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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 458 by gezelter, Fri Apr 4 19:47:19 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12 | SimInfo* currentInfo;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #ifdef IS_MPI
16 + #include "mpiSimulation.hpp"
17 + #endif
18 +
19 + inline double roundMe( double x ){
20 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21 + }
22 +          
23 +
24   SimInfo* currentInfo;
25  
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 +  origRcut = -1.0;
41 +  ecr = 0.0;
42 +  origEcr = -1.0;
43 +  est = 0.0;
44 +  oldEcr = 0.0;
45 +  oldRcut = 0.0;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 31 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64    wrapMeSimInfo( this );
65   }
66  
67 +
68 + SimInfo::~SimInfo(){
69 +
70 +  delete myConfiguration;
71 +
72 +  map<string, GenericData*>::iterator i;
73 +  
74 +  for(i = properties.begin(); i != properties.end(); i++)
75 +    delete (*i).second;
76 +    
77 + }
78 +
79   void SimInfo::setBox(double newBox[3]) {
80 <  box_x = newBox[0];
81 <  box_y = newBox[1];
82 <  box_z = newBox[2];
83 <  setFortranBoxSize(newBox);
80 >  
81 >  int i, j;
82 >  double tempMat[3][3];
83 >
84 >  for(i=0; i<3; i++)
85 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
86 >
87 >  tempMat[0][0] = newBox[0];
88 >  tempMat[1][1] = newBox[1];
89 >  tempMat[2][2] = newBox[2];
90 >
91 >  setBoxM( tempMat );
92 >
93   }
94  
95 < void SimInfo::getBox(double theBox[3]) {
96 <  theBox[0] = box_x;
97 <  theBox[1] = box_y;
98 <  theBox[2] = box_z;
95 > void SimInfo::setBoxM( double theBox[3][3] ){
96 >  
97 >  int i, j;
98 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
99 >                         // ordering in the array is as follows:
100 >                         // [ 0 3 6 ]
101 >                         // [ 1 4 7 ]
102 >                         // [ 2 5 8 ]
103 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
104 >
105 >  
106 >  if( !boxIsInit ) boxIsInit = 1;
107 >
108 >  for(i=0; i < 3; i++)
109 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
110 >  
111 >  calcBoxL();
112 >  calcHmatInv();
113 >
114 >  for(i=0; i < 3; i++) {
115 >    for (j=0; j < 3; j++) {
116 >      FortranHmat[3*j + i] = Hmat[i][j];
117 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
118 >    }
119 >  }
120 >
121 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122 >
123   }
124  
125 +
126 + void SimInfo::getBoxM (double theBox[3][3]) {
127 +
128 +  int i, j;
129 +  for(i=0; i<3; i++)
130 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
131 + }
132 +
133 +
134 + void SimInfo::scaleBox(double scale) {
135 +  double theBox[3][3];
136 +  int i, j;
137 +
138 +  // cerr << "Scaling box by " << scale << "\n";
139 +
140 +  for(i=0; i<3; i++)
141 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
142 +
143 +  setBoxM(theBox);
144 +
145 + }
146 +
147 + void SimInfo::calcHmatInv( void ) {
148 +  
149 +  int oldOrtho;
150 +  int i,j;
151 +  double smallDiag;
152 +  double tol;
153 +  double sanity[3][3];
154 +
155 +  invertMat3( Hmat, HmatInv );
156 +
157 +  // check to see if Hmat is orthorhombic
158 +  
159 +  oldOrtho = orthoRhombic;
160 +
161 +  smallDiag = fabs(Hmat[0][0]);
162 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
163 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
164 +  tol = smallDiag * 1E-6;
165 +
166 +  orthoRhombic = 1;
167 +  
168 +  for (i = 0; i < 3; i++ ) {
169 +    for (j = 0 ; j < 3; j++) {
170 +      if (i != j) {
171 +        if (orthoRhombic) {
172 +          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
173 +        }        
174 +      }
175 +    }
176 +  }
177 +
178 +  if( oldOrtho != orthoRhombic ){
179 +    
180 +    if( orthoRhombic ){
181 +      sprintf( painCave.errMsg,
182 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
184 +      simError();
185 +    }
186 +    else {
187 +      sprintf( painCave.errMsg,
188 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
189 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
190 +      simError();
191 +    }
192 +  }
193 + }
194 +
195 + double SimInfo::matDet3(double a[3][3]) {
196 +  int i, j, k;
197 +  double determinant;
198 +
199 +  determinant = 0.0;
200 +
201 +  for(i = 0; i < 3; i++) {
202 +    j = (i+1)%3;
203 +    k = (i+2)%3;
204 +
205 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 +  }
207 +
208 +  return determinant;
209 + }
210 +
211 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212 +  
213 +  int  i, j, k, l, m, n;
214 +  double determinant;
215 +
216 +  determinant = matDet3( a );
217 +
218 +  if (determinant == 0.0) {
219 +    sprintf( painCave.errMsg,
220 +             "Can't invert a matrix with a zero determinant!\n");
221 +    painCave.isFatal = 1;
222 +    simError();
223 +  }
224 +
225 +  for (i=0; i < 3; i++) {
226 +    j = (i+1)%3;
227 +    k = (i+2)%3;
228 +    for(l = 0; l < 3; l++) {
229 +      m = (l+1)%3;
230 +      n = (l+2)%3;
231 +      
232 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233 +    }
234 +  }
235 + }
236 +
237 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239 +
240 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243 +  
244 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 +  
248 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 +  
252 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255 + }
256 +
257 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 +  double a0, a1, a2;
259 +
260 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 +
262 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 + }
266 +
267 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 +  double temp[3][3];
269 +  int i, j;
270 +
271 +  for (i = 0; i < 3; i++) {
272 +    for (j = 0; j < 3; j++) {
273 +      temp[j][i] = in[i][j];
274 +    }
275 +  }
276 +  for (i = 0; i < 3; i++) {
277 +    for (j = 0; j < 3; j++) {
278 +      out[i][j] = temp[i][j];
279 +    }
280 +  }
281 + }
282 +  
283 + void SimInfo::printMat3(double A[3][3] ){
284 +
285 +  std::cerr
286 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 + }
290 +
291 + void SimInfo::printMat9(double A[9] ){
292 +
293 +  std::cerr
294 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 + }
298 +
299 +
300 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301 +
302 +      out[0] = a[1] * b[2] - a[2] * b[1];
303 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
304 +      out[2] = a[0] * b[1] - a[1] * b[0];
305 +      
306 + }
307 +
308 + double SimInfo::dotProduct3(double a[3], double b[3]){
309 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
310 + }
311 +
312 + double SimInfo::length3(double a[3]){
313 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
314 + }
315 +
316 + void SimInfo::calcBoxL( void ){
317 +
318 +  double dx, dy, dz, dsq;
319 +
320 +  // boxVol = Determinant of Hmat
321 +
322 +  boxVol = matDet3( Hmat );
323 +
324 +  // boxLx
325 +  
326 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
327 +  dsq = dx*dx + dy*dy + dz*dz;
328 +  boxL[0] = sqrt( dsq );
329 +  //maxCutoff = 0.5 * boxL[0];
330 +
331 +  // boxLy
332 +  
333 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
334 +  dsq = dx*dx + dy*dy + dz*dz;
335 +  boxL[1] = sqrt( dsq );
336 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
337 +
338 +
339 +  // boxLz
340 +  
341 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
342 +  dsq = dx*dx + dy*dy + dz*dz;
343 +  boxL[2] = sqrt( dsq );
344 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
345 +
346 +  //calculate the max cutoff
347 +  maxCutoff =  calcMaxCutOff();
348 +  
349 +  checkCutOffs();
350 +
351 + }
352 +
353 +
354 + double SimInfo::calcMaxCutOff(){
355 +
356 +  double ri[3], rj[3], rk[3];
357 +  double rij[3], rjk[3], rki[3];
358 +  double minDist;
359 +
360 +  ri[0] = Hmat[0][0];
361 +  ri[1] = Hmat[1][0];
362 +  ri[2] = Hmat[2][0];
363 +
364 +  rj[0] = Hmat[0][1];
365 +  rj[1] = Hmat[1][1];
366 +  rj[2] = Hmat[2][1];
367 +
368 +  rk[0] = Hmat[0][2];
369 +  rk[1] = Hmat[1][2];
370 +  rk[2] = Hmat[2][2];
371 +  
372 +  crossProduct3(ri,rj, rij);
373 +  distXY = dotProduct3(rk,rij) / length3(rij);
374 +
375 +  crossProduct3(rj,rk, rjk);
376 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
377 +
378 +  crossProduct3(rk,ri, rki);
379 +  distZX = dotProduct3(rj,rki) / length3(rki);
380 +
381 +  minDist = min(min(distXY, distYZ), distZX);
382 +  return minDist/2;
383 +  
384 + }
385 +
386 + void SimInfo::wrapVector( double thePos[3] ){
387 +
388 +  int i;
389 +  double scaled[3];
390 +
391 +  if( !orthoRhombic ){
392 +    // calc the scaled coordinates.
393 +  
394 +
395 +    matVecMul3(HmatInv, thePos, scaled);
396 +    
397 +    for(i=0; i<3; i++)
398 +      scaled[i] -= roundMe(scaled[i]);
399 +    
400 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
401 +    
402 +    matVecMul3(Hmat, scaled, thePos);
403 +
404 +  }
405 +  else{
406 +    // calc the scaled coordinates.
407 +    
408 +    for(i=0; i<3; i++)
409 +      scaled[i] = thePos[i]*HmatInv[i][i];
410 +    
411 +    // wrap the scaled coordinates
412 +    
413 +    for(i=0; i<3; i++)
414 +      scaled[i] -= roundMe(scaled[i]);
415 +    
416 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
417 +    
418 +    for(i=0; i<3; i++)
419 +      thePos[i] = scaled[i]*Hmat[i][i];
420 +  }
421 +    
422 + }
423 +
424 +
425   int SimInfo::getNDF(){
426 <  int ndf_local, ndf;
426 >  int ndf_local;
427    
428    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429  
# Line 58 | Line 433 | int SimInfo::getNDF(){
433    ndf = ndf_local;
434   #endif
435  
436 <  ndf = ndf - 3;
436 >  ndf = ndf - 3 - nZconstraints;
437  
438    return ndf;
439   }
440  
441   int SimInfo::getNDFraw() {
442 <  int ndfRaw_local, ndfRaw;
442 >  int ndfRaw_local;
443  
444    // Raw degrees of freedom that we have to set
445    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 77 | Line 452 | int SimInfo::getNDFraw() {
452  
453    return ndfRaw;
454   }
455 <
455 >
456 > int SimInfo::getNDFtranslational() {
457 >  int ndfTrans_local;
458 >
459 >  ndfTrans_local = 3 * n_atoms - n_constraints;
460 >
461 > #ifdef IS_MPI
462 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
463 > #else
464 >  ndfTrans = ndfTrans_local;
465 > #endif
466 >
467 >  ndfTrans = ndfTrans - 3 - nZconstraints;
468 >
469 >  return ndfTrans;
470 > }
471 >
472   void SimInfo::refreshSim(){
473  
474    simtype fInfo;
475    int isError;
476 +  int n_global;
477    int* excl;
478  
479 <  fInfo.box[0] = box_x;
88 <  fInfo.box[1] = box_y;
89 <  fInfo.box[2] = box_z;
479 >  fInfo.dielect = 0.0;
480  
481 <  fInfo.rlist = rList;
482 <  fInfo.rcut = rCut;
483 <  fInfo.rrf = ecr;
94 <  fInfo.rt = ecr - est;
95 <  fInfo.dielect = dielectric;
481 >  if( useDipole ){
482 >    if( useReactionField )fInfo.dielect = dielectric;
483 >  }
484  
485    fInfo.SIM_uses_PBC = usePBC;
486    //fInfo.SIM_uses_LJ = 0;
# Line 108 | Line 496 | void SimInfo::refreshSim(){
496  
497    excl = Exclude::getArray();
498  
499 + #ifdef IS_MPI
500 +  n_global = mpiSim->getTotAtoms();
501 + #else
502 +  n_global = n_atoms;
503 + #endif
504 +
505    isError = 0;
506  
507 < //   fInfo;
508 < //   n_atoms;
509 < //   identArray;
116 < //   n_exclude;
117 < //   excludes;
118 < //   nGlobalExcludes;
119 < //   globalExcludes;
120 < //   isError;
507 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
508 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
509 >                  &isError );
510  
122 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
123 –                  &nGlobalExcludes, globalExcludes, &isError );
124 –
511    if( isError ){
512  
513      sprintf( painCave.errMsg,
# Line 136 | Line 522 | void SimInfo::refreshSim(){
522    MPIcheckPoint();
523   #endif // is_mpi
524  
525 <  ndf = this->getNDF();
526 <  ndfRaw = this->getNDFraw();
525 >  this->ndf = this->getNDF();
526 >  this->ndfRaw = this->getNDFraw();
527 >  this->ndfTrans = this->getNDFtranslational();
528 > }
529  
530 +
531 + void SimInfo::setRcut( double theRcut ){
532 +
533 +  rCut = theRcut;
534 +  checkCutOffs();
535   }
536  
537 + void SimInfo::setDefaultRcut( double theRcut ){
538 +
539 +  haveOrigRcut = 1;
540 +  origRcut = theRcut;
541 +  rCut = theRcut;
542 +
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr ){
549 +
550 +  ecr = theEcr;
551 +  checkCutOffs();
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr ){
555 +
556 +  haveOrigEcr = 1;
557 +  origEcr = theEcr;
558 +  
559 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 +
561 +  ecr = theEcr;
562 +
563 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
564 + }
565 +
566 + void SimInfo::setEcr( double theEcr, double theEst ){
567 +
568 +  est = theEst;
569 +  setEcr( theEcr );
570 + }
571 +
572 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573 +
574 +  est = theEst;
575 +  setDefaultEcr( theEcr );
576 + }
577 +
578 +
579 + void SimInfo::checkCutOffs( void ){
580 +
581 +  int cutChanged = 0;
582 +  
583 +  if( boxIsInit ){
584 +    
585 +    //we need to check cutOffs against the box
586 +
587 +    //detect the change of rCut
588 +    if(( maxCutoff > rCut )&&(usePBC)){
589 +      if( rCut < origRcut ){
590 +        rCut = origRcut;
591 +        
592 +        if (rCut > maxCutoff)
593 +          rCut = maxCutoff;
594 +  
595 +          sprintf( painCave.errMsg,
596 +                    "New Box size is setting the long range cutoff radius "
597 +                    "to %lf at time %lf\n",
598 +                    rCut, currentTime );
599 +          painCave.isFatal = 0;
600 +          simError();
601 +      }
602 +    }
603 +    else if ((rCut > maxCutoff)&&(usePBC)) {
604 +      sprintf( painCave.errMsg,
605 +               "New Box size is setting the long range cutoff radius "
606 +               "to %lf at time %lf\n",
607 +               maxCutoff, currentTime );
608 +      painCave.isFatal = 0;
609 +      simError();
610 +      rCut = maxCutoff;
611 +    }
612 +
613 +
614 +    //detect the change of ecr
615 +    if( maxCutoff > ecr ){
616 +      if( ecr < origEcr ){
617 +        ecr = origEcr;
618 +        if (ecr > maxCutoff) ecr = maxCutoff;
619 +  
620 +          sprintf( painCave.errMsg,
621 +                    "New Box size is setting the electrostaticCutoffRadius "
622 +                    "to %lf at time %lf\n",
623 +                    ecr, currentTime );
624 +            painCave.isFatal = 0;
625 +            simError();
626 +      }
627 +    }
628 +    else if( ecr > maxCutoff){
629 +      sprintf( painCave.errMsg,
630 +               "New Box size is setting the electrostaticCutoffRadius "
631 +               "to %lf at time %lf\n",
632 +               maxCutoff, currentTime  );
633 +      painCave.isFatal = 0;
634 +      simError();      
635 +      ecr = maxCutoff;
636 +    }
637 +
638 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 +    
640 +    // rlist is the 1.0 plus max( rcut, ecr )
641 +    
642 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643 +    
644 +    if( cutChanged ){
645 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 +    }
647 +    
648 +    oldEcr = ecr;
649 +    oldRcut = rCut;
650 +    
651 +  } else {
652 +    // initialize this stuff before using it, OK?
653 +    sprintf( painCave.errMsg,
654 +             "Trying to check cutoffs without a box. Be smarter.\n" );
655 +    painCave.isFatal = 1;
656 +    simError();      
657 +  }
658 +  
659 + }
660 +
661 + void SimInfo::addProperty(GenericData* prop){
662 +
663 +  map<string, GenericData*>::iterator result;
664 +  result = properties.find(prop->getID());
665 +  
666 +  //we can't simply use  properties[prop->getID()] = prop,
667 +  //it will cause memory leak if we already contain a propery which has the same name of prop
668 +  
669 +  if(result != properties.end()){
670 +    
671 +    delete (*result).second;
672 +    (*result).second = prop;
673 +      
674 +  }
675 +  else{
676 +
677 +    properties[prop->getID()] = prop;
678 +
679 +  }
680 +    
681 + }
682 +
683 + GenericData* SimInfo::getProperty(const string& propName){
684 +
685 +  map<string, GenericData*>::iterator result;
686 +  
687 +  //string lowerCaseName = ();
688 +  
689 +  result = properties.find(propName);
690 +  
691 +  if(result != properties.end())
692 +    return (*result).second;  
693 +  else  
694 +    return NULL;  
695 + }
696 +
697 + vector<GenericData*> SimInfo::getProperties(){
698 +
699 +  vector<GenericData*> result;
700 +  map<string, GenericData*>::iterator i;
701 +  
702 +  for(i = properties.begin(); i != properties.end(); i++)
703 +    result.push_back((*i).second);
704 +    
705 +  return result;
706 + }
707 +
708 + double SimInfo::matTrace3(double m[3][3]){
709 +  double trace;
710 +  trace = m[0][0] + m[1][1] + m[2][2];
711 +
712 +  return trace;
713 + }

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