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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 618 by mmeineke, Tue Jul 15 21:34:56 2003 UTC vs.
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC

# Line 33 | Line 33 | SimInfo::SimInfo(){
33    the_integrator = NULL;
34    setTemp = 0;
35    thermalTime = 0.0;
36 +  currentTime = 0.0;
37    rCut = 0.0;
38    ecr = 0.0;
39 +  est = 0.0;
40 +  oldEcr = 0.0;
41 +  oldRcut = 0.0;
42  
43 +  haveOrigRcut = 0;
44 +  haveOrigEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  
48 +
49    usePBC = 0;
50    useLJ = 0;
51    useSticky = 0;
# Line 47 | Line 57 | SimInfo::SimInfo(){
57    wrapMeSimInfo( this );
58   }
59  
60 + SimInfo::~SimInfo(){
61 +
62 +  map<string, GenericData*>::iterator i;
63 +  
64 +  for(i = properties.begin(); i != properties.end(); i++)
65 +    delete (*i).second;
66 +
67 +  
68 + }
69 +
70   void SimInfo::setBox(double newBox[3]) {
71    
72    int i, j;
# Line 74 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94                           // [ 2 5 8 ]
95    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
96  
97 +  
98 +  if( !boxIsInit ) boxIsInit = 1;
99  
100    for(i=0; i < 3; i++)
101      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
102    
81 –  //  cerr
82 –  // << "setting Hmat ->\n"
83 –  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 –  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 –  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
86 –
103    calcBoxL();
104    calcHmatInv();
105  
# Line 96 | Line 112 | void SimInfo::setBoxM( double theBox[3][3] ){
112  
113    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
114  
99 –  smallestBoxL = boxLx;
100 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
101 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
102 –
103 –  maxCutoff = smallestBoxL / 2.0;
104 –
105 –  if (rList > maxCutoff) {
106 –    sprintf( painCave.errMsg,
107 –             "New Box size is forcing neighborlist radius down to %lf\n",
108 –             maxCutoff );
109 –    painCave.isFatal = 0;
110 –    simError();
111 –
112 –    rList = maxCutoff;
113 –
114 –    sprintf( painCave.errMsg,
115 –             "New Box size is forcing cutoff radius down to %lf\n",
116 –             maxCutoff - 1.0 );
117 –    painCave.isFatal = 0;
118 –    simError();
119 –
120 –    rCut = rList - 1.0;
121 –
122 –    // list radius changed so we have to refresh the simulation structure.
123 –    refreshSim();
124 –  }
125 –
126 –  if( ecr > maxCutoff ){
127 –
128 –    sprintf( painCave.errMsg,
129 –             "New Box size is forcing electrostatic cutoff radius "
130 –             "down to %lf\n",
131 –             maxCutoff );
132 –    painCave.isFatal = 0;
133 –    simError();
134 –
135 –    ecr = maxCutoff;
136 –    est = 0.05 * ecr;
137 –
138 –    refreshSim();
139 –  }
140 –    
115   }
116  
117  
# Line 312 | Line 286 | void SimInfo::calcBoxL( void ){
286    
287    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
288    dsq = dx*dx + dy*dy + dz*dz;
289 <  boxLx = sqrt( dsq );
289 >  boxL[0] = sqrt( dsq );
290 >  maxCutoff = 0.5 * boxL[0];
291  
292    // boxLy
293    
294    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
295    dsq = dx*dx + dy*dy + dz*dz;
296 <  boxLy = sqrt( dsq );
296 >  boxL[1] = sqrt( dsq );
297 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
298  
299    // boxLz
300    
301    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
302    dsq = dx*dx + dy*dy + dz*dz;
303 <  boxLz = sqrt( dsq );
304 <  
303 >  boxL[2] = sqrt( dsq );
304 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
305 >
306   }
307  
308  
# Line 405 | Line 382 | void SimInfo::refreshSim(){
382    int isError;
383    int n_global;
384    int* excl;
385 <  
409 <  fInfo.rrf = 0.0;
410 <  fInfo.rt = 0.0;
385 >
386    fInfo.dielect = 0.0;
387  
413 –  fInfo.rlist = rList;
414 –  fInfo.rcut = rCut;
415 –
388    if( useDipole ){
417 –    fInfo.rrf = ecr;
418 –    fInfo.rt = ecr - est;
389      if( useReactionField )fInfo.dielect = dielectric;
390    }
391  
# Line 461 | Line 431 | void SimInfo::refreshSim(){
431  
432    this->ndf = this->getNDF();
433    this->ndfRaw = this->getNDFraw();
434 +
435 + }
436 +
437 +
438 + void SimInfo::setRcut( double theRcut ){
439 +
440 +  if( !haveOrigRcut ){
441 +    haveOrigRcut = 1;
442 +    origRcut = theRcut;
443 +  }
444 +
445 +  rCut = theRcut;
446 +  checkCutOffs();
447 + }
448 +
449 + void SimInfo::setEcr( double theEcr ){
450 +
451 +  if( !haveOrigEcr ){
452 +    haveOrigEcr = 1;
453 +    origEcr = theEcr;
454 +  }
455 +
456 +  ecr = theEcr;
457 +  checkCutOffs();
458 + }
459 +
460 + void SimInfo::setEcr( double theEcr, double theEst ){
461 +
462 +  est = theEst;
463 +  setEcr( theEcr );
464 + }
465 +
466 +
467 + void SimInfo::checkCutOffs( void ){
468  
469 +  int cutChanged = 0;
470 +
471 +  if( boxIsInit ){
472 +    
473 +    //we need to check cutOffs against the box
474 +    
475 +    if( maxCutoff > rCut ){
476 +      if( rCut < origRcut ){
477 +        rCut = origRcut;
478 +        if (rCut > maxCutoff) rCut = maxCutoff;
479 +        
480 +        sprintf( painCave.errMsg,
481 +                 "New Box size is setting the long range cutoff radius "
482 +                 "to %lf\n",
483 +                 rCut );
484 +        painCave.isFatal = 0;
485 +        simError();
486 +      }
487 +    }
488 +
489 +    if( maxCutoff > ecr ){
490 +      if( ecr < origEcr ){
491 +        rCut = origEcr;
492 +        if (ecr > maxCutoff) ecr = maxCutoff;
493 +        
494 +        sprintf( painCave.errMsg,
495 +                 "New Box size is setting the electrostaticCutoffRadius "
496 +                 "to %lf\n",
497 +                 ecr );
498 +        painCave.isFatal = 0;
499 +        simError();
500 +      }
501 +    }
502 +
503 +
504 +    if (rCut > maxCutoff) {
505 +      sprintf( painCave.errMsg,
506 +               "New Box size is setting the long range cutoff radius "
507 +               "to %lf\n",
508 +               maxCutoff );
509 +      painCave.isFatal = 0;
510 +      simError();
511 +      rCut = maxCutoff;
512 +    }
513 +
514 +    if( ecr > maxCutoff){
515 +      sprintf( painCave.errMsg,
516 +               "New Box size is setting the electrostaticCutoffRadius "
517 +               "to %lf\n",
518 +               maxCutoff  );
519 +      painCave.isFatal = 0;
520 +      simError();      
521 +      ecr = maxCutoff;
522 +    }
523 +
524 +    
525 +  }
526 +  
527 +
528 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
529 +
530 +  // rlist is the 1.0 plus max( rcut, ecr )
531 +  
532 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
533 +
534 +  if( cutChanged ){
535 +    
536 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537 +  }
538 +
539 +  oldEcr = ecr;
540 +  oldRcut = rCut;
541   }
542  
543 + void SimInfo::addProperty(GenericData* prop){
544 +
545 +  map<string, GenericData*>::iterator result;
546 +  result = properties.find(prop->getID());
547 +  
548 +  //we can't simply use  properties[prop->getID()] = prop,
549 +  //it will cause memory leak if we already contain a propery which has the same name of prop
550 +  
551 +  if(result != properties.end()){
552 +    
553 +    delete (*result).second;
554 +    (*result).second = prop;
555 +      
556 +  }
557 +  else{
558 +
559 +    properties[prop->getID()] = prop;
560 +
561 +  }
562 +    
563 + }
564 +
565 + GenericData* SimInfo::getProperty(const string& propName){
566 +
567 +  map<string, GenericData*>::iterator result;
568 +  
569 +  //string lowerCaseName = ();
570 +  
571 +  result = properties.find(propName);
572 +  
573 +  if(result != properties.end())
574 +    return (*result).second;  
575 +  else  
576 +    return NULL;  
577 + }
578 +
579 + vector<GenericData*> SimInfo::getProperties(){
580 +
581 +  vector<GenericData*> result;
582 +  map<string, GenericData*>::iterator i;
583 +  
584 +  for(i = properties.begin(); i != properties.end(); i++)
585 +    result.push_back((*i).second);
586 +    
587 +  return result;
588 + }
589 +
590 +

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