--- trunk/OOPSE/staticProps/staticProps.cpp	2003/10/10 17:10:22	803
+++ trunk/OOPSE/staticProps/staticProps.cpp	2004/02/09 20:38:38	1043
@@ -39,6 +39,10 @@ int main(int argC,char* argV[]){
   bool haveMaxLength;
   double maxLength;
   
+  bool separateOut;
+  bool havePairCorrs;
+  bool haveStaticCorrs;
+
   int nBins;
 
   vector<PairCorrList> theList;
@@ -59,8 +63,7 @@ int main(int argC,char* argV[]){
   
   // first things first, all of the initializations
 
-  printf("Initializing stuff ....\n");
-  fflush(sdtout);
+  fflush(stdout);
   srand48( 1337 );          // the random number generator.
   initSimError();           // the error handler
 
@@ -72,11 +75,15 @@ int main(int argC,char* argV[]){
  
   havePrefix = false;
   haveMaxLength = false;
+
+  haveStaticCorrs = false;
+  havePairCorrs = false;
+  separateOut = false;
   
   maxLength = 1.0;
   nBins = 100;
 
-  programName = argv[0]; /*save the program name in case we need it*/
+  programName = argV[0]; /*save the program name in case we need it*/
 
   for( i = 1; i < argC; i++){
     
@@ -89,7 +96,7 @@ int main(int argC,char* argV[]){
 	// parse long word options
 	
 	if( !strcmp( argV[i], "--gofr" ) ){
-	  
+
 	  i++;
 	  if( i>=argC ){
 	    sprintf( painCave.errMsg,
@@ -113,7 +120,66 @@ int main(int argC,char* argV[]){
 	  pair2 = argV[i];
 
 	  pairType = gofr;
+	  theList.push_back(PairCorrList( pairType, pair1, pair2 ));
+	  havePairCorrs = true;
+	}
+
+	else if( !strcmp( argV[i], "--gofrTheta" ) ){
+	  
+	  i++;
+	  if( i>=argC ){
+	    sprintf( painCave.errMsg,
+		     "\n"
+		     "not enough arguments for --gofrTheta\n");
+	    usage();
+	    painCave.isFatal = 1;
+	    simError();
+	  }	  
+	  pair1 = argV[i];
+
+	  i++;
+	  if( i>=argC ){
+	    sprintf( painCave.errMsg,
+		     "\n"
+		     "not enough arguments for --gofrTheta\n");
+	    usage();
+	    painCave.isFatal = 1;
+	    simError();
+	  }	  
+	  pair2 = argV[i];
+
+	  pairType = gofrTheta;
+	  theList.push_back(PairCorrList( pairType, pair1, pair2 ));
+	  havePairCorrs = true;
+	}
+
+	else if( !strcmp( argV[i], "--gofrOmega" ) ){
+	  
+	  i++;
+	  if( i>=argC ){
+	    sprintf( painCave.errMsg,
+		     "\n"
+		     "not enough arguments for --gofrOmega\n");
+	    usage();
+	    painCave.isFatal = 1;
+	    simError();
+	  }	  
+	  pair1 = argV[i];
+
+	  i++;
+	  if( i>=argC ){
+	    sprintf( painCave.errMsg,
+		     "\n"
+		     "not enough arguments for --gofrOmega\n");
+	    usage();
+	    painCave.isFatal = 1;
+	    simError();
+	  }	  
+	  pair2 = argV[i];
+
+	  pairType = gofrOmega;
 	  theList.push_back(PairCorrList( pairType, pair1, pair2 ));
+	  havePairCorrs = true;
 	}
 
 	else if( !strcmp( argV[i], "--version") ){
@@ -245,6 +311,12 @@ int main(int argC,char* argV[]){
 
 	    break;
 
+	  case 's':
+	    // -s turn on separate output files
+
+	    separateOut = true;
+	    break;
+
 	  case 'n':
 	    // -n <int>    set <int> to the nBins
 
@@ -369,14 +441,15 @@ int main(int argC,char* argV[]){
 	 nFrames );
   fflush(stdout);
 
-  infoArray = new SimInfo[nFrames];
+  infoArray = new SimInfo;
 
   printf("Parsing the bass file, and initializing the "
 	 "Simulation Frames..." );
   fflush(stdout);
   
   startMe = new SimSetup();
-  startMe->setSimInfo( infoArray, nFrames );
+  startMe->setSimInfo( infoArray );
+  startMe->suspendInit();
   startMe->parseFile( inName );
   startMe->createSim();
 
@@ -394,7 +467,8 @@ int main(int argC,char* argV[]){
   theCorrs.setNbins( nBins );
   theCorrs.setFrames( infoArray, nFrames, reader );
   theCorrs.setPairCorrList( theList );
-  theCorrs.initCorrelations( outPrefix );
+  theCorrs.initCorrelations( outPrefix, separateOut, havePairCorrs,
+			     haveStaticCorrs );
 
   printf("done\n");
   fflush(stdout);
@@ -428,10 +502,14 @@ void usage(){
 		"\n"
 		"   long:\n"
 		"   -----\n"
-		"   --gofr <atom1> <atom2>    g(r) for atom1 and atom2\n"
-		"                                *note: \"_ALL_\" matches all atoms/n"
-		"   --version                 displays the version number\n"
-		"   --help                    displays this help message.\n"
+		"   --gofr <atom1> <atom2>         g(r) for atom1 and atom2\n"
+		"                                    *note: \"_ALL_\" matches all atoms\n"
+		"   --gofrTheta <atom1> <atom2>    g(r, theta) for atom1 and atom2\n"
+		"                                    *note: \"_ALL_\" matches all atoms\n"
+		"   --gofrOmega <atom1> <atom2>    g(r, omega) for atom1 and atom2\n"
+		"                                    *note: \"_ALL_\" matches all atoms\n"
+		"   --version                      displays the version number\n"
+		"   --help                         displays this help message.\n"
 		
 		"\n"
 		"\n",