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https://bitbucket.org/cosmicvoids/vide_public.git
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now includes automatic detection and handling of periodic boxes; all logic for dealing with this moved to pruneVoids
This commit is contained in:
P.M. Sutter
parent
390fb2f4e2
commit
292afacaf5
3 changed files with 87 additions and 47 deletions
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@ -39,7 +39,7 @@ typedef struct voidZoneStruct {
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typedef struct voidStruct {
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float vol, coreDens, zoneVol, densCon, voidProb, radius;
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int voidID, numPart, numZones, coreParticle, zoneNumPart;
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float maxRadius, nearestMock, centralDen, redshift;
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float maxRadius, nearestMock, centralDen, redshift, redshiftInMpc;
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float center[3], barycenter[3];
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int accepted;
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} VOID;
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@ -89,16 +89,34 @@ int main(int argc, char **argv) {
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double ranges[2][3], boxLen[3], mul;
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double volNorm, radius;
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int clock1, clock2;
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int periodicX=0, periodicY=0, periodicZ=0;
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numVoids = args_info.numVoids_arg;
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mockIndex = args_info.mockIndex_arg;
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tolerance = args_info.tolerance_arg;
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clock1 = clock();
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printf("Pruning parameters: %f %f %f\n", args_info.zMin_arg,
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args_info.zMax_arg,
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args_info.rMin_arg);
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printf("Pruning parameters: %f %f %f %s\n", args_info.zMin_arg,
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args_info.zMax_arg,
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args_info.rMin_arg,
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args_info.periodic_arg);
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// check for periodic box
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if (!args_info.isObservation_flag) {
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if ( strchr(args_info.periodic_arg, 'x') != NULL) {
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periodicX = 1;
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printf("Will assume x-direction is periodic.\n");
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}
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if ( strchr(args_info.periodic_arg, 'y') != NULL) {
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periodicY = 1;
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printf("Will assume y-direction is periodic.\n");
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}
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if ( strchr(args_info.periodic_arg, 'z') != NULL) {
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periodicZ = 1;
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printf("Will assume z-direction is periodic.\n");
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}
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}
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// load box size
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printf("\n Getting info...\n");
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NcFile f_info(args_info.extraInfo_arg);
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@ -291,17 +309,14 @@ int main(int argc, char **argv) {
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voids[iVoid].barycenter[1] = 0.;
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voids[iVoid].barycenter[2] = 0.;
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// TODO handle periodic boundaries?
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for (p = 0; p < voids[iVoid].numPart; p++) {
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dist[0] = voidPart[p].x - voids[iVoid].center[0];
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dist[1] = voidPart[p].y - voids[iVoid].center[1];
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dist[2] = voidPart[p].z - voids[iVoid].center[2];
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//if (!args_info.isObservation_flag) {
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// dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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// dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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// dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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//}
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if (periodicX) dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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if (periodicY) dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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if (periodicZ) dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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voids[iVoid].barycenter[0] += voidPart[p].vol*(dist[0]);
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voids[iVoid].barycenter[1] += voidPart[p].vol*(dist[1]);
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@ -324,11 +339,9 @@ int main(int argc, char **argv) {
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dist[1] = voidPart[p].y - voids[iVoid].barycenter[1];
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dist[2] = voidPart[p].z - voids[iVoid].barycenter[2];
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//if (!args_info.isObservation_flag) {
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// dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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// dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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// dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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//}
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if (periodicX) dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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if (periodicY) dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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if (periodicZ) dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 < centralRad) centralDen += 1;
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@ -336,21 +349,21 @@ int main(int argc, char **argv) {
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voids[iVoid].centralDen = centralDen / (4./3. * M_PI * pow(centralRad, 3./2.));
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// compute maximum extent
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if (args_info.isObservation_flag) {
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maxDist = 0.;
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for (p = 0; p < voids[iVoid].numPart; p++) {
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for (p2 = p; p2 < voids[iVoid].numPart; p2++) {
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//if (args_info.isObservation_flag) {
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// maxDist = 0.;
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// for (p = 0; p < voids[iVoid].numPart; p++) {
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// for (p2 = p; p2 < voids[iVoid].numPart; p2++) {
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dist[0] = voidPart[p].x - voidPart[p2].x;
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dist[1] = voidPart[p].y - voidPart[p2].y;
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dist[2] = voidPart[p].z - voidPart[p2].z;
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// dist[0] = voidPart[p].x - voidPart[p2].x;
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// dist[1] = voidPart[p].y - voidPart[p2].y;
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// dist[2] = voidPart[p].z - voidPart[p2].z;
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 > maxDist) maxDist = dist2;
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}
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}
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voids[iVoid].maxRadius = sqrt(maxDist)/2.;
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} else {
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// dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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// if (dist2 > maxDist) maxDist = dist2;
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// }
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// }
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// voids[iVoid].maxRadius = sqrt(maxDist)/2.;
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// } else {
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maxDist = 0.;
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for (p = 0; p < voids[iVoid].numPart; p++) {
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@ -358,11 +371,15 @@ int main(int argc, char **argv) {
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dist[0] = voidPart[p].y - voids[iVoid].barycenter[1];
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dist[0] = voidPart[p].z - voids[iVoid].barycenter[2];
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if (periodicX) dist[0] = fmin(dist[0], abs(boxLen[0]-dist[0]));
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if (periodicY) dist[1] = fmin(dist[1], abs(boxLen[1]-dist[1]));
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if (periodicZ) dist[2] = fmin(dist[2], abs(boxLen[2]-dist[2]));
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dist2 = pow(dist[0],2) + pow(dist[1],2) + pow(dist[2],2);
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if (dist2 > maxDist) maxDist = dist2;
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}
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voids[iVoid].maxRadius = sqrt(maxDist);
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}
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// }
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if (args_info.isObservation_flag) {
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// compute distance from center to nearest mock
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@ -382,28 +399,41 @@ int main(int argc, char **argv) {
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}
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if (args_info.isObservation_flag) {
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voids[iVoid].redshift =
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voids[iVoid].redshiftInMpc =
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sqrt(pow(voids[iVoid].barycenter[0] - boxLen[0]/2.,2) +
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pow(voids[iVoid].barycenter[1] - boxLen[1]/2.,2) +
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pow(voids[iVoid].barycenter[2] - boxLen[2]/2.,2));
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voids[iVoid].redshift = voids[iVoid].redshift;
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redshift = voids[iVoid].redshift;
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nearestEdge = fmin(fabs(redshift-args_info.zMin_arg*LIGHT_SPEED),
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fabs(redshift-args_info.zMax_arg*LIGHT_SPEED));
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voids[iVoid].redshiftInMpc = voids[iVoid].redshiftInMpc;
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redshift = voids[iVoid].redshiftInMpc;
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nearestEdge = fmin(fabs(redshift-args_info.zMin_arg*LIGHT_SPEED/100.),
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fabs(redshift-args_info.zMax_arg*LIGHT_SPEED/100.));
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voids[iVoid].redshift = voids[iVoid].redshiftInMpc/LIGHT_SPEED*100.;
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} else {
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voids[iVoid].redshiftInMpc = voids[iVoid].barycenter[2];
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voids[iVoid].redshift = voids[iVoid].barycenter[2]/LIGHT_SPEED*100.;
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nearestEdge = 1.e99;
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nearestEdge = fmin(
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fabs(voids[iVoid].barycenter[0] - ranges[0][0]),
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fabs(voids[iVoid].barycenter[0] - ranges[0][1]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[1] - ranges[1][0]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[1] - ranges[1][1]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[2] - ranges[2][0]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[2] - ranges[2][1]));
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if (!periodicX) {
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[0] - ranges[0][0]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[0] - ranges[0][1]));
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}
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if (!periodicY) {
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[1] - ranges[1][0]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[1] - ranges[1][1]));
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}
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if (!periodicZ) {
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[2] - ranges[2][0]));
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nearestEdge = fmin(nearestEdge,
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fabs(voids[iVoid].barycenter[2] - ranges[2][1]));
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}
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}
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if (nearestEdge < voids[iVoid].nearestMock) {
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@ -505,7 +535,7 @@ int main(int argc, char **argv) {
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fprintf(fpSkyPositions, "%.2f %.2f %.5f %.2f %d\n",
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atan((voids[iVoid].barycenter[1]-boxLen[1]/2.)/(voids[iVoid].barycenter[0]-boxLen[0]/2.)) * 180/M_PI + 180,
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asin((voids[iVoid].barycenter[2]-boxLen[2]/2.)/voids[iVoid].redshift) * 180/M_PI,
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asin((voids[iVoid].barycenter[2]-boxLen[2]/2.)/voids[iVoid].redshiftInMpc) * 180/M_PI,
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voids[iVoid].redshift,
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voids[iVoid].radius,
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voids[iVoid].voidID);
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@ -40,6 +40,8 @@ option "outSkyPositions" - "output sky positions of voids" string required
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option "dataPortion" - "all, central, or edge" string required
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option "periodic" - "Set of edges which are periodic" string optional default="xy"
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option "tolerance" - "Fraction of void width to consider edge" double optional default="1.0"
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option "centralRadFrac" - "Fraction of void radii to consider central region" double optional default="4"
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@ -244,11 +244,18 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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totalPart = open(zobovDir+"/total_particles.txt", "r").read()
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maxDen = 0.2*float(mockIndex)/float(totalPart)
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observationLine = " --isObservation"
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periodicLine = "--periodic=''"
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else:
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mockIndex = -1
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maxDen = 0.2
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observationLine = ""
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periodicLine = " --periodic='"
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if sample.numSubvolumes == 1: periodicLine += "xy"
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if sample.zBoundaryMpc[0] == 0 and \
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sample.zBoundaryMpc[1] == sample.boxLen : periodicLine += "z"
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periodicLine += "' "
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if not (continueRun and jobSuccessful(logFile, "NetCDF: Not a valid ID\n")):
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cmd = binPath
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cmd += " --partFile=" + zobovDir+"/zobov_slice_"+str(sampleName)
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@ -267,6 +274,7 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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cmd += " --rMin=" + str(sample.minVoidRadius)
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cmd += " --numVoids=" + str(numVoids)
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cmd += observationLine
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cmd += periodicLine
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cmd += " --output=" + zobovDir+"/voidDesc_"+\
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str(thisDataPortion)+"_"+\
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str(sampleName)+".out"
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