--- trunk/tcProps/tcProps.c	2004/02/18 21:20:51	1058
+++ trunk/tcProps/tcProps.c	2004/02/28 16:45:57	1073
@@ -2,12 +2,16 @@
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 
 #include "params.h"
 #include "tcProps.h"
 #include "readWrite.h"
 #include "scdCorr.h"
+#include "directorHead.h"
+#include "directorWhole.h"
+#include "rmsd.h"
 
 
 #define VERSION_MAJOR 0
@@ -30,13 +34,12 @@ int main( int argC, char *argV[] ){
   
   struct atomCoord atoms[nAtoms];
   int i,j,k;
-  char* inName;
-  int nFrames;
   
   char* outPrefix; // the output prefix
   char currentFlag; // used in parsing the flags
   int done = 0; // multipurpose boolean
   int havePrefix; // boolean for the output prefix  
+  int haveMaxLength;
   char* conversionCheck;
   int conversionError;
   int optionError;
@@ -44,6 +47,9 @@ int main( int argC, char *argV[] ){
   char* pair2;
   int scdCorr;
   double startTime;
+  double maxLength;
+  int directorHead, directorWhole, doRMSD;
+  enum atomNames rmsdType;
 
   // system initialization
   
@@ -55,11 +61,15 @@ int main( int argC, char *argV[] ){
   outPrefix = NULL;
   inName = NULL;
   
+  haveMaxLength = 0;
   conversionError = 0;
   optionError = 0;
   havePrefix = 0;
   scdCorr = 0;
   startTime = 0.0;
+  directorHead = 0;
+  directorWhole = 0;
+  doRMSD = 0;
   
 
   // parse the command line
@@ -76,27 +86,31 @@ int main( int argC, char *argV[] ){
 
 	// parse long word options
 	
-	if( !strcmp( argV[i], "--gofr" ) ){
+	if( !strcmp( argV[i], "--rmsd" ) ){
 
+	  doRMSD = 1;
 	  i++;
 	  if( i>=argC ){
 	    fprintf( stderr,
 		     "\n"
-		     "not enough arguments for --gofr\n");
+		     "not enough arguments for --rmsd\n");
 	    usage();
 	    exit(0);
 	  }	  
 	  pair1 = argV[i];
 
-	  i++;
-	  if( i>=argC ){
+	  if( !strcmp(pair1, "HEAD") )    rmsdType = HEAD;
+	  else if( !strcmp(pair1, "CH") ) rmsdType = CH;
+	  else if( !strcmp(pair1, "CH2") )rmsdType = CH2;
+	  else if( !strcmp(pair1, "CH3") )rmsdType = CH3;
+	  else if( !strcmp(pair1, "SSD") )rmsdType = SSD;
+	  else if( !strcmp(pair1, "COM") )rmsdType = COM;
+	  else{
 	    fprintf( stderr,
-		     "\n"
-		     "not enough arguments for --gofr\n");
-	    usage();
+		     "Unrecognized rmsd atom type \"%s\"\n",
+		     pair1 );
 	    exit(0);
-	  }	  
-	  pair2 = argV[i];
+	  }
 
 	}
 
@@ -231,7 +245,7 @@ int main( int argC, char *argV[] ){
 	  case 'l':
 	    // -l <double>    set <double> to the maxLength
 
-	    haveMaxLength = true;
+	    haveMaxLength = 1;
 	    j++;
 	    currentFlag = argV[i][j];
 	      
@@ -292,15 +306,27 @@ int main( int argC, char *argV[] ){
 	    break;
 
 	  case 's':
-	    // -s turn on separate output files
+	    // -s turn on Scd corr
 
 	    scdCorr = 1;
+	    break;
+
+	  case 'h':
+	    // -h turn on director head
+
+	    directorHead = 1;
+	    break;
+
+	  case 'w':
+	    // -h turn on director head
+
+	    directorWhole = 1;
 	    break;
 
 
 	  default:
 
-	    sprintf(painCave.errMsg, 
+	    fprintf( stderr, 
 		    "\n"
 		    "Bad option \"-%c\"\n", currentFlag);
 	    usage();
@@ -336,56 +362,80 @@ int main( int argC, char *argV[] ){
     exit(0);
   }
 
+  if( outPrefix == NULL )
+    outPrefix = inName;
 
+
   // initialize the arrays
 
   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;
@@ -393,7 +443,7 @@ int main( int argC, char *argV[] ){
 
   // read and set the frames
   
-  openFile( inName );
+  openFile();
 
   fprintf( stdout,
 	   "\n"
@@ -401,11 +451,11 @@ int main( int argC, char *argV[] ){
 	   inName );
   fflush(stdout);
 
-  setFrames( inName );
+  setFrames();
   
   fprintf( stdout,
 	   "done.\n"
-	   "nFrames = %d\n.",
+	   "nFrames = %d.\n",
 	   nFrames );
   fflush(stdout);
 
@@ -415,10 +465,39 @@ int main( int argC, char *argV[] ){
 	      "Calculating the Scd correlation\n" );
     fflush( stdout );
     
-    calcScdCorr( startTime );
+    calcScdCorr( startTime, atoms, outPrefix );
   }
+
+  if(directorHead){
+
+    fprintf ( stdout,
+	      "Calculating the Head director\n" );
+    fflush( stdout );
+    
+    calcDirHeadCorr( startTime, atoms, outPrefix );
+  }
+
+  if(directorWhole){
+
+    fprintf ( stdout,
+	      "Calculating the bilayer director\n" );
+    fflush( stdout );
+    
+    calcDirWholeCorr( startTime, atoms, outPrefix );
+  }
+
+  if(doRMSD){
+
+    fprintf ( stdout,
+	      "Calculating the RMSD\n" );
+    fflush( stdout );
+    
+    rmsd( rmsdType, startTime, outPrefix );
+  }
   
 
+  closeFile();
+
 }
 
 
@@ -440,10 +519,12 @@ 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"
-		"   --gofr <atom1> <atom2>         g(r) for atom1 and atom2\n"
+		"   --rmsd <atom1>                 rmsd for atom1\n"
 		"   --gofrTheta <atom1> <atom2>    g(r, theta) for atom1 and atom2\n"
 		"   --gofrOmega <atom1> <atom2>    g(r, omega) for atom1 and atom2\n"
 		"   --version                      displays the version number\n"