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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 617 by gezelter, Tue Jul 15 19:56:08 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;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  ecr = 0.0;
41 +  est = 0.0;
42  
43 +  haveRcut = 0;
44 +  haveEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  resetTime = 1e99;
48 +
49 +  orthoTolerance = 1E-6;
50 +  useInitXSstate = true;
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 43 | 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 64 | Line 92 | void SimInfo::setBoxM( double theBox[3][3] ){
92  
93   void SimInfo::setBoxM( double theBox[3][3] ){
94    
95 <  int i, j, status;
68 <  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 73 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){
100                           // [ 2 5 8 ]
101    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
103 +  if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
106      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107    
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 –
108    calcBoxL();
109    calcHmatInv();
110  
# Line 95 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){
117  
118    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119  
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 –  }
120   }
121  
122  
# Line 164 | 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 171 | Line 151 | void SimInfo::calcHmatInv( void ) {
151  
152    invertMat3( Hmat, HmatInv );
153  
174 –  // Check the inverse to make sure it is sane:
175 –
176 –  matMul3( Hmat, HmatInv, sanity );
177 –    
154    // check to see if Hmat is orthorhombic
155    
156 <  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;
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 299 | Line 295 | void SimInfo::calcBoxL( void ){
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;
305 –  int i;
318  
319    // boxVol = Determinant of Hmat
320  
# Line 312 | Line 324 | void SimInfo::calcBoxL( void ){
324    
325    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
326    dsq = dx*dx + dy*dy + dz*dz;
327 <  boxLx = sqrt( dsq );
327 >  boxL[0] = sqrt( dsq );
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 <  boxLy = sqrt( dsq );
334 >  boxL[1] = sqrt( dsq );
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 <  boxLz = sqrt( dsq );
342 >  boxL[2] = sqrt( dsq );
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 369 | 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 379 | 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 398 | 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;
474    int isError;
475    int n_global;
476    int* excl;
477 <  
409 <  fInfo.rrf = 0.0;
410 <  fInfo.rt = 0.0;
477 >
478    fInfo.dielect = 0.0;
479  
413 –  fInfo.rlist = rList;
414 –  fInfo.rcut = rCut;
415 –
480    if( useDipole ){
417 –    fInfo.rrf = ecr;
418 –    fInfo.rt = ecr - est;
481      if( useReactionField )fInfo.dielect = dielectric;
482    }
483  
# Line 461 | Line 523 | void SimInfo::refreshSim(){
523  
524    this->ndf = this->getNDF();
525    this->ndfRaw = this->getNDFraw();
526 +  this->ndfTrans = this->getNDFtranslational();
527 + }
528  
529 + void SimInfo::setDefaultRcut( double theRcut ){
530 +
531 +  haveRcut = 1;
532 +  rCut = theRcut;
533 +
534 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535 +
536 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537   }
538  
539 + void SimInfo::setDefaultEcr( double theEcr ){
540 +
541 +  haveEcr = 1;
542 +  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  ecr = theEcr;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551 +
552 +  est = theEst;
553 +  setDefaultEcr( theEcr );
554 + }
555 +
556 +
557 + void SimInfo::checkCutOffs( void ){
558 +  
559 +  if( boxIsInit ){
560 +    
561 +    //we need to check cutOffs against the box
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( haveEcr ){
573 +      if( ecr > maxCutoff ){
574 +        sprintf( painCave.errMsg,
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 +  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 +  else{
607 +
608 +    properties[prop->getID()] = prop;
609 +
610 +  }
611 +    
612 + }
613 +
614 + GenericData* SimInfo::getProperty(const string& propName){
615 +
616 +  map<string, GenericData*>::iterator result;
617 +  
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 + 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 +  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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