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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 841 by mmeineke, Wed Oct 29 17:55:28 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 279 | Line 279 | void SimInfo::printMat9(double A[9] ){
279              << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280              << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 + }
283 +
284 +
285 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
286 +
287 +      out[0] = a[1] * b[2] - a[2] * b[1];
288 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
289 +      out[2] = a[0] * b[1] - a[1] * b[0];
290 +      
291 + }
292 +
293 + double SimInfo::dotProduct3(double a[3], double b[3]){
294 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
295 + }
296 +
297 + double SimInfo::length3(double a[3]){
298 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
299   }
300  
301   void SimInfo::calcBoxL( void ){
302  
303    double dx, dy, dz, dsq;
287 –  int i;
304  
305    // boxVol = Determinant of Hmat
306  
# Line 295 | Line 311 | void SimInfo::calcBoxL( void ){
311    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
312    dsq = dx*dx + dy*dy + dz*dz;
313    boxL[0] = sqrt( dsq );
314 <  maxCutoff = 0.5 * boxL[0];
314 >  //maxCutoff = 0.5 * boxL[0];
315  
316    // boxLy
317    
318    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
319    dsq = dx*dx + dy*dy + dz*dz;
320    boxL[1] = sqrt( dsq );
321 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
321 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
322  
323 +
324    // boxLz
325    
326    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327    dsq = dx*dx + dy*dy + dz*dz;
328    boxL[2] = sqrt( dsq );
329 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
329 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
330 >
331 >  //calculate the max cutoff
332 >  maxCutoff =  calcMaxCutOff();
333    
334    checkCutOffs();
335  
336   }
337  
338  
339 + double SimInfo::calcMaxCutOff(){
340 +
341 +  double ri[3], rj[3], rk[3];
342 +  double rij[3], rjk[3], rki[3];
343 +  double minDist;
344 +
345 +  ri[0] = Hmat[0][0];
346 +  ri[1] = Hmat[1][0];
347 +  ri[2] = Hmat[2][0];
348 +
349 +  rj[0] = Hmat[0][1];
350 +  rj[1] = Hmat[1][1];
351 +  rj[2] = Hmat[2][1];
352 +
353 +  rk[0] = Hmat[0][2];
354 +  rk[1] = Hmat[1][2];
355 +  rk[2] = Hmat[2][2];
356 +  
357 +  crossProduct3(ri,rj, rij);
358 +  distXY = dotProduct3(rk,rij) / length3(rij);
359 +
360 +  crossProduct3(rj,rk, rjk);
361 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
362 +
363 +  crossProduct3(rk,ri, rki);
364 +  distZX = dotProduct3(rj,rki) / length3(rki);
365 +
366 +  minDist = min(min(distXY, distYZ), distZX);
367 +  return minDist/2;
368 +  
369 + }
370 +
371   void SimInfo::wrapVector( double thePos[3] ){
372  
373 <  int i, j, k;
373 >  int i;
374    double scaled[3];
375  
376    if( !orthoRhombic ){
# Line 356 | Line 408 | int SimInfo::getNDF(){
408  
409  
410   int SimInfo::getNDF(){
411 <  int ndf_local, ndf;
411 >  int ndf_local;
412    
413    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
414  
# Line 372 | Line 424 | int SimInfo::getNDFraw() {
424   }
425  
426   int SimInfo::getNDFraw() {
427 <  int ndfRaw_local, ndfRaw;
427 >  int ndfRaw_local;
428  
429    // Raw degrees of freedom that we have to set
430    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 387 | Line 439 | int SimInfo::getNDFtranslational() {
439   }
440  
441   int SimInfo::getNDFtranslational() {
442 <  int ndfTrans_local, ndfTrans;
442 >  int ndfTrans_local;
443  
444    ndfTrans_local = 3 * n_atoms - n_constraints;
445  
# Line 463 | Line 515 | void SimInfo::setRcut( double theRcut ){
515  
516   void SimInfo::setRcut( double theRcut ){
517  
466 –  if( !haveOrigRcut ){
467 –    haveOrigRcut = 1;
468 –    origRcut = theRcut;
469 –  }
470 –
518    rCut = theRcut;
519    checkCutOffs();
520   }
521  
522 < void SimInfo::setEcr( double theEcr ){
522 > void SimInfo::setDefaultRcut( double theRcut ){
523  
524 <  if( !haveOrigEcr ){
525 <    haveOrigEcr = 1;
526 <    origEcr = theEcr;
527 <  }
524 >  haveOrigRcut = 1;
525 >  origRcut = theRcut;
526 >  rCut = theRcut;
527 > }
528  
529 + void SimInfo::setEcr( double theEcr ){
530 +
531    ecr = theEcr;
532    checkCutOffs();
533 + }
534 +
535 + void SimInfo::setDefaultEcr( double theEcr ){
536 +
537 +  haveOrigEcr = 1;
538 +  origEcr = theEcr;
539 +  
540 +  ecr = theEcr;
541   }
542  
543   void SimInfo::setEcr( double theEcr, double theEst ){
# Line 489 | Line 546 | void SimInfo::setEcr( double theEcr, double theEst ){
546    setEcr( theEcr );
547   }
548  
549 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
550  
551 < void SimInfo::checkCutOffs( void ){
551 >  est = theEst;
552 >  setDefaultEcr( theEcr );
553 > }
554  
495 –  int cutChanged = 0;
555  
556 + void SimInfo::checkCutOffs( void ){
557  
558 <
558 >  int cutChanged = 0;
559 >  
560    if( boxIsInit ){
561      
562      //we need to check cutOffs against the box
563 <  
563 >
564 >    //detect the change of rCut
565      if(( maxCutoff > rCut )&&(usePBC)){
566        if( rCut < origRcut ){
567 <        rCut = origRcut;
568 <        if (rCut > maxCutoff) rCut = maxCutoff;
569 <        
570 <        sprintf( painCave.errMsg,
571 <                 "New Box size is setting the long range cutoff radius "
572 <                 "to %lf\n",
573 <                 rCut );
574 <        painCave.isFatal = 0;
575 <        simError();
567 >        rCut = origRcut;
568 >        
569 >        if (rCut > maxCutoff)
570 >          rCut = maxCutoff;
571 >  
572 >          sprintf( painCave.errMsg,
573 >                    "New Box size is setting the long range cutoff radius "
574 >                    "to %lf at time %lf\n",
575 >                    rCut, currentTime );
576 >          painCave.isFatal = 0;
577 >          simError();
578        }
579      }
580 <
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)) {
580 >    else if ((rCut > maxCutoff)&&(usePBC)) {
581        sprintf( painCave.errMsg,
582                 "New Box size is setting the long range cutoff radius "
583 <               "to %lf\n",
584 <               maxCutoff );
583 >               "to %lf at time %lf\n",
584 >               maxCutoff, currentTime );
585        painCave.isFatal = 0;
586        simError();
587        rCut = maxCutoff;
588      }
589  
590 <    if( ecr > maxCutoff){
590 >
591 >    //detect the change of ecr
592 >    if( maxCutoff > ecr ){
593 >      if( ecr < origEcr ){
594 >        ecr = origEcr;
595 >        if (ecr > maxCutoff) ecr = maxCutoff;
596 >  
597 >          sprintf( painCave.errMsg,
598 >                    "New Box size is setting the electrostaticCutoffRadius "
599 >                    "to %lf at time %lf\n",
600 >                    ecr, currentTime );
601 >            painCave.isFatal = 0;
602 >            simError();
603 >      }
604 >    }
605 >    else if( ecr > maxCutoff){
606        sprintf( painCave.errMsg,
607                 "New Box size is setting the electrostaticCutoffRadius "
608 <               "to %lf\n",
609 <               maxCutoff  );
608 >               "to %lf at time %lf\n",
609 >               maxCutoff, currentTime  );
610        painCave.isFatal = 0;
611        simError();      
612        ecr = maxCutoff;
613      }
614  
552 –
615      if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
616 <
616 >    
617      // rlist is the 1.0 plus max( rcut, ecr )
618      
619      ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
# Line 563 | Line 625 | void SimInfo::checkCutOffs( void ){
625      
626      oldEcr = ecr;
627      oldRcut = rCut;
628 <
628 >    
629    } else {
630      // initialize this stuff before using it, OK?
631 <      sprintf( painCave.errMsg,
632 <               "Trying to check cutoffs without a box. Be smarter.\n" );
633 <      painCave.isFatal = 1;
634 <      simError();      
631 >    sprintf( painCave.errMsg,
632 >             "Trying to check cutoffs without a box. Be smarter.\n" );
633 >    painCave.isFatal = 1;
634 >    simError();      
635    }
636 <
636 >  
637   }
638  
639   void SimInfo::addProperty(GenericData* prop){

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