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root/group/branches/no-template-branch/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 617 by gezelter, Tue Jul 15 19:56:08 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 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 73 | Line 84 | void SimInfo::setBoxM( double theBox[3][3] ){
84                           // [ 2 5 8 ]
85    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
86  
87 +  
88 +  if( !boxIsInit ) boxIsInit = 1;
89  
90    for(i=0; i < 3; i++)
91      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
92    
80 –  //  cerr
81 –  // << "setting Hmat ->\n"
82 –  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 –  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 –  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85 –
93    calcBoxL();
94    calcHmatInv();
95  
# Line 95 | Line 102 | void SimInfo::setBoxM( double theBox[3][3] ){
102  
103    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
104  
98 –  smallestBoxL = boxLx;
99 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
100 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
101 –
102 –  maxCutoff = smallestBoxL / 2.0;
103 –
104 –  if (rList > maxCutoff) {
105 –    sprintf( painCave.errMsg,
106 –             "New Box size is forcing neighborlist radius down to %lf\n",
107 –             maxCutoff );
108 –    painCave.isFatal = 0;
109 –    simError();
110 –
111 –    rList = maxCutoff;
112 –
113 –    sprintf( painCave.errMsg,
114 –             "New Box size is forcing cutoff radius down to %lf\n",
115 –             maxCutoff - 1.0 );
116 –    painCave.isFatal = 0;
117 –    simError();
118 –
119 –    rCut = rList - 1.0;
120 –
121 –    // list radius changed so we have to refresh the simulation structure.
122 –    refreshSim();
123 –  }
124 –
125 –  if (rCut > maxCutoff) {
126 –    sprintf( painCave.errMsg,
127 –             "New Box size is forcing cutoff radius down to %lf\n",
128 –             maxCutoff );
129 –    painCave.isFatal = 0;
130 –    simError();
131 –
132 –    status = 0;
133 –    LJ_new_rcut(&rCut, &status);
134 –    if (status != 0) {
135 –      sprintf( painCave.errMsg,
136 –               "Error in recomputing LJ shifts based on new rcut\n");
137 –      painCave.isFatal = 1;
138 –      simError();
139 –    }
140 –  }
105   }
106  
107  
# Line 312 | Line 276 | void SimInfo::calcBoxL( void ){
276    
277    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
278    dsq = dx*dx + dy*dy + dz*dz;
279 <  boxLx = sqrt( dsq );
279 >  boxL[0] = sqrt( dsq );
280 >  maxCutoff = 0.5 * boxL[0];
281  
282    // boxLy
283    
284    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
285    dsq = dx*dx + dy*dy + dz*dz;
286 <  boxLy = sqrt( dsq );
286 >  boxL[1] = sqrt( dsq );
287 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
288  
289    // boxLz
290    
291    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
292    dsq = dx*dx + dy*dy + dz*dz;
293 <  boxLz = sqrt( dsq );
294 <  
293 >  boxL[2] = sqrt( dsq );
294 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
295 >
296   }
297  
298  
# Line 405 | Line 372 | void SimInfo::refreshSim(){
372    int isError;
373    int n_global;
374    int* excl;
375 <  
409 <  fInfo.rrf = 0.0;
410 <  fInfo.rt = 0.0;
375 >
376    fInfo.dielect = 0.0;
377  
413 –  fInfo.rlist = rList;
414 –  fInfo.rcut = rCut;
415 –
378    if( useDipole ){
417 –    fInfo.rrf = ecr;
418 –    fInfo.rt = ecr - est;
379      if( useReactionField )fInfo.dielect = dielectric;
380    }
381  
# Line 461 | Line 421 | void SimInfo::refreshSim(){
421  
422    this->ndf = this->getNDF();
423    this->ndfRaw = this->getNDFraw();
424 +
425 + }
426 +
427 +
428 + void SimInfo::setRcut( double theRcut ){
429 +
430 +  if( !haveOrigRcut ){
431 +    haveOrigRcut = 1;
432 +    origRcut = theRcut;
433 +  }
434 +
435 +  rCut = theRcut;
436 +  checkCutOffs();
437 + }
438 +
439 + void SimInfo::setEcr( double theEcr ){
440 +
441 +  if( !haveOrigEcr ){
442 +    haveOrigEcr = 1;
443 +    origEcr = theEcr;
444 +  }
445 +
446 +  ecr = theEcr;
447 +  checkCutOffs();
448 + }
449 +
450 + void SimInfo::setEcr( double theEcr, double theEst ){
451 +
452 +  est = theEst;
453 +  setEcr( theEcr );
454 + }
455 +
456 +
457 + void SimInfo::checkCutOffs( void ){
458 +
459 +  int cutChanged = 0;
460 +
461 +  if( boxIsInit ){
462 +    
463 +    //we need to check cutOffs against the box
464 +    
465 +    if( maxCutoff > rCut ){
466 +      if( rCut < origRcut ){
467 +        rCut = origRcut;
468 +        if (rCut > maxCutoff) rCut = maxCutoff;
469 +        
470 +        sprintf( painCave.errMsg,
471 +                 "New Box size is setting the long range cutoff radius "
472 +                 "to %lf\n",
473 +                 rCut );
474 +        painCave.isFatal = 0;
475 +        simError();
476 +      }
477 +    }
478  
479 +    if( maxCutoff > ecr ){
480 +      if( ecr < origEcr ){
481 +        rCut = origEcr;
482 +        if (ecr > maxCutoff) ecr = maxCutoff;
483 +        
484 +        sprintf( painCave.errMsg,
485 +                 "New Box size is setting the electrostaticCutoffRadius "
486 +                 "to %lf\n",
487 +                 ecr );
488 +        painCave.isFatal = 0;
489 +        simError();
490 +      }
491 +    }
492 +
493 +
494 +    if (rCut > maxCutoff) {
495 +      sprintf( painCave.errMsg,
496 +               "New Box size is setting the long range cutoff radius "
497 +               "to %lf\n",
498 +               maxCutoff );
499 +      painCave.isFatal = 0;
500 +      simError();
501 +      rCut = maxCutoff;
502 +    }
503 +
504 +    if( ecr > maxCutoff){
505 +      sprintf( painCave.errMsg,
506 +               "New Box size is setting the electrostaticCutoffRadius "
507 +               "to %lf\n",
508 +               maxCutoff  );
509 +      painCave.isFatal = 0;
510 +      simError();      
511 +      ecr = maxCutoff;
512 +    }
513 +
514 +    
515 +  }
516 +  
517 +
518 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
519 +
520 +  // rlist is the 1.0 plus max( rcut, ecr )
521 +  
522 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
523 +
524 +  if( cutChanged ){
525 +    
526 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
527 +  }
528 +
529 +  oldEcr = ecr;
530 +  oldRcut = rCut;
531   }
532  
533 + void SimInfo::addProperty(GenericData* prop){
534 +
535 +  map<string, GenericData*>::iterator result;
536 +  result = properties.find(prop->getID());
537 +  
538 +  //we can't simply use  properties[prop->getID()] = prop,
539 +  //it will cause memory leak if we already contain a propery which has the same name of prop
540 +  
541 +  if(result != properties.end()){
542 +    
543 +    delete (*result).second;
544 +    (*result).second = prop;
545 +      
546 +  }
547 +  else{
548 +
549 +    properties[prop->getID()] = prop;
550 +
551 +  }
552 +    
553 + }
554 +
555 + GenericData* SimInfo::getProperty(const string& propName){
556 +
557 +  map<string, GenericData*>::iterator result;
558 +  
559 +  //string lowerCaseName = ();
560 +  
561 +  result = properties.find(propName);
562 +  
563 +  if(result != properties.end())
564 +    return (*result).second;  
565 +  else  
566 +    return NULL;  
567 + }
568 +
569 + vector<GenericData*> SimInfo::getProperties(){
570 +
571 +  vector<GenericData*> result;
572 +  map<string, GenericData*>::iterator i;
573 +  
574 +  for(i = properties.begin(); i != properties.end(); i++)
575 +    result.push_back((*i).second);
576 +    
577 +  return result;
578 + }
579 +
580 +

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