gmx | Generic GROMACS namespace |
test | Testing utilities namespace |
AnalysisDataTestInputPointSet | Represents a single set of points in AnalysisDataTestInputFrame structure |
AnalysisDataTestInputFrame | Represents a single frame in AnalysisDataTestInput structure |
AnalysisDataTestInput | Represents static input data for AbstractAnalysisData tests |
AnalysisDataTestFixture | Test fixture for AbstractAnalysisData testing |
MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
CommandLine | Helper class for tests that need to construct command lines |
CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
CommandLineTestBase | Test fixture for tests that call a single command-line program with input/output files |
ConfMatch | Match the contents as an gro file |
IntegrationTestFixture | Test fixture for integration tests |
InteractiveTestHelper | Helper class for testing interactive sessions |
TestReferenceChecker | Handles comparison to test reference data |
TestReferenceData | Handles creation of and comparison to test reference data |
StringTestBase | Test fixture for tests that check string formatting |
FloatingPointDifference | Computes and represents a floating-point difference value |
FloatingPointTolerance | Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance |
TestException | Exception class for reporting errors in tests |
TestFileManager | Helper for tests that need input and output files |
TestFileInputRedirector | In-memory implementation for IFileInputRedirector for tests |
TestFileOutputRedirector | In-memory implementation of IFileOutputRedirector for tests |
TestOptionsProvider | Provides additional options for the test executable |
ITextBlockMatcher | Represents a text matcher, matching text stream contents against reference data |
ITextBlockMatcherSettings | Represents a factory for creating a text matcher |
ExactTextMatch | Use an exact text match (the contents should be exactly equal) |
NoTextMatch | Do not match the text (the contents are ignored) |
XvgMatch | Match the contents as an xvg file |
AbstractAnalysisData | Abstract base class for all objects that provide data |
AnalysisData | Parallelizable data container for raw data |
AnalysisDataHandle | Handle for inserting data into AnalysisData |
AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
AnalysisArrayData | Simple in-memory data array |
AnalysisDataValue | Value type for representing a single value in analysis data objects |
AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
AnalysisDataModuleManager | Encapsulates handling of data modules attached to AbstractAnalysisData |
AnalysisDataStorageFrame | Allows assigning values for a data frame in AnalysisDataStorage |
AnalysisDataStorage | Helper class that implements storage of data |
AnalysisDataAverageModule | Data module for independently averaging each column in input data |
AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
AnalysisDataDisplacementModule | Data module for calculating displacements |
AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
AbstractAverageHistogram | Base class for representing histograms averaged over frames |
AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
AnalysisDataBinAverageModule | Data module for bin averages |
AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
AnalysisDataPlotSettings | Common settings for data plots |
AbstractPlotModule | Abstract data module for writing data into a file |
AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
AnalysisDataParallelOptions | Parallelization options for analysis data objects |
CommandLineHelpContext | Context information for writing out command-line help |
GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
ConstArrayRef | STL-like container for non-mutable interface to a C array (or part of a std::vector) |
CommandLineHelpWriter | Writes help information for Options |
CommandLineModuleSettings | Settings to pass information between a module and the general runner |
ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
CommandLineModuleGroup | Handle to add content to a group added with CommandLineModuleManager::addModuleGroup() |
ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
CommandLineParser | Implements command-line parsing for Options objects |
IExecutableEnvironment | Allows customization of the way various directories are found by CommandLineProgramContext |
CommandLineProgramContext | Program context implementation for command line programs |
CpuInfo | Detect CPU capabilities and basic logical processor info |
LogicalProcessor | Entry with basic information for a single logical processor |
HardwareTopology | Information about sockets, cores, threads, numa, caches |
Cache | Information about a single cache level |
Core | Information about a single core in a socket |
Device | Information about a single PCI device |
HWThread | Information about a single hardware thread in a core |
LogicalProcessor | Information about socket, core and hwthread for a logical processor |
Machine | Hardware topology information about the entire machine |
Numa | Information about a single numa node |
NumaNode | Information about each numa node in system |
Socket | Information about a single socket in the system |
StaticLog2 | Evaluate log2(n) for integer n statically at compile time |
StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
BasicVector | C++ class for 3D vectors |
ArrayRef | STL-like container for an interface to a C array (or part of a std::vector) |
TextTableFormatter | Formats rows of a table for text output |
HelpManager | Helper for providing interactive online help |
AbstractSimpleHelpTopic | Abstract base class for help topics that have simple text and no subtopics |
AbstractCompositeHelpTopic | Abstract base class for help topics that have simple text and subtopics |
SimpleHelpTopic | Template for simple implementation of AbstractSimpleHelpTopic |
CompositeHelpTopic | Template for simple implementation of AbstractCompositeHelpTopic |
HelpLinks | Hyperlink data for writing out help |
HelpWriterContext | Context information for writing out help |
IHelpTopic | Provides a single online help topic |
OptionStorageTemplate | Templated base class for constructing option value storage classes |
AbstractOption | Abstract base class for specifying option properties |
OptionTemplate | Templated base class for constructing concrete option settings classes |
OptionInfo | Gives information and allows modifications to an option after creation |
AbstractOptionStorage | Abstract base class for converting, validating, and storing option values |
BooleanOption | Specifies an option that provides boolean values |
IntegerOption | Specifies an option that provides integer values |
Int64Option | Specifies an option that provides 64-bit integer values |
DoubleOption | Specifies an option that provides floating-point (double) values |
FloatOption | Specifies an option that provides floating-point (float) values |
StringOption | Specifies an option that provides string values |
EnumOption | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
BooleanOptionInfo | Wrapper class for accessing boolean option information |
IntegerOptionInfo | Wrapper class for accessing integer option information |
Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
DoubleOptionInfo | Wrapper class for accessing floating-point option information |
FloatOptionInfo | Wrapper class for accessing floating-point option information |
StringOptionInfo | Wrapper class for accessing string option information |
EnumOptionInfo | Wrapper class for accessing enum option information |
OptionsBehaviorCollection | Container for IOptionsBehavior objects |
FileNameOption | Specifies an option that provides file names |
FileNameOptionInfo | Wrapper class for accessing file name option information |
FileNameOptionManager | Handles interaction of file name options with global options |
IOptionsBehavior | Interface to provide extension points for options parsing |
IOptionsContainer | Interface for adding input options |
OptionManagerContainer | Container to keep managers added with Options::addManager() and pass them to options |
IOptionManager | Base class for option managers |
Options | Collection of options |
OptionsAssigner | Decorator class for assigning values to Options |
OptionsVisitor | Pure interface for visiting options in a Options object |
OptionsTypeVisitor | Abstract base class for visiting options of a particular type |
OptionsIterator | Decorator class for visiting options in a Options object |
OptionsModifyingVisitor | Pure interface for visiting options in a Options object, allowing modifications |
OptionsModifyingTypeVisitor | Abstract base class for visiting options of a particular type, allowing modifications |
OptionsModifyingIterator | Decorator class for visiting options in a Options object, allowing changes |
TimeUnitManager | Provides common functionality for time unit conversions |
TimeUnitBehavior | Options behavior to add a time unit option |
ExponentialDistribution | Exponential distribution |
param_type | Exponential distribution parameters |
GammaDistribution | Gamma distribution |
param_type | Gamma distribution parameters |
NormalDistribution | Normal distribution |
param_type | Normal distribution parameters |
TabulatedNormalDistribution | Tabulated normal random distribution |
param_type | Normal distribution parameter class (mean and stddev) |
ThreeFry2x64General | General implementation class for ThreeFry counter-based random engines |
ThreeFry2x64 | ThreeFry2x64 random engine with 20 iteractions |
ThreeFry2x64Fast | ThreeFry2x64 random engine with 13 iteractions |
UniformIntDistribution | Uniform integer distribution |
param_type | Uniform int distribution parameters |
UniformRealDistribution | Uniform real distribution |
param_type | Uniform real distribution parameters |
AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
AnalysisNeighborhood | Neighborhood searching for analysis tools |
AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
Selection | Provides access to a single selection |
SelectionPosition | Provides access to information about a single selected position |
SelectionCollection | Collection of selections |
SelectionFileOption | Specifies a special option that provides selections from a file |
SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
SelectionOption | Specifies an option that provides selection(s) |
SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
ITopologyProvider | Provides topology information to SelectionOptionBehavior |
SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
SelectionOptionManager | Handles interaction of selection options with other options and user input |
Simd4Double | SIMD4 double type |
Simd4DBool | SIMD4 variable type to use for logical comparisons on doubles |
Simd4Float | SIMD4 float type |
Simd4FBool | SIMD4 variable type to use for logical comparisons on floats |
SimdDouble | Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1 |
SimdDInt32 | Integer SIMD variable type to use for conversions to/from double |
SimdDBool | Boolean type for double SIMD data |
SimdDIBool | Boolean type for integer datatypes corresponding to double SIMD |
SimdFloat | Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1 |
SimdFInt32 | Integer SIMD variable type to use for conversions to/from float |
SimdFBool | Boolean type for float SIMD data |
SimdFIBool | Boolean type for integer datatypes corresponding to float SIMD |
SimdLoadFProxyInternal | Proxy object to enable load() for SIMD and float types |
SimdLoadUFProxyInternal | Proxy object to enable loadU() for SIMD and float types |
SimdLoadDProxyInternal | Proxy object to enable load() for SIMD and double types |
SimdLoadUDProxyInternal | Proxy object to enable loadU() for SIMD and double types |
SimdLoadIProxyInternal | Proxy object load() for SimdFInt32, SImdDInt32, and int32 |
SimdLoadUIProxyInternal | Proxy object - loadU() for SimdFInt32, SImdDInt32, and int32 |
SimdSetZeroProxyInternal | Proxy object to enable setZero() for SIMD and real types |
TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
TrajectoryAnalysisModule | Base class for trajectory analysis modules |
TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
TopologyInformation | Topology information passed to a trajectory analysis module |
TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
AlignedAllocator | Aligned memory allocator |
rebind | Standard-required typedef to use allocator with different class |
EmptyArrayRef | Tag type to initialize empty array references |
BinaryInformationSettings | Settings for printBinaryInformation() |
PrivateImplPointer | Helper class to manage a pointer to a private implementation class |
DataFileOptions | Search parameters for DataFileFinder |
DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
DataFileFinder | Searches data files from a set of paths |
DirectoryEnumerator | Lists files in a directory |
ExceptionInfo | Stores additional context information for exceptions |
ExceptionInitializer | Provides information for Gromacs exception constructors |
GromacsException | Base class for all exception objects in Gromacs |
FileIOError | Exception class for file I/O errors |
UserInputError | Exception class for user input errors |
InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
InconsistentInputError | Exception class for situations where user input is inconsistent |
SimulationInstabilityError | Exception class for simulation instabilities |
InternalError | Exception class for internal errors |
APIError | Exception class for incorrect use of an API |
NotImplementedError | Exception class for use of an unimplemented feature |
IFileInputRedirector | Allows overriding file existence checks from code that supports it |
IFileOutputRedirector | Allows capturing stdout and file output from code that supports it |
StandardInputStream | Text input stream implementation for reading from stdin |
TextInputFile | Text input stream implementation for reading from a file |
TextOutputFile | Text output stream implementation for writing to a file |
FlagsTemplate | Template class for typesafe handling of combination of flags |
Regex | Represents a regular expression |
MessageStringCollector | Helper class for collecting message strings, optionally with context |
MessageStringContext | Convenience class for creating a message context |
no_delete | Deleter for std::shared_ptr that does nothing |
InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
IProgramContext | Provides context information about the program that is calling the library |
scoped_cptr | Stripped-down version of scoped_ptr that uses sfree() or custom deleter |
StringOutputStream | Text output stream implementation for writing to an in-memory string |
StringInputStream | Helper class to convert static string data to a stream |
StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
TextLineWrapperSettings | Stores settings for line wrapping |
TextLineWrapper | Wraps lines to a predefined length |
TextReader | Reads text from a TextInputStream |
TextInputStream | Interface for reading text |
TextOutputStream | Interface for writing text |
TextWriter | Writes text into a TextOutputStream |
gmx_ana_index_t | Stores a single index group |
gmx_ana_indexmap_t | Data structure for calculating index group mappings |
gmx_ana_pos_t | Stores a set of positions together with their origins |
gmx_ga2la_t | Structure for all global to local mapping information |
gmx_laa_t | Structure for the local atom info for a plain list |
gmx_lal_t | Structure for the local atom info for a hash table |
gmx_sparsematrix | Sparse matrix storage format |
t_cosines | Declares inputrec data structure and utilities |
t_filenm | File name option definition for C code |
t_mdatoms | Declares mdatom data structure |
t_pargs | Command-line argument definition for C code |
t_pbc | Structure containing info on periodic boundary conditions |