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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 642 by mmeineke, Mon Jul 21 16:23:57 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 26 | Line 26 | SimInfo::SimInfo(){
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32    ndf = 0;
33    ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38    currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41    ecr = 0.0;
42 +  origEcr = -1.0;
43    est = 0.0;
44    oldEcr = 0.0;
45    oldRcut = 0.0;
# Line 44 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 +  resetTime = 1e99;
52    
53  
54    usePBC = 0;
# Line 54 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64    wrapMeSimInfo( this );
65   }
66  
67 +
68 + SimInfo::~SimInfo(){
69 +
70 +  delete myConfiguration;
71 +
72 +  map<string, GenericData*>::iterator i;
73 +  
74 +  for(i = properties.begin(); i != properties.end(); i++)
75 +    delete (*i).second;
76 +    
77 + }
78 +
79   void SimInfo::setBox(double newBox[3]) {
80    
81    int i, j;
# Line 75 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94  
95   void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, j, status;
79 <  double smallestBoxL, maxCutoff;
97 >  int i, j;
98    double FortranHmat[9]; // to preserve compatibility with Fortran the
99                           // ordering in the array is as follows:
100                           // [ 0 3 6 ]
# Line 261 | Line 279 | void SimInfo::printMat9(double A[9] ){
279              << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280              << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 + }
283 +
284 +
285 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
286 +
287 +      out[0] = a[1] * b[2] - a[2] * b[1];
288 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
289 +      out[2] = a[0] * b[1] - a[1] * b[0];
290 +      
291 + }
292 +
293 + double SimInfo::dotProduct3(double a[3], double b[3]){
294 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
295   }
296  
297 + double SimInfo::length3(double a[3]){
298 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
299 + }
300 +
301   void SimInfo::calcBoxL( void ){
302  
303    double dx, dy, dz, dsq;
269 –  int i;
304  
305    // boxVol = Determinant of Hmat
306  
# Line 277 | Line 311 | void SimInfo::calcBoxL( void ){
311    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
312    dsq = dx*dx + dy*dy + dz*dz;
313    boxL[0] = sqrt( dsq );
314 <  maxCutoff = 0.5 * boxL[0];
314 >  //maxCutoff = 0.5 * boxL[0];
315  
316    // boxLy
317    
318    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
319    dsq = dx*dx + dy*dy + dz*dz;
320    boxL[1] = sqrt( dsq );
321 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
321 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
322  
323 +
324    // boxLz
325    
326    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327    dsq = dx*dx + dy*dy + dz*dz;
328    boxL[2] = sqrt( dsq );
329 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
329 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
330  
331 +  //calculate the max cutoff
332 +  maxCutoff =  calcMaxCutOff();
333 +  
334 +  checkCutOffs();
335 +
336   }
337  
338  
339 + double SimInfo::calcMaxCutOff(){
340 +
341 +  double ri[3], rj[3], rk[3];
342 +  double rij[3], rjk[3], rki[3];
343 +  double minDist;
344 +
345 +  ri[0] = Hmat[0][0];
346 +  ri[1] = Hmat[1][0];
347 +  ri[2] = Hmat[2][0];
348 +
349 +  rj[0] = Hmat[0][1];
350 +  rj[1] = Hmat[1][1];
351 +  rj[2] = Hmat[2][1];
352 +
353 +  rk[0] = Hmat[0][2];
354 +  rk[1] = Hmat[1][2];
355 +  rk[2] = Hmat[2][2];
356 +  
357 +  crossProduct3(ri,rj, rij);
358 +  distXY = dotProduct3(rk,rij) / length3(rij);
359 +
360 +  crossProduct3(rj,rk, rjk);
361 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
362 +
363 +  crossProduct3(rk,ri, rki);
364 +  distZX = dotProduct3(rj,rki) / length3(rki);
365 +
366 +  minDist = min(min(distXY, distYZ), distZX);
367 +  return minDist/2;
368 +  
369 + }
370 +
371   void SimInfo::wrapVector( double thePos[3] ){
372  
373 <  int i, j, k;
373 >  int i;
374    double scaled[3];
375  
376    if( !orthoRhombic ){
# Line 346 | Line 418 | int SimInfo::getNDF(){
418    ndf = ndf_local;
419   #endif
420  
421 <  ndf = ndf - 3;
421 >  ndf = ndf - 3 - nZconstraints;
422  
423    return ndf;
424   }
# Line 365 | Line 437 | int SimInfo::getNDFraw() {
437  
438    return ndfRaw;
439   }
440 <
440 >
441 > int SimInfo::getNDFtranslational() {
442 >  int ndfTrans_local, ndfTrans;
443 >
444 >  ndfTrans_local = 3 * n_atoms - n_constraints;
445 >
446 > #ifdef IS_MPI
447 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
448 > #else
449 >  ndfTrans = ndfTrans_local;
450 > #endif
451 >
452 >  ndfTrans = ndfTrans - 3 - nZconstraints;
453 >
454 >  return ndfTrans;
455 > }
456 >
457   void SimInfo::refreshSim(){
458  
459    simtype fInfo;
# Line 421 | Line 509 | void SimInfo::refreshSim(){
509  
510    this->ndf = this->getNDF();
511    this->ndfRaw = this->getNDFraw();
512 <
512 >  this->ndfTrans = this->getNDFtranslational();
513   }
514  
515  
# Line 457 | Line 545 | void SimInfo::checkCutOffs( void ){
545   void SimInfo::checkCutOffs( void ){
546  
547    int cutChanged = 0;
548 <
548 >  
549    if( boxIsInit ){
550      
551      //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 –    }
552  
553 <    if( maxCutoff > ecr ){
554 <      if( ecr < origEcr ){
555 <        rCut = origEcr;
556 <        if (ecr > maxCutoff) ecr = maxCutoff;
557 <        
558 <        sprintf( painCave.errMsg,
559 <                 "New Box size is setting the electrostaticCutoffRadius "
560 <                 "to %lf\n",
561 <                 ecr );
562 <        painCave.isFatal = 0;
563 <        simError();
553 >    //detect the change of rCut
554 >    if(( maxCutoff > rCut )&&(usePBC)){
555 >      if( rCut < origRcut ){
556 >        rCut = origRcut;
557 >        
558 >        if (rCut > maxCutoff)
559 >          rCut = maxCutoff;
560 >  
561 >          sprintf( painCave.errMsg,
562 >                    "New Box size is setting the long range cutoff radius "
563 >                    "to %lf at time %lf\n",
564 >                    rCut, currentTime );
565 >          painCave.isFatal = 0;
566 >          simError();
567        }
568      }
569 <
493 <
494 <    if (rCut > maxCutoff) {
569 >    else if ((rCut > maxCutoff)&&(usePBC)) {
570        sprintf( painCave.errMsg,
571                 "New Box size is setting the long range cutoff radius "
572 <               "to %lf\n",
573 <               maxCutoff );
572 >               "to %lf at time %lf\n",
573 >               maxCutoff, currentTime );
574        painCave.isFatal = 0;
575        simError();
576        rCut = maxCutoff;
577      }
578  
579 <    if( ecr > maxCutoff){
579 >
580 >    //detect the change of ecr
581 >    if( maxCutoff > ecr ){
582 >      if( ecr < origEcr ){
583 >        ecr = origEcr;
584 >        if (ecr > maxCutoff) ecr = maxCutoff;
585 >  
586 >          sprintf( painCave.errMsg,
587 >                    "New Box size is setting the electrostaticCutoffRadius "
588 >                    "to %lf at time %lf\n",
589 >                    ecr, currentTime );
590 >            painCave.isFatal = 0;
591 >            simError();
592 >      }
593 >    }
594 >    else if( ecr > maxCutoff){
595        sprintf( painCave.errMsg,
596                 "New Box size is setting the electrostaticCutoffRadius "
597 <               "to %lf\n",
598 <               maxCutoff  );
597 >               "to %lf at time %lf\n",
598 >               maxCutoff, currentTime  );
599        painCave.isFatal = 0;
600        simError();      
601        ecr = maxCutoff;
602      }
603  
604 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
605      
606 +    // rlist is the 1.0 plus max( rcut, ecr )
607 +    
608 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
609 +    
610 +    if( cutChanged ){
611 +      
612 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
613 +    }
614 +    
615 +    oldEcr = ecr;
616 +    oldRcut = rCut;
617 +    
618 +  } else {
619 +    // initialize this stuff before using it, OK?
620 +    sprintf( painCave.errMsg,
621 +             "Trying to check cutoffs without a box. Be smarter.\n" );
622 +    painCave.isFatal = 1;
623 +    simError();      
624    }
625 <  
625 >  
626 > }
627  
628 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
628 > void SimInfo::addProperty(GenericData* prop){
629  
630 <  // rlist is the 1.0 plus max( rcut, ecr )
630 >  map<string, GenericData*>::iterator result;
631 >  result = properties.find(prop->getID());
632    
633 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
634 <
635 <  if( cutChanged ){
633 >  //we can't simply use  properties[prop->getID()] = prop,
634 >  //it will cause memory leak if we already contain a propery which has the same name of prop
635 >  
636 >  if(result != properties.end()){
637      
638 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
638 >    delete (*result).second;
639 >    (*result).second = prop;
640 >      
641    }
642 +  else{
643  
644 <  oldEcr = ecr;
645 <  oldRcut = rCut;
644 >    properties[prop->getID()] = prop;
645 >
646 >  }
647 >    
648   }
649 +
650 + GenericData* SimInfo::getProperty(const string& propName){
651 +
652 +  map<string, GenericData*>::iterator result;
653 +  
654 +  //string lowerCaseName = ();
655 +  
656 +  result = properties.find(propName);
657 +  
658 +  if(result != properties.end())
659 +    return (*result).second;  
660 +  else  
661 +    return NULL;  
662 + }
663 +
664 + vector<GenericData*> SimInfo::getProperties(){
665 +
666 +  vector<GenericData*> result;
667 +  map<string, GenericData*>::iterator i;
668 +  
669 +  for(i = properties.begin(); i != properties.end(); i++)
670 +    result.push_back((*i).second);
671 +    
672 +  return result;
673 + }
674 +
675 + double SimInfo::matTrace3(double m[3][3]){
676 +  double trace;
677 +  trace = m[0][0] + m[1][1] + m[2][2];
678 +
679 +  return trace;
680 + }

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