Library API

Collaboration diagram for Library API:

Description

Classes and other symbols that are publicly accessible within the GROMACS library.

See Also

Public API

Classes
class	gmx::AbstractAnalysisData
	Abstract base class for all objects that provide data. More...
class	gmx::AbstractAnalysisArrayData
	Abstract base class for data objects that present in-memory data. More...
class	gmx::IAnalysisDataModule
	Interface for a module that gets notified whenever data is added. More...
class	gmx::AnalysisDataModuleSerial
	Convenience base class for serial analysis data modules. More...
class	gmx::AnalysisDataModuleParallel
	Convenience base class for parallel analysis data modules. More...
class	gmx::AnalysisDataModuleManager
	Encapsulates handling of data modules attached to AbstractAnalysisData. More...
class	gmx::AnalysisDataStorageFrame
	Allows assigning values for a data frame in AnalysisDataStorage. More...
class	gmx::AnalysisDataStorage
	Helper class that implements storage of data. More...
class	gmx::AnalysisDataParallelOptions
	Parallelization options for analysis data objects. More...
class	gmx::test::AnalysisDataTestInputPointSet
	Represents a single set of points in AnalysisDataTestInputFrame structure. More...
class	gmx::test::AnalysisDataTestInputFrame
	Represents a single frame in AnalysisDataTestInput structure. More...
class	gmx::test::AnalysisDataTestInput
	Represents static input data for AbstractAnalysisData tests. More...
class	gmx::test::AnalysisDataTestFixture
	Test fixture for AbstractAnalysisData testing. More...
class	gmx::GlobalCommandLineHelpContext
	Helper for passing CommandLineHelpContext into parse_common_args(). More...
class	gmx::CommandLineModuleManager
	Implements a wrapper command-line interface for multiple modules. More...
class	gmx::CommandLineModuleGroup
	Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More...
class	gmx::IExecutableEnvironment
	Allows customization of the way various directories are found by CommandLineProgramContext. More...
class	gmx::CommandLineProgramContext
	Program context implementation for command line programs. More...
class	gmx::MDModules
	Manages the collection of all modules used for mdrun. More...
class	gmx::IForceProvider
	Interface for a component that provides forces during MD. More...
struct	ForceProviders
	Evaluates forces from a collection of gmx::IForceProvider. More...
class	gmx::IMDModule
	Extension module for GROMACS simulations. More...
class	gmx::IMDOutputProvider
	Interface for handling additional output files during a simulation. More...
class	gmx::IMdpOptionProvider
	Interface for handling mdp/tpr input to a mdrun module. More...
class	gmx::TextTableFormatter
	Formats rows of a table for text output. More...
class	gmx::HelpManager
	Helper for providing interactive online help. More...
class	gmx::AbstractSimpleHelpTopic
	Abstract base class for help topics that have simple text and no subtopics. More...
class	gmx::AbstractCompositeHelpTopic
	Abstract base class for help topics that have simple text and subtopics. More...
class	gmx::SimpleHelpTopic< HelpText >
	Template for simple implementation of AbstractSimpleHelpTopic. More...
class	gmx::CompositeHelpTopic< HelpText >
	Template for simple implementation of AbstractCompositeHelpTopic. More...
class	gmx::HelpWriterContext
	Context information for writing out help. More...
class	gmx::IHelpTopic
	Provides a single online help topic. More...
class	gmx::OptionTemplate< T, U >
	Templated base class for constructing concrete option settings classes. More...
class	gmx::AbstractOptionStorage
	Abstract base class for converting, validating, and storing option values. More...
class	gmx::OptionsBehaviorCollection
	Container for IOptionsBehavior objects. More...
class	gmx::OptionManagerContainer
	Container to keep managers added with Options::addManager() and pass them to options. More...
class	gmx::IOptionManager
	Base class for option managers. More...
class	gmx::OptionsAssigner
	Decorator class for assigning values to Options. More...
class	gmx::OptionStorageTemplate< T >
	Templated base class for constructing option value storage classes. More...
class	gmx::OptionStorageTemplateSimple< T >
	Simplified option storage template for options that have one-to-one value conversion. More...
class	gmx::OptionsVisitor
	Pure interface for visiting options in a Options object. More...
class	gmx::OptionsTypeVisitor< InfoType >
	Abstract base class for visiting options of a particular type. More...
class	gmx::OptionsIterator
	Decorator class for visiting options in a Options object. More...
class	gmx::OptionsModifyingVisitor
	Pure interface for visiting options in a Options object, allowing modifications. More...
class	gmx::OptionsModifyingTypeVisitor< InfoType >
	Abstract base class for visiting options of a particular type, allowing modifications. More...
class	gmx::OptionsModifyingIterator
	Decorator class for visiting options in a Options object, allowing changes. More...
class	gmx::OptionValueConverterSimple< OutType >
	Helper for converting from Variant to a given type. More...
class	gmx::SelectionFileOption
	Specifies a special option that provides selections from a file. More...
class	gmx::SelectionFileOptionInfo
	Wrapper class for accessing and modifying selection file option information. More...
class	gmx::Allocator< T, AllocationPolicy >
	Policy-based memory allocator. More...
class	gmx::BinaryInformationSettings
	Settings for printBinaryInformation(). More...
class	gmx::PrivateImplPointer< Impl >
	Helper class to manage a pointer to a private implementation class. More...
class	gmx::DirectoryEnumerator
	Lists files in a directory. More...
class	gmx::IFileInputRedirector
	Allows overriding file existence checks from code that supports it. More...
class	gmx::IFileOutputRedirector
	Allows capturing stdout and file output from code that supports it. More...
class	gmx::StandardInputStream
	Text input stream implementation for reading from stdin. More...
class	gmx::TextInputFile
	Text input stream implementation for reading from a file. More...
class	gmx::TextOutputFile
	Text output stream implementation for writing to a file. More...
class	gmx::FlagsTemplate< FlagType >
	Template class for typesafe handling of combination of flags. More...
class	gmx::Regex
	Represents a regular expression. More...
class	gmx::KeyValueTreePath
	Identifies an entry in a key-value tree. More...
class	gmx::KeyValueTreeBuilder
	Root builder for creating trees that have an object at the root. More...
class	gmx::KeyValueTreeValueBuilder
	Builder for KeyValueTreeValue objects. More...
class	gmx::KeyValueTreeUniformArrayBuilder< T >
	Builder for KeyValueTreeArray objects where all elements are of type T. More...
class	gmx::KeyValueTreeObjectArrayBuilder
	Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects. More...
class	gmx::KeyValueTreeObjectBuilder
	Builder for KeyValueTreeObject objects. More...
class	gmx::IKeyValueTreeTransformRules
	Interface to declare rules for transforming key-value trees. More...
class	gmx::KeyValueTreeTransformRulesScoped
	Helper object returned from IKeyValueTreeTransformRules::scopedTransform(). More...
class	gmx::KeyValueTreeTransformRuleBuilder
	Provides methods to specify one transformation rule. More...
class	gmx::MessageStringCollector
	Helper class for collecting message strings, optionally with context. More...
class	gmx::MessageStringContext
	Convenience class for creating a message context. More...
struct	gmx::no_delete< T >
	Deleter for std::shared_ptr that does nothing. More...
class	gmx::StringCompare
	Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare. More...
class	gmx::StringOutputStream
	Text output stream implementation for writing to an in-memory string. More...
class	gmx::TextReader
	Reads text from a TextInputStream. More...
class	gmx::TextInputStream
	Interface for reading text. More...
class	gmx::TextOutputStream
	Interface for writing text. More...
class	gmx::TextWriter
	Writes text into a TextOutputStream. More...
class	gmx::test::CommandLine
	Helper class for tests that need to construct command lines. More...
class	gmx::test::CommandLineTestHelper
	Helper class for tests that construct command lines that need to reference existing files. More...
class	gmx::test::CommandLineTestBase
	Test fixture for tests that call a single command-line program with input/output files. More...
class	gmx::test::ConfMatch
	Match the contents as an gro file. More...
class	gmx::test::IFileMatcher
	Represents a file matcher, matching file contents against reference (or other) data. More...
class	gmx::test::IFileMatcherSettings
	Represents a factory for creating a file matcher. More...
class	gmx::test::TextFileMatch
	Use a ITextStreamMatcher for matching the contents. More...
class	gmx::test::NoContentsMatch
	Do not check the contents of the file. More...
class	gmx::test::InteractiveTestHelper
	Helper class for testing interactive sessions. More...
class	gmx::test::LoggerTestHelper
	Helper class for tests to check output written to a logger. More...
class	gmx::test::TestReferenceData
	Handles creation of and comparison to test reference data. More...
class	gmx::test::TestReferenceChecker
	Handles comparison to test reference data. More...
class	gmx::test::StdioTestHelper
	Helper class for tests where code reads directly from stdin. More...
class	gmx::test::StringTestBase
	Test fixture for tests that check string formatting. More...
class	gmx::test::TestFileManager
	Helper for tests that need input and output files. More...
class	gmx::test::TestFileInputRedirector
	In-memory implementation for IFileInputRedirector for tests. More...
class	gmx::test::TestOptionsProvider
	Provides additional options for the test executable. More...
class	gmx::test::ITextBlockMatcher
	Represents a text matcher, matching text stream contents against reference data. More...
class	gmx::test::ITextBlockMatcherSettings
	Represents a factory for creating a text matcher. More...
class	gmx::test::ExactTextMatch
	Use an exact text match (the contents should be exactly equal). More...
class	gmx::test::NoTextMatch
	Do not match the text (the contents are ignored). More...
class	gmx::test::XvgMatch
	Match the contents as an xvg file. More...

Typedefs
typedef std::unique_ptr < AbstractCompositeHelpTopic >	gmx::CompositeHelpTopicPointer
	Smart pointer type to manage a AbstractCompositeHelpTopic object.

Files
file	gmxpre.h
	Prerequisite header file for GROMACS build.
file	abstractdata.h
	Declares gmx::AbstractAnalysisData.
file	datamodule.h
	Declares gmx::IAnalysisDataModule and related convenience classes.
file	datamodulemanager.h
	Declares gmx::AnalysisDataModuleManager.
file	datastorage.h
	Declares gmx::AnalysisDataStorage.
file	paralleloptions.h
	Declares gmx::AnalysisDataParallelOptions.
file	datatest.h
	Helper classes for testing classes that derive from AbstractAnalysisData.
file	mock_datamodule.h
	Declares mock implementation of gmx::IAnalysisDataModule.
file	awh.h
	Declares the Awh class.
file	read-params.h
	Declares functions needed for reading, initializing and setting the AWH parameter data types.
file	cmdlinehelpcontext.h
	Declares gmx::CommandLineHelpContext.
file	cmdlinemodulemanager.h
	Declares gmx::CommandLineModuleManager.
file	cmdlineprogramcontext.h
	Declares gmx::CommandLineProgramContext.
file	make_unique.h
	Provides template gmx::compat::make_unique.
file	autocorr.h
	Declares routine for computing autocorrelation functions.
file	crosscorr.h
	Declares routine for computing a cross correlation between two data sets.
file	expfit.h
	Declares routine for fitting a data set to a curve.
file	integrate.h
	Declares routines for integrating a data set.
file	manyautocorrelation.h
	Declares routine for computing many correlation functions using OpenMP.
file	polynomials.h
	Declares routine for computing a Legendre polynomial.
file	dlbtiming.h
	This file declares functions for timing the load imbalance due to domain decomposition.
file	domdec.h
	This file declares functions for mdrun to call to manage the details of its domain decomposition.
file	domdec_network.h
	This file declares functions for (mostly) the domdec module to use MPI functionality.
file	domdec_struct.h
	Declares structures related to domain decomposition.
file	ga2la.h
	Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined.
file	edsam.h
	Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces.
file	ewald-utils.h
	Declares utility functions related to Ewald.
file	ewald.h
	This file contains function declarations necessary for computing energies and forces for the plain-Ewald long-ranged part, and the correction for overall system charge for all Ewald-family methods.
file	long-range-correction.h
	This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
file	pme-load-balancing.h
	This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ).
file	pme.h
	This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
file	keyvaluetreemdpwriter.h
	Declares a function to write a flat key-value tree to look like old-style mdp output.
file	gmxopencl.h
	Wraps the complexity of including OpenCL in Gromacs.
file	gpu_utils.h
	Declare functions for detection and initialization for GPU devices.
file	gpuregiontimer_ocl.h
	Implements the GPU region timer for OpenCL.
file	ocl_compiler.h
	Declare infrastructure for OpenCL JIT compilation.
file	oclutils.h
	Declare utility routines for OpenCL.
file	pinning.h
	Declares functions for pinning memory to be suitable for efficient GPU transfers on CUDA.
file	pmalloc_cuda.h
	Declare functions for host-side memory handling when using CUDA devices.
file	cpuinfo.h
	Declares gmx::CpuInfo.
file	hardwaretopology.h
	Declares gmx::HardwareTopology.
file	identifyavx512fmaunits.h
	Defines a routine to check the number of AVX512 fma units.
file	imd.h
	This file contains datatypes and function declarations necessary for mdrun to interface with VMD via the interactive molecular dynamics protocol.
file	imdsocket.h
	Implements the parts of the vmdsock.h interface needed for IMD communication.
file	bonded.h
	This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.
file	disre.h
	Declares functions for handling distance restraints.
file	manage-threading.h
	Declares functions for managing threading of listed forces.
file	orires.h
	Declares functions for handling orientation restraints.
file	pairs.h
	This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
file	position-restraints.h
	This file contains declarations necessary for low-level functions for computing energies and forces for position restraints.
file	invertmatrix.h
	Declares routines to invert 3x3 matrices.
file	broadcaststructs.h
	Convenience wrappers for broadcasting structs.
file	groupcoord.h
	Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
file	mdrun.h
	This file declares types and functions for initializing an MD run.
file	nb_verlet.h
	This file contains the public interface of the non-bonded Verlet module that implements the NxN cluster non-bonded algorithm to efficiently compute pair forces.
file	nbnxn_gpu_data_mgmt.h
	Declare interface for GPU data transfer for NBNXN module.
file	nbnxn_tuning.h
	Declares functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels.
file	simulationsignal.h
	This file declares functions for inter-rank signalling by mdrun.
file	handlerestart.h
	This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files).
file	mdmodules.h
	Declares gmx::MDModules.
file	threadaffinity.h
	Declares functions for managing mdrun thread affinity.
file	awh-correlation-history.h
	Contains datatypes and function declarations needed by AWH to have its force correlation data checkpointed.
file	awh-history.h
	Contains datatypes and function declarations needed by AWH to have its data checkpointed.
file	awh-params.h
	Declares AWH parameter data types.
file	energyhistory.h
	This file contains datatypes for energy statistics history.
file	forceoutput.h
	This file contains the definition of a container for force and virial output.
file	iforceprovider.h
	Declares gmx::IForceProvider and ForceProviders.
file	imdmodule.h
	Declares gmx::IMDModule.
file	imdoutputprovider.h
	Declares gmx::IMDOutputProvider.
file	imdpoptionprovider.h
	Declares gmx::IMdpOptionProvider.
file	observableshistory.h
	This file contains the definition of a container for history data for simulation observables.
file	pull-params.h
	This file contains datatypes for the mdp options used by the pull code.
file	state.h
	This file contains the definition of the microstate of the simulated system.
file	helpformat.h
	Declares common string formatting routines for online help.
file	helpmanager.h
	Declares gmx::HelpManager.
file	helptopic.h
	Declares helper classes for implementing gmx::IHelpTopic.
file	helpwritercontext.h
	Declares gmx::HelpWriterContext.
file	ihelptopic.h
	Declares gmx::IHelpTopic.
file	mock_helptopic.h
	Declares mock implementation of gmx::IHelpTopic.
file	abstractoption.h
	Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo.
file	abstractoptionstorage.h
	Declares gmx::AbstractOptionStorage.
file	behaviorcollection.h
	Declares gmx::OptionsBehaviorCollection.
file	optionmanagercontainer.h
	Declares gmx::OptionManagerContainer.
file	optionsassigner.h
	Declares gmx::OptionsAssigner.
file	optionstoragetemplate.h
	Defines gmx::OptionStorageTemplate template.
file	optionsvisitor.h
	Declares gmx::OptionsVisitor interface and supporting classes.
file	treesupport.h
	Declares functions for using keyvaluetree.h with Options.
file	pbc-simd.h
	This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations.
file	pull.h
	This file contains datatypes and function declarations necessary for mdrun to interface with the pull code.
file	pull_internal.h
	This file contains datatypes and function declarations for internal use in the pull code.
file	pull_rotation.h
	Declares functions to enforce rotational motion upon a group of particles.
file	indexutil.h
	API for handling index files and index groups.
file	selectionfileoption.h
	Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo.
file	selhelp.h
	Functions for initializing online help for selections.
file	scalar.h
	Scalar float functions corresponding to GROMACS SIMD functions.
file	scalar_math.h
	Scalar math functions mimicking GROMACS SIMD math functions.
file	scalar_util.h
	Scalar utility functions mimicking GROMACS SIMD utility functions.
file	simd.h
	Definitions, capabilities, and wrappers for SIMD module.
file	simd_math.h
	Math functions for SIMD datatypes.
file	simd_memory.h
	Declares SimdArrayRef.
file	support.h
	Functions to query compiled and supported SIMD architectures.
file	vector_operations.h
	SIMD operations corresponding to Gromacs rvec datatypes.
file	statistics.h
	Declares simple statistics toolbox.
file	swapcoords.h
	The "Computational Electrophysiology" protocol for ion/water position swapping.
file	cubicsplinetable.h
	Declares classes for cubic spline table.
file	forcetable.h
	Old routines for table generation (will eventually be replaced)
file	quadraticsplinetable.h
	Declares classes for quadratic spline table.
file	tableinput.h
	Declares structures for analytical or numerical input data to construct tables.
file	decidegpuusage.h
	Declares functionality for deciding whether tasks will run on GPUs.
file	resourcedivision.h
	Declares utility functionality for dividing resources and checking for consistency and usefulness.
file	taskassignment.h
	Declares high-level functionality for managing assigning tasks on ranks of a node to hardware on that node, and the factory function to build the correct flavours of gmx::INodeTaskAssigner required to implement the user's requirements.
file	usergpuids.h
	Declares routines for handling user-specified GPU IDs.
file	cyclecounter.h
	High-resolution timestamp or CPU clock cycle counters.
file	gpu_timing.h
	Declares data types for GPU timing.
file	atomsbuilder.h
	Utility classes for manipulating t_atoms structures.
file	mtop_lookup.h
	This file contains inline functions to look up atom information using the global atom index.
file	modules.h
	Generic interface for accessing trajectory analysis modules.
file	basenetwork.h
	Utility functions for basic MPI and network functionality.
file	binaryinformation.h
	Helper functionality for information about the currently running binary.
file	bitmask.h
	Declares gmx_bitmask_t and associated functions.
file	classhelpers.h
	Declares common utility classes and macros.
file	compare.h
	Utilities for comparing data structures (for gmx check).
file	coolstuff.h
	Functionality for printing cool strings.
file	dir_separator.h
	Provides OS-specific directory-name separator.
file	directoryenumerator.h
	Declares gmx::DirectoryEnumerator.
file	fileredirector.h
	Declares gmx::IFileOutputRedirector.
file	filestream.h
	Declares implementations for textstream.h interfaces for file input/output.
file	flags.h
	Declares gmx::FlagsTemplate.
file	gmxmpi.h
	Wraps mpi.h usage in Gromacs.
file	gmxomp.h
	Declares OpenMP wrappers to avoid conditional compilation.
file	gmxregex.h
	Declares simple wrapper for regular expression functionality.
file	ikeyvaluetreeerror.h
	Declares an error handling interface for key-value tree operations.
file	inmemoryserializer.h
	Declares gmx::ISerializer implementation for in-memory serialization.
file	int64_to_int.h
	Low-level utility for converting 64 bit int to int (the size of which is hardware dependent), printing a warning if an overflow will occur.
file	iserializer.h
	Declares a generic serialization interface that supports both directions.
file	keyvaluetree.h
	Declares a data structure for JSON-like structured key-value mapping.
file	keyvaluetreebuilder.h
	Declares classes for building the data structures in keyvaluetree.h.
file	keyvaluetreeserializer.h
	Declares serialization routines for KeyValueTree objects.
file	keyvaluetreetransform.h
	Declares utilities for transforming key-value trees.
file	logger.h
	Declares functionality for logging.
file	loggerbuilder.h
	Declares functionality for initializing logging.
file	messagestringcollector.h
	Declares gmx::MessageStringCollector.
file	mutex.h
	Declares C++11-style basic threading primitives (gmx::Mutex, gmx::lock_guard).
file	niceheader.h
	Declares function for printing a nice header for text output files.
file	nodelete.h
	Declares no_delete deleter for std::shared_ptr.
file	path.h
	Declares functions for OS-independent path handling.
file	pleasecite.h
	Declares please_cite() for printing out literature references.
file	qsort_threadsafe.h
	Portable implementation of threadsafe quicksort.
file	snprintf.h
	Provide snprintf symbol on all OS (for internal Gromacs use)
file	strconvert.h
	Declares common utility functions for conversions to and from strings.
file	strdb.h
	Declares C functions for reading files with a list of strings.
file	stringcompare.h
	Declares utility functionst for string comparison.
file	stringstream.h
	Declares implementations for textstream.h interfaces for input/output to in-memory strings.
file	sysinfo.h
	Declares functions that wrap platform-specific calls for obtaining information about the operating environment and the current process.
file	alignedallocator-impl.h
	Tests for allocators that offer a minimum alignment.
file	textreader.h
	Declares gmx::TextReader.
file	textstream.h
	Declares interfaces for simple input/output streams.
file	textwriter.h
	Declares gmx::TextWriter.
file	txtdump.h
	Declares helper functions for dumping basic data structures as text.
file	typetraits.h
	Declares type traits.
file	unique_cptr.h
	Declares gmx::unique_cptr and gmx::sfree_guard.
file	variant.h
	Declares gmx::Variant.
file	cmdlinetest.h
	Declares utilities testing command-line programs.
file	conftest.h
	Declares function to add the content of a conf file to a checker.
file	filematchers.h
	Declares utility classes for testing file contents.
file	interactivetest.h
	Provides helper classes for testing interactive prompts.
file	loggertest.h
	Declares gmx::test::LoggerTestHelper.
file	mpitest.h
	Helper functions for MPI tests to make thread-MPI look like real MPI.
file	refdata.h
	Functionality for writing tests that can produce their own reference data.
file	stdiohelper.h
	Declares gmx::test::StdioTestHelper.
file	stringtest.h
	Declares gmx::test::StringTestBase.
file	testasserts.h
	Extra assertions for unit tests.
file	testexceptions.h
	Exception classes for errors in tests.
file	testfilemanager.h
	Declares gmx::test::TestFileManager.
file	testfileredirector.h
	Declares generic mock implementations for interfaces in fileredirector.h.
file	testoptions.h
	Functions for accessing test command-line options.
file	textblockmatchers.h
	Declares utility classes for testing multi-line strings against reference data.
file	xvgtest.h
	Declares function to add the content of an xvg file to a checker.