diff --git a/c_tools/CMakeLists.txt b/c_tools/CMakeLists.txt
index 9247018..a1f620e 100644
--- a/c_tools/CMakeLists.txt
+++ b/c_tools/CMakeLists.txt
@@ -45,4 +45,4 @@ add_genopt(computeAverageDistortion_SRCS computeAverageDistortion.ggo computeAve
 #add_executable(computeAverageDistortion ${computeAverageDistortion_SRCS})
 #target_link_libraries(computeAverageDistortion ${ZOB_LIBS})
 
-subdirs(libzobov mock  stacking analysis zobov2 hod)
+subdirs(libzobov mock  stacking)
diff --git a/c_tools/analysis/CMakeLists.txt b/c_tools/analysis/CMakeLists.txt
deleted file mode 100644
index 202b97f..0000000
--- a/c_tools/analysis/CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
-
-SET(voidOverlap_SRCS voidOverlap.cpp)
-add_genopt(voidOverlap_SRCS voidOverlap.ggo voidOverlap_conf STRUCTNAME voidOverlap_info)
-add_executable(voidOverlap ${voidOverlap_SRCS})
-target_link_libraries(voidOverlap  ${ZOB_LIBS})
-
-install(TARGETS voidOverlap DESTINATION ${VIDE_BIN})
diff --git a/c_tools/analysis/voidOverlap.cpp b/c_tools/analysis/voidOverlap.cpp
deleted file mode 100644
index 9e51598..0000000
--- a/c_tools/analysis/voidOverlap.cpp
+++ /dev/null
@@ -1,825 +0,0 @@
-/*+
-    VIDE -- Void IDentification and Examination -- ./c_tools/analysis/voidOverlap.cpp
-    Copyright (C) 2010-2014 Guilhem Lavaux
-    Copyright (C) 2011-2014 P. M. Sutter
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; version 2 of the License.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-+*/
-
-
-
-// =============================================================================
-//
-//   Program: voidOverlap
-//
-//   Description: Takes two void catalogs and reports the "overlap" between
-//                them.
-//
-// ============================================================================
-
-
-#include "string.h"
-#include "ctype.h"
-#include "stdlib.h"
-#include <stdio.h>
-#include <math.h>
-#include "voidOverlap_conf.h"
-#include <vector>
-#include <netcdf>
-#include <iostream>
-#include <sstream>
-#include <fstream>
-
-using namespace std;
-
-typedef struct partStruct {
-  float x, y, z, volume;
-  float ra, dec, redshift;
-  long uniqueID;
-} PART;
-
-typedef struct zoneStruct {
-  int numPart;
-  int *partIDs;
-} ZONE2PART;
-
-typedef struct voidZoneStruct {
-  int numZones;
-  int *zoneIDs;
-} VOID2ZONE;
-
-typedef struct matchProps {
-  int matchID;
-  float commonVolOrig, commonVolProg;
-  float dist;
-  float merit;
-} MATCHPROPS;
-
-typedef struct voidStruct {
-  float vol, coreDens, zoneVol, densCon, voidProb, radius;
-  int voidID, numPart, numZones, coreParticle, zoneNumPart;
-  float maxRadius, nearestMock, centralDen, redshift, redshiftInMpc;
-  float nearestEdge;
-  float macrocenter[3];
-  float ellipticity;
-  float eigv1[3], eigv2[3], eigv3[3], eig[3];
-  std::vector<MATCHPROPS> matches;
-  int numMatches;
-  int numBigMatches;
-  float radiusMpc;
-} VOID;
-
-typedef struct catalog {
-  int numVoids, numPartTot, numZonesTot;
-  float boxLen[3];
-  std::vector<PART> part;
-  std::vector<ZONE2PART> zones2Parts;
-  std::vector<VOID2ZONE> void2Zones;
-  std::vector<VOID> voids;
-} CATALOG;
-
-void loadCatalog(const char *partFile, const char *volFile, 
-                 const char *voidFile, const char *zoneFile,
-                 const char *infoFile, const char *centerFile,
-                 const char *shapeFile,
-                 const char *zonePartFile, CATALOG& catalog,
-                 bool isObservation);
-
-float getDist(CATALOG& catalog1, CATALOG& catalog2, int& iVoid1, int& iVoid2,
-               bool periodicX, bool periodicY, bool operiodicZ);
-
-void sortMatches(std::vector<MATCHPROPS>& matches, 
-                 CATALOG& catalog2, int mode);
-
-// ----------------------------------------------------------------------------
-
-int main(int argc, char **argv) {
-
-  int p1, p2, iZ1, iZ2, iVoid1, iVoid2, iVoid, zoneID1, zoneID2, iMatch;
-  int partID1, partID2;
-  int voidID1, voidID2;
-  bool periodicX=false, periodicY=false, periodicZ=false, match;
-  float dist[3], rdist, r1, r2;
-  FILE *fp;
-  int closestMatchID;
-  float closestMatchDist;
-  float commonVolRatio;
-  MATCHPROPS newMatch;
-  int MAX_MATCHES = 300;
-  float matchDist = 0.25;
-  bool alreadyMatched;
-  int clock1, clock2;
-
-  CATALOG catalog1, catalog2;
-
-  // initialize arguments
-  voidOverlap_info args;
-  voidOverlap_conf_params params;
-
-  voidOverlap_conf_init(&args);
-  voidOverlap_conf_params_init(&params);
-
-  params.check_required = 0;
-  if (voidOverlap_conf_ext (argc, argv, &args, &params))
-    return 1;
-
-  if (!args.configFile_given) {
-    if (voidOverlap_conf_required (&args, VOIDOVERLAP_CONF_PACKAGE))
-      return 1;
-  } else {
-    params.check_required = 1;
-    params.initialize = 0;
-    if (voidOverlap_conf_config_file (args.configFile_arg, &args, &params))
-    return 1;
-  }
-
-  matchDist = args.overlapFrac_arg;
-
-  loadCatalog(args.partFile1_arg, args.volFile1_arg, args.voidFile1_arg,
-              args.zoneFile1_arg, args.infoFile1_arg, args.centerFile1_arg,
-              args.shapeFile1_arg,
-              args.zonePartFile1_arg, catalog1, args.isObservation_flag);
-
-  loadCatalog(args.partFile2_arg, args.volFile2_arg, args.voidFile2_arg,
-              args.zoneFile2_arg, args.infoFile2_arg, args.centerFile2_arg,
-              args.shapeFile2_arg,
-              args.zonePartFile2_arg, catalog2, args.isObservation_flag);
-
-  // check for periodic box
-    if ( strchr(args.periodic_arg, 'x') != NULL) {
-      periodicX = true;
-      printf("Will assume x-direction is periodic.\n");
-    }
-    if ( strchr(args.periodic_arg, 'y') != NULL) {
-      periodicY = true;
-      printf("Will assume y-direction is periodic.\n");
-    }
-    if ( strchr(args.periodic_arg, 'z') != NULL) {
-      periodicZ = true;
-      printf("Will assume z-direction is periodic.\n");
-    }
-
-  // find closest voids
-  printf(" Finding nearest matches...\n");
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    printf("  Matching for void %d of %d...", iVoid1, catalog1.numVoids);
-    fflush(stdout);
-    clock1 = clock();
-    for (iVoid2 = 0; iVoid2 < catalog2.numVoids; iVoid2++) {
-      rdist = getDist(catalog1, catalog2, iVoid1, iVoid2, 
-                      periodicX, periodicY, periodicZ);
-
-      newMatch.matchID = iVoid2;
-      newMatch.commonVolOrig = 0;
-      newMatch.commonVolProg = 0;
-      newMatch.dist = rdist; 
-
-      //if (rdist > 1.5) continue;
-      if (rdist/catalog1.voids[iVoid1].radius > 1.5) continue;
-
-      // see if center is contained in void
-      match = false;
-      voidID1 = catalog1.voids[iVoid1].voidID;
-      for (iZ1 = 0; iZ1 < catalog1.void2Zones[voidID1].numZones; iZ1++) {
-        zoneID1 = catalog1.void2Zones[voidID1].zoneIDs[iZ1];
-        for (p1 = 0; p1 < catalog1.zones2Parts[zoneID1].numPart; p1++) {
-          partID1 = catalog1.zones2Parts[zoneID1].partIDs[p1];     
-
-          dist[0] = fabs(catalog1.part[partID1].x - 
-                         catalog2.voids[iVoid2].macrocenter[0]);
-          dist[1] = fabs(catalog1.part[partID1].y - 
-                         catalog2.voids[iVoid2].macrocenter[1]);
-          dist[2] = fabs(catalog1.part[partID1].z - 
-                         catalog2.voids[iVoid2].macrocenter[2]);
-
-          if (periodicX) dist[0] = fmin(dist[0], 1.0 - dist[0]);
-          if (periodicY) dist[1] = fmin(dist[1], 1.0 - dist[1]);
-          if (periodicZ) dist[2] = fmin(dist[2], 1.0 - dist[2]);
-
-          rdist = sqrt(dist[0]*dist[0] + dist[1]*dist[1] + dist[2]*dist[2]);
-
-          r1 = pow(3./4./M_PI*catalog1.part[partID1].volume / 
-                   catalog1.numPartTot, 1./3.);
-          if (rdist <= matchDist*8*r1) {
-            match = true;
-            break;
-          }
-        }
-      }
-       
-      if (!match) continue; 
-      //if (rdist/catalog1.voids[iVoid1].radius > 1.) continue;
-
-      //if (catalog1.voids[iVoid1].matches.size() < MAX_MATCHES) {
-        catalog1.voids[iVoid1].matches.push_back(newMatch);
-      //} else {
-      //  // find the farthest match
-      //  float farthestMatchDist = 0;
-      //  int   farthestMatchID = 0;
-      //  for (iMatch = 0; iMatch < MAX_MATCHES; iMatch++) {
-      //    if (catalog1.voids[iVoid1].matches[iMatch].dist > farthestMatchDist){
-      //      farthestMatchDist = catalog1.voids[iVoid1].matches[iMatch].dist;
-       //     farthestMatchID   = iMatch;
-       //   }           
-       // } 
-       // if (rdist < farthestMatchDist)
-       //   catalog1.voids[iVoid1].matches[farthestMatchID] = newMatch;
-      //}
-    }
-
-    clock2 = clock();
-    printf("Time: %f sec\n", (1.*clock2-clock1)/CLOCKS_PER_SEC);
-    clock1 = clock();
-  } 
-
-  // pick the closest matches to speed up computation
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    int numPotential = catalog1.voids[iVoid1].matches.size();
-    catalog1.voids[iVoid1].numMatches = numPotential;
-    
-    if (numPotential > MAX_MATCHES) {
-      sortMatches(catalog1.voids[iVoid1].matches, catalog2, 1);
-      catalog1.voids[iVoid1].matches.resize(MAX_MATCHES); 
-    }
-  }
-
-  printf(" Determining overlap...\n");
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    printf("  Working on void %d of %d...", iVoid1+1, catalog1.numVoids); 
-    fflush(stdout);
-    clock1 = clock();
-    voidID1 = catalog1.voids[iVoid1].voidID;
-
-    for (iMatch = 0; iMatch < catalog1.voids[iVoid1].matches.size();iMatch++) {
-      iVoid2 = catalog1.voids[iVoid1].matches[iMatch].matchID;
-      voidID2 = catalog2.voids[iVoid2].voidID;
-
-      for (iZ1 = 0; iZ1 < catalog1.void2Zones[voidID1].numZones; iZ1++) {
-        zoneID1 = catalog1.void2Zones[voidID1].zoneIDs[iZ1];
-
-        for (p1 = 0; p1 < catalog1.zones2Parts[zoneID1].numPart; p1++) {
-          partID1 = catalog1.zones2Parts[zoneID1].partIDs[p1];
-
-          alreadyMatched = false;
-
-          for (iZ2 = 0; iZ2 < catalog2.void2Zones[voidID2].numZones; iZ2++) {
-            zoneID2 = catalog2.void2Zones[voidID2].zoneIDs[iZ2];
-
-            for (p2 = 0; p2 < catalog2.zones2Parts[zoneID2].numPart; p2++) {
-              partID2 = catalog2.zones2Parts[zoneID2].partIDs[p2];     
-
-              match = false;
-
-              if (args.useID_flag) {
-                if (catalog1.part[partID1].uniqueID == 
-                    catalog2.part[partID2].uniqueID) match = true;
-              } else {
-                dist[0] = fabs(catalog1.part[partID1].x - 
-                               catalog2.part[partID2].x);
-                dist[1] = fabs(catalog1.part[partID1].y - 
-                               catalog2.part[partID2].y);
-                dist[2] = fabs(catalog1.part[partID1].z - 
-                               catalog2.part[partID2].z);
-
-                if (periodicX) dist[0] = fmin(dist[0], 1.0 - dist[0]);
-                if (periodicY) dist[1] = fmin(dist[1], 1.0 - dist[1]);
-                if (periodicZ) dist[2] = fmin(dist[2], 1.0 - dist[2]);
-
-                rdist = sqrt(dist[0]*dist[0] + dist[1]*dist[1] + 
-                             dist[2]*dist[2]);
-
-                r1 = pow(3./4./M_PI*catalog1.part[partID1].volume / 
-                         catalog1.numPartTot, 1./3.);
-                r2 = pow(3./4./M_PI*catalog2.part[partID2].volume / 
-                         catalog2.numPartTot, 1./3.);
-                if (rdist <= matchDist*(r1+r2)) match = true;
-              }
-       
-              if (match) {
-                if (!alreadyMatched) {
-                  catalog1.voids[iVoid1].matches[iMatch].commonVolOrig += 
-                    catalog1.part[partID1].volume;
-                } 
-                catalog1.voids[iVoid1].matches[iMatch].commonVolProg += 
-                  catalog2.part[partID2].volume;
-                alreadyMatched = true;
-              } // end if match
-
-            } // end p2
-          } // end iZ2
-        } // end p1
-      } // end iZ1
-    } // end iVoid2
-
-    for (iMatch = 0; iMatch < catalog1.voids[iVoid1].matches.size(); iMatch++) {
-      int matchID = catalog1.voids[iVoid1].matches[iMatch].matchID;
-      catalog1.voids[iVoid1].matches[iMatch].merit = 
-        catalog1.voids[iVoid1].matches[iMatch].commonVolOrig * 
-        catalog1.voids[iVoid1].matches[iMatch].commonVolOrig / 
-        catalog1.voids[iVoid1].vol /
-        catalog2.voids[iVoid2].vol;
-        //catalog1.voids[iVoid1].matches[iMatch].commonVolOrig * 
-        //catalog1.voids[iVoid1].matches[iMatch].commonVolProg / 
-        //catalog1.voids[iVoid1].vol /
-        //catalog2.voids[matchID].vol;
-        //pow(catalog1.voids[iVoid1].matches[iMatch].commonVol,2) / 
-        //catalog1.voids[iVoid1].vol /
-        //catalog2.voids[matchID].vol;
-    }
-//    sortMatches(catalog1.voids[iVoid1].matches, catalog2);
-    clock2 = clock();
-    printf("Time: %f sec\n", (1.*clock2-clock1)/CLOCKS_PER_SEC);
-    clock1 = clock();
-//printf("BEST VOL %e\n", catalog2.voids[catalog1.voids[iVoid1].matches[0].matchID].vol/catalog1.voids[iVoid1].vol);
-  } // end match finding
-
-  printf(" Sorting matches...\n");
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    sortMatches(catalog1.voids[iVoid1].matches, catalog2, 0);
-    if (catalog1.voids[iVoid1].matches.size() > 0 && 
-        catalog1.voids[iVoid1].matches[0].merit < 1.e-6)
-      sortMatches(catalog1.voids[iVoid1].matches, catalog2, 1);
-  }
-
-  // count up significant matches
-  printf(" Categorizing matches...\n");
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    closestMatchDist = 0.;
-    for (iMatch = 0; iMatch < catalog1.voids[iVoid1].matches.size(); iMatch++) {
-      commonVolRatio = catalog1.voids[iVoid1].matches[iMatch].commonVolOrig / 
-                     //  catalog1.voids[iVoid1].numPart;
-                     catalog1.voids[iVoid1].vol;
-      if (commonVolRatio > 0.2) catalog1.voids[iVoid1].numBigMatches++;
-    } 
-  }
-
-  // output summary
-  printf(" Output...\n");
-  std::string filename;
-  filename = string(args.outfile_arg);
-  filename = filename.append("summary.out");
-  fp = fopen(filename.c_str(), "w");
-  fprintf(fp, "# void ID, radius, radius ratio, common volume ratio (to original), common volume ratio (to match), relative dist, num matches, num significant matches, match ID, merit, ellipticity ratio, density contrast, cosTheta, major axis ratio, minor axis ratio, ellipticity\n");
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    int voidID = catalog1.voids[iVoid1].voidID;
-    if (catalog1.voids[iVoid1].numMatches > 0) {
-      iVoid2 = catalog1.voids[iVoid1].matches[0].matchID;
-      float rRatio = catalog2.voids[iVoid2].radius / 
-                     catalog1.voids[iVoid1].radius;
-      float ellipRatio = catalog2.voids[iVoid2].ellipticity / 
-                         catalog1.voids[iVoid1].ellipticity;
-
-      // find angles between major axes, etc.
-     int iMaj1, iMed1, iMin1;
-     int iMaj2, iMed2, iMin2;
-     float eig1[3], eig2[3];
-     float eigv1[6], eigv2[6];
-     float cosThetaMaj, cosThetaMed, cosThetaMin;
- 
-     for (int i = 0; i < 3; i++) {
-       eig1[i] = catalog1.voids[iVoid1].eig[i];
-       eigv1[0,i] = catalog1.voids[iVoid1].eigv1[i];
-       eigv1[1,i] = catalog1.voids[iVoid1].eigv2[i];
-       eigv1[2,i] = catalog1.voids[iVoid1].eigv3[i];
-       eig2[i] = catalog2.voids[iVoid2].eig[i];
-       eigv2[0,i] = catalog2.voids[iVoid2].eigv1[i];
-       eigv2[1,i] = catalog2.voids[iVoid2].eigv2[i];
-       eigv2[2,i] = catalog2.voids[iVoid2].eigv3[i];
-     }
-  
-     if (eig1[0] > eig1[1] && eig1[0] > eig1[2]) iMaj1 = 0;
-     if (eig1[1] > eig1[2] && eig1[1] > eig1[0]) iMaj1 = 1;
-     if (eig1[2] > eig1[1] && eig1[2] > eig1[0]) iMaj1 = 2;
-     if (eig1[0] > eig1[1] && eig1[0] < eig1[2]) iMed1 = 0;
-     if (eig1[1] > eig1[2] && eig1[1] < eig1[0]) iMed1 = 1;
-     if (eig1[2] > eig1[1] && eig1[2] < eig1[0]) iMed1 = 2;
-     if (eig1[0] < eig1[1] && eig1[0] < eig1[2]) iMin1 = 0;
-     if (eig1[1] < eig1[2] && eig1[1] < eig1[0]) iMin1 = 1;
-     if (eig1[2] < eig1[1] && eig1[2] < eig1[0]) iMin1 = 2;
-
-     if (eig2[0] > eig2[1] && eig2[0] > eig2[2]) iMaj2 = 0;
-     if (eig2[1] > eig2[2] && eig2[1] > eig2[0]) iMaj2 = 1;
-     if (eig2[2] > eig2[1] && eig2[2] > eig2[0]) iMaj2 = 2;
-     if (eig2[0] > eig2[1] && eig2[0] < eig2[2]) iMed2 = 0;
-     if (eig2[1] > eig2[2] && eig2[1] < eig2[0]) iMed2 = 1;
-     if (eig2[2] > eig2[1] && eig2[2] < eig2[0]) iMed2 = 2;
-     if (eig2[0] < eig2[1] && eig2[0] < eig2[2]) iMin2 = 0;
-     if (eig2[1] < eig2[2] && eig2[1] < eig2[0]) iMin2 = 1;
-     if (eig2[2] < eig2[1] && eig2[2] < eig2[0]) iMin2 = 2;
-
-//printf("EIG CHECK %d %d %e %e %e %d %e %e %e %d\n", iVoid1, iVoid2, eig1[0], eig1[1], eig1[2], iMin1, eig2[0], eig2[1], eig2[2], iMin2);
-     cosThetaMaj = (eigv1[iMaj1,0]*eigv2[iMaj2,0] + 
-                          eigv1[iMaj1,1]*eigv2[iMaj2,1] +    
-                          eigv1[iMaj1,2]*eigv2[iMaj2,2]);
-//printf("EIG CHECK %d %d %e %e %e %e %e %e %e\n", iVoid1, iVoid2, eigv1[iMaj1,0], eigv1[iMaj1,1], eigv1[iMaj1,2], eigv2[iMaj2,0], eigv2[iMaj2,1], eigv2[iMaj2,2], cosThetaMaj);
-
-  
-     if (fabs(cosThetaMaj) > 0.) cosThetaMaj = acos(fabs(cosThetaMaj));
-
-     float majAxisRatio = eig2[iMaj2]/eig1[iMaj1];
-     float minAxisRatio = eig2[iMin2]/eig1[iMin1];
-
-// TEST 
-/*
-  if (catalog1.voids[iVoid1].voidID == 267 &&
-      catalog2.voids[iVoid2].voidID == 346) {
-
-    int voidID1 = catalog1.voids[iVoid1].voidID;
-    for (iZ1 = 0; iZ1 < catalog1.void2Zones[voidID1].numZones; iZ1++) {
-      zoneID1 = catalog1.void2Zones[voidID1].zoneIDs[iZ1];
-      for (p1 = 0; p1 < catalog1.zones2Parts[zoneID1].numPart; p1++) {
-        partID1 = catalog1.zones2Parts[zoneID1].partIDs[p1];     
-        printf("VOID1 %e %e %e\n", catalog1.part[partID1].x,
-                                       catalog1.part[partID1].y,
-                                       catalog1.part[partID1].z);
-      }
-    }
-
-    int voidID2 = catalog2.voids[iVoid2].voidID;
-    for (iZ2 = 0; iZ2 < catalog2.void2Zones[voidID2].numZones; iZ2++) {
-      zoneID2 = catalog2.void2Zones[voidID2].zoneIDs[iZ2];
-      for (p2 = 0; p2 < catalog2.zones2Parts[zoneID2].numPart; p2++) {
-        partID2 = catalog2.zones2Parts[zoneID2].partIDs[p2];     
-        printf("VOID1 %e %e %e\n", catalog2.part[partID2].x,
-                                       catalog2.part[partID2].y,
-                                       catalog2.part[partID2].z);
-      }
-    }
-  
-  }
-*/
-// END TEST
-      commonVolRatio = catalog1.voids[iVoid1].matches[0].commonVolOrig / 
-                       //catalog1.voids[iVoid1].numPart;
-                       catalog1.voids[iVoid1].vol;
-      float volRatio = catalog1.voids[iVoid1].matches[0].commonVolProg / 
-                       catalog2.voids[iVoid2].vol;
-      rdist = catalog1.voids[iVoid1].matches[0].dist;
-      rdist /= catalog1.voids[iVoid1].radius;
-
-      fprintf(fp, "%d %.4f %.4f %e %e %.4f %d %d %d %e %e %e %e %e %e %e\n", voidID, 
-      //fprintf(fp, "%d %.4f %.4f %.4f %.4f %.4f %d %d %d\n", voidID, 
-                                   catalog1.voids[iVoid1].radiusMpc,
-                                   rRatio, 
-                                   commonVolRatio,
-                                   volRatio,
-                                   rdist, 
-                                   catalog1.voids[iVoid1].numMatches,
-                                   catalog1.voids[iVoid1].numBigMatches,
-                                   catalog2.voids[iVoid2].voidID,
-                                   catalog1.voids[iVoid1].matches[0].merit,
-                                   ellipRatio,
-                                   catalog1.voids[iVoid1].densCon,
-                                   cosThetaMaj,
-                                   majAxisRatio,
-                                   minAxisRatio,
-                                   catalog1.voids[iVoid1].ellipticity
-                                   );
-
-    } else {
-      fprintf(fp, "%d %.4f 0.0 0.0 0.0 0.0 0.0 0 0 0 0.0 0.0 0.0 0.0 0.0 %e\n", voidID, 
-                                           catalog1.voids[iVoid1].radiusMpc, catalog1.voids[iVoid1].ellipticity);
-    }
-  } // end printing
-  fclose(fp);
-
-  // output detail
-  printf(" Output detail...\n");
-  filename = string(args.outfile_arg);
-  filename = filename.append("detail.out");
-  fp = fopen(filename.c_str(), "w");
-  fprintf(fp, "# match ID, merit, relative dist, relative radius\n");
-  for (iVoid1 = 0; iVoid1 < catalog1.numVoids; iVoid1++) {
-    int voidID = catalog1.voids[iVoid1].voidID;
-    fprintf(fp,"#%d (%.4f Mpc/h):\n", voidID, catalog1.voids[iVoid1].radiusMpc);
-    for (iMatch = 0; iMatch < catalog1.voids[iVoid1].matches.size(); iMatch++) {
-      commonVolRatio = catalog1.voids[iVoid1].matches[iMatch].commonVolOrig / 
-                       //catalog1.voids[iVoid1].numPart;
-                       catalog1.voids[iVoid1].vol;
-
-      int matchID = catalog1.voids[iVoid1].matches[iMatch].matchID;
-      fprintf(fp, "%d %e %.4f %.4f\n", matchID, 
-                                   catalog1.voids[iVoid1].matches[iMatch].merit,
-                                   catalog1.voids[iVoid1].matches[iMatch].dist/
-                                     catalog1.voids[iVoid1].radius,
-                                   catalog2.voids[matchID].radius/
-                                     catalog1.voids[iVoid1].radius);
-    }
-
-    fprintf(fp, "\n ");
-    fprintf(fp, "\n ");
-  } // end printing detail
-  fclose(fp);
-
-
-  printf("\nDone!\n");
-  return 0;
-} // end main
-
-// ----------------------------------------------------------------------------
-// ----------------------------------------------------------------------------
-void loadCatalog(const char *partFile, const char *volFile, 
-                 const char *voidFile, const char *zoneFile,
-                 const char *infoFile, const char *centerFile,
-                 const char *shapeFile,
-                 const char *zonePartFile, CATALOG& catalog,
-                 bool isObservation) {
-
-  int i, p, numPartTot, numZonesTot, dummy, iVoid, iZ, numVolTot, zoneNumPart;
-  FILE *fp;
-  float *temp, junk, voidVol, coreParticle, coreDens, zoneVol;
-  float densCon, voidProb, volNorm;
-  long *temp2;
-  int junkInt, voidID, numPart, numZones, zoneID, partID;
-  char line[500], junkStr[10];
-  float ranges[3][2];
-
-  printf("Loading info...\n");
-  netCDF::NcFile f_info(infoFile, netCDF::NcFile::read);
-  f_info.getAtt("range_x_min").getValues(&ranges[0][0]);
-  f_info.getAtt("range_x_max").getValues(&ranges[0][1]);
-  f_info.getAtt("range_y_min").getValues(&ranges[1][0]);
-  f_info.getAtt("range_y_max").getValues(&ranges[1][1]);
-  f_info.getAtt("range_z_min").getValues(&ranges[2][0]);
-  f_info.getAtt("range_z_max").getValues(&ranges[2][1]);
-
-  catalog.boxLen[0] = ranges[0][1] - ranges[0][0];
-  catalog.boxLen[1] = ranges[1][1] - ranges[1][0];
-  catalog.boxLen[2] = ranges[2][1] - ranges[2][0];
-  f_info.close();
-  
-  // read in all particle positions
-  printf("Loading particles...\n");
-  fp = fopen(partFile, "r");
-  fread(&dummy, 1, 4, fp); 
-  fread(&numPartTot, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-
-  catalog.part.resize(numPartTot);
-  catalog.numPartTot = numPartTot;
-
-  volNorm = numPartTot/(catalog.boxLen[0]*catalog.boxLen[1]*catalog.boxLen[2]);
-
-  temp = (float *) malloc(numPartTot * sizeof(float));
-  temp2 = (long *) malloc(numPartTot * sizeof(long));
-
-  fread(&dummy, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].x = temp[p];
-  fread(&dummy, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].y = temp[p];
-  fread(&dummy, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].z = temp[p];
-  fread(&dummy, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].ra = temp[p];
-  fread(&dummy, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].dec = temp[p];
-  fread(&dummy, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].redshift = temp[p];
-  fread(&dummy, 1, 4, fp);
-  fread(&dummy, 1, 4, fp);
-  fread(temp2, numPartTot, 8, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].uniqueID = temp2[p];
- 
-  free(temp2);
-  fclose(fp); 
-
-  printf(" Read %d particles...\n", catalog.numPartTot);
-
-  // read in all particle volumes
-  printf(" Loading volumes...\n");
-  fp = fopen(volFile, "r");
-  fread(&numVolTot, 1, 4, fp);
-  fread(temp, numPartTot, 4, fp);
-  for (p = 0; p < numPartTot; p++) 
-    catalog.part[p].volume = temp[p];
-  fclose(fp); 
-  free(temp);
-
-  // read in desired voids
-  printf(" Loading voids...\n");
-  fp = fopen(voidFile ,"r");
-  fgets(line, sizeof(line), fp);
-  sscanf(line, "%d %s %d %s", &junkInt, junkStr, &catalog.numVoids, junkStr);
-  fgets(line, sizeof(line), fp);
-  
-  catalog.voids.resize(catalog.numVoids);
-  i = 0;
-  while (fgets(line, sizeof(line), fp) != NULL) {
-   sscanf(line, "%d %d %d %f %f %d %d %f %d %f %f\n", &iVoid, &voidID,
-           &coreParticle, &coreDens, &zoneVol, &zoneNumPart, &numZones,
-           &voidVol, &numPart, &densCon, &voidProb);
-
-    catalog.voids[i].coreParticle = coreParticle;
-    catalog.voids[i].zoneNumPart = zoneNumPart;
-    catalog.voids[i].coreDens = coreDens;
-    catalog.voids[i].zoneVol = zoneVol;
-    catalog.voids[i].voidID = voidID;
-    catalog.voids[i].vol = voidVol;
-    catalog.voids[i].numPart = numPart;
-    catalog.voids[i].numZones = numZones;
-    catalog.voids[i].densCon = densCon;
-    catalog.voids[i].voidProb = voidProb;
-
-    catalog.voids[i].radius = pow(voidVol/catalog.numPartTot*3./4./M_PI, 1./3.);
-    catalog.voids[i].numMatches = 0;
-    catalog.voids[i].numBigMatches = 0;
-  
-    catalog.voids[i].radiusMpc = pow(voidVol/volNorm*3./4./M_PI, 1./3.);
-
-    i++;
-  }
-  fclose(fp);
-
-  catalog.numVoids = i - 1;
-  catalog.voids.resize(catalog.numVoids);
-  printf("  Read %d voids.\n", catalog.numVoids);
-
-  printf(" Loading macrocenters\n");
-  fp = fopen(centerFile, "r");
-  float tempBary[3];
-  float tempFloat;
-  int   tempInt;
-  iVoid = 0;
-  //fgets(line, sizeof(line), fp);
-  while (fgets(line, sizeof(line), fp) != NULL) {
-    sscanf(line, "%d %f %f %f\n", 
-           &tempInt, &tempBary[0], &tempBary[1], &tempBary[2]);
-    //sscanf(line, "%f %f %f %f %f %f %f %d %f %d %d %d %d\n", 
-    //       &tempBary[0], &tempBary[1], &tempBary[2],
-    //       &tempFloat, &tempFloat, &tempFloat, &tempFloat, &tempInt,
-    //       &tempFloat, &tempInt, &tempInt, &tempInt, &tempInt);
-
-    // convert back to ZOBOV-normalized units
-//if (iVoid < 10) printf("BARY %d %d %e %e %e\n", iVoid, catalog.voids[iVoid].voidID, tempBary[0], tempBary[1], tempBary[2]);
-    tempBary[0] = (tempBary[0] - ranges[0][0])/catalog.boxLen[0];
-    tempBary[1] = (tempBary[1] - ranges[1][0])/catalog.boxLen[1];
-    tempBary[2] = (tempBary[2] - ranges[2][0])/catalog.boxLen[2];
-
-    if (isObservation) {
-      tempBary[0] -= 0.5;
-      tempBary[1] -= 0.5;
-      tempBary[2] -= 0.5;
-    }
-
-    catalog.voids[iVoid].macrocenter[0] = tempBary[0];
-    catalog.voids[iVoid].macrocenter[1] = tempBary[1];
-    catalog.voids[iVoid].macrocenter[2] = tempBary[2];
-    iVoid++;
-  }
-  fclose(fp);
-
-  printf(" Loading shapes\n");
-  fp = fopen(shapeFile, "r");
-  iVoid = 0;
-  float tempEllip, eig[3], eigv1[3], eigv2[3], eigv3[3];
-  fgets(line, sizeof(line), fp);
-  while (fgets(line, sizeof(line), fp) != NULL) {
-    sscanf(line, "%d %f %f %f %f %f %f %f %f %f %f %f %f %f\n", 
-           &tempInt, &tempEllip, &eig[0], &eig[1], &eig[2],
-           &eigv1[0], &eigv1[1], &eigv1[2],
-           &eigv2[0], &eigv2[1], &eigv2[2],
-           &eigv3[0], &eigv3[1], &eigv3[2]);
-
-//if (iVoid < 10) printf("SHAPE %d %d %e\n", iVoid, catalog.voids[iVoid].voidID, tempEllip);
-    catalog.voids[iVoid].ellipticity = tempEllip;
-    catalog.voids[iVoid].eig[0] = eig[0];
-    catalog.voids[iVoid].eig[1] = eig[1];
-    catalog.voids[iVoid].eig[2] = eig[2];
-    catalog.voids[iVoid].eigv1[0] = eigv1[0];
-    catalog.voids[iVoid].eigv1[1] = eigv1[1];
-    catalog.voids[iVoid].eigv1[2] = eigv1[2];
-    catalog.voids[iVoid].eigv2[0] = eigv2[0];
-    catalog.voids[iVoid].eigv2[1] = eigv2[1];
-    catalog.voids[iVoid].eigv2[2] = eigv2[2];
-    catalog.voids[iVoid].eigv3[0] = eigv3[0];
-    catalog.voids[iVoid].eigv3[1] = eigv3[1];
-    catalog.voids[iVoid].eigv3[2] = eigv3[2];
-    iVoid++;
-  }
-  fclose(fp);
-
-
-  // load up the zone membership for each void
-  printf(" Loading zone-void membership info...\n");
-  fp = fopen(zoneFile, "r");
-  fread(&catalog.numZonesTot, 1, 4, fp);
-
-  catalog.void2Zones.resize(catalog.numZonesTot);
-    
-  for (iZ = 0; iZ < catalog.numZonesTot; iZ++) {
-    fread(&numZones, 1, 4, fp);
-
-    catalog.void2Zones[iZ].numZones = numZones;
-    catalog.void2Zones[iZ].zoneIDs = (int *) malloc(numZones * sizeof(int));
-
-    for (p = 0; p < numZones; p++) {
-      fread(&catalog.void2Zones[iZ].zoneIDs[p], 1, 4, fp);
-    }
-  }
-  fclose(fp);
-
-  // now the zone membership
-  printf(" Loading particle-zone membership info...\n");
-  fp = fopen(zonePartFile, "r");
-  fread(&dummy, 1, 4, fp);
-  fread(&numZonesTot, 1, 4, fp);
-
-  catalog.zones2Parts.resize(numZonesTot); 
-
-  for (iZ = 0; iZ < numZonesTot; iZ++) {
-    fread(&numPart, 1, 4, fp);
-    
-    catalog.zones2Parts[iZ].numPart = numPart;
-    catalog.zones2Parts[iZ].partIDs = (int *) malloc(numPart * sizeof(int));
-
-    for (p = 0; p < numPart; p++) {
-      fread(&catalog.zones2Parts[iZ].partIDs[p], 1, 4, fp);
-    }
-  }
-
-  fclose(fp);
-
-} // end loadCatalog
-
-// ----------------------------------------------------------------------------
-float getDist(CATALOG& catalog1, CATALOG& catalog2, int& iVoid1, int& iVoid2,
-              bool periodicX, bool periodicY, bool periodicZ) {
-
-  float rdist, dist[3];
-
-  dist[0] = fabs(catalog1.voids[iVoid1].macrocenter[0] - 
-                 catalog2.voids[iVoid2].macrocenter[0]);
-  dist[1] = fabs(catalog1.voids[iVoid1].macrocenter[1] - 
-                 catalog2.voids[iVoid2].macrocenter[1]);
-  dist[2] = fabs(catalog1.voids[iVoid1].macrocenter[2] - 
-                 catalog2.voids[iVoid2].macrocenter[2]);
-
-  if (periodicX) dist[0] = fmin(dist[0], 1.0 - dist[0]);
-  if (periodicY) dist[1] = fmin(dist[1], 1.0 - dist[1]);
-  if (periodicZ) dist[2] = fmin(dist[2], 1.0 - dist[2]);
-
-  rdist = sqrt(dist[0]*dist[0] + dist[1]*dist[1] + dist[2]*dist[2]);
-
-  return rdist;
-
-} // end getDist
-
-
-// ----------------------------------------------------------------------------
-void sortMatches(std::vector<MATCHPROPS>& matches, 
-                 CATALOG& catalog2, int mode) {
-
-  //printf("SORTING %d\n", matches.size());
-  MATCHPROPS tempMatch;
-  bool swapped;
-  int matchID, matchID2;
-
-  if (matches.size() <= 1) return;
-
-  swapped = true;
-  while (swapped) {
-    swapped = false;
-    for (int iMatch = 0; iMatch < matches.size() - 1; iMatch++) {
-      matchID = matches[iMatch].matchID;
-      matchID2 = matches[iMatch+1].matchID;
-      if ((mode == 0 && matches[iMatch].merit < matches[iMatch+1].merit) ||
-          (mode == 1 && matches[iMatch].dist > matches[iMatch+1].dist)) {
-        tempMatch = matches[iMatch+1];
-        matches[iMatch+1] = matches[iMatch];
-        matches[iMatch] = tempMatch;
-        swapped = true;
-      }
-    }
-  }
-
-  return;
-} // end sortMatches
diff --git a/c_tools/analysis/voidOverlap.ggo b/c_tools/analysis/voidOverlap.ggo
deleted file mode 100644
index 97e9496..0000000
--- a/c_tools/analysis/voidOverlap.ggo
+++ /dev/null
@@ -1,31 +0,0 @@
-package "voidOverlap"
-version "0"
-
-option "configFile"	 -	"Configuration file path"	string optional
-
-# void data for catalog 1
-option "partFile1" - "Particle file for catalog 1"	string yes
-option "volFile1" -	"Volume file for catalog 1"	string yes
-option "voidFile1" -	"Void info file for catalog 1"	string yes
-option "infoFile1" -	"Extra info file for catalog 1"	string yes
-option "zoneFile1" - "Zone file for catalog 1"	string yes
-option "zonePartFile1" -	"Zone-particle file for catalog 1"	string yes
-option "centerFile1" - "Barycenter file for catalog 1" string yes
-option "shapeFile1" - "Shape file for catalog 1" string yes
-
-# void data for file 2
-option "partFile2" - "Particle file for catalog 2"	string yes
-option "volFile2"	- "Volume file for catalog 2"	string yes
-option "voidFile2" - "Void info file for catalog 2"	string yes
-option "infoFile2" -	"Extra info file for catalog 2"	string yes
-option "zoneFile2" - "Zone file for catalog 2"	string yes
-option "zonePartFile2"	- "Zone-particle file for catalog 2"	string yes
-option "centerFile2" - "Barycenter file for catalog 2" string yes
-option "shapeFile2" - "Shape file for catalog 2" string yes
-
-# options
-option "isObservation" - "We are working with observational data" flag off
-option "outfile" - "Output file" string yes
-option "useID" - "Use unique catalog ID to match voids; otherwise use volumes" flag off
-option "overlapFrac" - "threshold fraction of voronoi radius to count as matched" double optional default="0.25"
-option "periodic" - "Set of edges which are periodic" string optional default="xy"