From 091cf5d1dcf52063dbc641f9471c89564c19a2a1 Mon Sep 17 00:00:00 2001
From: "Paul M. Sutter" <pmsutter@gmail.com>
Date: Thu, 9 Jan 2025 18:21:26 +0800
Subject: [PATCH] First steps in purging the tracking of mock particles: no
 longer present in jovoz2

---
 c_source/jozov2/jozov2.cpp         | 15 +++------------
 c_source/jozov2/jozov2.hpp         |  3 +--
 c_source/jozov2/jozov2_io.cpp      |  5 ++---
 c_source/zobov/voz.h               |  4 ++--
 python_source/backend/launchers.py |  3 ++-
 5 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/c_source/jozov2/jozov2.cpp b/c_source/jozov2/jozov2.cpp
index f4cb142..ea14344 100644
--- a/c_source/jozov2/jozov2.cpp
+++ b/c_source/jozov2/jozov2.cpp
@@ -51,9 +51,7 @@ int main(int argc,char **argv)
   double *sorter;
   int *iord;
 
-  int mockIndex;
-
-  if (argc != 8) {
+  if (argc != 7) {
     printf("Wrong number of arguments.\n");
     printf("arg1: adjacency file\n");
     printf("arg2: volume file\n");
@@ -61,7 +59,6 @@ int main(int argc,char **argv)
     printf("arg4: output file containing zones in each void\n");
     printf("arg5: output text file\n");
     printf("arg6: Density threshold (0 for no threshold)\n");
-    printf("arg7: Beginning index of mock galaxies\n\n");
     exit(0);
   }
   adjfile = argv[1];
@@ -73,10 +70,6 @@ int main(int argc,char **argv)
     printf("Bad density threshold.\n");
     exit(0);
   }
-  if (sscanf(argv[7],"%d",&mockIndex) == 0) {
-    printf("Bad mock galaxy index.\n");
-    exit(0);
-  }
   printf("TOLERANCE: %f\n", voltol);
   if (voltol <= 0.) {
     printf("Proceeding without a density threshold.\n");
@@ -91,13 +84,11 @@ int main(int argc,char **argv)
     {
       return 1;
     }
-  if (mockIndex < 0)
-    mockIndex = np;
 
   /* Check that we got all the pairs */
   for (int i = 0; i < np; i++)
     {
-      if (p[i].ncnt != p[i].nadj && i < mockIndex) {
+      if (p[i].ncnt != p[i].nadj) {
 	cout
 	  << format("We didn't get all of %d's adj's; %d != %d.") 
 	  % i % p[i].ncnt % p[i].nadj
@@ -109,7 +100,7 @@ int main(int argc,char **argv)
   /* Volumes */
   try
     {
-      readVolumeFile(volfile, p, np, mockIndex);
+      readVolumeFile(volfile, p, np);
     }
   catch (const FileError& e)
     {
diff --git a/c_source/jozov2/jozov2.hpp b/c_source/jozov2/jozov2.hpp
index 5def611..5475c4b 100644
--- a/c_source/jozov2/jozov2.hpp
+++ b/c_source/jozov2/jozov2.hpp
@@ -34,8 +34,7 @@ class FileError: virtual std::exception
 void readAdjacencyFile(const std::string& adjfile, PARTICLE*& p, pid_t& np)
   throw(FileError);
 
-void readVolumeFile(const std::string& volfile, PARTICLE *p, pid_t np, 
-                    pid_t mockIndex)
+void readVolumeFile(const std::string& volfile, PARTICLE *p, pid_t np)
   throw(FileError);
 
 void buildInitialZones(PARTICLE *p, pid_t np, pid_t* jumped, 
diff --git a/c_source/jozov2/jozov2_io.cpp b/c_source/jozov2/jozov2_io.cpp
index cc6abf7..72c5db2 100644
--- a/c_source/jozov2/jozov2_io.cpp
+++ b/c_source/jozov2/jozov2_io.cpp
@@ -103,8 +103,7 @@ void readAdjacencyFile(const string& adjfile, PARTICLE*& p, pid_t& np)
     }
 }
 
-void readVolumeFile(const std::string& volfile, PARTICLE *p, pid_t np, 
-                    pid_t mockIndex)
+void readVolumeFile(const std::string& volfile, PARTICLE *p, pid_t np)
   throw(FileError)
 {
   ifstream vol(volfile.c_str());
@@ -125,7 +124,7 @@ void readVolumeFile(const std::string& volfile, PARTICLE *p, pid_t np,
 
   for (pid_t i = 0; i < np; i++) {
     vol.read((char*)&p[i].dens, sizeof(float));
-    if (((p[i].dens < 1e-30) || (p[i].dens > 1e30)) && (i < mockIndex)) {
+    if ((p[i].dens < 1e-30) || (p[i].dens > 1e30)) {
       cout << format("Whacked-out volume found, of particle %d: %f") % i % p[i].dens << endl;
       p[i].dens = 1.;
     }
diff --git a/c_source/zobov/voz.h b/c_source/zobov/voz.h
index fb56279..f71e1fb 100644
--- a/c_source/zobov/voz.h
+++ b/c_source/zobov/voz.h
@@ -1,7 +1,7 @@
 #define MAXVERVER 100000
-#define NGUARD 84 /*Actually, the number of SPACES between guard points
-##define NGUARD 42 /*Actually, the number of SPACES between guard points
+#define NGUARD 42 /*Actually, the number of SPACES between guard points
 		    in each dim */
+//#define NGUARD 84 /*Actually, the number of SPACES between guard points
 
 typedef int pid_t;
 
diff --git a/python_source/backend/launchers.py b/python_source/backend/launchers.py
index 84c8606..44e5be2 100644
--- a/python_source/backend/launchers.py
+++ b/python_source/backend/launchers.py
@@ -500,7 +500,8 @@ def launchZobov(sample, binPath, outputDir=None, logDir=None, continueRun=None,
            outputDir+"/voidPart_"+sampleName+".dat", \
            outputDir+"/voidZone_"+sampleName+".dat", \
            outputDir+"/voidDesc_"+sampleName+".out", \
-           str(maxDen), str(maskIndex)]
+           str(maxDen)
+           ]
     log = open(logFile, 'a')
     subprocess.call(cmd, stdout=log, stderr=log)
     log.close()