  gmx::ArrayRef< ValueType > | |
| gmx::ConstArrayRef< AnalysisDataValue > | |
| gmx::ConstArrayRef< const char * > | |
| gmx::ConstArrayRef< real > | |
| gmx::FlagsTemplate< Flag > | |
| gmx::FlagsTemplate< OptionFlag > | |
 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< 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, 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::OptionStorageTemplate< bool > | |
| gmx::OptionStorageTemplate< double > | |
| gmx::OptionStorageTemplate< float > | |
| gmx::OptionStorageTemplate< gmx_int64_t > | |
| gmx::OptionStorageTemplate< int > | |
| gmx::OptionStorageTemplate< Selection > | |
| gmx::OptionStorageTemplate< std::string > | |
| gmx::AlignedAllocator< T > | Aligned memory allocator |
| gmx::AlignedAllocator< T >::rebind< U > | Standard-required typedef to use allocator with different class |
| 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::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::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::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::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::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::HelpManager | Helper for providing interactive online help |
| gmx::HelpWriterContext | Context information for writing out help |
| 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::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::InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| 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::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::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::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::PrivateImplPointer< Impl > | Helper class to manage a pointer to a private implementation class |
| gmx::Regex | Represents a regular expression |
| 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::SelectionPosition | Provides access to information about a single selected position |
| 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::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::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::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::IntegrationTestFixture | Test fixture for integration tests |
| 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::NoTextMatch | Do not match the text (the contents are ignored) |
| gmx::test::XvgMatch | Match the contents as an xvg file |
| gmx::test::MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
| 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 passed 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_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_ga2la_t | Structure for all global to local mapping information |
| 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_sparsematrix | Sparse matrix storage format |
| 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 |
| t_cosines | Declares inputrec data structure and utilities |
| 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 |
| 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 |
1.8.5
