MD-Bench/gromacs/includes/neighbor.h

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/*
* 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.
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*/
#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
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typedef struct {
int every;
int ncalls;
int maxneighs;
int* numneigh;
int* numneigh_masked;
int half_neigh;
int* neighbors;
unsigned int* neighbors_imask;
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} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*, Atom*);
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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*);
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#endif