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 real > | |
gmx::ArrayRef< const t_filenm > | |
gmx::ArrayRef< gmx::BasicVector > | |
gmx::ArrayRef< gmx::RVec > | |
gmx::ArrayRef< nbnxn_bb_t > | |
gmx::ArrayRef< ValueType > | |
gmx::BasicVector< double > | |
gmx::BasicVector< real > | |
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 |
EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
gmx::FlagsTemplate< Flag > | |
gmx::FlagsTemplate< OptionFlag > | |
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 |
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 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::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::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::Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
gmx::BasicVector< ValueType > | C++ class for 3D vectors |
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::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::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::DirectoryEnumerator | Lists files in a directory |
gmx::EmptyArrayRef | Tag type to initialize empty array references |
gmx::ExceptionInfo< Tag, T > | Stores additional context information for exceptions |
gmx::ExceptionInitializer | Provides information for Gromacs exception constructors |
gmx::ExponentialDistribution< RealType > | Exponential distribution |
gmx::ExponentialDistribution< RealType >::param_type | Exponential distribution parameters |
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::GammaDistribution< RealType > | Gamma distribution |
gmx::GammaDistribution< RealType >::param_type | Gamma distribution parameters |
gmx::GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
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::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::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::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::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::LegacyMdrunOptions | This class provides the same command-line option functionality to both CLI and API sessions |
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::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::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::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 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::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::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::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::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::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::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::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::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::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_indexmap_t | Data structure for calculating index group mappings |
gmx_ana_pos_t | Stores a set of positions together with their origins |
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_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_sparsematrix | Sparse matrix storage format |
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 |
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 |
MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
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 |
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::RVec > | |
gmx::PaddedVector< real > | |
gmx::PrivateImplPointer< internal::FileStreamImpl > | |
gmx::PrivateImplPointer< internal::KeyValueTreeTransformerImpl > | |
gmx::PrivateImplPointer< internal::OptionsImpl > | |
ReplicaExchangeParameters | The parameters for the replica exchange algorithm |
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 |
t_filenm | File name option definition for C code |
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 |
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 |
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 > | |