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Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC vs.
Revision 726 by tim, Tue Aug 26 20:37:30 2003 UTC

# Line 2 | Line 2 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
2   #include "simError.h"
3   #include <cmath>
4   template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5 <                                    : T(theInfo, the_ff), fz(NULL),
6 <                                      indexOfZConsMols(NULL)
5 >                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL),
6 >                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
7   {
8  
9    //get properties from SimInfo
10    GenericData* data;
11 <  IndexData* index;
11 >  ZConsParaData* zConsParaData;
12    DoubleData* sampleTime;
13 +  DoubleData* tolerance;
14 +  StringData* policy;
15    StringData* filename;
16 +  double COM[3];
17 +
18 +  //by default, the direction of constraint is z
19 +  // 0 --> x
20 +  // 1 --> y
21 +  // 2 --> z
22 +  whichDirection = 2;
23 +
24 +  //estimate the force constant of harmonical potential
25 +  double Kb = 1.986E-3 ; //in kcal/K
26    
27 <  //retrieve index of z-constraint molecules
28 <  data = info->getProperty("zconsindex");
17 <  if(!data) {
27 >  double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
28 >  zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
29  
30 +  //creat force substraction policy
31 +  data = info->getProperty(ZCONSFORCEPOLICY_ID);
32 +  if(!data){
33      sprintf( painCave.errMsg,
34 <               "ZConstraint error: If you use an ZConstraint\n"
35 <               " , you must set index of z-constraint molecules.\n");
36 <    painCave.isFatal = 1;
37 <    simError();  
34 >               "ZConstraint Warning: User does not set force substraction policy, "
35 >               "PolicyByMass is used\n");
36 >    painCave.isFatal = 0;
37 >    simError();      
38 >
39 >    forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
40    }
41    else{
42 <    index = dynamic_cast<IndexData*>(data);
42 >    policy = dynamic_cast<StringData*>(data);
43      
44 <    if(!index){
29 <
44 >    if(!policy){
45        sprintf( painCave.errMsg,
46 <                 "ZConstraint error: Can not get property from SimInfo\n");
47 <      painCave.isFatal = 1;
48 <      simError();  
49 <    
46 >                 "ZConstraint Error: Convertion from GenericData to StringData failure, "
47 >                 "PolicyByMass is used\n");
48 >      painCave.isFatal = 0;
49 >      simError();      
50 >
51 >      forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
52      }
53      else{
54 <          
55 <      indexOfAllZConsMols = index->getIndexData();
56 <      
57 <      //the maximum value of index is the last one(we sorted the index data in SimSetup.cpp)
58 <      int maxIndex;
42 <        int minIndex;
43 <      int totalNumMol;
44 <
45 <      minIndex = indexOfAllZConsMols[0];
46 <      if(minIndex < 0){
54 >      if(policy->getData() == "BYNUMBER")
55 >        forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
56 >      else if(policy->getData() == "BYMASS")
57 >        forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this);
58 >      else{
59          sprintf( painCave.errMsg,
60 <               "ZConstraint error: index is out of range\n");
61 <        painCave.isFatal = 1;
62 <        simError();
63 <        }
64 <          
53 <      maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1];
54 <
55 < #ifndef IS_MPI
56 <      totalNumMol = nMols;
57 < #else
58 <      totalNumMol = mpiSim->getTotNmol();  
59 < #endif      
60 <      
61 <      if(maxIndex > totalNumMol - 1){
62 <        sprintf( painCave.errMsg,
63 <               "ZConstraint error: index is out of range\n");
64 <        painCave.isFatal = 1;
65 <        simError();
66 <                
67 <      }
68 <      
60 >                  "ZConstraint Warning: unknown force substraction policy, "
61 >                  "average force substraction policy is used\n");
62 >        painCave.isFatal = 0;
63 >        simError();      
64 >      }  
65      }
70 –        
66    }
67    
68 +  
69    //retrieve sample time of z-contraint
70 <  data = info->getProperty("zconstime");
70 >  data = info->getProperty(ZCONSTIME_ID);
71    
72    if(!data) {
73        
# Line 99 | Line 95 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
95  
96    }
97    
102 –  
98    //retrieve output filename of z force
99 <  data = info->getProperty("zconsfilename");
99 >  data = info->getProperty(ZCONSFILENAME_ID);
100    if(!data) {
101  
102        
# Line 114 | Line 109 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
109    }
110    else{
111  
112 <     filename = dynamic_cast<StringData*>(data);
112 >    filename = dynamic_cast<StringData*>(data);
113      
114      if(!filename){
115  
# Line 128 | Line 123 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
123        this->zconsOutput = filename->getData();
124      }
125      
126 +  }
127  
128 +  //retrieve tolerance for z-constraint molecuels
129 +  data = info->getProperty(ZCONSTOL_ID);
130 +  
131 +  if(!data) {
132 +      
133 +    sprintf( painCave.errMsg,
134 +               "ZConstraint error: can not get tolerance \n");
135 +    painCave.isFatal = 1;
136 +    simError();      
137    }
138 +  else{
139    
140 +    tolerance = dynamic_cast<DoubleData*>(data);
141 +    
142 +    if(!tolerance){
143 +
144 +      sprintf( painCave.errMsg,
145 +                 "ZConstraint error: Can not get property from SimInfo\n");
146 +      painCave.isFatal = 1;
147 +      simError();  
148 +      
149 +    }
150 +    else{
151 +      this->zconsTol = tolerance->getData();
152 +    }
153 +
154 +  }
155 +  
156 +  //retrieve index of z-constraint molecules
157 +  data = info->getProperty(ZCONSPARADATA_ID);
158 +  if(!data) {
159 +
160 +    sprintf( painCave.errMsg,
161 +               "ZConstraint error: If you use an ZConstraint\n"
162 +               " , you must set index of z-constraint molecules.\n");
163 +    painCave.isFatal = 1;
164 +    simError();  
165 +  }
166 +  else{
167 +  
168 +    zConsParaData = dynamic_cast<ZConsParaData*>(data);
169 +    
170 +    if(!zConsParaData){
171 +
172 +      sprintf( painCave.errMsg,
173 +                 "ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
174 +      painCave.isFatal = 1;
175 +      simError();  
176 +    
177 +    }
178 +    else{
179 +      
180 +      parameters = zConsParaData->getData();
181 +
182 +      //check the range of zconsIndex
183 +      //and the minimum value of index is the first one (we already sorted the data)
184 +      //the maximum value of index is the last one
185 +
186 +      int maxIndex;
187 +      int minIndex;
188 +      int totalNumMol;
189 +
190 +      minIndex = (*parameters)[0].zconsIndex;
191 +      if(minIndex < 0){
192 +        sprintf( painCave.errMsg,
193 +               "ZConstraint error: index is out of range\n");
194 +        painCave.isFatal = 1;
195 +        simError();
196 +        }
197 +
198 +      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
199 +
200 + #ifndef IS_MPI
201 +      totalNumMol = nMols;
202 + #else
203 +      totalNumMol = mpiSim->getTotNmol();  
204 + #endif      
205 +      
206 +      if(maxIndex > totalNumMol - 1){
207 +        sprintf( painCave.errMsg,
208 +               "ZConstraint error: index is out of range\n");
209 +        painCave.isFatal = 1;
210 +        simError();                  
211 +      }
212 +
213 +      //if user does not specify the zpos for the zconstraint molecule
214 +      //its initial z coordinate  will be used as default
215 +      for(int i = 0; i < parameters->size(); i++){
216 +
217 +        if(!(*parameters)[i].havingZPos){
218 + #ifndef IS_MPI
219 +          for(int j = 0; j < nMols; j++){
220 +            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
221 +              molecules[j].getCOM(COM);
222 +        break;
223 +            }
224 +          }
225 + #else
226 +            //query which processor current zconstraint molecule belongs to
227 +          int *MolToProcMap;
228 +          int whichNode;
229 +    double initZPos;
230 +          MolToProcMap = mpiSim->getMolToProcMap();
231 +          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
232 +        
233 +          //broadcast the zpos of current z-contraint molecule
234 +          //the node which contain this
235 +          
236 +          if (worldRank == whichNode ){
237 +            
238 +            for(int j = 0; j < nMols; j++)
239 +              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
240 +                molecules[j].getCOM(COM);
241 +          break;
242 +              }
243 +        
244 +          }
245 +
246 +          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
247 + #endif
248 +            
249 +          (*parameters)[i].zPos = COM[whichDirection];
250 +
251 +          sprintf( painCave.errMsg,
252 +                     "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
253 +                     "initial z coornidate will be used \n");
254 +           painCave.isFatal = 0;
255 +           simError();  
256 +    
257 +  }
258 +      }
259 +      
260 +    }//end if (!zConsParaData)
261 +  }//end  if (!data)
262 +            
263 + //  
264   #ifdef IS_MPI
265    update();
266   #else  
267    int searchResult;
138 –  double COM[3];
268        
269    for(int i = 0; i < nMols; i++){
270      
# Line 145 | Line 274 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
274      
275        zconsMols.push_back(&molecules[i]);      
276        massOfZConsMols.push_back(molecules[i].getTotalMass());  
277 +
278 +      zPos.push_back((*parameters)[searchResult].zPos);
279 + //       cout << "index: "<< (*parameters)[searchResult].zconsIndex
280 + //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
281 +      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
282        
283        molecules[i].getCOM(COM);
284      }
# Line 158 | Line 292 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
292    }
293  
294    fz = new double[zconsMols.size()];
295 +  curZPos = new double[zconsMols.size()];
296    indexOfZConsMols = new int [zconsMols.size()];
297  
298 <  if(!fz || !indexOfZConsMols){
298 >  if(!fz || !curZPos || !indexOfZConsMols){
299      sprintf( painCave.errMsg,
300               "Memory allocation failure in class Zconstraint\n");
301      painCave.isFatal = 1;
302      simError();
303    }
304  
305 <  for(int i = 0; i < zconsMols.size(); i++)
305 >  //determine the states of z-constraint molecules
306 >  for(int i = 0; i < zconsMols.size(); i++){
307      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
308 +
309 +    zconsMols[i]->getCOM(COM);
310 +    if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
311 +      states.push_back(zcsFixed);
312 +    else
313 +      states.push_back(zcsMoving);
314 +  }
315    
316   #endif
317 +
318 +  //get total masss of unconstraint molecules
319 +  double totalMassOfUncons_local;
320 +  totalMassOfUncons_local = 0;
321 +  
322 +  for(int i = 0; i < unconsMols.size(); i++)
323 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
324 +    
325 + #ifndef IS_MPI
326 +  totalMassOfUncons = totalMassOfUncons_local;
327 + #else
328 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
329 +                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
330 + #endif
331  
332 +
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
# Line 181 | Line 339 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
339   #ifndef IS_MPI
340    totNumOfUnconsAtoms = nUnconsAtoms_local;
341   #else
342 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
343 < #endif
342 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1,
343 >                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
344 > #endif  
345  
346 <
346 >  // creat zconsWriter  
347 >  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
348    
189 –  fzOut = new ZConsWriter(zconsOutput.c_str());  
190 –  
349    if(!fzOut){
350      sprintf( painCave.errMsg,
351               "Memory allocation failure in class Zconstraint\n");
352      painCave.isFatal = 1;
353      simError();
354    }
355 <  
355 >
356 >  forcePolicy->update();
357   }
358  
359   template<typename T> ZConstraint<T>::~ZConstraint()
360   {
361    if(fz)
362      delete[] fz;
363 +
364 +  if(curZPos)
365 +    delete[] curZPos;
366    
367    if(indexOfZConsMols)
368      delete[] indexOfZConsMols;
369    
370    if(fzOut)
371      delete fzOut;
372 +  
373 +  if(forcePolicy)
374 +    delete forcePolicy;
375   }
376  
377 +
378 + /**
379 + *
380 + */
381 +
382   #ifdef IS_MPI
383   template<typename T> void ZConstraint<T>::update()
384   {
# Line 217 | Line 387 | template<typename T> void ZConstraint<T>::update()
387    
388    zconsMols.clear();
389    massOfZConsMols.clear();
390 +  zPos.clear();
391 +  kz.clear();
392    
393    unconsMols.clear();
394    massOfUnconsMols.clear();
# Line 230 | Line 402 | template<typename T> void ZConstraint<T>::update()
402      if(index > -1){
403      
404        zconsMols.push_back(&molecules[i]);      
405 +      zPos.push_back((*parameters)[index].zPos);
406 +      kz.push_back((*parameters)[index].kRatio * zForceConst);
407 +      
408        massOfZConsMols.push_back(molecules[i].getTotalMass());  
409        
410        molecules[i].getCOM(COM);
# Line 242 | Line 417 | template<typename T> void ZConstraint<T>::update()
417  
418      }
419    }
420 +
421 +  //determine the states of z-constraint molecules
422 +  for(int i = 0; i < zconsMols.size(); i++){
423 +     zconsMols[i]->getCOM(COM);
424 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
425 +      states.push_back(zcsFixed);
426 +     else
427 +      states.push_back(zcsMoving);
428 +  }
429 +
430      
431    //The reason to declare fz and indexOfZconsMols as pointer to array is
432    // that we want to make the MPI communication simple
433    if(fz)
434      delete[] fz;
435 +  
436 +  if(curZPos)
437 +    delete[] curZPos;
438      
439    if(indexOfZConsMols)
440      delete[] indexOfZConsMols;
441      
442    if (zconsMols.size() > 0){
443      fz = new double[zconsMols.size()];
444 +   curZPos = new double[zconsMols.size()];
445      indexOfZConsMols =  new int[zconsMols.size()];
446      
447 <    if(!fz || !indexOfZConsMols){
447 >    if(!fz || !curZPos || !indexOfZConsMols){
448        sprintf( painCave.errMsg,
449                 "Memory allocation failure in class Zconstraint\n");
450        painCave.isFatal = 1;
# Line 269 | Line 458 | template<typename T> void ZConstraint<T>::update()
458    }
459    else{
460      fz = NULL;
461 +   curZPos = NULL;
462      indexOfZConsMols = NULL;
463    }
464    
465 +  //
466 +  forcePolicy->update();
467 +  
468   }
469  
470   #endif
471  
472 < /**  Function Name: isZConstraintMol
473 < **  Parameter
474 < **    Molecule* mol
475 < **  Return value:
476 < **    -1, if the molecule is not z-constraint molecule,
477 < **    other non-negative values, its index in indexOfAllZConsMols vector
472 > /**
473 > *  Function Name: isZConstraintMol
474 > *  Parameter
475 > *    Molecule* mol
476 > *  Return value:
477 > *    -1, if the molecule is not z-constraint molecule,
478 > *    other non-negative values, its index in indexOfAllZConsMols vector
479   */
480  
481   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 294 | Line 488 | template<typename T> int ZConstraint<T>::isZConstraint
488    index = mol->getGlobalIndex();
489    
490    low = 0;
491 <  high = indexOfAllZConsMols.size() - 1;
491 >  high = parameters->size() - 1;
492    
493    //Binary Search (we have sorted the array)  
494    while(low <= high){
495      mid = (low + high) /2;
496 <    if (indexOfAllZConsMols[mid] == index)
496 >    if ((*parameters)[mid].zconsIndex == index)
497        return mid;
498 <    else if (indexOfAllZConsMols[mid] > index )
498 >    else if ((*parameters)[mid].zconsIndex > index )
499         high = mid -1;
500      else    
501        low = mid + 1;
# Line 310 | Line 504 | template<typename T> int ZConstraint<T>::isZConstraint
504    return -1;
505   }
506  
313 – /**
314 – * Description:
315 – *  Reset the z coordinates
316 – */
507   template<typename T> void ZConstraint<T>::integrate(){
508    
509    //zero out the velocities of center of mass of unconstrained molecules
510    //and the velocities of center of mass of every single z-constrained molecueles
511    zeroOutVel();
512 +
513 +  curZconsTime = zconsTime + info->getTime();
514    
515    T::integrate();
516  
# Line 330 | Line 522 | template<typename T> void ZConstraint<T>::integrate(){
522   *
523   *
524   *
525 < */
334 <
335 <
525 > */
526   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
527 +  double zsys;
528 +  double COM[3];
529 +  double force[3];
530 +  double zSysCOMVel;
531  
532    T::calcForce(calcPot, calcStress);
533  
534 <  if (checkZConsState())
534 >  if (checkZConsState()){
535 >    
536 > #ifdef IS_MPI
537 >    if(worldRank == 0){
538 > #endif
539 > //       std::cerr << "\n"
540 > //              << "*******************************************\n"
541 > //              << " about to call zeroOutVel()\n"
542 > //              << "*******************************************\n"
543 > //              << "\n";
544 > #ifdef IS_MPI
545 >    }
546 > #endif
547      zeroOutVel();
548  
549 + #ifdef IS_MPI
550 +    if(worldRank == 0){
551 + #endif
552 + //       std::cerr << "\n"
553 + //              << "*******************************************\n"
554 + //              << " finished zeroOutVel()\n"
555 + //              << "*******************************************\n"
556 + //              << "\n";
557 + #ifdef IS_MPI
558 +    }
559 + #endif
560 +    
561 +    forcePolicy->update();
562 +  }  
563 +  
564 +  zsys = calcZSys();
565 +  zSysCOMVel = calcSysCOMVel();
566 + #ifdef IS_MPI
567 +  if(worldRank == 0){
568 + #endif
569 + //     cout << "---------------------------------------------------------------------" <<endl;
570 + //     cout << "current time: " << info->getTime() << endl;
571 + //     cout << "center of mass at z: " << zsys << endl;    
572 + //     cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
573 +
574 + #ifdef IS_MPI
575 +  }
576 + #endif
577 +
578    //do zconstraint force;
579    if (haveFixedZMols())
580      this->doZconstraintForce();
581 <  
581 >    
582    //use harmonical poteintial to move the molecules to the specified positions
583    if (haveMovingZMols())
584 <    //this->doHarmonic();
585 <  
586 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
587 <      
584 >    this->doHarmonic();
585 >
586 >  //write out forces and current positions of z-constraint molecules
587 >  if(info->getTime() >= curZconsTime){    
588 >   for(int i = 0; i < zconsMols.size(); i++){
589 >      zconsMols[i]->getCOM(COM);
590 >    curZPos[i] = COM[whichDirection];
591 >
592 >    //if the z-constraint molecule is still moving, just record its force
593 >    if(states[i] == zcsMoving){
594 >         fz[i] = 0;
595 >      Atom** movingZAtoms;
596 >      movingZAtoms = zconsMols[i]->getMyAtoms();
597 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
598 >           movingZAtoms[j]->getFrc(force);
599 >           fz[i] += force[whichDirection];
600 >      }
601 >     }
602 >   }
603 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
604 >   curZconsTime += zconsTime;
605 >  }
606 >
607 >  zSysCOMVel = calcSysCOMVel();  
608 > #ifdef IS_MPI
609 >  if(worldRank == 0){
610 > #endif
611 > //    cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
612 > #ifdef IS_MPI
613 >  }
614 > #endif
615 >
616   }
617 +
618 +
619 + /**
620 + *
621 + */
622  
623   template<typename T> double ZConstraint<T>::calcZSys()
624   {
# Line 359 | Line 627 | template<typename T> double ZConstraint<T>::calcZSys()
627    double totalMass;
628    double totalMZ_local;
629    double totalMZ;
362 –  double massOfUncons_local;
630    double massOfCurMol;
631    double COM[3];
632    
633    totalMass_local = 0;
367 –  totalMass = 0;
634    totalMZ_local = 0;
369 –  totalMZ = 0;
370 –  massOfUncons_local = 0;
371 –    
635    
636    for(int i = 0; i < nMols; i++){
637      massOfCurMol = molecules[i].getTotalMass();
# Line 376 | Line 639 | template<typename T> double ZConstraint<T>::calcZSys()
639      
640      totalMass_local += massOfCurMol;
641      totalMZ_local += massOfCurMol * COM[whichDirection];
642 <    
380 <    if(isZConstraintMol(&molecules[i]) == -1){
381 <    
382 <      massOfUncons_local += massOfCurMol;
383 <    }  
384 <    
642 >
643    }
644 +
645    
387 –  
646   #ifdef IS_MPI  
647 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
648 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
649 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
650 < #else
647 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
648 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
649 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
650 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
651 > #else
652    totalMass = totalMass_local;
653    totalMZ = totalMZ_local;
654 <  totalMassOfUncons = massOfUncons_local;
396 < #endif  
654 > #endif  
655  
656    double zsys;
657    zsys = totalMZ / totalMass;
# Line 412 | Line 670 | template<typename T> void ZConstraint<T>::thermalize(
670  
671   /**
672   *
415 – *
416 – *
673   */
674  
675   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 421 | Line 677 | template<typename T> void ZConstraint<T>::zeroOutVel()
677    Atom** fixedZAtoms;  
678    double COMvel[3];
679    double vel[3];
680 <  
680 >  double zSysCOMVel;
681 >
682    //zero out the velocities of center of mass of fixed z-constrained molecules
683    
684    for(int i = 0; i < zconsMols.size(); i++){
685  
686 <    if (states[i] == zcsFixed){
686 >    if (states[i] == zcsFixed){
687  
688 <        zconsMols[i]->getCOMvel(COMvel);      
688 >     zconsMols[i]->getCOMvel(COMvel);      
689 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
690 >
691        fixedZAtoms = zconsMols[i]->getMyAtoms();
692 <          
692 >    
693        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
694          fixedZAtoms[j]->getVel(vel);
695 <          vel[whichDirection] -= COMvel[whichDirection];
696 <          fixedZAtoms[j]->setVel(vel);
695 >       vel[whichDirection] -= COMvel[whichDirection];
696 >       fixedZAtoms[j]->setVel(vel);
697        }
698 <          
698 >
699 >    zconsMols[i]->getCOMvel(COMvel);
700 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
701      }
441 –        
442 –  }
702    
703 +  }
704 +
705 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
706 +
707 +  zSysCOMVel = calcSysCOMVel();
708 + #ifdef IS_MPI
709 +  if(worldRank == 0){
710 + #endif
711 + //     cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
712 + #ifdef IS_MPI
713 +  }
714 + #endif
715 +      
716    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
717    double MVzOfMovingMols_local;
718    double MVzOfMovingMols;
# Line 455 | Line 727 | template<typename T> void ZConstraint<T>::zeroOutVel()
727      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
728    }
729  
730 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
459 <
730 >  for(int i = 0; i < zconsMols.size(); i++){
731      if (states[i] == zcsMoving){
732        zconsMols[i]->getCOMvel(COMvel);
733        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
734 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
734 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
735      }
736 <                
736 >    
737    }
738  
739   #ifndef IS_MPI
# Line 491 | Line 762 | template<typename T> void ZConstraint<T>::zeroOutVel()
762  
763    //modify the velocities of moving z-constrained molecuels
764    Atom** movingZAtoms;
765 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
765 >  for(int i = 0; i < zconsMols.size(); i++){
766  
767      if (states[i] ==zcsMoving){
768    
769        movingZAtoms = zconsMols[i]->getMyAtoms();
770 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
770 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
771          movingZAtoms[j]->getVel(vel);
772          vel[whichDirection] -= vzOfMovingMols;
773 <          movingZAtoms[j]->setVel(vel);
503 <        }
504 <          
773 >       movingZAtoms[j]->setVel(vel);
774      }
775 +    
776 +   }
777  
778 + }
779 +
780 +
781 +  zSysCOMVel = calcSysCOMVel();
782 + #ifdef IS_MPI
783 +  if(worldRank == 0){
784 + #endif
785 + //     cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
786 + #ifdef IS_MPI
787    }
788 + #endif
789  
790   }
791  
792 + /**
793 + *
794 + */
795 +
796   template<typename T> void ZConstraint<T>::doZconstraintForce(){
797  
798    Atom** zconsAtoms;
# Line 516 | Line 801 | template<typename T> void ZConstraint<T>::doZconstrain
801    double COMvel[3];  
802    double COM[3];
803    double force[3];
519 –  double zsys;
804  
521 –  int nMovingZMols_local;
522 –  int nMovingZMols;
805  
524 –  //constrain the molecules which do not reach the specified positions  
806  
807 <   zsys = calcZSys();
527 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
807 >  //constrain the molecules which do not reach the specified positions  
808      
809    //Zero Out the force of z-contrained molecules    
810    totalFZ_local = 0;
811  
812    //calculate the total z-contrained force of fixed z-contrained molecules
813 +
814    for(int i = 0; i < zconsMols.size(); i++){
815 <                
815 >    
816      if (states[i] == zcsFixed){
817 <                
817 >      
818        zconsMols[i]->getCOM(COM);
819        zconsAtoms = zconsMols[i]->getMyAtoms();  
820  
# Line 541 | Line 822 | template<typename T> void ZConstraint<T>::doZconstrain
822        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
823          zconsAtoms[j]->getFrc(force);
824          fz[i] += force[whichDirection];      
825 <      }
825 >      }
826        totalFZ_local += fz[i];
827  
828 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
828 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
829 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
830 >      //       << "\tcurrent fz: " <<fz[i] << endl;
831  
832 +
833      }
834 <          
834 >    
835    }
836  
837 <  //calculate the number of atoms of moving z-constrained molecules
554 <  nMovingZMols_local = 0;
555 <  for(int i = 0; zconsMols.size(); i++){
556 <    if(states[i] == zcsMoving)
557 <        nMovingZMols_local += massOfZConsMols[i];
558 <  }
837 >  //calculate total z-constraint force
838   #ifdef IS_MPI
839    MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
561 –  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
840   #else
841    totalFZ = totalFZ_local;
564 –  nMovingZMols = nMovingZMols_local;
842   #endif
843  
844 +  
845 +  // apply negative to fixed z-constrained molecues;
846    force[0]= 0;
847    force[1]= 0;
848    force[2]= 0;
570 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
849  
850 <  //modify the velocites of unconstrained molecules
850 >  for(int i = 0; i < zconsMols.size(); i++){
851 >
852 >    if (states[i] == zcsFixed){  
853 >  
854 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
855 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
856 >    
857 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
858 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
859 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
860 >        zconsAtoms[j]->addFrc(force);
861 >      }
862 >    
863 >    }
864 >  
865 >  }
866 >
867 > //   cout << "after zero out z-constraint force on fixed z-constraint molecuels "
868 > //        << "total force is " << calcTotalForce() << endl;
869 >
870 >  //calculate the number of atoms of moving z-constrained molecules
871 >  int nMovingZAtoms_local;
872 >  int nMovingZAtoms;
873 >  
874 >  nMovingZAtoms_local = 0;
875 >  for(int i = 0; i < zconsMols.size(); i++)
876 >    if(states[i] == zcsMoving)
877 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
878 >  
879 > #ifdef IS_MPI
880 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
881 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
882 > #else
883 >  nMovingZAtoms = nMovingZAtoms_local;
884 > #endif
885 >
886 >  force[0]= 0;
887 >  force[1]= 0;
888 >  force[2]= 0;
889 >
890 >  //modify the forces of unconstrained molecules
891    for(int i = 0; i < unconsMols.size(); i++){
892      
893       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
894      
895 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
895 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
896 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
897 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
898         unconsAtoms[j]->addFrc(force);
899 +     }
900      
901    }      
902  
903 < //modify the velocities of moving z-constrained molecules
903 > //modify the forces of moving z-constrained molecules
904    for(int i = 0; i < zconsMols.size(); i++) {
905 <   if (states[i] == zcsMoving){
906 <                
907 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
905 >    if (states[i] == zcsMoving){
906 >    
907 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
908  
909 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
910 <       movingZAtoms[j]->addFrc(force);
911 <     }
909 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
910 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
911 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
912 >        movingZAtoms[j]->addFrc(force);
913 >      }
914 >    }
915    }
916  
917 <  // apply negative to fixed z-constrained molecues;
918 <  force[0]= 0;
595 <  force[1]= 0;
596 <  force[2]= 0;
917 >  //cout << "after substracting z-constraint force from moving molecuels "
918 >  //      << "total force is " << calcTotalForce()  << endl;
919  
920 <  for(int i = 0; i < zconsMols.size(); i++){
920 > }
921  
922 <    if (states[i] == zcsFixed){  
923 <        
924 <      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
925 <      zconsAtoms = zconsMols[i]->getMyAtoms();  
922 > /**
923 >  *
924 >  *
925 >  */
926 >
927 > template<typename T> void ZConstraint<T>::doHarmonic(){
928 >  double force[3];
929 >  double harmonicU;
930 >  double harmonicF;
931 >  double COM[3];
932 >  double diff;
933 >  double totalFZ_local;
934 >  double totalFZ;
935 >  
936 >  force[0] = 0;
937 >  force[1] = 0;
938 >  force[2] = 0;
939 >
940 >  totalFZ_local = 0;
941 >
942 >  for(int i = 0; i < zconsMols.size(); i++) {
943 >
944 >    if (states[i] == zcsMoving){
945 >      zconsMols[i]->getCOM(COM);
946 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
947 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
948 >
949 >      diff = COM[whichDirection] -zPos[i];
950      
951 <      for(int j =0; j < nAtomOfCurZConsMol; j++) {
952 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
953 <        zconsAtoms[j]->addFrc(force);
954 <      }
955 <                
951 >      harmonicU = 0.5 * kz[i] * diff * diff;  
952 >      info->lrPot += harmonicU;
953 >
954 >      harmonicF =  - kz[i] * diff;
955 >      totalFZ_local += harmonicF;
956 >
957 >       //adjust force
958 >    
959 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
960 >
961 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
962 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
963 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
964 >         movingZAtoms[j]->addFrc(force);
965 >       }
966      }
611 –        
612 –  }
967  
968 +  }
969 +
970 + #ifndef IS_MPI
971 +  totalFZ = totalFZ_local;
972 + #else
973 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
974 + #endif
975 +
976 +  force[0]= 0;
977 +  force[1]= 0;
978 +  force[2]= 0;
979 +
980 +  //modify the forces of unconstrained molecules
981 +  for(int i = 0; i < unconsMols.size(); i++){
982 +    
983 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
984 +    
985 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
986 +       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
987 +       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
988 +       unconsAtoms[j]->addFrc(force);    
989 +     }
990 +  }  
991 +
992   }
993  
994 + /**
995 + *
996 + */
997 +
998   template<typename T> bool ZConstraint<T>::checkZConsState(){
999    double COM[3];
1000    double diff;
1001    
1002 <  bool changed;
1002 >  int changed_local;
1003 >  int changed;
1004    
1005 <  changed = false;
1005 >  changed_local = 0;
1006    
1007    for(int i =0; i < zconsMols.size(); i++){
1008  
1009      zconsMols[i]->getCOM(COM);
1010 <    diff = fabs(COM[whichDirection] - ZPos[i]);  
1011 <    if (  diff <= ztol && states[i] == zcsMoving){
1010 >    diff = fabs(COM[whichDirection] - zPos[i]);  
1011 >    if (  diff <= zconsTol && states[i] == zcsMoving){
1012        states[i] = zcsFixed;
1013 <        changed = true;
1013 >     changed_local = 1;
1014      }
1015 <    else if ( diff > ztol && states[i] == zcsFixed){
1015 >    else if ( diff > zconsTol && states[i] == zcsFixed){
1016        states[i] = zcsMoving;
1017 <        changed = true;  
1017 >     changed_local = 1;  
1018      }
1019    
1020    }
1021  
1022 <  return changed;
1022 > #ifndef IS_MPI
1023 >  changed =changed_local;
1024 > #else
1025 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1026 > #endif
1027 >
1028 >  return (changed > 0);
1029 >
1030   }
1031  
1032   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
643 –  for(int i = 0; i < zconsMols.size(); i++)
644 –    if (states[i] == zcsFixed)
645 –      return true;
1033  
1034 <  return false;
1034 >  int havingFixed_local;
1035 >  int havingFixed;
1036 >
1037 >  havingFixed_local = 0;
1038 >
1039 >  for(int i = 0; i < zconsMols.size(); i++)
1040 >    if (states[i] == zcsFixed){
1041 >      havingFixed_local = 1;
1042 >    break;
1043 >    }
1044 >
1045 > #ifndef IS_MPI
1046 >  havingFixed = havingFixed_local;
1047 > #else
1048 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1049 > #endif
1050 >
1051 >  return (havingFixed > 0);
1052   }
1053  
1054  
# Line 652 | Line 1056 | template<typename T> bool ZConstraint<T>::haveMovingZM
1056   *
1057   */
1058   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1059 +
1060 +  int havingMoving_local;
1061 +  int havingMoving;
1062 +
1063 +  havingMoving_local = 0;
1064 +
1065    for(int i = 0; i < zconsMols.size(); i++)
1066 <    if (states[i] == zcsMoving)
1067 <      return true;
1066 >    if (states[i] == zcsMoving){
1067 >      havingMoving_local = 1;
1068 >    break;
1069 >    }
1070  
1071 <  return false;
1071 > #ifndef IS_MPI
1072 >  havingMoving = havingMoving_local;
1073 > #else
1074 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1075 > #endif
1076 >
1077 >  return (havingMoving > 0);
1078    
1079 < }
1079 > }
1080 >
1081 > /**
1082 > *
1083 > */
1084 >
1085 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1086 > {
1087 >  double MVzOfMovingMols_local;
1088 >  double MVzOfMovingMols;
1089 >  double totalMassOfMovingZMols_local;
1090 >  double totalMassOfMovingZMols;
1091 >  double COMvel[3];
1092 >      
1093 >  MVzOfMovingMols_local = 0;
1094 >  totalMassOfMovingZMols_local = 0;
1095 >
1096 >  for(int i =0; i < unconsMols.size(); i++){
1097 >    unconsMols[i]->getCOMvel(COMvel);
1098 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1099 >  }
1100 >
1101 >  for(int i = 0; i < zconsMols.size(); i++){
1102 >
1103 >    if (states[i] == zcsMoving){
1104 >      zconsMols[i]->getCOMvel(COMvel);
1105 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1106 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1107 >    }
1108 >    
1109 >  }
1110 >
1111 > #ifndef IS_MPI
1112 >  MVzOfMovingMols = MVzOfMovingMols_local;
1113 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1114 > #else
1115 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1116 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1117 > #endif
1118 >
1119 >  double vzOfMovingMols;
1120 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1121 >
1122 >  return vzOfMovingMols;
1123 > }
1124 >
1125 > /**
1126 > *
1127 > */
1128 >
1129 > template<typename T> double ZConstraint<T>::calcSysCOMVel()
1130 > {
1131 >  double COMvel[3];
1132 >  double tempMVz_local;
1133 >  double tempMVz;
1134 >  double massOfZCons_local;
1135 >  double massOfZCons;
1136 >
1137 >
1138 > tempMVz_local = 0;
1139 >
1140 >  for(int i =0 ; i < nMols; i++){
1141 >    molecules[i].getCOMvel(COMvel);
1142 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1143 >  }
1144 >
1145 >  massOfZCons_local = 0;
1146 >  
1147 >  for(int i = 0; i < massOfZConsMols.size(); i++){
1148 >    massOfZCons_local += massOfZConsMols[i];
1149 >  }
1150 > #ifndef IS_MPI
1151 >  massOfZCons = massOfZCons_local;
1152 >  tempMVz = tempMVz_local;
1153 > #else
1154 >  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1155 >  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1156 > #endif
1157 >
1158 >  return tempMVz /(totalMassOfUncons + massOfZCons);
1159 > }
1160 >
1161 > /**
1162 > *
1163 > */
1164 >
1165 > template<typename T> double ZConstraint<T>::calcTotalForce(){
1166 >
1167 >  double force[3];  
1168 >  double totalForce_local;
1169 >  double totalForce;
1170 >
1171 >  totalForce_local = 0;
1172 >
1173 >  for(int i = 0; i < nAtoms; i++){
1174 >    atoms[i]->getFrc(force);
1175 >    totalForce_local += force[whichDirection];
1176 >  }
1177 >
1178 > #ifndef IS_MPI
1179 >  totalForce = totalForce_local;
1180 > #else
1181 >  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1182 > #endif
1183 >
1184 >  return totalForce;
1185 >
1186 > }
1187 >
1188 > /**
1189 > *
1190 > */
1191 >
1192 > template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1193 >  //calculate the number of atoms of moving z-constrained molecules
1194 >  int nMovingZAtoms_local;
1195 >  int nMovingZAtoms;
1196 >  
1197 >  nMovingZAtoms_local = 0;
1198 >  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1199 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1200 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1201 >  
1202 > #ifdef IS_MPI
1203 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1204 > #else
1205 >  nMovingZAtoms = nMovingZAtoms_local;
1206 > #endif
1207 >  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1208 >
1209 > #ifdef IS_MPI
1210 >  if(worldRank == 0){
1211 > #endif
1212 > //    std::cerr << "\n"
1213 > //            << "*******************************************\n"
1214 > //            << " fiished Policy by numbr()\n"
1215 > //            << "*******************************************\n"
1216 > //            << "\n";
1217 > #ifdef IS_MPI
1218 >  }
1219 > #endif
1220 > }
1221 >
1222 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1223 >  return totalForce / mol->getNAtoms();
1224 > }
1225 >
1226 > template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1227 >  return totalForce / totNumOfMovingAtoms;
1228 > }
1229 >
1230 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1231 >    return totalForce / mol->getNAtoms();
1232 > }
1233 >
1234 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1235 >  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1236 > }
1237 >
1238 > /**
1239 > *
1240 > */
1241 >
1242 > template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1243 >  //calculate the number of atoms of moving z-constrained molecules
1244 >  double massOfMovingZAtoms_local;
1245 >  double massOfMovingZAtoms;
1246 >  
1247 >  massOfMovingZAtoms_local = 0;
1248 >  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1249 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1250 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1251 >  
1252 > #ifdef IS_MPI
1253 >  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1254 > #else
1255 >  massOfMovingZAtoms = massOfMovingZAtoms_local;
1256 > #endif
1257 >  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1258 > }
1259 >
1260 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1261 >  return totalForce * atom->getMass() / mol->getTotalMass();
1262 > }
1263 >
1264 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1265 >    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1266 > }
1267 >
1268 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1269 >  return totalForce * atom->getMass() / mol->getTotalMass();
1270 > }
1271 >
1272 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1273 >    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1274 > }
1275 >

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