![o](ftv2mnode.png) docs | Build system and source code for various documentation items |
![|](ftv2vertline.png) ![\](ftv2mlastnode.png) doxygen | Doxygen build system and general documentation content |
![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) directories.cpp | Doxygen documentation file for directories in the source tree |
![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) misc.cpp | Doxygen documentation file for group declarations etc |
![o](ftv2mnode.png) share | Directory that contains installed data files |
![|](ftv2vertline.png) ![\](ftv2mlastnode.png) template | Template code for writing analysis programs |
![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) template.cpp | Template code for writing analysis programs |
![\](ftv2mlastnode.png) src | Main source code directory |
![](ftv2blank.png) ![o](ftv2mnode.png) gromacs | Source code for building the libgromacs library |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) analysisdata | Parallelizable Handling of Output Data (analysisdata) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) modules | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) average.cpp | Implements gmx::AnalysisDataAverageModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) average.h | Declares gmx::AnalysisDataAverageModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) displacement.cpp | Implements gmx::AnalysisDataDisplacementModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) displacement.h | Declares gmx::AnalysisDataDisplacementModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) frameaverager.cpp | Implements gmx::AnalysisDataFrameAverager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) frameaverager.h | Declares gmx::AnalysisDataFrameAverager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) histogram.cpp | Implements classes in histogram.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) histogram.h | Declares analysis data modules for calculating histograms |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) lifetime.cpp | Implements gmx::AnalysisDataLifetimeModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) lifetime.h | Declares gmx::AnalysisDataLifetimeModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) plot.cpp | Implements classes in plot.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) plot.h | Declares gmx::AnalysisDataPlotModule for plotting data (into a file) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Parallelizable Handling of Output Data (analysisdata) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysisdata.cpp | Tests for analysis data functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) arraydata.cpp | Tests for gmx::AnalysisArrayData functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) average.cpp | Tests for functionality of analysis data averaging modules |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datatest.cpp | Implements classes in datatest.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datatest.h | Helper classes for testing classes that derive from AbstractAnalysisData |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) histogram.cpp | Tests for functionality of analysis data histogram modules |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) lifetime.cpp | Tests for functionality of analysis data lifetime module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mock_datamodule.cpp | Implements classes in mock_datamodule.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) mock_datamodule.h | Declares mock implementation of gmx::IAnalysisDataModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) abstractdata.cpp | Implements gmx::AbstractAnalysisData |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) abstractdata.h | Declares gmx::AbstractAnalysisData |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysisdata.cpp | Implements classes in analysisdata.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysisdata.h | Declares gmx::AnalysisData and gmx::AnalysisDataHandle |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) arraydata.cpp | Implements classes in arraydata.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) arraydata.h | Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) dataframe.cpp | Implements classes in dataframe.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) dataframe.h | Declares classes for accessing data frame information |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datamodule.cpp | Implements classes from datamodule.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datamodule.h | Declares gmx::IAnalysisDataModule and related convenience classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datamodulemanager.cpp | Implements gmx::AnalysisDataModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datamodulemanager.h | Declares gmx::AnalysisDataModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) dataproxy.cpp | Implements gmx::AnalysisDataProxy |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) dataproxy.h | Declares gmx::AnalysisDataProxy |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datastorage.cpp | Implements classes in datastorage.h and paralleloptions.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datastorage.h | Declares gmx::AnalysisDataStorage |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) framelocaldata.h | Defines gmx::AnalysisDataFrameLocalData and supporting types |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) paralleloptions.h | Declares gmx::AnalysisDataParallelOptions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) commandline | Command Line Program Management (commandline) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Command Line Program Management (commandline) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpmodule.cpp | Tests gmx::CommandLineHelpModule through gmx::CommandLineModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpwriter.cpp | Tests gmx::CommandLineHelpWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodulemanager.cpp | Tests gmx::CommandLineModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodulemanagertest.cpp | Implements classes from cmdlinemodulemanagertest.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodulemanagertest.h | Test fixture and helper classes for tests using gmx::CommandLineModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineparser.cpp | Tests gmx::CommandLineParser |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineprogramcontext.cpp | Tests for gmx::CommandLineProgramContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pargs.cpp | Tests parse_common_args() |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpcontext.cpp | Implements gmx::CommandLineHelpContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpcontext.h | Declares gmx::CommandLineHelpContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpmodule.cpp | Implements gmx::CommandLineHelpModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpmodule.h | Declares gmx::CommandLineHelpModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpwriter.cpp | Implements gmx::CommandLineHelpWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinehelpwriter.h | Declares gmx::CommandLineHelpWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineinit.cpp | Implements functions from cmdlineinit.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineinit.h | Declares functions for initializing the GROMACS library for command line use |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodule.cpp | Implements classes from cmdlinemodule.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodule.h | Declares gmx::ICommandLineModule and supporting classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodulemanager-impl.h | Declares implementation types for gmx::CommandLineModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodulemanager.cpp | Implements gmx::CommandLineModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinemodulemanager.h | Declares gmx::CommandLineModuleManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineoptionsmodule.cpp | Implements supporting routines for gmx::ICommandLineOptionsModule |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineoptionsmodule.h | Declares gmx::ICommandLineOptionsModule and supporting routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineparser.cpp | Implements gmx::CommandLineParser |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineparser.h | Declares gmx::CommandLineParser |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineprogramcontext.cpp | Implements gmx::CommandLineProgramContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlineprogramcontext.h | Declares gmx::CommandLineProgramContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenm.h | Declares t_filenm for old-style command-line parsing of file name options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pargs.h | Declares t_pargs , parse_common_args() and related methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) shellcompletions.cpp | Implements gmx::ShellCompletionWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) shellcompletions.h | Declares gmx::ShellCompletionWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) viewit.h | Provides function to open output files automatically (with some X11 programs) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) correlationfunctions | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) autocorr.cpp | Implements test of autocorrelation function routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) correlationdataset.cpp | Implements helper class for autocorrelation tests |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) correlationdataset.h | Declares helper class for autocorrelation tests |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) expfit.cpp | Implements test of exponential fitting routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) autocorr.cpp | Implements function to compute many autocorrelation functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) autocorr.h | Declares routine for computing autocorrelation functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) crosscorr.cpp | Implements routine for computing a cross correlation between two data sets |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) crosscorr.h | Declares routine for computing a cross correlation between two data sets |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) expfit.cpp | Implements routine for fitting a data set to a curve |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) expfit.h | Declares routine for fitting a data set to a curve |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmx_lmcurve.cpp | Defines a driver routine for lmfit, and a callback for it to use |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmx_lmcurve.h | Declares a driver routine for lmfit |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) integrate.h | Declares routines for integrating a data set |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) manyautocorrelation.cpp | Implements function to compute many autocorrelation functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) manyautocorrelation.h | Declares routine for computing many correlation functions using OpenMP |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) polynomials.cpp | Implements help function to compute Legendre polynomials |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) polynomials.h | Declares routine for computing a Legendre polynomial |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) domdec | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec.h | This file declares functions for mdrun to call to manage the details of its domain decomposition |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_box.cpp | This file defines functions used by the domdec module for (bounding) box and pbc information generation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_constraints.cpp | This file implements functions for domdec to use while managing inter-atomic constraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_constraints.h | This file declares functions for domdec to use while managing inter-atomic constraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_internal.h | Declares implementation functions and types for the domain decomposition module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_network.cpp | This file defines functions for (mostly) the domdec module to use MPI functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_network.h | This file declares functions for (mostly) the domdec module to use MPI functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_setup.cpp | This file defines functions used by the domdec module in its initial setup phase |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_specatomcomm.cpp | This file implements functions for domdec to use while managing inter-atomic constraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_specatomcomm.h | This file declares functions for domdec to use while managing communication of atoms required for special purposes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_struct.h | Declares structures related to domain decomposition |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_vsite.cpp | This file implements functions for domdec to use while managing inter-atomic constraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domdec_vsite.h | This file declares functions for domdec to use while managing virtual sites |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ga2la.h | Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) hash.h | This file declares functions for a simple hash map used by domain decomposition |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) essentialdynamics | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) edsam.h | Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) ewald | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) long-range-correction.h | This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pme-internal.h | This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pme-load-balancing.cpp | This file contains function definitions necessary for managing automatic load balance of PME calculations (Coulomb and LJ) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pme-load-balancing.h | This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pme.cpp | This file contains function definitions necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pme.h | This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) fft | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) fft.cpp | Tests utilities for fft calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) fft.h | Fast Fourier Transforms |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) fileio | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) confio.cpp | Tests for reading/writing different structure file formats |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) readinp.cpp | Tests utilities for routines that parse fields e.g. from grompp input |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) tngio.cpp | Tests for file I/O routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) gmxfio-impl.h | Internal definitions shared by gmxfio*.c files |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) gmxana | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) legacytests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) gmx_traj_tests.cpp | Tests for gmx traj |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) gmx_wham.cpp | Implementation of the Weighted Histogram Analysis Method (WHAM) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) gmxpreprocess | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) genconf.cpp | Tests for genconf |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![o](ftv2node.png) insert-molecules.cpp | Tests for insertion of molecules |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![](ftv2blank.png) ![\](ftv2lastnode.png) solvate.cpp | Tests for solvation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) gpu_utils | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gpu_utils.cpp | Stub functions for non-GPU builds |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gpu_utils.h | Declare functions for detection and initialization for GPU devices |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gpu_utils_ocl.cpp | Define functions for detection and initialization for OpenCL devices |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ocl_caching.cpp | Define infrastructure for OpenCL JIT compilation for Gromacs |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ocl_caching.h | Declare infrastructure for managing caching of OpenCL JIT-ted binaries |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ocl_compiler.cpp | Define infrastructure for OpenCL JIT compilation for Gromacs |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ocl_compiler.h | Declare infrastructure for OpenCL JIT compilation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) oclutils.cpp | Define utility routines for OpenCL |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) oclutils.h | Declare utility routines for OpenCL |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pmalloc_cuda.h | Declare functions for host-side memory handling when using CUDA devices |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) hardware | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cpuinfo.cpp | Tests for gmx::CpuInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) hardwaretopology.cpp | Tests for gmx::HardwareTopology |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cpuinfo.cpp | Implements gmx::CpuInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cpuinfo.h | Declares gmx::CpuInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) hardwaretopology.cpp | Implements gmx::HardwareTopology |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) hardwaretopology.h | Declares gmx::HardwareTopology |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) imd | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) imd.cpp | Implements functions of imd.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) imd.h | This file contains datatypes and function declarations necessary for mdrun to interface with VMD via the interactive molecular dynamics protocol |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) imdsocket.cpp | Implements functions of imdsocket.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) imdsocket.h | Implements the parts of the vmdsock.h interface needed for IMD communication |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) linearalgebra | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmx_arpack.h | Selected routines from ARPACK |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmx_blas.h | Header definitions for the standard BLAS library |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) gmx_lapack.h | Header definitions for the standard LAPACK library |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) listed-forces | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) bonded.cpp | This file defines low-level functions necessary for computing energies and forces for listed interactions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) bonded.h | This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) disre.h | Declares functions for handling distance restraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) listed-forces.cpp | This file defines high-level functions for mdrun to compute energies and forces for listed interactions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) listed-forces.h | This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) listed-internal.cpp | This file defines functions needed internally by the module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) listed-internal.h | This file contains declarations for functions needed internally by the module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) manage-threading.cpp | This file defines functions for managing threading of listed interactions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) manage-threading.h | Declares functions for managing threading of listed forces |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) orires.h | Declares functions for handling orientation restraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pairs.cpp | This file defines functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pairs.h | This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) position-restraints.cpp | This file defines low-level functions necessary for computing energies and forces for position restraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) position-restraints.h | This file contains declarations necessary for low-level functions for computing energies and forces for position restraints |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) restcbt.cpp | This file contains function definitions necessary for computations of forces due to restricted angle, restricted dihedral and combined bending-torsion potentials |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) restcbt.h | This file contains function declarations necessary for computations of forces due to restricted angle, restricted dihedral and combined bending-torsion potentials |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) math | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) functions.cpp | Tests for simple math functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) invertmatrix.cpp | Tests matrix inversion routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) vectypes.cpp | Tests various corners of gmx::RVec implementation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) calculate-ewald-splitting-coefficient.h | Declares functions for computing Ewald splitting coefficients |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) functions.cpp | Implements simple math functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) functions.h | Declares simple math functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) invertmatrix.cpp | Routines to invert 3x3 matrices |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) invertmatrix.h | Declares routines to invert 3x3 matrices |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) mdlib | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) nbnxn_cuda | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) nbnxn_cuda_types.h | Data types used internally in the nbnxn_cuda module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) nbnxn_ocl | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_ocl.cpp | Define OpenCL implementation of nbnxn_gpu.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_ocl_data_mgmt.cpp | Define OpenCL implementation of nbnxn_gpu_data_mgmt.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_ocl_internal.h | Internal API of the OpenCL non-bonded module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_ocl_jit_support.cpp | Defines functions that support JIT compilation (e.g. for OpenCL) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) nbnxn_ocl_types.h | Data types used internally in the nbnxn_ocl module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) simulationsignal.cpp | Tests for the mdrun signalling functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) groupcoord.h | Assemble atomic positions of a (small) subset of atoms and distribute to all nodes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) minimize.cpp | This file defines integrators for energy minimization |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_gpu.h | Declare interface for GPU execution for NBNXN module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_gpu_data_mgmt.h | Declare interface for GPU data transfer for NBNXN module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbnxn_gpu_jit_support.h | Declares functions that support JIT compilation (e.g. for OpenCL) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) simulationsignal.cpp | This file defines functions for inter- and intra-simulation signalling by mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) simulationsignal.h | This file declares functions for inter-rank signalling by mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) tpi.cpp | This file defines the integrator for test particle insertion |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) mdrunutility | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) handlerestart.cpp | This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) handlerestart.h | This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) threadaffinity.h | Declares functions for managing mdrun thread affinity |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) mdtypes | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) md_enums.h | Declares enumerated types used throughout the code |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pull-params.h | This file contains datatypes for the mdp options used by the pull code |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) onlinehelp | Help Formatting for Online Help (onlinehelp) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Help Formatting for Online Help (onlinehelp) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpformat.cpp | Tests for help string formatting functions and classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpmanager.cpp | Tests for help topic management and help topic formatting |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpwritercontext.cpp | Tests for help text formatting |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mock_helptopic.cpp | Implements classes in mock_helptopic.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) mock_helptopic.h | Declares mock implementation of gmx::IHelpTopic |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpformat.cpp | Implements functions in helpformat.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpformat.h | Declares common string formatting routines for online help |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpmanager.cpp | Implements gmx::HelpManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpmanager.h | Declares gmx::HelpManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helptopic.cpp | Implements classes and functions from helptopic.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helptopic.h | Declares helper classes for implementing gmx::IHelpTopic |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpwritercontext.cpp | Implements gmx::HelpWriterContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) helpwritercontext.h | Declares gmx::HelpWriterContext |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ihelptopic.h | Declares gmx::IHelpTopic |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) rstparser.cpp | Implements classes from rstparser.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) rstparser.h | Declares classes for (partial) parsing of reStructuredText |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) options | Extensible Handling of Options (options) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Extensible Handling of Options (options) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) abstractoptionstorage.cpp | Tests proper handling of option storage |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoption.cpp | Tests basic file name option implementation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoptionmanager.cpp | Tests file name option implementation dependent on gmx::FileNameOptionManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) option.cpp | Tests creation of basic option types |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionsassigner.cpp | Tests option assignment |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) timeunitmanager.cpp | Tests handling of time units with gmx::TimeUnitManager and gmx::TimeUnitBehavior |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) abstractoption.cpp | Implements classes in abstractoption.h and abstractoptionstorage.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) abstractoption.h | Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) abstractoptionstorage.h | Declares gmx::AbstractOptionStorage |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) basicoptions.cpp | Implements classes in basicoptions.h and basicoptionstorage.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) basicoptions.h | Declares option objects for basic option types |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) basicoptionstorage.h | Declares storage classes for basic option types |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) behaviorcollection.cpp | Implements gmx::OptionsBehaviorCollection |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) behaviorcollection.h | Declares gmx::OptionsBehaviorCollection |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoption.cpp | Implements classes in filenameoption.h and filenameoptionstorage.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoption.h | Declares gmx::FileNameOption and gmx::FileNameOptionInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoptionmanager.cpp | Implements gmx::FileNameOptionManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoptionmanager.h | Declares gmx::FileNameOptionManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filenameoptionstorage.h | Declares gmx::FileNameOptionStorage |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ioptionsbehavior.h | Declares gmx::IOptionsBehavior |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) ioptionscontainer.h | Declares gmx::IOptionsContainer |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionfiletype.h | Defines an enumeration type for specifying file types for options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionflags.h | Defines flags used in option implementation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionmanagercontainer.h | Declares gmx::OptionManagerContainer |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) options-impl.h | Declares private implementation class for gmx::Options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) options.cpp | Implements gmx::Options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) options.h | Declares gmx::Options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionsassigner.cpp | Implements gmx::OptionsAssigner |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionsassigner.h | Declares gmx::OptionsAssigner |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionstoragetemplate.h | Defines gmx::OptionStorageTemplate template |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionsvisitor.cpp | Implements classes in optionsvisitor.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) optionsvisitor.h | Declares gmx::OptionsVisitor interface and supporting classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) timeunitmanager.cpp | Implements gmx::TimeUnitManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) timeunitmanager.h | Declares gmx::TimeUnitManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) pbcutil | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) boxutilities.cpp | Implements routines in boxutilities.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pbc-simd.cpp | This file defines a low-level function for SIMD PBC calculation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pbc-simd.h | This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pbc.cpp | Implements routines in pbc.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) pulling | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pull.cpp | Implements test of some pulling routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pull.h | This file contains datatypes and function declarations necessary for mdrun to interface with the pull code |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pull_internal.h | This file contains datatypes and function declarations for internal use in the pull code |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) pull_rotation.h | Declares functions to enforce rotational motion upon a group of particles |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) random | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) exponentialdistribution.cpp | Tests for GROMACS exponential distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gammadistribution.cpp | Tests for GROMACS gamma distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) normaldistribution.cpp | Tests for GROMACS normal distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) seed.cpp | Tests for random seed functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) tabulatednormaldistribution.cpp | Tests for GROMACS tabulated normal distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) threefry.cpp | Tests for the ThreeFry random engine |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) uniformintdistribution.cpp | Tests for GROMACS uniform integer distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) uniformrealdistribution.cpp | Tests for GROMACS uniform real distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) exponentialdistribution.h | The exponential distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gammadistribution.h | The gamma distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) normaldistribution.h | The normal distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) seed.h | Random seed and domain utilities |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) tabulatednormaldistribution.h | Tabulated normal distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) threefry.h | Implementation of the 2x64 ThreeFry random engine |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) uniformintdistribution.h | The uniform integer distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) uniformrealdistribution.h | The uniform real distribution |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) selection | Parsing and Evaluation of Analysis Selections (selection) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Parsing and Evaluation of Analysis Selections (selection) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) indexutil.cpp | Tests the index group handling in the selection engine |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbsearch.cpp | Tests selection neighborhood searching |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) poscalc.cpp | Tests the position mapping engine |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectioncollection.cpp | Tests selection parsing and compilation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoption.cpp | Tests handling of selection options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) toputils.cpp | Implements test helper routines from toputils.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) toputils.h | Helper routines for constructing topologies for tests |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) centerofmass.cpp | Implements functions in centerofmass.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) centerofmass.h | API for calculation of centers of mass/geometry |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) compiler.cpp | Selection compilation and optimization |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) compiler.h | Declares gmx::SelectionCompiler |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) evaluate.cpp | Implements functions in evaluate.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) evaluate.h | Evaluation functions for sel_evalfunc() |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) indexutil.cpp | Implements functions in indexutil.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) indexutil.h | API for handling index files and index groups |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) keywords.h | Definitions of generic keyword evaluation structures |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mempool.cpp | Implements functions in mempool.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mempool.h | Declarations for memory pooling functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbsearch.cpp | Implements neighborhood searching for analysis (from nbsearch.h) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nbsearch.h | API for neighborhood searching for analysis |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) params.cpp | Implements functions in selparam.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) parser_internal.h | Helper functions for the selection parser |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) parsetree.cpp | Implements functions in parsetree.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) parsetree.h | Handling of intermediate selection parser data |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) poscalc.cpp | Implements gmx::PositionCalculationCollection and functions in poscalc.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) poscalc.h | API for structured and optimized calculation of positions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) position.cpp | Implements functions in position.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) position.h | API for handling positions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) scanner.h | Parser/scanner interaction functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) scanner_internal.cpp | Helper functions for the selection tokenizer |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) scanner_internal.h | Internal header file used by the selection tokenizer |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selection.cpp | Implements classes in selection.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selection.h | Declares gmx::Selection and supporting classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectioncollection-impl.h | Declares private implementation class for gmx::SelectionCollection |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectioncollection.cpp | Implements gmx::SelectionCollection |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectioncollection.h | Declares gmx::SelectionCollection |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionenums.h | Declares common types used in selections |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionfileoption.h | Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionfileoptionstorage.h | Declares gmx::SelectionFileOptionStorage |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoption.cpp | Implements classes in selectionoption.h and selectionoptionstorage.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoption.h | Declares gmx::SelectionOption and gmx::SelectionOptionInfo |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoptionbehavior.cpp | Implements gmx::SelectionOptionBehavior |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoptionbehavior.h | Declares gmx::SelectionOptionBehavior |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoptionmanager.cpp | Implements gmx::SelectionOptionManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoptionmanager.h | Declares gmx::SelectionOptionManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selectionoptionstorage.h | Declares gmx::SelectionOptionStorage |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selelem.cpp | Implements functions in selelem.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selelem.h | Declares gmx::SelectionTreeElement and related things |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selhelp.cpp | Implements functions in selhelp.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selhelp.h | Functions for initializing online help for selections |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selmethod.cpp | Implements functions in selmethod.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selmethod.h | API for handling selection methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selparam.h | API for handling parameters used in selections |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selvalue.cpp | Implements functions in selvalue.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selvalue.h | Declares gmx_ana_selvalue_t |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_compare.cpp | Implements internal selection method for comparison expressions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_distance.cpp | Implements distance-based selection methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_insolidangle.cpp | Implements the insolidangle selection method |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_keywords.cpp | Implements internal selection methods for numeric and string keyword evaluation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_merge.cpp | Implements the merge and plus selection modifiers |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_permute.cpp | Implements the permute selection modifier |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_position.cpp | Implements position evaluation selection methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_same.cpp | Implements the same selection method |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sm_simple.cpp | Implements simple keyword selection methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) symrec.cpp | Implements classes in symrec.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) symrec.h | Handling of selection parser symbol table |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) simd | SIMD intrinsics interface (simd) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) impl_reference | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference.h | Reference SIMD implementation, including SIMD documentation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_definitions.h | Reference SIMD implementation, including SIMD documentation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_general.h | Reference SIMD implementation, general utility functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_simd4_double.h | Reference implementation, SIMD4 single precision |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_simd4_float.h | Reference implementation, SIMD4 single precision |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_simd_double.h | Reference implementation, SIMD double precision |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_simd_float.h | Reference implementation, SIMD single precision |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) impl_reference_util_double.h | Reference impl., higher-level double prec. SIMD utility functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) impl_reference_util_float.h | Reference impl., higher-level single prec. SIMD utility functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) scalar | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) scalar.h | Scalar float functions corresponding to GROMACS SIMD functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) scalar_math.h | Scalar math functions mimicking GROMACS SIMD math functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) scalar_util.h | Scalar utility functions mimicking GROMACS SIMD utility functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for SIMD intrinsics interface (simd) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) base.h | Declares common base class for testing SIMD and SIMD4 |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) bootstrap_loadstore.cpp | Separate test of SIMD load/store, before we use them in the SIMD test classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) simd.h | Declares fixture for testing of normal SIMD (not SIMD4) functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) simd4.h | Declares fixture for testing of SIMD4 functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) simd.h | Definitions, capabilities, and wrappers for SIMD module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) simd_math.h | Math functions for SIMD datatypes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) support.cpp | Implements SIMD architecture support query routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) support.h | Functions to query compiled and supported SIMD architectures |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) vector_operations.h | SIMD operations corresponding to Gromacs rvec datatypes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) statistics | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) statistics.h | Declares simple statistics toolbox |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) swap | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) swapcoords.cpp | Implements functions in swapcoords.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) swapcoords.h | The "Computational Electrophysiology" protocol for ion/water position swapping |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) timing | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cyclecounter.h | High-resolution timestamp or CPU clock cycle counters |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) gpu_timing.h | Declares data types for GPU timing |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) topology | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) atomsbuilder.cpp | Implements classes from atomsbuilder.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) atomsbuilder.h | Utility classes for manipulating t_atoms structures |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) trajectoryanalysis | Framework for Trajectory Analysis (trajectoryanalysis) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) modules | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) angle.cpp | Implements gmx::analysismodules::Angle |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) angle.h | Declares trajectory analysis module for angle calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) distance.cpp | Implements gmx::analysismodules::Distance |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) distance.h | Declares trajectory analysis module for distance calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) freevolume.cpp | Implements gmx::analysismodules::Freevolume |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) freevolume.h | Declares trajectory analysis module for free volume calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pairdist.cpp | Implements gmx::analysismodules::PairDistance |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pairdist.h | Declares trajectory analysis module for pairwise distance calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) rdf.cpp | Implements gmx::analysismodules::Rdf |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) rdf.h | Declares trajectory analysis module for RDF calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sasa.cpp | Implements gmx::analysismodules::Sasa |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sasa.h | Declares trajectory analysis module for surface area calculations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) select.cpp | Implements gmx::analysismodules::Select |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) select.h | Declares trajectory analysis module for basic selection information |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Framework for Trajectory Analysis (trajectoryanalysis) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) angle.cpp | Tests for functionality of the "angle" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinerunner.cpp | Tests for general functionality in gmx::TrajectoryAnalysisCommandLineRunner |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) distance.cpp | Tests for functionality of the "distance" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) freevolume.cpp | Tests for functionality of the "angle" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) moduletest.cpp | Implements classes in moduletest.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) moduletest.h | Declares test fixture for TrajectoryAnalysisModule subclasses |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pairdist.cpp | Tests for functionality of the "pairdist" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) rdf.cpp | Tests for functionality of the "rdf" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sasa.cpp | Tests for functionality of the "sasa" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) select.cpp | Tests for functionality of the "select" trajectory analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) surfacearea.cpp | Tests for the surface area calculation used by the sasa analysis module |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) test_selection.cpp | Testing/debugging tool for the selection engine |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysismodule.cpp | Implements classes in analysismodule.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysismodule.h | Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysissettings-impl.h | Declares private implementation class for gmx::TrajectoryAnalysisSettings |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysissettings.cpp | Implements classes in analysissettings.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysissettings.h | Declares gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinerunner.cpp | Implements gmx::TrajectoryAnalysisCommandLineRunner |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinerunner.h | Declares gmx::TrajectoryAnalysisCommandLineRunner |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) modules.cpp | Implements registerTrajectoryAnalysisModules() |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) modules.h | Generic interface for accessing trajectory analysis modules |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) runnercommon.cpp | Implements gmx::TrajectoryAnalysisRunnerCommon |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) runnercommon.h | Declares gmx::TrajectoryAnalysisRunnerCommon |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) utility | Low-Level Utilities (utility) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Low-Level Utilities (utility) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) alignedallocator.cpp | Tests for gmx::AlignedAllocator |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) arrayref.cpp | Tests for gmx::ArrayRef and gmx::ConstArrayRef |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) basedefinitions.cpp | Tests for base definitions (only alignment attributes for now) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) bitmask.h | Tests for bitmask functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) path.cpp | Tests for (some) functions in path.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringutil.cpp | Tests for string utility functions and classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) textwriter.cpp | Tests for gmx::TextWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) alignedallocator.cpp | Implements AlignedAllocator |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) alignedallocator.h | Declares gmx::AlignedAllocator that is used to make standard library containers compatible with SIMD contents that require aligned load/store |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) arrayref.h | Declares gmx::ArrayRef and gmx::ConstArrayRef |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) arraysize.h | Provides asize() macro for calculating the static size of an array |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) basedefinitions.h | Basic types and macros used throughout GROMACS |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) basenetwork.h | Utility functions for basic MPI and network functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) baseversion-gen.h | Declares variables that hold generated version information |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) baseversion.h | Declares functions to get basic version information |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) binaryinformation.cpp | Implements functionality for printing information about the currently running binary |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) binaryinformation.h | Helper functionality for information about the currently running binary |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) bitmask.h | Declares gmx_bitmask_t and associated functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) classhelpers.h | Declares common utility classes and macros |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) coolstuff.cpp | Functionality for printing cool strings |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) coolstuff.h | Functionality for printing cool strings |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cstringutil.h | Generic C string handling functions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) current_function.h | Declares GMX_CURRENT_FUNCTION for getting the current function name |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datafilefinder.cpp | Implements gmx::DataFileFinder |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) datafilefinder.h | Declares gmx::DataFileFinder and related classes |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) dir_separator.h | Provides OS-specific directory-name separator |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) directoryenumerator.cpp | Implements gmx::DirectoryEnumerator |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) directoryenumerator.h | Declares gmx::DirectoryEnumerator |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) errorcodes.cpp | Implements functions in errorcodes.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) errorcodes.h | Declares error codes and related functions for fatal error handling |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) errorformat.cpp | Implements functions declared in errorformat.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) errorformat.h | Declares an internal helper function for formatting standard error messages |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) exceptions.cpp | Implements classes and functions in exceptions.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) exceptions.h | Declares common exception classes and macros for fatal error handling |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) fatalerror.h | Declares fatal error handling and debugging routines for C code |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) fileredirector.cpp | Implements classes and functions from fileredirector.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) fileredirector.h | Declares gmx::IFileOutputRedirector |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filestream.cpp | Implements classes from filestream.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) filestream.h | Declares implementations for textstream.h interfaces for file input/output |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) flags.h | Declares gmx::FlagsTemplate |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) futil.h | Low-level wrappers for OS-specific file handling with some GROMACS customizations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxassert.cpp | Implements assertion handlers |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxassert.h | Defines assert macros customized for Gromacs |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxmpi.h | Wraps <mpi.h> usage in Gromacs |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxomp.cpp | Implements functions from gmxomp.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxomp.h | Declares OpenMP wrappers to avoid conditional compilation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxregex.cpp | Implements regular expression wrappers |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) gmxregex.h | Declares simple wrapper for regular expression functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) init.cpp | Implements functions from init.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) init.h | Declares functions for initializing the GROMACS library |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) 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 |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) messagestringcollector.cpp | Implements gmx::MessageStringCollector |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) messagestringcollector.h | Declares gmx::MessageStringCollector |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mutex.h | Declares C++11-style basic threading primitives (gmx::Mutex, gmx::lock_guard) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) nodelete.h | Declares no_delete deleter for std::shared_ptr |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) path.cpp | Implements functions in path.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) path.h | Declares functions for OS-independent path handling |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) pleasecite.h | Declares please_cite() for printing out literature references |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) programcontext.cpp | Implements gmx::IProgramContext and related methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) programcontext.h | Declares gmx::IProgramContext and related methods |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) qsort_threadsafe.h | Portable implementation of threadsafe quicksort |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) real.h | Declares real and related constants |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) scoped_cptr.h | Declares gmx::scoped_cptr and gmx::scoped_guard_sfree |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) smalloc.h | C memory allocation routines for GROMACS |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) snprintf.h | Provide snprintf symbol on all OS (for internal Gromacs use) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) strdb.h | Declares C functions for reading files with a list of strings |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringstream.cpp | Implements classes from stringstream.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringstream.h | Declares implementations for textstream.h interfaces for input/output to in-memory strings |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringutil.cpp | Implements functions and classes in stringutil.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringutil.h | Declares common string utility and formatting routines |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sysinfo.cpp | Implements functions from sysinfo.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) sysinfo.h | Declares functions for obtaining information about the operating environment and the current process |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textreader.cpp | Implements gmx::TextReader |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textreader.h | Declares gmx::TextReader |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textstream.h | Declares interfaces for simple input/output streams |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textwriter.cpp | Implements gmx::TextWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textwriter.h | Declares gmx::TextWriter |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) txtdump.h | Declares helper functions for dumping basic data structures as text |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) analysisdata.h | Public API convenience header for analysis data handling |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) commandline.h | Public API convenience header for managing command line programs |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) onlinehelp-doc.h | Dummy header for Help Formatting for Online Help (onlinehelp) documentation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) options.h | Public API convenience header for handling of options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) random.h | Public API convenience header for random engines and distributions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) selection.h | Public API convenience header for selection handling |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) trajectoryanalysis.h | Public API convenience header for trajectory analysis framework |
![](ftv2blank.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) utility.h | Public API convenience header for low-level utilities |
![](ftv2blank.png) ![o](ftv2mnode.png) programs | Source code for building executables, see Wrapper binary implementation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) mdrun | Source code specific to mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) compressed_x_output.cpp | Tests for the mdrun -x functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) domain_decomposition.cpp | Tests special cases in domain decomposition |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) energyreader.cpp | Implementions of related classes for tests that want to inspect energies produced by mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) energyreader.h | Interfaces of related classes for tests that want to inspect energies produced by mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) grompp.cpp | Tests for basic grompp functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) interactiveMD.cpp | Tests utilities for interactive molecular dynamics (IMD) setups |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mdruncomparisonfixture.cpp | Implements classes in mdruncomparisonfixture.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) moduletest.cpp | Implements classes in moduletest.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) moduletest.h | Declares test fixtures for general mdrun functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) multisim.cpp | Tests for the mdrun multi-simulation functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) multisimtest.cpp | Tests for the mdrun multi-simulation functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) multisimtest.h | Declares test fixture for the mdrun multi-simulation functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) replicaexchange.cpp | Tests for the mdrun replica-exchange functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) rerun.cpp | Tests for the mdrun -rerun functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) swapcoords.cpp | Tests utilities for "Computational Electrophysiology" setups |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) tabulated_bonded_interactions.cpp | Tests for tabulated bonded interactions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) termination.cpp | Tests for the mdrun termination functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) terminationhelper.cpp | Defines functionality used to test mdrun termination functionality under different conditions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) terminationhelper.h | Declares functionality used to test mdrun termination functionality under different conditions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) trajectory_writing.cpp | Tests for the .mdp nst*out functionality |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) trajectoryreader.cpp | Implementions of related classes for tests that want to inspect trajectories produced by mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) trajectoryreader.h | Declares interface of a class for tests that want to inspect trajectories produced by mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) md.h | Declares the integrators for molecular dynamics simulations |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mdrun.cpp | This file implements mdrun |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) runner.cpp | Implements the MD runner routine calling all integrators |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) runner.h | Declares the routine running the inetgrators |
![](ftv2blank.png) ![|](ftv2vertline.png) ![\](ftv2plastnode.png) view | Source code specific to gmx view , including all X11-dependent code |
![](ftv2blank.png) ![o](ftv2mnode.png) testutils | Testing Utilities (testutils) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2pnode.png) tests | Unit tests for Testing Utilities (testutils) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) interactivetest.cpp | Self-tests for interactive test helpers |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata_tests.cpp | Tests utilities for test reference data |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testasserts_tests.cpp | Tests GROMACS-specific test assertions |
![](ftv2blank.png) ![|](ftv2vertline.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) xvgtest_tests.cpp | Tests utilities for testing xvg files |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinetest.cpp | Implements classes from cmdlinetest.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) cmdlinetest.h | Declares utilities testing command-line programs |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) conftest.cpp | Implements routine to check the content of conf files |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) conftest.h | Declares function to add the content of a conf file to a checker |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) integrationtests.cpp | Implements classes in integrationtests.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) integrationtests.h | Declares test fixture for integration tests |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) interactivetest.cpp | Implements classes from interactivetest.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) interactivetest.h | Provides helper classes for testing interactive prompts |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) mpi-printer.h | Declares gmx::test::initMPIOutput() |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata-checkers.h | Declares internal helper classes for the reference data framework to check reference data values of different types |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata-impl.h | Declares internal data structures for the reference data framework |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata-xml.cpp | Implements reference data XML persistence |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata-xml.h | Declares functions for reference data XML persistence |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata.cpp | Implements classes and functions from refdata.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) refdata.h | Functionality for writing tests that can produce their own reference data |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringtest.cpp | Implements gmx::test::StringTestBase |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) stringtest.h | Declares gmx::test::StringTestBase |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testasserts.cpp | Implements floating-point comparison routines from testasserts.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testasserts.h | Extra assertions for unit tests |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testexceptions.h | Exception classes for errors in tests |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testfilemanager.cpp | Implements gmx::test::TestFileManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testfilemanager.h | Declares gmx::test::TestFileManager |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testfileredirector.cpp | Implements classes from testfileredirector.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testfileredirector.h | Declares generic mock implementations for interfaces in fileredirector.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testinit.cpp | Implements functions in testinit.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testinit.h | Functions for initialing GROMACS unit test executables |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testoptions.cpp | Implements functions in testoptions.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testoptions.h | Functions for accessing test command-line options |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) testutils-doc.h | Dummy header for Testing Utilities (testutils) documentation |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textblockmatchers.cpp | Implements classes from textblockmatchers.h |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) textblockmatchers.h | Declares utility classes for testing multi-line strings against reference data |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) unittest_main.cpp | Main() for unit tests that use Testing Utilities (testutils) |
![](ftv2blank.png) ![|](ftv2vertline.png) ![o](ftv2node.png) xvgtest.cpp | Implements routine to check the content of xvg files |
![](ftv2blank.png) ![|](ftv2vertline.png) ![\](ftv2lastnode.png) xvgtest.h | Declares function to add the content of an xvg file to a checker |
![](ftv2blank.png) ![\](ftv2lastnode.png) gmxpre.h | Prerequisite header file for GROMACS build |