Gromacs  2024.2
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123456]
oNanonymous_namespace{legacymodules.cpp}Registers command-line modules for pre-5.0 binaries
oNgmxGeneric GROMACS namespace
oNNbnxmNamespace for non-bonded kernels
oCAllVsiteBondedInteractionsWraps the datastructures for the different vsite bondeds
oCAmdPackedFloat3Special packed Float3 flavor to help compiler optimizations on AMD CDNA2 devices
oCAnalysisTemplateTemplate class to serve as a basis for user analysis tools
oCAtom2VsiteBondHelper type for conversion of bonded parameters to virtual sites
oCAtomDistributionDistribution of atom groups over the domain (only available on the main rank)
oCAtomIndexSetContainer for returning molecule type and index information for an atom
oCAtomInMolblockContainer for returning molecule type and index information for an atom
oCAtomIteratorObject that allows looping over all atoms in an mtop
oCAtomPropertiesHolds all the atom property information loaded
oCAtomPropertyConglomeration of atom property entries
oCAtomProxyProxy object returned from AtomIterator
oCAtomRangeRange over all atoms of topology
oCAtomsAdjacencyListElementHelper type for discovering coupled constraints
oCAwhReaderAll options and meta-data needed for the AWH output
oCBalanceRegionObject that describes a DLB balancing region
oCBaseEntryBasic entries in AtomProperty
oCBiasOutputSetupAll meta-data that is shared for all output files for one bias
oCbonded_threading_tStruct contain all data for bonded force threading
oCBondedInteractionInformation about single bonded interaction
oCBondedInteractionListAccumulation of different bonded types for preprocessing
oCCalcVerletBufferParametersStruct with references for most parameters for calling calcVerletBufferSize()
oCChainIdFillerConstructs plausible chain IDs for multi-molecule systems, e.g. when read from .tpr files
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCcl_nbparam_paramsData structure shared between the OpenCL device code and OpenCL host code
oCdd_corners_tDomain corners for communication, a maximum of 4 i-zones see a j domain
oCDDBalanceRegionHandlerManager for starting and stopping the dynamic load balancing region
oCDDGridSetupDescribes the DD grid setup
oCDDPairInteractionRangesPair interaction zone and atom range for an i-zone
oCDeviceInformationPlatform-dependent device information
oCDeviceStreamDeclaration of platform-agnostic device stream/queue
oCdf_history_tFree-energy sampling history struct
oCDipoleDataData structure to hold dipole-related data and staging arrays
oCekinstate_tStruct used for checkpointing only
oCem_stateUtility structure for manipulating states during EM
oCEwaldBoxZScalerClass to handle box scaling for Ewald and PME
oCFEPStateValueTemplate wrapper struct for particle FEP state values
oCForceHelperBuffersHelper force buffers for ForceOutputs
oCForeignLambdaTermsAccumulates free-energy foreign lambda energies and dH/dlamba
oCFreeEnergyDispatchTemporary data and methods for handling dispatching of the nbnxm free-energy kernels
oCgmx_ana_index_tStores a single index group
oCgmx_ana_indexgrps_tStores a set of index groups
oCgmx_ana_indexmap_tData structure for calculating index group mappings
oCgmx_ana_pos_tStores a set of positions together with their origins
oCgmx_ana_poscalc_tData structure for position calculation
oCgmx_ana_selcollection_tInformation for a collection of selections
oCgmx_ana_selmethod_help_tHelp information for a selection method
oCgmx_ana_selmethod_tDescribes a selection method
oCgmx_ana_selparam_tDescribes a single parameter for a selection method
oCgmx_ana_selvalue_tDescribes a value of a selection expression or of a selection method parameter
oCgmx_cache_protect_tCache-line protection buffer
oCgmx_device_runtime_data_tOpenCL GPU runtime data
oCgmx_domdec_constraints_tStruct used during constraint setup with domain decomposition
oCgmx_domdec_specat_comm_tStruct with setup and buffers for special atom communication
oCgmx_enerdata_tStruct for accumulating all potential energy terms and some kinetic energy terms
oCgmx_enfrotEnforced rotation data for all groups
oCgmx_enfrotgrpEnforced rotation data for a single rotation group
oCgmx_ffparams_tStruct that holds all force field parameters for the simulated system
oCgmx_fft_fftpackContents of the FFTPACK fft datatype
oCgmx_fft_fftw3Contents of the FFTW3 fft datatype
oCgmx_fft_mklContents of the Intel MKL FFT fft datatype
oCgmx_ga2la_tGlobal to local atom mapping
oCgmx_help_make_index_groupData necessary to construct a single (protein) index group in analyse_prot()
oCgmx_hw_opt_tThreading and GPU options, can be set automatically or by the user
oCgmx_kernel_timing_data_tGPU kernel time and call count
oCgmx_localtop_tThe fully written out topology for a domain over its lifetime
oCgmx_molblock_tBlock of molecules of the same type, used in gmx_mtop_t
oCgmx_moltype_tMolecules type data: atoms, interactions and exclusions
oCgmx_multisim_tCoordinate multi-simulation resources for mdrun
oCgmx_nodecomm_tSettings and communicators for two-step communication: intra + inter-node
oCgmx_pme_comm_n_box_tHelper struct for PP-PME communication of parameters
oCgmx_pme_comm_vir_ene_tHelper struct for PP-PME communication of virial and energy
oCgmx_pme_ppMain PP-PME communication data structure
oCgmx_potfitHelper structure for potential fitting
oCgmx_repl_exWorking data for replica exchange
oCgmx_reverse_top_tReverse topology class
oCgmx_sel_evaluate_tData structure for passing information required during evaluation
oCgmx_sel_lexer_tInternal data structure for the selection tokenizer state
oCgmx_sel_mempool_block_tDescribes a single block allocated from the memory pool
oCgmx_sel_mempool_tDescribes a memory pool
oCgmx_slabdataEnforced rotation / flexible: determine the angle of each slab
oCgmx_sparsematrixSparse matrix storage format
oCgmx_specatsend_tThe communication setup along a single dimension
oCgmx_tng_trajectoryGromacs Wrapper around tng datatype
oCgmx_wallclock_gpu_nbnxn_tGPU NB timings for kernels and H2d/D2H transfers
oCgmx_wallclock_gpu_pme_tGPU timings for PME
oCgmx_walltime_accountingManages caching wall-clock time measurements for simulations
oCGpuRegionTimerImplThe 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
oCGpuRegionTimerWrapperThis 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
oCGridConverterBuilds a kernel to convert between PME and FFT grids
oChistory_tHistory information for NMR distance and orientation restraints
oCilist_data_tStruct for passing all data required for a function type
oCIListIteratorObject that allows looping over all atoms in an mtop
oCIListProxyProxy object returned from IListIterator
oCIListRangeRange over all interaction lists of topology
oCIndexGroupAn index group consisting or a name and list of atom indices
oCInteractionListHandleType for returning a list of InteractionList references
oCInteractionOfTypeDescribes an interaction of a given type, plus its parameters
oCInteractionsOfTypeA set of interactions of a given type (found in the enumeration in ifunc.h), complete with atom indices and force field function parameters
oCJClusterListSimple j-cluster list
oCKernelLaunchConfigGPU kernels scheduling description. This is same in OpenCL/CUDA. Provides reasonable defaults, one typically only needs to set the GPU stream and non-1 work sizes
oCLeapFrogKernelClass name for leap-frog kernel
oCListedForcesClass for calculating listed interactions, uses OpenMP parallelization
oCLocalSettleDataLocal settle data
oCmethoddata_insolidangleData structure for the insolidangle selection method
oCmethoddata_mergeData structure for the merging selection modifiers
oCmethoddata_permuteData structure for the permute selection modifier
oCMolecularTopologyAtomIndicesMolecular topology indices of a global molecule a global atom belongs to
oCMoleculeBlockIndicesIndices for a gmx_molblock_t, derived from other gmx_mtop_t contents
oCMoleculeInformationHolds the molecule information during preprocessing
oCMoleculePatchBlock to modify individual residues
oCMoleculePatchDatabaseA set of modifications to apply to atoms
oCMoleculeTypeDescribes a molecule type, and keeps track of the number of these molecules
oCNBAtomDataGpuNonbonded atom data - both inputs and outputs
oCNbnxmGpuMain data structure for CUDA nonbonded force calculations
oCNbnxmKernelClass name for NBNXM kernel
oCNbnxmKernelPruneOnlyClass name for NBNXM prune-only kernel
oCnbnxn_atomdata_output_tStruct that holds force and energy output buffers
oCnbnxn_atomdata_tStruct that stores atom related data for the nbnxn module
oCnbnxn_ci_tSimple pair-list i-unit
oCnbnxn_cj_packed_tPacked j-cluster list element
oCnbnxn_cj_tThis is the actual cluster-pair list j-entry
oCnbnxn_cycle_tLocal cycle count struct for profiling
oCnbnxn_excl_tStruct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist
oCnbnxn_im_ei_tInteraction data for a j-group for one warp
oCnbnxn_sciGrouped pair-list i-unit
oCNbnxnPairlistCpuCluster pairlist type for use on CPUs
oCNbnxnPairlistCpuWorkWorking data for the actual i-supercell during pair search
oCNBParamGpuParameters required for the GPU nonbonded calculations
oCNBStagingDataStaging area for temporary data downloaded from the GPU
oCnonbonded_verlet_tTop-level non-bonded data structure for the Verlet-type cut-off scheme
oCNumPmeDomainsStruct for passing around the number of PME domains
oCObservablesHistoryObservables history, for writing/reading to/from checkpoint file
oComp_module_nthreads_tStructure with the number of threads for each OpenMP multi-threaded algorithmic module in mdrun
oCOutputFileAll meta-data that is shared for one output file type for one bias
oCPackedJClusterListPacked j-cluster list
oCPackHaloExternalHandles a kernel which packs non-contiguous overlap data in all 8 neighboring directions
oCPackHaloInternalHandles a kernel which packs non-contiguous overlap data in all 8 neighboring directions
oCPairlistParamsThe setup for generating and pruning the nbnxn pair list
oCPairlistSetAn object that holds the local or non-local pairlists
oCPairlistSetsContains sets of pairlists
oCPairSearchMain pair-search struct, contains the grid(s), not the pair-list(s)
oCPairsearchWorkThread-local work struct, contains working data for Grid
oCPartialDeserializedTprFileContains the partly deserialized contents of a TPR file
oCpartitionInternal data structure for the insolidangle selection method
oCPbcAiucCompact and ordered version of the PBC matrix
oCPdbAtomEntryContains information for a single particle in a PDB file
oCpme_setup_tParameters and settings for one PP-PME setup
oCPmeGpuThe main PME GPU host structure, included in the PME CPU structure by pointer
oCPmeGpuAtomParamsA GPU data structure for storing the PME data of the atoms, local to this process' domain partition. This only has to be updated every DD step
oCPmeGpuConstParamsA GPU data structure for storing the constant PME data. This only has to be initialized once
oCPmeGpuDynamicParamsA GPU data structure for storing the PME data which might change for each new PME computation
oCPmeGpuGridParamsA GPU data structure for storing the PME data related to the grid sizes and cut-off. This only has to be updated at every DD step
oCPmeGpuHaloExchangeHost data structure used to store data related to PME halo exchange, staging buffers for MPI communication
oCPmeGpuKernelParamsBaseA single structure encompassing all the PME data used in GPU kernels on device. To extend the list with platform-specific parameters, this can be inherited by the GPU framework-specific structure
oCPmeGpuProgramStores PME data derived from the GPU context or devices
oCPmeGpuProgramImplPME GPU persistent host program/kernel data, which should be initialized once for the whole execution
oCPmeGpuSettingsThe PME GPU settings structure, included in the main PME GPU structure by value
oCPmeGpuSpecificThe main PME CUDA/OpenCL-specific host data structure, included in the PME GPU structure by the archSpecific pointer
oCPmeGpuStagingThe PME GPU intermediate buffers structure, included in the main PME GPU structure by value. Buffers are managed by the PME GPU module
oCPmeSharedThe PME GPU structure for all the data copied directly from the CPU PME structure. The copying is done when the CPU PME structure is already (re-)initialized (pme_gpu_reinit is called at the end of gmx_pme_init). All the variables here are named almost the same way as in gmx_pme_t. The types are different: pointers are replaced by vectors. TODO: use the shared data with the PME CPU. Included in the main PME GPU structure by value
oCPmeSolveKernelThe kernel for PME solve
oCPpRanksContains information about the PP ranks that partner this PME rank
oCPpRanksSendFInfoContains information about the PP ranks that partners this PME rank. used in the pme gather kernel for nvshmem purpose
oCPreprocessingAtomTypesStorage of all atom types used during preprocessing of a simulation input
oCPreprocessingBondAtomTypeStorage for all bonded atomtypes during simulation preprocessing
oCPreprocessResidueInformation about preprocessing residues
oCpull_coord_work_tStruct with parameters and force evaluation local data for a pull coordinate
oCpull_group_work_tPull group data used during pulling
oCReduceKernelClass name for reduction kernel
oCReplicaExchangeParametersThe parameters for the replica exchange algorithm
oCReverseTopOptionsOptions for setting up gmx_reverse_top_t
oCScalarDataTypesScalar (non-SIMD) data types
oCSearchCycleCountingStruct for collecting detailed cycle counts for the search
oCSettleWaterTopologyComposite data for settle initialization
oCSimulationGroupsContains the simulation atom groups
oCSimulationParticleSingle particle in a simulation
oCSolveKernelParamsContains most of the parameters used by the solve kernel
oCsort_along_vec_tHelper structure for sorting positions along rotation vector
oCspheresurfacebinInternal data structure for the insolidangle selection method
oCStringTableA class to store strings for lookup
oCStringTableBuilderBuilds a memory efficient storage for strings of characters
oCStringTableEntryHelper class to access members in StringTable
oCswap_compartmentStructure containing compartment-specific data
oCswap_groupThis structure contains data needed for the groups involved in swapping: split group 0, split group 1, solvent group, ion groups
oCSystemMomentaSystem momenta used with with the box deform option
oCSystemMomentumThe momentum and mass of the whole system
oCt_bbStruct containing properties of a residue in a protein backbone
oCt_compare_valueData structure for comparison expression operand values
oCt_compiler_dataInternal data structure used by the compiler
oCt_coordselectionSelection of pull coordinates to be used in WHAM (one structure for each tpr file)
oCt_filenmFile name option definition for C code
oCt_forcetableStructure describing the data in a single table
oCt_mappingMaps an XPM element to an RGB color and a string description
oCt_matrixA matrix of integers, plus supporting values, such as used in XPM output
oCt_mdatomsDeclares mdatom data structure
oCt_methoddata_compareData structure for comparison expression evaluation
oCt_methoddata_distanceData structure for distance-based selection method
oCt_methoddata_kwevalData structure for keyword evaluation in arbitrary groups
oCt_methoddata_kwintData structure for integer keyword expression evaluation
oCt_methoddata_kwrealData structure for real keyword expression evaluation
oCt_methoddata_posData structure for position keyword evaluation
oCt_methoddata_sameData structure for the same selection method
oCt_nbparamUsed to temporarily store the explicit non-bonded parameter combinations, which will be copied to InteractionsOfType
oCt_oriresdataOrientation restraining stuff
oCt_pargsCommand-line argument definition for C code
oCt_partition_itemInternal data structure for the insolidangle selection method
oCt_pbcStructure containing info on periodic boundary conditions
oCt_pullcoordParameters of one pull coordinate
oCt_register_methodHelper structure for defining selection methods
oCt_stateThe microstate of the system
oCt_swapMain (private) data structure for the position swapping protocol
oCt_symbufLegacy symbol table entry as linked list
oCt_UmbrellaHeaderParameters of the umbrella potentials
oCt_UmbrellaWindowData in the umbrella histograms
oCt_xpmelmtModels an XPM element
oCthread_work_tStruct for thread local work data for local topology generation
oCTpxFileHeaderFirst part of the TPR file structure containing information about the general aspect of the system
oCUmbrellaOptionsParameters of WHAM
oCUnitCellInfoProvides information about properties of the unit cell
oCUnpackAndAddHaloInternalHandles a kernel which adds grid overlap data received from neighboring ranks
oCUnpackHaloExternalHandles a kernel which gathers data from halo region in all 8 neighboring directions
oCVirtualSiteConfigurationThe configuration describing a virtual site
oCVirtualSiteTopologyVirtual site topology datastructure
oCVsiteAtomMappingConvenience typedef for linking function type to parameter numbers
oCVsiteBondedInteractionData type to store information about bonded interactions for virtual sites
oCVsiteBondParameterStores information about single virtual site bonded parameter
oCwallcc_tCounters for an individual wallcycle timing region
oCWarningHandlerGeneral warning handling object
oCWaterMoleculeIndices of atoms in a water molecule
\CWorkDivisionThe division of bonded interactions of the threads