--- trunk/tcProps/readWrite.c	2004/02/18 21:20:51	1058
+++ trunk/tcProps/readWrite.c	2004/02/19 21:10:06	1060
@@ -17,8 +17,8 @@ FILE* inFile;
 int nFrames;
 double *frameTimes;
 FILE* inFile;
+char* inName;
 
-
 struct linkedPos{
   
   fpos_t *myPos;
@@ -39,9 +39,9 @@ void openFile( char* inName ){
 void setU( double q[4], double u[3] );
 void normalizeQ( double q[4] );
 
-void openFile( char* inName ){
+void openFile( void ){
   
-  inFile = fopen(inName);
+  inFile = fopen(inName, "r");
   if(inFile ==NULL){
     fprintf(stderr,
 	    "Error opening file \"%s\"\n",
@@ -59,7 +59,7 @@ int setFrames( void ){
   fileOpen = 0;
 }
 
-int setFrames( void ){
+void setFrames( void ){
 
   int i,j,k;
   struct linkedPos* headPos;
@@ -81,21 +81,22 @@ int setFrames( void ){
   nFrames = 0;
   headPos = (struct linkedPos*)malloc(sizeof(struct linkedPos));
   currPos = headPos;
+
+  currPT = (fpos_t *)malloc(sizeof(fpos_t));
+  fgetpos(inFile, currPT);
+  
+  fgets( readBuffer, sizeof( readBuffer ), inFile );
+  lineNum++;
+  if( feof( inFile ) ){
+    fprintf( stderr,
+	     "File \"%s\" ended unexpectedly at line %d\n", 
+	     inName,
+	     lineNum );
+    exit(0);
+  }
+
   while( !feof( inFile ) ){
 
-    currPT = (fpos_t *)malloc(sizeof(fpos_t));
-    fgetpos(inFile, currPT);
-    
-    fgets( readBuffer, sizeof( readBuffer ), inFile );
-    lineNum++;
-    if( feof( inFile ) ){
-      fprintf( stderr,
-	       "File \"%s\" ended unexpectedly at line %d\n", 
-	       inName,
-	       lineNum );
-      exit(0);
-    }
-    
     currPos->next = (struct linkedPos*)malloc(sizeof(struct linkedPos));
     currPos = currPos->next;
     currPos->myPos = currPT;      
@@ -229,6 +230,12 @@ int setFrames( void ){
 	exit(0);
       }
     }
+
+    currPT = (fpos_t *)malloc(sizeof(fpos_t));
+    fgetpos(inFile, currPT);
+    
+    fgets( readBuffer, sizeof( readBuffer ), inFile );
+    lineNum++;
   }
   
   // allocate the static position array
@@ -303,7 +310,7 @@ void readFrame(int theFrame, struct atomCoord* atoms, 
   if( !fileOpen ){
     
     fprintf( stderr,
-	     "File is closed, cannot read frame %d.\n"
+	     "File is closed, cannot read frame %d.\n",
 	     theFrame );
     exit(0);
   }
@@ -311,7 +318,7 @@ void readFrame(int theFrame, struct atomCoord* atoms, 
   // access the frame
   
   framePos = posArray[theFrame].myPos;
-  fsetPos( inFile, framePos );
+  fsetpos( inFile, framePos );
 
   for(j=0;j<3;j++){
     for(k=0;k<3;k++){
@@ -370,6 +377,13 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
 
 void parseDumpLine( char readLine[BUFFER_SIZE], int i, 
 		    struct atomCoord* atoms ){
+  
+  const int nLipAtoms = NL_ATOMS;
+  const int nBonds    = NBONDS;
+  const int nLipids   = NLIPIDS;
+  const int nSSD      = NSSD;
+  const int nAtoms    = nLipAtoms * nLipids + nSSD;
+
   char* foo;
   double q[4];
 
@@ -384,7 +398,7 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
   case HEAD:
     if( strcmp(foo, "HEAD") ){
       fprintf( stderr,
-	       "Atom %s does not match master array type \"HEAD\".\n"
+	       "Atom %s does not match master array type \"HEAD\".\n",
 	       foo );
       exit(0);
     }
@@ -393,7 +407,7 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
   case CH:
     if( strcmp(foo, "CH") ){
       fprintf( stderr,
-	       "Atom %s does not match master array type \"CH\".\n"
+	       "Atom %s does not match master array type \"CH\".\n",
 	       foo );
       exit(0);
     }
@@ -402,7 +416,7 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
   case CH2:
     if( strcmp(foo, "CH2") ){
       fprintf( stderr,
-	       "Atom %s does not match master array type \"CH2\".\n"
+	       "Atom %s does not match master array type \"CH2\".\n",
 	       foo );
       exit(0);
     }
@@ -411,7 +425,7 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
   case CH3:
     if( strcmp(foo, "CH3") ){
       fprintf( stderr,
-	       "Atom %s does not match master array type \"CH3\".\n"
+	       "Atom %s does not match master array type \"CH3\".\n",
 	       foo );
       exit(0);
     }
@@ -420,7 +434,7 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
   case SSD:
     if( strcmp(foo, "SSD") ){
       fprintf( stderr,
-	       "Atom %s does not match master array type \"SSD\".\n"
+	       "Atom %s does not match master array type \"SSD\".\n",
 	       foo );
       exit(0);
     }
@@ -505,10 +519,10 @@ void parseDumpLine( char readLine[BUFFER_SIZE], int i,
       
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      sprintf(painCave.errMsg,
-	      "error in reading quaternion 0 from %s\n"
-	      "natoms  = %d, i = %d\n",
-	      inName, nAtoms, i );
+      fprintf( stderr,
+	       "error in reading quaternion 0 from %s\n"
+	       "natoms  = %d, i = %d\n",
+	       inName, nAtoms, i );
       exit(0);
     }
     q[0] = atof( foo );
@@ -555,6 +569,7 @@ void setU( double the_q[4], double u[3] ){
   double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
   double A[3][3];
   double rb[3];
+  int i,j,k;
 
   // initialize the axis