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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::IAnalysisDataModule
 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::IExecutableEnvironment
 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::HelpWriterContext
 Context information for writing out help. More...
 
class  gmx::IHelpTopic
 Provides a single online help topic. 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::OptionsBehaviorCollection
 Container for IOptionsBehavior objects. More...
 
class  gmx::OptionManagerContainer
 Container to keep managers added with Options::addManager() and pass them to options. More...
 
class  gmx::IOptionManager
 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::AlignedAllocator< T >
 Aligned memory allocator. More...
 
class  gmx::BinaryInformationSettings
 Settings for printBinaryInformation(). 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::IFileInputRedirector
 Allows overriding file existence checks from code that supports it. More...
 
class  gmx::IFileOutputRedirector
 Allows capturing stdout and file output from code that supports it. More...
 
class  gmx::StandardInputStream
 Text input stream implementation for reading from stdin. More...
 
class  gmx::TextInputFile
 Text input stream implementation for reading from a file. More...
 
class  gmx::TextOutputFile
 Text output stream implementation for writing to a file. 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...
 
struct  gmx::no_delete< T >
 Deleter for std::shared_ptr that does nothing. More...
 
class  gmx::scoped_cptr< T, D >
 Stripped-down version of scoped_ptr that uses sfree() or custom deleter. More...
 
class  gmx::StringOutputStream
 Text output stream implementation for writing to an in-memory string. More...
 
class  gmx::TextReader
 Reads text from a TextInputStream. More...
 
class  gmx::TextInputStream
 Interface for reading text. More...
 
class  gmx::TextOutputStream
 Interface for writing text. More...
 
class  gmx::TextWriter
 Writes text into a TextOutputStream. 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::ConfMatch
 Match the contents as an gro file. More...
 
class  gmx::test::IntegrationTestFixture
 Test fixture for integration tests. More...
 
class  gmx::test::InteractiveTestHelper
 Helper class for testing interactive sessions. 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 IFileInputRedirector for tests. More...
 
class  gmx::test::TestOptionsProvider
 Provides additional options for the test executable. More...
 
class  gmx::test::ITextBlockMatcher
 Represents a text matcher, matching text stream contents against reference data. More...
 
class  gmx::test::ITextBlockMatcherSettings
 Represents a factory for creating a text matcher. More...
 
class  gmx::test::ExactTextMatch
 Use an exact text match (the contents should be exactly equal). More...
 
class  gmx::test::NoTextMatch
 Do not match the text (the contents are ignored). More...
 
class  gmx::test::XvgMatch
 Match the contents as an xvg file. More...
 

Typedefs

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

Files

file  gmxpre.h
 Prerequisite header file for GROMACS build.
 
file  abstractdata.h
 Declares gmx::AbstractAnalysisData.
 
file  datamodule.h
 Declares gmx::IAnalysisDataModule 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::IAnalysisDataModule.
 
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  domdec_struct.h
 Declares structures related to domain decomposition.
 
file  ga2la.h
 Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined.
 
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  gpu_utils.h
 Declare functions for detection and initialization for GPU devices.
 
file  ocl_compiler.h
 Declare infrastructure for OpenCL JIT compilation.
 
file  oclutils.h
 Declare utility routines for OpenCL.
 
file  pmalloc_cuda.h
 Declare functions for host-side memory handling when using CUDA devices.
 
file  cpuinfo.h
 Declares gmx::CpuInfo.
 
file  hardwaretopology.h
 Declares gmx::HardwareTopology.
 
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  disre.h
 Declares functions for handling distance restraints.
 
file  manage-threading.h
 Declares functions for managing threading of listed forces.
 
file  orires.h
 Declares functions for handling orientation restraints.
 
file  pairs.h
 This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
 
file  position-restraints.h
 This file contains declarations necessary for low-level functions for computing energies and forces for position restraints.
 
file  invertmatrix.h
 Declares routines to invert 3x3 matrices.
 
file  groupcoord.h
 Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
 
file  nbnxn_gpu_data_mgmt.h
 Declare interface for GPU data transfer for NBNXN module.
 
file  simulationsignal.h
 This file declares functions for inter-rank signalling by mdrun.
 
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  threadaffinity.h
 Declares functions for managing mdrun thread affinity.
 
file  pull-params.h
 This file contains datatypes for the mdp options used by the pull code.
 
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::IHelpTopic.
 
file  helpwritercontext.h
 Declares gmx::HelpWriterContext.
 
file  ihelptopic.h
 Declares gmx::IHelpTopic.
 
file  mock_helptopic.h
 Declares mock implementation of gmx::IHelpTopic.
 
file  abstractoption.h
 Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo.
 
file  abstractoptionstorage.h
 Declares gmx::AbstractOptionStorage.
 
file  behaviorcollection.h
 Declares gmx::OptionsBehaviorCollection.
 
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  scalar.h
 Scalar float functions corresponding to GROMACS SIMD functions.
 
file  scalar_math.h
 Scalar math functions mimicking GROMACS SIMD math functions.
 
file  scalar_util.h
 Scalar utility functions mimicking GROMACS SIMD utility functions.
 
file  simd.h
 Definitions, capabilities, and wrappers for SIMD module.
 
file  simd_math.h
 Math functions for SIMD datatypes.
 
file  support.h
 Functions to query compiled and supported SIMD architectures.
 
file  vector_operations.h
 SIMD operations corresponding to Gromacs rvec datatypes.
 
file  statistics.h
 Declares simple statistics toolbox.
 
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  alignedallocator.h
 Declares gmx::AlignedAllocator that is used to make standard library containers compatible with SIMD contents that require aligned load/store.
 
file  basenetwork.h
 Utility functions for basic MPI and network functionality.
 
file  binaryinformation.h
 Helper functionality for information about the currently running binary.
 
file  bitmask.h
 Declares gmx_bitmask_t and associated functions.
 
file  classhelpers.h
 Declares common utility classes and macros.
 
file  coolstuff.h
 Functionality for printing cool strings.
 
file  dir_separator.h
 Provides OS-specific directory-name separator.
 
file  directoryenumerator.h
 Declares gmx::DirectoryEnumerator.
 
file  fileredirector.h
 Declares gmx::IFileOutputRedirector.
 
file  filestream.h
 Declares implementations for textstream.h interfaces for file input/output.
 
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  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.
 
file  messagestringcollector.h
 Declares gmx::MessageStringCollector.
 
file  mutex.h
 Declares C++11-style basic threading primitives (gmx::Mutex, gmx::lock_guard).
 
file  nodelete.h
 Declares no_delete deleter for std::shared_ptr.
 
file  path.h
 Declares functions for OS-independent path handling.
 
file  pleasecite.h
 Declares please_cite() for printing out literature references.
 
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  strdb.h
 Declares C functions for reading files with a list of strings.
 
file  stringstream.h
 Declares implementations for textstream.h interfaces for input/output to in-memory strings.
 
file  sysinfo.h
 Declares functions for obtaining information about the operating environment and the current process.
 
file  textreader.h
 Declares gmx::TextReader.
 
file  textstream.h
 Declares interfaces for simple input/output streams.
 
file  textwriter.h
 Declares gmx::TextWriter.
 
file  txtdump.h
 Declares helper functions for dumping basic data structures as text.
 
file  cmdlinetest.h
 Declares utilities testing command-line programs.
 
file  conftest.h
 Declares function to add the content of a conf file to a checker.
 
file  integrationtests.h
 Declares test fixture for integration tests.
 
file  interactivetest.h
 Provides helper classes for testing interactive prompts.
 
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.
 
file  textblockmatchers.h
 Declares utility classes for testing multi-line strings against reference data.
 
file  xvgtest.h
 Declares function to add the content of an xvg file to a checker.