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root/group/trunk/tcProps/tcProps.c
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Comparing trunk/tcProps/tcProps.c (file contents):
Revision 1058 by mmeineke, Wed Feb 18 21:20:51 2004 UTC vs.
Revision 1062 by mmeineke, Fri Feb 20 21:20:37 2004 UTC

# Line 2 | Line 2
2  
3   #include <stdio.h>
4   #include <stdlib.h>
5 + #include <string.h>
6  
7  
8   #include "params.h"
9   #include "tcProps.h"
10   #include "readWrite.h"
11   #include "scdCorr.h"
12 + #include "directorHead.h"
13  
14  
15   #define VERSION_MAJOR 0
# Line 30 | Line 32 | int main( int argC, char *argV[] ){
32    
33    struct atomCoord atoms[nAtoms];
34    int i,j,k;
33 –  char* inName;
34 –  int nFrames;
35    
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 +  int haveMaxLength;
41    char* conversionCheck;
42    int conversionError;
43    int optionError;
# Line 44 | Line 45 | int main( int argC, char *argV[] ){
45    char* pair2;
46    int scdCorr;
47    double startTime;
48 +  double maxLength;
49 +  int directorHead, directorWhole;
50  
51    // system initialization
52    
# Line 55 | Line 58 | int main( int argC, char *argV[] ){
58    outPrefix = NULL;
59    inName = NULL;
60    
61 +  haveMaxLength = 0;
62    conversionError = 0;
63    optionError = 0;
64    havePrefix = 0;
65    scdCorr = 0;
66    startTime = 0.0;
67 +  directorHead = 0;
68 +  directorWhole = 0;
69    
70  
71    // parse the command line
# Line 231 | Line 237 | int main( int argC, char *argV[] ){
237            case 'l':
238              // -l <double>    set <double> to the maxLength
239  
240 <            haveMaxLength = true;
240 >            haveMaxLength = 1;
241              j++;
242              currentFlag = argV[i][j];
243                
# Line 292 | Line 298 | int main( int argC, char *argV[] ){
298              break;
299  
300            case 's':
301 <            // -s turn on separate output files
301 >            // -s turn on Scd corr
302  
303              scdCorr = 1;
304 +            break;
305 +
306 +          case 'h':
307 +            // -h turn on director head
308 +
309 +            directorHead = 1;
310 +            break;
311 +
312 +          case 'w':
313 +            // -h turn on director head
314 +
315 +            directorWhole = 1;
316              break;
317  
318  
319            default:
320  
321 <            sprintf(painCave.errMsg,
321 >            fprintf( stderr,
322                      "\n"
323                      "Bad option \"-%c\"\n", currentFlag);
324              usage();
# Line 336 | Line 354 | int main( int argC, char *argV[] ){
354      exit(0);
355    }
356  
357 +  if( outPrefix == NULL )
358 +    outPrefix = inName;
359  
360 +
361    // initialize the arrays
362  
363    for(i=0;i<nLipids;i++){
364  
365      atoms[nLipAtoms*i+0].type = HEAD;
366 +    atoms[nLipAtoms*i+0].mass = 72;
367      atoms[nLipAtoms*i+0].u[0] = 0.0;
368      atoms[nLipAtoms*i+0].u[1] = 0.0;
369      atoms[nLipAtoms*i+0].u[2] = 1.0;
370      
371 +    
372  
373      atoms[nLipAtoms*i+1].type = CH2;
374 +    atoms[nLipAtoms*i+1].mass = 14.03;
375  
376      atoms[nLipAtoms*i+2].type = CH;
377 +    atoms[nLipAtoms*i+2].mass = 13.02;
378  
379      atoms[nLipAtoms*i+3].type = CH2;
380 +    atoms[nLipAtoms*i+3].mass = 14.03;
381  
382      atoms[nLipAtoms*i+4].type = CH2;
383 +    atoms[nLipAtoms*i+4].mass = 14.03;
384  
385      atoms[nLipAtoms*i+5].type = CH2;
386 +    atoms[nLipAtoms*i+5].mass = 14.03;
387  
388      atoms[nLipAtoms*i+6].type = CH2;
389 +    atoms[nLipAtoms*i+6].mass = 14.03;
390  
391      atoms[nLipAtoms*i+7].type = CH2;
392 +    atoms[nLipAtoms*i+7].mass = 14.03;
393  
394      atoms[nLipAtoms*i+8].type = CH2;
395 +    atoms[nLipAtoms*i+8].mass = 14.03;
396  
397      atoms[nLipAtoms*i+9].type = CH2;
398 +    atoms[nLipAtoms*i+9].mass = 14.03;
399  
400      atoms[nLipAtoms*i+10].type = CH3;
401 +    atoms[nLipAtoms*i+10].mass = 15.04;
402  
403      atoms[nLipAtoms*i+11].type = CH2;
404 +    atoms[nLipAtoms*i+11].mass = 14.03;
405  
406      atoms[nLipAtoms*i+12].type = CH2;
407 +    atoms[nLipAtoms*i+12].mass = 14.03;
408  
409 <    atoms[nLipAtoms*i+13].type = CH2;
409 >    atoms[nLipAtoms*i+13].type = CH2;    
410 >    atoms[nLipAtoms*i+13].mass = 14.03;
411  
412      atoms[nLipAtoms*i+14].type = CH2;
413 +    atoms[nLipAtoms*i+14].mass = 14.03;
414    
415      atoms[nLipAtoms*i+15].type = CH2;
416 +    atoms[nLipAtoms*i+15].mass = 14.03;
417    
418      atoms[nLipAtoms*i+16].type = CH2;
419 +    atoms[nLipAtoms*i+16].mass = 14.03;
420    
421      atoms[nLipAtoms*i+17].type = CH2;
422 +    atoms[nLipAtoms*i+17].mass = 14.03;
423    
424      atoms[nLipAtoms*i+18].type = CH3;
425 +    atoms[nLipAtoms*i+18].mass = 15.04;
426    }
427    
428    for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
429      atoms[i].type = SSD;
430 +    atoms[i].mass = 18.03;
431      atoms[i].u[0] = 0.0;
432      atoms[i].u[1] = 0.0;
433      atoms[i].u[2] = 1.0;
# Line 393 | Line 435 | int main( int argC, char *argV[] ){
435  
436    // read and set the frames
437    
438 <  openFile( inName );
438 >  openFile();
439  
440    fprintf( stdout,
441             "\n"
# Line 401 | Line 443 | int main( int argC, char *argV[] ){
443             inName );
444    fflush(stdout);
445  
446 <  setFrames( inName );
446 >  setFrames();
447    
448    fprintf( stdout,
449             "done.\n"
450 <           "nFrames = %d\n.",
450 >           "nFrames = %d.\n",
451             nFrames );
452    fflush(stdout);
453  
# Line 415 | Line 457 | int main( int argC, char *argV[] ){
457                "Calculating the Scd correlation\n" );
458      fflush( stdout );
459      
460 <    calcScdCorr( startTime );
460 >    calcScdCorr( startTime, atoms, outPrefix );
461    }
462 +
463 +  if(directorHead){
464 +
465 +    fprintf ( stdout,
466 +              "Calculating the Head director\n" );
467 +    fflush( stdout );
468 +    
469 +    calcDirHeadCorr( startTime, atoms, outPrefix );
470 +  }
471 +
472 +  if(directorWhole){
473 +
474 +    fprintf ( stdout,
475 +              "Calculating the bilayer director\n" );
476 +    fflush( stdout );
477 +    
478 +    calcDirWholeCorr( startTime, atoms, outPrefix );
479 +  }
480    
481  
482 +  closeFile();
483 +
484   }
485  
486  
# Line 440 | Line 502 | void usage(){
502                  "   -l <maxLength>  set the maximum value of r\n"
503                  "                     *Defaults to 1/2 smallest length of first frame.\n"
504                  "   -s              Calculate the Scd chain correlation.\n"
505 +                "   -h              Calculate the directors for the head groups\n"
506 +                "   -w              Calculate the director fro the bilayers\n"
507                  "\n"
508                  "   long:\n"
509                  "   -----\n"

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