--- trunk/tcProps/tcProps.c	2004/02/13 22:13:06	1052
+++ trunk/tcProps/tcProps.c	2004/02/20 21:20:37	1062
@@ -2,84 +2,432 @@
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 
 #include "params.h"
 #include "tcProps.h"
 #include "readWrite.h"
+#include "scdCorr.h"
+#include "directorHead.h"
 
 
+#define VERSION_MAJOR 0
+#define VERSION_MINOR 1
+
+char *programName; /*the name of the program */
+void usage(void);
+
 int main( int argC, char *argV[] ){
 
   // list of 'a priori' constants
 
-  const int nLipAtoms = 19;
-  const int nBonds = 18;
-  const int nLipids = NLIPIDS;
-  const int nSSD = NSSD;
-  const int nAtoms = nLipAtoms * nLipids + nSSD;
+  const int nLipAtoms = NL_ATOMS;
+  const int nBonds    = NBONDS;
+  const int nLipids   = NLIPIDS;
+  const int nSSD      = NSSD;
+  const int nAtoms    = nLipAtoms * nLipids + nSSD;
 
   // different needed variables
   
   struct atomCoord atoms[nAtoms];
   int i,j,k;
-  char* inName;
-  int nFrames;
+  
+  char* outPrefix; // the output prefix
+  char currentFlag; // used in parsing the flags
+  int done = 0; // multipurpose boolean
+  int havePrefix; // boolean for the output prefix  
+  int haveMaxLength;
+  char* conversionCheck;
+  int conversionError;
+  int optionError;
+  char* pair1;
+  char* pair2;
+  int scdCorr;
+  double startTime;
+  double maxLength;
+  int directorHead, directorWhole;
 
   // system initialization
   
   isScanned = 0;
+  fileOpen = 0;
+  nFrames = 0;
+  frameTimes = NULL;
+
+  outPrefix = NULL;
+  inName = NULL;
+  
+  haveMaxLength = 0;
+  conversionError = 0;
+  optionError = 0;
+  havePrefix = 0;
+  scdCorr = 0;
+  startTime = 0.0;
+  directorHead = 0;
+  directorWhole = 0;
+  
+
+  // parse the command line
+
+  programName = argV[0]; /*save the program name in case we need it*/
+
+  for( i = 1; i < argC; i++){
+    
+    if(argV[i][0] =='-'){
+
+      // parse the option
+      
+      if(argV[i][1] == '-' ){
+
+	// parse long word options
+	
+	if( !strcmp( argV[i], "--gofr" ) ){
+
+	  i++;
+	  if( i>=argC ){
+	    fprintf( stderr,
+		     "\n"
+		     "not enough arguments for --gofr\n");
+	    usage();
+	    exit(0);
+	  }	  
+	  pair1 = argV[i];
+
+	  i++;
+	  if( i>=argC ){
+	    fprintf( stderr,
+		     "\n"
+		     "not enough arguments for --gofr\n");
+	    usage();
+	    exit(0);
+	  }	  
+	  pair2 = argV[i];
+
+	}
+
+	else if( !strcmp( argV[i], "--gofrTheta" ) ){
+	  
+	  i++;
+	  if( i>=argC ){
+	    fprintf( stderr,
+		     "\n"
+		     "not enough arguments for --gofrTheta\n");
+	    usage();
+	    exit(0);
+	  }	  
+	  pair1 = argV[i];
+
+	  i++;
+	  if( i>=argC ){
+	    fprintf( stderr,
+		     "\n"
+		     "not enough arguments for --gofrTheta\n");
+	    usage();
+	    exit(0);
+	  }	  
+	  pair2 = argV[i];
+
+	}
+
+	else if( !strcmp( argV[i], "--gofrOmega" ) ){
+	  
+	  i++;
+	  if( i>=argC ){
+	    fprintf( stderr,
+		     "\n"
+		     "not enough arguments for --gofrOmega\n");
+	    usage();
+	    exit(0);
+	  }	  
+	  pair1 = argV[i];
+
+	  i++;
+	  if( i>=argC ){
+	    fprintf( stderr,
+		     "\n"
+		     "not enough arguments for --gofrOmega\n");
+	    usage();
+	    exit(0);
+	  }	  
+	  pair2 = argV[i];
+
+	}
+
+	else if( !strcmp( argV[i], "--version") ){
+	  
+	  printf("\n"
+		 "tcProps version %d.%d\n"
+		 "\n",
+		 VERSION_MAJOR, VERSION_MINOR );
+	  exit(0);
+	  
+	}
+
+	else if( !strcmp( argV[i], "--help") ){
+	  
+	  usage();
+	  exit(0);
+	}
+	
+	// anything else is an error
+
+	else{
+	  fprintf( stderr, 
+		   "Invalid option \"%s\"\n", argV[i] );
+	  usage();
+	  exit(0);
+	}
+      }
+      
+      else{
+	
+	// parse single character options
+	
+	done =0;
+	j = 1;
+	currentFlag = argV[i][j];
+	while( (currentFlag != '\0') && (!done) ){
+	  
+	  switch(currentFlag){
+
+	  case 'o':
+	    // -o <prefix> => the output prefix.
+
+	    j++;
+	    currentFlag = argV[i][j];
+	      
+	    if( currentFlag != '\0' ) optionError = 1;
+	    
+	    if( optionError ){
+	      fprintf( stderr, 
+		       "\n"
+		       "The -o flag should end an option sequence.\n"
+		       "   example: -r <outname> *NOT* -or <outname>\n" );
+	      usage();
+	      exit(0);
+	    }
+	      
+	    i++;
+	    if( i>=argC ){
+	      fprintf( stderr, 
+		       "\n"
+		       "not enough arguments for -o\n");
+	      usage();
+	      exit(0);
+	    }	  
+	    
+	    outPrefix = argV[i];
+	    if( outPrefix[0] == '-' ) optionError = 1;
+	    	
+	    if( optionError ){
+	      fprintf( stderr, 
+		       "\n"
+		       "\"%s\" is not a valid out prefix/name.\n"
+		       "Out prefix/name should not begin with a dash.\n",
+		       outPrefix );
+	      usage();
+	      exit(0);
+	    }
+	    
+	    havePrefix = 1;
+	    done = 1;
+	    break;
+
+	  case 'l':
+	    // -l <double>    set <double> to the maxLength
+
+	    haveMaxLength = 1;
+	    j++;
+	    currentFlag = argV[i][j];
+	      
+	    if( currentFlag != '\0' ) optionError = 1;
+	    
+	    if( optionError ){
+	      fprintf( stderr,
+		       "\n"
+		       "The -l flag should end an option sequence.\n"
+		       "   example: -sl <double> *NOT* -ls <double>\n" );
+	      usage();
+	      exit(0);
+	    }
 
+	    i++;
+	    if( i>=argC ){
+	      fprintf( stderr,
+		       "\n"
+		       "not enough arguments for -l\n");
+	      usage();
+	      exit(0);
+	    }	  
 
+	    maxLength = atof( argV[i] );
+	    
+	    done = 1;
+
+	    break;
+
+	  case 't':
+	    // -t <double>    set <double> to the startTime
+
+	    j++;
+	    currentFlag = argV[i][j];
+	      
+	    if( currentFlag != '\0' ) optionError = 1;
+	    
+	    if( optionError ){
+	      fprintf( stderr,
+		       "\n"
+		       "The -t flag should end an option sequence.\n"
+		       "   example: -st <double> *NOT* -ts <double>\n" );
+	      usage();
+	      exit(0);
+	    }
+
+	    i++;
+	    if( i>=argC ){
+	      fprintf( stderr,
+		       "\n"
+		       "not enough arguments for -t\n");
+	      usage();
+	      exit(0);
+	    }	  
+
+	    startTime = atof( argV[i] );
+	    done = 1;
+	    break;
+
+	  case 's':
+	    // -s turn on Scd corr
+
+	    scdCorr = 1;
+	    break;
+
+	  case 'h':
+	    // -h turn on director head
+
+	    directorHead = 1;
+	    break;
+
+	  case 'w':
+	    // -h turn on director head
+
+	    directorWhole = 1;
+	    break;
+
+
+	  default:
+
+	    fprintf( stderr, 
+		    "\n"
+		    "Bad option \"-%c\"\n", currentFlag);
+	    usage();
+	    exit(0);
+	  }
+	  j++;
+	  currentFlag = argV[i][j];
+	}
+      }
+    }
+
+    else{
+      
+      if( inName != NULL ){
+	fprintf( stderr,
+		 "Error at \"%s\", program does not currently support\n"
+		 "more than one input dump file.\n"
+		 "\n",
+		 argV[i]);
+	usage();
+	exit(0);
+      }
+      
+      inName = argV[i];
+      
+    }
+  }  
+  
+  if( inName == NULL ){
+    fprintf( stderr,
+	     "Error, dump file is needed to run.\n" );
+    usage();
+    exit(0);
+  }
+
+  if( outPrefix == NULL )
+    outPrefix = inName;
+
+
   // initialize the arrays
 
   for(i=0;i<nLipids;i++){
 
     atoms[nLipAtoms*i+0].type = HEAD;
+    atoms[nLipAtoms*i+0].mass = 72;
     atoms[nLipAtoms*i+0].u[0] = 0.0;
     atoms[nLipAtoms*i+0].u[1] = 0.0;
     atoms[nLipAtoms*i+0].u[2] = 1.0;
     
+    
 
     atoms[nLipAtoms*i+1].type = CH2;
+    atoms[nLipAtoms*i+1].mass = 14.03;
 
     atoms[nLipAtoms*i+2].type = CH;
+    atoms[nLipAtoms*i+2].mass = 13.02;
 
     atoms[nLipAtoms*i+3].type = CH2;
+    atoms[nLipAtoms*i+3].mass = 14.03;
 
     atoms[nLipAtoms*i+4].type = CH2;
+    atoms[nLipAtoms*i+4].mass = 14.03;
 
     atoms[nLipAtoms*i+5].type = CH2;
+    atoms[nLipAtoms*i+5].mass = 14.03;
 
     atoms[nLipAtoms*i+6].type = CH2;
+    atoms[nLipAtoms*i+6].mass = 14.03;
 
     atoms[nLipAtoms*i+7].type = CH2;
+    atoms[nLipAtoms*i+7].mass = 14.03;
 
     atoms[nLipAtoms*i+8].type = CH2;
+    atoms[nLipAtoms*i+8].mass = 14.03;
 
     atoms[nLipAtoms*i+9].type = CH2;
+    atoms[nLipAtoms*i+9].mass = 14.03;
 
     atoms[nLipAtoms*i+10].type = CH3;
+    atoms[nLipAtoms*i+10].mass = 15.04;
 
     atoms[nLipAtoms*i+11].type = CH2;
+    atoms[nLipAtoms*i+11].mass = 14.03;
 
     atoms[nLipAtoms*i+12].type = CH2;
+    atoms[nLipAtoms*i+12].mass = 14.03;
 
-    atoms[nLipAtoms*i+13].type = CH2;
+    atoms[nLipAtoms*i+13].type = CH2;    
+    atoms[nLipAtoms*i+13].mass = 14.03;
 
     atoms[nLipAtoms*i+14].type = CH2;
+    atoms[nLipAtoms*i+14].mass = 14.03;
   
     atoms[nLipAtoms*i+15].type = CH2;
+    atoms[nLipAtoms*i+15].mass = 14.03;
   
     atoms[nLipAtoms*i+16].type = CH2;
+    atoms[nLipAtoms*i+16].mass = 14.03;
   
     atoms[nLipAtoms*i+17].type = CH2;
+    atoms[nLipAtoms*i+17].mass = 14.03;
   
     atoms[nLipAtoms*i+18].type = CH3;
+    atoms[nLipAtoms*i+18].mass = 15.04;
   }
   
   for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
     atoms[i].type = SSD;
+    atoms[i].mass = 18.03;
     atoms[i].u[0] = 0.0;
     atoms[i].u[1] = 0.0;
     atoms[i].u[2] = 1.0;
@@ -87,5 +435,85 @@ int main( int argC, char *argV[] ){
 
   // read and set the frames
   
-  nFrames = setFrames( inName );
+  openFile();
+
+  fprintf( stdout,
+	   "\n"
+	   "Counting the number of frames in \"%s\"...",
+	   inName );
+  fflush(stdout);
+
+  setFrames();
   
+  fprintf( stdout,
+	   "done.\n"
+	   "nFrames = %d.\n",
+	   nFrames );
+  fflush(stdout);
+
+  if(scdCorr){
+
+    fprintf ( stdout,
+	      "Calculating the Scd correlation\n" );
+    fflush( stdout );
+    
+    calcScdCorr( startTime, atoms, outPrefix );
+  }
+
+  if(directorHead){
+
+    fprintf ( stdout,
+	      "Calculating the Head director\n" );
+    fflush( stdout );
+    
+    calcDirHeadCorr( startTime, atoms, outPrefix );
+  }
+
+  if(directorWhole){
+
+    fprintf ( stdout,
+	      "Calculating the bilayer director\n" );
+    fflush( stdout );
+    
+    calcDirWholeCorr( startTime, atoms, outPrefix );
+  }
+  
+
+  closeFile();
+
+}
+
+
+/***************************************************************************
+ * prints out the usage for the command line arguments, then exits.
+ ***************************************************************************/
+
+void usage(){
+  (void)fprintf(stdout, 
+		"\n"
+		"The proper usage is: %s [options] <input_file>\n"
+		"\n"
+		"Options:\n"
+		"\n"
+		"   short:\n"
+		"   ------\n"
+		"   -o <name>       The output prefix\n"
+		"   -t <time>       Set the start time for correlations\n"
+		"   -l <maxLength>  set the maximum value of r\n"
+		"                     *Defaults to 1/2 smallest length of first frame.\n"
+		"   -s              Calculate the Scd chain correlation.\n"
+		"   -h              Calculate the directors for the head groups\n"
+		"   -w              Calculate the director fro the bilayers\n"
+		"\n"
+		"   long:\n"
+		"   -----\n"
+		"   --gofr <atom1> <atom2>         g(r) for atom1 and atom2\n"
+		"   --gofrTheta <atom1> <atom2>    g(r, theta) for atom1 and atom2\n"
+		"   --gofrOmega <atom1> <atom2>    g(r, omega) for atom1 and atom2\n"
+		"   --version                      displays the version number\n"
+		"   --help                         displays this help message.\n"
+		
+		"\n"
+		"\n",
+		programName);
+}