  gmx::accessor_basic< float > | |
| gmx::accessor_basic< value_type > | |
| AllVsiteBondedInteractions | Wraps the datastructures for the different vsite bondeds |
| gmx::AnalysisDataFrameLocalData< double > | |
| gmx::AnalysisDataFrameLocalData< int64_t > | |
| anonymous_namespace{edsam.cpp}::t_edflood | Essential 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) |
| anonymous_namespace{edsam.cpp}::t_edvecs | Essential dynamics vectors per method implementation |
| anonymous_namespace{edsam.cpp}::t_eigvec | Essential 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 |
| anonymous_namespace{evaluate.cpp}::MempoolGroupReserver | Reserves memory for an index group from the evaluation memory pool |
| anonymous_namespace{evaluate.cpp}::MempoolSelelemReserver | Reserves memory for a selection element from the evaluation memory pool |
| anonymous_namespace{evaluate.cpp}::SelelemTemporaryValueAssigner | Assigns a temporary value for a selection element |
| anonymous_namespace{indexutil.cpp}::IndexBlockTest | Text fixture for index block operations |
| anonymous_namespace{minimize.cpp}::EnergyEvaluator | Class to handle the work of setting and doing an energy evaluation |
| anonymous_namespace{resourcedivision.cpp}::SingleRankChecker | Handles checks for algorithms that must use a single rank |
| anonymous_namespace{sm_keywords.cpp}::StringKeywordMatchItem | Single item in the list of strings/regular expressions to match |
| anonymous_namespace{sm_keywords.cpp}::t_methoddata_kwstr | Data structure for string keyword expression evaluation |
| gmx::ArrayRef< const AnalysisDataValue > | |
| gmx::ArrayRef< const char *const > | |
| gmx::ArrayRef< const char > | |
| gmx::ArrayRef< const double > | |
| gmx::ArrayRef< const float > | |
| gmx::ArrayRef< const gmx::analysismodules::anonymous_namespace{msd.cpp}::MoleculeData > | |
| gmx::ArrayRef< const gmx::BasicVector > | |
| gmx::ArrayRef< const int > | |
| gmx::ArrayRef< const InteractionList > | |
| gmx::ArrayRef< const real > | |
| gmx::ArrayRef< const t_filenm > | |
| gmx::ArrayRef< const t_iparams > | |
| gmx::ArrayRef< const unsigned short > | |
| gmx::ArrayRef< double > | |
| gmx::ArrayRef< gmx::BasicVector > | |
| gmx::ArrayRef< gmx::gmx::BasicVector > | |
| gmx::ArrayRef< gmx::RVec > | |
| gmx::ArrayRef< Nbnxm::BoundingBox > | |
| gmx::ArrayRef< PpRanks > | |
| gmx::ArrayRef< real > | |
| gmx::ArrayRef< rvec > | |
| gmx::ArrayRef< ValueType > | |
| gmx::ArrayRefWithPadding< gmx::BasicVector > | |
| gmx::ArrayRefWithPadding< gmx::gmx::BasicVector > | |
| Atom2VsiteBond | Helper type for conversion of bonded parameters to virtual sites |
| AtomDistribution | Distribution of atom groups over the domain (only available on the master rank) |
| AtomDistribution::DomainAtomGroups | Collection of local group and atom counts for a domain |
| AtomIndexSet | Container for returning molecule type and index information for an atom |
| AtomInMolblock | Container for returning molecule type and index information for an atom |
| AtomIterator | Object that allows looping over all atoms in an mtop |
| AtomProperties | Holds all the atom property information loaded |
| AtomProperties::Impl | Implementation detail type for Atomproperties |
| AtomProperty | Conglomeration of atom property entries |
| AtomProxy | Proxy object returned from AtomIterator |
| AtomRange | Range over all atoms of topology |
| AwhReader | All options and meta-data needed for the AWH output |
| BalanceRegion | Struct for timing the region for dynamic load balancing |
| BaseEntry | Basic entries in AtomProperty |
| gmx::basic_mdspan< value_type, dynamic_extents_type, layout_right > | |
| gmx::basic_mdspan< value_type, Extents, layout_right > | |
| gmx::basic_mdspan< value_type, Extents, LayoutPolicy > | |
| gmx::basic_mdspan< value_type, gmx::extents, layout_right > | |
| gmx::basic_mdspan< value_type, gmx::extents< dynamic_extent, dynamic_extent >, layout_right > | |
| gmx::basic_mdspan< value_type, static_extents_type, layout_right > | |
| gmx::BasicVector< double > | |
| gmx::BasicVector< int > | |
| gmx::BasicVector< real > | |
| BiasOutputSetup | All meta-data that is shared for all output files for one bias |
| bonded_threading_t | Struct contain all data for bonded force threading |
| BondedInteraction | Information about single bonded interaction |
| BondedInteractionList | Accumulation of different bonded types for preprocessing |
| gmx::BuildMDModulesNotifier< const gmx::CoordinatesAndBoxPreprocessed &, const gmx::MDLogger &, warninp *, gmx::EnergyCalculationFrequencyErrors *, gmx_mtop_t *, const gmx::IndexGroupsAndNames &, gmx::KeyValueTreeObjectBuilder, const gmx::QMInputFileName & > | |
| gmx::BuildMDModulesNotifier< const KeyValueTreeObject &, gmx::LocalAtomSetManager *, const gmx::MDLogger &, const gmx_mtop_t &, gmx::MDModulesEnergyOutputToDensityFittingRequestChecker *, gmx::MDModulesEnergyOutputToQMMMRequestChecker *, gmx::SeparatePmeRanksPermitted *, const PbcType &, const gmx::SimulationTimeStep &, const t_commrec &, const gmx::MdRunInputFilename & > | |
| gmx::BuildMDModulesNotifier< gmx::MDModulesCheckpointReadingDataOnMaster, gmx::MDModulesCheckpointReadingBroadcast, gmx::MDModulesWriteCheckpointData > | |
| ChainIdFiller | Constructs plausible chain IDs for multi-molecule systems, e.g. when read from .tpr files |
| CheckpointHeaderContents | Header explaining the context of a checkpoint file |
| cl_nbparam_params | Data structure shared between the OpenCL device code and OpenCL host code |
| dd_corners_t | Domain corners for communication, a maximum of 4 i-zones see a j domain |
| DDBalanceRegionHandler | Manager for starting and stopping the dynamic load balancing region |
| DDGridSetup | Describes the DD grid setup |
| DDPairInteractionRanges | Pair interaction zone and atom range for an i-zone |
| DeviceInformation | Platform-dependent device information |
| DeviceStream | Declaration of platform-agnostic device stream/queue |
| df_history_t | Free-energy sampling history struct |
| DipoleData | Data structure to hold dipole-related data and staging arrays |
| DispersionCorrection::Correction | Struct for returning all dispersion correction quantities |
| ekinstate_t | Struct used for checkpointing only |
| em_state | Utility structure for manipulating states during EM |
| gmx::EnumerationArray< AtomLocality, const DeviceStream * > | |
| gmx::EnumerationArray< AtomLocality, GpuEventSynchronizer > | |
| gmx::EnumerationArray< AtomLocality, Nbnxm::GpuTimers::XFTransfers > | |
| gmx::EnumerationArray< BondedTypes, BondedInteractionList > | |
| gmx::EnumerationArray< Channel, int * > | |
| gmx::EnumerationArray< Channel, int > | |
| gmx::EnumerationArray< Channel, rvec * > | |
| gmx::EnumerationArray< Channel, rvec ** > | |
| gmx::EnumerationArray< Compartment, int * > | |
| gmx::EnumerationArray< Compartment, int > | |
| gmx::EnumerationArray< Compartment, real > | |
| gmx::EnumerationArray< Compartment, swap_compartment > | |
| gmx::EnumerationArray< CoordinateFileFlags, OutputAdapterPointer > | |
| gmx::EnumerationArray< DeviceStreamType, std::unique_ptr< DeviceStream > > | |
| gmx::EnumerationArray< FftDirection, RocfftPlan > | |
| gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, bool > | |
| gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, double > | |
| gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, real > | |
| gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, std::string > | |
| gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double > > | |
| gmx::EnumerationArray< gmx::AtomLocality, std::unique_ptr< gmx::GpuForceReduction > > | |
| gmx::EnumerationArray< InteractionLocality, Nbnxm::Nbnxm::GpuTimers::Nbnxm::GpuTimers::Interaction > | |
| gmx::EnumerationArray< ModuleMultiThread, int > | |
| gmx::EnumerationArray< Nbnxm::InteractionLocality, bool > | |
| gmx::EnumerationArray< Nbnxm::InteractionLocality, const DeviceStream * > | |
| gmx::EnumerationArray< Nbnxm::InteractionLocality, Nbnxm::gpu_plist * > | |
| gmx::EnumerationArray< NonBondedEnergyTerms, bool > | |
| gmx::EnumerationArray< NonBondedEnergyTerms, std::vector< real > > | |
| gmx::EnumerationArray< PmeStage, gmx_kernel_timing_data_t > | |
| gmx::EnumerationArray< PmeStage, GpuRegionTimerWrapper > | |
| gmx::EnumerationArray< PmeTestFlavor, std::string > | |
| gmx::EnumerationArray< ReplicaExchangeType, real * > | |
| gmx::EnumerationArray< SimulationAtomGroupType, AtomGroupIndices > | |
| gmx::EnumerationArray< SimulationAtomGroupType, std::vector< unsigned char > > | |
| gmx::EnumerationArray< WallCycleCounter, wallcc_t > | |
| gmx::EnumerationArray< WallCycleSubCounter, wallcc_t > | |
| EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
| gmx::extents< dynamic_extent, dynamic_extent, dynamic_extent > | |
| gmx::extents< E_STATIC...> | |
| gmx::FixedCapacityVector< GpuEventSynchronizer *, 3 > | |
| gmx::FlagsTemplate< Flag > | |
| gmx::FlagsTemplate< OptionFlag > | |
| gmx::FlagsTemplate< SelectionFlag > | |
| gmx::FlagsTemplate< TestFlag > | |
| ForceHelperBuffers | Helper force buffers for ForceOutputs |
| ForeignLambdaTerms | Accumulates free-energy foreign lambda energies and dH/dlamba |
| FreeEnergyDispatch | Temporary data and methods for handling dispatching of the nbnxm free-energy kernels |
 gmx::AbstractAnalysisData | Abstract base class for all objects that provide data |
 gmx::AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
| gmx::AbstractAverageHistogram | Base class for representing histograms averaged over frames |
| anonymous_namespace{histogram.cpp}::MockAverageHistogram | Mock object for testing gmx::AbstractAverageHistogram |
| gmx::anonymous_namespace{histogram.cpp}::StaticAverageHistogram | Represents copies of average histograms |
 gmx::internal::BasicAverageHistogramModule | Implements average histogram module that averages per-frame histograms |
| gmx::AnalysisArrayData | Simple in-memory data array |
| gmx::AnalysisDataAverageModule | Data module for independently averaging each column in input data |
| gmx::AnalysisDataBinAverageModule | Data module for bin averages |
| gmx::AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
| gmx::AnalysisData | Parallelizable data container for raw data |
| gmx::AnalysisDataDisplacementModule | Data module for calculating displacements |
| gmx::AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
| gmx::AnalysisDataProxy | Internal implementation class used to implement column modules |
| gmx::AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
| gmx::AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| gmx::AbstractAnalysisData::Impl | Private implementation class for AbstractAnalysisData |
| gmx::AbstractCompositeHelpTopic::Impl | Private implementation class for AbstractCompositeHelpTopic |
| gmx::AbstractOption | Abstract base class for specifying option properties |
| gmx::OptionTemplate< T, U > | Templated base class for constructing concrete option settings classes |
| gmx::SelectionFileOption | Specifies a special option that provides selections from a file |
| gmx::OptionTemplate< bool, BooleanOption > | |
| gmx::BooleanOption | Specifies an option that provides boolean values |
| gmx::OptionTemplate< double, DoubleOption > | |
| gmx::DoubleOption | Specifies an option that provides floating-point (double) values |
| gmx::OptionTemplate< EnumType, EnumOption< EnumType > > | |
| gmx::EnumOption< EnumType > | Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable |
| gmx::OptionTemplate< EnumType, LegacyEnumOption< EnumType > > | |
| gmx::LegacyEnumOption< EnumType > | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
| gmx::OptionTemplate< float, FloatOption > | |
| gmx::FloatOption | Specifies an option that provides floating-point (float) values |
| gmx::OptionTemplate< int, IntegerOption > | |
| gmx::IntegerOption | Specifies an option that provides integer values |
| gmx::OptionTemplate< int64_t, Int64Option > | |
| gmx::Int64Option | Specifies an option that provides 64-bit integer values |
| gmx::OptionTemplate< Selection, SelectionOption > | |
| gmx::SelectionOption | Specifies an option that provides selection(s) |
| gmx::OptionTemplate< std::string, FileNameOption > | |
| gmx::FileNameOption | Specifies an option that provides file names |
| gmx::OptionTemplate< std::string, MockOption > | |
| anonymous_namespace{abstractoptionstorage.cpp}::MockOption | Specifies an option that has a mock storage object for unit testing |
 gmx::OptionTemplate< std::string, StringOption > | |
 gmx::StringOption | Specifies an option that provides string values |
| gmx::AbstractOptionSection | Base class for specifying option section properties |
| gmx::OptionSection | Declares a simple option section |
| gmx::RepeatingOptionSection< T > | Declares an option section that creates a structure for each instance |
| gmx::AbstractOptionStorage | Abstract base class for converting, validating, and storing option values |
| gmx::OptionStorageTemplate< T > | Templated base class for constructing option value storage classes |
| gmx::OptionStorageTemplateSimple< T > | Simplified option storage template for options that have one-to-one value conversion |
| gmx::SelectionFileOptionStorage | Implementation for a special option for reading selections from files |
| gmx::OptionStorageTemplate< bool > | |
| gmx::OptionStorageTemplateSimple< bool > | |
| gmx::BooleanOptionStorage | Converts, validates, and stores boolean values |
| gmx::OptionStorageTemplate< double > | |
| gmx::OptionStorageTemplateSimple< double > | |
| gmx::DoubleOptionStorage | Converts, validates, and stores floating-point (double) values |
| gmx::OptionStorageTemplate< float > | |
| gmx::OptionStorageTemplateSimple< float > | |
| gmx::FloatOptionStorage | Converts, validates, and stores floating-point (float) values |
| gmx::OptionStorageTemplate< int > | |
| gmx::OptionStorageTemplateSimple< int > | |
| gmx::EnumOptionStorage | Converts, validates, and stores enum values |
| gmx::IntegerOptionStorage | Converts, validates, and stores integer values |
| gmx::OptionStorageTemplate< int64_t > | |
| gmx::OptionStorageTemplateSimple< int64_t > | |
| gmx::Int64OptionStorage | Converts, validates, and stores integer values |
| gmx::OptionStorageTemplate< Selection > | |
| gmx::SelectionOptionStorage | Converts, validates, and stores selection values |
| gmx::OptionStorageTemplate< std::string > | |
| anonymous_namespace{abstractoptionstorage.cpp}::MockOptionStorage | Mock implementation of an option storage class for unit testing |
| gmx::OptionStorageTemplateSimple< std::string > | |
| gmx::FileNameOptionStorage | Converts, validates, and stores file names |
| gmx::StringOptionStorage | Converts, validates, and stores string values |
| gmx::accessor_basic< ElementType > | The most basic memory access model for mdspan |
| gmx::AffineTransformation | Affine transformation of three-dimensional coordinates |
| gmx::AlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code |
| gmx::Allocator< T, AllocationPolicy > | Policy-based memory allocator |
| gmx::AnalysisData::Impl | Private implementation class for AnalysisData |
| gmx::AnalysisDataDisplacementModule::Impl | Private implementation class for AnalysisDataDisplacementModule |
| gmx::AnalysisDataFrameAverager | Helper class for modules that average values over frames |
| gmx::AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
| gmx::AnalysisDataFrameLocalData< ValueType > | Container for an array of frame-local values that supports parallel data processing |
| gmx::AnalysisDataFrameLocalDataHandle< ValueType > | Handle to a single frame data within frame-local data array |
| gmx::AnalysisDataFrameLocalDataSetHandle< ValueType > | Handle to a single data set within frame-local data array |
| gmx::AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
| gmx::AnalysisDataHandle | Handle for inserting data into AnalysisData |
| gmx::AnalysisDataLifetimeModule::Impl | Private implementation class for AnalysisDataLifetimeModule |
| gmx::AnalysisDataModuleManager | Encapsulates handling of data modules attached to AbstractAnalysisData |
| gmx::AnalysisDataModuleManager::Impl | Private implementation class for AnalysisDataModuleManager |
| gmx::AnalysisDataModuleManager::Impl::ModuleInfo | Stores information about an attached module |
| gmx::AnalysisDataParallelOptions | Parallelization options for analysis data objects |
| gmx::AnalysisDataPlotSettings | Common settings for data plots |
| gmx::AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
| gmx::AnalysisDataStorage | Helper class that implements storage of data |
| gmx::AnalysisDataStorageFrame | Allows assigning values for a data frame in AnalysisDataStorage |
| gmx::AnalysisDataValue | Value type for representing a single value in analysis data objects |
| gmx::AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
| gmx::AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
| gmx::analysismodules::anonymous_namespace{angle.cpp}::AnglePositionIterator | Helper to encapsulate logic for looping over input selections |
| gmx::analysismodules::anonymous_namespace{msd.cpp}::MoleculeData | Holds data needed for MSD calculations for a single molecule, if requested |
| gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager | Handles coordinate operations for MSD calculations |
| gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData | Mean Squared Displacement data accumulator |
| gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy | Proxy to a MsdData tau column vector. Supports only push_back |
| gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData | Holds per-group coordinates, analysis, and results |
| gmx::analysismodules::anonymous_namespace{sasa.cpp}::t_conect | Tracks information on two nearest neighbors of a single surface dot |
| gmx::AnalysisNeighborhood | Neighborhood searching for analysis tools |
| gmx::AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
| gmx::AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
| gmx::AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
| gmx::AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
| gmx::AnalyticalSplineTableInput | Specification for analytical table function (name, function, derivative) |
| gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::IHelpExport | Callbacks for exporting help information for command-line modules |
| gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportCompletion | Implements export for command-line completion |
| gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::HelpExportReStructuredText | Implements export for web pages as reStructuredText |
| gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::IOptionsFormatter | Interface for output format specific formatting of options |
| gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsListFormatter | Formatter implementation for help export |
| gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::SynopsisFormatter | Formatter implementation for synopsis |
| gmx::anonymous_namespace{cpuinfo.cpp}::ApicIdLayout | The layout of the bits in the APIC ID |
| gmx::anonymous_namespace{cpuinfo.cpp}::ApicInfo | Internal structure to return os logical cpu id together with APIC info for it |
| gmx::anonymous_namespace{densityfit.cpp}::CrossCorrelationEvaluationHelperValues | Helper values for evaluating the cross correlation |
| gmx::anonymous_namespace{densityfit.cpp}::CrossCorrelationGradientAtVoxel | Calculate a single cross correlation gradient entry at a voxel |
| gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityCrossCorrelation | Implementation for DensitySimilarityCrossCorrelation |
| gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityInnerProduct | Implementation for DensitySimilarityInnerProduct |
| gmx::anonymous_namespace{densityfit.cpp}::DensitySimilarityRelativeEntropy | Implementation for DensitySimilarityRelativeEntropy |
| gmx::anonymous_namespace{densityfitting.cpp}::DensityFittingSimulationParameterSetup | Collect density fitting parameters only available during simulation setup |
| gmx::anonymous_namespace{electricfield.cpp}::ElectricFieldDimension | Describes an applied electric field in a coordinate dimension |
| gmx::anonymous_namespace{exceptions.cpp}::ErrorMessage | Error message or error context text item |
| gmx::anonymous_namespace{exceptions.cpp}::IMessageWriter | Abstracts actual output from the other logic in exception formatting |
| gmx::anonymous_namespace{exceptions.cpp}::MessageWriterFileNoThrow | Exception information writer for cases where exceptions should be avoided |
| gmx::anonymous_namespace{exceptions.cpp}::MessageWriterString | Exception information writer to format into an std::string |
| gmx::anonymous_namespace{exceptions.cpp}::MessageWriterTextWriter | Exception information writer to format into a TextOutputStream |
| gmx::anonymous_namespace{filenameoption.cpp}::FileTypeHandler | Handles a single file type known to FileNameOptionStorage |
| gmx::anonymous_namespace{filenameoption.cpp}::FileTypeMapping | Mapping from OptionFileType to a file type in filetypes.h |
| gmx::anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}::PlanSetupData | Helper struct to reduce repetitive code setting up a 3D FFT plan |
| gmx::anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}::RocfftInitializer | Provides RAII-style initialization of rocFFT library |
| gmx::anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}::RocfftPlan | All the persistent data for planning an executing a 3D FFT |
| gmx::anonymous_namespace{handlerestart.cpp}::StartingBehaviorHandler | Describes how mdrun will (re)start and provides supporting functionality based on that data |
| gmx::anonymous_namespace{helpwritercontext.cpp}::IWrapper | Custom output interface for HelpWriterContext::Impl::processMarkup() |
| gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToString | Wraps markup output into a single string |
| gmx::anonymous_namespace{helpwritercontext.cpp}::WrapperToVector | Wraps markup output into a vector of string (one line per element) |
| gmx::anonymous_namespace{nbsearch.cpp}::MindistAction | Search action find the minimum distance |
| gmx::anonymous_namespace{neldermead.cpp}::NelderMeadParameters | The parameters for a Nelder-Mead optimisation |
| gmx::anonymous_namespace{pargs.cpp}::OptionsAdapter | Conversion helper between t_pargs/t_filenm and Options |
| gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup | Helper class that holds simulation data and callback functions for simulation setup time notifications |
| gmx::anonymous_namespace{shake.cpp}::ShakeTest | Test fixture for testing SHAKE |
| gmx::anonymous_namespace{updategroups.cpp}::UpdateGroupsTest | Test fixture class |
| gmx::Any | Represents a dynamically typed value of an arbitrary type - deprecated |
| gmx::ArrayRef< typename > | STL-like interface to a C array of T (or part of a std container of T) |
| gmx::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 |
| gmx::AtomIndex | List of atom indices belonging to a task |
| gmx::AtomIndexExtremes | Struct for returning an atom range |
| gmx::AtomInfoWithinMoleculeBlock | Contains information about each atom in a molecule block of the global topology |
| gmx::AtomPair | A pair of atoms indexes |
| gmx::AtomsAdjacencyListElement | Helper type for discovering coupled constraints |
| gmx::Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
| gmx::AwhEnergyBlock | AWH output data block that can be written to an energy file block |
| gmx::AwhParams | Structure holding parameter information for AWH |
| gmx::basic_mdspan< ElementType, Extents, LayoutPolicy, AccessorPolicy > | Multidimensional array indexing and memory access with flexible mapping and access model |
| gmx::BasicVector< ValueType > | C++ class for 3D vectors |
| gmx::BenchmarkSystem | Description of the system used for benchmarking |
| gmx::Bias | A bias acting on a multidimensional coordinate |
| gmx::BiasCoupledToSystem | A bias and its coupling to the system |
| gmx::BiasGrid | The grid for a single bias, generally multidimensional and periodic |
| gmx::BiasParams | Constant parameters for the bias |
| gmx::BiasState | The state of a bias |
| gmx::BiasWriter | Class organizing the output data storing and writing of an AWH bias |
| gmx::BinaryInformationSettings | Settings for printBinaryInformation() |
| gmx::BoxDeformationHandle | Handle to information about the box |
| gmx::BuildMDModulesNotifier< CallParameter > | Aide to avoid nested MDModulesNotifier definition |
| gmx::BuildMDModulesNotifier< CurrentCallParameter, CallParameter...> | Template specialization to assemble MDModulesNotifier |
| gmx::BuildMDModulesNotifier<> | Template specialization to end parameter unpacking recursion |
| gmx::BuildMDModulesNotifier<>::NoCallParameter | Do nothing but be base class of MDModulesNotifier |
| gmx::CacheLineAlignedFlag | Class with interfaces and data for CUDA version of PME Force sending functionality |
| gmx::cellInfo | Structure to hold cell information for any nbat-format forces |
| gmx::CheckpointData< operation > | } |
| gmx::CheckpointHandler | Class handling the checkpoint signal |
| gmx::CheckpointHelperBuilder | Builder for the checkpoint helper |
| gmx::CheckpointOptions | Options for writing checkpoint files |
| gmx::ClfftInitializer | Handle clFFT library init and tear down in RAII style also with mutual exclusion |
| gmx::ClHandle< cl_type > | Wrapper of OpenCL type cl_type to implement RAII |
| gmx::CommandLineCommonOptionsHolder | Encapsulates some handling of common options to the wrapper binary |
| gmx::CommandLineHelpContext | Context information for writing out command-line help |
| gmx::CommandLineHelpContext::Impl | Private implementation class for CommandLineHelpContext |
| gmx::CommandLineHelpWriter | Writes help information for Options |
| gmx::CommandLineHelpWriter::Impl | Private implementation class for CommandLineHelpWriter |
| gmx::CommandLineModuleGroup | Handle to add content to a group added with CommandLineModuleManager::addModuleGroup() |
| gmx::CommandLineModuleGroupData | Internal data for a CommandLineModuleManager module group |
| gmx::CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
| gmx::CommandLineModuleManager::Impl | Private implementation class for CommandLineModuleManager |
| gmx::CommandLineModuleSettings | Settings to pass information between a module and the general runner |
| gmx::CommandLineParser | Implements command-line parsing for Options objects |
| gmx::CommandLineParser::Impl | Private implementation class for CommandLineParser |
| gmx::compat::not_null< T > | Restricts a pointer or smart pointer to only hold non-null values |
| gmx::Constraints | Handles constraints |
| gmx::Constraints::CreationHelper | Support type to help implement makeConstraints() |
| gmx::ConstraintsParam | Collection of constraint parameters |
| gmx::ConvertTprInfo | Declares gmx convert-tpr |
| gmx::CoordinatesAndBoxPreprocessed | Provides coordinates and simulation box |
| gmx::CoordState | Keeps track of the current coordinate value, grid index and umbrella location |
| gmx::CorrelationBlockData | Correlation block averaging weight-only data |
| gmx::CorrelationBlockData::CoordData | Correlation block averaging data |
| gmx::CorrelationGrid | BiasGrid of local correlation tensors |
| gmx::CorrelationTensor | Correlation data for computing the correlation tensor of one grid point |
| gmx::CpuInfo | Detect CPU capabilities and basic logical processor info |
| gmx::CpuInfo::LogicalProcessor | Entry with basic information for a single processing unit |
| gmx::CrystallographicLabels | Crystallographic labels for mrc data |
| gmx::CubicSplineTable | Cubic spline interpolation table |
| gmx::DataFileFinder | Searches data files from a set of paths |
| gmx::DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
| gmx::DataFileOptions | Search parameters for DataFileFinder |
| gmx::DefaultInitializationAllocator< T, A > | Allocator adaptor that interposes construct() calls to convert value initialization into default initialization |
| gmx::DensityFittingAmplitudeLookup | Class that translates atom properties into amplitudes |
| gmx::DensityFittingForce | Manages evaluation of density-fitting forces for particles that were spread with a kernel |
| gmx::DensityFittingForce::Impl | Private implementation class for DensityFittingForce |
| gmx::DensityFittingForceProviderState | Parameters defining the internal density fitting force provider state |
| gmx::DensityFittingModuleInfo | Information about the density fitting module |
| gmx::DensityFittingParameters | Holding all directly user-provided parameters for density fitting |
| gmx::DensitySimilarityMeasure | Measure similarity and gradient between densities |
| gmx::detail::extents_analyse< 0 > | Specialisation for rank 0 extents analysis. Ends recursive rank analysis |
| gmx::detail::extents_analyse< R, dynamic_extent, StaticExtents...> | Enable querying extent of specific rank by splitting a dynamic extent off the variadic template arguments |
| gmx::detail::extents_analyse< R, E0, StaticExtents...> | Enable querying extent of specific rank by splitting a static extents off the variadic template arguments |
| gmx::detail::PaddingTraits< T > | Traits classes for handling padding for types used with PaddedVector |
| gmx::detail::SimulationInputHandleImplDeleter | Explicit deleter details for SimulationInputHolderImpl |
| gmx::DevelopmentFeatureFlags | Structure that holds boolean flags corresponding to the development features present enabled through environment variables |
| gmx::DeviceDetectionResult | Convenience macro to help us avoid ifdefs each time we use sysconf |
| gmx::DeviceStreamManager | Device stream and context manager |
| gmx::DeviceStreamManager::Impl | Impl class to manages the lifetime of the GPU streams |
| gmx::DimParams | Constant parameters for each dimension of the coordinate |
| gmx::DimParams::FepDimParams | Type for storing dimension parameters for free-energy lamdba type dimensions |
| gmx::DimParams::PullDimParams | Type for storing dimension parameters for pull type dimensions |
| gmx::DirectoryEnumerator | Lists files in a directory |
| gmx::DomainDecompositionBuilder | Builds a domain decomposition management object |
| gmx::DomainDecompositionBuilder::Impl | Impl class for DD builder |
| gmx::DomainInfo | Information on PBC and domain decomposition for virtual sites |
| gmx::DomainLifetimeWorkload | Describes work done on this domain on every step of its lifetime, but which might change after the next domain paritioning |
| gmx::DomDecHelperBuilder | Builder for DomDecHelper |
| gmx::DomdecOptions | Structure containing all (command line) options for the domain decomposition |
| gmx::EnergyCalculationFrequencyErrors | Collect errors for the energy calculation frequency |
| gmx::EnergyData | Data class managing energies |
| gmx::EnergyDriftTracker | Class for tracking and printing the drift in the conserved energy quantity |
| gmx::EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
| gmx::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 |
| gmx::EnumerationIterator< EnumType, Last, Step > | Allows iterating sequential enumerators |
| gmx::EnumerationWrapper< EnumType, Last, Step > | Allows constructing iterators for looping over sequential enumerators |
| gmx::EqualCaseInsensitive | Function object for comparisons with equalCaseInsensitive |
| gmx::ExceptionInitializer | Provides information for Gromacs exception constructors |
| gmx::ExclusionBlock | Describes exclusions for a single atom |
| gmx::ExponentialDistribution< RealType > | Exponential distribution |
| gmx::ExponentialDistribution< RealType >::param_type | Exponential distribution parameters |
| gmx::ExponentialMovingAverage | Evaluate the exponential moving average with bias correction |
| gmx::ExponentialMovingAverageState | Store the state of exponential moving averages |
| gmx::extents< StaticExtents > | Multidimensional extents with static and dynamic dimensions |
| gmx::FepStateSetting | Allows external clients to specify how to change the FEP state |
| gmx::FileNameOptionManager::Impl | Private implemention class for FileNameOptionManager |
| gmx::FixedCapacityVector< typename, size_t > | Vector that behaves likes std::vector but has fixed capacity |
| gmx::FlagsTemplate< FlagType > | Template class for typesafe handling of combination of flags |
| gmx::ForceBuffers | Object that holds the force buffers |
| gmx::ForceBuffersView | A view of the force buffer |
| gmx::ForceOutputs | Force and virial output buffers for use in force computation |
| gmx::ForceProviderInput | Helper struct that bundles data for passing it over to the force providers |
| gmx::ForceProviderOutput | Helper struct bundling the output data of a force provider |
| gmx::ForceProviders | Evaluates forces from a collection of gmx::IForceProvider |
| gmx::ForceWithShiftForces | Container for force and virial for algorithms that compute shift forces for virial calculation |
| gmx::ForceWithVirial | Container for force and virial for algorithms that provide their own virial tensor contribution |
| gmx::FreeEnergyPerturbationData | The free energy perturbation data |
| gmx::functor_wrapper< T, D > | Wrap function into functor to be used as deleter |
| gmx::GammaDistribution< RealType > | Gamma distribution |
| gmx::GammaDistribution< RealType >::param_type | Gamma distribution parameters |
| gmx::GaussianOn1DLattice | Provide result of Gaussian function evaluation on a one-dimensional lattice |
| gmx::GaussianSpreadKernelParameters | Parameters for density spreading kernels |
| gmx::GaussianSpreadKernelParameters::PositionAndAmplitude | Parameters that describe the kernel position and amplitude |
| gmx::GaussianSpreadKernelParameters::Shape | Shape parameters for Gaussian spreading kernels describe the kernel shape |
| gmx::GaussTransform3D | Sums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as  |
| gmx::GaussTransform3D::Impl | Private implementation class for GaussTransform3D |
| gmx::GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
| gmx::GlobalCommunicationHelper | Helper container with data connected to global communication |
| gmx::Gpu3dFft | A 3D FFT class for performing R2C/C2R transforms |
| gmx::Gpu3dFft::Impl | Impl base class for all FFT backends |
| gmx::Gpu3dFft::ImplCuFft | A 3D FFT wrapper class for performing R2C/C2R transforms using cuFFT |
| gmx::Gpu3dFft::ImplOcl | A 3D FFT wrapper class for performing R2C/C2R transforms using clFFT |
| gmx::Gpu3dFft::ImplSycl | A 3D FFT wrapper class for performing R2C/C2R transforms using SYCL. Not yet implemented |
| gmx::Gpu3dFft::ImplSyclMkl | A 3D FFT wrapper class for performing R2C/C2R transforms using SYCL + MKL |
| gmx::Gpu3dFft::ImplSyclRocfft | A 3D FFT wrapper class for performing R2C/C2R transforms using rocFFT for hipSYCL targetting ROCm devices |
| gmx::Gpu3dFft::ImplSyclRocfft::Impl | Impl class |
| gmx::GpuForceReduction | Manages the force reduction directly in GPU memory |
| gmx::GpuHaloExchange | Manages GPU Halo Exchange object |
| gmx::GpuHaloExchange::Impl | Impl class stub |
| gmx::GpuTaskAssignments | Contains the GPU task assignment for all ranks on this physical node |
| gmx::GpuTaskAssignmentsBuilder | Builder for the GpuTaskAssignments for all ranks on this node |
| gmx::GpuTaskMapping | Specifies the GPU deviceID_ available for task_ to use |
| gmx::GridAxis | An axis, i.e. dimension, of the grid |
| gmx::GridPoint | A point in the grid |
| gmx::GromppMtsOpts | Struct for passing the MTS mdp options to setupMtsLevels() |
| gmx::HardwareTopology | Information about packages, cores, processing units, numa, caches |
| gmx::HardwareTopology::Cache | Information about a single cache level |
| gmx::HardwareTopology::Core | Information about a single core in a package |
| gmx::HardwareTopology::Device | Information about a single PCI device |
| gmx::HardwareTopology::LogicalProcessor | Information about package, core and processing unit for a logical processor |
| gmx::HardwareTopology::Machine | Hardware topology information about the entire machine |
| gmx::HardwareTopology::Numa | Information about all numa nodes |
| gmx::HardwareTopology::NumaNode | Information about each numa node in system |
| gmx::HardwareTopology::Package | Information about a single package in the system |
| gmx::HardwareTopology::ProcessingUnit | Information about a single processing unit (in a core) |
| gmx::HashedMap< T > | Unordered key to value mapping |
| gmx::HelpLinks | Hyperlink data for writing out help |
| gmx::HelpLinks::Impl | Private implementation class for HelpLinks |
| gmx::HelpManager | Helper for providing interactive online help |
| gmx::HelpManager::Impl | Private implementation class for HelpManager |
| gmx::HelpWriterContext | Context information for writing out help |
| gmx::HelpWriterContext::Impl | Private implementation class for HelpWriterContext |
| gmx::HelpWriterContext::Impl::SharedState | Shared, non-modifiable state for context objects |
| gmx::HistogramSize | Tracks global size related properties of the bias histogram |
| gmx::HostAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers |
| gmx::HostInteractionList | Version of InteractionList that supports pinning |
| gmx::IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
| gmx::AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
| gmx::AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
| gmx::AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| gmx::AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
| gmx::AbstractPlotModule | Abstract data module for writing data into a file |
| gmx::AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
| gmx::AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
| gmx::AnalysisDataAverageModule | Data module for independently averaging each column in input data |
| gmx::AnalysisDataBinAverageModule | Data module for bin averages |
| gmx::AnalysisDataDisplacementModule | Data module for calculating displacements |
| gmx::AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
| gmx::AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
| gmx::analysismodules::anonymous_namespace{select.cpp}::IndexFileWriterModule | Data module for writing index files |
| gmx::internal::BasicAverageHistogramModule | Implements average histogram module that averages per-frame histograms |
| gmx::AnalysisDataProxy | Internal implementation class used to implement column modules |
| gmx::ICheckpointHelperClient | Client that needs to store data during checkpointing |
| gmx::EnergyData::Element | Element for EnergyData |
| gmx::ExpandedEnsembleElement | The expanded ensemble element |
| gmx::FirstOrderPressureCoupling | Element performing first-order pressure coupling |
| gmx::FreeEnergyPerturbationData::Element | The free energy perturbation data element |
| gmx::MttkData | Class holding the extra dof and parameters used by the MTTK algorithm |
| gmx::NoseHooverChainsData | Class holding data used by the Nose-Hoover chains |
| gmx::ParrinelloRahmanBarostat | Element implementing the Parrinello-Rahman barostat |
| gmx::PullElement | Element calling pull functionality |
| gmx::StatePropagatorData::Element | Element for StatePropagatorData |
| gmx::VelocityScalingTemperatureCoupling | Element implementing the a velocity-scaling thermostat |
| gmx::ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
| anonymous_namespace{legacymodules.cpp}::ObsoleteToolModule | Command line module that provides information about obsolescence |
| gmx::anonymous_namespace{cmdlinemodulemanager.cpp}::CMainCommandLineModule | Implements a ICommandLineModule, given a function with C/C++ main() signature |
| gmx::CommandLineHelpModule | Command-line module for producing help |
| gmx::test::MockModule | Mock implementation of gmx::ICommandLineModule |
| gmx::ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
| gmx::test::MockOptionsModule | Mock implementation of gmx::ICommandLineOptionsModule |
| gmx::ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
| gmx::IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
| gmx::IDomDecHelperClient | Client interface of the DomDecHelper class |
| gmx::ForceElement | Force element |
| gmx::FreeEnergyPerturbationData::Element | The free energy perturbation data element |
| gmx::TopologyHolder | Object holding the topology |
| gmx::IEnergySignallerClient | Interface for clients of the EnergySignaller |
| gmx::ComputeGlobalsElement< algorithm > | Encapsulate the calls to compute_globals |
| gmx::ConstraintsElement< variable > | Constraints element |
| gmx::EnergyData::Element | Element for EnergyData |
| gmx::ForceElement | Force element |
| gmx::ParrinelloRahmanBarostat | Element implementing the Parrinello-Rahman barostat |
| gmx::VelocityScalingTemperatureCoupling | Element implementing the a velocity-scaling thermostat |
| gmx::IExecutableEnvironment | Allows customization of the way various directories are found by CommandLineProgramContext |
| gmx::anonymous_namespace{cmdlineprogramcontext.cpp}::DefaultExecutableEnvironment | Default implementation for IExecutableEnvironment |
| gmx::IFileInputRedirector | Allows overriding file existence checks from code that supports it |
| gmx::anonymous_namespace{fileredirector.cpp}::DefaultInputRedirector | Implements the redirector returned by defaultFileInputRedirector() |
| gmx::test::TestFileInputRedirector | In-memory implementation for IFileInputRedirector for tests |
| gmx::IFileOutputRedirector | Allows capturing stdout and file output from code that supports it |
| gmx::anonymous_namespace{fileredirector.cpp}::DefaultOutputRedirector | Implements the redirector returned by defaultFileOutputRedirector() |
| gmx::test::TestFileOutputRedirector | In-memory implementation of IFileOutputRedirector for tests |
| gmx::IForceProvider | Interface for a component that provides forces during MD |
| gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
| gmx::DensityFittingForceProvider | Implements IForceProvider for density-fitting forces |
| gmx::QMMMForceProvider | Implements IForceProvider for QM/MM |
| gmx::RestraintForceProvider | Provide IForceProvider for RestraintMDModuleImpl |
| gmx::IHelpTopic | Provides a single online help topic |
| gmx::AbstractCompositeHelpTopic | Abstract base class for help topics that have simple text and subtopics |
| gmx::CompositeHelpTopic< KeywordsHelpText > | |
| gmx::anonymous_namespace{selhelp.cpp}::KeywordsHelpTopic | Custom help topic for printing a list of selection keywords |
| gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::RootHelpTopic | Help topic that forms the root of the help tree for the help subcommand |
| gmx::CompositeHelpTopic< HelpText > | Template for simple implementation of AbstractCompositeHelpTopic |
| gmx::AbstractSimpleHelpTopic | Abstract base class for help topics that have simple text and no subtopics |
| gmx::anonymous_namespace{selhelp.cpp}::KeywordDetailsHelpTopic | Help topic implementation for an individual selection method |
| gmx::SimpleHelpTopic< HelpText > | Template for simple implementation of AbstractSimpleHelpTopic |
| gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::CommandsHelpTopic | Help topic for listing the commands |
| gmx::anonymous_namespace{cmdlinehelpmodule.cpp}::ModuleHelpTopic | Help topic wrapper for a command-line module |
| gmx::IKeyValueTreeTransformRules | Interface to declare rules for transforming key-value trees |
| gmx::ILastStepSignallerClient | Interface for clients of the LastStepSignaller |
| gmx::CheckpointHelper | Checkpoint helper |
| gmx::LoggingSignaller | Element signalling a logging step |
| gmx::StatePropagatorData::Element | Element for StatePropagatorData |
| gmx::TrajectorySignaller | Element signalling trajectory writing |
| gmx::ILoggingSignallerClient | Interface for clients of the LoggingSignaller |
| gmx::ConstraintsElement< variable > | Constraints element |
| gmx::EnergySignaller | Element signalling energy related special steps |
| gmx::ExpandedEnsembleElement | The expanded ensemble element |
| gmx::TrajectoryElement | Trajectory element signals and handles trajectory writing |
| gmx::ILogTarget | Target where log output can be written |
| gmx::IMDEnergyBlock | IMD (interactive molecular dynamics) energy record |
| gmx::IMDHeader | IMD (interactive molecular dynamics) communication structure |
| gmx::IMDModule | Extension module for GROMACS simulations |
| gmx::anonymous_namespace{densityfitting.cpp}::DensityFitting | Density fitting |
| gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
| gmx::anonymous_namespace{qmmm.cpp}::QMMM | QMMM module |
| gmx::InteractiveMolecularDynamics | Implement interactive molecular dynamics |
| gmx::RestraintMDModule | MDModule wrapper for Restraint implementations |
| gmx::SwapCoordinates | Implement Computational Electrophysiology swapping |
| gmx::ImdOptions | Options for IMD |
| gmx::IMDOutputProvider | Interface for handling additional output files during a simulation |
| gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
| gmx::anonymous_namespace{qmmm.cpp}::QMMMOutputProvider | Handle file output for QMMM simulations. empty implementation as QMMM does not use that |
| gmx::DensityFittingOutputProvider | Handle file output for density guided simulations |
| gmx::IMdpOptionProvider | Interface for handling mdp/tpr input to a mdrun module |
| gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
| gmx::DensityFittingOptions | Input data storage for density fitting |
| gmx::QMMMOptions | Input data storage for QM/MM |
| gmx::ImdSession::Impl | Implementation type for the IMD session |
| gmx::IMDSocket | IMD (interactive molecular dynamics) socket structure |
| gmx::IndexGroupsAndNames | Bundle index groups with their names |
| gmx::INeighborSearchSignallerClient | Interface for clients of the NeighborSearchSignaller |
| gmx::DomDecHelper | Infrastructure element responsible for domain decomposition |
| gmx::ForceElement | Force element |
| gmx::LastStepSignaller | Element signalling the last step |
| gmx::PmeLoadBalanceHelper | Infrastructure element responsible for PME load balancing |
| gmx::InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| gmx::IntegerBox | A 3-orthotope over integer intervals |
| gmx::InteractiveMD | SimulatorBuilder parameter type for InteractiveMD |
| gmx::InterdependentTask | Data structure for thread tasks that use constructing atoms outside their own atom range |
| gmx::internal::AnalysisDataHandleImpl | Private implementation class for AnalysisDataHandle |
| gmx::internal::AnalysisDataStorageFrameData | Internal representation for a single stored frame |
| gmx::internal::AnalysisDataStorageImpl | Private implementation class for AnalysisDataStorage |
| gmx::internal::BasicHistogramImpl | Base class for private implementation classes for histogram modules |
| gmx::AnalysisDataSimpleHistogramModule::Impl | Private implementation class for AnalysisDataSimpleHistogramModule |
| gmx::AnalysisDataWeightedHistogramModule::Impl | Private implementation class for AnalysisDataWeightedHistogramModule |
| gmx::internal::IExceptionInfo | Base class for ExceptionInfo |
| gmx::ExceptionInfo< Tag, T > | Stores additional context information for exceptions |
| gmx::internal::OptionsImpl | Private implementation class for Options |
| gmx::internal::SelectionData | Internal data for a single selection |
| gmx::internal::SimdArrayRef< T > | STL-like container for aligned SIMD type. Used as ArrayRef<SimdReal> |
| gmx::internal::SimdTraits< T > | Simd traits |
| gmx::IonSwapping | Parameter type for IonSwapping SimulatorBuilder component |
| gmx::IOptionManager | Base class for option managers |
| gmx::FileNameOptionManager | Handles interaction of file name options with global options |
| gmx::SelectionOptionManager | Handles interaction of selection options with other options and user input |
| gmx::IOptionsBehavior | Interface to provide extension points for options parsing |
| gmx::SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
| gmx::TimeUnitBehavior | Options behavior to add a time unit option |
| gmx::IOptionsContainer | Interface for adding input options |
| gmx::internal::OptionSectionImpl::Group | Describes a group of options (see Options::addGroup()) |
| gmx::IOptionsContainerWithSections | Interface for adding input options with sections |
| gmx::AbstractOptionSectionHandle | Base class for handles to option sections |
| gmx::OptionSectionHandle | Allows adding options to an OptionSection |
| gmx::RepeatingOptionSectionHandle< T > | Allows adding options to an RepeatingOptionSection |
| gmx::internal::OptionSectionImpl | Internal implementation class for storing an option section |
| gmx::Options | Collection of options |
| gmx::IOptionSectionStorage | Provides behavior specific to a certain option section type |
| gmx::RepeatingOptionSectionStorage< T > | Implements handling of the structures that stores per-section values |
| gmx::IOptionValueStore< T > | Represents the final storage location of option values |
| gmx::OptionValueStoreNull< T > | Value storage that does not store anywhere |
| gmx::IOutputAdapter | OutputAdapter class for handling trajectory file flag setting and processing |
| gmx::OutputSelector | OutputSelector class controls setting which coordinates are actually written |
| gmx::SetAtoms | SetAtoms class controls availability of atoms data |
| gmx::SetBox | Allows changing box information when writing a coordinate file |
| gmx::SetForces | SetForces class allows changing writing of forces to file |
| gmx::SetPrecision | SetPrecision class allows changing file writing precision |
| gmx::SetStartTime | SetStartTime class allows changing trajectory time information |
| gmx::SetTimeStep | SetTimeStep class allows changing trajectory time information |
| gmx::SetVelocities | SetVelocities class allows changing writing of velocities to file |
| gmx::IProgramContext | Provides context information about the program that is calling the library |
| gmx::anonymous_namespace{programcontext.cpp}::DefaultProgramContext | Default implementation of IProgramContext |
| gmx::CommandLineProgramContext | Program context implementation for command line programs |
| gmx::test::anonymous_namespace{testinit.cpp}::TestProgramContext | Custom program context for test binaries |
| gmx::IRestraintPotential | Interface for Restraint potentials |
| gmx::ISerializer | Interface for types that convert standard data types into a form suitable for storage or transfer |
| gmx::FileIOXdrSerializer | Serializer to read/write XDR data |
| gmx::ISignaller | The general Signaller interface |
| gmx::EnergySignaller | Element signalling energy related special steps |
| gmx::LastStepSignaller | Element signalling the last step |
| gmx::LoggingSignaller | Element signalling a logging step |
| gmx::NeighborSearchSignaller | Element signalling a neighbor search step |
| gmx::TrajectorySignaller | Element signalling trajectory writing |
| gmx::ISimulator | The Simulator interface |
| gmx::LegacySimulator | Struct to handle setting up and running the different simulation types |
| gmx::ModularSimulator | The modular simulator |
| gmx::ISimulatorElement | The general interface for elements of the modular simulator |
| gmx::AndersenTemperatureCoupling | Element implementing the Andersen thermostat |
| gmx::CheckpointHelper | Checkpoint helper |
| gmx::CompositeSimulatorElement | Composite simulator element |
| gmx::ComputeGlobalsElement< algorithm > | Encapsulate the calls to compute_globals |
| gmx::ConstraintsElement< variable > | Constraints element |
| gmx::EnergyData::Element | Element for EnergyData |
| gmx::ExpandedEnsembleElement | The expanded ensemble element |
| gmx::FirstOrderPressureCoupling | Element performing first-order pressure coupling |
| gmx::ForceElement | Force element |
| gmx::FreeEnergyPerturbationData::Element | The free energy perturbation data element |
| gmx::MttkBoxScaling | This element scales the box based on the MTTK dof |
| gmx::MttkElement | Element propagating the MTTK degree of freedom |
| gmx::NoseHooverChainsElement | Element propagating the Nose-Hoover chains |
| gmx::ParrinelloRahmanBarostat | Element implementing the Parrinello-Rahman barostat |
| gmx::Propagator< integrationStage > | Propagator element |
| gmx::PullElement | Element calling pull functionality |
| gmx::StatePropagatorData::Element | Element for StatePropagatorData |
| gmx::TrajectoryElement | Trajectory element signals and handles trajectory writing |
| gmx::VelocityScalingTemperatureCoupling | Element implementing the a velocity-scaling thermostat |
| gmx::isIntegralConstant< T, Int > | Is true if type is a std::integral_constant |
| gmx::IsSerializableEnum< T, bool > | Struct allowing to check if enum has a serializable underlying type |
| gmx::IsSerializableType< T > | Struct allowing to check if data is serializable through the KeyValueTree serializer |
| gmx::ITemperatureCouplingImpl | Interface for temperature coupling implementations |
| gmx::BerendsenTemperatureCoupling | Implements Berendsen temperature coupling |
| gmx::NoseHooverTemperatureCoupling | Implements the Nose-Hoover temperature coupling |
| gmx::VRescaleTemperatureCoupling | Implements v-rescale temperature coupling |
| gmx::ITopologyHolderClient | Client requiring read access to the local topology |
| gmx::ForceElement | Force element |
| gmx::ITopologyProvider | Provides topology information to SelectionOptionBehavior |
| gmx::ITrajectorySignallerClient | Interface for signaller clients of the TrajectoryElement |
| gmx::ComputeGlobalsElement< algorithm > | Encapsulate the calls to compute_globals |
| gmx::ConstraintsElement< variable > | Constraints element |
| gmx::EnergyData::Element | Element for EnergyData |
| gmx::EnergySignaller | Element signalling energy related special steps |
| gmx::StatePropagatorData::Element | Element for StatePropagatorData |
| gmx::TrajectoryElement | Trajectory element signals and handles trajectory writing |
| gmx::ITrajectoryWriterClient | Interface for writer clients of the TrajectoryElement |
| gmx::EnergyData::Element | Element for EnergyData |
| gmx::StatePropagatorData::Element | Element for StatePropagatorData |
| gmx::KeyValueTreeBuilder | Root builder for creating trees that have an object at the root |
| gmx::KeyValueTreeObjectArrayBuilder | Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects |
| gmx::KeyValueTreeObjectBuilder | Builder for KeyValueTreeObject objects |
| gmx::KeyValueTreePath | Identifies an entry in a key-value tree |
| gmx::KeyValueTreeTransformRuleBuilder | Provides methods to specify one transformation rule |
| gmx::KeyValueTreeTransformRuleBuilder::Base | Base class used for implementing parameter provider objects |
| gmx::KeyValueTreeTransformRuleBuilder::AfterFrom< FromType > | Properties that can be specified after from() |
| gmx::KeyValueTreeTransformRuleBuilder::ToObject< FromType > | Properties that can be specified after from().toObject() |
| gmx::KeyValueTreeTransformRuleBuilder::ToValue< FromType, ToType > | Properties that can be specified after from().to() |
| gmx::KeyValueTreeTransformRulesScoped | Helper object returned from IKeyValueTreeTransformRules::scopedTransform() |
| gmx::KeyValueTreeUniformArrayBuilder< T > | Builder for KeyValueTreeArray objects where all elements are of type T |
| gmx::KeyValueTreeValueBuilder | Builder for KeyValueTreeValue objects |
| gmx::layout_right | Right-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number |
| gmx::layout_right::mapping< Extents > | Mapping from multidimensional indices within extents to 1D index |
| gmx::LegacyInput | Collection of legacy input information |
| gmx::LegacyMdrunOptions | This class provides the same command-line option functionality to both CLI and API sessions |
| gmx::LegacySimulatorData | The legacy simulator data |
| gmx::LegacySimulator | Struct to handle setting up and running the different simulation types |
| gmx::Lincs | Data for LINCS algorithm |
| gmx::LincsDeviations | Status information about how well LINCS satisified the constraints in this domain |
| gmx::LincsGpu | Class with interfaces and data for GPU version of LINCS |
| gmx::LinkFrontier | Helper 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 |
| gmx::ListedForcesGpu::Impl | Implements GPU bondeds |
| gmx::ListOfLists< typename > | A list of lists, optimized for performance |
| gmx::LocalAtomSet | A 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 |
| gmx::LocalAtomSetManager | Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel |
| gmx::LocalAtomSetManager::Impl | Private implementation class for LocalAtomSetManager |
| gmx::LocalTopologyChecker | Has responsibility for checking that the local topology distributed across domains describes a total number of bonded interactions that matches the system topology |
| gmx::LocalTopologyChecker::Impl | Data to help check local topology construction |
| gmx::LogEntryWriter | Helper class for creating log entries with GMX_LOG |
| gmx::LoggerBuilder | Initializes loggers |
| gmx::LoggerOwner | Manages memory for a logger built with LoggerBuilder |
| gmx::LogLevelHelper | Represents a single logging level |
| gmx::LogWriteHelper | Helper class for implementing GMX_LOG |
| gmx::MappedUnionFinder | Extension of UnionFind that supports non-consecutive integer indices as items |
| gmx::MDAtoms | Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators |
| gmx::MDLogger | Declares a logging interface |
| gmx::MDModules | Manages the collection of all modules used for mdrun |
| gmx::MDModulesCheckpointReadingBroadcast | Provides the MDModules with the communication record to broadcast |
| gmx::MDModulesCheckpointReadingDataOnMaster | Provides the MDModules with the checkpointed data on the master rank |
| gmx::MDModulesEnergyOutputToDensityFittingRequestChecker | Check if module outputs energy to a specific field |
| gmx::MDModulesEnergyOutputToQMMMRequestChecker | Check if QMMM module outputs energy to a specific field |
| gmx::MDModulesNotifier< CallParameter, MDModulesNotifierBase > | Organizes notifications about an event of interest to modules |
| gmx::MDModulesNotifiers | Group of notifers to organize that MDModules can receive callbacks they subscribe to |
| gmx::MDModulesWriteCheckpointData | Writing the MDModules data to a checkpoint file |
| gmx::MdRunInputFilename | Mdrun input filename |
| gmx::Mdrunner | Runner object for supporting setup and execution of mdrun |
| gmx::MdrunnerBuilder | Build a gmx::Mdrunner |
| gmx::MdrunOptions | Collection of all options of mdrun that are not processed separately |
| gmx::MembedHolder | Membed SimulatorBuilder parameter type |
| gmx::MessageStringCollector | Helper class for collecting message strings, optionally with context |
| gmx::MessageStringContext | Convenience class for creating a message context |
| gmx::MimicCommunicator | Class-wrapper around MiMiC communication library It uses GROMACS' unit conversion to switch from GROMACS' units to a.u |
| gmx::ModularSimulatorAlgorithm | The modular simulator |
| gmx::ModularSimulatorAlgorithmBuilder | Builder for ModularSimulatorAlgorithm objects |
| gmx::ModularSimulatorAlgorithmBuilderHelper | Helper for element addition |
| gmx::MrcDataStatistics | Statistics about mrc data arrays |
| gmx::MrcDensityMapHeader | A container for the data in mrc density map file formats |
| gmx::MrcDensityMapOfFloatFromFileReader | Read an mrc density map from a given file |
| gmx::MrcDensityMapOfFloatReader | Read an mrc/ccp4 file that contains float values |
| gmx::MrcDensityMapOfFloatReader::Impl | Private implementation class for MrcDensityMapOfFloatReader |
| gmx::MrcDensityMapOfFloatWriter | Write an mrc/ccp4 file that contains float values |
| gmx::MrcDensityMapOfFloatWriter::Impl | Private implementation class for MrcDensityMapOfFloatWriter |
| gmx::MrcDensitySkewData | Skew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" |
| gmx::MtsLevel | Setting for a single level for multiple time step integration |
| gmx::MttkPropagatorConnection | Object holding the callbacks and scaling views for the connection of MTTKElement objects to propagators |
| gmx::MttkPropagatorConnectionDetails | Struct collecting the propagator tags and offsets used by the MTTK pressure coupling |
| gmx::MultiDimArray< TContainer, Extents, LayoutPolicy > | Multidimensional array that manages its own memory |
| gmx::NelderMeadSimplex | The simplex for the Nelder-Mead algorithm |
| gmx::no_delete< T > | Deleter for std::shared_ptr that does nothing |
| gmx::NonbondedBenchmarkInfo | Declares gmx nonbonded-bench |
| gmx::NormalDistribution< RealType > | Normal distribution |
| gmx::NormalDistribution< RealType >::param_type | Normal distribution parameters |
| gmx::NoseHooverGroup | The current state of the Nose-Hoover chain degree of freedom for a temperature group |
| gmx::NumericalSplineTableInput | Specification for vector table function (name, function, derivative, spacing) |
| gmx::ObservablesReducer | Manage reduction of observables for registered subscribers |
| gmx::ObservablesReducer::Impl | Impl class for ObservablesReducer |
| gmx::ObservablesReducerBuilder | Builder for ObservablesReducer |
| gmx::ObservablesReducerBuilder::Impl | Impl class for ObservablesReducerBuilder |
| gmx::ObservablesReducerBuilder::Impl::Subscription | Data required to set up a subscription |
| gmx::Offset | Strong type used to denote scheduling offsets |
| gmx::OpenClTraits< cl_type > | Stub for OpenCL type traits |
| gmx::OpenClTraitsBase< cl_type > | Implements common trait infrastructure for OpenCL types |
| gmx::OptimisationResult | Compiles results of an a function optimisation |
| gmx::OptionInfo | Gives information and allows modifications to an option after creation |
| gmx::BooleanOptionInfo | Wrapper class for accessing boolean option information |
| gmx::DoubleOptionInfo | Wrapper class for accessing floating-point option information |
| gmx::EnumOptionInfo | Wrapper class for accessing enum option information |
| gmx::FileNameOptionInfo | Wrapper class for accessing file name option information |
| gmx::FloatOptionInfo | Wrapper class for accessing floating-point option information |
| gmx::Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
| gmx::IntegerOptionInfo | Wrapper class for accessing integer option information |
| gmx::SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
| gmx::SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
| gmx::StringOptionInfo | Wrapper class for accessing string option information |
| gmx::OptionManagerContainer | Container to keep managers added with Options::addManager() and pass them to options |
| gmx::OptionsAssigner | Decorator class for assigning values to Options |
| gmx::OptionsAssigner::Impl | Private implementation class for OptionsAssigner |
| gmx::OptionsBehaviorCollection | Container for IOptionsBehavior objects |
| gmx::OptionsIterator | Decorator class for visiting options in a Options object |
| gmx::OptionsModifyingIterator | Decorator class for visiting options in a Options object, allowing changes |
| gmx::OptionsModifyingVisitor | Pure interface for visiting options in a Options object, allowing modifications |
| gmx::OptionsModifyingTypeVisitor< InfoType > | Abstract base class for visiting options of a particular type, allowing modifications |
| gmx::OptionsModifyingTypeVisitor< FloatingPointOptionInfo > | |
| gmx::anonymous_namespace{timeunitmanager.cpp}::TimeOptionScaler< FloatingPointOptionInfo > | Option visitor that scales time options |
| gmx::OptionsVisitor | Pure interface for visiting options in a Options object |
| gmx::anonymous_namespace{cmdlinehelpwriter.cpp}::OptionsFilter | Output format independent processing of options |
| gmx::OptionsTypeVisitor< InfoType > | Abstract base class for visiting options of a particular type |
| gmx::OptionValueConverterSimple< OutType > | Helper for converting from Any to a given type |
| gmx::OuterProductEvaluator | Evaluate the outer product of two number ranges. Keeps the memory for the outer product allocated |
| gmx::OutputAdapterContainer | Storage for output adapters that modify the state of a t_trxframe object |
| gmx::OutputRequirementOptionDirector | Container 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 |
| gmx::OutputRequirements | Finalized version of requirements after processing |
| gmx::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 |
| gmx::PageAlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices |
| gmx::PhysicalNodeCommunicator | Holds a communicator for the physical node of this rank |
| gmx::PmeCoordinateReceiverGpu::Impl | Class with interfaces and data for CUDA version of PME coordinate receiving functionality |
| gmx::PmeForceSenderGpu | Manages sending forces from PME-only ranks to their PP ranks |
| gmx::PmeForceSenderGpu::Impl | Impl class stub |
| gmx::PmePpCommGpu | Manages communication related to GPU buffers between this PME rank and its PP rank |
| gmx::PmePpCommGpu::Impl | Class with interfaces and data for CUDA version of PME-PP Communication |
| gmx::PointState | The state of a coordinate point |
| gmx::PositionCalculationCollection | Collection of gmx_ana_poscalc_t structures for the same topology |
| gmx::PositionCalculationCollection::Impl | Private implementation class for PositionCalculationCollection |
| gmx::PotentialPointData | Structure to hold the results of IRestraintPotential::evaluate() |
| gmx::PpCommManager | Object to manage communications with a specific PP rank |
| gmx::Profiling | Collection of profiling information |
| gmx::PropagatorConnection | Information needed to connect a propagator to a temperature and / or pressure coupling element |
| gmx::PropagatorTag | Strong type used to name propagators |
| gmx::PTCouplingArrays | Arrays connected to Pressure and Temperature coupling |
| gmx::PullCoordExpressionParser | Class with a mathematical expression and parser |
| gmx::QMInputFileName | Notification for QM program input filename provided by user as command-line argument for grompp |
| gmx::QMMMInputGenerator | Class 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 |
| gmx::QMMMModuleInfo | Information about the QM/MM module |
| gmx::QMMMParameters | Holding all parameters needed for QM/MM simulation. Also used for setting all default parameter values |
| gmx::QMMMTopologyInfo | Contains various information about topology modifications Used for statistics during topology pre-processing within QMMMTopologyPreprocessor class |
| gmx::QMMMTopologyPreprocessor | Class 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) |
| gmx::QuadraticSplineTable | Quadratic spline interpolation table |
| gmx::Range< typename > | Defines a range of integer numbers and accompanying operations |
| gmx::Range< typename >::iterator | An iterator that loops over a range of integers |
| gmx::RangePartitioning | Division of a range of indices into consecutive blocks |
| gmx::ReadCheckpointDataHolder | Holder for read checkpoint data |
| gmx::RealFunctionvalueAtCoordinate | Tie together coordinate and function value at this coordinate |
| gmx::ReferenceTemperatureManager | Object managing reference temperature changes |
| gmx::ResetHandler | Class handling the reset of counters |
| gmx::RestraintManager | Manage the Restraint potentials available for Molecular Dynamics |
| gmx::RestraintManager::Impl | Implementation class for restraint manager |
| gmx::RestraintMDModuleImpl | IMDModule implementation for RestraintMDModule |
| gmx::RstParagraphIterator | Iterator over reStructuredText paragraphs |
| gmx::ScalingMatrix | Scaling matrix struct |
| gmx::Selection | Provides access to a single selection |
| gmx::SelectionCollection | Collection of selections |
| gmx::SelectionCollection::Impl | Private implemention class for SelectionCollection |
| gmx::SelectionEvaluator | Implements selection evaluation |
| gmx::SelectionLocation | Stores the location of a selection element in the selection text |
| gmx::SelectionOptionManager::Impl | Private implemention class for SelectionOptionManager |
| gmx::SelectionOptionManager::Impl::RequestsClearer | Helper class that clears a request list on scope exit |
| gmx::SelectionOptionManager::Impl::SelectionRequest | Request for postponed parsing of selections |
| gmx::SelectionParserParameter | Describes a parsed method parameter |
| gmx::SelectionParserSymbol | Single symbol for the selection parser |
| gmx::SelectionParserSymbol::Impl | Private implementation class for SelectionParserSymbol |
| gmx::SelectionParserSymbolIterator | Forward iterator for iterating symbols of a given type |
| gmx::SelectionParserSymbolIterator::Impl | Private implementation class for SelectionParserSymbolIterator |
| gmx::SelectionParserSymbolTable | Symbol table for the selection parser |
| gmx::SelectionParserSymbolTable::Impl | Private implementation class for SelectionParserSymbolTable |
| gmx::SelectionParserValue | Describes a parsed value, possibly resulting from expression evaluation |
| gmx::SelectionPosition | Provides access to information about a single selected position |
| gmx::SelectionTopologyProperties | Describes topology properties required for selection evaluation |
| gmx::SelectionTreeElement | Represents an element of a selection expression |
| gmx::SelMethodEvalContext | Evaluation context for selection methods |
| gmx::SeparatePmeRanksPermitted | Class for managing usage of separate PME-only ranks |
| gmx::SettleData | Data for executing SETTLE constraining |
| gmx::SettleGpu | Class with interfaces and data for GPU version of SETTLE |
| gmx::shakedata | Working data for the SHAKE algorithm |
| gmx::SignallerBuilder< Signaller > | Builder for signallers |
| gmx::Simd4DBool | SIMD4 variable type to use for logical comparisons on doubles |
| gmx::Simd4Double | SIMD4 double type |
| gmx::Simd4FBool | SIMD4 variable type to use for logical comparisons on floats |
| gmx::Simd4Float | SIMD4 float type |
| gmx::SimdDBool | Boolean type for double SIMD data |
| gmx::SimdDIBool | Boolean type for integer datatypes corresponding to double SIMD |
| gmx::SimdDInt32 | Integer SIMD variable type to use for conversions to/from double |
| gmx::SimdDInt32Tag | Tag type to select to load SimdDInt32 with simdLoad(U) |
| gmx::SimdDouble | Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1 |
| gmx::SimdDoubleTag | Tag type to select to load SimdDouble with simdLoad(U) |
| gmx::SimdFBool | Boolean type for float SIMD data |
| gmx::SimdFIBool | Boolean type for integer datatypes corresponding to float SIMD |
| gmx::SimdFInt32 | Integer SIMD variable type to use for conversions to/from float |
| gmx::SimdFInt32Tag | Tag type to select to load SimdFInt32 with simdLoad(U) |
| gmx::SimdFloat | Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1 |
| gmx::SimdFloatTag | Tag type to select to load SimdFloat with simdLoad(U) |
| gmx::SimdSetZeroProxy | Proxy object to enable setZero() for SIMD and real types |
| gmx::SimulationContext | Simulation environment and configuration |
| gmx::SimulationInputHandle | Owning handle to a SimulationInput object |
| gmx::SimulationSignal | POD-style object used by mdrun ranks to set and receive signals within and between simulations |
| gmx::SimulationSignaller | Object used by mdrun ranks to signal to each other at this step |
| gmx::SimulationTimeStep | Provides the simulation time step in ps |
| gmx::SimulationWorkload | Manage what computation is required during the simulation |
| gmx::SimulatorBuilder | Class preparing the creation of Simulator objects |
| gmx::SimulatorConfig | Simulation configuation settings |
| gmx::SimulatorEnv | Collection of environmental information for a simulation |
| gmx::SimulatorStateData | Data for a specific simulation state |
| gmx::Site | Abstraction for a restraint interaction site |
| gmx::StatePropagatorData | StatePropagatorData and associated data |
| gmx::StatePropagatorData::ReferenceTemperatureHelper | Helper object to scale velocities according to reference temperature change |
| gmx::StaticLog2< n > | Evaluate log2(n) for integer n statically at compile time |
| gmx::StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
| gmx::StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
| gmx::StepWorkload | Describes work done on this domain by the current rank that may change per-step |
| gmx::StopConditionSignal | Class setting the stop signal based on gmx_get_stop_condition() |
| gmx::StopConditionTime | Class setting the stop signal based on maximal run time |
| gmx::StopHandler | Class handling the stop signal |
| gmx::StopHandlerBuilder | Class preparing the creation of a StopHandler |
| gmx::StringCompare | Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare |
| gmx::StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
| gmx::StringToEnumValueConverter< EnumType,, stringCompareType, stripStrings > | A class to convert a string to an enum value of type EnumType |
| gmx::SurfaceAreaCalculator | Computes surface areas for a group of atoms/spheres |
| gmx::TabulatedNormalDistribution< RealType, tableBits > | Tabulated normal random distribution |
| gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type | Normal distribution parameter class (mean and stddev) |
| gmx::Task | Unit of work within LINCS |
| gmx::TemperatureCouplingData | Data used by the concrete temperature coupling implementations |
| gmx::test::AllocatorTest< T > | Templated test fixture |
| gmx::test::AllowAnyRankCount | Helper for GMX_MPI_TEST to permit any rank count |
| gmx::test::AnalysisDataTestFixture | Test fixture for AbstractAnalysisData testing |
| gmx::test::AnalysisDataTestInput | Represents static input data for AbstractAnalysisData tests |
| gmx::test::AnalysisDataTestInputFrame | Represents a single frame in AnalysisDataTestInput structure |
| gmx::test::AnalysisDataTestInputPointSet | Represents a single set of points in AnalysisDataTestInputFrame structure |
| gmx::test::anonymous_namespace{bonded.cpp}::iListInput | Input structure for listed forces tests |
| gmx::test::anonymous_namespace{bonded.cpp}::OutputQuantities | Output from bonded kernels |
| gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest | CheckpointData test fixture |
| gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType< T > | Struct allowing to check if type is vector of serializable data |
| gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues | Unified looping over test data |
| gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator< T > | Helper class allowing to loop over test values |
| gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator< T >::Iterator | Custom iterator |
| gmx::test::anonymous_namespace{com.cpp}::COMInPlaceTest | Test fixture for checking correct molecule COM treatment |
| gmx::test::anonymous_namespace{constr.cpp}::ConstraintsTest | Test fixture for constraints |
| gmx::test::anonymous_namespace{device_stream_manager.cpp}::DeviceStreamManagerTest | Test fixture |
| gmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTest | Test fixture to test energy output |
| gmx::test::anonymous_namespace{energyoutput.cpp}::EnergyOutputTestParameters | Test parameters space |
| gmx::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 |
| gmx::test::anonymous_namespace{expanded.cpp}::CalculateAcceptanceWeightSimple | Test fixture accepting a value to pass into calculateAcceptanceWeight |
| gmx::test::anonymous_namespace{extract_cluster.cpp}::ManualOutputFile | Helper struct to combine filename, path and FileMatcher |
| gmx::test::anonymous_namespace{freeenergyparameters.cpp}::FreeEnergyParameterTest | Test for setting free energy parameters |
| gmx::test::anonymous_namespace{freeenergyparameters.cpp}::FreeEnergyParameterTestParameters | Parameters that will vary from test to test |
| gmx::test::anonymous_namespace{leapfrog.cpp}::LeapFrogTest | Test fixture for LeapFrog integrator |
| gmx::test::anonymous_namespace{leapfrog.cpp}::LeapFrogTestParameters | The parameters for the test |
| gmx::test::anonymous_namespace{mock_datamodule.cpp}::DataStorageRequester | Functor for requesting data storage |
| gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataFrameHeaderChecker | Functor for checking data frame header against static test input data |
| gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsChecker | Functor for checking data frame points against static test input data |
| gmx::test::anonymous_namespace{mock_datamodule.cpp}::StaticDataPointsStorageChecker | Functor for checking data frame points and storage against static test input data |
| gmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTest | Mocking test with data collected from a few systems |
| gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData | Utility structure to hold atoms data |
| gmx::test::anonymous_namespace{nb_free_energy.cpp}::ListInput | Input structure for nonbonded fep kernel |
| gmx::test::anonymous_namespace{nb_free_energy.cpp}::OutputQuantities | Output from nonbonded fep kernel |
| gmx::test::anonymous_namespace{observablesreducer.cpp}::ObservablesReducerIntegrationTest | Test fixture class |
| gmx::test::anonymous_namespace{observablesreducer.cpp}::ObservablesReducerIntegrationTest::RankData | Helper struct to model data on a single MPI rank |
| gmx::test::anonymous_namespace{observablesreducer.cpp}::Subscriber | Helper class that models an MD module that needs to make a subscription to ObservablesReducer |
| gmx::test::anonymous_namespace{pairs.cpp}::ListInput | Input structure for listed forces tests |
| gmx::test::anonymous_namespace{pairs.cpp}::OutputQuantities | Output from pairs kernels |
| gmx::test::anonymous_namespace{pmebsplinetest.cpp}::PmeBSplineModuliTest | Test fixture for testing PME B-spline moduli creation |
| gmx::test::anonymous_namespace{pmegathertest.cpp}::GatherTest | Test fixture |
| gmx::test::anonymous_namespace{pmegathertest.cpp}::GatherTestBody | Test case whose body checks that gather works |
| gmx::test::anonymous_namespace{pmegathertest.cpp}::SplineData | A structure for all the spline data which depends in size both on the PME order and atom count |
| gmx::test::anonymous_namespace{pmegathertest.cpp}::TestSystem | A structure for the input atom data, which depends in size on atom count |
| gmx::test::anonymous_namespace{pmesolvetest.cpp}::SolveTest | Test fixture |
| gmx::test::anonymous_namespace{pmesolvetest.cpp}::SolveTestBody | Test case whose body checks that spline and spread work |
| gmx::test::anonymous_namespace{pmesplinespreadtest.cpp}::SplineAndSpreadTest | Test fixture for testing both atom spline parameter computation and charge spreading. These 2 stages of PME are tightly coupled in the code |
| gmx::test::anonymous_namespace{pmesplinespreadtest.cpp}::SplineAndSpreadTestBody | Test case whose body checks that spline and spread work |
| gmx::test::anonymous_namespace{settle.cpp}::SettleTest | Test fixture for testing SETTLE |
| gmx::test::anonymous_namespace{settle.cpp}::SettleTestParameters | Parameters that will vary from test to test |
| gmx::test::anonymous_namespace{splinetable.cpp}::SplineTableTest< T > | Test fixture for table comparision with analytical/numerical functions |
| gmx::test::anonymous_namespace{testinit.cpp}::SuccessListener | Makes GoogleTest non-failures more verbose |
| gmx::test::anonymous_namespace{testoptions.cpp}::TestOptionsRegistry | Singleton registry for test options added with GMX_TEST_OPTIONS |
| gmx::test::anonymous_namespace{textreader.cpp}::TextReaderTest | Test fixture |
| gmx::test::anonymous_namespace{textreader.cpp}::TextReaderTestParams | Helper struct |
| gmx::test::anonymous_namespace{threadaffinity_mpi.cpp}::RequireEvenRankCountWithAtLeastFourRanks | Helper to establish test requirements on MPI ranks |
| gmx::test::anonymous_namespace{timing.cpp}::TimingTest | Test Fixture for timing tests |
| gmx::test::anonymous_namespace{virtualsites.cpp}::VirtualSiteTest::VirtualSite | Holds parameters of virtual site and allows calculation |
| gmx::test::AwhTestParameters | Struct that gathers all input for setting up and using a Bias |
| gmx::test::BiasFepLambdaStateTest | Test fixture for testing Bias updates |
| gmx::test::BiasStateTest | Test fixture for testing Bias updates |
| gmx::test::BiasTest | Test fixture for testing Bias updates |
| gmx::test::CommandLine | Helper class for tests that need to construct command lines |
| gmx::test::CommandLineTestBase | Test fixture for tests that call a single command-line program with input/output files |
| gmx::test::AbstractTrajectoryAnalysisModuleTestFixture | Test fixture for trajectory analysis modules |
| gmx::test::anonymous_namespace{extract_cluster.cpp}::ExtractClusterModuleTest | Test fixture for the convert-trj analysis module |
| gmx::test::TrajectoryAnalysisModuleTestFixture< ModuleInfo > | Test fixture for a trajectory analysis module |
| gmx::test::TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::MsdInfo > | |
| gmx::test::FlagTest | Test fixture to test user inputs |
| gmx::test::ModuleTest | Test fixture to test matching file types for modules |
| gmx::test::AnyOutputSupportedFiles | Helper to test supported file names |
| gmx::test::NoOptionalOutput | Helper to test support for disabling all output options |
| gmx::test::OutputSelectorDeathTest | Helper to test that invalid selection is rejected |
| gmx::test::SetAtomsSupportedFiles | Helper to test supported file names |
| gmx::test::SetAtomsUnSupportedFiles | Helper to test supported file names |
| gmx::test::SetForceSupportedFiles | Helper to test supported file names |
| gmx::test::SetForceUnSupportedFiles | Helper to test supported file names |
| gmx::test::SetPrecisionSupportedFiles | Helper to test supported file names |
| gmx::test::SetPrecisionUnSupportedFiles | Helper to test supported file names |
| gmx::test::SetVelocitySupportedFiles | Helper to test supported file names |
| gmx::test::SetVelocityUnSupportedFiles | Helper to test supported file names |
| gmx::test::TrajectoryFrameWriterTest | Test fixture to test different file types are supported by the CoordinateFile |
| gmx::test::SetAtomsTest | Test fixture to prepare a setatoms object to pass data through |
| gmx::test::SetBothTimeTest | Test fixture to prepare a setatoms object to pass data through |
| gmx::test::SetStartTimeTest | Test fixture to prepare a setatoms object to pass data through |
| gmx::test::SetTimeStepTest | Test fixture to prepare a setatoms object to pass data through |
| gmx::test::CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
| gmx::test::EnergyComparison | Function object to compare all energy terms of reference with all matching terms from test within the given tolerances |
| gmx::test::EnergyFrameReader | Manages returning an EnergyFrame containing required energy term values read from successive frames of an .edr file |
| gmx::test::FloatingPointDifference | Computes and represents a floating-point difference value |
| gmx::test::FloatingPointTolerance | Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance |
| gmx::test::FloatTypeMatcher< FloatType > | Implementation class for RealEq matcher |
| gmx::test::FramePairManager< FrameReader > | Manages returning a pair of frames from two equivalent simulations that are meaningful to compare |
| gmx::test::HostAllocatorTestNoMem< T > | Typed test fixture (no mem/gpu initializtion - much faster) |
| gmx::test::HostAllocatorTestNoMemCopyable< T > | Typed test fixture for tests requiring a copyable type |
| gmx::test::HostMemoryTest< T > | Typed test fixture for infrastructure for host-side memory used for GPU transfers |
| gmx::test::HostAllocatorTest< T > | Typed test fixture |
| gmx::test::IFileMatcher | Represents a file matcher, matching file contents against reference (or other) data |
| gmx::test::IFileMatcherSettings | Represents a factory for creating a file matcher |
| gmx::test::NoContentsMatch | Do not check the contents of the file |
| gmx::test::TextFileMatch | Use a ITextBlockMatcher for matching the contents |
| gmx::test::InteractiveTestHelper | Helper class for testing interactive sessions |
| gmx::test::internal::TestReferenceDataImpl | Private implementation class for TestReferenceData |
| gmx::test::ITextBlockMatcher | Represents a text matcher, matching text stream contents against reference data |
| gmx::test::anonymous_namespace{msd.cpp}::MsdMatcher | MsdMatcher is effectively an extension of XvgMatcher for gmx msd results |
| gmx::test::ITextBlockMatcherSettings | Represents a factory for creating a text matcher |
| gmx::test::ConfMatch | Match the contents as an gro file |
| gmx::test::ExactTextMatch | Use an exact text match (the contents should be exactly equal) |
| gmx::test::FilteringExactTextMatch | Use an exact text match after scrubbing lines of the text that match the supplied regular expressions |
| gmx::test::NoTextMatch | Do not match the text (the contents are ignored) |
| gmx::test::XvgMatch | Match the contents as an xvg file |
| gmx::test::LoggerTestHelper | Helper class for tests to check output written to a logger |
| gmx::test::MaxNumFrames | Named struct indicating the max number of frames to be compared |
| gmx::test::MdrunTestFixtureBase | Declares test fixture base class for integration tests of mdrun functionality |
| gmx::test::MdrunTestFixture | Declares test fixture class for integration tests of mdrun functionality that use a single call of mdrun |
| anonymous_namespace{compressed_x_output.cpp}::MdrunCompressedXOutputTest | Test fixture for mdrun -x |
| anonymous_namespace{domain_decomposition.cpp}::DomainDecompositionSpecialCasesTest | Test fixture for domain decomposition special cases |
| anonymous_namespace{grompp.cpp}::GromppTest | Test fixture for grompp |
| gmx::test::anonymous_namespace{ewaldsurfaceterm.cpp}::EwaldSurfaceTermTest | Test fixture base for simple mdrun systems |
| gmx::test::anonymous_namespace{exactcontinuation.cpp}::MdrunNoAppendContinuationIsExact | Test fixture for mdrun exact continuations |
| gmx::test::anonymous_namespace{initialconstraints.cpp}::InitialConstraintsTest | Test fixture parametrized on integrators |
| gmx::test::anonymous_namespace{minimize.cpp}::EnergyMinimizationTest | Test fixture base for energy minimizaiton |
| gmx::test::anonymous_namespace{normalmodes.cpp}::NormalModesTest | Test fixture base for normal mode analysis |
| gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest | Test fixture for end-to-end execution of PME |
| gmx::test::anonymous_namespace{pull.cpp}::PullIntegrationTest | Test fixture base for simple mdrun systems |
| gmx::test::anonymous_namespace{rerun.cpp}::MdrunRerunTest | Test fixture base for mdrun -rerun |
| gmx::test::anonymous_namespace{simple_mdrun.cpp}::SimpleMdrunTest | Test fixture base for simple mdrun systems |
| gmx::test::anonymous_namespace{tpitest.cpp}::TpiTest | A basic TPI runner. The only input parameter used currently: input system random seed (ld-seed) |
| gmx::test::BondedInteractionsTest | Test fixture for bonded interactions |
| gmx::test::DensityFittingTest | End to end test for the density fitting functionality in mdrun |
| gmx::test::MimicTest | Test fixture for bonded interactions |
| gmx::test::ParameterizedMdrunTestFixture | Parameterized test fixture for mdrun integration tests |
| gmx::test::PeriodicActionsTest | Test fixture base for comparing a simulator with one that does everything every step |
| gmx::test::MultiSimTest | Test fixture for multi-sim functionality |
| gmx::test::MockAnalysisDataModule::Impl | Private implementation class for gmx::test::MockAnalysisDataModule |
| gmx::test::ModuleSelection | Helper class for tests that need an initialized selection |
| gmx::test::AnyOutputSupportedFiles | Helper to test supported file names |
| gmx::test::OutputSelectorDeathTest | Helper to test that invalid selection is rejected |
| gmx::test::NumRanksPerSimulation | Test flag setting the number of ranks per simulation |
| gmx::test::PaddedVectorTest< T > | Typed test fixture |
| gmx::test::PrintReplicaExchangeParametersToString | Helper struct printing custom test name |
| gmx::test::ReferenceFileNames | Helper type of output file names for the reference mdrun call |
| gmx::test::RequireMinimumRankCount< minimumNumRanks > | Helper for GMX_MPI_TEST to permit only a specific rank count |
| gmx::test::RequireRankCount< requiredNumRanks > | Helper for GMX_MPI_TEST to permit only a specific rank count |
| gmx::test::RVecMatcher< FloatType > | Implementation class for RvecEq matcher |
| gmx::test::SignalTest | Test fixture for mdrun signalling |
| gmx::test::SimdBaseTest | Base class for SIMD test fixtures |
| gmx::test::Simd4Test | Test fixture for SIMD4 tests - contains test settings |
| gmx::test::SimdTest | Test fixture for SIMD tests |
| gmx::test::anonymous_namespace{simd_floatingpoint_util.cpp}::SimdFloatingpointUtilTest | Test fixture for higher-level floating-point utility functions |
| gmx::test::SimdMathTest::CompareSettings | Settings used for simd math function comparisons |
| gmx::test::SimulationRunner | Helper object for running grompp and mdrun in integration tests of mdrun functionality |
| gmx::test::StdioTestHelper | Helper class for tests where code reads directly from stdin |
| gmx::test::StringTestBase | Test fixture for tests that check string formatting |
| gmx::test::CommandLineModuleManagerTestBase | Test fixture for tests using gmx::CommandLineModuleManager |
| gmx::test::TerminationHelper | Help test mdrun termination behaviour |
| gmx::test::TestDevice | A structure to describe a hardware context that persists over the lifetime of the test binary |
| gmx::test::TestFileManager | Helper for tests that need input and output files |
| gmx::test::TestFileManager::Impl | Private implementation class for TestFileManager |
| gmx::test::TestHardwareEnvironment | This class performs one-time test initialization, enumerating the hardware |
| gmx::test::TestOptionsProvider | Provides additional options for the test executable |
| gmx::test::TestReferenceChecker | Handles comparison to test reference data |
| gmx::test::TestReferenceChecker::Impl | Private implementation class for TestReferenceChecker |
| gmx::test::TestReferenceData | Handles creation of and comparison to test reference data |
| gmx::test::TopologyManager | Helps create and manage the lifetime of topology and related data structures |
| gmx::test::TprAndFileManager | Helper to bundle generated TPR and the file manager to clean it up |
| gmx::test::TrajectoryComparison | Function object to compare the fields of two frames vs each others or one frame vs reference data for equality given the matchSettings_ and tolerances_ |
| gmx::test::TrajectoryFrameMatchSettings | Helper struct to specify the expected behaviour of compareFrames() |
| gmx::test::TrajectoryFrameReader | Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file |
| gmx::test::TrajectoryTolerances | Helper struct for testing different trajectory components with different tolerances |
| gmx::TextInputStream | Interface for reading text |
| gmx::StandardInputStream | Text input stream implementation for reading from stdin |
| gmx::StringInputStream | Helper class to convert static string data to a stream |
| gmx::TextInputFile | Text input stream implementation for reading from a file |
| gmx::TextLineWrapper | Wraps lines to a predefined length |
| gmx::TextLineWrapperSettings | Stores settings for line wrapping |
| gmx::TextOutputStream | Interface for writing text |
| gmx::StringOutputStream | Text output stream implementation for writing to an in-memory string |
| gmx::TextOutputFile | Text output stream implementation for writing to a file |
| gmx::TextReader | Reads text from a TextInputStream |
| gmx::TextReader::Impl | Implementation class |
| gmx::TextTableFormatter | Formats rows of a table for text output |
| gmx::TextTableFormatter::Impl | Private implementation class for TextTableFormatter |
| gmx::TextTableFormatter::Impl::ColumnData | Manages a single column for TextTableFormatter |
| gmx::TextWriter | Writes text into a TextOutputStream |
| gmx::ThreadedForceBuffer< ForceBufferElementType > | Class for accumulating and reducing forces and energies on threads in parallel |
| gmx::ThreadForceBuffer< ForceBufferElementType > | Object that holds force and energies buffers plus a mask for a thread |
| gmx::ThreadingInfo | Information on how the virtual site work is divided over thread tasks |
| gmx::ThreeFry2x64General< rounds, internalCounterBits > | General implementation class for ThreeFry counter-based random engines |
| gmx::ThrowLocation | Stores the location from which an exception was thrown |
| gmx::TimeStep | Strong type used to denote propagation time steps |
| gmx::TimeUnitManager | Provides common functionality for time unit conversions |
| gmx::TimingOptions | Options for timing (parts of) mdrun |
| gmx::TopologyData | Collection of handles to topology information |
| gmx::TopologyHolder::Builder | Builder for the topology holder |
| gmx::TopologyInformation | Topology information available to a trajectory analysis module |
| gmx::TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
| gmx::TrajectoryAnalysisModule | Base class for trajectory analysis modules |
| AnalysisTemplate | Template class to serve as a basis for user analysis tools |
| gmx::analysismodules::anonymous_namespace{freevolume.cpp}::FreeVolume | Class used to compute free volume in a simulations box |
| gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistance | Implements gmx pairdist trajectory analysis module |
| gmx::analysismodules::anonymous_namespace{rdf.cpp}::Rdf | Implements gmx rdf trajectory analysis module |
| gmx::analysismodules::anonymous_namespace{sasa.cpp}::Sasa | Implements gmx sas trajectory analysis module |
| gmx::analysismodules::Msd | Implements the gmx msd module |
| gmx::TrajectoryAnalysisModule::Impl | Private implementation class for TrajectoryAnalysisModule |
| gmx::TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
| gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData | Temporary memory for use within a single-frame calculation |
| gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData | Temporary memory for use within a single-frame calculation |
| gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData | Temporary memory for use within a single-frame calculation |
| gmx::anonymous_namespace{analysismodule.cpp}::TrajectoryAnalysisModuleDataBasic | Basic thread-local trajectory analysis data storage class |
| gmx::TrajectoryAnalysisModuleData::Impl | Private implementation class for TrajectoryAnalysisModuleData |
| gmx::TrajectoryAnalysisRunnerCommon | Implements common trajectory analysis runner functionality |
| gmx::TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
| gmx::TrajectoryAnalysisSettings::Impl | Private implementation class for TrajectoryAnalysisSettings |
| gmx::TrajectoryElementBuilder | Build the TrajectoryElement |
| gmx::TrajectoryFileOpener | Low level method to take care of only file opening and closing |
| gmx::TrajectoryFrame | Contains a valid trajectory frame |
| gmx::TrajectoryFrameWriter | Writes coordinate frames to a sink, e.g. a trajectory file |
| gmx::TranslateAndScale | Transform coordinates in three dimensions by first translating, then scaling them |
| gmx::UniformIntDistribution< IntType > | Uniform integer distribution |
| gmx::UniformIntDistribution< IntType >::param_type | Uniform int distribution parameters |
| gmx::UniformRealDistribution< RealType > | Uniform real distribution |
| gmx::UniformRealDistribution< RealType >::param_type | Uniform real distribution parameters |
| gmx::UnionFinder | Union-find data structure for keeping track of disjoint sets |
| gmx::Update | Contains data for update phase |
| gmx::UpdateConstrainGpu::Impl | Class with interfaces and data for GPU version of Update-Constraint |
| gmx::UpdateGroups | Owns the update grouping and related data |
| gmx::UpdateGroupsCog | Class for managing and computing centers of geometry of update groups |
| gmx::VirtualSitesHandler | Class that handles construction of vsites and spreading of vsite forces |
| gmx::VirtualSitesHandler::Impl | Impl class for VirtualSitesHandler |
| gmx::VsiteThread | Vsite thread task data structure |
| gmx::WaterMolecule | Indices of atoms in a water molecule |
| gmx::WholeMoleculeTransform | This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules |
| gmx::WriteCheckpointDataHolder | Holder for write checkpoint data |
| gmx_ana_index_t | Stores a single index group |
| gmx_ana_indexgrps_t | Stores a set of index groups |
| gmx_ana_indexmap_t | Data structure for calculating index group mappings |
| gmx_ana_pos_t | Stores a set of positions together with their origins |
| gmx_ana_poscalc_t | Data structure for position calculation |
| gmx_ana_selcollection_t | Information for a collection of selections |
| gmx_ana_selmethod_help_t | Help information for a selection method |
| gmx_ana_selmethod_t | Describes a selection method |
| gmx_ana_selparam_t | Describes a single parameter for a selection method |
| gmx_ana_selvalue_t | Describes a value of a selection expression or of a selection method parameter |
| gmx_cache_protect_t | Cache-line protection buffer |
| gmx_device_runtime_data_t | OpenCL GPU runtime data |
| gmx_domdec_constraints_t | Struct used during constraint setup with domain decomposition |
| gmx_domdec_specat_comm_t | Struct with setup and buffers for special atom communication |
| gmx_enerdata_t | Struct for accumulating all potential energy terms and some kinetic energy terms |
| gmx_enfrot | Enforced rotation data for all groups |
| gmx_enfrotgrp | Enforced rotation data for a single rotation group |
| gmx_ffparams_t | Struct that holds all force field parameters for the simulated system |
| gmx_fft_fftpack | Contents of the FFTPACK fft datatype |
| gmx_fft_fftw3 | Contents of the FFTW3 fft datatype |
| gmx_fft_mkl | Contents of the Intel MKL FFT fft datatype |
| gmx_ga2la_t | Global to local atom mapping |
| gmx_ga2la_t::Entry | Structure for the local atom info |
| gmx_help_make_index_group | Data necessary to construct a single (protein) index group in analyse_prot() |
| gmx_hw_opt_t | Threading and GPU options, can be set automatically or by the user |
| gmx_kernel_timing_data_t | GPU kernel time and call count |
| gmx_localtop_t | The fully written out topology for a domain over its lifetime |
| gmx_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
| gmx_moltype_t | Molecules type data: atoms, interactions and exclusions |
| gmx_multisim_t | Coordinate multi-simulation resources for mdrun |
| gmx_pme_comm_n_box_t | Helper struct for PP-PME communication of parameters |
| gmx_pme_comm_vir_ene_t | Helper struct for PP-PME communication of virial and energy |
| gmx_pme_pp | Master PP-PME communication data structure |
| gmx_potfit | Helper structure for potential fitting |
| gmx_repl_ex | Working data for replica exchange |
| gmx_reverse_top_t | Reverse topology class |
| gmx_reverse_top_t::Impl | Struct for the reverse topology: links bonded interactions to atoms |
| gmx_sel_evaluate_t | Data structure for passing information required during evaluation |
| gmx_sel_lexer_t | Internal data structure for the selection tokenizer state |
| gmx_sel_mempool_block_t | Describes a single block allocated from the memory pool |
| gmx_sel_mempool_t | Describes a memory pool |
| gmx_slabdata | Enforced rotation / flexible: determine the angle of each slab |
| gmx_sparsematrix | Sparse matrix storage format |
| gmx_specatsend_t | The communication setup along a single dimension |
| gmx_tng_trajectory | Gromacs Wrapper around tng datatype |
| gmx_wallclock_gpu_nbnxn_t | GPU NB timings for kernels and H2d/D2H transfers |
| gmx_wallclock_gpu_pme_t | GPU timings for PME |
| gmx_walltime_accounting | Manages caching wall-clock time measurements for simulations |
| GpuEventSynchronizer | A class which allows for CPU thread to mark and wait for certain GPU stream execution point |
| GpuRegionTimerImpl | The 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 |
| GpuRegionTimerWrapper< 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 |
| gmx::HashedMap< gmx_ga2la_t::Entry > | |
| gmx::HashedMap< int > | |
| history_t | History information for NMR distance and orientation restraints |
| ilist_data_t | Struct for passing all data required for a function type |
| IListIterator | Object that allows looping over all atoms in an mtop |
| IListProxy | Proxy object returned from IListIterator |
| IListRange | Range over all interaction lists of topology |
| InteractionListHandle | Type for returning a list of InteractionList references |
| InteractionOfType | Describes an interaction of a given type, plus its parameters |
| InteractionsOfType | A set of interactions of a given type (found in the enumeration in ifunc.h), complete with atom indices and force field function parameters |
| gmx::IOptionValueStore< bool > | |
| gmx::IOptionValueStore< int > | |
| gmx::internal::EnumIndexStore< EnumType > | Type-specific implementation for IOptionValueStore for an enum option |
| KernelLaunchConfig | GPU 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 |
| LeapFrogKernel< numTempScaleValues, velocityScaling > | Class name for leap-frog kernel |
| ListedForces | Class for calculating listed interactions, uses OpenMP parallelization |
| gmx::ListOfLists< int > | |
| MD5Checksum | Helper struct for returning the MD5 checksum and the amount of the file that contributed to it |
| methoddata_insolidangle | Data structure for the insolidangle selection method |
| methoddata_merge | Data structure for the merging selection modifiers |
| methoddata_permute | Data structure for the permute selection modifier |
| MolecularTopologyAtomIndices | Molecular topology indices of a global molecule a global atom belongs to |
| MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
| MoleculeInformation | Holds the molecule information during preprocessing |
| MoleculePatch | Block to modify individual residues |
| MoleculePatchDatabase | A set of modifications to apply to atoms |
| MoleculeType | Describes a molecule type, and keeps track of the number of these molecules |
| gmx::MultiDimArray< dynamic_container_type, dynamic_extents_type > | |
| gmx::MultiDimArray< real > | |
| gmx::MultiDimArray< static_container_type, static_extents_type > | |
| gmx::MultiDimArray< std::vector< float >, gmx::extents > | |
| gmx::MultiDimArray< std::vector< float >, gmx::extents< dynamic_extent, dynamic_extent > > | |
| gmx::MultiDimArray< t_matelmt > | |
| NBAtomDataGpu | Nonbonded atom data - both inputs and outputs |
| Nbnxm::BoundingBox | Bounding box for a nbnxm atom cluster |
| Nbnxm::BoundingBox1D | Bounding box for one dimension of a grid cell |
| Nbnxm::BoundingBox::Corner | Corner for the bounding box, padded with one element to enable 4-wide SIMD operations |
| Nbnxm::EnergyFunctionProperties< elecType, vdwType > | Set of boolean constants mimicking preprocessor macros |
| Nbnxm::gpu_plist | GPU pair list structure |
| Nbnxm::GpuTimers | GPU region timers used for timing GPU kernels and H2D/D2H transfers |
| Nbnxm::GpuTimers::Interaction | Timers for local or non-local interaction related operations |
| Nbnxm::GpuTimers::XFTransfers | Timers for local or non-local coordinate/force transfers |
| Nbnxm::Grid | A pair-search grid object for one domain decomposition zone |
| Nbnxm::Grid::Dimensions | The physical dimensions of a grid |
| Nbnxm::Grid::Geometry | The cluster and cell geometry of a grid |
| Nbnxm::GridSet | Holds a set of search grids for the local + non-local DD zones |
| Nbnxm::GridSet::DomainSetup | Description of the domain setup: PBC and the connections between domains |
| Nbnxm::GridSetData | Struct that holds grid data that is shared over all grids |
| Nbnxm::GridWork | Working arrays for constructing a grid |
| Nbnxm::KernelBenchOptions | The options for the kernel benchmarks |
| NbnxmGpu | Main data structure for CUDA nonbonded force calculations |
| NbnxmKernel< doPruneNBL, doCalcEnergies, elecType, vdwType > | Class name for NBNXM kernel |
| NbnxmKernelPruneOnly< haveFreshList > | Class name for NBNXM prune-only kernel |
| nbnxn_atomdata_output_t | Struct that holds force and energy output buffers |
| nbnxn_atomdata_t | Struct that stores atom related data for the nbnxn module |
| nbnxn_atomdata_t::Params | The actual atom data parameter values |
| nbnxn_atomdata_t::SimdMasks | Diagonal and topology exclusion helper data for all SIMD kernels |
| nbnxn_ci_t | Simple pair-list i-unit |
| nbnxn_cj4_t | Four-way j-cluster lists |
| nbnxn_cj_t | This is the actual cluster-pair list j-entry |
| nbnxn_cycle_t | Local cycle count struct for profiling |
| nbnxn_excl_t | Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist |
| nbnxn_im_ei_t | Interaction data for a j-group for one warp |
| nbnxn_sci | Grouped pair-list i-unit |
| NbnxnPairlistCpu | Cluster pairlist type for use on CPUs |
| NbnxnPairlistCpuWork | Working data for the actual i-supercell during pair search |
| NbnxnPairlistCpuWork::IClusterData | Struct for storing coordinates and bounding box for an i-entry during search |
| NBParamGpu | Parameters required for the GPU nonbonded calculations |
| NBStagingData | Staging area for temporary data downloaded from the GPU |
| nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
| gmx::compat::not_null< gmx::ISimulatorElement * > | |
| gmx::compat::not_null< gmx::LegacySimulatorData * > | |
| NumPmeDomains | Struct for passing around the number of PME domains |
| ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
| omp_module_nthreads_t | Structure with the number of threads for each OpenMP multi-threaded algorithmic module in mdrun |
| gmx::OpenClTraitsBase< cl_command_queue > | |
| gmx::OpenClTraits< cl_command_queue > | Implements traits for cl_command_queue |
| gmx::OpenClTraitsBase< cl_context > | |
| gmx::OpenClTraits< cl_context > | Implements traits for cl_context |
| gmx::OpenClTraitsBase< cl_kernel > | |
| gmx::OpenClTraits< cl_kernel > | Implements traits for cl_kernel |
| gmx::OpenClTraitsBase< cl_program > | |
| gmx::OpenClTraits< cl_program > | Implements traits for cl_program |
| gmx::OptionValueConverterSimple< bool > | |
| gmx::OptionValueConverterSimple< double > | |
| gmx::OptionValueConverterSimple< float > | |
| gmx::OptionValueConverterSimple< int > | |
| gmx::OptionValueConverterSimple< int64_t > | |
| gmx::OptionValueConverterSimple< std::string > | |
| gmx::OptionValueConverterSimple< T > | |
| OutputFile | All meta-data that is shared for one output file type for one bias |
| gmx::PaddedVector< gmx::BasicVector > | |
| gmx::PaddedVector< gmx::gmx::BasicVector > | |
| gmx::PaddedVector< gmx::RVec > | |
| gmx::PaddedVector< real > | |
| gmx::PaddedVector< RVec > | |
| PairlistParams | The setup for generating and pruning the nbnxn pair list |
| PairlistSet | An object that holds the local or non-local pairlists |
| PairlistSets | Contains sets of pairlists |
| PairSearch | Main pair-search struct, contains the grid(s), not the pair-list(s) |
| PairsearchWork | Thread-local work struct, contains working data for Grid |
| PartialDeserializedTprFile | Contains the partly deserialized contents of a TPR file |
| partition | Internal data structure for the insolidangle selection method |
| PbcAiuc | Compact and ordered version of the PBC matrix |
| pme_setup_t | Parameters and settings for one PP-PME setup |
| PmeGpu | The main PME GPU host structure, included in the PME CPU structure by pointer |
| PmeGpuAtomParams | A 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 |
| PmeGpuConstParams | A GPU data structure for storing the constant PME data. This only has to be initialized once |
| PmeGpuDynamicParams | A GPU data structure for storing the PME data which might change for each new PME computation |
| PmeGpuGridParams | A 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 |
| PmeGpuKernelParamsBase | A 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 |
| PmeGpuProgram | Stores PME data derived from the GPU context or devices |
| PmeGpuProgramImpl | PME GPU persistent host program/kernel data, which should be initialized once for the whole execution |
| PmeGpuSettings | The PME GPU settings structure, included in the main PME GPU structure by value |
| PmeGpuSpecific | The main PME CUDA/OpenCL-specific host data structure, included in the PME GPU structure by the archSpecific pointer |
| PmeGpuStaging | The PME GPU intermediate buffers structure, included in the main PME GPU structure by value. Buffers are managed by the PME GPU module |
| PmeShared | The 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 |
| PmeSolveKernel< gridOrdering, computeEnergyAndVirial, gridIndex, subGroupSize > | The kernel for PME solve |
| PpRanks | Contains information about the PP ranks that partner this PME rank |
| PreprocessingAtomTypes | Storage of all atom types used during preprocessing of a simulation input |
| PreprocessingBondAtomType | Storage for all bonded atomtypes during simulation preprocessing |
| PreprocessResidue | Information about preprocessing residues |
| pull_coord_work_t | Struct with parameters and force evaluation local data for a pull coordinate |
| pull_group_work_t | Pull group data used during pulling |
| gmx::Range< int > | |
| ReduceKernel< addRvecForce, accumulateForce > | Class name for reduction kernel |
| ReplicaExchangeParameters | The parameters for the replica exchange algorithm |
| ReverseTopOptions | Options for setting up gmx_reverse_top_t |
| ScalarDataTypes | Scalar (non-SIMD) data types |
| SearchCycleCounting | Struct for collecting detailed cycle counts for the search |
| gmx::SignallerBuilder< gmx::EnergySignaller > | |
| gmx::SignallerBuilder< gmx::LastStepSignaller > | |
| gmx::SignallerBuilder< gmx::LoggingSignaller > | |
| gmx::SignallerBuilder< gmx::NeighborSearchSignaller > | |
| gmx::SignallerBuilder< gmx::TrajectorySignaller > | |
| gmx::internal::SimdArrayRef< const SimdInt32 > | |
| gmx::internal::SimdArrayRef< SimdInt32 > | |
| SimdDataTypes | SIMD data types |
| SimulationGroups | Contains the simulation atom groups |
| SolveKernelParams | Contains most of the parameters used by the solve kernel |
| sort_along_vec_t | Helper structure for sorting positions along rotation vector |
| spheresurfacebin | Internal data structure for the insolidangle selection method |
| std::array< T > | STL class |
| gmx::AlignedArray< double, N > | Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
| gmx::AlignedArray< float, N > | Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
| std::exception | STL class |
| gmx::GromacsException | Base class for all exception objects in Gromacs |
| gmx::APIError | Exception class for incorrect use of an API |
| gmx::NotImplementedError | Exception class for use of an unimplemented feature |
| gmx::ParallelConsistencyError | Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion |
| gmx::FileIOError | Exception class for file I/O errors |
| gmx::InternalError | Exception class for internal errors |
| gmx::ModularSimulatorError | Exception class for modular simulator |
| gmx::CheckpointError | Exception class signalling an error in reading or writing modular checkpoints |
| gmx::ElementNotFoundError | Exception class signalling that a requested element was not found |
| gmx::MissingElementConnectionError | Exception class signalling that elements were not connected properly |
| gmx::SimulationAlgorithmSetupError | Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way |
| gmx::RangeError | Exception class for out-of-range values or indices |
| gmx::SimulationInstabilityError | Exception class for simulation instabilities |
| gmx::test::TestException | Exception class for reporting errors in tests |
| gmx::ToleranceError | Exception class when a specified tolerance cannot be achieved |
| gmx::UserInputError | Exception class for user input errors |
| gmx::InconsistentInputError | Exception class for situations where user input is inconsistent |
| gmx::InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
| StringTable | A class to store strings for lookup |
| StringTableBuilder | Builds a memory efficient storage for strings of characters |
| StringTableEntry | Helper class to access members in StringTable |
| swap_compartment | Structure containing compartment-specific data |
| swap_group | This structure contains data needed for the groups involved in swapping: split group 0, split group 1, solvent group, ion groups |
| t_bb | Struct containing properties of a residue in a protein backbone |
| t_compare_value | Data structure for comparison expression operand values |
| t_compiler_data | Internal data structure used by the compiler |
| t_coordselection | Selection of pull coordinates to be used in WHAM (one structure for each tpr file) |
| t_filenm | File name option definition for C code |
| t_forcetable | Structure describing the data in a single table |
| t_mapping | Maps an XPM element to an RGB color and a string description |
| t_matrix | A matrix of integers, plus supporting values, such as used in XPM output |
| t_mdatoms | Declares mdatom data structure |
| t_methoddata_compare | Data structure for comparison expression evaluation |
| t_methoddata_distance | Data structure for distance-based selection method |
| t_methoddata_kweval | Data structure for keyword evaluation in arbitrary groups |
| t_methoddata_kwint | Data structure for integer keyword expression evaluation |
| t_methoddata_kwreal | Data structure for real keyword expression evaluation |
| t_methoddata_pos | Data structure for position keyword evaluation |
| t_methoddata_same | Data structure for the same selection method |
| t_nbparam | Used to temporarily store the explicit non-bonded parameter combinations, which will be copied to InteractionsOfType |
| t_oriresdata | Orientation restraining stuff |
| t_pargs | Command-line argument definition for C code |
| t_partition_item | Internal data structure for the insolidangle selection method |
| t_pbc | Structure containing info on periodic boundary conditions |
| t_pullcoord | Parameters of one pull coordinate |
| t_register_method | Helper structure for defining selection methods |
| t_state | The microstate of the system |
| t_swap | Main (private) data structure for the position swapping protocol |
| t_symbuf | Legacy symbol table entry as linked list |
| t_UmbrellaHeader | Parameters of the umbrella potentials |
| t_UmbrellaWindow | Data in the umbrella histograms |
| t_xpmelmt | Models an XPM element |
| thread_work_t | Struct for thread local work data for local topology generation |
| gmx::ThreadedForceBuffer< gmx::RVec > | |
| gmx::ThreadedForceBuffer< rvec4 > | |
| gmx::ThreadForceBuffer< gmx::RVec > | |
| gmx::ThreadForceBuffer< rvec4 > | |
| gmx::ThreeFry2x64General< 13, internalCounterBits > | |
| gmx::ThreeFry2x64Fast< internalCounterBits > | ThreeFry2x64 random engine with 13 iteractions |
| gmx::ThreeFry2x64General< 20, internalCounterBits > | |
| gmx::ThreeFry2x64< internalCounterBits > | ThreeFry2x64 random engine with 20 iteractions |
| TpxFileHeader | First part of the TPR file structure containing information about the general aspect of the system |
| UmbrellaOptions | Parameters of WHAM |
| UnitCellInfo | Provides information about properties of the unit cell |
| gmx::Update::Impl | PImpled implementation for Update |
| VirtualSiteConfiguration | The configuration describing a virtual site |
| VirtualSiteTopology | Virtual site topology datastructure |
| VirtualSiteTopology::VirtualSiteAngle | Helper struct for single angle in virtual site |
| VirtualSiteTopology::VirtualSiteBond | Helper struct for single bond in virtual site |
| VsiteAtomMapping | Convenience typedef for linking function type to parameter numbers |
| VsiteBondedInteraction | Data type to store information about bonded interactions for virtual sites |
| VsiteBondParameter | Stores information about single virtual site bonded parameter |
| WorkDivision | The division of bonded interactions of the threads |
1.8.5
