Gromacs  2023.2
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
oNgmxGeneric GROMACS namespace
oNNbnxmNamespace for non-bonded kernels
oCAtomIteratorObject that allows looping over all atoms in an mtop
oCAtomPropertiesHolds all the atom property information loaded
oCAtomProxyProxy object returned from AtomIterator
oCAtomRangeRange over all atoms of topology
oCAtomsAdjacencyListElementHelper type for discovering coupled constraints
oCBalanceRegionObject that describes a DLB balancing region
oCBondedInteractionInformation about single bonded interaction
oCBondedInteractionListAccumulation of different bonded types for preprocessing
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCDDBalanceRegionHandlerManager for starting and stopping the dynamic load balancing region
oCDeviceInformationPlatform-dependent device information
oCDeviceStreamDeclaration of platform-agnostic device stream/queue
oCdf_history_tFree-energy sampling history struct
oCekinstate_tStruct used for checkpointing only
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
oCgmx_ana_index_tStores a single index group
oCgmx_ana_indexmap_tData structure for calculating index group mappings
oCgmx_ana_pos_tStores a set of positions together with their origins
oCgmx_cache_protect_tCache-line protection buffer
oCgmx_domdec_constraints_tStruct used during constraint setup with domain decomposition
oCgmx_enerdata_tStruct for accumulating all potential energy terms and some kinetic energy terms
oCgmx_ffparams_tStruct that holds all force field parameters for the simulated system
oCgmx_ga2la_tGlobal to local atom mapping
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_sparsematrixSparse matrix storage format
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
oChistory_tHistory information for NMR distance and orientation restraints
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
oCListedForcesClass for calculating listed interactions, uses OpenMP parallelization
oCLocalSettleDataLocal settle data
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
oCNbnxmKernelClass name for NBNXM kernel
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
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
oCPackedJClusterListPacked j-cluster list
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
oCPbcAiucCompact and ordered version of the PBC matrix
oCPdbAtomEntryContains information for a single particle in a PDB file
oCPmeGpuProgramStores PME data derived from the GPU context or devices
oCPpRanksContains information about the PP ranks that partner this PME rank
oCPreprocessingAtomTypesStorage of all atom types used during preprocessing of a simulation input
oCPreprocessingBondAtomTypeStorage for all bonded atomtypes during simulation preprocessing
oCPreprocessResidueInformation about preprocessing residues
oCReplicaExchangeParametersThe parameters for the replica exchange algorithm
oCSettleWaterTopologyComposite data for settle initialization
oCSimulationGroupsContains the simulation atom groups
oCSimulationInputHandleOwning handle to a SimulationInput object
oCSimulationParticleSingle particle in a simulation
oCStringTableA class to store strings for lookup
oCStringTableBuilderBuilds a memory efficient storage for strings of characters
oCStringTableEntryHelper class to access members in StringTable
oCt_filenmFile name option definition for C code
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_oriresdataOrientation restraining stuff
oCt_pargsCommand-line argument definition for C code
oCt_pbcStructure containing info on periodic boundary conditions
oCt_stateThe microstate of the system
oCt_symbufLegacy symbol table entry as linked list
oCt_xpmelmtModels an XPM element
oCTpxFileHeaderFirst part of the TPR file structure containing information about the general aspect of the system
oCWarningHandlerGeneral warning handling object
\CWaterMoleculeIndices of atoms in a water molecule