Gromacs  2020.1
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1234]
oNanonymous_namespace{legacymodules.cpp}Registers command-line modules for pre-5.0 binaries
oNgmxGeneric GROMACS namespace
oCAllVsiteBondedInteractionsWraps the datastructures for the different vsite bondeds
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 master rank)
oCAtomIndexList of atom indices belonging to a task
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
oCAwhReaderAll options and meta-data needed for the AWH output
oCBalanceRegionStruct for timing the region for dynamic load balancing
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
oCChainIdFillerConstructs plausible chain IDs for multi-molecule systems, e.g. when read from .tpr files
oCCheckpointHeaderContentsHeader explaining the context of a checkpoint file
oCcl_atomdataNonbonded atom data - both inputs and outputs
oCcl_nb_stagingStaging area for temporary data downloaded from the GPU
oCcl_nbparamParameters required for the OpenCL nonbonded calculations
oCcl_nbparam_paramsData structure shared between the OpenCL device code and OpenCL host code
oCcu_atomdataNonbonded atom data - both inputs and outputs
oCcu_nbparamParameters required for the CUDA nonbonded calculations
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
oCdf_history_tFree-energy sampling history struct
oCekinstate_tStruct used for checkpointing only
oCem_state_tUtility structure for manipulating states during EM
oCEwaldBoxZScalerClass to handle box scaling for Ewald and PME
oCf_thread_tStruct with output for bonded forces, used per thread
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_device_info_tOpenCL device information
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_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_gpu_info_tInformation about GPU devices on this physical node
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_nbnxn_cuda_tMain data structure for CUDA nonbonded force calculations
oCgmx_nbnxn_ocl_tMain data structure for OpenCL nonbonded force calculations
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_ppMaster PP-PME communication data structure
oCgmx_potfitHelper structure for potential fitting
oCgmx_repl_exWorking data for replica exchange
oCgmx_reverse_top_tStruct for the reverse topology: links bonded interactions to atomsx
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
oCGpuEventSynchronizerA class which allows for CPU thread to mark and wait for certain GPU stream execution point. The event can be put into the stream with markEvent() and then later waited on with waitForEvent(). This can be repeated as necessary, but the current implementation does not allow waiting on completed event more than once, expecting only exact pairs of markEvent(stream); waitForEvent(). The class generally attempts to track the correctness of its state transitions, but please note that calling waitForEvent() right after the construction will fail with OpenCL but succeed with CUDA
oCGpuParallel3dFftA 3D FFT class for performing R2C/C2R transforms
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
oCilist_data_tStruct for passing all data required for a function type
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
oCInterdependentTaskData structure for thread tasks that use constructing atoms outside their own atom range
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
oCMD5ChecksumHelper struct for returning the MD5 checksum and the amount of the file that contributed to it
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
oCnb_stagingStaging 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
oCocl_gpu_id_tOpenCL GPU device identificator
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
oCPairlistParamsThe setup for generating and pruning the nbnxn pair list
oCPairlistSetAn object that holds the local or non-local pairlists
oCPartialDeserializedTprFileContains the partly deserialized contents of a TPR file
oCPbcAiucCompact and ordered version of the PBC matrix
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
oCPmeGpuKernelParamsBaseA single structure encompassing almost all the PME data used in GPU kernels on device. This is inherited by the GPU framework-specific structure (PmeGpuCudaKernelParams in pme.cuh). This way, most code preparing the kernel parameters can be GPU-agnostic by casting the kernel parameter data pointer to PmeGpuKernelParamsBase
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
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
oCProxyPtrWrapper around proxy object to implement operator->
oCpull_group_work_tPull group data used during pulling
oCReplicaExchangeParametersThe parameters for the replica exchange algorithm
oCResidueTypeEntrySingle ResidueType entry object
oCSearchCycleCountingStruct for collecting detailed cycle counts for the search
oCSimulationGroupsContains the simulation atom groups
oCSoftCoreRealMost treatments are fine with float in mixed-precision mode
oCSoftCoreReal< SoftCoreTreatment::RPower48 >This treatment requires double precision for some computations
oCsort_along_vec_tHelper structure for sorting positions along rotation vector
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
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_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_insolidangleData structure for the insolidangle 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_mergeData structure for the merging selection modifiers
oCt_methoddata_permuteData structure for the permute selection modifier
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_pargsCommand-line argument definition for C code
oCt_partitionInternal data structure for the insolidangle selection method
oCt_partition_itemInternal data structure for the insolidangle selection method
oCt_pbcStructure containing info on periodic boundary conditions
oCt_pullcoordParameters of one pull coodinate
oCt_register_methodHelper structure for defining selection methods
oCt_spheresurfacebinInternal data structure for the insolidangle selection method
oCt_stateThe microstate of the system
oCt_swapMain (private) data structure for the position swapping protocol
oCt_UmbrellaHeaderParameters of the umbrella potentials
oCt_UmbrellaOptionsParameters of WHAM
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
oCUnitCellInfoProvides information about properties of the unit cell
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
oCVsiteThreadVsite thread task data structure
\CWorkDivisionThe division of bonded interactions of the threads