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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 1234 by tim, Fri Jun 4 03:15:31 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 + #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 146 | Line 166 | void SimInfo::calcHmatInv( void ) {
166  
167   void SimInfo::calcHmatInv( void ) {
168    
169 +  int oldOrtho;
170    int i,j;
171    double smallDiag;
172    double tol;
# Line 153 | Line 174 | void SimInfo::calcHmatInv( void ) {
174  
175    invertMat3( Hmat, HmatInv );
176  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
177    // check to see if Hmat is orthorhombic
178    
179 <  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;
179 >  oldOrtho = orthoRhombic;
180  
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 * orthoTolerance;
185 +
186    orthoRhombic = 1;
187    
188    for (i = 0; i < 3; i++ ) {
189      for (j = 0 ; j < 3; j++) {
190        if (i != j) {
191          if (orthoRhombic) {
192 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
192 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
193          }        
194        }
195      }
196    }
178 – }
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 <  }
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;
198 >  if( oldOrtho != orthoRhombic ){
199 >    
200 >    if( orthoRhombic ) {
201 >      sprintf( painCave.errMsg,
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 <  }
212 < }
213 <
214 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
215 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
216 <
217 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
218 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
219 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
220 <  
221 <  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];
211 >    else {
212 >      sprintf( painCave.errMsg,
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    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
224   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
225  
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 –
226   void SimInfo::calcBoxL( void ){
227  
228    double dx, dy, dz, dsq;
# Line 353 | 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 408 | Line 333 | int SimInfo::getNDF(){
333  
334  
335   int SimInfo::getNDF(){
336 <  int ndf_local, ndf;
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;
366   }
367  
368   int SimInfo::getNDFraw() {
369 <  int ndfRaw_local, ndfRaw;
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 439 | Line 391 | int SimInfo::getNDFtranslational() {
391   }
392  
393   int SimInfo::getNDFtranslational() {
394 <  int ndfTrans_local, ndfTrans;
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 454 | 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 463 | 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 472 | 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  
492 <
493 < void SimInfo::setRcut( double theRcut ){
494 <
518 <  if( !haveOrigRcut ){
519 <    haveOrigRcut = 1;
520 <    origRcut = theRcut;
521 <  }
522 <
492 > void SimInfo::setDefaultRcut( double theRcut ){
493 >  
494 >  haveRcut = 1;
495    rCut = theRcut;
496 <  checkCutOffs();
496 >  rList = rCut + 1.0;
497 >  
498 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
499   }
500  
501 < void SimInfo::setEcr( double theEcr ){
501 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
502  
503 <  if( !haveOrigEcr ){
504 <    haveOrigEcr = 1;
531 <    origEcr = theEcr;
532 <  }
533 <
534 <  ecr = theEcr;
535 <  checkCutOffs();
503 >  rSw = theRsw;
504 >  setDefaultRcut( theRcut );
505   }
506  
538 – void SimInfo::setEcr( double theEcr, double theEst ){
507  
540 –  est = theEst;
541 –  setEcr( theEcr );
542 – }
543 –
544 –
508   void SimInfo::checkCutOffs( void ){
546 –
547 –  int cutChanged = 0;
509    
510    if( boxIsInit ){
511      
512      //we need to check cutOffs against the box
513 <
514 <    //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)) {
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;
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 <    
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 661 | Line 577 | GenericData* SimInfo::getProperty(const string& propNa
577      return NULL;  
578   }
579  
664 – 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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