Gromacs
2026.0-dev-20241106-9ba7f4d
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#include <cstdint>
#include <cstdio>
#include <memory>
#include <optional>
#include <vector>
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/hostallocator.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/locality.h"
#include "gromacs/nbnxm/nbnxm_enums.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/real.h"
Functionality for per-atom data in the nbnxm module.
Classes | |
class | gmx::EnergyAccumulator< bool, bool > |
Base energy accumulator class, only specializations are used. More... | |
struct | gmx::nbnxn_atomdata_output_t |
Struct that holds force and energy output buffers. More... | |
struct | gmx::nbnxn_atomdata_t |
Struct that stores atom related data for the nbnxn module. More... | |
struct | gmx::nbnxn_atomdata_t::Params |
The actual atom data parameter values. More... | |
struct | gmx::nbnxn_atomdata_t::SimdMasks |
Diagonal and topology exclusion helper data for all SIMD kernels. More... | |
Macros | |
#define | NBNXN_BUFFERFLAG_SIZE 16 |
Block size in atoms for the non-bonded thread force-buffer reduction. More... | |
#define | NBNXN_BUFFERFLAG_MAX_THREADS (BITMASK_SIZE) |
We store the reduction flags as gmx_bitmask_t. This limits the number of flags to BITMASK_SIZE. | |
Enumerations | |
enum | { nbatXYZ, nbatXYZQ, nbatX4, nbatX8 } |
enum | gmx::LJCombinationRule : int { gmx::LJCombinationRule::Geometric, gmx::LJCombinationRule::LorentzBerthelot, gmx::LJCombinationRule::None, gmx::LJCombinationRule::Count } |
LJ combination rules. More... | |
Functions | |
template<int packSize> | |
static int | gmx::atom_to_x_index (int a) |
Returns the index in a coordinate array corresponding to atom a. | |
const char * | gmx::enumValueToString (LJCombinationRule enumValue) |
String corresponding to LJ combination rule. | |
void | gmx::copy_rvec_to_nbat_real (const int *a, int na, int na_round, const rvec *x, int nbatFormat, real *xnb, int a0) |
Copy na rvec elements from x to xnb using nbatFormat, start dest a0, and fills up to na_round with coordinates that are far away. | |
void | gmx::nbnxn_atomdata_set (nbnxn_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const int > atomTypes, ArrayRef< const real > atomCharges, ArrayRef< const int32_t > atomInfo) |
Sets the atomdata after pair search. | |
void | gmx::nbnxn_atomdata_copy_shiftvec (bool dynamic_box, ArrayRef< RVec > shift_vec, nbnxn_atomdata_t *nbat) |
Copy the shift vectors to nbat. | |
void | gmx::nbnxn_atomdata_copy_x_to_nbat_x (const GridSet &gridSet, AtomLocality locality, const rvec *coordinates, nbnxn_atomdata_t *nbat) |
Transform coordinates to xbat layout. More... | |
void | gmx::nbnxn_atomdata_x_to_nbat_x_gpu (const GridSet &gridSet, AtomLocality locality, NbnxmGpu *gpu_nbv, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice) |
Transform coordinates to xbat layout on GPU. More... | |
void | gmx::nbnxn_atomdata_add_nbat_fshift_to_fshift (const nbnxn_atomdata_t &nbat, ArrayRef< RVec > fshift) |
Add the fshift force stored in nbat to fshift. | |
Variables | |
static constexpr int | gmx::STRIDE_XYZ = 3 |
Stride for coordinate/force arrays with xyz coordinate storage. | |
static constexpr int | gmx::STRIDE_XYZQ = 4 |
Stride for coordinate/force arrays with xyzq coordinate storage. | |
static constexpr int | gmx::c_packX4 = 4 |
Size of packs of x, y or z with SIMD 4-grouped packed coordinates/forces. | |
static constexpr int | gmx::c_packX8 = 8 |
Size of packs of x, y or z with SIMD 8-grouped packed coordinates/forces. | |
static constexpr int | gmx::STRIDE_P4 = DIM * c_packX4 |
Stridefor a pack of 4 coordinates/forces. | |
static constexpr int | gmx::STRIDE_P8 = DIM * c_packX8 |
Stridefor a pack of 8 coordinates/forces. | |
#define NBNXN_BUFFERFLAG_SIZE 16 |
Block size in atoms for the non-bonded thread force-buffer reduction.
Should be a multiple of all cell and x86 SIMD sizes (i.e. 2, 4 and 8). Should be small to reduce the reduction and zeroing cost, but too small will result in overhead. Currently the block size is NBNXN_BUFFERFLAG_SIZE*3*sizeof(real)=192 bytes.