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#include "dump2analysis.h"
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/* DOCUMENT */
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/* -m gr */
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/* lammpstrjから2原子間の動径分布関数を計算する */
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/* またカットオフ距離内の平均結合距離を求める */
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/* A原子(-a, -x, -s)とB原子(-c, -z, -u)を指定する。 */
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/* --rmaxは動径分布関数を計算する最大距離 default:10.005 */
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/* --rminは動径分布関数を計算する最小距離 default:0.01 */
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/* --drは動径分布関数を計算する刻み距離 default:0.01 */
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/* --rcutは結合距離を計算するカットオフ default:2.3 */
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void ErrorGr(){
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printf("Required arguments atoms A and atoms B\n");
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printf("(-a, -x, -s) atom A\n");
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printf("(-b, -y, -t) atom B\n");
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printf("------------------------------------------------------------\n");
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printf("Optional arguments for Gr analysis:\n");
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printf("--dr distance step for g(r) [0.01]\n");
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printf("--rmax maximum distance for g(r) [10.005]\n");
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printf("--rmin minimum distance for g(r) [0.005]\n");
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printf("--rcut cut-off for alculation of mean distance [2.3]\n");
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printf("------------------------------------------------------------\n");
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printf("Example:\n");
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printf("dump2analysis -m gr -x Si -y O -i hoge.lammpstrj -o hoge.gr\n");
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exit(0);
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}
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void OutputGr(PARAM *p, double *gr, double *cn, ATOMS *a, ATOMS *b,
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double ave, double std, int pairs){
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int i, RDATA;
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double rp, rcn=0;
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FILE *fp;
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RDATA = floor((RMAX-RMIN)/DR);
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fp = fopen(p->outfile, "w");
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fprintf(fp, "# Total step: %d\n", p->steps);
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/* fprintf(fp, "# atom-A:"); */
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/* for(i=0; i<a->atoms; i++) */
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/* fprintf(fp, " %s(%d)", a->elem[i], a->id[i]); */
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/* fprintf(fp, "\n"); */
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/* fprintf(fp, "# atom-B:"); */
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/* for(i=0; i<b->atoms; i++) */
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/* fprintf(fp, " %s(%d)", b->elem[i], b->id[i]); */
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/* fprintf(fp, "\n"); */
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fprintf(fp, "# (Rmin, Rmax, dr)=(%g, %g, %g)\n", RMIN, RMAX, DR);
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fprintf(fp, "# RDATA=%d\n", RDATA);
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fprintf(fp, "\n");
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fprintf(fp, "# Total pairs: %d\n", pairs);
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fprintf(fp, "# Rcut : %lf\n", RCUT);
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fprintf(fp, "# distance: %lf +/- %lf\n", ave, std);
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fprintf(fp, "# %10s %12s %12s\n", "r", "g(r)", "cn(r)");
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fprintf(fp, "%12g %12g %12g\n", 0.0, 0.0, 0.0);
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for(i=0; i<RDATA; i++){
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rp = RMIN + (double)i*DR + 0.5*DR;
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rcn = rcn + (double)cn[i];
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fprintf(fp, "%12g ", rp);
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fprintf(fp, "%12g ", gr[i]/(double)p->steps);
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fprintf(fp, "%12g ", rcn/(double)p->steps);
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fprintf(fp, "\n");
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}
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fclose(fp);
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}
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void EstimateGr(PARAM *param){
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FILE *f;
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HEAD head;
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int i, j, k, l, p, s, RDATA;
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double *gr, *cn, *cr;
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double volume, bunbo, sflag = 0.0;
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double xa, ya, za, xb, yb, zb, xp, yp, zp, r;
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double ave = 0.0, std = 0.0, *d = NULL;
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int rp, pairs=0;
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ATOMS a, b;
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if (ArgCheckInputOutput(param) != 0) ErrorGr();
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SetAtomsSteps(param);
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if (CheckArgAtomSelect(param) != 3) ErrorGr();
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Allocate(&a, param->atoms);
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Allocate(&b, param->atoms);
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f = fopen(param->infile, "r");
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RDATA = floor((RMAX-RMIN)/DR);
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gr = malloc(sizeof(double)*RDATA);
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cn = malloc(sizeof(double)*RDATA);
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cr = malloc(sizeof(double)*RDATA);
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/* grの計算 */
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for (i=0; i<RDATA; i++) gr[i] = 0.0;
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for (s=0; s<param->steps; s++){
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if (s%10 == 0) {
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printf("Calculating Gr step: %d\r", s);
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fflush(stdout);
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}
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/* 初期化 */
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for (i=0; i<RDATA; i++) cr[i] = 0.0;
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/* 原子の選択 */
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GetData(f, param, &head, &a, &b, NULL);
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/* 同一原子かのチェック */
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if (a.atoms == b.atoms){
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sflag = 1.0;
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for (i=0; i<a.atoms; i++)
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if (a.id[i] != b.id[i]) sflag = 0.0;
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}
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volume = head.A[0][0] * head.A[1][1] * head.A[2][2];
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for(i=0; i<a.atoms; i++){
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/* 絶対座標に変換 */
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xa = a.x[i]*head.A[0][0] + a.y[i]*head.A[1][0] + a.z[i]*head.A[2][0];
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ya = a.x[i]*head.A[0][1] + a.y[i]*head.A[1][1] + a.z[i]*head.A[2][1];
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za = a.x[i]*head.A[0][2] + a.y[i]*head.A[1][2] + a.z[i]*head.A[2][2];
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/* x-1, x+1, y-1,y+1, z-1, z+1 のb原子を作る */
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for (j=-1; j<2; j++){
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for (k=-1; k<2; k++){
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for (l=-1; l<2; l++){
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for (p=0; p<b.atoms; p++){
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xp = b.x[p] + j;
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yp = b.y[p] + k;
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zp = b.z[p] + l;
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xb = xp*head.A[0][0] + yp*head.A[1][0] + zp*head.A[2][0];
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yb = xp*head.A[0][1] + yp*head.A[1][1] + zp*head.A[2][1];
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zb = xp*head.A[0][2] + yp*head.A[1][2] + zp*head.A[2][2];
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r = sqrt(pow((xa-xb), 2) + pow((ya-yb), 2) + pow((za-zb), 2));
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if (RMIN < r && r < RMAX) {
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rp = (int)floor((r-RMIN)/DR);
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cr[rp]++;
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cn[rp] = cn[rp] + 1.0/(double)a.atoms;
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}
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if (0 < r && r < RCUT){
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d = realloc(d, sizeof(double) * (pairs+1));
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d[pairs] = r;
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pairs++;
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}
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}
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}
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}
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}
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}
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/* 1ステップ毎にgrの計算 */
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for (i=0; i<RDATA; i++){
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if(cr[i] != 0){
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r = RMIN + (double)i*DR + 0.5*DR;
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bunbo = 4.0 * M_PI * r*r * DR * (a.atoms) * (b.atoms - sflag);
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gr[i] = gr[i] + (double)cr[i] * volume / bunbo;
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}
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}
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}
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printf("\n");
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fclose(f);
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Deallocate(&a, param->atoms);
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Deallocate(&b, param->atoms);
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/* 平均値の計算 */
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for (i=0; i<pairs; i++) ave = ave + d[i];
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ave = ave/pairs;
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/* 標準偏差の計算 */
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for (i=0; i<pairs; i++) std = std + (d[i] - ave)*(d[i] - ave);
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std = sqrt(std/pairs);
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/* 出力 */
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OutputGr(param, gr, cn, &a, &b, ave, std, pairs);
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free(gr);
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free(cn);
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free(cr);
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free(d);
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}
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