  anonymous_namespace{abstractoptionstorage.cpp} | |
   MockOptionStorage | Mock implementation of an option storage class for unit testing |
 MockOption | Specifies an option that has a mock storage object for unit testing |
| anonymous_namespace{analysisdata.cpp} | |
| anonymous_namespace{angle.cpp} | |
| anonymous_namespace{arraydata.cpp} | |
| anonymous_namespace{average.cpp} | |
| anonymous_namespace{basicoptions.cpp} | |
| anonymous_namespace{binaryinformation.cpp} | |
| anonymous_namespace{cmdlinehelpmodule.cpp} | |
| anonymous_namespace{cmdlinehelpwriter.cpp} | |
| anonymous_namespace{cmdlinemodulemanager.cpp} | |
| anonymous_namespace{cmdlineparser.cpp} | |
| anonymous_namespace{cmdlineprogramcontext.cpp} | |
| anonymous_namespace{cmdlinerunner.cpp} | |
| anonymous_namespace{compressed_x_output.cpp} | |
| MdrunCompressedXOutputTest | Test fixture for mdrun -x |
| anonymous_namespace{confio.cpp} | |
| anonymous_namespace{cpuinfo.cpp} | |
| anonymous_namespace{distance.cpp} | |
| anonymous_namespace{domain_decomposition.cpp} | |
| DomainDecompositionSpecialCasesTest | Test fixture for domain decomposition special cases |
| anonymous_namespace{evaluate.cpp} | |
| MempoolSelelemReserver | Reserves memory for a selection element from the evaluation memory pool |
| MempoolGroupReserver | Reserves memory for an index group from the evaluation memory pool |
| SelelemTemporaryValueAssigner | Assigns a temporary value for a selection element |
| anonymous_namespace{fft.cpp} | |
| anonymous_namespace{filenameoption.cpp} | |
| anonymous_namespace{filenameoptionmanager.cpp} | |
| anonymous_namespace{freevolume.cpp} | |
| anonymous_namespace{functions.cpp} | |
| anonymous_namespace{genconf.cpp} | |
| anonymous_namespace{gmx_traj_tests.cpp} | |
| anonymous_namespace{grompp.cpp} | |
| GromppTest | Test fixture for grompp |
| anonymous_namespace{hardwaretopology.cpp} | |
| anonymous_namespace{helpformat.cpp} | |
| anonymous_namespace{helpmanager.cpp} | |
| anonymous_namespace{helpwritercontext.cpp} | |
| anonymous_namespace{histogram.cpp} | |
| MockAverageHistogram | Mock object for testing gmx::AbstractAverageHistogram |
| anonymous_namespace{indexutil.cpp} | |
| anonymous_namespace{insert-molecules.cpp} | |
| anonymous_namespace{interactivetest.cpp} | |
| anonymous_namespace{invertmatrix.cpp} | |
| anonymous_namespace{legacymodules.cpp} | Registers command-line modules for pre-5.0 binaries |
| ObsoleteToolModule | Command line module that provides information about obsolescence |
| anonymous_namespace{lifetime.cpp} | |
| anonymous_namespace{listed-forces.cpp} | |
| anonymous_namespace{mdrun_main.cpp} | |
| anonymous_namespace{nbsearch.cpp} | |
| anonymous_namespace{option.cpp} | |
| anonymous_namespace{optionsassigner.cpp} | |
| anonymous_namespace{pairdist.cpp} | |
| anonymous_namespace{pargs.cpp} | |
| anonymous_namespace{parsetree.cpp} | |
| anonymous_namespace{path.cpp} | |
| anonymous_namespace{plot.cpp} | |
| anonymous_namespace{poscalc.cpp} | |
| anonymous_namespace{position-restraints.cpp} | |
| anonymous_namespace{rdf.cpp} | |
| anonymous_namespace{refdata_tests.cpp} | |
| anonymous_namespace{rerun.cpp} | |
| MdrunRerun | Test fixture for mdrun -rerun |
| anonymous_namespace{sasa.cpp} | |
| anonymous_namespace{select.cpp} | |
| anonymous_namespace{selectioncollection.cpp} | |
| anonymous_namespace{selectionoption.cpp} | |
| anonymous_namespace{selhelp.cpp} | |
| 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 |
| t_methoddata_kwstr | Data structure for string keyword expression evaluation |
| anonymous_namespace{solvate.cpp} | |
| anonymous_namespace{stringutil.cpp} | |
| anonymous_namespace{surfacearea.cpp} | |
| anonymous_namespace{sysinfo.cpp} | |
| anonymous_namespace{testasserts_tests.cpp} | |
| anonymous_namespace{textwriter.cpp} | |
| anonymous_namespace{timeunitmanager.cpp} | |
| anonymous_namespace{tngio.cpp} | |
| anonymous_namespace{trajectory_writing.cpp} | |
| anonymous_namespace{vectypes.cpp} | |
| anonymous_namespace{xvgtest_tests.cpp} | |
| gmx | Generic GROMACS namespace |
| analysismodules | |
| anonymous_namespace{angle.cpp} | |
| AnglePositionIterator | Helper to encapsulate logic for looping over input selections |
| anonymous_namespace{distance.cpp} | |
| anonymous_namespace{freevolume.cpp} | |
| FreeVolume | Class used to compute free volume in a simulations box |
| anonymous_namespace{pairdist.cpp} | |
| PairDistance | Implements gmx pairdist trajectory analysis module |
| PairDistanceModuleData | Temporary memory for use within a single-frame calculation |
| anonymous_namespace{rdf.cpp} | |
| Rdf | Implements gmx rdf trajectory analysis module |
| RdfModuleData | Temporary memory for use within a single-frame calculation |
| anonymous_namespace{sasa.cpp} | |
| t_conect | Tracks information on two nearest neighbors of a single surface dot |
| Sasa | Implements gmx sas trajectory analysis module |
| SasaModuleData | Temporary memory for use within a single-frame calculation |
 anonymous_namespace{select.cpp} | |
 IndexFileWriterModule | Data module for writing index files |
| anonymous_namespace{analysismodule.cpp} | |
| TrajectoryAnalysisModuleDataBasic | Basic thread-local trajectory analysis data storage class |
| anonymous_namespace{arrayref.cpp} | |
| anonymous_namespace{autocorr.cpp} | |
| anonymous_namespace{cmdlinehelpcontext.cpp} | |
| anonymous_namespace{cmdlinehelpmodule.cpp} | |
| RootHelpTopic | Help topic that forms the root of the help tree for the help subcommand |
| IHelpExport | Callbacks for exporting help information for command-line modules |
| CommandsHelpTopic | Help topic for listing the commands |
| ModuleHelpTopic | Help topic wrapper for a command-line module |
| HelpExportReStructuredText | Implements export for web pages as reStructuredText |
| HelpExportCompletion | Implements export for command-line completion |
| anonymous_namespace{cmdlinehelpwriter.cpp} | |
| IOptionsFormatter | Interface for output format specific formatting of options |
| OptionsFilter | Output format independent processing of options |
| SynopsisFormatter | Formatter implementation for synopsis |
| OptionsListFormatter | Formatter implementation for help export |
| anonymous_namespace{cmdlineinit.cpp} | |
| anonymous_namespace{cmdlinemodulemanager.cpp} | |
| CMainCommandLineModule | Implements a ICommandLineModule, given a function with C/C++ main() signature |
| anonymous_namespace{cmdlineoptionsmodule.cpp} | |
| anonymous_namespace{cmdlineprogramcontext.cpp} | |
| DefaultExecutableEnvironment | Default implementation for IExecutableEnvironment |
| anonymous_namespace{cmdlinerunner.cpp} | |
| anonymous_namespace{coolstuff.cpp} | |
| anonymous_namespace{cpuinfo.cpp} | |
| anonymous_namespace{errorcodes.cpp} | |
| anonymous_namespace{exceptions.cpp} | |
| ErrorMessage | Error message or error context text item |
| IMessageWriter | Abstracts actual output from the other logic in exception formatting |
| MessageWriterFileNoThrow | Exception information writer for cases where exceptions should be avoided |
| MessageWriterTextWriter | Exception information writer to format into a TextOutputStream |
| MessageWriterString | Exception information writer to format into an std::string |
| anonymous_namespace{expfit.cpp} | |
| anonymous_namespace{exponentialdistribution.cpp} | |
| anonymous_namespace{filenameoption.cpp} | |
| FileTypeMapping | Mapping from OptionFileType to a file type in filetypes.h |
| FileTypeHandler | Handles a single file type known to FileNameOptionStorage |
| anonymous_namespace{filenameoptionmanager.cpp} | |
| anonymous_namespace{fileredirector.cpp} | |
| DefaultInputRedirector | Implements the redirector returned by defaultFileInputRedirector() |
| DefaultOutputRedirector | Implements the redirector returned by defaultFileOutputRedirector() |
| anonymous_namespace{filestream.cpp} | |
| anonymous_namespace{futil.cpp} | |
| anonymous_namespace{gammadistribution.cpp} | |
| anonymous_namespace{hardwaretopology.cpp} | |
| anonymous_namespace{helpwritercontext.cpp} | |
| IWrapper | Custom output interface for HelpWriterContext::Impl::processMarkup() |
| WrapperToString | Wraps markup output into a single string |
| WrapperToVector | Wraps markup output into a vector of string (one line per element) |
| anonymous_namespace{histogram.cpp} | |
| StaticAverageHistogram | Represents copies of average histograms |
| anonymous_namespace{init.cpp} | |
| anonymous_namespace{insert-molecules.cpp} | |
| anonymous_namespace{modules.cpp} | |
| anonymous_namespace{nbsearch.cpp} | |
| MindistAction | Search action find the minimum distance |
| anonymous_namespace{normaldistribution.cpp} | |
| anonymous_namespace{optionsvisitor.cpp} | |
| anonymous_namespace{pargs.cpp} | |
| OptionsAdapter | Conversion helper between t_pargs/t_filenm and Options |
| anonymous_namespace{programcontext.cpp} | |
| DefaultProgramContext | Default implementation of IProgramContext |
| anonymous_namespace{pull.cpp} | |
| anonymous_namespace{rstparser.cpp} | |
| anonymous_namespace{seed.cpp} | |
| anonymous_namespace{selectioncollection.cpp} | |
| anonymous_namespace{selhelp.cpp} | |
| KeywordDetailsHelpTopic | Help topic implementation for an individual selection method |
| KeywordsHelpTopic | Custom help topic for printing a list of selection keywords |
| anonymous_namespace{shellcompletions.cpp} | |
| anonymous_namespace{stringutil.cpp} | |
| anonymous_namespace{tabulatednormaldistribution.cpp} | |
| anonymous_namespace{tabulatednormaldistribution.h} | |
| anonymous_namespace{threefry.cpp} | |
| anonymous_namespace{timeunitmanager.cpp} | |
| TimeOptionScaler | Option visitor that scales time options |
| anonymous_namespace{uniformintdistribution.cpp} | |
| anonymous_namespace{uniformrealdistribution.cpp} | |
| internal | Internal GROMACS namespace |
| anonymous_namespace{selection.cpp} | |
| AnalysisDataHandleImpl | Private implementation class for AnalysisDataHandle |
| AnalysisDataStorageImpl | Private implementation class for AnalysisDataStorage |
| AnalysisDataStorageFrameData | Internal representation for a single stored frame |
| BasicAverageHistogramModule | Implements average histogram module that averages per-frame histograms |
| BasicHistogramImpl | Base class for private implementation classes for histogram modules |
| EnumIndexStoreInterface | Interface for handling storage of the enum indexes |
| EnumIndexStore | Type-specific implementation for EnumIndexStoreInterface |
| OptionsImpl | Private implementation class for Options |
| Group | Describes a group of options (see Options::addGroup()) |
| SelectionData | Internal data for a single selection |
| IExceptionInfo | Base class for ExceptionInfo |
| test | Testing utilities namespace |
| anonymous_namespace{base.cpp} | |
| anonymous_namespace{bootstrap_loadstore.cpp} | |
| anonymous_namespace{cmdlinemodulemanagertest.cpp} | |
| anonymous_namespace{cmdlinetest.cpp} | |
| anonymous_namespace{conftest.cpp} | |
| anonymous_namespace{mdruncomparisonfixture.cpp} | |
| anonymous_namespace{mock_datamodule.cpp} | |
| StaticDataFrameHeaderChecker | Functor for checking data frame header against static test input data |
| StaticDataPointsChecker | Functor for checking data frame points against static test input data |
| DataStorageRequester | Functor for requesting data storage |
| StaticDataPointsStorageChecker | Functor for checking data frame points and storage against static test input data |
| anonymous_namespace{moduletest.cpp} | |
| anonymous_namespace{refdata-xml.cpp} | |
| anonymous_namespace{refdata.cpp} | |
| anonymous_namespace{scalar.cpp} | |
| anonymous_namespace{scalar_math.cpp} | |
| anonymous_namespace{scalar_util.cpp} | |
| anonymous_namespace{simd4_floatingpoint.cpp} | |
| anonymous_namespace{simd4_math.cpp} | |
| anonymous_namespace{simd4_vector_operations.cpp} | |
| anonymous_namespace{simd_floatingpoint.cpp} | |
| anonymous_namespace{simd_floatingpoint_util.cpp} | |
| SimdFloatingpointUtilTest | Test fixture for higher-level floating-point utility functions |
| anonymous_namespace{simd_integer.cpp} | |
| anonymous_namespace{simd_math.cpp} | |
| anonymous_namespace{simd_vector_operations.cpp} | |
| anonymous_namespace{stringtest.cpp} | |
| anonymous_namespace{testasserts.cpp} | |
| anonymous_namespace{testinit.cpp} | |
| TestProgramContext | Custom program context for test binaries |
| anonymous_namespace{testoptions.cpp} | |
| TestOptionsRegistry | Singleton registry for test options added with GMX_TEST_OPTIONS |
| anonymous_namespace{textblockmatchers.cpp} | |
| anonymous_namespace{xvgtest.cpp} | |
| internal | |
| TestReferenceDataImpl | Private implementation class for TestReferenceData |
| 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 |
| MockModule | Mock implementation of gmx::ICommandLineModule |
| MockOptionsModule | Mock implementation of gmx::ICommandLineOptionsModule |
| CommandLineModuleManagerTestBase | Test fixture for tests using gmx::CommandLineModuleManager |
| SettleTest | Test fixture for testing SETTLE position updates |
| SignalTest | Test fixture for mdrun signalling |
| SimdBaseTest | Base class for SIMD test fixtures |
| SimdTest | Test fixture for SIMD tests |
| Simd4Test | Test fixture for SIMD4 tests - contains test settings |
| AbstractTrajectoryAnalysisModuleTestFixture | Test fixture for trajectory analysis modules |
| TrajectoryAnalysisModuleTestFixture | Test fixture for a trajectory analysis module |
| EnergyFrameReader | Manages returning an EnergyFrame containing required energy field values read from successive frames of an .edr file |
| EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
| MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
| SimulationRunner | Helper object for running grompp and mdrun in integration tests of mdrun functionality |
| MdrunTestFixtureBase | Declares test fixture base class for integration tests of mdrun functionality |
| MdrunTestFixture | Declares test fixture class for integration tests of mdrun functionality that use a single call of mdrun |
| ParameterizedMdrunTestFixture | Parameterized test fixture for mdrun integration tests |
| MultiSimTest | Test fixture for multi-sim functionality |
| BondedInteractionsTest | Test fixture for bonded interactions |
| TerminationHelper | Help test mdrun termination behaviour |
| TrajectoryFrameReader | Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file |
| TrajectoryFrame | Contains the content of a trajectory frame read by an TrajectoryFrameReader |
| 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 |
| Impl | Private implementation class for TestReferenceChecker |
| 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 |
| Impl | Private implementation class for TestFileManager |
| 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 |
| Impl | Private implementation class for AbstractAnalysisData |
| AnalysisData | Parallelizable data container for raw data |
| Impl | Private implementation class for AnalysisData |
| 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 |
| Impl | Private implementation class for AnalysisDataModuleManager |
| ModuleInfo | Stores information about an attached module |
| AnalysisDataProxy | Internal implementation class used to implement column modules |
| AnalysisDataStorageFrame | Allows assigning values for a data frame in AnalysisDataStorage |
| AnalysisDataStorage | Helper class that implements storage of data |
| AnalysisDataFrameLocalDataSetHandle | Handle to a single data set within frame-local data array |
| AnalysisDataFrameLocalDataHandle | Handle to a single frame data within frame-local data array |
| AnalysisDataFrameLocalData | Container for an array of frame-local values that supports parallel data processing |
| 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 |
| Impl | Private implementation class for AnalysisDataDisplacementModule |
| AnalysisDataFrameAverager | Helper class for modules that average values over frames |
| 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 |
| Impl | Private implementation class for AnalysisDataSimpleHistogramModule |
| AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| Impl | Private implementation class for AnalysisDataWeightedHistogramModule |
| AnalysisDataBinAverageModule | Data module for bin averages |
| AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
| Impl | Private implementation class for AnalysisDataLifetimeModule |
| 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 |
| Impl | Private implementation class for CommandLineHelpContext |
| GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
| CommandLineHelpModule | Command-line module for producing help |
| ConstArrayRef | STL-like container for non-mutable interface to a C array (or part of a std::vector) |
| CommandLineHelpWriter | Writes help information for Options |
| Impl | Private implementation class for CommandLineHelpWriter |
| CommandLineModuleSettings | Settings to pass information between a module and the general runner |
| ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
| CommandLineModuleGroupData | Internal data for a CommandLineModuleManager module group |
| CommandLineCommonOptionsHolder | Encapsulates some handling of common options to the wrapper binary |
| CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
| Impl | Private implementation class for CommandLineModuleManager |
| 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 |
| Impl | Private implementation class for CommandLineParser |
| 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) |
| SimulationSignal | POD-style object used by mdrun ranks to set and receive signals within and between simulations |
| SimulationSignaller | Object used by mdrun ranks to signal to each other at this step |
| TextTableFormatter | Formats rows of a table for text output |
| Impl | Private implementation class for TextTableFormatter |
| ColumnData | Manages a single column for TextTableFormatter |
| HelpManager | Helper for providing interactive online help |
| Impl | Private implementation class for HelpManager |
| 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 |
| Impl | Private implementation class for AbstractCompositeHelpTopic |
| SimpleHelpTopic | Template for simple implementation of AbstractSimpleHelpTopic |
| CompositeHelpTopic | Template for simple implementation of AbstractCompositeHelpTopic |
| HelpLinks | Hyperlink data for writing out help |
| Impl | Private implementation class for HelpLinks |
| HelpWriterContext | Context information for writing out help |
| Impl | Private implementation class for HelpWriterContext |
| SharedState | Shared, non-modifiable state for context objects |
| IHelpTopic | Provides a single online help topic |
| RstParagraphIterator | Iterator over reStructuredText paragraphs |
| 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 |
| BooleanOptionStorage | Converts, validates, and stores boolean values |
| IntegerOptionStorage | Converts, validates, and stores integer values |
| Int64OptionStorage | Converts, validates, and stores integer values |
| DoubleOptionStorage | Converts, validates, and stores floating-point (double) values |
| FloatOptionStorage | Converts, validates, and stores floating-point (float) values |
| StringOptionStorage | Converts, validates, and stores string values |
| EnumOptionStorage | Converts, validates, and stores enum values |
| 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 |
| Impl | Private implemention class for FileNameOptionManager |
| FileNameOptionStorage | Converts, validates, and stores file names |
| 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 |
| Impl | Private implementation class for OptionsAssigner |
| 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 |
| SelectionCompiler | Implements selection compilation |
| 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 |
| SelectionParserValue | Describes a parsed value, possibly resulting from expression evaluation |
| SelectionParserParameter | Describes a parsed method parameter |
| PositionCalculationCollection | Collection of gmx_ana_poscalc_t structures for the same topology |
| Impl | Private implementation class for PositionCalculationCollection |
| Selection | Provides access to a single selection |
| SelectionPosition | Provides access to information about a single selected position |
| SelectionEvaluator | Implements selection evaluation |
| SelectionCollection | Collection of selections |
| Impl | Private implemention class for SelectionCollection |
| SelectionFileOption | Specifies a special option that provides selections from a file |
| SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
| SelectionFileOptionStorage | Implementation for a special option for reading selections from files |
| 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 |
| Impl | Private implemention class for SelectionOptionManager |
| RequestsClearer | Helper class that clears a request list on scope exit |
| SelectionRequest | Request for postponed parsing of selections |
| SelectionOptionStorage | Converts, validates, and stores selection values |
| SelectionLocation | Stores the location of a selection element in the selection text |
| SelectionTreeElement | Represents an element of a selection expression |
| SelectionParserSymbol | Single symbol for the selection parser |
| Impl | Private implementation class for SelectionParserSymbol |
| SelectionParserSymbolIterator | Input iterator for iterating symbols of a given type |
| Impl | Private implementation class for SelectionParserSymbolIterator |
| SelectionParserSymbolTable | Symbol table for the selection parser |
| Impl | Private implementation class for SelectionParserSymbolTable |
| 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 |
| Impl | Private implementation class for TrajectoryAnalysisModuleData |
| TrajectoryAnalysisModule | Base class for trajectory analysis modules |
| Impl | Private implementation class for TrajectoryAnalysisModule |
| TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
| Impl | Private implementation class for TrajectoryAnalysisSettings |
| TopologyInformation | Topology information passed to a trajectory analysis module |
| TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
| SurfaceAreaCalculator | Computes surface areas for a group of atoms/spheres |
| TrajectoryAnalysisRunnerCommon | Implements common trajectory analysis runner functionality |
| 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 |
| ThrowLocation | Stores the location from which an exception was thrown |
| 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 |
| AnalysisTemplate | Template class to serve as a basis for user analysis tools |
| 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 |
| 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_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 |
| 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 |
| VsiteThread | Vsite thread task data structure |
1.8.5
