File List

Here is a list of all documented files with brief descriptions:

[detail level 1234567]

api
legacy
include
gromacs
analysisdata
modules
average.h	Declares gmx::AnalysisDataAverageModule
displacement.h	Declares gmx::AnalysisDataDisplacementModule
histogram.h	Declares analysis data modules for calculating histograms
lifetime.h	Declares gmx::AnalysisDataLifetimeModule
plot.h	Declares gmx::AnalysisDataPlotModule for plotting data (into a file)
abstractdata.h	Declares gmx::AbstractAnalysisData
analysisdata.h	Declares gmx::AnalysisData and gmx::AnalysisDataHandle
arraydata.h	Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData
dataframe.h	Declares classes for accessing data frame information
datamodule.h	Declares gmx::IAnalysisDataModule and related convenience classes
math
functions.h	Declares simple math functions
mdtypes
md_enums.h	Declares enumerated types used throughout the code
options
abstractoption.h	Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo
basicoptions.h	Declares option objects for basic option types
filenameoption.h	Declares gmx::FileNameOption and gmx::FileNameOptionInfo
filenameoptionmanager.h	Declares gmx::FileNameOptionManager
ioptionsbehavior.h	Declares gmx::IOptionsBehavior
ioptionscontainer.h	Declares gmx::IOptionsContainer
ioptionscontainerwithsections.h	Declares gmx::IOptionsContainerWithSections
ivaluestore.h	Declares gmx::IOptionValueStore
optionfiletype.h	Defines an enumeration type for specifying file types for options
optionflags.h	Defines flags used in option implementation
options.h	Declares gmx::Options
timeunitmanager.h	Declares gmx::TimeUnitManager
restraint
restraintpotential.h	Declare generic interface for restraint implementations
selection
indexutil.h	API for handling index files and index groups
nbsearch.h	API for neighborhood searching for analysis
position.h	API for handling positions
selection.h	Declares gmx::Selection and supporting classes
selectioncollection.h	Declares gmx::SelectionCollection
selectionenums.h	Declares common types used in selections
selectionoption.h	Declares gmx::SelectionOption and gmx::SelectionOptionInfo
selectionoptionbehavior.h	Declares gmx::SelectionOptionBehavior
selectionoptionmanager.h	Declares gmx::SelectionOptionManager
topology
symtab.h	Declares modern and legacy symbol table used to store strings of characters
trajectoryanalysis
analysismodule.h	Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData
analysissettings.h	Declares gmx::TrajectoryAnalysisSettings
cmdlinerunner.h	Declares gmx::TrajectoryAnalysisCommandLineRunner
topologyinformation.h	Declares gmx::TopologyInformation
utility
arrayref.h	Declares gmx::ArrayRef
basedefinitions.h	Basic types and macros used throughout GROMACS
baseversion.h	Declares functions to get basic version information
classhelpers.h	Declares common utility classes and macros
current_function.h	Declares GMX_CURRENT_FUNCTION for getting the current function name
enumerationhelpers.h	Defines helper types for class enumerations
exceptions.h	Declares common exception classes and macros for fatal error handling
fileptr.h	Declares guard pointer for RAII-style handling of cstdio FILE pointers
flags.h	Declares gmx::FlagsTemplate
futil.h	Low-level wrappers for OS-specific file handling with some GROMACS customizations
gmxassert.h	Defines assert macros customized for Gromacs
listoflists.h	Declares gmx::ListOfLists
programcontext.h	Declares gmx::IProgramContext and related methods
range.h	Declares gmx::Range
real.h	Declares real and related constants
smalloc.h	C-style memory allocation routines for GROMACS
stringutil.h	Declares common string utility and formatting routines
unique_cptr.h	Declares gmx::unique_cptr and gmx::sfree_guard
share	Directory that contains installed data files
template	Template code for writing analysis programs
template.cpp	Template code for writing analysis programs
src	Main source code directory
gromacs	Source code for building the libgromacs library
analysisdata	Parallelizable Handling of Output Data (analysisdata)
commandline	Command Line Program Management (commandline)
cmdlinehelpwriter.h	Declares gmx::CommandLineHelpWriter
cmdlineinit.h	Declares functions for initializing the GROMACS library for command line use
cmdlinemodule.h	Declares gmx::ICommandLineModule and supporting classes
cmdlineoptionsmodule.h	Declares gmx::ICommandLineOptionsModule and supporting routines
cmdlineparser.h	Declares gmx::CommandLineParser
cmdlineprogramcontext.h	Declares gmx::CommandLineProgramContext
filenm.h	Declares t_filenm for old-style command-line parsing of file name options
pargs.h	Declares t_pargs, parse_common_args() and related methods
viewit.h	Provides function to open output files automatically (with some X11 programs)
coordinateio
frameconverters
register.cpp
register.h	Declares gmx::ProcessFrameConversion
outputadapters
outputselector.h	Declares gmx::OutputSelector
setatoms.h	Declares gmx::SetAtoms
setbox.h	Declares gmx::SetBox
setforces.h	Declares gmx::SetForces
setprecision.h	Declares gmx::SetPrecision
setstarttime.h	Declares gmx::SetStartTime
settimestep.h	Declares gmx::SetTimeStep
setvelocities.h	Declares gmx:SetVelocities
tests
coordinate_test.h
frameconverter.h
outputadapters.h
register.cpp
requirements.h
testmodule.h
coordinatefile.h	CoordinateFile takes care of opening files and writing output to them
coordinatefileenums.h	Defines enum class defining the different requirements that outputadapters have for the output file type. OutputManager objects can only be built with OutputAdapters whose requirements can be implemented with the available input
frameconverterenums.h	Defines enum class defining the guarantees provided by different frameconverters for the coordiante file manipulations done by them
iframeconverter.h	Interface class for frame handling, provides handles for all calls
ioutputadapter.h	Declares gmx::IOutputAdapter interface for modifying coordinate file structures before writing them to disk
outputadaptercontainer.h	Declares gmx::OutputAdapterContainer, a storage object for multiple outputadapters derived from the IOutputadaper interface
outputadapters.h	Public API convenience header for accessing outputadapters
requirements.h	Storage object for requirements to build coordinate file writer
domdec
localatomset.cpp
localatomset.h
localatomsetdata.cpp
localatomsetdata.h
energyanalysis
analysismodule.h	Public API convenience header for energy analysis framework
fft
fft.h	Fast Fourier Transforms
gmxpreprocess
hackblock.h
resall.h
gpu_utils
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
sycl_kernel_utils.h	SYCL kernel helper functions
math
include
gromacs
math
arrayrefwithpadding.h	Declares gmx::ArrayRefWithPadding that refers to memory whose size includes padding for SIMD operations
paddedvector.h	Declares gmx::PaddedRVecVector
mdlib
simulationsignal.h	This file declares functions for inter-rank signalling by mdrun
mdrun
simulationinputhandle.h	Public interface for SimulationInput facilities
mdtypes
state.h	This file contains the definition of the microstate of the simulated system
nbnxm
benchmark
bench_system.h	This file declares functions for setting up a benchmark system
boundingboxes.h
options	Extensible Handling of Options (options)
abstractsection.h	Declares base classes for declaring option sections
isectionstorage.h	Declares gmx::IOptionSectionStorage
optionsection.h	Declares gmx::OptionSection and gmx::OptionSectionInfo
repeatingsection.h	Declares gmx::RepeatingOptionSection and related classes
valuestore.h	Declares implementations for IOptionValueStore
pbcutil
include
gromacs
pbcutil
com.h	Helper methods to place particle COM in boxes
pbc_aiuc.h	Structure and basic routines to handle periodic boundary conditions
pbcenums.h	Defines enum classes for centering and unit cell types
com.cpp
pbcenums.cpp
random
exponentialdistribution.h	The exponential distribution
gammadistribution.h	The gamma distribution
normaldistribution.h	The normal distribution
seed.h	Random seed and domain utilities
tabulatednormaldistribution.h	Tabulated normal distribution
threefry.h	Implementation of the 2x64 ThreeFry random engine
uniformintdistribution.h	The uniform integer distribution
uniformrealdistribution.h	The uniform real distribution
selection	Parsing and Evaluation of Analysis Selections (selection)
trajectoryanalysis	Framework for Trajectory Analysis (trajectoryanalysis)
utility	Low-Level Utilities (utility)
include
gromacs
utility
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
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
arraysize.h	Provides asize() function for calculating the static size of an array at compile time
cstringutil.h	Generic C string handling functions
datafilefinder.h	Declares gmx::DataFileFinder and related classes
fatalerror.h	Declares fatal error handling and debugging routines for C code
fixedcapacityvector.h	Declares gmx::FixedCapacityVector
init.h	Declares functions for initializing the GROMACS library
stringtoenumvalueconverter.h	Defines helper function object for class enumerations
errorcodes.h	Declares error codes and related functions for fatal error handling
utility.h	Public API convenience header for low-level utilities
programs
mdrun
nonbonded_bench.h	Declares the nonbonded benchmarking tool
testutils
topologyhelpers.h