gmx | Generic GROMACS namespace |
compat | Compatibility aliases for standard library features |
not_null | Restricts a pointer or smart pointer to only hold non-null values |
detail | |
extents_analyse< R, E0, StaticExtents...> | Enable querying extent of specific rank by splitting a static extents off the variadic template arguments |
extents_analyse< R, dynamic_extent, StaticExtents...> | Enable querying extent of specific rank by splitting a dynamic extent off the variadic template arguments |
extents_analyse< 0 > | Specialisation for rank 0 extents analysis. Ends recursive rank analysis |
internal | |
SimdTraits | Simd traits |
test | Testing utilities namespace |
detail | |
FormatterVariant | Single-component variant for a formatting callable for variables of type T |
FormatterVariant< Enum, typename std::enable_if_t< std::is_enum_v< Enum > > > | Specialization for formatting function of variables whose type is an enum |
ParamsToFormatterVariants | Template for mapping parameter types to formatter variants |
ParamsToFormatterVariants< std::tuple< Ts...> > | Specialization for tuple of parameter types to tuple of formatter variants |
IsTuple | Type trait for whether T is a std::tuple |
IsTuple< std::tuple< Ts...> > | Specialization to successfully match a std::tuple |
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 |
ModuleSelection | Helper class for tests that need an initialized selection |
ModuleTest | Test fixture to test matching file types for modules |
SetAtomsSupportedFiles | Helper to test supported file names |
SetAtomsUnSupportedFiles | Helper to test supported file names |
AnyOutputSupportedFiles | Helper to test supported file names |
NoOptionalOutput | Helper to test support for disabling all output options |
OutputSelectorDeathTest | Helper to test that invalid selection is rejected |
SetVelocitySupportedFiles | Helper to test supported file names |
SetVelocityUnSupportedFiles | Helper to test supported file names |
SetForceSupportedFiles | Helper to test supported file names |
SetForceUnSupportedFiles | Helper to test supported file names |
SetPrecisionSupportedFiles | Helper to test supported file names |
SetPrecisionUnSupportedFiles | Helper to test supported file names |
FlagTest | Test fixture to test user inputs |
TestSystem | Description of the system used for testing |
AllocatorTest | Templated test fixture |
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 ITextBlockMatcher 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 |
NameOfTestFromTuple | Function object that helps GoogleTest name our test cases |
RefDataFilenameMaker | Functor to name a refdata filename for this test |
PrefixFormatter | Functor to add a prefix to the return from formatter for T |
TestReferenceData | Handles creation of and comparison to test reference data |
TestReferenceChecker | Handles 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) |
FilteringExactTextMatch | Use an exact text match after scrubbing lines of the text that match the supplied regular expressions |
TprAndFileManager | Helper to bundle generated TPR and the file manager to clean it up |
XvgMatch | Match the contents as an xvg file |
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 |
ArrayRef | STL-like interface to a C array of T (or part of a std container of T) |
AnalysisDataParallelOptions | Parallelization options for analysis data objects |
Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
DensityFittingModuleInfo | Information about the density fitting module |
INNPotModel | NNPot Module |
NNPotTopologyPreprocessor | Class responsible for all modifications of the topology during input pre-processing |
TorchModel | Class responsible for loading and evaluating a TorchScript-compiled neural network model. Inherits from NNPotModel |
CommandLineHelpContext | Context information for writing out command-line help |
GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
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 |
TrajectoryFileOpener | Low level method to take care of only file opening and closing |
TrajectoryFrameWriter | Writes coordinate frames to a sink, e.g. a trajectory file |
ProcessFrameConversion | ProcessFrameConversion class for handling the running of several analysis steps |
IFrameConverter | IFrameConverter interface for manipulating coordinate information |
IOutputAdapter | OutputAdapter class for handling trajectory file flag setting and processing |
OutputAdapterContainer | Storage for output adapters that modify the state of a t_trxframe object |
OutputSelector | OutputSelector class controls setting which coordinates are actually written |
SetAtoms | SetAtoms class controls availability of atoms data |
SetBox | Allows changing box information when writing a coordinate file |
SetForces | SetForces class allows changing writing of forces to file |
SetPrecision | SetPrecision class allows changing file writing precision |
SetStartTime | SetStartTime class allows changing trajectory time information |
SetTimeStep | SetTimeStep class allows changing trajectory time information |
SetVelocities | SetVelocities class allows changing writing of velocities to file |
OutputRequirementOptionDirector | Container for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer |
OutputRequirements | Finalized version of requirements after processing |
DomainDecompositionBuilder | Builds a domain decomposition management object |
FixedCapacityVector | Vector that behaves likes std::vector but has fixed capacity |
HashedMap | Unordered key to value mapping |
GpuHaloExchange | Manages GPU Halo Exchange object |
LocalAtomSet | A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator |
LocalAtomSetManager | Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel |
LocalTopologyChecker | Has responsibility for checking that the local topology distributed across domains describes a total number of bonded interactions that matches the system topology |
DomdecOptions | Structure containing all (command line) options for the domain decomposition |
EnergyAnalysisFrame | Class describing an energy frame, that is the all the data stored for one energy term at one time step in an energy file |
EnergyTerm | Class describing the whole time series of an energy term |
EnergyNameUnit | Convenience structure for keeping energy name and unit together |
IEnergyAnalysis | Interface class overloaded by the separate energy modules |
SeparatePmeRanksPermitted | Class for managing usage of separate PME-only ranks |
PmeForceSenderGpu | Manages sending forces from PME-only ranks to their PP ranks |
PmePpCommGpu | Manages communication related to GPU buffers between this PME rank and its PP rank |
RocfftInitializer | Provides RAII-style initialization of rocFFT library |
RocfftPlan | All the persistent data for planning an executing a 3D FFT |
PlanSetupData | Helper struct to reduce repetitive code setting up a 3D FFT plan |
MDModulesCheckpointReadingDataOnMain | Provides the MDModules with the checkpointed data on the main rank |
MDModulesCheckpointReadingBroadcast | Provides the MDModules with the communication record to broadcast |
MDModulesWriteCheckpointData | Writing the MDModules data to a checkpoint file |
H5md | Manager of an H5MD filehandle. The class is designed to read/write data according to de Buyl et al., 2014 (https://doi.org/10.1016/j.cpc.2014.01.018) and https://www.nongnu.org/h5md/h5md.html |
MrcDensityMapOfFloatReader | Read an mrc/ccp4 file that contains float values |
MrcDensityMapOfFloatFromFileReader | Read an mrc density map from a given file |
MrcDensityMapOfFloatWriter | Write an mrc/ccp4 file that contains float values |
MrcDataStatistics | Statistics about mrc data arrays |
MrcDensitySkewData | Skew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" |
CrystallographicLabels | Crystallographic labels for mrc data |
MrcDensityMapHeader | A container for the data in mrc density map file formats |
ArrayRefWithPadding | Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses |
ListOfLists | A list of lists, optimized for performance |
ClfftInitializer | Handle clFFT library init and tear down in RAII style also with mutual exclusion |
DeviceStreamManager | Device stream and context manager |
HostAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers |
OpenClTraits | Stub for OpenCL type traits |
OpenClTraitsBase | Implements common trait infrastructure for OpenCL types |
OpenClTraits< cl_context > | Implements traits for cl_context |
OpenClTraits< cl_command_queue > | Implements traits for cl_command_queue |
OpenClTraits< cl_program > | Implements traits for cl_program |
OpenClTraits< cl_kernel > | Implements traits for cl_kernel |
ClHandle | Wrapper of OpenCL type cl_type to implement RAII |
CpuInfo | Detect CPU capabilities and basic logical processor info |
LogicalProcessor | Entry with basic information for a single processing unit |
HardwareTopology | Information about packages, cores, processing units, numa, caches |
Cache | Information about a single cache level |
Core | Information about a single core in a package |
Device | Information about a single PCI device |
LogicalProcessor | Information about package, core and processing unit for a logical processor |
Machine | Hardware topology information about the entire machine |
Numa | Information about all numa nodes |
NumaNode | Information about each numa node in system |
Package | Information about a single package in the system |
ProcessingUnit | Information about a single processing unit (in a core) |
EnumerationArray | Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type |
TranslateAndScale | Transform coordinates in three dimensions by first translating, then scaling them |
AffineTransformation | Affine transformation of three-dimensional coordinates |
DensitySimilarityMeasure | Measure similarity and gradient between densities |
DensityFittingForce | Manages evaluation of density-fitting forces for particles that were spread with a kernel |
ExponentialMovingAverageState | Store the state of exponential moving averages |
ExponentialMovingAverage | Evaluate the exponential moving average with bias correction |
GaussianSpreadKernelParameters | Parameters for density spreading kernels |
PositionAndAmplitude | Parameters that describe the kernel position and amplitude |
Shape | Shape parameters for Gaussian spreading kernels describe the kernel shape |
GaussTransform3D | Sums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as |
MultiDimArray | Multidimensional array that manages its own memory |
PaddedVector | PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS |
CheckpointHandler | Class handling the checkpoint signal |
Constraints | Handles constraints |
AtomPair | A pair of atoms indexes |
MDAtoms | Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators |
ResetHandler | Class handling the reset of counters |
SettleData | Data for executing SETTLE constraining |
shakedata | Working data for the SHAKE algorithm |
SimulationSignal | POD-style object used by mdrun ranks to set and receive signals within and between simulations |
SimulationSignaller | Object used by mdrun ranks to signal to each other at this step |
StopHandler | Class handling the stop signal |
StopConditionSignal | Class setting the stop signal based on gmx_get_stop_condition() |
StopConditionTime | Class setting the stop signal based on maximal run time |
StopHandlerBuilder | Class preparing the creation of a StopHandler |
Update | Contains data for update phase |
UpdateGroups | Owns the update grouping and related data |
Range | Defines a range of integer numbers and accompanying operations |
iterator | An iterator that loops over a range of integers |
UpdateGroupsCog | Class for managing and computing centers of geometry of update groups |
VirtualSitesHandler | Class that handles construction of vsites and spreading of vsite forces |
WholeMoleculeTransform | This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules |
LegacyMdrunOptions | This class provides the same command-line option functionality to both CLI and API sessions |
MDModules | Manages the collection of all modules used for mdrun |
MembedHolder | Membed SimulatorBuilder parameter type |
Mdrunner | Runner object for supporting setup and execution of mdrun |
MdrunnerBuilder | Build a gmx::Mdrunner |
SimulationContext | Simulation environment and configuration |
SimulatorConfig | Simulation configuation settings |
SimulatorStateData | Data for a specific simulation state |
SimulatorEnv | Collection of environmental information for a simulation |
Profiling | Collection of profiling information |
ConstraintsParam | Collection of constraint parameters |
LegacyInput | Collection of legacy input information |
InteractiveMD | SimulatorBuilder parameter type for InteractiveMD |
IonSwapping | Parameter type for IonSwapping SimulatorBuilder component |
TopologyData | Collection of handles to topology information |
BoxDeformationHandle | Handle to information about the box |
SimulatorBuilder | Class preparing the creation of Simulator objects |
MDModulesNotifier | Organizes notifications about an event of interest to modules |
BuildMDModulesNotifier< CurrentCallParameter, CallParameter...> | Template specialization to assemble MDModulesNotifier |
MDModulesAtomsRedistributedSignal | Notification that atoms may have been redistributed |
MDModulesEnergyOutputToDensityFittingRequestChecker | Check if module outputs energy to a specific field |
MDModulesEnergyOutputToQMMMRequestChecker | Check if QMMM module outputs energy to a specific field |
EnergyCalculationFrequencyErrors | Collect errors for the energy calculation frequency |
SimulationTimeStep | Provides the simulation time step in ps |
CoordinatesAndBoxPreprocessed | Provides coordinates and simulation box |
MdRunInputFilename | Mdrun input filename |
EdrOutputFilename | Energy trajectory output filename from Mdrun |
QMInputFileName | Notification for QM program input filename provided by user as command-line argument for grompp |
PlumedInputFilename | Notification for the optianal plumed input filename provided by user as command-line argument for mdrun |
EnsembleTemperature | Provides the constant ensemble temperature |
MDModulesNotifiers | Group of notifers to organize that MDModules can receive callbacks they subscribe to |
accessor_basic | The most basic memory access model for mdspan |
extents | Multidimensional extents with static and dynamic dimensions |
layout_right | Right-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number |
mapping | Mapping from multidimensional indices within extents to 1D index |
basic_mdspan | Multidimensional array indexing and memory access with flexible mapping and access model |
CheckpointData | } |
IsSerializableEnum | { |
ReadCheckpointDataHolder | Holder for read checkpoint data |
WriteCheckpointDataHolder | Holder for write checkpoint data |
ForceBuffersView | A view of the force buffer |
ForceBuffers | Object that holds the force buffers |
ForceWithShiftForces | Container for force and virial for algorithms that compute shift forces for virial calculation |
ForceWithVirial | Container for force and virial for algorithms that provide their own virial tensor contribution |
ForceOutputs | Force and virial output buffers for use in force computation |
ForceProviderInput | Helper struct that bundles data for passing it over to the force providers |
ForceProviderOutput | Helper struct bundling the output data of a force provider |
IForceProvider | Interface for a component that provides forces during MD |
ForceProviders | Evaluates forces from a collection of gmx::IForceProvider |
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 |
MtsLevel | Setting for a single level for multiple time step integration |
GromppMtsOpts | Struct for passing the MTS mdp options to setupMtsLevels() |
ObservablesReducerBuilder | Builder for ObservablesReducer |
ObservablesReducer | Manage reduction of observables for registered subscribers |
StepWorkload | Describes work done on this domain by the current rank that may change per-step |
DomainLifetimeWorkload | Describes work done on this domain on every step of its lifetime, but which might change after the next domain partitioning |
SimulationWorkload | Manage what computation is required during the simulation |
ModularSimulator | The modular simulator |
ElementNotFoundError | Exception class signalling that a requested element was not found |
MissingElementConnectionError | Exception class signalling that elements were not connected properly |
SimulationAlgorithmSetupError | Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way |
CheckpointError | Exception class signalling an error in reading or writing modular checkpoints |
EnergyAccumulator | Base energy accumulator class, only specializations are used |
BenchmarkSystem | Description of the system used for benchmarking |
EnergyFunctionProperties | Set of boolean constants mimicking preprocessor macros |
GridDimensions | The physical dimensions of a grid |
nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
gmx_cache_protect_t | Cache-line protection buffer |
nbnxn_cj_t | This is the actual cluster-pair list j-entry |
JClusterList | Simple j-cluster list |
nbnxn_sci_t | Grouped pair-list i-unit |
nbnxn_im_ei_t | Interaction data for a j-group for one warp |
nbnxn_cj_packed_t | Packed j-cluster list element |
PackedJClusterList | Packed j-cluster list |
nbnxn_excl_t | Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist |
NbnxnPairlistCpu | Cluster pairlist type for use on CPUs |
PairlistSets | Contains sets of pairlists |
NbnxmPairlistCpuWork | Working data for the actual i-supercell during pair search |
IClusterData | Struct for storing coordinates and bounding box for an i-entry during search |
nbnxn_cycle_t | Local cycle count struct for profiling |
PairsearchWork | Thread-local work struct, contains working data for Grid |
PairSearch | Main pair-search struct, contains the grid(s), not the pair-list(s) |
CoulombCalculator | Base Coulomb calculator class, only specializations are used |
CoulombCalculator< KernelCoulombType::RF > | Specialized calculator for RF |
CoulombCalculator< KernelCoulombType::EwaldAnalytical > | Specialized calculator for Ewald using an analytic approximation |
CoulombCalculator< KernelCoulombType::EwaldTabulated > | Specialized calculator for Ewald using tabulated functions |
DiagonalMasker | Base Coulomb calculator class, only specializations are used |
DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > | Specialized masker for JSizeEqualsISize |
DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > | Specialized masker for JSizeIsDoubleISize |
DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > | Specialized masker for JSizeIsHalfISize |
EnergyAccumulator< useEnergyGroups, false > | Specialized energy accumulator class for no energy calculation |
EnergyAccumulator< false, true > | Specialized energy accumulator class for energy accumulation without energy groups |
EnergyAccumulator< true, true > | Specialized energy accumulator class for energy accumulation with energy groups |
EnergyGroupsPerCluster | Holds energy group indices for use in EnergyAccumulator<true, true> |
LennardJonesCalculator | Base LJ calculator class, only specializations are used |
LennardJonesCalculator< false, InteractionModifiers::PotShift > | Specialized calculator for LJ with potential shift and no energy calculation |
LennardJonesCalculator< true, InteractionModifiers::PotShift > | Specialized calculator for LJ with potential shift and energy calculation |
LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > | Specialized calculator for LJ with force switch |
LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > | Specialized calculator for LJ with potential switch |
NbnxmKernel | Class name for NBNXM kernel |
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 |
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 |
OptionsBehaviorCollection | Container for IOptionsBehavior objects |
OptionManagerContainer | Container to keep managers added with Options::addManager() and pass them to options |
OptionsAssigner | Decorator class for assigning values to Options |
OptionSection | Declares a simple option section |
OptionSectionHandle | Allows adding options to an OptionSection |
OptionStorageTemplate | Templated base class for constructing option value storage classes |
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 |
OptionValueConverterSimple | Helper for converting from Any to a given type |
PullCoordExpressionParser | Class with a mathematical expression and parser |
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 |
RestraintManager | Manage the Restraint potentials available for Molecular Dynamics |
RestraintMDModule | MDModule wrapper for Restraint implementations |
Site | Abstraction for a restraint interaction site |
SelectionFileOption | Specifies a special option that provides selections from a file |
SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
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) |
SimdSetZeroProxy | 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) |
DevelopmentFeatureFlags | Structure that holds boolean flags corresponding to the development features present enabled through environment variables |
GpuTaskMapping | Specifies the GPU deviceID_ available for task_ to use |
GpuTaskAssignmentsBuilder | Builder for the GpuTaskAssignments for all ranks on this node |
GpuTaskAssignments | Contains the GPU task assignment for all ranks on this physical node |
ConvertTprInfo | Declares gmx convert-tpr |
ExclusionBlock | Describes exclusions for a single atom |
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 |
Any | Represents a dynamically typed value of an arbitrary type - deprecated |
BinaryInformationSettings | Settings for printBinaryInformation() |
BoolType | A clone of a bool as a workaround on the template specialization of std::vector<bool> that is incompatible with ArrayRef |
DataFileOptions | Search parameters for DataFileFinder |
DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
DataFileFinder | Searches data files from a set of paths |
DefaultInitializationAllocator | Allocator adaptor that interposes construct() calls to convert value initialization into default initialization |
DirectoryEnumerator | Lists files in a directory |
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 |
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 |
PhysicalNodeCommunicator | Holds a communicator for the physical node of this rank |
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 |
StringToEnumValueConverter | A class to convert a string to an enum value of type EnumType |
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 |
no_delete | Deleter for std::shared_ptr that does nothing |
NonbondedBenchmarkInfo | Declares gmx nonbonded-bench |
BasicVector | C++ class for 3D vectors |
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 |
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 |
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 |
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 |
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 an EnumerationArray of string values and writes the selected index into an enum variable |
LegacyEnumOption | 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 |
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 |
IOptionManager | Base class for option managers |
Options | Collection of options |
TimeUnitManager | Provides common functionality for time unit conversions |
TimeUnitBehavior | Options behavior to add a time unit option |
PotentialPointData | Structure to hold the results of IRestraintPotential::evaluate() |
IRestraintPotential | Interface for Restraint potentials |
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 |
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 |
RangePartitioning | Division of a range of indices into consecutive blocks |
TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
TrajectoryAnalysisModule | Base class for trajectory analysis modules |
TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
TopologyInformation | Topology information available to a trajectory analysis module |
EnumerationIterator | Allows iterating sequential enumerators |
EnumerationWrapper | Allows constructing iterators for looping over sequential enumerators |
EnumClassSuitsEnumerationArray | Helper class to determine whether a template type that is an enum class has a Count field |
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 |
ParallelConsistencyError | Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion |
ModularSimulatorError | Exception class for modular simulator |
FlagsTemplate | Template class for typesafe handling of combination of flags |
InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
IProgramContext | Provides context information about the program that is calling the library |
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 |
EqualCaseInsensitive | Function object for comparisons with equalCaseInsensitive |
TextLineWrapperSettings | Stores settings for line wrapping |
TextLineWrapper | Wraps lines to a predefined length |
CompileTimeStringJoin | Combines string literals at compile time to final string |
AtomIterator | Object that allows looping over all atoms in an mtop |
AtomProperties | Holds all the atom property information loaded |
AtomProxy | Proxy object returned from AtomIterator |
AtomRange | Range over all atoms of topology |
AtomsAdjacencyListElement | Helper type for discovering coupled constraints |
BalanceRegion | Object that describes a DLB balancing region |
BondedInteraction | Information about single bonded interaction |
BondedInteractionList | Accumulation of different bonded types for preprocessing |
CheckpointHeaderContents | Header explaining the context of a checkpoint file |
DDBalanceRegionHandler | Manager for starting and stopping the dynamic load balancing region |
DeviceInformation | Platform-dependent device information |
DeviceStream | Declaration of platform-agnostic device stream/queue |
df_history_t | Free-energy sampling history struct |
ekinstate_t | Struct used for checkpointing only |
EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
FEPStateValue | Template wrapper struct for particle FEP state values |
ForceHelperBuffers | Helper force buffers for ForceOutputs |
ForeignLambdaTerms | Accumulates free-energy foreign lambda energies and dH/dlamba |
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_cmap_t | CMAP grids |
gmx_cmapdata_t | CMAP data for a single grid |
gmx_domdec_constraints_t | Struct used during constraint setup with domain decomposition |
gmx_enerdata_t | Struct for accumulating all potential energy terms and some kinetic energy terms |
gmx_ffparams_t | Struct that holds all force field parameters for the simulated system |
gmx_ga2la_t | Global to local atom mapping |
Entry | Structure for the local atom info |
gmx_localtop_t | The fully written out topology for a domain over its lifetime |
gmx_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
gmx_moltype_t | Molecules type data: atoms, interactions and exclusions |
gmx_multisim_t | Coordinate multi-simulation resources for mdrun |
gmx_nodecomm_t | Settings and communicators for two-step communication: intra + inter-node |
gmx_sparsematrix | Sparse matrix storage format |
GpuRegionTimerImpl | The OpenCL implementation of the GPU code region timing. With OpenCL, one has to use cl_event handle for each API call that has to be timed, and accumulate the timing afterwards. As we would like to avoid overhead on API calls, we only query and accumulate cl_event timing at the end of time steps, not after the API calls. Thus, this implementation does not reuse a single cl_event for multiple calls, but instead maintains an array of cl_events to be used within any single code region. The array size is fixed at a small but sufficiently large value for the number of cl_events that might contribute to a timer region, currently 10 |
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 |
history_t | History information for NMR distance and orientation restraints |
IListIterator | Object that allows looping over all atoms in an mtop |
IListProxy | Proxy object returned from IListIterator |
IListRange | Range over all interaction lists of topology |
IndexGroup | An index group consisting or a name and list of atom indices |
InteractionDefinitions | Struct with list of interaction parameters and lists of interactions |
InteractionList | List of listed interactions |
InteractionListHandle | Type for returning a list of InteractionList references |
InteractionOfType | Describes an interaction of a given type, plus its parameters |
InteractionsOfType | A set of interactions of a given type (found in the enumeration in ifunc.h), complete with atom indices and force field function parameters |
ListedForces | Class for calculating listed interactions, uses OpenMP parallelization |
LocalSettleData | Local settle data |
MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
MoleculeInformation | Holds the molecule information during preprocessing |
MoleculePatch | Block to modify individual residues |
MoleculePatchDatabase | A set of modifications to apply to atoms |
NumPmeDomains | Struct for passing around the number of PME domains |
ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
PartialDeserializedTprFile | Contains the partly deserialized contents of a TPR file |
PbcAiuc | Compact and ordered version of the PBC matrix |
PdbAtomEntry | Contains information for a single particle in a PDB file |
PmeGpuProgram | Stores PME data derived from the GPU context or devices |
PmeSolve | Class for solving PME for Coulomb and LJ |
PpRanks | Contains information about the PP ranks that partner this PME rank |
PreprocessingAtomTypes | Storage of all atom types used during preprocessing of a simulation input |
PreprocessingBondAtomType | Storage for all bonded atomtypes during simulation preprocessing |
PreprocessResidue | Information about preprocessing residues |
ReplicaExchangeParameters | The parameters for the replica exchange algorithm |
SettleWaterTopology | Composite data for settle initialization |
SimulationGroups | Contains the simulation atom groups |
SimulationInputHandle | Owning handle to a SimulationInput object |
SimulationParticle | Single particle in a simulation |
StringTable | A class to store strings for lookup |
StringTableBuilder | Builds a memory efficient storage for strings of characters |
StringTableEntry | Helper class to access members in StringTable |
SystemMomenta | System momenta used with with the box deform option |
SystemMomentum | The momentum and mass of the whole system |
t_filenm | File name option definition for C code |
t_idef | Deprecated interation definitions, used in t_topology |
t_ilist | Deprecated list of listed interactions |
t_interaction_function | Interaction function |
t_iparams | Union of various interaction paramters |
t_mapping | Maps an XPM element to an RGB color and a string description |
t_matrix | A matrix of integers, plus supporting values, such as used in XPM output |
t_mdatoms | Declares mdatom data structure |
t_nblist | A plain atom pair list, used only for perturbed non-bonded interactions |
IEntry | An i-entry |
JEntry | A j-entry |
t_oriresdata | Orientation restraining stuff |
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 |
t_symbuf | Legacy symbol table entry as linked list |
t_xpmelmt | Models an XPM element |
TpxFileHeader | First part of the TPR file structure containing information about the general aspect of the system |
wallcc_t | Counters for an individual wallcycle timing region |
WarningHandler | General warning handling object |
WaterMolecule | Indices of atoms in a water molecule |