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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 941 by gezelter, Tue Jan 13 23:01:43 2004 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 + 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;
41 +  currentTime = 0.0;
42 +  rCut = 0.0;
43 +  ecr = 0.0;
44 +  est = 0.0;
45  
46 +  haveRcut = 0;
47 +  haveEcr = 0;
48 +  boxIsInit = 0;
49 +  
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  
32 –
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;
84 +  double tempMat[3][3];
85 +
86 +  for(i=0; i<3; i++)
87 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
88 +
89 +  tempMat[0][0] = newBox[0];
90 +  tempMat[1][1] = newBox[1];
91 +  tempMat[2][2] = newBox[2];
92 +
93 +  setBoxM( tempMat );
94 +
95 + }
96 +
97 + void SimInfo::setBoxM( double theBox[3][3] ){
98 +  
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 ]
103 +                         // [ 1 4 7 ]
104 +                         // [ 2 5 8 ]
105 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
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 oldOrtho;
151 +  int i,j;
152 +  double smallDiag;
153 +  double tol;
154 +  double sanity[3][3];
155 +
156 +  invertMat3( Hmat, HmatInv );
157 +
158 +  // check to see if Hmat is orthorhombic
159 +  
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 ( 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\n"
184 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
185 +               orthoTolerance);
186 +      simError();
187 +    }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
192 +               orthoTolerance);
193 +      simError();
194 +    }
195 +  }
196 + }
197 +
198 + double SimInfo::matDet3(double a[3][3]) {
199 +  int i, j, k;
200 +  double determinant;
201 +
202 +  determinant = 0.0;
203 +
204 +  for(i = 0; i < 3; i++) {
205 +    j = (i+1)%3;
206 +    k = (i+2)%3;
207 +
208 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
209 +  }
210 +
211 +  return determinant;
212 + }
213 +
214 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215 +  
216 +  int  i, j, k, l, m, n;
217 +  double determinant;
218 +
219 +  determinant = matDet3( a );
220 +
221 +  if (determinant == 0.0) {
222 +    sprintf( painCave.errMsg,
223 +             "Can't invert a matrix with a zero determinant!\n");
224 +    painCave.isFatal = 1;
225 +    simError();
226 +  }
227 +
228 +  for (i=0; i < 3; i++) {
229 +    j = (i+1)%3;
230 +    k = (i+2)%3;
231 +    for(l = 0; l < 3; l++) {
232 +      m = (l+1)%3;
233 +      n = (l+2)%3;
234 +      
235 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
236 +    }
237 +  }
238 + }
239 +
240 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242 +
243 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
244 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
245 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
246 +  
247 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
248 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
249 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
250 +  
251 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
252 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
253 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
254 +  
255 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
257 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
258 + }
259 +
260 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261 +  double a0, a1, a2;
262 +
263 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
264 +
265 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
266 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
267 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
268 + }
269 +
270 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271 +  double temp[3][3];
272 +  int i, j;
273 +
274 +  for (i = 0; i < 3; i++) {
275 +    for (j = 0; j < 3; j++) {
276 +      temp[j][i] = in[i][j];
277 +    }
278 +  }
279 +  for (i = 0; i < 3; i++) {
280 +    for (j = 0; j < 3; j++) {
281 +      out[i][j] = temp[i][j];
282 +    }
283 +  }
284 + }
285 +  
286 + void SimInfo::printMat3(double A[3][3] ){
287 +
288 +  std::cerr
289 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292 + }
293 +
294 + void SimInfo::printMat9(double A[9] ){
295 +
296 +  std::cerr
297 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300 + }
301 +
302 +
303 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
304 +
305 +      out[0] = a[1] * b[2] - a[2] * b[1];
306 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
307 +      out[2] = a[0] * b[1] - a[1] * b[0];
308 +      
309 + }
310 +
311 + double SimInfo::dotProduct3(double a[3], double b[3]){
312 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
313 + }
314 +
315 + double SimInfo::length3(double a[3]){
316 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
317 + }
318 +
319 + void SimInfo::calcBoxL( void ){
320 +
321 +  double dx, dy, dz, dsq;
322 +
323 +  // boxVol = Determinant of Hmat
324 +
325 +  boxVol = matDet3( Hmat );
326 +
327 +  // boxLx
328 +  
329 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
330 +  dsq = dx*dx + dy*dy + dz*dz;
331 +  boxL[0] = sqrt( dsq );
332 +  //maxCutoff = 0.5 * boxL[0];
333 +
334 +  // boxLy
335 +  
336 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
337 +  dsq = dx*dx + dy*dy + dz*dz;
338 +  boxL[1] = sqrt( dsq );
339 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
340 +
341 +
342 +  // boxLz
343 +  
344 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
345 +  dsq = dx*dx + dy*dy + dz*dz;
346 +  boxL[2] = sqrt( dsq );
347 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
348 +
349 +  //calculate the max cutoff
350 +  maxCutoff =  calcMaxCutOff();
351 +  
352 +  checkCutOffs();
353 +
354   }
355  
356 +
357 + double SimInfo::calcMaxCutOff(){
358 +
359 +  double ri[3], rj[3], rk[3];
360 +  double rij[3], rjk[3], rki[3];
361 +  double minDist;
362 +
363 +  ri[0] = Hmat[0][0];
364 +  ri[1] = Hmat[1][0];
365 +  ri[2] = Hmat[2][0];
366 +
367 +  rj[0] = Hmat[0][1];
368 +  rj[1] = Hmat[1][1];
369 +  rj[2] = Hmat[2][1];
370 +
371 +  rk[0] = Hmat[0][2];
372 +  rk[1] = Hmat[1][2];
373 +  rk[2] = Hmat[2][2];
374 +  
375 +  crossProduct3(ri,rj, rij);
376 +  distXY = dotProduct3(rk,rij) / length3(rij);
377 +
378 +  crossProduct3(rj,rk, rjk);
379 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
380 +
381 +  crossProduct3(rk,ri, rki);
382 +  distZX = dotProduct3(rj,rki) / length3(rki);
383 +
384 +  minDist = min(min(distXY, distYZ), distZX);
385 +  return minDist/2;
386 +  
387 + }
388 +
389 + void SimInfo::wrapVector( double thePos[3] ){
390 +
391 +  int i;
392 +  double scaled[3];
393 +
394 +  if( !orthoRhombic ){
395 +    // calc the scaled coordinates.
396 +  
397 +
398 +    matVecMul3(HmatInv, thePos, scaled);
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 +    matVecMul3(Hmat, scaled, thePos);
406 +
407 +  }
408 +  else{
409 +    // calc the scaled coordinates.
410 +    
411 +    for(i=0; i<3; i++)
412 +      scaled[i] = thePos[i]*HmatInv[i][i];
413 +    
414 +    // wrap the scaled coordinates
415 +    
416 +    for(i=0; i<3; i++)
417 +      scaled[i] -= roundMe(scaled[i]);
418 +    
419 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
420 +    
421 +    for(i=0; i<3; i++)
422 +      thePos[i] = scaled[i]*Hmat[i][i];
423 +  }
424 +    
425 + }
426 +
427 +
428 + int SimInfo::getNDF(){
429 +  int ndf_local;
430 +  
431 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
432 +
433 + #ifdef IS_MPI
434 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
435 + #else
436 +  ndf = ndf_local;
437 + #endif
438 +
439 +  ndf = ndf - 3 - nZconstraints;
440 +
441 +  return ndf;
442 + }
443 +
444 + int SimInfo::getNDFraw() {
445 +  int ndfRaw_local;
446 +
447 +  // Raw degrees of freedom that we have to set
448 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
449 +  
450 + #ifdef IS_MPI
451 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
452 + #else
453 +  ndfRaw = ndfRaw_local;
454 + #endif
455 +
456 +  return ndfRaw;
457 + }
458 +
459 + int SimInfo::getNDFtranslational() {
460 +  int ndfTrans_local;
461 +
462 +  ndfTrans_local = 3 * n_atoms - n_constraints;
463 +
464 + #ifdef IS_MPI
465 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
466 + #else
467 +  ndfTrans = ndfTrans_local;
468 + #endif
469 +
470 +  ndfTrans = ndfTrans - 3 - nZconstraints;
471 +
472 +  return ndfTrans;
473 + }
474 +
475   void SimInfo::refreshSim(){
476  
477    simtype fInfo;
478    int isError;
479 +  int n_global;
480 +  int* excl;
481  
482 <  fInfo.box[0] = box_x;
42 <  fInfo.box[1] = box_y;
43 <  fInfo.box[2] = box_z;
482 >  fInfo.dielect = 0.0;
483  
484 <  fInfo.rlist = rList;
485 <  fInfo.rcut = rCut;
486 <  fInfo.rrf = rRF;
48 <  fInfo.rt = 0.95 * rRF;
49 <  fInfo.dielect = dielectric;
50 <
484 >  if( useDipoles ){
485 >    if( useReactionField )fInfo.dielect = dielectric;
486 >  }
487  
488    fInfo.SIM_uses_PBC = usePBC;
489 +  //fInfo.SIM_uses_LJ = 0;
490    fInfo.SIM_uses_LJ = useLJ;
491    fInfo.SIM_uses_sticky = useSticky;
492 <  fInfo.SIM_uses_dipoles = useDipole;
493 <  fInfo.SIM_uses_RF = useReactionField;
492 >  //fInfo.SIM_uses_sticky = 0;
493 >  fInfo.SIM_uses_charges = useCharges;
494 >  fInfo.SIM_uses_dipoles = useDipoles;
495 >  //fInfo.SIM_uses_dipoles = 0;
496 >  //fInfo.SIM_uses_RF = useReactionField;
497 >  fInfo.SIM_uses_RF = 0;
498    fInfo.SIM_uses_GB = useGB;
499    fInfo.SIM_uses_EAM = useEAM;
500  
501 +  excl = Exclude::getArray();
502  
503 + #ifdef IS_MPI
504 +  n_global = mpiSim->getTotAtoms();
505 + #else
506 +  n_global = n_atoms;
507 + #endif
508 +
509    isError = 0;
510  
511 <  fInfo;
512 <  n_atoms;
513 <  identArray;
66 <  n_exclude;
67 <  excludes;
68 <  nGlobalExcludes;
69 <  globalExcludes;
70 <  isError;
511 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
512 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
513 >                  &isError );
514  
72 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
73 –
515    if( isError ){
516  
517      sprintf( painCave.errMsg,
# Line 84 | Line 525 | void SimInfo::refreshSim(){
525             "succesfully sent the simulation information to fortran.\n");
526    MPIcheckPoint();
527   #endif // is_mpi
528 +
529 +  this->ndf = this->getNDF();
530 +  this->ndfRaw = this->getNDFraw();
531 +  this->ndfTrans = this->getNDFtranslational();
532   }
533  
534 + void SimInfo::setDefaultRcut( double theRcut ){
535 +
536 +  haveRcut = 1;
537 +  rCut = theRcut;
538 +
539 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
540 +
541 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
542 + }
543 +
544 + void SimInfo::setDefaultEcr( double theEcr ){
545 +
546 +  haveEcr = 1;
547 +  ecr = theEcr;
548 +  
549 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
550 +
551 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555 +
556 +  est = theEst;
557 +  setDefaultEcr( theEcr );
558 + }
559 +
560 +
561 + void SimInfo::checkCutOffs( void ){
562 +  
563 +  if( boxIsInit ){
564 +    
565 +    //we need to check cutOffs against the box
566 +    
567 +    if( rCut > maxCutoff ){
568 +      sprintf( painCave.errMsg,
569 +               "Box size is too small for the long range cutoff radius, "
570 +               "%G, at time %G\n"
571 +               "  [ %G %G %G ]\n"
572 +               "  [ %G %G %G ]\n"
573 +               "  [ %G %G %G ]\n",
574 +               rCut, currentTime,
575 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
576 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
577 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
578 +      painCave.isFatal = 1;
579 +      simError();
580 +    }
581 +    
582 +    if( haveEcr ){
583 +      if( ecr > maxCutoff ){
584 +        sprintf( painCave.errMsg,
585 +                 "Box size is too small for the electrostatic cutoff radius, "
586 +                 "%G, at time %G\n"
587 +                 "  [ %G %G %G ]\n"
588 +                 "  [ %G %G %G ]\n"
589 +                 "  [ %G %G %G ]\n",
590 +                 ecr, currentTime,
591 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
592 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
593 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
594 +        painCave.isFatal = 1;
595 +        simError();
596 +      }
597 +    }
598 +  } else {
599 +    // initialize this stuff before using it, OK?
600 +    sprintf( painCave.errMsg,
601 +             "Trying to check cutoffs without a box. Be smarter.\n" );
602 +    painCave.isFatal = 1;
603 +    simError();      
604 +  }
605 +  
606 + }
607 +
608 + void SimInfo::addProperty(GenericData* prop){
609 +
610 +  map<string, GenericData*>::iterator result;
611 +  result = properties.find(prop->getID());
612 +  
613 +  //we can't simply use  properties[prop->getID()] = prop,
614 +  //it will cause memory leak if we already contain a propery which has the same name of prop
615 +  
616 +  if(result != properties.end()){
617 +    
618 +    delete (*result).second;
619 +    (*result).second = prop;
620 +      
621 +  }
622 +  else{
623 +
624 +    properties[prop->getID()] = prop;
625 +
626 +  }
627 +    
628 + }
629 +
630 + GenericData* SimInfo::getProperty(const string& propName){
631 +
632 +  map<string, GenericData*>::iterator result;
633 +  
634 +  //string lowerCaseName = ();
635 +  
636 +  result = properties.find(propName);
637 +  
638 +  if(result != properties.end())
639 +    return (*result).second;  
640 +  else  
641 +    return NULL;  
642 + }
643 +
644 + vector<GenericData*> SimInfo::getProperties(){
645 +
646 +  vector<GenericData*> result;
647 +  map<string, GenericData*>::iterator i;
648 +  
649 +  for(i = properties.begin(); i != properties.end(); i++)
650 +    result.push_back((*i).second);
651 +    
652 +  return result;
653 + }
654 +
655 + double SimInfo::matTrace3(double m[3][3]){
656 +  double trace;
657 +  trace = m[0][0] + m[1][1] + m[2][2];
658 +
659 +  return trace;
660 + }

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