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Library API
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Description

Classes and other symbols that are publicly accessible within the GROMACS library.

See Also
Public API

Classes

class  gmx::AbstractAnalysisData
 Abstract base class for all objects that provide data. More...
 
class  gmx::AbstractAnalysisArrayData
 Abstract base class for data objects that present in-memory data. More...
 
class  gmx::AnalysisDataModuleInterface
 Interface for a module that gets notified whenever data is added. More...
 
class  gmx::AnalysisDataModuleSerial
 Convenience base class for serial analysis data modules. More...
 
class  gmx::AnalysisDataModuleParallel
 Convenience base class for parallel analysis data modules. More...
 
class  gmx::AnalysisDataModuleManager
 Encapsulates handling of data modules attached to AbstractAnalysisData. More...
 
class  gmx::AnalysisDataStorageFrame
 Allows assigning values for a data frame in AnalysisDataStorage. More...
 
class  gmx::AnalysisDataStorage
 Helper class that implements storage of data. More...
 
class  gmx::AnalysisDataParallelOptions
 Parallelization options for analysis data objects. More...
 
class  gmx::test::AnalysisDataTestInputPointSet
 Represents a single set of points in AnalysisDataTestInputFrame structure. More...
 
class  gmx::test::AnalysisDataTestInputFrame
 Represents a single frame in AnalysisDataTestInput structure. More...
 
class  gmx::test::AnalysisDataTestInput
 Represents static input data for AbstractAnalysisData tests. More...
 
class  gmx::test::AnalysisDataTestFixture
 Test fixture for AbstractAnalysisData testing. More...
 
class  gmx::GlobalCommandLineHelpContext
 Helper for passing CommandLineHelpContext into parse_common_args(). More...
 
class  gmx::CommandLineModuleManager
 Implements a wrapper command-line interface for multiple modules. More...
 
class  gmx::CommandLineModuleGroup
 Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More...
 
class  gmx::ExecutableEnvironmentInterface
 Allows customization of the way various directories are found by CommandLineProgramContext. More...
 
class  gmx::CommandLineProgramContext
 Program context implementation for command line programs. More...
 
class  gmx::TextTableFormatter
 Formats rows of a table for text output. More...
 
class  gmx::HelpManager
 Helper for providing interactive online help. More...
 
class  gmx::AbstractSimpleHelpTopic
 Abstract base class for help topics that have simple text and no subtopics. More...
 
class  gmx::AbstractCompositeHelpTopic
 Abstract base class for help topics that have simple text and subtopics. More...
 
class  gmx::SimpleHelpTopic< HelpText >
 Template for simple implementation of AbstractSimpleHelpTopic. More...
 
class  gmx::CompositeHelpTopic< HelpText >
 Template for simple implementation of AbstractCompositeHelpTopic. More...
 
class  gmx::HelpTopicInterface
 Provides a single online help topic. More...
 
class  gmx::HelpWriterContext
 Context information for writing out help. More...
 
class  gmx::OptionTemplate< T, U >
 Templated base class for constructing concrete option settings classes. More...
 
class  gmx::AbstractOptionStorage
 Abstract base class for converting, validating, and storing option values. More...
 
class  gmx::OptionManagerContainer
 Container to keep managers added with Options::addManager() and pass them to options. More...
 
class  gmx::OptionManagerInterface
 Base class for option managers. More...
 
class  gmx::OptionsAssigner
 Decorator class for assigning values to Options. More...
 
class  gmx::OptionStorageTemplate< T >
 Templated base class for constructing option value storage classes. More...
 
class  gmx::OptionsVisitor
 Pure interface for visiting options in a Options object. More...
 
class  gmx::OptionsTypeVisitor< InfoType >
 Abstract base class for visiting options of a particular type. More...
 
class  gmx::OptionsIterator
 Decorator class for visiting options in a Options object. More...
 
class  gmx::OptionsModifyingVisitor
 Pure interface for visiting options in a Options object, allowing modifications. More...
 
class  gmx::OptionsModifyingTypeVisitor< InfoType >
 Abstract base class for visiting options of a particular type, allowing modifications. More...
 
class  gmx::OptionsModifyingIterator
 Decorator class for visiting options in a Options object, allowing changes. More...
 
class  gmx::SelectionFileOption
 Specifies a special option that provides selections from a file. More...
 
class  gmx::SelectionFileOptionInfo
 Wrapper class for accessing and modifying selection file option information. More...
 
class  gmx::PrivateImplPointer< Impl >
 Helper class to manage a pointer to a private implementation class. More...
 
class  gmx::DirectoryEnumerator
 Lists files in a directory. More...
 
class  gmx::FileInputRedirectorInterface
 Allows overriding file existence checks from code that supports it. More...
 
class  gmx::FileOutputRedirectorInterface
 Allows capturing stdout and file output from code that supports it. More...
 
class  gmx::FlagsTemplate< FlagType >
 Template class for typesafe handling of combination of flags. More...
 
class  gmx::Regex
 Represents a regular expression. More...
 
class  gmx::MessageStringCollector
 Helper class for collecting message strings, optionally with context. More...
 
class  gmx::MessageStringContext
 Convenience class for creating a message context. More...
 
class  gmx::scoped_cptr< T, D >
 Stripped-down version of scoped_ptr that uses sfree() or custom deleter. More...
 
class  gmx::test::CommandLine
 Helper class for tests that need to construct command lines. More...
 
class  gmx::test::CommandLineTestHelper
 Helper class for tests that construct command lines that need to reference existing files. More...
 
class  gmx::test::CommandLineTestBase
 Test fixture for tests that call a single command-line program with input/output files. More...
 
class  gmx::test::IntegrationTestFixture
 Test fixture for integration tests. More...
 
class  gmx::test::TestReferenceData
 Handles creation of and comparison to test reference data. More...
 
class  gmx::test::TestReferenceChecker
 Handles comparison to test reference data. More...
 
class  gmx::test::StringTestBase
 Test fixture for tests that check string formatting. More...
 
class  gmx::test::TestFileManager
 Helper for tests that need input and output files. More...
 
class  gmx::test::TestFileInputRedirector
 In-memory implementation for FileInputRedirectorInterface for tests. More...
 
class  gmx::test::TestOptionsProvider
 Provides additional options for the test executable. More...
 
class  gmx::gmx_unique_ptr< T >
 Smart pointer for unique ownership. More...
 

Typedefs

typedef gmx_unique_ptr
< AbstractCompositeHelpTopic >
::type 
gmx::CompositeHelpTopicPointer
 Smart pointer type to manage a AbstractCompositeHelpTopic object.
 

Functions

template<typename T >
boost::shared_ptr< T > & gmx::move (boost::shared_ptr< T > &ptr)
 Moves gmx::gmx_unique_ptr type pointers. More...
 

Files

file  gmxpre.h
 Prerequisite header file for GROMACS build.
 
file  abstractdata.h
 Declares gmx::AbstractAnalysisData.
 
file  datamodule.h
 Declares gmx::AnalysisDataModuleInterface and related convenience classes.
 
file  datamodulemanager.h
 Declares gmx::AnalysisDataModuleManager.
 
file  datastorage.h
 Declares gmx::AnalysisDataStorage.
 
file  paralleloptions.h
 Declares gmx::AnalysisDataParallelOptions.
 
file  datatest.h
 Helper classes for testing classes that derive from AbstractAnalysisData.
 
file  mock_datamodule.h
 Declares mock implementation of gmx::AnalysisDataModuleInterface.
 
file  cmdlinehelpcontext.h
 Declares gmx::CommandLineHelpContext.
 
file  cmdlinemodulemanager.h
 Declares gmx::CommandLineModuleManager.
 
file  cmdlineprogramcontext.h
 Declares gmx::CommandLineProgramContext.
 
file  autocorr.h
 Declares routine for computing autocorrelation functions.
 
file  crosscorr.h
 Declares routine for computing a cross correlation between two data sets.
 
file  expfit.h
 Declares routine for fitting a data set to a curve.
 
file  integrate.h
 Declares routines for integrating a data set.
 
file  manyautocorrelation.h
 Declares routine for computing many correlation functions using OpenMP.
 
file  polynomials.h
 Declares routine for computing a Legendre polynomial.
 
file  domdec.h
 This file declares functions for mdrun to call to manage the details of its domain decomposition.
 
file  domdec_network.h
 This file declares functions for (mostly) the domdec module to use MPI functionality.
 
file  edsam.h
 Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces.
 
file  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.
 
file  long-range-correction.h
 This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
 
file  pme-load-balancing.h
 This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ).
 
file  pme.h
 This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
 
file  pmalloc_cuda.h
 Declare functions for host-side memory handling when using CUDA devices.
 
file  gpu_utils.h
 Declare functions for detection and initialization for GPU devices.
 
file  ocl_compiler.h
 Declare infrastructure for OpenCL JIT compilation for Gromacs.
 
file  oclutils.h
 Declare utility routines for OpenCL.
 
file  imd.h
 This file contains datatypes and function declarations necessary for mdrun to interface with VMD via the interactive molecular dynamics protocol.
 
file  imdsocket.h
 Implements the parts of the vmdsock.h interface needed for IMD communication.
 
file  bonded.h
 This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.
 
file  manage-threading.h
 Declares functions for managing threading of listed forces.
 
file  position-restraints.h
 This file contains declarations necessary for low-level functions for computing energies and forces for position restraints.
 
file  groupcoord.h
 Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
 
file  mdrun_signalling.h
 This file declares functions for inter-rank signalling by mdrun.
 
file  nbnxn_gpu_data_mgmt.h
 Declare interface for GPU data transfer for NBNXN module.
 
file  handlerestart.h
 This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files).
 
file  helpformat.h
 Declares common string formatting routines for online help.
 
file  helpmanager.h
 Declares gmx::HelpManager.
 
file  helptopic.h
 Declares helper classes for implementing gmx::HelpTopicInterface.
 
file  helptopicinterface.h
 Declares gmx::HelpTopicInterface.
 
file  helpwritercontext.h
 Declares gmx::HelpWriterContext.
 
file  mock_helptopic.h
 Declares mock implementation of gmx::HelpTopicInterface.
 
file  abstractoption.h
 Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo.
 
file  abstractoptionstorage.h
 Declares gmx::AbstractOptionStorage.
 
file  optionmanagercontainer.h
 Declares gmx::OptionManagerContainer.
 
file  optionsassigner.h
 Declares gmx::OptionsAssigner.
 
file  optionstoragetemplate.h
 Defines gmx::OptionStorageTemplate template.
 
file  optionsvisitor.h
 Declares gmx::OptionsVisitor interface and supporting classes.
 
file  pbc-simd.h
 This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations.
 
file  pull.h
 This file contains datatypes and function declarations necessary for mdrun to interface with the pull code.
 
file  pull_internal.h
 This file contains datatypes and function declarations for internal use in the pull code.
 
file  pull_rotation.h
 Declares functions to enforce rotational motion upon a group of particles.
 
file  indexutil.h
 API for handling index files and index groups.
 
file  selectionfileoption.h
 Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo.
 
file  selhelp.h
 Functions for initializing online help for selections.
 
file  simd.h
 Definitions, capabilities, and wrappers for SIMD module.
 
file  simd_math.h
 Math functions for SIMD datatypes.
 
file  vector_operations.h
 SIMD operations corresponding to Gromacs rvec datatypes.
 
file  statistics.h
 Declares simple statistics toolbox.
 
file  enums.h
 Enumerated types used in the "Computational Electrophysiology" module.
 
file  swapcoords.h
 The "Computational Electrophysiology" protocol for ion/water position swapping.
 
file  cyclecounter.h
 High-resolution timestamp or CPU clock cycle counters.
 
file  gpu_timing.h
 Declares data types for GPU timing.
 
file  atomsbuilder.h
 Utility classes for manipulating t_atoms structures.
 
file  modules.h
 Generic interface for accessing trajectory analysis modules.
 
file  basenetwork.h
 Utility functions for basic MPI and network functionality.
 
file  baseversion.h
 Declares functions to get basic version information.
 
file  bitmask.h
 Declares gmx_bitmask_t and associated functions.
 
file  classhelpers.h
 Declares common utility classes and macros.
 
file  dir_separator.h
 Provides OS-specific directory-name separator.
 
file  directoryenumerator.h
 Declares gmx::DirectoryEnumerator.
 
file  fileredirector.h
 Declares gmx::FileOutputRedirectorInterface.
 
file  flags.h
 Declares gmx::FlagsTemplate.
 
file  gmxmpi.h
 Wraps <mpi.h> usage in Gromacs.
 
file  gmxomp.h
 Declares OpenMP wrappers to avoid conditional compilation.
 
file  gmxregex.h
 Declares simple wrapper for regular expression functionality.
 
file  messagestringcollector.h
 Declares gmx::MessageStringCollector.
 
file  path.h
 Declares functions for OS-independent path handling.
 
file  qsort_threadsafe.h
 Portable implementation of threadsafe quicksort.
 
file  scoped_cptr.h
 Declares gmx::scoped_cptr and gmx::scoped_guard_sfree.
 
file  snprintf.h
 Provide snprintf symbol on all OS (for internal Gromacs use)
 
file  sysinfo.h
 Declares functions for obtaining information about the operating environment and the current process.
 
file  uniqueptr.h
 Declares gmx::gmx_unique_ptr and supporting functionality.
 
file  cmdlinetest.h
 Declares utilities testing command-line programs.
 
file  integrationtests.h
 Declares test fixture for integration tests.
 
file  refdata.h
 Functionality for writing tests that can produce their own reference data.
 
file  stringtest.h
 Declares gmx::test::StringTestBase.
 
file  testasserts.h
 Extra assertions for unit tests.
 
file  testexceptions.h
 Exception classes for errors in tests.
 
file  testfilemanager.h
 Declares gmx::test::TestFileManager.
 
file  testfileredirector.h
 Declares generic mock implementations for interfaces in fileredirector.h.
 
file  testoptions.h
 Functions for accessing test command-line options.
 

Function Documentation

template<typename T >
boost::shared_ptr< T > & gmx::move ( boost::shared_ptr< T > &  ptr)

Moves gmx::gmx_unique_ptr type pointers.

For C++11 gmx::move is the std::move, for non-C++11 compilers, the move operation is a no-op.