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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 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 –  
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 161 | Line 175 | void SimInfo::calcHmatInv( void ) {
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 * 1E-6;
178 >  tol = smallDiag * orthoTolerance;
179  
180    orthoRhombic = 1;
181    
# Line 179 | Line 193 | void SimInfo::calcHmatInv( void ) {
193      
194      if( orthoRhombic ){
195        sprintf( painCave.errMsg,
196 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
197 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
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      else {
205        sprintf( painCave.errMsg,
206 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
207 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
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    }
216   }
217  
195 – double SimInfo::matDet3(double a[3][3]) {
196 –  int i, j, k;
197 –  double determinant;
198 –
199 –  determinant = 0.0;
200 –
201 –  for(i = 0; i < 3; i++) {
202 –    j = (i+1)%3;
203 –    k = (i+2)%3;
204 –
205 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 –  }
207 –
208 –  return determinant;
209 – }
210 –
211 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212 –  
213 –  int  i, j, k, l, m, n;
214 –  double determinant;
215 –
216 –  determinant = matDet3( a );
217 –
218 –  if (determinant == 0.0) {
219 –    sprintf( painCave.errMsg,
220 –             "Can't invert a matrix with a zero determinant!\n");
221 –    painCave.isFatal = 1;
222 –    simError();
223 –  }
224 –
225 –  for (i=0; i < 3; i++) {
226 –    j = (i+1)%3;
227 –    k = (i+2)%3;
228 –    for(l = 0; l < 3; l++) {
229 –      m = (l+1)%3;
230 –      n = (l+2)%3;
231 –      
232 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233 –    }
234 –  }
235 – }
236 –
237 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239 –
240 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243 –  
244 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 –  
248 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 –  
252 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255 – }
256 –
257 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 –  double a0, a1, a2;
259 –
260 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 –
262 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 – }
266 –
267 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 –  double temp[3][3];
269 –  int i, j;
270 –
271 –  for (i = 0; i < 3; i++) {
272 –    for (j = 0; j < 3; j++) {
273 –      temp[j][i] = in[i][j];
274 –    }
275 –  }
276 –  for (i = 0; i < 3; i++) {
277 –    for (j = 0; j < 3; j++) {
278 –      out[i][j] = temp[i][j];
279 –    }
280 –  }
281 – }
282 –  
283 – void SimInfo::printMat3(double A[3][3] ){
284 –
285 –  std::cerr
286 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 – }
290 –
291 – void SimInfo::printMat9(double A[9] ){
292 –
293 –  std::cerr
294 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 – }
298 –
299 –
300 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301 –
302 –      out[0] = a[1] * b[2] - a[2] * b[1];
303 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
304 –      out[2] = a[0] * b[1] - a[1] * b[0];
305 –      
306 – }
307 –
308 – double SimInfo::dotProduct3(double a[3], double b[3]){
309 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
310 – }
311 –
312 – double SimInfo::length3(double a[3]){
313 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
314 – }
315 –
218   void SimInfo::calcBoxL( void ){
219  
220    double dx, dy, dz, dsq;
# Line 368 | 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 424 | Line 326 | int SimInfo::getNDF(){
326  
327   int SimInfo::getNDF(){
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;
# Line 442 | Line 361 | int SimInfo::getNDFraw() {
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 456 | Line 385 | int SimInfo::getNDFtranslational() {
385   int SimInfo::getNDFtranslational() {
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);
393   #else
# Line 469 | 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 478 | 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 487 | 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 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
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, &groupList[0], &groupStart[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  
530 –
531 – void SimInfo::setRcut( double theRcut ){
532 –
533 –  rCut = theRcut;
534 –  checkCutOffs();
535 – }
536 –
483   void SimInfo::setDefaultRcut( double theRcut ){
484 <
485 <  haveOrigRcut = 1;
540 <  origRcut = theRcut;
484 >  
485 >  haveRcut = 1;
486    rCut = theRcut;
487 <
543 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 <
545 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 < }
547 <
548 < void SimInfo::setEcr( double theEcr ){
549 <
550 <  ecr = theEcr;
551 <  checkCutOffs();
552 < }
553 <
554 < void SimInfo::setDefaultEcr( double theEcr ){
555 <
556 <  haveOrigEcr = 1;
557 <  origEcr = theEcr;
487 >  rList = rCut + 1.0;
488    
489 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 <
561 <  ecr = theEcr;
562 <
563 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
489 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
490   }
491  
492 < void SimInfo::setEcr( double theEcr, double theEst ){
492 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
493  
494 <  est = theEst;
495 <  setEcr( theEcr );
494 >  rSw = theRsw;
495 >  setDefaultRcut( theRcut );
496   }
497  
572 – void SimInfo::setDefaultEcr( double theEcr, double theEst ){
498  
574 –  est = theEst;
575 –  setDefaultEcr( theEcr );
576 – }
577 –
578 –
499   void SimInfo::checkCutOffs( void ){
580 –
581 –  int cutChanged = 0;
500    
501    if( boxIsInit ){
502      
503      //we need to check cutOffs against the box
504 <
505 <    //detect the change of rCut
588 <    if(( maxCutoff > rCut )&&(usePBC)){
589 <      if( rCut < origRcut ){
590 <        rCut = origRcut;
591 <        
592 <        if (rCut > maxCutoff)
593 <          rCut = maxCutoff;
594 <  
595 <          sprintf( painCave.errMsg,
596 <                    "New Box size is setting the long range cutoff radius "
597 <                    "to %lf at time %lf\n",
598 <                    rCut, currentTime );
599 <          painCave.isFatal = 0;
600 <          simError();
601 <      }
602 <    }
603 <    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;
611 <    }
612 <
613 <
614 <    //detect the change of ecr
615 <    if( maxCutoff > ecr ){
616 <      if( ecr < origEcr ){
617 <        ecr = origEcr;
618 <        if (ecr > maxCutoff) ecr = maxCutoff;
619 <  
620 <          sprintf( painCave.errMsg,
621 <                    "New Box size is setting the electrostaticCutoffRadius "
622 <                    "to %lf at time %lf\n",
623 <                    ecr, currentTime );
624 <            painCave.isFatal = 0;
625 <            simError();
626 <      }
627 <    }
628 <    else if( ecr > maxCutoff){
629 <      sprintf( painCave.errMsg,
630 <               "New Box size is setting the electrostaticCutoffRadius "
631 <               "to %lf at time %lf\n",
632 <               maxCutoff, currentTime  );
633 <      painCave.isFatal = 0;
634 <      simError();      
635 <      ecr = maxCutoff;
636 <    }
637 <
638 <    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 <    
640 <    // rlist is the 1.0 plus max( rcut, ecr )
641 <    
642 <    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643 <    
644 <    if( cutChanged ){
645 <      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 <    }
647 <    
648 <    oldEcr = ecr;
649 <    oldRcut = rCut;
650 <    
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 694 | Line 566 | GenericData* SimInfo::getProperty(const string& propNa
566      return NULL;  
567   }
568  
697 – vector<GenericData*> SimInfo::getProperties(){
569  
570 <  vector<GenericData*> result;
571 <  map<string, GenericData*>::iterator i;
570 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
571 >                          vector<int>& groupList, vector<int>& groupStart){
572 >  Molecule* myMols;
573 >  Atom** myAtoms;
574 >  int numAtom;
575 >  int curIndex;
576 >  double mtot;
577 >  int numMol;
578 >  int numCutoffGroups;
579 >  CutoffGroup* myCutoffGroup;
580 >  vector<CutoffGroup*>::iterator iterCutoff;
581 >  Atom* cutoffAtom;
582 >  vector<Atom*>::iterator iterAtom;
583 >  int atomIndex;
584 >  double totalMass;
585    
586 <  for(i = properties.begin(); i != properties.end(); i++)
587 <    result.push_back((*i).second);
588 <    
589 <  return result;
590 < }
586 >  mfact.clear();
587 >  groupList.clear();
588 >  groupStart.clear();
589 >  
590 >  //Be careful, fortran array begin at 1
591 >  curIndex = 1;
592  
593 < double SimInfo::matTrace3(double m[3][3]){
594 <  double trace;
595 <  trace = m[0][0] + m[1][1] + m[2][2];
593 >  myMols = info->molecules;
594 >  numMol = info->n_mol;
595 >  for(int i  = 0; i < numMol; i++){
596 >    numCutoffGroups = myMols[i].getNCutoffGroups();
597 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
598 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
599  
600 <  return trace;
600 >      totalMass = myCutoffGroup->getMass();
601 >      
602 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
603 >                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
604 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
605 > #ifdef IS_MPI        
606 >        groupList.push_back(cutoffAtom->getGlobalIndex() + 1);
607 > #else
608 >        groupList.push_back(cutoffAtom->getIndex() + 1);
609 > #endif
610 >      }  
611 >                              
612 >      groupStart.push_back(curIndex);
613 >      curIndex += myCutoffGroup->getNumAtom();
614 >
615 >    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
616 >
617 >  }//end for(int i  = 0; i < numMol; i++)
618 >
619 >
620 >  //The last cutoff group need more element to indicate the end of the cutoff
621 >  ngroup = groupStart.size();
622   }

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