File List

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

[detail level 12345]

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)
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
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)
compat
make_unique.h	Provides template gmx::compat::make_unique
domdec
localatomset.cpp
localatomset.h
localatomsetdata.cpp
localatomsetdata.h
fft
fft.h	Fast Fourier Transforms
gpu_utils
hostallocator.h	Declares gmx::HostAllocationPolicy, gmx::HostAllocator, and gmx::HostVector, 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
math
arrayrefwithpadding.h	Declares gmx::ArrayRefWithPadding that refers to memory whose size includes padding for SIMD operations
functions.h	Declares simple math functions
paddedvector.h	Declares gmx::PaddedRVecVector
mdlib
simulationsignal.h	This file declares functions for inter-rank signalling by mdrun
mdtypes
md_enums.h	Declares enumerated types used throughout the code
state.h	This file contains the definition of the microstate of the simulated system
options	Extensible Handling of Options (options)
abstractoption.h	Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo
abstractsection.h	Declares base classes for declaring option sections
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
isectionstorage.h	Declares gmx::IOptionSectionStorage
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
optionsection.h	Declares gmx::OptionSection and gmx::OptionSectionInfo
repeatingsection.h	Declares gmx::RepeatingOptionSection and related classes
timeunitmanager.h	Declares gmx::TimeUnitManager
valuestore.h	Declares implementations for IOptionValueStore
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
restraint
restraintpotential.h	Declare generic interface for restraint implementations
selection	Parsing and Evaluation of Analysis Selections (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
trajectoryanalysis	Framework for Trajectory Analysis (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	Low-Level Utilities (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
arrayref.h	Declares gmx::ArrayRef
arraysize.h	Provides asize() function for calculating the static size of an array at compile time
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
cstringutil.h	Generic C string handling functions
current_function.h	Declares GMX_CURRENT_FUNCTION for getting the current function name
datafilefinder.h	Declares gmx::DataFileFinder and related classes
errorcodes.h	Declares error codes and related functions for fatal error handling
exceptions.h	Declares common exception classes and macros for fatal error handling
fatalerror.h	Declares fatal error handling and debugging routines for C code
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
init.h	Declares functions for initializing the GROMACS library
programcontext.h	Declares gmx::IProgramContext and related methods
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
analysisdata.h	Public API convenience header for analysis data handling
commandline.h	Public API convenience header for managing command line programs
options.h	Public API convenience header for handling of options
random.h	Public API convenience header for random engines and distributions
selection.h	Public API convenience header for selection handling
trajectoryanalysis.h	Public API convenience header for trajectory analysis framework
utility.h	Public API convenience header for low-level utilities