  docs | Build system and source code for various documentation items |
  doxygen | Doxygen build system and general documentation content |
   directories.cpp | Doxygen documentation file for directories in the source tree |
 misc.cpp | Doxygen documentation file for group declarations etc |
| 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.cpp | Implements gmx::AnalysisDataAverageModule |
| average.h | Declares gmx::AnalysisDataAverageModule |
| displacement.cpp | Implements gmx::AnalysisDataDisplacementModule |
| displacement.h | Declares gmx::AnalysisDataDisplacementModule |
| frameaverager.cpp | Implements gmx::AnalysisDataFrameAverager |
| frameaverager.h | Declares gmx::AnalysisDataFrameAverager |
| histogram.cpp | Implements classes in histogram.h |
| histogram.h | Declares analysis data modules for calculating histograms |
| lifetime.cpp | Implements gmx::AnalysisDataLifetimeModule |
| lifetime.h | Declares gmx::AnalysisDataLifetimeModule |
| plot.cpp | Implements classes in plot.h |
| plot.h | Declares gmx::AnalysisDataPlotModule for plotting data (into a file) |
| tests | Unit tests for Parallelizable Handling of Output Data (analysisdata) |
| analysisdata.cpp | Tests for analysis data functionality |
| arraydata.cpp | Tests for gmx::AnalysisArrayData functionality |
| average.cpp | Tests for functionality of analysis data averaging modules |
| datatest.cpp | Implements classes in datatest.h |
| datatest.h | Helper classes for testing classes that derive from AbstractAnalysisData |
| histogram.cpp | Tests for functionality of analysis data histogram modules |
| lifetime.cpp | Tests for functionality of analysis data lifetime module |
| mock_datamodule.cpp | Implements classes in mock_datamodule.h |
| mock_datamodule.h | Declares mock implementation of gmx::IAnalysisDataModule |
| abstractdata.cpp | Implements gmx::AbstractAnalysisData |
| abstractdata.h | Declares gmx::AbstractAnalysisData |
| analysisdata.cpp | Implements classes in analysisdata.h |
| analysisdata.h | Declares gmx::AnalysisData and gmx::AnalysisDataHandle |
| arraydata.cpp | Implements classes in arraydata.h |
| arraydata.h | Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData |
| dataframe.cpp | Implements classes in dataframe.h |
| dataframe.h | Declares classes for accessing data frame information |
| datamodule.cpp | Implements classes from datamodule.h |
| datamodule.h | Declares gmx::IAnalysisDataModule and related convenience classes |
| datamodulemanager.cpp | Implements gmx::AnalysisDataModuleManager |
| datamodulemanager.h | Declares gmx::AnalysisDataModuleManager |
| dataproxy.cpp | Implements gmx::AnalysisDataProxy |
| dataproxy.h | Declares gmx::AnalysisDataProxy |
| datastorage.cpp | Implements classes in datastorage.h and paralleloptions.h |
| datastorage.h | Declares gmx::AnalysisDataStorage |
| framelocaldata.h | Defines gmx::AnalysisDataFrameLocalData and supporting types |
| paralleloptions.h | Declares gmx::AnalysisDataParallelOptions |
| commandline | Command Line Program Management (commandline) |
| tests | Unit tests for Command Line Program Management (commandline) |
| cmdlinehelpmodule.cpp | Tests gmx::CommandLineHelpModule through gmx::CommandLineModuleManager |
| cmdlinehelpwriter.cpp | Tests gmx::CommandLineHelpWriter |
| cmdlinemodulemanager.cpp | Tests gmx::CommandLineModuleManager |
| cmdlinemodulemanagertest.cpp | Implements classes from cmdlinemodulemanagertest.h |
| cmdlinemodulemanagertest.h | Test fixture and helper classes for tests using gmx::CommandLineModuleManager |
| cmdlineparser.cpp | Tests gmx::CommandLineParser |
| cmdlineprogramcontext.cpp | Tests for gmx::CommandLineProgramContext |
| pargs.cpp | Tests parse_common_args() |
| cmdlinehelpcontext.cpp | Implements gmx::CommandLineHelpContext |
| cmdlinehelpcontext.h | Declares gmx::CommandLineHelpContext |
| cmdlinehelpmodule.cpp | Implements gmx::CommandLineHelpModule |
| cmdlinehelpmodule.h | Declares gmx::CommandLineHelpModule |
| cmdlinehelpwriter.cpp | Implements gmx::CommandLineHelpWriter |
| cmdlinehelpwriter.h | Declares gmx::CommandLineHelpWriter |
| cmdlineinit.cpp | Implements functions from cmdlineinit.h |
| cmdlineinit.h | Declares functions for initializing the GROMACS library for command line use |
| cmdlinemodule.cpp | Implements classes from cmdlinemodule.h |
| cmdlinemodule.h | Declares gmx::ICommandLineModule and supporting classes |
| cmdlinemodulemanager-impl.h | Declares implementation types for gmx::CommandLineModuleManager |
| cmdlinemodulemanager.cpp | Implements gmx::CommandLineModuleManager |
| cmdlinemodulemanager.h | Declares gmx::CommandLineModuleManager |
| cmdlineoptionsmodule.cpp | Implements supporting routines for gmx::ICommandLineOptionsModule |
| cmdlineoptionsmodule.h | Declares gmx::ICommandLineOptionsModule and supporting routines |
| cmdlineparser.cpp | Implements gmx::CommandLineParser |
| cmdlineparser.h | Declares gmx::CommandLineParser |
| cmdlineprogramcontext.cpp | Implements gmx::CommandLineProgramContext |
| 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 |
| shellcompletions.cpp | Implements gmx::ShellCompletionWriter |
| shellcompletions.h | Declares gmx::ShellCompletionWriter |
| viewit.h | Provides function to open output files automatically (with some X11 programs) |
| correlationfunctions | |
| tests | |
| autocorr.cpp | Implements test of autocorrelation function routines |
| correlationdataset.cpp | Implements helper class for autocorrelation tests |
| correlationdataset.h | Declares helper class for autocorrelation tests |
| expfit.cpp | Implements test of exponential fitting routines |
| autocorr.cpp | Implements function to compute many autocorrelation functions |
| autocorr.h | Declares routine for computing autocorrelation functions |
| crosscorr.cpp | Implements routine for computing a cross correlation between two data sets |
| crosscorr.h | Declares routine for computing a cross correlation between two data sets |
| expfit.cpp | Implements routine for fitting a data set to a curve |
| expfit.h | Declares routine for fitting a data set to a curve |
| gmx_lmcurve.cpp | Defines a driver routine for lmfit, and a callback for it to use |
| gmx_lmcurve.h | Declares a driver routine for lmfit |
| integrate.h | Declares routines for integrating a data set |
| manyautocorrelation.cpp | Implements function to compute many autocorrelation functions |
| manyautocorrelation.h | Declares routine for computing many correlation functions using OpenMP |
| polynomials.cpp | Implements help function to compute Legendre polynomials |
| polynomials.h | Declares routine for computing a Legendre polynomial |
| domdec | |
| domdec.h | This file declares functions for mdrun to call to manage the details of its domain decomposition |
| domdec_box.cpp | This file defines functions used by the domdec module for (bounding) box and pbc information generation |
| domdec_constraints.cpp | This file implements functions for domdec to use while managing inter-atomic constraints |
| domdec_constraints.h | This file declares functions for domdec to use while managing inter-atomic constraints |
| domdec_internal.h | Declares implementation functions and types for the domain decomposition module |
| domdec_network.cpp | This file defines functions for (mostly) the domdec module to use MPI functionality |
| domdec_network.h | This file declares functions for (mostly) the domdec module to use MPI functionality |
| domdec_setup.cpp | This file defines functions used by the domdec module in its initial setup phase |
| domdec_specatomcomm.cpp | This file implements functions for domdec to use while managing inter-atomic constraints |
| domdec_specatomcomm.h | This file declares functions for domdec to use while managing communication of atoms required for special purposes |
| domdec_struct.h | Declares structures related to domain decomposition |
| domdec_topology.cpp | This file defines functions used by the domdec module while managing the construction, use and error checking for topologies local to a DD rank |
| domdec_vsite.cpp | This file implements functions for domdec to use while managing inter-atomic constraints |
| domdec_vsite.h | This file declares functions for domdec to use while managing virtual sites |
| ga2la.h | Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined |
| hash.h | This file declares functions for a simple hash map used by domain decomposition |
| essentialdynamics | |
| edsam.h | Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces |
| ewald | |
| ewald.cpp | This file contains function definitions 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 |
| 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-internal.h | This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
| pme-load-balancing.cpp | This file contains function definitions necessary for managing automatic load balance of PME calculations (Coulomb and LJ) |
| pme-load-balancing.h | This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ) |
| pme-pp.cpp | This file contains function definitions necessary for managing the offload of long-ranged PME work to separate MPI rank, for computing energies and forces (Coulomb and LJ) |
| pme.cpp | This file contains function definitions necessary for computing energies and forces for the PME long-ranged part (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 | |
| tests | |
| fft.cpp | Tests utilities for fft calculations |
| fft.h | Fast Fourier Transforms |
| fileio | |
| tests | |
| confio.cpp | Tests for reading/writing different structure file formats |
| readinp.cpp | Tests utilities for routines that parse fields e.g. from grompp input |
| tngio.cpp | Tests for file I/O routines |
| gmxfio-impl.h | Internal definitions shared by gmxfio*.c files |
| gmxana | |
| legacytests | |
| gmx_traj_tests.cpp | Tests for gmx traj |
| gmx_wham.cpp | Implementation of the Weighted Histogram Analysis Method (WHAM) |
| gmxpreprocess | |
 tests | |
| genconf.cpp | Tests for genconf |
| insert-molecules.cpp | Tests for insertion of molecules |
| solvate.cpp | Tests for solvation |
| gpu_utils | |
| gpu_utils.cpp | Stub functions for non-GPU builds |
| gpu_utils.h | Declare functions for detection and initialization for GPU devices |
| gpu_utils_ocl.cpp | Define functions for detection and initialization for OpenCL devices |
| ocl_caching.cpp | Define infrastructure for OpenCL JIT compilation for Gromacs |
| ocl_caching.h | Declare infrastructure for managing caching of OpenCL JIT-ted binaries |
| ocl_compiler.cpp | Define infrastructure for OpenCL JIT compilation for Gromacs |
| ocl_compiler.h | Declare infrastructure for OpenCL JIT compilation |
| oclutils.cpp | Define utility routines for OpenCL |
| oclutils.h | Declare utility routines for OpenCL |
| pmalloc_cuda.h | Declare functions for host-side memory handling when using CUDA devices |
| hardware | |
| tests | |
| cpuinfo.cpp | Tests for gmx::CpuInfo |
| hardwaretopology.cpp | Tests for gmx::HardwareTopology |
| cpuinfo.cpp | Implements gmx::CpuInfo |
| cpuinfo.h | Declares gmx::CpuInfo |
| hardwaretopology.cpp | Implements gmx::HardwareTopology |
| hardwaretopology.h | Declares gmx::HardwareTopology |
| imd | |
| imd.cpp | Implements functions of imd.h |
| imd.h | This file contains datatypes and function declarations necessary for mdrun to interface with VMD via the interactive molecular dynamics protocol |
| imdsocket.cpp | Implements functions of imdsocket.h |
| imdsocket.h | Implements the parts of the vmdsock.h interface needed for IMD communication |
| linearalgebra | |
| gmx_arpack.h | Selected routines from ARPACK |
| gmx_blas.h | Header definitions for the standard BLAS library |
| gmx_lapack.h | Header definitions for the standard LAPACK library |
| listed-forces | |
| bonded.cpp | This file defines low-level functions necessary for computing energies and forces for listed interactions |
| 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.cpp | This file defines high-level functions for mdrun to compute energies and forces for listed interactions |
| listed-forces.h | This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions |
| listed-internal.cpp | This file defines functions needed internally by the module |
| listed-internal.h | This file contains declarations for functions needed internally by the module |
| manage-threading.cpp | This file defines functions for managing threading of listed interactions |
| manage-threading.h | Declares functions for managing threading of listed forces |
| orires.h | Declares functions for handling orientation restraints |
| pairs.cpp | This file defines functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions) |
| pairs.h | This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions) |
| position-restraints.cpp | This file defines low-level functions necessary for computing energies and forces for position restraints |
| position-restraints.h | This file contains declarations necessary for low-level functions for computing energies and forces for position restraints |
| restcbt.cpp | This file contains function definitions necessary for computations of forces due to restricted angle, restricted dihedral and combined bending-torsion potentials |
| restcbt.h | This file contains function declarations necessary for computations of forces due to restricted angle, restricted dihedral and combined bending-torsion potentials |
| math | |
| tests | |
| functions.cpp | Tests for simple math functions |
| invertmatrix.cpp | Tests matrix inversion routines |
| vectypes.cpp | Tests various corners of gmx::RVec implementation |
| calculate-ewald-splitting-coefficient.h | Declares functions for computing Ewald splitting coefficients |
| functions.cpp | Implements simple math functions |
| functions.h | Declares simple math functions |
| invertmatrix.cpp | Routines to invert 3x3 matrices |
| invertmatrix.h | Declares routines to invert 3x3 matrices |
| mdlib | |
| nbnxn_cuda | |
| nbnxn_cuda_types.h | Data types used internally in the nbnxn_cuda module |
| nbnxn_ocl | |
| nbnxn_ocl.cpp | Define OpenCL implementation of nbnxn_gpu.h |
| nbnxn_ocl_data_mgmt.cpp | Define OpenCL implementation of nbnxn_gpu_data_mgmt.h |
| nbnxn_ocl_internal.h | Internal API of the OpenCL non-bonded module |
| nbnxn_ocl_jit_support.cpp | Defines functions that support JIT compilation (e.g. for OpenCL) |
| nbnxn_ocl_types.h | Data types used internally in the nbnxn_ocl module |
| tests | |
| simulationsignal.cpp | Tests for the mdrun signalling functionality |
| groupcoord.h | Assemble atomic positions of a (small) subset of atoms and distribute to all nodes |
| minimize.cpp | This file defines integrators for energy minimization |
| nbnxn_gpu.h | Declare interface for GPU execution for NBNXN module |
| nbnxn_gpu_data_mgmt.h | Declare interface for GPU data transfer for NBNXN module |
| nbnxn_gpu_jit_support.h | Declares functions that support JIT compilation (e.g. for OpenCL) |
| simulationsignal.cpp | This file defines functions for inter- and intra-simulation signalling by mdrun |
| simulationsignal.h | This file declares functions for inter-rank signalling by mdrun |
| tpi.cpp | This file defines the integrator for test particle insertion |
| mdrunutility | |
| handlerestart.cpp | This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files) |
| handlerestart.h | This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files) |
| threadaffinity.h | Declares functions for managing mdrun thread affinity |
| mdtypes | |
| md_enums.h | Declares enumerated types used throughout the code |
| pull-params.h | This file contains datatypes for the mdp options used by the pull code |
| onlinehelp | Help Formatting for Online Help (onlinehelp) |
| tests | Unit tests for Help Formatting for Online Help (onlinehelp) |
| helpformat.cpp | Tests for help string formatting functions and classes |
| helpmanager.cpp | Tests for help topic management and help topic formatting |
| helpwritercontext.cpp | Tests for help text formatting |
| mock_helptopic.cpp | Implements classes in mock_helptopic.h |
| mock_helptopic.h | Declares mock implementation of gmx::IHelpTopic |
| helpformat.cpp | Implements functions in helpformat.h |
| helpformat.h | Declares common string formatting routines for online help |
| helpmanager.cpp | Implements gmx::HelpManager |
| helpmanager.h | Declares gmx::HelpManager |
| helptopic.cpp | Implements classes and functions from helptopic.h |
| helptopic.h | Declares helper classes for implementing gmx::IHelpTopic |
| helpwritercontext.cpp | Implements gmx::HelpWriterContext |
| helpwritercontext.h | Declares gmx::HelpWriterContext |
| ihelptopic.h | Declares gmx::IHelpTopic |
| rstparser.cpp | Implements classes from rstparser.h |
| rstparser.h | Declares classes for (partial) parsing of reStructuredText |
| options | Extensible Handling of Options (options) |
| tests | Unit tests for Extensible Handling of Options (options) |
| abstractoptionstorage.cpp | Tests proper handling of option storage |
| filenameoption.cpp | Tests basic file name option implementation |
| filenameoptionmanager.cpp | Tests file name option implementation dependent on gmx::FileNameOptionManager |
| option.cpp | Tests creation of basic option types |
| optionsassigner.cpp | Tests option assignment |
| timeunitmanager.cpp | Tests handling of time units with gmx::TimeUnitManager and gmx::TimeUnitBehavior |
| abstractoption.cpp | Implements classes in abstractoption.h and abstractoptionstorage.h |
| abstractoption.h | Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo |
| abstractoptionstorage.h | Declares gmx::AbstractOptionStorage |
| basicoptions.cpp | Implements classes in basicoptions.h and basicoptionstorage.h |
| basicoptions.h | Declares option objects for basic option types |
| basicoptionstorage.h | Declares storage classes for basic option types |
| behaviorcollection.cpp | Implements gmx::OptionsBehaviorCollection |
| behaviorcollection.h | Declares gmx::OptionsBehaviorCollection |
| filenameoption.cpp | Implements classes in filenameoption.h and filenameoptionstorage.h |
| filenameoption.h | Declares gmx::FileNameOption and gmx::FileNameOptionInfo |
| filenameoptionmanager.cpp | Implements gmx::FileNameOptionManager |
| filenameoptionmanager.h | Declares gmx::FileNameOptionManager |
| filenameoptionstorage.h | Declares gmx::FileNameOptionStorage |
| ioptionsbehavior.h | Declares gmx::IOptionsBehavior |
| ioptionscontainer.h | Declares gmx::IOptionsContainer |
| 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-impl.h | Declares private implementation class for gmx::Options |
| options.cpp | Implements gmx::Options |
| options.h | Declares gmx::Options |
| optionsassigner.cpp | Implements gmx::OptionsAssigner |
| optionsassigner.h | Declares gmx::OptionsAssigner |
| optionstoragetemplate.h | Defines gmx::OptionStorageTemplate template |
| optionsvisitor.cpp | Implements classes in optionsvisitor.h |
| optionsvisitor.h | Declares gmx::OptionsVisitor interface and supporting classes |
| timeunitmanager.cpp | Implements gmx::TimeUnitManager |
| timeunitmanager.h | Declares gmx::TimeUnitManager |
| pbcutil | |
| boxutilities.cpp | Implements routines in boxutilities.h |
| pbc-simd.cpp | This file defines a low-level function for SIMD PBC calculation |
| pbc-simd.h | This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations |
| pbc.cpp | Implements routines in pbc.h |
| pulling | |
| tests | |
| pull.cpp | Implements test of some pulling routines |
| 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 | |
| tests | |
| exponentialdistribution.cpp | Tests for GROMACS exponential distribution |
| gammadistribution.cpp | Tests for GROMACS gamma distribution |
| normaldistribution.cpp | Tests for GROMACS normal distribution |
| seed.cpp | Tests for random seed functions |
| tabulatednormaldistribution.cpp | Tests for GROMACS tabulated normal distribution |
| threefry.cpp | Tests for the ThreeFry random engine |
| uniformintdistribution.cpp | Tests for GROMACS uniform integer distribution |
| uniformrealdistribution.cpp | Tests for GROMACS uniform real distribution |
| 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.cpp | Tests the index group handling in the selection engine |
| nbsearch.cpp | Tests selection neighborhood searching |
| poscalc.cpp | Tests the position mapping engine |
| selectioncollection.cpp | Tests selection parsing and compilation |
| selectionoption.cpp | Tests handling of selection options |
| toputils.cpp | Implements test helper routines from toputils.h |
| toputils.h | Helper routines for constructing topologies for tests |
| centerofmass.cpp | Implements functions in centerofmass.h |
| centerofmass.h | API for calculation of centers of mass/geometry |
| compiler.cpp | Selection compilation and optimization |
| compiler.h | Declares gmx::SelectionCompiler |
| evaluate.cpp | Implements functions in evaluate.h |
| evaluate.h | Evaluation functions for sel_evalfunc() |
| indexutil.cpp | Implements functions in indexutil.h |
| indexutil.h | API for handling index files and index groups |
| keywords.h | Definitions of generic keyword evaluation structures |
| mempool.cpp | Implements functions in mempool.h |
| mempool.h | Declarations for memory pooling functions |
| nbsearch.cpp | Implements neighborhood searching for analysis (from nbsearch.h) |
| nbsearch.h | API for neighborhood searching for analysis |
| params.cpp | Implements functions in selparam.h |
| parser_internal.h | Helper functions for the selection parser |
| parsetree.cpp | Implements functions in parsetree.h |
| parsetree.h | Handling of intermediate selection parser data |
| poscalc.cpp | Implements gmx::PositionCalculationCollection and functions in poscalc.h |
| poscalc.h | API for structured and optimized calculation of positions |
| position.cpp | Implements functions in position.h |
| position.h | API for handling positions |
| scanner.h | Parser/scanner interaction functions |
| scanner_internal.cpp | Helper functions for the selection tokenizer |
| scanner_internal.h | Internal header file used by the selection tokenizer |
| selection.cpp | Implements classes in selection.h |
| selection.h | Declares gmx::Selection and supporting classes |
| selectioncollection-impl.h | Declares private implementation class for gmx::SelectionCollection |
| selectioncollection.cpp | Implements gmx::SelectionCollection |
| selectioncollection.h | Declares gmx::SelectionCollection |
| selectionenums.h | Declares common types used in selections |
| selectionfileoption.h | Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo |
| selectionfileoptionstorage.h | Declares gmx::SelectionFileOptionStorage |
| selectionoption.cpp | Implements classes in selectionoption.h and selectionoptionstorage.h |
| selectionoption.h | Declares gmx::SelectionOption and gmx::SelectionOptionInfo |
| selectionoptionbehavior.cpp | Implements gmx::SelectionOptionBehavior |
| selectionoptionbehavior.h | Declares gmx::SelectionOptionBehavior |
| selectionoptionmanager.cpp | Implements gmx::SelectionOptionManager |
| selectionoptionmanager.h | Declares gmx::SelectionOptionManager |
| selectionoptionstorage.h | Declares gmx::SelectionOptionStorage |
| selelem.cpp | Implements functions in selelem.h |
| selelem.h | Declares gmx::SelectionTreeElement and related things |
| selhelp.cpp | Implements functions in selhelp.h |
| selhelp.h | Functions for initializing online help for selections |
| selmethod.cpp | Implements functions in selmethod.h |
| selmethod.h | API for handling selection methods |
| selparam.h | API for handling parameters used in selections |
| selvalue.cpp | Implements functions in selvalue.h |
| selvalue.h | Declares gmx_ana_selvalue_t |
| sm_compare.cpp | Implements internal selection method for comparison expressions |
| sm_distance.cpp | Implements distance-based selection methods |
| sm_insolidangle.cpp | Implements the insolidangle selection method |
| sm_keywords.cpp | Implements internal selection methods for numeric and string keyword evaluation |
| sm_merge.cpp | Implements the merge and plus selection modifiers |
| sm_permute.cpp | Implements the permute selection modifier |
| sm_position.cpp | Implements position evaluation selection methods |
| sm_same.cpp | Implements the same selection method |
| sm_simple.cpp | Implements simple keyword selection methods |
| symrec.cpp | Implements classes in symrec.h |
| symrec.h | Handling of selection parser symbol table |
| 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) |
| base.h | Declares common base class for testing SIMD and SIMD4 |
| bootstrap_loadstore.cpp | Separate test of SIMD load/store, before we use them in the SIMD test classes |
| simd.h | Declares fixture for testing of normal SIMD (not SIMD4) functionality |
| simd4.h | Declares fixture for testing of SIMD4 functionality |
| simd.h | Definitions, capabilities, and wrappers for SIMD module |
| simd_math.h | Math functions for SIMD datatypes |
| support.cpp | Implements SIMD architecture support query routines |
| 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.cpp | Implements functions in swapcoords.h |
| swapcoords.h | The "Computational Electrophysiology" protocol for ion/water position swapping |
| timing | |
| cyclecounter.h | High-resolution timestamp or CPU clock cycle counters |
| gpu_timing.h | Declares data types for GPU timing |
| topology | |
| atomsbuilder.cpp | Implements classes from atomsbuilder.h |
| atomsbuilder.h | Utility classes for manipulating t_atoms structures |
| trajectoryanalysis | Framework for Trajectory Analysis (trajectoryanalysis) |
| modules | |
| angle.cpp | Implements gmx::analysismodules::Angle |
| angle.h | Declares trajectory analysis module for angle calculations |
| distance.cpp | Implements gmx::analysismodules::Distance |
| distance.h | Declares trajectory analysis module for distance calculations |
| freevolume.cpp | Implements gmx::analysismodules::Freevolume |
| freevolume.h | Declares trajectory analysis module for free volume calculations |
| pairdist.cpp | Implements gmx::analysismodules::PairDistance |
| pairdist.h | Declares trajectory analysis module for pairwise distance calculations |
| rdf.cpp | Implements gmx::analysismodules::Rdf |
| rdf.h | Declares trajectory analysis module for RDF calculations |
| sasa.cpp | Implements gmx::analysismodules::Sasa |
| sasa.h | Declares trajectory analysis module for surface area calculations |
| select.cpp | Implements gmx::analysismodules::Select |
| select.h | Declares trajectory analysis module for basic selection information |
| tests | Unit tests for Framework for Trajectory Analysis (trajectoryanalysis) |
| angle.cpp | Tests for functionality of the "angle" trajectory analysis module |
| cmdlinerunner.cpp | Tests for general functionality in gmx::TrajectoryAnalysisCommandLineRunner |
| distance.cpp | Tests for functionality of the "distance" trajectory analysis module |
| freevolume.cpp | Tests for functionality of the "angle" trajectory analysis module |
| moduletest.cpp | Implements classes in moduletest.h |
| moduletest.h | Declares test fixture for TrajectoryAnalysisModule subclasses |
| pairdist.cpp | Tests for functionality of the "pairdist" trajectory analysis module |
| rdf.cpp | Tests for functionality of the "rdf" trajectory analysis module |
| sasa.cpp | Tests for functionality of the "sasa" trajectory analysis module |
| select.cpp | Tests for functionality of the "select" trajectory analysis module |
| surfacearea.cpp | Tests for the surface area calculation used by the sasa analysis module |
| test_selection.cpp | Testing/debugging tool for the selection engine |
| analysismodule.cpp | Implements classes in analysismodule.h |
| analysismodule.h | Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData |
| analysissettings-impl.h | Declares private implementation class for gmx::TrajectoryAnalysisSettings |
| analysissettings.cpp | Implements classes in analysissettings.h |
| analysissettings.h | Declares gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation |
| cmdlinerunner.cpp | Implements gmx::TrajectoryAnalysisCommandLineRunner |
| cmdlinerunner.h | Declares gmx::TrajectoryAnalysisCommandLineRunner |
| modules.cpp | Implements registerTrajectoryAnalysisModules() |
| modules.h | Generic interface for accessing trajectory analysis modules |
| runnercommon.cpp | Implements gmx::TrajectoryAnalysisRunnerCommon |
| runnercommon.h | Declares gmx::TrajectoryAnalysisRunnerCommon |
| utility | Low-Level Utilities (utility) |
| tests | Unit tests for Low-Level Utilities (utility) |
| alignedallocator.cpp | Tests for gmx::AlignedAllocator |
| arrayref.cpp | Tests for gmx::ArrayRef and gmx::ConstArrayRef |
| basedefinitions.cpp | Tests for base definitions (only alignment attributes for now) |
| bitmask.h | Tests for bitmask functionality |
| path.cpp | Tests for (some) functions in path.h |
| stringutil.cpp | Tests for string utility functions and classes |
| textwriter.cpp | Tests for gmx::TextWriter |
| alignedallocator.cpp | Implements AlignedAllocator |
| alignedallocator.h | Declares gmx::AlignedAllocator that is used to make standard library containers compatible with SIMD contents that require aligned load/store |
| arrayref.h | Declares gmx::ArrayRef and gmx::ConstArrayRef |
| 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-gen.h | Declares variables that hold generated version information |
| baseversion.h | Declares functions to get basic version information |
| binaryinformation.cpp | Implements functionality for printing information about the currently running binary |
| 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 |
| coolstuff.cpp | Functionality for printing cool strings |
| 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.cpp | Implements gmx::DataFileFinder |
| datafilefinder.h | Declares gmx::DataFileFinder and related classes |
| dir_separator.h | Provides OS-specific directory-name separator |
| directoryenumerator.cpp | Implements gmx::DirectoryEnumerator |
| directoryenumerator.h | Declares gmx::DirectoryEnumerator |
| errorcodes.cpp | Implements functions in errorcodes.h |
| errorcodes.h | Declares error codes and related functions for fatal error handling |
| errorformat.cpp | Implements functions declared in errorformat.h |
| errorformat.h | Declares an internal helper function for formatting standard error messages |
| exceptions.cpp | Implements classes and functions in exceptions.h |
| 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.cpp | Implements classes and functions from fileredirector.h |
| fileredirector.h | Declares gmx::IFileOutputRedirector |
| filestream.cpp | Implements classes from filestream.h |
| 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.cpp | Implements assertion handlers |
| gmxassert.h | Defines assert macros customized for Gromacs |
| gmxmpi.h | Wraps <mpi.h> usage in Gromacs |
| gmxomp.cpp | Implements functions from gmxomp.h |
| gmxomp.h | Declares OpenMP wrappers to avoid conditional compilation |
| gmxregex.cpp | Implements regular expression wrappers |
| gmxregex.h | Declares simple wrapper for regular expression functionality |
| init.cpp | Implements functions from init.h |
| init.h | Declares functions for initializing the GROMACS library |
| 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 |
| messagestringcollector.cpp | Implements gmx::MessageStringCollector |
| messagestringcollector.h | Declares gmx::MessageStringCollector |
| mutex.h | Declares C++11-style basic threading primitives (gmx::Mutex, gmx::lock_guard) |
| nodelete.h | Declares no_delete deleter for std::shared_ptr |
| path.cpp | Implements functions in path.h |
| path.h | Declares functions for OS-independent path handling |
| pleasecite.h | Declares please_cite() for printing out literature references |
| programcontext.cpp | Implements gmx::IProgramContext and related methods |
| programcontext.h | Declares gmx::IProgramContext and related methods |
| qsort_threadsafe.h | Portable implementation of threadsafe quicksort |
| real.h | Declares real and related constants |
| scoped_cptr.h | Declares gmx::scoped_cptr and gmx::scoped_guard_sfree |
| smalloc.h | C memory allocation routines for GROMACS |
| snprintf.h | Provide snprintf symbol on all OS (for internal Gromacs use) |
| strdb.h | Declares C functions for reading files with a list of strings |
| stringstream.cpp | Implements classes from stringstream.h |
| stringstream.h | Declares implementations for textstream.h interfaces for input/output to in-memory strings |
| stringutil.cpp | Implements functions and classes in stringutil.h |
| stringutil.h | Declares common string utility and formatting routines |
| sysinfo.cpp | Implements functions from sysinfo.h |
| sysinfo.h | Declares functions for obtaining information about the operating environment and the current process |
| textreader.cpp | Implements gmx::TextReader |
| textreader.h | Declares gmx::TextReader |
| textstream.h | Declares interfaces for simple input/output streams |
| textwriter.cpp | Implements gmx::TextWriter |
| textwriter.h | Declares gmx::TextWriter |
| txtdump.h | Declares helper functions for dumping basic data structures as text |
| analysisdata.h | Public API convenience header for analysis data handling |
| commandline.h | Public API convenience header for managing command line programs |
| onlinehelp-doc.h | Dummy header for Help Formatting for Online Help (onlinehelp) documentation |
| 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 |
| tests | |
| compressed_x_output.cpp | Tests for the mdrun -x functionality |
| domain_decomposition.cpp | Tests special cases in domain decomposition |
| energyreader.cpp | Implementions of related classes for tests that want to inspect energies produced by mdrun |
| energyreader.h | Interfaces of related classes for tests that want to inspect energies produced by mdrun |
| grompp.cpp | Tests for basic grompp functionality |
| interactiveMD.cpp | Tests utilities for interactive molecular dynamics (IMD) setups |
| mdruncomparisonfixture.cpp | Implements classes in mdruncomparisonfixture.h |
| moduletest.cpp | Implements classes in moduletest.h |
| moduletest.h | Declares test fixtures for general mdrun functionality |
| multisim.cpp | Tests for the mdrun multi-simulation functionality |
| multisimtest.cpp | Tests for the mdrun multi-simulation functionality |
| multisimtest.h | Declares test fixture for the mdrun multi-simulation functionality |
| replicaexchange.cpp | Tests for the mdrun replica-exchange functionality |
| rerun.cpp | Tests for the mdrun -rerun functionality |
| swapcoords.cpp | Tests utilities for "Computational Electrophysiology" setups |
| tabulated_bonded_interactions.cpp | Tests for tabulated bonded interactions |
| termination.cpp | Tests for the mdrun termination functionality |
| terminationhelper.cpp | Defines functionality used to test mdrun termination functionality under different conditions |
| terminationhelper.h | Declares functionality used to test mdrun termination functionality under different conditions |
| trajectory_writing.cpp | Tests for the .mdp nst*out functionality |
| trajectoryreader.cpp | Implementions of related classes for tests that want to inspect trajectories produced by mdrun |
| trajectoryreader.h | Declares interface of a class for tests that want to inspect trajectories produced by mdrun |
| md.h | Declares the integrators for molecular dynamics simulations |
| mdrun.cpp | This file implements mdrun |
| runner.cpp | Implements the MD runner routine calling all integrators |
| 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) |
| interactivetest.cpp | Self-tests for interactive test helpers |
| refdata_tests.cpp | Tests utilities for test reference data |
| testasserts_tests.cpp | Tests GROMACS-specific test assertions |
| xvgtest_tests.cpp | Tests utilities for testing xvg files |
| cmdlinetest.cpp | Implements classes from cmdlinetest.h |
| cmdlinetest.h | Declares utilities testing command-line programs |
| conftest.cpp | Implements routine to check the content of conf files |
| conftest.h | Declares function to add the content of a conf file to a checker |
| integrationtests.cpp | Implements classes in integrationtests.h |
| integrationtests.h | Declares test fixture for integration tests |
| interactivetest.cpp | Implements classes from interactivetest.h |
| interactivetest.h | Provides helper classes for testing interactive prompts |
| mpi-printer.h | Declares gmx::test::initMPIOutput() |
| refdata-checkers.h | Declares internal helper classes for the reference data framework to check reference data values of different types |
| refdata-impl.h | Declares internal data structures for the reference data framework |
| refdata-xml.cpp | Implements reference data XML persistence |
| refdata-xml.h | Declares functions for reference data XML persistence |
| refdata.cpp | Implements classes and functions from refdata.h |
| refdata.h | Functionality for writing tests that can produce their own reference data |
| stringtest.cpp | Implements gmx::test::StringTestBase |
| stringtest.h | Declares gmx::test::StringTestBase |
| testasserts.cpp | Implements floating-point comparison routines from testasserts.h |
| testasserts.h | Extra assertions for unit tests |
| testexceptions.h | Exception classes for errors in tests |
| testfilemanager.cpp | Implements gmx::test::TestFileManager |
| testfilemanager.h | Declares gmx::test::TestFileManager |
| testfileredirector.cpp | Implements classes from testfileredirector.h |
| testfileredirector.h | Declares generic mock implementations for interfaces in fileredirector.h |
| testinit.cpp | Implements functions in testinit.h |
| testinit.h | Functions for initialing GROMACS unit test executables |
| testoptions.cpp | Implements functions in testoptions.h |
| testoptions.h | Functions for accessing test command-line options |
| testutils-doc.h | Dummy header for Testing Utilities (testutils) documentation |
| textblockmatchers.cpp | Implements classes from textblockmatchers.h |
| textblockmatchers.h | Declares utility classes for testing multi-line strings against reference data |
| unittest_main.cpp | Main() for unit tests that use Testing Utilities (testutils) |
| xvgtest.cpp | Implements routine to check the content of xvg files |
| 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
