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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 853 by mmeineke, Thu Nov 6 19:11:38 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 164 | Line 146 | void SimInfo::calcHmatInv( void ) {
146  
147   void SimInfo::calcHmatInv( void ) {
148    
149 +  int oldOrtho;
150    int i,j;
151    double smallDiag;
152    double tol;
# Line 171 | Line 154 | void SimInfo::calcHmatInv( void ) {
154  
155    invertMat3( Hmat, HmatInv );
156  
174 –  // Check the inverse to make sure it is sane:
175 –
176 –  matMul3( Hmat, HmatInv, sanity );
177 –    
157    // check to see if Hmat is orthorhombic
158    
159 <  smallDiag = Hmat[0][0];
160 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
161 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
159 >  oldOrtho = orthoRhombic;
160 >
161 >  smallDiag = fabs(Hmat[0][0]);
162 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
163 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
164    tol = smallDiag * 1E-6;
165  
166    orthoRhombic = 1;
# Line 188 | Line 169 | void SimInfo::calcHmatInv( void ) {
169      for (j = 0 ; j < 3; j++) {
170        if (i != j) {
171          if (orthoRhombic) {
172 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
172 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
173          }        
174        }
175 +    }
176 +  }
177 +
178 +  if( oldOrtho != orthoRhombic ){
179 +    
180 +    if( orthoRhombic ){
181 +      sprintf( painCave.errMsg,
182 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
184 +      simError();
185      }
186 +    else {
187 +      sprintf( painCave.errMsg,
188 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
189 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
190 +      simError();
191 +    }
192    }
193   }
194  
# Line 266 | Line 263 | void SimInfo::matVecMul3(double m[3][3], double inVec[
263    outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265   }
266 +
267 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 +  double temp[3][3];
269 +  int i, j;
270 +
271 +  for (i = 0; i < 3; i++) {
272 +    for (j = 0; j < 3; j++) {
273 +      temp[j][i] = in[i][j];
274 +    }
275 +  }
276 +  for (i = 0; i < 3; i++) {
277 +    for (j = 0; j < 3; j++) {
278 +      out[i][j] = temp[i][j];
279 +    }
280 +  }
281 + }
282    
283 + void SimInfo::printMat3(double A[3][3] ){
284 +
285 +  std::cerr
286 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 + }
290 +
291 + void SimInfo::printMat9(double A[9] ){
292 +
293 +  std::cerr
294 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 + }
298 +
299 +
300 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301 +
302 +      out[0] = a[1] * b[2] - a[2] * b[1];
303 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
304 +      out[2] = a[0] * b[1] - a[1] * b[0];
305 +      
306 + }
307 +
308 + double SimInfo::dotProduct3(double a[3], double b[3]){
309 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
310 + }
311 +
312 + double SimInfo::length3(double a[3]){
313 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
314 + }
315 +
316   void SimInfo::calcBoxL( void ){
317  
318    double dx, dy, dz, dsq;
273 –  int i;
319  
320    // boxVol = Determinant of Hmat
321  
# Line 280 | Line 325 | void SimInfo::calcBoxL( void ){
325    
326    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
327    dsq = dx*dx + dy*dy + dz*dz;
328 <  boxLx = sqrt( dsq );
328 >  boxL[0] = sqrt( dsq );
329 >  //maxCutoff = 0.5 * boxL[0];
330  
331    // boxLy
332    
333    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
334    dsq = dx*dx + dy*dy + dz*dz;
335 <  boxLy = sqrt( dsq );
335 >  boxL[1] = sqrt( dsq );
336 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
337  
338 +
339    // boxLz
340    
341    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
342    dsq = dx*dx + dy*dy + dz*dz;
343 <  boxLz = sqrt( dsq );
343 >  boxL[2] = sqrt( dsq );
344 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
345 >
346 >  //calculate the max cutoff
347 >  maxCutoff =  calcMaxCutOff();
348    
349 +  checkCutOffs();
350 +
351   }
352  
353  
354 + double SimInfo::calcMaxCutOff(){
355 +
356 +  double ri[3], rj[3], rk[3];
357 +  double rij[3], rjk[3], rki[3];
358 +  double minDist;
359 +
360 +  ri[0] = Hmat[0][0];
361 +  ri[1] = Hmat[1][0];
362 +  ri[2] = Hmat[2][0];
363 +
364 +  rj[0] = Hmat[0][1];
365 +  rj[1] = Hmat[1][1];
366 +  rj[2] = Hmat[2][1];
367 +
368 +  rk[0] = Hmat[0][2];
369 +  rk[1] = Hmat[1][2];
370 +  rk[2] = Hmat[2][2];
371 +  
372 +  crossProduct3(ri,rj, rij);
373 +  distXY = dotProduct3(rk,rij) / length3(rij);
374 +
375 +  crossProduct3(rj,rk, rjk);
376 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
377 +
378 +  crossProduct3(rk,ri, rki);
379 +  distZX = dotProduct3(rj,rki) / length3(rki);
380 +
381 +  minDist = min(min(distXY, distYZ), distZX);
382 +  return minDist/2;
383 +  
384 + }
385 +
386   void SimInfo::wrapVector( double thePos[3] ){
387  
388 <  int i, j, k;
388 >  int i;
389    double scaled[3];
390  
391    if( !orthoRhombic ){
# Line 337 | Line 423 | int SimInfo::getNDF(){
423  
424  
425   int SimInfo::getNDF(){
426 <  int ndf_local, ndf;
426 >  int ndf_local;
427    
428    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429  
# Line 347 | Line 433 | int SimInfo::getNDF(){
433    ndf = ndf_local;
434   #endif
435  
436 <  ndf = ndf - 3;
436 >  ndf = ndf - 3 - nZconstraints;
437  
438    return ndf;
439   }
440  
441   int SimInfo::getNDFraw() {
442 <  int ndfRaw_local, ndfRaw;
442 >  int ndfRaw_local;
443  
444    // Raw degrees of freedom that we have to set
445    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 366 | Line 452 | int SimInfo::getNDFraw() {
452  
453    return ndfRaw;
454   }
455 <
455 >
456 > int SimInfo::getNDFtranslational() {
457 >  int ndfTrans_local;
458 >
459 >  ndfTrans_local = 3 * n_atoms - n_constraints;
460 >
461 > #ifdef IS_MPI
462 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
463 > #else
464 >  ndfTrans = ndfTrans_local;
465 > #endif
466 >
467 >  ndfTrans = ndfTrans - 3 - nZconstraints;
468 >
469 >  return ndfTrans;
470 > }
471 >
472   void SimInfo::refreshSim(){
473  
474    simtype fInfo;
475    int isError;
476    int n_global;
477    int* excl;
478 <  
377 <  fInfo.rrf = 0.0;
378 <  fInfo.rt = 0.0;
478 >
479    fInfo.dielect = 0.0;
480  
381 –  fInfo.rlist = rList;
382 –  fInfo.rcut = rCut;
383 –
481    if( useDipole ){
385 –    fInfo.rrf = ecr;
386 –    fInfo.rt = ecr - est;
482      if( useReactionField )fInfo.dielect = dielectric;
483    }
484  
# Line 429 | Line 524 | void SimInfo::refreshSim(){
524  
525    this->ndf = this->getNDF();
526    this->ndfRaw = this->getNDFraw();
527 +  this->ndfTrans = this->getNDFtranslational();
528 + }
529  
530 +
531 + void SimInfo::setRcut( double theRcut ){
532 +
533 +  rCut = theRcut;
534 +  checkCutOffs();
535   }
536  
537 + void SimInfo::setDefaultRcut( double theRcut ){
538 +
539 +  haveOrigRcut = 1;
540 +  origRcut = theRcut;
541 +  rCut = theRcut;
542 +
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr ){
549 +
550 +  ecr = theEcr;
551 +  checkCutOffs();
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr ){
555 +
556 +  haveOrigEcr = 1;
557 +  origEcr = theEcr;
558 +  
559 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 +
561 +  ecr = theEcr;
562 +
563 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
564 + }
565 +
566 + void SimInfo::setEcr( double theEcr, double theEst ){
567 +
568 +  est = theEst;
569 +  setEcr( theEcr );
570 + }
571 +
572 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573 +
574 +  est = theEst;
575 +  setDefaultEcr( theEcr );
576 + }
577 +
578 +
579 + void SimInfo::checkCutOffs( void ){
580 +
581 +  int cutChanged = 0;
582 +  
583 +  if( boxIsInit ){
584 +    
585 +    //we need to check cutOffs against the box
586 +
587 +    //detect the change of rCut
588 +    if(( maxCutoff > rCut )&&(usePBC)){
589 +      if( rCut < origRcut ){
590 +        rCut = origRcut;
591 +        
592 +        if (rCut > maxCutoff)
593 +          rCut = maxCutoff;
594 +  
595 +          sprintf( painCave.errMsg,
596 +                    "New Box size is setting the long range cutoff radius "
597 +                    "to %lf at time %lf\n",
598 +                    rCut, currentTime );
599 +          painCave.isFatal = 0;
600 +          simError();
601 +      }
602 +    }
603 +    else if ((rCut > maxCutoff)&&(usePBC)) {
604 +      sprintf( painCave.errMsg,
605 +               "New Box size is setting the long range cutoff radius "
606 +               "to %lf at time %lf\n",
607 +               maxCutoff, currentTime );
608 +      painCave.isFatal = 0;
609 +      simError();
610 +      rCut = maxCutoff;
611 +    }
612 +
613 +
614 +    //detect the change of ecr
615 +    if( maxCutoff > ecr ){
616 +      if( ecr < origEcr ){
617 +        ecr = origEcr;
618 +        if (ecr > maxCutoff) ecr = maxCutoff;
619 +  
620 +          sprintf( painCave.errMsg,
621 +                    "New Box size is setting the electrostaticCutoffRadius "
622 +                    "to %lf at time %lf\n",
623 +                    ecr, currentTime );
624 +            painCave.isFatal = 0;
625 +            simError();
626 +      }
627 +    }
628 +    else if( ecr > maxCutoff){
629 +      sprintf( painCave.errMsg,
630 +               "New Box size is setting the electrostaticCutoffRadius "
631 +               "to %lf at time %lf\n",
632 +               maxCutoff, currentTime  );
633 +      painCave.isFatal = 0;
634 +      simError();      
635 +      ecr = maxCutoff;
636 +    }
637 +
638 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 +    
640 +    // rlist is the 1.0 plus max( rcut, ecr )
641 +    
642 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643 +    
644 +    if( cutChanged ){
645 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 +    }
647 +    
648 +    oldEcr = ecr;
649 +    oldRcut = rCut;
650 +    
651 +  } else {
652 +    // initialize this stuff before using it, OK?
653 +    sprintf( painCave.errMsg,
654 +             "Trying to check cutoffs without a box. Be smarter.\n" );
655 +    painCave.isFatal = 1;
656 +    simError();      
657 +  }
658 +  
659 + }
660 +
661 + void SimInfo::addProperty(GenericData* prop){
662 +
663 +  map<string, GenericData*>::iterator result;
664 +  result = properties.find(prop->getID());
665 +  
666 +  //we can't simply use  properties[prop->getID()] = prop,
667 +  //it will cause memory leak if we already contain a propery which has the same name of prop
668 +  
669 +  if(result != properties.end()){
670 +    
671 +    delete (*result).second;
672 +    (*result).second = prop;
673 +      
674 +  }
675 +  else{
676 +
677 +    properties[prop->getID()] = prop;
678 +
679 +  }
680 +    
681 + }
682 +
683 + GenericData* SimInfo::getProperty(const string& propName){
684 +
685 +  map<string, GenericData*>::iterator result;
686 +  
687 +  //string lowerCaseName = ();
688 +  
689 +  result = properties.find(propName);
690 +  
691 +  if(result != properties.end())
692 +    return (*result).second;  
693 +  else  
694 +    return NULL;  
695 + }
696 +
697 + vector<GenericData*> SimInfo::getProperties(){
698 +
699 +  vector<GenericData*> result;
700 +  map<string, GenericData*>::iterator i;
701 +  
702 +  for(i = properties.begin(); i != properties.end(); i++)
703 +    result.push_back((*i).second);
704 +    
705 +  return result;
706 + }
707 +
708 + double SimInfo::matTrace3(double m[3][3]){
709 +  double trace;
710 +  trace = m[0][0] + m[1][1] + m[2][2];
711 +
712 +  return trace;
713 + }

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