![o](ftv2pnode.png) gmx | Generic GROMACS namespace |
![|](ftv2vertline.png) ![o](ftv2pnode.png) detail | |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) PaddingTraits | Traits classes for handling padding for types used with PaddedVector |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractAnalysisData | Abstract base class for all objects that provide data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisData | Parallelizable data container for raw data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataHandle | Handle for inserting data into AnalysisData |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisArrayData | Simple in-memory data array |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataValue | Value type for representing a single value in analysis data objects |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
![|](ftv2vertline.png) ![o](ftv2node.png) IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
![|](ftv2vertline.png) ![o](ftv2node.png) ArrayRef | STL-like interface to a C array of T (or part of a std container of T) |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataAverageModule | Data module for independently averaging each column in input data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataDisplacementModule | Data module for calculating displacements |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractAverageHistogram | Base class for representing histograms averaged over frames |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataBinAverageModule | Data module for bin averages |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataPlotSettings | Common settings for data plots |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractPlotModule | Abstract data module for writing data into a file |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineHelpWriter | Writes help information for Options |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineModuleSettings | Settings to pass information between a module and the general runner |
![|](ftv2vertline.png) ![o](ftv2node.png) ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
![|](ftv2vertline.png) ![o](ftv2node.png) ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
![|](ftv2vertline.png) ![o](ftv2node.png) ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
![|](ftv2vertline.png) ![o](ftv2node.png) CommandLineParser | Implements command-line parsing for Options objects |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryFileOpener | Low level method to take care of only file opening and closing |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryFrameWriter | Writes coordinate frames to a sink, e.g. a trajectory file |
![|](ftv2vertline.png) ![o](ftv2node.png) IOutputAdapter | OutputAdapter class for handling trajectory file flag setting and processing |
![|](ftv2vertline.png) ![o](ftv2node.png) OutputSelector | OutputSelector class controls setting which coordinates are actually written |
![|](ftv2vertline.png) ![o](ftv2node.png) SetAtoms | SetAtoms class controls availability of atoms data |
![|](ftv2vertline.png) ![o](ftv2node.png) SetBox | Allows changing box information when writing a coordinate file |
![|](ftv2vertline.png) ![o](ftv2node.png) SetForces | SetForces class allows changing writing of forces to file |
![|](ftv2vertline.png) ![o](ftv2node.png) SetPrecision | SetPrecision class allows changing file writing precision |
![|](ftv2vertline.png) ![o](ftv2node.png) SetStartTime | SetStartTime class allows changing trajectory time information |
![|](ftv2vertline.png) ![o](ftv2node.png) SetTimeStep | SetTimeStep class allows changing trajectory time information |
![|](ftv2vertline.png) ![o](ftv2node.png) SetVelocities | SetVelocities class allows changing writing of velocities to file |
![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![|](ftv2vertline.png) ![o](ftv2node.png) OutputRequirements | Finalized version of requirements after processing |
![|](ftv2vertline.png) ![o](ftv2node.png) ListOfLists | A list of lists, optimized for performance |
![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![|](ftv2vertline.png) ![o](ftv2node.png) StaticLog2 | Evaluate log2(n) for integer n statically at compile time |
![|](ftv2vertline.png) ![o](ftv2node.png) StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
![|](ftv2vertline.png) ![o](ftv2node.png) StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
![|](ftv2vertline.png) ![o](ftv2node.png) PaddedVector | PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS |
![|](ftv2vertline.png) ![o](ftv2node.png) BasicVector | C++ class for 3D vectors |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationSignal | POD-style object used by mdrun ranks to set and receive signals within and between simulations |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationSignaller | Object used by mdrun ranks to signal to each other at this step |
![|](ftv2vertline.png) ![o](ftv2node.png) MembedHolder | Membed SimulatorBuilder parameter type |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulatorConfig | Simulation configuation settings |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulatorStateData | Data for a specific simulation state |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulatorEnv | Collection of environmental information for a simulation |
![|](ftv2vertline.png) ![o](ftv2node.png) Profiling | Collection of profiling information |
![|](ftv2vertline.png) ![o](ftv2node.png) ConstraintsParam | Collection of constraint parameters |
![|](ftv2vertline.png) ![o](ftv2node.png) LegacyInput | Collection of legacy input information |
![|](ftv2vertline.png) ![o](ftv2node.png) InteractiveMD | SimulatorBuilder parameter type for InteractiveMD |
![|](ftv2vertline.png) ![o](ftv2node.png) IonSwapping | Parameter type for IonSwapping SimulatorBuilder component |
![|](ftv2vertline.png) ![o](ftv2node.png) TopologyData | Collection of handles to topology information |
![|](ftv2vertline.png) ![o](ftv2node.png) BoxDeformationHandle | Handle to information about the box |
![|](ftv2vertline.png) ![o](ftv2node.png) IsSerializableEnum | { |
![|](ftv2vertline.png) ![o](ftv2node.png) CheckpointData | } |
![|](ftv2vertline.png) ![o](ftv2node.png) MtsLevel | Setting for a single level for multiple time step integration |
![|](ftv2vertline.png) ![o](ftv2node.png) ElementNotFoundError | Exception class signalling that a requested element was not found |
![|](ftv2vertline.png) ![o](ftv2node.png) MissingElementConnectionError | Exception class signalling that elements were not connected properly |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationAlgorithmSetupError | Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way |
![|](ftv2vertline.png) ![o](ftv2node.png) CheckpointError | Exception class signalling an error in reading or writing modular checkpoints |
![|](ftv2vertline.png) ![o](ftv2node.png) BenchmarkSystem | Description of the system used for benchmarking |
![|](ftv2vertline.png) ![o](ftv2pnode.png) Range | Defines a range of integer numbers and accompanying operations |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) iterator | An iterator that loops over a range of integers |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractOption | Abstract base class for specifying option properties |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionTemplate | Templated base class for constructing concrete option settings classes |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionInfo | Gives information and allows modifications to an option after creation |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractOptionSection | Base class for specifying option section properties |
![|](ftv2vertline.png) ![o](ftv2node.png) AbstractOptionSectionHandle | Base class for handles to option sections |
![|](ftv2vertline.png) ![o](ftv2node.png) BooleanOption | Specifies an option that provides boolean values |
![|](ftv2vertline.png) ![o](ftv2node.png) IntegerOption | Specifies an option that provides integer values |
![|](ftv2vertline.png) ![o](ftv2node.png) Int64Option | Specifies an option that provides 64-bit integer values |
![|](ftv2vertline.png) ![o](ftv2node.png) DoubleOption | Specifies an option that provides floating-point (double) values |
![|](ftv2vertline.png) ![o](ftv2node.png) FloatOption | Specifies an option that provides floating-point (float) values |
![|](ftv2vertline.png) ![o](ftv2node.png) StringOption | Specifies an option that provides string values |
![|](ftv2vertline.png) ![o](ftv2node.png) EnumOption | Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable |
![|](ftv2vertline.png) ![o](ftv2node.png) LegacyEnumOption | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
![|](ftv2vertline.png) ![o](ftv2node.png) BooleanOptionInfo | Wrapper class for accessing boolean option information |
![|](ftv2vertline.png) ![o](ftv2node.png) IntegerOptionInfo | Wrapper class for accessing integer option information |
![|](ftv2vertline.png) ![o](ftv2node.png) Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
![|](ftv2vertline.png) ![o](ftv2node.png) DoubleOptionInfo | Wrapper class for accessing floating-point option information |
![|](ftv2vertline.png) ![o](ftv2node.png) FloatOptionInfo | Wrapper class for accessing floating-point option information |
![|](ftv2vertline.png) ![o](ftv2node.png) StringOptionInfo | Wrapper class for accessing string option information |
![|](ftv2vertline.png) ![o](ftv2node.png) EnumOptionInfo | Wrapper class for accessing enum option information |
![|](ftv2vertline.png) ![o](ftv2node.png) FileNameOption | Specifies an option that provides file names |
![|](ftv2vertline.png) ![o](ftv2node.png) FileNameOptionInfo | Wrapper class for accessing file name option information |
![|](ftv2vertline.png) ![o](ftv2node.png) FileNameOptionManager | Handles interaction of file name options with global options |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionsBehavior | Interface to provide extension points for options parsing |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionsContainer | Interface for adding input options |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionsContainerWithSections | Interface for adding input options with sections |
![|](ftv2vertline.png) ![o](ftv2node.png) IOptionManager | Base class for option managers |
![|](ftv2vertline.png) ![o](ftv2node.png) Options | Collection of options |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionSection | Declares a simple option section |
![|](ftv2vertline.png) ![o](ftv2node.png) OptionSectionHandle | Allows adding options to an OptionSection |
![|](ftv2vertline.png) ![o](ftv2node.png) RepeatingOptionSectionHandle | Allows adding options to an RepeatingOptionSection |
![|](ftv2vertline.png) ![o](ftv2node.png) RepeatingOptionSection | Declares an option section that creates a structure for each instance |
![|](ftv2vertline.png) ![o](ftv2node.png) TimeUnitManager | Provides common functionality for time unit conversions |
![|](ftv2vertline.png) ![o](ftv2node.png) TimeUnitBehavior | Options behavior to add a time unit option |
![|](ftv2vertline.png) ![o](ftv2pnode.png) ExponentialDistribution | Exponential distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Exponential distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) GammaDistribution | Gamma distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Gamma distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) NormalDistribution | Normal distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Normal distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) TabulatedNormalDistribution | Tabulated normal random distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Normal distribution parameter class (mean and stddev) |
![|](ftv2vertline.png) ![o](ftv2node.png) ThreeFry2x64General | General implementation class for ThreeFry counter-based random engines |
![|](ftv2vertline.png) ![o](ftv2node.png) ThreeFry2x64 | ThreeFry2x64 random engine with 20 iteractions |
![|](ftv2vertline.png) ![o](ftv2node.png) ThreeFry2x64Fast | ThreeFry2x64 random engine with 13 iteractions |
![|](ftv2vertline.png) ![o](ftv2pnode.png) UniformIntDistribution | Uniform integer distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Uniform int distribution parameters |
![|](ftv2vertline.png) ![o](ftv2pnode.png) UniformRealDistribution | Uniform real distribution |
![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) param_type | Uniform real distribution parameters |
![|](ftv2vertline.png) ![o](ftv2node.png) PotentialPointData | Structure to hold the results of IRestraintPotential::evaluate() |
![|](ftv2vertline.png) ![o](ftv2node.png) IRestraintPotential | Interface for Restraint potentials |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhood | Neighborhood searching for analysis tools |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
![|](ftv2vertline.png) ![o](ftv2node.png) AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
![|](ftv2vertline.png) ![o](ftv2node.png) Selection | Provides access to a single selection |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionPosition | Provides access to information about a single selected position |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionCollection | Collection of selections |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionTopologyProperties | Describes topology properties required for selection evaluation |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOption | Specifies an option that provides selection(s) |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
![|](ftv2vertline.png) ![o](ftv2node.png) ITopologyProvider | Provides topology information to SelectionOptionBehavior |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
![|](ftv2vertline.png) ![o](ftv2node.png) SelectionOptionManager | Handles interaction of selection options with other options and user input |
![|](ftv2vertline.png) ![o](ftv2node.png) ConvertTprInfo | Declares gmx convert-tpr |
![|](ftv2vertline.png) ![o](ftv2node.png) RangePartitioning | Division of a range of indices into consecutive blocks |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisModule | Base class for trajectory analysis modules |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
![|](ftv2vertline.png) ![o](ftv2node.png) TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
![|](ftv2vertline.png) ![o](ftv2node.png) PrivateImplPointer | Helper class to manage a pointer to a private implementation class |
![|](ftv2vertline.png) ![o](ftv2node.png) DataFileOptions | Search parameters for DataFileFinder |
![|](ftv2vertline.png) ![o](ftv2node.png) DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
![|](ftv2vertline.png) ![o](ftv2node.png) DataFileFinder | Searches data files from a set of paths |
![|](ftv2vertline.png) ![o](ftv2node.png) ExceptionInfo | Stores additional context information for exceptions |
![|](ftv2vertline.png) ![o](ftv2node.png) ExceptionInitializer | Provides information for Gromacs exception constructors |
![|](ftv2vertline.png) ![o](ftv2node.png) GromacsException | Base class for all exception objects in Gromacs |
![|](ftv2vertline.png) ![o](ftv2node.png) FileIOError | Exception class for file I/O errors |
![|](ftv2vertline.png) ![o](ftv2node.png) UserInputError | Exception class for user input errors |
![|](ftv2vertline.png) ![o](ftv2node.png) InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
![|](ftv2vertline.png) ![o](ftv2node.png) InconsistentInputError | Exception class for situations where user input is inconsistent |
![|](ftv2vertline.png) ![o](ftv2node.png) ToleranceError | Exception class when a specified tolerance cannot be achieved |
![|](ftv2vertline.png) ![o](ftv2node.png) SimulationInstabilityError | Exception class for simulation instabilities |
![|](ftv2vertline.png) ![o](ftv2node.png) InternalError | Exception class for internal errors |
![|](ftv2vertline.png) ![o](ftv2node.png) APIError | Exception class for incorrect use of an API |
![|](ftv2vertline.png) ![o](ftv2node.png) RangeError | Exception class for out-of-range values or indices |
![|](ftv2vertline.png) ![o](ftv2node.png) NotImplementedError | Exception class for use of an unimplemented feature |
![|](ftv2vertline.png) ![o](ftv2node.png) ParallelConsistencyError | Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion |
![|](ftv2vertline.png) ![o](ftv2node.png) ModularSimulatorError | Exception class for modular simulator |
![|](ftv2vertline.png) ![o](ftv2node.png) FixedCapacityVector | Vector that behaves likes std::vector but has fixed capacity |
![|](ftv2vertline.png) ![o](ftv2node.png) FlagsTemplate | Template class for typesafe handling of combination of flags |
![|](ftv2vertline.png) ![o](ftv2node.png) InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
![|](ftv2vertline.png) ![o](ftv2node.png) IProgramContext | Provides context information about the program that is calling the library |
![|](ftv2vertline.png) ![o](ftv2node.png) StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
![|](ftv2vertline.png) ![o](ftv2node.png) IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
![|](ftv2vertline.png) ![o](ftv2node.png) TextLineWrapperSettings | Stores settings for line wrapping |
![|](ftv2vertline.png) ![o](ftv2node.png) TextLineWrapper | Wraps lines to a predefined length |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) NonbondedBenchmarkInfo | Declares gmx nonbonded-bench |
![o](ftv2node.png) AtomIterator | Object that allows looping over all atoms in an mtop |
![o](ftv2node.png) AtomProperties | Holds all the atom property information loaded |
![o](ftv2node.png) AtomProxy | Proxy object returned from AtomIterator |
![o](ftv2node.png) AtomRange | Range over all atoms of topology |
![o](ftv2node.png) CheckpointHeaderContents | Header explaining the context of a checkpoint file |
![o](ftv2node.png) df_history_t | Free-energy sampling history struct |
![o](ftv2node.png) ForceHelperBuffers | Helper force buffers for ForceOutputs |
![o](ftv2node.png) ForeignLambdaTerms | Accumulates free-energy foreign lambda energies and dH/dlamba |
![o](ftv2node.png) gmx_ana_index_t | Stores a single index group |
![o](ftv2node.png) gmx_ana_indexmap_t | Data structure for calculating index group mappings |
![o](ftv2node.png) gmx_ana_pos_t | Stores a set of positions together with their origins |
![o](ftv2node.png) gmx_cache_protect_t | Cache-line protection buffer |
![o](ftv2node.png) gmx_enerdata_t | Struct for accumulating all potential energy terms and some kinetic energy terms |
![o](ftv2node.png) gmx_ffparams_t | Struct that holds all force field parameters for the simulated system |
![o](ftv2node.png) gmx_localtop_t | The fully written out topology for a domain over its lifetime |
![o](ftv2node.png) gmx_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
![o](ftv2node.png) gmx_moltype_t | Molecules type data: atoms, interactions and exclusions |
![o](ftv2node.png) gmx_sparsematrix | Sparse matrix storage format |
![o](ftv2node.png) InteractionListHandle | Type for returning a list of InteractionList references |
![o](ftv2node.png) MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
![o](ftv2node.png) nbnxn_cj4_t | Four-way j-cluster lists |
![o](ftv2node.png) nbnxn_cj_t | This is the actual cluster-pair list j-entry |
![o](ftv2node.png) nbnxn_cycle_t | Local cycle count struct for profiling |
![o](ftv2node.png) nbnxn_excl_t | Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist |
![o](ftv2node.png) nbnxn_im_ei_t | Interaction data for a j-group for one warp |
![o](ftv2node.png) nbnxn_sci | Grouped pair-list i-unit |
![o](ftv2node.png) NbnxnPairlistCpu | Cluster pairlist type for use on CPUs |
![o](ftv2pnode.png) NbnxnPairlistCpuWork | Working data for the actual i-supercell during pair search |
![|](ftv2vertline.png) ![\](ftv2lastnode.png) IClusterData | Struct for storing coordinats and bounding box for an i-entry during search |
![o](ftv2node.png) PairlistSets | Contains sets of pairlists |
![o](ftv2node.png) PairSearch | Main pair-search struct, contains the grid(s), not the pair-list(s) |
![o](ftv2node.png) PairsearchWork | Thread-local work struct, contains working data for Grid |
![o](ftv2node.png) PartialDeserializedTprFile | Contains the partly deserialized contents of a TPR file |
![o](ftv2node.png) PbcAiuc | Compact and ordered version of the PBC matrix |
![o](ftv2node.png) SimulationGroups | Contains the simulation atom groups |
![o](ftv2node.png) SimulationInputHandle | Owning handle to a SimulationInput object |
![o](ftv2node.png) StringTable | A class to store strings for lookup |
![o](ftv2node.png) StringTableEntry | Helper class to access members in StringTable |
![o](ftv2node.png) t_filenm | File name option definition for C code |
![o](ftv2node.png) t_mapping | Maps an XPM element to an RGB color and a string description |
![o](ftv2node.png) t_matrix | A matrix of integers, plus supporting values, such as used in XPM output |
![o](ftv2node.png) t_mdatoms | Declares mdatom data structure |
![o](ftv2node.png) t_pargs | Command-line argument definition for C code |
![o](ftv2node.png) t_pbc | Structure containing info on periodic boundary conditions |
![o](ftv2node.png) t_state | The microstate of the system |
![\](ftv2lastnode.png) t_xpmelmt | Models an XPM element |