  gmx | Generic GROMACS namespace |
 test | |
  TestSystem | Description of the system used for testing |
 ArrayRef | STL-like interface to a C array of T (or part of a std container of T) |
| INNPotModel | NNPot Module |
| NNPotTopologyPreprocessor | Class responsible for all modifications of the topology during input pre-processing |
| TorchModel | Class responsible for loading and evaluating a TorchScript-compiled neural network model. Inherits from NNPotModel |
| CommandLineHelpWriter | Writes help information for Options |
| CommandLineModuleSettings | Settings to pass information between a module and the general runner |
| ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
| 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 |
| 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 |
| ProcessFrameConversion | ProcessFrameConversion class for handling the running of several analysis steps |
| IFrameConverter | IFrameConverter interface for manipulating coordinate information |
| IOutputAdapter | OutputAdapter class for handling trajectory file flag setting and processing |
| 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 |
| DomainCommBackward | Setup for selecting halo atoms to be sent and sending coordinates to another domain |
| ColumnInfo | Struct for collecting information on grid columns |
| DomainCommForward | Setup for receiving halo coordinates from another domain and sending halo forces |
| DomainPairComm | Setup for communication between pairs of domains, both backward and forward along the DD grid |
| FixedCapacityVector | Vector that behaves likes std::vector but has fixed capacity |
| HaloMpiRequests | Storage for MPI request for halo MPI receive and send operations |
| HaloExchange | Handles the halo communication of coordinates and forces |
| 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 |
| H5md | Manager of an H5MD filehandle. The class is designed to read/write data according to de Buyl et al., 2014 (https://doi.org/10.1016/j.cpc.2014.01.018) and https://www.nongnu.org/h5md/h5md.html |
| 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 |
| PaddedVector | PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS |
| AtomPair | A pair of atoms indexes |
| 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 |
| Range | Defines a range of integer numbers and accompanying operations |
| iterator | An iterator that loops over a range of integers |
| MembedHolder | Membed SimulatorBuilder parameter type |
| 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 |
| CheckpointData | } |
| IsSerializableEnum | { |
| MtsLevel | Setting for a single level for multiple time step integration |
| GromppMtsOpts | Struct for passing the MTS mdp options to setupMtsLevels() |
| 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 |
| EnergyAccumulator | Base energy accumulator class, only specializations are used |
| BenchmarkSystem | Description of the system used for benchmarking |
| EnergyFunctionProperties | Set of boolean constants mimicking preprocessor macros |
| GridDimensions | The physical dimensions of a grid |
| gmx_cache_protect_t | Cache-line protection buffer |
| nbnxn_cj_t | This is the actual cluster-pair list j-entry |
| JClusterList | Simple j-cluster list |
| nbnxn_sci_t | Grouped pair-list i-unit |
| nbnxn_im_ei_t | Interaction data for a j-group for one warp |
| nbnxn_cj_packed_t | Packed j-cluster list element |
| PackedJClusterList | Packed j-cluster list |
| nbnxn_excl_t | Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist |
| NbnxnPairlistCpu | Cluster pairlist type for use on CPUs |
| PairlistSets | Contains sets of pairlists |
| NbnxmPairlistCpuWork | Working data for the actual i-supercell during pair search |
| IClusterData | Struct for storing coordinates and bounding box for an i-entry during search |
| nbnxn_cycle_t | Local cycle count struct for profiling |
| PairsearchWork | Thread-local work struct, contains working data for Grid |
| PairSearch | Main pair-search struct, contains the grid(s), not the pair-list(s) |
| CoulombCalculator | Base Coulomb calculator class, only specializations are used |
| CoulombCalculator< KernelCoulombType::RF > | Specialized calculator for RF |
| CoulombCalculator< KernelCoulombType::EwaldAnalytical > | Specialized calculator for Ewald using an analytic approximation |
| CoulombCalculator< KernelCoulombType::EwaldTabulated > | Specialized calculator for Ewald using tabulated functions |
| DiagonalMasker | Base Coulomb calculator class, only specializations are used |
| DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > | Specialized masker for JSizeEqualsISize |
| DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > | Specialized masker for JSizeIsDoubleISize |
| DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > | Specialized masker for JSizeIsHalfISize |
| EnergyAccumulator< useEnergyGroups, false > | Specialized energy accumulator class for no energy calculation |
| EnergyAccumulator< false, true > | Specialized energy accumulator class for energy accumulation without energy groups |
| EnergyAccumulator< true, true > | Specialized energy accumulator class for energy accumulation with energy groups |
| EnergyGroupsPerCluster | Holds energy group indices for use in EnergyAccumulator<true, true> |
| LennardJonesCalculator | Base LJ calculator class, only specializations are used |
| LennardJonesCalculator< false, InteractionModifiers::PotShift > | Specialized calculator for LJ with potential shift and no energy calculation |
| LennardJonesCalculator< true, InteractionModifiers::PotShift > | Specialized calculator for LJ with potential shift and energy calculation |
| LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > | Specialized calculator for LJ with force switch |
| LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > | Specialized calculator for LJ with potential switch |
| NbnxmKernel | Class name for NBNXM kernel |
| AbstractOptionSection | Base class for specifying option section properties |
| AbstractOptionSectionHandle | Base class for handles to option sections |
| OptionSection | Declares a simple option section |
| OptionSectionHandle | Allows adding options to an OptionSection |
| RepeatingOptionSectionHandle | Allows adding options to an RepeatingOptionSection |
| RepeatingOptionSection | Declares an option section that creates a structure for each instance |
| 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 |
| ConvertTprInfo | Declares gmx convert-tpr |
| BoolType | A clone of a bool as a workaround on the template specialization of std::vector<bool> that is incompatible with ArrayRef |
| DataFileOptions | Search parameters for DataFileFinder |
| DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
| DataFileFinder | Searches data files from a set of paths |
| StringToEnumValueConverter | A class to convert a string to an enum value of type EnumType |
| NonbondedBenchmarkInfo | Declares gmx nonbonded-bench |
| BasicVector | C++ class for 3D vectors |
| AbstractAnalysisData | Abstract base class for all objects that provide data |
| AnalysisData | Parallelizable data container for raw data |
| AnalysisDataHandle | Handle for inserting data into AnalysisData |
| AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
| AnalysisArrayData | Simple in-memory data array |
| AnalysisDataValue | Value type for representing a single value in analysis data objects |
| AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
| AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
| AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
| IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
| AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
| AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
| AnalysisDataAverageModule | Data module for independently averaging each column in input data |
| AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
| AnalysisDataDisplacementModule | Data module for calculating displacements |
| AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
| AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
| AbstractAverageHistogram | Base class for representing histograms averaged over frames |
| AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
| AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| AnalysisDataBinAverageModule | Data module for bin averages |
| AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
| AnalysisDataPlotSettings | Common settings for data plots |
| AbstractPlotModule | Abstract data module for writing data into a file |
| AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
| AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
| 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 |
| 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 |
| 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 |
| FileNameOption | Specifies an option that provides file names |
| FileNameOptionInfo | Wrapper class for accessing file name option information |
| FileNameOptionManager | Handles interaction of file name options with global options |
| IOptionsBehavior | Interface to provide extension points for options parsing |
| IOptionsContainer | Interface for adding input options |
| IOptionsContainerWithSections | Interface for adding input options with sections |
| IOptionManager | Base class for option managers |
| Options | Collection of options |
| TimeUnitManager | Provides common functionality for time unit conversions |
| TimeUnitBehavior | Options behavior to add a time unit option |
| PotentialPointData | Structure to hold the results of IRestraintPotential::evaluate() |
| IRestraintPotential | Interface for Restraint potentials |
| AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
| AnalysisNeighborhood | Neighborhood searching for analysis tools |
| AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
| AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
| AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
| Selection | Provides access to a single selection |
| SelectionPosition | Provides access to information about a single selected position |
| SelectionCollection | Collection of selections |
| SelectionTopologyProperties | Describes topology properties required for selection evaluation |
| 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 |
| RangePartitioning | Division of a range of indices into consecutive blocks |
| TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
| TrajectoryAnalysisModule | Base class for trajectory analysis modules |
| TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
| TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
| EnumClassSuitsEnumerationArray | Helper class to determine whether a template type that is an enum class has a Count field |
| ExceptionInfo | Stores additional context information for exceptions |
| ExceptionInitializer | Provides information for Gromacs exception constructors |
| GromacsException | Base class for all exception objects in Gromacs |
| FileIOError | Exception class for file I/O errors |
| UserInputError | Exception class for user input errors |
| InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
| InconsistentInputError | Exception class for situations where user input is inconsistent |
| 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 |
| FlagsTemplate | Template class for typesafe handling of combination of flags |
| InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| IProgramContext | Provides context information about the program that is calling the library |
| 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 |
| CompileTimeStringJoin | Combines string literals at compile time to final string |
| AtomIterator | Object that allows looping over all atoms in an mtop |
| AtomProperties | Holds all the atom property information loaded |
| AtomProxy | Proxy object returned from AtomIterator |
| AtomRange | Range over all atoms of topology |
| AtomsAdjacencyListElement | Helper type for discovering coupled constraints |
| BalanceRegion | Object that describes a DLB balancing region |
| CheckpointHeaderContents | Header explaining the context of a checkpoint file |
| df_history_t | Free-energy sampling history struct |
| FEPStateValue | Template wrapper struct for particle FEP state values |
| ForceHelperBuffers | Helper force buffers for ForceOutputs |
| ForeignLambdaTerms | Accumulates free-energy foreign lambda energies and dH/dlamba |
| gmx_ana_index_t | Stores a single index group |
| gmx_ana_indexmap_t | Data structure for calculating index group mappings |
| gmx_ana_pos_t | Stores a set of positions together with their origins |
| gmx_cmap_t | CMAP grids |
| gmx_cmapdata_t | CMAP data for a single grid |
| gmx_domdec_constraints_t | Struct used during constraint setup with domain decomposition |
| gmx_enerdata_t | Struct for accumulating all potential energy terms and some kinetic energy terms |
| gmx_ffparams_t | Struct that holds all force field parameters for the simulated system |
| 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_nodecomm_t | Settings and communicators for two-step communication: intra + inter-node |
| gmx_sparsematrix | Sparse matrix storage format |
| 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 |
| IndexGroup | An index group consisting or a name and list of atom indices |
| InteractionDefinitions | Struct with list of interaction parameters and lists of interactions |
| InteractionList | List of listed interactions |
| InteractionListHandle | Type for returning a list of InteractionList references |
| LocalSettleData | Local settle data |
| MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
| PartialDeserializedTprFile | Contains the partly deserialized contents of a TPR file |
| PbcAiuc | Compact and ordered version of the PBC matrix |
| PdbAtomEntry | Contains information for a single particle in a PDB file |
| PmeSolve | Class for solving PME for Coulomb and LJ |
| SettleWaterTopology | Composite data for settle initialization |
| SimulationGroups | Contains the simulation atom groups |
| SimulationInputHandle | Owning handle to a SimulationInput object |
| SimulationParticle | Single particle in a simulation |
| StringTable | A class to store strings for lookup |
| StringTableEntry | Helper class to access members in StringTable |
| SystemMomenta | System momenta used with with the box deform option |
| SystemMomentum | The momentum and mass of the whole system |
| t_filenm | File name option definition for C code |
| t_idef | Deprecated interation definitions, used in t_topology |
| t_ilist | Deprecated list of listed interactions |
| t_interaction_function | Interaction function |
| t_iparams | Union of various interaction paramters |
| 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_nblist | A plain atom pair list, used only for perturbed non-bonded interactions |
| IEntry | An i-entry |
| JEntry | A j-entry |
| t_oriresdata | Orientation restraining stuff |
| t_pargs | Command-line argument definition for C code |
| t_pbc | Structure containing info on periodic boundary conditions |
| t_state | The microstate of the system |
| t_xpmelmt | Models an XPM element |
| VsiteTypeAndSign | Struct for handling vsite information for vsite generation inside grompp |
| wallcc_t | Counters for an individual wallcycle timing region |
| WarningHandler | General warning handling object |
| WaterMolecule | Indices of atoms in a water molecule |
1.8.5
