gmx::AnalysisDataFrameLocalData< double > | |
gmx::AnalysisDataFrameLocalData< gmx_int64_t > | |
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{shake.cpp}::ShakeTest | Test fixture for testing SHAKE |
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< ValueType > | |
AtomIndex | List of atom indices belonging to a task |
bonded_threading_t | Struct contain all data for bonded force threading |
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 |
cl_plist | Pair list data |
cl_timers | OpenCL events used for timing GPU kernels and H2D/D2H transfers |
gmx::ConstArrayRef< AnalysisDataValue > | |
gmx::ConstArrayRef< const char * > | |
gmx::ConstArrayRef< real > | |
cu_atomdata | Nonbonded atom data - both inputs and outputs |
cu_nbparam | Parameters required for the CUDA nonbonded calculations |
cu_plist | Pair list data |
cu_timers | CUDA events used for timing GPU kernels and H2D/D2H transfers |
eligible_gpu_ids | Helper struct so we can parse the string with eligible GPU IDs outside do_the_tests |
em_state_t | Utility structure for manipulating states during EM |
f_thread_t | Struct with output for bonded forces, used per thread |
gmx::FlagsTemplate< Flag > | |
gmx::FlagsTemplate< OptionFlag > | |
gmx::FlagsTemplate< SelectionFlag > | |
gmx::FlagsTemplate< TestFlag > | |
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< gmx_int64_t, Int64Option > | |
gmx::Int64Option | Specifies an option that provides 64-bit integer values |
gmx::OptionTemplate< int, IntegerOption > | |
gmx::IntegerOption | Specifies an option that provides 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::AbstractOptionStorage | Abstract base class for converting, validating, and storing option values |
gmx::OptionStorageTemplate< T > | Templated base class for constructing option value storage classes |
gmx::SelectionFileOptionStorage | Implementation for a special option for reading selections from files |
gmx::OptionStorageTemplate< bool > | |
gmx::BooleanOptionStorage | Converts, validates, and stores boolean values |
gmx::OptionStorageTemplate< double > | |
gmx::DoubleOptionStorage | Converts, validates, and stores floating-point (double) values |
gmx::OptionStorageTemplate< float > | |
gmx::FloatOptionStorage | Converts, validates, and stores floating-point (float) values |
gmx::OptionStorageTemplate< gmx_int64_t > | |
gmx::Int64OptionStorage | Converts, validates, and stores integer values |
gmx::OptionStorageTemplate< int > | |
gmx::EnumOptionStorage | Converts, validates, and stores enum values |
gmx::IntegerOptionStorage | 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::FileNameOptionStorage | Converts, validates, and stores file names |
gmx::StringOptionStorage | Converts, validates, and stores string values |
gmx::AlignedAllocator< T > | Aligned memory allocator |
gmx::AlignedAllocator< T >::rebind< U > | Standard-required typedef to use allocator with different class |
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::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{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::ArrayRef< T > | STL-like container for an interface to a C array (or part of a std::vector) |
gmx::BasicVector< ValueType > | C++ class for 3D vectors |
gmx::BinaryInformationSettings | Settings for printBinaryInformation() |
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::ConstArrayRef< T > | STL-like container for non-mutable interface to a C array (or part of a std::vector) |
gmx::CpuInfo | Detect CPU capabilities and basic logical processor info |
gmx::CpuInfo::LogicalProcessor | Entry with basic information for a single logical processor |
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::DirectoryEnumerator | Lists files in a directory |
gmx::EmptyArrayRef | Tag type to initialize empty array references |
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::GammaDistribution< RealType > | Gamma distribution |
gmx::GammaDistribution< RealType >::param_type | Gamma distribution parameters |
gmx::GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
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::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::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::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::InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
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::EnumIndexStoreInterface | Interface for handling storage of the enum indexes |
gmx::internal::EnumIndexStore< EnumType > | Type-specific implementation for EnumIndexStoreInterface |
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::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::OptionsImpl::Group | Describes a group of options (see Options::addGroup()) |
gmx::Options | Collection of options |
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::ITopologyProvider | Provides topology information to SelectionOptionBehavior |
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::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::PositionCalculationCollection | Collection of gmx_ana_poscalc_t structures for the same topology |
gmx::PositionCalculationCollection::Impl | Private implementation class for PositionCalculationCollection |
gmx::PrivateImplPointer< Impl > | Helper class to manage a pointer to a private implementation class |
gmx::Regex | Represents a regular expression |
gmx::RstParagraphIterator | Iterator over reStructuredText paragraphs |
gmx::scoped_cptr< T, D > | Stripped-down version of scoped_ptr that uses sfree() or custom deleter |
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::SelectionTreeElement | Represents an element of a selection expression |
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::SimdDouble | Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1 |
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::SimdFloat | Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1 |
gmx::SimdLoadDProxyInternal | Proxy object to enable load() for SIMD and double types |
gmx::SimdLoadFProxyInternal | Proxy object to enable load() for SIMD and float types |
gmx::SimdLoadIProxyInternal | Proxy object load() for SimdFInt32, SImdDInt32, and int32 |
gmx::SimdLoadUDProxyInternal | Proxy object to enable loadU() for SIMD and double types |
gmx::SimdLoadUFProxyInternal | Proxy object to enable loadU() for SIMD and float types |
gmx::SimdLoadUIProxyInternal | Proxy object - loadU() for SimdFInt32, SImdDInt32, and int32 |
gmx::SimdSetZeroProxyInternal | Proxy object to enable setZero() for SIMD and real types |
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::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::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::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{testoptions.cpp}::TestOptionsRegistry | Singleton registry for test options added with GMX_TEST_OPTIONS |
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::EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
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::IntegrationTestFixture | Test fixture for integration tests |
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 |
anonymous_namespace{rerun.cpp}::MdrunRerun | Test fixture for mdrun -rerun |
gmx::test::BondedInteractionsTest | Test fixture for bonded interactions |
gmx::test::MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
gmx::test::ParameterizedMdrunTestFixture | Parameterized test fixture for mdrun integration tests |
gmx::test::MultiSimTest | Test fixture for multi-sim functionality |
gmx::test::MdrunTestFixtureBase | Declares test fixture base class for integration tests of mdrun functionality |
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::NoTextMatch | Do not match the text (the contents are ignored) |
gmx::test::XvgMatch | Match the contents as an xvg file |
gmx::test::MockAnalysisDataModule::Impl | Private implementation class for gmx::test::MockAnalysisDataModule |
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::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::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::TrajectoryFrame | Contains the content of a trajectory frame read by an TrajectoryFrameReader |
gmx::test::TrajectoryFrameReader | Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file |
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::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 passed 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::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_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_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 | Structure for all global to local mapping information |
gmx_hash_e_t | Hashing key-generation helper struct |
gmx_hash_t | Hashing helper struct |
gmx_help_make_index_group | Cata necessary to construct a single (protein) index group in analyse_prot() |
gmx_laa_t | Structure for the local atom info for a plain list |
gmx_lal_t | Structure for the local atom info for a hash table |
gmx_nbnxn_cuda_t | Main data structure for CUDA nonbonded force calculations |
gmx_nbnxn_kernel_timing_data_t | Nonbonded kernel time and call count |
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_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_sparsematrix | Sparse matrix storage format |
gmx_wallclock_gpu_t | GPU timings for kernels and H2d/D2H transfers |
gmx_walltime_accounting | Manages caching wall-clock time measurements for simulations |
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 |
IMDSocket | IMD (interactive molecular dynamics) socket structure |
InterdependentTask | Data structure for thread tasks that use constructing atoms outside their own atom range |
nb_staging | Staging area for temporary data downloaded from the GPU |
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 |
pme_setup_t | Parameters and settings for one PP-PME setup |
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::HelpLinks::Impl > | |
gmx::PrivateImplPointer< gmx::HelpManager::Impl > | |
gmx::PrivateImplPointer< gmx::HelpWriterContext::Impl > | |
gmx::PrivateImplPointer< gmx::internal::AnalysisDataStorageImpl > | |
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::TextTableFormatter::Impl > | |
gmx::PrivateImplPointer< gmx::TrajectoryAnalysisModule::Impl > | |
gmx::PrivateImplPointer< gmx::TrajectoryAnalysisModuleData::Impl > | |
gmx::PrivateImplPointer< gmx::TrajectoryAnalysisSettings::Impl > | |
gmx::PrivateImplPointer< internal::FileStreamImpl > | |
gmx::PrivateImplPointer< internal::OptionsImpl > | |
gmx::scoped_cptr< ener_file, done_ener_file > | |
gmx::scoped_cptr< gmx_output_env_t, output_env_done > | |
gmx::scoped_cptr< struct warninp, free_warning > | |
gmx::scoped_cptr< t_enxframe, done_enxframe > | |
gmx::scoped_cptr< t_inpfile > | |
gmx::scoped_cptr< t_trxframe, done_trxframe > | |
gmx::scoped_cptr< t_trxstatus, close_trx > | |
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::SimulationInstabilityError | Exception class for simulation instabilities |
gmx::test::TestException | Exception class for reporting errors in tests |
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_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_cosines | Declares inputrec data structure and utilities |
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_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 |
VsiteThread | Vsite thread task data structure |