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568 lines
14 KiB
C
568 lines
14 KiB
C
#include <assert.h>
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/* jovoz.c by Mark Neyrinck */
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#define BIGFLT 1e30 /* Biggest possible floating-point number */
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#define NLINKS 1000 /* Number of possible links with the same rho_sl */
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#define FF fflush(stdout)
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typedef struct Particle {
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float dens;
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int nadj;
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int ncnt;
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int *adj;
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} PARTICLE;
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typedef struct Zone {
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int core; /* Identity of peak particle */
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int np; /* Number of particles in zone */
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int npjoin; /* Number of particles in the joined void */
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int nadj; /* Number of adjacent zones */
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int nhl; /* Number of zones in final joined void */
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float leak; /* Volume of last leak zone*/
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int *adj; /* Each adjacent zone, with ... */
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float *slv; /* Smallest Linking Volume */
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float denscontrast; /* density contrast */
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double vol; /* Total volume of all particles in the zone */
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double voljoin; /* Total volume of all particles in the joined void */
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} ZONE;
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typedef struct ZoneT {
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int nadj; /* Number of zones on border */
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int *adj; /* Each adjacent zone, with ... */
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float *slv; /* Smallest Linking Volume */
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} ZONET;
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void findrtop(double *a, int na, int *iord, int nb);
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int main(int argc,char **argv) {
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FILE *adj, *vol, *zon, *zon2, *txt;
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PARTICLE *p;
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ZONE *z;
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ZONET *zt;
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char *adjfile, *volfile, *zonfile, *zonfile2, *txtfile;
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int i, j,k,l, h, h2,hl,n,np, np2, nzones, nhl, nhlcount, nhl2;
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int *jumper, *jumped, *numinh;
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int *zonenum, *zonelist, *zonelist2;
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int link[NLINKS], link2, nl;
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float lowvol, voltol, prob;
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int q,q2;
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int za, nin;
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int testpart;
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char already, interior, *inyet, *inyet2, added, beaten;
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int *nm, **m;
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float maxvol, minvol;
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double *sorter, e1,maxdenscontrast;
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int *iord;
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e1 = exp(1.)-1.;
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if (argc != 8) {
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printf("Wrong number of arguments.\n");
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printf("arg1: adjacency file\n");
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printf("arg2: volume file\n");
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printf("arg3: output file containing particles in each zone\n");
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printf("arg4: output file containing zones in each void\n");
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printf("arg5: output text file\n");
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printf("arg6: Density threshold (0 for no threshold)\n");
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exit(0);
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}
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adjfile = argv[1];
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volfile = argv[2];
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zonfile = argv[3];
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zonfile2 = argv[4];
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txtfile = argv[5];
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if (sscanf(argv[6],"%f",&voltol) == 0) {
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printf("Bad density threshold.\n");
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exit(0);
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}
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printf("TOLERANCE: %f\n", voltol);
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if (voltol <= 0.) {
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printf("Proceeding without a density threshold.\n");
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voltol = 1e30;
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}
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adj = fopen(adjfile, "r");
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if (adj == NULL) {
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printf("Unable to open %s\n",adjfile);
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exit(0);
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}
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fread(&np,1, sizeof(int),adj);
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printf("adj: %d particles\n", np);
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FF;
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p = (PARTICLE *)malloc(np*sizeof(PARTICLE));
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/* Adjacencies*/
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for (i=0;i<np;i++) {
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fread(&p[i].nadj,1,sizeof(pid_t),adj);
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/* The number of adjacencies per particle */
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if (p[i].nadj > 0)
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p[i].adj = (pid_t *)malloc(p[i].nadj*sizeof(pid_t));
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else p[i].adj = 0;
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p[i].ncnt = 0; /* Temporarily, it's an adj counter */
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}
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for (i=0;i<np;i++) {
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fread(&nin,1,sizeof(pid_t),adj);
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if (nin > 0)
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for (k=0;k<nin;k++) {
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fread(&j,1,sizeof(pid_t),adj);
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if (j < np) {
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/* Set both halves of the pair */
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assert(i < j);
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if (p[i].ncnt == p[i].nadj)
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{
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int q;
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printf("OVERFLOW for particle %d (pending %d). List of accepted:\n", i, j);
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for (q=0;q<p[i].nadj;q++)
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printf(" %d\n", p[i].adj[q]);
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//abort();
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}
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if (p[j].ncnt == p[j].nadj)
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{
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int q;
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printf("OVERFLOW for particle %d (pending %d). List of accepted:\n", j, i);
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for (q=0;q<p[j].nadj;q++)
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printf(" %d\n", p[j].adj[q]);
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//abort();
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}
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p[i].adj[p[i].ncnt] = j;
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p[j].adj[p[j].ncnt] = i;
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p[i].ncnt++; p[j].ncnt++;
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} else {
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printf("%d: adj = %d\n",i,j);
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}
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}
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}
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fclose(adj);
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/* Check that we got all the pairs */
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/* adj = fopen(adjfile, "r");
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fread(&np,1, sizeof(int),adj);*/
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for (i=0;i<np;i++) {
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/* fread(&nin,1,sizeof(int),adj); /* actually nadj */
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// PMS
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if (p[i].ncnt != p[i].nadj && i < np) {
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/*if (p[i].ncnt != p[i].nadj) {*/
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// END PMS
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p[i].nadj = p[i].ncnt;
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printf("jovoz: We didn't get all of %d's adj's; %d != %d.\n",i,nin,p[i].nadj);
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/*exit(0);*/
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}
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}
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// fclose(adj);
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/* Volumes */
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vol = fopen(volfile, "r");
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if (vol == NULL) {
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printf("Unable to open volume file %s.\n\n",volfile);
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exit(0);
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}
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fread(&np2,1, sizeof(int),adj);
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if (np != np2) {
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printf("Number of particles doesn't match! %d != %d\n",np,np2);
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exit(0);
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}
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printf("%d particles\n", np);
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FF;
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for (i=0;i<np;i++) {
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fread(&p[i].dens,1,sizeof(float),vol);
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if ((p[i].dens < 1e-30) || (p[i].dens > 1e30)) {
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printf("Whacked-out volume found, of particle %d: %f\n",i,p[i].dens);
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p[i].dens = 1.;
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}
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p[i].dens = 1./p[i].dens; /* Get density from volume */
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}
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fclose(vol);
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jumped = (pid_t *)malloc(np*sizeof(pid_t));
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jumper = (pid_t *)malloc(np*sizeof(pid_t));
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numinh = (pid_t *)malloc(np*sizeof(pid_t));
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/* find jumper */
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for (i = 0; i < np; i++) {
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minvol = p[i].dens; jumper[i] = -1;
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for (j=0; j< p[i].nadj; j++) {
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if (p[p[i].adj[j]].dens < minvol) {
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jumper[i] = p[i].adj[j];
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minvol = p[jumper[i]].dens;
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}
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}
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numinh[i] = 0;
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}
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printf("About to jump ...\n"); FF;
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/* Jump */
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for (i = 0; i < np; i++) {
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jumped[i] = i;
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while (jumper[jumped[i]] > -1)
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jumped[i] = jumper[jumped[i]];
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numinh[jumped[i]]++;
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}
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printf("Post-jump ...\n"); FF;
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nzones = 0;
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for (i = 0; i < np; i++)
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if (numinh[i] > 0) nzones++;
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printf("%d initial zones found\n", nzones);
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z = (ZONE *)malloc(nzones*sizeof(ZONE));
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if (z == NULL) {
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printf("Unable to allocate z\n");
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exit(0);
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}
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zt = (ZONET *)malloc(nzones*sizeof(ZONET));
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if (zt == NULL) {
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printf("Unable to allocate zt\n");
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exit(0);
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}
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zonenum = (int *)malloc(np*sizeof(int));
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if (zonenum == NULL) {
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printf("Unable to allocate zonenum\n");
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exit(0);
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}
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h = 0;
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for (i = 0; i < np; i++)
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if (numinh[i] > 0) {
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z[h].core = i;
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zonenum[i] = h;
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h++;
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} else {
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zonenum[i] = -1;
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}
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/* Count border particles */
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for (i = 0; i < np; i++)
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for (j = 0; j < p[i].nadj; j++) {
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testpart = p[i].adj[j];
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if (jumped[i] != jumped[testpart])
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zt[zonenum[jumped[i]]].nadj++;
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}
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for (h=0;h<nzones;h++) {
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zt[h].adj = (pid_t *)malloc(zt[h].nadj*sizeof(pid_t));
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if (zt[h].adj == NULL) {
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printf("Unable to allocate %d adj's of zone %d\n",zt[h].nadj,h);
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exit(0);
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}
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zt[h].slv = (float *)malloc(zt[h].nadj*sizeof(float));
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if (zt[h].slv == NULL) {
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printf("Unable to allocate %d slv's of zone %d\n",zt[h].nadj,h);
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exit(0);
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}
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zt[h].nadj = 0;
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}
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/* Find "weakest links" */
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for (i = 0; i < np; i++) {
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h = zonenum[jumped[i]];
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for (j = 0; j < p[i].nadj; j++) {
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testpart = p[i].adj[j];
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if (h != zonenum[jumped[testpart]]) {
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if (p[testpart].dens > p[i].dens) {
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/* there could be a weakest link through testpart */
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already = 0;
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for (za = 0; za < zt[h].nadj; za++)
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if (zt[h].adj[za] == zonenum[jumped[testpart]]) {
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already = 1;
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if (p[testpart].dens < zt[h].slv[za]) {
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zt[h].slv[za] = p[testpart].dens;
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}
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}
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if (already == 0) {
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zt[h].adj[zt[h].nadj] = zonenum[jumped[testpart]];
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zt[h].slv[zt[h].nadj] = p[testpart].dens;
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zt[h].nadj++;
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}
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} else { /* There could be a weakest link through i */
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already = 0;
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for (za = 0; za < zt[h].nadj; za++)
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if (zt[h].adj[za] == zonenum[jumped[testpart]]) {
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already = 1;
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if (p[i].dens < zt[h].slv[za]) {
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zt[h].slv[za] = p[i].dens;
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}
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}
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if (already == 0) {
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zt[h].adj[zt[h].nadj] = zonenum[jumped[testpart]];
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zt[h].slv[zt[h].nadj] = p[i].dens;
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zt[h].nadj++;
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}
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}
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}
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}
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}
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printf("Found zone adjacencies\n"); FF;
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/* Free particle adjacencies */
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for (i=0;i<np; i++) if (p[i].adj != 0) free(p[i].adj);
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/* Use z instead of zt */
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for (h=0;h<nzones;h++) {
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/*printf("%d ",zt[h].nadj);*/
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z[h].nadj = zt[h].nadj;
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z[h].adj = (pid_t *)malloc(zt[h].nadj*sizeof(pid_t));
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z[h].slv = (float *)malloc(zt[h].nadj*sizeof(float));
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for (za = 0; za<zt[h].nadj; za++) {
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z[h].adj[za] = zt[h].adj[za];
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z[h].slv[za] = zt[h].slv[za];
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}
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free(zt[h].adj);
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free(zt[h].slv);
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z[h].np = numinh[z[h].core];
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}
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free(zt);
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free(numinh);
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m = (pid_t **)malloc(nzones*sizeof(pid_t *));
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/* Not in the zone struct since it'll be freed up (contiguously, we hope)
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soon */
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nm = (pid_t *)malloc(nzones*sizeof(pid_t));
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for (h=0; h<nzones; h++) {
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m[h] = (pid_t *)malloc(z[h].np*sizeof(pid_t));
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nm[h] = 0;
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z[h].vol = 0.;
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}
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for (i=0; i<np; i++) {
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h = zonenum[jumped[i]];
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if (i == z[h].core) {
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m[h][nm[h]] = m[h][0];
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m[h][0] = i; /* Put the core particle at the top of the list */
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} else {
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m[h][nm[h]] = i;
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}
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z[h].vol += 1.0/(double)p[i].dens;
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nm[h] ++;
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}
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free(nm);
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zon = fopen(zonfile,"w");
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if (zon == NULL) {
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printf("Problem opening zonefile %s.\n\n",zonfile);
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exit(0);
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}
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fwrite(&np,1,sizeof(pid_t),zon);
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fwrite(&nzones,1,sizeof(int),zon);
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for (h=0; h<nzones; h++) {
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// PMS
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//printf("%d %d %d", &(z[h].np), m[h], z[h].np);
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// END PMS
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fwrite(&(z[h].np),1,sizeof(pid_t),zon);
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fwrite(m[h],z[h].np,sizeof(pid_t),zon);
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free(m[h]);
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}
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free(m);
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close(zon);
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inyet = (char *)malloc(nzones*sizeof(char));
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inyet2 = (char *)malloc(nzones*sizeof(char));
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zonelist = (int *)malloc(nzones*sizeof(int));
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zonelist2 = (int *)malloc(nzones*sizeof(int));
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sorter = (double *)malloc((nzones+1)*sizeof(double));
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for (h = 0; h< nzones; h++) {
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inyet[h] = 0;
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inyet2[h] = 0;
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}
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nhl = 0;
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maxvol = 0.;
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minvol = BIGFLT;
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maxdenscontrast = 0.;
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for(i=0;i<np; i++){
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if (p[i].dens > maxvol) maxvol = p[i].dens;
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if (p[i].dens < minvol) minvol = p[i].dens;
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}
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printf("Densities range from %e to %e.\n",minvol,maxvol);FF;
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zon2 = fopen(zonfile2,"w");
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if (zon2 == NULL) {
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printf("Problem opening zonefile %s.\n\n",zonfile2);
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exit(0);
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}
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fwrite(&nzones,1,sizeof(int),zon2);
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for (h = 0; h<nzones; h++) {
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nhlcount = 0;
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for (hl = 0; hl < nhl; hl++)
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inyet[zonelist[hl]] = 0;
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zonelist[0] = h;
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inyet[h] = 1;
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nhl = 1;
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z[h].npjoin = z[h].np;
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do {
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/* Find the lowest-volume (highest-density) adjacency */
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lowvol = BIGFLT; nl = 0; beaten = 0;
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for (hl = 0; hl < nhl; hl++) {
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h2 = zonelist[hl];
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if (inyet[h2] == 1) { /* If it's not already identified as
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an interior zone, with inyet=2 */
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interior = 1;
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for (za = 0; za < z[h2].nadj; za ++) {
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if (inyet[z[h2].adj[za]] == 0) {
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interior = 0;
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if (z[h2].slv[za] == lowvol) {
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link[nl] = z[h2].adj[za];
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nl ++;
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if (nl == NLINKS) {
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printf("Too many links with the same rho_sl! Increase NLINKS from %d\n",nl);
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exit(0);
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}
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}
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if (z[h2].slv[za] < lowvol) {
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lowvol = z[h2].slv[za];
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link[0] = z[h2].adj[za];
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nl = 1;
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}
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}
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}
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if (interior == 1) inyet[h2] = 2; /* No bordering exter. zones */
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}
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}
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if (nl == 0) {
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beaten = 1;
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z[h].leak = maxvol;
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continue;
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}
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if (lowvol > voltol) {
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beaten = 1;
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z[h].leak = lowvol;
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continue;
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}
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for (l=0; l < nl; l++)
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if (p[z[link[l]].core].dens < p[z[h].core].dens)
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beaten = 1;
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if (beaten == 1) {
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z[h].leak = lowvol;
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continue;
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}
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/* Add everything linked to the link(s) */
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nhl2 = 0;
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for (l=0; l < nl; l++) {
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if (inyet2[link[l]] == 0) {
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zonelist2[nhl2] = link[l];
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inyet2[link[l]] = 1;
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nhl2 ++;
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added = 1;
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while ((added == 1) && (beaten == 0)) {
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added = 0;
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for (hl = 0; (hl < nhl2) && (beaten == 0); hl++) {
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h2 = zonelist2[hl];
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if (inyet2[h2] == 1) {
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interior = 1; /* Guilty until proven innocent */
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for (za = 0; za < z[h2].nadj; za ++) {
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link2 = z[h2].adj[za];
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if ((inyet[link2]+inyet2[link2]) == 0) {
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interior = 0;
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if (z[h2].slv[za] <= lowvol) {
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if (p[z[link2].core].dens < p[z[h].core].dens) {
|
|
beaten = 1;
|
|
break;
|
|
}
|
|
zonelist2[nhl2] = link2;
|
|
inyet2[link2] = 1;
|
|
nhl2++;
|
|
added = 1;
|
|
}
|
|
}
|
|
}
|
|
if (interior == 1) inyet2[h2] = 2;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
for (hl = 0; hl < nhl2; hl++)
|
|
inyet2[zonelist2[hl]] = 0;
|
|
|
|
/* See if there's a beater */
|
|
if (beaten == 1) {
|
|
z[h].leak = lowvol;
|
|
} else {
|
|
for (h2 = 0; h2 < nhl2; h2++) {
|
|
zonelist[nhl] = zonelist2[h2];
|
|
inyet[zonelist2[h2]] = 1;
|
|
nhl++;
|
|
z[h].npjoin += z[zonelist2[h2]].np;
|
|
}
|
|
}
|
|
if (nhl/10000 > nhlcount) {
|
|
nhlcount = nhl/10000;
|
|
printf(" %d",nhl); FF;
|
|
}
|
|
} while((lowvol < BIGFLT) && (beaten == 0));
|
|
|
|
z[h].denscontrast = z[h].leak/p[z[h].core].dens;
|
|
if (z[h].denscontrast < 1.) z[h].denscontrast = 1.;
|
|
|
|
/* find biggest denscontrast */
|
|
if (z[h].denscontrast > maxdenscontrast) {
|
|
maxdenscontrast = (double)z[h].denscontrast;
|
|
}
|
|
|
|
/* Don't sort; want the core zone to be first */
|
|
|
|
if (nhlcount > 0) { /* Outputs the number of zones in large voids */
|
|
printf(" h%d:%d\n",h,nhl);
|
|
FF;
|
|
}
|
|
/* Calculate volume */
|
|
z[h].voljoin = 0.;
|
|
for (q = 0; q<nhl; q++) {
|
|
z[h].voljoin += z[zonelist[q]].vol;
|
|
}
|
|
|
|
z[h].nhl = nhl;
|
|
|
|
fwrite(&nhl,1,sizeof(int),zon2);
|
|
fwrite(zonelist,nhl,sizeof(int),zon2);
|
|
}
|
|
fclose(zon2);
|
|
|
|
printf("Maxdenscontrast = %f.\n",maxdenscontrast);
|
|
|
|
/* Assign sorter by probability (could use volume instead) */
|
|
for (h=0; h< nzones; h++)
|
|
sorter[h] = (double)z[h].denscontrast;
|
|
|
|
/* Text output file */
|
|
|
|
printf("about to sort ...\n");FF;
|
|
|
|
iord = (int *)malloc(nzones*sizeof(int));
|
|
|
|
findrtop(sorter, nzones, iord, nzones);
|
|
|
|
txt = fopen(txtfile,"w");
|
|
fprintf(txt,"%d particles, %d voids.\n", np, nzones);
|
|
fprintf(txt,"Void# FileVoid# CoreParticle CoreDens ZoneVol Zone#Part Void#Zones VoidVol Void#Part VoidDensContrast VoidProb\n");
|
|
for (h=0; h<nzones; h++) {
|
|
i = iord[h];
|
|
prob = exp(-5.12*(z[i].denscontrast-1.) - 0.8*pow(z[i].denscontrast-1.,2.8));
|
|
// PMS
|
|
if (z[i].np == 1) continue;
|
|
// END PMS
|
|
fprintf(txt,"%d %d %d %e %e %d %d %e %d %f %6.2e\n",
|
|
h+1, i, z[i].core, p[z[i].core].dens, z[i].vol, z[i].np, z[i].nhl, z[i].voljoin, z[i].npjoin, z[i].denscontrast, prob);
|
|
|
|
} /* h+1 to start from 1, not zero */
|
|
fclose(txt);
|
|
|
|
printf("Done!\n");FF;
|
|
return(0);
|
|
}
|