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nonbonded_verlet_t Struct Reference

#include <gromacs/nbnxm/nbnxm.h>

Description

Top-level non-bonded data structure for the Verlet-type cut-off scheme.

Public Member Functions

 nonbonded_verlet_t (std::unique_ptr< PairlistSets > pairlistSets, std::unique_ptr< PairSearch > pairSearch, std::unique_ptr< nbnxn_atomdata_t > nbat, const Nbnxm::KernelSetup &kernelSetup, std::unique_ptr< ExclusionChecker > exclusionChecker, NbnxmGpu *gpu_nbv, gmx_wallcycle *wcycle)
 Constructs an object from its components. More...
 
 nonbonded_verlet_t (std::unique_ptr< PairlistSets > pairlistSets, std::unique_ptr< PairSearch > pairSearch, std::unique_ptr< nbnxn_atomdata_t > nbat, const Nbnxm::KernelSetup &kernelSetup, NbnxmGpu *gpu_nbv)
 Constructs an object from its, minimal, components. More...
 
bool useGpu () const
 Returns whether a GPU is use for the non-bonded calculations.
 
bool emulateGpu () const
 Returns whether a GPU is emulated for the non-bonded calculations.
 
bool pairlistIsSimple () const
 Return whether the pairlist is of simple, CPU type.
 
void putAtomsOnGrid (const matrix box, int gridIndex, const gmx::RVec &lowerCorner, const gmx::RVec &upperCorner, const gmx::UpdateGroupsCog *updateGroupsCog, gmx::Range< int > atomRange, real atomDensity, gmx::ArrayRef< const int64_t > atomInfo, gmx::ArrayRef< const gmx::RVec > x, int numAtomsMoved, const int *move)
 Put the atoms on the pair search grid. More...
 
gmx::ArrayRef< const int > getLocalAtomOrder () const
 Returns the order of the local atoms on the grid.
 
void setLocalAtomOrder () const
 Sets the order of the local atoms to the order grid atom ordering.
 
gmx::ArrayRef< const int > getGridIndices () const
 Returns the index position of the atoms on the search grid.
 
void constructPairlist (gmx::InteractionLocality iLocality, const gmx::ListOfLists< int > &exclusions, int64_t step, t_nrnb *nrnb) const
 Constructs the pairlist for the given locality. More...
 
void setAtomProperties (gmx::ArrayRef< const int > atomTypes, gmx::ArrayRef< const real > atomCharges, gmx::ArrayRef< const int64_t > atomInfo) const
 Updates all the atom properties in Nbnxm.
 
void convertCoordinates (gmx::AtomLocality locality, gmx::ArrayRef< const gmx::RVec > coordinates)
 Convert the coordinates to NBNXM format for the given locality. More...
 
void convertCoordinatesGpu (gmx::AtomLocality locality, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice)
 Convert the coordinates to NBNXM format on the GPU for the given locality. More...
 
void atomdata_init_copy_x_to_nbat_x_gpu () const
 Init for GPU version of setup coordinates in Nbnxm.
 
const PairlistSetspairlistSets () const
 Returns a reference to the pairlist sets.
 
bool isDynamicPruningStepCpu (int64_t step) const
 Returns whether step is a dynamic list pruning step, for CPU lists.
 
bool isDynamicPruningStepGpu (int64_t step) const
 Returns whether step is a dynamic list pruning step, for GPU lists.
 
void dispatchPruneKernelCpu (gmx::InteractionLocality iLocality, gmx::ArrayRef< const gmx::RVec > shift_vec) const
 Dispatches the dynamic pruning kernel for the given locality, for CPU lists.
 
void dispatchPruneKernelGpu (int64_t step)
 Dispatches the dynamic pruning kernel for GPU lists.
 
void dispatchNonbondedKernel (gmx::InteractionLocality iLocality, const interaction_const_t &ic, const gmx::StepWorkload &stepWork, int clearF, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< real > repulsionDispersionSR, gmx::ArrayRef< real > CoulombSR, t_nrnb *nrnb) const
 Executes the non-bonded kernel of the GPU or launches it on the GPU.
 
void dispatchFreeEnergyKernels (const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, gmx::ForceWithShiftForces *forceWithShiftForces, bool useSimd, int ntype, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< const real > nbfp, gmx::ArrayRef< const real > nbfp_grid, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const int > typeA, gmx::ArrayRef< const int > typeB, gmx::ArrayRef< const real > lambda, gmx_enerdata_t *enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb)
 Executes the non-bonded free-energy kernels, local + non-local, always runs on the CPU.
 
void atomdata_add_nbat_f_to_f (gmx::AtomLocality locality, gmx::ArrayRef< gmx::RVec > force)
 Add the forces stored in nbat to f, zeros the forces in nbat. More...
 
int getNumAtoms (gmx::AtomLocality locality) const
 Get the number of atoms for a given locality. More...
 
const Nbnxm::KernelSetup & kernelSetup () const
 Return the kernel setup.
 
real pairlistInnerRadius () const
 Returns the outer radius for the pair list.
 
real pairlistOuterRadius () const
 Returns the outer radius for the pair list.
 
void changePairlistRadii (real rlistOuter, real rlistInner) const
 Changes the pair-list outer and inner radius.
 
void setupGpuShortRangeWork (const gmx::ListedForcesGpu *listedForcesGpu, gmx::InteractionLocality iLocality) const
 Set up internal flags that indicate what type of short-range work there is.
 
void setupFepThreadedForceBuffer (int numAtomsForce)
 
nbnxn_atomdata_tnbat ()
 Returns a reference to the nbnxn_atomdata_t object.
 
const NbnxmGpugpuNbv () const
 Returns a pointer to the NbnxmGpu object, can return nullptr.
 
NbnxmGpugpuNbv ()
 Returns a pointer to the NbnxmGpu object, can return nullptr.
 

Constructor & Destructor Documentation

nonbonded_verlet_t::nonbonded_verlet_t ( std::unique_ptr< PairlistSets pairlistSets,
std::unique_ptr< PairSearch pairSearch,
std::unique_ptr< nbnxn_atomdata_t nbat,
const Nbnxm::KernelSetup &  kernelSetup,
std::unique_ptr< ExclusionChecker >  exclusionChecker,
NbnxmGpu gpu_nbv,
gmx_wallcycle *  wcycle 
)

Constructs an object from its components.

Parameters
[in]pairlistSetsThe pairlist sets, is consumed
[in]pairSearchThe pairsearch setup, is consumed
[in]nbatThe atom data, is consumed
[in]kernelSetupThe non-bonded kernel setup
[in]exclusionCheckerThe FEP exclusion checker, is consumed, can be nullptr
[in]gpu_nbvThe GPU non-bonded setup, ownership is transferred, can be nullptr
[in]wcyclePointer to wallcycle counters, can be nullptr
nonbonded_verlet_t::nonbonded_verlet_t ( std::unique_ptr< PairlistSets pairlistSets,
std::unique_ptr< PairSearch pairSearch,
std::unique_ptr< nbnxn_atomdata_t nbat,
const Nbnxm::KernelSetup &  kernelSetup,
NbnxmGpu gpu_nbv 
)

Constructs an object from its, minimal, components.

Parameters
[in]pairlistSetsThe pairlist sets, is consumed
[in]pairSearchThe pairsearch setup, is consumed
[in]nbatThe atom data, is consumed
[in]kernelSetupThe non-bonded kernel setup
[in]gpu_nbvThe GPU non-bonded setup, ownership is transferred, can be nullptr

Member Function Documentation

void nonbonded_verlet_t::atomdata_add_nbat_f_to_f ( gmx::AtomLocality  locality,
gmx::ArrayRef< gmx::RVec force 
)

Add the forces stored in nbat to f, zeros the forces in nbat.

Parameters
[in]localityLocal or non-local
[in,out]forceForce to be added to
void nonbonded_verlet_t::constructPairlist ( gmx::InteractionLocality  iLocality,
const gmx::ListOfLists< int > &  exclusions,
int64_t  step,
t_nrnb *  nrnb 
) const

Constructs the pairlist for the given locality.

When there are no non-self exclusions, exclusions can be empty. Otherwise the number of lists in exclusions should match the number of atoms when not using DD, or the total number of atoms in the i-zones when using DD.

Parameters
[in]iLocalityThe interaction locality: local or non-local
[in]exclusionsLists of exclusions for every atom.
[in]stepUsed to set the list creation step
[in,out]nrnbFlop accounting struct, can be nullptr
void nonbonded_verlet_t::convertCoordinates ( gmx::AtomLocality  locality,
gmx::ArrayRef< const gmx::RVec coordinates 
)

Convert the coordinates to NBNXM format for the given locality.

The API function for the transformation of the coordinates from one layout to another.

Parameters
[in]localityWhether coordinates for local or non-local atoms should be transformed.
[in]coordinatesCoordinates in plain rvec format to be transformed.
void nonbonded_verlet_t::convertCoordinatesGpu ( gmx::AtomLocality  locality,
DeviceBuffer< gmx::RVec d_x,
GpuEventSynchronizer *  xReadyOnDevice 
)

Convert the coordinates to NBNXM format on the GPU for the given locality.

The API function for the transformation of the coordinates from one layout to another in the GPU memory.

Parameters
[in]localityWhether coordinates for local or non-local atoms should be transformed.
[in]d_xGPU coordinates buffer in plain rvec format to be transformed.
[in]xReadyOnDeviceEvent synchronizer indicating that the coordinates are ready in the device memory.
int nonbonded_verlet_t::getNumAtoms ( gmx::AtomLocality  locality) const

Get the number of atoms for a given locality.

Parameters
[in]localityLocal or non-local
Returns
The number of atoms for given locality
void nonbonded_verlet_t::putAtomsOnGrid ( const matrix  box,
int  gridIndex,
const gmx::RVec lowerCorner,
const gmx::RVec upperCorner,
const gmx::UpdateGroupsCog updateGroupsCog,
gmx::Range< int >  atomRange,
real  atomDensity,
gmx::ArrayRef< const int64_t >  atomInfo,
gmx::ArrayRef< const gmx::RVec x,
int  numAtomsMoved,
const int *  move 
)

Put the atoms on the pair search grid.

Only atoms with indices wihtin atomRange in x are put on the grid. When updateGroupsCog != nullptr, atoms are put on the grid based on the center of geometry of the group they belong to. Atoms or COGs of groups should be within the bounding box provided, this is checked in debug builds when not using update groups. The atom density is used to determine the grid size when gridIndex = 0. When atomDensity <= 0, the density is determined from atomEnd-atomStart and the bounding box corners. With domain decomposition, part of the atoms might have migrated, but have not been removed yet. This count is given by numAtomsMoved. When move[i] < 0 particle i has migrated and will not be put on the grid.

Parameters
[in]boxBox used for periodic distance calculations
[in]gridIndexThe index of the grid to spread to, always 0 except with test particle insertion
[in]lowerCornerAtom groups to be gridded should have coordinates >= this corner
[in]upperCornerAtom groups to be gridded should have coordinates <= this corner
[in]updateGroupsCogCenters of geometry for update groups, pass nullptr when not using update groups
[in]atomRangeRange of atoms to grid
[in]atomDensityAn estimate of the atom density, used for peformance optimization and only with gridIndex = 0
[in]atomInfoAtom information flags
[in]xCoordinates for atoms to grid
[in]numAtomsMovedThe number of atoms that will move to another domain, pass 0 without DD
[in]moveMove flags for atoms, pass nullptr without DD

The documentation for this struct was generated from the following files: