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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 767 by tim, Tue Sep 16 20:02:11 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 48 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 +  resetTime = 1e99;
52    
53  
54    usePBC = 0;
# Line 93 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94  
95   void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, j, status;
97 <  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 146 | 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 153 | Line 154 | void SimInfo::calcHmatInv( void ) {
154  
155    invertMat3( Hmat, HmatInv );
156  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
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 170 | 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  
# Line 281 | Line 296 | void SimInfo::calcBoxL( void ){
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;
287 –  int i;
319  
320    // boxVol = Determinant of Hmat
321  
# Line 295 | 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 356 | 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 372 | Line 439 | int SimInfo::getNDFraw() {
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 387 | Line 454 | int SimInfo::getNDFtranslational() {
454   }
455  
456   int SimInfo::getNDFtranslational() {
457 <  int ndfTrans_local, ndfTrans;
457 >  int ndfTrans_local;
458  
459    ndfTrans_local = 3 * n_atoms - n_constraints;
460  
# Line 463 | Line 530 | void SimInfo::setRcut( double theRcut ){
530  
531   void SimInfo::setRcut( double theRcut ){
532  
466 –  if( !haveOrigRcut ){
467 –    haveOrigRcut = 1;
468 –    origRcut = theRcut;
469 –  }
470 –
533    rCut = theRcut;
534    checkCutOffs();
535   }
536  
537 < void SimInfo::setEcr( double theEcr ){
476 <
477 <  if( !haveOrigEcr ){
478 <    haveOrigEcr = 1;
479 <    origEcr = theEcr;
480 <  }
537 > void SimInfo::setDefaultRcut( double theRcut ){
538  
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 ){
567  
568    est = theEst;
569    setEcr( theEcr );
570   }
571  
572 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573  
574 < void SimInfo::checkCutOffs( void ){
574 >  est = theEst;
575 >  setDefaultEcr( theEcr );
576 > }
577  
495 –  int cutChanged = 0;
578  
579 + void SimInfo::checkCutOffs( void ){
580  
581 <
581 >  int cutChanged = 0;
582 >  
583    if( boxIsInit ){
584      
585      //we need to check cutOffs against the box
586 <  
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 <
517 <    if( maxCutoff > ecr ){
518 <      if( ecr < origEcr ){
519 <        ecr = origEcr;
520 <        if (ecr > maxCutoff) ecr = maxCutoff;
521 <        
522 <        sprintf( painCave.errMsg,
523 <                 "New Box size is setting the electrostaticCutoffRadius "
524 <                 "to %lf\n",
525 <                 ecr );
526 <        painCave.isFatal = 0;
527 <        simError();
528 <      }
529 <    }
530 <
531 <
532 <    if ((rCut > maxCutoff)&&(usePBC)) {
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  
552 –
638      if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 <
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 ){
560 –      
645        notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646      }
647      
648      oldEcr = ecr;
649      oldRcut = rCut;
650 <
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();      
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   void SimInfo::addProperty(GenericData* prop){

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