  gmx | Generic GROMACS namespace |
 test | Testing utilities namespace |
  AnalysisDataTestInputPointSet | Represents a single set of points in AnalysisDataTestInputFrame structure |
| AnalysisDataTestInputFrame | Represents a single frame in AnalysisDataTestInput structure |
| AnalysisDataTestInput | Represents static input data for AbstractAnalysisData tests |
| AnalysisDataTestFixture | Test fixture for AbstractAnalysisData testing |
| MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
| CommandLine | Helper class for tests that need to construct command lines |
| CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
| CommandLineTestBase | Test fixture for tests that call a single command-line program with input/output files |
| ConfMatch | Match the contents as an gro file |
| IntegrationTestFixture | Test fixture for integration tests |
| InteractiveTestHelper | Helper class for testing interactive sessions |
| TestReferenceChecker | Handles comparison to test reference data |
| TestReferenceData | Handles creation of and comparison to test reference data |
| StringTestBase | Test fixture for tests that check string formatting |
| FloatingPointDifference | Computes and represents a floating-point difference value |
| FloatingPointTolerance | Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance |
| TestException | Exception class for reporting errors in tests |
| TestFileManager | Helper for tests that need input and output files |
| TestFileInputRedirector | In-memory implementation for IFileInputRedirector for tests |
| TestFileOutputRedirector | In-memory implementation of IFileOutputRedirector for tests |
| TestOptionsProvider | Provides additional options for the test executable |
| ITextBlockMatcher | Represents a text matcher, matching text stream contents against reference data |
| ITextBlockMatcherSettings | Represents a factory for creating a text matcher |
| ExactTextMatch | Use an exact text match (the contents should be exactly equal) |
| NoTextMatch | Do not match the text (the contents are ignored) |
 XvgMatch | Match the contents as an xvg file |
| AbstractAnalysisData | Abstract base class for all objects that provide data |
| AnalysisData | Parallelizable data container for raw data |
| AnalysisDataHandle | Handle for inserting data into AnalysisData |
| AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
| AnalysisArrayData | Simple in-memory data array |
| AnalysisDataValue | Value type for representing a single value in analysis data objects |
| AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
| AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
| AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
| IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
| AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
| AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
| AnalysisDataModuleManager | Encapsulates handling of data modules attached to AbstractAnalysisData |
| AnalysisDataStorageFrame | Allows assigning values for a data frame in AnalysisDataStorage |
| AnalysisDataStorage | Helper class that implements storage of data |
| AnalysisDataAverageModule | Data module for independently averaging each column in input data |
| AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
| AnalysisDataDisplacementModule | Data module for calculating displacements |
| AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
| AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
| AbstractAverageHistogram | Base class for representing histograms averaged over frames |
| AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
| AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| AnalysisDataBinAverageModule | Data module for bin averages |
| AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
| AnalysisDataPlotSettings | Common settings for data plots |
| AbstractPlotModule | Abstract data module for writing data into a file |
| AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
| AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
| AnalysisDataParallelOptions | Parallelization options for analysis data objects |
| CommandLineHelpContext | Context information for writing out command-line help |
| GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
| ConstArrayRef | STL-like container for non-mutable interface to a C array (or part of a std::vector) |
| CommandLineHelpWriter | Writes help information for Options |
| CommandLineModuleSettings | Settings to pass information between a module and the general runner |
| ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
| CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
| CommandLineModuleGroup | Handle to add content to a group added with CommandLineModuleManager::addModuleGroup() |
| ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
| ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
| CommandLineParser | Implements command-line parsing for Options objects |
| IExecutableEnvironment | Allows customization of the way various directories are found by CommandLineProgramContext |
| CommandLineProgramContext | Program context implementation for command line programs |
| CpuInfo | Detect CPU capabilities and basic logical processor info |
| LogicalProcessor | Entry with basic information for a single logical processor |
| HardwareTopology | Information about sockets, cores, threads, numa, caches |
| Cache | Information about a single cache level |
| Core | Information about a single core in a socket |
| Device | Information about a single PCI device |
| HWThread | Information about a single hardware thread in a core |
| LogicalProcessor | Information about socket, core and hwthread for a logical processor |
| Machine | Hardware topology information about the entire machine |
| Numa | Information about a single numa node |
| NumaNode | Information about each numa node in system |
| Socket | Information about a single socket in the system |
| StaticLog2 | Evaluate log2(n) for integer n statically at compile time |
| StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
| StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
| BasicVector | C++ class for 3D vectors |
| ArrayRef | STL-like container for an interface to a C array (or part of a std::vector) |
| TextTableFormatter | Formats rows of a table for text output |
| HelpManager | Helper for providing interactive online help |
| AbstractSimpleHelpTopic | Abstract base class for help topics that have simple text and no subtopics |
| AbstractCompositeHelpTopic | Abstract base class for help topics that have simple text and subtopics |
| SimpleHelpTopic | Template for simple implementation of AbstractSimpleHelpTopic |
| CompositeHelpTopic | Template for simple implementation of AbstractCompositeHelpTopic |
| HelpLinks | Hyperlink data for writing out help |
| HelpWriterContext | Context information for writing out help |
| IHelpTopic | Provides a single online help topic |
| OptionStorageTemplate | Templated base class for constructing option value storage classes |
| AbstractOption | Abstract base class for specifying option properties |
| OptionTemplate | Templated base class for constructing concrete option settings classes |
| OptionInfo | Gives information and allows modifications to an option after creation |
| AbstractOptionStorage | Abstract base class for converting, validating, and storing option values |
| BooleanOption | Specifies an option that provides boolean values |
| IntegerOption | Specifies an option that provides integer values |
| Int64Option | Specifies an option that provides 64-bit integer values |
| DoubleOption | Specifies an option that provides floating-point (double) values |
| FloatOption | Specifies an option that provides floating-point (float) values |
| StringOption | Specifies an option that provides string values |
| EnumOption | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
| BooleanOptionInfo | Wrapper class for accessing boolean option information |
| IntegerOptionInfo | Wrapper class for accessing integer option information |
| Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
| DoubleOptionInfo | Wrapper class for accessing floating-point option information |
| FloatOptionInfo | Wrapper class for accessing floating-point option information |
| StringOptionInfo | Wrapper class for accessing string option information |
| EnumOptionInfo | Wrapper class for accessing enum option information |
| OptionsBehaviorCollection | Container for IOptionsBehavior objects |
| FileNameOption | Specifies an option that provides file names |
| FileNameOptionInfo | Wrapper class for accessing file name option information |
| FileNameOptionManager | Handles interaction of file name options with global options |
| IOptionsBehavior | Interface to provide extension points for options parsing |
| IOptionsContainer | Interface for adding input options |
| OptionManagerContainer | Container to keep managers added with Options::addManager() and pass them to options |
| IOptionManager | Base class for option managers |
| Options | Collection of options |
| OptionsAssigner | Decorator class for assigning values to Options |
| OptionsVisitor | Pure interface for visiting options in a Options object |
| OptionsTypeVisitor | Abstract base class for visiting options of a particular type |
| OptionsIterator | Decorator class for visiting options in a Options object |
| OptionsModifyingVisitor | Pure interface for visiting options in a Options object, allowing modifications |
| OptionsModifyingTypeVisitor | Abstract base class for visiting options of a particular type, allowing modifications |
| OptionsModifyingIterator | Decorator class for visiting options in a Options object, allowing changes |
| TimeUnitManager | Provides common functionality for time unit conversions |
| TimeUnitBehavior | Options behavior to add a time unit option |
| ExponentialDistribution | Exponential distribution |
| param_type | Exponential distribution parameters |
| GammaDistribution | Gamma distribution |
| param_type | Gamma distribution parameters |
| NormalDistribution | Normal distribution |
| param_type | Normal distribution parameters |
| TabulatedNormalDistribution | Tabulated normal random distribution |
| param_type | Normal distribution parameter class (mean and stddev) |
| ThreeFry2x64General | General implementation class for ThreeFry counter-based random engines |
| ThreeFry2x64 | ThreeFry2x64 random engine with 20 iteractions |
| ThreeFry2x64Fast | ThreeFry2x64 random engine with 13 iteractions |
| UniformIntDistribution | Uniform integer distribution |
| param_type | Uniform int distribution parameters |
| UniformRealDistribution | Uniform real distribution |
| param_type | Uniform real distribution parameters |
| AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
| AnalysisNeighborhood | Neighborhood searching for analysis tools |
| AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
| AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
| AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
| Selection | Provides access to a single selection |
| SelectionPosition | Provides access to information about a single selected position |
| SelectionCollection | Collection of selections |
| SelectionFileOption | Specifies a special option that provides selections from a file |
| SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
| SelectionOption | Specifies an option that provides selection(s) |
| SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
| ITopologyProvider | Provides topology information to SelectionOptionBehavior |
| SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
| SelectionOptionManager | Handles interaction of selection options with other options and user input |
| Simd4Double | SIMD4 double type |
| Simd4DBool | SIMD4 variable type to use for logical comparisons on doubles |
| Simd4Float | SIMD4 float type |
| Simd4FBool | SIMD4 variable type to use for logical comparisons on floats |
| SimdDouble | Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1 |
| SimdDInt32 | Integer SIMD variable type to use for conversions to/from double |
| SimdDBool | Boolean type for double SIMD data |
| SimdDIBool | Boolean type for integer datatypes corresponding to double SIMD |
| SimdFloat | Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1 |
| SimdFInt32 | Integer SIMD variable type to use for conversions to/from float |
| SimdFBool | Boolean type for float SIMD data |
| SimdFIBool | Boolean type for integer datatypes corresponding to float SIMD |
| SimdLoadFProxyInternal | Proxy object to enable load() for SIMD and float types |
| SimdLoadUFProxyInternal | Proxy object to enable loadU() for SIMD and float types |
| SimdLoadDProxyInternal | Proxy object to enable load() for SIMD and double types |
| SimdLoadUDProxyInternal | Proxy object to enable loadU() for SIMD and double types |
| SimdLoadIProxyInternal | Proxy object load() for SimdFInt32, SImdDInt32, and int32 |
| SimdLoadUIProxyInternal | Proxy object - loadU() for SimdFInt32, SImdDInt32, and int32 |
| SimdSetZeroProxyInternal | Proxy object to enable setZero() for SIMD and real types |
| TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
| TrajectoryAnalysisModule | Base class for trajectory analysis modules |
| TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
| TopologyInformation | Topology information passed to a trajectory analysis module |
| TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
| AlignedAllocator | Aligned memory allocator |
| rebind | Standard-required typedef to use allocator with different class |
| EmptyArrayRef | Tag type to initialize empty array references |
| BinaryInformationSettings | Settings for printBinaryInformation() |
| PrivateImplPointer | Helper class to manage a pointer to a private implementation class |
| DataFileOptions | Search parameters for DataFileFinder |
| DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
| DataFileFinder | Searches data files from a set of paths |
| DirectoryEnumerator | Lists files in a directory |
| ExceptionInfo | Stores additional context information for exceptions |
| ExceptionInitializer | Provides information for Gromacs exception constructors |
| GromacsException | Base class for all exception objects in Gromacs |
| FileIOError | Exception class for file I/O errors |
| UserInputError | Exception class for user input errors |
| InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
| InconsistentInputError | Exception class for situations where user input is inconsistent |
| SimulationInstabilityError | Exception class for simulation instabilities |
| InternalError | Exception class for internal errors |
| APIError | Exception class for incorrect use of an API |
| NotImplementedError | Exception class for use of an unimplemented feature |
| IFileInputRedirector | Allows overriding file existence checks from code that supports it |
| IFileOutputRedirector | Allows capturing stdout and file output from code that supports it |
| StandardInputStream | Text input stream implementation for reading from stdin |
| TextInputFile | Text input stream implementation for reading from a file |
| TextOutputFile | Text output stream implementation for writing to a file |
| FlagsTemplate | Template class for typesafe handling of combination of flags |
| Regex | Represents a regular expression |
| MessageStringCollector | Helper class for collecting message strings, optionally with context |
| MessageStringContext | Convenience class for creating a message context |
| no_delete | Deleter for std::shared_ptr that does nothing |
| InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| IProgramContext | Provides context information about the program that is calling the library |
| scoped_cptr | Stripped-down version of scoped_ptr that uses sfree() or custom deleter |
| StringOutputStream | Text output stream implementation for writing to an in-memory string |
| StringInputStream | Helper class to convert static string data to a stream |
| StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
| IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
| TextLineWrapperSettings | Stores settings for line wrapping |
| TextLineWrapper | Wraps lines to a predefined length |
| TextReader | Reads text from a TextInputStream |
| TextInputStream | Interface for reading text |
| TextOutputStream | Interface for writing text |
| TextWriter | Writes text into a TextOutputStream |
| 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 |
| 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 |
1.8.5
