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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 669 by chuckv, Thu Aug 7 00:47:33 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 <
67 <  
74 >    
75   }
76  
77   void SimInfo::setBox(double newBox[3]) {
# Line 85 | Line 92 | void SimInfo::setBoxM( double theBox[3][3] ){
92  
93   void SimInfo::setBoxM( double theBox[3][3] ){
94    
95 <  int i, j, status;
89 <  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 94 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){
100                           // [ 2 5 8 ]
101    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
97 –  
103    if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
# Line 138 | 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 145 | Line 151 | void SimInfo::calcHmatInv( void ) {
151  
152    invertMat3( Hmat, HmatInv );
153  
148 –  // Check the inverse to make sure it is sane:
149 –
150 –  matMul3( Hmat, HmatInv, sanity );
151 –    
154    // check to see if Hmat is orthorhombic
155    
156 <  smallDiag = Hmat[0][0];
155 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
156 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
157 <  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 273 | Line 295 | void SimInfo::printMat9(double A[9] ){
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;
279 –  int i;
318  
319    // boxVol = Determinant of Hmat
320  
# Line 287 | 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 348 | 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 358 | 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 377 | 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 433 | 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 + void SimInfo::setDefaultRcut( double theRcut ){
530  
531 < void SimInfo::setRcut( double theRcut ){
531 >  haveRcut = 1;
532 >  rCut = theRcut;
533  
534 <  if( !haveOrigRcut ){
443 <    haveOrigRcut = 1;
444 <    origRcut = theRcut;
445 <  }
534 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535  
536 <  rCut = theRcut;
448 <  checkCutOffs();
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;
456 <  }
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 <
471 <  int cutChanged = 0;
472 <
473 <
474 <
558 >  
559    if( boxIsInit ){
560      
561      //we need to check cutOffs against the box
562 <  
563 <    if(( maxCutoff > rCut )&&(usePBC)){
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 "
486 <                 "to %lf\n",
487 <                 rCut );
488 <        painCave.isFatal = 0;
489 <        simError();
490 <      }
562 >    
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 ){
495 <        rCut = origEcr;
496 <        if (ecr > maxCutoff) ecr = maxCutoff;
497 <        
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 <
583 <
584 <    if ((rCut > maxCutoff)&&(usePBC)) {
585 <      sprintf( painCave.errMsg,
586 <               "New Box size is setting the long range cutoff radius "
587 <               "to %lf\n",
512 <               maxCutoff );
513 <      painCave.isFatal = 0;
514 <      simError();
515 <      rCut = maxCutoff;
516 <    }
517 <
518 <    if( ecr > maxCutoff){
519 <      sprintf( painCave.errMsg,
520 <               "New Box size is setting the electrostaticCutoffRadius "
521 <               "to %lf\n",
522 <               maxCutoff  );
523 <      painCave.isFatal = 0;
524 <      simError();      
525 <      ecr = maxCutoff;
526 <    }
527 <
528 <    
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    }
530 –  
531 –
532 –  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
533 –
534 –  // rlist is the 1.0 plus max( rcut, ecr )
589    
536 –  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
537 –
538 –  if( cutChanged ){
539 –    
540 –    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
541 –  }
542 –
543 –  oldEcr = ecr;
544 –  oldRcut = rCut;
590   }
591  
592   void SimInfo::addProperty(GenericData* prop){
# Line 591 | Line 636 | vector<GenericData*> SimInfo::getProperties(){
636    return result;
637   }
638  
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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