--- branches/mmeineke/madProps/madProps.c	2002/07/19 01:37:38	38
+++ trunk/madProps/madProps.c	2002/08/16 04:05:45	82
@@ -3,23 +3,10 @@
 #include <string.h>
 #include <math.h>
 
+
+#include "madProps.h"
 #include "frameCount.h"
 
-struct coords{
-  double x;
-  double y;
-  double z;
-  char name[30];
-};
-
-
-struct xyz_frame{
-  int nAtoms;
-  double time;
-  double boxX, boxY, boxZ;
-  struct coords *r;
-};
-
 char *program_name; /*the name of the program */
 
 void usage(void);
@@ -35,46 +22,161 @@ int main(argc, argv)
   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
 
 
+
+  int done = 0; // multipurpose boolean
+  int have_prefix = 0; // prefix boolean
+  int calcRMSD = 0;
+
+  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*/
   
-  for( i = 0; i < argc; i++){
+  for( i = 1; i < argc; i++){
     
     if(argv[i][0] =='-'){
+
+      // parse the option
       
-      /* argv[i][1] is the actual option character */
+      if(argv[i][1] == '-' ){
+
+	// parse long word options
+	
+	if( !strcmp( argv[i], "--GofR" ) ){
+	  calcGofR = 1;
+	  i++;
+	  strcpy( gofR1, argv[i] );
+	  i++;
+	  strcpy( gofR2, argv[i] );
+	}
+
+	else if( !strcmp( argv[i], "--MuCorr") ){
+	  calcMuCorr = 1;
+	  i++;
+	  strcpy( muCorr, argv[i] );
+	}
+	
+	else if( !strcmp( argv[i], "--startFrame" ) ){
+	  haveStartFrame = 1;
+	  i++;
+	  startFrame = atoi(argv[i]);
+	}
+
+	else if( !strcmp( argv[i], "--endFrame" ) ){
+	  haveEndFrame = 1;
+	  i++;
+	  endFrame = atoi(argv[i]);
+	}
+
+	else{
+	  fprintf( stderr, 
+		   "Invalid option \"%s\"\n", argv[i] );
+	  usage();
+	}
+      }
       
-      switch(argv[i][1]){
+      else{
 	
-	/* -f <name> => the xyz input file
-	 *     [i+1] actually starts the name
-	 */
+	// parse single character options
+	
+	done =0;
+	j = 1;
+	current_flag = argv[i][j];
+	while( (current_flag != '\0') && (!done) ){
+	  
+	  switch(current_flag){
 
-      case 'f':
-	in_name = argv[i+1];
-	break;
+	  case 'o':
+	    // -o <prefix> => the output prefix.
 
-      default:
-	(void)fprintf(stderr, "Bad option %s\n", argv[i]);
+	    i++;
+	    out_prefix = argv[i];
+	    have_prefix = 1;
+	    done = 1;
+	    break;
+
+	  case 'h':
+	    // -h => give the usage
+	    
+	    usage();
+	    break;
+	
+	  case 'r':
+	    // calculates the rmsd
+
+	    calcRMSD = 1;
+	    break;
+
+	  case 'g':
+	    // calculate all to all g(r)
+
+	    calcGofR = 1;
+	    strcpy( gofR1, "all" );
+	    strcpy( gofR2, "all" );
+	    break;
+
+	  default:
+
+	    fprintf( stderr, "about to print bad option\n" );
+
+	    (void)fprintf(stderr, "Bad option \"-%s\"\n", current_flag);
+	    usage();
+	  }
+	  j++;
+	  current_flag = argv[i][j];
+	}
+      }
+    }
+
+    else{
+      
+      if( in_name != NULL ){
+	fprintf( stderr, 
+		 "Error at \"%s\", program does not currently support\n"
+		 "more than one input file.\n"
+		 "\n",
+		 argv[i]);
 	usage();
       }
+
+      in_name = argv[i];
     }
   }
 
   if(in_name == NULL){
     usage();
   }
+
+  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"
@@ -88,16 +190,27 @@ int main(argc, argv)
     exit(8);
   }
 
-  // create the array of frames
+  // 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
@@ -110,7 +223,18 @@ int main(argc, argv)
 
     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);
@@ -162,7 +286,7 @@ int main(argc, argv)
 	exit(8);
       }
       
-      strcpy(dumpArray[j].r[i].name, foo); /*copy the atom name */
+      strcpy(dumpArray[0].names[i], foo); /*copy the atom name */
 
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
@@ -187,7 +311,38 @@ int main(argc, argv)
       }
       
       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 );
+	}
+      }
+      
     }
   }
   
@@ -201,26 +356,113 @@ int main(argc, argv)
 
   // 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(stderr, 
-		"The proper usage is: %s [options] -f <xyz_file>\n\n"
-		"Options:\n",
+  (void)fprintf(stdout, 
+		"The proper usage is: %s [options] <xyz_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"
+		
+		"\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"
+		
+		"\n"
+		"\n",
 		program_name);
   exit(8);
 }