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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 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>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17 + #ifdef IS_MPI
18 + #include "mpiSimulation.hpp"
19 + #endif
20 +
21 + 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;
36    n_dipoles = 0;
37    ndf = 0;
38    ndfRaw = 0;
39 +  nZconstraints = 0;
40    the_integrator = NULL;
41    setTemp = 0;
42    thermalTime = 0.0;
43 +  currentTime = 0.0;
44    rCut = 0.0;
45 +  rSw = 0.0;
46  
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 +  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  
78 +
79 + SimInfo::~SimInfo(){
80 +
81 +  delete myConfiguration;
82 +
83 +  map<string, GenericData*>::iterator i;
84 +  
85 +  for(i = properties.begin(); i != properties.end(); i++)
86 +    delete (*i).second;
87 +  
88 + }
89 +
90   void SimInfo::setBox(double newBox[3]) {
91 <  double smallestBox, maxCutoff;
92 <  int status;
93 <  box_x = newBox[0];
41 <  box_y = newBox[1];
42 <  box_z = newBox[2];
43 <  setFortranBoxSize(newBox);
91 >  
92 >  int i, j;
93 >  double tempMat[3][3];
94  
95 <  smallestBox = box_x;
96 <  if (box_y < smallestBox) smallestBox = box_y;
47 <  if (box_z < smallestBox) smallestBox = box_z;
95 >  for(i=0; i<3; i++)
96 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
97  
98 <  maxCutoff = smallestBox / 2.0;
98 >  tempMat[0][0] = newBox[0];
99 >  tempMat[1][1] = newBox[1];
100 >  tempMat[2][2] = newBox[2];
101  
102 <  if (rList > maxCutoff) {
52 <    sprintf( painCave.errMsg,
53 <             "New Box size is forcing neighborlist radius down to %lf\n",
54 <             maxCutoff );
55 <    painCave.isFatal = 0;
56 <    simError();
102 >  setBoxM( tempMat );
103  
104 <    rList = maxCutoff;
104 > }
105  
106 <    sprintf( painCave.errMsg,
107 <             "New Box size is forcing cutoff radius down to %lf\n",
108 <             maxCutoff - 1.0 );
109 <    painCave.isFatal = 0;
110 <    simError();
106 > void SimInfo::setBoxM( double theBox[3][3] ){
107 >  
108 >  int i, j;
109 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
110 >                         // ordering in the array is as follows:
111 >                         // [ 0 3 6 ]
112 >                         // [ 1 4 7 ]
113 >                         // [ 2 5 8 ]
114 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
116 <    rCut = rList - 1.0;
116 >  if( !boxIsInit ) boxIsInit = 1;
117  
118 <    // list radius changed so we have to refresh the simulation structure.
119 <    refreshSim();
118 >  for(i=0; i < 3; i++)
119 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
120 >  
121 >  calcBoxL();
122 >  calcHmatInv();
123 >
124 >  for(i=0; i < 3; i++) {
125 >    for (j=0; j < 3; j++) {
126 >      FortranHmat[3*j + i] = Hmat[i][j];
127 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
128 >    }
129    }
130  
131 <  if (rCut > maxCutoff) {
132 <    sprintf( painCave.errMsg,
133 <             "New Box size is forcing cutoff radius down to %lf\n",
134 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
131 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
132 >
133 > }
134 >
135  
136 <    status = 0;
137 <    LJ_new_rcut(&rCut, &status);
138 <    if (status != 0) {
136 > void SimInfo::getBoxM (double theBox[3][3]) {
137 >
138 >  int i, j;
139 >  for(i=0; i<3; i++)
140 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
141 > }
142 >
143 >
144 > void SimInfo::scaleBox(double scale) {
145 >  double theBox[3][3];
146 >  int i, j;
147 >
148 >  // cerr << "Scaling box by " << scale << "\n";
149 >
150 >  for(i=0; i<3; i++)
151 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
152 >
153 >  setBoxM(theBox);
154 >
155 > }
156 >
157 > void SimInfo::calcHmatInv( void ) {
158 >  
159 >  int oldOrtho;
160 >  int i,j;
161 >  double smallDiag;
162 >  double tol;
163 >  double sanity[3][3];
164 >
165 >  invertMat3( Hmat, HmatInv );
166 >
167 >  // check to see if Hmat is orthorhombic
168 >  
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 ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183 >        }        
184 >      }
185 >    }
186 >  }
187 >
188 >  if( oldOrtho != orthoRhombic ){
189 >    
190 >    if( orthoRhombic ){
191        sprintf( painCave.errMsg,
192 <               "Error in recomputing LJ shifts based on new rcut\n");
193 <      painCave.isFatal = 1;
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 +    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    }
212   }
213  
214 < void SimInfo::getBox(double theBox[3]) {
215 <  theBox[0] = box_x;
216 <  theBox[1] = box_y;
217 <  theBox[2] = box_z;
214 > void SimInfo::calcBoxL( void ){
215 >
216 >  double dx, dy, dz, dsq;
217 >
218 >  // boxVol = Determinant of Hmat
219 >
220 >  boxVol = matDet3( Hmat );
221 >
222 >  // boxLx
223 >  
224 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
225 >  dsq = dx*dx + dy*dy + dz*dz;
226 >  boxL[0] = sqrt( dsq );
227 >  //maxCutoff = 0.5 * boxL[0];
228 >
229 >  // boxLy
230 >  
231 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
232 >  dsq = dx*dx + dy*dy + dz*dz;
233 >  boxL[1] = sqrt( dsq );
234 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
235 >
236 >
237 >  // boxLz
238 >  
239 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
240 >  dsq = dx*dx + dy*dy + dz*dz;
241 >  boxL[2] = sqrt( dsq );
242 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
243 >
244 >  //calculate the max cutoff
245 >  maxCutoff =  calcMaxCutOff();
246 >  
247 >  checkCutOffs();
248 >
249   }
250 <
251 < int SimInfo::getNDF(){
252 <  int ndf_local, ndf;
250 >
251 >
252 > double SimInfo::calcMaxCutOff(){
253 >
254 >  double ri[3], rj[3], rk[3];
255 >  double rij[3], rjk[3], rki[3];
256 >  double minDist;
257 >
258 >  ri[0] = Hmat[0][0];
259 >  ri[1] = Hmat[1][0];
260 >  ri[2] = Hmat[2][0];
261 >
262 >  rj[0] = Hmat[0][1];
263 >  rj[1] = Hmat[1][1];
264 >  rj[2] = Hmat[2][1];
265 >
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) / norm3(rij);
272 >
273 >  crossProduct3(rj,rk, rjk);
274 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275 >
276 >  crossProduct3(rk,ri, rki);
277 >  distZX = dotProduct3(rj,rki) / norm3(rki);
278 >
279 >  minDist = min(min(distXY, distYZ), distZX);
280 >  return minDist/2;
281    
282 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
282 > }
283  
284 + void SimInfo::wrapVector( double thePos[3] ){
285 +
286 +  int i;
287 +  double scaled[3];
288 +
289 +  if( !orthoRhombic ){
290 +    // calc the scaled coordinates.
291 +  
292 +
293 +    matVecMul3(HmatInv, thePos, scaled);
294 +    
295 +    for(i=0; i<3; i++)
296 +      scaled[i] -= roundMe(scaled[i]);
297 +    
298 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
299 +    
300 +    matVecMul3(Hmat, scaled, thePos);
301 +
302 +  }
303 +  else{
304 +    // calc the scaled coordinates.
305 +    
306 +    for(i=0; i<3; i++)
307 +      scaled[i] = thePos[i]*HmatInv[i][i];
308 +    
309 +    // wrap the scaled coordinates
310 +    
311 +    for(i=0; i<3; i++)
312 +      scaled[i] -= roundMe(scaled[i]);
313 +    
314 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
315 +    
316 +    for(i=0; i<3; i++)
317 +      thePos[i] = scaled[i]*Hmat[i][i];
318 +  }
319 +    
320 + }
321 +
322 +
323 + int SimInfo::getNDF(){
324 +  int ndf_local;
325 +
326 +  ndf_local = 0;
327 +  
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 <  ndf = ndf - 3;
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 123 | Line 377 | int SimInfo::getNDFraw() {
377  
378    return ndfRaw;
379   }
380 <
380 >
381 > int SimInfo::getNDFtranslational() {
382 >  int ndfTrans_local;
383 >
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
390 >  ndfTrans = ndfTrans_local;
391 > #endif
392 >
393 >  ndfTrans = ndfTrans - 3 - nZconstraints;
394 >
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;
418    int isError;
419 +  int n_global;
420    int* excl;
421 <  
133 <  fInfo.rrf = 0.0;
134 <  fInfo.rt = 0.0;
421 >
422    fInfo.dielect = 0.0;
423  
424 <  fInfo.box[0] = box_x;
138 <  fInfo.box[1] = box_y;
139 <  fInfo.box[2] = box_z;
140 <
141 <  fInfo.rlist = rList;
142 <  fInfo.rcut = rCut;
143 <
144 <  if( useDipole ){
145 <    fInfo.rrf = ecr;
146 <    fInfo.rt = ecr - est;
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 152 | 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;
434 <  fInfo.SIM_uses_dipoles = 0;
435 <  //fInfo.SIM_uses_RF = useReactionField;
436 <  fInfo.SIM_uses_RF = 0;
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;
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 >  
450    isError = 0;
451 <
452 < //   fInfo;
453 < //   n_atoms;
454 < //   identArray;
455 < //   n_exclude;
456 < //   excludes;
457 < //   nGlobalExcludes;
172 < //   globalExcludes;
173 < //   isError;
174 <
175 <  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
176 <                  &nGlobalExcludes, globalExcludes, &isError );
177 <
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 >                  &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 + void SimInfo::setDefaultRcut( double theRcut ){
478 +  
479 +  haveRcut = 1;
480 +  rCut = theRcut;
481 +  rList = rCut + 1.0;
482 +  
483 +  notifyFortranCutOffs( &rCut, &rSw, &rList );
484   }
485  
486 + void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
487 +
488 +  rSw = theRsw;
489 +  setDefaultRcut( theRcut );
490 + }
491 +
492 +
493 + void SimInfo::checkCutOffs( void ){
494 +  
495 +  if( boxIsInit ){
496 +    
497 +    //we need to check cutOffs against the box
498 +    
499 +    if( rCut > maxCutoff ){
500 +      sprintf( painCave.errMsg,
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 +    }    
516 +  } else {
517 +    // initialize this stuff before using it, OK?
518 +    sprintf( painCave.errMsg,
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 +  }
524 +  
525 + }
526 +
527 + void SimInfo::addProperty(GenericData* prop){
528 +
529 +  map<string, GenericData*>::iterator result;
530 +  result = properties.find(prop->getID());
531 +  
532 +  //we can't simply use  properties[prop->getID()] = prop,
533 +  //it will cause memory leak if we already contain a propery which has the same name of prop
534 +  
535 +  if(result != properties.end()){
536 +    
537 +    delete (*result).second;
538 +    (*result).second = prop;
539 +      
540 +  }
541 +  else{
542 +
543 +    properties[prop->getID()] = prop;
544 +
545 +  }
546 +    
547 + }
548 +
549 + GenericData* SimInfo::getProperty(const string& propName){
550 +
551 +  map<string, GenericData*>::iterator result;
552 +  
553 +  //string lowerCaseName = ();
554 +  
555 +  result = properties.find(propName);
556 +  
557 +  if(result != properties.end())
558 +    return (*result).second;  
559 +  else  
560 +    return NULL;  
561 + }
562 +
563 +
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 +  //Be careful, fortran array begin at 1
577 +  curIndex = 1;
578 +  
579 +  if(info->useMolecularCutoffs){
580 +    
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 +      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 +      }
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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