Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 1234]

AmdPackedFloat3	Special packed Float3 flavor to help compiler optimizations on AMD CDNA2 devices
gmx::ArrayRef< BoundingBox >
gmx::ArrayRef< const AnalysisDataValue >
gmx::ArrayRef< const char *const >
gmx::ArrayRef< const char >
gmx::ArrayRef< const double >
gmx::ArrayRef< const float >
gmx::ArrayRef< const gmx::BasicVector >
gmx::ArrayRef< const int >
gmx::ArrayRef< const InteractionList >
gmx::ArrayRef< const real >
gmx::ArrayRef< const t_filenm >
gmx::ArrayRef< const t_iparams >
gmx::ArrayRef< const unsigned short >
gmx::ArrayRef< double >
gmx::ArrayRef< gmx::BasicVector >
gmx::ArrayRef< gmx::gmx::BasicVector >
gmx::ArrayRef< gmx::RVec >
gmx::ArrayRef< PpRanks >
gmx::ArrayRef< real >
gmx::ArrayRef< ValueType >
gmx::ArrayRefWithPadding< gmx::BasicVector >
gmx::ArrayRefWithPadding< gmx::gmx::BasicVector >
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
gmx::BasicVector< double >
gmx::BasicVector< int >
gmx::BasicVector< real >
CheckpointHeaderContents	Header explaining the context of a checkpoint file
df_history_t	Free-energy sampling history struct
FEPStateValue< T >	Template wrapper struct for particle FEP state values
FEPStateValue< NameHolder >
FEPStateValue< real >
FEPStateValue< unsigned short >
gmx::FixedCapacityVector< GpuEventSynchronizer *, 3 >
gmx::FlagsTemplate< Flag >
ForceHelperBuffers	Helper force buffers for ForceOutputs
ForeignLambdaTerms	Accumulates free-energy foreign lambda energies and dH/dlamba
gmx::AbstractAnalysisData	Abstract base class for all objects that provide data
gmx::AbstractAnalysisArrayData	Abstract base class for data objects that present in-memory data
gmx::AbstractAverageHistogram	Base class for representing histograms averaged over frames
gmx::AnalysisArrayData	Simple in-memory data array
gmx::AnalysisDataAverageModule	Data module for independently averaging each column in input data
gmx::AnalysisDataBinAverageModule	Data module for bin averages
gmx::AnalysisDataLifetimeModule	Data module for computing lifetime histograms for columns in input data
gmx::AnalysisData	Parallelizable data container for raw data
gmx::AnalysisDataDisplacementModule	Data module for calculating displacements
gmx::AnalysisDataFrameAverageModule	Data module for averaging of columns for each frame
gmx::AnalysisDataSimpleHistogramModule	Data module for per-frame histograms
gmx::AnalysisDataWeightedHistogramModule	Data module for per-frame weighted histograms
gmx::AbstractOption	Abstract base class for specifying option properties
gmx::OptionTemplate< T, U >	Templated base class for constructing concrete option settings classes
gmx::OptionTemplate< bool, BooleanOption >
gmx::BooleanOption	Specifies an option that provides boolean values
gmx::OptionTemplate< double, DoubleOption >
gmx::DoubleOption	Specifies an option that provides floating-point (double) values
gmx::OptionTemplate< EnumType, EnumOption< EnumType > >
gmx::EnumOption< EnumType >	Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable
gmx::OptionTemplate< EnumType, LegacyEnumOption< EnumType > >
gmx::LegacyEnumOption< EnumType >	Specifies an option that accepts enumerated string values and writes the selected index into an enum variable
gmx::OptionTemplate< float, FloatOption >
gmx::FloatOption	Specifies an option that provides floating-point (float) values
gmx::OptionTemplate< int, IntegerOption >
gmx::IntegerOption	Specifies an option that provides integer values
gmx::OptionTemplate< int64_t, Int64Option >
gmx::Int64Option	Specifies an option that provides 64-bit integer values
gmx::OptionTemplate< Selection, SelectionOption >
gmx::SelectionOption	Specifies an option that provides selection(s)
gmx::OptionTemplate< std::string, FileNameOption >
gmx::FileNameOption	Specifies an option that provides file names
gmx::OptionTemplate< std::string, StringOption >
gmx::StringOption	Specifies an option that provides string values
gmx::AbstractOptionSection	Base class for specifying option section properties
gmx::OptionSection	Declares a simple option section
gmx::RepeatingOptionSection< T >	Declares an option section that creates a structure for each instance
gmx::AnalysisDataFrameHeader	Value type for storing frame-level information for analysis data
gmx::AnalysisDataFrameRef	Value type wrapper for non-mutable access to a data frame
gmx::AnalysisDataHandle	Handle for inserting data into AnalysisData
gmx::AnalysisDataPlotSettings	Common settings for data plots
gmx::AnalysisDataPointSetRef	Value type wrapper for non-mutable access to a set of data column values
gmx::AnalysisDataValue	Value type for representing a single value in analysis data objects
gmx::AnalysisHistogramSettings	Contains parameters that specify histogram bin locations
gmx::AnalysisHistogramSettingsInitializer	Provides "named parameter" idiom for constructing histograms
gmx::AnalysisNeighborhood	Neighborhood searching for analysis tools
gmx::AnalysisNeighborhoodPair	Value type to represent a pair of positions found in neighborhood searching
gmx::AnalysisNeighborhoodPairSearch	Initialized neighborhood pair search with a fixed set of positions
gmx::AnalysisNeighborhoodPositions	Input positions for neighborhood searching
gmx::AnalysisNeighborhoodSearch	Initialized neighborhood search with a fixed set of reference positions
gmx::ArrayRef< typename >	STL-like interface to a C array of T (or part of a std container of T)
gmx::ArrayRefWithPadding< typename >	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
gmx::AtomPair	A pair of atoms indexes
gmx::BasicVector< ValueType >	C++ class for 3D vectors
gmx::BenchmarkSystem	Description of the system used for benchmarking
gmx::BoolType	A clone of a bool as a workaround on the template specialization of std::vector<bool> that is incompatible with ArrayRef
gmx::BoxDeformationHandle	Handle to information about the box
gmx::CheckpointData< operation >	}
gmx::CommandLineHelpWriter	Writes help information for Options
gmx::CommandLineModuleSettings	Settings to pass information between a module and the general runner
gmx::CommandLineParser	Implements command-line parsing for Options objects
gmx::ConstraintsParam	Collection of constraint parameters
gmx::ConvertTprInfo	Declares gmx convert-tpr
gmx::CoulombCalculator< coulombType >	Base Coulomb calculator class, only specializations are used
gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical >	Specialized calculator for Ewald using an analytic approximation
gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated >	Specialized calculator for Ewald using tabulated functions
gmx::CoulombCalculator< KernelCoulombType::RF >	Specialized calculator for RF
gmx::DataFileFinder	Searches data files from a set of paths
gmx::DataFileInfo	Information about a data file found by DataFileFinder::enumerateFiles()
gmx::DataFileOptions	Search parameters for DataFileFinder
gmx::detail::PaddingTraits< T >	Traits classes for handling padding for types used with PaddedVector
gmx::DiagonalMasker< int, KernelLayout, KernelLayoutClusterRatio >	Base Coulomb calculator class, only specializations are used
gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize >	Specialized masker for JSizeEqualsISize
gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize >	Specialized masker for JSizeIsDoubleISize
gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize >	Specialized masker for JSizeIsHalfISize
gmx::EqualCaseInsensitive	Function object for comparisons with equalCaseInsensitive
gmx::ExceptionInfo< Tag, T >	Stores additional context information for exceptions
gmx::ExceptionInitializer	Provides information for Gromacs exception constructors
gmx::ExponentialDistribution< RealType >	Exponential distribution
gmx::ExponentialDistribution< RealType >::param_type	Exponential distribution parameters
gmx::FixedCapacityVector< typename, size_t >	Vector that behaves likes std::vector but has fixed capacity
gmx::FlagsTemplate< FlagType >	Template class for typesafe handling of combination of flags
gmx::GammaDistribution< RealType >	Gamma distribution
gmx::GammaDistribution< RealType >::param_type	Gamma distribution parameters
gmx::GromppMtsOpts	Struct for passing the MTS mdp options to setupMtsLevels()
gmx::IAnalysisDataModule	Interface for a module that gets notified whenever data is added
gmx::AnalysisDataModuleParallel	Convenience base class for parallel analysis data modules
gmx::AnalysisDataSimpleHistogramModule	Data module for per-frame histograms
gmx::AnalysisDataWeightedHistogramModule	Data module for per-frame weighted histograms
gmx::AnalysisDataModuleSerial	Convenience base class for serial analysis data modules
gmx::AbstractPlotModule	Abstract data module for writing data into a file
gmx::AnalysisDataPlotModule	Plotting module for straightforward plotting of data
gmx::AnalysisDataVectorPlotModule	Plotting module specifically for data consisting of vectors
gmx::AnalysisDataAverageModule	Data module for independently averaging each column in input data
gmx::AnalysisDataBinAverageModule	Data module for bin averages
gmx::AnalysisDataDisplacementModule	Data module for calculating displacements
gmx::AnalysisDataFrameAverageModule	Data module for averaging of columns for each frame
gmx::AnalysisDataLifetimeModule	Data module for computing lifetime histograms for columns in input data
gmx::ICommandLineModule	Module that can be run from command line using CommandLineModuleManager
gmx::ICommandLineOptionsModule	Module that can be run from a command line and uses gmx::Options for argument processing
gmx::ICommandLineOptionsModuleSettings	Settings to pass information between a CommandLineOptionsModule and generic code that runs it
gmx::IdentityFormatter	Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further
gmx::IFrameConverter	IFrameConverter interface for manipulating coordinate information
gmx::ProcessFrameConversion	ProcessFrameConversion class for handling the running of several analysis steps
gmx::InstallationPrefixInfo	Provides information about installation prefix (see IProgramContext::installationPrefix())
gmx::InteractiveMD	SimulatorBuilder parameter type for InteractiveMD
gmx::IonSwapping	Parameter type for IonSwapping SimulatorBuilder component
gmx::IOptionManager	Base class for option managers
gmx::FileNameOptionManager	Handles interaction of file name options with global options
gmx::SelectionOptionManager	Handles interaction of selection options with other options and user input
gmx::IOptionsBehavior	Interface to provide extension points for options parsing
gmx::SelectionOptionBehavior	Options behavior to allow using SelectionOptions
gmx::TimeUnitBehavior	Options behavior to add a time unit option
gmx::IOptionsContainer	Interface for adding input options
gmx::IOptionsContainerWithSections	Interface for adding input options with sections
gmx::AbstractOptionSectionHandle	Base class for handles to option sections
gmx::OptionSectionHandle	Allows adding options to an OptionSection
gmx::RepeatingOptionSectionHandle< T >	Allows adding options to an RepeatingOptionSection
gmx::Options	Collection of options
gmx::IOutputAdapter	OutputAdapter class for handling trajectory file flag setting and processing
gmx::OutputSelector	OutputSelector class controls setting which coordinates are actually written
gmx::SetAtoms	SetAtoms class controls availability of atoms data
gmx::SetBox	Allows changing box information when writing a coordinate file
gmx::SetForces	SetForces class allows changing writing of forces to file
gmx::SetPrecision	SetPrecision class allows changing file writing precision
gmx::SetStartTime	SetStartTime class allows changing trajectory time information
gmx::SetTimeStep	SetTimeStep class allows changing trajectory time information
gmx::SetVelocities	SetVelocities class allows changing writing of velocities to file
gmx::IProgramContext	Provides context information about the program that is calling the library
gmx::IRestraintPotential	Interface for Restraint potentials
gmx::IsSerializableEnum< T, bool >	{
gmx::ITopologyProvider	Provides topology information to SelectionOptionBehavior
gmx::LegacyInput	Collection of legacy input information
gmx::LennardJonesCalculator< calculateEnergies, vdwModifier >	Base LJ calculator class, only specializations are used
gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch >	Specialized calculator for LJ with force switch
gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch >	Specialized calculator for LJ with potential switch
gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift >	Specialized calculator for LJ with potential shift and no energy calculation
gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift >	Specialized calculator for LJ with potential shift and energy calculation
gmx::ListOfLists< typename >	A list of lists, optimized for performance
gmx::MembedHolder	Membed SimulatorBuilder parameter type
gmx::MtsLevel	Setting for a single level for multiple time step integration
gmx::NonbondedBenchmarkInfo	Declares gmx nonbonded-bench
gmx::NormalDistribution< RealType >	Normal distribution
gmx::NormalDistribution< RealType >::param_type	Normal distribution parameters
gmx::OptionInfo	Gives information and allows modifications to an option after creation
gmx::BooleanOptionInfo	Wrapper class for accessing boolean option information
gmx::DoubleOptionInfo	Wrapper class for accessing floating-point option information
gmx::EnumOptionInfo	Wrapper class for accessing enum option information
gmx::FileNameOptionInfo	Wrapper class for accessing file name option information
gmx::FloatOptionInfo	Wrapper class for accessing floating-point option information
gmx::Int64OptionInfo	Wrapper class for accessing 64-bit integer option information
gmx::IntegerOptionInfo	Wrapper class for accessing integer option information
gmx::SelectionOptionInfo	Wrapper class for accessing and modifying selection option information
gmx::StringOptionInfo	Wrapper class for accessing string option information
gmx::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
gmx::OutputRequirements	Finalized version of requirements after processing
gmx::PaddedVector< T, Allocator >	PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS
gmx::PotentialPointData	Structure to hold the results of IRestraintPotential::evaluate()
gmx::Profiling	Collection of profiling information
gmx::PullCoordExpressionParser	Class with a mathematical expression and parser
gmx::Range< typename >	Defines a range of integer numbers and accompanying operations
gmx::Range< typename >::iterator	An iterator that loops over a range of integers
gmx::RangePartitioning	Division of a range of indices into consecutive blocks
gmx::Selection	Provides access to a single selection
gmx::SelectionCollection	Collection of selections
gmx::SelectionPosition	Provides access to information about a single selected position
gmx::SelectionTopologyProperties	Describes topology properties required for selection evaluation
gmx::SimulationSignal	POD-style object used by mdrun ranks to set and receive signals within and between simulations
gmx::SimulationSignaller	Object used by mdrun ranks to signal to each other at this step
gmx::SimulatorConfig	Simulation configuation settings
gmx::SimulatorEnv	Collection of environmental information for a simulation
gmx::SimulatorStateData	Data for a specific simulation state
gmx::StaticLog2< n >	Evaluate log2(n) for integer n statically at compile time
gmx::StaticLog2< 0 >	Specialization of StaticLog2<n> for n==0
gmx::StaticLog2< 1 >	Specialization of StaticLog2<n> for n==1
gmx::StringFormatter	Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms
gmx::StringToEnumValueConverter< EnumType,, stringCompareType, stripStrings >	A class to convert a string to an enum value of type EnumType
gmx::TabulatedNormalDistribution< RealType, tableBits >	Tabulated normal random distribution
gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type	Normal distribution parameter class (mean and stddev)
gmx::TextLineWrapper	Wraps lines to a predefined length
gmx::TextLineWrapperSettings	Stores settings for line wrapping
gmx::ThreeFry2x64General< rounds, internalCounterBits >	General implementation class for ThreeFry counter-based random engines
gmx::TimeUnitManager	Provides common functionality for time unit conversions
gmx::TopologyData	Collection of handles to topology information
gmx::TrajectoryAnalysisCommandLineRunner	Runner for command-line trajectory analysis tools
gmx::TrajectoryAnalysisModule	Base class for trajectory analysis modules
gmx::TrajectoryAnalysisModuleData	Base class for thread-local data storage during trajectory analysis
gmx::TrajectoryAnalysisSettings	Trajectory analysis module configuration object
gmx::TrajectoryFileOpener	Low level method to take care of only file opening and closing
gmx::TrajectoryFrameWriter	Writes coordinate frames to a sink, e.g. a trajectory file
gmx::UniformIntDistribution< IntType >	Uniform integer distribution
gmx::UniformIntDistribution< IntType >::param_type	Uniform int distribution parameters
gmx::UniformRealDistribution< RealType >	Uniform real distribution
gmx::UniformRealDistribution< RealType >::param_type	Uniform real distribution parameters
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_cache_protect_t	Cache-line protection buffer
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
InteractionListHandle	Type for returning a list of InteractionList references
JClusterList	Simple j-cluster list
gmx::ListOfLists< int >
LocalSettleData	Local settle data
MoleculeBlockIndices	Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents
Nbnxm::EnergyFunctionProperties< elecType, vdwType >	Set of boolean constants mimicking preprocessor macros
Nbnxm::Grid::Dimensions	The physical dimensions of a grid
NbnxmKernel< doPruneNBL, doCalcEnergies, elecType, vdwType, subGroupSize >	Class name for NBNXM kernel
nbnxn_cj_packed_t	Packed j-cluster list element
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
NbnxnPairlistCpuWork::IClusterData	Struct for storing coordinates and bounding box for an i-entry during search
PackedJClusterList	Packed j-cluster list
gmx::PaddedVector< gmx::BasicVector >
gmx::PaddedVector< gmx::gmx::BasicVector >
gmx::PaddedVector< gmx::RVec >
gmx::PaddedVector< real >
gmx::PaddedVector< RVec >
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
PbcAiuc	Compact and ordered version of the PBC matrix
PdbAtomEntry	Contains information for a single particle in a PDB file
gmx::Range< int >
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
std::exception	STL class
gmx::GromacsException	Base class for all exception objects in Gromacs
gmx::APIError	Exception class for incorrect use of an API
gmx::NotImplementedError	Exception class for use of an unimplemented feature
gmx::ParallelConsistencyError	Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion
gmx::FileIOError	Exception class for file I/O errors
gmx::InternalError	Exception class for internal errors
gmx::ModularSimulatorError	Exception class for modular simulator
gmx::CheckpointError	Exception class signalling an error in reading or writing modular checkpoints
gmx::ElementNotFoundError	Exception class signalling that a requested element was not found
gmx::MissingElementConnectionError	Exception class signalling that elements were not connected properly
gmx::SimulationAlgorithmSetupError	Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way
gmx::RangeError	Exception class for out-of-range values or indices
gmx::SimulationInstabilityError	Exception class for simulation instabilities
gmx::ToleranceError	Exception class when a specified tolerance cannot be achieved
gmx::UserInputError	Exception class for user input errors
gmx::InconsistentInputError	Exception class for situations where user input is inconsistent
gmx::InvalidInputError	Exception class for situations where user input cannot be parsed/understood
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_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_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
gmx::ThreeFry2x64General< 13, internalCounterBits >
gmx::ThreeFry2x64Fast< internalCounterBits >	ThreeFry2x64 random engine with 13 iteractions
gmx::ThreeFry2x64General< 20, internalCounterBits >
gmx::ThreeFry2x64< internalCounterBits >	ThreeFry2x64 random engine with 20 iteractions
wallcc_t	Counters for an individual wallcycle timing region
WarningHandler	General warning handling object
WaterMolecule	Indices of atoms in a water molecule