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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC vs.
Revision 781 by tim, Mon Sep 22 23:07:57 2003 UTC

# Line 1 | Line 1
1   #include <cstdlib>
2   #include <cstring>
3 + #include <cmath>
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 29 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63  
33 –
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 +  
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::setBoxM( double theBox[3][3] ){
96 +  
97 +  int i, j, status;
98 +  double smallestBoxL, maxCutoff;
99 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
100 +                         // ordering in the array is as follows:
101 +                         // [ 0 3 6 ]
102 +                         // [ 1 4 7 ]
103 +                         // [ 2 5 8 ]
104 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
105 +
106 +  
107 +  if( !boxIsInit ) boxIsInit = 1;
108 +
109 +  for(i=0; i < 3; i++)
110 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
111 +  
112 +  calcBoxL();
113 +  calcHmatInv();
114 +
115 +  for(i=0; i < 3; i++) {
116 +    for (j=0; j < 3; j++) {
117 +      FortranHmat[3*j + i] = Hmat[i][j];
118 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
119 +    }
120 +  }
121 +
122 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123 +
124 + }
125 +
126 +
127 + void SimInfo::getBoxM (double theBox[3][3]) {
128 +
129 +  int i, j;
130 +  for(i=0; i<3; i++)
131 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
132 + }
133 +
134 +
135 + void SimInfo::scaleBox(double scale) {
136 +  double theBox[3][3];
137 +  int i, j;
138 +
139 +  // cerr << "Scaling box by " << scale << "\n";
140 +
141 +  for(i=0; i<3; i++)
142 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
143 +
144 +  setBoxM(theBox);
145 +
146 + }
147 +
148 + void SimInfo::calcHmatInv( void ) {
149 +  
150 +  int i,j;
151 +  double smallDiag;
152 +  double tol;
153 +  double sanity[3][3];
154 +
155 +  invertMat3( Hmat, HmatInv );
156 +
157 +  // Check the inverse to make sure it is sane:
158 +
159 +  matMul3( Hmat, HmatInv, sanity );
160 +    
161 +  // check to see if Hmat is orthorhombic
162 +  
163 +  smallDiag = Hmat[0][0];
164 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
165 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
166 +  tol = smallDiag * 1E-6;
167 +
168 +  orthoRhombic = 1;
169 +  
170 +  for (i = 0; i < 3; i++ ) {
171 +    for (j = 0 ; j < 3; j++) {
172 +      if (i != j) {
173 +        if (orthoRhombic) {
174 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
175 +        }        
176 +      }
177 +    }
178 +  }
179 + }
180 +
181 + double SimInfo::matDet3(double a[3][3]) {
182 +  int i, j, k;
183 +  double determinant;
184 +
185 +  determinant = 0.0;
186 +
187 +  for(i = 0; i < 3; i++) {
188 +    j = (i+1)%3;
189 +    k = (i+2)%3;
190 +
191 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
192 +  }
193 +
194 +  return determinant;
195 + }
196 +
197 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
198 +  
199 +  int  i, j, k, l, m, n;
200 +  double determinant;
201 +
202 +  determinant = matDet3( a );
203 +
204 +  if (determinant == 0.0) {
205 +    sprintf( painCave.errMsg,
206 +             "Can't invert a matrix with a zero determinant!\n");
207 +    painCave.isFatal = 1;
208 +    simError();
209 +  }
210 +
211 +  for (i=0; i < 3; i++) {
212 +    j = (i+1)%3;
213 +    k = (i+2)%3;
214 +    for(l = 0; l < 3; l++) {
215 +      m = (l+1)%3;
216 +      n = (l+2)%3;
217 +      
218 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
219 +    }
220 +  }
221 + }
222 +
223 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
224 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
225 +
226 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
227 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
228 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
229 +  
230 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
231 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
232 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
233 +  
234 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
235 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
236 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
237 +  
238 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
239 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
240 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
241 + }
242 +
243 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
244 +  double a0, a1, a2;
245 +
246 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
247 +
248 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
249 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
250 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
251 + }
252 +
253 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
254 +  double temp[3][3];
255 +  int i, j;
256 +
257 +  for (i = 0; i < 3; i++) {
258 +    for (j = 0; j < 3; j++) {
259 +      temp[j][i] = in[i][j];
260 +    }
261 +  }
262 +  for (i = 0; i < 3; i++) {
263 +    for (j = 0; j < 3; j++) {
264 +      out[i][j] = temp[i][j];
265 +    }
266 +  }
267 + }
268 +  
269 + void SimInfo::printMat3(double A[3][3] ){
270 +
271 +  std::cerr
272 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
273 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
274 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
275 + }
276 +
277 + void SimInfo::printMat9(double A[9] ){
278 +
279 +  std::cerr
280 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
281 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
282 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
283 + }
284 +
285 +
286 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
287 +
288 +      out[0] = a[1] * b[2] - a[2] * b[1];
289 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
290 +      out[2] = a[0] * b[1] - a[1] * b[0];
291 +      
292 + }
293 +
294 + double SimInfo::dotProduct3(double a[3], double b[3]){
295 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
296 + }
297 +
298 + double SimInfo::length3(double a[3]){
299 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
300 + }
301 +
302 + void SimInfo::calcBoxL( void ){
303 +
304 +  double dx, dy, dz, dsq;
305 +  int i;
306 +
307 +  // boxVol = Determinant of Hmat
308 +
309 +  boxVol = matDet3( Hmat );
310 +
311 +  // boxLx
312 +  
313 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314 +  dsq = dx*dx + dy*dy + dz*dz;
315 +  boxL[0] = sqrt( dsq );
316 +  //maxCutoff = 0.5 * boxL[0];
317 +
318 +  // boxLy
319 +  
320 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321 +  dsq = dx*dx + dy*dy + dz*dz;
322 +  boxL[1] = sqrt( dsq );
323 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
324 +
325 +
326 +  // boxLz
327 +  
328 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
329 +  dsq = dx*dx + dy*dy + dz*dz;
330 +  boxL[2] = sqrt( dsq );
331 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
332 +
333 +  //calculate the max cutoff
334 +  maxCutoff =  calcMaxCutOff();
335 +  
336 +  checkCutOffs();
337 +
338 + }
339 +
340 +
341 + double SimInfo::calcMaxCutOff(){
342 +
343 +  double ri[3], rj[3], rk[3];
344 +  double rij[3], rjk[3], rki[3];
345 +  double minDist;
346 +
347 +  ri[0] = Hmat[0][0];
348 +  ri[1] = Hmat[1][0];
349 +  ri[2] = Hmat[2][0];
350 +
351 +  rj[0] = Hmat[0][1];
352 +  rj[1] = Hmat[1][1];
353 +  rj[2] = Hmat[2][1];
354 +
355 +  rk[0] = Hmat[0][2];
356 +  rk[1] = Hmat[1][2];
357 +  rk[2] = Hmat[2][2];
358 +  
359 +  crossProduct3(ri,rj, rij);
360 +  distXY = dotProduct3(rk,rij) / length3(rij);
361 +
362 +  crossProduct3(rj,rk, rjk);
363 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
364 +
365 +  crossProduct3(rk,ri, rki);
366 +  distZX = dotProduct3(rj,rki) / length3(rki);
367 +
368 +  minDist = min(min(distXY, distYZ), distZX);
369 +  return minDist/2;
370 +  
371   }
372  
373 + void SimInfo::wrapVector( double thePos[3] ){
374 +
375 +  int i, j, k;
376 +  double scaled[3];
377 +
378 +  if( !orthoRhombic ){
379 +    // calc the scaled coordinates.
380 +  
381 +
382 +    matVecMul3(HmatInv, thePos, scaled);
383 +    
384 +    for(i=0; i<3; i++)
385 +      scaled[i] -= roundMe(scaled[i]);
386 +    
387 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
388 +    
389 +    matVecMul3(Hmat, scaled, thePos);
390 +
391 +  }
392 +  else{
393 +    // calc the scaled coordinates.
394 +    
395 +    for(i=0; i<3; i++)
396 +      scaled[i] = thePos[i]*HmatInv[i][i];
397 +    
398 +    // wrap the scaled coordinates
399 +    
400 +    for(i=0; i<3; i++)
401 +      scaled[i] -= roundMe(scaled[i]);
402 +    
403 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
404 +    
405 +    for(i=0; i<3; i++)
406 +      thePos[i] = scaled[i]*Hmat[i][i];
407 +  }
408 +    
409 + }
410 +
411 +
412 + int SimInfo::getNDF(){
413 +  int ndf_local, ndf;
414 +  
415 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
416 +
417 + #ifdef IS_MPI
418 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
419 + #else
420 +  ndf = ndf_local;
421 + #endif
422 +
423 +  ndf = ndf - 3 - nZconstraints;
424 +
425 +  return ndf;
426 + }
427 +
428 + int SimInfo::getNDFraw() {
429 +  int ndfRaw_local, ndfRaw;
430 +
431 +  // Raw degrees of freedom that we have to set
432 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
433 +  
434 + #ifdef IS_MPI
435 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
436 + #else
437 +  ndfRaw = ndfRaw_local;
438 + #endif
439 +
440 +  return ndfRaw;
441 + }
442 +
443 + int SimInfo::getNDFtranslational() {
444 +  int ndfTrans_local, ndfTrans;
445 +
446 +  ndfTrans_local = 3 * n_atoms - n_constraints;
447 +
448 + #ifdef IS_MPI
449 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
450 + #else
451 +  ndfTrans = ndfTrans_local;
452 + #endif
453 +
454 +  ndfTrans = ndfTrans - 3 - nZconstraints;
455 +
456 +  return ndfTrans;
457 + }
458 +
459   void SimInfo::refreshSim(){
460  
461    simtype fInfo;
462    int isError;
463 +  int n_global;
464    int* excl;
465  
466 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
466 >  fInfo.dielect = 0.0;
467  
468 <  fInfo.rlist = rList;
469 <  fInfo.rcut = rCut;
470 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
468 >  if( useDipole ){
469 >    if( useReactionField )fInfo.dielect = dielectric;
470 >  }
471  
472    fInfo.SIM_uses_PBC = usePBC;
473 <  //  fInfo.SIM_uses_LJ = useLJ;
474 <  fInfo.SIM_uses_LJ = 0;
475 <  //fInfo.SIM_uses_sticky = useSticky;
476 <  fInfo.SIM_uses_sticky = 0;
473 >  //fInfo.SIM_uses_LJ = 0;
474 >  fInfo.SIM_uses_LJ = useLJ;
475 >  fInfo.SIM_uses_sticky = useSticky;
476 >  //fInfo.SIM_uses_sticky = 0;
477    fInfo.SIM_uses_dipoles = useDipole;
478    //fInfo.SIM_uses_dipoles = 0;
479 <  fInfo.SIM_uses_RF = useReactionField;
479 >  //fInfo.SIM_uses_RF = useReactionField;
480 >  fInfo.SIM_uses_RF = 0;
481    fInfo.SIM_uses_GB = useGB;
482    fInfo.SIM_uses_EAM = useEAM;
483  
484    excl = Exclude::getArray();
485  
486 + #ifdef IS_MPI
487 +  n_global = mpiSim->getTotAtoms();
488 + #else
489 +  n_global = n_atoms;
490 + #endif
491 +
492    isError = 0;
493  
494 <  fInfo;
495 <  n_atoms;
496 <  identArray;
71 <  n_exclude;
72 <  excludes;
73 <  nGlobalExcludes;
74 <  globalExcludes;
75 <  isError;
494 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
495 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
496 >                  &isError );
497  
77 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
78 –                  &nGlobalExcludes, globalExcludes, &isError );
79 –
498    if( isError ){
499  
500      sprintf( painCave.errMsg,
# Line 90 | Line 508 | void SimInfo::refreshSim(){
508             "succesfully sent the simulation information to fortran.\n");
509    MPIcheckPoint();
510   #endif // is_mpi
511 +
512 +  this->ndf = this->getNDF();
513 +  this->ndfRaw = this->getNDFraw();
514 +  this->ndfTrans = this->getNDFtranslational();
515   }
516  
517 +
518 + void SimInfo::setRcut( double theRcut ){
519 +
520 +  if( !haveOrigRcut ){
521 +    haveOrigRcut = 1;
522 +    origRcut = theRcut;
523 +  }
524 +
525 +  rCut = theRcut;
526 +  checkCutOffs();
527 + }
528 +
529 + void SimInfo::setEcr( double theEcr ){
530 +
531 +  if( !haveOrigEcr ){
532 +    haveOrigEcr = 1;
533 +    origEcr = theEcr;
534 +  }
535 +
536 +  ecr = theEcr;
537 +  checkCutOffs();
538 + }
539 +
540 + void SimInfo::setEcr( double theEcr, double theEst ){
541 +
542 +  est = theEst;
543 +  setEcr( theEcr );
544 + }
545 +
546 +
547 + void SimInfo::checkCutOffs( void ){
548 +
549 +  int cutChanged = 0;
550 +  
551 +  if( boxIsInit ){
552 +    
553 +    //we need to check cutOffs against the box
554 +
555 +    //detect the change of rCut
556 +    if(( maxCutoff > rCut )&&(usePBC)){
557 +      if( rCut < origRcut ){
558 +        rCut = origRcut;
559 +        
560 +        if (rCut > maxCutoff)
561 +          rCut = maxCutoff;
562 +  
563 +          sprintf( painCave.errMsg,
564 +                    "New Box size is setting the long range cutoff radius "
565 +                    "to %lf at time %lf\n",
566 +                    rCut, currentTime );
567 +          painCave.isFatal = 0;
568 +          simError();
569 +      }
570 +    }
571 +    else if ((rCut > maxCutoff)&&(usePBC)) {
572 +      sprintf( painCave.errMsg,
573 +               "New Box size is setting the long range cutoff radius "
574 +               "to %lf at time %lf\n",
575 +               maxCutoff, currentTime );
576 +      painCave.isFatal = 0;
577 +      simError();
578 +      rCut = maxCutoff;
579 +    }
580 +
581 +
582 +    //detect the change of ecr
583 +    if( maxCutoff > ecr ){
584 +      if( ecr < origEcr ){
585 +        ecr = origEcr;
586 +        if (ecr > maxCutoff) ecr = maxCutoff;
587 +  
588 +          sprintf( painCave.errMsg,
589 +                    "New Box size is setting the electrostaticCutoffRadius "
590 +                    "to %lf at time %lf\n",
591 +                    ecr, currentTime );
592 +            painCave.isFatal = 0;
593 +            simError();
594 +      }
595 +    }
596 +    else if( ecr > maxCutoff){
597 +      sprintf( painCave.errMsg,
598 +               "New Box size is setting the electrostaticCutoffRadius "
599 +               "to %lf at time %lf\n",
600 +               maxCutoff, currentTime  );
601 +      painCave.isFatal = 0;
602 +      simError();      
603 +      ecr = maxCutoff;
604 +    }
605 +
606 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
607 +    
608 +    // rlist is the 1.0 plus max( rcut, ecr )
609 +    
610 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
611 +    
612 +    if( cutChanged ){
613 +      
614 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
615 +    }
616 +    
617 +    oldEcr = ecr;
618 +    oldRcut = rCut;
619 +    
620 +  } else {
621 +    // initialize this stuff before using it, OK?
622 +    sprintf( painCave.errMsg,
623 +             "Trying to check cutoffs without a box. Be smarter.\n" );
624 +    painCave.isFatal = 1;
625 +    simError();      
626 +  }
627 +  
628 + }
629 +
630 + void SimInfo::addProperty(GenericData* prop){
631 +
632 +  map<string, GenericData*>::iterator result;
633 +  result = properties.find(prop->getID());
634 +  
635 +  //we can't simply use  properties[prop->getID()] = prop,
636 +  //it will cause memory leak if we already contain a propery which has the same name of prop
637 +  
638 +  if(result != properties.end()){
639 +    
640 +    delete (*result).second;
641 +    (*result).second = prop;
642 +      
643 +  }
644 +  else{
645 +
646 +    properties[prop->getID()] = prop;
647 +
648 +  }
649 +    
650 + }
651 +
652 + GenericData* SimInfo::getProperty(const string& propName){
653 +
654 +  map<string, GenericData*>::iterator result;
655 +  
656 +  //string lowerCaseName = ();
657 +  
658 +  result = properties.find(propName);
659 +  
660 +  if(result != properties.end())
661 +    return (*result).second;  
662 +  else  
663 +    return NULL;  
664 + }
665 +
666 + vector<GenericData*> SimInfo::getProperties(){
667 +
668 +  vector<GenericData*> result;
669 +  map<string, GenericData*>::iterator i;
670 +  
671 +  for(i = properties.begin(); i != properties.end(); i++)
672 +    result.push_back((*i).second);
673 +    
674 +  return result;
675 + }
676 +
677 + double SimInfo::matTrace3(double m[3][3]){
678 +  double trace;
679 +  trace = m[0][0] + m[1][1] + m[2][2];
680 +
681 +  return trace;
682 + }

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