  gmx::accessor_basic< float > | |
| gmx::accessor_basic< value_type > | |
| gmx::ArrayRef< BoundingBox > | |
| 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::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< gmx::BasicVector > | |
| gmx::ArrayRef< gmx::gmx::BasicVector > | |
| gmx::ArrayRef< gmx::RVec > | |
| gmx::ArrayRef< PpRanks > | |
| gmx::ArrayRef< real > | |
| gmx::ArrayRef< rvec > | |
| gmx::ArrayRef< ValueType > | |
| gmx::ArrayRefWithPadding< gmx::BasicVector > | |
| gmx::ArrayRefWithPadding< gmx::gmx::BasicVector > | |
| AtomIterator | Object that allows looping over all atoms in an mtop |
| AtomProperties | Holds all the atom property information loaded |
| AtomProxy | Proxy object returned from AtomIterator |
| AtomRange | Range over all atoms of topology |
| 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::BasicVector< double > | |
| gmx::BasicVector< int > | |
| gmx::BasicVector< real > | |
| BondedInteraction | Information about single bonded interaction |
| BondedInteractionList | Accumulation of different bonded types for preprocessing |
| CheckpointHeaderContents | Header explaining the context of a checkpoint file |
| DDBalanceRegionHandler | Manager for starting and stopping the dynamic load balancing region |
| DeviceInformation | Platform-dependent device information |
| DeviceStream | Declaration of platform-agnostic device stream/queue |
| df_history_t | Free-energy sampling history struct |
| ekinstate_t | Struct used for checkpointing only |
| gmx::EnumerationArray< AtomLocality, const DeviceStream * > | |
| gmx::EnumerationArray< AtomLocality, GpuEventSynchronizer > | |
| gmx::EnumerationArray< AtomLocality, XFTransfers > | |
| gmx::EnumerationArray< CoordinateFileFlags, OutputAdapterPointer > | |
| gmx::EnumerationArray< DeviceStreamType, std::unique_ptr< DeviceStream > > | |
| gmx::EnumerationArray< gmx::AtomLocality, std::unique_ptr< gmx::GpuForceReduction > > | |
| gmx::EnumerationArray< InteractionLocality, Nbnxm::gpu_timers_t::Interaction > | |
| gmx::EnumerationArray< Nbnxm::InteractionLocality, bool > | |
| gmx::EnumerationArray< Nbnxm::InteractionLocality, const DeviceStream * > | |
| gmx::EnumerationArray< Nbnxm::InteractionLocality, Nbnxm::gpu_plist * > | |
| gmx::EnumerationArray< SimulationAtomGroupType, AtomGroupIndices > | |
| gmx::EnumerationArray< SimulationAtomGroupType, std::vector< unsigned char > > | |
| EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
| gmx::extents< E_STATIC...> | |
| gmx::FlagsTemplate< Flag > | |
| gmx::FlagsTemplate< OptionFlag > | |
| ForceHelperBuffers | Helper force buffers for ForceOutputs |
| ForeignLambdaTerms | Accumulates free-energy foreign lambda energies and dH/dlamba |
 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 |
| 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::AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
| gmx::AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| 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, 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::OptionStorageTemplate< bool > | |
| gmx::OptionStorageTemplateSimple< bool > | |
| gmx::OptionStorageTemplate< double > | |
| gmx::OptionStorageTemplateSimple< double > | |
| gmx::OptionStorageTemplate< float > | |
| gmx::OptionStorageTemplateSimple< float > | |
| gmx::OptionStorageTemplate< int > | |
| gmx::OptionStorageTemplateSimple< int > | |
| gmx::OptionStorageTemplate< int64_t > | |
| gmx::OptionStorageTemplateSimple< int64_t > | |
| gmx::OptionStorageTemplate< Selection > | |
| gmx::OptionStorageTemplate< std::string > | |
| gmx::OptionStorageTemplateSimple< std::string > | |
| 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::AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
| gmx::AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
| gmx::AnalysisDataHandle | Handle for inserting data into AnalysisData |
| gmx::AnalysisDataModuleManager | Encapsulates handling of data modules attached to AbstractAnalysisData |
| 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::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::Any | Represents a dynamically typed value of an arbitrary type |
| 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::Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
| 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::BinaryInformationSettings | Settings for printBinaryInformation() |
| gmx::BoxDeformationHandle | Handle to information about the box |
| gmx::CheckpointData< operation > | } |
| gmx::CheckpointHandler | Class handling the checkpoint signal |
| 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::CommandLineHelpContext | Context information for writing out command-line help |
| gmx::CommandLineHelpWriter | Writes help information for Options |
| gmx::CommandLineModuleGroup | Handle to add content to a group added with CommandLineModuleManager::addModuleGroup() |
| gmx::CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
| gmx::CommandLineModuleSettings | Settings to pass information between a module and the general runner |
| gmx::CommandLineParser | Implements command-line parsing for Options objects |
| gmx::compat::not_null< T > | Restricts a pointer or smart pointer to only hold non-null values |
| gmx::Constraints | Handles constraints |
| gmx::ConstraintsParam | Collection of constraint parameters |
| gmx::ConvertTprInfo | Declares gmx convert-tpr |
| gmx::CpuInfo | Detect CPU capabilities and basic logical processor info |
| gmx::CpuInfo::LogicalProcessor | Entry with basic information for a single logical processor |
| 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::DensityFittingForce | Manages evaluation of density-fitting forces for particles that were spread with a kernel |
| gmx::DensityFittingModuleInfo | Information about the density fitting module |
| 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::DevelopmentFeatureFlags | Structure that holds boolean flags corresponding to the development features present enabled through environment variables |
| gmx::DeviceStreamManager | Device stream and context manager |
| gmx::DirectoryEnumerator | Lists files in a directory |
| gmx::DomainDecompositionBuilder | Builds a domain decomposition management object |
| gmx::DomainLifetimeWorkload | Describes work done on this domain on every step of its lifetime, but which might change after the next domain paritioning |
| gmx::DomdecOptions | Structure containing all (command line) options for the domain decomposition |
| gmx::EnergyCalculationFrequencyErrors | Collect errors for the energy calculation frequency |
| 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::ExceptionInfo< Tag, T > | Stores additional context information for exceptions |
| 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::FixedCapacityVector< T, capacity > | 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::GammaDistribution< RealType > | Gamma distribution |
| gmx::GammaDistribution< RealType >::param_type | Gamma distribution parameters |
| 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::GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
| gmx::GpuHaloExchange | Manages GPU Halo Exchange object |
| 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::HardwareTopology | Information about sockets, cores, threads, numa, caches |
| gmx::HardwareTopology::Cache | Information about a single cache level |
| gmx::HardwareTopology::Core | Information about a single core in a socket |
| gmx::HardwareTopology::Device | Information about a single PCI device |
| gmx::HardwareTopology::HWThread | Information about a single hardware thread in a core |
| gmx::HardwareTopology::LogicalProcessor | Information about socket, core and hwthread for a logical processor |
| gmx::HardwareTopology::Machine | Hardware topology information about the entire machine |
| gmx::HardwareTopology::Numa | Information about a single numa node |
| gmx::HardwareTopology::NumaNode | Information about each numa node in system |
| gmx::HardwareTopology::Socket | Information about a single socket in the system |
| gmx::HashedMap< T > | Unordered key to value mapping |
| gmx::HelpLinks | Hyperlink data for writing out help |
| gmx::HelpManager | Helper for providing interactive online help |
| gmx::HelpWriterContext | Context information for writing out help |
| gmx::HostAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers |
| 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::ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
| gmx::ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
| 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::IExecutableEnvironment | Allows customization of the way various directories are found by CommandLineProgramContext |
| gmx::IFileInputRedirector | Allows overriding file existence checks from code that supports it |
| gmx::test::TestFileInputRedirector | In-memory implementation for IFileInputRedirector for tests |
| gmx::IFileOutputRedirector | Allows capturing stdout and file output from code that supports it |
| gmx::test::TestFileOutputRedirector | In-memory implementation of IFileOutputRedirector for tests |
| gmx::IForceProvider | Interface for a component that provides forces during MD |
| gmx::IHelpTopic | Provides a single online help topic |
| gmx::AbstractCompositeHelpTopic | Abstract base class for help topics that have simple text and subtopics |
| 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::SimpleHelpTopic< HelpText > | Template for simple implementation of AbstractSimpleHelpTopic |
| gmx::IKeyValueTreeTransformRules | Interface to declare rules for transforming key-value trees |
| gmx::ILogTarget | Target where log output can be written |
| gmx::IMDModule | Extension module for GROMACS simulations |
| gmx::RestraintMDModule | MDModule wrapper for Restraint implementations |
| gmx::IMDOutputProvider | Interface for handling additional output files during a simulation |
| gmx::IMdpOptionProvider | Interface for handling mdp/tpr input to a mdrun module |
| gmx::InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| gmx::InteractiveMD | SimulatorBuilder parameter type for InteractiveMD |
| 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::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::Options | Collection of options |
| 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::CommandLineProgramContext | Program context implementation for command line programs |
| 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::isIntegralConstant< T, Int > | Is true if type is a std::integral_constant |
| gmx::IsSerializableEnum< T, bool > | { |
| gmx::ITopologyProvider | Provides topology information to SelectionOptionBehavior |
| 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::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::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::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::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::MdModuleNotification< CallParameter, MdModuleNotificationBase > | Subscribe and trigger notification functions |
| 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::MdModulesNotifier | Collection of callbacks to MDModules at differnt run-times |
| gmx::MdModulesWriteCheckpointData | Writing the MdModules data to a checkpoint file |
| gmx::Mdrunner | Runner object for supporting setup and execution of mdrun |
| gmx::MdrunnerBuilder | Build a gmx::Mdrunner |
| 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::ModularSimulator | The modular simulator |
| 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::MrcDensityMapOfFloatWriter | Write an mrc/ccp4 file that contains float values |
| 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::MultiDimArray< TContainer, Extents, LayoutPolicy > | Multidimensional array that manages its own memory |
| 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::NumericalSplineTableInput | Specification for vector table function (name, function, derivative, spacing) |
| gmx::OpenClTraits< cl_type > | Stub for OpenCL type traits |
| gmx::OpenClTraitsBase< cl_type > | Implements common trait infrastructure for OpenCL types |
| 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::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::OptionsVisitor | Pure interface for visiting options in a Options object |
| 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::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::PmeForceSenderGpu | Manages sending forces from PME-only ranks to their PP ranks |
| gmx::PmePpCommGpu | Manages communication related to GPU buffers between this PME rank and its PP rank |
| gmx::PotentialPointData | Structure to hold the results of IRestraintPotential::evaluate() |
| gmx::PrivateImplPointer< Impl > | Helper class to manage a pointer to a private implementation class |
| gmx::Profiling | Collection of profiling information |
| 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::registerMdModuleNotification< CurrentCallParameter, CallParameter...> | Template specialization to assemble MdModuleNotification |
| gmx::ResetHandler | Class handling the reset of counters |
| gmx::RestraintManager | Manage the Restraint potentials available for Molecular Dynamics |
| gmx::Selection | Provides access to a single selection |
| gmx::SelectionCollection | Collection of selections |
| gmx::SelectionPosition | Provides access to information about a single selected position |
| gmx::SelectionTopologyProperties | Describes topology properties required for selection evaluation |
| gmx::SettleData | Data for executing SETTLE constraining |
| gmx::shakedata | Working data for the SHAKE algorithm |
| 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::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::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 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::TabulatedNormalDistribution< RealType, tableBits > | Tabulated normal random distribution |
| gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type | Normal distribution parameter class (mean and stddev) |
| gmx::test::AllocatorTest< T > | Templated test fixture |
| 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::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::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::CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
| 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::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::ITextBlockMatcher | Represents a text matcher, matching text stream contents against reference data |
| 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::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::StdioTestHelper | Helper class for tests where code reads directly from stdin |
| gmx::test::StringTestBase | Test fixture for tests that check string formatting |
| gmx::test::TestFileManager | Helper for tests that need input and output files |
| gmx::test::TestOptionsProvider | Provides additional options for the test executable |
| gmx::test::TestReferenceChecker | Handles comparison to test reference data |
| gmx::test::TestReferenceData | Handles creation of and comparison to test reference data |
| gmx::test::TprAndFileManager | Helper to bundle generated TPR and the file manager to clean it up |
| 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::TextTableFormatter | Formats rows of a table for text output |
| gmx::TextWriter | Writes text into a TextOutputStream |
| gmx::ThreeFry2x64General< rounds, internalCounterBits > | General implementation class for ThreeFry counter-based random engines |
| gmx::TimeUnitManager | Provides common functionality for time unit conversions |
| gmx::TopologyData | Collection of handles to topology information |
| 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 |
| gmx::TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
| gmx::TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
| gmx::TrajectoryFileOpener | Low level method to take care of only file opening and closing |
| 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::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::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_indexmap_t | Data structure for calculating index group mappings |
| gmx_ana_pos_t | Stores a set of positions together with their origins |
| gmx_cache_protect_t | Cache-line protection buffer |
| gmx_enerdata_t | Struct for accumulating all potential energy terms and some kinetic energy terms |
| gmx_ffparams_t | Struct that holds all force field parameters for the simulated system |
| gmx_ga2la_t | Global to local atom mapping |
| gmx_ga2la_t::Entry | Structure for the local atom info |
| 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_sparsematrix | Sparse matrix storage format |
| 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 |
| 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 |
| ListedForces | Class for calculating listed interactions, uses OpenMP parallelization |
| gmx::ListOfLists< int > | |
| 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 |
| gmx::MultiDimArray< real > | |
| gmx::MultiDimArray< std::vector< float >, gmx::extents > | |
| gmx::MultiDimArray< std::vector< float >, gmx::extents< dynamic_extent, dynamic_extent > > | |
| gmx::MultiDimArray< t_matelmt > | |
| Nbnxm::Grid::Dimensions | The physical dimensions of a grid |
| 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 coordinats and bounding box for an i-entry during search |
| nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
| gmx::compat::not_null< ISimulatorElement * > | |
| gmx::compat::not_null< LegacySimulatorData * > | |
| NumPmeDomains | Struct for passing around the number of PME domains |
| ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
| 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 > | |
| gmx::PaddedVector< gmx::BasicVector > | |
| gmx::PaddedVector< gmx::gmx::BasicVector > | |
| gmx::PaddedVector< gmx::RVec > | |
| gmx::PaddedVector< real > | |
| gmx::PaddedVector< RVec > | |
| 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 |
| PbcAiuc | Compact and ordered version of the PBC matrix |
| PmeGpuProgram | Stores PME data derived from the GPU context or devices |
| 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 |
| gmx::PrivateImplPointer< internal::FileStreamImpl > | |
| gmx::PrivateImplPointer< internal::KeyValueTreeTransformerImpl > | |
| gmx::PrivateImplPointer< internal::OptionsImpl > | |
| gmx::Range< int > | |
| ReplicaExchangeParameters | The parameters for the replica exchange algorithm |
| SimulationGroups | Contains the simulation atom groups |
| SimulationInputHandle | Owning handle to a SimulationInput object |
| 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 |
| t_filenm | File name option definition for C code |
| 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_pargs | Command-line argument definition for C code |
| t_pbc | Structure containing info on periodic boundary conditions |
| t_state | The microstate of the system |
| t_symbuf | Legacy symbol table entry as linked list |
| t_xpmelmt | Models an XPM element |
| 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 |
1.8.5
