--- trunk/madProps/madProps.c	2002/07/19 19:05:59	43
+++ trunk/madProps/madProps.c	2002/08/16 04:05:45	82
@@ -22,6 +22,7 @@ int main(argc, argv)
   int lineNum = 0; // keeps track of the line number
   int n_atoms; // the number of atoms
   int i,j; // loop counters
+  int isFirst;
 
   char read_buffer[2000]; /*the line buffer for reading */
   char *foo; /*the pointer to the current string token */
@@ -47,8 +48,11 @@ int main(argc, argv)
   char cosCorr1[30];
   char cosCorr2[30];
 
+  int startFrame = 0;
+  int haveStartFrame = 0;
+  int endFrame = 0;
+  int haveEndFrame = 0;
 
-
   program_name = argv[0]; /*save the program name in case we need it*/
   
   for( i = 1; i < argc; i++){
@@ -75,12 +79,16 @@ int main(argc, argv)
 	  strcpy( muCorr, argv[i] );
 	}
 	
-	else if( !strcmp( argv[i], "--CosCorr" ) ){
-	  calcCosCorr = 1;
+	else if( !strcmp( argv[i], "--startFrame" ) ){
+	  haveStartFrame = 1;
 	  i++;
-	  strcpy( cosCorr1, argv[i] );
+	  startFrame = atoi(argv[i]);
+	}
+
+	else if( !strcmp( argv[i], "--endFrame" ) ){
+	  haveEndFrame = 1;
 	  i++;
-	  strcpy( cosCorr2, argv[i] );
+	  endFrame = atoi(argv[i]);
 	}
 
 	else{
@@ -168,6 +176,7 @@ int main(argc, argv)
   fflush( stdout );
   
   nFrames = frameCount( in_name );
+  if( !haveEndFrame ) endFrame = nFrames;
 
   printf( "done.\n"
 	  "nframes = %d\n"
@@ -181,16 +190,27 @@ int main(argc, argv)
     exit(8);
   }
 
-  // create the array of frames
+  // create and initialize the array of frames
 
   dumpArray = (struct xyz_frame*)calloc( nFrames,
 					 sizeof( struct xyz_frame ) );
+  for( i=0; i<nFrames; i++ ){
+    dumpArray[i].nAtoms = 0;
+    dumpArray[i].time   = 0.0;
+    dumpArray[i].boxX   = 0.0;
+    dumpArray[i].boxY   = 0.0;
+    dumpArray[i].boxZ   = 0.0;
+    dumpArray[i].r      = NULL;
+    dumpArray[i].v      = NULL;
+    dumpArray[i].names  = NULL;
+  }
 
   // read the frames
   
   printf( "Reading the frames into the coordinate arrays..." );
   fflush( stdout );
 
+  isFirst = 1;
   for(j =0; j<nFrames; j++ ){
     
     // read the number of atoms
@@ -203,6 +223,12 @@ int main(argc, argv)
 
     dumpArray[j].r = 
       (struct coords *)calloc(n_atoms, sizeof(struct coords));
+    
+    if( isFirst ) {
+      dumpArray[0].names = 
+	(atomID *)calloc( n_atoms, sizeof(atomID) );
+      isFirst = 0;
+    }
 
     if( calcMuCorr || calcCosCorr ){
           dumpArray[j].v = 
@@ -260,7 +286,7 @@ int main(argc, argv)
 	exit(8);
       }
       
-      strcpy(dumpArray[j].r[i].name, foo); /*copy the atom name */
+      strcpy(dumpArray[0].names[i], foo); /*copy the atom name */
 
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
@@ -338,7 +364,7 @@ int main(argc, argv)
     fflush( stdout );
     
     // gofr call
-    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames );
+    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame );
     
     fprintf( stdout, 
 	     " done.\n"
@@ -384,8 +410,8 @@ int main(argc, argv)
 	     cosCorr1, cosCorr2 );
     fflush( stdout );
     
-    // cosCorr call
-
+    cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame, 
+	     endFrame );
     
     fprintf( stdout, 
 	     " done.\n"
@@ -393,13 +419,21 @@ int main(argc, argv)
     fflush(stdout);
   }
   
-  
   return 0;
   
 }
 
 
+void map( double *x, double *y, double *z, 
+	  double boxX, double boxY, double boxZ ){ 
+  
+  *x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5  );
+  *y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5  );
+  *z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5  );
 
+}
+
+
 /***************************************************************************
  * prints out the usage for the command line arguments, then exits.
  ***************************************************************************/
@@ -424,8 +458,9 @@ void usage(){
 		"                               -note: \"all\" will do all atoms\n"
 		"   --MuCorr <atom>           Calculate mu correlation of atom\n"
 		"   --CosCorr <atom1> <atom2> Calculate the cos correlation between atom1 and atom2\n"
+		"  --startFrame <frame#>      Specifies a frame to start correlating\n"
+		"  --endFrame <frame#>        Specifies a frame to stop correlating.\n"
 		
-		
 		"\n"
 		"\n",
 		program_name);