Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 123]

gmx	Generic GROMACS namespace
detail
PaddingTraits	Traits classes for handling padding for types used with PaddedVector
ArrayRef	STL-like interface to a C array of T (or part of a std container of T)
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
FixedCapacityVector	Vector that behaves likes std::vector but has fixed capacity
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
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
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
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, DiagonalMaskType::JSizeEqualsISize >	Specialized masker for JSizeEqualsISize
DiagonalMasker< nR, kernelLayout, DiagonalMaskType::JSizeIsDoubleISize >	Specialized masker for JSizeIsDoubleISize
DiagonalMasker< nR, kernelLayout, DiagonalMaskType::JSizeIsHalfISize >	Specialized masker for JSizeIsHalfISize
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
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
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
Nbnxm	Namespace for non-bonded kernels
EnergyFunctionProperties	Set of boolean constants mimicking preprocessor macros
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_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
LocalSettleData	Local settle data
MoleculeBlockIndices	Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents
NbnxmKernel	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
IClusterData	Struct for storing coordinates and bounding box for an i-entry during search
PackedJClusterList	Packed j-cluster list
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
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
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
WarningHandler	General warning handling object
WaterMolecule	Indices of atoms in a water molecule