Gromacs
2016.6
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Classes and other symbols that are publicly accessible within the GROMACS library.
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 | 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. | |