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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 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 12 | Line 12 | using namespace std;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
# Line 20 | Line 22 | inline double roundMe( double x ){
22    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23   }
24            
25 + inline double min( double a, double b ){
26 +  return (a < b ) ? a : b;
27 + }
28  
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34    nZconstraints = 0;
35    n_oriented = 0;
# Line 37 | Line 42 | SimInfo::SimInfo(){
42    thermalTime = 0.0;
43    currentTime = 0.0;
44    rCut = 0.0;
45 <  origRcut = -1.0;
41 <  ecr = 0.0;
42 <  origEcr = -1.0;
43 <  est = 0.0;
44 <  oldEcr = 0.0;
45 <  oldRcut = 0.0;
45 >  rSw = 0.0;
46  
47 <  haveOrigRcut = 0;
48 <  haveOrigEcr = 0;
47 >  haveRcut = 0;
48 >  haveRsw = 0;
49    boxIsInit = 0;
50    
51    resetTime = 1e99;
52 –  
52  
53 +  orthoRhombic = 0;
54 +  orthoTolerance = 1E-6;
55 +  useInitXSstate = true;
56 +
57    usePBC = 0;
58    useLJ = 0;
59    useSticky = 0;
60 <  useDipole = 0;
60 >  useCharges = 0;
61 >  useDipoles = 0;
62    useReactionField = 0;
63    useGB = 0;
64    useEAM = 0;
65 +  useSolidThermInt = 0;
66 +  useLiquidThermInt = 0;
67  
68 +  haveCutoffGroups = false;
69 +
70 +  excludes = Exclude::Instance();
71 +
72    myConfiguration = new SimState();
73  
74 +  has_minimizer = false;
75 +  the_minimizer =NULL;
76 +
77 +  ngroup = 0;
78 +
79    wrapMeSimInfo( this );
80   }
81  
# Line 73 | Line 88 | SimInfo::~SimInfo(){
88    
89    for(i = properties.begin(); i != properties.end(); i++)
90      delete (*i).second;
91 <    
91 >  
92   }
93  
94   void SimInfo::setBox(double newBox[3]) {
# Line 102 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){
117                           // [ 2 5 8 ]
118    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119  
105 –  
120    if( !boxIsInit ) boxIsInit = 1;
121  
122    for(i=0; i < 3; i++)
# Line 146 | Line 160 | void SimInfo::calcHmatInv( void ) {
160  
161   void SimInfo::calcHmatInv( void ) {
162    
163 +  int oldOrtho;
164    int i,j;
165    double smallDiag;
166    double tol;
# Line 153 | Line 168 | void SimInfo::calcHmatInv( void ) {
168  
169    invertMat3( Hmat, HmatInv );
170  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
171    // check to see if Hmat is orthorhombic
172    
173 <  smallDiag = Hmat[0][0];
163 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 <  tol = smallDiag * 1E-6;
173 >  oldOrtho = orthoRhombic;
174  
175 +  smallDiag = fabs(Hmat[0][0]);
176 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178 +  tol = smallDiag * orthoTolerance;
179 +
180    orthoRhombic = 1;
181    
182    for (i = 0; i < 3; i++ ) {
183      for (j = 0 ; j < 3; j++) {
184        if (i != j) {
185          if (orthoRhombic) {
186 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
186 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187          }        
188        }
189      }
190    }
178 – }
191  
192 < double SimInfo::matDet3(double a[3][3]) {
193 <  int i, j, k;
194 <  double determinant;
195 <
196 <  determinant = 0.0;
197 <
198 <  for(i = 0; i < 3; i++) {
199 <    j = (i+1)%3;
200 <    k = (i+2)%3;
201 <
202 <    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
191 <  }
192 <
193 <  return determinant;
194 < }
195 <
196 < void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
197 <  
198 <  int  i, j, k, l, m, n;
199 <  double determinant;
200 <
201 <  determinant = matDet3( a );
202 <
203 <  if (determinant == 0.0) {
204 <    sprintf( painCave.errMsg,
205 <             "Can't invert a matrix with a zero determinant!\n");
206 <    painCave.isFatal = 1;
207 <    simError();
208 <  }
209 <
210 <  for (i=0; i < 3; i++) {
211 <    j = (i+1)%3;
212 <    k = (i+2)%3;
213 <    for(l = 0; l < 3; l++) {
214 <      m = (l+1)%3;
215 <      n = (l+2)%3;
216 <      
217 <      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
192 >  if( oldOrtho != orthoRhombic ){
193 >    
194 >    if( orthoRhombic ){
195 >      sprintf( painCave.errMsg,
196 >               "OOPSE is switching from the default Non-Orthorhombic\n"
197 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
198 >               "\tThis is usually a good thing, but if you wan't the\n"
199 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200 >               "\tvariable ( currently set to %G ) smaller.\n",
201 >               orthoTolerance);
202 >      simError();
203      }
204 <  }
205 < }
206 <
207 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
208 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
209 <
210 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
211 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
212 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
213 <  
229 <  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
230 <  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
231 <  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
232 <  
233 <  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
234 <  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
235 <  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
236 <  
237 <  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
238 <  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
239 <  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
240 < }
241 <
242 < void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
243 <  double a0, a1, a2;
244 <
245 <  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
246 <
247 <  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
248 <  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
249 <  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
250 < }
251 <
252 < void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
253 <  double temp[3][3];
254 <  int i, j;
255 <
256 <  for (i = 0; i < 3; i++) {
257 <    for (j = 0; j < 3; j++) {
258 <      temp[j][i] = in[i][j];
204 >    else {
205 >      sprintf( painCave.errMsg,
206 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
207 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
208 >               "\tThis is usually because the box has deformed under\n"
209 >               "\tNPTf integration. If you wan't to live on the edge with\n"
210 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
211 >               "\tvariable ( currently set to %G ) larger.\n",
212 >               orthoTolerance);
213 >      simError();
214      }
215    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
216   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
217  
270 –  std::cerr
271 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
272 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
273 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
274 – }
275 –
276 – void SimInfo::printMat9(double A[9] ){
277 –
278 –  std::cerr
279 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 – }
283 –
284 –
285 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
286 –
287 –      out[0] = a[1] * b[2] - a[2] * b[1];
288 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
289 –      out[2] = a[0] * b[1] - a[1] * b[0];
290 –      
291 – }
292 –
293 – double SimInfo::dotProduct3(double a[3], double b[3]){
294 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
295 – }
296 –
297 – double SimInfo::length3(double a[3]){
298 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
299 – }
300 –
218   void SimInfo::calcBoxL( void ){
219  
220    double dx, dy, dz, dsq;
# Line 353 | Line 270 | double SimInfo::calcMaxCutOff(){
270    rk[0] = Hmat[0][2];
271    rk[1] = Hmat[1][2];
272    rk[2] = Hmat[2][2];
273 <  
274 <  crossProduct3(ri,rj, rij);
275 <  distXY = dotProduct3(rk,rij) / length3(rij);
273 >    
274 >  crossProduct3(ri, rj, rij);
275 >  distXY = dotProduct3(rk,rij) / norm3(rij);
276  
277    crossProduct3(rj,rk, rjk);
278 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
278 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
279  
280    crossProduct3(rk,ri, rki);
281 <  distZX = dotProduct3(rj,rki) / length3(rki);
281 >  distZX = dotProduct3(rj,rki) / norm3(rki);
282  
283    minDist = min(min(distXY, distYZ), distZX);
284    return minDist/2;
# Line 408 | Line 325 | int SimInfo::getNDF(){
325  
326  
327   int SimInfo::getNDF(){
328 <  int ndf_local, ndf;
328 >  int ndf_local;
329 >
330 >  ndf_local = 0;
331    
332 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
332 >  for(int i = 0; i < integrableObjects.size(); i++){
333 >    ndf_local += 3;
334 >    if (integrableObjects[i]->isDirectional()) {
335 >      if (integrableObjects[i]->isLinear())
336 >        ndf_local += 2;
337 >      else
338 >        ndf_local += 3;
339 >    }
340 >  }
341  
342 +  // n_constraints is local, so subtract them on each processor:
343 +
344 +  ndf_local -= n_constraints;
345 +
346   #ifdef IS_MPI
347    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
348   #else
349    ndf = ndf_local;
350   #endif
351  
352 +  // nZconstraints is global, as are the 3 COM translations for the
353 +  // entire system:
354 +
355    ndf = ndf - 3 - nZconstraints;
356  
357    return ndf;
358   }
359  
360   int SimInfo::getNDFraw() {
361 <  int ndfRaw_local, ndfRaw;
361 >  int ndfRaw_local;
362  
363    // Raw degrees of freedom that we have to set
364 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
365 <  
364 >  ndfRaw_local = 0;
365 >
366 >  for(int i = 0; i < integrableObjects.size(); i++){
367 >    ndfRaw_local += 3;
368 >    if (integrableObjects[i]->isDirectional()) {
369 >       if (integrableObjects[i]->isLinear())
370 >        ndfRaw_local += 2;
371 >      else
372 >        ndfRaw_local += 3;
373 >    }
374 >  }
375 >    
376   #ifdef IS_MPI
377    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378   #else
# Line 439 | Line 383 | int SimInfo::getNDFtranslational() {
383   }
384  
385   int SimInfo::getNDFtranslational() {
386 <  int ndfTrans_local, ndfTrans;
386 >  int ndfTrans_local;
387  
388 <  ndfTrans_local = 3 * n_atoms - n_constraints;
388 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
389 >
390  
391   #ifdef IS_MPI
392    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
# Line 454 | Line 399 | int SimInfo::getNDFtranslational() {
399    return ndfTrans;
400   }
401  
402 + int SimInfo::getTotIntegrableObjects() {
403 +  int nObjs_local;
404 +  int nObjs;
405 +
406 +  nObjs_local =  integrableObjects.size();
407 +
408 +
409 + #ifdef IS_MPI
410 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
411 + #else
412 +  nObjs = nObjs_local;
413 + #endif
414 +
415 +
416 +  return nObjs;
417 + }
418 +
419   void SimInfo::refreshSim(){
420  
421    simtype fInfo;
# Line 463 | Line 425 | void SimInfo::refreshSim(){
425  
426    fInfo.dielect = 0.0;
427  
428 <  if( useDipole ){
428 >  if( useDipoles ){
429      if( useReactionField )fInfo.dielect = dielectric;
430    }
431  
# Line 472 | Line 434 | void SimInfo::refreshSim(){
434    fInfo.SIM_uses_LJ = useLJ;
435    fInfo.SIM_uses_sticky = useSticky;
436    //fInfo.SIM_uses_sticky = 0;
437 <  fInfo.SIM_uses_dipoles = useDipole;
437 >  fInfo.SIM_uses_charges = useCharges;
438 >  fInfo.SIM_uses_dipoles = useDipoles;
439    //fInfo.SIM_uses_dipoles = 0;
440 <  //fInfo.SIM_uses_RF = useReactionField;
441 <  fInfo.SIM_uses_RF = 0;
440 >  fInfo.SIM_uses_RF = useReactionField;
441 >  //fInfo.SIM_uses_RF = 0;
442    fInfo.SIM_uses_GB = useGB;
443    fInfo.SIM_uses_EAM = useEAM;
444  
445 <  excl = Exclude::getArray();
446 <
445 >  n_exclude = excludes->getSize();
446 >  excl = excludes->getFortranArray();
447 >  
448   #ifdef IS_MPI
449 <  n_global = mpiSim->getTotAtoms();
449 >  n_global = mpiSim->getNAtomsGlobal();
450   #else
451    n_global = n_atoms;
452   #endif
453 <
453 >  
454    isError = 0;
455 <
455 >  
456 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
457 >  //it may not be a good idea to pass the address of first element in vector
458 >  //since c++ standard does not require vector to be stored continuously in meomory
459 >  //Most of the compilers will organize the memory of vector continuously
460    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
461 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 <                  &isError );
463 <
461 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
463 >  
464    if( isError ){
465 <
465 >    
466      sprintf( painCave.errMsg,
467 <             "There was an error setting the simulation information in fortran.\n" );
467 >             "There was an error setting the simulation information in fortran.\n" );
468      painCave.isFatal = 1;
469      simError();
470    }
471 <
471 >  
472   #ifdef IS_MPI
473    sprintf( checkPointMsg,
474             "succesfully sent the simulation information to fortran.\n");
475    MPIcheckPoint();
476   #endif // is_mpi
477 <
477 >  
478    this->ndf = this->getNDF();
479    this->ndfRaw = this->getNDFraw();
480    this->ndfTrans = this->getNDFtranslational();
481   }
482  
483 <
484 < void SimInfo::setRcut( double theRcut ){
485 <
518 <  if( !haveOrigRcut ){
519 <    haveOrigRcut = 1;
520 <    origRcut = theRcut;
521 <  }
522 <
483 > void SimInfo::setDefaultRcut( double theRcut ){
484 >  
485 >  haveRcut = 1;
486    rCut = theRcut;
487 <  checkCutOffs();
487 >  rList = rCut + 1.0;
488 >  
489 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
490   }
491  
492 < void SimInfo::setEcr( double theEcr ){
492 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
493  
494 <  if( !haveOrigEcr ){
495 <    haveOrigEcr = 1;
531 <    origEcr = theEcr;
532 <  }
533 <
534 <  ecr = theEcr;
535 <  checkCutOffs();
494 >  rSw = theRsw;
495 >  setDefaultRcut( theRcut );
496   }
497  
538 – void SimInfo::setEcr( double theEcr, double theEst ){
498  
540 –  est = theEst;
541 –  setEcr( theEcr );
542 – }
543 –
544 –
499   void SimInfo::checkCutOffs( void ){
546 –
547 –  int cutChanged = 0;
500    
501    if( boxIsInit ){
502      
503      //we need to check cutOffs against the box
504 <
505 <    //detect the change of rCut
554 <    if(( maxCutoff > rCut )&&(usePBC)){
555 <      if( rCut < origRcut ){
556 <        rCut = origRcut;
557 <        
558 <        if (rCut > maxCutoff)
559 <          rCut = maxCutoff;
560 <  
561 <          sprintf( painCave.errMsg,
562 <                    "New Box size is setting the long range cutoff radius "
563 <                    "to %lf at time %lf\n",
564 <                    rCut, currentTime );
565 <          painCave.isFatal = 0;
566 <          simError();
567 <      }
568 <    }
569 <    else if ((rCut > maxCutoff)&&(usePBC)) {
504 >    
505 >    if( rCut > maxCutoff ){
506        sprintf( painCave.errMsg,
507 <               "New Box size is setting the long range cutoff radius "
508 <               "to %lf at time %lf\n",
509 <               maxCutoff, currentTime );
510 <      painCave.isFatal = 0;
507 >               "cutoffRadius is too large for the current periodic box.\n"
508 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
509 >               "\tThis is larger than half of at least one of the\n"
510 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
511 >               "\n"
512 >               "\t[ %G %G %G ]\n"
513 >               "\t[ %G %G %G ]\n"
514 >               "\t[ %G %G %G ]\n",
515 >               rCut, currentTime,
516 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
517 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
518 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
519 >      painCave.isFatal = 1;
520        simError();
521 <      rCut = maxCutoff;
577 <    }
578 <
579 <
580 <    //detect the change of ecr
581 <    if( maxCutoff > ecr ){
582 <      if( ecr < origEcr ){
583 <        ecr = origEcr;
584 <        if (ecr > maxCutoff) ecr = maxCutoff;
585 <  
586 <          sprintf( painCave.errMsg,
587 <                    "New Box size is setting the electrostaticCutoffRadius "
588 <                    "to %lf at time %lf\n",
589 <                    ecr, currentTime );
590 <            painCave.isFatal = 0;
591 <            simError();
592 <      }
593 <    }
594 <    else if( ecr > maxCutoff){
595 <      sprintf( painCave.errMsg,
596 <               "New Box size is setting the electrostaticCutoffRadius "
597 <               "to %lf at time %lf\n",
598 <               maxCutoff, currentTime  );
599 <      painCave.isFatal = 0;
600 <      simError();      
601 <      ecr = maxCutoff;
602 <    }
603 <
604 <    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
605 <    
606 <    // rlist is the 1.0 plus max( rcut, ecr )
607 <    
608 <    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
609 <    
610 <    if( cutChanged ){
611 <      
612 <      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
613 <    }
614 <    
615 <    oldEcr = ecr;
616 <    oldRcut = rCut;
617 <    
521 >    }    
522    } else {
523      // initialize this stuff before using it, OK?
524      sprintf( painCave.errMsg,
525 <             "Trying to check cutoffs without a box. Be smarter.\n" );
525 >             "Trying to check cutoffs without a box.\n"
526 >             "\tOOPSE should have better programmers than that.\n" );
527      painCave.isFatal = 1;
528      simError();      
529    }
# Line 661 | Line 566 | GenericData* SimInfo::getProperty(const string& propNa
566      return NULL;  
567   }
568  
664 – vector<GenericData*> SimInfo::getProperties(){
569  
570 <  vector<GenericData*> result;
571 <  map<string, GenericData*>::iterator i;
570 > void SimInfo::getFortranGroupArrays(SimInfo* info,
571 >                                    vector<int>& FglobalGroupMembership,
572 >                                    vector<double>& mfact){
573    
574 <  for(i = properties.begin(); i != properties.end(); i++)
575 <    result.push_back((*i).second);
576 <    
577 <  return result;
578 < }
574 >  Molecule* myMols;
575 >  Atom** myAtoms;
576 >  int numAtom;
577 >  double mtot;
578 >  int numMol;
579 >  int numCutoffGroups;
580 >  CutoffGroup* myCutoffGroup;
581 >  vector<CutoffGroup*>::iterator iterCutoff;
582 >  Atom* cutoffAtom;
583 >  vector<Atom*>::iterator iterAtom;
584 >  int atomIndex;
585 >  double totalMass;
586 >  
587 >  mfact.clear();
588 >  FglobalGroupMembership.clear();
589 >  
590  
591 < double SimInfo::matTrace3(double m[3][3]){
592 <  double trace;
593 <  trace = m[0][0] + m[1][1] + m[2][2];
591 >  // Fix the silly fortran indexing problem
592 > #ifdef IS_MPI
593 >  numAtom = mpiSim->getNAtomsGlobal();
594 > #else
595 >  numAtom = n_atoms;
596 > #endif
597 >  for (int i = 0; i < numAtom; i++)
598 >    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
599  
600 <  return trace;
600 >  myMols = info->molecules;
601 >  numMol = info->n_mol;
602 >  for(int i  = 0; i < numMol; i++){
603 >    numCutoffGroups = myMols[i].getNCutoffGroups();
604 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
605 >        myCutoffGroup != NULL;
606 >        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
607 >
608 >      totalMass = myCutoffGroup->getMass();
609 >      
610 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
611 >          cutoffAtom != NULL;
612 >          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
613 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
614 >      }  
615 >    }
616 >  }
617 >
618   }

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