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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 1157 by tim, Tue May 11 20:33:41 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 +  
66 +  haveCutoffGroups = false;
67  
68 +  excludes = Exclude::Instance();
69 +
70    myConfiguration = new SimState();
71  
72 +  has_minimizer = false;
73 +  the_minimizer =NULL;
74 +
75 +  ngroup = 0;
76 +
77    wrapMeSimInfo( this );
78   }
79  
# Line 75 | Line 86 | SimInfo::~SimInfo(){
86    
87    for(i = properties.begin(); i != properties.end(); i++)
88      delete (*i).second;
89 <    
89 >  
90   }
91  
92   void SimInfo::setBox(double newBox[3]) {
# Line 104 | Line 115 | void SimInfo::setBoxM( double theBox[3][3] ){
115                           // [ 2 5 8 ]
116    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
117  
107 –  
118    if( !boxIsInit ) boxIsInit = 1;
119  
120    for(i=0; i < 3; i++)
# Line 181 | Line 191 | void SimInfo::calcHmatInv( void ) {
191      
192      if( orthoRhombic ){
193        sprintf( painCave.errMsg,
194 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
195 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
194 >               "OOPSE is switching from the default Non-Orthorhombic\n"
195 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
196 >               "\tThis is usually a good thing, but if you wan't the\n"
197 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
198 >               "\tvariable ( currently set to %G ) smaller.\n",
199                 orthoTolerance);
200        simError();
201      }
202      else {
203        sprintf( painCave.errMsg,
204 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
205 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
204 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
205 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
206 >               "\tThis is usually because the box has deformed under\n"
207 >               "\tNPTf integration. If you wan't to live on the edge with\n"
208 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
209 >               "\tvariable ( currently set to %G ) larger.\n",
210                 orthoTolerance);
211        simError();
195 –    }
196 –  }
197 – }
198 –
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];
212      }
213    }
280 –  for (i = 0; i < 3; i++) {
281 –    for (j = 0; j < 3; j++) {
282 –      out[i][j] = temp[i][j];
283 –    }
284 –  }
214   }
286 –  
287 – void SimInfo::printMat3(double A[3][3] ){
215  
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 –
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
# Line 372 | Line 268 | double SimInfo::calcMaxCutOff(){
268    rk[0] = Hmat[0][2];
269    rk[1] = Hmat[1][2];
270    rk[2] = Hmat[2][2];
271 <  
272 <  crossProduct3(ri,rj, rij);
273 <  distXY = dotProduct3(rk,rij) / length3(rij);
271 >    
272 >  crossProduct3(ri, rj, rij);
273 >  distXY = dotProduct3(rk,rij) / norm3(rij);
274  
275    crossProduct3(rj,rk, rjk);
276 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
276 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
277  
278    crossProduct3(rk,ri, rki);
279 <  distZX = dotProduct3(rj,rki) / length3(rki);
279 >  distZX = dotProduct3(rj,rki) / norm3(rki);
280  
281    minDist = min(min(distXY, distYZ), distZX);
282    return minDist/2;
# Line 428 | Line 324 | int SimInfo::getNDF(){
324  
325   int SimInfo::getNDF(){
326    int ndf_local;
327 +
328 +  ndf_local = 0;
329    
330 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
330 >  for(int i = 0; i < integrableObjects.size(); i++){
331 >    ndf_local += 3;
332 >    if (integrableObjects[i]->isDirectional()) {
333 >      if (integrableObjects[i]->isLinear())
334 >        ndf_local += 2;
335 >      else
336 >        ndf_local += 3;
337 >    }
338 >  }
339  
340 +  // n_constraints is local, so subtract them on each processor:
341 +
342 +  ndf_local -= n_constraints;
343 +
344   #ifdef IS_MPI
345    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
346   #else
347    ndf = ndf_local;
348   #endif
349  
350 +  // nZconstraints is global, as are the 3 COM translations for the
351 +  // entire system:
352 +
353    ndf = ndf - 3 - nZconstraints;
354  
355    return ndf;
# Line 446 | Line 359 | int SimInfo::getNDFraw() {
359    int ndfRaw_local;
360  
361    // Raw degrees of freedom that we have to set
362 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
363 <  
362 >  ndfRaw_local = 0;
363 >
364 >  for(int i = 0; i < integrableObjects.size(); i++){
365 >    ndfRaw_local += 3;
366 >    if (integrableObjects[i]->isDirectional()) {
367 >       if (integrableObjects[i]->isLinear())
368 >        ndfRaw_local += 2;
369 >      else
370 >        ndfRaw_local += 3;
371 >    }
372 >  }
373 >    
374   #ifdef IS_MPI
375    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
376   #else
# Line 460 | Line 383 | int SimInfo::getNDFtranslational() {
383   int SimInfo::getNDFtranslational() {
384    int ndfTrans_local;
385  
386 <  ndfTrans_local = 3 * n_atoms - n_constraints;
386 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
387  
388 +
389   #ifdef IS_MPI
390    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
391   #else
# Line 473 | Line 397 | void SimInfo::refreshSim(){
397    return ndfTrans;
398   }
399  
400 + int SimInfo::getTotIntegrableObjects() {
401 +  int nObjs_local;
402 +  int nObjs;
403 +
404 +  nObjs_local =  integrableObjects.size();
405 +
406 +
407 + #ifdef IS_MPI
408 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
409 + #else
410 +  nObjs = nObjs_local;
411 + #endif
412 +
413 +
414 +  return nObjs;
415 + }
416 +
417   void SimInfo::refreshSim(){
418  
419    simtype fInfo;
# Line 482 | Line 423 | void SimInfo::refreshSim(){
423  
424    fInfo.dielect = 0.0;
425  
426 <  if( useDipole ){
426 >  if( useDipoles ){
427      if( useReactionField )fInfo.dielect = dielectric;
428    }
429  
# Line 491 | Line 432 | void SimInfo::refreshSim(){
432    fInfo.SIM_uses_LJ = useLJ;
433    fInfo.SIM_uses_sticky = useSticky;
434    //fInfo.SIM_uses_sticky = 0;
435 <  fInfo.SIM_uses_dipoles = useDipole;
435 >  fInfo.SIM_uses_charges = useCharges;
436 >  fInfo.SIM_uses_dipoles = useDipoles;
437    //fInfo.SIM_uses_dipoles = 0;
438 <  //fInfo.SIM_uses_RF = useReactionField;
439 <  fInfo.SIM_uses_RF = 0;
438 >  fInfo.SIM_uses_RF = useReactionField;
439 >  //fInfo.SIM_uses_RF = 0;
440    fInfo.SIM_uses_GB = useGB;
441    fInfo.SIM_uses_EAM = useEAM;
442  
443 <  excl = Exclude::getArray();
444 <
443 >  n_exclude = excludes->getSize();
444 >  excl = excludes->getFortranArray();
445 >  
446   #ifdef IS_MPI
447    n_global = mpiSim->getTotAtoms();
448   #else
449    n_global = n_atoms;
450   #endif
451 <
451 >  
452    isError = 0;
453 <
453 >  
454 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
455 >  //it may not be a good idea to pass the address of first element in vector
456 >  //since c++ standard does not require vector to be stored continously in meomory
457 >  //Most of the compilers will organize the memory of vector continously
458    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
459 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 <                  &isError );
461 <
459 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
461 >  
462    if( isError ){
463 <
463 >    
464      sprintf( painCave.errMsg,
465 <             "There was an error setting the simulation information in fortran.\n" );
465 >             "There was an error setting the simulation information in fortran.\n" );
466      painCave.isFatal = 1;
467      simError();
468    }
469 <
469 >  
470   #ifdef IS_MPI
471    sprintf( checkPointMsg,
472             "succesfully sent the simulation information to fortran.\n");
473    MPIcheckPoint();
474   #endif // is_mpi
475 <
475 >  
476    this->ndf = this->getNDF();
477    this->ndfRaw = this->getNDFraw();
478    this->ndfTrans = this->getNDFtranslational();
479   }
480  
534 –
535 – void SimInfo::setRcut( double theRcut ){
536 –
537 –  rCut = theRcut;
538 –  checkCutOffs();
539 – }
540 –
481   void SimInfo::setDefaultRcut( double theRcut ){
482 <
483 <  haveOrigRcut = 1;
544 <  origRcut = theRcut;
482 >  
483 >  haveRcut = 1;
484    rCut = theRcut;
485 <
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;
485 >  rList = rCut + 1.0;
486    
487 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 <
565 <  ecr = theEcr;
566 <
567 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
487 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
488   }
489  
490 < void SimInfo::setEcr( double theEcr, double theEst ){
490 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
491  
492 <  est = theEst;
493 <  setEcr( theEcr );
492 >  rSw = theRsw;
493 >  setDefaultRcut( theRcut );
494   }
495  
576 – void SimInfo::setDefaultEcr( double theEcr, double theEst ){
496  
578 –  est = theEst;
579 –  setDefaultEcr( theEcr );
580 – }
581 –
582 –
497   void SimInfo::checkCutOffs( void ){
584 –
585 –  int cutChanged = 0;
498    
499    if( boxIsInit ){
500      
501      //we need to check cutOffs against the box
502 <
503 <    //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)) {
502 >    
503 >    if( rCut > maxCutoff ){
504        sprintf( painCave.errMsg,
505 <               "New Box size is setting the long range cutoff radius "
506 <               "to %lf at time %lf\n",
507 <               maxCutoff, currentTime );
508 <      painCave.isFatal = 0;
505 >               "cutoffRadius is too large for the current periodic box.\n"
506 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
507 >               "\tThis is larger than half of at least one of the\n"
508 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
509 >               "\n"
510 >               "\t[ %G %G %G ]\n"
511 >               "\t[ %G %G %G ]\n"
512 >               "\t[ %G %G %G ]\n",
513 >               rCut, currentTime,
514 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
515 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
516 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
517 >      painCave.isFatal = 1;
518        simError();
519 <      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 <    
519 >    }    
520    } else {
521      // initialize this stuff before using it, OK?
522      sprintf( painCave.errMsg,
523 <             "Trying to check cutoffs without a box. Be smarter.\n" );
523 >             "Trying to check cutoffs without a box.\n"
524 >             "\tOOPSE should have better programmers than that.\n" );
525      painCave.isFatal = 1;
526      simError();      
527    }
# Line 698 | Line 564 | vector<GenericData*> SimInfo::getProperties(){
564      return NULL;  
565   }
566  
701 – vector<GenericData*> SimInfo::getProperties(){
567  
568 <  vector<GenericData*> result;
569 <  map<string, GenericData*>::iterator i;
568 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
569 >                          vector<int>& groupList, vector<int>& groupStart){
570 >  Molecule* myMols;
571 >  Atom** myAtoms;
572 >  int numAtom;
573 >  int curIndex;
574 >  double mtot;
575 >  int numMol;
576 >  int numCutoffGroups;
577 >  CutoffGroup* myCutoffGroup;
578 >  vector<CutoffGroup*>::iterator iterCutoff;
579 >  Atom* cutoffAtom;
580 >  vector<Atom*>::iterator iterAtom;
581 >  int atomIndex;
582    
583 <  for(i = properties.begin(); i != properties.end(); i++)
584 <    result.push_back((*i).second);
583 >  mfact.clear();
584 >  groupList.clear();
585 >  groupStart.clear();
586 >  
587 >  //Be careful, fortran array begin at 1
588 >  curIndex = 1;
589 >
590 >  myMols = info->molecules;
591 >  numMol = info->n_mol;
592 >  for(int i  = 0; i < numMol; i++){
593 >    numAtom = myMols[i].getNAtoms();
594 >    myAtoms = myMols[i].getMyAtoms();
595 >
596      
597 <  return result;
710 < }
597 >    for(int j = 0; j < numAtom; j++){
598  
599 < double SimInfo::matTrace3(double m[3][3]){
600 <  double trace;
601 <  trace = m[0][0] + m[1][1] + m[2][2];
599 >    
600 > #ifdef IS_MPI      
601 >      atomIndex = myAtoms[j]->getGlobalIndex();
602 > #else
603 >      atomIndex = myAtoms[j]->getIndex();
604 > #endif
605  
606 <  return trace;
606 >      if(myMols[i].belongToCutoffGroup(atomIndex))
607 >        continue;
608 >      else{
609 >        mfact.push_back(myAtoms[j]->getMass());
610 >        groupList.push_back(myAtoms[j]->getIndex() + 1);
611 >        groupStart.push_back(curIndex++);  
612 >      }
613 >    }
614 >      
615 >    numCutoffGroups = myMols[i].getNCutoffGroups();
616 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
617 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
618 >      
619 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
620 >                                           cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
621 >        groupList.push_back(cutoffAtom->getIndex() + 1);
622 >      }  
623 >                              
624 >      groupStart.push_back(curIndex);
625 >      curIndex += myCutoffGroup->getNumAtom();
626 >    }
627 >    
628 >  }
629 >
630 >  ngroup = groupStart.size();
631   }

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