trunk/tcProps/tcProps.c

#define _FILE_OFFSET_BITS 64

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


#include "params.h"
#include "tcProps.h"
#include "readWrite.h"
#include "scdCorr.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* 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  
  char* conversionCheck;
  int conversionError;
  int optionError;
  char* pair1;
  char* pair2;
  int scdCorr;
  double startTime;

  // system initialization
  
  isScanned = 0;
  fileOpen = 0;
  nFrames = 0;
  frameTimes = NULL;

  outPrefix = NULL;
  inName = NULL;
  
  conversionError = 0;
  optionError = 0;
  havePrefix = 0;
  scdCorr = 0;
  startTime = 0.0;
  

  // 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 = true;
            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 separate output files

            scdCorr = 1;
            break;


          default:

            sprintf(painCave.errMsg, 
                    "\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);
  }


  // initialize the arrays

  for(i=0;i<nLipids;i++){

    atoms[nLipAtoms*i+0].type = HEAD;
    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+2].type = CH;

    atoms[nLipAtoms*i+3].type = CH2;

    atoms[nLipAtoms*i+4].type = CH2;

    atoms[nLipAtoms*i+5].type = CH2;

    atoms[nLipAtoms*i+6].type = CH2;

    atoms[nLipAtoms*i+7].type = CH2;

    atoms[nLipAtoms*i+8].type = CH2;

    atoms[nLipAtoms*i+9].type = CH2;

    atoms[nLipAtoms*i+10].type = CH3;

    atoms[nLipAtoms*i+11].type = CH2;

    atoms[nLipAtoms*i+12].type = CH2;

    atoms[nLipAtoms*i+13].type = CH2;

    atoms[nLipAtoms*i+14].type = CH2;
  
    atoms[nLipAtoms*i+15].type = CH2;
  
    atoms[nLipAtoms*i+16].type = CH2;
  
    atoms[nLipAtoms*i+17].type = CH2;
  
    atoms[nLipAtoms*i+18].type = CH3;
  }
  
  for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
    atoms[i].type = SSD;
    atoms[i].u[0] = 0.0;
    atoms[i].u[1] = 0.0;
    atoms[i].u[2] = 1.0;
  }

  // read and set the frames
  
  openFile( inName );

  fprintf( stdout,
           "\n"
           "Counting the number of frames in \"%s\"...",
           inName );
  fflush(stdout);

  setFrames( inName );
  
  fprintf( stdout,
           "done.\n"
           "nFrames = %d\n.",
           nFrames );
  fflush(stdout);

  if(scdCorr){

    fprintf ( stdout,
              "Calculating the Scd correlation\n" );
    fflush( stdout );
    
    calcScdCorr( startTime );
  }
  

}


/***************************************************************************
 * 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"
                "\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);
}
Revision:	1058
Committed:	Wed Feb 18 21:20:51 2004 UTC (21 years, 8 months ago) by mmeineke
Content type:	text/plain
File size:	8557 byte(s)
Log Message:	finished up the rough draft of tcProps with Scd corr
#	User	Rev	Content
1	mmeineke	1052	#define _FILE_OFFSET_BITS 64
2
3	mmeineke	1049	#include <stdio.h>
4			#include <stdlib.h>
5
6
7			#include "params.h"
8			#include "tcProps.h"
9	mmeineke	1052	#include "readWrite.h"
10	mmeineke	1058	#include "scdCorr.h"
11	mmeineke	1049
12
13	mmeineke	1058	#define VERSION_MAJOR 0
14			#define VERSION_MINOR 1
15
16			char programName; /the name of the program */
17			void usage(void);
18
19	mmeineke	1049	int main( int argC, char *argV[] ){
20
21			// list of 'a priori' constants
22
23	mmeineke	1056	const int nLipAtoms = NL_ATOMS;
24			const int nBonds = NBONDS;
25			const int nLipids = NLIPIDS;
26			const int nSSD = NSSD;
27			const int nAtoms = nLipAtoms * nLipids + nSSD;
28	mmeineke	1052
29			// different needed variables
30	mmeineke	1049
31			struct atomCoord atoms[nAtoms];
32	mmeineke	1052	int i,j,k;
33			char* inName;
34			int nFrames;
35	mmeineke	1058
36			char* outPrefix; // the output prefix
37			char currentFlag; // used in parsing the flags
38			int done = 0; // multipurpose boolean
39			int havePrefix; // boolean for the output prefix
40			char* conversionCheck;
41			int conversionError;
42			int optionError;
43			char* pair1;
44			char* pair2;
45			int scdCorr;
46			double startTime;
47	mmeineke	1049
48	mmeineke	1052	// system initialization
49	mmeineke	1049
50	mmeineke	1052	isScanned = 0;
51	mmeineke	1056	fileOpen = 0;
52			nFrames = 0;
53			frameTimes = NULL;
54	mmeineke	1049
55	mmeineke	1058	outPrefix = NULL;
56			inName = NULL;
57
58			conversionError = 0;
59			optionError = 0;
60			havePrefix = 0;
61			scdCorr = 0;
62			startTime = 0.0;
63
64	mmeineke	1052
65	mmeineke	1058	// parse the command line
66
67			programName = argV[0]; /save the program name in case we need it/
68
69			for( i = 1; i < argC; i++){
70
71			if(argV[i][0] =='-'){
72
73			// parse the option
74
75			if(argV[i][1] == '-' ){
76
77			// parse long word options
78
79			if( !strcmp( argV[i], "--gofr" ) ){
80
81			i++;
82			if( i>=argC ){
83			fprintf( stderr,
84			"\n"
85			"not enough arguments for --gofr\n");
86			usage();
87			exit(0);
88			}
89			pair1 = argV[i];
90
91			i++;
92			if( i>=argC ){
93			fprintf( stderr,
94			"\n"
95			"not enough arguments for --gofr\n");
96			usage();
97			exit(0);
98			}
99			pair2 = argV[i];
100
101			}
102
103			else if( !strcmp( argV[i], "--gofrTheta" ) ){
104
105			i++;
106			if( i>=argC ){
107			fprintf( stderr,
108			"\n"
109			"not enough arguments for --gofrTheta\n");
110			usage();
111			exit(0);
112			}
113			pair1 = argV[i];
114
115			i++;
116			if( i>=argC ){
117			fprintf( stderr,
118			"\n"
119			"not enough arguments for --gofrTheta\n");
120			usage();
121			exit(0);
122			}
123			pair2 = argV[i];
124
125			}
126
127			else if( !strcmp( argV[i], "--gofrOmega" ) ){
128
129			i++;
130			if( i>=argC ){
131			fprintf( stderr,
132			"\n"
133			"not enough arguments for --gofrOmega\n");
134			usage();
135			exit(0);
136			}
137			pair1 = argV[i];
138
139			i++;
140			if( i>=argC ){
141			fprintf( stderr,
142			"\n"
143			"not enough arguments for --gofrOmega\n");
144			usage();
145			exit(0);
146			}
147			pair2 = argV[i];
148
149			}
150
151			else if( !strcmp( argV[i], "--version") ){
152
153			printf("\n"
154			"tcProps version %d.%d\n"
155			"\n",
156			VERSION_MAJOR, VERSION_MINOR );
157			exit(0);
158
159			}
160
161			else if( !strcmp( argV[i], "--help") ){
162
163			usage();
164			exit(0);
165			}
166
167			// anything else is an error
168
169			else{
170			fprintf( stderr,
171			"Invalid option \"%s\"\n", argV[i] );
172			usage();
173			exit(0);
174			}
175			}
176
177			else{
178
179			// parse single character options
180
181			done =0;
182			j = 1;
183			currentFlag = argV[i][j];
184			while( (currentFlag != '\0') && (!done) ){
185
186			switch(currentFlag){
187
188			case 'o':
189			// -o <prefix> => the output prefix.
190
191			j++;
192			currentFlag = argV[i][j];
193
194			if( currentFlag != '\0' ) optionError = 1;
195
196			if( optionError ){
197			fprintf( stderr,
198			"\n"
199			"The -o flag should end an option sequence.\n"
200			" example: -r <outname> NOT -or <outname>\n" );
201			usage();
202			exit(0);
203			}
204
205			i++;
206			if( i>=argC ){
207			fprintf( stderr,
208			"\n"
209			"not enough arguments for -o\n");
210			usage();
211			exit(0);
212			}
213
214			outPrefix = argV[i];
215			if( outPrefix[0] == '-' ) optionError = 1;
216
217			if( optionError ){
218			fprintf( stderr,
219			"\n"
220			"\"%s\" is not a valid out prefix/name.\n"
221			"Out prefix/name should not begin with a dash.\n",
222			outPrefix );
223			usage();
224			exit(0);
225			}
226
227			havePrefix = 1;
228			done = 1;
229			break;
230
231			case 'l':
232			// -l <double> set <double> to the maxLength
233
234			haveMaxLength = true;
235			j++;
236			currentFlag = argV[i][j];
237
238			if( currentFlag != '\0' ) optionError = 1;
239
240			if( optionError ){
241			fprintf( stderr,
242			"\n"
243			"The -l flag should end an option sequence.\n"
244			" example: -sl <double> NOT -ls <double>\n" );
245			usage();
246			exit(0);
247			}
248
249			i++;
250			if( i>=argC ){
251			fprintf( stderr,
252			"\n"
253			"not enough arguments for -l\n");
254			usage();
255			exit(0);
256			}
257
258			maxLength = atof( argV[i] );
259
260			done = 1;
261
262			break;
263
264			case 't':
265			// -t <double> set <double> to the startTime
266
267			j++;
268			currentFlag = argV[i][j];
269
270			if( currentFlag != '\0' ) optionError = 1;
271
272			if( optionError ){
273			fprintf( stderr,
274			"\n"
275			"The -t flag should end an option sequence.\n"
276			" example: -st <double> NOT -ts <double>\n" );
277			usage();
278			exit(0);
279			}
280
281			i++;
282			if( i>=argC ){
283			fprintf( stderr,
284			"\n"
285			"not enough arguments for -t\n");
286			usage();
287			exit(0);
288			}
289
290			startTime = atof( argV[i] );
291			done = 1;
292			break;
293
294			case 's':
295			// -s turn on separate output files
296
297			scdCorr = 1;
298			break;
299
300
301			default:
302
303			sprintf(painCave.errMsg,
304			"\n"
305			"Bad option \"-%c\"\n", currentFlag);
306			usage();
307			exit(0);
308			}
309			j++;
310			currentFlag = argV[i][j];
311			}
312			}
313			}
314
315			else{
316
317			if( inName != NULL ){
318			fprintf( stderr,
319			"Error at \"%s\", program does not currently support\n"
320			"more than one input dump file.\n"
321			"\n",
322			argV[i]);
323			usage();
324			exit(0);
325			}
326
327			inName = argV[i];
328
329			}
330			}
331
332			if( inName == NULL ){
333			fprintf( stderr,
334			"Error, dump file is needed to run.\n" );
335			usage();
336			exit(0);
337			}
338
339
340	mmeineke	1049	// initialize the arrays
341
342			for(i=0;i<nLipids;i++){
343
344			atoms[nLipAtoms*i+0].type = HEAD;
345	mmeineke	1052	atoms[nLipAtoms*i+0].u[0] = 0.0;
346			atoms[nLipAtoms*i+0].u[1] = 0.0;
347			atoms[nLipAtoms*i+0].u[2] = 1.0;
348
349	mmeineke	1049
350			atoms[nLipAtoms*i+1].type = CH2;
351
352			atoms[nLipAtoms*i+2].type = CH;
353
354			atoms[nLipAtoms*i+3].type = CH2;
355
356			atoms[nLipAtoms*i+4].type = CH2;
357
358			atoms[nLipAtoms*i+5].type = CH2;
359
360			atoms[nLipAtoms*i+6].type = CH2;
361
362			atoms[nLipAtoms*i+7].type = CH2;
363
364			atoms[nLipAtoms*i+8].type = CH2;
365
366			atoms[nLipAtoms*i+9].type = CH2;
367
368			atoms[nLipAtoms*i+10].type = CH3;
369
370			atoms[nLipAtoms*i+11].type = CH2;
371
372			atoms[nLipAtoms*i+12].type = CH2;
373
374			atoms[nLipAtoms*i+13].type = CH2;
375
376			atoms[nLipAtoms*i+14].type = CH2;
377
378			atoms[nLipAtoms*i+15].type = CH2;
379
380			atoms[nLipAtoms*i+16].type = CH2;
381
382			atoms[nLipAtoms*i+17].type = CH2;
383
384			atoms[nLipAtoms*i+18].type = CH3;
385			}
386
387	mmeineke	1052	for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
388	mmeineke	1049	atoms[i].type = SSD;
389	mmeineke	1052	atoms[i].u[0] = 0.0;
390			atoms[i].u[1] = 0.0;
391			atoms[i].u[2] = 1.0;
392	mmeineke	1049	}
393	mmeineke	1052
394			// read and set the frames
395
396	mmeineke	1058	openFile( inName );
397
398			fprintf( stdout,
399			"\n"
400			"Counting the number of frames in \"%s\"...",
401			inName );
402			fflush(stdout);
403
404	mmeineke	1056	setFrames( inName );
405	mmeineke	1052
406	mmeineke	1058	fprintf( stdout,
407			"done.\n"
408			"nFrames = %d\n.",
409			nFrames );
410			fflush(stdout);
411
412			if(scdCorr){
413
414			fprintf ( stdout,
415			"Calculating the Scd correlation\n" );
416			fflush( stdout );
417
418			calcScdCorr( startTime );
419			}
420
421
422			}
423
424
425			/***************************************************************************
426			* prints out the usage for the command line arguments, then exits.
427			***************************************************************************/
428
429			void usage(){
430			(void)fprintf(stdout,
431			"\n"
432			"The proper usage is: %s [options] <input_file>\n"
433			"\n"
434			"Options:\n"
435			"\n"
436			" short:\n"
437			" ------\n"
438			" -o <name> The output prefix\n"
439			" -t <time> Set the start time for correlations\n"
440			" -l <maxLength> set the maximum value of r\n"
441			" *Defaults to 1/2 smallest length of first frame.\n"
442			" -s Calculate the Scd chain correlation.\n"
443			"\n"
444			" long:\n"
445			" -----\n"
446			" --gofr <atom1> <atom2> g(r) for atom1 and atom2\n"
447			" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n"
448			" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n"
449			" --version displays the version number\n"
450			" --help displays this help message.\n"
451
452			"\n"
453			"\n",
454			programName);
455			}