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Gromacs
2019
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Gromacs
2019
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  gmx | Generic GROMACS namespace |
 detail | |
  PaddingTraits | Traits classes for handling padding for types used with PaddedVector |
 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 |
| ArrayRef | STL-like interface to a C array of T (or part of a std container of 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 |
| 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 |
| 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 |
| 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 |
| PaddedVector | PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS |
| BasicVector | C++ class for 3D vectors |
| 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 |
| 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 |
| 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 |
| 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 |
| OptionSection | Declares a simple option section |
| OptionSectionHandle | Allows adding options to an OptionSection |
| 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 |
| 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 |
| 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 |
 Block | Struct for returning the range of a block |
 iterator | An iterator that loops over integers |
| 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 |
| EmptyArrayRef | Tag type to initialize empty array references |
| 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 |
| 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 |
| 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 |
| TextLineWrapperSettings | Stores settings for line wrapping |
| TextLineWrapper | Wraps lines to a predefined length |
| df_history_t | Free-energy sampling history struct |
| 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_ffparams_t | Struct that holds all force field parameters for the simulated system |
| 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_sparsematrix | Sparse matrix storage format |
| InteractionListHandle | Type for returning a list of InteractionList references |
| MoleculeBlockIndices | Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents |
| 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 |
1.8.5
