![o](ftv2pnode.png) anonymous_namespace{abstractoptionstorage.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) MockOptionStorage | Mock implementation of an option storage class for unit testing |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) MockOption | Specifies an option that has a mock storage object for unit testing |
![o](ftv2node.png) anonymous_namespace{analysisdata.cpp} | |
![o](ftv2node.png) anonymous_namespace{angle.cpp} | |
![o](ftv2node.png) anonymous_namespace{arraydata.cpp} | |
![o](ftv2node.png) anonymous_namespace{average.cpp} | |
![o](ftv2node.png) anonymous_namespace{basicoptions.cpp} | |
![o](ftv2node.png) anonymous_namespace{binaryinformation.cpp} | |
![o](ftv2node.png) anonymous_namespace{cmdlinehelpmodule.cpp} | |
![o](ftv2node.png) anonymous_namespace{cmdlinehelpwriter.cpp} | |
![o](ftv2node.png) anonymous_namespace{cmdlinemodulemanager.cpp} | |
![o](ftv2node.png) anonymous_namespace{cmdlineparser.cpp} | |
![o](ftv2node.png) anonymous_namespace{cmdlineprogramcontext.cpp} | |
![o](ftv2node.png) anonymous_namespace{cmdlinerunner.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{compressed_x_output.cpp} | |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) MdrunCompressedXOutputTest | Test fixture for mdrun -x |
![o](ftv2node.png) anonymous_namespace{confio.cpp} | |
![o](ftv2node.png) anonymous_namespace{cpuinfo.cpp} | |
![o](ftv2node.png) anonymous_namespace{distance.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{domain_decomposition.cpp} | |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) DomainDecompositionSpecialCasesTest | Test fixture for domain decomposition special cases |
![o](ftv2pnode.png) anonymous_namespace{evaluate.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) MempoolSelelemReserver | Reserves memory for a selection element from the evaluation memory pool |
![|](ftv2vertline.png) ![o](ftv2node.png) MempoolGroupReserver | Reserves memory for an index group from the evaluation memory pool |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) SelelemTemporaryValueAssigner | Assigns a temporary value for a selection element |
![o](ftv2node.png) anonymous_namespace{fft.cpp} | |
![o](ftv2node.png) anonymous_namespace{filenameoption.cpp} | |
![o](ftv2node.png) anonymous_namespace{filenameoptionmanager.cpp} | |
![o](ftv2node.png) anonymous_namespace{freevolume.cpp} | |
![o](ftv2node.png) anonymous_namespace{functions.cpp} | |
![o](ftv2node.png) anonymous_namespace{genconf.cpp} | |
![o](ftv2node.png) anonymous_namespace{gmx_traj_tests.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{grompp.cpp} | |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) GromppTest | Test fixture for grompp |
![o](ftv2node.png) anonymous_namespace{hardwaretopology.cpp} | |
![o](ftv2node.png) anonymous_namespace{helpformat.cpp} | |
![o](ftv2node.png) anonymous_namespace{helpmanager.cpp} | |
![o](ftv2node.png) anonymous_namespace{helpwritercontext.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{histogram.cpp} | |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) MockAverageHistogram | Mock object for testing gmx::AbstractAverageHistogram |
![o](ftv2node.png) anonymous_namespace{indexutil.cpp} | |
![o](ftv2node.png) anonymous_namespace{insert-molecules.cpp} | |
![o](ftv2node.png) anonymous_namespace{interactivetest.cpp} | |
![o](ftv2node.png) anonymous_namespace{invertmatrix.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{legacymodules.cpp} | Registers command-line modules for pre-5.0 binaries |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) ObsoleteToolModule | Command line module that provides information about obsolescence |
![o](ftv2node.png) anonymous_namespace{lifetime.cpp} | |
![o](ftv2node.png) anonymous_namespace{listed-forces.cpp} | |
![o](ftv2node.png) anonymous_namespace{mdrun_main.cpp} | |
![o](ftv2node.png) anonymous_namespace{nbsearch.cpp} | |
![o](ftv2node.png) anonymous_namespace{option.cpp} | |
![o](ftv2node.png) anonymous_namespace{optionsassigner.cpp} | |
![o](ftv2node.png) anonymous_namespace{pairdist.cpp} | |
![o](ftv2node.png) anonymous_namespace{pargs.cpp} | |
![o](ftv2node.png) anonymous_namespace{parsetree.cpp} | |
![o](ftv2node.png) anonymous_namespace{path.cpp} | |
![o](ftv2node.png) anonymous_namespace{plot.cpp} | |
![o](ftv2node.png) anonymous_namespace{poscalc.cpp} | |
![o](ftv2node.png) anonymous_namespace{position-restraints.cpp} | |
![o](ftv2node.png) anonymous_namespace{rdf.cpp} | |
![o](ftv2node.png) anonymous_namespace{refdata_tests.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{rerun.cpp} | |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) MdrunRerun | Test fixture for mdrun -rerun |
![o](ftv2node.png) anonymous_namespace{sasa.cpp} | |
![o](ftv2node.png) anonymous_namespace{select.cpp} | |
![o](ftv2node.png) anonymous_namespace{selectioncollection.cpp} | |
![o](ftv2node.png) anonymous_namespace{selectionoption.cpp} | |
![o](ftv2node.png) anonymous_namespace{selhelp.cpp} | |
![o](ftv2pnode.png) anonymous_namespace{shake.cpp} | |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) ShakeTest | Test fixture for testing SHAKE |
![o](ftv2pnode.png) anonymous_namespace{sm_keywords.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) StringKeywordMatchItem | Single item in the list of strings/regular expressions to match |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) t_methoddata_kwstr | Data structure for string keyword expression evaluation |
![o](ftv2node.png) anonymous_namespace{solvate.cpp} | |
![o](ftv2node.png) anonymous_namespace{stringutil.cpp} | |
![o](ftv2node.png) anonymous_namespace{surfacearea.cpp} | |
![o](ftv2node.png) anonymous_namespace{sysinfo.cpp} | |
![o](ftv2node.png) anonymous_namespace{testasserts_tests.cpp} | |
![o](ftv2node.png) anonymous_namespace{textwriter.cpp} | |
![o](ftv2node.png) anonymous_namespace{timeunitmanager.cpp} | |
![o](ftv2node.png) anonymous_namespace{tngio.cpp} | |
![o](ftv2node.png) anonymous_namespace{trajectory_writing.cpp} | |
![o](ftv2node.png) anonymous_namespace{vectypes.cpp} | |
![o](ftv2node.png) anonymous_namespace{xvgtest_tests.cpp} | |
![o](ftv2pnode.png) gmx | Generic GROMACS namespace |
![|](ftv2vertline.png) ![o](ftv2pnode.png) analysismodules | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{angle.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) AnglePositionIterator | Helper to encapsulate logic for looping over input selections |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{distance.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{freevolume.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) FreeVolume | Class used to compute free volume in a simulations box |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{pairdist.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) PairDistance | Implements gmx pairdist trajectory analysis module |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) PairDistanceModuleData | Temporary memory for use within a single-frame calculation |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{rdf.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Rdf | Implements gmx rdf trajectory analysis module |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) RdfModuleData | Temporary memory for use within a single-frame calculation |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{sasa.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) t_conect | Tracks information on two nearest neighbors of a single surface dot |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Sasa | Implements gmx sas trajectory analysis module |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) SasaModuleData | Temporary memory for use within a single-frame calculation |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) anonymous_namespace{select.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) IndexFileWriterModule | Data module for writing index files |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{analysismodule.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) TrajectoryAnalysisModuleDataBasic | Basic thread-local trajectory analysis data storage class |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{arrayref.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{autocorr.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cmdlinehelpcontext.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{cmdlinehelpmodule.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) RootHelpTopic | Help topic that forms the root of the help tree for the help subcommand |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) IHelpExport | Callbacks for exporting help information for command-line modules |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CommandsHelpTopic | Help topic for listing the commands |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ModuleHelpTopic | Help topic wrapper for a command-line module |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) HelpExportReStructuredText | Implements export for web pages as reStructuredText |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) HelpExportCompletion | Implements export for command-line completion |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{cmdlinehelpwriter.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) IOptionsFormatter | Interface for output format specific formatting of options |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) OptionsFilter | Output format independent processing of options |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SynopsisFormatter | Formatter implementation for synopsis |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) OptionsListFormatter | Formatter implementation for help export |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cmdlineinit.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{cmdlinemodulemanager.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) CMainCommandLineModule | Implements a ICommandLineModule, given a function with C/C++ main() signature |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cmdlineoptionsmodule.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{cmdlineprogramcontext.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) DefaultExecutableEnvironment | Default implementation for IExecutableEnvironment |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cmdlinerunner.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{coolstuff.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cpuinfo.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{errorcodes.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{exceptions.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ErrorMessage | Error message or error context text item |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) IMessageWriter | Abstracts actual output from the other logic in exception formatting |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MessageWriterFileNoThrow | Exception information writer for cases where exceptions should be avoided |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MessageWriterTextWriter | Exception information writer to format into a TextOutputStream |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) MessageWriterString | Exception information writer to format into an std::string |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{expfit.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{exponentialdistribution.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{filenameoption.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) FileTypeMapping | Mapping from OptionFileType to a file type in filetypes.h |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) FileTypeHandler | Handles a single file type known to FileNameOptionStorage |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{filenameoptionmanager.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{fileredirector.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) DefaultInputRedirector | Implements the redirector returned by defaultFileInputRedirector() |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) DefaultOutputRedirector | Implements the redirector returned by defaultFileOutputRedirector() |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{filestream.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{futil.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{gammadistribution.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{hardwaretopology.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{helpwritercontext.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) IWrapper | Custom output interface for HelpWriterContext::Impl::processMarkup() |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) WrapperToString | Wraps markup output into a single string |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) WrapperToVector | Wraps markup output into a vector of string (one line per element) |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{histogram.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) StaticAverageHistogram | Represents copies of average histograms |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{init.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{insert-molecules.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{modules.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{nbsearch.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) MindistAction | Search action find the minimum distance |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{normaldistribution.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{optionsvisitor.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{pargs.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) OptionsAdapter | Conversion helper between t_pargs/t_filenm and Options |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{programcontext.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) DefaultProgramContext | Default implementation of IProgramContext |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{pull.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{rstparser.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{seed.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{selectioncollection.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{selhelp.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) KeywordDetailsHelpTopic | Help topic implementation for an individual selection method |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) KeywordsHelpTopic | Custom help topic for printing a list of selection keywords |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{shellcompletions.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{stringutil.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{tabulatednormaldistribution.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{tabulatednormaldistribution.h} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{threefry.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{timeunitmanager.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) TimeOptionScaler | Option visitor that scales time options |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{uniformintdistribution.cpp} | |
![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{uniformrealdistribution.cpp} | |
![|](ftv2vertline.png) ![o](ftv2pnode.png) internal | Internal GROMACS namespace |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{selection.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataHandleImpl | Private implementation class for AnalysisDataHandle |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataStorageImpl | Private implementation class for AnalysisDataStorage |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataStorageFrameData | Internal representation for a single stored frame |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) BasicAverageHistogramModule | Implements average histogram module that averages per-frame histograms |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) BasicHistogramImpl | Base class for private implementation classes for histogram modules |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) EnumIndexStoreInterface | Interface for handling storage of the enum indexes |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) EnumIndexStore | Type-specific implementation for EnumIndexStoreInterface |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) OptionsImpl | Private implementation class for Options |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Group | Describes a group of options (see Options::addGroup()) |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SelectionData | Internal data for a single selection |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) IExceptionInfo | Base class for ExceptionInfo |
![|](ftv2vertline.png) ![o](ftv2pnode.png) test | Testing utilities namespace |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{base.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{bootstrap_loadstore.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cmdlinemodulemanagertest.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{cmdlinetest.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{mdruncomparisonfixture.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{mock_datamodule.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) StaticDataFrameHeaderChecker | Functor for checking data frame header against static test input data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) StaticDataPointsChecker | Functor for checking data frame points against static test input data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) DataStorageRequester | Functor for requesting data storage |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) StaticDataPointsStorageChecker | Functor for checking data frame points and storage against static test input data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{moduletest.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{refdata-xml.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{refdata.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{scalar.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{scalar_math.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{scalar_util.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd4_floatingpoint.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd4_math.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd4_vector_operations.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd_floatingpoint.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{simd_floatingpoint_util.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) SimdFloatingpointUtilTest | Test fixture for higher-level floating-point utility functions |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd_integer.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd_math.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{simd_vector_operations.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{stringtest.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{testasserts.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{testinit.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) TestProgramContext | Custom program context for test binaries |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) anonymous_namespace{testoptions.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) TestOptionsRegistry | Singleton registry for test options added with GMX_TEST_OPTIONS |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{textblockmatchers.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) anonymous_namespace{xvgtest.cpp} | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) internal | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) TestReferenceDataImpl | Private implementation class for TestReferenceData |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataTestInputPointSet | Represents a single set of points in AnalysisDataTestInputFrame structure |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataTestInputFrame | Represents a single frame in AnalysisDataTestInput structure |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataTestInput | Represents static input data for AbstractAnalysisData tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataTestFixture | Test fixture for AbstractAnalysisData testing |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MockModule | Mock implementation of gmx::ICommandLineModule |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MockOptionsModule | Mock implementation of gmx::ICommandLineOptionsModule |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineModuleManagerTestBase | Test fixture for tests using gmx::CommandLineModuleManager |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SettleTest | Test fixture for testing SETTLE position updates |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SignalTest | Test fixture for mdrun signalling |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SimdBaseTest | Base class for SIMD test fixtures |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SimdTest | Test fixture for SIMD tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Simd4Test | Test fixture for SIMD4 tests - contains test settings |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) AbstractTrajectoryAnalysisModuleTestFixture | Test fixture for trajectory analysis modules |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisModuleTestFixture | Test fixture for a trajectory analysis module |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) EnergyFrameReader | Manages returning an EnergyFrame containing required energy field values read from successive frames of an .edr file |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) SimulationRunner | Helper object for running grompp and mdrun in integration tests of mdrun functionality |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MdrunTestFixtureBase | Declares test fixture base class for integration tests of mdrun functionality |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MdrunTestFixture | Declares test fixture class for integration tests of mdrun functionality that use a single call of mdrun |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ParameterizedMdrunTestFixture | Parameterized test fixture for mdrun integration tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) MultiSimTest | Test fixture for multi-sim functionality |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) BondedInteractionsTest | Test fixture for bonded interactions |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TerminationHelper | Help test mdrun termination behaviour |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryFrameReader | Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryFrame | Contains the content of a trajectory frame read by an TrajectoryFrameReader |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CommandLine | Helper class for tests that need to construct command lines |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineTestBase | Test fixture for tests that call a single command-line program with input/output files |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) IntegrationTestFixture | Test fixture for integration tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) InteractiveTestHelper | Helper class for testing interactive sessions |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) TestReferenceChecker | Handles comparison to test reference data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for TestReferenceChecker |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TestReferenceData | Handles creation of and comparison to test reference data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) StringTestBase | Test fixture for tests that check string formatting |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) FloatingPointDifference | Computes and represents a floating-point difference value |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) FloatingPointTolerance | Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TestException | Exception class for reporting errors in tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) TestFileManager | Helper for tests that need input and output files |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for TestFileManager |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TestFileInputRedirector | In-memory implementation for IFileInputRedirector for tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TestFileOutputRedirector | In-memory implementation of IFileOutputRedirector for tests |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) TestOptionsProvider | Provides additional options for the test executable |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ITextBlockMatcher | Represents a text matcher, matching text stream contents against reference data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ITextBlockMatcherSettings | Represents a factory for creating a text matcher |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ExactTextMatch | Use an exact text match (the contents should be exactly equal) |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) NoTextMatch | Do not match the text (the contents are ignored) |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) XvgMatch | Match the contents as an xvg file |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AbstractAnalysisData | Abstract base class for all objects that provide data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AbstractAnalysisData |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AnalysisData | Parallelizable data container for raw data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AnalysisData |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataHandle | Handle for inserting data into AnalysisData |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisArrayData | Simple in-memory data array |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataValue | Value type for representing a single value in analysis data objects |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
![|](ftv2vertline.png) ![o](ftv2node.png) IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AnalysisDataModuleManager | Encapsulates handling of data modules attached to AbstractAnalysisData |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) Impl | Private implementation class for AnalysisDataModuleManager |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) ModuleInfo | Stores information about an attached module |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataProxy | Internal implementation class used to implement column modules |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataStorageFrame | Allows assigning values for a data frame in AnalysisDataStorage |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataStorage | Helper class that implements storage of data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameLocalDataSetHandle | Handle to a single data set within frame-local data array |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameLocalDataHandle | Handle to a single frame data within frame-local data array |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameLocalData | Container for an array of frame-local values that supports parallel data processing |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataAverageModule | Data module for independently averaging each column in input data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AnalysisDataDisplacementModule | Data module for calculating displacements |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AnalysisDataDisplacementModule |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameAverager | Helper class for modules that average values over frames |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractAverageHistogram | Base class for representing histograms averaged over frames |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AnalysisDataSimpleHistogramModule |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AnalysisDataWeightedHistogramModule |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataBinAverageModule | Data module for bin averages |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AnalysisDataLifetimeModule |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataPlotSettings | Common settings for data plots |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractPlotModule | Abstract data module for writing data into a file |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataParallelOptions | Parallelization options for analysis data objects |
![|](ftv2vertline.png) ![o](ftv2pnode.png) CommandLineHelpContext | Context information for writing out command-line help |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for CommandLineHelpContext |
![|](ftv2vertline.png) ![o](ftv2node.png) GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineHelpModule | Command-line module for producing help |
![|](ftv2vertline.png) ![o](ftv2node.png) ConstArrayRef | STL-like container for non-mutable interface to a C array (or part of a std::vector) |
![|](ftv2vertline.png) ![o](ftv2pnode.png) CommandLineHelpWriter | Writes help information for Options |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for CommandLineHelpWriter |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineModuleSettings | Settings to pass information between a module and the general runner |
![|](ftv2vertline.png) ![o](ftv2node.png) ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineModuleGroupData | Internal data for a CommandLineModuleManager module group |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineCommonOptionsHolder | Encapsulates some handling of common options to the wrapper binary |
![|](ftv2vertline.png) ![o](ftv2pnode.png) CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for CommandLineModuleManager |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineModuleGroup | Handle to add content to a group added with CommandLineModuleManager::addModuleGroup() |
![|](ftv2vertline.png) ![o](ftv2node.png) ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
![|](ftv2vertline.png) ![o](ftv2node.png) ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
![|](ftv2vertline.png) ![o](ftv2pnode.png) CommandLineParser | Implements command-line parsing for Options objects |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for CommandLineParser |
![|](ftv2vertline.png) ![o](ftv2node.png) IExecutableEnvironment | Allows customization of the way various directories are found by CommandLineProgramContext |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineProgramContext | Program context implementation for command line programs |
![|](ftv2vertline.png) ![o](ftv2pnode.png) CpuInfo | Detect CPU capabilities and basic logical processor info |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) LogicalProcessor | Entry with basic information for a single logical processor |
![|](ftv2vertline.png) ![o](ftv2pnode.png) HardwareTopology | Information about sockets, cores, threads, numa, caches |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Cache | Information about a single cache level |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Core | Information about a single core in a socket |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Device | Information about a single PCI device |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) HWThread | Information about a single hardware thread in a core |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) LogicalProcessor | Information about socket, core and hwthread for a logical processor |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Machine | Hardware topology information about the entire machine |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) Numa | Information about a single numa node |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) NumaNode | Information about each numa node in system |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Socket | Information about a single socket in the system |
![|](ftv2vertline.png) ![o](ftv2node.png) StaticLog2 | Evaluate log2(n) for integer n statically at compile time |
![|](ftv2vertline.png) ![o](ftv2node.png) StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
![|](ftv2vertline.png) ![o](ftv2node.png) StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
![|](ftv2vertline.png) ![o](ftv2node.png) BasicVector | C++ class for 3D vectors |
![|](ftv2vertline.png) ![o](ftv2node.png) ArrayRef | STL-like container for an interface to a C array (or part of a std::vector) |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationSignal | POD-style object used by mdrun ranks to set and receive signals within and between simulations |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationSignaller | Object used by mdrun ranks to signal to each other at this step |
![|](ftv2vertline.png) ![o](ftv2pnode.png) TextTableFormatter | Formats rows of a table for text output |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) Impl | Private implementation class for TextTableFormatter |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) ColumnData | Manages a single column for TextTableFormatter |
![|](ftv2vertline.png) ![o](ftv2pnode.png) HelpManager | Helper for providing interactive online help |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for HelpManager |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractSimpleHelpTopic | Abstract base class for help topics that have simple text and no subtopics |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AbstractCompositeHelpTopic | Abstract base class for help topics that have simple text and subtopics |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for AbstractCompositeHelpTopic |
![|](ftv2vertline.png) ![o](ftv2node.png) SimpleHelpTopic | Template for simple implementation of AbstractSimpleHelpTopic |
![|](ftv2vertline.png) ![o](ftv2node.png) CompositeHelpTopic | Template for simple implementation of AbstractCompositeHelpTopic |
![|](ftv2vertline.png) ![o](ftv2pnode.png) HelpLinks | Hyperlink data for writing out help |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for HelpLinks |
![|](ftv2vertline.png) ![o](ftv2pnode.png) HelpWriterContext | Context information for writing out help |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) Impl | Private implementation class for HelpWriterContext |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) SharedState | Shared, non-modifiable state for context objects |
![|](ftv2vertline.png) ![o](ftv2node.png) IHelpTopic | Provides a single online help topic |
![|](ftv2vertline.png) ![o](ftv2node.png) RstParagraphIterator | Iterator over reStructuredText paragraphs |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionStorageTemplate | Templated base class for constructing option value storage classes |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractOption | Abstract base class for specifying option properties |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionTemplate | Templated base class for constructing concrete option settings classes |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionInfo | Gives information and allows modifications to an option after creation |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractOptionStorage | Abstract base class for converting, validating, and storing option values |
![|](ftv2vertline.png) ![o](ftv2node.png) BooleanOption | Specifies an option that provides boolean values |
![|](ftv2vertline.png) ![o](ftv2node.png) IntegerOption | Specifies an option that provides integer values |
![|](ftv2vertline.png) ![o](ftv2node.png) Int64Option | Specifies an option that provides 64-bit integer values |
![|](ftv2vertline.png) ![o](ftv2node.png) DoubleOption | Specifies an option that provides floating-point (double) values |
![|](ftv2vertline.png) ![o](ftv2node.png) FloatOption | Specifies an option that provides floating-point (float) values |
![|](ftv2vertline.png) ![o](ftv2node.png) StringOption | Specifies an option that provides string values |
![|](ftv2vertline.png) ![o](ftv2node.png) EnumOption | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
![|](ftv2vertline.png) ![o](ftv2node.png) BooleanOptionInfo | Wrapper class for accessing boolean option information |
![|](ftv2vertline.png) ![o](ftv2node.png) IntegerOptionInfo | Wrapper class for accessing integer option information |
![|](ftv2vertline.png) ![o](ftv2node.png) Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
![|](ftv2vertline.png) ![o](ftv2node.png) DoubleOptionInfo | Wrapper class for accessing floating-point option information |
![|](ftv2vertline.png) ![o](ftv2node.png) FloatOptionInfo | Wrapper class for accessing floating-point option information |
![|](ftv2vertline.png) ![o](ftv2node.png) StringOptionInfo | Wrapper class for accessing string option information |
![|](ftv2vertline.png) ![o](ftv2node.png) EnumOptionInfo | Wrapper class for accessing enum option information |
![|](ftv2vertline.png) ![o](ftv2node.png) BooleanOptionStorage | Converts, validates, and stores boolean values |
![|](ftv2vertline.png) ![o](ftv2node.png) IntegerOptionStorage | Converts, validates, and stores integer values |
![|](ftv2vertline.png) ![o](ftv2node.png) Int64OptionStorage | Converts, validates, and stores integer values |
![|](ftv2vertline.png) ![o](ftv2node.png) DoubleOptionStorage | Converts, validates, and stores floating-point (double) values |
![|](ftv2vertline.png) ![o](ftv2node.png) FloatOptionStorage | Converts, validates, and stores floating-point (float) values |
![|](ftv2vertline.png) ![o](ftv2node.png) StringOptionStorage | Converts, validates, and stores string values |
![|](ftv2vertline.png) ![o](ftv2node.png) EnumOptionStorage | Converts, validates, and stores enum values |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsBehaviorCollection | Container for IOptionsBehavior objects |
![|](ftv2vertline.png) ![o](ftv2node.png) FileNameOption | Specifies an option that provides file names |
![|](ftv2vertline.png) ![o](ftv2node.png) FileNameOptionInfo | Wrapper class for accessing file name option information |
![|](ftv2vertline.png) ![o](ftv2pnode.png) FileNameOptionManager | Handles interaction of file name options with global options |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implemention class for FileNameOptionManager |
![|](ftv2vertline.png) ![o](ftv2node.png) FileNameOptionStorage | Converts, validates, and stores file names |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionsBehavior | Interface to provide extension points for options parsing |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionsContainer | Interface for adding input options |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionManagerContainer | Container to keep managers added with Options::addManager() and pass them to options |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionManager | Base class for option managers |
![|](ftv2vertline.png) ![o](ftv2node.png) Options | Collection of options |
![|](ftv2vertline.png) ![o](ftv2pnode.png) OptionsAssigner | Decorator class for assigning values to Options |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for OptionsAssigner |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsVisitor | Pure interface for visiting options in a Options object |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsTypeVisitor | Abstract base class for visiting options of a particular type |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsIterator | Decorator class for visiting options in a Options object |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsModifyingVisitor | Pure interface for visiting options in a Options object, allowing modifications |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsModifyingTypeVisitor | Abstract base class for visiting options of a particular type, allowing modifications |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionsModifyingIterator | Decorator class for visiting options in a Options object, allowing changes |
![|](ftv2vertline.png) ![o](ftv2node.png) TimeUnitManager | Provides common functionality for time unit conversions |
![|](ftv2vertline.png) ![o](ftv2node.png) TimeUnitBehavior | Options behavior to add a time unit option |
![|](ftv2vertline.png) ![o](ftv2pnode.png) ExponentialDistribution | Exponential distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Exponential distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) GammaDistribution | Gamma distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Gamma distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) NormalDistribution | Normal distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Normal distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) TabulatedNormalDistribution | Tabulated normal random distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Normal distribution parameter class (mean and stddev) |
![|](ftv2vertline.png) ![o](ftv2node.png) ThreeFry2x64General | General implementation class for ThreeFry counter-based random engines |
![|](ftv2vertline.png) ![o](ftv2node.png) ThreeFry2x64 | ThreeFry2x64 random engine with 20 iteractions |
![|](ftv2vertline.png) ![o](ftv2node.png) ThreeFry2x64Fast | ThreeFry2x64 random engine with 13 iteractions |
![|](ftv2vertline.png) ![o](ftv2pnode.png) UniformIntDistribution | Uniform integer distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Uniform int distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) UniformRealDistribution | Uniform real distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Uniform real distribution parameters |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionCompiler | Implements selection compilation |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhood | Neighborhood searching for analysis tools |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionParserValue | Describes a parsed value, possibly resulting from expression evaluation |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionParserParameter | Describes a parsed method parameter |
![|](ftv2vertline.png) ![o](ftv2pnode.png) PositionCalculationCollection | Collection of gmx_ana_poscalc_t structures for the same topology |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for PositionCalculationCollection |
![|](ftv2vertline.png) ![o](ftv2node.png) Selection | Provides access to a single selection |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionPosition | Provides access to information about a single selected position |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionEvaluator | Implements selection evaluation |
![|](ftv2vertline.png) ![o](ftv2pnode.png) SelectionCollection | Collection of selections |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implemention class for SelectionCollection |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionFileOption | Specifies a special option that provides selections from a file |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionFileOptionStorage | Implementation for a special option for reading selections from files |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOption | Specifies an option that provides selection(s) |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
![|](ftv2vertline.png) ![o](ftv2node.png) ITopologyProvider | Provides topology information to SelectionOptionBehavior |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
![|](ftv2vertline.png) ![o](ftv2pnode.png) SelectionOptionManager | Handles interaction of selection options with other options and user input |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) Impl | Private implemention class for SelectionOptionManager |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) RequestsClearer | Helper class that clears a request list on scope exit |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) SelectionRequest | Request for postponed parsing of selections |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOptionStorage | Converts, validates, and stores selection values |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionLocation | Stores the location of a selection element in the selection text |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionTreeElement | Represents an element of a selection expression |
![|](ftv2vertline.png) ![o](ftv2pnode.png) SelectionParserSymbol | Single symbol for the selection parser |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for SelectionParserSymbol |
![|](ftv2vertline.png) ![o](ftv2pnode.png) SelectionParserSymbolIterator | Input iterator for iterating symbols of a given type |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for SelectionParserSymbolIterator |
![|](ftv2vertline.png) ![o](ftv2pnode.png) SelectionParserSymbolTable | Symbol table for the selection parser |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for SelectionParserSymbolTable |
![|](ftv2vertline.png) ![o](ftv2node.png) Simd4Double | SIMD4 double type |
![|](ftv2vertline.png) ![o](ftv2node.png) Simd4DBool | SIMD4 variable type to use for logical comparisons on doubles |
![|](ftv2vertline.png) ![o](ftv2node.png) Simd4Float | SIMD4 float type |
![|](ftv2vertline.png) ![o](ftv2node.png) Simd4FBool | SIMD4 variable type to use for logical comparisons on floats |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdDouble | Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1 |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdDInt32 | Integer SIMD variable type to use for conversions to/from double |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdDBool | Boolean type for double SIMD data |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdDIBool | Boolean type for integer datatypes corresponding to double SIMD |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdFloat | Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1 |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdFInt32 | Integer SIMD variable type to use for conversions to/from float |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdFBool | Boolean type for float SIMD data |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdFIBool | Boolean type for integer datatypes corresponding to float SIMD |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdLoadFProxyInternal | Proxy object to enable load() for SIMD and float types |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdLoadUFProxyInternal | Proxy object to enable loadU() for SIMD and float types |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdLoadDProxyInternal | Proxy object to enable load() for SIMD and double types |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdLoadUDProxyInternal | Proxy object to enable loadU() for SIMD and double types |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdLoadIProxyInternal | Proxy object load() for SimdFInt32, SImdDInt32, and int32 |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdLoadUIProxyInternal | Proxy object - loadU() for SimdFInt32, SImdDInt32, and int32 |
![|](ftv2vertline.png) ![o](ftv2node.png) SimdSetZeroProxyInternal | Proxy object to enable setZero() for SIMD and real types |
![|](ftv2vertline.png) ![o](ftv2pnode.png) TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for TrajectoryAnalysisModuleData |
![|](ftv2vertline.png) ![o](ftv2pnode.png) TrajectoryAnalysisModule | Base class for trajectory analysis modules |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for TrajectoryAnalysisModule |
![|](ftv2vertline.png) ![o](ftv2pnode.png) TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) Impl | Private implementation class for TrajectoryAnalysisSettings |
![|](ftv2vertline.png) ![o](ftv2node.png) TopologyInformation | Topology information passed to a trajectory analysis module |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
![|](ftv2vertline.png) ![o](ftv2node.png) SurfaceAreaCalculator | Computes surface areas for a group of atoms/spheres |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisRunnerCommon | Implements common trajectory analysis runner functionality |
![|](ftv2vertline.png) ![o](ftv2pnode.png) AlignedAllocator | Aligned memory allocator |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) rebind | Standard-required typedef to use allocator with different class |
![|](ftv2vertline.png) ![o](ftv2node.png) EmptyArrayRef | Tag type to initialize empty array references |
![|](ftv2vertline.png) ![o](ftv2node.png) BinaryInformationSettings | Settings for printBinaryInformation() |
![|](ftv2vertline.png) ![o](ftv2node.png) PrivateImplPointer | Helper class to manage a pointer to a private implementation class |
![|](ftv2vertline.png) ![o](ftv2node.png) DataFileOptions | Search parameters for DataFileFinder |
![|](ftv2vertline.png) ![o](ftv2node.png) DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
![|](ftv2vertline.png) ![o](ftv2node.png) DataFileFinder | Searches data files from a set of paths |
![|](ftv2vertline.png) ![o](ftv2node.png) DirectoryEnumerator | Lists files in a directory |
![|](ftv2vertline.png) ![o](ftv2node.png) ExceptionInfo | Stores additional context information for exceptions |
![|](ftv2vertline.png) ![o](ftv2node.png) ThrowLocation | Stores the location from which an exception was thrown |
![|](ftv2vertline.png) ![o](ftv2node.png) ExceptionInitializer | Provides information for Gromacs exception constructors |
![|](ftv2vertline.png) ![o](ftv2node.png) GromacsException | Base class for all exception objects in Gromacs |
![|](ftv2vertline.png) ![o](ftv2node.png) FileIOError | Exception class for file I/O errors |
![|](ftv2vertline.png) ![o](ftv2node.png) UserInputError | Exception class for user input errors |
![|](ftv2vertline.png) ![o](ftv2node.png) InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
![|](ftv2vertline.png) ![o](ftv2node.png) InconsistentInputError | Exception class for situations where user input is inconsistent |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationInstabilityError | Exception class for simulation instabilities |
![|](ftv2vertline.png) ![o](ftv2node.png) InternalError | Exception class for internal errors |
![|](ftv2vertline.png) ![o](ftv2node.png) APIError | Exception class for incorrect use of an API |
![|](ftv2vertline.png) ![o](ftv2node.png) NotImplementedError | Exception class for use of an unimplemented feature |
![|](ftv2vertline.png) ![o](ftv2node.png) IFileInputRedirector | Allows overriding file existence checks from code that supports it |
![|](ftv2vertline.png) ![o](ftv2node.png) IFileOutputRedirector | Allows capturing stdout and file output from code that supports it |
![|](ftv2vertline.png) ![o](ftv2node.png) StandardInputStream | Text input stream implementation for reading from stdin |
![|](ftv2vertline.png) ![o](ftv2node.png) TextInputFile | Text input stream implementation for reading from a file |
![|](ftv2vertline.png) ![o](ftv2node.png) TextOutputFile | Text output stream implementation for writing to a file |
![|](ftv2vertline.png) ![o](ftv2node.png) FlagsTemplate | Template class for typesafe handling of combination of flags |
![|](ftv2vertline.png) ![o](ftv2node.png) Regex | Represents a regular expression |
![|](ftv2vertline.png) ![o](ftv2node.png) MessageStringCollector | Helper class for collecting message strings, optionally with context |
![|](ftv2vertline.png) ![o](ftv2node.png) MessageStringContext | Convenience class for creating a message context |
![|](ftv2vertline.png) ![o](ftv2node.png) no_delete | Deleter for std::shared_ptr that does nothing |
![|](ftv2vertline.png) ![o](ftv2node.png) InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
![|](ftv2vertline.png) ![o](ftv2node.png) IProgramContext | Provides context information about the program that is calling the library |
![|](ftv2vertline.png) ![o](ftv2node.png) scoped_cptr | Stripped-down version of scoped_ptr that uses sfree() or custom deleter |
![|](ftv2vertline.png) ![o](ftv2node.png) StringOutputStream | Text output stream implementation for writing to an in-memory string |
![|](ftv2vertline.png) ![o](ftv2node.png) StringInputStream | Helper class to convert static string data to a stream |
![|](ftv2vertline.png) ![o](ftv2node.png) StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
![|](ftv2vertline.png) ![o](ftv2node.png) IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
![|](ftv2vertline.png) ![o](ftv2node.png) TextLineWrapperSettings | Stores settings for line wrapping |
![|](ftv2vertline.png) ![o](ftv2node.png) TextLineWrapper | Wraps lines to a predefined length |
![|](ftv2vertline.png) ![o](ftv2node.png) TextReader | Reads text from a TextInputStream |
![|](ftv2vertline.png) ![o](ftv2node.png) TextInputStream | Interface for reading text |
![|](ftv2vertline.png) ![o](ftv2node.png) TextOutputStream | Interface for writing text |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) TextWriter | Writes text into a TextOutputStream |
![o](ftv2node.png) AnalysisTemplate | Template class to serve as a basis for user analysis tools |
![o](ftv2node.png) AtomIndex | List of atom indices belonging to a task |
![o](ftv2node.png) bonded_threading_t | Struct contain all data for bonded force threading |
![o](ftv2node.png) cl_atomdata | Nonbonded atom data - both inputs and outputs |
![o](ftv2node.png) cl_nb_staging | Staging area for temporary data downloaded from the GPU |
![o](ftv2node.png) cl_nbparam | Parameters required for the OpenCL nonbonded calculations |
![o](ftv2node.png) cl_nbparam_params | Data structure shared between the OpenCL device code and OpenCL host code |
![o](ftv2node.png) cl_plist | Pair list data |
![o](ftv2node.png) cl_timers | OpenCL events used for timing GPU kernels and H2D/D2H transfers |
![o](ftv2node.png) cu_atomdata | Nonbonded atom data - both inputs and outputs |
![o](ftv2node.png) cu_nbparam | Parameters required for the CUDA nonbonded calculations |
![o](ftv2node.png) cu_plist | Pair list data |
![o](ftv2node.png) cu_timers | CUDA events used for timing GPU kernels and H2D/D2H transfers |
![o](ftv2node.png) eligible_gpu_ids | Helper struct so we can parse the string with eligible GPU IDs outside do_the_tests |
![o](ftv2node.png) em_state_t | Utility structure for manipulating states during EM |
![o](ftv2node.png) f_thread_t | Struct with output for bonded forces, used per thread |
![o](ftv2node.png) gmx_ana_index_t | Stores a single index group |
![o](ftv2node.png) gmx_ana_indexgrps_t | Stores a set of index groups |
![o](ftv2node.png) gmx_ana_indexmap_t | Data structure for calculating index group mappings |
![o](ftv2node.png) gmx_ana_pos_t | Stores a set of positions together with their origins |
![o](ftv2node.png) gmx_ana_poscalc_t | Data structure for position calculation |
![o](ftv2node.png) gmx_ana_selcollection_t | Information for a collection of selections |
![o](ftv2node.png) gmx_ana_selmethod_help_t | Help information for a selection method |
![o](ftv2node.png) gmx_ana_selmethod_t | Describes a selection method |
![o](ftv2node.png) gmx_ana_selparam_t | Describes a single parameter for a selection method |
![o](ftv2node.png) gmx_ana_selvalue_t | Describes a value of a selection expression or of a selection method parameter |
![o](ftv2node.png) gmx_device_info_t | OpenCL device information |
![o](ftv2node.png) gmx_device_runtime_data_t | OpenCL GPU runtime data |
![o](ftv2node.png) gmx_domdec_constraints_t | Struct used during constraint setup with domain decomposition |
![o](ftv2node.png) gmx_domdec_specat_comm_t | Struct with setup and buffers for special atom communication |
![o](ftv2node.png) gmx_fft_fftpack | Contents of the FFTPACK fft datatype |
![o](ftv2node.png) gmx_fft_fftw3 | Contents of the FFTW3 fft datatype |
![o](ftv2node.png) gmx_fft_mkl | Contents of the Intel MKL FFT fft datatype |
![o](ftv2node.png) gmx_ga2la_t | Structure for all global to local mapping information |
![o](ftv2node.png) gmx_hash_e_t | Hashing key-generation helper struct |
![o](ftv2node.png) gmx_hash_t | Hashing helper struct |
![o](ftv2node.png) gmx_help_make_index_group | Cata necessary to construct a single (protein) index group in analyse_prot() |
![o](ftv2node.png) gmx_laa_t | Structure for the local atom info for a plain list |
![o](ftv2node.png) gmx_lal_t | Structure for the local atom info for a hash table |
![o](ftv2node.png) gmx_nbnxn_cuda_t | Main data structure for CUDA nonbonded force calculations |
![o](ftv2node.png) gmx_nbnxn_kernel_timing_data_t | Nonbonded kernel time and call count |
![o](ftv2node.png) gmx_nbnxn_ocl_t | Main data structure for OpenCL nonbonded force calculations |
![o](ftv2node.png) gmx_pme_comm_n_box_t | Helper struct for PP-PME communication of parameters |
![o](ftv2node.png) gmx_pme_comm_vir_ene_t | Helper struct for PP-PME communication of virial and energy |
![o](ftv2node.png) gmx_pme_pp | Master PP-PME communication data structure |
![o](ftv2node.png) gmx_reverse_top_t | Struct for the reverse topology: links bonded interactions to atomsx |
![o](ftv2node.png) gmx_sel_evaluate_t | Data structure for passing information required during evaluation |
![o](ftv2node.png) gmx_sel_lexer_t | Internal data structure for the selection tokenizer state |
![o](ftv2node.png) gmx_sel_mempool_block_t | Describes a single block allocated from the memory pool |
![o](ftv2node.png) gmx_sel_mempool_t | Describes a memory pool |
![o](ftv2node.png) gmx_sparsematrix | Sparse matrix storage format |
![o](ftv2node.png) gmx_wallclock_gpu_t | GPU timings for kernels and H2d/D2H transfers |
![o](ftv2node.png) gmx_walltime_accounting | Manages caching wall-clock time measurements for simulations |
![o](ftv2node.png) ilist_data_t | Struct for passing all data required for a function type |
![o](ftv2node.png) IMDEnergyBlock | IMD (interactive molecular dynamics) energy record |
![o](ftv2node.png) IMDHeader | IMD (interactive molecular dynamics) communication structure |
![o](ftv2node.png) IMDSocket | IMD (interactive molecular dynamics) socket structure |
![o](ftv2node.png) InterdependentTask | Data structure for thread tasks that use constructing atoms outside their own atom range |
![o](ftv2node.png) nb_staging | Staging area for temporary data downloaded from the GPU |
![o](ftv2node.png) ocl_gpu_id_t | OpenCL GPU device identificator |
![o](ftv2node.png) omp_module_nthreads_t | Structure with the number of threads for each OpenMP multi-threaded algorithmic module in mdrun |
![o](ftv2node.png) pme_setup_t | Parameters and settings for one PP-PME setup |
![o](ftv2node.png) swap_compartment | Structure containing compartment-specific data |
![o](ftv2node.png) swap_group | This structure contains data needed for the groups involved in swapping: split group 0, split group 1, solvent group, ion groups |
![o](ftv2node.png) t_compare_value | Data structure for comparison expression operand values |
![o](ftv2node.png) t_compiler_data | Internal data structure used by the compiler |
![o](ftv2node.png) t_coordselection | Selection of pull coordinates to be used in WHAM (one structure for each tpr file) |
![o](ftv2node.png) t_cosines | Declares inputrec data structure and utilities |
![o](ftv2node.png) t_filenm | File name option definition for C code |
![o](ftv2node.png) t_gmx_IMD | IMD (interactive molecular dynamics) main data structure |
![o](ftv2node.png) t_mdatoms | Declares mdatom data structure |
![o](ftv2node.png) t_methoddata_compare | Data structure for comparison expression evaluation |
![o](ftv2node.png) t_methoddata_distance | Data structure for distance-based selection method |
![o](ftv2node.png) t_methoddata_insolidangle | Data structure for the insolidangle selection method |
![o](ftv2node.png) t_methoddata_kweval | Data structure for keyword evaluation in arbitrary groups |
![o](ftv2node.png) t_methoddata_kwint | Data structure for integer keyword expression evaluation |
![o](ftv2node.png) t_methoddata_kwreal | Data structure for real keyword expression evaluation |
![o](ftv2node.png) t_methoddata_merge | Data structure for the merging selection modifiers |
![o](ftv2node.png) t_methoddata_permute | Data structure for the permute selection modifier |
![o](ftv2node.png) t_methoddata_pos | Data structure for position keyword evaluation |
![o](ftv2node.png) t_methoddata_same | Data structure for the same selection method |
![o](ftv2node.png) t_pargs | Command-line argument definition for C code |
![o](ftv2node.png) t_partition | Internal data structure for the insolidangle selection method |
![o](ftv2node.png) t_partition_item | Internal data structure for the insolidangle selection method |
![o](ftv2node.png) t_pbc | Structure containing info on periodic boundary conditions |
![o](ftv2node.png) t_pullcoord | Parameters of one pull coodinate |
![o](ftv2node.png) t_register_method | Helper structure for defining selection methods |
![o](ftv2node.png) t_spheresurfacebin | Internal data structure for the insolidangle selection method |
![o](ftv2node.png) t_swap | Main (private) data structure for the position swapping protocol |
![o](ftv2node.png) t_UmbrellaHeader | Parameters of the umbrella potentials |
![o](ftv2node.png) t_UmbrellaOptions | Parameters of WHAM |
![o](ftv2node.png) t_UmbrellaWindow | Data in the umbrella histograms |
![o](ftv2node.png) thread_work_t | Struct for thread local work data for local topology generation |
![\](ftv2lastnode.png) VsiteThread | Vsite thread task data structure |