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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 1154 by gezelter, Tue May 11 16:00:22 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  
66 +  excludes = Exclude::Instance();
67 +
68    myConfiguration = new SimState();
69  
70 +  has_minimizer = false;
71 +  the_minimizer =NULL;
72 +
73 +  ngroup = 0;
74 +
75    wrapMeSimInfo( this );
76   }
77  
# Line 73 | Line 84 | SimInfo::~SimInfo(){
84    
85    for(i = properties.begin(); i != properties.end(); i++)
86      delete (*i).second;
87 <    
87 >  
88   }
89  
90   void SimInfo::setBox(double newBox[3]) {
# Line 102 | Line 113 | void SimInfo::setBoxM( double theBox[3][3] ){
113                           // [ 2 5 8 ]
114    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
105 –  
116    if( !boxIsInit ) boxIsInit = 1;
117  
118    for(i=0; i < 3; i++)
# Line 146 | Line 156 | void SimInfo::calcHmatInv( void ) {
156  
157   void SimInfo::calcHmatInv( void ) {
158    
159 +  int oldOrtho;
160    int i,j;
161    double smallDiag;
162    double tol;
# Line 153 | Line 164 | void SimInfo::calcHmatInv( void ) {
164  
165    invertMat3( Hmat, HmatInv );
166  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
167    // check to see if Hmat is orthorhombic
168    
169 <  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;
169 >  oldOrtho = orthoRhombic;
170  
171 +  smallDiag = fabs(Hmat[0][0]);
172 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
173 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
174 +  tol = smallDiag * orthoTolerance;
175 +
176    orthoRhombic = 1;
177    
178    for (i = 0; i < 3; i++ ) {
179      for (j = 0 ; j < 3; j++) {
180        if (i != j) {
181          if (orthoRhombic) {
182 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
182 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183          }        
184        }
185      }
186    }
178 – }
187  
188 < double SimInfo::matDet3(double a[3][3]) {
189 <  int i, j, k;
190 <  double determinant;
191 <
192 <  determinant = 0.0;
193 <
194 <  for(i = 0; i < 3; i++) {
195 <    j = (i+1)%3;
196 <    k = (i+2)%3;
197 <
198 <    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
191 <  }
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;
188 >  if( oldOrtho != orthoRhombic ){
189 >    
190 >    if( orthoRhombic ){
191 >      sprintf( painCave.errMsg,
192 >               "OOPSE is switching from the default Non-Orthorhombic\n"
193 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
194 >               "\tThis is usually a good thing, but if you wan't the\n"
195 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
196 >               "\tvariable ( currently set to %G ) smaller.\n",
197 >               orthoTolerance);
198 >      simError();
199      }
200 <  }
201 < }
202 <
203 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
204 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
205 <
206 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
207 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
208 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
209 <  
229 <  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];
200 >    else {
201 >      sprintf( painCave.errMsg,
202 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
203 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
204 >               "\tThis is usually because the box has deformed under\n"
205 >               "\tNPTf integration. If you wan't to live on the edge with\n"
206 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
207 >               "\tvariable ( currently set to %G ) larger.\n",
208 >               orthoTolerance);
209 >      simError();
210      }
211    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
212   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
213  
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 –
214   void SimInfo::calcBoxL( void ){
215  
216    double dx, dy, dz, dsq;
# Line 353 | Line 266 | double SimInfo::calcMaxCutOff(){
266    rk[0] = Hmat[0][2];
267    rk[1] = Hmat[1][2];
268    rk[2] = Hmat[2][2];
269 <  
270 <  crossProduct3(ri,rj, rij);
271 <  distXY = dotProduct3(rk,rij) / length3(rij);
269 >    
270 >  crossProduct3(ri, rj, rij);
271 >  distXY = dotProduct3(rk,rij) / norm3(rij);
272  
273    crossProduct3(rj,rk, rjk);
274 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
274 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275  
276    crossProduct3(rk,ri, rki);
277 <  distZX = dotProduct3(rj,rki) / length3(rki);
277 >  distZX = dotProduct3(rj,rki) / norm3(rki);
278  
279    minDist = min(min(distXY, distYZ), distZX);
280    return minDist/2;
# Line 408 | Line 321 | int SimInfo::getNDF(){
321  
322  
323   int SimInfo::getNDF(){
324 <  int ndf_local, ndf;
324 >  int ndf_local;
325 >
326 >  ndf_local = 0;
327    
328 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
328 >  for(int i = 0; i < integrableObjects.size(); i++){
329 >    ndf_local += 3;
330 >    if (integrableObjects[i]->isDirectional()) {
331 >      if (integrableObjects[i]->isLinear())
332 >        ndf_local += 2;
333 >      else
334 >        ndf_local += 3;
335 >    }
336 >  }
337  
338 +  // n_constraints is local, so subtract them on each processor:
339 +
340 +  ndf_local -= n_constraints;
341 +
342   #ifdef IS_MPI
343    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344   #else
345    ndf = ndf_local;
346   #endif
347  
348 +  // nZconstraints is global, as are the 3 COM translations for the
349 +  // entire system:
350 +
351    ndf = ndf - 3 - nZconstraints;
352  
353    return ndf;
354   }
355  
356   int SimInfo::getNDFraw() {
357 <  int ndfRaw_local, ndfRaw;
357 >  int ndfRaw_local;
358  
359    // Raw degrees of freedom that we have to set
360 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
361 <  
360 >  ndfRaw_local = 0;
361 >
362 >  for(int i = 0; i < integrableObjects.size(); i++){
363 >    ndfRaw_local += 3;
364 >    if (integrableObjects[i]->isDirectional()) {
365 >       if (integrableObjects[i]->isLinear())
366 >        ndfRaw_local += 2;
367 >      else
368 >        ndfRaw_local += 3;
369 >    }
370 >  }
371 >    
372   #ifdef IS_MPI
373    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374   #else
# Line 439 | Line 379 | int SimInfo::getNDFtranslational() {
379   }
380  
381   int SimInfo::getNDFtranslational() {
382 <  int ndfTrans_local, ndfTrans;
382 >  int ndfTrans_local;
383  
384 <  ndfTrans_local = 3 * n_atoms - n_constraints;
384 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
385  
386 +
387   #ifdef IS_MPI
388    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389   #else
# Line 454 | Line 395 | int SimInfo::getNDFtranslational() {
395    return ndfTrans;
396   }
397  
398 + int SimInfo::getTotIntegrableObjects() {
399 +  int nObjs_local;
400 +  int nObjs;
401 +
402 +  nObjs_local =  integrableObjects.size();
403 +
404 +
405 + #ifdef IS_MPI
406 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
407 + #else
408 +  nObjs = nObjs_local;
409 + #endif
410 +
411 +
412 +  return nObjs;
413 + }
414 +
415   void SimInfo::refreshSim(){
416  
417    simtype fInfo;
# Line 463 | Line 421 | void SimInfo::refreshSim(){
421  
422    fInfo.dielect = 0.0;
423  
424 <  if( useDipole ){
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 472 | Line 430 | void SimInfo::refreshSim(){
430    fInfo.SIM_uses_LJ = useLJ;
431    fInfo.SIM_uses_sticky = useSticky;
432    //fInfo.SIM_uses_sticky = 0;
433 <  fInfo.SIM_uses_dipoles = useDipole;
433 >  fInfo.SIM_uses_charges = useCharges;
434 >  fInfo.SIM_uses_dipoles = useDipoles;
435    //fInfo.SIM_uses_dipoles = 0;
436 <  //fInfo.SIM_uses_RF = useReactionField;
437 <  fInfo.SIM_uses_RF = 0;
436 >  fInfo.SIM_uses_RF = useReactionField;
437 >  //fInfo.SIM_uses_RF = 0;
438    fInfo.SIM_uses_GB = useGB;
439    fInfo.SIM_uses_EAM = useEAM;
440  
441 <  excl = Exclude::getArray();
442 <
441 >  n_exclude = excludes->getSize();
442 >  excl = excludes->getFortranArray();
443 >  
444   #ifdef IS_MPI
445    n_global = mpiSim->getTotAtoms();
446   #else
447    n_global = n_atoms;
448   #endif
449 <
449 >  
450    isError = 0;
451 <
451 >  
452 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
453 >  
454    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
455 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 <                  &isError );
457 <
455 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
457 >  
458    if( isError ){
459 <
459 >    
460      sprintf( painCave.errMsg,
461 <             "There was an error setting the simulation information in fortran.\n" );
461 >             "There was an error setting the simulation information in fortran.\n" );
462      painCave.isFatal = 1;
463      simError();
464    }
465 <
465 >  
466   #ifdef IS_MPI
467    sprintf( checkPointMsg,
468             "succesfully sent the simulation information to fortran.\n");
469    MPIcheckPoint();
470   #endif // is_mpi
471 <
471 >  
472    this->ndf = this->getNDF();
473    this->ndfRaw = this->getNDFraw();
474    this->ndfTrans = this->getNDFtranslational();
475   }
476  
477 <
478 < void SimInfo::setRcut( double theRcut ){
479 <
518 <  if( !haveOrigRcut ){
519 <    haveOrigRcut = 1;
520 <    origRcut = theRcut;
521 <  }
522 <
477 > void SimInfo::setDefaultRcut( double theRcut ){
478 >  
479 >  haveRcut = 1;
480    rCut = theRcut;
481 <  checkCutOffs();
481 >  rList = rCut + 1.0;
482 >  
483 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
484   }
485  
486 < void SimInfo::setEcr( double theEcr ){
486 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
487  
488 <  if( !haveOrigEcr ){
489 <    haveOrigEcr = 1;
531 <    origEcr = theEcr;
532 <  }
533 <
534 <  ecr = theEcr;
535 <  checkCutOffs();
488 >  rSw = theRsw;
489 >  setDefaultRcut( theRcut );
490   }
491  
538 – void SimInfo::setEcr( double theEcr, double theEst ){
492  
540 –  est = theEst;
541 –  setEcr( theEcr );
542 – }
543 –
544 –
493   void SimInfo::checkCutOffs( void ){
546 –
547 –  int cutChanged = 0;
494    
495    if( boxIsInit ){
496      
497      //we need to check cutOffs against the box
498 <
499 <    //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)) {
498 >    
499 >    if( rCut > maxCutoff ){
500        sprintf( painCave.errMsg,
501 <               "New Box size is setting the long range cutoff radius "
502 <               "to %lf at time %lf\n",
503 <               maxCutoff, currentTime );
504 <      painCave.isFatal = 0;
501 >               "cutoffRadius is too large for the current periodic box.\n"
502 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
503 >               "\tThis is larger than half of at least one of the\n"
504 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 >               "\n"
506 >               "\t[ %G %G %G ]\n"
507 >               "\t[ %G %G %G ]\n"
508 >               "\t[ %G %G %G ]\n",
509 >               rCut, currentTime,
510 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 >      painCave.isFatal = 1;
514        simError();
515 <      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 <    
515 >    }    
516    } else {
517      // initialize this stuff before using it, OK?
518      sprintf( painCave.errMsg,
519 <             "Trying to check cutoffs without a box. Be smarter.\n" );
519 >             "Trying to check cutoffs without a box.\n"
520 >             "\tOOPSE should have better programmers than that.\n" );
521      painCave.isFatal = 1;
522      simError();      
523    }
# Line 661 | Line 560 | GenericData* SimInfo::getProperty(const string& propNa
560      return NULL;  
561   }
562  
664 – vector<GenericData*> SimInfo::getProperties(){
563  
564 <  vector<GenericData*> result;
565 <  map<string, GenericData*>::iterator i;
564 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
565 >                          vector<int>& groupList, vector<int>& groupStart){
566 >  Molecule* mol;
567 >  Atom** myAtoms;
568 >  int numAtom;
569 >  int curIndex;
570 >  double mtot;
571 >
572 >  mfact.clear();
573 >  groupList.clear();
574 >  groupStart.clear();
575    
576 <  for(i = properties.begin(); i != properties.end(); i++)
577 <    result.push_back((*i).second);
576 >  //Be careful, fortran array begin at 1
577 >  curIndex = 1;
578 >  
579 >  if(info->useMolecularCutoffs){
580      
581 <  return result;
582 < }
581 > #ifdef IS_MPI
582 >    ngroup = mpiSim->getMyNMol();
583 > #else
584 >    ngroup = info->n_mol;
585 > #endif
586 >    
587 >    for(int i = 0; i < ngroup; i ++){
588 >      mol = &(info->molecules[i]);
589 >      numAtom = mol->getNAtoms();
590 >      myAtoms = mol->getMyAtoms();
591 >      mtot = 0.0;
592  
593 < double SimInfo::matTrace3(double m[3][3]){
594 <  double trace;
595 <  trace = m[0][0] + m[1][1] + m[2][2];
593 >      for(int j=0; j < numAtom; j++)
594 >        mtot += myAtoms[j]->getMass();                
595 >      
596 >      for(int j=0; j < numAtom; j++){
597 >              
598 >        // We want the local Index:
599 >        groupList.push_back(myAtoms[j]->getIndex() + 1);
600 >        mfact.push_back(myAtoms[j]->getMass() / mtot);
601  
602 <  return trace;
602 >      }
603 >      
604 >      groupStart.push_back(curIndex);
605 >      curIndex += numAtom;
606 >      
607 >    } //end for(int i =0 ; i < ngroup; i++)    
608 >  }
609 >  else{
610 >    //using atomic cutoff, every single atom is just a group
611 >    
612 > #ifdef IS_MPI
613 >    ngroup = mpiSim->getMyNlocal();
614 > #else
615 >    ngroup = info->n_atoms;
616 > #endif
617 >    
618 >    for(int i =0 ; i < ngroup; i++){
619 >      groupStart.push_back(curIndex++);      
620 >      groupList.push_back((info->atoms[i])->getIndex() + 1);
621 >      mfact.push_back(1.0);
622 >      
623 >    }//end for(int i =0 ; i < ngroup; i++)
624 >    
625 >  }//end if (info->useMolecularCutoffs)
626 >  
627   }

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