Gromacs  2023
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File List
Here is a list of all documented files with brief descriptions:
[detail level 1234567]
o-api
|\-legacy
| \-include
|  \+gromacs
o-shareDirectory that contains installed data files
|\-templateTemplate code for writing analysis programs
| \*template.cppTemplate code for writing analysis programs
\-srcMain source code directory
 o-gromacsSource code for building the libgromacs library
 |o-analysisdataParallelizable Handling of Output Data (analysisdata)
 |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-coordinateio
 ||o+frameconverters
 ||o+outputadapters
 ||o+tests
 ||o*coordinatefile.hCoordinateFile takes care of opening files and writing output to them
 ||o*coordinatefileenums.hDefines 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
 ||o*frameconverterenums.hDefines enum class defining the guarantees provided by different frameconverters for the coordiante file manipulations done by them
 ||o*iframeconverter.hInterface class for frame handling, provides handles for all calls
 ||o*ioutputadapter.hDeclares gmx::IOutputAdapter interface for modifying coordinate file structures before writing them to disk
 ||o*outputadaptercontainer.hDeclares gmx::OutputAdapterContainer, a storage object for multiple outputadapters derived from the IOutputadaper interface
 ||o*outputadapters.hPublic API convenience header for accessing outputadapters
 ||\*requirements.hStorage object for requirements to build coordinate file writer
 |o-domdec
 ||o*localatomset.cpp
 ||o*localatomset.h
 ||o*localatomsetdata.cpp
 ||\*localatomsetdata.h
 |o-fft
 ||\*fft.hFast Fourier Transforms
 |o-gmxpreprocess
 ||o*hackblock.h
 ||\*resall.h
 |o-gpu_utils
 ||o*hostallocator.hDeclares 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.hSYCL kernel helper functions
 |o-math
 ||\+include
 |o-mdlib
 ||\*simulationsignal.hThis file declares functions for inter-rank signalling by mdrun
 |o-mdrun
 ||\*simulationinputhandle.hPublic interface for SimulationInput facilities
 |o-mdtypes
 ||\*state.hThis file contains the definition of the microstate of the simulated system
 |o-nbnxm
 ||o+benchmark
 ||\*boundingboxes.h
 |o-optionsExtensible Handling of Options (options)
 ||o*abstractsection.hDeclares base classes for declaring option sections
 ||o*isectionstorage.hDeclares gmx::IOptionSectionStorage
 ||o*optionsection.hDeclares gmx::OptionSection and gmx::OptionSectionInfo
 ||o*repeatingsection.hDeclares gmx::RepeatingOptionSection and related classes
 ||\*valuestore.hDeclares implementations for IOptionValueStore
 |o-pbcutil
 ||o+include
 ||o*com.cpp
 ||\*pbcenums.cpp
 |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-trajectoryanalysisFramework for Trajectory Analysis (trajectoryanalysis)
 |o-utilityLow-Level Utilities (utility)
 ||o+include
 ||\*errorcodes.hDeclares error codes and related functions for fatal error handling
 |\*utility.hPublic API convenience header for low-level utilities
 o-programs
 |\-mdrun
 | \*nonbonded_bench.hDeclares the nonbonded benchmarking tool
 \-testutils
  \*topologyhelpers.h