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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 12 | Line 12 | using namespace std;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17 + #include "ConstraintManager.hpp"
18 +
19   #ifdef IS_MPI
20   #include "mpiSimulation.hpp"
21   #endif
# Line 20 | Line 24 | inline double roundMe( double x ){
24    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25   }
26            
27 + inline double min( double a, double b ){
28 +  return (a < b ) ? a : b;
29 + }
30  
31   SimInfo* currentInfo;
32  
33   SimInfo::SimInfo(){
34 <  excludes = NULL;
34 >
35    n_constraints = 0;
36    nZconstraints = 0;
37    n_oriented = 0;
# Line 37 | Line 44 | SimInfo::SimInfo(){
44    thermalTime = 0.0;
45    currentTime = 0.0;
46    rCut = 0.0;
47 <  origRcut = -1.0;
41 <  ecr = 0.0;
42 <  origEcr = -1.0;
43 <  est = 0.0;
44 <  oldEcr = 0.0;
45 <  oldRcut = 0.0;
47 >  rSw = 0.0;
48  
49 <  haveOrigRcut = 0;
50 <  haveOrigEcr = 0;
49 >  haveRcut = 0;
50 >  haveRsw = 0;
51    boxIsInit = 0;
52    
53    resetTime = 1e99;
52 –  
54  
55 +  orthoRhombic = 0;
56 +  orthoTolerance = 1E-6;
57 +  useInitXSstate = true;
58 +
59    usePBC = 0;
60    useLJ = 0;
61    useSticky = 0;
62 <  useDipole = 0;
62 >  useCharges = 0;
63 >  useDipoles = 0;
64    useReactionField = 0;
65    useGB = 0;
66    useEAM = 0;
67 +  useSolidThermInt = 0;
68 +  useLiquidThermInt = 0;
69  
70 +  haveCutoffGroups = false;
71 +
72 +  excludes = Exclude::Instance();
73 +
74    myConfiguration = new SimState();
75  
76 +  has_minimizer = false;
77 +  the_minimizer =NULL;
78 +
79 +  ngroup = 0;
80 +
81 +  consMan = NULL;
82 +  
83    wrapMeSimInfo( this );
84   }
85  
# Line 73 | Line 92 | SimInfo::~SimInfo(){
92    
93    for(i = properties.begin(); i != properties.end(); i++)
94      delete (*i).second;
95 <    
95 >
96 >  if (!consMan)
97 >    delete consMan;  
98   }
99  
100   void SimInfo::setBox(double newBox[3]) {
# Line 102 | Line 123 | void SimInfo::setBoxM( double theBox[3][3] ){
123                           // [ 2 5 8 ]
124    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
125  
105 –  
126    if( !boxIsInit ) boxIsInit = 1;
127  
128    for(i=0; i < 3; i++)
# Line 161 | Line 181 | void SimInfo::calcHmatInv( void ) {
181    smallDiag = fabs(Hmat[0][0]);
182    if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
183    if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
184 <  tol = smallDiag * 1E-6;
184 >  tol = smallDiag * orthoTolerance;
185  
186    orthoRhombic = 1;
187    
# Line 177 | Line 197 | void SimInfo::calcHmatInv( void ) {
197  
198    if( oldOrtho != orthoRhombic ){
199      
200 <    if( orthoRhombic ){
200 >    if( orthoRhombic ) {
201        sprintf( painCave.errMsg,
202 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
203 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
202 >               "OOPSE is switching from the default Non-Orthorhombic\n"
203 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
204 >               "\tThis is usually a good thing, but if you wan't the\n"
205 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
206 >               "\tvariable ( currently set to %G ) smaller.\n",
207 >               orthoTolerance);
208 >      painCave.severity = OOPSE_INFO;
209        simError();
210      }
211      else {
212        sprintf( painCave.errMsg,
213 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
214 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
213 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
214 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
215 >               "\tThis is usually because the box has deformed under\n"
216 >               "\tNPTf integration. If you wan't to live on the edge with\n"
217 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
218 >               "\tvariable ( currently set to %G ) larger.\n",
219 >               orthoTolerance);
220 >      painCave.severity = OOPSE_WARNING;
221        simError();
222      }
223    }
224   }
225  
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 –
226   void SimInfo::calcBoxL( void ){
227  
228    double dx, dy, dz, dsq;
# Line 368 | Line 278 | double SimInfo::calcMaxCutOff(){
278    rk[0] = Hmat[0][2];
279    rk[1] = Hmat[1][2];
280    rk[2] = Hmat[2][2];
281 <  
282 <  crossProduct3(ri,rj, rij);
283 <  distXY = dotProduct3(rk,rij) / length3(rij);
281 >    
282 >  crossProduct3(ri, rj, rij);
283 >  distXY = dotProduct3(rk,rij) / norm3(rij);
284  
285    crossProduct3(rj,rk, rjk);
286 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
286 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
287  
288    crossProduct3(rk,ri, rki);
289 <  distZX = dotProduct3(rj,rki) / length3(rki);
289 >  distZX = dotProduct3(rj,rki) / norm3(rki);
290  
291    minDist = min(min(distXY, distYZ), distZX);
292    return minDist/2;
# Line 424 | Line 334 | int SimInfo::getNDF(){
334  
335   int SimInfo::getNDF(){
336    int ndf_local;
337 +
338 +  ndf_local = 0;
339    
340 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
340 >  for(int i = 0; i < integrableObjects.size(); i++){
341 >    ndf_local += 3;
342 >    if (integrableObjects[i]->isDirectional()) {
343 >      if (integrableObjects[i]->isLinear())
344 >        ndf_local += 2;
345 >      else
346 >        ndf_local += 3;
347 >    }
348 >  }
349  
350 +  // n_constraints is local, so subtract them on each processor:
351 +
352 +  ndf_local -= n_constraints;
353 +
354   #ifdef IS_MPI
355    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356   #else
357    ndf = ndf_local;
358   #endif
359  
360 +  // nZconstraints is global, as are the 3 COM translations for the
361 +  // entire system:
362 +
363    ndf = ndf - 3 - nZconstraints;
364  
365    return ndf;
# Line 442 | Line 369 | int SimInfo::getNDFraw() {
369    int ndfRaw_local;
370  
371    // Raw degrees of freedom that we have to set
372 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
373 <  
372 >  ndfRaw_local = 0;
373 >
374 >  for(int i = 0; i < integrableObjects.size(); i++){
375 >    ndfRaw_local += 3;
376 >    if (integrableObjects[i]->isDirectional()) {
377 >       if (integrableObjects[i]->isLinear())
378 >        ndfRaw_local += 2;
379 >      else
380 >        ndfRaw_local += 3;
381 >    }
382 >  }
383 >    
384   #ifdef IS_MPI
385    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
386   #else
# Line 456 | Line 393 | int SimInfo::getNDFtranslational() {
393   int SimInfo::getNDFtranslational() {
394    int ndfTrans_local;
395  
396 <  ndfTrans_local = 3 * n_atoms - n_constraints;
396 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
397  
398 +
399   #ifdef IS_MPI
400    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
401   #else
# Line 469 | Line 407 | int SimInfo::getNDFtranslational() {
407    return ndfTrans;
408   }
409  
410 + int SimInfo::getTotIntegrableObjects() {
411 +  int nObjs_local;
412 +  int nObjs;
413 +
414 +  nObjs_local =  integrableObjects.size();
415 +
416 +
417 + #ifdef IS_MPI
418 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
419 + #else
420 +  nObjs = nObjs_local;
421 + #endif
422 +
423 +
424 +  return nObjs;
425 + }
426 +
427   void SimInfo::refreshSim(){
428  
429    simtype fInfo;
# Line 478 | Line 433 | void SimInfo::refreshSim(){
433  
434    fInfo.dielect = 0.0;
435  
436 <  if( useDipole ){
436 >  if( useDipoles ){
437      if( useReactionField )fInfo.dielect = dielectric;
438    }
439  
# Line 487 | Line 442 | void SimInfo::refreshSim(){
442    fInfo.SIM_uses_LJ = useLJ;
443    fInfo.SIM_uses_sticky = useSticky;
444    //fInfo.SIM_uses_sticky = 0;
445 <  fInfo.SIM_uses_dipoles = useDipole;
445 >  fInfo.SIM_uses_charges = useCharges;
446 >  fInfo.SIM_uses_dipoles = useDipoles;
447    //fInfo.SIM_uses_dipoles = 0;
448 <  //fInfo.SIM_uses_RF = useReactionField;
449 <  fInfo.SIM_uses_RF = 0;
448 >  fInfo.SIM_uses_RF = useReactionField;
449 >  //fInfo.SIM_uses_RF = 0;
450    fInfo.SIM_uses_GB = useGB;
451    fInfo.SIM_uses_EAM = useEAM;
452  
453 <  excl = Exclude::getArray();
454 <
453 >  n_exclude = excludes->getSize();
454 >  excl = excludes->getFortranArray();
455 >  
456   #ifdef IS_MPI
457 <  n_global = mpiSim->getTotAtoms();
457 >  n_global = mpiSim->getNAtomsGlobal();
458   #else
459    n_global = n_atoms;
460   #endif
461 <
461 >  
462    isError = 0;
463 <
463 >  
464 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
465 >  //it may not be a good idea to pass the address of first element in vector
466 >  //since c++ standard does not require vector to be stored continuously in meomory
467 >  //Most of the compilers will organize the memory of vector continuously
468    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
469 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 <                  &isError );
469 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
471  
472    if( isError ){
473 <
473 >    
474      sprintf( painCave.errMsg,
475 <             "There was an error setting the simulation information in fortran.\n" );
475 >             "There was an error setting the simulation information in fortran.\n" );
476      painCave.isFatal = 1;
477 +    painCave.severity = OOPSE_ERROR;
478      simError();
479    }
480 <
480 >  
481   #ifdef IS_MPI
482    sprintf( checkPointMsg,
483             "succesfully sent the simulation information to fortran.\n");
484    MPIcheckPoint();
485   #endif // is_mpi
486 <
486 >  
487    this->ndf = this->getNDF();
488    this->ndfRaw = this->getNDFraw();
489    this->ndfTrans = this->getNDFtranslational();
490   }
491  
530 –
531 – void SimInfo::setRcut( double theRcut ){
532 –
533 –  rCut = theRcut;
534 –  checkCutOffs();
535 – }
536 –
492   void SimInfo::setDefaultRcut( double theRcut ){
493 <
494 <  haveOrigRcut = 1;
540 <  origRcut = theRcut;
493 >  
494 >  haveRcut = 1;
495    rCut = theRcut;
496 <
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;
496 >  rList = rCut + 1.0;
497    
498 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 <
561 <  ecr = theEcr;
562 <
563 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
498 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
499   }
500  
501 < void SimInfo::setEcr( double theEcr, double theEst ){
501 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
502  
503 <  est = theEst;
504 <  setEcr( theEcr );
503 >  rSw = theRsw;
504 >  setDefaultRcut( theRcut );
505   }
506  
572 – void SimInfo::setDefaultEcr( double theEcr, double theEst ){
507  
574 –  est = theEst;
575 –  setDefaultEcr( theEcr );
576 – }
577 –
578 –
508   void SimInfo::checkCutOffs( void ){
580 –
581 –  int cutChanged = 0;
509    
510    if( boxIsInit ){
511      
512      //we need to check cutOffs against the box
513 <
514 <    //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)) {
513 >    
514 >    if( rCut > maxCutoff ){
515        sprintf( painCave.errMsg,
516 <               "New Box size is setting the long range cutoff radius "
517 <               "to %lf at time %lf\n",
518 <               maxCutoff, currentTime );
519 <      painCave.isFatal = 0;
516 >               "cutoffRadius is too large for the current periodic box.\n"
517 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
518 >               "\tThis is larger than half of at least one of the\n"
519 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
520 >               "\n"
521 >               "\t[ %G %G %G ]\n"
522 >               "\t[ %G %G %G ]\n"
523 >               "\t[ %G %G %G ]\n",
524 >               rCut, currentTime,
525 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
526 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
527 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
528 >      painCave.severity = OOPSE_ERROR;
529 >      painCave.isFatal = 1;
530        simError();
531 <      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 <    
531 >    }    
532    } else {
533      // initialize this stuff before using it, OK?
534      sprintf( painCave.errMsg,
535 <             "Trying to check cutoffs without a box. Be smarter.\n" );
535 >             "Trying to check cutoffs without a box.\n"
536 >             "\tOOPSE should have better programmers than that.\n" );
537 >    painCave.severity = OOPSE_ERROR;
538      painCave.isFatal = 1;
539      simError();      
540    }
# Line 694 | Line 577 | GenericData* SimInfo::getProperty(const string& propNa
577      return NULL;  
578   }
579  
697 – vector<GenericData*> SimInfo::getProperties(){
580  
581 <  vector<GenericData*> result;
582 <  map<string, GenericData*>::iterator i;
581 > void SimInfo::getFortranGroupArrays(SimInfo* info,
582 >                                    vector<int>& FglobalGroupMembership,
583 >                                    vector<double>& mfact){
584    
585 <  for(i = properties.begin(); i != properties.end(); i++)
586 <    result.push_back((*i).second);
587 <    
588 <  return result;
589 < }
585 >  Molecule* myMols;
586 >  Atom** myAtoms;
587 >  int numAtom;
588 >  double mtot;
589 >  int numMol;
590 >  int numCutoffGroups;
591 >  CutoffGroup* myCutoffGroup;
592 >  vector<CutoffGroup*>::iterator iterCutoff;
593 >  Atom* cutoffAtom;
594 >  vector<Atom*>::iterator iterAtom;
595 >  int atomIndex;
596 >  double totalMass;
597 >  
598 >  mfact.clear();
599 >  FglobalGroupMembership.clear();
600 >  
601  
602 < double SimInfo::matTrace3(double m[3][3]){
603 <  double trace;
604 <  trace = m[0][0] + m[1][1] + m[2][2];
602 >  // Fix the silly fortran indexing problem
603 > #ifdef IS_MPI
604 >  numAtom = mpiSim->getNAtomsGlobal();
605 > #else
606 >  numAtom = n_atoms;
607 > #endif
608 >  for (int i = 0; i < numAtom; i++)
609 >    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
610 >  
611  
612 <  return trace;
612 >  myMols = info->molecules;
613 >  numMol = info->n_mol;
614 >  for(int i  = 0; i < numMol; i++){
615 >    numCutoffGroups = myMols[i].getNCutoffGroups();
616 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
617 >        myCutoffGroup != NULL;
618 >        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
619 >
620 >      totalMass = myCutoffGroup->getMass();
621 >      
622 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
623 >          cutoffAtom != NULL;
624 >          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
625 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
626 >      }  
627 >    }
628 >  }
629 >
630   }

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