MD-Bench/gromacs/includes/atom.h
Rafael Ravedutti cbe42b8149 Fix errors to make gromacs approach compilable so far
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-25 12:19:28 +01:00

85 lines
2.6 KiB
C

/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
*
* This file is part of MD-Bench.
*
* MD-Bench is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License along
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <parameter.h>
#ifndef __ATOM_H_
#define __ATOM_H_
#define CLUSTER_DIM_N 4
#define CLUSTER_DIM_M 4
typedef struct {
int bin;
int natoms;
int type[CLUSTER_DIM_N];
MD_FLOAT bbminx, bbmaxx;
MD_FLOAT bbminy, bbmaxy;
MD_FLOAT bbminz, bbmaxz;
} Cluster;
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *fx, *fy, *fz;
MD_FLOAT *cl_x;
int *border_map;
int *type;
int ntypes;
MD_FLOAT *epsilon;
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
Cluster *clusters;
int *PBCx, *PBCy, *PBCz;
} Atom;
extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);
#define cluster_ptr(ci) &(atom->cl_x[ci * CLUSTER_DIM_N * 3])
#ifdef AOS
#define POS_DATA_LAYOUT "AoS"
#define atom_x(i) atom->x[(i) * 3 + 0]
#define atom_y(i) atom->x[(i) * 3 + 1]
#define atom_z(i) atom->x[(i) * 3 + 2]
#define cluster_x(cptr, i) cptr[(i) * 3 + 0]
#define cluster_y(cptr, i) cptr[(i) * 3 + 1]
#define cluster_z(cptr, i) cptr[(i) * 3 + 2]
#else
#define POS_DATA_LAYOUT "SoA"
#define atom_x(i) atom->x[i]
#define atom_y(i) atom->y[i]
#define atom_z(i) atom->z[i]
#define cluster_x(cptr, i) cptr[0 * CLUSTER_DIM_N + (i)]
#define cluster_y(cptr, i) cptr[1 * CLUSTER_DIM_N + (i)]
#define cluster_z(cptr, i) cptr[2 * CLUSTER_DIM_N + (i)]
#endif
#endif