80 lines
2.6 KiB
C
80 lines
2.6 KiB
C
/*
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* =======================================================================================
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*
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* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
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* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
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*
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* This file is part of MD-Bench.
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*
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* MD-Bench is free software: you can redistribute it and/or modify it
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* under the terms of the GNU Lesser General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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* details.
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*
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* You should have received a copy of the GNU Lesser General Public License along
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* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
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* =======================================================================================
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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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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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} 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 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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