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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 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 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 146 | Line 147 | void SimInfo::calcHmatInv( void ) {
147  
148   void SimInfo::calcHmatInv( void ) {
149    
150 +  int oldOrtho;
151    int i,j;
152    double smallDiag;
153    double tol;
# Line 153 | Line 155 | void SimInfo::calcHmatInv( void ) {
155  
156    invertMat3( Hmat, HmatInv );
157  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
158    // check to see if Hmat is orthorhombic
159    
160 <  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;
160 >  oldOrtho = orthoRhombic;
161  
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 * orthoTolerance;
166 +
167    orthoRhombic = 1;
168    
169    for (i = 0; i < 3; i++ ) {
170      for (j = 0 ; j < 3; j++) {
171        if (i != j) {
172          if (orthoRhombic) {
173 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
173 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
174          }        
175        }
176 +    }
177 +  }
178 +
179 +  if( oldOrtho != orthoRhombic ){
180 +    
181 +    if( orthoRhombic ){
182 +      sprintf( painCave.errMsg,
183 +               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
184 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
185 +               "\tvariable ( currently set to %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188 +    }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
192 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
193 +               "\tvariable ( currently set to %G ).\n",
194 +               orthoTolerance);
195 +      simError();
196      }
197    }
198   }
# Line 408 | Line 428 | int SimInfo::getNDF(){
428  
429  
430   int SimInfo::getNDF(){
431 <  int ndf_local, ndf;
431 >  int ndf_local;
432    
433    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
434  
# Line 424 | Line 444 | int SimInfo::getNDFraw() {
444   }
445  
446   int SimInfo::getNDFraw() {
447 <  int ndfRaw_local, ndfRaw;
447 >  int ndfRaw_local;
448  
449    // Raw degrees of freedom that we have to set
450    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 439 | Line 459 | int SimInfo::getNDFtranslational() {
459   }
460  
461   int SimInfo::getNDFtranslational() {
462 <  int ndfTrans_local, ndfTrans;
462 >  int ndfTrans_local;
463  
464    ndfTrans_local = 3 * n_atoms - n_constraints;
465  
# Line 463 | Line 483 | void SimInfo::refreshSim(){
483  
484    fInfo.dielect = 0.0;
485  
486 <  if( useDipole ){
486 >  if( useDipoles ){
487      if( useReactionField )fInfo.dielect = dielectric;
488    }
489  
# Line 472 | Line 492 | void SimInfo::refreshSim(){
492    fInfo.SIM_uses_LJ = useLJ;
493    fInfo.SIM_uses_sticky = useSticky;
494    //fInfo.SIM_uses_sticky = 0;
495 <  fInfo.SIM_uses_dipoles = useDipole;
495 >  fInfo.SIM_uses_charges = useCharges;
496 >  fInfo.SIM_uses_dipoles = useDipoles;
497    //fInfo.SIM_uses_dipoles = 0;
498 <  //fInfo.SIM_uses_RF = useReactionField;
499 <  fInfo.SIM_uses_RF = 0;
498 >  fInfo.SIM_uses_RF = useReactionField;
499 >  //fInfo.SIM_uses_RF = 0;
500    fInfo.SIM_uses_GB = useGB;
501    fInfo.SIM_uses_EAM = useEAM;
502  
# Line 512 | Line 533 | void SimInfo::refreshSim(){
533    this->ndfTrans = this->getNDFtranslational();
534   }
535  
536 <
516 < void SimInfo::setRcut( double theRcut ){
517 <
518 <  if( !haveOrigRcut ){
519 <    haveOrigRcut = 1;
520 <    origRcut = theRcut;
521 <  }
536 > void SimInfo::setDefaultRcut( double theRcut ){
537  
538 +  haveRcut = 1;
539    rCut = theRcut;
524 –  checkCutOffs();
525 – }
540  
541 < void SimInfo::setEcr( double theEcr ){
541 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542  
543 <  if( !haveOrigEcr ){
544 <    haveOrigEcr = 1;
531 <    origEcr = theEcr;
532 <  }
543 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
544 > }
545  
546 + void SimInfo::setDefaultEcr( double theEcr ){
547 +
548 +  haveEcr = 1;
549    ecr = theEcr;
550 <  checkCutOffs();
550 >  
551 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
552 >
553 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
554   }
555  
556 < void SimInfo::setEcr( double theEcr, double theEst ){
556 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
557  
558    est = theEst;
559 <  setEcr( theEcr );
559 >  setDefaultEcr( theEcr );
560   }
561  
562  
563   void SimInfo::checkCutOffs( void ){
546 –
547 –  int cutChanged = 0;
564    
565    if( boxIsInit ){
566      
567      //we need to check cutOffs against the box
568 <
569 <    //detect the change of rCut
554 <    if(( maxCutoff > rCut )&&(usePBC)){
555 <      if( rCut < origRcut ){
556 <        rCut = origRcut;
557 <        
558 <        if (rCut > maxCutoff)
559 <          rCut = maxCutoff;
560 <  
561 <          sprintf( painCave.errMsg,
562 <                    "New Box size is setting the long range cutoff radius "
563 <                    "to %lf at time %lf\n",
564 <                    rCut, currentTime );
565 <          painCave.isFatal = 0;
566 <          simError();
567 <      }
568 <    }
569 <    else if ((rCut > maxCutoff)&&(usePBC)) {
568 >    
569 >    if( rCut > maxCutoff ){
570        sprintf( painCave.errMsg,
571 <               "New Box size is setting the long range cutoff radius "
572 <               "to %lf at time %lf\n",
573 <               maxCutoff, currentTime );
574 <      painCave.isFatal = 0;
571 >               "Box size is too small for the long range cutoff radius, "
572 >               "%G, at time %G\n"
573 >               "\t[ %G %G %G ]\n"
574 >               "\t[ %G %G %G ]\n"
575 >               "\t[ %G %G %G ]\n",
576 >               rCut, currentTime,
577 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
578 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
579 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
580 >      painCave.isFatal = 1;
581        simError();
576 –      rCut = maxCutoff;
582      }
583 <
584 <
585 <    //detect the change of ecr
586 <    if( maxCutoff > ecr ){
587 <      if( ecr < origEcr ){
588 <        ecr = origEcr;
589 <        if (ecr > maxCutoff) ecr = maxCutoff;
590 <  
591 <          sprintf( painCave.errMsg,
592 <                    "New Box size is setting the electrostaticCutoffRadius "
593 <                    "to %lf at time %lf\n",
594 <                    ecr, currentTime );
595 <            painCave.isFatal = 0;
596 <            simError();
583 >    
584 >    if( haveEcr ){
585 >      if( ecr > maxCutoff ){
586 >        sprintf( painCave.errMsg,
587 >                 "Box size is too small for the electrostatic cutoff radius, "
588 >                 "%G, at time %G\n"
589 >                 "\t[ %G %G %G ]\n"
590 >                 "\t[ %G %G %G ]\n"
591 >                 "\t[ %G %G %G ]\n",
592 >                 ecr, currentTime,
593 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
594 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
595 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
596 >        painCave.isFatal = 1;
597 >        simError();
598        }
599      }
594 –    else if( ecr > maxCutoff){
595 –      sprintf( painCave.errMsg,
596 –               "New Box size is setting the electrostaticCutoffRadius "
597 –               "to %lf at time %lf\n",
598 –               maxCutoff, currentTime  );
599 –      painCave.isFatal = 0;
600 –      simError();      
601 –      ecr = maxCutoff;
602 –    }
603 –
604 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
605 –    
606 –    // rlist is the 1.0 plus max( rcut, ecr )
607 –    
608 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
609 –    
610 –    if( cutChanged ){
611 –      
612 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
613 –    }
614 –    
615 –    oldEcr = ecr;
616 –    oldRcut = rCut;
617 –    
600    } else {
601      // initialize this stuff before using it, OK?
602      sprintf( painCave.errMsg,
603 <             "Trying to check cutoffs without a box. Be smarter.\n" );
603 >             "Trying to check cutoffs without a box.\n"
604 >             "\tOOPSE should have better programmers than that.\n" );
605      painCave.isFatal = 1;
606      simError();      
607    }

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