Gromacs  2016.6
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File List
Here is a list of all documented files with brief descriptions:
[detail level 12345]
o-shareDirectory that contains installed data files
|\-templateTemplate code for writing analysis programs
| \*template.cppTemplate code for writing analysis programs
\-srcMain source code directory
 \-gromacsSource code for building the libgromacs library
  o-analysisdataParallelizable Handling of Output Data (analysisdata)
  |o-modules
  ||o*average.hDeclares gmx::AnalysisDataAverageModule
  ||o*displacement.hDeclares gmx::AnalysisDataDisplacementModule
  ||o*histogram.hDeclares analysis data modules for calculating histograms
  ||o*lifetime.hDeclares gmx::AnalysisDataLifetimeModule
  ||\*plot.hDeclares gmx::AnalysisDataPlotModule for plotting data (into a file)
  |o*abstractdata.hDeclares gmx::AbstractAnalysisData
  |o*analysisdata.hDeclares gmx::AnalysisData and gmx::AnalysisDataHandle
  |o*arraydata.hDeclares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData
  |o*dataframe.hDeclares classes for accessing data frame information
  |\*datamodule.hDeclares gmx::IAnalysisDataModule and related convenience classes
  o-commandlineCommand Line Program Management (commandline)
  |o*cmdlinehelpwriter.hDeclares gmx::CommandLineHelpWriter
  |o*cmdlineinit.hDeclares functions for initializing the GROMACS library for command line use
  |o*cmdlinemodule.hDeclares gmx::ICommandLineModule and supporting classes
  |o*cmdlineoptionsmodule.hDeclares gmx::ICommandLineOptionsModule and supporting routines
  |o*cmdlineparser.hDeclares gmx::CommandLineParser
  |o*cmdlineprogramcontext.hDeclares gmx::CommandLineProgramContext
  |o*filenm.hDeclares t_filenm for old-style command-line parsing of file name options
  |o*pargs.hDeclares t_pargs, parse_common_args() and related methods
  |\*viewit.hProvides function to open output files automatically (with some X11 programs)
  o-fft
  |\*fft.hFast Fourier Transforms
  o-listed-forces
  |\*listed-forces.hThis file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions
  o-math
  |o*calculate-ewald-splitting-coefficient.hDeclares functions for computing Ewald splitting coefficients
  |\*functions.hDeclares simple math functions
  o-mdtypes
  |\*md_enums.hDeclares enumerated types used throughout the code
  o-optionsExtensible Handling of Options (options)
  |o*abstractoption.hDefines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo
  |o*basicoptions.hDeclares option objects for basic option types
  |o*filenameoption.hDeclares gmx::FileNameOption and gmx::FileNameOptionInfo
  |o*filenameoptionmanager.hDeclares gmx::FileNameOptionManager
  |o*ioptionsbehavior.hDeclares gmx::IOptionsBehavior
  |o*ioptionscontainer.hDeclares gmx::IOptionsContainer
  |o*optionfiletype.hDefines an enumeration type for specifying file types for options
  |o*optionflags.hDefines flags used in option implementation
  |o*options.hDeclares gmx::Options
  |\*timeunitmanager.hDeclares gmx::TimeUnitManager
  o-random
  |o*exponentialdistribution.hThe exponential distribution
  |o*gammadistribution.hThe gamma distribution
  |o*normaldistribution.hThe normal distribution
  |o*seed.hRandom seed and domain utilities
  |o*tabulatednormaldistribution.hTabulated normal distribution
  |o*threefry.hImplementation of the 2x64 ThreeFry random engine
  |o*uniformintdistribution.hThe uniform integer distribution
  |\*uniformrealdistribution.hThe uniform real distribution
  o-selectionParsing and Evaluation of Analysis Selections (selection)
  |o*indexutil.hAPI for handling index files and index groups
  |o*nbsearch.hAPI for neighborhood searching for analysis
  |o*position.hAPI for handling positions
  |o*selection.hDeclares gmx::Selection and supporting classes
  |o*selectioncollection.hDeclares gmx::SelectionCollection
  |o*selectionenums.hDeclares common types used in selections
  |o*selectionoption.hDeclares gmx::SelectionOption and gmx::SelectionOptionInfo
  |o*selectionoptionbehavior.hDeclares gmx::SelectionOptionBehavior
  |\*selectionoptionmanager.hDeclares gmx::SelectionOptionManager
  o-trajectoryanalysisFramework for Trajectory Analysis (trajectoryanalysis)
  |o*analysismodule.hDeclares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData
  |o*analysissettings.hDeclares gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation
  |\*cmdlinerunner.hDeclares gmx::TrajectoryAnalysisCommandLineRunner
  o-utilityLow-Level Utilities (utility)
  |o*arrayref.hDeclares gmx::ArrayRef and gmx::ConstArrayRef
  |o*arraysize.hProvides asize() macro for calculating the static size of an array
  |o*basedefinitions.hBasic types and macros used throughout GROMACS
  |o*baseversion.hDeclares functions to get basic version information
  |o*classhelpers.hDeclares common utility classes and macros
  |o*cstringutil.hGeneric C string handling functions
  |o*current_function.hDeclares GMX_CURRENT_FUNCTION for getting the current function name
  |o*datafilefinder.hDeclares gmx::DataFileFinder and related classes
  |o*errorcodes.hDeclares error codes and related functions for fatal error handling
  |o*exceptions.hDeclares common exception classes and macros for fatal error handling
  |o*fatalerror.hDeclares fatal error handling and debugging routines for C code
  |o*flags.hDeclares gmx::FlagsTemplate
  |o*futil.hLow-level wrappers for OS-specific file handling with some GROMACS customizations
  |o*gmxassert.hDefines assert macros customized for Gromacs
  |o*init.hDeclares functions for initializing the GROMACS library
  |o*programcontext.hDeclares gmx::IProgramContext and related methods
  |o*real.hDeclares real and related constants
  |o*smalloc.hC memory allocation routines for GROMACS
  |\*stringutil.hDeclares common string utility and formatting routines
  o*analysisdata.hPublic API convenience header for analysis data handling
  o*commandline.hPublic API convenience header for managing command line programs
  o*options.hPublic API convenience header for handling of options
  o*random.hPublic API convenience header for random engines and distributions
  o*selection.hPublic API convenience header for selection handling
  o*trajectoryanalysis.hPublic API convenience header for trajectory analysis framework
  \*utility.hPublic API convenience header for low-level utilities
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