Gromacs  2019
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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1234]
oNgmxGeneric GROMACS namespace
oCdf_history_tFree-energy sampling history struct
oCDomdecOptionsStructure containing all (command line) options for the domain decomposition
oCekinstate_tStruct used for checkpointing only
oCEwaldBoxZScalerClass to handle box scaling for Ewald and PME
oCForceProvidersEvaluates forces from a collection of gmx::IForceProvider
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_ffparams_tStruct that holds all force field parameters for the simulated system
oCgmx_ga2la_tGlobal to local atom mapping
oCgmx_molblock_tBlock of molecules of the same type, used in gmx_mtop_t
oCgmx_moltype_tMolecules type data: atoms, interactions and exclusions
oCgmx_sparsematrixSparse matrix storage format
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
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
oCInteractionListHandleType for returning a list of InteractionList references
oCMoleculeBlockIndicesIndices for a gmx_molblock_t, derived from other gmx_mtop_t contents
oCnonbonded_verlet_group_tNon-bonded interaction group data structure
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
oCReplicaExchangeParametersThe parameters for the replica exchange algorithm
oCt_filenmFile name option definition for C code
oCt_mdatomsDeclares mdatom data structure
oCt_pargsCommand-line argument definition for C code
oCt_pbcStructure containing info on periodic boundary conditions
oCt_stateThe microstate of the system
\CTypedClMemoryA minimal cl_mem wrapper that remembers its allocation type. The only point is making template type deduction possible