nbnxm.h File Reference

#include <memory>
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/locality.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"

Include dependency graph for nbnxm.h:

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Description

This file contains the public interface of the nbnxm module that implements the NxM atom cluster non-bonded algorithm to efficiently compute pair forces.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Szilárd Páll pall..nosp@m.szil.nosp@m.ard@g.nosp@m.mail.nosp@m..com

Classes
class	gmx::ArrayRefWithPadding< typename >
	Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses. More...
class	gmx::ListOfLists< typename >
	A list of lists, optimized for performance. More...
class	gmx::Range< typename >
	Defines a range of integer numbers and accompanying operations. More...
struct	nonbonded_verlet_t
	Top-level non-bonded data structure for the Verlet-type cut-off scheme. More...

Enumerations
enum	Nbnxm::ElecType : int {   Nbnxm::ElecType::Cut, Nbnxm::ElecType::RF, Nbnxm::ElecType::EwaldTab, Nbnxm::ElecType::EwaldTabTwin,   Nbnxm::ElecType::EwaldAna, Nbnxm::ElecType::EwaldAnaTwin, Nbnxm::ElecType::Count }
	Nbnxm electrostatic GPU kernel flavors. More...
enum	Nbnxm::VdwType : int {   Nbnxm::VdwType::Cut, Nbnxm::VdwType::CutCombGeom, Nbnxm::VdwType::CutCombLB, Nbnxm::VdwType::FSwitch,   Nbnxm::VdwType::PSwitch, Nbnxm::VdwType::EwaldGeom, Nbnxm::VdwType::EwaldLB, Nbnxm::VdwType::Count }
	Nbnxm VdW GPU kernel flavors. More...
enum	Nbnxm::KernelType : int {   NotSet = 0, Cpu4x4_PlainC, Cpu4xN_Simd_4xN, Cpu4xN_Simd_2xNN,   Gpu8x8x8, Cpu8x8x8_PlainC, Count }
	Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation.
enum	Nbnxm::EwaldExclusionType : int { NotSet = 0, Table, Analytical, DecidedByGpuModule }
	Ewald exclusion types.
enum	{ enbvClearFNo, enbvClearFYes }
	Flag to tell the nonbonded kernels whether to clear the force output buffers.

Functions
const char *	Nbnxm::lookup_kernel_name (Nbnxm::KernelType kernelType)
	Return a string identifying the kernel type. More...
std::unique_ptr < nonbonded_verlet_t >	Nbnxm::init_nb_verlet (const gmx::MDLogger &mdlog, const t_inputrec &inputrec, const t_forcerec &forcerec, const t_commrec *commrec, const gmx_hw_info_t &hardwareInfo, bool useGpuForNonbonded, const gmx::DeviceStreamManager *deviceStreamManager, const gmx_mtop_t &mtop, gmx::ObservablesReducerBuilder *observablesReducerBuilder, gmx::ArrayRef< const gmx::RVec > coordinates, matrix box, gmx_wallcycle *wcycle)
	Creates an Nbnxm object.
void	nbnxn_put_on_grid_nonlocal (nonbonded_verlet_t *nb_verlet, const struct gmx_domdec_zones_t *zones, gmx::ArrayRef< const int64_t > atomInfo, gmx::ArrayRef< const gmx::RVec > x)
	As nbnxn_put_on_grid, but for the non-local atoms. More...
bool	buildSupportsNonbondedOnGpu (std::string *error)
	Check if GROMACS has been built with GPU support. More...

Variables
constexpr int	Nbnxm::c_numElecTypes = static_cast<int>(ElecType::Count)
	Number of possible ElecType values.
constexpr int	Nbnxm::c_numVdwTypes = static_cast<int>(VdwType::Count)
	Number of possible VdwType values.

Function Documentation

bool buildSupportsNonbondedOnGpu

(

std::string *

error

)

Check if GROMACS has been built with GPU support.

Parameters

[in]

error

Pointer to error string or nullptr.

Todo:

Move this to NB module once it exists.

void nbnxn_put_on_grid_nonlocal	(	nonbonded_verlet_t *	nb_verlet,
		const struct gmx_domdec_zones_t *	zones,
		gmx::ArrayRef< const int64_t >	atomInfo,
		gmx::ArrayRef< const gmx::RVec >	x
	)

As nbnxn_put_on_grid, but for the non-local atoms.

with domain decomposition. Should be called after calling nbnxn_search_put_on_grid for the local atoms / home zone.