53 lines
1.7 KiB
C
53 lines
1.7 KiB
C
/*
|
|
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
|
|
* All rights reserved. This file is part of MD-Bench.
|
|
* Use of this source code is governed by a LGPL-3.0
|
|
* license that can be found in the LICENSE file.
|
|
*/
|
|
#include <atom.h>
|
|
#include <parameter.h>
|
|
|
|
#ifndef __NEIGHBOR_H_
|
|
#define __NEIGHBOR_H_
|
|
// Interaction masks from GROMACS, things to remember (maybe these confused just me):
|
|
// 1. These are not "exclusion" masks as the name suggests in GROMACS, but rather
|
|
// interaction masks (1 = interaction, 0 = no interaction)
|
|
// 2. These are inverted (maybe because that is how you use in AVX2/AVX512 masking),
|
|
// so read them from right to left (least significant to most significant bit)
|
|
// All interaction mask is the same for all kernels
|
|
#define NBNXN_INTERACTION_MASK_ALL 0xffffffffU
|
|
// 4x4 kernel diagonal mask
|
|
#define NBNXN_INTERACTION_MASK_DIAG 0x08ceU
|
|
// 4x2 kernel diagonal masks
|
|
#define NBNXN_INTERACTION_MASK_DIAG_J2_0 0x0002U
|
|
#define NBNXN_INTERACTION_MASK_DIAG_J2_1 0x002fU
|
|
// 4x8 kernel diagonal masks
|
|
#define NBNXN_INTERACTION_MASK_DIAG_J8_0 0xf0f8fcfeU
|
|
#define NBNXN_INTERACTION_MASK_DIAG_J8_1 0x0080c0e0U
|
|
|
|
typedef struct {
|
|
int cj;
|
|
unsigned int imask;
|
|
} NeighborCluster;
|
|
|
|
typedef struct {
|
|
int every;
|
|
int ncalls;
|
|
int maxneighs;
|
|
int* numneigh;
|
|
int half_neigh;
|
|
NeighborCluster* neighbors;
|
|
} Neighbor;
|
|
|
|
extern void initNeighbor(Neighbor*, Parameter*);
|
|
extern void setupNeighbor(Parameter*, Atom*);
|
|
extern void binatoms(Atom*);
|
|
extern void buildNeighbor(Atom*, Neighbor*);
|
|
extern void pruneNeighbor(Parameter*, Atom*, Neighbor*);
|
|
extern void sortAtom(Atom*);
|
|
extern void buildClusters(Atom*);
|
|
extern void defineJClusters(Atom*);
|
|
extern void binClusters(Atom*);
|
|
extern void updateSingleAtoms(Atom*);
|
|
#endif
|