286 lines
10 KiB
C
286 lines
10 KiB
C
/*
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* =======================================================================================
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*
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* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
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* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
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*
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* This file is part of MD-Bench.
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*
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* MD-Bench is free software: you can redistribute it and/or modify it
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* under the terms of the GNU Lesser General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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* details.
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*
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* You should have received a copy of the GNU Lesser General Public License along
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* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
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* =======================================================================================
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <allocate.h>
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#include <atom.h>
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#include <eam.h>
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#include <parameter.h>
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#include <util.h>
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#ifndef MAXLINE
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#define MAXLINE 4096
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#endif
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void initEam(Eam* eam, Parameter* param) {
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int ntypes = param->ntypes;
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eam->nmax = 0;
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eam->fp = NULL;
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coeff(eam, param);
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init_style(eam, param);
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}
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void coeff(Eam* eam, Parameter* param) {
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read_eam_file(&eam->file, param->eam_file);
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param->mass = eam->file.mass;
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param->cutforce = eam->file.cut;
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param->cutneigh = param->cutforce + 1.0;
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param->temp = 600.0;
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param->dt = 0.001;
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param->rho = 0.07041125;
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param->dtforce = 0.5 * param->dt / param->mass;
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}
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void init_style(Eam* eam, Parameter* param) {
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// convert read-in file(s) to arrays and spline them
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file2array(eam);
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array2spline(eam, param);
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}
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void read_eam_file(Funcfl* file, const char* filename) {
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FILE* fptr;
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char line[MAXLINE];
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fptr = fopen(filename, "r");
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if(fptr == NULL) {
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printf("Can't open EAM Potential file: %s\n", filename);
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exit(0);
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}
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int tmp;
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fgets(line, MAXLINE, fptr);
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fgets(line, MAXLINE, fptr);
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sscanf(line, "%d %lg", &tmp, &(file->mass));
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fgets(line, MAXLINE, fptr);
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sscanf(line, "%d %lg %d %lg %lg", &file->nrho, &file->drho, &file->nr, &file->dr, &file->cut);
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//printf("Read: %lf %i %lf %i %lf %lf\n",file->mass,file->nrho,file->drho,file->nr,file->dr,file->cut);
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file->frho = (MD_FLOAT *) allocate(ALIGNMENT, (file->nrho + 1) * sizeof(MD_FLOAT));
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file->rhor = (MD_FLOAT *) allocate(ALIGNMENT, (file->nr + 1) * sizeof(MD_FLOAT));
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file->zr = (MD_FLOAT *) allocate(ALIGNMENT, (file->nr + 1) * sizeof(MD_FLOAT));
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grab(fptr, file->nrho, file->frho);
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grab(fptr, file->nr, file->zr);
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grab(fptr, file->nr, file->rhor);
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for(int i = file->nrho; i > 0; i--) file->frho[i] = file->frho[i - 1];
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for(int i = file->nr; i > 0; i--) file->rhor[i] = file->rhor[i - 1];
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for(int i = file->nr; i > 0; i--) file->zr[i] = file->zr[i - 1];
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fclose(fptr);
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}
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void file2array(Eam* eam) {
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int i, j, k, m, n;
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double sixth = 1.0 / 6.0;
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// determine max function params from all active funcfl files
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// active means some element is pointing at it via map
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int active;
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double rmax, rhomax;
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eam->dr = eam->drho = rmax = rhomax = 0.0;
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active = 0;
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Funcfl* file = &eam->file;
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eam->dr = MAX(eam->dr, file->dr);
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eam->drho = MAX(eam->drho, file->drho);
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rmax = MAX(rmax, (file->nr - 1) * file->dr);
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rhomax = MAX(rhomax, (file->nrho - 1) * file->drho);
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// set nr,nrho from cutoff and spacings
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// 0.5 is for round-off in divide
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eam->nr = (int)(rmax / eam->dr + 0.5);
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eam->nrho = (int)(rhomax / eam->drho + 0.5);
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// ------------------------------------------------------------------
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// setup frho arrays
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// ------------------------------------------------------------------
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// allocate frho arrays
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// nfrho = # of funcfl files + 1 for zero array
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eam->frho = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nrho + 1) * sizeof(MD_FLOAT));
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// interpolate each file's frho to a single grid and cutoff
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double r, p, cof1, cof2, cof3, cof4;
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n = 0;
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for(m = 1; m <= eam->nrho; m++) {
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r = (m - 1) * eam->drho;
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p = r / file->drho + 1.0;
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k = (int)(p);
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k = MIN(k, file->nrho - 2);
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k = MAX(k, 2);
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p -= k;
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p = MIN(p, 2.0);
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cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
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cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
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cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
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cof4 = sixth * p * (p * p - 1.0);
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eam->frho[m] = cof1 * file->frho[k - 1] + cof2 * file->frho[k] +
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cof3 * file->frho[k + 1] + cof4 * file->frho[k + 2];
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}
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// ------------------------------------------------------------------
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// setup rhor arrays
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// ------------------------------------------------------------------
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// allocate rhor arrays
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// nrhor = # of funcfl files
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eam->rhor = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nr + 1) * sizeof(MD_FLOAT));
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// interpolate each file's rhor to a single grid and cutoff
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for(m = 1; m <= eam->nr; m++) {
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r = (m - 1) * eam->dr;
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p = r / file->dr + 1.0;
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k = (int)(p);
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k = MIN(k, file->nr - 2);
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k = MAX(k, 2);
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p -= k;
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p = MIN(p, 2.0);
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cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
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cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
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cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
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cof4 = sixth * p * (p * p - 1.0);
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eam->rhor[m] = cof1 * file->rhor[k - 1] + cof2 * file->rhor[k] +
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cof3 * file->rhor[k + 1] + cof4 * file->rhor[k + 2];
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//if(m==119)printf("BuildRho: %e %e %e %e %e %e\n",rhor[m],cof1,cof2,cof3,cof4,file->rhor[k]);
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}
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// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
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// for funcfl files, I,J mapping only depends on I
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// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
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// ------------------------------------------------------------------
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// setup z2r arrays
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// ------------------------------------------------------------------
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// allocate z2r arrays
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// nz2r = N*(N+1)/2 where N = # of funcfl files
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eam->z2r = (MD_FLOAT *) allocate(ALIGNMENT, (eam->nr + 1) * sizeof(MD_FLOAT));
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// create a z2r array for each file against other files, only for I >= J
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// interpolate zri and zrj to a single grid and cutoff
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double zri, zrj;
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Funcfl* ifile = &eam->file;
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Funcfl* jfile = &eam->file;
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for(m = 1; m <= eam->nr; m++) {
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r = (m - 1) * eam->dr;
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p = r / ifile->dr + 1.0;
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k = (int)(p);
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k = MIN(k, ifile->nr - 2);
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k = MAX(k, 2);
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p -= k;
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p = MIN(p, 2.0);
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cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
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cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
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cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
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cof4 = sixth * p * (p * p - 1.0);
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zri = cof1 * ifile->zr[k - 1] + cof2 * ifile->zr[k] +
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cof3 * ifile->zr[k + 1] + cof4 * ifile->zr[k + 2];
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p = r / jfile->dr + 1.0;
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k = (int)(p);
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k = MIN(k, jfile->nr - 2);
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k = MAX(k, 2);
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p -= k;
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p = MIN(p, 2.0);
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cof1 = -sixth * p * (p - 1.0) * (p - 2.0);
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cof2 = 0.5 * (p * p - 1.0) * (p - 2.0);
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cof3 = -0.5 * p * (p + 1.0) * (p - 2.0);
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cof4 = sixth * p * (p * p - 1.0);
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zrj = cof1 * jfile->zr[k - 1] + cof2 * jfile->zr[k] +
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cof3 * jfile->zr[k + 1] + cof4 * jfile->zr[k + 2];
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eam->z2r[m] = 27.2 * 0.529 * zri * zrj;
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}
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}
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void array2spline(Eam* eam, Parameter* param) {
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eam->rdr = 1.0 / eam->dr;
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eam->rdrho = 1.0 / eam->drho;
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eam->nrho_tot = (eam->nrho + 1) * 7 + 64;
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eam->nr_tot = (eam->nr + 1) * 7 + 64;
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eam->nrho_tot -= eam->nrho_tot%64;
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eam->nr_tot -= eam->nr_tot%64;
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int ntypes = param->ntypes;
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eam->frho_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nrho_tot * sizeof(MD_FLOAT));
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eam->rhor_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nr_tot * sizeof(MD_FLOAT));
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eam->z2r_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nr_tot * sizeof(MD_FLOAT));
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interpolate(eam->nrho, eam->drho, eam->frho, eam->frho_spline);
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interpolate(eam->nr, eam->dr, eam->rhor, eam->rhor_spline);
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interpolate(eam->nr, eam->dr, eam->z2r, eam->z2r_spline);
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// replicate data for multiple types;
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for(int tt = 0; tt < ntypes * ntypes; tt++) {
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for(int k = 0; k < eam->nrho_tot; k++)
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eam->frho_spline[tt*eam->nrho_tot + k] = eam->frho_spline[k];
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for(int k = 0; k < eam->nr_tot; k++)
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eam->rhor_spline[tt*eam->nr_tot + k] = eam->rhor_spline[k];
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for(int k = 0; k < eam->nr_tot; k++)
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eam->z2r_spline[tt*eam->nr_tot + k] = eam->z2r_spline[k];
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}
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}
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void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline) {
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for(int m = 1; m <= n; m++) spline[m * 7 + 6] = f[m];
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spline[1 * 7 + 5] = spline[2 * 7 + 6] - spline[1 * 7 + 6];
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spline[2 * 7 + 5] = 0.5 * (spline[3 * 7 + 6] - spline[1 * 7 + 6]);
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spline[(n - 1) * 7 + 5] = 0.5 * (spline[n * 7 + 6] - spline[(n - 2) * 7 + 6]);
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spline[n * 7 + 5] = spline[n * 7 + 6] - spline[(n - 1) * 7 + 6];
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for(int m = 3; m <= n - 2; m++)
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spline[m * 7 + 5] = ((spline[(m - 2) * 7 + 6] - spline[(m + 2) * 7 + 6]) +
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8.0 * (spline[(m + 1) * 7 + 6] - spline[(m - 1) * 7 + 6])) / 12.0;
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for(int m = 1; m <= n - 1; m++) {
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spline[m * 7 + 4] = 3.0 * (spline[(m + 1) * 7 + 6] - spline[m * 7 + 6]) -
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2.0 * spline[m * 7 + 5] - spline[(m + 1) * 7 + 5];
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spline[m * 7 + 3] = spline[m * 7 + 5] + spline[(m + 1) * 7 + 5] -
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2.0 * (spline[(m + 1) * 7 + 6] - spline[m * 7 + 6]);
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}
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spline[n * 7 + 4] = 0.0;
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spline[n * 7 + 3] = 0.0;
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for(int m = 1; m <= n; m++) {
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spline[m * 7 + 2] = spline[m * 7 + 5] / delta;
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spline[m * 7 + 1] = 2.0 * spline[m * 7 + 4] / delta;
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spline[m * 7 + 0] = 3.0 * spline[m * 7 + 3] / delta;
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}
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}
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void grab(FILE* fptr, int n, MD_FLOAT* list) {
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char* ptr;
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char line[MAXLINE];
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int i = 0;
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while(i < n) {
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fgets(line, MAXLINE, fptr);
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ptr = strtok(line, " \t\n\r\f");
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list[i++] = atof(ptr);
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while(ptr = strtok(NULL, " \t\n\r\f")) list[i++] = atof(ptr);
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}
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}
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