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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 >
oCAllVsiteBondedInteractionsWraps the datastructures for the different vsite bondeds
oCAmdPackedFloat3Special packed Float3 flavor to help compiler optimizations on AMD CDNA2 devices
oCgmx::AnalysisDataFrameLocalData< double >
oCgmx::AnalysisDataFrameLocalData< int64_t >
oCanonymous_namespace{edsam.cpp}::t_edfloodEssential dynamics flooding parameters and work data. TODO: split into working data and input parameters NOTE: The implementation here follows: O.E. Lange, L.V. Schafer, and H. Grubmuller, “Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics,” J. Comp. Chem., 27 1693–1702 (2006)
oCanonymous_namespace{edsam.cpp}::t_edvecsEssential dynamics vectors per method implementation
oCanonymous_namespace{edsam.cpp}::t_eigvecEssential dynamics vector. TODO: split into working data and input data NOTE: called eigvec, because traditionally eigenvectors from PCA analysis were used as essential dynamics vectors, however, vectors used for ED need not have any special properties
oCanonymous_namespace{evaluate.cpp}::MempoolGroupReserverReserves memory for an index group from the evaluation memory pool
oCanonymous_namespace{evaluate.cpp}::MempoolSelelemReserverReserves memory for a selection element from the evaluation memory pool
oCanonymous_namespace{evaluate.cpp}::SelelemTemporaryValueAssignerAssigns a temporary value for a selection element
oCanonymous_namespace{indexutil.cpp}::IndexBlockTestText fixture for index block operations
oCanonymous_namespace{lincs.cpp}::AtomPairIndices of the two atoms involved in a single constraint
oCanonymous_namespace{lincs.cpp}::TaskUnit of work within LINCS
oCanonymous_namespace{minimize.cpp}::EnergyEvaluatorClass to handle the work of setting and doing an energy evaluation
oCanonymous_namespace{resourcedivision.cpp}::SingleRankCheckerHandles checks for algorithms that must use a single rank
oCanonymous_namespace{sm_keywords.cpp}::StringKeywordMatchItemSingle item in the list of strings/regular expressions to match
oCanonymous_namespace{sm_keywords.cpp}::t_methoddata_kwstrData structure for string keyword expression evaluation
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::analysismodules::anonymous_namespace{msd.cpp}::MoleculeData >
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< Nbnxm::BoundingBox >
oCgmx::ArrayRef< PpRanks >
oCgmx::ArrayRef< real >
oCgmx::ArrayRef< ValueType >
oCgmx::ArrayRefWithPadding< gmx::BasicVector >
oCgmx::ArrayRefWithPadding< gmx::gmx::BasicVector >
oCAtom2VsiteBondHelper type for conversion of bonded parameters to virtual sites
oCAtomDistributionDistribution of atom groups over the domain (only available on the main rank)
oCAtomDistribution::DomainAtomGroupsCollection of local group and atom counts for a domain
oCAtomIndexSetContainer for returning molecule type and index information for an atom
oCAtomInMolblockContainer for returning molecule type and index information for an atom
oCAtomIteratorObject that allows looping over all atoms in an mtop
oCAtomPropertiesHolds all the atom property information loaded
oCAtomProperties::ImplImplementation detail type for Atomproperties
oCAtomPropertyConglomeration of atom property entries
oCAtomProxyProxy object returned from AtomIterator
oCAtomRangeRange over all atoms of topology
oCAtomsAdjacencyListElementHelper type for discovering coupled constraints
oCAwhReaderAll options and meta-data needed for the AWH output
oCBalanceRegionObject that describes a DLB balancing region
oCBalanceRegion::ImplStruct for timing the region for dynamic load balancing
oCBaseEntryBasic entries in AtomProperty
oCgmx::basic_mdspan< value_type, dynamic_extents_type, layout_right >
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::basic_mdspan< value_type, gmx::gmx::extents, layout_right >
oCgmx::basic_mdspan< value_type, static_extents_type, layout_right >
oCgmx::BasicVector< double >
oCgmx::BasicVector< int >
oCgmx::BasicVector< real >
oCBiasOutputSetupAll meta-data that is shared for all output files for one bias
oCbonded_threading_tStruct contain all data for bonded force threading
oCBondedInteractionInformation about single bonded interaction
oCBondedInteractionListAccumulation of different bonded types for preprocessing
oCgmx::BuildMDModulesNotifier< const gmx::CoordinatesAndBoxPreprocessed &, const gmx::MDLogger &, WarningHandler *, gmx::EnergyCalculationFrequencyErrors *, gmx_mtop_t *, const gmx::IndexGroupsAndNames &, gmx::KeyValueTreeObjectBuilder, const gmx::QMInputFileName &, const gmx::EnsembleTemperature & >
oCgmx::BuildMDModulesNotifier< const KeyValueTreeObject &, gmx::LocalAtomSetManager *, const gmx::MDLogger &, const gmx_mtop_t &, const gmx::MDModulesAtomsRedistributedSignal, gmx::MDModulesEnergyOutputToDensityFittingRequestChecker *, gmx::MDModulesEnergyOutputToQMMMRequestChecker *, gmx::SeparatePmeRanksPermitted *, const PbcType &, const gmx::SimulationTimeStep &, const t_commrec &, const gmx::MdRunInputFilename &, const gmx::EdrOutputFilename & >
oCgmx::BuildMDModulesNotifier< gmx::MDModulesCheckpointReadingDataOnMain, gmx::MDModulesCheckpointReadingBroadcast, gmx::MDModulesWriteCheckpointData >
oCCalcVerletBufferParametersStruct with references for most parameters for calling calcVerletBufferSize()
oCChainIdFillerConstructs plausible chain IDs for multi-molecule systems, e.g. when read from .tpr files
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCcl_nbparam_paramsData structure shared between the OpenCL device code and OpenCL host code
oCdd_corners_tDomain corners for communication, a maximum of 4 i-zones see a j domain
oCDDBalanceRegionHandlerManager for starting and stopping the dynamic load balancing region
oCDDGridSetupDescribes the DD grid setup
oCDDPairInteractionRangesPair interaction zone and atom range for an i-zone
oCDeviceInformationPlatform-dependent device information
oCDeviceStreamDeclaration of platform-agnostic device stream/queue
oCdf_history_tFree-energy sampling history struct
oCDipoleDataData structure to hold dipole-related data and staging arrays
oCDispersionCorrection::CorrectionStruct for returning all dispersion correction quantities
oCekinstate_tStruct used for checkpointing only
oCem_stateUtility structure for manipulating states during EM
oCgmx::EnumerationArray< AtomLocality, const DeviceStream * >
oCgmx::EnumerationArray< AtomLocality, GpuEventSynchronizer >
oCgmx::EnumerationArray< AtomLocality, Nbnxm::GpuTimers::XFTransfers >
oCgmx::EnumerationArray< BackboneAtomTypes, size_t >
oCgmx::EnumerationArray< BondedTypes, BondedInteractionList >
oCgmx::EnumerationArray< Channel, int * >
oCgmx::EnumerationArray< Channel, int >
oCgmx::EnumerationArray< Channel, rvec * >
oCgmx::EnumerationArray< Channel, rvec ** >
oCgmx::EnumerationArray< Compartment, int * >
oCgmx::EnumerationArray< Compartment, int >
oCgmx::EnumerationArray< Compartment, real >
oCgmx::EnumerationArray< Compartment, swap_compartment >
oCgmx::EnumerationArray< CoordinateFileFlags, OutputAdapterPointer >
oCgmx::EnumerationArray< DeviceStreamType, std::unique_ptr< DeviceStream > >
oCgmx::EnumerationArray< FftDirection, RocfftPlan >
oCgmx::EnumerationArray< FreeEnergyPerturbationCouplingType, bool >
oCgmx::EnumerationArray< FreeEnergyPerturbationCouplingType, double >
oCgmx::EnumerationArray< FreeEnergyPerturbationCouplingType, real >
oCgmx::EnumerationArray< FreeEnergyPerturbationCouplingType, std::string >
oCgmx::EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double > >
oCgmx::EnumerationArray< gmx::AtomLocality, std::unique_ptr< gmx::GpuForceReduction > >
oCgmx::EnumerationArray< gmx::DirectionX, gmx::EnumerationArray< gmx::DirectionY, DeviceBuffer< float > > >
oCgmx::EnumerationArray< gmx::DirectionX, gmx::EnumerationArray< gmx::DirectionY, int > >
oCgmx::EnumerationArray< gmx::DirectionX, int >
oCgmx::EnumerationArray< gmx::DirectionY, int >
oCgmx::EnumerationArray< HydrogenExchangeGroup, HydrogenCellType >
oCgmx::EnumerationArray< InteractionLocality, Nbnxm::Nbnxm::GpuTimers::Nbnxm::GpuTimers::Interaction >
oCgmx::EnumerationArray< MdGraphEvenOrOddStep, std::unique_ptr< gmx::MdGpuGraph > >
oCgmx::EnumerationArray< ModuleMultiThread, int >
oCgmx::EnumerationArray< Nbnxm::InteractionLocality, bool >
oCgmx::EnumerationArray< Nbnxm::InteractionLocality, const DeviceStream * >
oCgmx::EnumerationArray< Nbnxm::InteractionLocality, Nbnxm::gpu_plist * >
oCgmx::EnumerationArray< NonBondedEnergyTerms, bool >
oCgmx::EnumerationArray< NonBondedEnergyTerms, std::vector< real > >
oCgmx::EnumerationArray< PmeStage, gmx_kernel_timing_data_t >
oCgmx::EnumerationArray< PmeStage, GpuRegionTimerWrapper >
oCgmx::EnumerationArray< PmeTestFlavor, std::string >
oCgmx::EnumerationArray< ReplicaExchangeType, real * >
oCgmx::EnumerationArray< SimulationAtomGroupType, AtomGroupIndices >
oCgmx::EnumerationArray< SimulationAtomGroupType, std::vector< unsigned char > >
oCgmx::EnumerationArray< TurnsTypes, HelixPositions >
oCgmx::EnumerationArray< WallCycleCounter, wallcc_t >
oCgmx::EnumerationArray< WallCycleSubCounter, wallcc_t >
oCgmx::EnumerationArray< WarningType, int >
oCEwaldBoxZScalerClass to handle box scaling for Ewald and PME
oCExclusionChecker::ImplData to help check local topology construction
oCgmx::extents< dynamic_extent, dynamic_extent, dynamic_extent >
oCgmx::extents< E_STATIC...>
oCFEPStateValue< T >Template wrapper struct for particle FEP state values
oCFEPStateValue< NameHolder >
oCFEPStateValue< real >
oCFEPStateValue< unsigned short >
oCgmx::FixedCapacityVector< GpuEventSynchronizer *, 3 >
oCgmx::FlagsTemplate< Flag >
oCgmx::FlagsTemplate< OptionFlag >
oCgmx::FlagsTemplate< SelectionFlag >
oCgmx::FlagsTemplate< TestFlag >
oCForceHelperBuffersHelper force buffers for ForceOutputs
oCForeignLambdaTermsAccumulates free-energy foreign lambda energies and dH/dlamba
oCFreeEnergyDispatchTemporary data and methods for handling dispatching of the nbnxm free-energy kernels
oCgmx::AbstractAnalysisDataAbstract base class for all objects that provide data
oCgmx::AbstractAnalysisData::ImplPrivate implementation class for AbstractAnalysisData
oCgmx::AbstractCompositeHelpTopic::ImplPrivate implementation class for AbstractCompositeHelpTopic
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::AnalysisData::ImplPrivate implementation class for AnalysisData
oCgmx::AnalysisDataDisplacementModule::ImplPrivate implementation class for AnalysisDataDisplacementModule
oCgmx::AnalysisDataFrameAveragerHelper class for modules that average values over frames
oCgmx::AnalysisDataFrameHeaderValue type for storing frame-level information for analysis data
oCgmx::AnalysisDataFrameLocalData< ValueType >Container for an array of frame-local values that supports parallel data processing
oCgmx::AnalysisDataFrameLocalDataHandle< ValueType >Handle to a single frame data within frame-local data array
oCgmx::AnalysisDataFrameLocalDataSetHandle< ValueType >Handle to a single data set within frame-local data array
oCgmx::AnalysisDataFrameRefValue type wrapper for non-mutable access to a data frame
oCgmx::AnalysisDataHandleHandle for inserting data into AnalysisData
oCgmx::AnalysisDataLifetimeModule::ImplPrivate implementation class for AnalysisDataLifetimeModule
oCgmx::AnalysisDataModuleManagerEncapsulates handling of data modules attached to AbstractAnalysisData
oCgmx::AnalysisDataModuleManager::ImplPrivate implementation class for AnalysisDataModuleManager
oCgmx::AnalysisDataModuleManager::Impl::ModuleInfoStores information about an attached module
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::analysismodules::anonymous_namespace{angle.cpp}::AnglePositionIteratorHelper to encapsulate logic for looping over input selections
oCgmx::analysismodules::anonymous_namespace{dssp.cpp}::DsspStorageClass that stores frame information in storage and, upon request, can return it
oCgmx::analysismodules::anonymous_namespace{dssp.cpp}::DsspStorageFrameStructure that contains storage information from different frames
oCgmx::analysismodules::anonymous_namespace{dssp.cpp}::ResInfoStructure of residues' information that can operate with atoms' indices
oCgmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructuresClass that provides search of specific h-bond patterns within residues
oCgmx::analysismodules::anonymous_namespace{dssp.cpp}::SecondaryStructuresDataDescribes and manipulates secondary structure attributes of a residue
oCgmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageClass that stores frame information in storage and, upon request, can return it
oCgmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageFrameStructure that contains storage information from different frames
oCgmx::analysismodules::anonymous_namespace{msd.cpp}::MoleculeDataHolds data needed for MSD calculations for a single molecule, if requested
oCgmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManagerHandles coordinate operations for MSD calculations
oCgmx::analysismodules::anonymous_namespace{msd.cpp}::MsdDataMean Squared Displacement data accumulator
oCgmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxyProxy to a MsdData tau column vector. Supports only push_back
oCgmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupDataHolds per-group coordinates, analysis, and results
oCgmx::analysismodules::anonymous_namespace{sasa.cpp}::t_conectTracks information on two nearest neighbors of a single surface dot
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::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExportCallbacks for exporting help information for command-line modules
oCgmx::anonymous_namespace{cmdlinehelpwriter.cpp}::IOptionsFormatterInterface for output format specific formatting of options
oCgmx::anonymous_namespace{cpuinfo.cpp}::ApicIdLayoutThe layout of the bits in the APIC ID
oCgmx::anonymous_namespace{cpuinfo.cpp}::ApicInfoInternal structure to return os logical cpu id together with APIC info for it
oCgmx::anonymous_namespace{densityfit.cpp}::CrossCorrelationEvaluationHelperValuesHelper values for evaluating the cross correlation
oCgmx::anonymous_namespace{densityfit.cpp}::CrossCorrelationGradientAtVoxelCalculate a single cross correlation gradient entry at a voxel
oCgmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityCrossCorrelationImplementation for DensitySimilarityCrossCorrelation
oCgmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityInnerProductImplementation for DensitySimilarityInnerProduct
oCgmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityRelativeEntropyImplementation for DensitySimilarityRelativeEntropy
oCgmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetupCollect density fitting parameters only available during simulation setup
oCgmx::anonymous_namespace{electricfield.cpp}::ElectricFieldDimensionDescribes an applied electric field in a coordinate dimension
oCgmx::anonymous_namespace{exceptions.cpp}::ErrorMessageError message or error context text item
oCgmx::anonymous_namespace{exceptions.cpp}::IMessageWriterAbstracts actual output from the other logic in exception formatting
oCgmx::anonymous_namespace{filenameoption.cpp}::FileTypeHandlerHandles a single file type known to FileNameOptionStorage
oCgmx::anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}::PlanSetupDataHelper struct to reduce repetitive code setting up a 3D FFT plan
oCgmx::anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}::RocfftInitializerProvides RAII-style initialization of rocFFT library
oCgmx::anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}::RocfftPlanAll the persistent data for planning an executing a 3D FFT
oCgmx::anonymous_namespace{handlerestart.cpp}::StartingBehaviorHandlerDescribes how mdrun will (re)start and provides supporting functionality based on that data
oCgmx::anonymous_namespace{helpwritercontext.cpp}::IWrapperCustom output interface for HelpWriterContext::Impl::processMarkup()
oCgmx::anonymous_namespace{nbsearch.cpp}::MindistActionSearch action find the minimum distance
oCgmx::anonymous_namespace{neldermead.cpp}::NelderMeadParametersThe parameters for a Nelder-Mead optimisation
oCgmx::anonymous_namespace{pargs.cpp}::OptionsAdapterConversion helper between t_pargs/t_filenm and Options
oCgmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetupHelper class that holds simulation data and callback functions for simulation setup time notifications
oCgmx::anonymous_namespace{shake.cpp}::ShakeTestTest fixture for testing SHAKE
oCgmx::anonymous_namespace{updategroups.cpp}::UpdateGroupsTestTest fixture class
oCgmx::AnyRepresents a dynamically typed value of an arbitrary type - deprecated
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::AtomicStructureFactorNeutron scattering factor parameters for an atom type
oCgmx::AtomIndexList of atom indices belonging to a task
oCgmx::AtomIndexExtremesStruct for returning an atom range
oCgmx::AtomInfoWithinMoleculeBlockContains information about each atom in a molecule block of the global topology
oCgmx::AtomPairA pair of atoms indexes
oCgmx::AwhCoupling of the accelerated weight histogram method (AWH) with the system
oCgmx::AwhEnergyBlockAWH output data block that can be written to an energy file block
oCgmx::AwhParamsStructure holding parameter information for AWH
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::BiasA bias acting on a multidimensional coordinate
oCgmx::BiasCoupledToSystemA bias and its coupling to the system
oCgmx::BiasGridThe grid for a single bias, generally multidimensional and periodic
oCgmx::BiasParamsConstant parameters for the bias
oCgmx::BiasStateThe state of a bias
oCgmx::BiasWriterClass organizing the output data storing and writing of an AWH bias
oCgmx::BinaryInformationSettingsSettings for printBinaryInformation()
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::BuildMDModulesNotifier< CallParameter >Aide to avoid nested MDModulesNotifier definition
oCgmx::BuildMDModulesNotifier< CurrentCallParameter, CallParameter...>Template specialization to assemble MDModulesNotifier
oCgmx::BuildMDModulesNotifier<>Template specialization to end parameter unpacking recursion
oCgmx::BuildMDModulesNotifier<>::NoCallParameterDo nothing but be base class of MDModulesNotifier
oCgmx::CacheLineAlignedFlagClass with interfaces and data for CUDA version of PME Force sending functionality
oCgmx::cellInfoStructure to hold cell information for any nbat-format forces
oCgmx::CheckpointData< operation >}
oCgmx::CheckpointHandlerClass handling the checkpoint signal
oCgmx::CheckpointHelperBuilderBuilder for the checkpoint helper
oCgmx::CheckpointOptionsOptions for writing checkpoint files
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::ColvarProxyGromacsImplements a GROMACS version of colvarproxy. This class hold for the communication between colvars and GROMACS. 2 child class will inherit from this one: one during pre processing (ColvarsPreProcessor) and one during the simulation (ColvarsForceProvider). Most of the work needed for the communication will be implemented in this class
oCgmx::ColvarsForceProviderStateParameters defining the internal colvars force provider state
oCgmx::ColvarsModuleInfoInformation about the colvars module
oCgmx::ColvarsSimulationsParametersCollect colvars parameters only available during simulation setup
oCgmx::CommandLineCommonOptionsHolderEncapsulates some handling of common options to the wrapper binary
oCgmx::CommandLineHelpContextContext information for writing out command-line help
oCgmx::CommandLineHelpContext::ImplPrivate implementation class for CommandLineHelpContext
oCgmx::CommandLineHelpWriterWrites help information for Options
oCgmx::CommandLineHelpWriter::ImplPrivate implementation class for CommandLineHelpWriter
oCgmx::CommandLineModuleGroupHandle to add content to a group added with CommandLineModuleManager::addModuleGroup()
oCgmx::CommandLineModuleGroupDataInternal data for a CommandLineModuleManager module group
oCgmx::CommandLineModuleManagerImplements a wrapper command-line interface for multiple modules
oCgmx::CommandLineModuleManager::ImplPrivate implementation class for CommandLineModuleManager
oCgmx::CommandLineModuleSettingsSettings to pass information between a module and the general runner
oCgmx::CommandLineParserImplements command-line parsing for Options objects
oCgmx::CommandLineParser::ImplPrivate implementation class for CommandLineParser
oCgmx::compat::not_null< T >Restricts a pointer or smart pointer to only hold non-null values
oCgmx::ComputeDebyeScatteringBase class for computing SANS and SAXS using Debye Method
oCgmx::ConstraintsHandles constraints
oCgmx::ConstraintsParamCollection of constraint parameters
oCgmx::ConvertTprInfoDeclares gmx convert-tpr
oCgmx::CoordinatesAndBoxPreprocessedProvides coordinates and simulation box
oCgmx::CoordStateKeeps track of the current coordinate value, grid index and umbrella location
oCgmx::CorrelationBlockDataCorrelation block averaging weight-only data
oCgmx::CorrelationBlockData::CoordDataCorrelation block averaging data
oCgmx::CorrelationGridBiasGrid of local correlation tensors
oCgmx::CorrelationTensorCorrelation data for computing the correlation tensor of one grid point
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::CpuInfoDetect CPU capabilities and basic logical processor info
oCgmx::CpuInfo::LogicalProcessorEntry with basic information for a single processing unit
oCgmx::CromerMannParametersCromer-Mann scattering factor parameters to compute structure factor dependent on Q
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::DensityFittingAmplitudeLookupClass that translates atom properties into amplitudes
oCgmx::DensityFittingForceManages evaluation of density-fitting forces for particles that were spread with a kernel
oCgmx::DensityFittingForce::ImplPrivate implementation class for DensityFittingForce
oCgmx::DensityFittingForceProviderStateParameters defining the internal density fitting force provider state
oCgmx::DensityFittingModuleInfoInformation about the density fitting module
oCgmx::DensityFittingParametersHolding all directly user-provided parameters for density fitting
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::detail::SimulationInputHandleImplDeleterExplicit deleter details for SimulationInputHolderImpl
oCgmx::DevelopmentFeatureFlagsStructure that holds boolean flags corresponding to the development features present enabled through environment variables
oCgmx::DeviceDetectionResultConvenience macro to help us avoid ifdefs each time we use sysconf
oCgmx::DeviceStreamManagerDevice stream and context manager
oCgmx::DeviceStreamManager::ImplImpl class to manages the lifetime of the GPU streams
oCgmx::DiagonalMasker< int, KernelLayout, KernelLayoutClusterRatio >Base Coulomb calculator class, only specializations are used
oCgmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize >Specialized masker for JSizeEqualsISize
oCgmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize >Specialized masker for JSizeIsDoubleISize
oCgmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize >Specialized masker for JSizeIsHalfISize
oCgmx::DimParamsConstant parameters for each dimension of the coordinate
oCgmx::DimParams::FepDimParamsType for storing dimension parameters for free-energy lambda type dimensions
oCgmx::DimParams::PullDimParamsType for storing dimension parameters for pull type dimensions
oCgmx::DirectoryEnumeratorLists files in a directory
oCgmx::DomainDecompositionBuilderBuilds a domain decomposition management object
oCgmx::DomainDecompositionBuilder::ImplImpl class for DD builder
oCgmx::DomainInfoInformation on PBC and domain decomposition for virtual sites
oCgmx::DomainLifetimeWorkloadDescribes work done on this domain on every step of its lifetime, but which might change after the next domain partitioning
oCgmx::DomDecHelperBuilderBuilder for DomDecHelper
oCgmx::DomdecOptionsStructure containing all (command line) options for the domain decomposition
oCgmx::EdrOutputFilenameEnergy trajectory output filename from Mdrun
oCgmx::EnergyAnalysisFrameClass describing an energy frame, that is the all the data stored for one energy term at one time step in an energy file
oCgmx::EnergyCalculationFrequencyErrorsCollect errors for the energy calculation frequency
oCgmx::EnergyDataData class managing energies
oCgmx::EnergyDriftTrackerClass for tracking and printing the drift in the conserved energy quantity
oCgmx::EnergyFrameContains the content of an .edr frame read by an EnergyFrameReader
oCgmx::EnergyNameUnitConvenience structure for keeping energy name and unit together
oCgmx::EnergyTermClass describing the whole time series of an energy term
oCgmx::EnsembleTemperatureProvides the constant ensemble temperature
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::EqualCaseInsensitiveFunction object for comparisons with equalCaseInsensitive
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::FepStateSettingAllows external clients to specify how to change the FEP state
oCgmx::FileNameOptionManager::ImplPrivate implemention class for FileNameOptionManager
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::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::FreeEnergyPerturbationDataThe free energy perturbation data
oCgmx::functor_wrapper< T, D >Wrap function into functor to be used as deleter
oCgmx::GammaDistribution< RealType >Gamma distribution
oCgmx::GammaDistribution< RealType >::param_typeGamma distribution parameters
oCgmx::GaussianOn1DLatticeProvide result of Gaussian function evaluation on a one-dimensional lattice
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::GaussTransform3D::ImplPrivate implementation class for GaussTransform3D
oCgmx::GlobalCommandLineHelpContextHelper for passing CommandLineHelpContext into parse_common_args()
oCgmx::GlobalCommunicationHelperHelper container with data connected to global communication
oCgmx::Gpu3dFftA 3D FFT class for performing R2C/C2R transforms
oCgmx::Gpu3dFft::ImplImpl base class for all FFT backends
oCgmx::Gpu3dFft::ImplOclVkfft::ImplImpl class
oCgmx::Gpu3dFft::ImplSyclRocfft::ImplImpl class
oCgmx::Gpu3dFft::ImplSyclVkfft::ImplImpl class
oCgmx::GpuForceReductionManages the force reduction directly in GPU memory
oCgmx::GpuHaloExchangeManages GPU Halo Exchange object
oCgmx::GpuHaloExchange::ImplImpl class stub
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::GridAxisAn axis, i.e. dimension, of the grid
oCgmx::GridPointA point in the grid
oCgmx::GromppMtsOptsStruct for passing the MTS mdp options to setupMtsLevels()
oCgmx::HardwareTopologyInformation about packages, cores, processing units, numa, caches
oCgmx::HardwareTopology::CacheInformation about a single cache level
oCgmx::HardwareTopology::CoreInformation about a single core in a package
oCgmx::HardwareTopology::DeviceInformation about a single PCI device
oCgmx::HardwareTopology::LogicalProcessorInformation about package, core and processing unit for a logical processor
oCgmx::HardwareTopology::MachineHardware topology information about the entire machine
oCgmx::HardwareTopology::NumaInformation about all numa nodes
oCgmx::HardwareTopology::NumaNodeInformation about each numa node in system
oCgmx::HardwareTopology::PackageInformation about a single package in the system
oCgmx::HardwareTopology::ProcessingUnitInformation about a single processing unit (in a core)
oCgmx::HashedMap< T >Unordered key to value mapping
oCgmx::HelpLinksHyperlink data for writing out help
oCgmx::HelpLinks::ImplPrivate implementation class for HelpLinks
oCgmx::HelpManagerHelper for providing interactive online help
oCgmx::HelpManager::ImplPrivate implementation class for HelpManager
oCgmx::HelpWriterContextContext information for writing out help
oCgmx::HelpWriterContext::ImplPrivate implementation class for HelpWriterContext
oCgmx::HelpWriterContext::Impl::SharedStateShared, non-modifiable state for context objects
oCgmx::HistogramSizeTracks global size related properties of the bias histogram
oCgmx::HostAllocationPolicyPolicy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers
oCgmx::HostInteractionListVersion of InteractionList that supports pinning
oCgmx::IAnalysisDataModuleInterface for a module that gets notified whenever data is added
oCgmx::ICheckpointHelperClientClient that needs to store data during checkpointing
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::IDomDecHelperClientClient interface of the DomDecHelper class
oCgmx::IEnergyAnalysisInterface class overloaded by the separate energy modules
oCgmx::IEnergySignallerClientInterface for clients of the EnergySignaller
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::IFrameConverterIFrameConverter interface for manipulating coordinate information
oCgmx::IHelpTopicProvides a single online help topic
oCgmx::IKeyValueTreeTransformRulesInterface to declare rules for transforming key-value trees
oCgmx::ILastStepSignallerClientInterface for clients of the LastStepSignaller
oCgmx::ILoggingSignallerClientInterface for clients of the LoggingSignaller
oCgmx::ILogTargetTarget where log output can be written
oCgmx::IMDEnergyBlockIMD (interactive molecular dynamics) energy record
oCgmx::IMDHeaderIMD (interactive molecular dynamics) communication structure
oCgmx::IMDModuleExtension module for GROMACS simulations
oCgmx::ImdOptionsOptions for IMD
oCgmx::IMDOutputProviderInterface for handling additional output files during a simulation
oCgmx::IMdpOptionProviderInterface for handling mdp/tpr input to a mdrun module
oCgmx::ImdSession::ImplImplementation type for the IMD session
oCgmx::IMDSocketIMD (interactive molecular dynamics) socket structure
oCgmx::IndexGroupsAndNamesBundle index groups with their names
oCgmx::INeighborSearchSignallerClientInterface for clients of the NeighborSearchSignaller
oCgmx::InstallationPrefixInfoProvides information about installation prefix (see IProgramContext::installationPrefix())
oCgmx::IntegerBoxA 3-orthotope over integer intervals
oCgmx::InteractiveMDSimulatorBuilder parameter type for InteractiveMD
oCgmx::InterdependentTaskData structure for thread tasks that use constructing atoms outside their own atom range
oCgmx::internal::AnalysisDataHandleImplPrivate implementation class for AnalysisDataHandle
oCgmx::internal::AnalysisDataStorageFrameDataInternal representation for a single stored frame
oCgmx::internal::AnalysisDataStorageImplPrivate implementation class for AnalysisDataStorage
oCgmx::internal::BasicHistogramImplBase class for private implementation classes for histogram modules
oCgmx::internal::IExceptionInfoBase class for ExceptionInfo
oCgmx::internal::OptionsImplPrivate implementation class for Options
oCgmx::internal::SelectionDataInternal data for a single selection
oCgmx::internal::SimdArrayRef< T >STL-like container for aligned SIMD type. Used as ArrayRef<SimdReal>
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::IOptionSectionStorageProvides behavior specific to a certain option section type
oCgmx::IOptionValueStore< T >Represents the final storage location of option values
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::ISignallerThe general Signaller interface
oCgmx::ISimulatorThe Simulator interface
oCgmx::ISimulatorElementThe general interface for elements of the modular simulator
oCgmx::isIntegralConstant< T, Int >Is true if type is a std::integral_constant
oCgmx::IsSerializableEnum< T, bool >Struct allowing to check if enum has a serializable underlying type
oCgmx::IsSerializableType< T >Struct allowing to check if data is serializable through the KeyValueTree serializer
oCgmx::ITemperatureCouplingImplInterface for temperature coupling implementations
oCgmx::ITopologyHolderClientClient requiring read access to the local topology
oCgmx::ITopologyProviderProvides topology information to SelectionOptionBehavior
oCgmx::ITrajectorySignallerClientInterface for signaller clients of the TrajectoryElement
oCgmx::ITrajectoryWriterClientInterface for writer clients of the TrajectoryElement
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::BaseBase class used for implementing parameter provider objects
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::LegacySimulatorDataThe legacy simulator data
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::LincsData for LINCS algorithm
oCgmx::LincsDeviationsStatus information about how well LINCS satisfied the constraints in this domain
oCgmx::LincsGpuClass with interfaces and data for GPU version of LINCS
oCgmx::LinkFrontierHelper structure with indexes of broken bonds between QM and MM Used to determine and store pair of QM and MM atoms between which chemical bond is broken
oCgmx::ListedForcesGpu::ImplImplements GPU bondeds
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::LocalAtomSetManager::ImplPrivate implementation class for LocalAtomSetManager
oCgmx::LocalTopologyCheckerHas responsibility for checking that the local topology distributed across domains describes a total number of bonded interactions that matches the system topology
oCgmx::LocalTopologyChecker::ImplData to help check local topology construction
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::LogWriteHelperHelper class for implementing GMX_LOG
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::MdGpuGraph::ImplImpl class stub
oCgmx::MDLoggerDeclares a logging interface
oCgmx::MDModulesManages the collection of all modules used for mdrun
oCgmx::MDModulesAtomsRedistributedSignalNotification that atoms may have been redistributed
oCgmx::MDModulesCheckpointReadingBroadcastProvides the MDModules with the communication record to broadcast
oCgmx::MDModulesCheckpointReadingDataOnMainProvides the MDModules with the checkpointed data on the main rank
oCgmx::MDModulesEnergyOutputToDensityFittingRequestCheckerCheck if module outputs energy to a specific field
oCgmx::MDModulesEnergyOutputToQMMMRequestCheckerCheck if QMMM module outputs energy to a specific field
oCgmx::MDModulesNotifier< CallParameter, MDModulesNotifierBase >Organizes notifications about an event of interest to modules
oCgmx::MDModulesNotifiersGroup of notifers to organize that MDModules can receive callbacks they subscribe to
oCgmx::MDModulesWriteCheckpointDataWriting the MDModules data to a checkpoint file
oCgmx::MdRunInputFilenameMdrun input filename
oCgmx::MdrunnerRunner object for supporting setup and execution of mdrun
oCgmx::MdrunnerBuilderBuild a gmx::Mdrunner
oCgmx::MdrunOptionsCollection of all options of mdrun that are not processed separately
oCgmx::MembedHolderMembed SimulatorBuilder parameter type
oCgmx::MessageStringCollectorHelper class for collecting message strings, optionally with context
oCgmx::MessageStringContextConvenience class for creating a message context
oCgmx::MimicCommunicatorClass-wrapper around MiMiC communication library It uses GROMACS' unit conversion to switch from GROMACS' units to a.u
oCgmx::ModularSimulatorAlgorithmThe modular simulator
oCgmx::ModularSimulatorAlgorithmBuilderBuilder for ModularSimulatorAlgorithm objects
oCgmx::ModularSimulatorAlgorithmBuilderHelperHelper for element addition
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::MrcDensityMapOfFloatReader::ImplPrivate implementation class for MrcDensityMapOfFloatReader
oCgmx::MrcDensityMapOfFloatWriterWrite an mrc/ccp4 file that contains float values
oCgmx::MrcDensityMapOfFloatWriter::ImplPrivate implementation class for MrcDensityMapOfFloatWriter
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::MttkPropagatorConnectionObject holding the callbacks and scaling views for the connection of MTTKElement objects to propagators
oCgmx::MttkPropagatorConnectionDetailsStruct collecting the propagator tags and offsets used by the MTTK pressure coupling
oCgmx::MultiDimArray< TContainer, Extents, LayoutPolicy >Multidimensional array that manages its own memory
oCgmx::NelderMeadSimplexThe simplex for the Nelder-Mead algorithm
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::NoseHooverGroupThe current state of the Nose-Hoover chain degree of freedom for a temperature group
oCgmx::NumericalSplineTableInputSpecification for vector table function (name, function, derivative, spacing)
oCgmx::ObservablesReducerManage reduction of observables for registered subscribers
oCgmx::ObservablesReducer::ImplImpl class for ObservablesReducer
oCgmx::ObservablesReducerBuilderBuilder for ObservablesReducer
oCgmx::ObservablesReducerBuilder::ImplImpl class for ObservablesReducerBuilder
oCgmx::ObservablesReducerBuilder::Impl::SubscriptionData required to set up a subscription
oCgmx::OffsetStrong type used to denote scheduling offsets
oCgmx::OpenClTraits< cl_type >Stub for OpenCL type traits
oCgmx::OpenClTraitsBase< cl_type >Implements common trait infrastructure for OpenCL types
oCgmx::OptimisationResultCompiles results of an a function optimisation
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::OptionsAssigner::ImplPrivate implementation class for OptionsAssigner
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::OuterProductEvaluatorEvaluate the outer product of two number ranges. Keeps the memory for the outer product allocated
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::PairDistValueStructure to store pair dist units
oCgmx::pairHashHash function to allow use of pair in unordered_map
oCgmx::PhysicalNodeCommunicatorHolds a communicator for the physical node of this rank
oCgmx::PmeCoordinateReceiverGpu::ImplClass with interfaces and data for CUDA version of PME coordinate receiving functionality
oCgmx::PmeForceSenderGpuManages sending forces from PME-only ranks to their PP ranks
oCgmx::PmeForceSenderGpu::ImplImpl class stub
oCgmx::PmePpCommGpuManages communication related to GPU buffers between this PME rank and its PP rank
oCgmx::PmePpCommGpu::ImplClass with interfaces and data for GPU version of PME-PP Communication
oCgmx::PointStateThe state of a coordinate point
oCgmx::PositionCalculationCollectionCollection of gmx_ana_poscalc_t structures for the same topology
oCgmx::PositionCalculationCollection::ImplPrivate implementation class for PositionCalculationCollection
oCgmx::PotentialPointDataStructure to hold the results of IRestraintPotential::evaluate()
oCgmx::PpCommManagerObject to manage communications with a specific PP rank
oCgmx::PpForceCommManagerObject to manage communications with a specific PP rank
oCgmx::ProfilingCollection of profiling information
oCgmx::PropagatorConnectionInformation needed to connect a propagator to a temperature and / or pressure coupling element
oCgmx::PropagatorTagStrong type used to name propagators
oCgmx::PTCouplingArraysArrays connected to Pressure and Temperature coupling
oCgmx::PullCoordExpressionParserClass with a mathematical expression and parser
oCgmx::QMInputFileNameNotification for QM program input filename provided by user as command-line argument for grompp
oCgmx::QMMMInputGeneratorClass that takes QMMMParameters, Coordinates, Point charges, Box dimensions, pbcType. Generates QM/MM sample input parameters and pdb-style coordinates for CP2K. Input are generated as std::string objects which can be stored in tpr KVT and/or flushed into the files
oCgmx::QMMMModuleInfoInformation about the QM/MM module
oCgmx::QMMMParametersHolding all parameters needed for QM/MM simulation. Also used for setting all default parameter values
oCgmx::QMMMTopologyInfoContains various information about topology modifications Used for statistics during topology pre-processing within QMMMTopologyPreprocessor class
oCgmx::QMMMTopologyPreprocessorClass implementing gmx_mtop_t QMMM modifications during preprocessing 1) Split QM-containing molecules from other molecules in blocks 2) Nullify charges on all virtual sites consisting of QM only atoms 3) Nullifies charges on all QM atoms 4) Excludes LJ interactions between QM atoms 5) Builds vector with atomic numbers of all atoms 6) Makes F_CONNBOND between atoms within QM region 7) Removes angles and settles containing 2 or more QM atoms 8) Removes dihedrals containing 3 or more QM atoms 9) Builds vector containing pairs of bonded QM - MM atoms (Link frontier)
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::RealFunctionvalueAtCoordinateTie together coordinate and function value at this coordinate
oCgmx::ReferenceTemperatureManagerObject managing reference temperature changes
oCgmx::ResetHandlerClass handling the reset of counters
oCgmx::RestraintManagerManage the Restraint potentials available for Molecular Dynamics
oCgmx::RestraintManager::ImplImplementation class for restraint manager
oCgmx::RestraintMDModuleImplIMDModule implementation for RestraintMDModule
oCgmx::RstParagraphIteratorIterator over reStructuredText paragraphs
oCgmx::ScalingMatrixScaling matrix struct
oCgmx::SelectionProvides access to a single selection
oCgmx::SelectionCollectionCollection of selections
oCgmx::SelectionCollection::ImplPrivate implemention class for SelectionCollection
oCgmx::SelectionEvaluatorImplements selection evaluation
oCgmx::SelectionLocationStores the location of a selection element in the selection text
oCgmx::SelectionOptionManager::ImplPrivate implemention class for SelectionOptionManager
oCgmx::SelectionOptionManager::Impl::RequestsClearerHelper class that clears a request list on scope exit
oCgmx::SelectionOptionManager::Impl::SelectionRequestRequest for postponed parsing of selections
oCgmx::SelectionParserParameterDescribes a parsed method parameter
oCgmx::SelectionParserSymbolSingle symbol for the selection parser
oCgmx::SelectionParserSymbol::ImplPrivate implementation class for SelectionParserSymbol
oCgmx::SelectionParserSymbolIteratorForward iterator for iterating symbols of a given type
oCgmx::SelectionParserSymbolIterator::ImplPrivate implementation class for SelectionParserSymbolIterator
oCgmx::SelectionParserSymbolTableSymbol table for the selection parser
oCgmx::SelectionParserSymbolTable::ImplPrivate implementation class for SelectionParserSymbolTable
oCgmx::SelectionParserValueDescribes a parsed value, possibly resulting from expression evaluation
oCgmx::SelectionPositionProvides access to information about a single selected position
oCgmx::SelectionTopologyPropertiesDescribes topology properties required for selection evaluation
oCgmx::SelectionTreeElementRepresents an element of a selection expression
oCgmx::SelMethodEvalContextEvaluation context for selection methods
oCgmx::SeparatePmeRanksPermittedClass for managing usage of separate PME-only ranks
oCgmx::SettleDataData for executing SETTLE constraining
oCgmx::SettleGpuClass with interfaces and data for GPU version of SETTLE
oCgmx::shakedataWorking data for the SHAKE algorithm
oCgmx::SignallerBuilder< Signaller >Builder for signallers
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::SimulationInputHandleOwning handle to a SimulationInput object
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::StatePropagatorDataStatePropagatorData and associated data
oCgmx::StatePropagatorData::ReferenceTemperatureHelperHelper object to scale velocities according to reference temperature change
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 by the current rank 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::StringToEnumValueConverter< EnumType,, stringCompareType, stripStrings >A class to convert a string to an enum value of type EnumType
oCgmx::SurfaceAreaCalculatorComputes surface areas for a group of atoms/spheres
oCgmx::TabulatedNormalDistribution< RealType, tableBits >Tabulated normal random distribution
oCgmx::TabulatedNormalDistribution< RealType, tableBits >::param_typeNormal distribution parameter class (mean and stddev)
oCgmx::TemperatureCouplingDataData used by the concrete temperature coupling implementations
oCgmx::test::AllocatorTest< T >Templated test fixture
oCgmx::test::AllowAnyRankCountHelper for GMX_MPI_TEST to permit any rank count
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::anonymous_namespace{bonded.cpp}::iListInputInput structure for listed forces tests
oCgmx::test::anonymous_namespace{bonded.cpp}::OutputQuantitiesOutput from bonded kernels
oCgmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTestCheckpointData test fixture
oCgmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType< T >Struct allowing to check if type is vector of serializable data
oCgmx::test::anonymous_namespace{checkpointdata.cpp}::TestValuesUnified looping over test data
oCgmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator< T >Helper class allowing to loop over test values
oCgmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator< T >::IteratorCustom iterator
oCgmx::test::anonymous_namespace{com.cpp}::COMInPlaceTestTest fixture for checking correct molecule COM treatment
oCgmx::test::anonymous_namespace{constr.cpp}::ConstraintsTestTest fixture for constraints
oCgmx::test::anonymous_namespace{device_stream_manager.cpp}::DeviceStreamManagerTestTest fixture
oCgmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTestTest fixture to test energy output
oCgmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTestParametersTest parameters space
oCgmx::test::anonymous_namespace{exactcontinuation.cpp}::ContinuationFramePairManager< FrameReader >Manages comparing a pair of matching energy frames from a normal run and the same run in two parts
oCgmx::test::anonymous_namespace{expanded.cpp}::CalculateAcceptanceWeightSimpleTest fixture accepting a value to pass into calculateAcceptanceWeight
oCgmx::test::anonymous_namespace{extract_cluster.cpp}::ManualOutputFileHelper struct to combine filename, path and FileMatcher
oCgmx::test::anonymous_namespace{freeenergyparameters.cpp}::FreeEnergyParameterTestTest for setting free energy parameters
oCgmx::test::anonymous_namespace{freeenergyparameters.cpp}::FreeEnergyParameterTestParametersParameters that will vary from test to test
oCgmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParametersConvenience typedef of the test input parameters
oCgmx::test::anonymous_namespace{kernel_test.cpp}::KernelOptionsThe options for the kernel
oCgmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTestClass that sets up and holds a set of N atoms and a full NxM pairlist
oCgmx::test::anonymous_namespace{kernel_test.cpp}::TestSystemDescription of the system used for benchmarking
oCgmx::test::anonymous_namespace{leapfrog.cpp}::LeapFrogTestTest fixture for LeapFrog integrator
oCgmx::test::anonymous_namespace{leapfrog.cpp}::LeapFrogTestParametersThe parameters for the test
oCgmx::test::anonymous_namespace{mock_datamodule.cpp}::DataStorageRequesterFunctor for requesting data storage
oCgmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataFrameHeaderCheckerFunctor for checking data frame header against static test input data
oCgmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsCheckerFunctor for checking data frame points against static test input data
oCgmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsStorageCheckerFunctor for checking data frame points and storage against static test input data
oCgmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTestMocking test with data collected from a few systems
oCgmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomDataUtility structure to hold atoms data
oCgmx::test::anonymous_namespace{nb_free_energy.cpp}::ListInputInput structure for nonbonded fep kernel
oCgmx::test::anonymous_namespace{nb_free_energy.cpp}::OutputQuantitiesOutput from nonbonded fep kernel
oCgmx::test::anonymous_namespace{observablesreducer.cpp}::ObservablesReducerIntegrationTestTest fixture class
oCgmx::test::anonymous_namespace{observablesreducer.cpp}::ObservablesReducerIntegrationTest::RankDataHelper struct to model data on a single MPI rank
oCgmx::test::anonymous_namespace{observablesreducer.cpp}::SubscriberHelper class that models an MD module that needs to make a subscription to ObservablesReducer
oCgmx::test::anonymous_namespace{pairs.cpp}::ListInputInput structure for listed forces tests
oCgmx::test::anonymous_namespace{pairs.cpp}::OutputQuantitiesOutput from pairs kernels
oCgmx::test::anonymous_namespace{pmebsplinetest.cpp}::PmeBSplineModuliTestTest fixture for testing PME B-spline moduli creation
oCgmx::test::anonymous_namespace{pmegathertest.cpp}::GatherTestTest fixture
oCgmx::test::anonymous_namespace{pmegathertest.cpp}::SplineDataA structure for all the spline data which depends in size both on the PME order and atom count
oCgmx::test::anonymous_namespace{pmegathertest.cpp}::TestSystemA structure for the input atom data, which depends in size on atom count
oCgmx::test::anonymous_namespace{pmesolvetest.cpp}::SolveTestTest fixture
oCgmx::test::anonymous_namespace{pmesplinespreadtest.cpp}::SplineAndSpreadTestTest fixture for testing both atom spline parameter computation and charge spreading. These 2 stages of PME are tightly coupled in the code
oCgmx::test::anonymous_namespace{settle.cpp}::SettleTestTest fixture for testing SETTLE
oCgmx::test::anonymous_namespace{settle.cpp}::SettleTestParametersParameters that will vary from test to test
oCgmx::test::anonymous_namespace{splinetable.cpp}::SplineTableTest< T >Test fixture for table comparision with analytical/numerical functions
oCgmx::test::anonymous_namespace{testinit.cpp}::SuccessListenerMakes GoogleTest non-failures more verbose
oCgmx::test::anonymous_namespace{testoptions.cpp}::TestOptionsRegistrySingleton registry for test options added with GMX_TEST_OPTIONS
oCgmx::test::anonymous_namespace{textreader.cpp}::TextReaderTestTest fixture
oCgmx::test::anonymous_namespace{textreader.cpp}::TextReaderTestParamsHelper struct
oCgmx::test::anonymous_namespace{threadaffinity_mpi.cpp}::RequireEvenRankCountWithAtLeastFourRanksHelper to establish test requirements on MPI ranks
oCgmx::test::anonymous_namespace{timing.cpp}::TimingTestTest Fixture for timing tests
oCgmx::test::anonymous_namespace{virtualsites.cpp}::VirtualSiteTest::VirtualSiteHolds parameters of virtual site and allows calculation
oCgmx::test::AwhTestParametersStruct that gathers all input for setting up and using a Bias
oCgmx::test::BiasFepLambdaStateTestTest fixture for testing Bias updates
oCgmx::test::BiasStateTestTest fixture for testing Bias updates
oCgmx::test::BiasTestTest fixture for testing Bias updates
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::EnergyComparisonFunction object to compare all energy terms of reference with all matching terms from test within the given tolerances
oCgmx::test::EnergyFrameReaderManages returning an EnergyFrame containing required energy term values read from successive frames of an .edr file
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::FloatTypeMatcher< FloatType >Implementation class for RealEq matcher
oCgmx::test::FramePairManager< FrameReader >Manages returning a pair of frames from two equivalent simulations that are meaningful to compare
oCgmx::test::FrictionMetricTestTest fixture for testing Friction metric, including storing to, and restoring from, history
oCgmx::test::HostAllocatorTestNoMem< T >Typed test fixture (no mem/gpu initializtion - much faster)
oCgmx::test::HostMemoryTest< T >Typed test fixture for infrastructure for host-side memory used for GPU transfers
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::internal::TestReferenceDataImplPrivate implementation class for TestReferenceData
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::MaxNumFramesNamed struct indicating the max number of frames to be compared
oCgmx::test::MdrunTestFixtureBaseDeclares test fixture base class for integration tests of mdrun functionality
oCgmx::test::MockAnalysisDataModule::ImplPrivate implementation class for gmx::test::MockAnalysisDataModule
oCgmx::test::ModuleSelectionHelper class for tests that need an initialized selection
oCgmx::test::NbnxmKernelTestBodyTest case whose body checks that the NBNxM kernel produces correct output
oCgmx::test::NumRanksPerSimulationTest flag setting the number of ranks per simulation
oCgmx::test::PaddedVectorTest< T >Typed test fixture
oCgmx::test::PrintReplicaExchangeParametersToStringHelper struct printing custom test name
oCgmx::test::ReferenceFileNamesHelper type of output file names for the reference mdrun call
oCgmx::test::RequireMinimumRankCount< minimumNumRanks >Helper for GMX_MPI_TEST to permit only a specific rank count
oCgmx::test::RequireRankCount< requiredNumRanks >Helper for GMX_MPI_TEST to permit only a specific rank count
oCgmx::test::RVecMatcher< FloatType >Implementation class for RvecEq matcher
oCgmx::test::SignalTestTest fixture for mdrun signalling
oCgmx::test::SimdBaseTestBase class for SIMD test fixtures
oCgmx::test::SimulationRunnerHelper object for running grompp and mdrun in integration tests of mdrun functionality
oCgmx::test::StdioTestHelperHelper class for tests where code reads directly from stdin
oCgmx::test::StringTestBaseTest fixture for tests that check string formatting
oCgmx::test::TerminationHelperHelp test mdrun termination behaviour
oCgmx::test::TestDeviceA structure to describe a hardware context that persists over the lifetime of the test binary
oCgmx::test::TestFileManagerHelper for tests that need input and output files
oCgmx::test::TestFileManager::ImplPrivate implementation class for TestFileManager
oCgmx::test::TestHardwareEnvironmentThis class performs one-time test initialization, enumerating the hardware
oCgmx::test::TestOptionsProviderProvides additional options for the test executable
oCgmx::test::TestReferenceCheckerHandles comparison to test reference data
oCgmx::test::TestReferenceChecker::ImplPrivate implementation class for TestReferenceChecker
oCgmx::test::TestReferenceDataHandles creation of and comparison to test reference data
oCgmx::test::TopologyManagerHelps create and manage the lifetime of topology and related data structures
oCgmx::test::TprAndFileManagerHelper to bundle generated TPR and the file manager to clean it up
oCgmx::test::TrajectoryComparisonFunction object to compare the fields of two frames vs each others or one frame vs reference data for equality given the matchSettings_ and tolerances_
oCgmx::test::TrajectoryFrameMatchSettingsHelper struct to specify the expected behaviour of compareFrames()
oCgmx::test::TrajectoryFrameReaderManages returning a t_trxframe whose contents were read from successive frames of an trajectory file
oCgmx::test::TrajectoryTolerancesHelper struct for testing different trajectory components with different tolerances
oCgmx::test::UserInputTestTest user input data reading
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::TextReader::ImplImplementation class
oCgmx::TextTableFormatterFormats rows of a table for text output
oCgmx::TextTableFormatter::ImplPrivate implementation class for TextTableFormatter
oCgmx::TextTableFormatter::Impl::ColumnDataManages a single column for TextTableFormatter
oCgmx::TextWriterWrites text into a TextOutputStream
oCgmx::ThreadedForceBuffer< ForceBufferElementType >Class for accumulating and reducing forces and energies on threads in parallel
oCgmx::ThreadForceBuffer< ForceBufferElementType >Object that holds force and energies buffers plus a mask for a thread
oCgmx::ThreadingInfoInformation on how the virtual site work is divided over thread tasks
oCgmx::ThreeFry2x64General< rounds, internalCounterBits >General implementation class for ThreeFry counter-based random engines
oCgmx::ThrowLocationStores the location from which an exception was thrown
oCgmx::TimeStepStrong type used to denote propagation time steps
oCgmx::TimeUnitManagerProvides common functionality for time unit conversions
oCgmx::TimingOptionsOptions for timing (parts of) mdrun
oCgmx::TopologyDataCollection of handles to topology information
oCgmx::TopologyHolder::BuilderBuilder for the topology holder
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::TrajectoryAnalysisModule::ImplPrivate implementation class for TrajectoryAnalysisModule
oCgmx::TrajectoryAnalysisModuleDataBase class for thread-local data storage during trajectory analysis
oCgmx::TrajectoryAnalysisModuleData::ImplPrivate implementation class for TrajectoryAnalysisModuleData
oCgmx::TrajectoryAnalysisRunnerCommonImplements common trajectory analysis runner functionality
oCgmx::TrajectoryAnalysisSettingsTrajectory analysis module configuration object
oCgmx::TrajectoryAnalysisSettings::ImplPrivate implementation class for TrajectoryAnalysisSettings
oCgmx::TrajectoryElementBuilderBuild the TrajectoryElement
oCgmx::TrajectoryFileOpenerLow level method to take care of only file opening and closing
oCgmx::TrajectoryFrameContains a valid trajectory frame
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::UpdateConstrainGpu::ImplClass with interfaces and data for GPU version of Update-Constraint
oCgmx::UpdateGroupsOwns the update grouping and related data
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::VirtualSitesHandler::ImplImpl class for VirtualSitesHandler
oCgmx::VsiteThreadVsite thread task data structure
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_indexgrps_tStores a set of index groups
oCgmx_ana_indexmap_tData structure for calculating index group mappings
oCgmx_ana_pos_tStores a set of positions together with their origins
oCgmx_ana_poscalc_tData structure for position calculation
oCgmx_ana_selcollection_tInformation for a collection of selections
oCgmx_ana_selmethod_help_tHelp information for a selection method
oCgmx_ana_selmethod_tDescribes a selection method
oCgmx_ana_selparam_tDescribes a single parameter for a selection method
oCgmx_ana_selvalue_tDescribes a value of a selection expression or of a selection method parameter
oCgmx_cache_protect_tCache-line protection buffer
oCgmx_device_runtime_data_tOpenCL GPU runtime data
oCgmx_domdec_constraints_tStruct used during constraint setup with domain decomposition
oCgmx_domdec_specat_comm_tStruct with setup and buffers for special atom communication
oCgmx_enerdata_tStruct for accumulating all potential energy terms and some kinetic energy terms
oCgmx_enfrotEnforced rotation data for all groups
oCgmx_enfrotgrpEnforced rotation data for a single rotation group
oCgmx_ffparams_tStruct that holds all force field parameters for the simulated system
oCgmx_fft_fftpackContents of the FFTPACK fft datatype
oCgmx_fft_fftw3Contents of the FFTW3 fft datatype
oCgmx_fft_mklContents of the Intel MKL FFT fft datatype
oCgmx_ga2la_tGlobal to local atom mapping
oCgmx_ga2la_t::EntryStructure for the local atom info
oCgmx_help_make_index_groupData necessary to construct a single (protein) index group in analyse_prot()
oCgmx_hw_opt_tThreading and GPU options, can be set automatically or by the user
oCgmx_kernel_timing_data_tGPU kernel time and call count
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_nodecomm_tSettings and communicators for two-step communication: intra + inter-node
oCgmx_pme_comm_n_box_tHelper struct for PP-PME communication of parameters
oCgmx_pme_comm_vir_ene_tHelper struct for PP-PME communication of virial and energy
oCgmx_pme_ppMain PP-PME communication data structure
oCgmx_potfitHelper structure for potential fitting
oCgmx_repl_exWorking data for replica exchange
oCgmx_reverse_top_tReverse topology class
oCgmx_reverse_top_t::ImplStruct for the reverse topology: links bonded interactions to atoms
oCgmx_sel_evaluate_tData structure for passing information required during evaluation
oCgmx_sel_lexer_tInternal data structure for the selection tokenizer state
oCgmx_sel_mempool_block_tDescribes a single block allocated from the memory pool
oCgmx_sel_mempool_tDescribes a memory pool
oCgmx_slabdataEnforced rotation / flexible: determine the angle of each slab
oCgmx_sparsematrixSparse matrix storage format
oCgmx_specatsend_tThe communication setup along a single dimension
oCgmx_tng_trajectoryGromacs Wrapper around tng datatype
oCgmx_wallclock_gpu_nbnxn_tGPU NB timings for kernels and H2d/D2H transfers
oCgmx_wallclock_gpu_pme_tGPU timings for PME
oCgmx_walltime_accountingManages caching wall-clock time measurements for simulations
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
oCGridConverter< pmeToFft >Builds a kernel to convert between PME and FFT grids
oCgmx::HashedMap< gmx_ga2la_t::Entry >
oCgmx::HashedMap< int >
oChistory_tHistory information for NMR distance and orientation restraints
oCilist_data_tStruct for passing all data required for a function type
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
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
oCgmx::IOptionValueStore< bool >
oCgmx::IOptionValueStore< int >
oCJClusterListSimple j-cluster list
oCKernelLaunchConfigGPU kernels scheduling description. This is same in OpenCL/CUDA. Provides reasonable defaults, one typically only needs to set the GPU stream and non-1 work sizes
oCLeapFrogKernel< numTempScaleValues, parrinelloRahmanVelocityScaling >Class name for leap-frog kernel
oCListedForcesClass for calculating listed interactions, uses OpenMP parallelization
oCgmx::ListOfLists< int >
oCLocalSettleDataLocal settle data
oCmethoddata_insolidangleData structure for the insolidangle selection method
oCmethoddata_mergeData structure for the merging selection modifiers
oCmethoddata_permuteData structure for the permute selection modifier
oCMolecularTopologyAtomIndicesMolecular topology indices of a global molecule a global atom belongs to
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
oCMoleculeTypeDescribes a molecule type, and keeps track of the number of these molecules
oCgmx::MultiDimArray< dynamic_container_type, dynamic_extents_type >
oCgmx::MultiDimArray< real >
oCgmx::MultiDimArray< static_container_type, static_extents_type >
oCgmx::MultiDimArray< std::vector< double >, gmx::gmx::extents >
oCgmx::MultiDimArray< std::vector< float >, gmx::extents >
oCgmx::MultiDimArray< std::vector< float >, gmx::extents< dynamic_extent, dynamic_extent > >
oCgmx::MultiDimArray< t_matelmt >
oCNBAtomDataGpuNonbonded atom data - both inputs and outputs
oCNbnxm::BoundingBoxBounding box for a nbnxm atom cluster
oCNbnxm::BoundingBox1DBounding box for one dimension of a grid cell
oCNbnxm::BoundingBox::CornerCorner for the bounding box, padded with one element to enable 4-wide SIMD operations
oCNbnxm::EnergyFunctionProperties< elecType, vdwType >Set of boolean constants mimicking preprocessor macros
oCNbnxm::gpu_plistGPU pair list structure
oCNbnxm::gpuPlistSortingSorted pair list on GPU and data required for performing the sorting
oCNbnxm::GpuTimersGPU region timers used for timing GPU kernels and H2D/D2H transfers
oCNbnxm::GpuTimers::InteractionTimers for local or non-local interaction related operations
oCNbnxm::GpuTimers::XFTransfersTimers for local or non-local coordinate/force transfers
oCNbnxm::GridA pair-search grid object for one domain decomposition zone
oCNbnxm::Grid::DimensionsThe physical dimensions of a grid
oCNbnxm::Grid::GeometryThe cluster and cell geometry of a grid
oCNbnxm::GridSetHolds a set of search grids for the local + non-local DD zones
oCNbnxm::GridSet::DomainSetupDescription of the domain setup: PBC and the connections between domains
oCNbnxm::GridSetDataStruct that holds grid data that is shared over all grids
oCNbnxm::GridWorkWorking arrays for constructing a grid
oCNbnxm::KernelBenchOptionsThe options for the kernel benchmarks
oCNbnxmGpuMain data structure for CUDA nonbonded force calculations
oCNbnxmKernel< doPruneNBL, doCalcEnergies, elecType, vdwType, subGroupSize >Class name for NBNXM kernel
oCNbnxmKernelPruneOnly< haveFreshList >Class name for NBNXM prune-only kernel
oCnbnxn_atomdata_output_tStruct that holds force and energy output buffers
oCnbnxn_atomdata_tStruct that stores atom related data for the nbnxn module
oCnbnxn_atomdata_t::ParamsThe actual atom data parameter values
oCnbnxn_atomdata_t::SimdMasksDiagonal and topology exclusion helper data for all SIMD kernels
oCnbnxn_ci_tSimple pair-list i-unit
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
oCNBParamGpuParameters required for the GPU nonbonded calculations
oCNBStagingDataStaging area for temporary data downloaded from the GPU
oCnonbonded_verlet_tTop-level non-bonded data structure for the Verlet-type cut-off scheme
oCgmx::compat::not_null< gmx::ISimulatorElement * >
oCgmx::compat::not_null< gmx::LegacySimulatorData * >
oCNumPmeDomainsStruct for passing around the number of PME domains
oCObservablesHistoryObservables history, for writing/reading to/from checkpoint file
oComp_module_nthreads_tStructure with the number of threads for each OpenMP multi-threaded algorithmic module in mdrun
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 >
oCOutputFileAll meta-data that is shared for one output file type for one bias
oCPackedJClusterListPacked j-cluster list
oCPackHaloExternalHandles a kernel which packs non-contiguous overlap data in all 8 neighboring directions
oCPackHaloInternalHandles a kernel which packs non-contiguous overlap data in all 8 neighboring directions
oCgmx::PaddedVector< gmx::BasicVector >
oCgmx::PaddedVector< gmx::gmx::BasicVector >
oCgmx::PaddedVector< gmx::RVec >
oCgmx::PaddedVector< real >
oCgmx::PaddedVector< RVec >
oCPairlistParamsThe setup for generating and pruning the nbnxn pair list
oCPairlistSetAn object that holds the local or non-local pairlists
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
oCpartitionInternal data structure for the insolidangle selection method
oCPbcAiucCompact and ordered version of the PBC matrix
oCPdbAtomEntryContains information for a single particle in a PDB file
oCpme_setup_tParameters and settings for one PP-PME setup
oCPmeGpuThe main PME GPU host structure, included in the PME CPU structure by pointer
oCPmeGpuAtomParamsA GPU data structure for storing the PME data of the atoms, local to this process' domain partition. This only has to be updated every DD step
oCPmeGpuConstParamsA GPU data structure for storing the constant PME data. This only has to be initialized once
oCPmeGpuDynamicParamsA GPU data structure for storing the PME data which might change for each new PME computation
oCPmeGpuGridParamsA GPU data structure for storing the PME data related to the grid sizes and cut-off. This only has to be updated at every DD step
oCPmeGpuHaloExchangeHost data structure used to store data related to PME halo exchange, staging buffers for MPI communication
oCPmeGpuKernelParamsBaseA single structure encompassing all the PME data used in GPU kernels on device. To extend the list with platform-specific parameters, this can be inherited by the GPU framework-specific structure
oCPmeGpuProgramStores PME data derived from the GPU context or devices
oCPmeGpuProgramImplPME GPU persistent host program/kernel data, which should be initialized once for the whole execution
oCPmeGpuSettingsThe PME GPU settings structure, included in the main PME GPU structure by value
oCPmeGpuSpecificThe main PME CUDA/OpenCL-specific host data structure, included in the PME GPU structure by the archSpecific pointer
oCPmeGpuStagingThe PME GPU intermediate buffers structure, included in the main PME GPU structure by value. Buffers are managed by the PME GPU module
oCPmeSharedThe PME GPU structure for all the data copied directly from the CPU PME structure. The copying is done when the CPU PME structure is already (re-)initialized (pme_gpu_reinit is called at the end of gmx_pme_init). All the variables here are named almost the same way as in gmx_pme_t. The types are different: pointers are replaced by vectors. TODO: use the shared data with the PME CPU. Included in the main PME GPU structure by value
oCPmeSolveKernel< gridOrdering, computeEnergyAndVirial, gridIndex, subGroupSize >The kernel for PME solve
oCPpRanksContains information about the PP ranks that partner this PME rank
oCPpRanksSendFInfoContains information about the PP ranks that partners this PME rank. used in the pme gather kernel for nvshmem purpose
oCPreprocessingAtomTypesStorage of all atom types used during preprocessing of a simulation input
oCPreprocessingBondAtomTypeStorage for all bonded atomtypes during simulation preprocessing
oCPreprocessResidueInformation about preprocessing residues
oCpull_coord_work_tStruct with parameters and force evaluation local data for a pull coordinate
oCpull_group_work_tPull group data used during pulling
oCgmx::Range< int >
oCReduceKernel< addRvecForce, accumulateForce >Class name for reduction kernel
oCReplicaExchangeParametersThe parameters for the replica exchange algorithm
oCReverseTopOptionsOptions for setting up gmx_reverse_top_t
oCScalarDataTypesScalar (non-SIMD) data types
oCSearchCycleCountingStruct for collecting detailed cycle counts for the search
oCSettleWaterTopologyComposite data for settle initialization
oCgmx::SignallerBuilder< gmx::EnergySignaller >
oCgmx::SignallerBuilder< gmx::LastStepSignaller >
oCgmx::SignallerBuilder< gmx::LoggingSignaller >
oCgmx::SignallerBuilder< gmx::NeighborSearchSignaller >
oCgmx::SignallerBuilder< gmx::TrajectorySignaller >
oCSimulationGroupsContains the simulation atom groups
oCSimulationParticleSingle particle in a simulation
oCSolveKernelParamsContains most of the parameters used by the solve kernel
oCsort_along_vec_tHelper structure for sorting positions along rotation vector
oCspheresurfacebinInternal data structure for the insolidangle selection method
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
oCswap_compartmentStructure containing compartment-specific data
oCswap_groupThis structure contains data needed for the groups involved in swapping: split group 0, split group 1, solvent group, ion groups
oCSystemMomentaSystem momenta used with with the box deform option
oCSystemMomentumThe momentum and mass of the whole system
oCt_bbStruct containing properties of a residue in a protein backbone
oCt_compare_valueData structure for comparison expression operand values
oCt_compiler_dataInternal data structure used by the compiler
oCt_coordselectionSelection of pull coordinates to be used in WHAM (one structure for each tpr file)
oCt_filenmFile name option definition for C code
oCt_forcetableStructure describing the data in a single table
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_methoddata_compareData structure for comparison expression evaluation
oCt_methoddata_distanceData structure for distance-based selection method
oCt_methoddata_kwevalData structure for keyword evaluation in arbitrary groups
oCt_methoddata_kwintData structure for integer keyword expression evaluation
oCt_methoddata_kwrealData structure for real keyword expression evaluation
oCt_methoddata_posData structure for position keyword evaluation
oCt_methoddata_sameData structure for the same selection method
oCt_nbparamUsed to temporarily store the explicit non-bonded parameter combinations, which will be copied to InteractionsOfType
oCt_oriresdataOrientation restraining stuff
oCt_pargsCommand-line argument definition for C code
oCt_partition_itemInternal data structure for the insolidangle selection method
oCt_pbcStructure containing info on periodic boundary conditions
oCt_pullcoordParameters of one pull coordinate
oCt_register_methodHelper structure for defining selection methods
oCt_stateThe microstate of the system
oCt_swapMain (private) data structure for the position swapping protocol
oCt_symbufLegacy symbol table entry as linked list
oCt_UmbrellaHeaderParameters of the umbrella potentials
oCt_UmbrellaWindowData in the umbrella histograms
oCt_xpmelmtModels an XPM element
oCthread_work_tStruct for thread local work data for local topology generation
oCgmx::ThreadedForceBuffer< gmx::RVec >
oCgmx::ThreadedForceBuffer< rvec4 >
oCgmx::ThreadForceBuffer< gmx::RVec >
oCgmx::ThreadForceBuffer< rvec4 >
oCgmx::ThreeFry2x64General< 13, internalCounterBits >
oCgmx::ThreeFry2x64General< 20, internalCounterBits >
oCTpxFileHeaderFirst part of the TPR file structure containing information about the general aspect of the system
oCUmbrellaOptionsParameters of WHAM
oCUnitCellInfoProvides information about properties of the unit cell
oCUnpackAndAddHaloInternalHandles a kernel which adds grid overlap data received from neighboring ranks
oCUnpackHaloExternalHandles a kernel which gathers data from halo region in all 8 neighboring directions
oCgmx::Update::ImplPImpled implementation for Update
oCVirtualSiteConfigurationThe configuration describing a virtual site
oCVirtualSiteTopologyVirtual site topology datastructure
oCVirtualSiteTopology::VirtualSiteAngleHelper struct for single angle in virtual site
oCVirtualSiteTopology::VirtualSiteBondHelper struct for single bond in virtual site
oCVsiteAtomMappingConvenience typedef for linking function type to parameter numbers
oCVsiteBondedInteractionData type to store information about bonded interactions for virtual sites
oCVsiteBondParameterStores information about single virtual site bonded parameter
oCwallcc_tCounters for an individual wallcycle timing region
oCWarningHandlerGeneral warning handling object
oCWaterMoleculeIndices of atoms in a water molecule
\CWorkDivisionThe division of bonded interactions of the threads