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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC vs.
Revision 941 by gezelter, Tue Jan 13 23:01:43 2004 UTC

# Line 20 | Line 20 | inline double roundMe( double x ){
20    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21   }
22            
23 + inline double min( double a, double b ){
24 +  return (a < b ) ? a : b;
25 + }
26  
27   SimInfo* currentInfo;
28  
# Line 37 | Line 40 | SimInfo::SimInfo(){
40    thermalTime = 0.0;
41    currentTime = 0.0;
42    rCut = 0.0;
40 –  origRcut = -1.0;
43    ecr = 0.0;
42 –  origEcr = -1.0;
44    est = 0.0;
44 –  oldEcr = 0.0;
45 –  oldRcut = 0.0;
45  
46 <  haveOrigRcut = 0;
47 <  haveOrigEcr = 0;
46 >  haveRcut = 0;
47 >  haveEcr = 0;
48    boxIsInit = 0;
49    
50    resetTime = 1e99;
52 –  
51  
52 +  orthoTolerance = 1E-6;
53 +  useInitXSstate = true;
54 +
55    usePBC = 0;
56    useLJ = 0;
57    useSticky = 0;
58 <  useDipole = 0;
58 >  useCharges = 0;
59 >  useDipoles = 0;
60    useReactionField = 0;
61    useGB = 0;
62    useEAM = 0;
# Line 102 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){
104                           // [ 2 5 8 ]
105    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106  
105 –  
107    if( !boxIsInit ) boxIsInit = 1;
108  
109    for(i=0; i < 3; i++)
# Line 161 | Line 162 | void SimInfo::calcHmatInv( void ) {
162    smallDiag = fabs(Hmat[0][0]);
163    if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
164    if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
165 <  tol = smallDiag * 1E-6;
165 >  tol = smallDiag * orthoTolerance;
166  
167    orthoRhombic = 1;
168    
# Line 180 | Line 181 | void SimInfo::calcHmatInv( void ) {
181      if( orthoRhombic ){
182        sprintf( painCave.errMsg,
183                 "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
184 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
184 >               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
185 >               orthoTolerance);
186        simError();
187      }
188      else {
189        sprintf( painCave.errMsg,
190                 "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
191 >               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
192 >               orthoTolerance);
193        simError();
194      }
195    }
# Line 478 | Line 481 | void SimInfo::refreshSim(){
481  
482    fInfo.dielect = 0.0;
483  
484 <  if( useDipole ){
484 >  if( useDipoles ){
485      if( useReactionField )fInfo.dielect = dielectric;
486    }
487  
# Line 487 | Line 490 | void SimInfo::refreshSim(){
490    fInfo.SIM_uses_LJ = useLJ;
491    fInfo.SIM_uses_sticky = useSticky;
492    //fInfo.SIM_uses_sticky = 0;
493 <  fInfo.SIM_uses_dipoles = useDipole;
493 >  fInfo.SIM_uses_charges = useCharges;
494 >  fInfo.SIM_uses_dipoles = useDipoles;
495    //fInfo.SIM_uses_dipoles = 0;
496    //fInfo.SIM_uses_RF = useReactionField;
497    fInfo.SIM_uses_RF = 0;
# Line 527 | Line 531 | void SimInfo::refreshSim(){
531    this->ndfTrans = this->getNDFtranslational();
532   }
533  
530 –
531 – void SimInfo::setRcut( double theRcut ){
532 –
533 –  rCut = theRcut;
534 –  checkCutOffs();
535 – }
536 –
534   void SimInfo::setDefaultRcut( double theRcut ){
535  
536 <  haveOrigRcut = 1;
540 <  origRcut = theRcut;
536 >  haveRcut = 1;
537    rCut = theRcut;
538  
539    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
# Line 545 | Line 541 | void SimInfo::setEcr( double theEcr ){
541    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
542   }
543  
548 – void SimInfo::setEcr( double theEcr ){
549 –
550 –  ecr = theEcr;
551 –  checkCutOffs();
552 – }
553 –
544   void SimInfo::setDefaultEcr( double theEcr ){
545  
546 <  haveOrigEcr = 1;
547 <  origEcr = theEcr;
546 >  haveEcr = 1;
547 >  ecr = theEcr;
548    
549    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
550  
561 –  ecr = theEcr;
562 –
551    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
552   }
553  
566 – void SimInfo::setEcr( double theEcr, double theEst ){
567 –
568 –  est = theEst;
569 –  setEcr( theEcr );
570 – }
571 –
554   void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555  
556    est = theEst;
# Line 577 | Line 559 | void SimInfo::checkCutOffs( void ){
559  
560  
561   void SimInfo::checkCutOffs( void ){
580 –
581 –  int cutChanged = 0;
562    
563    if( boxIsInit ){
564      
565      //we need to check cutOffs against the box
566 <
567 <    //detect the change of rCut
588 <    if(( maxCutoff > rCut )&&(usePBC)){
589 <      if( rCut < origRcut ){
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 <    else if ((rCut > maxCutoff)&&(usePBC)) {
566 >    
567 >    if( rCut > maxCutoff ){
568        sprintf( painCave.errMsg,
569 <               "New Box size is setting the long range cutoff radius "
570 <               "to %lf at time %lf\n",
571 <               maxCutoff, currentTime );
572 <      painCave.isFatal = 0;
569 >               "Box size is too small for the long range cutoff radius, "
570 >               "%G, at time %G\n"
571 >               "  [ %G %G %G ]\n"
572 >               "  [ %G %G %G ]\n"
573 >               "  [ %G %G %G ]\n",
574 >               rCut, currentTime,
575 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
576 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
577 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
578 >      painCave.isFatal = 1;
579        simError();
610 –      rCut = maxCutoff;
580      }
581 <
582 <
583 <    //detect the change of ecr
584 <    if( maxCutoff > ecr ){
585 <      if( ecr < origEcr ){
586 <        ecr = origEcr;
587 <        if (ecr > maxCutoff) ecr = maxCutoff;
588 <  
589 <          sprintf( painCave.errMsg,
590 <                    "New Box size is setting the electrostaticCutoffRadius "
591 <                    "to %lf at time %lf\n",
592 <                    ecr, currentTime );
593 <            painCave.isFatal = 0;
594 <            simError();
581 >    
582 >    if( haveEcr ){
583 >      if( ecr > maxCutoff ){
584 >        sprintf( painCave.errMsg,
585 >                 "Box size is too small for the electrostatic cutoff radius, "
586 >                 "%G, at time %G\n"
587 >                 "  [ %G %G %G ]\n"
588 >                 "  [ %G %G %G ]\n"
589 >                 "  [ %G %G %G ]\n",
590 >                 ecr, currentTime,
591 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
592 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
593 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
594 >        painCave.isFatal = 1;
595 >        simError();
596        }
597      }
628 –    else if( ecr > maxCutoff){
629 –      sprintf( painCave.errMsg,
630 –               "New Box size is setting the electrostaticCutoffRadius "
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 –    
598    } else {
599      // initialize this stuff before using it, OK?
600      sprintf( painCave.errMsg,

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