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::IOutputAdapter
	OutputAdapter class for handling trajectory file flag setting and processing. More...
class	gmx::LocalAtomSet
	A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator. More...
class	gmx::LocalAtomSetManager
	Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...
class	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. More...
class	gmx::MDModules
	Manages the collection of all modules used for mdrun. More...
class	gmx::SimulationContext
	Simulation environment and configuration. More...
class	gmx::IForceProvider
	Interface for a component that provides forces during MD. More...
class	gmx::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::ObservablesReducer
	Manage reduction of observables for registered subscribers. More...
class	gmx::MimicCommunicator
	Class-wrapper around MiMiC communication library It uses GROMACS' unit conversion to switch from GROMACS' units to a.u. 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 Any to a given type. More...
class	gmx::Site
	Abstraction for a restraint interaction site. 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::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::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 ITextBlockMatcher 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::FilteringExactTextMatch
	Use an exact text match after scrubbing lines of the text that match the supplied regular expressions. 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	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	electricfield.h
	Declares module creation function for applied electric fields.
file	cmdlinehelpcontext.h
	Declares gmx::CommandLineHelpContext.
file	cmdlinemodulemanager.h
	Declares gmx::CommandLineModuleManager.
file	cmdlineprogramcontext.h
	Declares gmx::CommandLineProgramContext.
file	mp11.h
	Provides ported functions/classes from boost::mp11.
file	pointers.h
	Provides ported functions/classes from gsl/pointers.
file	utility.h
	Provides backported functions/classes from utility.
file	ioutputadapter.h
	Declares gmx::IOutputAdapter interface for modifying coordinate file structures before writing them to disk.
file	outputadaptercontainer.h
	Declares gmx::OutputAdapterContainer, a storage object for multiple outputadapters derived from the IOutputadaper interface.
file	requirements.h
	Storage object for requirements to build coordinate file writer.
file	coordinate_test.h
	Helper classes for coordinatefile and coordinateio tests.
file	outputadapters.h
	Helpers and data for outputadapter module tests.
file	requirements.h
	Helpers and data for flag setting method.
file	coordinateio.h
	Public API convenience header for coordinate file output.
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	builder.h
	This file declares a builder class for the manager of domain decomposition.
file	collect.h
	Declares functions to collect state data to the master rank.
file	computemultibodycutoffs.h
	This file declares the function for computing the required cutoff distance for inter-domain multi-body interactions, when those exist.
file	dlb.h
	This file declares functions to interact with the dynamic load balancing machinery.
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	gpuhaloexchange.h
	Declaration of GPU halo exchange.
file	hashedmap.h
	Defines structures and functions for mapping from keys to entries indices using a hash table. The functions are performance critical and should be inlined.
file	localatomset.h
	Declares gmx::LocalAtomSet.
file	localatomsetmanager.h
	Declares gmx::LocalAtomSetManager.
file	localtopology.h
	This file makes declarations used for building the local topology.
file	localtopologychecker.h
	This file declares functionality for checking whether local topologies describe all bonded interactions.
file	makebondedlinks.h
	Declares a function that makes the list of links between atoms connected by bonded interactions.
file	mdsetup.h
	Contains functions relevant to simulation setup in MD drivers.
file	options.h
	This file declares command-line options for mdrun related to domain decomposition.
file	partition.h
	This file declares functions for mdrun to call to make a new domain decomposition, and check it.
file	reversetopology.h
	This file makes declarations used for building the reverse topology.
file	edsam.h
	Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces.
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	ewald_utils.h
	Declares utility functions related to Ewald.
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.h
	This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
file	pme_coordinate_receiver_gpu.h
	Declaration of class which receives coordinates to GPU memory on PME task.
file	pme_force_sender_gpu.h
	Declaration of class which sends PME Force from GPU memory to PP task.
file	pme_gpu_program.h
	Declares PmeGpuProgram to store data derived from the GPU context or devices for PME, such as (compiled) kernel handles and the warp sizes they work with.
file	pme_load_balancing.h
	This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ).
file	pme_only.h
	This file contains function declarations necessary for running on an MPI rank doing only PME long-ranged work.
file	pme_pp_comm_gpu.h
	Declaration of GPU PME-PP Communication.
file	mrcdensitymap.h
	Declars mrc/ccp4-file format handling.
file	mrcdensitymapheader.h
	Implement mrc/ccp4-file metadata.
file	gpp_atomtype.h
	Declares PreprocessingAtomType.
file	gpp_bond_atomtype.h
	Declares PreprocessingBondAtomType.
file	clfftinitializer.h
	Declares ClfftInitializer class, which initializes and tears down the clFFT library resources in OpenCL builds, and does nothing in other builds, and a factory function for it.
file	device_context.h
	Declarations for DeviceContext class.
file	device_event.h
	Declares DeviceEvent for all build configuraitons.
file	device_event_ocl.h
	Implements a DeviceEvent class for OpenCL.
file	device_event_sycl.h
	Implements a GpuEventSynchronizer class for SYCL.
file	device_stream.h
	Declarations for DeviceStream class.
file	device_stream_manager.h
	This file declares a manager of GPU context and streams needed for running workloads on GPUs.
file	devicebuffer.h
	Implements the logic for handling of DeviceBuffer types in OpenCL, CUDA and SYCL.
file	devicebuffer_datatype.h
	Declares the DeviceBuffer data type.
file	devicebuffer_ocl.h
	Implements the DeviceBuffer type and routines for OpenCL. Should only be included directly by the main DeviceBuffer file devicebuffer.h. TODO: the intent is for DeviceBuffer to become a class.
file	devicebuffer_sycl.h
	Implements the DeviceBuffer type and routines for SYCL. Should only be included directly by the main DeviceBuffer file devicebuffer.h. TODO: the intent is for DeviceBuffer to become a class.
file	gmxopencl.h
	Wraps the complexity of including OpenCL in Gromacs.
file	gmxsycl.h
	Wraps the complexity of including SYCL in GROMACS.
file	gpu_utils.h
	Declare functions for detection and initialization for GPU devices.
file	gpueventsynchronizer.h
	Implements a GpuEventSynchronizer class.
file	gpuregiontimer_ocl.h
	Implements the GPU region timer for OpenCL.
file	gpuregiontimer_sycl.h
	Implements the GPU region timer for SYCL.
file	gputraits.h
	Declares the GPU type traits for non-GPU builds.
file	gputraits_ocl.h
	Declares the OpenCL type traits.
file	gputraits_sycl.h
	Declares the SYCL type traits.
file	ocl_compiler.h
	Declare infrastructure for OpenCL JIT compilation.
file	oclraii.h
	Declare RAII helpers for OpenCL types, along with supporting type traits.
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.h
	Declare functions for host-side memory handling.
file	syclutils.h
	Declare utility routines for SYCL.
file	cpuinfo.h
	Declares gmx::CpuInfo.
file	device_management.h
	Declares functions to manage GPU resources.
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 declares the class that coordinates with VMD via the Interactive Molecular Dynamics protocol, along with supporting free functions.
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	listed_forces.h
	This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions.
file	listed_forces_gpu.h
	This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions.
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	coordinatetransformation.h
	Declares coordinate transformation routines.
file	densityfit.h
	Declares density similarity measures and their derivatives.
file	densityfittingforce.h
	Declares classes to calculate density fitting forces.
file	exponentialmovingaverage.h
	Declares an exponential moving average class.
file	gausstransform.h
	Declares Gaussian function evaluations on lattices and related functionality.
file	invertmatrix.h
	Declares routines to invert 3x3 matrices.
file	multidimarray.h
	Declares MultiDimArray.
file	testarrayrefs.h
	Declares functions for comparing views of vector-like data.
file	boxdeformation.h
	Declares interface to box deformation code.
file	broadcaststructs.h
	Convenience wrappers for broadcasting structs.
file	checkpointhandler.h
	Declares the checkpoint handler class.
file	constr.h
	Declares interface to constraint code.
file	energyoutput.h
	Header for the code that writes energy-like quantities.
file	groupcoord.h
	Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
file	leapfrog_gpu.h
	Declarations for GPU implementation of Leap-Frog.
file	leapfrog_gpu_internal.h
	Declarations for backend specific GPU functions for Leap-Frog.
file	lincs.h
	Declares interface to LINCS code.
file	lincs_gpu.h
	Declares the class for GPU implementation of LINCS.
file	makeconstraints.h
	Declares and implements factory function for Constraints.
file	resethandler.h
	Declares the reset handler class.
file	settle.h
	Declares interface to SETTLE code.
file	shake.h
	Declares interface to SHAKE code.
file	simulationsignal.h
	This file declares functions for inter-rank signalling by mdrun.
file	stophandler.h
	Declares StopHandler, a helper class and two stop conditions.
file	update_constrain_gpu.h
	Declaration of high-level functions of GPU implementation of update and constrain class.
file	updategroups.h
	Declares the functions for generating update groups.
file	updategroupscog.h
	Declares the UpdateGroupsCog class for managing centers of mass of update groups.
file	vsite.h
	Declares the VirtualSitesHandler class and vsite standalone functions.
file	wholemoleculetransform.h
	Declares the WholeMolecules class for generating whole molecules.
file	legacymdrunoptions.h
	This file declares helper functionality for legacy option handling for mdrun.
file	mdmodules.h
	Declares gmx::MDModules.
file	simulationcontext.h
	Provide ways for client code to own simulation resources.
file	simulationinput.h
	Utilities for interacting with SimulationInput.
file	freeenergy.cpp
	Defines helper functions for mdrun pertaining to free energy calculations.
file	freeenergy.h
	Declares helper functions for mdrun pertaining to free energy calculations.
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	logging.h
	Declares the MD log file handling routines.
file	multisim.h
	Declares the multi-simulation support routines.
file	printtime.h
	Declares functions that write timestamps to e.g. log files.
file	threadaffinity.h
	Declares functions for managing mdrun thread affinity.
file	extensions.h
	GROMACS extensions to mdspan.
file	mdspan.h
	Declares gmx::mdspan.
file	atominfo.h
	This file makes declarations used for storing bitfields describing each atom so that other modules can efficiently process them.
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	forcebuffers.h
	This file contains the definition of a container for force buffers.
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	mdrunoptions.h
	This file declares helper functionality for legacy option handling for mdrun.
file	observableshistory.h
	This file contains the definition of a container for history data for simulation observables.
file	observablesreducer.cpp
	Defines gmx::ObservablesReducer and its builder.
file	observablesreducer.h
	Declares gmx::ObservablesReducer and builder.
file	pull_params.h
	This file contains datatypes for the mdp options used by the pull code.
file	pullhistory.h
	This file contains datatypes for pull statistics history.
file	simulation_workload.h
	Declares step, domain-lifetime, and run workload managers.
file	state.h
	This file contains the definition of the microstate of the simulated system.
file	state_propagator_data_gpu.h
	Declaration of interfaces for GPU state data propagator object.
file	utilities.h
	Provides utility functions for MiMiC QM/MM.
file	atomdata.h
	Functionality for per-atom data in the nbnxm module.
file	bench_setup.h
	This file declares functions for setting up kernel benchmarks.
file	gpu_data_mgmt.h
	Declare interface for GPU data transfer for NBNXN module.
file	nbnxm.h
	This file contains the public interface of the nbnxm module that implements the NxM atom cluster non-bonded algorithm to efficiently compute pair forces.
file	pairlist_tuning.h
	Declares functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels.
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	com.h
	Helper methods to place particle COM in boxes.
file	pbc_aiuc.h
	Structure and basic routines to handle periodic boundary conditions.
file	pbc_aiuc_sycl.h
	Basic routines to handle periodic boundary conditions with SYCL.
file	pbc_simd.h
	This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations.
file	output.h
	This file declares functions for pull output writing.
file	pull.h
	This file contains datatypes and function declarations necessary for mdrun to interface with the pull code.
file	pull_rotation.h
	Declares functions to enforce rotational motion upon a group of particles.
file	manager.h
	Declare the Manager for restraint potentials.
file	restraintmdmodule.h
	Library interface for RestraintMDModule.
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	symtab.h
	Declares modern and legacy symbol table used to store strings of characters.
file	modules.h
	Generic interface for accessing trajectory analysis modules.
file	topologyinformation.h
	Declares gmx::TopologyInformation.
file	any.h
	Declares gmx::Any.
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	defaultinitializationallocator.h
	Declares an allocator that can use default initialization instead of values initialization. This is useful for improving performance of resize() in standard vectors for buffers in performance critical code.
file	dir_separator.h
	Provides OS-specific directory-name separator.
file	directoryenumerator.h
	Declares gmx::DirectoryEnumerator.
file	enumerationhelpers.h
	Defines helper types for class enumerations.
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	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	keyvaluetreemdpwriter.h
	Declares a function to write a flat key-value tree to look like old-style mdp output.
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	mdmodulesnotifier.h
	Declares gmx::MDModulesNotifier and builder.
file	mdmodulesnotifiers.h
	Declares gmx::MDModulesNotifiers.
file	message_string_collector.h
	Declares gmx::MessageStringCollector.
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	physicalnodecommunicator.h
	Declares functionality for communicators across physical nodes.
file	pleasecite.h
	Declares please_cite() for printing out literature references. Declares writeSourceDoi for printing of source code DOI.
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	stringtoenumvalueconverter.h
	Defines helper function object for class enumerations.
file	sysinfo.h
	Declares functions that wrap platform-specific calls for obtaining information about the operating environment and the current process.
file	template_mp.h
	Declares utilities for template metaprogramming.
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	gmxpre.h
	Prerequisite header file for GROMACS build.
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	setenv.h
	Helper functions to have identical behavior of setenv and unsetenv on Unix and Windows systems.
file	simulationdatabase.h
	Functionality for testing whether calls to mdrun produce the same energy and force quantities when they should do so.
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	testmatchers.h
	Extra GoogleMock matchers for unit tests.
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.