mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
FIXED zobov bug when only using one subdomain; added zobov buffer as tunable parameter
This commit is contained in:
Paul M. Sutter
parent
8730193e71
commit
23d665f7bd
6 changed files with 139 additions and 83 deletions
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@ -17,7 +17,7 @@ int main(int argc, char *argv[]) {
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coordT rtemp[3], *parts;
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coordT deladjs[3*MAXVERVER], points[3*MAXVERVER];
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pointT intpoints[3*MAXVERVER];
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FILE *pos, *out;
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FILE *pos, *out, *testFile;
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char *posfile, outfile[200], *suffix, *outDir;
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PARTADJ *adjs;
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float *vols;
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@ -33,8 +33,11 @@ int main(int argc, char *argv[]) {
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realT c[3];
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int b[3];
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double totalvol;
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int isObs = 0;
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if (argc != 10) {
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printf("Routine: voz1b1\n");
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if (argc != 11) {
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printf("Wrong number of arguments.\n");
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printf("arg1: position file\n");
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printf("arg2: border size\n");
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@ -43,6 +46,7 @@ int main(int argc, char *argv[]) {
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printf("arg5: number of divisions\n");
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printf("arg6-8: b[0-2]\n\n");
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printf("arg9: output directory\n");
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printf("arg10: observation flag\n");
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exit(0);
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}
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posfile = argv[1];
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@ -79,8 +83,15 @@ int main(int argc, char *argv[]) {
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exit(0);
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}
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outDir = argv[9];
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if (sscanf(argv[10],"%d",&isObs) != 1) {
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printf("That's no observation mode; try again.\n");
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exit(0);
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}
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printf("Working with subdomain b=[%d,%d,%d]\n", b[0], b[1], b[2]);
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/* Boxsize should be the range in r, yielding a range 0-1 */
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printf("Reading particle file...\n");
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np = posread(posfile,&r,1./boxsize);
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printf("%d particles\n",np);fflush(stdout);
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@ -90,7 +101,8 @@ int main(int argc, char *argv[]) {
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if (r[i][1]<ymin) ymin = r[i][1]; if (r[i][1]>ymax) ymax = r[i][1];
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if (r[i][2]<zmin) zmin = r[i][2]; if (r[i][2]>zmax) zmax = r[i][2];
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}
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printf("np: %d, x: %f,%f; y: %f,%f; z: %f,%f\n",np,xmin,xmax, ymin,ymax, zmin,zmax); fflush(stdout);
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printf("Full box particle stats: np: %d, x: %f,%f; y: %f,%f; z: %f,%f\n",np,
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xmin,xmax, ymin,ymax, zmin,zmax); fflush(stdout);
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width = 1./(float)numdiv;
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width2 = 0.5*width;
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@ -108,7 +120,7 @@ int main(int argc, char *argv[]) {
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exit(0);
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}
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g = (bf / 2.)*(1. + sqrt(1 - 2.*s*s/(bf*bf)));
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printf("s = %f, bf = %f, g = %f.\n",s,bf,g);
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printf("Guard particle information: s = %f, bf = %f, g = %f.\n",s,bf,g);
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fflush(stdout);
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@ -118,11 +130,10 @@ int main(int argc, char *argv[]) {
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exit(1);
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}
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DL c[d] = ((float)b[d])*width;
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printf("c: %f,%f,%f\n",c[0],c[1],c[2]);
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DL c[d] = ((float)b[d]+0.5)*width;
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printf("Counting particles in subdomain...\n");
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/* Assign temporary array*/
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nvpbuf = 0; /* Number of particles to tesselate, including
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buffer */
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nvpbuf = 0; /* Number of particles to tesselate, includng ibuffer */
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nvp = 0; /* Without the buffer */
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for (i=0; i<np; i++) {
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isitinbuf = 1;
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@ -139,8 +150,7 @@ int main(int argc, char *argv[]) {
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if (isitinmain) nvp++;
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}
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nvpbuf += 6*(NGUARD+1)*(NGUARD+1); /* number of guard
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points */
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nvpbuf += 6*(NGUARD+1)*(NGUARD+1); /* number of guard points */
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parts = (coordT *)malloc(3*nvpbuf*sizeof(coordT));
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orig = (pid_t *)malloc(nvpbuf*sizeof(pid_t));
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@ -156,6 +166,7 @@ int main(int argc, char *argv[]) {
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exit(1);
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}
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printf("Placing particles in subdomain...\n");
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nvp = 0; nvpall = 0; /* nvp = number of particles without buffer */
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xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
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for (i=0; i<np; i++) {
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@ -180,8 +191,13 @@ int main(int argc, char *argv[]) {
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if (rtemp[2] > zmax) zmax = rtemp[2];
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}
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}
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printf("nvp = %d\n",nvp);
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printf("x: %f,%f; y: %f,%f; z:%f,%f\n",xmin,xmax,ymin,ymax,zmin,zmax);
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printf("Subdomain: b=(%d,%d,%d), c=(%f,%f,%f)\n",
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b[0],b[1],b[2],c[0],c[1],c[2]);
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printf(" nvp=%d, nvpbuf=%d\n", nvp,nvpbuf);
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printf(" Particle ranges: x: %f,%f; y: %f,%f; z:%f,%f\n",
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xmin,xmax,ymin,ymax,zmin,zmax);
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printf("Adding particles to buffer regions...\n");
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nvpbuf = nvp;
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for (i=0; i<np; i++) {
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isitinbuf = 1;
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@ -195,9 +211,6 @@ int main(int argc, char *argv[]) {
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isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
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}
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if (isitinbuf && !isitinmain) {
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/*printf("%3.3f ",sqrt(rtemp[0]*rtemp[0] + rtemp[1]*rtemp[1] +
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rtemp[2]*rtemp[2]));
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printf("|%2.2f,%2.2f,%2.2f,%f,%f",r[i][0],r[i][1],r[i][2],width2,totwidth2);*/
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parts[3*nvpbuf] = rtemp[0];
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parts[3*nvpbuf+1] = rtemp[1];
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parts[3*nvpbuf+2] = rtemp[2];
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@ -212,16 +225,19 @@ int main(int argc, char *argv[]) {
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if (rtemp[2] > zmax) zmax = rtemp[2];
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}
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}
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printf("nvpbuf = %d\n",nvpbuf);
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printf("x: %f,%f; y: %f,%f; z:%f,%f\n",xmin,xmax,ymin,ymax,zmin,zmax);
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nvpall = nvpbuf;
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predict = pow(width+2.*bf,3)*(float)np;
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printf("There should be ~ %f points; there are %d\n",predict,nvpbuf);
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printf("Total particles including buffer = %d (predicted ~%f)\n",
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nvpbuf, predict);
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printf(" Particle ranges including buffer: x: %f,%f; y: %f,%f; z:%f,%f\n",
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xmin,xmax,ymin,ymax,zmin,zmax);
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for (i=0;i<np;i++) free(r[i]);
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free(r);
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/* Add guard points */
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printf("Adding guard points to subdomain faces...\n");
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for (i=0; i<NGUARD+1; i++) {
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for (j=0; j<NGUARD+1; j++) {
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/* Bottom */
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@ -262,6 +278,23 @@ int main(int argc, char *argv[]) {
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nvpall++;
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}
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}
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/*
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// TEST TEMP
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testFile = fopen("test.txt", "a");
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for (i=0; i<nvpall; i++){
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int itype = 0;
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if (i > nvp) itype = 1; // it's a buffer particle
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if (i > nvpbuf) itype = 2; // it's a guard particle
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fprintf(testFile, "%f %f %f %d %f %f %f\n", c[0], c[1], c[2],
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itype,
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parts[3*i],
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parts[3*i+1],
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parts[3*i+2]);
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}
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fclose(testFile);
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*/
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xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
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for (i=nvpbuf;i<nvpall;i++) {
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if (parts[3*i] < xmin) xmin = parts[3*i];
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@ -274,7 +307,8 @@ int main(int argc, char *argv[]) {
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printf("Added guard points to total %d points (should be %d)\n",nvpall,
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nvpbuf + 6*(NGUARD+1)*(NGUARD+1));
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printf("x: %f,%f; y: %f,%f; z:%f,%f\n",xmin,xmax,ymin,ymax,zmin,zmax);
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printf("New particle ranges including guards: x: %f,%f; y: %f,%f; z:%f,%f\n",
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xmin,xmax,ymin,ymax,zmin,zmax);
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/* Do tesselation*/
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printf("File read. Tessellating ...\n"); fflush(stdout);
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@ -28,8 +28,11 @@ int main(int argc, char *argv[]) {
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int numGuards;
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int b[3];
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int numThreads;
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int isObs = 0;
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if (argc != 9) {
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printf("Routine: vozinit\n");
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if (argc != 10) {
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printf("Wrong number of arguments.\n");
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printf("arg1: position file\n");
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printf("arg2: buffer size (default 0.1)\n");
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@ -39,6 +42,7 @@ int main(int argc, char *argv[]) {
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printf("arg6: number of parallel threads\n");
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printf("arg7: location of voboz executables\n");
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printf("arg8: output directory\n");
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printf("arg9: observation flag (set to 1 for observation mode)\n");
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exit(0);
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}
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posfile = argv[1];
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@ -70,8 +74,13 @@ int main(int argc, char *argv[]) {
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}
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vobozPath = argv[7];
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outDir = argv[8];
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if (sscanf(argv[9],"%d",&isObs) != 1) {
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printf("That's no observation mode; try again.\n");
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exit(0);
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}
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/* Read the position file */
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printf("Reading particle file and calculating box sizes...\n");
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np = posread(posfile,&rfloat,1./boxsize);
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/* Boxsize should be the range in r, yielding a range 0-1 */
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@ -96,61 +105,67 @@ int main(int argc, char *argv[]) {
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printf("s = %f, bf = %f, g = %f.\n",s,bf,g);
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nvpmax = 0; nvpbufmax = 0; nvpmin = np; nvpbufmin = np;
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// count particles in each sub-domain
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printf("Counting particles in each subdomain...\n");
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for (b[0] = 0; b[0] < numdiv; b[0]++) {
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c[0] = ((float)b[0]+0.5)*width;
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for (b[1] = 0; b[1] < numdiv; b[1]++) {
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c[0] = ((float)b[0]+0.5)*width;
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for (b[1] = 0; b[1] < numdiv; b[1]++) {
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c[1] = ((float)b[1]+0.5)*width;
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for (b[2] = 0; b[2] < numdiv; b[2]++) {
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c[2] = ((float)b[2]+0.5)*width;
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for (b[2] = 0; b[2] < numdiv; b[2]++) {
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c[2] = ((float)b[2]+0.5)*width;
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nvp = 0; /* Number of particles excluding buffer */
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nvpbuf = 0; /* Number of particles to tesselate, including
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buffer */
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xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
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for (i=0; i<np; i++) {
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isitinbuf = 1; isitinmain = 1;
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for (d=0; d<3; d++) {
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rtemp[d] = rfloat[i][d] - c[d];
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if (rtemp[d] > 0.5) rtemp[d] --;
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if (rtemp[d] < -0.5) rtemp[d] ++;
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isitinbuf = isitinbuf && (fabs(rtemp[d]) < totwidth2);
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isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
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}
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if (isitinbuf) {
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nvpbuf++;
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}
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if (isitinmain) {
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nvp++;
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if (rtemp[0] < xmin) xmin = rtemp[0];
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if (rtemp[0] > xmax) xmax = rtemp[0];
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if (rtemp[1] < ymin) ymin = rtemp[1];
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if (rtemp[1] > ymax) ymax = rtemp[1];
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if (rtemp[2] < zmin) zmin = rtemp[2];
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if (rtemp[2] > zmax) zmax = rtemp[2];
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}
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}
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if (nvp > nvpmax) nvpmax = nvp;
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if (nvpbuf > nvpbufmax) nvpbufmax = nvpbuf;
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if (nvp < nvpmin) nvpmin = nvp;
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if (nvpbuf < nvpbufmin) nvpbufmin = nvpbuf;
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printf("b=(%d,%d,%d), c=(%f,%f,%f), nvp=%d, nvpbuf=%d\n",
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b[0],b[1],b[2],c[0],c[1],c[2],nvp,nvpbuf);
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nvp = 0; /* Number of particles excluding buffer */
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nvpbuf = 0; /* Number of particles to tesselate, including buffer */
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xmin = BF; xmax = -BF; ymin = BF; ymax = -BF; zmin = BF; zmax = -BF;
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for (i=0; i<np; i++) {
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isitinbuf = 1; isitinmain = 1;
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for (d=0; d<3; d++) {
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rtemp[d] = rfloat[i][d] - c[d];
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//if (isObs == 0) {
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if (rtemp[d] > 0.5) rtemp[d] --;
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if (rtemp[d] < -0.5) rtemp[d] ++;
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//}
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isitinbuf = isitinbuf && (fabs(rtemp[d]) < totwidth2);
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isitinmain = isitinmain && (fabs(rtemp[d]) <= width2);
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}
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if (isitinbuf) { nvpbuf++; }
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if (isitinmain) {
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nvp++;
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if (rtemp[0] < xmin) xmin = rtemp[0];
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if (rtemp[0] > xmax) xmax = rtemp[0];
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if (rtemp[1] < ymin) ymin = rtemp[1];
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if (rtemp[1] > ymax) ymax = rtemp[1];
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if (rtemp[2] < zmin) zmin = rtemp[2];
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if (rtemp[2] > zmax) zmax = rtemp[2];
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}
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}
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}
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if (nvp > nvpmax) nvpmax = nvp;
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if (nvpbuf > nvpbufmax) nvpbufmax = nvpbuf;
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if (nvp < nvpmin) nvpmin = nvp;
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if (nvpbuf < nvpbufmin) nvpbufmin = nvpbuf;
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printf("Subdomain: b=(%d,%d,%d), c=(%f,%f,%f)\n",
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b[0],b[1],b[2],c[0],c[1],c[2]);
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printf(" nvp=%d, nvpbuf=%d\n", nvp,nvpbuf);
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printf(" Particle ranges: x: %f,%f; y: %f,%f; z:%f,%f\n",
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xmin,xmax,ymin,ymax,zmin,zmax);
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}
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}
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}
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printf("Nvp range: %d,%d\n",nvpmin,nvpmax);
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printf("Nvpbuf range: %d,%d\n",nvpbufmin,nvpbufmax);
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numGuards = 6*(NGUARD+1)*(NGUARD+1);
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printf("Num guards = %d\n", numGuards);
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printf("Total max particles: %d\n" , nvpbufmax+numGuards);
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if (nvpbufmax+numGuards >= QHULL_MAX_PARTICLES)
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{
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if (nvpbufmax+numGuards >= QHULL_MAX_PARTICLES) {
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printf("Too many particles to tesselate per division (Qhull will overflow). Increase divisions or reduce buffer size.\n");
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fflush(stdout);
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exit(1);
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}
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}
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/* Output script file */
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sprintf(scrfile,"scr%s",suffix);
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@ -164,23 +179,19 @@ int main(int argc, char *argv[]) {
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fprintf(scr,"#!/bin/bash -f\n");
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p = 0;
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for (b[0]=0;b[0]<numdiv; b[0]++) {
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for (b[1] = 0; b[1] < numdiv; b[1]++) {
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for (b[2] = 0; b[2] < numdiv; b[2]++) {
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//fprintf(scr,"%s/../c_tools/zobov2/voz1b1/voz1b1_2 %s %f %f %f %f %s %d %d %d %d %d %d %s&\n",
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// vobozPath,
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// posfile,border,boxsize,boxsize,boxsize,suffix,numdiv,numdiv, numdiv,b[0],b[1],b[2],
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// outDir);
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fprintf(scr,"%s/voz1b1 %s %f %f %s %d %d %d %d %s&\n",
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for (b[1] = 0; b[1] < numdiv; b[1]++) {
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for (b[2] = 0; b[2] < numdiv; b[2]++) {
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fprintf(scr,"%s/voz1b1 %s %f %f %s %d %d %d %d %s %d\n",
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vobozPath,
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posfile,border,boxsize,suffix,numdiv,b[0],b[1],b[2],
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outDir);
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outDir, isObs);
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p++;
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if ((p == numThreads)) { fprintf(scr, "wait\n"); p = 0; }
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}
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}
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}
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}
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}
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fprintf(scr,"wait\n");
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fprintf(scr,"%s/voztie %d %s %s %d\n", vobozPath, numdiv,suffix, outDir);
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fprintf(scr,"%s/voztie %d %s %s %d\n", vobozPath, numdiv,suffix, outDir, isObs);
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fclose(scr);
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sprintf(systemstr,"chmod u+x %s",scrfile);
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@ -33,13 +33,14 @@ int main(int argc, char *argv[]) {
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double avgnadj, avgvol;
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int numRemoved = 0;
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int isObs = 0;
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||||
if (argc != 5) {
|
||||
printf("Wrong number of arguments.\n");
|
||||
printf("Voztie: Wrong number of arguments.\n");
|
||||
printf("arg1: number of divisions (default 2)\n");
|
||||
printf("arg2: suffix describing this run\n");
|
||||
printf("arg3: file directory\n");
|
||||
printf("arg4: Beginning index of mock particles\n\n");
|
||||
printf("arg5: observation flag\n");
|
||||
exit(0);
|
||||
}
|
||||
if (sscanf(argv[1],"%d",&numdiv) != 1) {
|
||||
|
|
@ -53,6 +54,11 @@ int main(int argc, char *argv[]) {
|
|||
|
||||
suffix = argv[2];
|
||||
outDir = argv[3];
|
||||
|
||||
if (sscanf(argv[4],"%d",&isObs) != 1) {
|
||||
printf("That's no observation flag; try again.\n");
|
||||
exit(0);
|
||||
}
|
||||
|
||||
np = -1; nvpmax = -1; nvpsum = 0;
|
||||
|
||||
|
|
@ -204,7 +210,7 @@ int main(int argc, char *argv[]) {
|
|||
|
||||
npnotdone = 0; avgnadj = 0.; avgvol = 0.;
|
||||
for (p=0;p<np;p++) {
|
||||
// PMS
|
||||
// PMS - TOTO KEEP THIS HERE???
|
||||
if (vols[p] == 1.e-29) continue;
|
||||
// END PMS
|
||||
if (vols[p] == -1.) npnotdone++;
|
||||
|
|
|
|||
|
|
@ -353,6 +353,7 @@ def launchPrep(sample, binPath, workDir=None, inputDataDir=None,
|
|||
# -----------------------------------------------------------------------------
|
||||
def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
|
||||
numZobovDivisions=None, numZobovThreads=None,
|
||||
zobovBuffer=0.1,
|
||||
mergingThreshold=0.2):
|
||||
|
||||
startTime = time.time()
|
||||
|
|
@ -382,9 +383,14 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
|
|||
if os.access(outputDir+"/voidDesc_"+sampleName+".out", os.F_OK):
|
||||
os.unlink(outputDir+"/voidDesc_"+sampleName+".out")
|
||||
|
||||
cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \
|
||||
isObs = 0
|
||||
if sample.dataType == "observation":
|
||||
isObs = 1
|
||||
|
||||
cmd = [binPath+"/vozinit", datafile, str(zobovBuffer), \
|
||||
"1.0", str(numZobovDivisions), \
|
||||
"_"+sampleName, str(numZobovThreads), \
|
||||
binPath, outputDir]
|
||||
binPath, outputDir, str(isObs)]
|
||||
log = open(logFile, 'w')
|
||||
subprocess.call(cmd, stdout=log, stderr=log)
|
||||
log.close()
|
||||
|
|
|
|||
|
|
@ -101,6 +101,7 @@ for sample in dataSampleList:
|
|||
launchZobov(sample, ZOBOV_PATH, outputDir=outputDir, logDir=logDir,
|
||||
continueRun=continueRun, numZobovDivisions=numZobovDivisions,
|
||||
numZobovThreads=numZobovThreads,
|
||||
zobovBuffer=zobovBuffer,
|
||||
mergingThreshold=mergingThreshold)
|
||||
|
||||
# -------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -258,9 +258,7 @@ def loadVoidCatalog(sampleDir,
|
|||
# clearNearBoundaries: remove voids where the maximum extent is
|
||||
# greater than the distance to nearest edge
|
||||
# maxHighCentralDen: if != -1, filters based on based on central density
|
||||
|
||||
# NOTE: we are moving away from the cumbersome void catalog outputs of
|
||||
# older versions, and will eventually just output a single catalog.
|
||||
#
|
||||
# To replicate the old "central" catalog, choose:
|
||||
# clearEdges = True
|
||||
# clearTree = True
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue