diff --git a/src/atom.c b/src/atom.c index 4e28d7a..9964a14 100644 --- a/src/atom.c +++ b/src/atom.c @@ -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 } diff --git a/src/eam_utils.c b/src/eam_utils.c index d52626d..7d2ef77 100644 --- a/src/eam_utils.c +++ b/src/eam_utils.c @@ -1,16 +1,23 @@ #include #include +#include #include #include #include #include +#include + +#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); } void coeff(Eam* eam, const char* arg) { @@ -46,7 +53,7 @@ void read_file(Funcfl* file, const char* filename) { 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->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); @@ -66,18 +73,18 @@ void file2array(Eam* eam) { // active means some element is pointing at it via map int active; double rmax, rhomax; - dr = drho = rmax = rhomax = 0.0; + eam->dr = eam->drho = rmax = rhomax = 0.0; active = 0; Funcfl* file = eam->file; - dr = MAX(dr, file->dr); - drho = MAX(drho, file->drho); + 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 = static_cast(rmax / dr + 0.5); - eam->nrho = static_cast(rhomax / drho + 0.5); + eam->nr = (int)(rmax / eam->dr + 0.5); + eam->nrho = (int)(rhomax / eam->drho + 0.5); // ------------------------------------------------------------------ // setup frho arrays @@ -85,16 +92,16 @@ void file2array(Eam* eam) { // allocate frho arrays // nfrho = # of funcfl files + 1 for zero array - eam->frho = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nhro + 1) * sizeof(MD_FLOAT)); + 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) * drho; + r = (m - 1) * eam->drho; p = r / file->drho + 1.0; - k = static_cast(p); + k = (int)(p); k = MIN(k, file->nrho - 2); k = MAX(k, 2); p -= k; @@ -118,9 +125,9 @@ void file2array(Eam* eam) { // interpolate each file's rhor to a single grid and cutoff for(m = 1; m <= eam->nr; m++) { - r = (m - 1) * dr; + r = (m - 1) * eam->dr; p = r / file->dr + 1.0; - k = static_cast(p); + k = (int)(p); k = MIN(k, file->nr - 2); k = MAX(k, 2); p -= k; @@ -153,9 +160,9 @@ void file2array(Eam* eam) { Funcfl* jfile = eam->file; for(m = 1; m <= eam->nr; m++) { - r = (m - 1) * dr; + r = (m - 1) * eam->dr; p = r / ifile->dr + 1.0; - k = static_cast(p); + k = (int)(p); k = MIN(k, ifile->nr - 2); k = MAX(k, 2); p -= k; @@ -168,7 +175,7 @@ void file2array(Eam* eam) { cof3 * ifile->zr[k + 1] + cof4 * ifile->zr[k + 2]; p = r / jfile->dr + 1.0; - k = static_cast(p); + k = (int)(p); k = MIN(k, jfile->nr - 2); k = MAX(k, 2); p -= k; @@ -185,33 +192,33 @@ void file2array(Eam* eam) { } 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; + 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 * 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)); + 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 < 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]; + 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(MMD_int n, MMD_float delta, MMD_float* f, MMD_float* spline) { +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]; @@ -240,7 +247,7 @@ void interpolate(MMD_int n, MMD_float delta, MMD_float* f, MMD_float* spline) { } } -void grab(FILE* fptr, MMD_int n, MMD_float* list) { +void grab(FILE* fptr, int n, MD_FLOAT* list) { char* ptr; char line[MAXLINE]; int i = 0; diff --git a/src/force_eam.c b/src/force_eam.c index 5ab58da..1e5bb72 100644 --- a/src/force_eam.c +++ b/src/force_eam.c @@ -21,6 +21,7 @@ * ======================================================================================= */ #include +#include #include #include @@ -29,18 +30,21 @@ #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->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)); + 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; + 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"); @@ -67,7 +71,7 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i if(rsq < cutforcesq) { MD_FLOAT p = sqrt(rsq) * rdr + 1.0; - int m = static_cast(p); + int m = (int)(p); m = m < nr - 1 ? m : nr - 1; p -= m; p = p < 1.0 ? p : 1.0; @@ -81,7 +85,7 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i const int type_ii = type_i * type_i; MD_FLOAT p = 1.0 * rhoi * rdrho + 1.0; - int m = static_cast(p); + int m = (int)(p); m = MAX(1, MIN(m, nrho - 1)); p -= m; p = MIN(p, 1.0); @@ -116,9 +120,9 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i 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); + 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; @@ -134,24 +138,24 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i // 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 + + 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]; - MMD_float z2p = (z2r_spline[type_ij * nr_tot + m * 7 + 0] * p + + 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]; - MMD_float z2 = ((z2r_spline[type_ij * nr_tot + m * 7 + 3] * p + + 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]; - 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; + 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; diff --git a/src/includes/atom.h b/src/includes/atom.h index ed1a0f9..98d2117 100644 --- a/src/includes/atom.h +++ b/src/includes/atom.h @@ -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*); diff --git a/src/includes/eam.h b/src/includes/eam.h index be23d41..0ac250d 100644 --- a/src/includes/eam.h +++ b/src/includes/eam.h @@ -20,6 +20,8 @@ * with MD-Bench. If not, see . * ======================================================================================= */ +#include + #include #include @@ -34,6 +36,7 @@ typedef struct { typedef struct { MD_FLOAT* fp; int nmax; + int ntypes; int nrho, nr; int nrho_tot, nr_tot; MD_FLOAT dr, rdr, drho, rdrho; @@ -43,12 +46,12 @@ typedef struct { Funcfl* file; } Eam; -void init_eam(Eam* eam, int ntypes); +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(MMD_int n, MMD_float delta, MMD_float* f, MMD_float* spline); -void grab(FILE* fptr, MMD_int n, MMD_float* list); +void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline); +void grab(FILE* fptr, int n, MD_FLOAT* list); #endif diff --git a/src/includes/parameter.h b/src/includes/parameter.h index e8eef2b..ac6c737 100644 --- a/src/includes/parameter.h +++ b/src/includes/parameter.h @@ -33,6 +33,7 @@ #endif typedef struct { + int force_field; char* input_file; MD_FLOAT epsilon; MD_FLOAT sigma6; diff --git a/src/main-stub.c b/src/main-stub.c index 72521f2..07fbbe8 100644 --- a/src/main-stub.c +++ b/src/main-stub.c @@ -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++; }