--- trunk/tcProps/directorWhole.c	2004/02/24 16:36:33	1066
+++ trunk/tcProps/directorWhole.c	2004/02/24 17:13:06	1067
@@ -74,10 +74,10 @@ void calcDirWholeCorr(double startTime, struct atomCoo
     percentComplete = 
       (int)( 100.0 * (double)framesFinished / (double) corrFrames );
     
-//     fprintf( stdout,
-// 	     "\rDirector bilayer corr %3d%% complete.",
-// 	     percentComplete );
-//     fflush( stdout );
+    fprintf( stdout,
+	     "\rDirector bilayer corr %3d%% complete.",
+	     percentComplete );
+    fflush( stdout );
 
     readFrame( i, atoms, Hmat );
     
@@ -88,14 +88,26 @@ void calcDirWholeCorr(double startTime, struct atomCoo
     framesFinished++;
   }
 
-//   sprintf( outName, "%s.dirHead", outPrefix );
-//   outFile = fopen( outName, "w" );
+  sprintf( outName, "%s.dirWhole", outPrefix );
+  outFile = fopen( outName, "w" );
 
+  fprintf( outFile,
+	   "#time\torderParam\tx\ty\tz\n");
+  
+  for(i=0;i<corrFrames;i++){
+    fprintf( outFile,
+	     "%6G\t%6G\t%6G\t%6G\t%6G\n",
+	     directorWhole[i].time,
+	     directorWhole[i].order,
+	     directorWhole[i].u[0],
+	     directorWhole[i].u[1],
+	     directorWhole[i].u[2]);
+  }
 
   
 
-//   fflush(outFile);
-//   fclose(outFile);
+  fflush(outFile);
+  fclose(outFile);
 
   percentComplete = 
     (int)( 100.0 * (double)framesFinished / (double) corrFrames );
@@ -127,6 +139,7 @@ void accumDWFrame( int index, struct atomCoord *atoms 
 
   double oMat[3][3];   
   double iMat[3][3];
+  double matWrap[9];
   double com[3];
   double totMass;
   double lenPrinc, distl;
@@ -172,10 +185,10 @@ void accumDWFrame( int index, struct atomCoord *atoms 
     for(j=0;j<nLipAtoms;j++){
       l=k+j;
       
-      for(m=0;m<3;m++){
+      for(m=0;m<3;m++)
 	com[m] += atoms[l].mass * atoms[l].pos[m];
-	totMass += atoms[l].mass;
-      }
+      
+      totMass += atoms[l].mass;
     }
     for(m=0;m<3;m++) com[m] /= totMass;
 
@@ -197,26 +210,45 @@ void accumDWFrame( int index, struct atomCoord *atoms 
       
       
     }
+    
+//     fprintf(stderr, "iMat (before) = %6G, %6G, %6G\n"
+// 	            "                %6G, %6G, %6G\n"
+// 	            "                %6G, %6G, %6G\n\n",
+// 	    iMat[0][0], iMat[0][1], iMat[0][2],
+// 	    iMat[1][0], iMat[1][1], iMat[1][2],
+// 	    iMat[2][0], iMat[2][1], iMat[2][2]);
 
+    // matWrap to fortran convention
+
+    for(j=0;j<3;j++)
+      for(l=0;l<3;l++)
+	matWrap[l+3*j] = iMat[l][j];
+
     ifail = 0;
-    dsyev(&job, &uplo, &nfilled, iMat, &ndiag, evals, work, &lWork, &ifail);
+    dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail);
     
     if (ifail) {
       fprintf(stderr, "dsyev screwed something up!\n");
       exit(0);
     }
 
-    fprintf(stderr, "evals = %6G, %6G, %6G\n\n",
-	    evals[0], evals[1], evals[2]);
+    // matWrap from fortran convention
 
-    fprintf(stderr, "iMat = %6G, %6G, %6G\n"
-	            "       %6G, %6G, %6G\n"
-	            "       %6G, %6G, %6G\n\n",
-	    iMat[0][0], iMat[0][1], iMat[0][2],
-	    iMat[1][0], iMat[1][1], iMat[1][2],
-	    iMat[2][0], iMat[2][1], iMat[2][2]);
+    for(j=0;j<3;j++)
+      for(l=0;l<3;l++)
+	iMat[l][j] = matWrap[l+3*j];
 
+//     fprintf(stderr, "evals = %6G, %6G, %6G\n\n",
+// 	    evals[0], evals[1], evals[2]);
 
+//     fprintf(stderr, "iMat (after) = %6G, %6G, %6G\n"
+// 	            "               %6G, %6G, %6G\n"
+// 	            "               %6G, %6G, %6G\n\n",
+// 	    iMat[0][0], iMat[0][1], iMat[0][2],
+// 	    iMat[1][0], iMat[1][1], iMat[1][2],
+// 	    iMat[2][0], iMat[2][1], iMat[2][2]);
+
+
       
     smallest = fabs(evals[0]);
     which = 0;
@@ -230,6 +262,7 @@ void accumDWFrame( int index, struct atomCoord *atoms 
     lenPrinc = 0.0;
     for(j=0;j<3;j++)
       lenPrinc +=  iMat[j][which] * iMat[j][which];
+    lenPrinc = sqrt( lenPrinc );
     
     for(j=0;j<3;j++)
       principal[i].u[j] = iMat[j][which]/lenPrinc;
@@ -259,15 +292,26 @@ void accumDWFrame( int index, struct atomCoord *atoms 
     for(j=0;j<3;j++)
       oMat[i][j] /= (double)nLipids;
 
+  // matWrap to fortran convention
+  
+  for(j=0;j<3;j++)
+    for(l=0;l<3;l++)
+      matWrap[l+3*j] = oMat[l][j];
+  
   ifail = 0;
+  dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail);
 
-  dsyev(&job, &uplo, &nfilled, oMat, &ndiag, evals, work, &lWork, &ifail);
-
   if (ifail) {
     fprintf(stderr, "dsyev screwed something up!\n");
     exit(0);
   }
+
+  // matWrap from fortran convention
   
+  for(j=0;j<3;j++)
+    for(l=0;l<3;l++)
+      oMat[l][j] = matWrap[l+3*j];
+  
   max = 0.0;
   for (i=0; i<3;i++) {
     if (fabs(evals[i]) > max) {
@@ -282,13 +326,13 @@ void accumDWFrame( int index, struct atomCoord *atoms 
 
   directorWhole[index].order = 1.5 * max;
 
-  fprintf(stderr,
-	  "frame[%d] => order = %6G; < %6G, %6G, %6G >\n",
-	  index,
-	  directorWhole[index].order,
-	  directorWhole[index].u[0],
-	  directorWhole[index].u[1],
-	  directorWhole[index].u[2] );
+//   fprintf(stderr,
+// 	  "frame[%d] => order = %6G; < %6G, %6G, %6G >\n",
+// 	  index,
+// 	  directorWhole[index].order,
+// 	  directorWhole[index].u[0],
+// 	  directorWhole[index].u[1],
+// 	  directorWhole[index].u[2] );
 
 //   fprintf(stdout,
 // 	  "%6g\t%6G\n",