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root/group/branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp
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Comparing:
trunk/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 852 by mmeineke, Thu Nov 6 18:20:47 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 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 54 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64 +  properties = new GenericData();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70   SimInfo::~SimInfo(){
71  
72 <  map<string, GenericData*>::iterator i;
73 <  
64 <  for(i = properties.begin(); i != properties.end(); i++)
65 <    delete (*i).second;
66 <
67 <  
72 >  delete myConfiguration;
73 >  delete properties;    
74   }
75  
76   void SimInfo::setBox(double newBox[3]) {
# Line 85 | Line 91 | void SimInfo::setBoxM( double theBox[3][3] ){
91  
92   void SimInfo::setBoxM( double theBox[3][3] ){
93    
94 <  int i, j, status;
89 <  double smallestBoxL, maxCutoff;
94 >  int i, j;
95    double FortranHmat[9]; // to preserve compatibility with Fortran the
96                           // ordering in the array is as follows:
97                           // [ 0 3 6 ]
# Line 137 | Line 142 | void SimInfo::calcHmatInv( void ) {
142   }
143  
144   void SimInfo::calcHmatInv( void ) {
145 <  
145 >
146 >  int oldOrtho;
147    int i,j;
148    double smallDiag;
149    double tol;
# Line 147 | Line 153 | void SimInfo::calcHmatInv( void ) {
153  
154    // Check the inverse to make sure it is sane:
155  
156 <  matMul3( Hmat, HmatInv, sanity );
156 >  // matMul3( Hmat, HmatInv, sanity );
157      
158    // check to see if Hmat is orthorhombic
159 +
160    
161 <  smallDiag = Hmat[0][0];
162 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
163 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
161 >  oldOrtho = orthoRhombic;
162 >
163 >  smallDiag = fabs(Hmat[0][0]);
164 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166    tol = smallDiag * 1E-6;
167  
168    orthoRhombic = 1;
# Line 162 | Line 171 | void SimInfo::calcHmatInv( void ) {
171      for (j = 0 ; j < 3; j++) {
172        if (i != j) {
173          if (orthoRhombic) {
174 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175          }        
176        }
177      }
178    }
179 +  
180 +  if( oldOrtho != orthoRhombic ){
181 +    
182 +    if( orthoRhombic ){
183 +      sprintf( painCave.errMsg,
184 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
186 +      simError();
187 +    }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
192 +      simError();
193 +    }
194 +  }
195   }
196  
197   double SimInfo::matDet3(double a[3][3]) {
# Line 273 | Line 298 | void SimInfo::printMat9(double A[9] ){
298              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
299   }
300  
301 +
302 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
303 +
304 +      out[0] = a[1] * b[2] - a[2] * b[1];
305 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
306 +      out[2] = a[0] * b[1] - a[1] * b[0];
307 +      
308 + }
309 +
310 + double SimInfo::dotProduct3(double a[3], double b[3]){
311 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
312 + }
313 +
314 + double SimInfo::length3(double a[3]){
315 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
316 + }
317 +
318   void SimInfo::calcBoxL( void ){
319  
320    double dx, dy, dz, dsq;
279 –  int i;
321  
322    // boxVol = Determinant of Hmat
323  
# Line 287 | Line 328 | void SimInfo::calcBoxL( void ){
328    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
329    dsq = dx*dx + dy*dy + dz*dz;
330    boxL[0] = sqrt( dsq );
331 <  maxCutoff = 0.5 * boxL[0];
331 >  //maxCutoff = 0.5 * boxL[0];
332  
333    // boxLy
334    
335    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
336    dsq = dx*dx + dy*dy + dz*dz;
337    boxL[1] = sqrt( dsq );
338 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
338 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
339  
340 +
341    // boxLz
342    
343    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
344    dsq = dx*dx + dy*dy + dz*dz;
345    boxL[2] = sqrt( dsq );
346 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
346 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
347 >
348 >  //calculate the max cutoff
349 >  maxCutoff =  calcMaxCutOff();
350 >  
351 >  checkCutOffs();
352  
353   }
354  
355  
356 + double SimInfo::calcMaxCutOff(){
357 +
358 +  double ri[3], rj[3], rk[3];
359 +  double rij[3], rjk[3], rki[3];
360 +  double minDist;
361 +
362 +  ri[0] = Hmat[0][0];
363 +  ri[1] = Hmat[1][0];
364 +  ri[2] = Hmat[2][0];
365 +
366 +  rj[0] = Hmat[0][1];
367 +  rj[1] = Hmat[1][1];
368 +  rj[2] = Hmat[2][1];
369 +
370 +  rk[0] = Hmat[0][2];
371 +  rk[1] = Hmat[1][2];
372 +  rk[2] = Hmat[2][2];
373 +  
374 +  crossProduct3(ri,rj, rij);
375 +  distXY = dotProduct3(rk,rij) / length3(rij);
376 +
377 +  crossProduct3(rj,rk, rjk);
378 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
379 +
380 +  crossProduct3(rk,ri, rki);
381 +  distZX = dotProduct3(rj,rki) / length3(rki);
382 +
383 +  minDist = min(min(distXY, distYZ), distZX);
384 +  return minDist/2;
385 +  
386 + }
387 +
388   void SimInfo::wrapVector( double thePos[3] ){
389  
390 <  int i, j, k;
390 >  int i;
391    double scaled[3];
392  
393    if( !orthoRhombic ){
# Line 346 | Line 425 | int SimInfo::getNDF(){
425  
426  
427   int SimInfo::getNDF(){
428 <  int ndf_local, ndf;
428 >  int ndf_local;
429    
430    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
431  
# Line 356 | Line 435 | int SimInfo::getNDF(){
435    ndf = ndf_local;
436   #endif
437  
438 <  ndf = ndf - 3;
438 >  ndf = ndf - 3 - nZconstraints;
439  
440    return ndf;
441   }
442  
443   int SimInfo::getNDFraw() {
444 <  int ndfRaw_local, ndfRaw;
444 >  int ndfRaw_local;
445  
446    // Raw degrees of freedom that we have to set
447    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 375 | Line 454 | int SimInfo::getNDFraw() {
454  
455    return ndfRaw;
456   }
457 <
457 >
458 > int SimInfo::getNDFtranslational() {
459 >  int ndfTrans_local;
460 >
461 >  ndfTrans_local = 3 * n_atoms - n_constraints;
462 >
463 > #ifdef IS_MPI
464 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
465 > #else
466 >  ndfTrans = ndfTrans_local;
467 > #endif
468 >
469 >  ndfTrans = ndfTrans - 3 - nZconstraints;
470 >
471 >  return ndfTrans;
472 > }
473 >
474   void SimInfo::refreshSim(){
475  
476    simtype fInfo;
# Line 431 | Line 526 | void SimInfo::refreshSim(){
526  
527    this->ndf = this->getNDF();
528    this->ndfRaw = this->getNDFraw();
529 <
529 >  this->ndfTrans = this->getNDFtranslational();
530   }
531  
532  
533   void SimInfo::setRcut( double theRcut ){
534  
440 –  if( !haveOrigRcut ){
441 –    haveOrigRcut = 1;
442 –    origRcut = theRcut;
443 –  }
444 –
535    rCut = theRcut;
536    checkCutOffs();
537   }
538  
539 < void SimInfo::setEcr( double theEcr ){
539 > void SimInfo::setDefaultRcut( double theRcut ){
540  
541 <  if( !haveOrigEcr ){
542 <    haveOrigEcr = 1;
543 <    origEcr = theEcr;
454 <  }
541 >  haveOrigRcut = 1;
542 >  origRcut = theRcut;
543 >  rCut = theRcut;
544  
545 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setEcr( double theEcr ){
551 +
552    ecr = theEcr;
553    checkCutOffs();
554   }
555  
556 + void SimInfo::setDefaultEcr( double theEcr ){
557 +
558 +  haveOrigEcr = 1;
559 +  origEcr = theEcr;
560 +  
561 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
562 +
563 +  ecr = theEcr;
564 +
565 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
566 + }
567 +
568   void SimInfo::setEcr( double theEcr, double theEst ){
569  
570    est = theEst;
571    setEcr( theEcr );
572   }
573  
574 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
575  
576 +  est = theEst;
577 +  setDefaultEcr( theEcr );
578 + }
579 +
580 +
581   void SimInfo::checkCutOffs( void ){
582  
583    int cutChanged = 0;
584 <
584 >  
585    if( boxIsInit ){
586      
587      //we need to check cutOffs against the box
588 <    
589 <    if( maxCutoff > rCut ){
588 >
589 >    //detect the change of rCut
590 >    if(( maxCutoff > rCut )&&(usePBC)){
591        if( rCut < origRcut ){
592 <        rCut = origRcut;
593 <        if (rCut > maxCutoff) rCut = maxCutoff;
594 <        
595 <        sprintf( painCave.errMsg,
596 <                 "New Box size is setting the long range cutoff radius "
597 <                 "to %lf\n",
598 <                 rCut );
599 <        painCave.isFatal = 0;
600 <        simError();
592 >        rCut = origRcut;
593 >        
594 >        if (rCut > maxCutoff)
595 >          rCut = maxCutoff;
596 >  
597 >          sprintf( painCave.errMsg,
598 >                    "New Box size is setting the long range cutoff radius "
599 >                    "to %lf at time %lf\n",
600 >                    rCut, currentTime );
601 >          painCave.isFatal = 0;
602 >          simError();
603        }
604      }
605 <
489 <    if( maxCutoff > ecr ){
490 <      if( ecr < origEcr ){
491 <        rCut = origEcr;
492 <        if (ecr > maxCutoff) ecr = maxCutoff;
493 <        
494 <        sprintf( painCave.errMsg,
495 <                 "New Box size is setting the electrostaticCutoffRadius "
496 <                 "to %lf\n",
497 <                 ecr );
498 <        painCave.isFatal = 0;
499 <        simError();
500 <      }
501 <    }
502 <
503 <
504 <    if (rCut > maxCutoff) {
605 >    else if ((rCut > maxCutoff)&&(usePBC)) {
606        sprintf( painCave.errMsg,
607                 "New Box size is setting the long range cutoff radius "
608 <               "to %lf\n",
609 <               maxCutoff );
608 >               "to %lf at time %lf\n",
609 >               maxCutoff, currentTime );
610        painCave.isFatal = 0;
611        simError();
612        rCut = maxCutoff;
613      }
614  
615 <    if( ecr > maxCutoff){
615 >
616 >    //detect the change of ecr
617 >    if( maxCutoff > ecr ){
618 >      if( ecr < origEcr ){
619 >        ecr = origEcr;
620 >        if (ecr > maxCutoff) ecr = maxCutoff;
621 >  
622 >          sprintf( painCave.errMsg,
623 >                    "New Box size is setting the electrostaticCutoffRadius "
624 >                    "to %lf at time %lf\n",
625 >                    ecr, currentTime );
626 >            painCave.isFatal = 0;
627 >            simError();
628 >      }
629 >    }
630 >    else if( ecr > maxCutoff){
631        sprintf( painCave.errMsg,
632                 "New Box size is setting the electrostaticCutoffRadius "
633 <               "to %lf\n",
634 <               maxCutoff  );
633 >               "to %lf at time %lf\n",
634 >               maxCutoff, currentTime  );
635        painCave.isFatal = 0;
636        simError();      
637        ecr = maxCutoff;
638      }
639  
640 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
641      
642 <  }
526 <  
527 <
528 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
529 <
530 <  // rlist is the 1.0 plus max( rcut, ecr )
531 <  
532 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
533 <
534 <  if( cutChanged ){
642 >    // rlist is the 1.0 plus max( rcut, ecr )
643      
644 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537 <  }
538 <
539 <  oldEcr = ecr;
540 <  oldRcut = rCut;
541 < }
542 <
543 < void SimInfo::addProperty(GenericData* prop){
544 <
545 <  map<string, GenericData*>::iterator result;
546 <  result = properties.find(prop->getID());
547 <  
548 <  //we can't simply use  properties[prop->getID()] = prop,
549 <  //it will cause memory leak if we already contain a propery which has the same name of prop
550 <  
551 <  if(result != properties.end()){
644 >    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
645      
646 <    delete (*result).second;
647 <    (*result).second = prop;
648 <      
556 <  }
557 <  else{
558 <
559 <    properties[prop->getID()] = prop;
560 <
561 <  }
646 >    if( cutChanged ){
647 >      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
648 >    }
649      
650 < }
651 <
652 < GenericData* SimInfo::getProperty(const string& propName){
653 <
654 <  map<string, GenericData*>::iterator result;
650 >    oldEcr = ecr;
651 >    oldRcut = rCut;
652 >    
653 >  } else {
654 >    // initialize this stuff before using it, OK?
655 >    sprintf( painCave.errMsg,
656 >             "Trying to check cutoffs without a box. Be smarter.\n" );
657 >    painCave.isFatal = 1;
658 >    simError();      
659 >  }
660    
569 –  //string lowerCaseName = ();
570 –  
571 –  result = properties.find(propName);
572 –  
573 –  if(result != properties.end())
574 –    return (*result).second;  
575 –  else  
576 –    return NULL;  
661   }
662  
663 < vector<GenericData*> SimInfo::getProperties(){
663 > GenericData* SimInfo::getProperty(char* propName){
664  
665 <  vector<GenericData*> result;
582 <  map<string, GenericData*>::iterator i;
583 <  
584 <  for(i = properties.begin(); i != properties.end(); i++)
585 <    result.push_back((*i).second);
586 <    
587 <  return result;
665 >  return properties->find( propName );
666   }
667  
668 + double SimInfo::matTrace3(double m[3][3]){
669 +  double trace;
670 +  trace = m[0][0] + m[1][1] + m[2][2];
671  
672 +  return trace;
673 + }

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