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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 999 by chrisfen, Fri Jan 30 15:01:09 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 Box.\n"
184 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
185 +               "\tvariable ( currently set to %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188 +    }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
192 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
193 +               "\tvariable ( currently set to %G ).\n",
194 +               orthoTolerance);
195 +      simError();
196 +    }
197 +  }
198   }
199  
200   double SimInfo::matDet3(double a[3][3]) {
# Line 263 | Line 301 | void SimInfo::calcBoxL( void ){
301              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
302   }
303  
304 +
305 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
306 +
307 +      out[0] = a[1] * b[2] - a[2] * b[1];
308 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
309 +      out[2] = a[0] * b[1] - a[1] * b[0];
310 +      
311 + }
312 +
313 + double SimInfo::dotProduct3(double a[3], double b[3]){
314 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
315 + }
316 +
317 + double SimInfo::length3(double a[3]){
318 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
319 + }
320 +
321   void SimInfo::calcBoxL( void ){
322  
323    double dx, dy, dz, dsq;
269 –  int i;
324  
325    // boxVol = Determinant of Hmat
326  
# Line 277 | Line 331 | void SimInfo::calcBoxL( void ){
331    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
332    dsq = dx*dx + dy*dy + dz*dz;
333    boxL[0] = sqrt( dsq );
334 <  maxCutoff = 0.5 * boxL[0];
334 >  //maxCutoff = 0.5 * boxL[0];
335  
336    // boxLy
337    
338    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
339    dsq = dx*dx + dy*dy + dz*dz;
340    boxL[1] = sqrt( dsq );
341 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
342  
343 +
344    // boxLz
345    
346    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
347    dsq = dx*dx + dy*dy + dz*dz;
348    boxL[2] = sqrt( dsq );
349 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
350  
351 +  //calculate the max cutoff
352 +  maxCutoff =  calcMaxCutOff();
353 +  
354 +  checkCutOffs();
355 +
356   }
357  
358  
359 + double SimInfo::calcMaxCutOff(){
360 +
361 +  double ri[3], rj[3], rk[3];
362 +  double rij[3], rjk[3], rki[3];
363 +  double minDist;
364 +
365 +  ri[0] = Hmat[0][0];
366 +  ri[1] = Hmat[1][0];
367 +  ri[2] = Hmat[2][0];
368 +
369 +  rj[0] = Hmat[0][1];
370 +  rj[1] = Hmat[1][1];
371 +  rj[2] = Hmat[2][1];
372 +
373 +  rk[0] = Hmat[0][2];
374 +  rk[1] = Hmat[1][2];
375 +  rk[2] = Hmat[2][2];
376 +  
377 +  crossProduct3(ri,rj, rij);
378 +  distXY = dotProduct3(rk,rij) / length3(rij);
379 +
380 +  crossProduct3(rj,rk, rjk);
381 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
382 +
383 +  crossProduct3(rk,ri, rki);
384 +  distZX = dotProduct3(rj,rki) / length3(rki);
385 +
386 +  minDist = min(min(distXY, distYZ), distZX);
387 +  return minDist/2;
388 +  
389 + }
390 +
391   void SimInfo::wrapVector( double thePos[3] ){
392  
393 <  int i, j, k;
393 >  int i;
394    double scaled[3];
395  
396    if( !orthoRhombic ){
# Line 336 | Line 428 | int SimInfo::getNDF(){
428  
429  
430   int SimInfo::getNDF(){
431 <  int ndf_local, ndf;
431 >  int ndf_local;
432    
433    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
434  
# Line 346 | Line 438 | int SimInfo::getNDF(){
438    ndf = ndf_local;
439   #endif
440  
441 <  ndf = ndf - 3;
441 >  ndf = ndf - 3 - nZconstraints;
442  
443    return ndf;
444   }
445  
446   int SimInfo::getNDFraw() {
447 <  int ndfRaw_local, ndfRaw;
447 >  int ndfRaw_local;
448  
449    // Raw degrees of freedom that we have to set
450    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 365 | Line 457 | int SimInfo::getNDFraw() {
457  
458    return ndfRaw;
459   }
460 <
460 >
461 > int SimInfo::getNDFtranslational() {
462 >  int ndfTrans_local;
463 >
464 >  ndfTrans_local = 3 * n_atoms - n_constraints;
465 >
466 > #ifdef IS_MPI
467 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
468 > #else
469 >  ndfTrans = ndfTrans_local;
470 > #endif
471 >
472 >  ndfTrans = ndfTrans - 3 - nZconstraints;
473 >
474 >  return ndfTrans;
475 > }
476 >
477   void SimInfo::refreshSim(){
478  
479    simtype fInfo;
# Line 375 | Line 483 | void SimInfo::refreshSim(){
483  
484    fInfo.dielect = 0.0;
485  
486 <  if( useDipole ){
486 >  if( useDipoles ){
487      if( useReactionField )fInfo.dielect = dielectric;
488    }
489  
# Line 384 | Line 492 | void SimInfo::refreshSim(){
492    fInfo.SIM_uses_LJ = useLJ;
493    fInfo.SIM_uses_sticky = useSticky;
494    //fInfo.SIM_uses_sticky = 0;
495 <  fInfo.SIM_uses_dipoles = useDipole;
495 >  fInfo.SIM_uses_charges = useCharges;
496 >  fInfo.SIM_uses_dipoles = useDipoles;
497    //fInfo.SIM_uses_dipoles = 0;
498 <  //fInfo.SIM_uses_RF = useReactionField;
499 <  fInfo.SIM_uses_RF = 0;
498 >  fInfo.SIM_uses_RF = useReactionField;
499 >  //fInfo.SIM_uses_RF = 0;
500    fInfo.SIM_uses_GB = useGB;
501    fInfo.SIM_uses_EAM = useEAM;
502  
# Line 421 | Line 530 | void SimInfo::refreshSim(){
530  
531    this->ndf = this->getNDF();
532    this->ndfRaw = this->getNDFraw();
533 <
533 >  this->ndfTrans = this->getNDFtranslational();
534   }
535  
536 + void SimInfo::setDefaultRcut( double theRcut ){
537  
538 < void SimInfo::setRcut( double theRcut ){
538 >  haveRcut = 1;
539 >  rCut = theRcut;
540  
541 <  if( !haveOrigRcut ){
431 <    haveOrigRcut = 1;
432 <    origRcut = theRcut;
433 <  }
541 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542  
543 <  rCut = theRcut;
436 <  checkCutOffs();
543 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
544   }
545  
546 < void SimInfo::setEcr( double theEcr ){
546 > void SimInfo::setDefaultEcr( double theEcr ){
547  
548 <  if( !haveOrigEcr ){
442 <    haveOrigEcr = 1;
443 <    origEcr = theEcr;
444 <  }
445 <
548 >  haveEcr = 1;
549    ecr = theEcr;
550 <  checkCutOffs();
550 >  
551 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
552 >
553 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
554   }
555  
556 < void SimInfo::setEcr( double theEcr, double theEst ){
556 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
557  
558    est = theEst;
559 <  setEcr( theEcr );
559 >  setDefaultEcr( theEcr );
560   }
561  
562  
563   void SimInfo::checkCutOffs( void ){
564 <
459 <  int cutChanged = 0;
460 <
564 >  
565    if( boxIsInit ){
566      
567      //we need to check cutOffs against the box
568      
569 <    if( maxCutoff > rCut ){
570 <      if( rCut < origRcut ){
571 <        rCut = origRcut;
572 <        if (rCut > maxCutoff) rCut = maxCutoff;
573 <        
574 <        sprintf( painCave.errMsg,
575 <                 "New Box size is setting the long range cutoff radius "
576 <                 "to %lf\n",
577 <                 rCut );
578 <        painCave.isFatal = 0;
579 <        simError();
580 <      }
569 >    if( rCut > maxCutoff ){
570 >      sprintf( painCave.errMsg,
571 >               "Box size is too small for the long range cutoff radius, "
572 >               "%G, at time %G\n"
573 >               "\t[ %G %G %G ]\n"
574 >               "\t[ %G %G %G ]\n"
575 >               "\t[ %G %G %G ]\n",
576 >               rCut, currentTime,
577 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
578 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
579 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
580 >      painCave.isFatal = 1;
581 >      simError();
582      }
583 <
584 <    if( maxCutoff > ecr ){
585 <      if( ecr < origEcr ){
481 <        rCut = origEcr;
482 <        if (ecr > maxCutoff) ecr = maxCutoff;
483 <        
583 >    
584 >    if( haveEcr ){
585 >      if( ecr > maxCutoff ){
586          sprintf( painCave.errMsg,
587 <                 "New Box size is setting the electrostaticCutoffRadius "
588 <                 "to %lf\n",
589 <                 ecr );
590 <        painCave.isFatal = 0;
587 >                 "Box size is too small for the electrostatic cutoff radius, "
588 >                 "%G, at time %G\n"
589 >                 "\t[ %G %G %G ]\n"
590 >                 "\t[ %G %G %G ]\n"
591 >                 "\t[ %G %G %G ]\n",
592 >                 ecr, currentTime,
593 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
594 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
595 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
596 >        painCave.isFatal = 1;
597          simError();
598        }
599      }
600 +  } else {
601 +    // initialize this stuff before using it, OK?
602 +    sprintf( painCave.errMsg,
603 +             "Trying to check cutoffs without a box.\n"
604 +             "\tOOPSE should have better programmers than that.\n" );
605 +    painCave.isFatal = 1;
606 +    simError();      
607 +  }
608 +  
609 + }
610  
611 + void SimInfo::addProperty(GenericData* prop){
612  
613 <    if (rCut > maxCutoff) {
614 <      sprintf( painCave.errMsg,
615 <               "New Box size is setting the long range cutoff radius "
616 <               "to %lf\n",
617 <               maxCutoff );
618 <      painCave.isFatal = 0;
619 <      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 <
613 >  map<string, GenericData*>::iterator result;
614 >  result = properties.find(prop->getID());
615 >  
616 >  //we can't simply use  properties[prop->getID()] = prop,
617 >  //it will cause memory leak if we already contain a propery which has the same name of prop
618 >  
619 >  if(result != properties.end()){
620      
621 +    delete (*result).second;
622 +    (*result).second = prop;
623 +      
624    }
625 <  
625 >  else{
626  
627 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
627 >    properties[prop->getID()] = prop;
628  
629 <  // rlist is the 1.0 plus max( rcut, ecr )
629 >  }
630 >    
631 > }
632 >
633 > GenericData* SimInfo::getProperty(const string& propName){
634 >
635 >  map<string, GenericData*>::iterator result;
636    
637 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
637 >  //string lowerCaseName = ();
638 >  
639 >  result = properties.find(propName);
640 >  
641 >  if(result != properties.end())
642 >    return (*result).second;  
643 >  else  
644 >    return NULL;  
645 > }
646  
647 <  if( cutChanged ){
647 > vector<GenericData*> SimInfo::getProperties(){
648 >
649 >  vector<GenericData*> result;
650 >  map<string, GenericData*>::iterator i;
651 >  
652 >  for(i = properties.begin(); i != properties.end(); i++)
653 >    result.push_back((*i).second);
654      
655 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
656 <  }
655 >  return result;
656 > }
657  
658 <  oldEcr = ecr;
659 <  oldRcut = rCut;
658 > double SimInfo::matTrace3(double m[3][3]){
659 >  double trace;
660 >  trace = m[0][0] + m[1][1] + m[2][2];
661 >
662 >  return trace;
663   }

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