Public API

Collaboration diagram for Public API:

Description

Classes and other symbols that are publicly accessible from user code.

Modules
	MD restraints
	Apply restraints during MD integration.

Namespaces
	gmx
	Generic GROMACS namespace.

Classes
class	gmx::CommandLineHelpWriter
	Writes help information for Options. More...
class	gmx::ICommandLineModule
	Module that can be run from command line using CommandLineModuleManager. More...
class	gmx::CommandLineModuleSettings
	Settings to pass information between a module and the general runner. More...
class	gmx::ICommandLineOptionsModuleSettings
	Settings to pass information between a CommandLineOptionsModule and generic code that runs it. More...
class	gmx::ICommandLineOptionsModule
	Module that can be run from a command line and uses gmx::Options for argument processing. More...
class	gmx::CommandLineParser
	Implements command-line parsing for Options objects. More...
struct	t_filenm
	File name option definition for C code. More...
struct	t_pargs
	Command-line argument definition for C code. More...
class	gmx::TrajectoryFileOpener
	Low level method to take care of only file opening and closing. More...
class	gmx::TrajectoryFrameWriter
	Writes coordinate frames to a sink, e.g. a trajectory file. More...
class	gmx::OutputSelector
	OutputSelector class controls setting which coordinates are actually written. More...
class	gmx::SetAtoms
	SetAtoms class controls availability of atoms data. More...
class	gmx::SetBox
	Allows changing box information when writing a coordinate file. More...
class	gmx::SetForces
	SetForces class allows changing writing of forces to file. More...
class	gmx::SetPrecision
	SetPrecision class allows changing file writing precision. More...
class	gmx::SetStartTime
	SetStartTime class allows changing trajectory time information. More...
class	gmx::SetTimeStep
	SetTimeStep class allows changing trajectory time information. More...
class	gmx::SetVelocities
	SetVelocities class allows changing writing of velocities to file. More...
class	gmx::OptionSection
	Declares a simple option section. More...
class	gmx::OptionSectionHandle
	Allows adding options to an OptionSection. More...
class	gmx::RepeatingOptionSection< T >
	Declares an option section that creates a structure for each instance. More...
class	gmx::RepeatingOptionSectionHandle< T >
	Allows adding options to an RepeatingOptionSection. More...
class	gmx::DataFileOptions
	Search parameters for DataFileFinder. More...
struct	gmx::DataFileInfo
	Information about a data file found by DataFileFinder::enumerateFiles(). More...
class	gmx::DataFileFinder
	Searches data files from a set of paths. More...
class	gmx::FixedCapacityVector< typename, size_t >
	Vector that behaves likes std::vector but has fixed capacity. More...
class	gmx::AnalysisData
	Parallelizable data container for raw data. More...
class	gmx::AnalysisDataHandle
	Handle for inserting data into AnalysisData. More...
class	gmx::AnalysisArrayData
	Simple in-memory data array. More...
class	gmx::AnalysisDataValue
	Value type for representing a single value in analysis data objects. More...
class	gmx::AnalysisDataFrameHeader
	Value type for storing frame-level information for analysis data. More...
class	gmx::AnalysisDataPointSetRef
	Value type wrapper for non-mutable access to a set of data column values. More...
class	gmx::AnalysisDataFrameRef
	Value type wrapper for non-mutable access to a data frame. More...
class	gmx::AnalysisDataAverageModule
	Data module for independently averaging each column in input data. More...
class	gmx::AnalysisDataFrameAverageModule
	Data module for averaging of columns for each frame. More...
class	gmx::AnalysisDataDisplacementModule
	Data module for calculating displacements. More...
class	gmx::AnalysisHistogramSettingsInitializer
	Provides "named parameter" idiom for constructing histograms. More...
class	gmx::AnalysisHistogramSettings
	Contains parameters that specify histogram bin locations. More...
class	gmx::AbstractAverageHistogram
	Base class for representing histograms averaged over frames. More...
class	gmx::AnalysisDataSimpleHistogramModule
	Data module for per-frame histograms. More...
class	gmx::AnalysisDataWeightedHistogramModule
	Data module for per-frame weighted histograms. More...
class	gmx::AnalysisDataBinAverageModule
	Data module for bin averages. More...
class	gmx::AnalysisDataLifetimeModule
	Data module for computing lifetime histograms for columns in input data. More...
class	gmx::AnalysisDataPlotSettings
	Common settings for data plots. More...
class	gmx::AnalysisDataPlotModule
	Plotting module for straightforward plotting of data. More...
class	gmx::AnalysisDataVectorPlotModule
	Plotting module specifically for data consisting of vectors. More...
class	gmx::OptionInfo
	Gives information and allows modifications to an option after creation. More...
class	gmx::BooleanOption
	Specifies an option that provides boolean values. More...
class	gmx::IntegerOption
	Specifies an option that provides 32-bit integer values. More...
class	gmx::UnsignedIntegerOption
	Specifies an option that provides unsigned 32-bit integer values. More...
class	gmx::Int64Option
	Specifies an option that provides 64-bit integer values. More...
class	gmx::UnsignedInt64Option
	Specifies an option that provides 64-bit unsigned integer values. More...
class	gmx::DoubleOption
	Specifies an option that provides floating-point (double) values. More...
class	gmx::FloatOption
	Specifies an option that provides floating-point (float) values. More...
class	gmx::StringOption
	Specifies an option that provides string values. More...
class	gmx::EnumOption< EnumType >
	Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable. More...
class	gmx::LegacyEnumOption< EnumType >
	Specifies an option that accepts enumerated string values and writes the selected index into an enum variable. More...
class	gmx::BooleanOptionInfo
	Wrapper class for accessing boolean option information. More...
class	gmx::IntegerOptionInfo
	Wrapper class for accessing 32-bit integer option information. More...
class	gmx::UnsignedIntegerOptionInfo
	Wrapper class for accessing unsigned 32-bit integer option information. More...
class	gmx::Int64OptionInfo
	Wrapper class for accessing 64-bit integer option information. More...
class	gmx::UnsignedInt64OptionInfo
	Wrapper class for accessing 64-bit unsigned integer option information. More...
class	gmx::DoubleOptionInfo
	Wrapper class for accessing floating-point option information. More...
class	gmx::FloatOptionInfo
	Wrapper class for accessing floating-point option information. More...
class	gmx::StringOptionInfo
	Wrapper class for accessing string option information. More...
class	gmx::EnumOptionInfo
	Wrapper class for accessing enum option information. More...
class	gmx::FileNameOption
	Specifies an option that provides file names. More...
class	gmx::FileNameOptionInfo
	Wrapper class for accessing file name option information. More...
class	gmx::FileNameOptionManager
	Handles interaction of file name options with global options. More...
class	gmx::IOptionsBehavior
	Interface to provide extension points for options parsing. More...
class	gmx::IOptionsContainer
	Interface for adding input options. More...
class	gmx::IOptionsContainerWithSections
	Interface for adding input options with sections. More...
class	gmx::Options
	Collection of options. More...
class	gmx::TimeUnitManager
	Provides common functionality for time unit conversions. More...
class	gmx::TimeUnitBehavior
	Options behavior to add a time unit option. More...
class	gmx::AnalysisNeighborhoodPositions
	Input positions for neighborhood searching. More...
class	gmx::AnalysisNeighborhood
	Neighborhood searching for analysis tools. More...
class	gmx::AnalysisNeighborhoodPair
	Value type to represent a pair of positions found in neighborhood searching. More...
class	gmx::AnalysisNeighborhoodSearch
	Initialized neighborhood search with a fixed set of reference positions. More...
class	gmx::AnalysisNeighborhoodPairSearch
	Initialized neighborhood pair search with a fixed set of positions. More...
class	gmx::Selection
	Provides access to a single selection. More...
class	gmx::SelectionPosition
	Provides access to information about a single selected position. More...
class	gmx::SelectionCollection
	Collection of selections. More...
struct	gmx::SelectionTopologyProperties
	Describes topology properties required for selection evaluation. More...
class	gmx::SelectionOption
	Specifies an option that provides selection(s). More...
class	gmx::SelectionOptionInfo
	Wrapper class for accessing and modifying selection option information. More...
class	gmx::ITopologyProvider
	Provides topology information to SelectionOptionBehavior. More...
class	gmx::SelectionOptionBehavior
	Options behavior to allow using SelectionOptions. More...
class	gmx::SelectionOptionManager
	Handles interaction of selection options with other options and user input. More...
class	gmx::TrajectoryAnalysisModuleData
	Base class for thread-local data storage during trajectory analysis. More...
class	gmx::TrajectoryAnalysisModule
	Base class for trajectory analysis modules. More...
class	gmx::TrajectoryAnalysisSettings
	Trajectory analysis module configuration object. More...
class	gmx::TrajectoryAnalysisCommandLineRunner
	Runner for command-line trajectory analysis tools. More...
class	gmx::ArrayRef< typename >
	STL-like interface to a C array of T (or part of a std container of T). More...
class	gmx::ExceptionInfo< Tag, T >
	Stores additional context information for exceptions. More...
class	gmx::GromacsException
	Base class for all exception objects in Gromacs. More...
class	gmx::FileIOError
	Exception class for file I/O errors. More...
class	gmx::UserInputError
	Exception class for user input errors. More...
class	gmx::InvalidInputError
	Exception class for situations where user input cannot be parsed/understood. More...
class	gmx::InconsistentInputError
	Exception class for situations where user input is inconsistent. More...
class	gmx::ToleranceError
	Exception class when a specified tolerance cannot be achieved. More...
class	gmx::SimulationInstabilityError
	Exception class for simulation instabilities. More...
class	gmx::InternalError
	Exception class for internal errors. More...
class	gmx::APIError
	Exception class for incorrect use of an API. More...
class	gmx::RangeError
	Exception class for out-of-range values or indices. More...
class	gmx::NotImplementedError
	Exception class for use of an unimplemented feature. More...
class	gmx::ParallelConsistencyError
	Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion. More...
class	gmx::ModularSimulatorError
	Exception class for modular simulator. More...
class	gmx::MDModuleSetupError
	Exception class for MD module setup/initialization failures. More...
struct	gmx::InstallationPrefixInfo
	Provides information about installation prefix (see IProgramContext::installationPrefix()). More...
class	gmx::IProgramContext
	Provides context information about the program that is calling the library. More...
class	gmx::TextLineWrapperSettings
	Stores settings for line wrapping. More...
class	gmx::TextLineWrapper
	Wraps lines to a predefined length. More...
class	gmx::BasicVector< ValueType >
	C++ class for 3D vectors. More...

Enumerations
enum	gmx::TimeUnit : int {   Femtoseconds, Picoseconds, Nanoseconds, Microseconds,   Milliseconds, Seconds, Count, Default = Picoseconds }
	Time values for TimeUnitManager and legacy oenv module.
enum	e_coverfrac_t { CFRAC_NONE, CFRAC_SOLIDANGLE }
	Defines the type of covered fraction. More...

Functions
AnalysisHistogramSettingsInitializer	gmx::histogramFromRange (real min, real max)
	Initializes a histogram using a range and a bin width. More...
AnalysisHistogramSettingsInitializer	gmx::histogramFromBins (real start, size_t nbins, real binwidth)
	Initializes a histogram using bin width and the number of bins. More...

Files
file	cmdlinehelpwriter.h
	Declares gmx::CommandLineHelpWriter.
file	cmdlineinit.h
	Declares functions for initializing the GROMACS library for command line use.
file	cmdlinemodule.h
	Declares gmx::ICommandLineModule and supporting classes.
file	cmdlinemodulesettings.h
	Declares gmx::CommandLineModuleSettings.
file	cmdlineoptionsmodule.h
	Declares gmx::ICommandLineOptionsModule and supporting routines.
file	cmdlineparser.h
	Declares gmx::CommandLineParser.
file	filenm.h
	Declares t_filenm for old-style command-line parsing of file name options.
file	pargs.h
	Declares t_pargs, parse_common_args() and related methods.
file	viewit.h
	Provides function to open output files automatically (with some X11 programs).
file	coordinatefile.h
	CoordinateFile takes care of opening files and writing output to them.
file	outputselector.h
	Declares gmx::OutputSelector.
file	setatoms.h
	Declares gmx::SetAtoms.
file	setbox.h
	Declares gmx::SetBox.
file	setforces.h
	Declares gmx::SetForces.
file	setprecision.h
	Declares gmx::SetPrecision.
file	setstarttime.h
	Declares gmx::SetStartTime.
file	settimestep.h
	Declares gmx::SetTimeStep.
file	setvelocities.h
	Declares gmx:SetVelocities.
file	outputadapters.h
	Public API convenience header for accessing outputadapters.
file	analysismodule.h
	Public API convenience header for energy analysis framework.
file	fft.h
	Fast Fourier Transforms.
file	hostallocator.h
	Declares gmx::HostAllocationPolicy, gmx::HostAllocator, gmx::HostVector and gmx::PaddedHostVector, which are used to make/be standard library containers that can allocate memory suitable for transfers. Currently the only supported transfers using pinned memory are to CUDA GPUs, but other possibilities exist in future.
file	arrayrefwithpadding.h
	Declares gmx::ArrayRefWithPadding that refers to memory whose size includes padding for SIMD operations.
file	paddedvector.h
	Declares gmx::PaddedRVecVector.
file	simulationinputhandle.h
	Public interface for SimulationInput facilities.
file	optionsection.h
	Declares gmx::OptionSection and gmx::OptionSectionInfo.
file	repeatingsection.h
	Declares gmx::RepeatingOptionSection and related classes.
file	exponentialdistribution.h
	The exponential distribution.
file	gammadistribution.h
	The gamma distribution.
file	normaldistribution.h
	The normal distribution.
file	seed.h
	Random seed and domain utilities.
file	tabulatednormaldistribution.h
	Tabulated normal distribution.
file	threefry.h
	Implementation of the 2x64 ThreeFry random engine.
file	uniformintdistribution.h
	The uniform integer distribution.
file	uniformrealdistribution.h
	The uniform real distribution.
file	alignedallocator.h
	Declares allocation policy classes and allocators that are used to make library containers compatible with alignment requirements of particular hardware, e.g. memory operations for SIMD or accelerators.
file	allocator.h
	Declares gmx::Allocator template whose allocation functionality is configured both by type of object allocated and a policy class that configures the necessary matching malloc and free operation.
file	arraysize.h
	Provides asize() function for calculating the static size of an array at compile time.
file	cstringutil.h
	Generic C string handling functions.
file	datafilefinder.h
	Declares gmx::DataFileFinder and related classes.
file	fatalerror.h
	Declares fatal error handling and debugging routines for C code.
file	fixedcapacityvector.h
	Declares gmx::FixedCapacityVector.
file	init.h
	Declares functions for initializing the GROMACS library.
file	utility.h
	Public API convenience header for low-level utilities.
file	analysisdata.h
	Declares gmx::AnalysisData and gmx::AnalysisDataHandle.
file	arraydata.h
	Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData.
file	dataframe.h
	Declares classes for accessing data frame information.
file	average.h
	Declares gmx::AnalysisDataAverageModule.
file	displacement.h
	Declares gmx::AnalysisDataDisplacementModule.
file	histogram.h
	Declares analysis data modules for calculating histograms.
file	lifetime.h
	Declares gmx::AnalysisDataLifetimeModule.
file	plot.h
	Declares gmx::AnalysisDataPlotModule for plotting data (into a file).
file	functions.h
	Declares simple math functions.
file	md_enums.h
	Declares enumerated types used throughout the code.
file	basicoptions.h
	Declares option objects for basic option types.
file	filenameoption.h
	Declares gmx::FileNameOption and gmx::FileNameOptionInfo.
file	filenameoptionmanager.h
	Declares gmx::FileNameOptionManager.
file	ioptionsbehavior.h
	Declares gmx::IOptionsBehavior.
file	ioptionscontainer.h
	Declares gmx::IOptionsContainer.
file	ioptionscontainerwithsections.h
	Declares gmx::IOptionsContainerWithSections.
file	optionfiletype.h
	Defines an enumeration type for specifying file types for options.
file	options.h
	Declares gmx::Options.
file	timeunitmanager.h
	Declares gmx::TimeUnitManager.
file	restraintpotential.h
	Declare generic interface for restraint implementations.
file	nbsearch.h
	API for neighborhood searching for analysis.
file	selection.h
	Declares gmx::Selection and supporting classes.
file	selectioncollection.h
	Declares gmx::SelectionCollection.
file	selectionoption.h
	Declares gmx::SelectionOption and gmx::SelectionOptionInfo.
file	selectionoptionbehavior.h
	Declares gmx::SelectionOptionBehavior.
file	selectionoptionmanager.h
	Declares gmx::SelectionOptionManager.
file	analysismodule.h
	Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData.
file	analysissettings.h
	Declares gmx::TrajectoryAnalysisSettings.
file	cmdlinerunner.h
	Declares gmx::TrajectoryAnalysisCommandLineRunner.
file	arrayref.h
	Declares gmx::ArrayRef.
file	basedefinitions.h
	Basic types and macros used throughout GROMACS.
file	baseversion.h
	Declares functions to get basic version information.
file	exceptions.h
	Declares common exception classes and macros for fatal error handling.
file	fileptr.h
	Declares guard pointer for RAII-style handling of cstdio FILE pointers.
file	futil.h
	Low-level wrappers for OS-specific file handling with some GROMACS customizations.
file	gmxassert.h
	Defines assert macros customized for Gromacs.
file	listoflists.h
	Declares gmx::ListOfLists.
file	programcontext.h
	Declares gmx::IProgramContext and related methods.
file	range.h
	Declares gmx::Range.
file	real.h
	Declares real and related constants.
file	smalloc.h
	C-style memory allocation routines for GROMACS.
file	stringutil.h
	Declares common string utility and formatting routines.

Enumeration Type Documentation

enum e_coverfrac_t

Defines the type of covered fraction.

Enumerator
CFRAC_NONE	No covered fraction (everything covered).
CFRAC_SOLIDANGLE	Fraction of a solid (3D) angle covered.

Function Documentation

AnalysisHistogramSettingsInitializer gmx::histogramFromBins ( real  start, size_t  nbins, real  binwidth  )

inline

Initializes a histogram using bin width and the number of bins.

Does not throw.

AnalysisHistogramSettingsInitializer gmx::histogramFromRange ( real  min, real  max  )

inline

Initializes a histogram using a range and a bin width.

Does not throw.