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Include Likwid Markers. Allow to switch between SP and DP floats.

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This commit is contained in:
Jan Eitzinger 2020-11-05 12:41:44 +01:00
parent b45ab26e03
commit b39957421c
11 changed files with 333 additions and 133 deletions
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2
include_CLANG.mk
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@ -12,6 +12,6 @@ ASFLAGS = -masm=intel
CXXFLAGS = $(CFLAGS)
FCFLAGS =
LFLAGS =
DEFINES = -D_GNU_SOURCE -DALIGNMENT=64
DEFINES = -D_GNU_SOURCE -DALIGNMENT=64 -DPRECISION=2
INCLUDES =
LIBS = -lomp

23
include_ICC.mk
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@ -2,18 +2,19 @@ CC = icc
CXX = icpc
LINKER = $(CC)
PROFILE = #-g -pg
OPTS = -Ofast -xCORE-AVX512 -qopt-zmm-usage=high $(PROFILE)
#OPTS = -O3 -xCORE-AVX2 $(PROFILE)
#OPTS = -O3 -xAVX $(PROFILE)
#OPTS = -O3 -xSSE4.2 $(PROFILE)
#OPTS = -O3 -no-vec $(PROFILE)
#OPTS = -Ofast -xHost $(PROFILE)
CFLAGS = $(PROFILE) -restrict $(OPTS)
OPENMP = #-qopenmp
PROFILE = #-profile-functions -g -pg
# OPTS = -fast -xCORE-AVX512 -qopt-zmm-usage=high $(PROFILE)
#OPTS = -fast -xCORE-AVX2 $(PROFILE)
#OPTS = -fast -xAVX $(PROFILE)
#OPTS = -fast -xSSE4.2 $(PROFILE)
#OPTS = -fast -no-vec $(PROFILE)
OPTS = -fast -xHost $(PROFILE)
CFLAGS = $(PROFILE) -restrict $(OPENMP) $(OPTS)
CXXFLAGS = $(CFLAGS)
ASFLAGS = -masm=intel
FCFLAGS =
LFLAGS = $(PROFILE) $(OPTS)
LFLAGS = $(PROFILE) $(OPTS) $(OPENMP)
DEFINES = -D_GNU_SOURCE -DALIGNMENT=64 # -DLIKWID_PERFMON -DPRECISION=1
INCLUDES =
LIBS =
INCLUDES = #$(LIKWID_INC)
LIBS = #$(LIKWID_LIB) -llikwid

28
src/atom.c
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@ -43,12 +43,12 @@ void initAtom(Atom *atom)
void createAtom(Atom *atom, Parameter *param)
{
double xlo = 0.0; double xhi = param->xprd;
double ylo = 0.0; double yhi = param->yprd;
double zlo = 0.0; double zhi = param->zprd;
MD_FLOAT xlo = 0.0; MD_FLOAT xhi = param->xprd;
MD_FLOAT ylo = 0.0; MD_FLOAT yhi = param->yprd;
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = param->zprd;
atom->Natoms = 4 * param->nx * param->ny * param->nz;
atom->Nlocal = 0;
double alat = pow((4.0 / param->rho), (1.0 / 3.0));
MD_FLOAT alat = pow((4.0 / param->rho), (1.0 / 3.0));
int ilo = (int) (xlo / (0.5 * alat) - 1);
int ihi = (int) (xhi / (0.5 * alat) + 1);
int jlo = (int) (ylo / (0.5 * alat) - 1);
@ -63,7 +63,7 @@ void createAtom(Atom *atom, Parameter *param)
klo = MAX(klo, 0);
khi = MIN(khi, 2 * param->nz - 1);
double xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
MD_FLOAT xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
int i, j, k, m, n;
int sx = 0; int sy = 0; int sz = 0;
int ox = 0; int oy = 0; int oz = 0;
@ -136,15 +136,15 @@ void growAtom(Atom *atom)
int nold = atom->Nmax;
atom->Nmax += DELTA;
atom->x = (double*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->y = (double*) reallocate(atom->y, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->z = (double*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->vx = (double*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->vy = (double*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->vz = (double*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->fx = (double*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->fy = (double*) reallocate(atom->fy, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->fz = (double*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(double), nold * sizeof(double));
atom->x = (MD_FLOAT*) reallocate(atom->x, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->y = (MD_FLOAT*) reallocate(atom->y, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->z = (MD_FLOAT*) reallocate(atom->z, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vx = (MD_FLOAT*) reallocate(atom->vx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vy = (MD_FLOAT*) reallocate(atom->vy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->vz = (MD_FLOAT*) reallocate(atom->vz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fx = (MD_FLOAT*) reallocate(atom->fx, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fy = (MD_FLOAT*) reallocate(atom->fy, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
atom->fz = (MD_FLOAT*) reallocate(atom->fz, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
}

6
src/includes/atom.h
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@ -27,9 +27,9 @@
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
double *x, *y, *z;
double *vx, *vy, *vz;
double *fx, *fy, *fz;
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *fx, *fy, *fz;
} Atom;
extern void initAtom(Atom*);

170
src/includes/likwid-marker.h Normal file
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@ -0,0 +1,170 @@
/*
* =======================================================================================
*
* 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 */

1
src/includes/neighbor.h
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@ -26,7 +26,6 @@
#ifndef __NEIGHBOR_H_
#define __NEIGHBOR_H_
typedef struct {
/* double cutneigh; // neighbor cutoff */
int every;
int ncalls;
int* neighbors;

29
src/includes/parameter.h
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@ -23,20 +23,29 @@
#ifndef __PARAMETER_H_
#define __PARAMETER_H_
#ifndef PRECISION
#define PRECISION 2
#endif
#if PRECISION == 1
#define MD_FLOAT float
#else
#define MD_FLOAT double
#endif
typedef struct {
double epsilon;
double sigma6;
double temp;
double rho;
double mass;
MD_FLOAT epsilon;
MD_FLOAT sigma6;
MD_FLOAT temp;
MD_FLOAT rho;
MD_FLOAT mass;
int ntimes;
int nstat;
int every;
double dt;
double dtforce;
double cutforce;
double cutneigh;
MD_FLOAT dt;
MD_FLOAT dtforce;
MD_FLOAT cutforce;
MD_FLOAT cutneigh;
int nx, ny, nz;
double xprd, yprd, zprd;
MD_FLOAT xprd, yprd, zprd;
} Parameter;
#endif

69
src/main.c
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@ -28,6 +28,8 @@
#include <math.h>
#include <float.h>
#include <likwid-marker.h>
#include <timing.h>
#include <allocate.h>
#include <neighbor.h>
@ -100,11 +102,13 @@ double reneighbour(
double S, E;
S = getTimeStamp();
LIKWID_MARKER_START("reneighbour");
updateAtomsPbc(atom, param);
setupPbc(atom, param);
updatePbc(atom, param);
/* sortAtom(); */
buildNeighbor(atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();
return E-S;
@ -112,9 +116,9 @@ double reneighbour(
void initialIntegrate(Parameter *param, Atom *atom)
{
double* x = atom->x; double* y = atom->y; double* z = atom->z;
double* fx = atom->fx; double* fy = atom->fy; double* fz = atom->fz;
double* vx = atom->vx; double* vy = atom->vy; double* vz = atom->vz;
MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
@ -128,8 +132,8 @@ void initialIntegrate(Parameter *param, Atom *atom)
void finalIntegrate(Parameter *param, Atom *atom)
{
double* fx = atom->fx; double* fy = atom->fy; double* fz = atom->fz;
double* vx = atom->vx; double* vy = atom->vy; double* vz = atom->vz;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
@ -142,12 +146,12 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
{
int Nlocal = atom->Nlocal;
int* neighs;
double cutforcesq = param->cutforce * param->cutforce;
double sigma6 = param->sigma6;
double epsilon = param->epsilon;
double* x = atom->x; double* y = atom->y; double* z = atom->z;
double* fx = atom->fx; double* fy = atom->fy; double* fz = atom->fz;
double S, E;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT S, E;
S = getTimeStamp();
for(int i = 0; i < Nlocal; i++) {
@ -156,29 +160,31 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
fz[i] = 0.0;
}
LIKWID_MARKER_START("force");
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
double xtmp = x[i];
double ytmp = y[i];
double ztmp = z[i];
MD_FLOAT xtmp = x[i];
MD_FLOAT ytmp = y[i];
MD_FLOAT ztmp = z[i];
double fix = 0;
double fiy = 0;
double fiz = 0;
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
double delx = xtmp - x[j];
double dely = ytmp - y[j];
double delz = ztmp - z[j];
double rsq = delx * delx + dely * dely + delz * delz;
MD_FLOAT delx = xtmp - x[j];
MD_FLOAT dely = ytmp - y[j];
MD_FLOAT delz = ztmp - z[j];
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) {
double sr2 = 1.0 / rsq;
double sr6 = sr2 * sr2 * sr2 * sigma6;
double force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
@ -189,6 +195,7 @@ double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
fy[i] += fiy;
fz[i] += fiz;
}
LIKWID_MARKER_STOP("force");
E = getTimeStamp();
return E-S;
@ -214,6 +221,13 @@ int main (int argc, char** argv)
Neighbor neighbor;
Parameter param;
LIKWID_MARKER_INIT;
#pragma omp parallel
{
LIKWID_MARKER_REGISTER("force");
LIKWID_MARKER_REGISTER("reneighbour");
LIKWID_MARKER_REGISTER("pbc");
}
init(&param);
for(int i = 0; i < argc; i++)
@ -279,6 +293,12 @@ int main (int argc, char** argv)
computeThermo(-1, &param, &atom);
printf(HLINE);
#if PRECISION == 1
printf("Using single precision floating point.\n");
#else
printf("Using double precision floating point.\n");
#endif
printf(HLINE);
printf("System: %d atoms %d ghost atoms, Steps: %d\n", atom.Natoms, atom.Nghost, param.ntimes);
printf("TOTAL %.2fs FORCE %.2fs NEIGH %.2fs REST %.2fs\n",
timer[TOTAL], timer[FORCE], timer[NEIGH], timer[TOTAL]-timer[FORCE]-timer[NEIGH]);
@ -286,5 +306,6 @@ int main (int argc, char** argv)
printf("Performance: %.2f million atom updates per second\n",
1e-6 * (double) atom.Natoms * param.ntimes / timer[TOTAL]);
LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS;
}

62
src/neighbor.c
View File

@ -31,8 +31,8 @@
#define SMALL 1.0e-6
#define FACTOR 0.999
static double xprd, yprd, zprd;
static double bininvx, bininvy, bininvz;
static MD_FLOAT xprd, yprd, zprd;
static MD_FLOAT bininvx, bininvy, bininvz;
static int mbinxlo, mbinylo, mbinzlo;
static int nbinx, nbiny, nbinz;
static int mbinx, mbiny, mbinz; // n bins in x, y, z
@ -40,21 +40,21 @@ static int *bincount;
static int *bins;
static int mbins; //total number of bins
static int atoms_per_bin; // max atoms per bin
static double cutneigh;
static double cutneighsq; // neighbor cutoff squared
static MD_FLOAT cutneigh;
static MD_FLOAT cutneighsq; // neighbor cutoff squared
static int nmax;
static int nstencil; // # of bins in stencil
static int* stencil; // stencil list of bin offsets
static double binsizex, binsizey, binsizez;
static int nstencil; // # of bins in stencil
static int* stencil; // stencil list of bin offsets
static MD_FLOAT binsizex, binsizey, binsizez;
static int coord2bin(double, double , double);
static double bindist(int, int, int);
static int coord2bin(MD_FLOAT, MD_FLOAT , MD_FLOAT);
static MD_FLOAT bindist(int, int, int);
/* exported subroutines */
void initNeighbor(Neighbor *neighbor, Parameter *param)
{
double lattice = pow((4.0 / param->rho), (1.0 / 3.0));
double neighscale = 5.0 / 6.0;
MD_FLOAT lattice = pow((4.0 / param->rho), (1.0 / 3.0));
MD_FLOAT neighscale = 5.0 / 6.0;
xprd = param->nx * lattice;
yprd = param->ny * lattice;
zprd = param->nz * lattice;
@ -74,12 +74,12 @@ void initNeighbor(Neighbor *neighbor, Parameter *param)
void setupNeighbor()
{
double coord;
MD_FLOAT coord;
int mbinxhi, mbinyhi, mbinzhi;
int nextx, nexty, nextz;
double xlo = 0.0; double xhi = xprd;
double ylo = 0.0; double yhi = yprd;
double zlo = 0.0; double zhi = zprd;
MD_FLOAT xlo = 0.0; MD_FLOAT xhi = xprd;
MD_FLOAT ylo = 0.0; MD_FLOAT yhi = yprd;
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = zprd;
cutneighsq = cutneigh * cutneigh;
binsizex = xprd / nbinx;
@ -184,9 +184,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
/* bin local & ghost atoms */
binatoms(atom);
int resize = 1;
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
/* loop over each atom, storing neighbors */
while(resize) {
@ -196,9 +196,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
for(int i = 0; i < atom->Nlocal; i++) {
int* neighptr = &(neighbor->neighbors[i * neighbor->maxneighs]);
int n = 0;
double xtmp = x[i];
double ytmp = y[i];
double ztmp = z[i];
MD_FLOAT xtmp = x[i];
MD_FLOAT ytmp = y[i];
MD_FLOAT ztmp = z[i];
int ibin = coord2bin(xtmp, ytmp, ztmp);
for(int k = 0; k < nstencil; k++) {
@ -212,10 +212,10 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
continue;
}
double delx = xtmp - x[j];
double dely = ytmp - y[j];
double delz = ztmp - z[j];
double rsq = delx * delx + dely * dely + delz * delz;
MD_FLOAT delx = xtmp - x[j];
MD_FLOAT dely = ytmp - y[j];
MD_FLOAT delz = ztmp - z[j];
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if( rsq <= cutneighsq ) {
neighptr[n++] = j;
@ -244,9 +244,9 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
}
/* internal subroutines */
double bindist(int i, int j, int k)
MD_FLOAT bindist(int i, int j, int k)
{
double delx, dely, delz;
MD_FLOAT delx, dely, delz;
if(i > 0) {
delx = (i - 1) * binsizex;
@ -275,7 +275,7 @@ double bindist(int i, int j, int k)
return (delx * delx + dely * dely + delz * delz);
}
int coord2bin(double xin, double yin, double zin)
int coord2bin(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin)
{
int ix, iy, iz;
@ -309,9 +309,9 @@ int coord2bin(double xin, double yin, double zin)
void binatoms(Atom *atom)
{
int nall = atom->Nlocal + atom->Nghost;
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
int resize = 1;
while(resize > 0) {

34
src/pbc.c
View File

@ -48,12 +48,12 @@ void initPbc()
void updatePbc(Atom *atom, Parameter *param)
{
int nlocal = atom->Nlocal;
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
double xprd = param->xprd;
double yprd = param->yprd;
double zprd = param->zprd;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nghost; i++) {
x[nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd;
@ -66,12 +66,12 @@ void updatePbc(Atom *atom, Parameter *param)
* to periodic boundary conditions */
void updateAtomsPbc(Atom *atom, Parameter *param)
{
double* x = atom->x;
double* y = atom->y;
double* z = atom->z;
double xprd = param->xprd;
double yprd = param->yprd;
double zprd = param->zprd;
MD_FLOAT* x = atom->x;
MD_FLOAT* y = atom->y;
MD_FLOAT* z = atom->z;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
for(int i = 0; i < atom->Nlocal; i++) {
@ -102,11 +102,11 @@ void updateAtomsPbc(Atom *atom, Parameter *param)
#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
void setupPbc(Atom *atom, Parameter *param)
{
double* x = atom->x; double* y = atom->y; double* z = atom->z;
double xprd = param->xprd;
double yprd = param->yprd;
double zprd = param->zprd;
double Cutneigh = param->cutneigh;
MD_FLOAT* x = atom->x; MD_FLOAT* y = atom->y; MD_FLOAT* z = atom->z;
MD_FLOAT xprd = param->xprd;
MD_FLOAT yprd = param->yprd;
MD_FLOAT zprd = param->zprd;
MD_FLOAT Cutneigh = param->cutneigh;
int Nghost = -1;
for(int i = 0; i < atom->Nlocal; i++) {

42
src/thermo.c
View File

@ -27,17 +27,17 @@
#include <thermo.h>
static int *steparr;
static double *tmparr;
static double *engarr;
static double *prsarr;
static double mvv2e;
static MD_FLOAT *tmparr;
static MD_FLOAT *engarr;
static MD_FLOAT *prsarr;
static MD_FLOAT mvv2e;
static int dof_boltz;
static double t_scale;
static double p_scale;
static double e_scale;
static double t_act;
static double p_act;
static double e_act;
static MD_FLOAT t_scale;
static MD_FLOAT p_scale;
static MD_FLOAT e_scale;
static MD_FLOAT t_act;
static MD_FLOAT p_act;
static MD_FLOAT e_act;
static int mstat;
/* exported subroutines */
@ -46,9 +46,9 @@ void setupThermo(Parameter *param, int natoms)
int maxstat = param->ntimes / param->nstat + 2;
steparr = (int*) malloc(maxstat * sizeof(int));
tmparr = (double*) malloc(maxstat * sizeof(double));
engarr = (double*) malloc(maxstat * sizeof(double));
prsarr = (double*) malloc(maxstat * sizeof(double));
tmparr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
engarr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
prsarr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
mvv2e = 1.0;
dof_boltz = (natoms * 3 - 3);
@ -61,10 +61,10 @@ void setupThermo(Parameter *param, int natoms)
void computeThermo(int iflag, Parameter *param, Atom *atom)
{
double t = 0.0, p;
double* vx = atom->vx;
double* vy = atom->vy;
double* vz = atom->vz;
MD_FLOAT t = 0.0, p;
MD_FLOAT* vx = atom->vx;
MD_FLOAT* vy = atom->vy;
MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
@ -92,8 +92,8 @@ void computeThermo(int iflag, Parameter *param, Atom *atom)
void adjustThermo(Parameter *param, Atom *atom)
{
/* zero center-of-mass motion */
double vxtot = 0.0; double vytot = 0.0; double vztot = 0.0;
double* vx = atom->vx; double* vy = atom->vy; double* vz = atom->vz;
MD_FLOAT vxtot = 0.0; MD_FLOAT vytot = 0.0; MD_FLOAT vztot = 0.0;
MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
for(int i = 0; i < atom->Nlocal; i++) {
vxtot += vx[i];
@ -112,14 +112,14 @@ void adjustThermo(Parameter *param, Atom *atom)
}
t_act = 0;
double t = 0.0;
MD_FLOAT t = 0.0;
for(int i = 0; i < atom->Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t *= t_scale;
double factor = sqrt(param->temp / t);
MD_FLOAT factor = sqrt(param->temp / t);
for(int i = 0; i < atom->Nlocal; i++) {
vx[i] *= factor;