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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC

# Line 37 | Line 37 | SimInfo::SimInfo(){
37    thermalTime = 0.0;
38    currentTime = 0.0;
39    rCut = 0.0;
40 –  origRcut = -1.0;
40    ecr = 0.0;
42 –  origEcr = -1.0;
41    est = 0.0;
44 –  oldEcr = 0.0;
45 –  oldRcut = 0.0;
42  
43 <  haveOrigRcut = 0;
44 <  haveOrigEcr = 0;
43 >  haveRcut = 0;
44 >  haveEcr = 0;
45    boxIsInit = 0;
46    
47    resetTime = 1e99;
52 –  
48  
49 +  orthoTolerance = 1E-6;
50 +  useInitXSstate = true;
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 102 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){
100                           // [ 2 5 8 ]
101    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
105 –  
103    if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
# Line 146 | Line 143 | void SimInfo::calcHmatInv( void ) {
143  
144   void SimInfo::calcHmatInv( void ) {
145    
146 +  int oldOrtho;
147    int i,j;
148    double smallDiag;
149    double tol;
# Line 153 | Line 151 | void SimInfo::calcHmatInv( void ) {
151  
152    invertMat3( Hmat, HmatInv );
153  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
154    // check to see if Hmat is orthorhombic
155    
156 <  smallDiag = Hmat[0][0];
163 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 <  tol = smallDiag * 1E-6;
156 >  oldOrtho = orthoRhombic;
157  
158 +  smallDiag = fabs(Hmat[0][0]);
159 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
160 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
161 +  tol = smallDiag * orthoTolerance;
162 +
163    orthoRhombic = 1;
164    
165    for (i = 0; i < 3; i++ ) {
166      for (j = 0 ; j < 3; j++) {
167        if (i != j) {
168          if (orthoRhombic) {
169 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
169 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
170          }        
171        }
172 +    }
173 +  }
174 +
175 +  if( oldOrtho != orthoRhombic ){
176 +    
177 +    if( orthoRhombic ){
178 +      sprintf( painCave.errMsg,
179 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
180 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
181 +               orthoTolerance);
182 +      simError();
183      }
184 +    else {
185 +      sprintf( painCave.errMsg,
186 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
187 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
188 +               orthoTolerance);
189 +      simError();
190 +    }
191    }
192   }
193  
# Line 512 | Line 526 | void SimInfo::refreshSim(){
526    this->ndfTrans = this->getNDFtranslational();
527   }
528  
515 –
516 – void SimInfo::setRcut( double theRcut ){
517 –
518 –  rCut = theRcut;
519 –  checkCutOffs();
520 – }
521 –
529   void SimInfo::setDefaultRcut( double theRcut ){
530  
531 <  haveOrigRcut = 1;
525 <  origRcut = theRcut;
531 >  haveRcut = 1;
532    rCut = theRcut;
533  
534    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535  
536    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
531 – }
532 –
533 – void SimInfo::setEcr( double theEcr ){
534 –
535 –  ecr = theEcr;
536 –  checkCutOffs();
537   }
538  
539   void SimInfo::setDefaultEcr( double theEcr ){
540  
541 <  haveOrigEcr = 1;
542 <  origEcr = theEcr;
541 >  haveEcr = 1;
542    
543    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544  
# Line 548 | Line 547 | void SimInfo::setEcr( double theEcr, double theEst ){
547    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548   }
549  
551 – void SimInfo::setEcr( double theEcr, double theEst ){
552 –
553 –  est = theEst;
554 –  setEcr( theEcr );
555 – }
556 –
550   void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551  
552    est = theEst;
# Line 562 | Line 555 | void SimInfo::checkCutOffs( void ){
555  
556  
557   void SimInfo::checkCutOffs( void ){
565 –
566 –  int cutChanged = 0;
558    
559    if( boxIsInit ){
560      
561      //we need to check cutOffs against the box
562 <
563 <    //detect the change of rCut
573 <    if(( maxCutoff > rCut )&&(usePBC)){
574 <      if( rCut < origRcut ){
575 <        rCut = origRcut;
576 <        
577 <        if (rCut > maxCutoff)
578 <          rCut = maxCutoff;
579 <  
580 <          sprintf( painCave.errMsg,
581 <                    "New Box size is setting the long range cutoff radius "
582 <                    "to %lf at time %lf\n",
583 <                    rCut, currentTime );
584 <          painCave.isFatal = 0;
585 <          simError();
586 <      }
587 <    }
588 <    else if ((rCut > maxCutoff)&&(usePBC)) {
562 >    
563 >    if( rCut > maxCutoff ){
564        sprintf( painCave.errMsg,
565 <               "New Box size is setting the long range cutoff radius "
566 <               "to %lf at time %lf\n",
567 <               maxCutoff, currentTime );
568 <      painCave.isFatal = 0;
565 >               "Box size is too small for the long range cutoff radius, "
566 >               "%lf, at time %lf\n",
567 >               rCut, currentTime );
568 >      painCave.isFatal = 1;
569        simError();
595 –      rCut = maxCutoff;
570      }
571 <
572 <
573 <    //detect the change of ecr
574 <    if( maxCutoff > ecr ){
575 <      if( ecr < origEcr ){
576 <        ecr = origEcr;
577 <        if (ecr > maxCutoff) ecr = maxCutoff;
578 <  
579 <          sprintf( painCave.errMsg,
606 <                    "New Box size is setting the electrostaticCutoffRadius "
607 <                    "to %lf at time %lf\n",
608 <                    ecr, currentTime );
609 <            painCave.isFatal = 0;
610 <            simError();
571 >    
572 >    if( haveEcr ){
573 >      if( ecr > maxCutoff ){
574 >        sprintf( painCave.errMsg,
575 >                 "Box size is too small for the electrostatic cutoff radius, "
576 >                 "%lf, at time %lf\n",
577 >                 ecr, currentTime );
578 >        painCave.isFatal = 1;
579 >        simError();
580        }
581      }
613 –    else if( ecr > maxCutoff){
614 –      sprintf( painCave.errMsg,
615 –               "New Box size is setting the electrostaticCutoffRadius "
616 –               "to %lf at time %lf\n",
617 –               maxCutoff, currentTime  );
618 –      painCave.isFatal = 0;
619 –      simError();      
620 –      ecr = maxCutoff;
621 –    }
622 –
623 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
624 –    
625 –    // rlist is the 1.0 plus max( rcut, ecr )
626 –    
627 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
628 –    
629 –    if( cutChanged ){
630 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
631 –    }
632 –    
633 –    oldEcr = ecr;
634 –    oldRcut = rCut;
635 –    
582    } else {
583      // initialize this stuff before using it, OK?
584      sprintf( painCave.errMsg,

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