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Rename default directory to lammps and reorganize gromacs variant steps

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-01-25 21:00:11 +01:00
parent cbe42b8149
commit aa0f4048d0
34 changed files with 12 additions and 9 deletions
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29
lammps/includes/allocate.h Normal file
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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <stdlib.h>
#ifndef __ALLOCATE_H_
#define __ALLOCATE_H_
extern void* allocate (int alignment, size_t bytesize);
extern void* reallocate (void* ptr, int alignment, size_t newBytesize, size_t oldBytesize);
#endif

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/*
* =======================================================================================
*
* 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <parameter.h>
#ifndef __ATOM_H_
#define __ATOM_H_
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;
} Atom;
extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern int readAtom(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]
#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]
#endif
#endif

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <stdio.h>
#include <atom.h>
#include <parameter.h>
#ifndef __EAM_H_
#define __EAM_H_
typedef struct {
int nrho, nr;
MD_FLOAT drho, dr, cut, mass;
MD_FLOAT *frho, *rhor, *zr;
} Funcfl;
typedef struct {
MD_FLOAT* fp;
int nmax;
int nrho, nr;
int nrho_tot, nr_tot;
MD_FLOAT dr, rdr, drho, rdrho;
MD_FLOAT *frho, *rhor, *z2r;
MD_FLOAT *rhor_spline, *frho_spline, *z2r_spline;
Funcfl file;
} Eam;
void initEam(Eam* eam, Parameter* param);
void coeff(Eam* eam, Parameter* param);
void init_style(Eam* eam, Parameter *param);
void read_eam_file(Funcfl* file, const char* filename);
void file2array(Eam* eam);
void array2spline(Eam* eam, Parameter* param);
void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline);
void grab(FILE* fptr, int n, MD_FLOAT* list);
#endif

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/*
* =======================================================================================
*
* Filename: likwid-marker.h
*
* Description: Header File of likwid Marker API
*
* Version: <VERSION>
* Released: <DATE>
*
* Authors: Thomas Gruber (tg), thomas.roehl@googlemail.com
*
* Project: likwid
*
* Copyright (C) 2016 RRZE, University Erlangen-Nuremberg
*
* This program is free software: you can redistribute it and/or modify it under
* the terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* this program. If not, see <http://www.gnu.org/licenses/>.
*
* =======================================================================================
*/
#ifndef LIKWID_MARKER_H
#define LIKWID_MARKER_H
/** \addtogroup MarkerAPI Marker API module
* @{
*/
/*!
\def LIKWID_MARKER_INIT
Shortcut for likwid_markerInit() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_THREADINIT
Shortcut for likwid_markerThreadInit() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_REGISTER(regionTag)
Shortcut for likwid_markerRegisterRegion() with \a regionTag if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_START(regionTag)
Shortcut for likwid_markerStartRegion() with \a regionTag if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_STOP(regionTag)
Shortcut for likwid_markerStopRegion() with \a regionTag if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_GET(regionTag, nevents, events, time, count)
Shortcut for likwid_markerGetResults() for \a regionTag if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_SWITCH
Shortcut for likwid_markerNextGroup() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_RESET(regionTag)
Shortcut for likwid_markerResetRegion() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_MARKER_CLOSE
Shortcut for likwid_markerClose() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/** @}*/
#ifdef LIKWID_PERFMON
#include <likwid.h>
#define LIKWID_MARKER_INIT likwid_markerInit()
#define LIKWID_MARKER_THREADINIT likwid_markerThreadInit()
#define LIKWID_MARKER_SWITCH likwid_markerNextGroup()
#define LIKWID_MARKER_REGISTER(regionTag) likwid_markerRegisterRegion(regionTag)
#define LIKWID_MARKER_START(regionTag) likwid_markerStartRegion(regionTag)
#define LIKWID_MARKER_STOP(regionTag) likwid_markerStopRegion(regionTag)
#define LIKWID_MARKER_CLOSE likwid_markerClose()
#define LIKWID_MARKER_RESET(regionTag) likwid_markerResetRegion(regionTag)
#define LIKWID_MARKER_GET(regionTag, nevents, events, time, count) likwid_markerGetRegion(regionTag, nevents, events, time, count)
#else /* LIKWID_PERFMON */
#define LIKWID_MARKER_INIT
#define LIKWID_MARKER_THREADINIT
#define LIKWID_MARKER_SWITCH
#define LIKWID_MARKER_REGISTER(regionTag)
#define LIKWID_MARKER_START(regionTag)
#define LIKWID_MARKER_STOP(regionTag)
#define LIKWID_MARKER_CLOSE
#define LIKWID_MARKER_GET(regionTag, nevents, events, time, count)
#define LIKWID_MARKER_RESET(regionTag)
#endif /* LIKWID_PERFMON */
/** \addtogroup NvMarkerAPI NvMarker API module (MarkerAPI for Nvidia GPUs)
* @{
*/
/*!
\def LIKWID_NVMARKER_INIT
Shortcut for likwid_gpuMarkerInit() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_THREADINIT
Shortcut for likwid_gpuMarkerThreadInit() if compiled with -DLIKWID_PERFMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_REGISTER(regionTag)
Shortcut for likwid_gpuMarkerRegisterRegion() with \a regionTag if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_START(regionTag)
Shortcut for likwid_gpuMarkerStartRegion() with \a regionTag if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_STOP(regionTag)
Shortcut for likwid_gpuMarkerStopRegion() with \a regionTag if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_GET(regionTag, ngpus, nevents, events, time, count)
Shortcut for likwid_gpuMarkerGetRegion() for \a regionTag if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_SWITCH
Shortcut for likwid_gpuMarkerNextGroup() if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_RESET(regionTag)
Shortcut for likwid_gpuMarkerResetRegion() if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/*!
\def LIKWID_NVMARKER_CLOSE
Shortcut for likwid_gpuMarkerClose() if compiled with -DLIKWID_NVMON. Otherwise no operation is performed
*/
/** @}*/
#ifdef LIKWID_NVMON
#ifndef LIKWID_WITH_NVMON
#define LIKWID_WITH_NVMON
#endif
#include <likwid.h>
#define LIKWID_NVMARKER_INIT likwid_gpuMarkerInit()
#define LIKWID_NVMARKER_THREADINIT likwid_gpuMarkerThreadInit()
#define LIKWID_NVMARKER_SWITCH likwid_gpuMarkerNextGroup()
#define LIKWID_NVMARKER_REGISTER(regionTag) likwid_gpuMarkerRegisterRegion(regionTag)
#define LIKWID_NVMARKER_START(regionTag) likwid_gpuMarkerStartRegion(regionTag)
#define LIKWID_NVMARKER_STOP(regionTag) likwid_gpuMarkerStopRegion(regionTag)
#define LIKWID_NVMARKER_CLOSE likwid_gpuMarkerClose()
#define LIKWID_NVMARKER_RESET(regionTag) likwid_gpuMarkerResetRegion(regionTag)
#define LIKWID_NVMARKER_GET(regionTag, ngpus, nevents, events, time, count) \
likwid_gpuMarkerGetRegion(regionTag, ngpus, nevents, events, time, count)
#else /* LIKWID_NVMON */
#define LIKWID_NVMARKER_INIT
#define LIKWID_NVMARKER_THREADINIT
#define LIKWID_NVMARKER_SWITCH
#define LIKWID_NVMARKER_REGISTER(regionTag)
#define LIKWID_NVMARKER_START(regionTag)
#define LIKWID_NVMARKER_STOP(regionTag)
#define LIKWID_NVMARKER_CLOSE
#define LIKWID_NVMARKER_GET(regionTag, nevents, events, time, count)
#define LIKWID_NVMARKER_RESET(regionTag)
#endif /* LIKWID_NVMON */
#endif /* LIKWID_MARKER_H */

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <atom.h>
#include <parameter.h>
#ifndef __NEIGHBOR_H_
#define __NEIGHBOR_H_
typedef struct {
int every;
int ncalls;
int* neighbors;
int maxneighs;
int* numneigh;
} Neighbor;
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*);
extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*);
extern void sortAtom(Atom*);
#endif

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#ifndef __PARAMETER_H_
#define __PARAMETER_H_
#if PRECISION == 1
#define MD_FLOAT float
#else
#define MD_FLOAT double
#endif
typedef struct {
int force_field;
char* input_file;
char* vtk_file;
MD_FLOAT epsilon;
MD_FLOAT sigma6;
MD_FLOAT temp;
MD_FLOAT rho;
MD_FLOAT mass;
int ntypes;
int ntimes;
int nstat;
int every;
MD_FLOAT dt;
MD_FLOAT dtforce;
MD_FLOAT cutforce;
MD_FLOAT cutneigh;
int nx, ny, nz;
MD_FLOAT lattice;
MD_FLOAT xlo, xhi, ylo, yhi, zlo, zhi;
MD_FLOAT xprd, yprd, zprd;
double proc_freq;
char* eam_file;
} Parameter;
#endif

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <atom.h>
#include <parameter.h>
#ifndef __PBC_H_
#define __PBC_H_
extern void initPbc();
extern void updatePbc(Atom*, Parameter*);
extern void updateAtomsPbc(Atom*, Parameter*);
extern void setupPbc(Atom*, Parameter*);
#endif

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <atom.h>
#include <parameter.h>
#ifndef __STATS_H_
#define __STATS_H_
typedef struct {
long long int total_force_neighs;
long long int total_force_iters;
} Stats;
void initStats(Stats *s);
void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer);
#ifdef COMPUTE_STATS
# define addStat(stat, value) stat += value;
# define beginStatTimer() double Si = getTimeStamp();
# define endStatTimer(stat) stat += getTimeStamp() - Si;
#else
# define addStat(stat, value)
# define beginStatTimer()
# define endStatTimer(stat)
#endif
#endif

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <parameter.h>
#include <atom.h>
#ifndef __THERMO_H_
#define __THERMO_H_
extern void setupThermo(Parameter*, int);
extern void computeThermo(int, Parameter*, Atom*);
extern void adjustThermo(Parameter*, Atom*);
#endif

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#ifndef __TIMERS_H_
#define __TIMERS_H_
typedef enum {
TOTAL = 0,
NEIGH,
FORCE,
NUMTIMER
} timertype;
#endif

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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#ifndef __TIMING_H_
#define __TIMING_H_
extern double getTimeStamp();
extern double getTimeResolution();
extern double getTimeStamp_();
#endif

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/*
* =======================================================================================
*
* 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#if defined(MEM_TRACER) || defined(INDEX_TRACER)
#include <stdio.h>
#include <stdlib.h>
#endif
#ifndef VECTOR_WIDTH
# define VECTOR_WIDTH 8
#endif
#ifndef TRACER_CONDITION
# define TRACER_CONDITION (!(timestep % param->every))
#endif
#ifdef MEM_TRACER
# define MEM_TRACER_INIT FILE *mem_tracer_fp; \
if(TRACER_CONDITION) { \
char mem_tracer_fn[128]; \
snprintf(mem_tracer_fn, sizeof mem_tracer_fn, "mem_tracer_%d.out", timestep); \
mem_tracer_fp = fopen(mem_tracer_fn, "w");
}
# define MEM_TRACER_END if(TRACER_CONDITION) { fclose(mem_tracer_fp); }
# define MEM_TRACE(addr, op) if(TRACER_CONDITION) { fprintf(mem_tracer_fp, "%c: %p\n", op, (void *)(&(addr))); }
#else
# define MEM_TRACER_INIT
# define MEM_TRACER_END
# define MEM_TRACE(addr, op)
#endif
#ifdef INDEX_TRACER
# define INDEX_TRACER_INIT FILE *index_tracer_fp; \
if(TRACER_CONDITION) { \
char index_tracer_fn[128]; \
snprintf(index_tracer_fn, sizeof index_tracer_fn, "index_tracer_%d.out", timestep); \
index_tracer_fp = fopen(index_tracer_fn, "w"); \
}
# define INDEX_TRACER_END if(TRACER_CONDITION) { fclose(index_tracer_fp); }
# define INDEX_TRACE_NATOMS(nl, ng, mn) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "N: %d %d %d\n", nl, ng, mn); }
# define INDEX_TRACE_ATOM(a) if(TRACER_CONDITION) { fprintf(index_tracer_fp, "A: %d\n", a); }
# define INDEX_TRACE(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
fprintf(index_tracer_fp, "I: "); \
for(int __j = 0; __j < __e; ++__j) { \
fprintf(index_tracer_fp, "%d ", l[__i + __j]); \
} \
fprintf(index_tracer_fp, "\n"); \
} \
}
# define DIST_TRACE_SORT(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
if(__e > 1) { \
for(int __j = __i; __j < __i + __e - 1; ++__j) { \
for(int __k = __i; __k < __i + __e - (__j - __i) - 1; ++__k) { \
if(l[__k] > l[__k + 1]) { \
int __t = l[__k]; \
l[__k] = l[__k + 1]; \
l[__k + 1] = __t; \
} \
} \
} \
} \
} \
}
# define DIST_TRACE(l, e) if(TRACER_CONDITION) { \
for(int __i = 0; __i < (e); __i += VECTOR_WIDTH) { \
int __e = (((e) - __i) < VECTOR_WIDTH) ? ((e) - __i) : VECTOR_WIDTH; \
if(__e > 1) { \
fprintf(index_tracer_fp, "D: "); \
for(int __j = 0; __j < __e - 1; ++__j) { \
int __dist = abs(l[__i + __j + 1] - l[__i + __j]); \
fprintf(index_tracer_fp, "%d ", __dist); \
} \
fprintf(index_tracer_fp, "\n"); \
} \
} \
}
#else
# define INDEX_TRACER_INIT
# define INDEX_TRACER_END
# define INDEX_TRACE_NATOMS(nl, ng, mn)
# define INDEX_TRACE_ATOM(a)
# define INDEX_TRACE(l, e)
# define DIST_TRACE_SORT(l, e)
# define DIST_TRACE(l, e)
#endif
extern void traceAddresses(Parameter *param, Atom *atom, Neighbor *neighbor, int timestep);

43
lammps/includes/util.h Normal file
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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#ifndef __UTIL_H_
#define __UTIL_H_
#ifndef MIN
#define MIN(x,y) ((x)<(y)?(x):(y))
#endif
#ifndef MAX
#define MAX(x,y) ((x)>(y)?(x):(y))
#endif
#ifndef ABS
#define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif
#define FF_LJ 0
#define FF_EAM 1
extern double myrandom(int*);
extern void random_reset(int *seed, int ibase, double *coord);
extern int str2ff(const char *string);
extern const char* ff2str(int ff);
#endif

28
lammps/includes/vtk.h Normal file
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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 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 <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <atom.h>
#ifndef __VTK_H_
#define __VTK_H_
extern int write_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
#endif