Gromacs
2024.4
|
Classes and other symbols that are publicly accessible from user code.
Modules | |
MD restraints | |
Apply restraints during MD integration. | |
Namespaces | |
gmx | |
Generic GROMACS namespace. | |
Classes | |
class | gmx::CommandLineHelpWriter |
Writes help information for Options. More... | |
class | gmx::CommandLineModuleSettings |
Settings to pass information between a module and the general runner. More... | |
class | gmx::ICommandLineModule |
Module that can be run from command line using CommandLineModuleManager. More... | |
class | gmx::ICommandLineOptionsModuleSettings |
Settings to pass information between a CommandLineOptionsModule and generic code that runs it. More... | |
class | gmx::ICommandLineOptionsModule |
Module that can be run from a command line and uses gmx::Options for argument processing. More... | |
class | gmx::CommandLineParser |
Implements command-line parsing for Options objects. More... | |
struct | t_filenm |
File name option definition for C code. More... | |
struct | t_pargs |
Command-line argument definition for C code. More... | |
class | gmx::TrajectoryFileOpener |
Low level method to take care of only file opening and closing. More... | |
class | gmx::TrajectoryFrameWriter |
Writes coordinate frames to a sink, e.g. a trajectory file. More... | |
class | gmx::OutputSelector |
OutputSelector class controls setting which coordinates are actually written. More... | |
class | gmx::SetAtoms |
SetAtoms class controls availability of atoms data. More... | |
class | gmx::SetBox |
Allows changing box information when writing a coordinate file. More... | |
class | gmx::SetForces |
SetForces class allows changing writing of forces to file. More... | |
class | gmx::SetPrecision |
SetPrecision class allows changing file writing precision. More... | |
class | gmx::SetStartTime |
SetStartTime class allows changing trajectory time information. More... | |
class | gmx::SetTimeStep |
SetTimeStep class allows changing trajectory time information. More... | |
class | gmx::SetVelocities |
SetVelocities class allows changing writing of velocities to file. More... | |
class | gmx::OptionSection |
Declares a simple option section. More... | |
class | gmx::OptionSectionHandle |
Allows adding options to an OptionSection. More... | |
class | gmx::RepeatingOptionSection< T > |
Declares an option section that creates a structure for each instance. More... | |
class | gmx::RepeatingOptionSectionHandle< T > |
Allows adding options to an RepeatingOptionSection. More... | |
class | gmx::DataFileOptions |
Search parameters for DataFileFinder. More... | |
struct | gmx::DataFileInfo |
Information about a data file found by DataFileFinder::enumerateFiles(). More... | |
class | gmx::DataFileFinder |
Searches data files from a set of paths. More... | |
class | gmx::FixedCapacityVector< typename, size_t > |
Vector that behaves likes std::vector but has fixed capacity. More... | |
class | gmx::AnalysisData |
Parallelizable data container for raw data. More... | |
class | gmx::AnalysisDataHandle |
Handle for inserting data into AnalysisData. More... | |
class | gmx::AnalysisArrayData |
Simple in-memory data array. More... | |
class | gmx::AnalysisDataValue |
Value type for representing a single value in analysis data objects. More... | |
class | gmx::AnalysisDataFrameHeader |
Value type for storing frame-level information for analysis data. More... | |
class | gmx::AnalysisDataPointSetRef |
Value type wrapper for non-mutable access to a set of data column values. More... | |
class | gmx::AnalysisDataFrameRef |
Value type wrapper for non-mutable access to a data frame. More... | |
class | gmx::AnalysisDataAverageModule |
Data module for independently averaging each column in input data. More... | |
class | gmx::AnalysisDataFrameAverageModule |
Data module for averaging of columns for each frame. More... | |
class | gmx::AnalysisDataDisplacementModule |
Data module for calculating displacements. More... | |
class | gmx::AnalysisHistogramSettingsInitializer |
Provides "named parameter" idiom for constructing histograms. More... | |
class | gmx::AnalysisHistogramSettings |
Contains parameters that specify histogram bin locations. More... | |
class | gmx::AbstractAverageHistogram |
Base class for representing histograms averaged over frames. More... | |
class | gmx::AnalysisDataSimpleHistogramModule |
Data module for per-frame histograms. More... | |
class | gmx::AnalysisDataWeightedHistogramModule |
Data module for per-frame weighted histograms. More... | |
class | gmx::AnalysisDataBinAverageModule |
Data module for bin averages. More... | |
class | gmx::AnalysisDataLifetimeModule |
Data module for computing lifetime histograms for columns in input data. More... | |
class | gmx::AnalysisDataPlotSettings |
Common settings for data plots. More... | |
class | gmx::AnalysisDataPlotModule |
Plotting module for straightforward plotting of data. More... | |
class | gmx::AnalysisDataVectorPlotModule |
Plotting module specifically for data consisting of vectors. More... | |
class | gmx::BasicVector< ValueType > |
C++ class for 3D vectors. More... | |
class | gmx::OptionInfo |
Gives information and allows modifications to an option after creation. More... | |
class | gmx::BooleanOption |
Specifies an option that provides boolean values. More... | |
class | gmx::IntegerOption |
Specifies an option that provides integer values. More... | |
class | gmx::Int64Option |
Specifies an option that provides 64-bit integer values. More... | |
class | gmx::DoubleOption |
Specifies an option that provides floating-point (double) values. More... | |
class | gmx::FloatOption |
Specifies an option that provides floating-point (float) values. More... | |
class | gmx::StringOption |
Specifies an option that provides string values. More... | |
class | gmx::EnumOption< EnumType > |
Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable. More... | |
class | gmx::LegacyEnumOption< EnumType > |
Specifies an option that accepts enumerated string values and writes the selected index into an enum variable. More... | |
class | gmx::BooleanOptionInfo |
Wrapper class for accessing boolean option information. More... | |
class | gmx::IntegerOptionInfo |
Wrapper class for accessing integer option information. More... | |
class | gmx::Int64OptionInfo |
Wrapper class for accessing 64-bit integer option information. More... | |
class | gmx::DoubleOptionInfo |
Wrapper class for accessing floating-point option information. More... | |
class | gmx::FloatOptionInfo |
Wrapper class for accessing floating-point option information. More... | |
class | gmx::StringOptionInfo |
Wrapper class for accessing string option information. More... | |
class | gmx::EnumOptionInfo |
Wrapper class for accessing enum option information. More... | |
class | gmx::FileNameOption |
Specifies an option that provides file names. More... | |
class | gmx::FileNameOptionInfo |
Wrapper class for accessing file name option information. More... | |
class | gmx::FileNameOptionManager |
Handles interaction of file name options with global options. More... | |
class | gmx::IOptionsBehavior |
Interface to provide extension points for options parsing. More... | |
class | gmx::IOptionsContainer |
Interface for adding input options. More... | |
class | gmx::IOptionsContainerWithSections |
Interface for adding input options with sections. More... | |
class | gmx::Options |
Collection of options. More... | |
class | gmx::TimeUnitManager |
Provides common functionality for time unit conversions. More... | |
class | gmx::TimeUnitBehavior |
Options behavior to add a time unit option. More... | |
class | gmx::AnalysisNeighborhoodPositions |
Input positions for neighborhood searching. More... | |
class | gmx::AnalysisNeighborhood |
Neighborhood searching for analysis tools. More... | |
class | gmx::AnalysisNeighborhoodPair |
Value type to represent a pair of positions found in neighborhood searching. More... | |
class | gmx::AnalysisNeighborhoodSearch |
Initialized neighborhood search with a fixed set of reference positions. More... | |
class | gmx::AnalysisNeighborhoodPairSearch |
Initialized neighborhood pair search with a fixed set of positions. More... | |
class | gmx::Selection |
Provides access to a single selection. More... | |
class | gmx::SelectionPosition |
Provides access to information about a single selected position. More... | |
class | gmx::SelectionCollection |
Collection of selections. More... | |
struct | gmx::SelectionTopologyProperties |
Describes topology properties required for selection evaluation. More... | |
class | gmx::SelectionOption |
Specifies an option that provides selection(s). More... | |
class | gmx::SelectionOptionInfo |
Wrapper class for accessing and modifying selection option information. More... | |
class | gmx::ITopologyProvider |
Provides topology information to SelectionOptionBehavior. More... | |
class | gmx::SelectionOptionBehavior |
Options behavior to allow using SelectionOptions. More... | |
class | gmx::SelectionOptionManager |
Handles interaction of selection options with other options and user input. More... | |
class | gmx::TrajectoryAnalysisModuleData |
Base class for thread-local data storage during trajectory analysis. More... | |
class | gmx::TrajectoryAnalysisModule |
Base class for trajectory analysis modules. More... | |
class | gmx::TrajectoryAnalysisSettings |
Trajectory analysis module configuration object. More... | |
class | gmx::TrajectoryAnalysisCommandLineRunner |
Runner for command-line trajectory analysis tools. More... | |
class | gmx::ArrayRef< typename > |
STL-like interface to a C array of T (or part of a std container of T). More... | |
class | gmx::ExceptionInfo< Tag, T > |
Stores additional context information for exceptions. More... | |
class | gmx::GromacsException |
Base class for all exception objects in Gromacs. More... | |
class | gmx::FileIOError |
Exception class for file I/O errors. More... | |
class | gmx::UserInputError |
Exception class for user input errors. More... | |
class | gmx::InvalidInputError |
Exception class for situations where user input cannot be parsed/understood. More... | |
class | gmx::InconsistentInputError |
Exception class for situations where user input is inconsistent. More... | |
class | gmx::ToleranceError |
Exception class when a specified tolerance cannot be achieved. More... | |
class | gmx::SimulationInstabilityError |
Exception class for simulation instabilities. More... | |
class | gmx::InternalError |
Exception class for internal errors. More... | |
class | gmx::APIError |
Exception class for incorrect use of an API. More... | |
class | gmx::RangeError |
Exception class for out-of-range values or indices. More... | |
class | gmx::NotImplementedError |
Exception class for use of an unimplemented feature. More... | |
class | gmx::ParallelConsistencyError |
Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion. More... | |
class | gmx::ModularSimulatorError |
Exception class for modular simulator. More... | |
struct | gmx::InstallationPrefixInfo |
Provides information about installation prefix (see IProgramContext::installationPrefix()). More... | |
class | gmx::IProgramContext |
Provides context information about the program that is calling the library. More... | |
class | gmx::TextLineWrapperSettings |
Stores settings for line wrapping. More... | |
class | gmx::TextLineWrapper |
Wraps lines to a predefined length. More... | |
Enumerations | |
enum | gmx::TimeUnit : int { Femtoseconds, Picoseconds, Nanoseconds, Microseconds, Milliseconds, Seconds, Count, Default = Picoseconds } |
Time values for TimeUnitManager and legacy oenv module. | |
enum | e_coverfrac_t { CFRAC_NONE, CFRAC_SOLIDANGLE } |
Defines the type of covered fraction. More... | |
Functions | |
AnalysisHistogramSettingsInitializer | gmx::histogramFromRange (real min, real max) |
Initializes a histogram using a range and a bin width. More... | |
AnalysisHistogramSettingsInitializer | gmx::histogramFromBins (real start, int nbins, real binwidth) |
Initializes a histogram using bin width and the number of bins. More... | |
Files | |
file | cmdlinehelpwriter.h |
Declares gmx::CommandLineHelpWriter. | |
file | cmdlineinit.h |
Declares functions for initializing the GROMACS library for command line use. | |
file | cmdlinemodule.h |
Declares gmx::ICommandLineModule and supporting classes. | |
file | cmdlineoptionsmodule.h |
Declares gmx::ICommandLineOptionsModule and supporting routines. | |
file | cmdlineparser.h |
Declares gmx::CommandLineParser. | |
file | filenm.h |
Declares t_filenm for old-style command-line parsing of file name options. | |
file | pargs.h |
Declares t_pargs , parse_common_args() and related methods. | |
file | viewit.h |
Provides function to open output files automatically (with some X11 programs). | |
file | coordinatefile.h |
CoordinateFile takes care of opening files and writing output to them. | |
file | outputselector.h |
Declares gmx::OutputSelector. | |
file | setatoms.h |
Declares gmx::SetAtoms. | |
file | setbox.h |
Declares gmx::SetBox. | |
file | setforces.h |
Declares gmx::SetForces. | |
file | setprecision.h |
Declares gmx::SetPrecision. | |
file | setstarttime.h |
Declares gmx::SetStartTime. | |
file | settimestep.h |
Declares gmx::SetTimeStep. | |
file | setvelocities.h |
Declares gmx:SetVelocities. | |
file | outputadapters.h |
Public API convenience header for accessing outputadapters. | |
file | analysismodule.h |
Public API convenience header for energy analysis framework. | |
file | fft.h |
Fast Fourier Transforms. | |
file | hostallocator.h |
Declares gmx::HostAllocationPolicy, gmx::HostAllocator, gmx::HostVector and gmx::PaddedHostVector, which are used to make/be standard library containers that can allocate memory suitable for transfers. Currently the only supported transfers using pinned memory are to CUDA GPUs, but other possibilities exist in future. | |
file | arrayrefwithpadding.h |
Declares gmx::ArrayRefWithPadding that refers to memory whose size includes padding for SIMD operations. | |
file | paddedvector.h |
Declares gmx::PaddedRVecVector. | |
file | simulationinputhandle.h |
Public interface for SimulationInput facilities. | |
file | optionsection.h |
Declares gmx::OptionSection and gmx::OptionSectionInfo. | |
file | repeatingsection.h |
Declares gmx::RepeatingOptionSection and related classes. | |
file | exponentialdistribution.h |
The exponential distribution. | |
file | gammadistribution.h |
The gamma distribution. | |
file | normaldistribution.h |
The normal distribution. | |
file | seed.h |
Random seed and domain utilities. | |
file | tabulatednormaldistribution.h |
Tabulated normal distribution. | |
file | threefry.h |
Implementation of the 2x64 ThreeFry random engine. | |
file | uniformintdistribution.h |
The uniform integer distribution. | |
file | uniformrealdistribution.h |
The uniform real distribution. | |
file | alignedallocator.h |
Declares allocation policy classes and allocators that are used to make library containers compatible with alignment requirements of particular hardware, e.g. memory operations for SIMD or accelerators. | |
file | allocator.h |
Declares gmx::Allocator template whose allocation functionality is configured both by type of object allocated and a policy class that configures the necessary matching malloc and free operation. | |
file | arraysize.h |
Provides asize() function for calculating the static size of an array at compile time. | |
file | cstringutil.h |
Generic C string handling functions. | |
file | datafilefinder.h |
Declares gmx::DataFileFinder and related classes. | |
file | fatalerror.h |
Declares fatal error handling and debugging routines for C code. | |
file | fixedcapacityvector.h |
Declares gmx::FixedCapacityVector. | |
file | init.h |
Declares functions for initializing the GROMACS library. | |
file | utility.h |
Public API convenience header for low-level utilities. | |
file | analysisdata.h |
Declares gmx::AnalysisData and gmx::AnalysisDataHandle. | |
file | arraydata.h |
Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData. | |
file | dataframe.h |
Declares classes for accessing data frame information. | |
file | average.h |
Declares gmx::AnalysisDataAverageModule. | |
file | displacement.h |
Declares gmx::AnalysisDataDisplacementModule. | |
file | histogram.h |
Declares analysis data modules for calculating histograms. | |
file | lifetime.h |
Declares gmx::AnalysisDataLifetimeModule. | |
file | plot.h |
Declares gmx::AnalysisDataPlotModule for plotting data (into a file). | |
file | functions.h |
Declares simple math functions. | |
file | md_enums.h |
Declares enumerated types used throughout the code. | |
file | basicoptions.h |
Declares option objects for basic option types. | |
file | filenameoption.h |
Declares gmx::FileNameOption and gmx::FileNameOptionInfo. | |
file | filenameoptionmanager.h |
Declares gmx::FileNameOptionManager. | |
file | ioptionsbehavior.h |
Declares gmx::IOptionsBehavior. | |
file | ioptionscontainer.h |
Declares gmx::IOptionsContainer. | |
file | ioptionscontainerwithsections.h |
Declares gmx::IOptionsContainerWithSections. | |
file | optionfiletype.h |
Defines an enumeration type for specifying file types for options. | |
file | options.h |
Declares gmx::Options. | |
file | timeunitmanager.h |
Declares gmx::TimeUnitManager. | |
file | restraintpotential.h |
Declare generic interface for restraint implementations. | |
file | nbsearch.h |
API for neighborhood searching for analysis. | |
file | selection.h |
Declares gmx::Selection and supporting classes. | |
file | selectioncollection.h |
Declares gmx::SelectionCollection. | |
file | selectionoption.h |
Declares gmx::SelectionOption and gmx::SelectionOptionInfo. | |
file | selectionoptionbehavior.h |
Declares gmx::SelectionOptionBehavior. | |
file | selectionoptionmanager.h |
Declares gmx::SelectionOptionManager. | |
file | analysismodule.h |
Declares gmx::TrajectoryAnalysisModule and gmx::TrajectoryAnalysisModuleData. | |
file | analysissettings.h |
Declares gmx::TrajectoryAnalysisSettings. | |
file | cmdlinerunner.h |
Declares gmx::TrajectoryAnalysisCommandLineRunner. | |
file | arrayref.h |
Declares gmx::ArrayRef. | |
file | basedefinitions.h |
Basic types and macros used throughout GROMACS. | |
file | baseversion.h |
Declares functions to get basic version information. | |
file | exceptions.h |
Declares common exception classes and macros for fatal error handling. | |
file | fileptr.h |
Declares guard pointer for RAII-style handling of cstdio FILE pointers. | |
file | futil.h |
Low-level wrappers for OS-specific file handling with some GROMACS customizations. | |
file | gmxassert.h |
Defines assert macros customized for Gromacs. | |
file | listoflists.h |
Declares gmx::ListOfLists. | |
file | programcontext.h |
Declares gmx::IProgramContext and related methods. | |
file | range.h |
Declares gmx::Range. | |
file | real.h |
Declares real and related constants. | |
file | smalloc.h |
C-style memory allocation routines for GROMACS. | |
file | stringutil.h |
Declares common string utility and formatting routines. | |
enum e_coverfrac_t |
|
inline |
Initializes a histogram using bin width and the number of bins.
Does not throw.