  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{bonded.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{convert_trj.cpp} | |
| anonymous_namespace{cpuinfo.cpp} | |
| anonymous_namespace{device_management.cpp} | |
| anonymous_namespace{distance.cpp} | |
| anonymous_namespace{dofit.cpp} | |
| anonymous_namespace{domain_decomposition.cpp} | |
| DomainDecompositionSpecialCasesTest | Test fixture for domain decomposition special cases |
| anonymous_namespace{edsam.cpp} | |
| t_eigvec | Essential dynamics vector. TODO: split into working data and input data NOTE: called eigvec, because traditionally eigenvectors from PCA analysis were used as essential dynamics vectors, however, vectors used for ED need not have any special properties |
| t_edvecs | Essential dynamics vectors per method implementation |
| t_edflood | Essential dynamics flooding parameters and work data. TODO: split into working data and input parameters NOTE: The implementation here follows: O.E. Lange, L.V. Schafer, and H. Grubmuller, “Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics,” J. Comp. Chem., 27 1693–1702 (2006) |
| 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{filenameoption.cpp} | |
| anonymous_namespace{filenameoptionmanager.cpp} | |
| anonymous_namespace{filenm.cpp} | |
| anonymous_namespace{freeenergydispatch.cpp} | |
| anonymous_namespace{freevolume.cpp} | |
| anonymous_namespace{functions.cpp} | |
| anonymous_namespace{genconf.cpp} | |
| anonymous_namespace{gmx_awh.cpp} | |
| anonymous_namespace{gmx_make_ndx.cpp} | |
| anonymous_namespace{gmx_mindist.cpp} | |
| anonymous_namespace{gmx_traj.cpp} | |
| anonymous_namespace{grompp.cpp} | |
| GromppTest | Test fixture for grompp |
| anonymous_namespace{grompp_directives.cpp} | |
| anonymous_namespace{hardwaretopology.cpp} | |
| anonymous_namespace{hashedmap.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} | |
| IndexBlockTest | Text fixture for index block operations |
| anonymous_namespace{insert_molecules.cpp} | |
| anonymous_namespace{invertmatrix.cpp} | |
| anonymous_namespace{keyvaluetreeserializer.cpp} | |
| anonymous_namespace{keyvaluetreetransform.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{logger.cpp} | |
| anonymous_namespace{manager.cpp} | |
| anonymous_namespace{mdrun_main.cpp} | |
| anonymous_namespace{minimize.cpp} | |
| EnergyEvaluator | Class to handle the work of setting and doing an energy evaluation |
| anonymous_namespace{nbsearch.cpp} | |
| anonymous_namespace{option.cpp} | |
| anonymous_namespace{optionsassigner.cpp} | |
| anonymous_namespace{orires.cpp} | |
| anonymous_namespace{pairdist.cpp} | |
| anonymous_namespace{pargs.cpp} | |
| anonymous_namespace{parsetree.cpp} | |
| anonymous_namespace{path.cpp} | |
| anonymous_namespace{pdb2gmx.cpp} | |
| anonymous_namespace{pleasecite.cpp} | |
| anonymous_namespace{pme_gpu_calculate_splines_sycl.h} | |
| anonymous_namespace{poscalc.cpp} | |
| anonymous_namespace{position_restraints.cpp} | |
| anonymous_namespace{rdf.cpp} | |
| anonymous_namespace{readir.cpp} | |
| anonymous_namespace{repeatingsection.cpp} | |
| anonymous_namespace{resourcedivision.cpp} | |
| SingleRankChecker | Handles checks for algorithms that must use a single rank |
| anonymous_namespace{sasa.cpp} | |
| anonymous_namespace{select.cpp} | |
| anonymous_namespace{selectioncollection.cpp} | |
| anonymous_namespace{selectionoption.cpp} | |
| anonymous_namespace{selhelp.cpp} | |
| 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{state.cpp} | |
| anonymous_namespace{surfacearea.cpp} | |
| anonymous_namespace{sysinfo.cpp} | |
| anonymous_namespace{testasserts_tests.cpp} | |
| anonymous_namespace{textwriter.cpp} | |
| anonymous_namespace{threadaffinity.cpp} | |
| anonymous_namespace{timeunitmanager.cpp} | |
| anonymous_namespace{tngio.cpp} | |
| anonymous_namespace{trajectory.cpp} | |
| anonymous_namespace{trajectory_writing.cpp} | |
| anonymous_namespace{treesupport.cpp} | |
| anonymous_namespace{unionfind.cpp} | |
| anonymous_namespace{vectypes.cpp} | |
| gmx | Generic GROMACS namespace |
| analysismodules | |
| anonymous_namespace{angle.cpp} | |
| AnglePositionIterator | Helper to encapsulate logic for looping over input selections |
| anonymous_namespace{convert_trj.cpp} | |
| anonymous_namespace{distance.cpp} | |
| anonymous_namespace{extract_cluster.cpp} | |
| anonymous_namespace{freevolume.cpp} | |
| FreeVolume | Class used to compute free volume in a simulations box |
| anonymous_namespace{msd.cpp} | |
| MsdData | Mean Squared Displacement data accumulator |
| MsdColumnProxy | Proxy to a MsdData tau column vector. Supports only push_back |
| MoleculeData | Holds data needed for MSD calculations for a single molecule, if requested |
| MsdCoordinateManager | Handles coordinate operations for MSD calculations |
| MsdGroupData | Holds per-group coordinates, analysis, and results |
| 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{trajectory.cpp} | |
| Msd | Implements the gmx msd module |
| anonymous_namespace{alignedallocator.cpp} | |
| anonymous_namespace{analysismodule.cpp} | |
| TrajectoryAnalysisModuleDataBasic | Basic thread-local trajectory analysis data storage class |
| anonymous_namespace{arrayref.cpp} | |
| anonymous_namespace{arrayrefwithpadding.cpp} | |
| anonymous_namespace{autocorr.cpp} | |
| anonymous_namespace{awh_history.cpp} | |
| anonymous_namespace{bench_system.cpp} | |
| anonymous_namespace{biasgrid.cpp} | |
| anonymous_namespace{biasparams.cpp} | |
| anonymous_namespace{biassharing.cpp} | |
| anonymous_namespace{biasstate.cpp} | |
| anonymous_namespace{biaswriter.cpp} | |
| anonymous_namespace{boxutilities.cpp} | |
| anonymous_namespace{calc_verletbuf.cpp} | |
| anonymous_namespace{clfftinitializer.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{com.cpp} | |
| anonymous_namespace{computeglobalselement.cpp} | |
| anonymous_namespace{convert_tpr.cpp} | |
| anonymous_namespace{coolstuff.cpp} | |
| anonymous_namespace{coordstate.cpp} | |
| anonymous_namespace{correlationgrid.cpp} | |
| anonymous_namespace{correlationtensor.cpp} | |
| anonymous_namespace{cpuinfo.cpp} | |
| ApicInfo | Internal structure to return os logical cpu id together with APIC info for it |
| ApicIdLayout | The layout of the bits in the APIC ID |
| anonymous_namespace{cubicsplinetable.cpp} | |
| anonymous_namespace{decidegpuusage.cpp} | |
| anonymous_namespace{densityfit.cpp} | |
| DensitySimilarityInnerProduct | Implementation for DensitySimilarityInnerProduct |
| DensitySimilarityRelativeEntropy | Implementation for DensitySimilarityRelativeEntropy |
| CrossCorrelationEvaluationHelperValues | Helper values for evaluating the cross correlation |
| CrossCorrelationGradientAtVoxel | Calculate a single cross correlation gradient entry at a voxel |
| DensitySimilarityCrossCorrelation | Implementation for DensitySimilarityCrossCorrelation |
| anonymous_namespace{densityfitting.cpp} | |
| DensityFittingSimulationParameterSetup | Collect density fitting parameters only available during simulation setup |
| DensityFitting | Density fitting |
| anonymous_namespace{densityfittingamplitudelookup.cpp} | |
| anonymous_namespace{densityfittingforceprovider.cpp} | |
| anonymous_namespace{densityfittingoptions.cpp} | |
| anonymous_namespace{devicetransfers_ocl.cpp} | |
| anonymous_namespace{dump.cpp} | |
| anonymous_namespace{electricfield.cpp} | |
| ElectricFieldDimension | Describes an applied electric field in a coordinate dimension |
| ElectricField | Describe time dependent electric field |
| anonymous_namespace{energydata.cpp} | |
| anonymous_namespace{energydrifttracker.cpp} | |
| anonymous_namespace{entropy.cpp} | |
| anonymous_namespace{enumerationhelpers.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{exclusionblocks.cpp} | |
| anonymous_namespace{expandedensembleelement.cpp} | |
| 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{findallgputasks.cpp} | |
| anonymous_namespace{firstorderpressurecoupling.cpp} | |
| anonymous_namespace{fixedcapacityvector.cpp} | |
| anonymous_namespace{freeenergyparameters.cpp} | |
| anonymous_namespace{freeenergyperturbationdata.cpp} | |
| anonymous_namespace{futil.cpp} | |
| anonymous_namespace{gammadistribution.cpp} | |
| anonymous_namespace{gausstransform.cpp} | |
| anonymous_namespace{gmx_covar.cpp} | |
| anonymous_namespace{gpp_atomtype.cpp} | |
| anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp} | |
| RocfftInitializer | Provides RAII-style initialization of rocFFT library |
| RocfftPlan | All the persistent data for planning an executing a 3D FFT |
| PlanSetupData | Helper struct to reduce repetitive code setting up a 3D FFT plan |
| anonymous_namespace{handlerestart.cpp} | |
| StartingBehaviorHandler | Describes how mdrun will (re)start and provides supporting functionality based on that data |
| 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{histogramsize.cpp} | |
| anonymous_namespace{idef.cpp} | |
| anonymous_namespace{identifyavx512fmaunits.cpp} | |
| anonymous_namespace{ikeyvaluetreeerror.cpp} | |
| anonymous_namespace{init.cpp} | |
| anonymous_namespace{inmemoryserializer.cpp} | |
| anonymous_namespace{insert_molecules.cpp} | |
| anonymous_namespace{keyvaluetree.cpp} | |
| anonymous_namespace{keyvaluetreeserializer.cpp} | |
| anonymous_namespace{keyvaluetreetransform.cpp} | |
| anonymous_namespace{listoflists.cpp} | |
| anonymous_namespace{logger.cpp} | |
| anonymous_namespace{manyautocorrelation.cpp} | |
| anonymous_namespace{mdmodulesnotifier.cpp} | |
| anonymous_namespace{mdspan.cpp} | |
| anonymous_namespace{message_string_collector.cpp} | |
| anonymous_namespace{modules.cpp} | |
| anonymous_namespace{mrcdensitymap.cpp} | |
| anonymous_namespace{mrcdensitymapheader.cpp} | |
| anonymous_namespace{mrcserializer.cpp} | |
| anonymous_namespace{mtop.cpp} | |
| anonymous_namespace{mttk.cpp} | |
| anonymous_namespace{multipletimestepping.cpp} | |
| anonymous_namespace{nbsearch.cpp} | |
| MindistAction | Search action find the minimum distance |
| anonymous_namespace{neldermead.cpp} | |
| NelderMeadParameters | The parameters for a Nelder-Mead optimisation |
| anonymous_namespace{nonbonded_bench.cpp} | |
| anonymous_namespace{normaldistribution.cpp} | |
| anonymous_namespace{nosehooverchains.cpp} | |
| anonymous_namespace{optionsection.cpp} | |
| anonymous_namespace{optionsvisitor.cpp} | |
| anonymous_namespace{pargs.cpp} | |
| OptionsAdapter | Conversion helper between t_pargs/t_filenm and Options |
| anonymous_namespace{parrinellorahmanbarostat.cpp} | |
| anonymous_namespace{path.cpp} | |
| anonymous_namespace{pdb2gmx.cpp} | |
| anonymous_namespace{physicalnodecommunicator.cpp} | |
| anonymous_namespace{pointstate.cpp} | |
| anonymous_namespace{poscalc.cpp} | |
| anonymous_namespace{programcontext.cpp} | |
| DefaultProgramContext | Default implementation of IProgramContext |
| anonymous_namespace{propagator.cpp} | |
| anonymous_namespace{pull.cpp} | |
| anonymous_namespace{pullelement.cpp} | |
| anonymous_namespace{qmmm.cpp} | |
| QMMMSimulationParameterSetup | Helper class that holds simulation data and callback functions for simulation setup time notifications |
| QMMMOutputProvider | Handle file output for QMMM simulations. empty implementation as QMMM does not use that |
| QMMM | QMMM module |
| anonymous_namespace{qmmmforceprovider.cpp} | |
| anonymous_namespace{qmmmoptions.cpp} | |
| anonymous_namespace{quadraticsplinetable.cpp} | |
| anonymous_namespace{range.cpp} | |
| anonymous_namespace{read_params.cpp} | |
| anonymous_namespace{report_methods.cpp} | |
| anonymous_namespace{reportgpuusage.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{shake.cpp} | |
| ShakeTest | Test fixture for testing SHAKE |
| anonymous_namespace{shellcompletions.cpp} | |
| anonymous_namespace{simd_memory.cpp} | |
| anonymous_namespace{statepropagatordata.cpp} | |
| anonymous_namespace{stringtoenumvalueconverter.cpp} | |
| anonymous_namespace{stringutil.cpp} | |
| anonymous_namespace{tabulatednormaldistribution.cpp} | |
| anonymous_namespace{taskassignment.cpp} | |
| anonymous_namespace{template_mp.cpp} | |
| anonymous_namespace{threaded_force_buffer.cpp} | |
| anonymous_namespace{threefry.cpp} | |
| anonymous_namespace{timeunitmanager.cpp} | |
| TimeOptionScaler | Option visitor that scales time options |
| anonymous_namespace{topologyinformation.cpp} | |
| anonymous_namespace{topsort.cpp} | |
| anonymous_namespace{transformationcoordinate.cpp} | |
| anonymous_namespace{treesupport.cpp} | |
| anonymous_namespace{uniformintdistribution.cpp} | |
| anonymous_namespace{uniformrealdistribution.cpp} | |
| anonymous_namespace{updategroups.cpp} | |
| UpdateGroupsTest | Test fixture class |
| anonymous_namespace{updategroupscog.cpp} | |
| anonymous_namespace{velocityscalingtemperaturecoupling.cpp} | |
| anonymous_namespace{wholemoleculetransform.cpp} | |
| compat | Compatibility aliases for standard library features |
| anonymous_namespace{pointers.cpp} | |
| not_null | Restricts a pointer or smart pointer to only hold non-null values |
| detail | |
| PaddingTraits | Traits classes for handling padding for types used with PaddedVector |
| SimulationInputHandleImplDeleter | Explicit deleter details for SimulationInputHolderImpl |
| extents_analyse< R, E0, StaticExtents...> | Enable querying extent of specific rank by splitting a static extents off the variadic template arguments |
| extents_analyse< R, dynamic_extent, StaticExtents...> | Enable querying extent of specific rank by splitting a dynamic extent off the variadic template arguments |
| extents_analyse< 0 > | Specialisation for rank 0 extents analysis. Ends recursive rank analysis |
| 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 |
| EnumIndexStore | Type-specific implementation for IOptionValueStore for an enum option |
| OptionSectionImpl | Internal implementation class for storing an option section |
| Group | Describes a group of options (see Options::addGroup()) |
| OptionsImpl | Private implementation class for Options |
| SelectionData | Internal data for a single selection |
| SimdTraits | Simd traits |
| SimdArrayRef | STL-like container for aligned SIMD type. Used as ArrayRef<SimdReal> |
| IExceptionInfo | Base class for ExceptionInfo |
| test | Testing utilities namespace |
| anonymous_namespace{base.cpp} | |
| anonymous_namespace{bonded.cpp} | |
| OutputQuantities | Output from bonded kernels |
| iListInput | Input structure for listed forces tests |
| anonymous_namespace{bootstrap_loadstore.cpp} | |
| anonymous_namespace{calcvir.cpp} | |
| anonymous_namespace{checkpoint.cpp} | |
| anonymous_namespace{checkpointdata.cpp} | |
| IsVectorOfSerializableType | Struct allowing to check if type is vector of serializable data |
| TestValues | Unified looping over test data |
 TestValueGenerator | Helper class allowing to loop over test values |
 Iterator | Custom iterator |
| CheckpointDataTest | CheckpointData test fixture |
| anonymous_namespace{clustsize.cpp} | |
| anonymous_namespace{cmdlinemodulemanagertest.cpp} | |
| anonymous_namespace{cmdlinetest.cpp} | |
| anonymous_namespace{com.cpp} | |
| COMInPlaceTest | Test fixture for checking correct molecule COM treatment |
| anonymous_namespace{conftest.cpp} | |
| anonymous_namespace{constantacceleration.cpp} | |
| anonymous_namespace{constr.cpp} | |
| ConstraintsTest | Test fixture for constraints |
| anonymous_namespace{convert-tpr.cpp} | |
| anonymous_namespace{cstringutil.cpp} | |
| anonymous_namespace{defaultinitializationallocator.cpp} | |
| anonymous_namespace{densityfittingforce.cpp} | |
| anonymous_namespace{device_stream_manager.cpp} | |
| DeviceStreamManagerTest | Test fixture |
| anonymous_namespace{ebin.cpp} | |
| anonymous_namespace{editconf.cpp} | |
| anonymous_namespace{electricfield.cpp} | |
| anonymous_namespace{energyoutput.cpp} | |
| EnergyOutputTestParameters | Test parameters space |
| EnergyOutputTest | Test fixture to test energy output |
| anonymous_namespace{ewaldsurfaceterm.cpp} | |
| EwaldSurfaceTermTest | Test fixture base for simple mdrun systems |
| anonymous_namespace{exactcontinuation.cpp} | |
| ContinuationFramePairManager | Manages comparing a pair of matching energy frames from a normal run and the same run in two parts |
| MdrunNoAppendContinuationIsExact | Test fixture for mdrun exact continuations |
| anonymous_namespace{expanded.cpp} | |
| CalculateAcceptanceWeightSimple | Test fixture accepting a value to pass into calculateAcceptanceWeight |
| anonymous_namespace{exponentialmovingaverage.cpp} | |
| anonymous_namespace{extract_cluster.cpp} | |
| ManualOutputFile | Helper struct to combine filename, path and FileMatcher |
| ExtractClusterModuleTest | Test fixture for the convert-trj analysis module |
| anonymous_namespace{fft.cpp} | |
| anonymous_namespace{fileioxdrserializer.cpp} | |
| anonymous_namespace{filematchers.cpp} | |
| anonymous_namespace{filemd5.cpp} | |
| anonymous_namespace{filenm.cpp} | |
| anonymous_namespace{freeenergy.cpp} | |
| anonymous_namespace{freeenergyparameters.cpp} | |
| FreeEnergyParameterTestParameters | Parameters that will vary from test to test |
| FreeEnergyParameterTest | Test for setting free energy parameters |
| anonymous_namespace{freezegroups.cpp} | |
| anonymous_namespace{gausstransform.cpp} | |
| anonymous_namespace{genion.cpp} | |
| anonymous_namespace{gmx_chi.cpp} | |
| anonymous_namespace{gpueventsynchronizer.cpp} | |
| anonymous_namespace{haloexchange_mpi.cpp} | |
| anonymous_namespace{helpwriting.cpp} | |
| anonymous_namespace{initialconstraints.cpp} | |
| InitialConstraintsTest | Test fixture parametrized on integrators |
| anonymous_namespace{inmemoryserializer.cpp} | |
| anonymous_namespace{interactivetest.cpp} | |
| anonymous_namespace{kernelsetup.cpp} | |
| anonymous_namespace{leapfrog.cpp} | |
| LeapFrogTestParameters | The parameters for the test |
| LeapFrogTest | Test fixture for LeapFrog integrator |
| anonymous_namespace{legacyenergy.cpp} | |
| anonymous_namespace{loggertest.cpp} | |
| anonymous_namespace{matrix.cpp} | |
| anonymous_namespace{minimize.cpp} | |
| EnergyMinimizationTest | Test fixture base for energy minimizaiton |
| 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{mockhardwaretopology.cpp} | |
| MockHardwareTopologyTest | Mocking test with data collected from a few systems |
| anonymous_namespace{moduletest.cpp} | |
| anonymous_namespace{mpitest.cpp} | |
| anonymous_namespace{mrcdensitymap.cpp} | |
| anonymous_namespace{msd.cpp} | |
| MsdMatcher | MsdMatcher is effectively an extension of XvgMatcher for gmx msd results |
| anonymous_namespace{mshift.cpp} | |
| anonymous_namespace{multidimarray.cpp} | |
| anonymous_namespace{multiple_time_stepping.cpp} | |
| anonymous_namespace{multipletimestepping.cpp} | |
| anonymous_namespace{nb_free_energy.cpp} | |
| OutputQuantities | Output from nonbonded fep kernel |
| AtomData | Utility structure to hold atoms data |
| ListInput | Input structure for nonbonded fep kernel |
| anonymous_namespace{neldermead.cpp} | |
| anonymous_namespace{nonbonded_bench.cpp} | |
| anonymous_namespace{normalmodes.cpp} | |
| NormalModesTest | Test fixture base for normal mode analysis |
| anonymous_namespace{observablesreducer.cpp} | |
| Subscriber | Helper class that models an MD module that needs to make a subscription to ObservablesReducer |
| ObservablesReducerIntegrationTest | Test fixture class |
| RankData | Helper struct to model data on a single MPI rank |
| anonymous_namespace{optimization.cpp} | |
| anonymous_namespace{outputfiles.cpp} | |
| anonymous_namespace{pairs.cpp} | |
| OutputQuantities | Output from pairs kernels |
| ListInput | Input structure for listed forces tests |
| anonymous_namespace{path.cpp} | |
| anonymous_namespace{pdb2gmx.cpp} | |
| anonymous_namespace{physicalnodecommunicator_mpi.cpp} | |
| anonymous_namespace{pmebsplinetest.cpp} | |
| PmeBSplineModuliTest | Test fixture for testing PME B-spline moduli creation |
| anonymous_namespace{pmegathertest.cpp} | |
| SplineData | A structure for all the spline data which depends in size both on the PME order and atom count |
| TestSystem | A structure for the input atom data, which depends in size on atom count |
| GatherTest | Test fixture |
| GatherTestBody | Test case whose body checks that gather works |
| anonymous_namespace{pmesolvetest.cpp} | |
| SolveTest | Test fixture |
| SolveTestBody | Test case whose body checks that spline and spread work |
| anonymous_namespace{pmesplinespreadtest.cpp} | |
| SplineAndSpreadTest | Test fixture for testing both atom spline parameter computation and charge spreading. These 2 stages of PME are tightly coupled in the code |
| SplineAndSpreadTestBody | Test case whose body checks that spline and spread work |
| anonymous_namespace{pmetest.cpp} | |
| PmeTest | Test fixture for end-to-end execution of PME |
| anonymous_namespace{position_restraints.cpp} | |
| anonymous_namespace{pull.cpp} | |
| PullIntegrationTest | Test fixture base for simple mdrun systems |
| anonymous_namespace{refdata.cpp} | |
| anonymous_namespace{refdata_tests.cpp} | |
| anonymous_namespace{refdata_xml.cpp} | |
| anonymous_namespace{rerun.cpp} | |
| MdrunRerunTest | Test fixture base for mdrun -rerun |
| anonymous_namespace{scalar.cpp} | |
| anonymous_namespace{scalar_math.cpp} | |
| anonymous_namespace{scalar_util.cpp} | |
| anonymous_namespace{settle.cpp} | |
| SettleTestParameters | Parameters that will vary from test to test |
| SettleTest | Test fixture for testing SETTLE |
| 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{simple_mdrun.cpp} | |
| SimpleMdrunTest | Test fixture base for simple mdrun systems |
| anonymous_namespace{simulationdatabase.cpp} | |
| anonymous_namespace{simulator.cpp} | |
| anonymous_namespace{splinetable.cpp} | |
| SplineTableTest | Test fixture for table comparision with analytical/numerical functions |
| anonymous_namespace{strconvert.cpp} | |
| anonymous_namespace{stringtest.cpp} | |
| anonymous_namespace{stringutil.cpp} | |
| anonymous_namespace{symtab.cpp} | |
| anonymous_namespace{testasserts.cpp} | |
| anonymous_namespace{testinit.cpp} | |
| TestProgramContext | Custom program context for test binaries |
| SuccessListener | Makes GoogleTest non-failures more verbose |
| anonymous_namespace{testoptions.cpp} | |
| TestOptionsRegistry | Singleton registry for test options added with GMX_TEST_OPTIONS |
| anonymous_namespace{textblockmatchers.cpp} | |
| anonymous_namespace{textreader.cpp} | |
| TextReaderTestParams | Helper struct |
| TextReaderTest | Test fixture |
| anonymous_namespace{threadaffinity_mpi.cpp} | |
| RequireEvenRankCountWithAtLeastFourRanks | Helper to establish test requirements on MPI ranks |
| anonymous_namespace{timing.cpp} | |
| TimingTest | Test Fixture for timing tests |
| anonymous_namespace{topologyinformation.cpp} | |
| anonymous_namespace{tpitest.cpp} | |
| TpiTest | A basic TPI runner. The only input parameter used currently: input system random seed (ld-seed) |
| anonymous_namespace{trjconv.cpp} | |
| anonymous_namespace{usergpuids.cpp} | |
| anonymous_namespace{virtualsites.cpp} | |
| anonymous_namespace{xvgtest.cpp} | |
| anonymous_namespace{xvgtest_tests.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 |
| AwhTestParameters | Struct that gathers all input for setting up and using a Bias |
| BiasTest | Test fixture for testing Bias updates |
| BiasFepLambdaStateTest | Test fixture for testing Bias updates |
| BiasStateTest | Test fixture for testing Bias updates |
| MockModule | Mock implementation of gmx::ICommandLineModule |
| MockOptionsModule | Mock implementation of gmx::ICommandLineOptionsModule |
| CommandLineModuleManagerTestBase | Test fixture for tests using gmx::CommandLineModuleManager |
| TrajectoryFrameWriterTest | Test fixture to test different file types are supported by the CoordinateFile |
| ModuleSelection | Helper class for tests that need an initialized selection |
| ModuleTest | Test fixture to test matching file types for modules |
| SetAtomsSupportedFiles | Helper to test supported file names |
| SetAtomsUnSupportedFiles | Helper to test supported file names |
| AnyOutputSupportedFiles | Helper to test supported file names |
| NoOptionalOutput | Helper to test support for disabling all output options |
| OutputSelectorDeathTest | Helper to test that invalid selection is rejected |
| SetVelocitySupportedFiles | Helper to test supported file names |
| SetVelocityUnSupportedFiles | Helper to test supported file names |
| SetForceSupportedFiles | Helper to test supported file names |
| SetForceUnSupportedFiles | Helper to test supported file names |
| SetPrecisionSupportedFiles | Helper to test supported file names |
| SetPrecisionUnSupportedFiles | Helper to test supported file names |
| FlagTest | Test fixture to test user inputs |
| SetAtomsTest | Test fixture to prepare a setatoms object to pass data through |
| SetBothTimeTest | Test fixture to prepare a setatoms object to pass data through |
| SetStartTimeTest | Test fixture to prepare a setatoms object to pass data through |
| SetTimeStepTest | Test fixture to prepare a setatoms object to pass data through |
| HostMemoryTest | Typed test fixture for infrastructure for host-side memory used for GPU transfers |
| HostAllocatorTest | Typed test fixture |
| HostAllocatorTestNoMem | Typed test fixture (no mem/gpu initializtion - much faster) |
| HostAllocatorTestNoMemCopyable | Typed test fixture for tests requiring a copyable type |
| PaddedVectorTest | Typed test fixture |
| SignalTest | Test fixture for mdrun signalling |
| TopologyManager | Helps create and manage the lifetime of topology and related data structures |
| 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 |
| AllocatorTest | Templated test fixture |
| MaxNumFrames | Named struct indicating the max number of frames to be compared |
| DensityFittingTest | End to end test for the density fitting functionality in mdrun |
| EnergyComparison | Function object to compare all energy terms of reference with all matching terms from test within the given tolerances |
| EnergyFrameReader | Manages returning an EnergyFrame containing required energy term values read from successive frames of an .edr file |
| FramePairManager | Manages returning a pair of frames from two equivalent simulations that are meaningful to compare |
| MimicTest | Test fixture for bonded interactions |
| 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 |
| NumRanksPerSimulation | Test flag setting the number of ranks per simulation |
| MultiSimTest | Test fixture for multi-sim functionality |
| ReferenceFileNames | Helper type of output file names for the reference mdrun call |
| PeriodicActionsTest | Test fixture base for comparing a simulator with one that does everything every step |
| PrintReplicaExchangeParametersToString | Helper struct printing custom test name |
| BondedInteractionsTest | Test fixture for bonded interactions |
| TerminationHelper | Help test mdrun termination behaviour |
| TrajectoryTolerances | Helper struct for testing different trajectory components with different tolerances |
| TrajectoryFrameMatchSettings | Helper struct to specify the expected behaviour of compareFrames() |
| TrajectoryComparison | Function object to compare the fields of two frames vs each others or one frame vs reference data for equality given the matchSettings_ and tolerances_ |
| 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 |
| IFileMatcher | Represents a file matcher, matching file contents against reference (or other) data |
| IFileMatcherSettings | Represents a factory for creating a file matcher |
| TextFileMatch | Use a ITextBlockMatcher for matching the contents |
| NoContentsMatch | Do not check the contents of the file |
| InteractiveTestHelper | Helper class for testing interactive sessions |
| LoggerTestHelper | Helper class for tests to check output written to a logger |
| AllowAnyRankCount | Helper for GMX_MPI_TEST to permit any rank count |
| RequireRankCount | Helper for GMX_MPI_TEST to permit only a specific rank count |
| RequireMinimumRankCount | Helper for GMX_MPI_TEST to permit only a specific rank count |
| TestReferenceData | Handles creation of and comparison to test reference data |
| TestReferenceChecker | Handles comparison to test reference data |
| Impl | Private implementation class for TestReferenceChecker |
| StdioTestHelper | Helper class for tests where code reads directly from stdin |
| StringTestBase | Test fixture for tests that check string formatting |
| TestDevice | A structure to describe a hardware context that persists over the lifetime of the test binary |
| TestHardwareEnvironment | This class performs one-time test initialization, enumerating the hardware |
| 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) |
| FilteringExactTextMatch | Use an exact text match after scrubbing lines of the text that match the supplied regular expressions |
| TprAndFileManager | Helper to bundle generated TPR and the file manager to clean it up |
| TrajectoryFrameReader | Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file |
| XvgMatch | Match the contents as an xvg file |
| FloatTypeMatcher | Implementation class for RealEq matcher |
| RVecMatcher | Implementation class for RvecEq matcher |
| testing | |
| anonymous_namespace{exclusionblocks.cpp} | |
| 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 |
| ArrayRef | STL-like interface to a C array of T (or part of a std container of T) |
| 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 |
| BiasCoupledToSystem | A bias and its coupling to the system |
| Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
| Bias | A bias acting on a multidimensional coordinate |
| GridAxis | An axis, i.e. dimension, of the grid |
| GridPoint | A point in the grid |
| BiasGrid | The grid for a single bias, generally multidimensional and periodic |
| BiasParams | Constant parameters for the bias |
| BiasState | The state of a bias |
| AwhEnergyBlock | AWH output data block that can be written to an energy file block |
| BiasWriter | Class organizing the output data storing and writing of an AWH bias |
| CoordState | Keeps track of the current coordinate value, grid index and umbrella location |
| CorrelationGrid | BiasGrid of local correlation tensors |
| CorrelationBlockData | Correlation block averaging weight-only data |
| CoordData | Correlation block averaging data |
| CorrelationTensor | Correlation data for computing the correlation tensor of one grid point |
| DimParams | Constant parameters for each dimension of the coordinate |
| FepDimParams | Type for storing dimension parameters for free-energy lamdba type dimensions |
| PullDimParams | Type for storing dimension parameters for pull type dimensions |
| HistogramSize | Tracks global size related properties of the bias histogram |
| PointState | The state of a coordinate point |
| DensityFittingModuleInfo | Information about the density fitting module |
| DensityFittingAmplitudeLookup | Class that translates atom properties into amplitudes |
| DensityFittingForceProviderState | Parameters defining the internal density fitting force provider state |
| DensityFittingForceProvider | Implements IForceProvider for density-fitting forces |
| DensityFittingOptions | Input data storage for density fitting |
| DensityFittingOutputProvider | Handle file output for density guided simulations |
| DensityFittingParameters | Holding all directly user-provided parameters for density fitting |
| QMMMModuleInfo | Information about the QM/MM module |
| QMMMForceProvider | Implements IForceProvider for QM/MM |
| QMMMInputGenerator | Class that takes QMMMParameters, Coordinates, Point charges, Box dimensions, pbcType. Generates QM/MM sample input parameters and pdb-style coordinates for CP2K. Input are generated as std::string objects which can be stored in tpr KVT and/or flushed into the files |
| QMMMOptions | Input data storage for QM/MM |
| QMMMTopologyInfo | Contains various information about topology modifications Used for statistics during topology pre-processing within QMMMTopologyPreprocessor class |
| QMMMTopologyPreprocessor | Class implementing gmx_mtop_t QMMM modifications during preprocessing 1) Split QM-containing molecules from other molecules in blocks 2) Nullify charges on all virtual sites consisting of QM only atoms 3) Nullifies charges on all QM atoms 4) Excludes LJ interactions between QM atoms 5) Builds vector with atomic numbers of all atoms 6) Makes F_CONNBOND between atoms within QM region 7) Removes angles and settles containing 2 or more QM atoms 8) Removes dihedrals containing 3 or more QM atoms 9) Builds vector containing pairs of bonded QM - MM atoms (Link frontier) |
| LinkFrontier | Helper structure with indexes of broken bonds between QM and MM Used to determine and store pair of QM and MM atoms between which chemical bond is broken |
| QMMMParameters | Holding all parameters needed for QM/MM simulation. Also used for setting all default parameter values |
| 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 |
| 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 |
| 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() |
| CommandLineModuleGroupData | Internal data for a CommandLineModuleManager module group |
| CommandLineCommonOptionsHolder | Encapsulates some handling of common options to the wrapper binary |
| 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 |
| TrajectoryFileOpener | Low level method to take care of only file opening and closing |
| TrajectoryFrameWriter | Writes coordinate frames to a sink, e.g. a trajectory file |
| IOutputAdapter | OutputAdapter class for handling trajectory file flag setting and processing |
| OutputAdapterContainer | Storage for output adapters that modify the state of a t_trxframe object |
| OutputSelector | OutputSelector class controls setting which coordinates are actually written |
| SetAtoms | SetAtoms class controls availability of atoms data |
| SetBox | Allows changing box information when writing a coordinate file |
| SetForces | SetForces class allows changing writing of forces to file |
| SetPrecision | SetPrecision class allows changing file writing precision |
| SetStartTime | SetStartTime class allows changing trajectory time information |
| SetTimeStep | SetTimeStep class allows changing trajectory time information |
| SetVelocities | SetVelocities class allows changing writing of velocities to file |
| OutputRequirementOptionDirector | Container for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer |
| OutputRequirements | Finalized version of requirements after processing |
| DomainDecompositionBuilder | Builds a domain decomposition management object |
| Impl | Impl class for DD builder |
| FixedCapacityVector | Vector that behaves likes std::vector but has fixed capacity |
| HashedMap | Unordered key to value mapping |
| GpuHaloExchange | Manages GPU Halo Exchange object |
| Impl | Impl class stub |
| LocalAtomSet | A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator |
| LocalAtomSetManager | Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel |
| Impl | Private implementation class for LocalAtomSetManager |
| LocalTopologyChecker | Has responsibility for checking that the local topology distributed across domains describes a total number of bonded interactions that matches the system topology |
| Impl | Data to help check local topology construction |
| DomdecOptions | Structure containing all (command line) options for the domain decomposition |
| SeparatePmeRanksPermitted | Class for managing usage of separate PME-only ranks |
| PpCommManager | Object to manage communications with a specific PP rank |
| PmeForceSenderGpu | Manages sending forces from PME-only ranks to their PP ranks |
| Impl | Impl class stub |
| CacheLineAlignedFlag | Class with interfaces and data for CUDA version of PME Force sending functionality |
| PmePpCommGpu | Manages communication related to GPU buffers between this PME rank and its PP rank |
| Impl | Class with interfaces and data for CUDA version of PME-PP Communication |
| Gpu3dFft | A 3D FFT class for performing R2C/C2R transforms |
| Impl | Impl base class for all FFT backends |
| ImplCuFft | A 3D FFT wrapper class for performing R2C/C2R transforms using cuFFT |
| ImplOcl | A 3D FFT wrapper class for performing R2C/C2R transforms using clFFT |
| ImplSycl | A 3D FFT wrapper class for performing R2C/C2R transforms using SYCL. Not yet implemented |
| ImplSyclMkl | A 3D FFT wrapper class for performing R2C/C2R transforms using SYCL + MKL |
| ImplSyclRocfft | A 3D FFT wrapper class for performing R2C/C2R transforms using rocFFT for hipSYCL targetting ROCm devices |
| Impl | Impl class |
| MDModulesCheckpointReadingDataOnMaster | Provides the MDModules with the checkpointed data on the master rank |
| MDModulesCheckpointReadingBroadcast | Provides the MDModules with the communication record to broadcast |
| MDModulesWriteCheckpointData | Writing the MDModules data to a checkpoint file |
| FileIOXdrSerializer | Serializer to read/write XDR data |
| MrcDensityMapOfFloatReader | Read an mrc/ccp4 file that contains float values |
| Impl | Private implementation class for MrcDensityMapOfFloatReader |
| MrcDensityMapOfFloatFromFileReader | Read an mrc density map from a given file |
| MrcDensityMapOfFloatWriter | Write an mrc/ccp4 file that contains float values |
| Impl | Private implementation class for MrcDensityMapOfFloatWriter |
| MrcDataStatistics | Statistics about mrc data arrays |
| MrcDensitySkewData | Skew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" |
| CrystallographicLabels | Crystallographic labels for mrc data |
| MrcDensityMapHeader | A container for the data in mrc density map file formats |
| ArrayRefWithPadding | Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses |
| ListOfLists | A list of lists, optimized for performance |
| ClfftInitializer | Handle clFFT library init and tear down in RAII style also with mutual exclusion |
| DeviceStreamManager | Device stream and context manager |
| Impl | Impl class to manages the lifetime of the GPU streams |
| HostAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers |
| OpenClTraits | Stub for OpenCL type traits |
| OpenClTraitsBase | Implements common trait infrastructure for OpenCL types |
| OpenClTraits< cl_context > | Implements traits for cl_context |
| OpenClTraits< cl_command_queue > | Implements traits for cl_command_queue |
| OpenClTraits< cl_program > | Implements traits for cl_program |
| OpenClTraits< cl_kernel > | Implements traits for cl_kernel |
| ClHandle | Wrapper of OpenCL type cl_type to implement RAII |
| CpuInfo | Detect CPU capabilities and basic logical processor info |
| LogicalProcessor | Entry with basic information for a single processing unit |
| DeviceDetectionResult | Convenience macro to help us avoid ifdefs each time we use sysconf |
| HardwareTopology | Information about packages, cores, processing units, numa, caches |
| Cache | Information about a single cache level |
| Core | Information about a single core in a package |
| Device | Information about a single PCI device |
| LogicalProcessor | Information about package, core and processing unit for a logical processor |
| Machine | Hardware topology information about the entire machine |
| Numa | Information about all numa nodes |
| NumaNode | Information about each numa node in system |
| Package | Information about a single package in the system |
| ProcessingUnit | Information about a single processing unit (in a core) |
| IMDEnergyBlock | IMD (interactive molecular dynamics) energy record |
| IMDHeader | IMD (interactive molecular dynamics) communication structure |
| InteractiveMolecularDynamics | Implement interactive molecular dynamics |
| IMDSocket | IMD (interactive molecular dynamics) socket structure |
| EnumerationArray | Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type |
| HostInteractionList | Version of InteractionList that supports pinning |
| TranslateAndScale | Transform coordinates in three dimensions by first translating, then scaling them |
| AffineTransformation | Affine transformation of three-dimensional coordinates |
| DensitySimilarityMeasure | Measure similarity and gradient between densities |
| DensityFittingForce | Manages evaluation of density-fitting forces for particles that were spread with a kernel |
| Impl | Private implementation class for DensityFittingForce |
| ExponentialMovingAverageState | Store the state of exponential moving averages |
| ExponentialMovingAverage | Evaluate the exponential moving average with bias correction |
| GaussianOn1DLattice | Provide result of Gaussian function evaluation on a one-dimensional lattice |
| GaussianSpreadKernelParameters | Parameters for density spreading kernels |
| PositionAndAmplitude | Parameters that describe the kernel position and amplitude |
| Shape | Shape parameters for Gaussian spreading kernels describe the kernel shape |
| GaussTransform3D | Sums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as  |
| Impl | Private implementation class for GaussTransform3D |
| IntegerBox | A 3-orthotope over integer intervals |
| OuterProductEvaluator | Evaluate the outer product of two number ranges. Keeps the memory for the outer product allocated |
| MultiDimArray | Multidimensional array that manages its own memory |
| RealFunctionvalueAtCoordinate | Tie together coordinate and function value at this coordinate |
| NelderMeadSimplex | The simplex for the Nelder-Mead algorithm |
| OptimisationResult | Compiles results of an a function optimisation |
| PaddedVector | PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS |
| CheckpointHandler | Class handling the checkpoint signal |
| Constraints | Handles constraints |
| CreationHelper | Support type to help implement makeConstraints() |
| EnergyDriftTracker | Class for tracking and printing the drift in the conserved energy quantity |
| PTCouplingArrays | Arrays connected to Pressure and Temperature coupling |
| GpuForceReduction | Manages the force reduction directly in GPU memory |
| cellInfo | Structure to hold cell information for any nbat-format forces |
| AtomPair | A pair of atoms indexes |
| Task | Unit of work within LINCS |
| Lincs | Data for LINCS algorithm |
| LincsDeviations | Status information about how well LINCS satisified the constraints in this domain |
| AtomsAdjacencyListElement | Helper type for discovering coupled constraints |
| LincsGpu | Class with interfaces and data for GPU version of LINCS |
| MDAtoms | Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators |
| ResetHandler | Class handling the reset of counters |
| SettleData | Data for executing SETTLE constraining |
| WaterMolecule | Indices of atoms in a water molecule |
| SettleGpu | Class with interfaces and data for GPU version of SETTLE |
| shakedata | Working data for the SHAKE algorithm |
| 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 |
| StopHandler | Class handling the stop signal |
| StopConditionSignal | Class setting the stop signal based on gmx_get_stop_condition() |
| StopConditionTime | Class setting the stop signal based on maximal run time |
| StopHandlerBuilder | Class preparing the creation of a StopHandler |
| Update | Contains data for update phase |
| Impl | PImpled implementation for Update |
| ScalingMatrix | Scaling matrix struct |
| AtomIndexExtremes | Struct for returning an atom range |
| UpdateGroups | Owns the update grouping and related data |
| UpdateGroupsCog | Class for managing and computing centers of geometry of update groups |
| DomainInfo | Information on PBC and domain decomposition for virtual sites |
| AtomIndex | List of atom indices belonging to a task |
| InterdependentTask | Data structure for thread tasks that use constructing atoms outside their own atom range |
| VsiteThread | Vsite thread task data structure |
| ThreadingInfo | Information on how the virtual site work is divided over thread tasks |
| VirtualSitesHandler | Class that handles construction of vsites and spreading of vsite forces |
| Impl | Impl class for VirtualSitesHandler |
| WholeMoleculeTransform | This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules |
| ISimulator | The Simulator interface |
| LegacySimulatorData | The legacy simulator data |
| LegacyMdrunOptions | This class provides the same command-line option functionality to both CLI and API sessions |
| LegacySimulator | Struct to handle setting up and running the different simulation types |
| MDModules | Manages the collection of all modules used for mdrun |
| MembedHolder | Membed SimulatorBuilder parameter type |
| Mdrunner | Runner object for supporting setup and execution of mdrun |
| MdrunnerBuilder | Build a gmx::Mdrunner |
| SimulationContext | Simulation environment and configuration |
| SimulationInputHandle | Owning handle to a SimulationInput object |
| SimulatorConfig | Simulation configuation settings |
| SimulatorStateData | Data for a specific simulation state |
| SimulatorEnv | Collection of environmental information for a simulation |
| Profiling | Collection of profiling information |
| ConstraintsParam | Collection of constraint parameters |
| LegacyInput | Collection of legacy input information |
| InteractiveMD | SimulatorBuilder parameter type for InteractiveMD |
| IonSwapping | Parameter type for IonSwapping SimulatorBuilder component |
| TopologyData | Collection of handles to topology information |
| BoxDeformationHandle | Handle to information about the box |
| SimulatorBuilder | Class preparing the creation of Simulator objects |
| accessor_basic | The most basic memory access model for mdspan |
| extents | Multidimensional extents with static and dynamic dimensions |
| layout_right | Right-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number |
| mapping | Mapping from multidimensional indices within extents to 1D index |
| basic_mdspan | Multidimensional array indexing and memory access with flexible mapping and access model |
| AtomInfoWithinMoleculeBlock | Contains information about each atom in a molecule block of the global topology |
| CheckpointData | } |
| AwhParams | Structure holding parameter information for AWH |
| IsSerializableType | Struct allowing to check if data is serializable through the KeyValueTree serializer |
| IsSerializableEnum | Struct allowing to check if enum has a serializable underlying type |
| ReadCheckpointDataHolder | Holder for read checkpoint data |
| WriteCheckpointDataHolder | Holder for write checkpoint data |
| ForceBuffersView | A view of the force buffer |
| ForceBuffers | Object that holds the force buffers |
| ForceWithShiftForces | Container for force and virial for algorithms that compute shift forces for virial calculation |
| ForceWithVirial | Container for force and virial for algorithms that provide their own virial tensor contribution |
| ForceOutputs | Force and virial output buffers for use in force computation |
| ForceProviderInput | Helper struct that bundles data for passing it over to the force providers |
| ForceProviderOutput | Helper struct bundling the output data of a force provider |
| IForceProvider | Interface for a component that provides forces during MD |
| ForceProviders | Evaluates forces from a collection of gmx::IForceProvider |
| IMDModule | Extension module for GROMACS simulations |
| IMDOutputProvider | Interface for handling additional output files during a simulation |
| IMdpOptionProvider | Interface for handling mdp/tpr input to a mdrun module |
| CheckpointOptions | Options for writing checkpoint files |
| TimingOptions | Options for timing (parts of) mdrun |
| ImdOptions | Options for IMD |
| MdrunOptions | Collection of all options of mdrun that are not processed separately |
| MtsLevel | Setting for a single level for multiple time step integration |
| GromppMtsOpts | Struct for passing the MTS mdp options to setupMtsLevels() |
| ObservablesReducerBuilder | Builder for ObservablesReducer |
| Impl | Impl class for ObservablesReducerBuilder |
| Subscription | Data required to set up a subscription |
| ObservablesReducer | Manage reduction of observables for registered subscribers |
| Impl | Impl class for ObservablesReducer |
| StepWorkload | Describes work done on this domain by the current rank that may change per-step |
| DomainLifetimeWorkload | Describes work done on this domain on every step of its lifetime, but which might change after the next domain paritioning |
| SimulationWorkload | Manage what computation is required during the simulation |
| ThreadForceBuffer | Object that holds force and energies buffers plus a mask for a thread |
| ThreadedForceBuffer | Class for accumulating and reducing forces and energies on threads in parallel |
| MimicCommunicator | Class-wrapper around MiMiC communication library It uses GROMACS' unit conversion to switch from GROMACS' units to a.u |
| AndersenTemperatureCoupling | Element implementing the Andersen thermostat |
| CheckpointHelper | Checkpoint helper |
| CheckpointHelperBuilder | Builder for the checkpoint helper |
| CompositeSimulatorElement | Composite simulator element |
| ComputeGlobalsElement | Encapsulate the calls to compute_globals |
| ConstraintsElement | Constraints element |
| DomDecHelper | Infrastructure element responsible for domain decomposition |
| DomDecHelperBuilder | Builder for DomDecHelper |
| EnergyData | Data class managing energies |
| Element | Element for EnergyData |
| ExpandedEnsembleElement | The expanded ensemble element |
| FirstOrderPressureCoupling | Element performing first-order pressure coupling |
| ForceElement | Force element |
| FreeEnergyPerturbationData | The free energy perturbation data |
| Element | The free energy perturbation data element |
| FepStateSetting | Allows external clients to specify how to change the FEP state |
| ModularSimulator | The modular simulator |
| SignallerBuilder | Builder for signallers |
| ISimulatorElement | The general interface for elements of the modular simulator |
| ISignaller | The general Signaller interface |
| INeighborSearchSignallerClient | Interface for clients of the NeighborSearchSignaller |
| ILastStepSignallerClient | Interface for clients of the LastStepSignaller |
| ILoggingSignallerClient | Interface for clients of the LoggingSignaller |
| IEnergySignallerClient | Interface for clients of the EnergySignaller |
| ITrajectorySignallerClient | Interface for signaller clients of the TrajectoryElement |
| ITrajectoryWriterClient | Interface for writer clients of the TrajectoryElement |
| ITopologyHolderClient | Client requiring read access to the local topology |
| ICheckpointHelperClient | Client that needs to store data during checkpointing |
| ElementNotFoundError | Exception class signalling that a requested element was not found |
| MissingElementConnectionError | Exception class signalling that elements were not connected properly |
| SimulationAlgorithmSetupError | Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way |
| CheckpointError | Exception class signalling an error in reading or writing modular checkpoints |
| PropagatorTag | Strong type used to name propagators |
| TimeStep | Strong type used to denote propagation time steps |
| Offset | Strong type used to denote scheduling offsets |
| PropagatorConnection | Information needed to connect a propagator to a temperature and / or pressure coupling element |
| IDomDecHelperClient | Client interface of the DomDecHelper class |
| MttkPropagatorConnectionDetails | Struct collecting the propagator tags and offsets used by the MTTK pressure coupling |
| MttkData | Class holding the extra dof and parameters used by the MTTK algorithm |
| MttkPropagatorConnection | Object holding the callbacks and scaling views for the connection of MTTKElement objects to propagators |
| MttkElement | Element propagating the MTTK degree of freedom |
| MttkBoxScaling | This element scales the box based on the MTTK dof |
| NoseHooverGroup | The current state of the Nose-Hoover chain degree of freedom for a temperature group |
| NoseHooverChainsData | Class holding data used by the Nose-Hoover chains |
| NoseHooverChainsElement | Element propagating the Nose-Hoover chains |
| ParrinelloRahmanBarostat | Element implementing the Parrinello-Rahman barostat |
| PmeLoadBalanceHelper | Infrastructure element responsible for PME load balancing |
| Propagator | Propagator element |
| PullElement | Element calling pull functionality |
| ReferenceTemperatureManager | Object managing reference temperature changes |
| NeighborSearchSignaller | Element signalling a neighbor search step |
| LastStepSignaller | Element signalling the last step |
| LoggingSignaller | Element signalling a logging step |
| TrajectorySignaller | Element signalling trajectory writing |
| EnergySignaller | Element signalling energy related special steps |
| ModularSimulatorAlgorithm | The modular simulator |
| GlobalCommunicationHelper | Helper container with data connected to global communication |
| ModularSimulatorAlgorithmBuilderHelper | Helper for element addition |
| ModularSimulatorAlgorithmBuilder | Builder for ModularSimulatorAlgorithm objects |
| StatePropagatorData | StatePropagatorData and associated data |
| Element | Element for StatePropagatorData |
| ReferenceTemperatureHelper | Helper object to scale velocities according to reference temperature change |
| TopologyHolder | Object holding the topology |
| Builder | Builder for the topology holder |
| TrajectoryElement | Trajectory element signals and handles trajectory writing |
| TrajectoryElementBuilder | Build the TrajectoryElement |
| TemperatureCouplingData | Data used by the concrete temperature coupling implementations |
| ITemperatureCouplingImpl | Interface for temperature coupling implementations |
| VRescaleTemperatureCoupling | Implements v-rescale temperature coupling |
| BerendsenTemperatureCoupling | Implements Berendsen temperature coupling |
| NoseHooverTemperatureCoupling | Implements the Nose-Hoover temperature coupling |
| VelocityScalingTemperatureCoupling | Element implementing the a velocity-scaling thermostat |
| BenchmarkSystem | Description of the system used for benchmarking |
| Range | Defines a range of integer numbers and accompanying operations |
| iterator | An iterator that loops over a range of integers |
| 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 |
| AbstractOptionSection | Base class for specifying option section properties |
| AbstractOptionSectionHandle | Base class for handles to option sections |
| 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 an EnumerationArray of string values and writes the selected index into an enum variable |
| LegacyEnumOption | 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 |
| IOptionsContainerWithSections | Interface for adding input options with sections |
| IOptionSectionStorage | Provides behavior specific to a certain option section type |
| IOptionValueStore | Represents the final storage location of option values |
| 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 |
| OptionSection | Declares a simple option section |
| OptionSectionHandle | Allows adding options to an OptionSection |
| OptionStorageTemplateSimple | Simplified option storage template for options that have one-to-one value conversion |
| 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 |
| RepeatingOptionSectionHandle | Allows adding options to an RepeatingOptionSection |
| RepeatingOptionSectionStorage | Implements handling of the structures that stores per-section values |
| RepeatingOptionSection | Declares an option section that creates a structure for each instance |
| TimeUnitManager | Provides common functionality for time unit conversions |
| TimeUnitBehavior | Options behavior to add a time unit option |
| OptionValueConverterSimple | Helper for converting from Any to a given type |
| OptionValueStoreNull | Value storage that does not store anywhere |
| PullCoordExpressionParser | Class with a mathematical expression and parser |
| 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 |
| RestraintManager | Manage the Restraint potentials available for Molecular Dynamics |
| Impl | Implementation class for restraint manager |
| RestraintMDModule | MDModule wrapper for Restraint implementations |
| Site | Abstraction for a restraint interaction site |
| RestraintForceProvider | Provide IForceProvider for RestraintMDModuleImpl |
| RestraintMDModuleImpl | IMDModule implementation for RestraintMDModule |
| IndexGroupsAndNames | Bundle index groups with their names |
| 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 |
| SelectionCollection | Collection of selections |
| Impl | Private implemention class for SelectionCollection |
| SelectionEvaluator | Implements selection evaluation |
| SelectionTopologyProperties | Describes topology properties required for selection evaluation |
| 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 |
| SelMethodEvalContext | Evaluation context for selection methods |
| SelectionParserSymbol | Single symbol for the selection parser |
| Impl | Private implementation class for SelectionParserSymbol |
| SelectionParserSymbolIterator | Forward 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 |
| SimdFloatTag | Tag type to select to load SimdFloat with simdLoad(U) |
| SimdDoubleTag | Tag type to select to load SimdDouble with simdLoad(U) |
| SimdFInt32Tag | Tag type to select to load SimdFInt32 with simdLoad(U) |
| SimdDInt32Tag | Tag type to select to load SimdDInt32 with simdLoad(U) |
| AlignedArray< float, N > | Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
| AlignedArray< double, N > | Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
| SimdSetZeroProxy | Proxy object to enable setZero() for SIMD and real types |
| SwapCoordinates | Implement Computational Electrophysiology swapping |
| CubicSplineTable | Cubic spline interpolation table |
| QuadraticSplineTable | Quadratic spline interpolation table |
| AnalyticalSplineTableInput | Specification for analytical table function (name, function, derivative) |
| NumericalSplineTableInput | Specification for vector table function (name, function, derivative, spacing) |
| DevelopmentFeatureFlags | Structure that holds boolean flags corresponding to the development features present enabled through environment variables |
| GpuTaskMapping | Specifies the GPU deviceID_ available for task_ to use |
| GpuTaskAssignmentsBuilder | Builder for the GpuTaskAssignments for all ranks on this node |
| GpuTaskAssignments | Contains the GPU task assignment for all ranks on this physical node |
| ConvertTprInfo | Declares gmx convert-tpr |
| RangePartitioning | Division of a range of indices into consecutive blocks |
| ExclusionBlock | Describes exclusions for a single atom |
| EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
| TrajectoryFrame | Contains a valid trajectory frame |
| 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 |
| TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
| SurfaceAreaCalculator | Computes surface areas for a group of atoms/spheres |
| UnionFinder | Union-find data structure for keeping track of disjoint sets |
| MappedUnionFinder | Extension of UnionFind that supports non-consecutive integer indices as items |
| TrajectoryAnalysisRunnerCommon | Implements common trajectory analysis runner functionality |
| TopologyInformation | Topology information available to a trajectory analysis module |
| AlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code |
| PageAlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices |
| Allocator | Policy-based memory allocator |
| Any | Represents a dynamically typed value of an arbitrary type - deprecated |
| BinaryInformationSettings | Settings for printBinaryInformation() |
| DataFileOptions | Search parameters for DataFileFinder |
| DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
| DataFileFinder | Searches data files from a set of paths |
| DefaultInitializationAllocator | Allocator adaptor that interposes construct() calls to convert value initialization into default initialization |
| DirectoryEnumerator | Lists files in a directory |
| EnumerationIterator | Allows iterating sequential enumerators |
| EnumerationWrapper | Allows constructing iterators for looping over sequential enumerators |
| 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 |
| ISerializer | Interface for types that convert standard data types into a form suitable for storage or transfer |
| KeyValueTreePath | Identifies an entry in a key-value tree |
| KeyValueTreeBuilder | Root builder for creating trees that have an object at the root |
| KeyValueTreeValueBuilder | Builder for KeyValueTreeValue objects |
| KeyValueTreeUniformArrayBuilder | Builder for KeyValueTreeArray objects where all elements are of type T |
| KeyValueTreeObjectArrayBuilder | Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects |
| KeyValueTreeObjectBuilder | Builder for KeyValueTreeObject objects |
| IKeyValueTreeTransformRules | Interface to declare rules for transforming key-value trees |
| KeyValueTreeTransformRulesScoped | Helper object returned from IKeyValueTreeTransformRules::scopedTransform() |
| KeyValueTreeTransformRuleBuilder | Provides methods to specify one transformation rule |
| AfterFrom | Properties that can be specified after from() |
| Base | Base class used for implementing parameter provider objects |
| ToObject | Properties that can be specified after from().toObject() |
| ToValue | Properties that can be specified after from().to() |
| ILogTarget | Target where log output can be written |
| LogEntryWriter | Helper class for creating log entries with GMX_LOG |
| LogWriteHelper | Helper class for implementing GMX_LOG |
| LogLevelHelper | Represents a single logging level |
| MDLogger | Declares a logging interface |
| LoggerBuilder | Initializes loggers |
| LoggerOwner | Manages memory for a logger built with LoggerBuilder |
| MDModulesNotifier | Organizes notifications about an event of interest to modules |
| BuildMDModulesNotifier | Aide to avoid nested MDModulesNotifier definition |
| BuildMDModulesNotifier<> | Template specialization to end parameter unpacking recursion |
| NoCallParameter | Do nothing but be base class of MDModulesNotifier |
| BuildMDModulesNotifier< CurrentCallParameter, CallParameter...> | Template specialization to assemble MDModulesNotifier |
| MDModulesEnergyOutputToDensityFittingRequestChecker | Check if module outputs energy to a specific field |
| MDModulesEnergyOutputToQMMMRequestChecker | Check if QMMM module outputs energy to a specific field |
| EnergyCalculationFrequencyErrors | Collect errors for the energy calculation frequency |
| SimulationTimeStep | Provides the simulation time step in ps |
| CoordinatesAndBoxPreprocessed | Provides coordinates and simulation box |
| MdRunInputFilename | Mdrun input filename |
| QMInputFileName | Notification for QM program input filename provided by user as command-line argument for grompp |
| MDModulesNotifiers | Group of notifers to organize that MDModules can receive callbacks they subscribe to |
| 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 |
| PhysicalNodeCommunicator | Holds a communicator for the physical node of this rank |
| InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| IProgramContext | Provides context information about the program that is calling the library |
| StringCompare | Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare |
| StringOutputStream | Text output stream implementation for writing to an in-memory string |
| StringInputStream | Helper class to convert static string data to a stream |
| StringToEnumValueConverter | A class to convert a string to an enum value of type EnumType |
| 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 |
| EqualCaseInsensitive | Function object for comparisons with equalCaseInsensitive |
| TextLineWrapperSettings | Stores settings for line wrapping |
| TextLineWrapper | Wraps lines to a predefined length |
| TextReader | Reads text from a TextInputStream |
| Impl | Implementation class |
| TextInputStream | Interface for reading text |
| TextOutputStream | Interface for writing text |
| TextWriter | Writes text into a TextOutputStream |
| isIntegralConstant | Is true if type is a std::integral_constant |
| functor_wrapper | Wrap function into functor to be used as deleter |
| NonbondedBenchmarkInfo | Declares gmx nonbonded-bench |
| BasicVector | C++ class for 3D vectors |
| 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 |
| PotentialPointData | Structure to hold the results of IRestraintPotential::evaluate() |
| IRestraintPotential | Interface for Restraint potentials |
| 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 |
| ToleranceError | Exception class when a specified tolerance cannot be achieved |
| SimulationInstabilityError | Exception class for simulation instabilities |
| InternalError | Exception class for internal errors |
| APIError | Exception class for incorrect use of an API |
| RangeError | Exception class for out-of-range values or indices |
| NotImplementedError | Exception class for use of an unimplemented feature |
| ParallelConsistencyError | Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion |
| ModularSimulatorError | Exception class for modular simulator |
| Nbnxm | Namespace for non-bonded kernels |
| KernelBenchOptions | The options for the kernel benchmarks |
| GpuTimers | GPU region timers used for timing GPU kernels and H2D/D2H transfers |
| Interaction | Timers for local or non-local interaction related operations |
| XFTransfers | Timers for local or non-local coordinate/force transfers |
| gpu_plist | GPU pair list structure |
| BoundingBox | Bounding box for a nbnxm atom cluster |
| Corner | Corner for the bounding box, padded with one element to enable 4-wide SIMD operations |
| BoundingBox1D | Bounding box for one dimension of a grid cell |
| Grid | A pair-search grid object for one domain decomposition zone |
| Dimensions | The physical dimensions of a grid |
| Geometry | The cluster and cell geometry of a grid |
| GridSet | Holds a set of search grids for the local + non-local DD zones |
| DomainSetup | Description of the domain setup: PBC and the connections between domains |
| GridSetData | Struct that holds grid data that is shared over all grids |
| GridWork | Working arrays for constructing a grid |
| EnergyFunctionProperties | Set of boolean constants mimicking preprocessor macros |
| AllVsiteBondedInteractions | Wraps the datastructures for the different vsite bondeds |
| AnalysisTemplate | Template class to serve as a basis for user analysis tools |
| Atom2VsiteBond | Helper type for conversion of bonded parameters to virtual sites |
| AtomDistribution | Distribution of atom groups over the domain (only available on the master rank) |
| DomainAtomGroups | Collection of local group and atom counts for a domain |
| AtomIndexSet | Container for returning molecule type and index information for an atom |
| AtomInMolblock | Container for returning molecule type and index information for an atom |
| AtomIterator | Object that allows looping over all atoms in an mtop |
| AtomProperties | Holds all the atom property information loaded |
| Impl | Implementation detail type for Atomproperties |
| AtomProperty | Conglomeration of atom property entries |
| AtomProxy | Proxy object returned from AtomIterator |
| AtomRange | Range over all atoms of topology |
| AwhReader | All options and meta-data needed for the AWH output |
| BalanceRegion | Struct for timing the region for dynamic load balancing |
| BaseEntry | Basic entries in AtomProperty |
| BiasOutputSetup | All meta-data that is shared for all output files for one bias |
| bonded_threading_t | Struct contain all data for bonded force threading |
| BondedInteraction | Information about single bonded interaction |
| BondedInteractionList | Accumulation of different bonded types for preprocessing |
| ChainIdFiller | Constructs plausible chain IDs for multi-molecule systems, e.g. when read from .tpr files |
| CheckpointHeaderContents | Header explaining the context of a checkpoint file |
| cl_nbparam_params | Data structure shared between the OpenCL device code and OpenCL host code |
| dd_corners_t | Domain corners for communication, a maximum of 4 i-zones see a j domain |
| DDBalanceRegionHandler | Manager for starting and stopping the dynamic load balancing region |
| DDGridSetup | Describes the DD grid setup |
| DDPairInteractionRanges | Pair interaction zone and atom range for an i-zone |
| DeviceInformation | Platform-dependent device information |
| DeviceStream | Declaration of platform-agnostic device stream/queue |
| df_history_t | Free-energy sampling history struct |
| DipoleData | Data structure to hold dipole-related data and staging arrays |
| ekinstate_t | Struct used for checkpointing only |
| em_state | Utility structure for manipulating states during EM |
| EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
| ForceHelperBuffers | Helper force buffers for ForceOutputs |
| ForeignLambdaTerms | Accumulates free-energy foreign lambda energies and dH/dlamba |
| FreeEnergyDispatch | Temporary data and methods for handling dispatching of the nbnxm free-energy kernels |
| 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_cache_protect_t | Cache-line protection buffer |
| 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_enerdata_t | Struct for accumulating all potential energy terms and some kinetic energy terms |
| gmx_enfrot | Enforced rotation data for all groups |
| gmx_enfrotgrp | Enforced rotation data for a single rotation group |
| gmx_ffparams_t | Struct that holds all force field parameters for the simulated system |
| 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 | Global to local atom mapping |
| Entry | Structure for the local atom info |
| gmx_help_make_index_group | Data necessary to construct a single (protein) index group in analyse_prot() |
| gmx_hw_opt_t | Threading and GPU options, can be set automatically or by the user |
| gmx_kernel_timing_data_t | GPU kernel time and call count |
| gmx_localtop_t | The fully written out topology for a domain over its lifetime |
| gmx_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
| gmx_moltype_t | Molecules type data: atoms, interactions and exclusions |
| gmx_multisim_t | Coordinate multi-simulation resources for mdrun |
| 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_potfit | Helper structure for potential fitting |
| gmx_repl_ex | Working data for replica exchange |
| gmx_reverse_top_t | Reverse topology class |
| Impl | Struct for the reverse topology: links bonded interactions to atoms |
| 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_slabdata | Enforced rotation / flexible: determine the angle of each slab |
| gmx_sparsematrix | Sparse matrix storage format |
| gmx_specatsend_t | The communication setup along a single dimension |
| gmx_tng_trajectory | Gromacs Wrapper around tng datatype |
| gmx_wallclock_gpu_nbnxn_t | GPU NB timings for kernels and H2d/D2H transfers |
| gmx_wallclock_gpu_pme_t | GPU timings for PME |
| gmx_walltime_accounting | Manages caching wall-clock time measurements for simulations |
| GpuEventSynchronizer | A class which allows for CPU thread to mark and wait for certain GPU stream execution point |
| GpuRegionTimerImpl | The OpenCL implementation of the GPU code region timing. With OpenCL, one has to use cl_event handle for each API call that has to be timed, and accumulate the timing afterwards. As we would like to avoid overhead on API calls, we only query and accumulate cl_event timing at the end of time steps, not after the API calls. Thus, this implementation does not reuse a single cl_event for multiple calls, but instead maintains an array of cl_events to be used within any single code region. The array size is fixed at a small but sufficiently large value for the number of cl_events that might contribute to a timer region, currently 10 |
| GpuRegionTimerWrapper | This is a GPU region timing wrapper class. It allows for host-side tracking of the accumulated execution timespans in GPU code (measuring kernel or transfers duration). It also partially tracks the correctness of the timer state transitions, as far as current implementation allows (see TODO in getLastRangeTime() for a disabled check). Internally it uses GpuRegionTimerImpl for measuring regions |
| history_t | History information for NMR distance and orientation restraints |
| ilist_data_t | Struct for passing all data required for a function type |
| IListIterator | Object that allows looping over all atoms in an mtop |
| IListProxy | Proxy object returned from IListIterator |
| IListRange | Range over all interaction lists of topology |
| InteractionListHandle | Type for returning a list of InteractionList references |
| InteractionOfType | Describes an interaction of a given type, plus its parameters |
| InteractionsOfType | A set of interactions of a given type (found in the enumeration in ifunc.h), complete with atom indices and force field function parameters |
| KernelLaunchConfig | GPU kernels scheduling description. This is same in OpenCL/CUDA. Provides reasonable defaults, one typically only needs to set the GPU stream and non-1 work sizes |
| LeapFrogKernel | Class name for leap-frog kernel |
| ListedForces | Class for calculating listed interactions, uses OpenMP parallelization |
| MD5Checksum | Helper struct for returning the MD5 checksum and the amount of the file that contributed to it |
| methoddata_insolidangle | Data structure for the insolidangle selection method |
| methoddata_merge | Data structure for the merging selection modifiers |
| methoddata_permute | Data structure for the permute selection modifier |
| MolecularTopologyAtomIndices | Molecular topology indices of a global molecule a global atom belongs to |
| MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
| MoleculeInformation | Holds the molecule information during preprocessing |
| MoleculePatch | Block to modify individual residues |
| MoleculePatchDatabase | A set of modifications to apply to atoms |
| MoleculeType | Describes a molecule type, and keeps track of the number of these molecules |
| NBAtomDataGpu | Nonbonded atom data - both inputs and outputs |
| NbnxmGpu | Main data structure for CUDA nonbonded force calculations |
| NbnxmKernel | Class name for NBNXM kernel |
| NbnxmKernelPruneOnly | Class name for NBNXM prune-only kernel |
| nbnxn_atomdata_output_t | Struct that holds force and energy output buffers |
| nbnxn_atomdata_t | Struct that stores atom related data for the nbnxn module |
| Params | The actual atom data parameter values |
| SimdMasks | Diagonal and topology exclusion helper data for all SIMD kernels |
| nbnxn_ci_t | Simple pair-list i-unit |
| nbnxn_cj4_t | Four-way j-cluster lists |
| nbnxn_cj_t | This is the actual cluster-pair list j-entry |
| nbnxn_cycle_t | Local cycle count struct for profiling |
| nbnxn_excl_t | Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist |
| nbnxn_im_ei_t | Interaction data for a j-group for one warp |
| nbnxn_sci | Grouped pair-list i-unit |
| NbnxnPairlistCpu | Cluster pairlist type for use on CPUs |
| NbnxnPairlistCpuWork | Working data for the actual i-supercell during pair search |
| IClusterData | Struct for storing coordinates and bounding box for an i-entry during search |
| NBParamGpu | Parameters required for the GPU nonbonded calculations |
| NBStagingData | Staging area for temporary data downloaded from the GPU |
| nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
| NumPmeDomains | Struct for passing around the number of PME domains |
| ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
| omp_module_nthreads_t | Structure with the number of threads for each OpenMP multi-threaded algorithmic module in mdrun |
| OutputFile | All meta-data that is shared for one output file type for one bias |
| PairlistParams | The setup for generating and pruning the nbnxn pair list |
| PairlistSet | An object that holds the local or non-local pairlists |
| PairlistSets | Contains sets of pairlists |
| PairSearch | Main pair-search struct, contains the grid(s), not the pair-list(s) |
| PairsearchWork | Thread-local work struct, contains working data for Grid |
| PartialDeserializedTprFile | Contains the partly deserialized contents of a TPR file |
| partition | Internal data structure for the insolidangle selection method |
| PbcAiuc | Compact and ordered version of the PBC matrix |
| pme_setup_t | Parameters and settings for one PP-PME setup |
| PmeGpu | The main PME GPU host structure, included in the PME CPU structure by pointer |
| PmeGpuAtomParams | A GPU data structure for storing the PME data of the atoms, local to this process' domain partition. This only has to be updated every DD step |
| PmeGpuConstParams | A GPU data structure for storing the constant PME data. This only has to be initialized once |
| PmeGpuDynamicParams | A GPU data structure for storing the PME data which might change for each new PME computation |
| PmeGpuGridParams | A GPU data structure for storing the PME data related to the grid sizes and cut-off. This only has to be updated at every DD step |
| PmeGpuKernelParamsBase | A single structure encompassing all the PME data used in GPU kernels on device. To extend the list with platform-specific parameters, this can be inherited by the GPU framework-specific structure |
| PmeGpuProgram | Stores PME data derived from the GPU context or devices |
| PmeGpuProgramImpl | PME GPU persistent host program/kernel data, which should be initialized once for the whole execution |
| PmeGpuSettings | The PME GPU settings structure, included in the main PME GPU structure by value |
| PmeGpuSpecific | The main PME CUDA/OpenCL-specific host data structure, included in the PME GPU structure by the archSpecific pointer |
| PmeGpuStaging | The PME GPU intermediate buffers structure, included in the main PME GPU structure by value. Buffers are managed by the PME GPU module |
| PmeShared | The PME GPU structure for all the data copied directly from the CPU PME structure. The copying is done when the CPU PME structure is already (re-)initialized (pme_gpu_reinit is called at the end of gmx_pme_init). All the variables here are named almost the same way as in gmx_pme_t. The types are different: pointers are replaced by vectors. TODO: use the shared data with the PME CPU. Included in the main PME GPU structure by value |
| PmeSolveKernel | The kernel for PME solve |
| PpRanks | Contains information about the PP ranks that partner this PME rank |
| PreprocessingAtomTypes | Storage of all atom types used during preprocessing of a simulation input |
| PreprocessingBondAtomType | Storage for all bonded atomtypes during simulation preprocessing |
| PreprocessResidue | Information about preprocessing residues |
| pull_coord_work_t | Struct with parameters and force evaluation local data for a pull coordinate |
| pull_group_work_t | Pull group data used during pulling |
| ReduceKernel | Class name for reduction kernel |
| ReplicaExchangeParameters | The parameters for the replica exchange algorithm |
| ReverseTopOptions | Options for setting up gmx_reverse_top_t |
| ScalarDataTypes | Scalar (non-SIMD) data types |
| SearchCycleCounting | Struct for collecting detailed cycle counts for the search |
| SimdDataTypes | SIMD data types |
| SimulationGroups | Contains the simulation atom groups |
| SolveKernelParams | Contains most of the parameters used by the solve kernel |
| sort_along_vec_t | Helper structure for sorting positions along rotation vector |
| spheresurfacebin | Internal data structure for the insolidangle selection method |
| StringTable | A class to store strings for lookup |
| StringTableBuilder | Builds a memory efficient storage for strings of characters |
| StringTableEntry | Helper class to access members in StringTable |
| 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_bb | Struct containing properties of a residue in a protein backbone |
| 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_filenm | File name option definition for C code |
| t_forcetable | Structure describing the data in a single table |
| t_mapping | Maps an XPM element to an RGB color and a string description |
| t_matrix | A matrix of integers, plus supporting values, such as used in XPM output |
| 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_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_pos | Data structure for position keyword evaluation |
| t_methoddata_same | Data structure for the same selection method |
| t_nbparam | Used to temporarily store the explicit non-bonded parameter combinations, which will be copied to InteractionsOfType |
| t_oriresdata | Orientation restraining stuff |
| t_pargs | Command-line argument definition for C code |
| 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 coordinate |
| t_register_method | Helper structure for defining selection methods |
| t_state | The microstate of the system |
| t_swap | Main (private) data structure for the position swapping protocol |
| t_symbuf | Legacy symbol table entry as linked list |
| t_UmbrellaHeader | Parameters of the umbrella potentials |
| t_UmbrellaWindow | Data in the umbrella histograms |
| t_xpmelmt | Models an XPM element |
| thread_work_t | Struct for thread local work data for local topology generation |
| TpxFileHeader | First part of the TPR file structure containing information about the general aspect of the system |
| UmbrellaOptions | Parameters of WHAM |
| UnitCellInfo | Provides information about properties of the unit cell |
| VirtualSiteConfiguration | The configuration describing a virtual site |
| VirtualSiteTopology | Virtual site topology datastructure |
| VirtualSiteAngle | Helper struct for single angle in virtual site |
| VirtualSiteBond | Helper struct for single bond in virtual site |
| VsiteAtomMapping | Convenience typedef for linking function type to parameter numbers |
| VsiteBondedInteraction | Data type to store information about bonded interactions for virtual sites |
| VsiteBondParameter | Stores information about single virtual site bonded parameter |
| WorkDivision | The division of bonded interactions of the threads |
1.8.5
