ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/tcProps/tcProps.c
(Generate patch)

Comparing trunk/tcProps/tcProps.c (file contents):
Revision 1058 by mmeineke, Wed Feb 18 21:20:51 2004 UTC vs.
Revision 1073 by mmeineke, Sat Feb 28 16:45:57 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  
16  
17   #define VERSION_MAJOR 0
# Line 30 | Line 34 | int main( int argC, char *argV[] ){
34    
35    struct atomCoord atoms[nAtoms];
36    int i,j,k;
33 –  char* inName;
34 –  int nFrames;
37    
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 +  int haveMaxLength;
43    char* conversionCheck;
44    int conversionError;
45    int optionError;
# Line 44 | Line 47 | int main( int argC, char *argV[] ){
47    char* pair2;
48    int scdCorr;
49    double startTime;
50 +  double maxLength;
51 +  int directorHead, directorWhole, doRMSD;
52 +  enum atomNames rmsdType;
53  
54    // system initialization
55    
# Line 55 | Line 61 | int main( int argC, char *argV[] ){
61    outPrefix = NULL;
62    inName = NULL;
63    
64 +  haveMaxLength = 0;
65    conversionError = 0;
66    optionError = 0;
67    havePrefix = 0;
68    scdCorr = 0;
69    startTime = 0.0;
70 +  directorHead = 0;
71 +  directorWhole = 0;
72 +  doRMSD = 0;
73    
74  
75    // parse the command line
# Line 76 | Line 86 | int main( int argC, char *argV[] ){
86  
87          // parse long word options
88          
89 <        if( !strcmp( argV[i], "--gofr" ) ){
89 >        if( !strcmp( argV[i], "--rmsd" ) ){
90  
91 +          doRMSD = 1;
92            i++;
93            if( i>=argC ){
94              fprintf( stderr,
95                       "\n"
96 <                     "not enough arguments for --gofr\n");
96 >                     "not enough arguments for --rmsd\n");
97              usage();
98              exit(0);
99            }      
100            pair1 = argV[i];
101  
102 <          i++;
103 <          if( i>=argC ){
102 >          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              fprintf( stderr,
110 <                     "\n"
111 <                     "not enough arguments for --gofr\n");
96 <            usage();
110 >                     "Unrecognized rmsd atom type \"%s\"\n",
111 >                     pair1 );
112              exit(0);
113 <          }      
99 <          pair2 = argV[i];
113 >          }
114  
115          }
116  
# Line 231 | Line 245 | int main( int argC, char *argV[] ){
245            case 'l':
246              // -l <double>    set <double> to the maxLength
247  
248 <            haveMaxLength = true;
248 >            haveMaxLength = 1;
249              j++;
250              currentFlag = argV[i][j];
251                
# Line 292 | Line 306 | int main( int argC, char *argV[] ){
306              break;
307  
308            case 's':
309 <            // -s turn on separate output files
309 >            // -s turn on Scd corr
310  
311              scdCorr = 1;
312 +            break;
313 +
314 +          case 'h':
315 +            // -h turn on director head
316 +
317 +            directorHead = 1;
318 +            break;
319 +
320 +          case 'w':
321 +            // -h turn on director head
322 +
323 +            directorWhole = 1;
324              break;
325  
326  
327            default:
328  
329 <            sprintf(painCave.errMsg,
329 >            fprintf( stderr,
330                      "\n"
331                      "Bad option \"-%c\"\n", currentFlag);
332              usage();
# Line 336 | Line 362 | int main( int argC, char *argV[] ){
362      exit(0);
363    }
364  
365 +  if( outPrefix == NULL )
366 +    outPrefix = inName;
367  
368 +
369    // initialize the arrays
370  
371    for(i=0;i<nLipids;i++){
372  
373      atoms[nLipAtoms*i+0].type = HEAD;
374 +    atoms[nLipAtoms*i+0].mass = 72;
375      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 +    
380  
381      atoms[nLipAtoms*i+1].type = CH2;
382 +    atoms[nLipAtoms*i+1].mass = 14.03;
383  
384      atoms[nLipAtoms*i+2].type = CH;
385 +    atoms[nLipAtoms*i+2].mass = 13.02;
386  
387      atoms[nLipAtoms*i+3].type = CH2;
388 +    atoms[nLipAtoms*i+3].mass = 14.03;
389  
390      atoms[nLipAtoms*i+4].type = CH2;
391 +    atoms[nLipAtoms*i+4].mass = 14.03;
392  
393      atoms[nLipAtoms*i+5].type = CH2;
394 +    atoms[nLipAtoms*i+5].mass = 14.03;
395  
396      atoms[nLipAtoms*i+6].type = CH2;
397 +    atoms[nLipAtoms*i+6].mass = 14.03;
398  
399      atoms[nLipAtoms*i+7].type = CH2;
400 +    atoms[nLipAtoms*i+7].mass = 14.03;
401  
402      atoms[nLipAtoms*i+8].type = CH2;
403 +    atoms[nLipAtoms*i+8].mass = 14.03;
404  
405      atoms[nLipAtoms*i+9].type = CH2;
406 +    atoms[nLipAtoms*i+9].mass = 14.03;
407  
408      atoms[nLipAtoms*i+10].type = CH3;
409 +    atoms[nLipAtoms*i+10].mass = 15.04;
410  
411      atoms[nLipAtoms*i+11].type = CH2;
412 +    atoms[nLipAtoms*i+11].mass = 14.03;
413  
414      atoms[nLipAtoms*i+12].type = CH2;
415 +    atoms[nLipAtoms*i+12].mass = 14.03;
416  
417 <    atoms[nLipAtoms*i+13].type = CH2;
417 >    atoms[nLipAtoms*i+13].type = CH2;    
418 >    atoms[nLipAtoms*i+13].mass = 14.03;
419  
420      atoms[nLipAtoms*i+14].type = CH2;
421 +    atoms[nLipAtoms*i+14].mass = 14.03;
422    
423      atoms[nLipAtoms*i+15].type = CH2;
424 +    atoms[nLipAtoms*i+15].mass = 14.03;
425    
426      atoms[nLipAtoms*i+16].type = CH2;
427 +    atoms[nLipAtoms*i+16].mass = 14.03;
428    
429      atoms[nLipAtoms*i+17].type = CH2;
430 +    atoms[nLipAtoms*i+17].mass = 14.03;
431    
432      atoms[nLipAtoms*i+18].type = CH3;
433 +    atoms[nLipAtoms*i+18].mass = 15.04;
434    }
435    
436    for(i=(nLipAtoms*nLipids);i<nAtoms;i++){
437      atoms[i].type = SSD;
438 +    atoms[i].mass = 18.03;
439      atoms[i].u[0] = 0.0;
440      atoms[i].u[1] = 0.0;
441      atoms[i].u[2] = 1.0;
# Line 393 | Line 443 | int main( int argC, char *argV[] ){
443  
444    // read and set the frames
445    
446 <  openFile( inName );
446 >  openFile();
447  
448    fprintf( stdout,
449             "\n"
# Line 401 | Line 451 | int main( int argC, char *argV[] ){
451             inName );
452    fflush(stdout);
453  
454 <  setFrames( inName );
454 >  setFrames();
455    
456    fprintf( stdout,
457             "done.\n"
458 <           "nFrames = %d\n.",
458 >           "nFrames = %d.\n",
459             nFrames );
460    fflush(stdout);
461  
# Line 415 | Line 465 | int main( int argC, char *argV[] ){
465                "Calculating the Scd correlation\n" );
466      fflush( stdout );
467      
468 <    calcScdCorr( startTime );
468 >    calcScdCorr( startTime, atoms, outPrefix );
469    }
470 +
471 +  if(directorHead){
472 +
473 +    fprintf ( stdout,
474 +              "Calculating the Head director\n" );
475 +    fflush( stdout );
476 +    
477 +    calcDirHeadCorr( startTime, atoms, outPrefix );
478 +  }
479 +
480 +  if(directorWhole){
481 +
482 +    fprintf ( stdout,
483 +              "Calculating the bilayer director\n" );
484 +    fflush( stdout );
485 +    
486 +    calcDirWholeCorr( startTime, atoms, outPrefix );
487 +  }
488 +
489 +  if(doRMSD){
490 +
491 +    fprintf ( stdout,
492 +              "Calculating the RMSD\n" );
493 +    fflush( stdout );
494 +    
495 +    rmsd( rmsdType, startTime, outPrefix );
496 +  }
497    
498  
499 +  closeFile();
500 +
501   }
502  
503  
# Line 440 | Line 519 | void usage(){
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 +                "   -h              Calculate the directors for the head groups\n"
523 +                "   -w              Calculate the director fro the bilayers\n"
524                  "\n"
525                  "   long:\n"
526                  "   -----\n"
527 <                "   --gofr <atom1> <atom2>         g(r) for atom1 and atom2\n"
527 >                "   --rmsd <atom1>                 rmsd for atom1\n"
528                  "   --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"

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines