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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 UTC

# 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  
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 +  useThermInt = 0;
66  
67 +  haveCutoffGroups = false;
68 +
69 +  excludes = Exclude::Instance();
70 +
71    myConfiguration = new SimState();
72  
73 +  has_minimizer = false;
74 +  the_minimizer =NULL;
75 +
76 +  ngroup = 0;
77 +
78    wrapMeSimInfo( this );
79   }
80  
# Line 75 | Line 87 | SimInfo::~SimInfo(){
87    
88    for(i = properties.begin(); i != properties.end(); i++)
89      delete (*i).second;
90 <    
90 >  
91   }
92  
93   void SimInfo::setBox(double newBox[3]) {
# Line 104 | Line 116 | void SimInfo::setBoxM( double theBox[3][3] ){
116                           // [ 2 5 8 ]
117    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
118  
107 –  
119    if( !boxIsInit ) boxIsInit = 1;
120  
121    for(i=0; i < 3; i++)
# Line 181 | Line 192 | void SimInfo::calcHmatInv( void ) {
192      
193      if( orthoRhombic ){
194        sprintf( painCave.errMsg,
195 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
196 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
195 >               "OOPSE is switching from the default Non-Orthorhombic\n"
196 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
197 >               "\tThis is usually a good thing, but if you wan't the\n"
198 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
199 >               "\tvariable ( currently set to %G ) smaller.\n",
200                 orthoTolerance);
201        simError();
202      }
203      else {
204        sprintf( painCave.errMsg,
205 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
206 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
205 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
206 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
207 >               "\tThis is usually because the box has deformed under\n"
208 >               "\tNPTf integration. If you wan't to live on the edge with\n"
209 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
210 >               "\tvariable ( currently set to %G ) larger.\n",
211                 orthoTolerance);
212        simError();
213      }
214    }
215   }
216  
199 – double SimInfo::matDet3(double a[3][3]) {
200 –  int i, j, k;
201 –  double determinant;
202 –
203 –  determinant = 0.0;
204 –
205 –  for(i = 0; i < 3; i++) {
206 –    j = (i+1)%3;
207 –    k = (i+2)%3;
208 –
209 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
210 –  }
211 –
212 –  return determinant;
213 – }
214 –
215 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216 –  
217 –  int  i, j, k, l, m, n;
218 –  double determinant;
219 –
220 –  determinant = matDet3( a );
221 –
222 –  if (determinant == 0.0) {
223 –    sprintf( painCave.errMsg,
224 –             "Can't invert a matrix with a zero determinant!\n");
225 –    painCave.isFatal = 1;
226 –    simError();
227 –  }
228 –
229 –  for (i=0; i < 3; i++) {
230 –    j = (i+1)%3;
231 –    k = (i+2)%3;
232 –    for(l = 0; l < 3; l++) {
233 –      m = (l+1)%3;
234 –      n = (l+2)%3;
235 –      
236 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
237 –    }
238 –  }
239 – }
240 –
241 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
242 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
243 –
244 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
245 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
246 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
247 –  
248 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
249 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
250 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
251 –  
252 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
253 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
254 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
255 –  
256 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
257 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
258 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
259 – }
260 –
261 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
262 –  double a0, a1, a2;
263 –
264 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
265 –
266 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
267 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
268 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
269 – }
270 –
271 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272 –  double temp[3][3];
273 –  int i, j;
274 –
275 –  for (i = 0; i < 3; i++) {
276 –    for (j = 0; j < 3; j++) {
277 –      temp[j][i] = in[i][j];
278 –    }
279 –  }
280 –  for (i = 0; i < 3; i++) {
281 –    for (j = 0; j < 3; j++) {
282 –      out[i][j] = temp[i][j];
283 –    }
284 –  }
285 – }
286 –  
287 – void SimInfo::printMat3(double A[3][3] ){
288 –
289 –  std::cerr
290 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293 – }
294 –
295 – void SimInfo::printMat9(double A[9] ){
296 –
297 –  std::cerr
298 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301 – }
302 –
303 –
304 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
305 –
306 –      out[0] = a[1] * b[2] - a[2] * b[1];
307 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
308 –      out[2] = a[0] * b[1] - a[1] * b[0];
309 –      
310 – }
311 –
312 – double SimInfo::dotProduct3(double a[3], double b[3]){
313 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
314 – }
315 –
316 – double SimInfo::length3(double a[3]){
317 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
318 – }
319 –
217   void SimInfo::calcBoxL( void ){
218  
219    double dx, dy, dz, dsq;
# Line 372 | Line 269 | double SimInfo::calcMaxCutOff(){
269    rk[0] = Hmat[0][2];
270    rk[1] = Hmat[1][2];
271    rk[2] = Hmat[2][2];
272 <  
273 <  crossProduct3(ri,rj, rij);
274 <  distXY = dotProduct3(rk,rij) / length3(rij);
272 >    
273 >  crossProduct3(ri, rj, rij);
274 >  distXY = dotProduct3(rk,rij) / norm3(rij);
275  
276    crossProduct3(rj,rk, rjk);
277 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
277 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
278  
279    crossProduct3(rk,ri, rki);
280 <  distZX = dotProduct3(rj,rki) / length3(rki);
280 >  distZX = dotProduct3(rj,rki) / norm3(rki);
281  
282    minDist = min(min(distXY, distYZ), distZX);
283    return minDist/2;
# Line 428 | Line 325 | int SimInfo::getNDF(){
325  
326   int SimInfo::getNDF(){
327    int ndf_local;
328 +
329 +  ndf_local = 0;
330    
331 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
331 >  for(int i = 0; i < integrableObjects.size(); i++){
332 >    ndf_local += 3;
333 >    if (integrableObjects[i]->isDirectional()) {
334 >      if (integrableObjects[i]->isLinear())
335 >        ndf_local += 2;
336 >      else
337 >        ndf_local += 3;
338 >    }
339 >  }
340  
341 +  // n_constraints is local, so subtract them on each processor:
342 +
343 +  ndf_local -= n_constraints;
344 +
345   #ifdef IS_MPI
346    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
347   #else
348    ndf = ndf_local;
349   #endif
350  
351 +  // nZconstraints is global, as are the 3 COM translations for the
352 +  // entire system:
353 +
354    ndf = ndf - 3 - nZconstraints;
355  
356    return ndf;
# Line 446 | Line 360 | int SimInfo::getNDFraw() {
360    int ndfRaw_local;
361  
362    // Raw degrees of freedom that we have to set
363 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
364 <  
363 >  ndfRaw_local = 0;
364 >
365 >  for(int i = 0; i < integrableObjects.size(); i++){
366 >    ndfRaw_local += 3;
367 >    if (integrableObjects[i]->isDirectional()) {
368 >       if (integrableObjects[i]->isLinear())
369 >        ndfRaw_local += 2;
370 >      else
371 >        ndfRaw_local += 3;
372 >    }
373 >  }
374 >    
375   #ifdef IS_MPI
376    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
377   #else
# Line 460 | Line 384 | int SimInfo::getNDFtranslational() {
384   int SimInfo::getNDFtranslational() {
385    int ndfTrans_local;
386  
387 <  ndfTrans_local = 3 * n_atoms - n_constraints;
387 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
388  
389 +
390   #ifdef IS_MPI
391    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
392   #else
# Line 473 | Line 398 | int SimInfo::getNDFtranslational() {
398    return ndfTrans;
399   }
400  
401 + int SimInfo::getTotIntegrableObjects() {
402 +  int nObjs_local;
403 +  int nObjs;
404 +
405 +  nObjs_local =  integrableObjects.size();
406 +
407 +
408 + #ifdef IS_MPI
409 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
410 + #else
411 +  nObjs = nObjs_local;
412 + #endif
413 +
414 +
415 +  return nObjs;
416 + }
417 +
418   void SimInfo::refreshSim(){
419  
420    simtype fInfo;
# Line 482 | Line 424 | void SimInfo::refreshSim(){
424  
425    fInfo.dielect = 0.0;
426  
427 <  if( useDipole ){
427 >  if( useDipoles ){
428      if( useReactionField )fInfo.dielect = dielectric;
429    }
430  
# Line 491 | Line 433 | void SimInfo::refreshSim(){
433    fInfo.SIM_uses_LJ = useLJ;
434    fInfo.SIM_uses_sticky = useSticky;
435    //fInfo.SIM_uses_sticky = 0;
436 <  fInfo.SIM_uses_dipoles = useDipole;
436 >  fInfo.SIM_uses_charges = useCharges;
437 >  fInfo.SIM_uses_dipoles = useDipoles;
438    //fInfo.SIM_uses_dipoles = 0;
439 <  //fInfo.SIM_uses_RF = useReactionField;
440 <  fInfo.SIM_uses_RF = 0;
439 >  fInfo.SIM_uses_RF = useReactionField;
440 >  //fInfo.SIM_uses_RF = 0;
441    fInfo.SIM_uses_GB = useGB;
442    fInfo.SIM_uses_EAM = useEAM;
443  
444 <  excl = Exclude::getArray();
445 <
444 >  n_exclude = excludes->getSize();
445 >  excl = excludes->getFortranArray();
446 >  
447   #ifdef IS_MPI
448    n_global = mpiSim->getTotAtoms();
449   #else
450    n_global = n_atoms;
451   #endif
452 <
452 >  
453    isError = 0;
454 <
454 >  
455 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
456 >  //it may not be a good idea to pass the address of first element in vector
457 >  //since c++ standard does not require vector to be stored continuously in meomory
458 >  //Most of the compilers will organize the memory of vector continuously
459    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
460 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
461 <                  &isError );
462 <
460 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
461 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
462 >  
463    if( isError ){
464 <
464 >    
465      sprintf( painCave.errMsg,
466 <             "There was an error setting the simulation information in fortran.\n" );
466 >             "There was an error setting the simulation information in fortran.\n" );
467      painCave.isFatal = 1;
468      simError();
469    }
470 <
470 >  
471   #ifdef IS_MPI
472    sprintf( checkPointMsg,
473             "succesfully sent the simulation information to fortran.\n");
474    MPIcheckPoint();
475   #endif // is_mpi
476 <
476 >  
477    this->ndf = this->getNDF();
478    this->ndfRaw = this->getNDFraw();
479    this->ndfTrans = this->getNDFtranslational();
480   }
481  
534 –
535 – void SimInfo::setRcut( double theRcut ){
536 –
537 –  rCut = theRcut;
538 –  checkCutOffs();
539 – }
540 –
482   void SimInfo::setDefaultRcut( double theRcut ){
483 <
484 <  haveOrigRcut = 1;
544 <  origRcut = theRcut;
483 >  
484 >  haveRcut = 1;
485    rCut = theRcut;
486 <
547 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 <
549 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550 < }
551 <
552 < void SimInfo::setEcr( double theEcr ){
553 <
554 <  ecr = theEcr;
555 <  checkCutOffs();
556 < }
557 <
558 < void SimInfo::setDefaultEcr( double theEcr ){
559 <
560 <  haveOrigEcr = 1;
561 <  origEcr = theEcr;
486 >  rList = rCut + 1.0;
487    
488 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 <
565 <  ecr = theEcr;
566 <
567 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
488 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
489   }
490  
491 < void SimInfo::setEcr( double theEcr, double theEst ){
491 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
492  
493 <  est = theEst;
494 <  setEcr( theEcr );
493 >  rSw = theRsw;
494 >  setDefaultRcut( theRcut );
495   }
496  
576 – void SimInfo::setDefaultEcr( double theEcr, double theEst ){
497  
578 –  est = theEst;
579 –  setDefaultEcr( theEcr );
580 – }
581 –
582 –
498   void SimInfo::checkCutOffs( void ){
584 –
585 –  int cutChanged = 0;
499    
500    if( boxIsInit ){
501      
502      //we need to check cutOffs against the box
503 <
504 <    //detect the change of rCut
592 <    if(( maxCutoff > rCut )&&(usePBC)){
593 <      if( rCut < origRcut ){
594 <        rCut = origRcut;
595 <        
596 <        if (rCut > maxCutoff)
597 <          rCut = maxCutoff;
598 <  
599 <          sprintf( painCave.errMsg,
600 <                    "New Box size is setting the long range cutoff radius "
601 <                    "to %lf at time %lf\n",
602 <                    rCut, currentTime );
603 <          painCave.isFatal = 0;
604 <          simError();
605 <      }
606 <    }
607 <    else if ((rCut > maxCutoff)&&(usePBC)) {
503 >    
504 >    if( rCut > maxCutoff ){
505        sprintf( painCave.errMsg,
506 <               "New Box size is setting the long range cutoff radius "
507 <               "to %lf at time %lf\n",
508 <               maxCutoff, currentTime );
509 <      painCave.isFatal = 0;
506 >               "cutoffRadius is too large for the current periodic box.\n"
507 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
508 >               "\tThis is larger than half of at least one of the\n"
509 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
510 >               "\n"
511 >               "\t[ %G %G %G ]\n"
512 >               "\t[ %G %G %G ]\n"
513 >               "\t[ %G %G %G ]\n",
514 >               rCut, currentTime,
515 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
516 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
517 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
518 >      painCave.isFatal = 1;
519        simError();
520 <      rCut = maxCutoff;
615 <    }
616 <
617 <
618 <    //detect the change of ecr
619 <    if( maxCutoff > ecr ){
620 <      if( ecr < origEcr ){
621 <        ecr = origEcr;
622 <        if (ecr > maxCutoff) ecr = maxCutoff;
623 <  
624 <          sprintf( painCave.errMsg,
625 <                    "New Box size is setting the electrostaticCutoffRadius "
626 <                    "to %lf at time %lf\n",
627 <                    ecr, currentTime );
628 <            painCave.isFatal = 0;
629 <            simError();
630 <      }
631 <    }
632 <    else if( ecr > maxCutoff){
633 <      sprintf( painCave.errMsg,
634 <               "New Box size is setting the electrostaticCutoffRadius "
635 <               "to %lf at time %lf\n",
636 <               maxCutoff, currentTime  );
637 <      painCave.isFatal = 0;
638 <      simError();      
639 <      ecr = maxCutoff;
640 <    }
641 <
642 <    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
643 <    
644 <    // rlist is the 1.0 plus max( rcut, ecr )
645 <    
646 <    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647 <    
648 <    if( cutChanged ){
649 <      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650 <    }
651 <    
652 <    oldEcr = ecr;
653 <    oldRcut = rCut;
654 <    
520 >    }    
521    } else {
522      // initialize this stuff before using it, OK?
523      sprintf( painCave.errMsg,
524 <             "Trying to check cutoffs without a box. Be smarter.\n" );
524 >             "Trying to check cutoffs without a box.\n"
525 >             "\tOOPSE should have better programmers than that.\n" );
526      painCave.isFatal = 1;
527      simError();      
528    }
# Line 698 | Line 565 | GenericData* SimInfo::getProperty(const string& propNa
565      return NULL;  
566   }
567  
701 – vector<GenericData*> SimInfo::getProperties(){
568  
569 <  vector<GenericData*> result;
570 <  map<string, GenericData*>::iterator i;
569 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
570 >                          vector<int>& groupList, vector<int>& groupStart){
571 >  Molecule* myMols;
572 >  Atom** myAtoms;
573 >  int numAtom;
574 >  int curIndex;
575 >  double mtot;
576 >  int numMol;
577 >  int numCutoffGroups;
578 >  CutoffGroup* myCutoffGroup;
579 >  vector<CutoffGroup*>::iterator iterCutoff;
580 >  Atom* cutoffAtom;
581 >  vector<Atom*>::iterator iterAtom;
582 >  int atomIndex;
583 >  double totalMass;
584    
585 <  for(i = properties.begin(); i != properties.end(); i++)
586 <    result.push_back((*i).second);
587 <    
588 <  return result;
589 < }
585 >  mfact.clear();
586 >  groupList.clear();
587 >  groupStart.clear();
588 >  
589 >  //Be careful, fortran array begin at 1
590 >  curIndex = 1;
591  
592 < double SimInfo::matTrace3(double m[3][3]){
593 <  double trace;
594 <  trace = m[0][0] + m[1][1] + m[2][2];
592 >  myMols = info->molecules;
593 >  numMol = info->n_mol;
594 >  for(int i  = 0; i < numMol; i++){
595 >    numCutoffGroups = myMols[i].getNCutoffGroups();
596 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
597 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
598  
599 <  return trace;
599 >      totalMass = myCutoffGroup->getMass();
600 >      
601 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
602 >                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
603 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
604 >        groupList.push_back(cutoffAtom->getIndex() + 1);
605 >      }  
606 >                              
607 >      groupStart.push_back(curIndex);
608 >      curIndex += myCutoffGroup->getNumAtom();
609 >
610 >    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
611 >
612 >  }//end for(int i  = 0; i < numMol; i++)
613 >
614 >
615 >  //The last cutoff group need more element to indicate the end of the cutoff
616 >  groupStart.push_back(curIndex);
617 >  ngroup = groupStart.size() - 1;
618   }

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