gmx | Generic GROMACS namespace |
compat | Compatibility aliases for standard library features |
internal | |
SimdTraits | Simd traits |
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 |
AllocatorTest | Templated test fixture |
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 |
IFileMatcher | Represents a file matcher, matching file contents against reference (or other) data |
IFileMatcherSettings | Represents a factory for creating a file matcher |
TextFileMatch | Use a ITextStreamMatcher for matching the contents |
NoContentsMatch | Do not check the contents of the file |
InteractiveTestHelper | Helper class for testing interactive sessions |
LoggerTestHelper | Helper class for tests to check output written to a logger |
TestReferenceChecker | Handles comparison to test reference data |
TestReferenceData | Handles creation of and comparison to test reference data |
StdioTestHelper | Helper class for tests where code reads directly from stdin |
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 |
Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
CommandLineHelpContext | Context information for writing out command-line help |
GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
ArrayRef | STL-like container for an interface to a C array of T (or part of a std::vector<T, A> or std::array<T>) |
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 |
HostAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers |
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 |
MDAtoms | Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators |
MDModules | Manages the collection of all modules used for mdrun |
ForceWithVirial | Container for force and virial for algorithms that provide their own virial tensor contribution |
IForceProvider | Interface for a component that provides forces during MD |
IMDModule | Extension module for GROMACS simulations |
IMDOutputProvider | Interface for handling additional output files during a simulation |
IMdpOptionProvider | Interface for handling mdp/tpr input to a mdrun module |
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 |
AbstractOptionSection | Base class for specifying option section properties |
AbstractOptionSectionHandle | Base class for handles to option sections |
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 |
IOptionsContainerWithSections | Interface for adding input options with sections |
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 |
OptionSection | Declares a simple option section |
OptionSectionHandle | Allows adding options to an OptionSection |
OptionStorageTemplateSimple | Simplified option storage template for options that have one-to-one value conversion |
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 |
RepeatingOptionSectionHandle | Allows adding options to an RepeatingOptionSection |
RepeatingOptionSection | Declares an option section that creates a structure for each instance |
TimeUnitManager | Provides common functionality for time unit conversions |
TimeUnitBehavior | Options behavior to add a time unit option |
OptionValueConverterSimple | Helper for converting from Variant to a given type |
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 |
SelectionTopologyProperties | Describes topology properties required for selection evaluation |
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 |
SimdFloatTag | Tag type to select to load SimdFloat with simdLoad(U) |
SimdDoubleTag | Tag type to select to load SimdDouble with simdLoad(U) |
SimdFInt32Tag | Tag type to select to load SimdFInt32 with simdLoad(U) |
SimdDInt32Tag | Tag type to select to load SimdDInt32 with simdLoad(U) |
AlignedArray< float, N > | Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
AlignedArray< double, N > | Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
SimdSetZeroProxyInternal | Proxy object to enable setZero() for SIMD and real types |
CubicSplineTable | Cubic spline interpolation table |
QuadraticSplineTable | Quadratic spline interpolation table |
AnalyticalSplineTableInput | Specification for analytical table function (name, function, derivative) |
NumericalSplineTableInput | Specification for vector table function (name, function, derivative, spacing) |
GpuTaskMapping | Specifies the GPU deviceID_ available for task_ to use |
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 |
UnionFinder | Union-find data structure for keeping track of disjoint sets |
MappedUnionFinder | Extension of UnionFind that supports non-consecutive integer indices as items |
AlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code |
PageAlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices |
Allocator | Policy-based 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 |
ToleranceError | Exception class when a specified tolerance cannot be achieved |
SimulationInstabilityError | Exception class for simulation instabilities |
InternalError | Exception class for internal errors |
APIError | Exception class for incorrect use of an API |
RangeError | Exception class for out-of-range values or indices |
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 |
ISerializer | Interface for types that convert standard data types into a form suitable for storage or transfer |
KeyValueTreePath | Identifies an entry in a key-value tree |
KeyValueTreeBuilder | Root builder for creating trees that have an object at the root |
KeyValueTreeValueBuilder | Builder for KeyValueTreeValue objects |
KeyValueTreeUniformArrayBuilder | Builder for KeyValueTreeArray objects where all elements are of type T |
KeyValueTreeObjectArrayBuilder | Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects |
KeyValueTreeObjectBuilder | Builder for KeyValueTreeObject objects |
IKeyValueTreeTransformRules | Interface to declare rules for transforming key-value trees |
KeyValueTreeTransformRulesScoped | Helper object returned from IKeyValueTreeTransformRules::scopedTransform() |
KeyValueTreeTransformRuleBuilder | Provides methods to specify one transformation rule |
AfterFrom | Properties that can be specified after from() |
ToObject | Properties that can be specified after from().toObject() |
ToValue | Properties that can be specified after from().to() |
ILogTarget | Target where log output can be written |
LogEntryWriter | Helper class for creating log entries with GMX_LOG |
LogLevelHelper | Represents a single logging level |
MDLogger | Declares a logging interface |
LoggerBuilder | Initializes loggers |
LoggerOwner | Manages memory for a logger built with LoggerBuilder |
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 |
StringCompare | Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare |
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 |
isIntegralConstant | Is true if type is a std::integral_constant |
Variant | Represents a dynamically typed value of an arbitrary type |
Mdrunner | Runner object for supporting setup and execution of mdrun |
df_history_t | Free-energy sampling history struct |
DomdecOptions | Structure containing all (command line) options for the domain decomposition |
ekinstate_t | Struct used for checkpointing only |
EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
ForceProviders | Evaluates forces from a collection of gmx::IForceProvider |
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_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
gmx_sparsematrix | Sparse matrix storage format |
GpuRegionTimerImpl | This is a GPU region timing implementation interface. It should provide methods for measuring the last timespan. Copying/assignment is disabled since the underlying timing events are owned by this |
GpuRegionTimerWrapper | This is a GPU region timing wrapper class. It allows for host-side tracking of the accumulated execution timespans in GPU code (measuring kernel or transfers duration). It also partially tracks the correctness of the timer state transitions, as far as current implementation allows (see TODO in getLastRangeTime() for a disabled check). Internally it uses GpuRegionTimerImpl for measuring regions |
GpuTraits | GPU build-path traits such as types |
history_t | History information for NMR distance and orientation restraints |
nonbonded_verlet_group_t | Non-bonded interaction group data structure |
nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
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 |
t_state | The microstate of the system |