gmx::ArrayRef< const AnalysisDataValue > | |
gmx::ArrayRef< const char *const > | |
gmx::ArrayRef< const double > | |
gmx::ArrayRef< const real > | |
gmx::ArrayRef< gmx::BasicVector > | |
gmx::ArrayRef< ValueType > | |
df_history_t | Free-energy sampling history struct |
gmx::FlagsTemplate< Flag > | |
gmx::AbstractAnalysisData | Abstract base class for all objects that provide data |
gmx::AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
gmx::AbstractAverageHistogram | Base class for representing histograms averaged over frames |
gmx::AnalysisArrayData | Simple in-memory data array |
gmx::AnalysisDataAverageModule | Data module for independently averaging each column in input data |
gmx::AnalysisDataBinAverageModule | Data module for bin averages |
gmx::AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
gmx::AnalysisData | Parallelizable data container for raw data |
gmx::AnalysisDataDisplacementModule | Data module for calculating displacements |
gmx::AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
gmx::AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
gmx::AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
gmx::AbstractOption | Abstract base class for specifying option properties |
gmx::OptionTemplate< T, U > | Templated base class for constructing concrete option settings classes |
gmx::OptionTemplate< bool, BooleanOption > | |
gmx::BooleanOption | Specifies an option that provides boolean values |
gmx::OptionTemplate< double, DoubleOption > | |
gmx::DoubleOption | Specifies an option that provides floating-point (double) values |
gmx::OptionTemplate< EnumType, EnumOption< EnumType > > | |
gmx::EnumOption< EnumType > | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
gmx::OptionTemplate< float, FloatOption > | |
gmx::FloatOption | Specifies an option that provides floating-point (float) values |
gmx::OptionTemplate< gmx_int64_t, Int64Option > | |
gmx::Int64Option | Specifies an option that provides 64-bit integer values |
gmx::OptionTemplate< int, IntegerOption > | |
gmx::IntegerOption | Specifies an option that provides integer values |
gmx::OptionTemplate< Selection, SelectionOption > | |
gmx::SelectionOption | Specifies an option that provides selection(s) |
gmx::OptionTemplate< std::string, FileNameOption > | |
gmx::FileNameOption | Specifies an option that provides file names |
gmx::OptionTemplate< std::string, StringOption > | |
gmx::StringOption | Specifies an option that provides string values |
gmx::AbstractOptionSection | Base class for specifying option section properties |
gmx::OptionSection | Declares a simple option section |
gmx::RepeatingOptionSection< T > | Declares an option section that creates a structure for each instance |
gmx::AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
gmx::AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
gmx::AnalysisDataHandle | Handle for inserting data into AnalysisData |
gmx::AnalysisDataPlotSettings | Common settings for data plots |
gmx::AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
gmx::AnalysisDataValue | Value type for representing a single value in analysis data objects |
gmx::AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
gmx::AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
gmx::AnalysisNeighborhood | Neighborhood searching for analysis tools |
gmx::AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
gmx::AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
gmx::AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
gmx::AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
gmx::ArrayRef< T > | STL-like container for an interface to a C array of T (or part of a std::vector<T, A> or std::array<T>) |
gmx::BasicVector< ValueType > | C++ class for 3D vectors |
gmx::CommandLineHelpWriter | Writes help information for Options |
gmx::CommandLineModuleSettings | Settings to pass information between a module and the general runner |
gmx::CommandLineParser | Implements command-line parsing for Options objects |
gmx::DataFileFinder | Searches data files from a set of paths |
gmx::DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
gmx::DataFileOptions | Search parameters for DataFileFinder |
gmx::EmptyArrayRef | Tag type to initialize empty array references |
gmx::ExceptionInfo< Tag, T > | Stores additional context information for exceptions |
gmx::ExceptionInitializer | Provides information for Gromacs exception constructors |
gmx::ExponentialDistribution< RealType > | Exponential distribution |
gmx::ExponentialDistribution< RealType >::param_type | Exponential distribution parameters |
gmx::FlagsTemplate< FlagType > | Template class for typesafe handling of combination of flags |
gmx::GammaDistribution< RealType > | Gamma distribution |
gmx::GammaDistribution< RealType >::param_type | Gamma distribution parameters |
gmx::IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
gmx::AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
gmx::AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
gmx::AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
gmx::AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
gmx::AbstractPlotModule | Abstract data module for writing data into a file |
gmx::AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
gmx::AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
gmx::AnalysisDataAverageModule | Data module for independently averaging each column in input data |
gmx::AnalysisDataBinAverageModule | Data module for bin averages |
gmx::AnalysisDataDisplacementModule | Data module for calculating displacements |
gmx::AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
gmx::AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
gmx::ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
gmx::ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
gmx::ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
gmx::IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
gmx::InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
gmx::IOptionManager | Base class for option managers |
gmx::FileNameOptionManager | Handles interaction of file name options with global options |
gmx::SelectionOptionManager | Handles interaction of selection options with other options and user input |
gmx::IOptionsBehavior | Interface to provide extension points for options parsing |
gmx::SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
gmx::TimeUnitBehavior | Options behavior to add a time unit option |
gmx::IOptionsContainer | Interface for adding input options |
gmx::IOptionsContainerWithSections | Interface for adding input options with sections |
gmx::AbstractOptionSectionHandle | Base class for handles to option sections |
gmx::OptionSectionHandle | Allows adding options to an OptionSection |
gmx::RepeatingOptionSectionHandle< T > | Allows adding options to an RepeatingOptionSection |
gmx::Options | Collection of options |
gmx::IProgramContext | Provides context information about the program that is calling the library |
gmx::ITopologyProvider | Provides topology information to SelectionOptionBehavior |
gmx::NormalDistribution< RealType > | Normal distribution |
gmx::NormalDistribution< RealType >::param_type | Normal distribution parameters |
gmx::OptionInfo | Gives information and allows modifications to an option after creation |
gmx::BooleanOptionInfo | Wrapper class for accessing boolean option information |
gmx::DoubleOptionInfo | Wrapper class for accessing floating-point option information |
gmx::EnumOptionInfo | Wrapper class for accessing enum option information |
gmx::FileNameOptionInfo | Wrapper class for accessing file name option information |
gmx::FloatOptionInfo | Wrapper class for accessing floating-point option information |
gmx::Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
gmx::IntegerOptionInfo | Wrapper class for accessing integer option information |
gmx::SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
gmx::StringOptionInfo | Wrapper class for accessing string option information |
gmx::PrivateImplPointer< Impl > | Helper class to manage a pointer to a private implementation class |
gmx::Selection | Provides access to a single selection |
gmx::SelectionCollection | Collection of selections |
gmx::SelectionPosition | Provides access to information about a single selected position |
gmx::SelectionTopologyProperties | Describes topology properties required for selection evaluation |
gmx::StaticLog2< n > | Evaluate log2(n) for integer n statically at compile time |
gmx::StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
gmx::StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
gmx::StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
gmx::TabulatedNormalDistribution< RealType, tableBits > | Tabulated normal random distribution |
gmx::TabulatedNormalDistribution< RealType, tableBits >::param_type | Normal distribution parameter class (mean and stddev) |
gmx::TextLineWrapper | Wraps lines to a predefined length |
gmx::TextLineWrapperSettings | Stores settings for line wrapping |
gmx::ThreeFry2x64General< rounds, internalCounterBits > | General implementation class for ThreeFry counter-based random engines |
gmx::TimeUnitManager | Provides common functionality for time unit conversions |
gmx::TopologyInformation | Topology information passed to a trajectory analysis module |
gmx::TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
gmx::TrajectoryAnalysisModule | Base class for trajectory analysis modules |
gmx::TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
gmx::TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
gmx::UniformIntDistribution< IntType > | Uniform integer distribution |
gmx::UniformIntDistribution< IntType >::param_type | Uniform int distribution parameters |
gmx::UniformRealDistribution< RealType > | Uniform real distribution |
gmx::UniformRealDistribution< RealType >::param_type | Uniform real distribution parameters |
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_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
gmx_sparsematrix | Sparse matrix storage format |
gmx::PrivateImplPointer< internal::FileStreamImpl > | |
gmx::PrivateImplPointer< internal::KeyValueTreeTransformerImpl > | |
gmx::PrivateImplPointer< internal::OptionsImpl > | |
std::exception | STL class |
gmx::GromacsException | Base class for all exception objects in Gromacs |
gmx::APIError | Exception class for incorrect use of an API |
gmx::NotImplementedError | Exception class for use of an unimplemented feature |
gmx::FileIOError | Exception class for file I/O errors |
gmx::InternalError | Exception class for internal errors |
gmx::RangeError | Exception class for out-of-range values or indices |
gmx::SimulationInstabilityError | Exception class for simulation instabilities |
gmx::ToleranceError | Exception class when a specified tolerance cannot be achieved |
gmx::UserInputError | Exception class for user input errors |
gmx::InconsistentInputError | Exception class for situations where user input is inconsistent |
gmx::InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
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 |
gmx::ThreeFry2x64General< 13, internalCounterBits > | |
gmx::ThreeFry2x64Fast< internalCounterBits > | ThreeFry2x64 random engine with 13 iteractions |
gmx::ThreeFry2x64General< 20, internalCounterBits > | |
gmx::ThreeFry2x64< internalCounterBits > | ThreeFry2x64 random engine with 20 iteractions |