Cleanup. Remove copyright year. Reformat.
This commit is contained in:
103
verletlist/includes/atom.h
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103
verletlist/includes/atom.h
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/*
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* Copyright (C) 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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34
verletlist/includes/integrate.h
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34
verletlist/includes/integrate.h
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/*
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* Copyright (C) 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 <stdbool.h>
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//---
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#include <parameter.h>
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#include <atom.h>
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void initialIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom) {
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for(int i = 0; i < atom->Nlocal; i++) {
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atom_vx(i) += param->dtforce * atom_fx(i);
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atom_vy(i) += param->dtforce * atom_fy(i);
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atom_vz(i) += param->dtforce * atom_fz(i);
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atom_x(i) = atom_x(i) + param->dt * atom_vx(i);
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atom_y(i) = atom_y(i) + param->dt * atom_vy(i);
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atom_z(i) = atom_z(i) + param->dt * atom_vz(i);
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}
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}
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void finalIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom) {
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for(int i = 0; i < atom->Nlocal; i++) {
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atom_vx(i) += param->dtforce * atom_fx(i);
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atom_vy(i) += param->dtforce * atom_fy(i);
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atom_vz(i) += param->dtforce * atom_fz(i);
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}
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}
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#ifdef CUDA_TARGET
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void initialIntegrate_cuda(bool, Parameter*, Atom*);
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void finalIntegrate_cuda(bool, Parameter*, Atom*);
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#endif
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55
verletlist/includes/neighbor.h
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55
verletlist/includes/neighbor.h
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/*
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* Copyright (C) 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 <atom.h>
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#include <parameter.h>
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#ifndef __NEIGHBOR_H_
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#define __NEIGHBOR_H_
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typedef struct {
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int *neighbors;
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int *numneigh;
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} DeviceNeighbor;
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typedef struct {
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int every;
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int ncalls;
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int maxneighs;
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int half_neigh;
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int *neighbors;
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int *numneigh;
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// Device data
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DeviceNeighbor d_neighbor;
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} Neighbor;
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typedef struct {
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MD_FLOAT xprd; MD_FLOAT yprd; MD_FLOAT zprd;
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MD_FLOAT bininvx; MD_FLOAT bininvy; MD_FLOAT bininvz;
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int mbinxlo; int mbinylo; int mbinzlo;
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int nbinx; int nbiny; int nbinz;
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int mbinx; int mbiny; int mbinz;
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} Neighbor_params;
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typedef struct {
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int* bincount;
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int* bins;
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int mbins;
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int atoms_per_bin;
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} Binning;
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extern void initNeighbor(Neighbor*, Parameter*);
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extern void setupNeighbor(Parameter*);
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extern void binatoms(Atom*);
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extern void buildNeighbor_cpu(Atom*, Neighbor*);
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extern void sortAtom(Atom*);
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#ifdef CUDA_TARGET
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extern void buildNeighbor_cuda(Atom*, Neighbor*);
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#endif
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#endif
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24
verletlist/includes/pbc.h
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24
verletlist/includes/pbc.h
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/*
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* Copyright (C) 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 <stdbool.h>
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//---
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#include <atom.h>
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#include <parameter.h>
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#ifndef __PBC_H_
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#define __PBC_H_
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extern void initPbc(Atom*);
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extern void updatePbc_cpu(Atom*, Parameter*, bool);
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extern void updateAtomsPbc_cpu(Atom*, Parameter*);
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extern void setupPbc(Atom*, Parameter*);
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#ifdef CUDA_TARGET
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extern void updatePbc_cuda(Atom*, Parameter*, bool);
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extern void updateAtomsPbc_cuda(Atom*, Parameter*);
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#endif
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#endif
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32
verletlist/includes/stats.h
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32
verletlist/includes/stats.h
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/*
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* Copyright (C) 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 <atom.h>
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#include <parameter.h>
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#ifndef __STATS_H_
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#define __STATS_H_
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typedef struct {
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long long int total_force_neighs;
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long long int total_force_iters;
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long long int atoms_within_cutoff;
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long long int atoms_outside_cutoff;
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} Stats;
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void initStats(Stats *s);
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void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer);
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#ifdef COMPUTE_STATS
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# define addStat(stat, value) stat += value;
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# define beginStatTimer() double Si = getTimeStamp();
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# define endStatTimer(stat) stat += getTimeStamp() - Si;
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#else
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# define addStat(stat, value)
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# define beginStatTimer()
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# define endStatTimer(stat)
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#endif
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#endif
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102
verletlist/includes/tracing.h
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102
verletlist/includes/tracing.h
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/*
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* Copyright (C) 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 <neighbor.h>
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#include <parameter.h>
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#include <atom.h>
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#if defined(MEM_TRACER) || defined(INDEX_TRACER)
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#include <stdio.h>
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#include <stdlib.h>
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#endif
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#ifndef VECTOR_WIDTH
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# define VECTOR_WIDTH 8
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#endif
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#ifndef TRACER_CONDITION
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# define TRACER_CONDITION (!(timestep % param->every))
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#endif
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#ifdef MEM_TRACER
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# define MEM_TRACER_INIT FILE *mem_tracer_fp; \
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if(TRACER_CONDITION) { \
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char mem_tracer_fn[128]; \
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snprintf(mem_tracer_fn, sizeof mem_tracer_fn, "mem_tracer_%d.out", timestep); \
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mem_tracer_fp = fopen(mem_tracer_fn, "w");
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}
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# define MEM_TRACER_END if(TRACER_CONDITION) { fclose(mem_tracer_fp); }
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# define MEM_TRACE(addr, op) if(TRACER_CONDITION) { fprintf(mem_tracer_fp, "%c: %p\n", op, (void *)(&(addr))); }
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#else
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# define MEM_TRACER_INIT
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# define MEM_TRACER_END
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# define MEM_TRACE(addr, op)
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#endif
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#ifdef INDEX_TRACER
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# define INDEX_TRACER_INIT FILE *index_tracer_fp; \
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if(TRACER_CONDITION) { \
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char index_tracer_fn[128]; \
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snprintf(index_tracer_fn, sizeof index_tracer_fn, "index_tracer_%d.out", timestep); \
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index_tracer_fp = fopen(index_tracer_fn, "w"); \
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}
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# define INDEX_TRACER_END if(TRACER_CONDITION) { fclose(index_tracer_fp); }
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# define INDEX_TRACE_NATOMS(nl, ng, mn) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "N: %d %d %d\n", nl, ng, mn); }
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# define INDEX_TRACE_ATOM(a) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "A: %d\n", a); }
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# define INDEX_TRACE(l, e) if(TRACER_CONDITION) { \
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for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
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int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
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fprintf(index_tracer_fp, "I: "); \
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for(int __j = 0; __j < __e; ++__j) { \
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fprintf(index_tracer_fp, "%d ", l[__i + __j]); \
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} \
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fprintf(index_tracer_fp, "\n"); \
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} \
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}
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# define DIST_TRACE_SORT(l, e) if(TRACER_CONDITION) { \
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for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
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int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
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if(__e > 1) { \
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for(int __j = __i; __j < __i + __e - 1; ++__j) { \
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for(int __k = __i; __k < __i + __e - (__j - __i) - 1; ++__k) { \
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if(l[__k] > l[__k + 1]) { \
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int __t = l[__k]; \
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l[__k] = l[__k + 1]; \
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l[__k + 1] = __t; \
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} \
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} \
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} \
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} \
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} \
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}
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# define DIST_TRACE(l, e) if(TRACER_CONDITION) { \
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for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
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int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
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if(__e > 1) { \
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fprintf(index_tracer_fp, "D: "); \
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for(int __j = 0; __j < __e - 1; ++__j) { \
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int __dist = abs(l[__i + __j + 1] - l[__i + __j]); \
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fprintf(index_tracer_fp, "%d ", __dist); \
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} \
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fprintf(index_tracer_fp, "\n"); \
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} \
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} \
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}
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#else
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# define INDEX_TRACER_INIT
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# define INDEX_TRACER_END
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# define INDEX_TRACE_NATOMS(nl, ng, mn)
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# define INDEX_TRACE_ATOM(a)
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# define INDEX_TRACE(l, e)
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# define DIST_TRACE_SORT(l, e)
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# define DIST_TRACE(l, e)
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#endif
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extern void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timestep);
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12
verletlist/includes/vtk.h
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12
verletlist/includes/vtk.h
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@@ -0,0 +1,12 @@
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/*
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* Copyright (C) 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 <atom.h>
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#ifndef __VTK_H_
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#define __VTK_H_
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extern int write_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
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#endif
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