atmtobnd.c

c++编写的并行拉马克遗传算法的程序。实现分析对接程序

	/* pointtovu: connect-up XYZ points into a vu file by distance.
	 * Input:  lines with X,Y,Z in first three fields, or possibly
	 * with an initial "s" or "l" field (for compatibility with .vu
	 * files.) Lines beginning with a # or lines without three numeric
	 * values are ignored (not even counted in line numbering)
	 *  Mike Pique
	 *
	 * options:
	 * -r radius     uses radius (float) as connection distance limit
	 * Typical usage to make a bondlist might be: -r 1.85 
	 *
	 */
#define DEFAULTDIST 1.8 /* connect points closer than this */
#define MAXNPOINTS 14000

#include <stdio.h>
#include <math.h>

int nflag = 1;

int dflag = 0;
int kflag = 0;
int hflag = 0;
double rad = DEFAULTDIST;
#define HDIST 1.15
char *pgmname;
double atof();

main(argc,argv)
int argc;
char **argv;
{

FILE *f = NULL; /* input file */

/* option cracking: see getopt(3) */
extern char *optarg;
extern int optind;
int c;

	pgmname = argv[0];
	rad = DEFAULTDIST;

	while(( c = getopt(argc, argv, "r:ndkh")) != -1) switch(c) {
	case 'r': rad = atof(optarg);
		break;
	case 'n': nflag++; break;
	case 'd': dflag++; break;
	case 'k': kflag++; break;
	case 'h': hflag++; break;
	case '?': usage(); break;
	default: usage(); exit(-1); break;
	}/*while for getopt*/

	if(rad<0 || rad>1E9) {
		fprintf(stderr,"%s: bad radius %g\n",
		 pgmname, rad);
		usage();
		exit(-3);
	}/*if radius no good*/

	for(; optind < argc; optind++) {
		f = fopen(argv[optind], "r");

		if(f==NULL) {
			fprintf(stderr,"%s: can't open %s.\n", pgmname, argv[optind]);
			usage();
			exit(-1);
		}/*can't read file*/

		do_dist(f, argv[optind]);
		fclose(f);
	}/*for each file argument*/

	if(f == NULL) do_dist(stdin, "stdin");
	exit(0);
}/*main*/

do_dist(f, filename)
FILE * f;
char *filename;
{
typedef struct {
	float x, y, z;
	char *key;
	} point;
static point pos[MAXNPOINTS];
register point *point_ptr;
float x, y, z;
float dx, dy, dz;
register float dist = rad;
char linebuf[1000];
/* char *malloc(); */

register int p;
int npoints, i;
char *w;
	npoints = 0;

	while(fgets(linebuf,sizeof(linebuf),f) != NULL) {
/*for each line of data in the input file do this*/
		int nmatches = 0;
		char keybuffer[1024];
		float d; /* distance */
		if(linebuf[0] == '#') continue;
		if(linebuf[0] == 's' || linebuf[0]== 'l') linebuf[0]=' ';
		if(3 > sscanf(linebuf, "%f %f %f %[^\n]", &x, &y, &z, keybuffer)) continue;
		/* enter this point into list */
		pos[npoints].x = x;
		pos[npoints].y = y;
		pos[npoints].z = z;
		pos[npoints].key = (char *)malloc((size_t)(1+strlen(keybuffer)));	/* DEC Alpha */
		/*pos[npoints].key = (char *)malloc((size_t)(1+strlen(keybuffer)));*/
		if(pos[npoints].key != NULL) strcpy(pos[npoints].key, keybuffer);
			
#ifdef TRIPLET
#define min(a,b) ((a)<(b)?(a):(b))
#define max(a,b) ((a)>(b)?(a):(b))
#define dist_pos(a,b) hypot(hypot(pos[a].x-pos[b].x, pos[a].y-pos[b].y),pos[a].z-pos[b].z)
		{register int j,k;
		for(j=0; j<npoints;j++) for(k=0;k<j;k++)  {
			float dij, djk, dki;
			float d1, d2, d3;
			dij = dist_pos(npoints,j);
			djk = dist_pos(j,k);
			dki = dist_pos(npoints,k);
			/* sort increasing - is there an easier way? mp */
			d1 = min(dij,min(djk,dki)); /* min */
			d2 = min(max(dij,djk), max(djk,dki)); /* middle */
			d3 = max(dij,max(djk,dki)); /* max */
			if(dflag)printf("%.4f %.4f %.4f", d1, d2, d3);
#define out1(i) printf(" %g %g %g", pos[i].x, pos[i].y, pos[i].z)
			out1(k);
			out1(j);
			out1(npoints);
			if(kflag) printf(" %s %s %s",
			  pos[k].key, pos[j].key, pos[npoints].key);
			printf("\n");
			}/*for j=0 to npoints*/
		npoints++;/*now do whole loop again for one more point*/
		continue;
		}/*register j,k*/
#endif /* TRIPLET */
		/* search for points within 'd' of this one */
		point_ptr = pos;
		for( p= 0; p<npoints; p++ ) {
			dx = x- point_ptr->x;
			dy = y- point_ptr->y;
 		w=pos[npoints].key+16;

			if( (dx<dist|| dx> -dist) && (dy<dist|| dy> -dist) 
			 && (d=hypot( z- point_ptr->z, hypot(dx,dy)))<dist &&
			 (strncmp("H",point_ptr->key+16,1)||strncmp("H",pos[npoints].key+16,1))) {
				/* accept */
				if(nflag) printf("%d %d",p+1,npoints+1); /* 1-origin */
				else
				out(point_ptr->x,point_ptr->y, point_ptr->z,
				 x,y,z);
				if(kflag) printf(" %s %s", point_ptr->key, pos[npoints].key);
				if(dflag) printf(" %g", d);
				printf("\n");
				nmatches++;
				if(hflag&& d <= HDIST) break;
				}
			point_ptr++;
/*printf("\n");*/
			}
		/* if no matches, emit the point as a point */
		/* ?? what is right? mp  if(nmatches==0) out(x,y,z,x,y,z); */
		npoints++;
	}/*while fgets*/

	if(kflag) for(p=0;p<npoints;p++) free(pos[p].key);
}/*do_dist*/

out(x1,y1,z1, x2, y2, z2)
float x1,y1,z1,x2,y2,z2;
{
#define map(a) (a)
	printf("%g %g %g %g %g %g",
	map(x1), map(y1), map(z1),
	map(x2), map(y2), map(z2));
}/*out*/

usage()
{
	fprintf(stderr,"%s: usage:  %s [-r radius (%g)] [-k] [-n] [-h]\n",
	 pgmname, pgmname, DEFAULTDIST);
}/*usage*/