MD-Bench/lammps/includes/atom.h

/*
 * 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 <parameter.h>

#ifndef __ATOM_H_
#define __ATOM_H_

#ifdef CUDA_TARGET
#   define KERNEL_NAME                  "CUDA"
#   define computeForceLJFullNeigh      computeForceLJFullNeigh_cuda
#   define initialIntegrate             initialIntegrate_cuda
#   define finalIntegrate               finalIntegrate_cuda
#   define buildNeighbor                buildNeighbor_cuda
#   define updatePbc                    updatePbc_cuda
#   define updateAtomsPbc               updateAtomsPbc_cuda
#else
#   ifdef USE_SIMD_KERNEL
#       define KERNEL_NAME              "SIMD"
#       define computeForceLJFullNeigh  computeForceLJFullNeigh_simd
#   else
#       define KERNEL_NAME              "plain-C"
#       define computeForceLJFullNeigh  computeForceLJFullNeigh_plain_c
#   endif
#   define initialIntegrate             initialIntegrate_cpu
#   define finalIntegrate               finalIntegrate_cpu
#   define buildNeighbor                buildNeighbor_cpu
#   define updatePbc                    updatePbc_cpu
#   define updateAtomsPbc               updateAtomsPbc_cpu
#endif

typedef struct {
    MD_FLOAT *x, *y, *z;
    MD_FLOAT *vx, *vy, *vz;
    MD_FLOAT *fx, *fy, *fz;
    int *border_map;
    int *type;
    MD_FLOAT *epsilon;
    MD_FLOAT *sigma6;
    MD_FLOAT *cutforcesq;
    MD_FLOAT *cutneighsq;
} DeviceAtom;

typedef struct {
    int Natoms, Nlocal, Nghost, Nmax;
    MD_FLOAT *x, *y, *z;
    MD_FLOAT *vx, *vy, *vz;
    MD_FLOAT *fx, *fy, *fz;
    int *border_map;
    int *type;
    int ntypes;
    MD_FLOAT *epsilon;
    MD_FLOAT *sigma6;
    MD_FLOAT *cutforcesq;
    MD_FLOAT *cutneighsq;

    // DEM
    MD_FLOAT *radius;
    MD_FLOAT *av;
    MD_FLOAT *r;

    // Device data
    DeviceAtom d_atom;
} 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 int readAtom_in(Atom*, Parameter*);
extern void growAtom(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]
#   define atom_vx(i)          atom->vx[(i) * 3 + 0]
#   define atom_vy(i)          atom->vx[(i) * 3 + 1]
#   define atom_vz(i)          atom->vx[(i) * 3 + 2]
#   define atom_fx(i)          atom->fx[(i) * 3 + 0]
#   define atom_fy(i)          atom->fx[(i) * 3 + 1]
#   define atom_fz(i)          atom->fx[(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 atom_vx(i)          atom->vx[i]
#   define atom_vy(i)          atom->vy[i]
#   define atom_vz(i)          atom->vz[i]
#   define atom_fx(i)          atom->fx[i]
#   define atom_fy(i)          atom->fy[i]
#   define atom_fz(i)          atom->fz[i]
#endif

#endif