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root/group/branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp
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Comparing:
trunk/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
3 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5   #include <iostream>
6   using namespace std;
# 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;
# Line 47 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 +  resetTime = 1e99;
52    
53  
54    usePBC = 0;
# Line 59 | Line 61 | SimInfo::SimInfo(){
61  
62    myConfiguration = new SimState();
63  
64 +  properties = new GenericData();
65 +
66    wrapMeSimInfo( this );
67   }
68  
# Line 66 | Line 70 | SimInfo::~SimInfo(){
70   SimInfo::~SimInfo(){
71  
72    delete myConfiguration;
73 <
70 <  map<string, GenericData*>::iterator i;
71 <  
72 <  for(i = properties.begin(); i != properties.end(); i++)
73 <    delete (*i).second;
74 <    
73 >  delete properties;    
74   }
75  
76   void SimInfo::setBox(double newBox[3]) {
# Line 92 | Line 91 | void SimInfo::setBoxM( double theBox[3][3] ){
91  
92   void SimInfo::setBoxM( double theBox[3][3] ){
93    
94 <  int i, j, status;
96 <  double smallestBoxL, maxCutoff;
94 >  int i, j;
95    double FortranHmat[9]; // to preserve compatibility with Fortran the
96                           // ordering in the array is as follows:
97                           // [ 0 3 6 ]
# Line 280 | Line 278 | void SimInfo::printMat9(double A[9] ){
278              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
279   }
280  
281 +
282 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
283 +
284 +      out[0] = a[1] * b[2] - a[2] * b[1];
285 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
286 +      out[2] = a[0] * b[1] - a[1] * b[0];
287 +      
288 + }
289 +
290 + double SimInfo::dotProduct3(double a[3], double b[3]){
291 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
292 + }
293 +
294 + double SimInfo::length3(double a[3]){
295 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
296 + }
297 +
298   void SimInfo::calcBoxL( void ){
299  
300    double dx, dy, dz, dsq;
286 –  int i;
301  
302    // boxVol = Determinant of Hmat
303  
# Line 294 | Line 308 | void SimInfo::calcBoxL( void ){
308    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
309    dsq = dx*dx + dy*dy + dz*dz;
310    boxL[0] = sqrt( dsq );
311 <  maxCutoff = 0.5 * boxL[0];
311 >  //maxCutoff = 0.5 * boxL[0];
312  
313    // boxLy
314    
315    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
316    dsq = dx*dx + dy*dy + dz*dz;
317    boxL[1] = sqrt( dsq );
318 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
318 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
319  
320 +
321    // boxLz
322    
323    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
324    dsq = dx*dx + dy*dy + dz*dz;
325    boxL[2] = sqrt( dsq );
326 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
326 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
327 >
328 >  //calculate the max cutoff
329 >  maxCutoff =  calcMaxCutOff();
330    
331    checkCutOffs();
332  
333   }
334  
335  
336 + double SimInfo::calcMaxCutOff(){
337 +
338 +  double ri[3], rj[3], rk[3];
339 +  double rij[3], rjk[3], rki[3];
340 +  double minDist;
341 +
342 +  ri[0] = Hmat[0][0];
343 +  ri[1] = Hmat[1][0];
344 +  ri[2] = Hmat[2][0];
345 +
346 +  rj[0] = Hmat[0][1];
347 +  rj[1] = Hmat[1][1];
348 +  rj[2] = Hmat[2][1];
349 +
350 +  rk[0] = Hmat[0][2];
351 +  rk[1] = Hmat[1][2];
352 +  rk[2] = Hmat[2][2];
353 +  
354 +  crossProduct3(ri,rj, rij);
355 +  distXY = dotProduct3(rk,rij) / length3(rij);
356 +
357 +  crossProduct3(rj,rk, rjk);
358 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
359 +
360 +  crossProduct3(rk,ri, rki);
361 +  distZX = dotProduct3(rj,rki) / length3(rki);
362 +
363 +  minDist = min(min(distXY, distYZ), distZX);
364 +  return minDist/2;
365 +  
366 + }
367 +
368   void SimInfo::wrapVector( double thePos[3] ){
369  
370 <  int i, j, k;
370 >  int i;
371    double scaled[3];
372  
373    if( !orthoRhombic ){
# Line 355 | Line 405 | int SimInfo::getNDF(){
405  
406  
407   int SimInfo::getNDF(){
408 <  int ndf_local, ndf;
408 >  int ndf_local;
409    
410    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
411  
# Line 371 | Line 421 | int SimInfo::getNDFraw() {
421   }
422  
423   int SimInfo::getNDFraw() {
424 <  int ndfRaw_local, ndfRaw;
424 >  int ndfRaw_local;
425  
426    // Raw degrees of freedom that we have to set
427    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 384 | Line 434 | int SimInfo::getNDFraw() {
434  
435    return ndfRaw;
436   }
437 <
437 >
438 > int SimInfo::getNDFtranslational() {
439 >  int ndfTrans_local;
440 >
441 >  ndfTrans_local = 3 * n_atoms - n_constraints;
442 >
443 > #ifdef IS_MPI
444 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
445 > #else
446 >  ndfTrans = ndfTrans_local;
447 > #endif
448 >
449 >  ndfTrans = ndfTrans - 3 - nZconstraints;
450 >
451 >  return ndfTrans;
452 > }
453 >
454   void SimInfo::refreshSim(){
455  
456    simtype fInfo;
# Line 440 | Line 506 | void SimInfo::refreshSim(){
506  
507    this->ndf = this->getNDF();
508    this->ndfRaw = this->getNDFraw();
509 <
509 >  this->ndfTrans = this->getNDFtranslational();
510   }
511  
512  
513   void SimInfo::setRcut( double theRcut ){
514  
449 –  if( !haveOrigRcut ){
450 –    haveOrigRcut = 1;
451 –    origRcut = theRcut;
452 –  }
453 –
515    rCut = theRcut;
516    checkCutOffs();
517   }
518  
519 < void SimInfo::setEcr( double theEcr ){
519 > void SimInfo::setDefaultRcut( double theRcut ){
520  
521 <  if( !haveOrigEcr ){
522 <    haveOrigEcr = 1;
523 <    origEcr = theEcr;
463 <  }
521 >  haveOrigRcut = 1;
522 >  origRcut = theRcut;
523 >  rCut = theRcut;
524  
525 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
526 +
527 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
528 + }
529 +
530 + void SimInfo::setEcr( double theEcr ){
531 +
532    ecr = theEcr;
533    checkCutOffs();
534   }
535  
536 + void SimInfo::setDefaultEcr( double theEcr ){
537 +
538 +  haveOrigEcr = 1;
539 +  origEcr = theEcr;
540 +  
541 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542 +
543 +  ecr = theEcr;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548   void SimInfo::setEcr( double theEcr, double theEst ){
549  
550    est = theEst;
551    setEcr( theEcr );
552   }
553  
554 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555  
556 < void SimInfo::checkCutOffs( void ){
556 >  est = theEst;
557 >  setDefaultEcr( theEcr );
558 > }
559  
478 –  int cutChanged = 0;
560  
561 + void SimInfo::checkCutOffs( void ){
562  
563 <
563 >  int cutChanged = 0;
564 >  
565    if( boxIsInit ){
566      
567      //we need to check cutOffs against the box
568 <  
568 >
569 >    //detect the change of rCut
570      if(( maxCutoff > rCut )&&(usePBC)){
571        if( rCut < origRcut ){
572 <        rCut = origRcut;
573 <        if (rCut > maxCutoff) rCut = maxCutoff;
574 <        
575 <        sprintf( painCave.errMsg,
576 <                 "New Box size is setting the long range cutoff radius "
577 <                 "to %lf\n",
578 <                 rCut );
579 <        painCave.isFatal = 0;
580 <        simError();
572 >        rCut = origRcut;
573 >        
574 >        if (rCut > maxCutoff)
575 >          rCut = maxCutoff;
576 >  
577 >          sprintf( painCave.errMsg,
578 >                    "New Box size is setting the long range cutoff radius "
579 >                    "to %lf at time %lf\n",
580 >                    rCut, currentTime );
581 >          painCave.isFatal = 0;
582 >          simError();
583        }
584      }
585 <
500 <    if( maxCutoff > ecr ){
501 <      if( ecr < origEcr ){
502 <        rCut = origEcr;
503 <        if (ecr > maxCutoff) ecr = maxCutoff;
504 <        
505 <        sprintf( painCave.errMsg,
506 <                 "New Box size is setting the electrostaticCutoffRadius "
507 <                 "to %lf\n",
508 <                 ecr );
509 <        painCave.isFatal = 0;
510 <        simError();
511 <      }
512 <    }
513 <
514 <
515 <    if ((rCut > maxCutoff)&&(usePBC)) {
585 >    else if ((rCut > maxCutoff)&&(usePBC)) {
586        sprintf( painCave.errMsg,
587                 "New Box size is setting the long range cutoff radius "
588 <               "to %lf\n",
589 <               maxCutoff );
588 >               "to %lf at time %lf\n",
589 >               maxCutoff, currentTime );
590        painCave.isFatal = 0;
591        simError();
592        rCut = maxCutoff;
593      }
594  
595 <    if( ecr > maxCutoff){
595 >
596 >    //detect the change of ecr
597 >    if( maxCutoff > ecr ){
598 >      if( ecr < origEcr ){
599 >        ecr = origEcr;
600 >        if (ecr > maxCutoff) ecr = maxCutoff;
601 >  
602 >          sprintf( painCave.errMsg,
603 >                    "New Box size is setting the electrostaticCutoffRadius "
604 >                    "to %lf at time %lf\n",
605 >                    ecr, currentTime );
606 >            painCave.isFatal = 0;
607 >            simError();
608 >      }
609 >    }
610 >    else if( ecr > maxCutoff){
611        sprintf( painCave.errMsg,
612                 "New Box size is setting the electrostaticCutoffRadius "
613 <               "to %lf\n",
614 <               maxCutoff  );
613 >               "to %lf at time %lf\n",
614 >               maxCutoff, currentTime  );
615        painCave.isFatal = 0;
616        simError();      
617        ecr = maxCutoff;
618      }
619  
620 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
621      
622 <  }
537 <  
538 <
539 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
540 <
541 <  // rlist is the 1.0 plus max( rcut, ecr )
542 <  
543 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 <
545 <  if( cutChanged ){
622 >    // rlist is the 1.0 plus max( rcut, ecr )
623      
624 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 <  }
549 <
550 <  oldEcr = ecr;
551 <  oldRcut = rCut;
552 < }
553 <
554 < void SimInfo::addProperty(GenericData* prop){
555 <
556 <  map<string, GenericData*>::iterator result;
557 <  result = properties.find(prop->getID());
558 <  
559 <  //we can't simply use  properties[prop->getID()] = prop,
560 <  //it will cause memory leak if we already contain a propery which has the same name of prop
561 <  
562 <  if(result != properties.end()){
624 >    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
625      
626 <    delete (*result).second;
627 <    (*result).second = prop;
628 <      
567 <  }
568 <  else{
569 <
570 <    properties[prop->getID()] = prop;
571 <
572 <  }
626 >    if( cutChanged ){
627 >      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
628 >    }
629      
630 < }
631 <
632 < GenericData* SimInfo::getProperty(const string& propName){
633 <
634 <  map<string, GenericData*>::iterator result;
630 >    oldEcr = ecr;
631 >    oldRcut = rCut;
632 >    
633 >  } else {
634 >    // initialize this stuff before using it, OK?
635 >    sprintf( painCave.errMsg,
636 >             "Trying to check cutoffs without a box. Be smarter.\n" );
637 >    painCave.isFatal = 1;
638 >    simError();      
639 >  }
640    
580 –  //string lowerCaseName = ();
581 –  
582 –  result = properties.find(propName);
583 –  
584 –  if(result != properties.end())
585 –    return (*result).second;  
586 –  else  
587 –    return NULL;  
641   }
642  
643 < vector<GenericData*> SimInfo::getProperties(){
643 > GenericData* SimInfo::getProperty(char* propName){
644  
645 <  vector<GenericData*> result;
593 <  map<string, GenericData*>::iterator i;
594 <  
595 <  for(i = properties.begin(); i != properties.end(); i++)
596 <    result.push_back((*i).second);
597 <    
598 <  return result;
645 >  return properties->find( propName );
646   }
647  
648 + double SimInfo::matTrace3(double m[3][3]){
649 +  double trace;
650 +  trace = m[0][0] + m[1][1] + m[2][2];
651  
652 +  return trace;
653 + }

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