--- trunk/tcProps/tcProps.c	2004/02/20 17:52:57	1061
+++ trunk/tcProps/tcProps.c	2004/02/20 21:20:37	1062
@@ -46,7 +46,7 @@ int main( int argC, char *argV[] ){
   int scdCorr;
   double startTime;
   double maxLength;
-  int directorHead;
+  int directorHead, directorWhole;
 
   // system initialization
   
@@ -65,6 +65,7 @@ int main( int argC, char *argV[] ){
   scdCorr = 0;
   startTime = 0.0;
   directorHead = 0;
+  directorWhole = 0;
   
 
   // parse the command line
@@ -308,7 +309,13 @@ int main( int argC, char *argV[] ){
 	    directorHead = 1;
 	    break;
 
+	  case 'w':
+	    // -h turn on director head
 
+	    directorWhole = 1;
+	    break;
+
+
 	  default:
 
 	    fprintf( stderr, 
@@ -356,50 +363,71 @@ int main( int argC, char *argV[] ){
   for(i=0;i<nLipids;i++){
 
     atoms[nLipAtoms*i+0].type = HEAD;
+    atoms[nLipAtoms*i+0].mass = 72;
     atoms[nLipAtoms*i+0].u[0] = 0.0;
     atoms[nLipAtoms*i+0].u[1] = 0.0;
     atoms[nLipAtoms*i+0].u[2] = 1.0;
+    
     
 
     atoms[nLipAtoms*i+1].type = CH2;
+    atoms[nLipAtoms*i+1].mass = 14.03;
 
     atoms[nLipAtoms*i+2].type = CH;
+    atoms[nLipAtoms*i+2].mass = 13.02;
 
     atoms[nLipAtoms*i+3].type = CH2;
+    atoms[nLipAtoms*i+3].mass = 14.03;
 
     atoms[nLipAtoms*i+4].type = CH2;
+    atoms[nLipAtoms*i+4].mass = 14.03;
 
     atoms[nLipAtoms*i+5].type = CH2;
+    atoms[nLipAtoms*i+5].mass = 14.03;
 
     atoms[nLipAtoms*i+6].type = CH2;
+    atoms[nLipAtoms*i+6].mass = 14.03;
 
     atoms[nLipAtoms*i+7].type = CH2;
+    atoms[nLipAtoms*i+7].mass = 14.03;
 
     atoms[nLipAtoms*i+8].type = CH2;
+    atoms[nLipAtoms*i+8].mass = 14.03;
 
     atoms[nLipAtoms*i+9].type = CH2;
+    atoms[nLipAtoms*i+9].mass = 14.03;
 
     atoms[nLipAtoms*i+10].type = CH3;
+    atoms[nLipAtoms*i+10].mass = 15.04;
 
     atoms[nLipAtoms*i+11].type = CH2;
+    atoms[nLipAtoms*i+11].mass = 14.03;
 
     atoms[nLipAtoms*i+12].type = CH2;
+    atoms[nLipAtoms*i+12].mass = 14.03;
 
-    atoms[nLipAtoms*i+13].type = CH2;
+    atoms[nLipAtoms*i+13].type = CH2;    
+    atoms[nLipAtoms*i+13].mass = 14.03;
 
     atoms[nLipAtoms*i+14].type = CH2;
+    atoms[nLipAtoms*i+14].mass = 14.03;
   
     atoms[nLipAtoms*i+15].type = CH2;
+    atoms[nLipAtoms*i+15].mass = 14.03;
   
     atoms[nLipAtoms*i+16].type = CH2;
+    atoms[nLipAtoms*i+16].mass = 14.03;
   
     atoms[nLipAtoms*i+17].type = CH2;
+    atoms[nLipAtoms*i+17].mass = 14.03;
   
     atoms[nLipAtoms*i+18].type = CH3;
+    atoms[nLipAtoms*i+18].mass = 15.04;
   }
   
   for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
     atoms[i].type = SSD;
+    atoms[i].mass = 18.03;
     atoms[i].u[0] = 0.0;
     atoms[i].u[1] = 0.0;
     atoms[i].u[2] = 1.0;
@@ -440,6 +468,15 @@ int main( int argC, char *argV[] ){
     
     calcDirHeadCorr( startTime, atoms, outPrefix );
   }
+
+  if(directorWhole){
+
+    fprintf ( stdout,
+	      "Calculating the bilayer director\n" );
+    fflush( stdout );
+    
+    calcDirWholeCorr( startTime, atoms, outPrefix );
+  }
   
 
   closeFile();
@@ -465,6 +502,8 @@ void usage(){
 		"   -l <maxLength>  set the maximum value of r\n"
 		"                     *Defaults to 1/2 smallest length of first frame.\n"
 		"   -s              Calculate the Scd chain correlation.\n"
+		"   -h              Calculate the directors for the head groups\n"
+		"   -w              Calculate the director fro the bilayers\n"
 		"\n"
 		"   long:\n"
 		"   -----\n"