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Move common modules to common directory

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-08-17 17:56:31 +02:00
parent 47db9e86b0
commit 28d3946072
31 changed files with 40 additions and 1102 deletions
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29
lammps/includes/allocate.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 <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

55
lammps/includes/eam.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 <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

170
lammps/includes/likwid-marker.h
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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 */

73
lammps/includes/parameter.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/>.
* =======================================================================================
*/
#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* param_file;
char* input_file;
char* vtk_file;
MD_FLOAT epsilon;
MD_FLOAT sigma;
MD_FLOAT sigma6;
MD_FLOAT temp;
MD_FLOAT rho;
MD_FLOAT mass;
int ntypes;
int ntimes;
int nstat;
int reneigh_every;
int x_out_every;
int v_out_every;
int half_neigh;
MD_FLOAT dt;
MD_FLOAT dtforce;
MD_FLOAT skin;
MD_FLOAT cutforce;
MD_FLOAT cutneigh;
int nx, ny, nz;
int pbc_x, pbc_y, pbc_z;
MD_FLOAT lattice;
MD_FLOAT xlo, xhi, ylo, yhi, zlo, zhi;
MD_FLOAT xprd, yprd, zprd;
double proc_freq;
char* eam_file;
// DEM
MD_FLOAT k_s;
MD_FLOAT k_dn;
MD_FLOAT gx, gy, gz;
MD_FLOAT reflect_x, reflect_y, reflect_z;
} Parameter;
void initParameter(Parameter*);
void readParameter(Parameter*, const char*);
void printParameter(Parameter*);
#endif

31
lammps/includes/thermo.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 <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

11
lammps/includes/timers.h
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#ifndef __TIMERS_H_
#define __TIMERS_H_
typedef enum {
TOTAL = 0,
NEIGH,
FORCE,
NUMTIMER
} timertype;
#endif

30
lammps/includes/timing.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/>.
* =======================================================================================
*/
#ifndef __TIMING_H_
#define __TIMING_H_
extern double getTimeStamp();
extern double getTimeResolution();
extern double getTimeStamp_();
#endif