--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2004/01/07 19:26:12	905
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2004/04/12 20:32:20	1097
@@ -327,7 +327,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
   double pos[3]; // position place holders
   double vel[3]; // velocity placeholders
   double q[4]; // the quaternions
-  double jx, jy, jz; // angular velocity placeholders;
+  double ji[3]; // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
 
   Atom **atoms = simnfo->atoms;
@@ -490,7 +490,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	       c_in_name, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jx = atof( foo );
+    ji[0] = atof( foo );
 
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
@@ -500,7 +500,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	       c_in_name, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jy = atof(foo );
+    ji[1] = atof(foo );
 
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
@@ -510,7 +510,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	       c_in_name, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jz = atof( foo );
+    ji[2] = atof( foo );
 
     dAtom = ( DirectionalAtom* )atoms[atomIndex];
 
@@ -528,9 +528,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 
     // add the angular velocities
 
-    dAtom->setJx( jx );
-    dAtom->setJy( jy );
-    dAtom->setJz( jz );
+    dAtom->setJ( ji );
   }
 
   // add the positions and velocities to the atom
@@ -587,54 +585,63 @@ char* InitializeFromFile::parseCommentLine(char* readL
   entry_plug->setBoxM( theBoxMat3 );
 
   //get chi and integralOfChidt, they should appear by pair
-  foo = strtok(NULL, " ,;\t\n");
-  if(foo != NULL){
-    chi = atof(foo);
 
+  if( entry_plug->useInitXSstate ){
     foo = strtok(NULL, " ,;\t\n");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-               "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
-      return strdup( painCave.errMsg );
+    if(foo != NULL){
+      chi = atof(foo);
+      
+      foo = strtok(NULL, " ,;\t\n");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
+	return strdup( painCave.errMsg );
+      }
+      integralOfChidt = atof( foo );
+      
+      //push chi and integralOfChidt into SimInfo::properties which can be
+      //retrieved by integrator later
+      DoubleData* chiValue = new DoubleData();
+      chiValue->setID(CHIVALUE_ID);
+      chiValue->setData(chi);
+      entry_plug->addProperty(chiValue);
+      
+      DoubleData* integralOfChidtValue = new DoubleData();
+      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
+      integralOfChidtValue->setData(integralOfChidt);
+      entry_plug->addProperty(integralOfChidtValue);
+      
     }
-    integralOfChidt = atof( foo );
-
-    //push chi and integralOfChidt into SimInfo::properties which can be
+    else
+      return NULL;
+    
+    //get eta
+    foo = strtok(NULL, " ,;\t\n");
+    if(foo != NULL ){
+  
+      for(int i = 0 ; i < 9; i++){
+	
+	if(foo == NULL){
+	  sprintf( painCave.errMsg,
+		   "error in reading eta[%d] from %s\n", i, c_in_name );
+	  return strdup( painCave.errMsg );
+	}
+	eta[i] = atof( foo );
+	foo = strtok(NULL, " ,;\t\n");
+      }
+    }
+    else
+      return NULL;
+    
+    //push eta into SimInfo::properties which can be
     //retrieved by integrator later
-    DoubleData* chiValue = new DoubleData();
-    chiValue->setID(CHIVALUE_ID);
-    chiValue->setData(chi);
-    entry_plug->addProperty(chiValue);
-
-    DoubleData* integralOfChidtValue = new DoubleData();
-    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
-    integralOfChidtValue->setData(integralOfChidt);
-    entry_plug->addProperty(integralOfChidtValue);
-
+    //entry_plug->setBoxM( theBoxMat3 );
+    DoubleArrayData* etaValue = new DoubleArrayData();
+    etaValue->setID(ETAVALUE_ID);
+    etaValue->setData(eta, 9);
+    entry_plug->addProperty(etaValue);
   }
-  else
-    return NULL;
 
-  //get eta
-  for(int i = 0 ; i < 9; i++){
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      sprintf( painCave.errMsg,
-               "error in reading eta[%d] from %s\n", i, c_in_name );
-      return strdup( painCave.errMsg );
-    }
-    eta[i] = atof( foo );
-  }
-
-  //push eta into SimInfo::properties which can be
-  //retrieved by integrator later
-  //entry_plug->setBoxM( theBoxMat3 );
-  DoubleArrayData* etaValue = new DoubleArrayData();
-  etaValue->setID(ETAVALUE_ID);
-  etaValue->setData(eta, 9);
-  entry_plug->addProperty(etaValue);
-
-
   return NULL;
 }