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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 642 by mmeineke, Mon Jul 21 16:23:57 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 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;
# Line 37 | Line 39 | SimInfo::SimInfo(){
39    rCut = 0.0;
40    ecr = 0.0;
41    est = 0.0;
40 –  oldEcr = 0.0;
41 –  oldRcut = 0.0;
42  
43 <  haveOrigRcut = 0;
44 <  haveOrigEcr = 0;
43 >  haveRcut = 0;
44 >  haveEcr = 0;
45    boxIsInit = 0;
46    
47 <  
47 >  resetTime = 1e99;
48  
49 +  orthoTolerance = 1E-6;
50 +  useInitXSstate = true;
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 54 | Line 57 | SimInfo::SimInfo(){
57    useGB = 0;
58    useEAM = 0;
59  
60 +  myConfiguration = new SimState();
61 +
62    wrapMeSimInfo( this );
63   }
64  
65 +
66 + SimInfo::~SimInfo(){
67 +
68 +  delete myConfiguration;
69 +
70 +  map<string, GenericData*>::iterator i;
71 +  
72 +  for(i = properties.begin(); i != properties.end(); i++)
73 +    delete (*i).second;
74 +    
75 + }
76 +
77   void SimInfo::setBox(double newBox[3]) {
78    
79    int i, j;
# Line 75 | Line 92 | void SimInfo::setBoxM( double theBox[3][3] ){
92  
93   void SimInfo::setBoxM( double theBox[3][3] ){
94    
95 <  int i, j, status;
79 <  double smallestBoxL, maxCutoff;
95 >  int i, j;
96    double FortranHmat[9]; // to preserve compatibility with Fortran the
97                           // ordering in the array is as follows:
98                           // [ 0 3 6 ]
# Line 84 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){
100                           // [ 2 5 8 ]
101    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
87 –  
103    if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
# Line 128 | Line 143 | void SimInfo::calcHmatInv( void ) {
143  
144   void SimInfo::calcHmatInv( void ) {
145    
146 +  int oldOrtho;
147    int i,j;
148    double smallDiag;
149    double tol;
# Line 135 | Line 151 | void SimInfo::calcHmatInv( void ) {
151  
152    invertMat3( Hmat, HmatInv );
153  
138 –  // Check the inverse to make sure it is sane:
139 –
140 –  matMul3( Hmat, HmatInv, sanity );
141 –    
154    // check to see if Hmat is orthorhombic
155    
156 <  smallDiag = Hmat[0][0];
145 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
146 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
147 <  tol = smallDiag * 1E-6;
156 >  oldOrtho = orthoRhombic;
157  
158 +  smallDiag = fabs(Hmat[0][0]);
159 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
160 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
161 +  tol = smallDiag * orthoTolerance;
162 +
163    orthoRhombic = 1;
164    
165    for (i = 0; i < 3; i++ ) {
166      for (j = 0 ; j < 3; j++) {
167        if (i != j) {
168          if (orthoRhombic) {
169 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
169 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
170          }        
171        }
172      }
173    }
174 +
175 +  if( oldOrtho != orthoRhombic ){
176 +    
177 +    if( orthoRhombic ){
178 +      sprintf( painCave.errMsg,
179 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
180 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
181 +               orthoTolerance);
182 +      simError();
183 +    }
184 +    else {
185 +      sprintf( painCave.errMsg,
186 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
187 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
188 +               orthoTolerance);
189 +      simError();
190 +    }
191 +  }
192   }
193  
194   double SimInfo::matDet3(double a[3][3]) {
# Line 261 | Line 293 | void SimInfo::printMat9(double A[9] ){
293              << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
294              << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
295              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
296 + }
297 +
298 +
299 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
300 +
301 +      out[0] = a[1] * b[2] - a[2] * b[1];
302 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
303 +      out[2] = a[0] * b[1] - a[1] * b[0];
304 +      
305 + }
306 +
307 + double SimInfo::dotProduct3(double a[3], double b[3]){
308 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
309 + }
310 +
311 + double SimInfo::length3(double a[3]){
312 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
313   }
314  
315   void SimInfo::calcBoxL( void ){
316  
317    double dx, dy, dz, dsq;
269 –  int i;
318  
319    // boxVol = Determinant of Hmat
320  
# Line 277 | Line 325 | void SimInfo::calcBoxL( void ){
325    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
326    dsq = dx*dx + dy*dy + dz*dz;
327    boxL[0] = sqrt( dsq );
328 <  maxCutoff = 0.5 * boxL[0];
328 >  //maxCutoff = 0.5 * boxL[0];
329  
330    // boxLy
331    
332    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
333    dsq = dx*dx + dy*dy + dz*dz;
334    boxL[1] = sqrt( dsq );
335 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
335 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
336  
337 +
338    // boxLz
339    
340    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
341    dsq = dx*dx + dy*dy + dz*dz;
342    boxL[2] = sqrt( dsq );
343 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
343 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
344  
345 +  //calculate the max cutoff
346 +  maxCutoff =  calcMaxCutOff();
347 +  
348 +  checkCutOffs();
349 +
350   }
351  
352  
353 + double SimInfo::calcMaxCutOff(){
354 +
355 +  double ri[3], rj[3], rk[3];
356 +  double rij[3], rjk[3], rki[3];
357 +  double minDist;
358 +
359 +  ri[0] = Hmat[0][0];
360 +  ri[1] = Hmat[1][0];
361 +  ri[2] = Hmat[2][0];
362 +
363 +  rj[0] = Hmat[0][1];
364 +  rj[1] = Hmat[1][1];
365 +  rj[2] = Hmat[2][1];
366 +
367 +  rk[0] = Hmat[0][2];
368 +  rk[1] = Hmat[1][2];
369 +  rk[2] = Hmat[2][2];
370 +  
371 +  crossProduct3(ri,rj, rij);
372 +  distXY = dotProduct3(rk,rij) / length3(rij);
373 +
374 +  crossProduct3(rj,rk, rjk);
375 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
376 +
377 +  crossProduct3(rk,ri, rki);
378 +  distZX = dotProduct3(rj,rki) / length3(rki);
379 +
380 +  minDist = min(min(distXY, distYZ), distZX);
381 +  return minDist/2;
382 +  
383 + }
384 +
385   void SimInfo::wrapVector( double thePos[3] ){
386  
387 <  int i, j, k;
387 >  int i;
388    double scaled[3];
389  
390    if( !orthoRhombic ){
# Line 336 | Line 422 | int SimInfo::getNDF(){
422  
423  
424   int SimInfo::getNDF(){
425 <  int ndf_local, ndf;
425 >  int ndf_local;
426    
427    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
428  
# Line 346 | Line 432 | int SimInfo::getNDF(){
432    ndf = ndf_local;
433   #endif
434  
435 <  ndf = ndf - 3;
435 >  ndf = ndf - 3 - nZconstraints;
436  
437    return ndf;
438   }
439  
440   int SimInfo::getNDFraw() {
441 <  int ndfRaw_local, ndfRaw;
441 >  int ndfRaw_local;
442  
443    // Raw degrees of freedom that we have to set
444    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 451 | int SimInfo::getNDFraw() {
451  
452    return ndfRaw;
453   }
454 <
454 >
455 > int SimInfo::getNDFtranslational() {
456 >  int ndfTrans_local;
457 >
458 >  ndfTrans_local = 3 * n_atoms - n_constraints;
459 >
460 > #ifdef IS_MPI
461 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
462 > #else
463 >  ndfTrans = ndfTrans_local;
464 > #endif
465 >
466 >  ndfTrans = ndfTrans - 3 - nZconstraints;
467 >
468 >  return ndfTrans;
469 > }
470 >
471   void SimInfo::refreshSim(){
472  
473    simtype fInfo;
# Line 421 | Line 523 | void SimInfo::refreshSim(){
523  
524    this->ndf = this->getNDF();
525    this->ndfRaw = this->getNDFraw();
526 <
526 >  this->ndfTrans = this->getNDFtranslational();
527   }
528  
529 <
428 < void SimInfo::setRcut( double theRcut ){
429 <
430 <  if( !haveOrigRcut ){
431 <    haveOrigRcut = 1;
432 <    origRcut = theRcut;
433 <  }
529 > void SimInfo::setDefaultRcut( double theRcut ){
530  
531 +  haveRcut = 1;
532    rCut = theRcut;
533 <  checkCutOffs();
533 >
534 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535 >
536 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537   }
538  
539 < void SimInfo::setEcr( double theEcr ){
539 > void SimInfo::setDefaultEcr( double theEcr ){
540  
541 <  if( !haveOrigEcr ){
542 <    haveOrigEcr = 1;
543 <    origEcr = theEcr;
444 <  }
541 >  haveEcr = 1;
542 >  
543 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544  
545    ecr = theEcr;
546 <  checkCutOffs();
546 >
547 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548   }
549  
550 < void SimInfo::setEcr( double theEcr, double theEst ){
550 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551  
552    est = theEst;
553 <  setEcr( theEcr );
553 >  setDefaultEcr( theEcr );
554   }
555  
556  
557   void SimInfo::checkCutOffs( void ){
558 <
459 <  int cutChanged = 0;
460 <
558 >  
559    if( boxIsInit ){
560      
561      //we need to check cutOffs against the box
562      
563 <    if( maxCutoff > rCut ){
564 <      if( rCut < origRcut ){
565 <        rCut = origRcut;
566 <        if (rCut > maxCutoff) rCut = maxCutoff;
567 <        
568 <        sprintf( painCave.errMsg,
569 <                 "New Box size is setting the long range cutoff radius "
472 <                 "to %lf\n",
473 <                 rCut );
474 <        painCave.isFatal = 0;
475 <        simError();
476 <      }
563 >    if( rCut > maxCutoff ){
564 >      sprintf( painCave.errMsg,
565 >               "Box size is too small for the long range cutoff radius, "
566 >               "%lf, at time %lf\n",
567 >               rCut, currentTime );
568 >      painCave.isFatal = 1;
569 >      simError();
570      }
571 <
572 <    if( maxCutoff > ecr ){
573 <      if( ecr < origEcr ){
481 <        rCut = origEcr;
482 <        if (ecr > maxCutoff) ecr = maxCutoff;
483 <        
571 >    
572 >    if( haveEcr ){
573 >      if( ecr > maxCutoff ){
574          sprintf( painCave.errMsg,
575 <                 "New Box size is setting the electrostaticCutoffRadius "
576 <                 "to %lf\n",
577 <                 ecr );
578 <        painCave.isFatal = 0;
575 >                 "Box size is too small for the electrostatic cutoff radius, "
576 >                 "%lf, at time %lf\n",
577 >                 ecr, currentTime );
578 >        painCave.isFatal = 1;
579          simError();
580        }
581      }
582 +  } else {
583 +    // initialize this stuff before using it, OK?
584 +    sprintf( painCave.errMsg,
585 +             "Trying to check cutoffs without a box. Be smarter.\n" );
586 +    painCave.isFatal = 1;
587 +    simError();      
588 +  }
589 +  
590 + }
591  
592 + void SimInfo::addProperty(GenericData* prop){
593  
594 <    if (rCut > maxCutoff) {
595 <      sprintf( painCave.errMsg,
596 <               "New Box size is setting the long range cutoff radius "
597 <               "to %lf\n",
598 <               maxCutoff );
599 <      painCave.isFatal = 0;
600 <      simError();
501 <      rCut = maxCutoff;
502 <    }
503 <
504 <    if( ecr > maxCutoff){
505 <      sprintf( painCave.errMsg,
506 <               "New Box size is setting the electrostaticCutoffRadius "
507 <               "to %lf\n",
508 <               maxCutoff  );
509 <      painCave.isFatal = 0;
510 <      simError();      
511 <      ecr = maxCutoff;
512 <    }
513 <
594 >  map<string, GenericData*>::iterator result;
595 >  result = properties.find(prop->getID());
596 >  
597 >  //we can't simply use  properties[prop->getID()] = prop,
598 >  //it will cause memory leak if we already contain a propery which has the same name of prop
599 >  
600 >  if(result != properties.end()){
601      
602 +    delete (*result).second;
603 +    (*result).second = prop;
604 +      
605    }
606 <  
606 >  else{
607  
608 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
608 >    properties[prop->getID()] = prop;
609  
610 <  // rlist is the 1.0 plus max( rcut, ecr )
610 >  }
611 >    
612 > }
613 >
614 > GenericData* SimInfo::getProperty(const string& propName){
615 >
616 >  map<string, GenericData*>::iterator result;
617    
618 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
618 >  //string lowerCaseName = ();
619 >  
620 >  result = properties.find(propName);
621 >  
622 >  if(result != properties.end())
623 >    return (*result).second;  
624 >  else  
625 >    return NULL;  
626 > }
627  
628 <  if( cutChanged ){
628 > vector<GenericData*> SimInfo::getProperties(){
629 >
630 >  vector<GenericData*> result;
631 >  map<string, GenericData*>::iterator i;
632 >  
633 >  for(i = properties.begin(); i != properties.end(); i++)
634 >    result.push_back((*i).second);
635      
636 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
637 <  }
636 >  return result;
637 > }
638  
639 <  oldEcr = ecr;
640 <  oldRcut = rCut;
639 > double SimInfo::matTrace3(double m[3][3]){
640 >  double trace;
641 >  trace = m[0][0] + m[1][1] + m[2][2];
642 >
643 >  return trace;
644   }

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