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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 590 by mmeineke, Thu Jul 10 22:15:53 2003 UTC vs.
Revision 843 by mmeineke, Wed Oct 29 20:41:39 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;
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 64 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94  
95   void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, j, status;
68 <  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 73 | Line 102 | void SimInfo::setBoxM( double theBox[3][3] ){
102                           // [ 2 5 8 ]
103    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
104  
105 +  
106 +  if( !boxIsInit ) boxIsInit = 1;
107  
108    for(i=0; i < 3; i++)
109      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
110    
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 –
111    calcBoxL();
112    calcHmatInv();
113  
# Line 95 | Line 120 | void SimInfo::setBoxM( double theBox[3][3] ){
120  
121    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122  
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 –  }
123   }
124  
125  
# Line 153 | Line 135 | void SimInfo::scaleBox(double scale) {
135    double theBox[3][3];
136    int i, j;
137  
138 <  cerr << "Scaling box by " << scale << "\n";
138 >  // cerr << "Scaling box by " << scale << "\n";
139  
140    for(i=0; i<3; i++)
141      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 265 | Line 247 | void SimInfo::matVecMul3(double m[3][3], double inVec[
247    outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
248    outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
249    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
250 + }
251 +
252 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
253 +  double temp[3][3];
254 +  int i, j;
255 +
256 +  for (i = 0; i < 3; i++) {
257 +    for (j = 0; j < 3; j++) {
258 +      temp[j][i] = in[i][j];
259 +    }
260 +  }
261 +  for (i = 0; i < 3; i++) {
262 +    for (j = 0; j < 3; j++) {
263 +      out[i][j] = temp[i][j];
264 +    }
265 +  }
266   }
267    
268 + void SimInfo::printMat3(double A[3][3] ){
269 +
270 +  std::cerr
271 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
272 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
273 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
274 + }
275 +
276 + void SimInfo::printMat9(double A[9] ){
277 +
278 +  std::cerr
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;
273 –  int i;
304  
305    // boxVol = Determinant of Hmat
306  
# Line 280 | Line 310 | void SimInfo::calcBoxL( void ){
310    
311    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
312    dsq = dx*dx + dy*dy + dz*dz;
313 <  boxLx = sqrt( dsq );
313 >  boxL[0] = sqrt( dsq );
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 <  boxLy = sqrt( dsq );
320 >  boxL[1] = sqrt( dsq );
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 <  boxLz = sqrt( dsq );
328 >  boxL[2] = sqrt( dsq );
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 337 | 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 347 | Line 418 | int SimInfo::getNDF(){
418    ndf = ndf_local;
419   #endif
420  
421 <  ndf = ndf - 3;
421 >  ndf = ndf - 3 - nZconstraints;
422  
423    return ndf;
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 366 | Line 437 | int SimInfo::getNDFraw() {
437  
438    return ndfRaw;
439   }
440 <
440 >
441 > int SimInfo::getNDFtranslational() {
442 >  int ndfTrans_local;
443 >
444 >  ndfTrans_local = 3 * n_atoms - n_constraints;
445 >
446 > #ifdef IS_MPI
447 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
448 > #else
449 >  ndfTrans = ndfTrans_local;
450 > #endif
451 >
452 >  ndfTrans = ndfTrans - 3 - nZconstraints;
453 >
454 >  return ndfTrans;
455 > }
456 >
457   void SimInfo::refreshSim(){
458  
459    simtype fInfo;
460    int isError;
461    int n_global;
462    int* excl;
463 <  
377 <  fInfo.rrf = 0.0;
378 <  fInfo.rt = 0.0;
463 >
464    fInfo.dielect = 0.0;
465  
381 –  fInfo.rlist = rList;
382 –  fInfo.rcut = rCut;
383 –
466    if( useDipole ){
385 –    fInfo.rrf = ecr;
386 –    fInfo.rt = ecr - est;
467      if( useReactionField )fInfo.dielect = dielectric;
468    }
469  
# Line 429 | Line 509 | void SimInfo::refreshSim(){
509  
510    this->ndf = this->getNDF();
511    this->ndfRaw = this->getNDFraw();
512 +  this->ndfTrans = this->getNDFtranslational();
513 + }
514  
515 +
516 + void SimInfo::setRcut( double theRcut ){
517 +
518 +  rCut = theRcut;
519 +  checkCutOffs();
520   }
521  
522 + void SimInfo::setDefaultRcut( double theRcut ){
523 +
524 +  haveOrigRcut = 1;
525 +  origRcut = theRcut;
526 +  rCut = theRcut;
527 +
528 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
529 + }
530 +
531 + void SimInfo::setEcr( double theEcr ){
532 +
533 +  ecr = theEcr;
534 +  checkCutOffs();
535 + }
536 +
537 + void SimInfo::setDefaultEcr( double theEcr ){
538 +
539 +  haveOrigEcr = 1;
540 +  origEcr = theEcr;
541 +  
542 +  ecr = theEcr;
543 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
544 + }
545 +
546 + void SimInfo::setEcr( double theEcr, double theEst ){
547 +
548 +  est = theEst;
549 +  setEcr( theEcr );
550 + }
551 +
552 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
553 +
554 +  est = theEst;
555 +  setDefaultEcr( theEcr );
556 + }
557 +
558 +
559 + void SimInfo::checkCutOffs( void ){
560 +
561 +  int cutChanged = 0;
562 +  
563 +  if( boxIsInit ){
564 +    
565 +    //we need to check cutOffs against the box
566 +
567 +    //detect the change of rCut
568 +    if(( maxCutoff > rCut )&&(usePBC)){
569 +      if( rCut < origRcut ){
570 +        rCut = origRcut;
571 +        
572 +        if (rCut > maxCutoff)
573 +          rCut = maxCutoff;
574 +  
575 +          sprintf( painCave.errMsg,
576 +                    "New Box size is setting the long range cutoff radius "
577 +                    "to %lf at time %lf\n",
578 +                    rCut, currentTime );
579 +          painCave.isFatal = 0;
580 +          simError();
581 +      }
582 +    }
583 +    else if ((rCut > maxCutoff)&&(usePBC)) {
584 +      sprintf( painCave.errMsg,
585 +               "New Box size is setting the long range cutoff radius "
586 +               "to %lf at time %lf\n",
587 +               maxCutoff, currentTime );
588 +      painCave.isFatal = 0;
589 +      simError();
590 +      rCut = maxCutoff;
591 +    }
592 +
593 +
594 +    //detect the change of ecr
595 +    if( maxCutoff > ecr ){
596 +      if( ecr < origEcr ){
597 +        ecr = origEcr;
598 +        if (ecr > maxCutoff) ecr = maxCutoff;
599 +  
600 +          sprintf( painCave.errMsg,
601 +                    "New Box size is setting the electrostaticCutoffRadius "
602 +                    "to %lf at time %lf\n",
603 +                    ecr, currentTime );
604 +            painCave.isFatal = 0;
605 +            simError();
606 +      }
607 +    }
608 +    else if( ecr > maxCutoff){
609 +      sprintf( painCave.errMsg,
610 +               "New Box size is setting the electrostaticCutoffRadius "
611 +               "to %lf at time %lf\n",
612 +               maxCutoff, currentTime  );
613 +      painCave.isFatal = 0;
614 +      simError();      
615 +      ecr = maxCutoff;
616 +    }
617 +
618 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
619 +    
620 +    // rlist is the 1.0 plus max( rcut, ecr )
621 +    
622 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
623 +    
624 +    if( cutChanged ){
625 +      
626 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
627 +    }
628 +    
629 +    oldEcr = ecr;
630 +    oldRcut = rCut;
631 +    
632 +  } else {
633 +    // initialize this stuff before using it, OK?
634 +    sprintf( painCave.errMsg,
635 +             "Trying to check cutoffs without a box. Be smarter.\n" );
636 +    painCave.isFatal = 1;
637 +    simError();      
638 +  }
639 +  
640 + }
641 +
642 + void SimInfo::addProperty(GenericData* prop){
643 +
644 +  map<string, GenericData*>::iterator result;
645 +  result = properties.find(prop->getID());
646 +  
647 +  //we can't simply use  properties[prop->getID()] = prop,
648 +  //it will cause memory leak if we already contain a propery which has the same name of prop
649 +  
650 +  if(result != properties.end()){
651 +    
652 +    delete (*result).second;
653 +    (*result).second = prop;
654 +      
655 +  }
656 +  else{
657 +
658 +    properties[prop->getID()] = prop;
659 +
660 +  }
661 +    
662 + }
663 +
664 + GenericData* SimInfo::getProperty(const string& propName){
665 +
666 +  map<string, GenericData*>::iterator result;
667 +  
668 +  //string lowerCaseName = ();
669 +  
670 +  result = properties.find(propName);
671 +  
672 +  if(result != properties.end())
673 +    return (*result).second;  
674 +  else  
675 +    return NULL;  
676 + }
677 +
678 + vector<GenericData*> SimInfo::getProperties(){
679 +
680 +  vector<GenericData*> result;
681 +  map<string, GenericData*>::iterator i;
682 +  
683 +  for(i = properties.begin(); i != properties.end(); i++)
684 +    result.push_back((*i).second);
685 +    
686 +  return result;
687 + }
688 +
689 + double SimInfo::matTrace3(double m[3][3]){
690 +  double trace;
691 +  trace = m[0][0] + m[1][1] + m[2][2];
692 +
693 +  return trace;
694 + }

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