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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 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;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 43 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64    wrapMeSimInfo( this );
65   }
66  
67 +
68 + SimInfo::~SimInfo(){
69 +
70 +  delete myConfiguration;
71 +
72 +  map<string, GenericData*>::iterator i;
73 +  
74 +  for(i = properties.begin(); i != properties.end(); i++)
75 +    delete (*i).second;
76 +    
77 + }
78 +
79   void SimInfo::setBox(double newBox[3]) {
80    
81    int i, j;
# Line 73 | Line 103 | void SimInfo::setBoxM( double theBox[3][3] ){
103                           // [ 2 5 8 ]
104    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
105  
106 +  
107 +  if( !boxIsInit ) boxIsInit = 1;
108  
109    for(i=0; i < 3; i++)
110      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
111    
80 –  cerr
81 –    << "setting Hmat ->\n"
82 –    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 –    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 –    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85 –
112    calcBoxL();
113    calcHmatInv();
114  
# Line 93 | Line 119 | void SimInfo::setBoxM( double theBox[3][3] ){
119      }
120    }
121  
122 <  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
122 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123  
98 –  smallestBoxL = boxLx;
99 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
100 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
101 –
102 –  maxCutoff = smallestBoxL / 2.0;
103 –
104 –  if (rList > maxCutoff) {
105 –    sprintf( painCave.errMsg,
106 –             "New Box size is forcing neighborlist radius down to %lf\n",
107 –             maxCutoff );
108 –    painCave.isFatal = 0;
109 –    simError();
110 –
111 –    rList = maxCutoff;
112 –
113 –    sprintf( painCave.errMsg,
114 –             "New Box size is forcing cutoff radius down to %lf\n",
115 –             maxCutoff - 1.0 );
116 –    painCave.isFatal = 0;
117 –    simError();
118 –
119 –    rCut = rList - 1.0;
120 –
121 –    // list radius changed so we have to refresh the simulation structure.
122 –    refreshSim();
123 –  }
124 –
125 –  if (rCut > maxCutoff) {
126 –    sprintf( painCave.errMsg,
127 –             "New Box size is forcing cutoff radius down to %lf\n",
128 –             maxCutoff );
129 –    painCave.isFatal = 0;
130 –    simError();
131 –
132 –    status = 0;
133 –    LJ_new_rcut(&rCut, &status);
134 –    if (status != 0) {
135 –      sprintf( painCave.errMsg,
136 –               "Error in recomputing LJ shifts based on new rcut\n");
137 –      painCave.isFatal = 1;
138 –      simError();
139 –    }
140 –  }
124   }
125  
126  
# Line 153 | Line 136 | void SimInfo::scaleBox(double scale) {
136    double theBox[3][3];
137    int i, j;
138  
139 <  cerr << "Scaling box by " << scale << "\n";
139 >  // cerr << "Scaling box by " << scale << "\n";
140  
141    for(i=0; i<3; i++)
142      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 163 | Line 146 | void SimInfo::calcHmatInv( void ) {
146   }
147  
148   void SimInfo::calcHmatInv( void ) {
149 <
149 >  
150 >  int i,j;
151    double smallDiag;
152    double tol;
153    double sanity[3][3];
# Line 173 | Line 157 | void SimInfo::calcHmatInv( void ) {
157    // Check the inverse to make sure it is sane:
158  
159    matMul3( Hmat, HmatInv, sanity );
176 –
177 –  cerr << "sanity => \n"
178 –       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
179 –       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
180 –       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
181 –       << "\n";
160      
161    // check to see if Hmat is orthorhombic
162    
# Line 270 | Line 248 | void SimInfo::matVecMul3(double m[3][3], double inVec[
248    outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
249    outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
250    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
251 + }
252 +
253 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
254 +  double temp[3][3];
255 +  int i, j;
256 +
257 +  for (i = 0; i < 3; i++) {
258 +    for (j = 0; j < 3; j++) {
259 +      temp[j][i] = in[i][j];
260 +    }
261 +  }
262 +  for (i = 0; i < 3; i++) {
263 +    for (j = 0; j < 3; j++) {
264 +      out[i][j] = temp[i][j];
265 +    }
266 +  }
267   }
268    
269 + void SimInfo::printMat3(double A[3][3] ){
270 +
271 +  std::cerr
272 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
273 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
274 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
275 + }
276 +
277 + void SimInfo::printMat9(double A[9] ){
278 +
279 +  std::cerr
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 285 | Line 312 | void SimInfo::calcBoxL( void ){
312    
313    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314    dsq = dx*dx + dy*dy + dz*dz;
315 <  boxLx = sqrt( dsq );
315 >  boxL[0] = sqrt( dsq );
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 <  boxLy = sqrt( dsq );
322 >  boxL[1] = sqrt( dsq );
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 <  boxLz = sqrt( dsq );
330 >  boxL[2] = sqrt( dsq );
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 352 | 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 371 | 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;
462    int isError;
463    int n_global;
464    int* excl;
465 <  
382 <  fInfo.rrf = 0.0;
383 <  fInfo.rt = 0.0;
465 >
466    fInfo.dielect = 0.0;
467  
386 –  fInfo.rlist = rList;
387 –  fInfo.rcut = rCut;
388 –
468    if( useDipole ){
390 –    fInfo.rrf = ecr;
391 –    fInfo.rt = ecr - est;
469      if( useReactionField )fInfo.dielect = dielectric;
470    }
471  
# Line 434 | Line 511 | void SimInfo::refreshSim(){
511  
512    this->ndf = this->getNDF();
513    this->ndfRaw = this->getNDFraw();
514 +  this->ndfTrans = this->getNDFtranslational();
515 + }
516  
517 +
518 + void SimInfo::setRcut( double theRcut ){
519 +
520 +  if( !haveOrigRcut ){
521 +    haveOrigRcut = 1;
522 +    origRcut = theRcut;
523 +  }
524 +
525 +  rCut = theRcut;
526 +  checkCutOffs();
527   }
528  
529 + void SimInfo::setEcr( double theEcr ){
530 +
531 +  if( !haveOrigEcr ){
532 +    haveOrigEcr = 1;
533 +    origEcr = theEcr;
534 +  }
535 +
536 +  ecr = theEcr;
537 +  checkCutOffs();
538 + }
539 +
540 + void SimInfo::setEcr( double theEcr, double theEst ){
541 +
542 +  est = theEst;
543 +  setEcr( theEcr );
544 + }
545 +
546 +
547 + void SimInfo::checkCutOffs( void ){
548 +
549 +  int cutChanged = 0;
550 +  
551 +  if( boxIsInit ){
552 +    
553 +    //we need to check cutOffs against the box
554 +
555 +    //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)) {
572 +      sprintf( painCave.errMsg,
573 +               "New Box size is setting the long range cutoff radius "
574 +               "to %lf at time %lf\n",
575 +               maxCutoff, currentTime );
576 +      painCave.isFatal = 0;
577 +      simError();
578 +      rCut = maxCutoff;
579 +    }
580 +
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 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 +    
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 +  
628 + }
629 +
630 + void SimInfo::addProperty(GenericData* prop){
631 +
632 +  map<string, GenericData*>::iterator result;
633 +  result = properties.find(prop->getID());
634 +  
635 +  //we can't simply use  properties[prop->getID()] = prop,
636 +  //it will cause memory leak if we already contain a propery which has the same name of prop
637 +  
638 +  if(result != properties.end()){
639 +    
640 +    delete (*result).second;
641 +    (*result).second = prop;
642 +      
643 +  }
644 +  else{
645 +
646 +    properties[prop->getID()] = prop;
647 +
648 +  }
649 +    
650 + }
651 +
652 + GenericData* SimInfo::getProperty(const string& propName){
653 +
654 +  map<string, GenericData*>::iterator result;
655 +  
656 +  //string lowerCaseName = ();
657 +  
658 +  result = properties.find(propName);
659 +  
660 +  if(result != properties.end())
661 +    return (*result).second;  
662 +  else  
663 +    return NULL;  
664 + }
665 +
666 + vector<GenericData*> SimInfo::getProperties(){
667 +
668 +  vector<GenericData*> result;
669 +  map<string, GenericData*>::iterator i;
670 +  
671 +  for(i = properties.begin(); i != properties.end(); i++)
672 +    result.push_back((*i).second);
673 +    
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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