Classes and other symbols that are publicly accessible within the GROMACS library.
|
class | gmx::AbstractAnalysisData |
| Abstract base class for all objects that provide data. More...
|
|
class | gmx::AbstractAnalysisArrayData |
| Abstract base class for data objects that present in-memory data. More...
|
|
class | gmx::IAnalysisDataModule |
| Interface for a module that gets notified whenever data is added. More...
|
|
class | gmx::AnalysisDataModuleSerial |
| Convenience base class for serial analysis data modules. More...
|
|
class | gmx::AnalysisDataModuleParallel |
| Convenience base class for parallel analysis data modules. More...
|
|
class | gmx::AnalysisDataModuleManager |
| Encapsulates handling of data modules attached to AbstractAnalysisData. More...
|
|
class | gmx::AnalysisDataStorageFrame |
| Allows assigning values for a data frame in AnalysisDataStorage. More...
|
|
class | gmx::AnalysisDataStorage |
| Helper class that implements storage of data. More...
|
|
class | gmx::AnalysisDataParallelOptions |
| Parallelization options for analysis data objects. More...
|
|
class | gmx::test::AnalysisDataTestInputPointSet |
| Represents a single set of points in AnalysisDataTestInputFrame structure. More...
|
|
class | gmx::test::AnalysisDataTestInputFrame |
| Represents a single frame in AnalysisDataTestInput structure. More...
|
|
class | gmx::test::AnalysisDataTestInput |
| Represents static input data for AbstractAnalysisData tests. More...
|
|
class | gmx::test::AnalysisDataTestFixture |
| Test fixture for AbstractAnalysisData testing. More...
|
|
class | gmx::GlobalCommandLineHelpContext |
| Helper for passing CommandLineHelpContext into parse_common_args(). More...
|
|
class | gmx::CommandLineModuleManager |
| Implements a wrapper command-line interface for multiple modules. More...
|
|
class | gmx::CommandLineModuleGroup |
| Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More...
|
|
class | gmx::IExecutableEnvironment |
| Allows customization of the way various directories are found by CommandLineProgramContext. More...
|
|
class | gmx::CommandLineProgramContext |
| Program context implementation for command line programs. More...
|
|
class | gmx::IOutputAdapter |
| OutputAdapter class for handling trajectory file flag setting and processing. More...
|
|
class | gmx::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. More...
|
|
class | gmx::LocalAtomSetManager |
| Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...
|
|
class | gmx::ArrayRefWithPadding< typename > |
| 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. More...
|
|
class | gmx::MDModules |
| Manages the collection of all modules used for mdrun. More...
|
|
class | gmx::SimulationContext |
| Simulation environment and configuration. More...
|
|
class | gmx::IForceProvider |
| Interface for a component that provides forces during MD. More...
|
|
class | gmx::ForceProviders |
| Evaluates forces from a collection of gmx::IForceProvider. More...
|
|
class | gmx::IMDModule |
| Extension module for GROMACS simulations. More...
|
|
class | gmx::IMDOutputProvider |
| Interface for handling additional output files during a simulation. More...
|
|
class | gmx::IMdpOptionProvider |
| Interface for handling mdp/tpr input to a mdrun module. More...
|
|
class | gmx::ObservablesReducer |
| Manage reduction of observables for registered subscribers. More...
|
|
class | gmx::TextTableFormatter |
| Formats rows of a table for text output. More...
|
|
class | gmx::HelpManager |
| Helper for providing interactive online help. More...
|
|
class | gmx::AbstractSimpleHelpTopic |
| Abstract base class for help topics that have simple text and no subtopics. More...
|
|
class | gmx::AbstractCompositeHelpTopic |
| Abstract base class for help topics that have simple text and subtopics. More...
|
|
class | gmx::SimpleHelpTopic< HelpText > |
| Template for simple implementation of AbstractSimpleHelpTopic. More...
|
|
class | gmx::CompositeHelpTopic< HelpText > |
| Template for simple implementation of AbstractCompositeHelpTopic. More...
|
|
class | gmx::HelpWriterContext |
| Context information for writing out help. More...
|
|
class | gmx::IHelpTopic |
| Provides a single online help topic. More...
|
|
class | gmx::OptionTemplate< T, U > |
| Templated base class for constructing concrete option settings classes. More...
|
|
class | gmx::AbstractOptionStorage |
| Abstract base class for converting, validating, and storing option values. More...
|
|
class | gmx::OptionsBehaviorCollection |
| Container for IOptionsBehavior objects. More...
|
|
class | gmx::OptionManagerContainer |
| Container to keep managers added with Options::addManager() and pass them to options. More...
|
|
class | gmx::IOptionManager |
| Base class for option managers. More...
|
|
class | gmx::OptionsAssigner |
| Decorator class for assigning values to Options. More...
|
|
class | gmx::OptionStorageTemplate< T > |
| Templated base class for constructing option value storage classes. More...
|
|
class | gmx::OptionStorageTemplateSimple< T > |
| Simplified option storage template for options that have one-to-one value conversion. More...
|
|
class | gmx::OptionsVisitor |
| Pure interface for visiting options in a Options object. More...
|
|
class | gmx::OptionsTypeVisitor< InfoType > |
| Abstract base class for visiting options of a particular type. More...
|
|
class | gmx::OptionsIterator |
| Decorator class for visiting options in a Options object. More...
|
|
class | gmx::OptionsModifyingVisitor |
| Pure interface for visiting options in a Options object, allowing modifications. More...
|
|
class | gmx::OptionsModifyingTypeVisitor< InfoType > |
| Abstract base class for visiting options of a particular type, allowing modifications. More...
|
|
class | gmx::OptionsModifyingIterator |
| Decorator class for visiting options in a Options object, allowing changes. More...
|
|
class | gmx::OptionValueConverterSimple< OutType > |
| Helper for converting from Any to a given type. More...
|
|
class | gmx::Site |
| Abstraction for a restraint interaction site. More...
|
|
class | gmx::SelectionFileOption |
| Specifies a special option that provides selections from a file. More...
|
|
class | gmx::SelectionFileOptionInfo |
| Wrapper class for accessing and modifying selection file option information. More...
|
|
class | gmx::Allocator< T, AllocationPolicy > |
| Policy-based memory allocator. More...
|
|
class | gmx::BinaryInformationSettings |
| Settings for printBinaryInformation(). More...
|
|
class | gmx::DirectoryEnumerator |
| Lists files in a directory. More...
|
|
class | gmx::IFileInputRedirector |
| Allows overriding file existence checks from code that supports it. More...
|
|
class | gmx::IFileOutputRedirector |
| Allows capturing stdout and file output from code that supports it. More...
|
|
class | gmx::StandardInputStream |
| Text input stream implementation for reading from stdin . More...
|
|
class | gmx::TextInputFile |
| Text input stream implementation for reading from a file. More...
|
|
class | gmx::TextOutputFile |
| Text output stream implementation for writing to a file. More...
|
|
class | gmx::FlagsTemplate< FlagType > |
| Template class for typesafe handling of combination of flags. More...
|
|
class | gmx::KeyValueTreePath |
| Identifies an entry in a key-value tree. More...
|
|
class | gmx::KeyValueTreeBuilder |
| Root builder for creating trees that have an object at the root. More...
|
|
class | gmx::KeyValueTreeValueBuilder |
| Builder for KeyValueTreeValue objects. More...
|
|
class | gmx::KeyValueTreeUniformArrayBuilder< T > |
| Builder for KeyValueTreeArray objects where all elements are of type T . More...
|
|
class | gmx::KeyValueTreeObjectArrayBuilder |
| Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects. More...
|
|
class | gmx::KeyValueTreeObjectBuilder |
| Builder for KeyValueTreeObject objects. More...
|
|
class | gmx::IKeyValueTreeTransformRules |
| Interface to declare rules for transforming key-value trees. More...
|
|
class | gmx::KeyValueTreeTransformRulesScoped |
| Helper object returned from IKeyValueTreeTransformRules::scopedTransform(). More...
|
|
class | gmx::KeyValueTreeTransformRuleBuilder |
| Provides methods to specify one transformation rule. More...
|
|
class | gmx::MessageStringCollector |
| Helper class for collecting message strings, optionally with context. More...
|
|
class | gmx::MessageStringContext |
| Convenience class for creating a message context. More...
|
|
struct | gmx::no_delete< T > |
| Deleter for std::shared_ptr that does nothing. More...
|
|
class | gmx::StringCompare |
| Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare. More...
|
|
class | gmx::StringOutputStream |
| Text output stream implementation for writing to an in-memory string. More...
|
|
class | gmx::TextReader |
| Reads text from a TextInputStream. More...
|
|
class | gmx::TextInputStream |
| Interface for reading text. More...
|
|
class | gmx::TextOutputStream |
| Interface for writing text. More...
|
|
class | gmx::TextWriter |
| Writes text into a TextOutputStream. More...
|
|
class | gmx::test::CommandLine |
| Helper class for tests that need to construct command lines. More...
|
|
class | gmx::test::CommandLineTestHelper |
| Helper class for tests that construct command lines that need to reference existing files. More...
|
|
class | gmx::test::CommandLineTestBase |
| Test fixture for tests that call a single command-line program with input/output files. More...
|
|
class | gmx::test::ConfMatch |
| Match the contents as an gro file. More...
|
|
class | gmx::test::IFileMatcher |
| Represents a file matcher, matching file contents against reference (or other) data. More...
|
|
class | gmx::test::IFileMatcherSettings |
| Represents a factory for creating a file matcher. More...
|
|
class | gmx::test::TextFileMatch |
| Use a ITextBlockMatcher for matching the contents. More...
|
|
class | gmx::test::NoContentsMatch |
| Do not check the contents of the file. More...
|
|
class | gmx::test::InteractiveTestHelper |
| Helper class for testing interactive sessions. More...
|
|
class | gmx::test::LoggerTestHelper |
| Helper class for tests to check output written to a logger. More...
|
|
class | gmx::test::TestReferenceData |
| Handles creation of and comparison to test reference data. More...
|
|
class | gmx::test::TestReferenceChecker |
| Handles comparison to test reference data. More...
|
|
class | gmx::test::StdioTestHelper |
| Helper class for tests where code reads directly from stdin . More...
|
|
class | gmx::test::StringTestBase |
| Test fixture for tests that check string formatting. More...
|
|
class | gmx::test::TestFileManager |
| Helper for tests that need input and output files. More...
|
|
class | gmx::test::TestFileInputRedirector |
| In-memory implementation for IFileInputRedirector for tests. More...
|
|
class | gmx::test::TestOptionsProvider |
| Provides additional options for the test executable. More...
|
|
class | gmx::test::ITextBlockMatcher |
| Represents a text matcher, matching text stream contents against reference data. More...
|
|
class | gmx::test::ITextBlockMatcherSettings |
| Represents a factory for creating a text matcher. More...
|
|
class | gmx::test::ExactTextMatch |
| Use an exact text match (the contents should be exactly equal). More...
|
|
class | gmx::test::NoTextMatch |
| Do not match the text (the contents are ignored). More...
|
|
class | gmx::test::FilteringExactTextMatch |
| Use an exact text match after scrubbing lines of the text that match the supplied regular expressions. More...
|
|
class | gmx::test::XvgMatch |
| Match the contents as an xvg file. More...
|
|
|
file | abstractdata.h |
| Declares gmx::AbstractAnalysisData.
|
|
file | datamodule.h |
| Declares gmx::IAnalysisDataModule and related convenience classes.
|
|
file | datamodulemanager.h |
| Declares gmx::AnalysisDataModuleManager.
|
|
file | datastorage.h |
| Declares gmx::AnalysisDataStorage.
|
|
file | paralleloptions.h |
| Declares gmx::AnalysisDataParallelOptions.
|
|
file | datatest.h |
| Helper classes for testing classes that derive from AbstractAnalysisData.
|
|
file | mock_datamodule.h |
| Declares mock implementation of gmx::IAnalysisDataModule.
|
|
file | awh.h |
| Declares the Awh class.
|
|
file | read_params.h |
| Declares functions needed for reading, initializing and setting the AWH parameter data types.
|
|
file | electricfield.h |
| Declares module creation function for applied electric fields.
|
|
file | cmdlinehelpcontext.h |
| Declares gmx::CommandLineHelpContext.
|
|
file | cmdlinemodulemanager.h |
| Declares gmx::CommandLineModuleManager.
|
|
file | cmdlineprogramcontext.h |
| Declares gmx::CommandLineProgramContext.
|
|
file | mp11.h |
| Provides ported functions/classes from boost::mp11.
|
|
file | pointers.h |
| Provides ported functions/classes from gsl/pointers.
|
|
file | utility.h |
| Provides backported functions/classes from utility.
|
|
file | ioutputadapter.h |
| Declares gmx::IOutputAdapter interface for modifying coordinate file structures before writing them to disk.
|
|
file | outputadaptercontainer.h |
| Declares gmx::OutputAdapterContainer, a storage object for multiple outputadapters derived from the IOutputadaper interface.
|
|
file | requirements.h |
| Storage object for requirements to build coordinate file writer.
|
|
file | coordinate_test.h |
| Helper classes for coordinatefile and coordinateio tests.
|
|
file | outputadapters.h |
| Helpers and data for outputadapter module tests.
|
|
file | requirements.h |
| Helpers and data for flag setting method.
|
|
file | coordinateio.h |
| Public API convenience header for coordinate file output.
|
|
file | autocorr.h |
| Declares routine for computing autocorrelation functions.
|
|
file | crosscorr.h |
| Declares routine for computing a cross correlation between two data sets.
|
|
file | expfit.h |
| Declares routine for fitting a data set to a curve.
|
|
file | integrate.h |
| Declares routines for integrating a data set.
|
|
file | manyautocorrelation.h |
| Declares routine for computing many correlation functions using OpenMP.
|
|
file | polynomials.h |
| Declares routine for computing a Legendre polynomial.
|
|
file | builder.h |
| This file declares a builder class for the manager of domain decomposition.
|
|
file | collect.h |
| Declares functions to collect state data to the master rank.
|
|
file | computemultibodycutoffs.h |
| This file declares the function for computing the required cutoff distance for inter-domain multi-body interactions, when those exist.
|
|
file | dlb.h |
| This file declares functions to interact with the dynamic load balancing machinery.
|
|
file | dlbtiming.h |
| This file declares functions for timing the load imbalance due to domain decomposition.
|
|
file | domdec.h |
| This file declares functions for mdrun to call to manage the details of its domain decomposition.
|
|
file | domdec_network.h |
| This file declares functions for (mostly) the domdec module to use MPI functionality.
|
|
file | domdec_struct.h |
| Declares structures related to domain decomposition.
|
|
file | ga2la.h |
| Defines structures and functions for mapping from global to local atom indices. The functions are performance critical and should be inlined.
|
|
file | gpuhaloexchange.h |
| Declaration of GPU halo exchange.
|
|
file | hashedmap.h |
| Defines structures and functions for mapping from keys to entries indices using a hash table. The functions are performance critical and should be inlined.
|
|
file | localatomset.h |
| Declares gmx::LocalAtomSet.
|
|
file | localatomsetmanager.h |
| Declares gmx::LocalAtomSetManager.
|
|
file | localtopology.h |
| This file makes declarations used for building the local topology.
|
|
file | localtopologychecker.h |
| This file declares functionality for checking whether local topologies describe all bonded interactions.
|
|
file | makebondedlinks.h |
| Declares a function that makes the list of links between atoms connected by bonded interactions.
|
|
file | mdsetup.h |
| Contains functions relevant to simulation setup in MD drivers.
|
|
file | options.h |
| This file declares command-line options for mdrun related to domain decomposition.
|
|
file | partition.h |
| This file declares functions for mdrun to call to make a new domain decomposition, and check it.
|
|
file | reversetopology.h |
| This file makes declarations used for building the reverse topology.
|
|
file | edsam.h |
| Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces.
|
|
file | ewald.h |
| This file contains function declarations necessary for computing energies and forces for the plain-Ewald long-ranged part, and the correction for overall system charge for all Ewald-family methods.
|
|
file | ewald_utils.h |
| Declares utility functions related to Ewald.
|
|
file | long_range_correction.h |
| This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
|
|
file | pme.h |
| This file contains function declarations necessary for computing energies and forces for the PME long-ranged part (Coulomb and LJ).
|
|
file | pme_coordinate_receiver_gpu.h |
| Declaration of class which receives coordinates to GPU memory on PME task.
|
|
file | pme_force_sender_gpu.h |
| Declaration of class which sends PME Force from GPU memory to PP task.
|
|
file | pme_gpu_program.h |
| Declares PmeGpuProgram to store data derived from the GPU context or devices for PME, such as (compiled) kernel handles and the warp sizes they work with.
|
|
file | pme_load_balancing.h |
| This file contains function declarations necessary for managing automatic load balance of PME calculations (Coulomb and LJ).
|
|
file | pme_only.h |
| This file contains function declarations necessary for running on an MPI rank doing only PME long-ranged work.
|
|
file | pme_pp_comm_gpu.h |
| Declaration of GPU PME-PP Communication.
|
|
file | mrcdensitymap.h |
| Declars mrc/ccp4-file format handling.
|
|
|
file | gpp_atomtype.h |
| Declares PreprocessingAtomType.
|
|
file | gpp_bond_atomtype.h |
| Declares PreprocessingBondAtomType.
|
|
file | clfftinitializer.h |
| Declares ClfftInitializer class, which initializes and tears down the clFFT library resources in OpenCL builds, and does nothing in other builds, and a factory function for it.
|
|
file | device_context.h |
| Declarations for DeviceContext class.
|
|
file | device_event.h |
| Declares DeviceEvent for all build configuraitons.
|
|
file | device_event_ocl.h |
| Implements a DeviceEvent class for OpenCL.
|
|
file | device_event_sycl.h |
| Implements a GpuEventSynchronizer class for SYCL.
|
|
file | device_stream.h |
| Declarations for DeviceStream class.
|
|
file | device_stream_manager.h |
| This file declares a manager of GPU context and streams needed for running workloads on GPUs.
|
|
file | devicebuffer.h |
| Implements the logic for handling of DeviceBuffer types in OpenCL, CUDA and SYCL.
|
|
file | devicebuffer_datatype.h |
| Declares the DeviceBuffer data type.
|
|
file | devicebuffer_ocl.h |
| Implements the DeviceBuffer type and routines for OpenCL. Should only be included directly by the main DeviceBuffer file devicebuffer.h. TODO: the intent is for DeviceBuffer to become a class.
|
|
file | devicebuffer_sycl.h |
| Implements the DeviceBuffer type and routines for SYCL. Should only be included directly by the main DeviceBuffer file devicebuffer.h. TODO: the intent is for DeviceBuffer to become a class.
|
|
file | gmxopencl.h |
| Wraps the complexity of including OpenCL in Gromacs.
|
|
file | gmxsycl.h |
| Wraps the complexity of including SYCL in GROMACS.
|
|
file | gpu_utils.h |
| Declare functions for detection and initialization for GPU devices.
|
|
file | gpueventsynchronizer.h |
| Implements a GpuEventSynchronizer class.
|
|
file | gpuregiontimer_ocl.h |
| Implements the GPU region timer for OpenCL.
|
|
file | gpuregiontimer_sycl.h |
| Implements the GPU region timer for SYCL.
|
|
file | gputraits.h |
| Declares the GPU type traits for non-GPU builds.
|
|
file | gputraits_ocl.h |
| Declares the OpenCL type traits.
|
|
file | gputraits_sycl.h |
| Declares the SYCL type traits.
|
|
file | ocl_compiler.h |
| Declare infrastructure for OpenCL JIT compilation.
|
|
file | oclraii.h |
| Declare RAII helpers for OpenCL types, along with supporting type traits.
|
|
file | oclutils.h |
| Declare utility routines for OpenCL.
|
|
file | pinning.h |
| Declares functions for pinning memory to be suitable for efficient GPU transfers on CUDA.
|
|
file | pmalloc.h |
| Declare functions for host-side memory handling.
|
|
file | syclutils.h |
| Declare utility routines for SYCL.
|
|
file | cpuinfo.h |
| Declares gmx::CpuInfo.
|
|
file | device_management.h |
| Declares functions to manage GPU resources.
|
|
file | hardwaretopology.h |
| Declares gmx::HardwareTopology.
|
|
file | identifyavx512fmaunits.h |
| Defines a routine to check the number of AVX512 fma units.
|
|
file | imd.h |
| This file declares the class that coordinates with VMD via the Interactive Molecular Dynamics protocol, along with supporting free functions.
|
|
file | imdsocket.h |
| Implements the parts of the vmdsock.h interface needed for IMD communication.
|
|
file | bonded.h |
| This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.
|
|
file | disre.h |
| Declares functions for handling distance restraints.
|
|
file | listed_forces.h |
| This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions.
|
|
file | listed_forces_gpu.h |
| This file contains declarations of high-level functions used by mdrun to compute energies and forces for listed interactions.
|
|
file | orires.h |
| Declares functions for handling orientation restraints.
|
|
file | pairs.h |
| This file declares functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
|
|
file | position_restraints.h |
| This file contains declarations necessary for low-level functions for computing energies and forces for position restraints.
|
|
file | coordinatetransformation.h |
| Declares coordinate transformation routines.
|
|
file | densityfit.h |
| Declares density similarity measures and their derivatives.
|
|
file | densityfittingforce.h |
| Declares classes to calculate density fitting forces.
|
|
file | exponentialmovingaverage.h |
| Declares an exponential moving average class.
|
|
file | gausstransform.h |
| Declares Gaussian function evaluations on lattices and related functionality.
|
|
file | invertmatrix.h |
| Declares routines to invert 3x3 matrices.
|
|
file | multidimarray.h |
| Declares MultiDimArray.
|
|
file | testarrayrefs.h |
| Declares functions for comparing views of vector-like data.
|
|
file | boxdeformation.h |
| Declares interface to box deformation code.
|
|
file | broadcaststructs.h |
| Convenience wrappers for broadcasting structs.
|
|
file | checkpointhandler.h |
| Declares the checkpoint handler class.
|
|
file | constr.h |
| Declares interface to constraint code.
|
|
file | energyoutput.h |
| Header for the code that writes energy-like quantities.
|
|
file | groupcoord.h |
| Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
|
|
file | leapfrog_gpu.h |
| Declarations for GPU implementation of Leap-Frog.
|
|
file | leapfrog_gpu_internal.h |
| Declarations for backend specific GPU functions for Leap-Frog.
|
|
file | lincs.h |
| Declares interface to LINCS code.
|
|
file | lincs_gpu.h |
| Declares the class for GPU implementation of LINCS.
|
|
file | makeconstraints.h |
| Declares and implements factory function for Constraints.
|
|
file | resethandler.h |
| Declares the reset handler class.
|
|
file | settle.h |
| Declares interface to SETTLE code.
|
|
file | shake.h |
| Declares interface to SHAKE code.
|
|
file | simulationsignal.h |
| This file declares functions for inter-rank signalling by mdrun.
|
|
file | stophandler.h |
| Declares StopHandler, a helper class and two stop conditions.
|
|
file | update_constrain_gpu.h |
| Declaration of high-level functions of GPU implementation of update and constrain class.
|
|
file | updategroups.h |
| Declares the functions for generating update groups.
|
|
file | updategroupscog.h |
| Declares the UpdateGroupsCog class for managing centers of mass of update groups.
|
|
file | vsite.h |
| Declares the VirtualSitesHandler class and vsite standalone functions.
|
|
file | wholemoleculetransform.h |
| Declares the WholeMolecules class for generating whole molecules.
|
|
file | legacymdrunoptions.h |
| This file declares helper functionality for legacy option handling for mdrun.
|
|
file | mdmodules.h |
| Declares gmx::MDModules.
|
|
file | simulationcontext.h |
| Provide ways for client code to own simulation resources.
|
|
file | simulationinput.h |
| Utilities for interacting with SimulationInput.
|
|
file | freeenergy.cpp |
| Defines helper functions for mdrun pertaining to free energy calculations.
|
|
file | freeenergy.h |
| Declares helper functions for mdrun pertaining to free energy calculations.
|
|
file | handlerestart.h |
| This file declares functions for mdrun to call to manage the details of doing a restart (ie. reading checkpoints, appending output files).
|
|
file | logging.h |
| Declares the MD log file handling routines.
|
|
file | multisim.h |
| Declares the multi-simulation support routines.
|
|
file | printtime.h |
| Declares functions that write timestamps to e.g. log files.
|
|
file | threadaffinity.h |
| Declares functions for managing mdrun thread affinity.
|
|
file | extensions.h |
| GROMACS extensions to mdspan.
|
|
file | mdspan.h |
| Declares gmx::mdspan.
|
|
file | atominfo.h |
| This file makes declarations used for storing bitfields describing each atom so that other modules can efficiently process them.
|
|
file | awh_correlation_history.h |
| Contains datatypes and function declarations needed by AWH to have its force correlation data checkpointed.
|
|
file | awh_history.h |
| Contains datatypes and function declarations needed by AWH to have its data checkpointed.
|
|
file | awh_params.h |
| Declares AWH parameter data types.
|
|
file | energyhistory.h |
| This file contains datatypes for energy statistics history.
|
|
file | forcebuffers.h |
| This file contains the definition of a container for force buffers.
|
|
file | forceoutput.h |
| This file contains the definition of a container for force and virial output.
|
|
file | iforceprovider.h |
| Declares gmx::IForceProvider and ForceProviders.
|
|
file | imdmodule.h |
| Declares gmx::IMDModule.
|
|
file | imdoutputprovider.h |
| Declares gmx::IMDOutputProvider.
|
|
file | imdpoptionprovider.h |
| Declares gmx::IMdpOptionProvider.
|
|
file | mdrunoptions.h |
| This file declares helper functionality for legacy option handling for mdrun.
|
|
file | observableshistory.h |
| This file contains the definition of a container for history data for simulation observables.
|
|
file | observablesreducer.h |
| Declares gmx::ObservablesReducer and builder.
|
|
file | pull_params.h |
| This file contains datatypes for the mdp options used by the pull code.
|
|
file | pullhistory.h |
| This file contains datatypes for pull statistics history.
|
|
file | simulation_workload.h |
| Declares step, domain-lifetime, and run workload managers.
|
|
file | state.h |
| This file contains the definition of the microstate of the simulated system.
|
|
file | utilities.h |
| Provides utility functions for MiMiC QM/MM.
|
|
file | atomdata.h |
| Functionality for per-atom data in the nbnxm module.
|
|
file | bench_setup.h |
| This file declares functions for setting up kernel benchmarks.
|
|
file | gpu_data_mgmt.h |
| Declare interface for GPU data transfer for NBNXN module.
|
|
file | nbnxm.h |
| This file contains the public interface of the nbnxm module that implements the NxM atom cluster non-bonded algorithm to efficiently compute pair forces.
|
|
file | pairlist_tuning.h |
| Declares functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels.
|
|
file | helpformat.h |
| Declares common string formatting routines for online help.
|
|
file | helpmanager.h |
| Declares gmx::HelpManager.
|
|
file | helptopic.h |
| Declares helper classes for implementing gmx::IHelpTopic.
|
|
file | helpwritercontext.h |
| Declares gmx::HelpWriterContext.
|
|
file | ihelptopic.h |
| Declares gmx::IHelpTopic.
|
|
file | mock_helptopic.h |
| Declares mock implementation of gmx::IHelpTopic.
|
|
file | abstractoption.h |
| Defines gmx::AbstractOption, gmx::OptionTemplate and gmx::OptionInfo.
|
|
file | abstractoptionstorage.h |
| Declares gmx::AbstractOptionStorage.
|
|
file | behaviorcollection.h |
| Declares gmx::OptionsBehaviorCollection.
|
|
file | optionmanagercontainer.h |
| Declares gmx::OptionManagerContainer.
|
|
file | optionsassigner.h |
| Declares gmx::OptionsAssigner.
|
|
file | optionstoragetemplate.h |
| Defines gmx::OptionStorageTemplate template.
|
|
file | optionsvisitor.h |
| Declares gmx::OptionsVisitor interface and supporting classes.
|
|
file | treesupport.h |
| Declares functions for using keyvaluetree.h with Options.
|
|
file | com.h |
| Helper methods to place particle COM in boxes.
|
|
file | pbc_aiuc.h |
| Structure and basic routines to handle periodic boundary conditions.
|
|
file | pbc_aiuc_sycl.h |
| Basic routines to handle periodic boundary conditions with SYCL.
|
|
file | pbc_simd.h |
| This file contains a definition, declaration and inline function for SIMD accelerated PBC calculations.
|
|
file | output.h |
| This file declares functions for pull output writing.
|
|
file | pull.h |
| This file contains datatypes and function declarations necessary for mdrun to interface with the pull code.
|
|
file | pull_rotation.h |
| Declares functions to enforce rotational motion upon a group of particles.
|
|
file | manager.h |
| Declare the Manager for restraint potentials.
|
|
file | restraintmdmodule.h |
| Library interface for RestraintMDModule.
|
|
file | indexutil.h |
| API for handling index files and index groups.
|
|
file | selectionfileoption.h |
| Declares gmx::SelectionFileOption and gmx::SelectionFileOptionInfo.
|
|
file | selhelp.h |
| Functions for initializing online help for selections.
|
|
file | scalar.h |
| Scalar float functions corresponding to GROMACS SIMD functions.
|
|
file | scalar_math.h |
| Scalar math functions mimicking GROMACS SIMD math functions.
|
|
file | scalar_util.h |
| Scalar utility functions mimicking GROMACS SIMD utility functions.
|
|
file | simd.h |
| Definitions, capabilities, and wrappers for SIMD module.
|
|
file | simd_math.h |
| Math functions for SIMD datatypes.
|
|
file | simd_memory.h |
| Declares SimdArrayRef.
|
|
file | support.h |
| Functions to query compiled and supported SIMD architectures.
|
|
file | vector_operations.h |
| SIMD operations corresponding to Gromacs rvec datatypes.
|
|
file | statistics.h |
| Declares simple statistics toolbox.
|
|
file | swapcoords.h |
| The "Computational Electrophysiology" protocol for ion/water position swapping.
|
|
file | cubicsplinetable.h |
| Declares classes for cubic spline table.
|
|
file | forcetable.h |
| Old routines for table generation (will eventually be replaced)
|
|
file | quadraticsplinetable.h |
| Declares classes for quadratic spline table.
|
|
file | tableinput.h |
| Declares structures for analytical or numerical input data to construct tables.
|
|
file | decidegpuusage.h |
| Declares functionality for deciding whether tasks will run on GPUs.
|
|
file | resourcedivision.h |
| Declares utility functionality for dividing resources and checking for consistency and usefulness.
|
|
file | taskassignment.h |
| Declares high-level functionality for managing assigning tasks on ranks of a node to hardware on that node, and the factory function to build the correct flavours of gmx::INodeTaskAssigner required to implement the user's requirements.
|
|
file | usergpuids.h |
| Declares routines for handling user-specified GPU IDs.
|
|
file | cyclecounter.h |
| High-resolution timestamp or CPU clock cycle counters.
|
|
file | gpu_timing.h |
| Declares data types for GPU timing.
|
|
file | atomsbuilder.h |
| Utility classes for manipulating t_atoms structures.
|
|
file | mtop_lookup.h |
| This file contains inline functions to look up atom information using the global atom index.
|
|
file | symtab.h |
| Declares modern and legacy symbol table used to store strings of characters.
|
|
file | modules.h |
| Generic interface for accessing trajectory analysis modules.
|
|
file | topologyinformation.h |
| Declares gmx::TopologyInformation.
|
|
file | any.h |
| Declares gmx::Any.
|
|
file | basenetwork.h |
| Utility functions for basic MPI and network functionality.
|
|
file | binaryinformation.h |
| Helper functionality for information about the currently running binary.
|
|
file | bitmask.h |
| Declares gmx_bitmask_t and associated functions.
|
|
file | classhelpers.h |
| Declares common utility classes and macros.
|
|
file | compare.h |
| Utilities for comparing data structures (for gmx check).
|
|
file | coolstuff.h |
| Functionality for printing cool strings.
|
|
file | defaultinitializationallocator.h |
| Declares an allocator that can use default initialization instead of values initialization. This is useful for improving performance of resize() in standard vectors for buffers in performance critical code.
|
|
file | dir_separator.h |
| Provides OS-specific directory-name separator.
|
|
file | directoryenumerator.h |
| Declares gmx::DirectoryEnumerator.
|
|
file | enumerationhelpers.h |
| Defines helper types for class enumerations.
|
|
file | fileredirector.h |
| Declares gmx::IFileOutputRedirector.
|
|
file | filestream.h |
| Declares implementations for textstream.h interfaces for file input/output.
|
|
file | flags.h |
| Declares gmx::FlagsTemplate.
|
|
file | gmxmpi.h |
| Wraps mpi.h usage in Gromacs.
|
|
file | gmxomp.h |
| Declares OpenMP wrappers to avoid conditional compilation.
|
|
file | ikeyvaluetreeerror.h |
| Declares an error handling interface for key-value tree operations.
|
|
file | inmemoryserializer.h |
| Declares gmx::ISerializer implementation for in-memory serialization.
|
|
file | int64_to_int.h |
| Low-level utility for converting 64 bit int to int (the size of which is hardware dependent), printing a warning if an overflow will occur.
|
|
file | iserializer.h |
| Declares a generic serialization interface that supports both directions.
|
|
file | keyvaluetree.h |
| Declares a data structure for JSON-like structured key-value mapping.
|
|
file | keyvaluetreebuilder.h |
| Declares classes for building the data structures in keyvaluetree.h.
|
|
file | keyvaluetreemdpwriter.h |
| Declares a function to write a flat key-value tree to look like old-style mdp output.
|
|
file | keyvaluetreeserializer.h |
| Declares serialization routines for KeyValueTree objects.
|
|
file | keyvaluetreetransform.h |
| Declares utilities for transforming key-value trees.
|
|
file | logger.h |
| Declares functionality for logging.
|
|
file | loggerbuilder.h |
| Declares functionality for initializing logging.
|
|
file | mdmodulesnotifier.h |
| Declares gmx::MDModulesNotifier and builder.
|
|
file | mdmodulesnotifiers.h |
| Declares gmx::MDModulesNotifiers.
|
|
file | message_string_collector.h |
| Declares gmx::MessageStringCollector.
|
|
|
file | nodelete.h |
| Declares no_delete deleter for std::shared_ptr.
|
|
file | path.h |
| Declares functions for OS-independent path handling.
|
|
file | physicalnodecommunicator.h |
| Declares functionality for communicators across physical nodes.
|
|
file | pleasecite.h |
| Declares please_cite() for printing out literature references. Declares writeSourceDoi for printing of source code DOI.
|
|
file | snprintf.h |
| Provide snprintf symbol on all OS (for internal Gromacs use)
|
|
file | strconvert.h |
| Declares common utility functions for conversions to and from strings.
|
|
file | strdb.h |
| Declares C functions for reading files with a list of strings.
|
|
file | stringcompare.h |
| Declares utility functionst for string comparison.
|
|
file | stringstream.h |
| Declares implementations for textstream.h interfaces for input/output to in-memory strings.
|
|
file | stringtoenumvalueconverter.h |
| Defines helper function object for class enumerations.
|
|
file | sysinfo.h |
| Declares functions that wrap platform-specific calls for obtaining information about the operating environment and the current process.
|
|
file | template_mp.h |
| Declares utilities for template metaprogramming.
|
|
file | alignedallocator_impl.h |
| Tests for allocators that offer a minimum alignment.
|
|
file | textreader.h |
| Declares gmx::TextReader.
|
|
file | textstream.h |
| Declares interfaces for simple input/output streams.
|
|
file | textwriter.h |
| Declares gmx::TextWriter.
|
|
file | txtdump.h |
| Declares helper functions for dumping basic data structures as text.
|
|
file | typetraits.h |
| Declares type traits.
|
|
file | unique_cptr.h |
| Declares gmx::unique_cptr and gmx::sfree_guard.
|
|
file | gmxpre.h |
| Prerequisite header file for GROMACS build.
|
|
file | cmdlinetest.h |
| Declares utilities testing command-line programs.
|
|
file | conftest.h |
| Declares function to add the content of a conf file to a checker.
|
|
file | filematchers.h |
| Declares utility classes for testing file contents.
|
|
file | interactivetest.h |
| Provides helper classes for testing interactive prompts.
|
|
file | loggertest.h |
| Declares gmx::test::LoggerTestHelper.
|
|
file | mpitest.h |
| Helper functions for MPI tests to make thread-MPI look like real MPI.
|
|
file | refdata.h |
| Functionality for writing tests that can produce their own reference data.
|
|
file | setenv.h |
| Helper functions to have identical behavior of setenv and unsetenv on Unix and Windows systems.
|
|
file | simulationdatabase.h |
| Functionality for testing whether calls to mdrun produce the same energy and force quantities when they should do so.
|
|
file | stdiohelper.h |
| Declares gmx::test::StdioTestHelper.
|
|
file | stringtest.h |
| Declares gmx::test::StringTestBase.
|
|
file | testasserts.h |
| Extra assertions for unit tests.
|
|
file | testexceptions.h |
| Exception classes for errors in tests.
|
|
file | testfilemanager.h |
| Declares gmx::test::TestFileManager.
|
|
file | testfileredirector.h |
| Declares generic mock implementations for interfaces in fileredirector.h.
|
|
file | testmatchers.h |
| Extra GoogleMock matchers for unit tests.
|
|
file | testoptions.h |
| Functions for accessing test command-line options.
|
|
file | textblockmatchers.h |
| Declares utility classes for testing multi-line strings against reference data.
|
|
file | xvgtest.h |
| Declares function to add the content of an xvg file to a checker.
|
|