Gromacs
2016.1
|
share | Directory that contains installed data files |
template | Template code for writing analysis programs |
template.cpp | Template code for writing analysis programs |
src | Main source code directory |
gromacs | Source code for building the libgromacs library |
analysisdata | Parallelizable Handling of Output Data (analysisdata) |
modules | |
average.h | Declares gmx::AnalysisDataAverageModule |
displacement.h | Declares gmx::AnalysisDataDisplacementModule |
histogram.h | Declares analysis data modules for calculating histograms |
lifetime.h | Declares gmx::AnalysisDataLifetimeModule |
plot.h | Declares gmx::AnalysisDataPlotModule for plotting data (into a file) |
abstractdata.h | Declares gmx::AbstractAnalysisData |
analysisdata.h | Declares gmx::AnalysisData and gmx::AnalysisDataHandle |
arraydata.h | Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData |
dataframe.h | Declares classes for accessing data frame information |
datamodule.h | Declares gmx::IAnalysisDataModule and related convenience classes |
commandline | Command Line Program Management (commandline) |
cmdlinehelpwriter.h | Declares gmx::CommandLineHelpWriter |
cmdlineinit.h | Declares functions for initializing the GROMACS library for command line use |
cmdlinemodule.h | Declares gmx::ICommandLineModule and supporting classes |
cmdlineoptionsmodule.h | Declares gmx::ICommandLineOptionsModule and supporting routines |
cmdlineparser.h | Declares gmx::CommandLineParser |
cmdlineprogramcontext.h | Declares gmx::CommandLineProgramContext |
filenm.h | Declares t_filenm for old-style command-line parsing of file name options |
pargs.h | Declares t_pargs , parse_common_args() and related methods |
viewit.h | Provides function to open output files automatically (with some X11 programs) |
fft | |
fft.h | Fast Fourier Transforms |
listed-forces | |
listed-forces.h | This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions |
math | |
calculate-ewald-splitting-coefficient.h | Declares functions for computing Ewald splitting coefficients |
functions.h | Declares simple math functions |
mdtypes | |
md_enums.h | Declares enumerated types used throughout the code |
options | Extensible Handling of Options (options) |
abstractoption.h | Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo |
basicoptions.h | Declares option objects for basic option types |
filenameoption.h | Declares gmx::FileNameOption and gmx::FileNameOptionInfo |
filenameoptionmanager.h | Declares gmx::FileNameOptionManager |
ioptionsbehavior.h | Declares gmx::IOptionsBehavior |
ioptionscontainer.h | Declares gmx::IOptionsContainer |
optionfiletype.h | Defines an enumeration type for specifying file types for options |
optionflags.h | Defines flags used in option implementation |
options.h | Declares gmx::Options |
timeunitmanager.h | Declares gmx::TimeUnitManager |
random | |
exponentialdistribution.h | The exponential distribution |
gammadistribution.h | The gamma distribution |
normaldistribution.h | The normal distribution |
seed.h | Random seed and domain utilities |
tabulatednormaldistribution.h | Tabulated normal distribution |
threefry.h | Implementation of the 2x64 ThreeFry random engine |
uniformintdistribution.h | The uniform integer distribution |
uniformrealdistribution.h | The uniform real distribution |
selection | Parsing and Evaluation of Analysis Selections (selection) |
indexutil.h | API for handling index files and index groups |
nbsearch.h | API for neighborhood searching for analysis |
position.h | API for handling positions |
selection.h | Declares gmx::Selection and supporting classes |
selectioncollection.h | Declares gmx::SelectionCollection |
selectionenums.h | Declares common types used in selections |
selectionoption.h | Declares gmx::SelectionOption and gmx::SelectionOptionInfo |
selectionoptionbehavior.h | Declares gmx::SelectionOptionBehavior |
selectionoptionmanager.h | Declares gmx::SelectionOptionManager |
trajectoryanalysis | Framework for Trajectory Analysis (trajectoryanalysis) |
analysismodule.h | Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData |
analysissettings.h | Declares gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation |
cmdlinerunner.h | Declares gmx::TrajectoryAnalysisCommandLineRunner |
utility | Low-Level Utilities (utility) |
arrayref.h | Declares gmx::ArrayRef and gmx::ConstArrayRef |
arraysize.h | Provides asize() macro for calculating the static size of an array |
basedefinitions.h | Basic types and macros used throughout GROMACS |
baseversion.h | Declares functions to get basic version information |
classhelpers.h | Declares common utility classes and macros |
cstringutil.h | Generic C string handling functions |
current_function.h | Declares GMX_CURRENT_FUNCTION for getting the current function name |
datafilefinder.h | Declares gmx::DataFileFinder and related classes |
errorcodes.h | Declares error codes and related functions for fatal error handling |
exceptions.h | Declares common exception classes and macros for fatal error handling |
fatalerror.h | Declares fatal error handling and debugging routines for C code |
flags.h | Declares gmx::FlagsTemplate |
futil.h | Low-level wrappers for OS-specific file handling with some GROMACS customizations |
gmxassert.h | Defines assert macros customized for Gromacs |
init.h | Declares functions for initializing the GROMACS library |
programcontext.h | Declares gmx::IProgramContext and related methods |
real.h | Declares real and related constants |
smalloc.h | C memory allocation routines for GROMACS |
stringutil.h | Declares common string utility and formatting routines |
analysisdata.h | Public API convenience header for analysis data handling |
commandline.h | Public API convenience header for managing command line programs |
options.h | Public API convenience header for handling of options |
random.h | Public API convenience header for random engines and distributions |
selection.h | Public API convenience header for selection handling |
trajectoryanalysis.h | Public API convenience header for trajectory analysis framework |
utility.h | Public API convenience header for low-level utilities |