ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 841 by mmeineke, Wed Oct 29 17:55:28 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;
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 43 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 +  resetTime = 1e99;
52    
53  
54    usePBC = 0;
# Line 53 | 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]) {
# Line 74 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94  
95   void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, j, status;
78 <  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 262 | Line 281 | void SimInfo::calcBoxL( void ){
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;
268 –  int i;
304  
305    // boxVol = Determinant of Hmat
306  
# Line 276 | 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 335 | Line 408 | int SimInfo::getNDF(){
408  
409  
410   int SimInfo::getNDF(){
411 <  int ndf_local, ndf;
411 >  int ndf_local;
412    
413    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
414  
# Line 345 | 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   }
425  
426   int SimInfo::getNDFraw() {
427 <  int ndfRaw_local, ndfRaw;
427 >  int ndfRaw_local;
428  
429    // Raw degrees of freedom that we have to set
430    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 364 | Line 437 | int SimInfo::getNDFraw() {
437  
438    return ndfRaw;
439   }
440 <
440 >
441 > int SimInfo::getNDFtranslational() {
442 >  int ndfTrans_local;
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 420 | 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  
516   void SimInfo::setRcut( double theRcut ){
517  
429 –  if( !haveOrigRcut ){
430 –    haveOrigRcut = 1;
431 –    origRcut = theRcut;
432 –  }
433 –
518    rCut = theRcut;
519    checkCutOffs();
520   }
521  
522 < void SimInfo::setEcr( double theEcr ){
522 > void SimInfo::setDefaultRcut( double theRcut ){
523  
524 <  if( !haveOrigEcr ){
525 <    haveOrigEcr = 1;
526 <    origEcr = theEcr;
527 <  }
524 >  haveOrigRcut = 1;
525 >  origRcut = theRcut;
526 >  rCut = theRcut;
527 > }
528  
529 + void SimInfo::setEcr( double theEcr ){
530 +
531    ecr = theEcr;
532    checkCutOffs();
533   }
534  
535 + void SimInfo::setDefaultEcr( double theEcr ){
536 +
537 +  haveOrigEcr = 1;
538 +  origEcr = theEcr;
539 +  
540 +  ecr = theEcr;
541 + }
542 +
543   void SimInfo::setEcr( double theEcr, double theEst ){
544  
545    est = theEst;
546    setEcr( theEcr );
547   }
548  
549 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
550  
551 +  est = theEst;
552 +  setDefaultEcr( theEcr );
553 + }
554 +
555 +
556   void SimInfo::checkCutOffs( void ){
557  
558    int cutChanged = 0;
559 <
559 >  
560    if( boxIsInit ){
561      
562      //we need to check cutOffs against the box
563 <    
564 <    if( maxCutoff > rCut ){
563 >
564 >    //detect the change of rCut
565 >    if(( maxCutoff > rCut )&&(usePBC)){
566        if( rCut < origRcut ){
567 <        rCut = origRcut;
568 <        if (rCut > maxCutoff) rCut = maxCutoff;
569 <        
570 <        sprintf( painCave.errMsg,
571 <                 "New Box size is setting the long range cutoff radius "
572 <                 "to %lf\n",
573 <                 rCut );
574 <        painCave.isFatal = 0;
575 <        simError();
567 >        rCut = origRcut;
568 >        
569 >        if (rCut > maxCutoff)
570 >          rCut = maxCutoff;
571 >  
572 >          sprintf( painCave.errMsg,
573 >                    "New Box size is setting the long range cutoff radius "
574 >                    "to %lf at time %lf\n",
575 >                    rCut, currentTime );
576 >          painCave.isFatal = 0;
577 >          simError();
578        }
579      }
580 <
478 <    if( maxCutoff > ecr ){
479 <      if( ecr < origEcr ){
480 <        rCut = origEcr;
481 <        if (ecr > maxCutoff) ecr = maxCutoff;
482 <        
483 <        sprintf( painCave.errMsg,
484 <                 "New Box size is setting the electrostaticCutoffRadius "
485 <                 "to %lf\n",
486 <                 ecr );
487 <        painCave.isFatal = 0;
488 <        simError();
489 <      }
490 <    }
491 <
492 <
493 <    if (rCut > maxCutoff) {
580 >    else if ((rCut > maxCutoff)&&(usePBC)) {
581        sprintf( painCave.errMsg,
582                 "New Box size is setting the long range cutoff radius "
583 <               "to %lf\n",
584 <               maxCutoff );
583 >               "to %lf at time %lf\n",
584 >               maxCutoff, currentTime );
585        painCave.isFatal = 0;
586        simError();
587        rCut = maxCutoff;
588      }
589  
590 <    if( ecr > maxCutoff){
590 >
591 >    //detect the change of ecr
592 >    if( maxCutoff > ecr ){
593 >      if( ecr < origEcr ){
594 >        ecr = origEcr;
595 >        if (ecr > maxCutoff) ecr = maxCutoff;
596 >  
597 >          sprintf( painCave.errMsg,
598 >                    "New Box size is setting the electrostaticCutoffRadius "
599 >                    "to %lf at time %lf\n",
600 >                    ecr, currentTime );
601 >            painCave.isFatal = 0;
602 >            simError();
603 >      }
604 >    }
605 >    else if( ecr > maxCutoff){
606        sprintf( painCave.errMsg,
607                 "New Box size is setting the electrostaticCutoffRadius "
608 <               "to %lf\n",
609 <               maxCutoff  );
608 >               "to %lf at time %lf\n",
609 >               maxCutoff, currentTime  );
610        painCave.isFatal = 0;
611        simError();      
612        ecr = maxCutoff;
613      }
614  
615 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
616      
617 +    // rlist is the 1.0 plus max( rcut, ecr )
618 +    
619 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
620 +    
621 +    if( cutChanged ){
622 +      
623 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
624 +    }
625 +    
626 +    oldEcr = ecr;
627 +    oldRcut = rCut;
628 +    
629 +  } else {
630 +    // initialize this stuff before using it, OK?
631 +    sprintf( painCave.errMsg,
632 +             "Trying to check cutoffs without a box. Be smarter.\n" );
633 +    painCave.isFatal = 1;
634 +    simError();      
635    }
636 <  
636 >  
637 > }
638  
639 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 > void SimInfo::addProperty(GenericData* prop){
640  
641 <  // rlist is the 1.0 plus max( rcut, ecr )
641 >  map<string, GenericData*>::iterator result;
642 >  result = properties.find(prop->getID());
643    
644 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
645 <
646 <  if( cutChanged ){
644 >  //we can't simply use  properties[prop->getID()] = prop,
645 >  //it will cause memory leak if we already contain a propery which has the same name of prop
646 >  
647 >  if(result != properties.end()){
648      
649 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
649 >    delete (*result).second;
650 >    (*result).second = prop;
651 >      
652    }
653 +  else{
654  
655 <  oldEcr = ecr;
656 <  oldRcut = rCut;
655 >    properties[prop->getID()] = prop;
656 >
657 >  }
658 >    
659   }
660 +
661 + GenericData* SimInfo::getProperty(const string& propName){
662 +
663 +  map<string, GenericData*>::iterator result;
664 +  
665 +  //string lowerCaseName = ();
666 +  
667 +  result = properties.find(propName);
668 +  
669 +  if(result != properties.end())
670 +    return (*result).second;  
671 +  else  
672 +    return NULL;  
673 + }
674 +
675 + vector<GenericData*> SimInfo::getProperties(){
676 +
677 +  vector<GenericData*> result;
678 +  map<string, GenericData*>::iterator i;
679 +  
680 +  for(i = properties.begin(); i != properties.end(); i++)
681 +    result.push_back((*i).second);
682 +    
683 +  return result;
684 + }
685 +
686 + double SimInfo::matTrace3(double m[3][3]){
687 +  double trace;
688 +  trace = m[0][0] + m[1][1] + m[2][2];
689 +
690 +  return trace;
691 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines