Gromacs  2025-dev-20240710-afbd73d
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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
oCAmdPackedFloat3Special packed Float3 flavor to help compiler optimizations on AMD CDNA2 devices
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
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCdf_history_tFree-energy sampling history struct
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_cmap_tCMAP grids
oCgmx_cmapdata_tCMAP data for a single grid
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_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_nodecomm_tSettings and communicators for two-step communication: intra + inter-node
oCgmx_sparsematrixSparse matrix storage format
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
oCInteractionDefinitionsStruct with list of interaction parameters and lists of interactions
oCInteractionListList of listed interactions
oCInteractionListHandleType for returning a list of InteractionList references
oCJClusterListSimple j-cluster list
oCLocalSettleDataLocal settle data
oCMoleculeBlockIndicesIndices for a gmx_molblock_t, derived from other gmx_mtop_t contents
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_sci_tGrouped pair-list i-unit
oCNbnxnPairlistCpuCluster pairlist type for use on CPUs
oCNbnxnPairlistCpuWorkWorking data for the actual i-supercell during pair search
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
oCPmeSolveClass for solving PME for Coulomb and LJ
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
oCStringTableEntryHelper class to access members in StringTable
oCSystemMomentaSystem momenta used with with the box deform option
oCSystemMomentumThe momentum and mass of the whole system
oCt_filenmFile name option definition for C code
oCt_idefDeprecated interation definitions, used in t_topology
oCt_ilistDeprecated list of listed interactions
oCt_interaction_functionInteraction function
oCt_iparamsUnion of various interaction paramters
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_xpmelmtModels an XPM element
oCwallcc_tCounters for an individual wallcycle timing region
oCWarningHandlerGeneral warning handling object
\CWaterMoleculeIndices of atoms in a water molecule