MD-Bench/gromacs/includes/atom.h

/*
 * =======================================================================================
 *
 *   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 DELTA 20000

#define CLUSTER_M 4

// Nbnxn layouts (as of GROMACS):
// Simd4xN: M=4, N=VECTOR_WIDTH
// Simd2xNN: M=4, N=(VECTOR_WIDTH/2)

// Simd2XNN (here used for single-precision)
#if VECTOR_WIDTH > CLUSTER_M * 2
#   define CLUSTER_N                (VECTOR_WIDTH / 2)
// Simd4xN
#else
#   define CLUSTER_N                VECTOR_WIDTH
#endif

#if CLUSTER_M == CLUSTER_N
#   define CJ0_FROM_CI(a)           (a)
#   define CJ1_FROM_CI(a)           (a)
#   define CI_BASE_INDEX(a,b)       ((a) * CLUSTER_N * (b))
#   define CJ_BASE_INDEX(a,b)       ((a) * CLUSTER_N * (b))
#elif CLUSTER_M == CLUSTER_N * 2 // M > N
#   define CJ0_FROM_CI(a)           ((a) << 1)
#   define CJ1_FROM_CI(a)           (((a) << 1) | 0x1)
#   define CI_BASE_INDEX(a,b)       ((a) * CLUSTER_M * (b))
#   define CJ_BASE_INDEX(a,b)       (((a) >> 1) * CLUSTER_M * (b) + ((a) & 0x1) * (CLUSTER_M >> 1))
#elif CLUSTER_M == CLUSTER_N / 2 // M < N
#   define CJ0_FROM_CI(a)           ((a) >> 1)
#   define CJ1_FROM_CI(a)           ((a) >> 1)
#   define CI_BASE_INDEX(a,b)       (((a) >> 1) * CLUSTER_N * (b) + ((a) & 0x1) * (CLUSTER_N >> 1))
#   define CJ_BASE_INDEX(a,b)       ((a) * CLUSTER_N * (b))
#else
#   error "Invalid cluster configuration!"
#endif

#if CLUSTER_N != 2 && CLUSTER_N != 4 && CLUSTER_N != 8
#   error "Cluster N dimension can be only 2, 4 and 8"
#endif

#define CI_SCALAR_BASE_INDEX(a)     (CI_BASE_INDEX(a, 1))
#define CI_VECTOR_BASE_INDEX(a)     (CI_BASE_INDEX(a, 3))
#define CJ_SCALAR_BASE_INDEX(a)     (CJ_BASE_INDEX(a, 1))
#define CJ_VECTOR_BASE_INDEX(a)     (CJ_BASE_INDEX(a, 3))

#if CLUSTER_M >= CLUSTER_N
#   define CL_X_OFFSET              (0 * CLUSTER_M)
#   define CL_Y_OFFSET              (1 * CLUSTER_M)
#   define CL_Z_OFFSET              (2 * CLUSTER_M)
#else
#   define CL_X_OFFSET              (0 * CLUSTER_N)
#   define CL_Y_OFFSET              (1 * CLUSTER_N)
#   define CL_Z_OFFSET              (2 * CLUSTER_N)
#endif

typedef struct {
    int natoms;
    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;
    int *border_map;
    int *type;
    int ntypes;
    MD_FLOAT *epsilon;
    MD_FLOAT *sigma6;
    MD_FLOAT *cutforcesq;
    MD_FLOAT *cutneighsq;
    int *PBCx, *PBCy, *PBCz;
    // Data in cluster format
    MD_FLOAT *cl_x;
    MD_FLOAT *cl_v;
    MD_FLOAT *cl_f;
    int *cl_type;
    Cluster *iclusters, *jclusters;
} Atom;

extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*);
extern int readAtom_pdb(Atom*, Parameter*);
extern int readAtom_gro(Atom*, Parameter*);
extern int readAtom_dmp(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);

#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]
#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]
#endif

#endif