--- trunk/dumpCat/dumpCat.c	2002/07/24 16:51:43	48
+++ trunk/dumpCat/dumpCat.c	2002/09/06 21:47:13	105
@@ -3,6 +3,7 @@
 #include <string.h>
 #include <unistd.h>
 
+#define MAX_FILES 1000
 
 void usage( void );
 
@@ -14,22 +15,113 @@ int main( int argc, char* argv[] ){
   double realTime, currentTime, lastTime;
   double boxX, boxY, boxZ;
   char* foo;
-  char* in_name;
-  char* out_name;
+  char* in_name[MAX_FILES];
   char readBuffer[2000];
   int i,j,k;
   int lineNum;
 
+  int current_flag;
+  int done;
+  
+  char* out_name;
+  int have_out = 0;
+
+  int timeMod = 1;
+
+  int nFiles;
+  int index;
+  
+  int printMe = 0;
+  int skipFirst = 0;
+
   FILE *in_file;
   FILE *out_file;
   
   program_name = argv[0];
+
+  nFiles = 0;
+  for( i = 1; i < argc; i++){
+    
+    if(argv[i][0] =='-'){
+
+      // parse the option
+      
+      if(argv[i][1] == '-' ){
+
+	// parse long word options
+	
+	fprintf( stderr, 
+		 "Invalid option \"%s\"\n", argv[i] );
+	usage();
+	
+      }
+      
+      else{
+	
+	// parse single character options
+	
+	done = 0;
+	j = 1;
+	current_flag = argv[i][j];
+	while( (current_flag != '\0') && (!done) ){
+	  
+	  switch(current_flag){
+
+	  case 'o':
+	    // -o <outFile> => the output file.
+
+	    i++;
+	    out_name = argv[i];
+	    have_out = 1;
+	    done = 1;
+	    break;
+
+	  case 't':
+	    // -t <#> => the time increment
+
+	    i++;
+	    timeMod = atoi( argv[i] );
+	    done = 1;
+	    break;
+
+	  case 'h':
+ 	    // -h => display help
+	    
+	    usage();
+	    break;
+	
+	  case 's':
+	    // -b => skip first frame
+
+	    skipFirst = 1;
+	    break;
+
+	  default:
+
+	    (void)fprintf(stderr, "Bad option \"-%c\"\n", current_flag);
+	    usage();
+	  }
+	  j++;
+	  current_flag = argv[i][j];
+	}
+      }
+    }
+
+    else{
+      
+      nFiles++;
+      if( nFiles >= MAX_FILES ){
+	printf( "Error, MAX_FILES, %d, exceeded at %s\n", MAX_FILES, argv[i] );
+	exit(0);
+      }
+      
+      in_name[(nFiles-1)] = argv[i];
+    }
+  }
   
-  out_name = argv[1];
-  
-  if( !access( out_name, F_OK ) ){
+  if( !have_out ){
     
-    in_file = fopen( out_name, "r" );
+    in_file = fopen( in_name[0], "r" );
     lineNum =0;
     if( in_file == NULL ){
       printf( "Error opening \"%s\"\n", out_name );
@@ -76,7 +168,7 @@ int main( int argc, char* argv[] ){
     
     fclose( in_file );
 
-    out_file = fopen( out_name, "a" );
+    out_file = fopen( in_name[0], "a" );
   }
   
   else{
@@ -84,92 +176,145 @@ int main( int argc, char* argv[] ){
     out_file = fopen( out_name, "w" );
     lastTime = 0.0;
     
-    in_name = argv[2];
-
-    in_file = fopen( in_name, "r" );
+    in_file = fopen( in_name[0], "r" );
     lineNum = 0;
     if( in_file == NULL ){
-      printf( "Error opening \"%s\"\n", in_name );
+      printf( "Error opening \"%s\"\n", in_name[0] );
       exit(8);
     }
 
     fgets( readBuffer, sizeof( readBuffer ), in_file );
     lineNum++;
     if( feof( in_file ) ){
-      printf( "File %s ended unexpectedly at line %d\n", in_name, lineNum );
+      printf( "File %s ended unexpectedly at line %d\n", in_name[0], lineNum );
       exit(8);
     }
+       
+    while( !feof( in_file ) ){
+      
+      
+      i = atoi(readBuffer);
+      
+      fgets(readBuffer, sizeof(readBuffer), in_file);
+      lineNum++;
+      if( feof( in_file ) ){
+	printf( "File %s ended unexpectedly at line %d\n", in_name[0], 
+		lineNum );
+	exit(8);
+      }
+      
+ 
+      foo = strtok(readBuffer, " ,;\t");
+      if(foo == NULL){
+	printf("error in reading time at line %d in %s\n", lineNum, 
+	       in_name[0]);
+	exit(8);
+      }
     
-    fprintf( out_file, "%s", readBuffer );
+      currentTime = atof( foo );
+      realTime = currentTime + lastTime;
+      
 
-    i = atoi(readBuffer);
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	printf("error in reading boxX at line %d in %s\n", lineNum, 
+	       in_name[0]);
+	exit(8);
+      }
     
-    fgets(readBuffer, sizeof(readBuffer), in_file);
-    lineNum++;
-    if( feof( in_file ) ){
-      printf( "File %s ended unexpectedly at line %d\n", in_name, lineNum );
-      exit(8);
-    }
-    
-    fprintf( out_file, "%s", readBuffer );
+      boxX = atof( foo );
 
-    for(j=0; j<i; j++){
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	printf("error in reading boxY at line %d in %s\n", lineNum, 
+	       in_name[0]);
+	exit(8);
+      }
       
-      fgets( readBuffer, sizeof( readBuffer ), in_file );
-      lineNum++;    
-      if( feof( in_file ) ){
-	printf( "File %s ended unexpectedly at line %d,"
-		" with atom %d\n", in_name, lineNum, j);
+      boxY = atof( foo );
+    
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	printf("error in reading boxZ at line %d in %s\n", lineNum, 
+	       in_name[0]);
 	exit(8);
       }
+      
+      boxZ = atof( foo );
 
-      fprintf( out_file, "%s", readBuffer );
-    }
+      printMe = !( ((int)realTime) % timeMod );
+      
+      if( printMe ){
+	fprintf( out_file, "%d\n", i );
+	fprintf( out_file, "%lf\t%lf\t%lf\t%lf\n",
+		 realTime, boxX, boxY, boxZ );
+      }
+      
+      for(j=0; j<i; j++){
+	
+	fgets( readBuffer, sizeof( readBuffer ), in_file );
+	lineNum++;    
+	if( feof( in_file ) ){
+	  printf( "File %s ended unexpectedly at line %d,"
+		  " with atom %d\n", in_name[0], lineNum, j);
+	  exit(8);
+	}
+	
+	if(printMe) fprintf( out_file, "%s", readBuffer );
 
+      }
+           
+      fgets( readBuffer, sizeof( readBuffer ), in_file );
+      lineNum++;
+    }
+    
+    lastTime = realTime;
     fclose( in_file );
   }
 
-  for( k=2; k<argc; k++ ){
+  for( k=1; k<nFiles; k++ ){
 
-    in_name = argv[k];
-
-    in_file = fopen( in_name, "r" );
+    in_file = fopen( in_name[k], "r" );
     lineNum = 0;
     if( in_file == NULL ){
-      printf( "Error opening \"%s\"\n", in_name );
+      printf( "Error opening \"%s\"\n", in_name[k] );
       exit(8);
     }
     
     
-    // skip the zero frame
+    // if this is a time = 0.0 frame then don't write it.
 
-    fgets( readBuffer, sizeof( readBuffer ), in_file );
-    lineNum++;
-    if( feof( in_file ) ){
-      printf( "File %s ended unexpectedly at line %d\n", in_name, lineNum );
-      exit(8);
-    }
-    
-    i = atoi(readBuffer);
-    
-    fgets(readBuffer, sizeof(readBuffer), in_file);
-    lineNum++;
-    if( feof( in_file ) ){
-      printf( "File %s ended unexpectedly at line %d\n", in_name, lineNum );
-      exit(8);
-    }
-    
-    for(j=0; j<i; j++){
-      
+    if( skipFirst ){
       fgets( readBuffer, sizeof( readBuffer ), in_file );
-      lineNum++;    
+      lineNum++;
       if( feof( in_file ) ){
-	printf( "File %s ended unexpectedly at line %d,"
-		" with atom %d\n", in_name, lineNum, j);
+	printf( "File %s ended unexpectedly at line %d\n", in_name[k], 
+		lineNum );
 	exit(8);
       }
+      
+      i = atoi(readBuffer);
+      
+      fgets(readBuffer, sizeof(readBuffer), in_file);
+      lineNum++;
+      if( feof( in_file ) ){
+	printf( "File %s ended unexpectedly at line %d\n", in_name[k], 
+		lineNum );
+	exit(8);
+      }
+      
+      for(j=0; j<i; j++){
+	
+	fgets( readBuffer, sizeof( readBuffer ), in_file );
+	lineNum++;    
+	if( feof( in_file ) ){
+	  printf( "File %s ended unexpectedly at line %d,"
+		  " with atom %d\n", in_name[k], lineNum, j);
+	  exit(8);
+	}
+      }
     }
-    
+
     // now start reading and writing
 
     fgets( readBuffer, sizeof( readBuffer ), in_file );
@@ -181,21 +326,21 @@ int main( int argc, char* argv[] ){
     
     while( !feof( in_file ) ){
       
-      fprintf( out_file, "%s", readBuffer );
-      
       i = atoi(readBuffer);
       
       fgets(readBuffer, sizeof(readBuffer), in_file);
       lineNum++;
       if( feof( in_file ) ){
-	printf( "File %s ended unexpectedly at line %d\n", in_name, lineNum );
+	printf( "File %s ended unexpectedly at line %d\n", in_name[k], 
+		lineNum );
 	exit(8);
       }
       
  
       foo = strtok(readBuffer, " ,;\t");
       if(foo == NULL){
-	printf("error in reading time at line %d in %s\n", lineNum, in_name);
+	printf("error in reading time at line %d in %s\n", lineNum, 
+	       in_name[k]);
 	exit(8);
       }
     
@@ -205,7 +350,8 @@ int main( int argc, char* argv[] ){
 
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading boxX at line %d in %s\n", lineNum, in_name);
+	printf("error in reading boxX at line %d in %s\n", lineNum, 
+	       in_name[k]);
 	exit(8);
       }
     
@@ -213,7 +359,8 @@ int main( int argc, char* argv[] ){
 
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading boxY at line %d in %s\n", lineNum, in_name);
+	printf("error in reading boxY at line %d in %s\n", lineNum, 
+	       in_name[k]);
 	exit(8);
       }
       
@@ -221,26 +368,32 @@ int main( int argc, char* argv[] ){
     
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading boxZ at line %d in %s\n", lineNum, in_name);
+	printf("error in reading boxZ at line %d in %s\n", lineNum, 
+	       in_name[k]);
 	exit(8);
       }
       
       boxZ = atof( foo );
 
-      fprintf( out_file, "%lf\t%lf\t%lf\t%lf\n",
-	       realTime, boxX, boxY, boxZ );
+      printMe = !( ((int)realTime) % timeMod );
       
+      if( printMe ){
+	fprintf( out_file, "%d\n", i );
+	fprintf( out_file, "%lf\t%lf\t%lf\t%lf\n",
+		 realTime, boxX, boxY, boxZ );
+      }
+      
       for(j=0; j<i; j++){
 	
 	fgets( readBuffer, sizeof( readBuffer ), in_file );
 	lineNum++;    
 	if( feof( in_file ) ){
 	  printf( "File %s ended unexpectedly at line %d,"
-		  " with atom %d\n", in_name, lineNum, j);
+		  " with atom %d\n", in_name[k], lineNum, j);
 	  exit(8);
 	}
 	
-	fprintf( out_file, "%s", readBuffer );
+	if(printMe) fprintf( out_file, "%s", readBuffer );
 
       }
            
@@ -256,3 +409,26 @@ int main( int argc, char* argv[] ){
   
   return 0;
 }
+
+
+/***************************************************************************
+ * prints out the usage for the command line arguments, then exits.
+ ***************************************************************************/
+
+void usage(){
+  (void)fprintf(stderr, 
+		"The proper usage is: %s [options] dumpFile1 dumpFile2...\n"
+		"\n"
+		"Options:\n"
+		"\n"
+		"   -o <outFile>  the output file\n"
+		"                     *default is to append to first file.\n"
+		"   -t <#>        only print out time steps that are\n"
+		"                      increments of <#>\n"
+		"   -s            skip the first frame (t = 0.0 )\n"
+		"\n"
+		"   -h            display this message\n"
+		"\n",
+		program_name);
+  exit(8);
+}