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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 781 by tim, Mon Sep 22 23:07:57 2003 UTC

# Line 26 | Line 26 | SimInfo::SimInfo(){
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32    ndf = 0;
33    ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38    currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41    ecr = 0.0;
42 +  origEcr = -1.0;
43    est = 0.0;
44    oldEcr = 0.0;
45    oldRcut = 0.0;
# Line 44 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 +  resetTime = 1e99;
52    
53  
54    usePBC = 0;
# Line 275 | Line 280 | void SimInfo::printMat9(double A[9] ){
280              << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
281              << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
282              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
283 + }
284 +
285 +
286 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
287 +
288 +      out[0] = a[1] * b[2] - a[2] * b[1];
289 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
290 +      out[2] = a[0] * b[1] - a[1] * b[0];
291 +      
292   }
293  
294 + double SimInfo::dotProduct3(double a[3], double b[3]){
295 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
296 + }
297 +
298 + double SimInfo::length3(double a[3]){
299 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
300 + }
301 +
302   void SimInfo::calcBoxL( void ){
303  
304    double dx, dy, dz, dsq;
# Line 291 | Line 313 | void SimInfo::calcBoxL( void ){
313    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314    dsq = dx*dx + dy*dy + dz*dz;
315    boxL[0] = sqrt( dsq );
316 <  maxCutoff = 0.5 * boxL[0];
316 >  //maxCutoff = 0.5 * boxL[0];
317  
318    // boxLy
319    
320    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321    dsq = dx*dx + dy*dy + dz*dz;
322    boxL[1] = sqrt( dsq );
323 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
323 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
324  
325 +
326    // boxLz
327    
328    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
329    dsq = dx*dx + dy*dy + dz*dz;
330    boxL[2] = sqrt( dsq );
331 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
331 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
332 >
333 >  //calculate the max cutoff
334 >  maxCutoff =  calcMaxCutOff();
335    
336    checkCutOffs();
337  
338   }
339  
340  
341 + double SimInfo::calcMaxCutOff(){
342 +
343 +  double ri[3], rj[3], rk[3];
344 +  double rij[3], rjk[3], rki[3];
345 +  double minDist;
346 +
347 +  ri[0] = Hmat[0][0];
348 +  ri[1] = Hmat[1][0];
349 +  ri[2] = Hmat[2][0];
350 +
351 +  rj[0] = Hmat[0][1];
352 +  rj[1] = Hmat[1][1];
353 +  rj[2] = Hmat[2][1];
354 +
355 +  rk[0] = Hmat[0][2];
356 +  rk[1] = Hmat[1][2];
357 +  rk[2] = Hmat[2][2];
358 +  
359 +  crossProduct3(ri,rj, rij);
360 +  distXY = dotProduct3(rk,rij) / length3(rij);
361 +
362 +  crossProduct3(rj,rk, rjk);
363 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
364 +
365 +  crossProduct3(rk,ri, rki);
366 +  distZX = dotProduct3(rj,rki) / length3(rki);
367 +
368 +  minDist = min(min(distXY, distYZ), distZX);
369 +  return minDist/2;
370 +  
371 + }
372 +
373   void SimInfo::wrapVector( double thePos[3] ){
374  
375    int i, j, k;
# Line 362 | Line 420 | int SimInfo::getNDF(){
420    ndf = ndf_local;
421   #endif
422  
423 <  ndf = ndf - 3;
423 >  ndf = ndf - 3 - nZconstraints;
424  
425    return ndf;
426   }
# Line 381 | Line 439 | int SimInfo::getNDFraw() {
439  
440    return ndfRaw;
441   }
442 <
442 >
443 > int SimInfo::getNDFtranslational() {
444 >  int ndfTrans_local, ndfTrans;
445 >
446 >  ndfTrans_local = 3 * n_atoms - n_constraints;
447 >
448 > #ifdef IS_MPI
449 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
450 > #else
451 >  ndfTrans = ndfTrans_local;
452 > #endif
453 >
454 >  ndfTrans = ndfTrans - 3 - nZconstraints;
455 >
456 >  return ndfTrans;
457 > }
458 >
459   void SimInfo::refreshSim(){
460  
461    simtype fInfo;
# Line 437 | Line 511 | void SimInfo::refreshSim(){
511  
512    this->ndf = this->getNDF();
513    this->ndfRaw = this->getNDFraw();
514 <
514 >  this->ndfTrans = this->getNDFtranslational();
515   }
516  
517  
# Line 473 | Line 547 | void SimInfo::checkCutOffs( void ){
547   void SimInfo::checkCutOffs( void ){
548  
549    int cutChanged = 0;
550 <
477 <
478 <
550 >  
551    if( boxIsInit ){
552      
553      //we need to check cutOffs against the box
554 <  
554 >
555 >    //detect the change of rCut
556      if(( maxCutoff > rCut )&&(usePBC)){
557        if( rCut < origRcut ){
558 <        rCut = origRcut;
559 <        if (rCut > maxCutoff) rCut = maxCutoff;
560 <        
561 <        sprintf( painCave.errMsg,
562 <                 "New Box size is setting the long range cutoff radius "
563 <                 "to %lf\n",
564 <                 rCut );
565 <        painCave.isFatal = 0;
566 <        simError();
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 <
497 <    if( maxCutoff > ecr ){
498 <      if( ecr < origEcr ){
499 <        rCut = origEcr;
500 <        if (ecr > maxCutoff) ecr = maxCutoff;
501 <        
502 <        sprintf( painCave.errMsg,
503 <                 "New Box size is setting the electrostaticCutoffRadius "
504 <                 "to %lf\n",
505 <                 ecr );
506 <        painCave.isFatal = 0;
507 <        simError();
508 <      }
509 <    }
510 <
511 <
512 <    if ((rCut > maxCutoff)&&(usePBC)) {
571 >    else if ((rCut > maxCutoff)&&(usePBC)) {
572        sprintf( painCave.errMsg,
573                 "New Box size is setting the long range cutoff radius "
574 <               "to %lf\n",
575 <               maxCutoff );
574 >               "to %lf at time %lf\n",
575 >               maxCutoff, currentTime );
576        painCave.isFatal = 0;
577        simError();
578        rCut = maxCutoff;
579      }
580  
581 <    if( ecr > maxCutoff){
581 >
582 >    //detect the change of ecr
583 >    if( maxCutoff > ecr ){
584 >      if( ecr < origEcr ){
585 >        ecr = origEcr;
586 >        if (ecr > maxCutoff) ecr = maxCutoff;
587 >  
588 >          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();
594 >      }
595 >    }
596 >    else if( ecr > maxCutoff){
597        sprintf( painCave.errMsg,
598                 "New Box size is setting the electrostaticCutoffRadius "
599 <               "to %lf\n",
600 <               maxCutoff  );
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 <  }
534 <  
535 <
536 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
537 <
538 <  // rlist is the 1.0 plus max( rcut, ecr )
539 <  
540 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
541 <
542 <  if( cutChanged ){
608 >    // rlist is the 1.0 plus max( rcut, ecr )
609      
610 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
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 >    
620 >  } else {
621 >    // initialize this stuff before using it, OK?
622 >    sprintf( painCave.errMsg,
623 >             "Trying to check cutoffs without a box. Be smarter.\n" );
624 >    painCave.isFatal = 1;
625 >    simError();      
626    }
627 <
547 <  oldEcr = ecr;
548 <  oldRcut = rCut;
627 >  
628   }
629  
630   void SimInfo::addProperty(GenericData* prop){
# Line 595 | Line 674 | vector<GenericData*> SimInfo::getProperties(){
674    return result;
675   }
676  
677 + double SimInfo::matTrace3(double m[3][3]){
678 +  double trace;
679 +  trace = m[0][0] + m[1][1] + m[2][2];
680  
681 +  return trace;
682 + }

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