From 2dac10469cc56fc0303cb79ef6c763c01c7bcce5 Mon Sep 17 00:00:00 2001 From: Rafael Ravedutti Date: Tue, 26 Oct 2021 00:40:39 +0200 Subject: [PATCH] Add EAM force field Signed-off-by: Rafael Ravedutti --- src/eam_utils.c | 254 +++++++++++++++++++++++++++++++++++++++ src/force_eam.c | 173 ++++++++++++++++++++++++++ src/includes/eam.h | 54 +++++++++ src/includes/parameter.h | 4 + src/main.c | 59 ++++++++- 5 files changed, 538 insertions(+), 6 deletions(-) create mode 100644 src/eam_utils.c create mode 100644 src/force_eam.c create mode 100644 src/includes/eam.h diff --git a/src/eam_utils.c b/src/eam_utils.c new file mode 100644 index 0000000..d52626d --- /dev/null +++ b/src/eam_utils.c @@ -0,0 +1,254 @@ +#include +#include + +#include +#include +#include +#include + +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)); +} + +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; icutforcesq[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->nhro + 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; + dr = drho = rmax = rhomax = 0.0; + active = 0; + Funcfl* file = eam->file; + dr = MAX(dr, file->dr); + drho = MAX(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 = static_cast(rmax / dr + 0.5); + eam->nrho = static_cast(rhomax / drho + 0.5); + + // ------------------------------------------------------------------ + // setup frho arrays + // ------------------------------------------------------------------ + + // allocate frho arrays + // nfrho = # of funcfl files + 1 for zero array + eam->frho = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nhro + 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) * drho; + p = r / file->drho + 1.0; + k = static_cast(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) * dr; + p = r / file->dr + 1.0; + k = static_cast(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) * dr; + p = r / ifile->dr + 1.0; + k = static_cast(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 = static_cast(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) { + rdr = 1.0 / eam->dr; + rdrho = 1.0 / eam->drho; + nrho_tot = (eam->nrho + 1) * 7 + 64; + nr_tot = (eam->nr + 1) * 7 + 64; + nrho_tot -= nrho_tot%64; + nr_tot -= nr_tot%64; + + int ntypes = eam->ntypes; + eam->frho_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * nrho_tot * sizeof(MD_FLOAT)); + eam->rhor_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * nr_tot * sizeof(MD_FLOAT)); + eam->z2r_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * 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 < nrho_tot; k++) + eam->frho_spline[tt*nrho_tot + k] = eam->frho_spline[k]; + for(int k = 0; k < nr_tot; k++) + eam->rhor_spline[tt*nr_tot + k] = eam->rhor_spline[k]; + for(int k = 0; k < nr_tot; k++) + eam->z2r_spline[tt*nr_tot + k] = eam->z2r_spline[k]; + } +} + +void interpolate(MMD_int n, MMD_float delta, MMD_float* f, MMD_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, MMD_int n, MMD_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); + } +} diff --git a/src/force_eam.c b/src/force_eam.c new file mode 100644 index 0000000..5ab58da --- /dev/null +++ b/src/force_eam.c @@ -0,0 +1,173 @@ +/* + * ======================================================================================= + * + * 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 . + * ======================================================================================= + */ +#include + +#include +#include +#include +#include +#include +#include +#include + +double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, int first_exec, int timestep) { + if(atom->nmax > eam->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* fhro_spline = eam->fhro_spline; MD_FLOAT* z2r_spline = eam->z2r_spline; + 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 = static_cast(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 = static_cast(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) { + MMD_float r = sqrt(rsq); + MMD_float p = r * rdr + 1.0; + int m = static_cast(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 + + MMD_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]; + + MMD_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]; + + MMD_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]; + + MMD_float recip = 1.0 / r; + MMD_float phi = z2 * recip; + MMD_float phip = z2p * recip - phi * recip; + MMD_float psip = fp[i] * rhoip + fp[j] * rhoip + phip; + MMD_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; +} diff --git a/src/includes/eam.h b/src/includes/eam.h new file mode 100644 index 0000000..be23d41 --- /dev/null +++ b/src/includes/eam.h @@ -0,0 +1,54 @@ +/* + * ======================================================================================= + * + * 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 . + * ======================================================================================= + */ +#include +#include + +#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; + MD_FLOAT *cutforcesq; + Funcfl* file; +} Eam; + +void init_eam(Eam* eam, 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(MMD_int n, MMD_float delta, MMD_float* f, MMD_float* spline); +void grab(FILE* fptr, MMD_int n, MMD_float* list); +#endif diff --git a/src/includes/parameter.h b/src/includes/parameter.h index e95e1e8..e8eef2b 100644 --- a/src/includes/parameter.h +++ b/src/includes/parameter.h @@ -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 +33,7 @@ #endif typedef struct { + char* input_file; MD_FLOAT epsilon; MD_FLOAT sigma6; MD_FLOAT temp; diff --git a/src/main.c b/src/main.c index bff4422..00ae044 100644 --- a/src/main.c +++ b/src/main.c @@ -39,13 +39,17 @@ #include #include #include +#include #define HLINE "----------------------------------------------------------------------------\n" extern double computeForce(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; @@ -67,6 +71,7 @@ void init(Parameter *param) double setup( Parameter *param, + Eam *eam, Atom *atom, Neighbor *neighbor, Stats *stats) @@ -78,6 +83,7 @@ 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(); @@ -153,9 +159,24 @@ void printAtomState(Atom *atom) /* } */ } -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; @@ -172,6 +193,19 @@ 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]); @@ -192,7 +226,7 @@ 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; @@ -201,17 +235,24 @@ int main (int argc, char** argv) { printf("MD Bench: A minimalistic re-implementation of miniMD\n"); printf(HLINE); + printf("-f : force field (lj or eam), default lj\n"); + printf("-i : input file for EAM\n"); printf("-n / --nsteps : set number of timesteps for simulation\n"); printf("-nx/-ny/-nz : set linear dimension of systembox in x/y/z direction\n"); - printf("-f : processor frequency (GHz)\n"); + printf("--freq : processor frequency (GHz)\n"); printf(HLINE); exit(EXIT_SUCCESS); } } - setup(¶m, &atom, &neighbor, &stats); + setup(¶m, &eam, &atom, &neighbor, &stats); computeThermo(0, ¶m, &atom); - computeForce(¶m, &atom, &neighbor, &stats, 1, 0); + + if(param.force_field == FF_EAM) { + computeForceEam(&eam, &atom, &neighbor, &stats, 1, 0); + } else { + computeForce(¶m, &atom, &neighbor, &stats, 1, 0); + } timer[FORCE] = 0.0; timer[NEIGH] = 0.0; @@ -226,7 +267,12 @@ int main (int argc, char** argv) timer[NEIGH] += reneighbour(¶m, &atom, &neighbor); } - timer[FORCE] += computeForce(¶m, &atom, &neighbor, &stats, 0, n + 1); + if(param.force_field == FF_EAM) { + timer[FORCE] += computeForceEam(&eam, &atom, &neighbor, &stats, 0, n + 1); + } else { + timer[FORCE] += computeForce(¶m, &atom, &neighbor, &stats, 0, n + 1); + } + finalIntegrate(¶m, &atom); if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) { @@ -238,6 +284,7 @@ int main (int argc, char** argv) computeThermo(-1, ¶m, &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");