104 lines
3.2 KiB
C
104 lines
3.2 KiB
C
/*
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* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <parameter.h>
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#ifndef __ATOM_H_
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#define __ATOM_H_
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#ifdef CUDA_TARGET
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# define KERNEL_NAME "CUDA"
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# define computeForceLJFullNeigh computeForceLJFullNeigh_cuda
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# define initialIntegrate initialIntegrate_cuda
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# define finalIntegrate finalIntegrate_cuda
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# define buildNeighbor buildNeighbor_cuda
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# define updatePbc updatePbc_cuda
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# define updateAtomsPbc updateAtomsPbc_cuda
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#else
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# ifdef USE_SIMD_KERNEL
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# define KERNEL_NAME "SIMD"
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# define computeForceLJFullNeigh computeForceLJFullNeigh_simd
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# else
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# define KERNEL_NAME "plain-C"
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# define computeForceLJFullNeigh computeForceLJFullNeigh_plain_c
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# endif
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# define initialIntegrate initialIntegrate_cpu
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# define finalIntegrate finalIntegrate_cpu
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# define buildNeighbor buildNeighbor_cpu
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# define updatePbc updatePbc_cpu
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# define updateAtomsPbc updateAtomsPbc_cpu
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#endif
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typedef struct {
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MD_FLOAT *x, *y, *z;
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MD_FLOAT *vx, *vy, *vz;
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MD_FLOAT *fx, *fy, *fz;
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int *border_map;
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int *type;
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MD_FLOAT *epsilon;
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MD_FLOAT *sigma6;
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MD_FLOAT *cutforcesq;
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MD_FLOAT *cutneighsq;
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} DeviceAtom;
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typedef struct {
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int Natoms, Nlocal, Nghost, Nmax;
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MD_FLOAT *x, *y, *z;
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MD_FLOAT *vx, *vy, *vz;
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MD_FLOAT *fx, *fy, *fz;
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int *border_map;
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int *type;
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int ntypes;
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MD_FLOAT *epsilon;
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MD_FLOAT *sigma6;
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MD_FLOAT *cutforcesq;
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MD_FLOAT *cutneighsq;
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// DEM
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MD_FLOAT *radius;
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MD_FLOAT *av;
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MD_FLOAT *r;
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// Device data
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DeviceAtom d_atom;
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} Atom;
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extern void initAtom(Atom*);
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extern void createAtom(Atom*, Parameter*);
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extern int readAtom(Atom*, Parameter*);
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extern int readAtom_pdb(Atom*, Parameter*);
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extern int readAtom_gro(Atom*, Parameter*);
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extern int readAtom_dmp(Atom*, Parameter*);
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extern int readAtom_in(Atom*, Parameter*);
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extern void writeAtom(Atom*, Parameter*);
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extern void growAtom(Atom*);
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#ifdef AOS
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# define POS_DATA_LAYOUT "AoS"
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# define atom_x(i) atom->x[(i) * 3 + 0]
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# define atom_y(i) atom->x[(i) * 3 + 1]
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# define atom_z(i) atom->x[(i) * 3 + 2]
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# define atom_vx(i) atom->vx[(i) * 3 + 0]
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# define atom_vy(i) atom->vx[(i) * 3 + 1]
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# define atom_vz(i) atom->vx[(i) * 3 + 2]
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# define atom_fx(i) atom->fx[(i) * 3 + 0]
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# define atom_fy(i) atom->fx[(i) * 3 + 1]
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# define atom_fz(i) atom->fx[(i) * 3 + 2]
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#else
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# define POS_DATA_LAYOUT "SoA"
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# define atom_x(i) atom->x[i]
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# define atom_y(i) atom->y[i]
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# define atom_z(i) atom->z[i]
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# define atom_vx(i) atom->vx[i]
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# define atom_vy(i) atom->vy[i]
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# define atom_vz(i) atom->vz[i]
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# define atom_fx(i) atom->fx[i]
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# define atom_fy(i) atom->fy[i]
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# define atom_fz(i) atom->fz[i]
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#endif
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#endif
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