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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 855 by mmeineke, Thu Nov 6 22:01:37 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 +  orthoTolerance = 1E-6;
54 +  useInitXSstate = true;
55 +
56    usePBC = 0;
57    useLJ = 0;
58    useSticky = 0;
# Line 43 | Line 61 | SimInfo::SimInfo(){
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +
74 +  map<string, GenericData*>::iterator i;
75 +  
76 +  for(i = properties.begin(); i != properties.end(); i++)
77 +    delete (*i).second;
78 +    
79 + }
80 +
81   void SimInfo::setBox(double newBox[3]) {
82    
83    int i, j;
# Line 64 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){
96  
97   void SimInfo::setBoxM( double theBox[3][3] ){
98    
99 <  int i, j, status;
68 <  double smallestBoxL, maxCutoff;
99 >  int i, j;
100    double FortranHmat[9]; // to preserve compatibility with Fortran the
101                           // ordering in the array is as follows:
102                           // [ 0 3 6 ]
# Line 73 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){
104                           // [ 2 5 8 ]
105    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106  
107 +  
108 +  if( !boxIsInit ) boxIsInit = 1;
109  
110    for(i=0; i < 3; i++)
111      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
112    
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 –
113    calcBoxL();
114    calcHmatInv();
115  
# Line 95 | Line 122 | void SimInfo::setBoxM( double theBox[3][3] ){
122  
123    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
124  
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 –  }
125   }
126  
127  
# Line 153 | Line 137 | void SimInfo::scaleBox(double scale) {
137    double theBox[3][3];
138    int i, j;
139  
140 <  cerr << "Scaling box by " << scale << "\n";
140 >  // cerr << "Scaling box by " << scale << "\n";
141  
142    for(i=0; i<3; i++)
143      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 164 | Line 148 | void SimInfo::calcHmatInv( void ) {
148  
149   void SimInfo::calcHmatInv( void ) {
150    
151 +  int oldOrtho;
152    int i,j;
153    double smallDiag;
154    double tol;
# Line 171 | Line 156 | void SimInfo::calcHmatInv( void ) {
156  
157    invertMat3( Hmat, HmatInv );
158  
174 –  // Check the inverse to make sure it is sane:
175 –
176 –  matMul3( Hmat, HmatInv, sanity );
177 –    
159    // check to see if Hmat is orthorhombic
160    
161 <  smallDiag = Hmat[0][0];
181 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
182 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
183 <  tol = smallDiag * 1E-6;
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 * orthoTolerance;
167 +
168    orthoRhombic = 1;
169    
170    for (i = 0; i < 3; i++ ) {
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 orthoBoxTolerance( currently %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188      }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
192 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
193 +               orthoTolerance);
194 +      simError();
195 +    }
196    }
197   }
198  
# Line 266 | Line 267 | void SimInfo::matVecMul3(double m[3][3], double inVec[
267    outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
268    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
269   }
270 +
271 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272 +  double temp[3][3];
273 +  int i, j;
274 +
275 +  for (i = 0; i < 3; i++) {
276 +    for (j = 0; j < 3; j++) {
277 +      temp[j][i] = in[i][j];
278 +    }
279 +  }
280 +  for (i = 0; i < 3; i++) {
281 +    for (j = 0; j < 3; j++) {
282 +      out[i][j] = temp[i][j];
283 +    }
284 +  }
285 + }
286    
287 + void SimInfo::printMat3(double A[3][3] ){
288 +
289 +  std::cerr
290 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293 + }
294 +
295 + void SimInfo::printMat9(double A[9] ){
296 +
297 +  std::cerr
298 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301 + }
302 +
303 +
304 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
305 +
306 +      out[0] = a[1] * b[2] - a[2] * b[1];
307 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
308 +      out[2] = a[0] * b[1] - a[1] * b[0];
309 +      
310 + }
311 +
312 + double SimInfo::dotProduct3(double a[3], double b[3]){
313 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
314 + }
315 +
316 + double SimInfo::length3(double a[3]){
317 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
318 + }
319 +
320   void SimInfo::calcBoxL( void ){
321  
322    double dx, dy, dz, dsq;
273 –  int i;
323  
324    // boxVol = Determinant of Hmat
325  
# Line 280 | Line 329 | void SimInfo::calcBoxL( void ){
329    
330    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
331    dsq = dx*dx + dy*dy + dz*dz;
332 <  boxLx = sqrt( dsq );
332 >  boxL[0] = sqrt( dsq );
333 >  //maxCutoff = 0.5 * boxL[0];
334  
335    // boxLy
336    
337    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
338    dsq = dx*dx + dy*dy + dz*dz;
339 <  boxLy = sqrt( dsq );
339 >  boxL[1] = sqrt( dsq );
340 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341  
342 +
343    // boxLz
344    
345    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
346    dsq = dx*dx + dy*dy + dz*dz;
347 <  boxLz = sqrt( dsq );
347 >  boxL[2] = sqrt( dsq );
348 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349 >
350 >  //calculate the max cutoff
351 >  maxCutoff =  calcMaxCutOff();
352    
353 +  checkCutOffs();
354 +
355   }
356  
357  
358 + double SimInfo::calcMaxCutOff(){
359 +
360 +  double ri[3], rj[3], rk[3];
361 +  double rij[3], rjk[3], rki[3];
362 +  double minDist;
363 +
364 +  ri[0] = Hmat[0][0];
365 +  ri[1] = Hmat[1][0];
366 +  ri[2] = Hmat[2][0];
367 +
368 +  rj[0] = Hmat[0][1];
369 +  rj[1] = Hmat[1][1];
370 +  rj[2] = Hmat[2][1];
371 +
372 +  rk[0] = Hmat[0][2];
373 +  rk[1] = Hmat[1][2];
374 +  rk[2] = Hmat[2][2];
375 +  
376 +  crossProduct3(ri,rj, rij);
377 +  distXY = dotProduct3(rk,rij) / length3(rij);
378 +
379 +  crossProduct3(rj,rk, rjk);
380 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
381 +
382 +  crossProduct3(rk,ri, rki);
383 +  distZX = dotProduct3(rj,rki) / length3(rki);
384 +
385 +  minDist = min(min(distXY, distYZ), distZX);
386 +  return minDist/2;
387 +  
388 + }
389 +
390   void SimInfo::wrapVector( double thePos[3] ){
391  
392 <  int i, j, k;
392 >  int i;
393    double scaled[3];
394  
395    if( !orthoRhombic ){
# Line 337 | Line 427 | int SimInfo::getNDF(){
427  
428  
429   int SimInfo::getNDF(){
430 <  int ndf_local, ndf;
430 >  int ndf_local;
431    
432    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
433  
# Line 347 | Line 437 | int SimInfo::getNDF(){
437    ndf = ndf_local;
438   #endif
439  
440 <  ndf = ndf - 3;
440 >  ndf = ndf - 3 - nZconstraints;
441  
442    return ndf;
443   }
444  
445   int SimInfo::getNDFraw() {
446 <  int ndfRaw_local, ndfRaw;
446 >  int ndfRaw_local;
447  
448    // Raw degrees of freedom that we have to set
449    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 366 | Line 456 | int SimInfo::getNDFraw() {
456  
457    return ndfRaw;
458   }
459 <
459 >
460 > int SimInfo::getNDFtranslational() {
461 >  int ndfTrans_local;
462 >
463 >  ndfTrans_local = 3 * n_atoms - n_constraints;
464 >
465 > #ifdef IS_MPI
466 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
467 > #else
468 >  ndfTrans = ndfTrans_local;
469 > #endif
470 >
471 >  ndfTrans = ndfTrans - 3 - nZconstraints;
472 >
473 >  return ndfTrans;
474 > }
475 >
476   void SimInfo::refreshSim(){
477  
478    simtype fInfo;
479    int isError;
480    int n_global;
481    int* excl;
482 <  
377 <  fInfo.rrf = 0.0;
378 <  fInfo.rt = 0.0;
482 >
483    fInfo.dielect = 0.0;
484  
381 –  fInfo.rlist = rList;
382 –  fInfo.rcut = rCut;
383 –
485    if( useDipole ){
385 –    fInfo.rrf = ecr;
386 –    fInfo.rt = ecr - est;
486      if( useReactionField )fInfo.dielect = dielectric;
487    }
488  
# Line 429 | Line 528 | void SimInfo::refreshSim(){
528  
529    this->ndf = this->getNDF();
530    this->ndfRaw = this->getNDFraw();
531 +  this->ndfTrans = this->getNDFtranslational();
532 + }
533  
534 +
535 + void SimInfo::setRcut( double theRcut ){
536 +
537 +  rCut = theRcut;
538 +  checkCutOffs();
539   }
540  
541 + void SimInfo::setDefaultRcut( double theRcut ){
542 +
543 +  haveOrigRcut = 1;
544 +  origRcut = theRcut;
545 +  rCut = theRcut;
546 +
547 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 +
549 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550 + }
551 +
552 + void SimInfo::setEcr( double theEcr ){
553 +
554 +  ecr = theEcr;
555 +  checkCutOffs();
556 + }
557 +
558 + void SimInfo::setDefaultEcr( double theEcr ){
559 +
560 +  haveOrigEcr = 1;
561 +  origEcr = theEcr;
562 +  
563 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 +
565 +  ecr = theEcr;
566 +
567 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
568 + }
569 +
570 + void SimInfo::setEcr( double theEcr, double theEst ){
571 +
572 +  est = theEst;
573 +  setEcr( theEcr );
574 + }
575 +
576 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
577 +
578 +  est = theEst;
579 +  setDefaultEcr( theEcr );
580 + }
581 +
582 +
583 + void SimInfo::checkCutOffs( void ){
584 +
585 +  int cutChanged = 0;
586 +  
587 +  if( boxIsInit ){
588 +    
589 +    //we need to check cutOffs against the box
590 +
591 +    //detect the change of rCut
592 +    if(( maxCutoff > rCut )&&(usePBC)){
593 +      if( rCut < origRcut ){
594 +        rCut = origRcut;
595 +        
596 +        if (rCut > maxCutoff)
597 +          rCut = maxCutoff;
598 +  
599 +          sprintf( painCave.errMsg,
600 +                    "New Box size is setting the long range cutoff radius "
601 +                    "to %lf at time %lf\n",
602 +                    rCut, currentTime );
603 +          painCave.isFatal = 0;
604 +          simError();
605 +      }
606 +    }
607 +    else if ((rCut > maxCutoff)&&(usePBC)) {
608 +      sprintf( painCave.errMsg,
609 +               "New Box size is setting the long range cutoff radius "
610 +               "to %lf at time %lf\n",
611 +               maxCutoff, currentTime );
612 +      painCave.isFatal = 0;
613 +      simError();
614 +      rCut = maxCutoff;
615 +    }
616 +
617 +
618 +    //detect the change of ecr
619 +    if( maxCutoff > ecr ){
620 +      if( ecr < origEcr ){
621 +        ecr = origEcr;
622 +        if (ecr > maxCutoff) ecr = maxCutoff;
623 +  
624 +          sprintf( painCave.errMsg,
625 +                    "New Box size is setting the electrostaticCutoffRadius "
626 +                    "to %lf at time %lf\n",
627 +                    ecr, currentTime );
628 +            painCave.isFatal = 0;
629 +            simError();
630 +      }
631 +    }
632 +    else if( ecr > maxCutoff){
633 +      sprintf( painCave.errMsg,
634 +               "New Box size is setting the electrostaticCutoffRadius "
635 +               "to %lf at time %lf\n",
636 +               maxCutoff, currentTime  );
637 +      painCave.isFatal = 0;
638 +      simError();      
639 +      ecr = maxCutoff;
640 +    }
641 +
642 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
643 +    
644 +    // rlist is the 1.0 plus max( rcut, ecr )
645 +    
646 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647 +    
648 +    if( cutChanged ){
649 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650 +    }
651 +    
652 +    oldEcr = ecr;
653 +    oldRcut = rCut;
654 +    
655 +  } else {
656 +    // initialize this stuff before using it, OK?
657 +    sprintf( painCave.errMsg,
658 +             "Trying to check cutoffs without a box. Be smarter.\n" );
659 +    painCave.isFatal = 1;
660 +    simError();      
661 +  }
662 +  
663 + }
664 +
665 + void SimInfo::addProperty(GenericData* prop){
666 +
667 +  map<string, GenericData*>::iterator result;
668 +  result = properties.find(prop->getID());
669 +  
670 +  //we can't simply use  properties[prop->getID()] = prop,
671 +  //it will cause memory leak if we already contain a propery which has the same name of prop
672 +  
673 +  if(result != properties.end()){
674 +    
675 +    delete (*result).second;
676 +    (*result).second = prop;
677 +      
678 +  }
679 +  else{
680 +
681 +    properties[prop->getID()] = prop;
682 +
683 +  }
684 +    
685 + }
686 +
687 + GenericData* SimInfo::getProperty(const string& propName){
688 +
689 +  map<string, GenericData*>::iterator result;
690 +  
691 +  //string lowerCaseName = ();
692 +  
693 +  result = properties.find(propName);
694 +  
695 +  if(result != properties.end())
696 +    return (*result).second;  
697 +  else  
698 +    return NULL;  
699 + }
700 +
701 + vector<GenericData*> SimInfo::getProperties(){
702 +
703 +  vector<GenericData*> result;
704 +  map<string, GenericData*>::iterator i;
705 +  
706 +  for(i = properties.begin(); i != properties.end(); i++)
707 +    result.push_back((*i).second);
708 +    
709 +  return result;
710 + }
711 +
712 + double SimInfo::matTrace3(double m[3][3]){
713 +  double trace;
714 +  trace = m[0][0] + m[1][1] + m[2][2];
715 +
716 +  return trace;
717 + }

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