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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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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 853 by mmeineke, Thu Nov 6 19:11:38 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 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 128 | Line 146 | void SimInfo::calcHmatInv( void ) {
146  
147   void SimInfo::calcHmatInv( void ) {
148    
149 +  int oldOrtho;
150    int i,j;
151    double smallDiag;
152    double tol;
# Line 135 | Line 154 | void SimInfo::calcHmatInv( void ) {
154  
155    invertMat3( Hmat, HmatInv );
156  
138 –  // Check the inverse to make sure it is sane:
139 –
140 –  matMul3( Hmat, HmatInv, sanity );
141 –    
157    // check to see if Hmat is orthorhombic
158    
159 <  smallDiag = Hmat[0][0];
160 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
161 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
159 >  oldOrtho = orthoRhombic;
160 >
161 >  smallDiag = fabs(Hmat[0][0]);
162 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
163 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
164    tol = smallDiag * 1E-6;
165  
166    orthoRhombic = 1;
# Line 152 | Line 169 | void SimInfo::calcHmatInv( void ) {
169      for (j = 0 ; j < 3; j++) {
170        if (i != j) {
171          if (orthoRhombic) {
172 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
172 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
173          }        
174        }
175      }
176    }
177 +
178 +  if( oldOrtho != orthoRhombic ){
179 +    
180 +    if( orthoRhombic ){
181 +      sprintf( painCave.errMsg,
182 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
184 +      simError();
185 +    }
186 +    else {
187 +      sprintf( painCave.errMsg,
188 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
189 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
190 +      simError();
191 +    }
192 +  }
193   }
194  
195   double SimInfo::matDet3(double a[3][3]) {
# Line 263 | Line 296 | void SimInfo::printMat9(double A[9] ){
296              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297   }
298  
299 +
300 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301 +
302 +      out[0] = a[1] * b[2] - a[2] * b[1];
303 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
304 +      out[2] = a[0] * b[1] - a[1] * b[0];
305 +      
306 + }
307 +
308 + double SimInfo::dotProduct3(double a[3], double b[3]){
309 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
310 + }
311 +
312 + double SimInfo::length3(double a[3]){
313 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
314 + }
315 +
316   void SimInfo::calcBoxL( void ){
317  
318    double dx, dy, dz, dsq;
269 –  int i;
319  
320    // boxVol = Determinant of Hmat
321  
# Line 277 | Line 326 | void SimInfo::calcBoxL( void ){
326    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
327    dsq = dx*dx + dy*dy + dz*dz;
328    boxL[0] = sqrt( dsq );
329 <  maxCutoff = 0.5 * boxL[0];
329 >  //maxCutoff = 0.5 * boxL[0];
330  
331    // boxLy
332    
333    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
334    dsq = dx*dx + dy*dy + dz*dz;
335    boxL[1] = sqrt( dsq );
336 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
336 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
337  
338 +
339    // boxLz
340    
341    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
342    dsq = dx*dx + dy*dy + dz*dz;
343    boxL[2] = sqrt( dsq );
344 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
344 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
345  
346 +  //calculate the max cutoff
347 +  maxCutoff =  calcMaxCutOff();
348 +  
349 +  checkCutOffs();
350 +
351   }
352 +
353 +
354 + double SimInfo::calcMaxCutOff(){
355  
356 +  double ri[3], rj[3], rk[3];
357 +  double rij[3], rjk[3], rki[3];
358 +  double minDist;
359  
360 +  ri[0] = Hmat[0][0];
361 +  ri[1] = Hmat[1][0];
362 +  ri[2] = Hmat[2][0];
363 +
364 +  rj[0] = Hmat[0][1];
365 +  rj[1] = Hmat[1][1];
366 +  rj[2] = Hmat[2][1];
367 +
368 +  rk[0] = Hmat[0][2];
369 +  rk[1] = Hmat[1][2];
370 +  rk[2] = Hmat[2][2];
371 +  
372 +  crossProduct3(ri,rj, rij);
373 +  distXY = dotProduct3(rk,rij) / length3(rij);
374 +
375 +  crossProduct3(rj,rk, rjk);
376 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
377 +
378 +  crossProduct3(rk,ri, rki);
379 +  distZX = dotProduct3(rj,rki) / length3(rki);
380 +
381 +  minDist = min(min(distXY, distYZ), distZX);
382 +  return minDist/2;
383 +  
384 + }
385 +
386   void SimInfo::wrapVector( double thePos[3] ){
387  
388 <  int i, j, k;
388 >  int i;
389    double scaled[3];
390  
391    if( !orthoRhombic ){
# Line 336 | Line 423 | int SimInfo::getNDF(){
423  
424  
425   int SimInfo::getNDF(){
426 <  int ndf_local, ndf;
426 >  int ndf_local;
427    
428    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429  
# Line 346 | Line 433 | int SimInfo::getNDF(){
433    ndf = ndf_local;
434   #endif
435  
436 <  ndf = ndf - 3;
436 >  ndf = ndf - 3 - nZconstraints;
437  
438    return ndf;
439   }
440  
441   int SimInfo::getNDFraw() {
442 <  int ndfRaw_local, ndfRaw;
442 >  int ndfRaw_local;
443  
444    // Raw degrees of freedom that we have to set
445    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 452 | int SimInfo::getNDFraw() {
452  
453    return ndfRaw;
454   }
455 <
455 >
456 > int SimInfo::getNDFtranslational() {
457 >  int ndfTrans_local;
458 >
459 >  ndfTrans_local = 3 * n_atoms - n_constraints;
460 >
461 > #ifdef IS_MPI
462 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
463 > #else
464 >  ndfTrans = ndfTrans_local;
465 > #endif
466 >
467 >  ndfTrans = ndfTrans - 3 - nZconstraints;
468 >
469 >  return ndfTrans;
470 > }
471 >
472   void SimInfo::refreshSim(){
473  
474    simtype fInfo;
# Line 421 | Line 524 | void SimInfo::refreshSim(){
524  
525    this->ndf = this->getNDF();
526    this->ndfRaw = this->getNDFraw();
527 <
527 >  this->ndfTrans = this->getNDFtranslational();
528   }
529  
530  
531   void SimInfo::setRcut( double theRcut ){
532  
430 –  if( !haveOrigRcut ){
431 –    haveOrigRcut = 1;
432 –    origRcut = theRcut;
433 –  }
434 –
533    rCut = theRcut;
534    checkCutOffs();
535   }
536  
537 < void SimInfo::setEcr( double theEcr ){
537 > void SimInfo::setDefaultRcut( double theRcut ){
538  
539 <  if( !haveOrigEcr ){
540 <    haveOrigEcr = 1;
541 <    origEcr = theEcr;
444 <  }
539 >  haveOrigRcut = 1;
540 >  origRcut = theRcut;
541 >  rCut = theRcut;
542  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr ){
549 +
550    ecr = theEcr;
551    checkCutOffs();
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr ){
555 +
556 +  haveOrigEcr = 1;
557 +  origEcr = theEcr;
558 +  
559 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 +
561 +  ecr = theEcr;
562 +
563 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
564   }
565  
566   void SimInfo::setEcr( double theEcr, double theEst ){
# Line 453 | Line 569 | void SimInfo::setEcr( double theEcr, double theEst ){
569    setEcr( theEcr );
570   }
571  
572 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573  
574 +  est = theEst;
575 +  setDefaultEcr( theEcr );
576 + }
577 +
578 +
579   void SimInfo::checkCutOffs( void ){
580  
581    int cutChanged = 0;
582 <
582 >  
583    if( boxIsInit ){
584      
585      //we need to check cutOffs against the box
586 <    
587 <    if( maxCutoff > rCut ){
586 >
587 >    //detect the change of rCut
588 >    if(( maxCutoff > rCut )&&(usePBC)){
589        if( rCut < origRcut ){
590 <        rCut = origRcut;
591 <        if (rCut > maxCutoff) rCut = maxCutoff;
592 <        
593 <        sprintf( painCave.errMsg,
594 <                 "New Box size is setting the long range cutoff radius "
595 <                 "to %lf\n",
596 <                 rCut );
597 <        painCave.isFatal = 0;
598 <        simError();
590 >        rCut = origRcut;
591 >        
592 >        if (rCut > maxCutoff)
593 >          rCut = maxCutoff;
594 >  
595 >          sprintf( painCave.errMsg,
596 >                    "New Box size is setting the long range cutoff radius "
597 >                    "to %lf at time %lf\n",
598 >                    rCut, currentTime );
599 >          painCave.isFatal = 0;
600 >          simError();
601        }
602      }
603 <
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) {
603 >    else if ((rCut > maxCutoff)&&(usePBC)) {
604        sprintf( painCave.errMsg,
605                 "New Box size is setting the long range cutoff radius "
606 <               "to %lf\n",
607 <               maxCutoff );
606 >               "to %lf at time %lf\n",
607 >               maxCutoff, currentTime );
608        painCave.isFatal = 0;
609        simError();
610        rCut = maxCutoff;
611      }
612  
613 <    if( ecr > maxCutoff){
613 >
614 >    //detect the change of ecr
615 >    if( maxCutoff > ecr ){
616 >      if( ecr < origEcr ){
617 >        ecr = origEcr;
618 >        if (ecr > maxCutoff) ecr = maxCutoff;
619 >  
620 >          sprintf( painCave.errMsg,
621 >                    "New Box size is setting the electrostaticCutoffRadius "
622 >                    "to %lf at time %lf\n",
623 >                    ecr, currentTime );
624 >            painCave.isFatal = 0;
625 >            simError();
626 >      }
627 >    }
628 >    else if( ecr > maxCutoff){
629        sprintf( painCave.errMsg,
630                 "New Box size is setting the electrostaticCutoffRadius "
631 <               "to %lf\n",
632 <               maxCutoff  );
631 >               "to %lf at time %lf\n",
632 >               maxCutoff, currentTime  );
633        painCave.isFatal = 0;
634        simError();      
635        ecr = maxCutoff;
636      }
637  
638 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639      
640 +    // rlist is the 1.0 plus max( rcut, ecr )
641 +    
642 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643 +    
644 +    if( cutChanged ){
645 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 +    }
647 +    
648 +    oldEcr = ecr;
649 +    oldRcut = rCut;
650 +    
651 +  } else {
652 +    // initialize this stuff before using it, OK?
653 +    sprintf( painCave.errMsg,
654 +             "Trying to check cutoffs without a box. Be smarter.\n" );
655 +    painCave.isFatal = 1;
656 +    simError();      
657    }
658 <  
658 >  
659 > }
660  
661 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
661 > void SimInfo::addProperty(GenericData* prop){
662  
663 <  // rlist is the 1.0 plus max( rcut, ecr )
663 >  map<string, GenericData*>::iterator result;
664 >  result = properties.find(prop->getID());
665    
666 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
667 <
668 <  if( cutChanged ){
666 >  //we can't simply use  properties[prop->getID()] = prop,
667 >  //it will cause memory leak if we already contain a propery which has the same name of prop
668 >  
669 >  if(result != properties.end()){
670      
671 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
671 >    delete (*result).second;
672 >    (*result).second = prop;
673 >      
674    }
675 +  else{
676  
677 <  oldEcr = ecr;
678 <  oldRcut = rCut;
677 >    properties[prop->getID()] = prop;
678 >
679 >  }
680 >    
681   }
682 +
683 + GenericData* SimInfo::getProperty(const string& propName){
684 +
685 +  map<string, GenericData*>::iterator result;
686 +  
687 +  //string lowerCaseName = ();
688 +  
689 +  result = properties.find(propName);
690 +  
691 +  if(result != properties.end())
692 +    return (*result).second;  
693 +  else  
694 +    return NULL;  
695 + }
696 +
697 + vector<GenericData*> SimInfo::getProperties(){
698 +
699 +  vector<GenericData*> result;
700 +  map<string, GenericData*>::iterator i;
701 +  
702 +  for(i = properties.begin(); i != properties.end(); i++)
703 +    result.push_back((*i).second);
704 +    
705 +  return result;
706 + }
707 +
708 + double SimInfo::matTrace3(double m[3][3]){
709 +  double trace;
710 +  trace = m[0][0] + m[1][1] + m[2][2];
711 +
712 +  return trace;
713 + }

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