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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 781 by tim, Mon Sep 22 23:07:57 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 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 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 94 | Line 92 | void SimInfo::setBoxM( double theBox[3][3] ){
92  
93   void SimInfo::setBoxM( double theBox[3][3] ){
94    
95 <  int i, j, status;
98 <  double smallestBoxL, maxCutoff;
95 >  int i, j;
96    double FortranHmat[9]; // to preserve compatibility with Fortran the
97                           // ordering in the array is as follows:
98                           // [ 0 3 6 ]
# Line 103 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){
100                           // [ 2 5 8 ]
101    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
106 –  
103    if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
# Line 147 | 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 154 | Line 151 | void SimInfo::calcHmatInv( void ) {
151  
152    invertMat3( Hmat, HmatInv );
153  
157 –  // Check the inverse to make sure it is sane:
158 –
159 –  matMul3( Hmat, HmatInv, sanity );
160 –    
154    // check to see if Hmat is orthorhombic
155    
156 <  smallDiag = Hmat[0][0];
164 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
165 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
166 <  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  
194   double SimInfo::matDet3(double a[3][3]) {
# Line 302 | Line 315 | void SimInfo::calcBoxL( void ){
315   void SimInfo::calcBoxL( void ){
316  
317    double dx, dy, dz, dsq;
305 –  int i;
318  
319    // boxVol = Determinant of Hmat
320  
# Line 372 | Line 384 | void SimInfo::wrapVector( double thePos[3] ){
384  
385   void SimInfo::wrapVector( double thePos[3] ){
386  
387 <  int i, j, k;
387 >  int i;
388    double scaled[3];
389  
390    if( !orthoRhombic ){
# Line 410 | Line 422 | int SimInfo::getNDF(){
422  
423  
424   int SimInfo::getNDF(){
425 <  int ndf_local, ndf;
425 >  int ndf_local;
426    
427    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
428  
# Line 426 | Line 438 | int SimInfo::getNDFraw() {
438   }
439  
440   int SimInfo::getNDFraw() {
441 <  int ndfRaw_local, ndfRaw;
441 >  int ndfRaw_local;
442  
443    // Raw degrees of freedom that we have to set
444    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 441 | Line 453 | int SimInfo::getNDFtranslational() {
453   }
454  
455   int SimInfo::getNDFtranslational() {
456 <  int ndfTrans_local, ndfTrans;
456 >  int ndfTrans_local;
457  
458    ndfTrans_local = 3 * n_atoms - n_constraints;
459  
# Line 514 | Line 526 | void SimInfo::refreshSim(){
526    this->ndfTrans = this->getNDFtranslational();
527   }
528  
529 <
518 < void SimInfo::setRcut( double theRcut ){
519 <
520 <  if( !haveOrigRcut ){
521 <    haveOrigRcut = 1;
522 <    origRcut = theRcut;
523 <  }
529 > void SimInfo::setDefaultRcut( double theRcut ){
530  
531 +  haveRcut = 1;
532    rCut = theRcut;
533 <  checkCutOffs();
533 >
534 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535 >
536 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537   }
538  
539 < void SimInfo::setEcr( double theEcr ){
539 > void SimInfo::setDefaultEcr( double theEcr ){
540  
541 <  if( !haveOrigEcr ){
542 <    haveOrigEcr = 1;
543 <    origEcr = theEcr;
534 <  }
541 >  haveEcr = 1;
542 >  
543 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544  
545    ecr = theEcr;
546 <  checkCutOffs();
546 >
547 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548   }
549  
550 < void SimInfo::setEcr( double theEcr, double theEst ){
550 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551  
552    est = theEst;
553 <  setEcr( theEcr );
553 >  setDefaultEcr( theEcr );
554   }
555  
556  
557   void SimInfo::checkCutOffs( void ){
548 –
549 –  int cutChanged = 0;
558    
559    if( boxIsInit ){
560      
561      //we need to check cutOffs against the box
562 <
563 <    //detect the change of rCut
556 <    if(( maxCutoff > rCut )&&(usePBC)){
557 <      if( rCut < origRcut ){
558 <        rCut = origRcut;
559 <        
560 <        if (rCut > maxCutoff)
561 <          rCut = maxCutoff;
562 <  
563 <          sprintf( painCave.errMsg,
564 <                    "New Box size is setting the long range cutoff radius "
565 <                    "to %lf at time %lf\n",
566 <                    rCut, currentTime );
567 <          painCave.isFatal = 0;
568 <          simError();
569 <      }
570 <    }
571 <    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();
578 –      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,
589 <                    "New Box size is setting the electrostaticCutoffRadius "
590 <                    "to %lf at time %lf\n",
591 <                    ecr, currentTime );
592 <            painCave.isFatal = 0;
593 <            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      }
596 –    else if( ecr > maxCutoff){
597 –      sprintf( painCave.errMsg,
598 –               "New Box size is setting the electrostaticCutoffRadius "
599 –               "to %lf at time %lf\n",
600 –               maxCutoff, currentTime  );
601 –      painCave.isFatal = 0;
602 –      simError();      
603 –      ecr = maxCutoff;
604 –    }
605 –
606 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
607 –    
608 –    // rlist is the 1.0 plus max( rcut, ecr )
609 –    
610 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
611 –    
612 –    if( cutChanged ){
613 –      
614 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
615 –    }
616 –    
617 –    oldEcr = ecr;
618 –    oldRcut = rCut;
619 –    
582    } else {
583      // initialize this stuff before using it, OK?
584      sprintf( painCave.errMsg,

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