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Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCAmdPackedFloat3Special packed Float3 flavor to help compiler optimizations on AMD CDNA2 devices
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< const unsigned short >
oCgmx::ArrayRef< double >
oCgmx::ArrayRef< gmx::BasicVector >
oCgmx::ArrayRef< gmx::gmx::BasicVector >
oCgmx::ArrayRef< gmx::RVec >
oCgmx::ArrayRef< PpRanks >
oCgmx::ArrayRef< real >
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
oCAtomsAdjacencyListElementHelper type for discovering coupled constraints
oCBalanceRegionObject that describes a DLB balancing region
oCgmx::BasicVector< double >
oCgmx::BasicVector< int >
oCgmx::BasicVector< real >
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCdf_history_tFree-energy sampling history struct
oCFEPStateValue< T >Template wrapper struct for particle FEP state values
oCFEPStateValue< NameHolder >
oCFEPStateValue< real >
oCFEPStateValue< unsigned short >
oCgmx::FixedCapacityVector< GpuEventSynchronizer *, 3 >
oCgmx::FlagsTemplate< Flag >
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::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::AnalysisDataPlotSettingsCommon settings for data plots
oCgmx::AnalysisDataPointSetRefValue type wrapper for non-mutable access to a set of data column values
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::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::AtomPairA pair of atoms indexes
oCgmx::BasicVector< ValueType >C++ class for 3D vectors
oCgmx::BenchmarkSystemDescription of the system used for benchmarking
oCgmx::BoolTypeA clone of a bool as a workaround on the template specialization of std::vector<bool> that is incompatible with ArrayRef
oCgmx::BoxDeformationHandleHandle to information about the box
oCgmx::CheckpointData< operation >}
oCgmx::CommandLineHelpWriterWrites help information for Options
oCgmx::CommandLineModuleSettingsSettings to pass information between a module and the general runner
oCgmx::CommandLineParserImplements command-line parsing for Options objects
oCgmx::ConstraintsParamCollection of constraint parameters
oCgmx::ConvertTprInfoDeclares gmx convert-tpr
oCgmx::CoulombCalculator< coulombType >Base Coulomb calculator class, only specializations are used
oCgmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical >Specialized calculator for Ewald using an analytic approximation
oCgmx::CoulombCalculator< KernelCoulombType::EwaldTabulated >Specialized calculator for Ewald using tabulated functions
oCgmx::CoulombCalculator< KernelCoulombType::RF >Specialized calculator for RF
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::detail::PaddingTraits< T >Traits classes for handling padding for types used with PaddedVector
oCgmx::DiagonalMasker< int, KernelLayout, DiagonalMaskType >Base Coulomb calculator class, only specializations are used
oCgmx::DiagonalMasker< nR, kernelLayout, DiagonalMaskType::JSizeEqualsISize >Specialized masker for JSizeEqualsISize
oCgmx::DiagonalMasker< nR, kernelLayout, DiagonalMaskType::JSizeIsDoubleISize >Specialized masker for JSizeIsDoubleISize
oCgmx::DiagonalMasker< nR, kernelLayout, DiagonalMaskType::JSizeIsHalfISize >Specialized masker for JSizeIsHalfISize
oCgmx::EqualCaseInsensitiveFunction object for comparisons with equalCaseInsensitive
oCgmx::ExceptionInfo< Tag, T >Stores additional context information for exceptions
oCgmx::ExceptionInitializerProvides information for Gromacs exception constructors
oCgmx::ExponentialDistribution< RealType >Exponential distribution
oCgmx::ExponentialDistribution< RealType >::param_typeExponential distribution parameters
oCgmx::FixedCapacityVector< typename, size_t >Vector that behaves likes std::vector but has fixed capacity
oCgmx::FlagsTemplate< FlagType >Template class for typesafe handling of combination of flags
oCgmx::GammaDistribution< RealType >Gamma distribution
oCgmx::GammaDistribution< RealType >::param_typeGamma distribution parameters
oCgmx::GromppMtsOptsStruct for passing the MTS mdp options to setupMtsLevels()
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::IFrameConverterIFrameConverter interface for manipulating coordinate information
oCgmx::InstallationPrefixInfoProvides information about installation prefix (see IProgramContext::installationPrefix())
oCgmx::InteractiveMDSimulatorBuilder parameter type for InteractiveMD
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::IsSerializableEnum< T, bool >{
oCgmx::ITopologyProviderProvides topology information to SelectionOptionBehavior
oCgmx::LegacyInputCollection of legacy input information
oCgmx::LennardJonesCalculator< calculateEnergies, vdwModifier >Base LJ calculator class, only specializations are used
oCgmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch >Specialized calculator for LJ with force switch
oCgmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch >Specialized calculator for LJ with potential switch
oCgmx::LennardJonesCalculator< false, InteractionModifiers::PotShift >Specialized calculator for LJ with potential shift and no energy calculation
oCgmx::LennardJonesCalculator< true, InteractionModifiers::PotShift >Specialized calculator for LJ with potential shift and energy calculation
oCgmx::ListOfLists< typename >A list of lists, optimized for performance
oCgmx::MembedHolderMembed SimulatorBuilder parameter type
oCgmx::MtsLevelSetting for a single level for multiple time step integration
oCgmx::NonbondedBenchmarkInfoDeclares gmx nonbonded-bench
oCgmx::NormalDistribution< RealType >Normal distribution
oCgmx::NormalDistribution< RealType >::param_typeNormal distribution parameters
oCgmx::OptionInfoGives information and allows modifications to an option after creation
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::PotentialPointDataStructure to hold the results of IRestraintPotential::evaluate()
oCgmx::ProfilingCollection of profiling information
oCgmx::PullCoordExpressionParserClass with a mathematical expression and parser
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::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::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::SimulatorConfigSimulation configuation settings
oCgmx::SimulatorEnvCollection of environmental information for a simulation
oCgmx::SimulatorStateDataData for a specific simulation state
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::StringFormatterFunction object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms
oCgmx::StringToEnumValueConverter< EnumType,, stringCompareType, stripStrings >A class to convert a string to an enum value of type EnumType
oCgmx::TabulatedNormalDistribution< RealType, tableBits >Tabulated normal random distribution
oCgmx::TabulatedNormalDistribution< RealType, tableBits >::param_typeNormal distribution parameter class (mean and stddev)
oCgmx::TextLineWrapperWraps lines to a predefined length
oCgmx::TextLineWrapperSettingsStores settings for line wrapping
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::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::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_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_domdec_constraints_tStruct used during constraint setup with domain decomposition
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_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_nodecomm_tSettings and communicators for two-step communication: intra + inter-node
oCgmx_sparsematrixSparse matrix storage format
oCIListIteratorObject that allows looping over all atoms in an mtop
oCIListProxyProxy object returned from IListIterator
oCIListRangeRange over all interaction lists of topology
oCIndexGroupAn index group consisting or a name and list of atom indices
oCInteractionListHandleType for returning a list of InteractionList references
oCJClusterListSimple j-cluster list
oCgmx::ListOfLists< int >
oCLocalSettleDataLocal settle data
oCMoleculeBlockIndicesIndices for a gmx_molblock_t, derived from other gmx_mtop_t contents
oCNbnxm::EnergyFunctionProperties< elecType, vdwType >Set of boolean constants mimicking preprocessor macros
oCNbnxm::Grid::DimensionsThe physical dimensions of a grid
oCNbnxmKernel< doPruneNBL, doCalcEnergies, elecType, vdwType, subGroupSize >Class name for NBNXM kernel
oCnbnxn_cj_packed_tPacked j-cluster list element
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 coordinates and bounding box for an i-entry during search
oCPackedJClusterListPacked j-cluster list
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
oCPdbAtomEntryContains information for a single particle in a PDB file
oCgmx::Range< int >
oCSettleWaterTopologyComposite data for settle initialization
oCSimulationGroupsContains the simulation atom groups
oCSimulationInputHandleOwning handle to a SimulationInput object
oCSimulationParticleSingle particle in a simulation
oCstd::exceptionSTL class
oCStringTableA class to store strings for lookup
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_oriresdataOrientation restraining stuff
oCt_pargsCommand-line argument definition for C code
oCt_pbcStructure containing info on periodic boundary conditions
oCt_stateThe microstate of the system
oCt_xpmelmtModels an XPM element
oCgmx::ThreeFry2x64General< 13, internalCounterBits >
oCgmx::ThreeFry2x64General< 20, internalCounterBits >
oCWarningHandlerGeneral warning handling object
\CWaterMoleculeIndices of atoms in a water molecule