/* * ======================================================================================= * * 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 . * ======================================================================================= */ #include #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 { 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; } 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