--- trunk/commandLine/commandLine.c	2003/05/05 21:35:19	518
+++ trunk/commandLine/commandLine.c	2003/05/05 22:01:36	520
@@ -1,60 +1,28 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <math.h>
 
 
-#include "madProps.h"
-#include "frameCount.h"
-
 char *program_name; /*the name of the program */
-
 void usage(void);
 
 int main(argc, argv)
      int argc;
      char *argv[];
 {
-
-
-  struct xyz_frame *dumpArray;
-  int nFrames; // the nu8mvber of frames
-  int lineNum = 0; // keeps track of the line number
-  int n_atoms; // the number of atoms
   int i,j; // loop counters
-  int isFirst;
 
-  char read_buffer[2000]; /*the line buffer for reading */
-  char *foo; /*the pointer to the current string token */
-  FILE *in_file; /* the input file */
-  char *in_name = NULL; /*the name of the input file */
-  char *out_prefix; // the output prefix
-  char current_flag; // used in parseing the flags
-
-
-
+  char *in_name = NULL; // name of the input file
+  char* out_prefix = NULL; // the output prefix
+  char current_flag; // used in parsing the flags
   int done = 0; // multipurpose boolean
-  int have_prefix = 0; // prefix boolean
-  int calcRMSD = 0;
+  int have_prefix; // boolean for the output prefix
 
-  int calcGofR = 0;
-  char gofR1[30];
-  char gofR2[30];
-
-  int calcMuCorr = 0;
-  char muCorr[30];
-
-  int calcCosCorr = 0;
-  char cosCorr1[30];
-  char cosCorr2[30];
-
-  int startFrame = 0;
-  int haveStartFrame = 0;
-  int endFrame = 0;
-  int haveEndFrame = 0;
-
-  program_name = argv[0]; /*save the program name in case we need it*/
   
+  // here we set the name of the program need by the usage message
+  program_name = argv[0];
+  
+
   for( i = 1; i < argc; i++){
     
     if(argv[i][0] =='-'){
@@ -178,295 +146,33 @@ int main(argc, argv)
   }
 
   if( !have_prefix ) out_prefix = in_name;
-  
-  printf( "Counting number of frames..." );
-  fflush( stdout );
-  
-  nFrames = frameCount( in_name );
-  if( !haveEndFrame ) endFrame = nFrames;
-
-  printf( "done.\n"
-	  "nframes = %d\n"
-	  "\n",
-	  nFrames );
-  fflush( stdout );
-
-  in_file = fopen(in_name, "r");
-  if(in_file == NULL){
-    printf("Cannot open file: %s\n", in_name);
-    exit(8);
-  }
-
-  // create and initialize the array of frames
-
-  dumpArray = (struct xyz_frame*)calloc( nFrames,
-					 sizeof( struct xyz_frame ) );
-  for( i=0; i<nFrames; i++ ){
-    dumpArray[i].nAtoms = 0;
-    dumpArray[i].time   = 0.0;
-    dumpArray[i].boxX   = 0.0;
-    dumpArray[i].boxY   = 0.0;
-    dumpArray[i].boxZ   = 0.0;
-    dumpArray[i].r      = NULL;
-    dumpArray[i].v      = NULL;
-    dumpArray[i].names  = NULL;
-  }
-
-  // read the frames
-  
-  printf( "Reading the frames into the coordinate arrays..." );
-  fflush( stdout );
-
-  isFirst = 1;
-  for(j =0; j<nFrames; j++ ){
-    
-    // read the number of atoms
-
-    fgets(read_buffer, sizeof(read_buffer), in_file);
-    lineNum++;
-
-    n_atoms = atoi( read_buffer );
-    dumpArray[j].nAtoms = n_atoms;
-
-    dumpArray[j].r = 
-      (struct coords *)calloc(n_atoms, sizeof(struct coords));
-    
-    if( isFirst ) {
-      dumpArray[0].names = 
-	(atomID *)calloc( n_atoms, sizeof(atomID) );
-      isFirst = 0;
-    }
-
-    if( calcMuCorr || calcCosCorr ){
-          dumpArray[j].v = 
-	    (struct vect *)calloc(n_atoms, sizeof(struct vect));
-    }
-
-    //read the time and the box sizes
-
-    fgets(read_buffer, sizeof(read_buffer), in_file);
-    lineNum++;
-    
-    foo = strtok(read_buffer, " ,;\t");
-    if(foo == NULL){
-      printf("error in reading time at line %d\n", lineNum);
-      exit(8);
-    }
-    
-    dumpArray[j].time = atof( foo );
-    
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      printf("error in reading boxX at line %d\n", lineNum);
-      exit(8);
-    }
-    
-    dumpArray[j].boxX = atof( foo );
-
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      printf("error in reading boxY at line %d\n", lineNum);
-      exit(8);
-    }
-    
-    dumpArray[j].boxY = atof( foo );
-    
-    foo = strtok(NULL, " ,;\t");
-    if(foo == NULL){
-      printf("error in reading boxZ at line %d\n", lineNum);
-      exit(8);
-    }
-    
-    dumpArray[j].boxZ = atof( foo );
-
-
-    for( i=0; i < n_atoms; i++){
-      
-      fgets(read_buffer, sizeof(read_buffer), in_file);
-      lineNum++;
-      
-      // get the name and positions
-
-      foo = strtok(read_buffer, " ,;\t");
-      if(foo == NULL){
-	printf("error in reading atom name at line %d\n", lineNum );
-	exit(8);
-      }
-      
-      strcpy(dumpArray[0].names[i], foo); /*copy the atom name */
 
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	printf("error in reading position x at line %d\n", lineNum);
-	exit(8);
-      }
-      
-      dumpArray[j].r[i].x = atof( foo );
-
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	printf("error in reading position y at line %d\n", lineNum);
-	exit(8);
-      }
-      
-      dumpArray[j].r[i].y = atof( foo );
-
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	printf("error in reading position z at line %d\n", lineNum);
-	exit(8);
-      }
-      
-      dumpArray[j].r[i].z = atof( foo );
-
-      if( calcCosCorr || calcMuCorr ){
-	
-	foo = strtok(NULL, " ,;\t");
-	if(foo == NULL){
-	  	  
-	  dumpArray[j].v[i].x = 0.0;
-	  dumpArray[j].v[i].y = 0.0;
-	  dumpArray[j].v[i].z = 0.0;
-	}
-	else{
-
-	  dumpArray[j].v[i].x = atof( foo );
-	  
-	  foo = strtok(NULL, " ,;\t");
-	  if(foo == NULL){
-	    printf("error in reading vector y at line %d\n", lineNum);
-	    exit(8);
-	  }
-	  
-	  dumpArray[j].v[i].y = atof( foo );
-	  
-	  foo = strtok(NULL, " ,;\t");
-	  if(foo == NULL){
-	    printf("error in reading vector z at line %d\n", lineNum);
-	    exit(8);
-	  }
-	  
-	  dumpArray[j].v[i].z = atof( foo );
-	}
-      }
-      
-    }
-  }
-  
-  (void)fclose(in_file);
-  
-  printf( "done\n"
-	  "\n" );
-  fflush( stdout );
-  
-  
-
-  // do calculations here.
-
-  if( calcGofR ){
-    
-    fprintf( stdout,
-	     "Calculating the g(r) between atoms \"%s\" and \"%s\"...",
-	     gofR1, gofR2 );
-    fflush( stdout );
-    
-    // gofr call
-    GofR( out_prefix, gofR1, gofR2, dumpArray, nFrames, startFrame, endFrame );
-    
-    fprintf( stdout, 
-	     " done.\n"
-	     "\n");
-    fflush(stdout);
-  }
-
-  if( calcRMSD ){
-    
-    fprintf( stdout,
-	     "Calculating the RMSD..." );
-    fflush( stdout );
-    
-    // RMSD call
-
-    
-    fprintf( stdout, 
-	     " done.\n"
-	     "\n");
-    fflush(stdout);
-  }
-
-  if( calcMuCorr ){
-    
-    fprintf( stdout,
-	     "Calculating the mu correlation for \"%s\"...",
-	     muCorr);
-    fflush( stdout );
-    
-    // muCorr call
-
-    
-    fprintf( stdout, 
-	     " done.\n"
-	     "\n");
-    fflush(stdout);
-  }
-
-  if( calcCosCorr ){
-    
-    fprintf( stdout,
-	     "Calculating the cos correlation between \"%s\" and \"%s\"...",
-	     cosCorr1, cosCorr2 );
-    fflush( stdout );
-    
-    cosCorr( out_prefix, cosCorr1, cosCorr2, dumpArray, nFrames, startFrame, 
-	     endFrame );
-    
-    fprintf( stdout, 
-	     " done.\n"
-	     "\n");
-    fflush(stdout);
-  }
-  
-  return 0;
-  
 }
 
 
-void map( double *x, double *y, double *z, 
-	  double boxX, double boxY, double boxZ ){ 
-  
-  *x -= boxX * copysign(1.0,*x) * floor( fabs( *x/boxX ) + 0.5  );
-  *y -= boxY * copysign(1.0,*y) * floor( fabs( *y/boxY ) + 0.5  );
-  *z -= boxZ * copysign(1.0,*z) * floor( fabs( *z/boxZ ) + 0.5  );
-
-}
-
-
 /***************************************************************************
  * prints out the usage for the command line arguments, then exits.
  ***************************************************************************/
 
 void usage(){
   (void)fprintf(stdout, 
-		"The proper usage is: %s [options] <xyz_file>\n"
+		"The proper usage is: %s [options] <input_file>\n"
 		"\n"
 		"Options:\n"
 		"\n"
 		"   short:\n"
 		"   ------\n"
 		"   -h              Display this message\n"
-		"   -o <prefix>     The output prefix\n"
-		"   -r              Calculate the RMSD\n"
-		"   -g              Calculate all to all g(r)\n"
+		"   -o <name>       The output name/prefix\n"
+		"   -r              the r flag\n"
+		"   -i <#>          set number to <#>\n"
 		
 		"\n"
 		"   long:\n"
 		"   -----\n"
-		"   --GofR <atom1> <atom2>    Calculates g(r) between atom1 and atom 2\n"
-		"                               -note: \"all\" will do all atoms\n"
-		"   --MuCorr <atom>           Calculate mu correlation of atom\n"
-		"   --CosCorr <atom1> <atom2> Calculate the cos correlation between atom1 and atom2\n"
-		"   --startFrame <frame#>     Specifies a frame to start correlating\n"
-		"   --endFrame <frame#>       Specifies a frame to stop correlating.\n"
+		"   --flag1 <arg1> <arg2>     does flag 1 for arg1 and 2\n"
+		"   --flag2 <arg1>            does flag 2 for arg1\n"
+		"   --flag3                   does flag 3\n"
 		
 		"\n"
 		"\n",