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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 941 by gezelter, Tue Jan 13 23:01:43 2004 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 20 | Line 20 | inline double roundMe( double x ){
20    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21   }
22            
23 + inline double min( double a, double b ){
24 +  return (a < b ) ? a : b;
25 + }
26  
27   SimInfo* currentInfo;
28  
29   SimInfo::SimInfo(){
30    excludes = NULL;
31    n_constraints = 0;
32 +  nZconstraints = 0;
33    n_oriented = 0;
34    n_dipoles = 0;
35    ndf = 0;
36    ndfRaw = 0;
37 +  nZconstraints = 0;
38    the_integrator = NULL;
39    setTemp = 0;
40    thermalTime = 0.0;
# Line 37 | Line 42 | SimInfo::SimInfo(){
42    rCut = 0.0;
43    ecr = 0.0;
44    est = 0.0;
40 –  oldEcr = 0.0;
41 –  oldRcut = 0.0;
45  
46 <  haveOrigRcut = 0;
47 <  haveOrigEcr = 0;
46 >  haveRcut = 0;
47 >  haveEcr = 0;
48    boxIsInit = 0;
49    
50 <  
50 >  resetTime = 1e99;
51  
52 +  orthoTolerance = 1E-6;
53 +  useInitXSstate = true;
54 +
55    usePBC = 0;
56    useLJ = 0;
57    useSticky = 0;
58 <  useDipole = 0;
58 >  useCharges = 0;
59 >  useDipoles = 0;
60    useReactionField = 0;
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 75 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){
96  
97   void SimInfo::setBoxM( double theBox[3][3] ){
98    
99 <  int i, j, status;
79 <  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 84 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){
104                           // [ 2 5 8 ]
105    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106  
87 –  
107    if( !boxIsInit ) boxIsInit = 1;
108  
109    for(i=0; i < 3; i++)
# Line 128 | Line 147 | void SimInfo::calcHmatInv( void ) {
147  
148   void SimInfo::calcHmatInv( void ) {
149    
150 +  int oldOrtho;
151    int i,j;
152    double smallDiag;
153    double tol;
# Line 135 | Line 155 | void SimInfo::calcHmatInv( void ) {
155  
156    invertMat3( Hmat, HmatInv );
157  
138 –  // Check the inverse to make sure it is sane:
139 –
140 –  matMul3( Hmat, HmatInv, sanity );
141 –    
158    // check to see if Hmat is orthorhombic
159    
160 <  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;
160 >  oldOrtho = orthoRhombic;
161  
162 +  smallDiag = fabs(Hmat[0][0]);
163 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
164 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
165 +  tol = smallDiag * orthoTolerance;
166 +
167    orthoRhombic = 1;
168    
169    for (i = 0; i < 3; i++ ) {
170      for (j = 0 ; j < 3; j++) {
171        if (i != j) {
172          if (orthoRhombic) {
173 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
173 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
174          }        
175        }
176      }
177    }
178 +
179 +  if( oldOrtho != orthoRhombic ){
180 +    
181 +    if( orthoRhombic ){
182 +      sprintf( painCave.errMsg,
183 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
184 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
185 +               orthoTolerance);
186 +      simError();
187 +    }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
192 +               orthoTolerance);
193 +      simError();
194 +    }
195 +  }
196   }
197  
198   double SimInfo::matDet3(double a[3][3]) {
# Line 263 | Line 299 | void SimInfo::printMat9(double A[9] ){
299              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300   }
301  
302 +
303 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
304 +
305 +      out[0] = a[1] * b[2] - a[2] * b[1];
306 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
307 +      out[2] = a[0] * b[1] - a[1] * b[0];
308 +      
309 + }
310 +
311 + double SimInfo::dotProduct3(double a[3], double b[3]){
312 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
313 + }
314 +
315 + double SimInfo::length3(double a[3]){
316 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
317 + }
318 +
319   void SimInfo::calcBoxL( void ){
320  
321    double dx, dy, dz, dsq;
269 –  int i;
322  
323    // boxVol = Determinant of Hmat
324  
# Line 277 | Line 329 | void SimInfo::calcBoxL( void ){
329    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
330    dsq = dx*dx + dy*dy + dz*dz;
331    boxL[0] = sqrt( dsq );
332 <  maxCutoff = 0.5 * boxL[0];
332 >  //maxCutoff = 0.5 * boxL[0];
333  
334    // boxLy
335    
336    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
337    dsq = dx*dx + dy*dy + dz*dz;
338    boxL[1] = sqrt( dsq );
339 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
339 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
340  
341 +
342    // boxLz
343    
344    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
345    dsq = dx*dx + dy*dy + dz*dz;
346    boxL[2] = sqrt( dsq );
347 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
347 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
348  
349 +  //calculate the max cutoff
350 +  maxCutoff =  calcMaxCutOff();
351 +  
352 +  checkCutOffs();
353 +
354   }
355  
356  
357 + double SimInfo::calcMaxCutOff(){
358 +
359 +  double ri[3], rj[3], rk[3];
360 +  double rij[3], rjk[3], rki[3];
361 +  double minDist;
362 +
363 +  ri[0] = Hmat[0][0];
364 +  ri[1] = Hmat[1][0];
365 +  ri[2] = Hmat[2][0];
366 +
367 +  rj[0] = Hmat[0][1];
368 +  rj[1] = Hmat[1][1];
369 +  rj[2] = Hmat[2][1];
370 +
371 +  rk[0] = Hmat[0][2];
372 +  rk[1] = Hmat[1][2];
373 +  rk[2] = Hmat[2][2];
374 +  
375 +  crossProduct3(ri,rj, rij);
376 +  distXY = dotProduct3(rk,rij) / length3(rij);
377 +
378 +  crossProduct3(rj,rk, rjk);
379 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
380 +
381 +  crossProduct3(rk,ri, rki);
382 +  distZX = dotProduct3(rj,rki) / length3(rki);
383 +
384 +  minDist = min(min(distXY, distYZ), distZX);
385 +  return minDist/2;
386 +  
387 + }
388 +
389   void SimInfo::wrapVector( double thePos[3] ){
390  
391 <  int i, j, k;
391 >  int i;
392    double scaled[3];
393  
394    if( !orthoRhombic ){
# Line 336 | Line 426 | int SimInfo::getNDF(){
426  
427  
428   int SimInfo::getNDF(){
429 <  int ndf_local, ndf;
429 >  int ndf_local;
430    
431    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
432  
# Line 346 | Line 436 | int SimInfo::getNDF(){
436    ndf = ndf_local;
437   #endif
438  
439 <  ndf = ndf - 3;
439 >  ndf = ndf - 3 - nZconstraints;
440  
441    return ndf;
442   }
443  
444   int SimInfo::getNDFraw() {
445 <  int ndfRaw_local, ndfRaw;
445 >  int ndfRaw_local;
446  
447    // Raw degrees of freedom that we have to set
448    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 455 | int SimInfo::getNDFraw() {
455  
456    return ndfRaw;
457   }
458 <
458 >
459 > int SimInfo::getNDFtranslational() {
460 >  int ndfTrans_local;
461 >
462 >  ndfTrans_local = 3 * n_atoms - n_constraints;
463 >
464 > #ifdef IS_MPI
465 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
466 > #else
467 >  ndfTrans = ndfTrans_local;
468 > #endif
469 >
470 >  ndfTrans = ndfTrans - 3 - nZconstraints;
471 >
472 >  return ndfTrans;
473 > }
474 >
475   void SimInfo::refreshSim(){
476  
477    simtype fInfo;
# Line 375 | Line 481 | void SimInfo::refreshSim(){
481  
482    fInfo.dielect = 0.0;
483  
484 <  if( useDipole ){
484 >  if( useDipoles ){
485      if( useReactionField )fInfo.dielect = dielectric;
486    }
487  
# Line 384 | Line 490 | void SimInfo::refreshSim(){
490    fInfo.SIM_uses_LJ = useLJ;
491    fInfo.SIM_uses_sticky = useSticky;
492    //fInfo.SIM_uses_sticky = 0;
493 <  fInfo.SIM_uses_dipoles = useDipole;
493 >  fInfo.SIM_uses_charges = useCharges;
494 >  fInfo.SIM_uses_dipoles = useDipoles;
495    //fInfo.SIM_uses_dipoles = 0;
496    //fInfo.SIM_uses_RF = useReactionField;
497    fInfo.SIM_uses_RF = 0;
# Line 421 | Line 528 | void SimInfo::refreshSim(){
528  
529    this->ndf = this->getNDF();
530    this->ndfRaw = this->getNDFraw();
531 <
531 >  this->ndfTrans = this->getNDFtranslational();
532   }
533  
534 <
428 < void SimInfo::setRcut( double theRcut ){
429 <
430 <  if( !haveOrigRcut ){
431 <    haveOrigRcut = 1;
432 <    origRcut = theRcut;
433 <  }
534 > void SimInfo::setDefaultRcut( double theRcut ){
535  
536 +  haveRcut = 1;
537    rCut = theRcut;
436 –  checkCutOffs();
437 – }
538  
539 < void SimInfo::setEcr( double theEcr ){
539 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
540  
541 <  if( !haveOrigEcr ){
542 <    haveOrigEcr = 1;
443 <    origEcr = theEcr;
444 <  }
541 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
542 > }
543  
544 + void SimInfo::setDefaultEcr( double theEcr ){
545 +
546 +  haveEcr = 1;
547    ecr = theEcr;
548 <  checkCutOffs();
548 >  
549 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
550 >
551 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
552   }
553  
554 < void SimInfo::setEcr( double theEcr, double theEst ){
554 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555  
556    est = theEst;
557 <  setEcr( theEcr );
557 >  setDefaultEcr( theEcr );
558   }
559  
560  
561   void SimInfo::checkCutOffs( void ){
562 <
459 <  int cutChanged = 0;
460 <
562 >  
563    if( boxIsInit ){
564      
565      //we need to check cutOffs against the box
566      
567 <    if( maxCutoff > rCut ){
568 <      if( rCut < origRcut ){
569 <        rCut = origRcut;
570 <        if (rCut > maxCutoff) rCut = maxCutoff;
571 <        
572 <        sprintf( painCave.errMsg,
573 <                 "New Box size is setting the long range cutoff radius "
574 <                 "to %lf\n",
575 <                 rCut );
576 <        painCave.isFatal = 0;
577 <        simError();
578 <      }
567 >    if( rCut > maxCutoff ){
568 >      sprintf( painCave.errMsg,
569 >               "Box size is too small for the long range cutoff radius, "
570 >               "%G, at time %G\n"
571 >               "  [ %G %G %G ]\n"
572 >               "  [ %G %G %G ]\n"
573 >               "  [ %G %G %G ]\n",
574 >               rCut, currentTime,
575 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
576 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
577 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
578 >      painCave.isFatal = 1;
579 >      simError();
580      }
581 <
582 <    if( maxCutoff > ecr ){
583 <      if( ecr < origEcr ){
481 <        rCut = origEcr;
482 <        if (ecr > maxCutoff) ecr = maxCutoff;
483 <        
581 >    
582 >    if( haveEcr ){
583 >      if( ecr > maxCutoff ){
584          sprintf( painCave.errMsg,
585 <                 "New Box size is setting the electrostaticCutoffRadius "
586 <                 "to %lf\n",
587 <                 ecr );
588 <        painCave.isFatal = 0;
585 >                 "Box size is too small for the electrostatic cutoff radius, "
586 >                 "%G, at time %G\n"
587 >                 "  [ %G %G %G ]\n"
588 >                 "  [ %G %G %G ]\n"
589 >                 "  [ %G %G %G ]\n",
590 >                 ecr, currentTime,
591 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
592 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
593 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
594 >        painCave.isFatal = 1;
595          simError();
596        }
597      }
598 +  } else {
599 +    // initialize this stuff before using it, OK?
600 +    sprintf( painCave.errMsg,
601 +             "Trying to check cutoffs without a box. Be smarter.\n" );
602 +    painCave.isFatal = 1;
603 +    simError();      
604 +  }
605 +  
606 + }
607  
608 + void SimInfo::addProperty(GenericData* prop){
609  
610 <    if (rCut > maxCutoff) {
611 <      sprintf( painCave.errMsg,
612 <               "New Box size is setting the long range cutoff radius "
613 <               "to %lf\n",
614 <               maxCutoff );
615 <      painCave.isFatal = 0;
616 <      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 <
610 >  map<string, GenericData*>::iterator result;
611 >  result = properties.find(prop->getID());
612 >  
613 >  //we can't simply use  properties[prop->getID()] = prop,
614 >  //it will cause memory leak if we already contain a propery which has the same name of prop
615 >  
616 >  if(result != properties.end()){
617      
618 +    delete (*result).second;
619 +    (*result).second = prop;
620 +      
621    }
622 <  
622 >  else{
623  
624 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
624 >    properties[prop->getID()] = prop;
625  
626 <  // rlist is the 1.0 plus max( rcut, ecr )
626 >  }
627 >    
628 > }
629 >
630 > GenericData* SimInfo::getProperty(const string& propName){
631 >
632 >  map<string, GenericData*>::iterator result;
633    
634 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
634 >  //string lowerCaseName = ();
635 >  
636 >  result = properties.find(propName);
637 >  
638 >  if(result != properties.end())
639 >    return (*result).second;  
640 >  else  
641 >    return NULL;  
642 > }
643  
644 <  if( cutChanged ){
644 > vector<GenericData*> SimInfo::getProperties(){
645 >
646 >  vector<GenericData*> result;
647 >  map<string, GenericData*>::iterator i;
648 >  
649 >  for(i = properties.begin(); i != properties.end(); i++)
650 >    result.push_back((*i).second);
651      
652 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
653 <  }
652 >  return result;
653 > }
654  
655 <  oldEcr = ecr;
656 <  oldRcut = rCut;
655 > double SimInfo::matTrace3(double m[3][3]){
656 >  double trace;
657 >  trace = m[0][0] + m[1][1] + m[2][2];
658 >
659 >  return trace;
660   }

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