trunk/tcProps/tcProps.c

#define _FILE_OFFSET_BITS 64

#include <stdio.h>
#include <stdlib.h>
#include <string.h>


#include "params.h"
#include "tcProps.h"
#include "readWrite.h"
#include "scdCorr.h"
#include "directorHead.h"
#include "directorWhole.h"
#include "rmsd.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 = 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* 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, doRMSD;
  enum atomNames rmsdType;

  // 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;
  doRMSD = 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], "--rmsd" ) ){

          doRMSD = 1;
          i++;
          if( i>=argC ){
            fprintf( stderr,
                     "\n"
                     "not enough arguments for --rmsd\n");
            usage();
            exit(0);
          }       
          pair1 = argV[i];

          if( !strcmp(pair1, "HEAD") )    rmsdType = HEAD;
          else if( !strcmp(pair1, "CH") ) rmsdType = CH;
          else if( !strcmp(pair1, "CH2") )rmsdType = CH2;
          else if( !strcmp(pair1, "CH3") )rmsdType = CH3;
          else if( !strcmp(pair1, "SSD") )rmsdType = SSD;
          else if( !strcmp(pair1, "COM") )rmsdType = COM;
          else{
            fprintf( stderr,
                     "Unrecognized rmsd atom type \"%s\"\n",
                     pair1 );
            exit(0);
          }

        }

        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].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;
  }

  // read and set the frames
  
  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 );
  }

  if(doRMSD){

    fprintf ( stdout,
              "Calculating the RMSD\n" );
    fflush( stdout );
    
    rmsd( rmsdType, startTime, 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"
                "   --rmsd <atom1>                 rmsd for atom1\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);
}
Revision:	1073
Committed:	Sat Feb 28 16:45:57 2004 UTC (21 years, 8 months ago) by mmeineke
Content type:	text/plain
File size:	10691 byte(s)
Log Message:	finished the rmsd coding. hasn't been debugged
#	User	Rev	Content
1	mmeineke	1052	#define _FILE_OFFSET_BITS 64
2
3	mmeineke	1049	#include <stdio.h>
4			#include <stdlib.h>
5	mmeineke	1060	#include <string.h>
6	mmeineke	1049
7
8			#include "params.h"
9			#include "tcProps.h"
10	mmeineke	1052	#include "readWrite.h"
11	mmeineke	1058	#include "scdCorr.h"
12	mmeineke	1060	#include "directorHead.h"
13	mmeineke	1067	#include "directorWhole.h"
14	mmeineke	1073	#include "rmsd.h"
15	mmeineke	1049
16
17	mmeineke	1058	#define VERSION_MAJOR 0
18			#define VERSION_MINOR 1
19
20			char programName; /the name of the program */
21			void usage(void);
22
23	mmeineke	1049	int main( int argC, char *argV[] ){
24
25			// list of 'a priori' constants
26
27	mmeineke	1056	const int nLipAtoms = NL_ATOMS;
28			const int nBonds = NBONDS;
29			const int nLipids = NLIPIDS;
30			const int nSSD = NSSD;
31			const int nAtoms = nLipAtoms * nLipids + nSSD;
32	mmeineke	1052
33			// different needed variables
34	mmeineke	1049
35			struct atomCoord atoms[nAtoms];
36	mmeineke	1052	int i,j,k;
37	mmeineke	1058
38			char* outPrefix; // the output prefix
39			char currentFlag; // used in parsing the flags
40			int done = 0; // multipurpose boolean
41			int havePrefix; // boolean for the output prefix
42	mmeineke	1060	int haveMaxLength;
43	mmeineke	1058	char* conversionCheck;
44			int conversionError;
45			int optionError;
46			char* pair1;
47			char* pair2;
48			int scdCorr;
49			double startTime;
50	mmeineke	1060	double maxLength;
51	mmeineke	1073	int directorHead, directorWhole, doRMSD;
52			enum atomNames rmsdType;
53	mmeineke	1049
54	mmeineke	1052	// system initialization
55	mmeineke	1049
56	mmeineke	1052	isScanned = 0;
57	mmeineke	1056	fileOpen = 0;
58			nFrames = 0;
59			frameTimes = NULL;
60	mmeineke	1049
61	mmeineke	1058	outPrefix = NULL;
62			inName = NULL;
63
64	mmeineke	1060	haveMaxLength = 0;
65	mmeineke	1058	conversionError = 0;
66			optionError = 0;
67			havePrefix = 0;
68			scdCorr = 0;
69			startTime = 0.0;
70	mmeineke	1060	directorHead = 0;
71	mmeineke	1062	directorWhole = 0;
72	mmeineke	1073	doRMSD = 0;
73	mmeineke	1058
74	mmeineke	1052
75	mmeineke	1058	// parse the command line
76
77			programName = argV[0]; /save the program name in case we need it/
78
79			for( i = 1; i < argC; i++){
80
81			if(argV[i][0] =='-'){
82
83			// parse the option
84
85			if(argV[i][1] == '-' ){
86
87			// parse long word options
88
89	mmeineke	1073	if( !strcmp( argV[i], "--rmsd" ) ){
90	mmeineke	1058
91	mmeineke	1073	doRMSD = 1;
92	mmeineke	1058	i++;
93			if( i>=argC ){
94			fprintf( stderr,
95			"\n"
96	mmeineke	1073	"not enough arguments for --rmsd\n");
97	mmeineke	1058	usage();
98			exit(0);
99			}
100			pair1 = argV[i];
101
102	mmeineke	1073	if( !strcmp(pair1, "HEAD") ) rmsdType = HEAD;
103			else if( !strcmp(pair1, "CH") ) rmsdType = CH;
104			else if( !strcmp(pair1, "CH2") )rmsdType = CH2;
105			else if( !strcmp(pair1, "CH3") )rmsdType = CH3;
106			else if( !strcmp(pair1, "SSD") )rmsdType = SSD;
107			else if( !strcmp(pair1, "COM") )rmsdType = COM;
108			else{
109	mmeineke	1058	fprintf( stderr,
110	mmeineke	1073	"Unrecognized rmsd atom type \"%s\"\n",
111			pair1 );
112	mmeineke	1058	exit(0);
113	mmeineke	1073	}
114	mmeineke	1058
115			}
116
117			else if( !strcmp( argV[i], "--gofrTheta" ) ){
118
119			i++;
120			if( i>=argC ){
121			fprintf( stderr,
122			"\n"
123			"not enough arguments for --gofrTheta\n");
124			usage();
125			exit(0);
126			}
127			pair1 = argV[i];
128
129			i++;
130			if( i>=argC ){
131			fprintf( stderr,
132			"\n"
133			"not enough arguments for --gofrTheta\n");
134			usage();
135			exit(0);
136			}
137			pair2 = argV[i];
138
139			}
140
141			else if( !strcmp( argV[i], "--gofrOmega" ) ){
142
143			i++;
144			if( i>=argC ){
145			fprintf( stderr,
146			"\n"
147			"not enough arguments for --gofrOmega\n");
148			usage();
149			exit(0);
150			}
151			pair1 = argV[i];
152
153			i++;
154			if( i>=argC ){
155			fprintf( stderr,
156			"\n"
157			"not enough arguments for --gofrOmega\n");
158			usage();
159			exit(0);
160			}
161			pair2 = argV[i];
162
163			}
164
165			else if( !strcmp( argV[i], "--version") ){
166
167			printf("\n"
168			"tcProps version %d.%d\n"
169			"\n",
170			VERSION_MAJOR, VERSION_MINOR );
171			exit(0);
172
173			}
174
175			else if( !strcmp( argV[i], "--help") ){
176
177			usage();
178			exit(0);
179			}
180
181			// anything else is an error
182
183			else{
184			fprintf( stderr,
185			"Invalid option \"%s\"\n", argV[i] );
186			usage();
187			exit(0);
188			}
189			}
190
191			else{
192
193			// parse single character options
194
195			done =0;
196			j = 1;
197			currentFlag = argV[i][j];
198			while( (currentFlag != '\0') && (!done) ){
199
200			switch(currentFlag){
201
202			case 'o':
203			// -o <prefix> => the output prefix.
204
205			j++;
206			currentFlag = argV[i][j];
207
208			if( currentFlag != '\0' ) optionError = 1;
209
210			if( optionError ){
211			fprintf( stderr,
212			"\n"
213			"The -o flag should end an option sequence.\n"
214			" example: -r <outname> NOT -or <outname>\n" );
215			usage();
216			exit(0);
217			}
218
219			i++;
220			if( i>=argC ){
221			fprintf( stderr,
222			"\n"
223			"not enough arguments for -o\n");
224			usage();
225			exit(0);
226			}
227
228			outPrefix = argV[i];
229			if( outPrefix[0] == '-' ) optionError = 1;
230
231			if( optionError ){
232			fprintf( stderr,
233			"\n"
234			"\"%s\" is not a valid out prefix/name.\n"
235			"Out prefix/name should not begin with a dash.\n",
236			outPrefix );
237			usage();
238			exit(0);
239			}
240
241			havePrefix = 1;
242			done = 1;
243			break;
244
245			case 'l':
246			// -l <double> set <double> to the maxLength
247
248	mmeineke	1060	haveMaxLength = 1;
249	mmeineke	1058	j++;
250			currentFlag = argV[i][j];
251
252			if( currentFlag != '\0' ) optionError = 1;
253
254			if( optionError ){
255			fprintf( stderr,
256			"\n"
257			"The -l flag should end an option sequence.\n"
258			" example: -sl <double> NOT -ls <double>\n" );
259			usage();
260			exit(0);
261			}
262
263			i++;
264			if( i>=argC ){
265			fprintf( stderr,
266			"\n"
267			"not enough arguments for -l\n");
268			usage();
269			exit(0);
270			}
271
272			maxLength = atof( argV[i] );
273
274			done = 1;
275
276			break;
277
278			case 't':
279			// -t <double> set <double> to the startTime
280
281			j++;
282			currentFlag = argV[i][j];
283
284			if( currentFlag != '\0' ) optionError = 1;
285
286			if( optionError ){
287			fprintf( stderr,
288			"\n"
289			"The -t flag should end an option sequence.\n"
290			" example: -st <double> NOT -ts <double>\n" );
291			usage();
292			exit(0);
293			}
294
295			i++;
296			if( i>=argC ){
297			fprintf( stderr,
298			"\n"
299			"not enough arguments for -t\n");
300			usage();
301			exit(0);
302			}
303
304			startTime = atof( argV[i] );
305			done = 1;
306			break;
307
308			case 's':
309	mmeineke	1060	// -s turn on Scd corr
310	mmeineke	1058
311			scdCorr = 1;
312			break;
313
314	mmeineke	1060	case 'h':
315			// -h turn on director head
316	mmeineke	1058
317	mmeineke	1060	directorHead = 1;
318			break;
319
320	mmeineke	1062	case 'w':
321			// -h turn on director head
322	mmeineke	1060
323	mmeineke	1062	directorWhole = 1;
324			break;
325
326
327	mmeineke	1058	default:
328
329	mmeineke	1060	fprintf( stderr,
330	mmeineke	1058	"\n"
331			"Bad option \"-%c\"\n", currentFlag);
332			usage();
333			exit(0);
334			}
335			j++;
336			currentFlag = argV[i][j];
337			}
338			}
339			}
340
341			else{
342
343			if( inName != NULL ){
344			fprintf( stderr,
345			"Error at \"%s\", program does not currently support\n"
346			"more than one input dump file.\n"
347			"\n",
348			argV[i]);
349			usage();
350			exit(0);
351			}
352
353			inName = argV[i];
354
355			}
356			}
357
358			if( inName == NULL ){
359			fprintf( stderr,
360			"Error, dump file is needed to run.\n" );
361			usage();
362			exit(0);
363			}
364
365	mmeineke	1060	if( outPrefix == NULL )
366			outPrefix = inName;
367	mmeineke	1058
368	mmeineke	1060
369	mmeineke	1049	// initialize the arrays
370
371			for(i=0;i<nLipids;i++){
372
373			atoms[nLipAtoms*i+0].type = HEAD;
374	mmeineke	1062	atoms[nLipAtoms*i+0].mass = 72;
375	mmeineke	1052	atoms[nLipAtoms*i+0].u[0] = 0.0;
376			atoms[nLipAtoms*i+0].u[1] = 0.0;
377			atoms[nLipAtoms*i+0].u[2] = 1.0;
378
379	mmeineke	1062
380	mmeineke	1049
381			atoms[nLipAtoms*i+1].type = CH2;
382	mmeineke	1062	atoms[nLipAtoms*i+1].mass = 14.03;
383	mmeineke	1049
384			atoms[nLipAtoms*i+2].type = CH;
385	mmeineke	1062	atoms[nLipAtoms*i+2].mass = 13.02;
386	mmeineke	1049
387			atoms[nLipAtoms*i+3].type = CH2;
388	mmeineke	1062	atoms[nLipAtoms*i+3].mass = 14.03;
389	mmeineke	1049
390			atoms[nLipAtoms*i+4].type = CH2;
391	mmeineke	1062	atoms[nLipAtoms*i+4].mass = 14.03;
392	mmeineke	1049
393			atoms[nLipAtoms*i+5].type = CH2;
394	mmeineke	1062	atoms[nLipAtoms*i+5].mass = 14.03;
395	mmeineke	1049
396			atoms[nLipAtoms*i+6].type = CH2;
397	mmeineke	1062	atoms[nLipAtoms*i+6].mass = 14.03;
398	mmeineke	1049
399			atoms[nLipAtoms*i+7].type = CH2;
400	mmeineke	1062	atoms[nLipAtoms*i+7].mass = 14.03;
401	mmeineke	1049
402			atoms[nLipAtoms*i+8].type = CH2;
403	mmeineke	1062	atoms[nLipAtoms*i+8].mass = 14.03;
404	mmeineke	1049
405			atoms[nLipAtoms*i+9].type = CH2;
406	mmeineke	1062	atoms[nLipAtoms*i+9].mass = 14.03;
407	mmeineke	1049
408			atoms[nLipAtoms*i+10].type = CH3;
409	mmeineke	1062	atoms[nLipAtoms*i+10].mass = 15.04;
410	mmeineke	1049
411			atoms[nLipAtoms*i+11].type = CH2;
412	mmeineke	1062	atoms[nLipAtoms*i+11].mass = 14.03;
413	mmeineke	1049
414			atoms[nLipAtoms*i+12].type = CH2;
415	mmeineke	1062	atoms[nLipAtoms*i+12].mass = 14.03;
416	mmeineke	1049
417	mmeineke	1062	atoms[nLipAtoms*i+13].type = CH2;
418			atoms[nLipAtoms*i+13].mass = 14.03;
419	mmeineke	1049
420			atoms[nLipAtoms*i+14].type = CH2;
421	mmeineke	1062	atoms[nLipAtoms*i+14].mass = 14.03;
422	mmeineke	1049
423			atoms[nLipAtoms*i+15].type = CH2;
424	mmeineke	1062	atoms[nLipAtoms*i+15].mass = 14.03;
425	mmeineke	1049
426			atoms[nLipAtoms*i+16].type = CH2;
427	mmeineke	1062	atoms[nLipAtoms*i+16].mass = 14.03;
428	mmeineke	1049
429			atoms[nLipAtoms*i+17].type = CH2;
430	mmeineke	1062	atoms[nLipAtoms*i+17].mass = 14.03;
431	mmeineke	1049
432			atoms[nLipAtoms*i+18].type = CH3;
433	mmeineke	1062	atoms[nLipAtoms*i+18].mass = 15.04;
434	mmeineke	1049	}
435
436	mmeineke	1052	for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
437	mmeineke	1049	atoms[i].type = SSD;
438	mmeineke	1062	atoms[i].mass = 18.03;
439	mmeineke	1052	atoms[i].u[0] = 0.0;
440			atoms[i].u[1] = 0.0;
441			atoms[i].u[2] = 1.0;
442	mmeineke	1049	}
443	mmeineke	1052
444			// read and set the frames
445
446	mmeineke	1060	openFile();
447	mmeineke	1058
448			fprintf( stdout,
449			"\n"
450			"Counting the number of frames in \"%s\"...",
451			inName );
452			fflush(stdout);
453
454	mmeineke	1060	setFrames();
455	mmeineke	1052
456	mmeineke	1058	fprintf( stdout,
457			"done.\n"
458	mmeineke	1060	"nFrames = %d.\n",
459	mmeineke	1058	nFrames );
460			fflush(stdout);
461
462			if(scdCorr){
463
464			fprintf ( stdout,
465			"Calculating the Scd correlation\n" );
466			fflush( stdout );
467
468	mmeineke	1060	calcScdCorr( startTime, atoms, outPrefix );
469	mmeineke	1058	}
470	mmeineke	1060
471			if(directorHead){
472
473			fprintf ( stdout,
474			"Calculating the Head director\n" );
475			fflush( stdout );
476
477			calcDirHeadCorr( startTime, atoms, outPrefix );
478			}
479	mmeineke	1062
480			if(directorWhole){
481
482			fprintf ( stdout,
483			"Calculating the bilayer director\n" );
484			fflush( stdout );
485
486			calcDirWholeCorr( startTime, atoms, outPrefix );
487			}
488	mmeineke	1073
489			if(doRMSD){
490
491			fprintf ( stdout,
492			"Calculating the RMSD\n" );
493			fflush( stdout );
494
495			rmsd( rmsdType, startTime, outPrefix );
496			}
497	mmeineke	1058
498
499	mmeineke	1060	closeFile();
500
501	mmeineke	1058	}
502
503
504			/***************************************************************************
505			* prints out the usage for the command line arguments, then exits.
506			***************************************************************************/
507
508			void usage(){
509			(void)fprintf(stdout,
510			"\n"
511			"The proper usage is: %s [options] <input_file>\n"
512			"\n"
513			"Options:\n"
514			"\n"
515			" short:\n"
516			" ------\n"
517			" -o <name> The output prefix\n"
518			" -t <time> Set the start time for correlations\n"
519			" -l <maxLength> set the maximum value of r\n"
520			" *Defaults to 1/2 smallest length of first frame.\n"
521			" -s Calculate the Scd chain correlation.\n"
522	mmeineke	1062	" -h Calculate the directors for the head groups\n"
523			" -w Calculate the director fro the bilayers\n"
524	mmeineke	1058	"\n"
525			" long:\n"
526			" -----\n"
527	mmeineke	1073	" --rmsd <atom1> rmsd for atom1\n"
528	mmeineke	1058	" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n"
529			" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n"
530			" --version displays the version number\n"
531			" --help displays this help message.\n"
532
533			"\n"
534			"\n",
535			programName);
536			}