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root/group/trunk/tcProps/readWrite.c
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Comparing trunk/tcProps/readWrite.c (file contents):
Revision 1056 by mmeineke, Tue Feb 17 14:30:48 2004 UTC vs.
Revision 1058 by mmeineke, Wed Feb 18 21:20:51 2004 UTC

# Line 36 | Line 36 | void parseDumpLine( char readBuffer[BUFFER_SIZE], int
36  
37   void parseDumpLine( char readBuffer[BUFFER_SIZE], int index,
38                      struct atomCoord* atoms );
39 + void setU( double q[4], double u[3] );
40 + void normalizeQ( double q[4] );
41  
42   void openFile( char* inName ){
43    
# Line 366 | Line 368 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
368    }
369   }
370  
371 < void parseDumpLine( char readLine[BUFFER_SIZE], int index,
371 > void parseDumpLine( char readLine[BUFFER_SIZE], int i,
372                      struct atomCoord* atoms ){
373    char* foo;
374    double q[4];
# Line 377 | Line 379 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
379    
380    // check the atom ID
381  
382 <  switch( atoms[index].type ){
382 >  switch( atoms[i].type ){
383      
384    case HEAD:
385      if( strcmp(foo, "HEAD") ){
# Line 427 | Line 429 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
429    default:
430      fprintf(stderr,
431              "Atom %d is an unrecognized enumeration\n",
432 <            index );
432 >            i );
433      exit(0);
434    }
435    
# Line 437 | Line 439 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
439    if(foo == NULL){
440      fprintf( stderr,
441               "error in reading postition x from %s\n"
442 <             "natoms  = %d, index = %d\n",
443 <             inName, nAtoms, index );
442 >             "natoms  = %d, i = %d\n",
443 >             inName, nAtoms, i );
444      exit(0);
445    }
446    atoms[i].pos[0] = atof( foo );
# Line 447 | Line 449 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
449    if(foo == NULL){
450      fprintf( stderr,
451               "error in reading postition y from %s\n"
452 <             "natoms  = %d, index = %d\n",
453 <             inName, nAtoms, index );
452 >             "natoms  = %d, i = %d\n",
453 >             inName, nAtoms, i );
454      exit(0);
455    }
456    atoms[i].pos[1] = atof( foo );
# Line 457 | Line 459 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
459    if(foo == NULL){
460      fprintf( stderr,
461               "error in reading postition z from %s\n"
462 <             "natoms  = %d, index = %d\n",
463 <             inName, nAtoms, index );
462 >             "natoms  = %d, i = %d\n",
463 >             inName, nAtoms, i );
464      exit(0);
465    }
466    atoms[i].pos[2] = atof( foo );    
# Line 470 | Line 472 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
472    if(foo == NULL){
473      fprintf( stderr,
474               "error in reading velocity x from %s\n"
475 <             "natoms  = %d, index = %d\n",
476 <             inName, nAtoms, index );
475 >             "natoms  = %d, i = %d\n",
476 >             inName, nAtoms, i );
477      exit(0);
478    }
479    atoms[i].vel[0] = atof( foo );
# Line 480 | Line 482 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
482    if(foo == NULL){
483      fprintf( stderr,
484               "error in reading velocity y from %s\n"
485 <             "natoms  = %d, index = %d\n",
486 <             inName, nAtoms, index );
485 >             "natoms  = %d, i = %d\n",
486 >             inName, nAtoms, i );
487      exit(0);
488    }
489    atoms[i].vel[1] = atof( foo );
# Line 490 | Line 492 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
492    if(foo == NULL){
493      fprintf( stderr,
494               "error in reading velocity z from %s\n"
495 <             "natoms  = %d, index = %d\n",
496 <             inName, nAtoms, index );
495 >             "natoms  = %d, i = %d\n",
496 >             inName, nAtoms, i );
497      exit(0);
498    }
499    atoms[i].vel[2] = atof( foo );
# Line 505 | Line 507 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
507      if(foo == NULL){
508        sprintf(painCave.errMsg,
509                "error in reading quaternion 0 from %s\n"
510 <              "natoms  = %d, index = %d\n",
511 <              inName, nAtoms, index );
510 >              "natoms  = %d, i = %d\n",
511 >              inName, nAtoms, i );
512        exit(0);
513      }
514      q[0] = atof( foo );
# Line 515 | Line 517 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
517      if(foo == NULL){
518        fprintf( stderr,
519                 "error in reading quaternion 1 from %s\n"
520 <               "natoms  = %d, index = %d\n",
521 <               inName, nAtoms, index );
520 >               "natoms  = %d, i = %d\n",
521 >               inName, nAtoms, i );
522        exit(0);
523      }
524      q[1] = atof( foo );
# Line 525 | Line 527 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
527      if(foo == NULL){
528        fprintf( stderr,
529                 "error in reading quaternion 2 from %s\n"
530 <               "natoms  = %d, index = %d\n",
531 <               inName, nAtoms, index );
530 >               "natoms  = %d, i = %d\n",
531 >               inName, nAtoms, i );
532        exit(0);
533      }
534      q[2] = atof( foo );
# Line 535 | Line 537 | void parseDumpLine( char readLine[BUFFER_SIZE], int in
537      if(foo == NULL){
538        fprintf( stderr,
539                 "error in reading quaternion 3 from %s\n"
540 <               "natoms  = %d, index = %d\n",
541 <               inName, nAtoms, index );
540 >               "natoms  = %d, i = %d\n",
541 >               inName, nAtoms, i );
542        exit(0);
543      }
544      q[3] = atof( foo );
545 +  
546 +    normalizeQ( q );
547 +
548 +    setU( q, atoms[i].u );
549    }
550 + }
551  
552  
553 + void setU( double the_q[4], double u[3] ){
554  
555 +  double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
556 +  double A[3][3];
557 +  double rb[3];
558  
559 +  // initialize the axis
560  
561 +  rb[0] = 0.0;
562 +  rb[1] = 0.0;
563 +  rb[2] = 1.0;
564 +
565 +  // set the rotation matrix
566 +  
567 +  q0Sqr = the_q[0] * the_q[0];
568 +  q1Sqr = the_q[1] * the_q[1];
569 +  q2Sqr = the_q[2] * the_q[2];
570 +  q3Sqr = the_q[3] * the_q[3];
571 +  
572 +  A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr;
573 +  A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] );
574 +  A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] );
575 +  
576 +  A[1][0]  = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] );
577 +  A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr;
578 +  A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] );
579 +  
580 +  A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] );
581 +  A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] );
582 +  A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr;
583 +
584 +  // perform the rotation
585 +  
586 +  for( i=0; i<3; i++ ){
587 +    u[i] = 0.0;
588 +    
589 +    for( j=0; j<3; j++ ){
590 +      u[i] += A[j][i] * rb[j];
591 +    }
592 +  }
593   }
594 +
595 + void normalizeQ( double q[4] ){
596 +  
597 +  double qSqr, qL;
598 +  int i;
599 +  
600 +  qSqr = 0.0;
601 +  for(i=0;i<4;i++)
602 +    qSqr += q[i] * q[i];
603 +  
604 +  for(i=0;i<4;i++)
605 +    q[i] /= qSqr;
606 + }
607 +      

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