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Merge branch 'master' of github.com:RRZE-HPC/MD-Bench

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This commit is contained in:
Jan Eitzinger 2021-10-26 09:16:31 +02:00
commit 70e24d7c2c
11 changed files with 587 additions and 35 deletions
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3
Makefile
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@ -33,9 +33,6 @@ ifneq ($(NEIGHBORS_LOOP_RUNS),)
DEFINES += -DNEIGHBORS_LOOP_RUNS=$(NEIGHBORS_LOOP_RUNS)
endif
ifeq ($(strip $(PRINT_STATS)),true)
DEFINES += -DPRINT_STATS
endif
ifeq ($(strip $(EXPLICIT_TYPES)),true)
DEFINES += -DEXPLICIT_TYPES
endif

2
config.mk
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@ -9,8 +9,6 @@ DATA_LAYOUT ?= AOS
# Assembly syntax to generate (ATT/INTEL)
ASM_SYNTAX ?= ATT
# Output detailed statistics
PRINT_STATS ?= true
# Number of times to run the atoms loop on stubbed variant
ATOMS_LOOP_RUNS ?= 1
# Number of times to run the neighbors loop on stubbed variant

9
src/atom.c
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@ -41,14 +41,12 @@ void initAtom(Atom *atom)
atom->Nlocal = 0;
atom->Nghost = 0;
atom->Nmax = 0;
#ifdef EXPLICIT_TYPES
atom->type = NULL;
atom->ntypes = 0;
atom->epsilon = NULL;
atom->sigma6 = NULL;
atom->cutforcesq = NULL;
atom->cutneighsq = NULL;
#endif
}
void createAtom(Atom *atom, Parameter *param)
@ -58,8 +56,6 @@ void createAtom(Atom *atom, Parameter *param)
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = param->zprd;
atom->Natoms = 4 * param->nx * param->ny * param->nz;
atom->Nlocal = 0;
#ifdef EXPLICIT_TYPES
atom->ntypes = param->ntypes;
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
@ -71,7 +67,6 @@ void createAtom(Atom *atom, Parameter *param)
atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
atom->cutforcesq[i] = param->cutforce * param->cutforce;
}
#endif
MD_FLOAT alat = pow((4.0 / param->rho), (1.0 / 3.0));
int ilo = (int) (xlo / (0.5 * alat) - 1);
@ -142,9 +137,7 @@ void createAtom(Atom *atom, Parameter *param)
atom->vx[atom->Nlocal] = vxtmp;
atom->vy[atom->Nlocal] = vytmp;
atom->vz[atom->Nlocal] = vztmp;
#ifdef EXPLICIT_TYPES
atom->type[atom->Nlocal] = rand() % atom->ntypes;
#endif
atom->Nlocal++;
}
}
@ -177,9 +170,7 @@ void growAtom(Atom *atom)
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));
#ifdef EXPLICIT_TYPES
atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int));
#endif
}

284
src/eam_utils.c Normal file
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@ -0,0 +1,284 @@
/*
* =======================================================================================
*
* 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 <stdlib.h>
#include <string.h>
#include <allocate.h>
#include <atom.h>
#include <eam.h>
#include <parameter.h>
#include <util.h>
#ifndef MAXLINE
#define MAXLINE 4096
#endif
void initEam(Eam* eam, const char* input_file, int ntypes) {
eam->nmax = 0;
eam->fp = NULL;
eam->ntypes = ntypes;
eam->cutforcesq = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * sizeof(MD_FLOAT));
coeff(eam, input_file);
init_style(eam);
}
void coeff(Eam* eam, const char* arg) {
read_file(&eam->file, arg);
int n = strlen(arg) + 1;
int ntypes = eam->ntypes;
double cutmax = eam->file.cut;
for(int i=0; i<ntypes*ntypes; i++)
eam->cutforcesq[i] = cutmax * cutmax;
}
void init_style(Eam* eam) {
// convert read-in file(s) to arrays and spline them
file2array(eam);
array2spline(eam);
}
void read_file(Funcfl* file, const char* filename) {
FILE* fptr;
char line[MAXLINE];
fptr = fopen(filename, "r");
if(fptr == NULL) {
printf("Can't open EAM Potential file: %s\n", filename);
exit(0);
}
int tmp;
fgets(line, MAXLINE, fptr);
fgets(line, MAXLINE, fptr);
sscanf(line, "%d %lg", &tmp, &(file->mass));
fgets(line, MAXLINE, fptr);
sscanf(line, "%d %lg %d %lg %lg", &file->nrho, &file->drho, &file->nr, &file->dr, &file->cut);
//printf("Read: %lf %i %lf %i %lf %lf\n",file->mass,file->nrho,file->drho,file->nr,file->dr,file->cut);
file->frho = (MD_FLOAT *) allocate(ALIGNMENT, (file->nrho + 1) * sizeof(MD_FLOAT));
file->rhor = (MD_FLOAT *) allocate(ALIGNMENT, (file->nr + 1) * sizeof(MD_FLOAT));
file->zr = (MD_FLOAT *) allocate(ALIGNMENT, (file->nr + 1) * sizeof(MD_FLOAT));
grab(fptr, file->nrho, file->frho);
grab(fptr, file->nr, file->zr);
grab(fptr, file->nr, file->rhor);
for(int i = file->nrho; i > 0; i--) file->frho[i] = file->frho[i - 1];
for(int i = file->nr; i > 0; i--) file->rhor[i] = file->rhor[i - 1];
for(int i = file->nr; i > 0; i--) file->zr[i] = file->zr[i - 1];
fclose(fptr);
}
void file2array(Eam* eam) {
int i, j, k, m, n;
double sixth = 1.0 / 6.0;
// determine max function params from all active funcfl files
// active means some element is pointing at it via map
int active;
double rmax, rhomax;
eam->dr = eam->drho = rmax = rhomax = 0.0;
active = 0;
Funcfl* file = &eam->file;
eam->dr = MAX(eam->dr, file->dr);
eam->drho = MAX(eam->drho, file->drho);
rmax = MAX(rmax, (file->nr - 1) * file->dr);
rhomax = MAX(rhomax, (file->nrho - 1) * file->drho);
// set nr,nrho from cutoff and spacings
// 0.5 is for round-off in divide
eam->nr = (int)(rmax / eam->dr + 0.5);
eam->nrho = (int)(rhomax / eam->drho + 0.5);
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of funcfl files + 1 for zero array
eam->frho = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nrho + 1) * sizeof(MD_FLOAT));
// interpolate each file's frho to a single grid and cutoff
double r, p, cof1, cof2, cof3, cof4;
n = 0;
for(m = 1; m <= eam->nrho; m++) {
r = (m - 1) * eam->drho;
p = r / file->drho + 1.0;
k = (int)(p);
k = MIN(k, file->nrho - 2);
k = MAX(k, 2);
p -= k;
p = MIN(p, 2.0);
cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
cof4 = sixth * p * (p * p - 1.0);
eam->frho[m] = cof1 * file->frho[k - 1] + cof2 * file->frho[k] +
cof3 * file->frho[k + 1] + cof4 * file->frho[k + 2];
}
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate rhor arrays
// nrhor = # of funcfl files
eam->rhor = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nr + 1) * sizeof(MD_FLOAT));
// interpolate each file's rhor to a single grid and cutoff
for(m = 1; m <= eam->nr; m++) {
r = (m - 1) * eam->dr;
p = r / file->dr + 1.0;
k = (int)(p);
k = MIN(k, file->nr - 2);
k = MAX(k, 2);
p -= k;
p = MIN(p, 2.0);
cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
cof4 = sixth * p * (p * p - 1.0);
eam->rhor[m] = cof1 * file->rhor[k - 1] + cof2 * file->rhor[k] +
cof3 * file->rhor[k + 1] + cof4 * file->rhor[k + 2];
//if(m==119)printf("BuildRho: %e %e %e %e %e %e\n",rhor[m],cof1,cof2,cof3,cof4,file->rhor[k]);
}
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for funcfl files, I,J mapping only depends on I
// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of funcfl files
eam->z2r = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nr + 1) * sizeof(MD_FLOAT));
// create a z2r array for each file against other files, only for I >= J
// interpolate zri and zrj to a single grid and cutoff
double zri, zrj;
Funcfl* ifile = &eam->file;
Funcfl* jfile = &eam->file;
for(m = 1; m <= eam->nr; m++) {
r = (m - 1) * eam->dr;
p = r / ifile->dr + 1.0;
k = (int)(p);
k = MIN(k, ifile->nr - 2);
k = MAX(k, 2);
p -= k;
p = MIN(p, 2.0);
cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
cof4 = sixth * p * (p * p - 1.0);
zri = cof1 * ifile->zr[k - 1] + cof2 * ifile->zr[k] +
cof3 * ifile->zr[k + 1] + cof4 * ifile->zr[k + 2];
p = r / jfile->dr + 1.0;
k = (int)(p);
k = MIN(k, jfile->nr - 2);
k = MAX(k, 2);
p -= k;
p = MIN(p, 2.0);
cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
cof4 = sixth * p * (p * p - 1.0);
zrj = cof1 * jfile->zr[k - 1] + cof2 * jfile->zr[k] +
cof3 * jfile->zr[k + 1] + cof4 * jfile->zr[k + 2];
eam->z2r[m] = 27.2 * 0.529 * zri * zrj;
}
}
void array2spline(Eam* eam) {
eam->rdr = 1.0 / eam->dr;
eam->rdrho = 1.0 / eam->drho;
eam->nrho_tot = (eam->nrho + 1) * 7 + 64;
eam->nr_tot = (eam->nr + 1) * 7 + 64;
eam->nrho_tot -= eam->nrho_tot%64;
eam->nr_tot -= eam->nr_tot%64;
int ntypes = eam->ntypes;
eam->frho_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nrho_tot * sizeof(MD_FLOAT));
eam->rhor_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nr_tot * sizeof(MD_FLOAT));
eam->z2r_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nr_tot * sizeof(MD_FLOAT));
interpolate(eam->nrho, eam->drho, eam->frho, eam->frho_spline);
interpolate(eam->nr, eam->dr, eam->rhor, eam->rhor_spline);
interpolate(eam->nr, eam->dr, eam->z2r, eam->z2r_spline);
// replicate data for multiple types;
for(int tt = 0; tt < ntypes * ntypes; tt++) {
for(int k = 0; k < eam->nrho_tot; k++)
eam->frho_spline[tt*eam->nrho_tot + k] = eam->frho_spline[k];
for(int k = 0; k < eam->nr_tot; k++)
eam->rhor_spline[tt*eam->nr_tot + k] = eam->rhor_spline[k];
for(int k = 0; k < eam->nr_tot; k++)
eam->z2r_spline[tt*eam->nr_tot + k] = eam->z2r_spline[k];
}
}
void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline) {
for(int m = 1; m <= n; m++) spline[m * 7 + 6] = f[m];
spline[1 * 7 + 5] = spline[2 * 7 + 6] - spline[1 * 7 + 6];
spline[2 * 7 + 5] = 0.5 * (spline[3 * 7 + 6] - spline[1 * 7 + 6]);
spline[(n - 1) * 7 + 5] = 0.5 * (spline[n * 7 + 6] - spline[(n - 2) * 7 + 6]);
spline[n * 7 + 5] = spline[n * 7 + 6] - spline[(n - 1) * 7 + 6];
for(int m = 3; m <= n - 2; m++)
spline[m * 7 + 5] = ((spline[(m - 2) * 7 + 6] - spline[(m + 2) * 7 + 6]) +
8.0 * (spline[(m + 1) * 7 + 6] - spline[(m - 1) * 7 + 6])) / 12.0;
for(int m = 1; m <= n - 1; m++) {
spline[m * 7 + 4] = 3.0 * (spline[(m + 1) * 7 + 6] - spline[m * 7 + 6]) -
2.0 * spline[m * 7 + 5] - spline[(m + 1) * 7 + 5];
spline[m * 7 + 3] = spline[m * 7 + 5] + spline[(m + 1) * 7 + 5] -
2.0 * (spline[(m + 1) * 7 + 6] - spline[m * 7 + 6]);
}
spline[n * 7 + 4] = 0.0;
spline[n * 7 + 3] = 0.0;
for(int m = 1; m <= n; m++) {
spline[m * 7 + 2] = spline[m * 7 + 5] / delta;
spline[m * 7 + 1] = 2.0 * spline[m * 7 + 4] / delta;
spline[m * 7 + 0] = 3.0 * spline[m * 7 + 3] / delta;
}
}
void grab(FILE* fptr, int n, MD_FLOAT* list) {
char* ptr;
char line[MAXLINE];
int i = 0;
while(i < n) {
fgets(line, MAXLINE, fptr);
ptr = strtok(line, " \t\n\r\f");
list[i++] = atof(ptr);
while(ptr = strtok(NULL, " \t\n\r\f")) list[i++] = atof(ptr);
}
}

177
src/force_eam.c Normal file
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@ -0,0 +1,177 @@
/*
* =======================================================================================
*
* 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 <likwid-marker.h>
#include <math.h>
#include <allocate.h>
#include <timing.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <stats.h>
#include <eam.h>
#include <util.h>
double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep) {
if(eam->nmax < atom->Nmax) {
eam->nmax = atom->Nmax;
if(eam->fp != NULL) { free(eam->fp); }
eam->fp = (MD_FLOAT *) allocate(ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT));
}
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; MD_FLOAT* fp = eam->fp;
MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline;
int rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; int rdrho = eam->rdrho;
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot;
double S = getTimeStamp();
LIKWID_MARKER_START("force_eam_fp");
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT rhoi = 0;
const int type_i = atom->type[i];
#pragma ivdep
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
if(rsq < cutforcesq) {
MD_FLOAT p = sqrt(rsq) * rdr + 1.0;
int m = (int)(p);
m = m < nr - 1 ? m : nr - 1;
p -= m;
p = p < 1.0 ? p : 1.0;
rhoi += ((rhor_spline[type_ij * nr_tot + m * 7 + 3] * p +
rhor_spline[type_ij * nr_tot + m * 7 + 4]) * p +
rhor_spline[type_ij * nr_tot + m * 7 + 5]) * p +
rhor_spline[type_ij * nr_tot + m * 7 + 6];
}
}
const int type_ii = type_i * type_i;
MD_FLOAT p = 1.0 * rhoi * rdrho + 1.0;
int m = (int)(p);
m = MAX(1, MIN(m, nrho - 1));
p -= m;
p = MIN(p, 1.0);
fp[i] = (frho_spline[type_ii * nrho_tot + m * 7 + 0] * p +
frho_spline[type_ii * nrho_tot + m * 7 + 1]) * p +
frho_spline[type_ii * nrho_tot + m * 7 + 2];
}
LIKWID_MARKER_STOP("force_eam_fp");
LIKWID_MARKER_START("force_eam");
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
const int type_i = atom->type[i];
#pragma ivdep
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
if(rsq < cutforcesq) {
MD_FLOAT r = sqrt(rsq);
MD_FLOAT p = r * rdr + 1.0;
int m = (int)(p);
m = m < nr - 1 ? m : nr - 1;
p -= m;
p = p < 1.0 ? p : 1.0;
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
// phi = pair potential energy
// phip = phi'
// z2 = phi * r
// z2p = (phi * r)' = (phi' r) + phi
// psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
MD_FLOAT rhoip = (rhor_spline[type_ij * nr_tot + m * 7 + 0] * p +
rhor_spline[type_ij * nr_tot + m * 7 + 1]) * p +
rhor_spline[type_ij * nr_tot + m * 7 + 2];
MD_FLOAT z2p = (z2r_spline[type_ij * nr_tot + m * 7 + 0] * p +
z2r_spline[type_ij * nr_tot + m * 7 + 1]) * p +
z2r_spline[type_ij * nr_tot + m * 7 + 2];
MD_FLOAT z2 = ((z2r_spline[type_ij * nr_tot + m * 7 + 3] * p +
z2r_spline[type_ij * nr_tot + m * 7 + 4]) * p +
z2r_spline[type_ij * nr_tot + m * 7 + 5]) * p +
z2r_spline[type_ij * nr_tot + m * 7 + 6];
MD_FLOAT recip = 1.0 / r;
MD_FLOAT phi = z2 * recip;
MD_FLOAT phip = z2p * recip - phi * recip;
MD_FLOAT psip = fp[i] * rhoip + fp[j] * rhoip + phip;
MD_FLOAT fpair = -psip * recip;
fix += delx * fpair;
fiy += dely * fpair;
fiz += delz * fpair;
//fpair *= 0.5;
}
}
fx[i] = fix;
fy[i] = fiy;
fz[i] = fiz;
addStat(stats->total_force_neighs, numneighs);
addStat(stats->total_force_iters, (numneighs + VECTOR_WIDTH - 1) / VECTOR_WIDTH);
}
LIKWID_MARKER_STOP("force_eam");
double E = getTimeStamp();
return E-S;
}

2
src/includes/atom.h
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@ -30,14 +30,12 @@ typedef struct {
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *fx, *fy, *fz;
#ifdef EXPLICIT_TYPES
int *type;
int ntypes;
MD_FLOAT *epsilon;
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
#endif
} Atom;
extern void initAtom(Atom*);

57
src/includes/eam.h Normal file
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@ -0,0 +1,57 @@
/*
* =======================================================================================
*
* 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 ntypes;
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;
MD_FLOAT *cutforcesq;
Funcfl file;
} Eam;
void initEam(Eam* eam, const char* input_file, int ntypes);
void coeff(Eam* eam, const char* arg);
void init_style(Eam* eam);
void read_file(Funcfl* file, const char* filename);
void file2array(Eam* eam);
void array2spline(Eam* eam);
void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline);
void grab(FILE* fptr, int n, MD_FLOAT* list);
#endif

5
src/includes/parameter.h
View File

@ -23,6 +23,9 @@
#ifndef __PARAMETER_H_
#define __PARAMETER_H_
#define FF_LJ 0
#define FF_EAM 1
#if PRECISION == 1
#define MD_FLOAT float
#else
@ -30,6 +33,8 @@
#endif
typedef struct {
int force_field;
char* input_file;
MD_FLOAT epsilon;
MD_FLOAT sigma6;
MD_FLOAT temp;

4
src/main-stub.c
View File

@ -128,7 +128,6 @@ int main(int argc, const char *argv[]) {
initAtom(atom);
initStats(&stats);
#ifdef EXPLICIT_TYPES
atom->ntypes = param.ntypes;
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
@ -140,7 +139,6 @@ int main(int argc, const char *argv[]) {
atom->cutneighsq[i] = param.cutneigh * param.cutneigh;
atom->cutforcesq[i] = param.cutforce * param.cutforce;
}
#endif
DEBUG("Creating atoms...\n");
for(int i = 0; i < param.nx; ++i) {
@ -176,9 +174,7 @@ int main(int argc, const char *argv[]) {
for(int jj = 0; jj < fac_y; ++jj) {
for(int kk = 0; kk < fac_z; ++kk) {
if(added_atoms < atoms_per_unit_cell) {
#ifdef EXPLICIT_TYPES
atom->type[atom->Nlocal] = rand() % atom->ntypes;
#endif
ADD_ATOM(ii * offset_x, jj * offset_y, kk * offset_z, vx, vy, vz);
added_atoms++;
}

67
src/main.c
View File

@ -39,14 +39,18 @@
#include <thermo.h>
#include <pbc.h>
#include <timers.h>
#include <eam.h>
#define HLINE "----------------------------------------------------------------------------\n"
extern double computeForce(Parameter*, Atom*, Neighbor*);
extern double computeForceTracing(Parameter*, Atom*, Neighbor*, Stats*, int, int);
extern double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep);
void init(Parameter *param)
{
param->input_file = NULL;
param->force_field = FF_LJ;
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
@ -68,6 +72,7 @@ void init(Parameter *param)
double setup(
Parameter *param,
Eam *eam,
Atom *atom,
Neighbor *neighbor,
Stats *stats)
@ -79,6 +84,7 @@ double setup(
param->zprd = param->nz * param->lattice;
S = getTimeStamp();
if(param->force_field == FF_EAM) { initEam(eam, param->input_file, param->ntypes); }
initAtom(atom);
initNeighbor(neighbor, param);
initPbc();
@ -147,16 +153,31 @@ void printAtomState(Atom *atom)
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
atom->Natoms, atom->Nlocal, atom->Nghost, atom->Nmax);
/* int nall = atom->Nlocal + atom->Nghost; */
/* int nall = atom->Nlocal + atom->Nghost; */
/* for (int i=0; i<nall; i++) { */
/* printf("%d %f %f %f\n", i, atom->x[i], atom->y[i], atom->z[i]); */
/* } */
/* for (int i=0; i<nall; i++) { */
/* printf("%d %f %f %f\n", i, atom->x[i], atom->y[i], atom->z[i]); */
/* } */
}
int main (int argc, char** argv)
int str2ff(const char *string)
{
if(strncmp(string, "lj", 2) == 0) return FF_LJ;
if(strncmp(string, "eam", 3) == 0) return FF_EAM;
return -1;
}
const char* ff2str(int ff)
{
if(ff == FF_LJ) { return "lj"; }
if(ff == FF_EAM) { return "eam"; }
return "invalid";
}
int main(int argc, char** argv)
{
double timer[NUMTIMER];
Eam eam;
Atom atom;
Neighbor neighbor;
Stats stats;
@ -173,6 +194,19 @@ int main (int argc, char** argv)
for(int i = 0; i < argc; i++)
{
if((strcmp(argv[i], "-f") == 0))
{
if((param.force_field = str2ff(argv[++i])) < 0) {
fprintf(stderr, "Invalid force field!\n");
exit(-1);
}
continue;
}
if((strcmp(argv[i], "-i") == 0))
{
param.input_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0))
{
param.ntimes = atoi(argv[++i]);
@ -193,7 +227,7 @@ int main (int argc, char** argv)
param.nz = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-f") == 0))
if((strcmp(argv[i], "--freq") == 0))
{
param.proc_freq = atof(argv[++i]);
continue;
@ -202,21 +236,27 @@ int main (int argc, char** argv)
{
printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE);
printf("-f <string>: force field (lj or eam), default lj\n");
printf("-i <string>: input file for EAM\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf("-f <real>: processor frequency (GHz)\n");
printf("--freq <real>: processor frequency (GHz)\n");
printf(HLINE);
exit(EXIT_SUCCESS);
}
}
setup(&param, &atom, &neighbor, &stats);
setup(&param, &eam, &atom, &neighbor, &stats);
computeThermo(0, &param, &atom);
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(PRINT_STATS)
if(param.force_field == FF_EAM) {
computeForceEam(&eam, &atom, &neighbor, &stats, 1, 0);
} else {
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(COMPUTE_STATS)
computeForceTracing(&param, &atom, &neighbor, &stats, 1, 0);
#else
computeForce(&param, &atom, &neighbor);
#endif
}
timer[FORCE] = 0.0;
timer[NEIGH] = 0.0;
@ -231,11 +271,15 @@ int main (int argc, char** argv)
timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
}
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(PRINT_STATS)
if(param.force_field == FF_EAM) {
timer[FORCE] += computeForceEam(&eam, &atom, &neighbor, &stats, 0, n + 1);
} else {
#if defined(MEM_TRACER) || defined(INDEX_TRACER) || defined(COMPUTE_STATS)
timer[FORCE] += computeForceTracing(&param, &atom, &neighbor, &stats, 0, n + 1);
#else
timer[FORCE] += computeForce(&param, &atom, &neighbor);
#endif
}
finalIntegrate(&param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
@ -247,6 +291,7 @@ int main (int argc, char** argv)
computeThermo(-1, &param, &atom);
printf(HLINE);
printf("Force field: %s\n", ff2str(param.force_field));
printf("Data layout for positions: %s\n", POS_DATA_LAYOUT);
#if PRECISION == 1
printf("Using single precision floating point.\n");
@ -260,7 +305,7 @@ int main (int argc, char** argv)
printf(HLINE);
printf("Performance: %.2f million atom updates per second\n",
1e-6 * (double) atom.Natoms * param.ntimes / timer[TOTAL]);
#ifdef PRINT_STATS
#ifdef COMPUTE_STATS
displayStatistics(&atom, &param, &stats, timer);
#endif
LIKWID_MARKER_CLOSE;

4
src/stats.c
View File

@ -14,11 +14,15 @@ void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer
#ifdef COMPUTE_STATS
double force_useful_volume = 1e-9 * ( (double)(atom->Nlocal * (param->ntimes + 1)) * (sizeof(MD_FLOAT) * 6 + sizeof(int)) +
(double)(stats->total_force_neighs) * (sizeof(MD_FLOAT) * 3 + sizeof(int)) );
double avg_neigh = stats->total_force_neighs / (double)(atom->Nlocal * (param->ntimes + 1));
double avg_simd = stats->total_force_iters / (double)(atom->Nlocal * (param->ntimes + 1));
#ifdef EXPLICIT_TYPES
force_useful_volume += 1e-9 * (double)((atom.Nlocal * (param.ntimes + 1)) + stats.total_force_neighs) * sizeof(int);
#endif
printf("Statistics:\n");
printf("\tVector width: %d, Processor frequency: %.4f GHz\n", VECTOR_WIDTH, param->proc_freq);
printf("\tAverage neighbors per atom: %.4f\n", avg_neigh);
printf("\tAverage SIMD iterations per atom: %.4f\n", avg_simd);
printf("\tTotal number of computed pair interactions: %lld\n", stats->total_force_neighs);
printf("\tTotal number of SIMD iterations: %lld\n", stats->total_force_iters);
printf("\tUseful read data volume for force computation: %.2fGB\n", force_useful_volume);