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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 790 by mmeineke, Mon Sep 29 21:16:11 2003 UTC vs.
Revision 1218 by gezelter, Wed Jun 2 14:21:54 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]);
203 <  }
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 >               "\n\tOOPSE 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 >      painCave.severity = OOPSE_INFO;
203 >      simError();
204      }
205 <  }
206 < }
207 <
208 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
209 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
210 <
211 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
212 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
213 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
214 <  
215 <  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];
205 >    else {
206 >      sprintf( painCave.errMsg,
207 >               "\n\tOOPSE is switching from the faster Orthorhombic to the more\n"
208 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
209 >               "\tThis is usually because the box has deformed under\n"
210 >               "\tNPTf integration. If you wan't to live on the edge with\n"
211 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212 >               "\tvariable ( currently set to %G ) larger.\n",
213 >               orthoTolerance);
214 >      painCave.severity = OOPSE_WARNING;
215 >      simError();
216      }
217    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
218   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
219  
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 –
220   void SimInfo::calcBoxL( void ){
221  
222    double dx, dy, dz, dsq;
# Line 353 | Line 272 | double SimInfo::calcMaxCutOff(){
272    rk[0] = Hmat[0][2];
273    rk[1] = Hmat[1][2];
274    rk[2] = Hmat[2][2];
275 <  
276 <  crossProduct3(ri,rj, rij);
277 <  distXY = dotProduct3(rk,rij) / length3(rij);
275 >    
276 >  crossProduct3(ri, rj, rij);
277 >  distXY = dotProduct3(rk,rij) / norm3(rij);
278  
279    crossProduct3(rj,rk, rjk);
280 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
280 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
281  
282    crossProduct3(rk,ri, rki);
283 <  distZX = dotProduct3(rj,rki) / length3(rki);
283 >  distZX = dotProduct3(rj,rki) / norm3(rki);
284  
285    minDist = min(min(distXY, distYZ), distZX);
286    return minDist/2;
# Line 409 | Line 328 | int SimInfo::getNDF(){
328  
329   int SimInfo::getNDF(){
330    int ndf_local;
331 +
332 +  ndf_local = 0;
333    
334 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
334 >  for(int i = 0; i < integrableObjects.size(); i++){
335 >    ndf_local += 3;
336 >    if (integrableObjects[i]->isDirectional()) {
337 >      if (integrableObjects[i]->isLinear())
338 >        ndf_local += 2;
339 >      else
340 >        ndf_local += 3;
341 >    }
342 >  }
343  
344 +  // n_constraints is local, so subtract them on each processor:
345 +
346 +  ndf_local -= n_constraints;
347 +
348   #ifdef IS_MPI
349    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350   #else
351    ndf = ndf_local;
352   #endif
353  
354 +  // nZconstraints is global, as are the 3 COM translations for the
355 +  // entire system:
356 +
357    ndf = ndf - 3 - nZconstraints;
358  
359    return ndf;
# Line 427 | Line 363 | int SimInfo::getNDFraw() {
363    int ndfRaw_local;
364  
365    // Raw degrees of freedom that we have to set
366 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
367 <  
366 >  ndfRaw_local = 0;
367 >
368 >  for(int i = 0; i < integrableObjects.size(); i++){
369 >    ndfRaw_local += 3;
370 >    if (integrableObjects[i]->isDirectional()) {
371 >       if (integrableObjects[i]->isLinear())
372 >        ndfRaw_local += 2;
373 >      else
374 >        ndfRaw_local += 3;
375 >    }
376 >  }
377 >    
378   #ifdef IS_MPI
379    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380   #else
# Line 441 | Line 387 | int SimInfo::getNDFtranslational() {
387   int SimInfo::getNDFtranslational() {
388    int ndfTrans_local;
389  
390 <  ndfTrans_local = 3 * n_atoms - n_constraints;
390 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
391  
392 +
393   #ifdef IS_MPI
394    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395   #else
# Line 454 | Line 401 | int SimInfo::getNDFtranslational() {
401    return ndfTrans;
402   }
403  
404 + int SimInfo::getTotIntegrableObjects() {
405 +  int nObjs_local;
406 +  int nObjs;
407 +
408 +  nObjs_local =  integrableObjects.size();
409 +
410 +
411 + #ifdef IS_MPI
412 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
413 + #else
414 +  nObjs = nObjs_local;
415 + #endif
416 +
417 +
418 +  return nObjs;
419 + }
420 +
421   void SimInfo::refreshSim(){
422  
423    simtype fInfo;
# Line 463 | Line 427 | void SimInfo::refreshSim(){
427  
428    fInfo.dielect = 0.0;
429  
430 <  if( useDipole ){
430 >  if( useDipoles ){
431      if( useReactionField )fInfo.dielect = dielectric;
432    }
433  
# Line 472 | Line 436 | void SimInfo::refreshSim(){
436    fInfo.SIM_uses_LJ = useLJ;
437    fInfo.SIM_uses_sticky = useSticky;
438    //fInfo.SIM_uses_sticky = 0;
439 <  fInfo.SIM_uses_dipoles = useDipole;
439 >  fInfo.SIM_uses_charges = useCharges;
440 >  fInfo.SIM_uses_dipoles = useDipoles;
441    //fInfo.SIM_uses_dipoles = 0;
442 <  //fInfo.SIM_uses_RF = useReactionField;
443 <  fInfo.SIM_uses_RF = 0;
442 >  fInfo.SIM_uses_RF = useReactionField;
443 >  //fInfo.SIM_uses_RF = 0;
444    fInfo.SIM_uses_GB = useGB;
445    fInfo.SIM_uses_EAM = useEAM;
446  
447 <  excl = Exclude::getArray();
448 <
447 >  n_exclude = excludes->getSize();
448 >  excl = excludes->getFortranArray();
449 >  
450   #ifdef IS_MPI
451 <  n_global = mpiSim->getTotAtoms();
451 >  n_global = mpiSim->getNAtomsGlobal();
452   #else
453    n_global = n_atoms;
454   #endif
455 <
455 >  
456    isError = 0;
457 <
457 >  
458 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459 >  //it may not be a good idea to pass the address of first element in vector
460 >  //since c++ standard does not require vector to be stored continuously in meomory
461 >  //Most of the compilers will organize the memory of vector continuously
462    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
464 <                  &isError );
463 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
464 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
465  
466    if( isError ){
467 <
467 >    
468      sprintf( painCave.errMsg,
469 <             "There was an error setting the simulation information in fortran.\n" );
469 >             "There was an error setting the simulation information in fortran.\n" );
470      painCave.isFatal = 1;
471      simError();
472    }
473 <
473 >  
474   #ifdef IS_MPI
475    sprintf( checkPointMsg,
476             "succesfully sent the simulation information to fortran.\n");
477    MPIcheckPoint();
478   #endif // is_mpi
479 <
479 >  
480    this->ndf = this->getNDF();
481    this->ndfRaw = this->getNDFraw();
482    this->ndfTrans = this->getNDFtranslational();
483   }
484  
485 <
486 < void SimInfo::setRcut( double theRcut ){
487 <
518 <  if( !haveOrigRcut ){
519 <    haveOrigRcut = 1;
520 <    origRcut = theRcut;
521 <  }
522 <
485 > void SimInfo::setDefaultRcut( double theRcut ){
486 >  
487 >  haveRcut = 1;
488    rCut = theRcut;
489 <  checkCutOffs();
489 >  rList = rCut + 1.0;
490 >  
491 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
492   }
493  
494 < void SimInfo::setEcr( double theEcr ){
494 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
495  
496 <  if( !haveOrigEcr ){
497 <    haveOrigEcr = 1;
531 <    origEcr = theEcr;
532 <  }
533 <
534 <  ecr = theEcr;
535 <  checkCutOffs();
496 >  rSw = theRsw;
497 >  setDefaultRcut( theRcut );
498   }
499  
538 – void SimInfo::setEcr( double theEcr, double theEst ){
500  
540 –  est = theEst;
541 –  setEcr( theEcr );
542 – }
543 –
544 –
501   void SimInfo::checkCutOffs( void ){
546 –
547 –  int cutChanged = 0;
502    
503    if( boxIsInit ){
504      
505      //we need to check cutOffs against the box
506 <
507 <    //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)) {
506 >    
507 >    if( rCut > maxCutoff ){
508        sprintf( painCave.errMsg,
509 <               "New Box size is setting the long range cutoff radius "
510 <               "to %lf at time %lf\n",
511 <               maxCutoff, currentTime );
512 <      painCave.isFatal = 0;
509 >               "\n\tcutoffRadius is too large for the current periodic box.\n"
510 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
511 >               "\tThis is larger than half of at least one of the\n"
512 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
513 >               "\n"
514 >               "\t[ %G %G %G ]\n"
515 >               "\t[ %G %G %G ]\n"
516 >               "\t[ %G %G %G ]\n",
517 >               rCut, currentTime,
518 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
519 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
520 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
521 >      painCave.severity = OOPSE_ERROR;
522 >      painCave.isFatal = 1;
523        simError();
524 <      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 <    
524 >    }    
525    } else {
526      // initialize this stuff before using it, OK?
527      sprintf( painCave.errMsg,
528 <             "Trying to check cutoffs without a box. Be smarter.\n" );
528 >             "\n\tTrying to check cutoffs without a box.\n"
529 >             "\tOOPSE should have better programmers than that.\n" );
530 >    painCave.severity = OOPSE_ERROR;
531      painCave.isFatal = 1;
532      simError();      
533    }
# Line 661 | Line 570 | GenericData* SimInfo::getProperty(const string& propNa
570      return NULL;  
571   }
572  
664 – vector<GenericData*> SimInfo::getProperties(){
573  
574 <  vector<GenericData*> result;
575 <  map<string, GenericData*>::iterator i;
574 > void SimInfo::getFortranGroupArrays(SimInfo* info,
575 >                                    vector<int>& FglobalGroupMembership,
576 >                                    vector<double>& mfact){
577    
578 <  for(i = properties.begin(); i != properties.end(); i++)
579 <    result.push_back((*i).second);
580 <    
581 <  return result;
582 < }
578 >  Molecule* myMols;
579 >  Atom** myAtoms;
580 >  int numAtom;
581 >  double mtot;
582 >  int numMol;
583 >  int numCutoffGroups;
584 >  CutoffGroup* myCutoffGroup;
585 >  vector<CutoffGroup*>::iterator iterCutoff;
586 >  Atom* cutoffAtom;
587 >  vector<Atom*>::iterator iterAtom;
588 >  int atomIndex;
589 >  double totalMass;
590 >  
591 >  mfact.clear();
592 >  FglobalGroupMembership.clear();
593 >  
594  
595 < double SimInfo::matTrace3(double m[3][3]){
596 <  double trace;
597 <  trace = m[0][0] + m[1][1] + m[2][2];
595 >  // Fix the silly fortran indexing problem
596 > #ifdef IS_MPI
597 >  numAtom = mpiSim->getNAtomsGlobal();
598 > #else
599 >  numAtom = n_atoms;
600 > #endif
601 >  for (int i = 0; i < numAtom; i++)
602 >    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
603 >  
604  
605 <  return trace;
605 >  myMols = info->molecules;
606 >  numMol = info->n_mol;
607 >  for(int i  = 0; i < numMol; i++){
608 >    numCutoffGroups = myMols[i].getNCutoffGroups();
609 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
610 >        myCutoffGroup != NULL;
611 >        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
612 >
613 >      totalMass = myCutoffGroup->getMass();
614 >      
615 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
616 >          cutoffAtom != NULL;
617 >          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
618 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
619 >      }  
620 >    }
621 >  }
622 >
623   }

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