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{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 double > | |
gmx::ArrayRef< const gmx::BasicVector > | |
gmx::ArrayRef< const int > | |
gmx::ArrayRef< const IVec > | |
gmx::ArrayRef< const real > | |
gmx::ArrayRef< const t_filenm > | |
gmx::ArrayRef< gmx::BasicVector > | |
gmx::ArrayRef< gmx::RVec > | |
gmx::ArrayRef< nbnxn_bb_t > | |
gmx::ArrayRef< ValueType > | |
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 |
AtomIndex | List of atom indices belonging to a task |
AwhReader | All options and meta-data needed for the AWH output |
BalanceRegion | Struct for timing the region for dynamic load balancing |
gmx::BasicVector< double > | |
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 |
ChainIdFiller | Constructs plausible chain IDs for multi-molecule systems, e.g. when read from .tpr files |
CheckpointOptions | Options for writing checkpoint files |
cl_atomdata | Nonbonded atom data - both inputs and outputs |
cl_nb_staging | Staging area for temporary data downloaded from the GPU |
cl_nbparam | Parameters required for the OpenCL nonbonded calculations |
cl_nbparam_params | Data structure shared between the OpenCL device code and OpenCL host code |
ContinuationOptions | Options and settings for continuing from checkpoint |
cu_atomdata | Nonbonded atom data - both inputs and outputs |
cu_nbparam | Parameters required for the CUDA nonbonded calculations |
dd_corners_t | Domain corners for communication, a maximum of 4 i-zones see a j domain |
df_history_t | Free-energy sampling history struct |
DomdecOptions | Structure containing all (command line) options for the domain decomposition |
ekinstate_t | Struct used for checkpointing only |
em_state_t | Utility structure for manipulating states during EM |
EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
f_thread_t | Struct with output for bonded forces, used per thread |
gmx::FlagsTemplate< Flag > | |
gmx::FlagsTemplate< OptionFlag > | |
gmx::FlagsTemplate< SelectionFlag > | |
gmx::FlagsTemplate< TestFlag > | |
ForceProviders | Evaluates forces from a collection of gmx::IForceProvider |
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 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::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{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{electricfield.cpp}::ElectricFieldData | Declaration of storage unit for fields |
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{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{pargs.cpp}::OptionsAdapter | Conversion helper between t_pargs/t_filenm and Options |
gmx::anonymous_namespace{shake.cpp}::ShakeTest | Test fixture for testing SHAKE |
gmx::ArrayRef< T > | STL-like interface to a C array of T (or part of a std container of T) |
gmx::ArrayRefWithPadding< T > | 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::AtomIndexExtremes | Struct for returning an atom range |
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::BasicVector< ValueType > | C++ class for 3D vectors |
gmx::Bias | A bias acting on a multidimensional coordinate |
gmx::BiasCoupledToSystem | A bias and its coupling to the system |
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::CheckpointHandler | Class handling the checkpoint signal |
gmx::ClfftInitializer | Handle clFFT library init and tear down in RAII style |
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::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 | Grid 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 logical processor |
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::detail::PaddingTraits< T > | Traits classes for handling padding for types used with PaddedVector |
gmx::DimParams | Constant parameters for each dimension of the coordinate |
gmx::DirectoryEnumerator | Lists files in a directory |
gmx::EmptyArrayRef | Tag type to initialize empty array references |
gmx::EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
gmx::ExceptionInitializer | Provides information for Gromacs exception constructors |
gmx::ExponentialDistribution< RealType > | Exponential distribution |
gmx::ExponentialDistribution< RealType >::param_type | Exponential distribution parameters |
gmx::FileNameOptionManager::Impl | Private implemention class for FileNameOptionManager |
gmx::FlagsTemplate< FlagType > | Template class for typesafe handling of combination of flags |
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::ForceWithVirial | Container for force and virial for algorithms that provide their own virial tensor contribution |
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::GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
gmx::GpuBonded::Impl | Implements GPU bondeds |
gmx::GpuTaskMapping | Specifies the GPU deviceID_ available for task_ to use |
gmx::Grid | The grid, generally multidimensional and periodic |
gmx::GridAxis | An axis, i.e. dimension, of the grid |
gmx::GridPoint | A point in the grid |
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::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::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::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::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::ILogTarget | Target where log output can be written |
gmx::IMDModule | Extension module for GROMACS simulations |
gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
gmx::RestraintMDModule | MDModule wrapper for Restraint implementations |
gmx::IMDOutputProvider | Interface for handling additional output files during a simulation |
gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
gmx::IMdpOptionProvider | Interface for handling mdp/tpr input to a mdrun module |
gmx::anonymous_namespace{electricfield.cpp}::ElectricField | Describe time dependent electric field |
gmx::InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
gmx::Integrator | Struct to handle setting up and running the different "integrators" |
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::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::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::isIntegralConstant< T, Int > | Is true if type is a std::integral_constant |
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::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::LegacyMdrunOptions | This class provides the same command-line option functionality to both CLI and API sessions |
gmx::Lincs | Data for LINCS algorithm |
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::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::Mdrunner | Runner object for supporting setup and execution of mdrun |
gmx::MdrunnerBuilder | Build a gmx::Mdrunner |
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::no_delete< T > | Deleter for std::shared_ptr that does nothing |
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::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 Variant to a given type |
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::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::PpForceWorkload | Manage what force calculation work is required each step |
gmx::PrivateImplPointer< Impl > | Helper class to manage a pointer to a private implementation class |
gmx::QuadraticSplineTable | Quadratic spline interpolation table |
gmx::RangePartitioning | Division of a range of indices into consecutive blocks |
gmx::RangePartitioning::Block | Struct for returning the range of a block |
gmx::RangePartitioning::Block::iterator | An iterator that loops over integers |
gmx::Regex | Represents a regular expression |
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::Selection | Provides access to a single selection |
gmx::SelectionCollection | Collection of selections |
gmx::SelectionCollection::Impl | Private implemention class for SelectionCollection |
gmx::SelectionCompiler | Implements selection compilation |
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 | Input 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::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::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::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::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::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::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{mutex.cpp}::DifferentTasksTest | Parameterized test fixture |
gmx::test::anonymous_namespace{pmebsplinetest.cpp}::PmeBSplineModuliTest | Test fixture for testing PME B-spline moduli creation |
gmx::test::anonymous_namespace{pmegathertest.cpp}::AtomAndPmeOrderSizedData | 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}::AtomSizedData | A structure for all the input atom data which depends in size on atom count - including a range of spline data for different PME orders |
gmx::test::anonymous_namespace{pmegathertest.cpp}::PmeGatherTest | Test fixture |
gmx::test::anonymous_namespace{pmesolvetest.cpp}::PmeSolveTest | Test fixture |
gmx::test::anonymous_namespace{pmesplinespreadtest.cpp}::PmeSplineAndSpreadTest | 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{rerun.cpp}::EnergyComparator | Functor for comparing reference and test frames on particular energies to match |
gmx::test::anonymous_namespace{splinetable.cpp}::SplineTableTest< T > | Test fixture for table comparision with analytical/numerical functions |
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::AwhTestParameters | Struct that gathers all input for setting up and using a Bias |
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::TrajectoryAnalysisModuleTestFixture< ModuleInfo > | Test fixture for a trajectory analysis module |
gmx::test::CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
gmx::test::EnergyFrameReader | Manages returning an EnergyFrame containing required energy field 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, Frame > | 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::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::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{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{pmetest.cpp}::PmeTest | A basic PME runner |
gmx::test::anonymous_namespace{rerun.cpp}::MdrunRerunTest | Test fixture base for mdrun -rerun |
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::MimicTest | Test fixture for bonded interactions |
gmx::test::ParameterizedMdrunTestFixture | Parameterized test fixture for mdrun integration tests |
gmx::test::MdrunTestFixtureBase | Declares test fixture base class for integration tests of mdrun functionality |
gmx::test::MockAnalysisDataModule::Impl | Private implementation class for gmx::test::MockAnalysisDataModule |
gmx::test::MultiSimTest | Test fixture for multi-sim functionality |
gmx::test::PaddedVectorTest< T > | Typed test fixture |
gmx::test::PmeTestEnvironment | This class performs one-time test initialization (enumerating the hardware) |
gmx::test::RVecMatcher< FloatType > | Implementation class for RvecEq matcher |
gmx::test::SettleTest | Test fixture for testing SETTLE position updates |
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::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::TestFileManager | Helper for tests that need input and output files |
gmx::test::TestFileManager::Impl | Private implementation class for TestFileManager |
gmx::test::TestHardwareContext | A structure to describe a hardware context that persists over the lifetime of the test binary - an abstraction over PmeGpuProgram with a human-readable string |
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::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::ThreeFry2x64General< rounds, internalCounterBits > | General implementation class for ThreeFry counter-based random engines |
gmx::ThrowLocation | Stores the location from which an exception was thrown |
gmx::TimeUnitManager | Provides common functionality for time unit conversions |
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::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::TrajectoryFrame | Contains a valid trajectory frame |
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::UpdateGroupsCog | Class for managing and computing centers of geometry of update groups |
gmx::Variant | Represents a dynamically typed value of an arbitrary type |
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_device_info_t | OpenCL device information |
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_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_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_nbnxn_cuda_t | Main data structure for CUDA nonbonded force calculations |
gmx_nbnxn_ocl_t | Main data structure for OpenCL nonbonded force calculations |
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 | Struct for the reverse topology: links bonded interactions to atomsx |
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. The event can be put into the stream with markEvent() and then later waited on with waitForEvent(). This can be repeated as necessary, but the current implementation does not allow waiting on completed event more than once, expecting only exact pairs of markEvent(stream); waitForEvent(). The class generally attempts to track the correctness of its state transitions, but please note that calling waitForEvent() right after the construction will fail with OpenCL but succeed with CUDA |
GpuParallel3dFft | A 3D FFT class for performing R2C/C2R transforms |
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 |
IMDEnergyBlock | IMD (interactive molecular dynamics) energy record |
IMDHeader | IMD (interactive molecular dynamics) communication structure |
ImdOptions | Options for IMD |
IMDSocket | IMD (interactive molecular dynamics) socket structure |
InteractionListHandle | Type for returning a list of InteractionList references |
InterdependentTask | Data structure for thread tasks that use constructing atoms outside their own atom range |
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 |
MD5Checksum | Helper struct for returning the MD5 checksum and the amount of the file that contributed to it |
MdrunOptions | Collection of all options of mdrun that are not processed separately |
MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
nb_staging | Staging area for temporary data downloaded from the GPU |
nbnxn_gpu_timers_t | GPU region timers used for timing GPU kernels and H2D/D2H transfers |
nonbonded_verlet_group_t | Non-bonded interaction group data structure |
nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
NumPmeDomains | Struct for passing around the number of PME domains |
ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
ocl_gpu_id_t | OpenCL GPU device identificator |
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::RVec > | |
gmx::PaddedVector< real > | |
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 almost all the PME data used in GPU kernels on device. This is inherited by the GPU framework-specific structure (PmeGpuCudaKernelParams in pme.cuh). This way, most code preparing the kernel parameters can be GPU-agnostic by casting the kernel parameter data pointer to PmeGpuKernelParamsBase |
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 |
PpRanks | Contains information about the PP ranks that partner this PME rank |
gmx::PrivateImplPointer< gmx::AbstractAnalysisData::Impl > | |
gmx::PrivateImplPointer< gmx::AbstractCompositeHelpTopic::Impl > | |
gmx::PrivateImplPointer< gmx::AnalysisData::Impl > | |
gmx::PrivateImplPointer< gmx::AnalysisDataDisplacementModule::Impl > | |
gmx::PrivateImplPointer< gmx::AnalysisDataLifetimeModule::Impl > | |
gmx::PrivateImplPointer< gmx::AnalysisDataModuleManager::Impl > | |
gmx::PrivateImplPointer< gmx::AnalysisDataSimpleHistogramModule::Impl > | |
gmx::PrivateImplPointer< gmx::AnalysisDataWeightedHistogramModule::Impl > | |
gmx::PrivateImplPointer< gmx::CommandLineHelpContext::Impl > | |
gmx::PrivateImplPointer< gmx::CommandLineHelpWriter::Impl > | |
gmx::PrivateImplPointer< gmx::CommandLineModuleManager::Impl > | |
gmx::PrivateImplPointer< gmx::CommandLineParser::Impl > | |
gmx::PrivateImplPointer< gmx::FileNameOptionManager::Impl > | |
gmx::PrivateImplPointer< gmx::GpuBonded::Impl > | |
gmx::PrivateImplPointer< gmx::HelpLinks::Impl > | |
gmx::PrivateImplPointer< gmx::HelpManager::Impl > | |
gmx::PrivateImplPointer< gmx::HelpWriterContext::Impl > | |
gmx::PrivateImplPointer< gmx::internal::AnalysisDataStorageImpl > | |
gmx::PrivateImplPointer< gmx::LocalAtomSetManager::Impl > | |
gmx::PrivateImplPointer< gmx::OptionsAssigner::Impl > | |
gmx::PrivateImplPointer< gmx::PositionCalculationCollection::Impl > | |
gmx::PrivateImplPointer< gmx::SelectionCollection::Impl > | |
gmx::PrivateImplPointer< gmx::SelectionOptionManager::Impl > | |
gmx::PrivateImplPointer< gmx::SelectionParserSymbol::Impl > | |
gmx::PrivateImplPointer< gmx::SelectionParserSymbolIterator::Impl > | |
gmx::PrivateImplPointer< gmx::SelectionParserSymbolTable::Impl > | |
gmx::PrivateImplPointer< gmx::test::MockAnalysisDataModule::Impl > | |
gmx::PrivateImplPointer< gmx::test::TestFileManager::Impl > | |
gmx::PrivateImplPointer< gmx::test::TestReferenceChecker::Impl > | |
gmx::PrivateImplPointer< gmx::TextReader::Impl > | |
gmx::PrivateImplPointer< gmx::TextTableFormatter::Impl > | |
gmx::PrivateImplPointer< gmx::TrajectoryAnalysisModule::Impl > | |
gmx::PrivateImplPointer< gmx::TrajectoryAnalysisModuleData::Impl > | |
gmx::PrivateImplPointer< gmx::TrajectoryAnalysisSettings::Impl > | |
gmx::PrivateImplPointer< internal::FileStreamImpl > | |
gmx::PrivateImplPointer< internal::KeyValueTreeTransformerImpl > | |
gmx::PrivateImplPointer< internal::OptionsImpl > | |
pull_group_work_t | Pull group data used during pulling |
ReplicaExchangeParameters | The parameters for the replica exchange algorithm |
gmx::internal::SimdArrayRef< const SimdInt32 > | |
gmx::internal::SimdArrayRef< SimdInt32 > | |
sort_along_vec_t | Helper structure for sorting positions along rotation vector |
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::FileIOError | Exception class for file I/O errors |
gmx::InternalError | Exception class for internal errors |
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 |
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_gmx_IMD | IMD (interactive molecular dynamics) main data structure |
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_insolidangle | Data structure for the insolidangle 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_merge | Data structure for the merging selection modifiers |
t_methoddata_permute | Data structure for the permute selection modifier |
t_methoddata_pos | Data structure for position keyword evaluation |
t_methoddata_same | Data structure for the same selection method |
t_pargs | Command-line argument definition for C code |
t_partition | Internal data structure for the insolidangle selection method |
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 coodinate |
t_register_method | Helper structure for defining selection methods |
t_spheresurfacebin | Internal data structure for the insolidangle selection method |
t_state | The microstate of the system |
t_swap | Main (private) data structure for the position swapping protocol |
t_UmbrellaHeader | Parameters of the umbrella potentials |
t_UmbrellaOptions | Parameters of WHAM |
t_UmbrellaWindow | Data in the umbrella histograms |
thread_work_t | Struct for thread local work data for local topology generation |
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 |
TimingOptions | Options for timing (parts of) mdrun |
TypedClMemory< ValueType > | A minimal cl_mem wrapper that remembers its allocation type. The only point is making template type deduction possible |
TypedClMemory< float > | |
TypedClMemory< int > | |
TypedClMemory< nbnxn_cj4_t > | |
TypedClMemory< nbnxn_excl_t > | |
TypedClMemory< nbnxn_sci_t > | |
TypedClMemory< unsigned int > | |
VsiteThread | Vsite thread task data structure |