  docs | Build system and source code for various documentation items |
  doxygen | Doxygen build system and general documentation content |
| 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) |
| tests | Unit tests for Parallelizable Handling of Output Data (analysisdata) |
| datatest.h | Helper classes for testing classes that derive from AbstractAnalysisData |
| mock_datamodule.h | Declares mock implementation of gmx::IAnalysisDataModule |
| 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 |
| datamodulemanager.h | Declares gmx::AnalysisDataModuleManager |
| datastorage.h | Declares gmx::AnalysisDataStorage |
| paralleloptions.h | Declares gmx::AnalysisDataParallelOptions |
| awh | |
| awh.h | Declares the Awh class |
| read-params.h | Declares functions needed for reading, initializing and setting the AWH parameter data types |
| commandline | Command Line Program Management (commandline) |
| tests | Unit tests for Command Line Program Management (commandline) |
| cmdlinehelpcontext.h | Declares gmx::CommandLineHelpContext |
| 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 |
| cmdlinemodulemanager.h | Declares gmx::CommandLineModuleManager |
| 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 | C++ standard library compatibility helpers. |
| make_unique.h | Provides template gmx::compat::make_unique |
| correlationfunctions | |
| autocorr.h | Declares routine for computing autocorrelation functions |
| crosscorr.h | Declares routine for computing a cross correlation between two data sets |
| expfit.h | Declares routine for fitting a data set to a curve |
| gmx_lmcurve.h | Declares a driver routine for lmfit |
| integrate.h | Declares routines for integrating a data set |
| manyautocorrelation.h | Declares routine for computing many correlation functions using OpenMP |
| polynomials.h | Declares routine for computing a Legendre polynomial |
| domdec | |
| dlbtiming.h | This file declares functions for timing the load imbalance due to domain decomposition |
| domdec.h | This file declares functions for mdrun to call to manage the details of its domain decomposition |
| domdec_network.h | This file declares functions for (mostly) the domdec module to use MPI functionality |
| domdec_struct.h | Declares structures related to domain decomposition |
| ga2la.h | Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined |
| essentialdynamics | |
| edsam.h | Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces |
| ewald | |
| ewald-utils.h | Declares utility functions related to Ewald |
| 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 |
| long-range-correction.h | This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
| pme-gpu-types.h | Defines the GPU-agnostic PME GPU data structures (the host-side PME GPU data, and the GPU function parameters) |
| pme-load-balancing.h | This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ) |
| pme.h | This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
| fft | |
| fft.h | Fast Fourier Transforms |
| gmxpreprocess | |
| keyvaluetreemdpwriter.h | Declares a function to write a flat key-value tree to look like old-style mdp output |
| gpu_utils | |
| gmxopencl.h | Wraps the complexity of including OpenCL in Gromacs |
| gpu_utils.h | Declare functions for detection and initialization for GPU devices |
| gpuregiontimer.h | Defines the GPU region timer implementation/wrapper classes. The implementations live in gpuregiontimer.cuh for CUDA and gpuregiontimer_ocl.h for OpenCL |
| gpuregiontimer_ocl.h | Implements the GPU region timer for OpenCL |
| 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 |
| ocl_compiler.h | Declare infrastructure for OpenCL JIT compilation |
| oclutils.h | Declare utility routines for OpenCL |
| pinning.h | Declares functions for pinning memory to be suitable for efficient GPU transfers on CUDA |
| pmalloc_cuda.h | Declare functions for host-side memory handling when using CUDA devices |
| hardware | |
| cpuinfo.h | Declares gmx::CpuInfo |
| hardwaretopology.h | Declares gmx::HardwareTopology |
| identifyavx512fmaunits.h | Defines a routine to check the number of AVX512 fma units |
| imd | |
| imd.h | This file contains datatypes and function declarations necessary for mdrun to interface with VMD via the interactive molecular dynamics protocol |
| imdsocket.h | Implements the parts of the vmdsock.h interface needed for IMD communication |
| listed-forces | |
| bonded.h | This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions |
| disre.h | Declares functions for handling distance restraints |
| listed-forces.h | This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions |
| manage-threading.h | Declares functions for managing threading of listed forces |
| orires.h | Declares functions for handling orientation restraints |
| pairs.h | This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions) |
| position-restraints.h | This file contains declarations necessary for low-level functions for computing energies and forces for position restraints |
| math | |
| functions.h | Declares simple math functions |
| invertmatrix.h | Declares routines to invert 3x3 matrices |
| paddedvector.h | Declares gmx::PaddedRVecVector |
| mdlib | |
| nbnxn_kernels | |
| nbnxn_kernel_cpu.h | Declares the nbnxn pair interaction kernel dispatcher |
| nbnxn_kernel_prune.h | Declares the pair-list pruning kernel wrapper function |
| broadcaststructs.h | Convenience wrappers for broadcasting structs |
| groupcoord.h | Assemble atomic positions of a (small) subset of atoms and distribute to all nodes |
| mdrun.h | This file declares types and functions for initializing an MD run |
| nb_verlet.h | This file contains the public interface of the non-bonded Verlet module that implements the NxN cluster non-bonded algorithm to efficiently compute pair forces |
| nbnxn_gpu_data_mgmt.h | Declare interface for GPU data transfer for NBNXN module |
| nbnxn_tuning.h | Declares functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels |
| simulationsignal.h | This file declares functions for inter-rank signalling by mdrun |
| mdrunutility | |
| handlerestart.h | This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files) |
| mdmodules.h | Declares gmx::MDModules |
| threadaffinity.h | Declares functions for managing mdrun thread affinity |
| mdtypes | |
| awh-correlation-history.h | Contains datatypes and function declarations needed by AWH to have its force correlation data checkpointed |
| awh-history.h | Contains datatypes and function declarations needed by AWH to have its data checkpointed |
| awh-params.h | Declares AWH parameter data types |
| energyhistory.h | This file contains datatypes for energy statistics history |
| forceoutput.h | This file contains the definition of a container for force and virial output |
| iforceprovider.h | Declares gmx::IForceProvider and ForceProviders |
| imdmodule.h | Declares gmx::IMDModule |
| imdoutputprovider.h | Declares gmx::IMDOutputProvider |
| imdpoptionprovider.h | Declares gmx::IMdpOptionProvider |
| md_enums.h | Declares enumerated types used throughout the code |
| observableshistory.h | This file contains the definition of a container for history data for simulation observables |
| pull-params.h | This file contains datatypes for the mdp options used by the pull code |
| state.h | This file contains the definition of the microstate of the simulated system |
| onlinehelp | Help Formatting for Online Help (onlinehelp) |
| tests | Unit tests for Help Formatting for Online Help (onlinehelp) |
| mock_helptopic.h | Declares mock implementation of gmx::IHelpTopic |
| helpformat.h | Declares common string formatting routines for online help |
| helpmanager.h | Declares gmx::HelpManager |
| helptopic.h | Declares helper classes for implementing gmx::IHelpTopic |
| helpwritercontext.h | Declares gmx::HelpWriterContext |
| ihelptopic.h | Declares gmx::IHelpTopic |
| options | Extensible Handling of Options (options) |
| tests | Unit tests for Extensible Handling of Options (options) |
| abstractoption.h | Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo |
| abstractoptionstorage.h | Declares gmx::AbstractOptionStorage |
| abstractsection.h | Declares base classes for declaring option sections |
| basicoptions.h | Declares option objects for basic option types |
| behaviorcollection.h | Declares gmx::OptionsBehaviorCollection |
| 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 |
| optionmanagercontainer.h | Declares gmx::OptionManagerContainer |
| options.h | Declares gmx::Options |
| optionsassigner.h | Declares gmx::OptionsAssigner |
| optionsection.h | Declares gmx::OptionSection and gmx::OptionSectionInfo |
| optionstoragetemplate.h | Defines gmx::OptionStorageTemplate template |
| optionsvisitor.h | Declares gmx::OptionsVisitor interface and supporting classes |
| repeatingsection.h | Declares gmx::RepeatingOptionSection and related classes |
| timeunitmanager.h | Declares gmx::TimeUnitManager |
| treesupport.h | Declares functions for using keyvaluetree.h with Options |
| valueconverter.h | Provides gmx::OptionValueConverterSimple |
| valuestore.h | Declares implementations for IOptionValueStore |
| pbcutil | |
| pbc-simd.h | This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations |
| pulling | |
| pull.h | This file contains datatypes and function declarations necessary for mdrun to interface with the pull code |
| pull_internal.h | This file contains datatypes and function declarations for internal use in the pull code |
| pull_rotation.h | Declares functions to enforce rotational motion upon a group of particles |
| 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) |
| tests | Unit tests for 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 |
| selectionfileoption.h | Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo |
| selectionoption.h | Declares gmx::SelectionOption and gmx::SelectionOptionInfo |
| selectionoptionbehavior.h | Declares gmx::SelectionOptionBehavior |
| selectionoptionmanager.h | Declares gmx::SelectionOptionManager |
| selhelp.h | Functions for initializing online help for selections |
| simd | SIMD intrinsics interface (simd) |
| impl_reference | |
| impl_reference.h | Reference SIMD implementation, including SIMD documentation |
| impl_reference_definitions.h | Reference SIMD implementation, including SIMD documentation |
| impl_reference_general.h | Reference SIMD implementation, general utility functions |
| impl_reference_simd4_double.h | Reference implementation, SIMD4 single precision |
| impl_reference_simd4_float.h | Reference implementation, SIMD4 single precision |
| impl_reference_simd_double.h | Reference implementation, SIMD double precision |
| impl_reference_simd_float.h | Reference implementation, SIMD single precision |
| impl_reference_util_double.h | Reference impl., higher-level double prec. SIMD utility functions |
| impl_reference_util_float.h | Reference impl., higher-level single prec. SIMD utility functions |
| scalar | |
| scalar.h | Scalar float functions corresponding to GROMACS SIMD functions |
| scalar_math.h | Scalar math functions mimicking GROMACS SIMD math functions |
| scalar_util.h | Scalar utility functions mimicking GROMACS SIMD utility functions |
| tests | Unit tests for SIMD intrinsics interface (simd) |
| simd.h | Definitions, capabilities, and wrappers for SIMD module |
| simd_math.h | Math functions for SIMD datatypes |
| simd_memory.h | Declares SimdArrayRef |
| support.h | Functions to query compiled and supported SIMD architectures |
| vector_operations.h | SIMD operations corresponding to Gromacs rvec datatypes |
| statistics | |
| statistics.h | Declares simple statistics toolbox |
| swap | |
| swapcoords.h | The "Computational Electrophysiology" protocol for ion/water position swapping |
| tables | |
| cubicsplinetable.h | Declares classes for cubic spline table |
| forcetable.h | Old routines for table generation (will eventually be replaced) |
| quadraticsplinetable.h | Declares classes for quadratic spline table |
| tableinput.h | Declares structures for analytical or numerical input data to construct tables |
| taskassignment | |
| decidegpuusage.h | Declares functionality for deciding whether tasks will run on GPUs |
| resourcedivision.h | Declares utility functionality for dividing resources and checking for consistency and usefulness |
| 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 |
| usergpuids.h | Declares routines for handling user-specified GPU IDs |
| timing | |
| cyclecounter.h | High-resolution timestamp or CPU clock cycle counters |
| gpu_timing.h | Declares data types for GPU timing |
| topology | |
| atomsbuilder.h | Utility classes for manipulating t_atoms structures |
| mtop_lookup.h | This file contains inline functions to look up atom information using the global atom index |
| trajectoryanalysis | Framework for Trajectory Analysis (trajectoryanalysis) |
| modules | |
| unionfind.h | Implements gmx::UnionFinder and gmx::MappedUnionFinder |
| tests | Unit tests for Framework for Trajectory Analysis (trajectoryanalysis) |
| analysismodule.h | Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData |
| analysissettings.h | Declares gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation |
| cmdlinerunner.h | Declares gmx::TrajectoryAnalysisCommandLineRunner |
| modules.h | Generic interface for accessing trajectory analysis modules |
| utility | Low-Level Utilities (utility) |
| tests | Unit tests for Low-Level Utilities (utility) |
| alignedallocator-impl.h | Tests for allocators that offer a minimum alignment |
| 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() macro for calculating the static size of an array |
| basedefinitions.h | Basic types and macros used throughout GROMACS |
| basenetwork.h | Utility functions for basic MPI and network functionality |
| baseversion.h | Declares functions to get basic version information |
| binaryinformation.h | Helper functionality for information about the currently running binary |
| bitmask.h | Declares gmx_bitmask_t and associated functions |
| classhelpers.h | Declares common utility classes and macros |
| compare.h | Utilities for comparing data structures (for gmx check) |
| coolstuff.h | Functionality for printing cool strings |
| 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 |
| dir_separator.h | Provides OS-specific directory-name separator |
| directoryenumerator.h | Declares gmx::DirectoryEnumerator |
| 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 |
| fileredirector.h | Declares gmx::IFileOutputRedirector |
| filestream.h | Declares implementations for textstream.h interfaces for file input/output |
| 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 |
| gmxmpi.h | Wraps mpi.h usage in Gromacs |
| gmxomp.h | Declares OpenMP wrappers to avoid conditional compilation |
| gmxregex.h | Declares simple wrapper for regular expression functionality |
| ikeyvaluetreeerror.h | Declares an error handling interface for key-value tree operations |
| init.h | Declares functions for initializing the GROMACS library |
| inmemoryserializer.h | Declares gmx::ISerializer implementation for in-memory serialization |
| 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 |
| iserializer.h | Declares a generic serialization interface that supports both directions |
| keyvaluetree.h | Declares a data structure for JSON-like structured key-value mapping |
| keyvaluetreebuilder.h | Declares classes for building the data structures in keyvaluetree.h |
| keyvaluetreeserializer.h | Declares serialization routines for KeyValueTree objects |
| keyvaluetreetransform.h | Declares utilities for transforming key-value trees |
| logger.h | Declares functionality for logging |
| loggerbuilder.h | Declares functionality for initializing logging |
| messagestringcollector.h | Declares gmx::MessageStringCollector |
| mutex.h | Declares C++11-style basic threading primitives (gmx::Mutex, gmx::lock_guard) |
| niceheader.h | Declares function for printing a nice header for text output files |
| nodelete.h | Declares no_delete deleter for std::shared_ptr |
| path.h | Declares functions for OS-independent path handling |
| pleasecite.h | Declares please_cite() for printing out literature references |
| programcontext.h | Declares gmx::IProgramContext and related methods |
| qsort_threadsafe.h | Portable implementation of threadsafe quicksort |
| real.h | Declares real and related constants |
| smalloc.h | C memory allocation routines for GROMACS |
| snprintf.h | Provide snprintf symbol on all OS (for internal Gromacs use) |
| strconvert.h | Declares common utility functions for conversions to and from strings |
| strdb.h | Declares C functions for reading files with a list of strings |
| stringcompare.h | Declares utility functionst for string comparison |
| stringstream.h | Declares implementations for textstream.h interfaces for input/output to in-memory strings |
| stringutil.h | Declares common string utility and formatting routines |
| sysinfo.h | Declares functions that wrap platform-specific calls for obtaining information about the operating environment and the current process |
| textreader.h | Declares gmx::TextReader |
| textstream.h | Declares interfaces for simple input/output streams |
| textwriter.h | Declares gmx::TextWriter |
| txtdump.h | Declares helper functions for dumping basic data structures as text |
| typetraits.h | Declares type traits |
| unique_cptr.h | Declares gmx::unique_cptr and gmx::sfree_guard |
| variant.h | Declares gmx::Variant |
| 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 |
| programs | Source code for building executables, see Wrapper binary implementation |
| mdrun | Source code specific to mdrun |
| runner.h | Declares the routine running the inetgrators |
 view | Source code specific to gmx view, including all X11-dependent code |
| testutils | Testing Utilities (testutils) |
| tests | Unit tests for Testing Utilities (testutils) |
| cmdlinetest.h | Declares utilities testing command-line programs |
| conftest.h | Declares function to add the content of a conf file to a checker |
| filematchers.h | Declares utility classes for testing file contents |
| interactivetest.h | Provides helper classes for testing interactive prompts |
| loggertest.h | Declares gmx::test::LoggerTestHelper |
| mpitest.h | Helper functions for MPI tests to make thread-MPI look like real MPI |
| refdata.h | Functionality for writing tests that can produce their own reference data |
| stdiohelper.h | Declares gmx::test::StdioTestHelper |
| stringtest.h | Declares gmx::test::StringTestBase |
| testasserts.h | Extra assertions for unit tests |
| testexceptions.h | Exception classes for errors in tests |
| testfilemanager.h | Declares gmx::test::TestFileManager |
| testfileredirector.h | Declares generic mock implementations for interfaces in fileredirector.h |
| testoptions.h | Functions for accessing test command-line options |
| textblockmatchers.h | Declares utility classes for testing multi-line strings against reference data |
| xvgtest.h | Declares function to add the content of an xvg file to a checker |
| gmxpre.h | Prerequisite header file for GROMACS build |
1.8.5
