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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 1085 by mmeineke, Fri Mar 5 03:10:29 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 + #include "directorWhole.h"
14 + #include "rmsd.h"
15 + #include "gofz.h"
16  
17  
18   #define VERSION_MAJOR 0
# Line 30 | Line 35 | int main( int argC, char *argV[] ){
35    
36    struct atomCoord atoms[nAtoms];
37    int i,j,k;
33 –  char* inName;
34 –  int nFrames;
38    
39    char* outPrefix; // the output prefix
40    char currentFlag; // used in parsing the flags
41    int done = 0; // multipurpose boolean
42    int havePrefix; // boolean for the output prefix  
43 +  int haveMaxLength;
44    char* conversionCheck;
45    int conversionError;
46    int optionError;
47 +  char* rmsdName;
48    char* pair1;
49    char* pair2;
50    int scdCorr;
51    double startTime;
52 +  double avgXY;
53 +  double maxLength;
54  
55 +  int directorHead, directorWhole, doRMSD, doGofz, doAvgXY;
56 +  enum atomNames rmsdType;
57 +
58    // system initialization
59    
60    isScanned = 0;
# Line 55 | Line 65 | int main( int argC, char *argV[] ){
65    outPrefix = NULL;
66    inName = NULL;
67    
68 +  haveMaxLength = 0;
69    conversionError = 0;
70    optionError = 0;
71    havePrefix = 0;
72    scdCorr = 0;
73    startTime = 0.0;
74 +  directorHead = 0;
75 +  directorWhole = 0;
76 +  doRMSD = 0;
77 +  doGofz = 0;
78 +  doAvgXY = 0;
79    
80  
81    // parse the command line
# Line 76 | Line 92 | int main( int argC, char *argV[] ){
92  
93          // parse long word options
94          
95 <        if( !strcmp( argV[i], "--gofr" ) ){
95 >        if( !strcmp( argV[i], "--rmsd" ) ){
96  
97 +          doRMSD = 1;
98            i++;
99            if( i>=argC ){
100              fprintf( stderr,
101                       "\n"
102 <                     "not enough arguments for --gofr\n");
102 >                     "not enough arguments for --rmsd\n");
103              usage();
104              exit(0);
105            }      
106 <          pair1 = argV[i];
106 >          rmsdName = argV[i];
107  
108 <          i++;
109 <          if( i>=argC ){
108 >          if( !strcmp(rmsdName, "HEAD") )    rmsdType = HEAD;
109 >          else if( !strcmp(rmsdName, "CH") ) rmsdType = CH;
110 >          else if( !strcmp(rmsdName, "CH2") )rmsdType = CH2;
111 >          else if( !strcmp(rmsdName, "CH3") )rmsdType = CH3;
112 >          else if( !strcmp(rmsdName, "SSD") )rmsdType = SSD;
113 >          else if( !strcmp(rmsdName, "COM") )rmsdType = COM;
114 >          else{
115              fprintf( stderr,
116 <                     "\n"
117 <                     "not enough arguments for --gofr\n");
96 <            usage();
116 >                     "Unrecognized rmsd atom type \"%s\"\n",
117 >                     rmsdName );
118              exit(0);
119 <          }      
99 <          pair2 = argV[i];
119 >          }
120  
121          }
122  
# Line 231 | Line 251 | int main( int argC, char *argV[] ){
251            case 'l':
252              // -l <double>    set <double> to the maxLength
253  
254 <            haveMaxLength = true;
254 >            haveMaxLength = 1;
255              j++;
256              currentFlag = argV[i][j];
257                
# Line 292 | Line 312 | int main( int argC, char *argV[] ){
312              break;
313  
314            case 's':
315 <            // -s turn on separate output files
315 >            // -s turn on Scd corr
316  
317              scdCorr = 1;
318              break;
319  
320 +          case 'h':
321 +            // -h turn on director head
322  
323 +            directorHead = 1;
324 +            break;
325 +
326 +          case 'w':
327 +            // -w turn on director head
328 +
329 +            directorWhole = 1;
330 +            break;
331 +
332 +          case 'g':
333 +            // -g turn on gofZ
334 +
335 +            doGofz = 1;
336 +            break;
337 +
338 +          case 'v':
339 +            // -v turn on average XY
340 +
341 +            doAvgXY = 1;
342 +            break;
343 +
344 +
345            default:
346  
347 <            sprintf(painCave.errMsg,
347 >            fprintf( stderr,
348                      "\n"
349                      "Bad option \"-%c\"\n", currentFlag);
350              usage();
# Line 336 | Line 380 | int main( int argC, char *argV[] ){
380      exit(0);
381    }
382  
383 +  if( outPrefix == NULL )
384 +    outPrefix = inName;
385  
386 +
387    // initialize the arrays
388  
389    for(i=0;i<nLipids;i++){
390  
391      atoms[nLipAtoms*i+0].type = HEAD;
392 +    atoms[nLipAtoms*i+0].mass = 72;
393      atoms[nLipAtoms*i+0].u[0] = 0.0;
394      atoms[nLipAtoms*i+0].u[1] = 0.0;
395      atoms[nLipAtoms*i+0].u[2] = 1.0;
396      
397 +    
398  
399      atoms[nLipAtoms*i+1].type = CH2;
400 +    atoms[nLipAtoms*i+1].mass = 14.03;
401  
402      atoms[nLipAtoms*i+2].type = CH;
403 +    atoms[nLipAtoms*i+2].mass = 13.02;
404  
405      atoms[nLipAtoms*i+3].type = CH2;
406 +    atoms[nLipAtoms*i+3].mass = 14.03;
407  
408      atoms[nLipAtoms*i+4].type = CH2;
409 +    atoms[nLipAtoms*i+4].mass = 14.03;
410  
411      atoms[nLipAtoms*i+5].type = CH2;
412 +    atoms[nLipAtoms*i+5].mass = 14.03;
413  
414      atoms[nLipAtoms*i+6].type = CH2;
415 +    atoms[nLipAtoms*i+6].mass = 14.03;
416  
417      atoms[nLipAtoms*i+7].type = CH2;
418 +    atoms[nLipAtoms*i+7].mass = 14.03;
419  
420      atoms[nLipAtoms*i+8].type = CH2;
421 +    atoms[nLipAtoms*i+8].mass = 14.03;
422  
423      atoms[nLipAtoms*i+9].type = CH2;
424 +    atoms[nLipAtoms*i+9].mass = 14.03;
425  
426      atoms[nLipAtoms*i+10].type = CH3;
427 +    atoms[nLipAtoms*i+10].mass = 15.04;
428  
429      atoms[nLipAtoms*i+11].type = CH2;
430 +    atoms[nLipAtoms*i+11].mass = 14.03;
431  
432      atoms[nLipAtoms*i+12].type = CH2;
433 +    atoms[nLipAtoms*i+12].mass = 14.03;
434  
435 <    atoms[nLipAtoms*i+13].type = CH2;
435 >    atoms[nLipAtoms*i+13].type = CH2;    
436 >    atoms[nLipAtoms*i+13].mass = 14.03;
437  
438      atoms[nLipAtoms*i+14].type = CH2;
439 +    atoms[nLipAtoms*i+14].mass = 14.03;
440    
441      atoms[nLipAtoms*i+15].type = CH2;
442 +    atoms[nLipAtoms*i+15].mass = 14.03;
443    
444      atoms[nLipAtoms*i+16].type = CH2;
445 +    atoms[nLipAtoms*i+16].mass = 14.03;
446    
447      atoms[nLipAtoms*i+17].type = CH2;
448 +    atoms[nLipAtoms*i+17].mass = 14.03;
449    
450      atoms[nLipAtoms*i+18].type = CH3;
451 +    atoms[nLipAtoms*i+18].mass = 15.04;
452    }
453    
454    for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
455      atoms[i].type = SSD;
456 +    atoms[i].mass = 18.03;
457      atoms[i].u[0] = 0.0;
458      atoms[i].u[1] = 0.0;
459      atoms[i].u[2] = 1.0;
# Line 393 | Line 461 | int main( int argC, char *argV[] ){
461  
462    // read and set the frames
463    
464 <  openFile( inName );
464 >  openFile();
465  
466    fprintf( stdout,
467             "\n"
# Line 401 | Line 469 | int main( int argC, char *argV[] ){
469             inName );
470    fflush(stdout);
471  
472 <  setFrames( inName );
472 >  setFrames();
473    
474    fprintf( stdout,
475             "done.\n"
476 <           "nFrames = %d\n.",
476 >           "nFrames = %d.\n",
477             nFrames );
478    fflush(stdout);
479  
# Line 415 | Line 483 | int main( int argC, char *argV[] ){
483                "Calculating the Scd correlation\n" );
484      fflush( stdout );
485      
486 <    calcScdCorr( startTime );
486 >    calcScdCorr( startTime, atoms, outPrefix );
487    }
488 +
489 +  if(directorHead){
490 +
491 +    fprintf ( stdout,
492 +              "Calculating the Head director\n" );
493 +    fflush( stdout );
494 +    
495 +    calcDirHeadCorr( startTime, atoms, outPrefix );
496 +  }
497 +
498 +  if(directorWhole){
499 +
500 +    fprintf ( stdout,
501 +              "Calculating the bilayer director\n" );
502 +    fflush( stdout );
503 +    
504 +    calcDirWholeCorr( startTime, atoms, outPrefix );
505 +  }
506 +
507 +  if(doRMSD){
508 +
509 +    fprintf ( stdout,
510 +              "Calculating the RMSD\n" );
511 +    fflush( stdout );
512 +    
513 +    rmsd( rmsdType, startTime, outPrefix, rmsdName );
514 +  }
515 +
516 +  if(doGofz){
517 +
518 +    fprintf ( stdout,
519 +              "Calculating the gofZ\n" );
520 +    fflush( stdout );
521 +    
522 +    calcGofz( startTime, atoms, outPrefix );
523 +  }
524 +
525 +  if(doAvgXY){
526 +
527 +    fprintf ( stdout,
528 +              "Calculating the average XY\n" );
529 +    fflush( stdout );
530 +    
531 +    avgXY = calcAverageXY( startTime );
532 +    
533 +    fprintf ( stdout,
534 +              "Done, average XY = %6G\n", avgXY );
535 +    fflush( stdout );
536 +    
537 +  }
538    
539  
540 +  closeFile();
541 +
542   }
543  
544  
# Line 440 | Line 560 | void usage(){
560                  "   -l <maxLength>  set the maximum value of r\n"
561                  "                     *Defaults to 1/2 smallest length of first frame.\n"
562                  "   -s              Calculate the Scd chain correlation.\n"
563 +                "   -h              Calculate the directors for the head groups\n"
564 +                "   -w              Calculate the director from the bilayers\n"
565 +                "   -g              Calculate the gofz profile\n"
566                  "\n"
567                  "   long:\n"
568                  "   -----\n"
569 <                "   --gofr <atom1> <atom2>         g(r) for atom1 and atom2\n"
569 >                "   --rmsd <atom1>                 rmsd for atom1\n"
570                  "   --gofrTheta <atom1> <atom2>    g(r, theta) for atom1 and atom2\n"
571                  "   --gofrOmega <atom1> <atom2>    g(r, omega) for atom1 and atom2\n"
572                  "   --version                      displays the version number\n"

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