRef< PpRanks >
oCgmx::ArrayRef< real >
oCgmx::ArrayRef< rvec >
oCgmx::ArrayRef< ValueType >
oCgmx::ArrayRefWithPadding< gmx::BasicVector >
oCgmx::ArrayRefWithPadding< gmx::gmx::BasicVector >
oCAtomIteratorObject that allows looping over all atoms in an mtop
oCAtomPropertiesHolds all the atom property information loaded
oCAtomProxyProxy object returned from AtomIterator
oCAtomRangeRange over all atoms of topology
oCgmx::basic_mdspan< value_type, Extents, layout_right >
oCgmx::basic_mdspan< value_type, Extents, LayoutPolicy >
oCgmx::basic_mdspan< value_type, gmx::extents, layout_right >
oCgmx::basic_mdspan< value_type, gmx::extents< dynamic_extent, dynamic_extent >, layout_right >
oCgmx::BasicVector< double >
oCgmx::BasicVector< int >
oCgmx::BasicVector< real >
oCBondedInteractionInformation about single bonded interaction
oCBondedInteractionListAccumulation of different bonded types for preprocessing
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCDDBalanceRegionHandlerManager for starting and stopping the dynamic load balancing region
oCDeviceInformationPlatform-dependent device information
oCDeviceStreamDeclaration of platform-agnostic device stream/queue
oCdf_history_tFree-energy sampling history struct
oCekinstate_tStruct used for checkpointing only
oCgmx::EnumerationArray< AtomLocality, const DeviceStream * >
oCgmx::EnumerationArray< AtomLocality, GpuEventSynchronizer >
oCgmx::EnumerationArray< AtomLocality, XFTransfers >
oCgmx::EnumerationArray< CoordinateFileFlags, OutputAdapterPointer >
oCgmx::EnumerationArray< DeviceStreamType, std::unique_ptr< DeviceStream > >
oCgmx::EnumerationArray< gmx::AtomLocality, std::unique_ptr< gmx::GpuForceReduction > >
oCgmx::EnumerationArray< InteractionLocality, Nbnxm::gpu_timers_t::Interaction >
oCgmx::EnumerationArray< Nbnxm::InteractionLocality, bool >
oCgmx::EnumerationArray< Nbnxm::InteractionLocality, const DeviceStream * >
oCgmx::EnumerationArray< Nbnxm::InteractionLocality, Nbnxm::gpu_plist * >
oCgmx::EnumerationArray< SimulationAtomGroupType, AtomGroupIndices >
oCgmx::EnumerationArray< SimulationAtomGroupType, std::vector< unsigned char > >
oCEwaldBoxZScalerClass to handle box scaling for Ewald and PME
oCgmx::extents< E_STATIC...>
oCgmx::FlagsTemplate< Flag >
oCgmx::FlagsTemplate< OptionFlag >
oCForceHelperBuffersHelper force buffers for ForceOutputs
oCForeignLambdaTermsAccumulates free-energy foreign lambda energies and dH/dlamba
oCgmx::AbstractAnalysisDataAbstract base class for all objects that provide data
oCgmx::AbstractOptionAbstract base class for specifying option properties
oCgmx::AbstractOptionSectionBase class for specifying option section properties
oCgmx::AbstractOptionStorageAbstract base class for converting, validating, and storing option values
oCgmx::accessor_basic< ElementType >The most basic memory access model for mdspan
oCgmx::AffineTransformationAffine transformation of three-dimensional coordinates
oCgmx::AlignedAllocationPolicyPolicy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code
oCgmx::Allocator< T, AllocationPolicy >Policy-based memory allocator
oCgmx::AnalysisDataFrameHeaderValue type for storing frame-level information for analysis data
oCgmx::AnalysisDataFrameRefValue type wrapper for non-mutable access to a data frame
oCgmx::AnalysisDataHandleHandle for inserting data into AnalysisData
oCgmx::AnalysisDataModuleManagerEncapsulates handling of data modules attached to AbstractAnalysisData
oCgmx::AnalysisDataParallelOptionsParallelization options for analysis data objects
oCgmx::AnalysisDataPlotSettingsCommon settings for data plots
oCgmx::AnalysisDataPointSetRefValue type wrapper for non-mutable access to a set of data column values
oCgmx::AnalysisDataStorageHelper class that implements storage of data
oCgmx::AnalysisDataStorageFrameAllows assigning values for a data frame in AnalysisDataStorage
oCgmx::AnalysisDataValueValue type for representing a single value in analysis data objects
oCgmx::AnalysisHistogramSettingsContains parameters that specify histogram bin locations
oCgmx::AnalysisHistogramSettingsInitializerProvides "named parameter" idiom for constructing histograms
oCgmx::AnalysisNeighborhoodNeighborhood searching for analysis tools
oCgmx::AnalysisNeighborhoodPairValue type to represent a pair of positions found in neighborhood searching
oCgmx::AnalysisNeighborhoodPairSearchInitialized neighborhood pair search with a fixed set of positions
oCgmx::AnalysisNeighborhoodPositionsInput positions for neighborhood searching
oCgmx::AnalysisNeighborhoodSearchInitialized neighborhood search with a fixed set of reference positions
oCgmx::AnalyticalSplineTableInputSpecification for analytical table function (name, function, derivative)
oCgmx::AnyRepresents a dynamically typed value of an arbitrary type
oCgmx::ArrayRef< typename >STL-like interface to a C array of T (or part of a std container of T)
oCgmx::ArrayRefWithPadding< typename >Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses
oCgmx::AwhCoupling of the accelerated weight histogram method (AWH) with the system
oCgmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy >Multidimensional array indexing and memory access with flexible mapping and access model
oCgmx::BasicVector< ValueType >C++ class for 3D vectors
oCgmx::BenchmarkSystemDescription of the system used for benchmarking
oCgmx::BinaryInformationSettingsSettings for printBinaryInformation()
oCgmx::BoxDeformationHandleHandle to information about the box
oCgmx::CheckpointData< operation >}
oCgmx::CheckpointHandlerClass handling the checkpoint signal
oCgmx::ClfftInitializerHandle clFFT library init and tear down in RAII style also with mutual exclusion
oCgmx::ClHandle< cl_type >Wrapper of OpenCL type cl_type to implement RAII
oCgmx::CommandLineHelpContextContext information for writing out command-line help
oCgmx::CommandLineHelpWriterWrites help information for Options
oCgmx::CommandLineModuleGroupHandle to add content to a group added with CommandLineModuleManager::addModuleGroup()
oCgmx::CommandLineModuleManagerImplements a wrapper command-line interface for multiple modules
oCgmx::CommandLineModuleSettingsSettings to pass information between a module and the general runner
oCgmx::CommandLineParserImplements command-line parsing for Options objects
oCgmx::compat::not_null< T >Restricts a pointer or smart pointer to only hold non-null values
oCgmx::ConstraintsHandles constraints
oCgmx::ConstraintsParamCollection of constraint parameters
oCgmx::ConvertTprInfoDeclares gmx convert-tpr
oCgmx::CpuInfoDetect CPU capabilities and basic logical processor info
oCgmx::CpuInfo::LogicalProcessorEntry with basic information for a single logical processor
oCgmx::CrystallographicLabelsCrystallographic labels for mrc data
oCgmx::CubicSplineTableCubic spline interpolation table
oCgmx::DataFileFinderSearches data files from a set of paths
oCgmx::DataFileInfoInformation about a data file found by DataFileFinder::enumerateFiles()
oCgmx::DataFileOptionsSearch parameters for DataFileFinder
oCgmx::DefaultInitializationAllocator< T, A >Allocator adaptor that interposes construct() calls to convert value initialization into default initialization
oCgmx::DensityFittingForceManages evaluation of density-fitting forces for particles that were spread with a kernel
oCgmx::DensityFittingModuleInfoInformation about the density fitting module
oCgmx::DensitySimilarityMeasureMeasure similarity and gradient between densities
oCgmx::detail::extents_analyse< 0 >Specialisation for rank 0 extents analysis. Ends recursive rank analysis
oCgmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...>Enable querying extent of specific rank by splitting a dynamic extent off the variadic template arguments
oCgmx::detail::extents_analyse< R, E0, StaticExtents...>Enable querying extent of specific rank by splitting a static extents off the variadic template arguments
oCgmx::detail::PaddingTraits< T >Traits classes for handling padding for types used with PaddedVector
oCgmx::DevelopmentFeatureFlagsStructure that holds boolean flags corresponding to the development features present enabled through environment variables
oCgmx::DeviceStreamManagerDevice stream and context manager
oCgmx::DirectoryEnumeratorLists files in a directory
oCgmx::DomainDecompositionBuilderBuilds a domain decomposition management object
oCgmx::DomainLifetimeWorkloadDescribes work done on this domain on every step of its lifetime, but which might change after the next domain paritioning
oCgmx::DomdecOptionsStructure containing all (command line) options for the domain decomposition
oCgmx::EnergyCalculationFrequencyErrorsCollect errors for the energy calculation frequency
oCgmx::EnumerationArray< EnumType, DataType, ArraySize >Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type
oCgmx::EnumerationIterator< EnumType, Last, Step >Allows iterating sequential enumerators
oCgmx::EnumerationWrapper< EnumType, Last, Step >Allows constructing iterators for looping over sequential enumerators
oCgmx::ExceptionInfo< Tag, T >Stores additional context information for exceptions
oCgmx::ExceptionInitializerProvides information for Gromacs exception constructors
oCgmx::ExclusionBlockDescribes exclusions for a single atom
oCgmx::ExponentialDistribution< RealType >Exponential distribution
oCgmx::ExponentialDistribution< RealType >::param_typeExponential distribution parameters
oCgmx::ExponentialMovingAverageEvaluate the exponential moving average with bias correction
oCgmx::ExponentialMovingAverageStateStore the state of exponential moving averages
oCgmx::extents< StaticExtents >Multidimensional extents with static and dynamic dimensions
oCgmx::FixedCapacityVector< T, capacity >Vector that behaves likes std::vector but has fixed capacity
oCgmx::FlagsTemplate< FlagType >Template class for typesafe handling of combination of flags
oCgmx::ForceBuffersObject that holds the force buffers
oCgmx::ForceBuffersViewA view of the force buffer
oCgmx::ForceOutputsForce and virial output buffers for use in force computation
oCgmx::ForceProviderInputHelper struct that bundles data for passing it over to the force providers
oCgmx::ForceProviderOutputHelper struct bundling the output data of a force provider
oCgmx::ForceProvidersEvaluates forces from a collection of gmx::IForceProvider
oCgmx::ForceWithShiftForcesContainer for force and virial for algorithms that compute shift forces for virial calculation
oCgmx::ForceWithVirialContainer for force and virial for algorithms that provide their own virial tensor contribution
oCgmx::GammaDistribution< RealType >Gamma distribution
oCgmx::GammaDistribution< RealType >::param_typeGamma distribution parameters
oCgmx::GaussianSpreadKernelParametersParameters for density spreading kernels
oCgmx::GaussianSpreadKernelParameters::PositionAndAmplitudeParameters that describe the kernel position and amplitude
oCgmx::GaussianSpreadKernelParameters::ShapeShape parameters for Gaussian spreading kernels describe the kernel shape
oCgmx::GaussTransform3DSums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as $A \frac{1}{\sigma^3 \sqrt(2^3\pi^3)} * \exp(-\frac{(x-x0)^2}{2 \sigma^2})$
oCgmx::GlobalCommandLineHelpContextHelper for passing CommandLineHelpContext into parse_common_args()
oCgmx::GpuHaloExchangeManages GPU Halo Exchange object
oCgmx::GpuTaskAssignmentsContains the GPU task assignment for all ranks on this physical node
oCgmx::GpuTaskAssignmentsBuilderBuilder for the GpuTaskAssignments for all ranks on this node
oCgmx::GpuTaskMappingSpecifies the GPU deviceID_ available for task_ to use
oCgmx::HardwareTopologyInformation about sockets, cores, threads, numa, caches
oCgmx::HardwareTopology::CacheInformation about a single cache level
oCgmx::HardwareTopology::CoreInformation about a single core in a socket
oCgmx::HardwareTopology::DeviceInformation about a single PCI device
oCgmx::HardwareTopology::HWThreadInformation about a single hardware thread in a core
oCgmx::HardwareTopology::LogicalProcessorInformation about socket, core and hwthread for a logical processor
oCgmx::HardwareTopology::MachineHardware topology information about the entire machine
oCgmx::HardwareTopology::NumaInformation about a single numa node
oCgmx::HardwareTopology::NumaNodeInformation about each numa node in system
oCgmx::HardwareTopology::SocketInformation about a single socket in the system
oCgmx::HashedMap< T >Unordered key to value mapping
oCgmx::HelpLinksHyperlink data for writing out help
oCgmx::HelpManagerHelper for providing interactive online help
oCgmx::HelpWriterContextContext information for writing out help
oCgmx::HostAllocationPolicyPolicy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers
oCgmx::IAnalysisDataModuleInterface for a module that gets notified whenever data is added
oCgmx::ICommandLineModuleModule that can be run from command line using CommandLineModuleManager
oCgmx::ICommandLineOptionsModuleModule that can be run from a command line and uses gmx::Options for argument processing
oCgmx::ICommandLineOptionsModuleSettingsSettings to pass information between a CommandLineOptionsModule and generic code that runs it
oCgmx::IdentityFormatterFunction object to implement the same interface as StringFormatter to use with strings that should not be formatted further
oCgmx::IExecutableEnvironmentAllows customization of the way various directories are found by CommandLineProgramContext
oCgmx::IFileInputRedirectorAllows overriding file existence checks from code that supports it
oCgmx::IFileOutputRedirectorAllows capturing stdout and file output from code that supports it
oCgmx::IForceProviderInterface for a component that provides forces during MD
oCgmx::IHelpTopicProvides a single online help topic
oCgmx::IKeyValueTreeTransformRulesInterface to declare rules for transforming key-value trees
oCgmx::ILogTargetTarget where log output can be written
oCgmx::IMDModuleExtension module for GROMACS simulations
oCgmx::IMDOutputProviderInterface for handling additional output files during a simulation
oCgmx::IMdpOptionProviderInterface for handling mdp/tpr input to a mdrun module
oCgmx::InstallationPrefixInfoProvides information about installation prefix (see IProgramContext::installationPrefix())
oCgmx::InteractiveMDSimulatorBuilder parameter type for InteractiveMD
oCgmx::internal::SimdTraits< T >Simd traits
oCgmx::IonSwappingParameter type for IonSwapping SimulatorBuilder component
oCgmx::IOptionManagerBase class for option managers
oCgmx::IOptionsBehaviorInterface to provide extension points for options parsing
oCgmx::IOptionsContainerInterface for adding input options
oCgmx::IOutputAdapterOutputAdapter class for handling trajectory file flag setting and processing
oCgmx::IProgramContextProvides context information about the program that is calling the library
oCgmx::IRestraintPotentialInterface for Restraint potentials
oCgmx::ISerializerInterface for types that convert standard data types into a form suitable for storage or transfer
oCgmx::isIntegralConstant< T, Int >Is true if type is a std::integral_constant
oCgmx::IsSerializableEnum< T, bool >{
oCgmx::ITopologyProviderProvides topology information to SelectionOptionBehavior
oCgmx::KeyValueTreeBuilderRoot builder for creating trees that have an object at the root
oCgmx::KeyValueTreeObjectArrayBuilderBuilder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects
oCgmx::KeyValueTreeObjectBuilderBuilder for KeyValueTreeObject objects
oCgmx::KeyValueTreePathIdentifies an entry in a key-value tree
oCgmx::KeyValueTreeTransformRuleBuilderProvides methods to specify one transformation rule
oCgmx::KeyValueTreeTransformRuleBuilder::AfterFrom< FromType >Properties that can be specified after from()
oCgmx::KeyValueTreeTransformRuleBuilder::ToObject< FromType >Properties that can be specified after from().toObject()
oCgmx::KeyValueTreeTransformRuleBuilder::ToValue< FromType, ToType >Properties that can be specified after from().to()
oCgmx::KeyValueTreeTransformRulesScopedHelper object returned from IKeyValueTreeTransformRules::scopedTransform()
oCgmx::KeyValueTreeUniformArrayBuilder< T >Builder for KeyValueTreeArray objects where all elements are of type T
oCgmx::KeyValueTreeValueBuilderBuilder for KeyValueTreeValue objects
oCgmx::layout_rightRight-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number
oCgmx::layout_right::mapping< Extents >Mapping from multidimensional indices within extents to 1D index
oCgmx::LegacyInputCollection of legacy input information
oCgmx::LegacyMdrunOptionsThis class provides the same command-line option functionality to both CLI and API sessions
oCgmx::ListOfLists< typename >A list of lists, optimized for performance
oCgmx::LocalAtomSetA local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator
oCgmx::LocalAtomSetManagerHands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel
oCgmx::LogEntryWriterHelper class for creating log entries with GMX_LOG
oCgmx::LoggerBuilderInitializes loggers
oCgmx::LoggerOwnerManages memory for a logger built with LoggerBuilder
oCgmx::LogLevelHelperRepresents a single logging level
oCgmx::MappedUnionFinderExtension of UnionFind that supports non-consecutive integer indices as items
oCgmx::MDAtomsContains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators
oCgmx::MDLoggerDeclares a logging interface
oCgmx::MdModuleNotification< CallParameter, MdModuleNotificationBase >Subscribe and trigger notification functions
oCgmx::MDModulesManages the collection of all modules used for mdrun
oCgmx::MdModulesCheckpointReadingBroadcastProvides the MdModules with the communication record to broadcast
oCgmx::MdModulesCheckpointReadingDataOnMasterProvides the MdModules with the checkpointed data on the master rank
oCgmx::MdModulesEnergyOutputToDensityFittingRequestCheckerCheck if module outputs energy to a specific field
oCgmx::MdModulesNotifierCollection of callbacks to MDModules at differnt run-times
oCgmx::MdModulesWriteCheckpointDataWriting the MdModules data to a checkpoint file
oCgmx::MdrunnerRunner object for supporting setup and execution of mdrun
oCgmx::MdrunnerBuilderBuild a gmx::Mdrunner
oCgmx::MembedHolderMembed SimulatorBuilder parameter type
oCgmx::MessageStringCollectorHelper class for collecting message strings, optionally with context
oCgmx::MessageStringContextConvenience class for creating a message context
oCgmx::ModularSimulatorThe modular simulator
oCgmx::MrcDataStatisticsStatistics about mrc data arrays
oCgmx::MrcDensityMapHeaderA container for the data in mrc density map file formats
oCgmx::MrcDensityMapOfFloatFromFileReaderRead an mrc density map from a given file
oCgmx::MrcDensityMapOfFloatReaderRead an mrc/ccp4 file that contains float values
oCgmx::MrcDensityMapOfFloatWriterWrite an mrc/ccp4 file that contains float values
oCgmx::MrcDensitySkewDataSkew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) 2014"
oCgmx::MtsLevelSetting for a single level for multiple time step integration
oCgmx::MultiDimArray< TContainer, Extents, LayoutPolicy >Multidimensional array that manages its own memory
oCgmx::no_delete< T >Deleter for std::shared_ptr that does nothing
oCgmx::NonbondedBenchmarkInfoDeclares gmx nonbonded-bench
oCgmx::NormalDistribution< RealType >Normal distribution
oCgmx::NormalDistribution< RealType >::param_typeNormal distribution parameters
oCgmx::NumericalSplineTableInputSpecification for vector table function (name, function, derivative, spacing)
oCgmx::OpenClTraits< cl_type >Stub for OpenCL type traits
oCgmx::OpenClTraitsBase< cl_type >Implements common trait infrastructure for OpenCL types
oCgmx::OptionInfoGives information and allows modifications to an option after creation
oCgmx::OptionManagerContainerContainer to keep managers added with Options::addManager() and pass them to options
oCgmx::OptionsAssignerDecorator class for assigning values to Options
oCgmx::OptionsBehaviorCollectionContainer for IOptionsBehavior objects
oCgmx::OptionsIteratorDecorator class for visiting options in a Options object
oCgmx::OptionsModifyingIteratorDecorator class for visiting options in a Options object, allowing changes
oCgmx::OptionsModifyingVisitorPure interface for visiting options in a Options object, allowing modifications
oCgmx::OptionsVisitorPure interface for visiting options in a Options object
oCgmx::OptionValueConverterSimple< OutType >Helper for converting from Any to a given type
oCgmx::OutputAdapterContainerStorage for output adapters that modify the state of a t_trxframe object
oCgmx::OutputRequirementOptionDirectorContainer for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer
oCgmx::OutputRequirementsFinalized version of requirements after processing
oCgmx::PaddedVector< T, Allocator >PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS
oCgmx::PageAlignedAllocationPolicyPolicy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices
oCgmx::PhysicalNodeCommunicatorHolds a communicator for the physical node of this rank
oCgmx::PmeForceSenderGpuManages sending forces from PME-only ranks to their PP ranks
oCgmx::PmePpCommGpuManages communication related to GPU buffers between this PME rank and its PP rank
oCgmx::PotentialPointDataStructure to hold the results of IRestraintPotential::evaluate()
oCgmx::PrivateImplPointer< Impl >Helper class to manage a pointer to a private implementation class
oCgmx::ProfilingCollection of profiling information
oCgmx::QuadraticSplineTableQuadratic spline interpolation table
oCgmx::Range< typename >Defines a range of integer numbers and accompanying operations
oCgmx::Range< typename >::iteratorAn iterator that loops over a range of integers
oCgmx::RangePartitioningDivision of a range of indices into consecutive blocks
oCgmx::ReadCheckpointDataHolderHolder for read checkpoint data
oCgmx::registerMdModuleNotification< CurrentCallParameter, CallParameter...>Template specialization to assemble MdModuleNotification
oCgmx::ResetHandlerClass handling the reset of counters
oCgmx::RestraintManagerManage the Restraint potentials available for Molecular Dynamics
oCgmx::SelectionProvides access to a single selection
oCgmx::SelectionCollectionCollection of selections
oCgmx::SelectionPositionProvides access to information about a single selected position
oCgmx::SelectionTopologyPropertiesDescribes topology properties required for selection evaluation
oCgmx::SettleDataData for executing SETTLE constraining
oCgmx::shakedataWorking data for the SHAKE algorithm
oCgmx::Simd4DBoolSIMD4 variable type to use for logical comparisons on doubles
oCgmx::Simd4DoubleSIMD4 double type
oCgmx::Simd4FBoolSIMD4 variable type to use for logical comparisons on floats
oCgmx::Simd4FloatSIMD4 float type
oCgmx::SimdDBoolBoolean type for double SIMD data
oCgmx::SimdDIBoolBoolean type for integer datatypes corresponding to double SIMD
oCgmx::SimdDInt32Integer SIMD variable type to use for conversions to/from double
oCgmx::SimdDInt32TagTag type to select to load SimdDInt32 with simdLoad(U)
oCgmx::SimdDoubleDouble SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1
oCgmx::SimdDoubleTagTag type to select to load SimdDouble with simdLoad(U)
oCgmx::SimdFBoolBoolean type for float SIMD data
oCgmx::SimdFIBoolBoolean type for integer datatypes corresponding to float SIMD
oCgmx::SimdFInt32Integer SIMD variable type to use for conversions to/from float
oCgmx::SimdFInt32TagTag type to select to load SimdFInt32 with simdLoad(U)
oCgmx::SimdFloatFloat SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1
oCgmx::SimdFloatTagTag type to select to load SimdFloat with simdLoad(U)
oCgmx::SimdSetZeroProxyProxy object to enable setZero() for SIMD and real types
oCgmx::SimulationContextSimulation environment and configuration
oCgmx::SimulationSignalPOD-style object used by mdrun ranks to set and receive signals within and between simulations
oCgmx::SimulationSignallerObject used by mdrun ranks to signal to each other at this step
oCgmx::SimulationTimeStepProvides the simulation time step in ps
oCgmx::SimulationWorkloadManage what computation is required during the simulation
oCgmx::SimulatorBuilderClass preparing the creation of Simulator objects
oCgmx::SimulatorConfigSimulation configuation settings
oCgmx::SimulatorEnvCollection of environmental information for a simulation
oCgmx::SimulatorStateDataData for a specific simulation state
oCgmx::SiteAbstraction for a restraint interaction site
oCgmx::StaticLog2< n >Evaluate log2(n) for integer n statically at compile time
oCgmx::StaticLog2< 0 >Specialization of StaticLog2<n> for n==0
oCgmx::StaticLog2< 1 >Specialization of StaticLog2<n> for n==1
oCgmx::StepWorkloadDescribes work done on this domain that may change per-step
oCgmx::StopConditionSignalClass setting the stop signal based on gmx_get_stop_condition()
oCgmx::StopConditionTimeClass setting the stop signal based on maximal run time
oCgmx::StopHandlerClass handling the stop signal
oCgmx::StopHandlerBuilderClass preparing the creation of a StopHandler
oCgmx::StringCompareCompare object for std::string STL containers and algorithms that supports run-time decision on how to compare
oCgmx::StringFormatterFunction object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms
oCgmx::TabulatedNormalDistribution< RealType, tableBits >Tabulated normal random distribution
oCgmx::TabulatedNormalDistribution< RealType, tableBits >::param_typeNormal distribution parameter class (mean and stddev)
oCgmx::test::AllocatorTest< T >Templated test fixture
oCgmx::test::AnalysisDataTestFixtureTest fixture for AbstractAnalysisData testing
oCgmx::test::AnalysisDataTestInputRepresents static input data for AbstractAnalysisData tests
oCgmx::test::AnalysisDataTestInputFrameRepresents a single frame in AnalysisDataTestInput structure
oCgmx::test::AnalysisDataTestInputPointSetRepresents a single set of points in AnalysisDataTestInputFrame structure
oCgmx::test::CommandLineHelper class for tests that need to construct command lines
oCgmx::test::CommandLineTestBaseTest fixture for tests that call a single command-line program with input/output files
oCgmx::test::CommandLineTestHelperHelper class for tests that construct command lines that need to reference existing files
oCgmx::test::FloatingPointDifferenceComputes and represents a floating-point difference value
oCgmx::test::FloatingPointToleranceSpecifies a floating-point comparison tolerance and checks whether a difference is within the tolerance
oCgmx::test::IFileMatcherRepresents a file matcher, matching file contents against reference (or other) data
oCgmx::test::IFileMatcherSettingsRepresents a factory for creating a file matcher
oCgmx::test::InteractiveTestHelperHelper class for testing interactive sessions
oCgmx::test::ITextBlockMatcherRepresents a text matcher, matching text stream contents against reference data
oCgmx::test::ITextBlockMatcherSettingsRepresents a factory for creating a text matcher
oCgmx::test::LoggerTestHelperHelper class for tests to check output written to a logger
oCgmx::test::ModuleSelectionHelper class for tests that need an initialized selection
oCgmx::test::StdioTestHelperHelper class for tests where code reads directly from stdin
oCgmx::test::StringTestBaseTest fixture for tests that check string formatting
oCgmx::test::TestFileManagerHelper for tests that need input and output files
oCgmx::test::TestOptionsProviderProvides additional options for the test executable
oCgmx::test::TestReferenceCheckerHandles comparison to test reference data
oCgmx::test::TestReferenceDataHandles creation of and comparison to test reference data
oCgmx::test::TprAndFileManagerHelper to bundle generated TPR and the file manager to clean it up
oCgmx::TextInputStreamInterface for reading text
oCgmx::TextLineWrapperWraps lines to a predefined length
oCgmx::TextLineWrapperSettingsStores settings for line wrapping
oCgmx::TextOutputStreamInterface for writing text
oCgmx::TextReaderReads text from a TextInputStream
oCgmx::TextTableFormatterFormats rows of a table for text output
oCgmx::TextWriterWrites text into a TextOutputStream
oCgmx::ThreeFry2x64General< rounds, internalCounterBits >General implementation class for ThreeFry counter-based random engines
oCgmx::TimeUnitManagerProvides common functionality for time unit conversions
oCgmx::TopologyDataCollection of handles to topology information
oCgmx::TopologyInformationTopology information available to a trajectory analysis module
oCgmx::TrajectoryAnalysisCommandLineRunnerRunner for command-line trajectory analysis tools
oCgmx::TrajectoryAnalysisModuleBase class for trajectory analysis modules
oCgmx::TrajectoryAnalysisModuleDataBase class for thread-local data storage during trajectory analysis
oCgmx::TrajectoryAnalysisSettingsTrajectory analysis module configuration object
oCgmx::TrajectoryFileOpenerLow level method to take care of only file opening and closing
oCgmx::TrajectoryFrameWriterWrites coordinate frames to a sink, e.g. a trajectory file
oCgmx::TranslateAndScaleTransform coordinates in three dimensions by first translating, then scaling them
oCgmx::UniformIntDistribution< IntType >Uniform integer distribution
oCgmx::UniformIntDistribution< IntType >::param_typeUniform int distribution parameters
oCgmx::UniformRealDistribution< RealType >Uniform real distribution
oCgmx::UniformRealDistribution< RealType >::param_typeUniform real distribution parameters
oCgmx::UnionFinderUnion-find data structure for keeping track of disjoint sets
oCgmx::UpdateContains data for update phase
oCgmx::UpdateGroupsCogClass for managing and computing centers of geometry of update groups
oCgmx::VirtualSitesHandlerClass that handles construction of vsites and spreading of vsite forces
oCgmx::WholeMoleculeTransformThis class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules
oCgmx::WriteCheckpointDataHolderHolder for write checkpoint data
oCgmx_ana_index_tStores a single index group
oCgmx_ana_indexmap_tData structure for calculating index group mappings
oCgmx_ana_pos_tStores a set of positions together with their origins
oCgmx_cache_protect_tCache-line protection buffer
oCgmx_enerdata_tStruct for accumulating all potential energy terms and some kinetic energy terms
oCgmx_ffparams_tStruct that holds all force field parameters for the simulated system
oCgmx_ga2la_tGlobal to local atom mapping
oCgmx_ga2la_t::EntryStructure for the local atom info
oCgmx_localtop_tThe fully written out topology for a domain over its lifetime
oCgmx_molblock_tBlock of molecules of the same type, used in gmx_mtop_t
oCgmx_moltype_tMolecules type data: atoms, interactions and exclusions
oCgmx_multisim_tCoordinate multi-simulation resources for mdrun
oCgmx_sparsematrixSparse matrix storage format
oCGpuRegionTimerImplThe OpenCL implementation of the GPU code region timing. With OpenCL, one has to use cl_event handle for each API call that has to be timed, and accumulate the timing afterwards. As we would like to avoid overhead on API calls, we only query and accumulate cl_event timing at the end of time steps, not after the API calls. Thus, this implementation does not reuse a single cl_event for multiple calls, but instead maintains an array of cl_events to be used within any single code region. The array size is fixed at a small but sufficiently large value for the number of cl_events that might contribute to a timer region, currently 10
oCGpuRegionTimerWrapper< GpuRegionTimerImpl >This is a GPU region timing wrapper class. It allows for host-side tracking of the accumulated execution timespans in GPU code (measuring kernel or transfers duration). It also partially tracks the correctness of the timer state transitions, as far as current implementation allows (see TODO in getLastRangeTime() for a disabled check). Internally it uses GpuRegionTimerImpl for measuring regions
oCgmx::HashedMap< gmx_ga2la_t::Entry >
oCgmx::HashedMap< int >
oChistory_tHistory information for NMR distance and orientation restraints
oCInteractionListHandleType for returning a list of InteractionList references
oCInteractionOfTypeDescribes an interaction of a given type, plus its parameters
oCInteractionsOfTypeA set of interactions of a given type (found in the enumeration in ifunc.h), complete with atom indices and force field function parameters
oCListedForcesClass for calculating listed interactions, uses OpenMP parallelization
oCgmx::ListOfLists< int >
oCMoleculeBlockIndicesIndices for a gmx_molblock_t, derived from other gmx_mtop_t contents
oCMoleculeInformationHolds the molecule information during preprocessing
oCMoleculePatchBlock to modify individual residues
oCMoleculePatchDatabaseA set of modifications to apply to atoms
oCgmx::MultiDimArray< real >
oCgmx::MultiDimArray< std::vector< float >, gmx::extents >
oCgmx::MultiDimArray< std::vector< float >, gmx::extents< dynamic_extent, dynamic_extent > >
oCgmx::MultiDimArray< t_matelmt >
oCNbnxm::Grid::DimensionsThe physical dimensions of a grid
oCnbnxn_cj4_tFour-way j-cluster lists
oCnbnxn_cj_tThis is the actual cluster-pair list j-entry
oCnbnxn_cycle_tLocal cycle count struct for profiling
oCnbnxn_excl_tStruct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist
oCnbnxn_im_ei_tInteraction data for a j-group for one warp
oCnbnxn_sciGrouped pair-list i-unit
oCNbnxnPairlistCpuCluster pairlist type for use on CPUs
oCNbnxnPairlistCpuWorkWorking data for the actual i-supercell during pair search
oCNbnxnPairlistCpuWork::IClusterDataStruct for storing coordinats and bounding box for an i-entry during search
oCnonbonded_verlet_tTop-level non-bonded data structure for the Verlet-type cut-off scheme
oCgmx::compat::not_null< ISimulatorElement * >
oCgmx::compat::not_null< LegacySimulatorData * >
oCNumPmeDomainsStruct for passing around the number of PME domains
oCObservablesHistoryObservables history, for writing/reading to/from checkpoint file
oCgmx::OpenClTraitsBase< cl_command_queue >
oCgmx::OpenClTraitsBase< cl_context >
oCgmx::OpenClTraitsBase< cl_kernel >
oCgmx::OpenClTraitsBase< cl_program >
oCgmx::OptionValueConverterSimple< bool >
oCgmx::OptionValueConverterSimple< double >
oCgmx::OptionValueConverterSimple< float >
oCgmx::OptionValueConverterSimple< int >
oCgmx::OptionValueConverterSimple< int64_t >
oCgmx::OptionValueConverterSimple< std::string >
oCgmx::OptionValueConverterSimple< T >
oCgmx::PaddedVector< gmx::BasicVector >
oCgmx::PaddedVector< gmx::gmx::BasicVector >
oCgmx::PaddedVector< gmx::RVec >
oCgmx::PaddedVector< real >
oCgmx::PaddedVector< RVec >
oCPairlistSetsContains sets of pairlists
oCPairSearchMain pair-search struct, contains the grid(s), not the pair-list(s)
oCPairsearchWorkThread-local work struct, contains working data for Grid
oCPartialDeserializedTprFileContains the partly deserialized contents of a TPR file
oCPbcAiucCompact and ordered version of the PBC matrix
oCPmeGpuProgramStores PME data derived from the GPU context or devices
oCPpRanksContains information about the PP ranks that partner this PME rank
oCPreprocessingAtomTypesStorage of all atom types used during preprocessing of a simulation input
oCPreprocessingBondAtomTypeStorage for all bonded atomtypes during simulation preprocessing
oCPreprocessResidueInformation about preprocessing residues
oCgmx::PrivateImplPointer< internal::FileStreamImpl >
oCgmx::PrivateImplPointer< internal::KeyValueTreeTransformerImpl >
oCgmx::PrivateImplPointer< internal::OptionsImpl >
oCgmx::Range< int >
oCReplicaExchangeParametersThe parameters for the replica exchange algorithm
oCSimulationGroupsContains the simulation atom groups
oCSimulationInputHandleOwning handle to a SimulationInput object
oCstd::array< T >STL class
oCstd::exceptionSTL class
oCStringTableA class to store strings for lookup
oCStringTableBuilderBuilds a memory efficient storage for strings of characters
oCStringTableEntryHelper class to access members in StringTable
oCt_filenmFile name option definition for C code
oCt_mappingMaps an XPM element to an RGB color and a string description
oCt_matrixA matrix of integers, plus supporting values, such as used in XPM output
oCt_mdatomsDeclares mdatom data structure
oCt_pargsCommand-line argument definition for C code
oCt_pbcStructure containing info on periodic boundary conditions
oCt_stateThe microstate of the system
oCt_symbufLegacy symbol table entry as linked list
oCt_xpmelmtModels an XPM element
oCgmx::ThreeFry2x64General< 13, internalCounterBits >
oCgmx::ThreeFry2x64General< 20, internalCounterBits >
\CTpxFileHeaderFirst part of the TPR file structure containing information about the general aspect of the system