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root/group/trunk/OOPSE/libmdtools/ZConstraint.cpp
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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 701 by tim, Wed Aug 20 14:34:04 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 >               "average force substraction policy is used\n");
36 >    painCave.isFatal = 0;
37 >    simError();      
38 >
39 >    forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(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 >                 "average force substraction policy is used\n");
48 >      painCave.isFatal = 0;
49 >      simError();      
50 >
51 >      forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(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
# Line 330 | Line 520 | template<typename T> void ZConstraint<T>::integrate(){
520   *
521   *
522   *
523 < */
334 <
335 <
523 > */
524   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
525 +  double zsys;
526 +  double COM[3];
527 +  double force[3];
528  
529    T::calcForce(calcPot, calcStress);
530  
531 <  if (checkZConsState())
531 >  if (checkZConsState()){
532      zeroOutVel();
533 +   forcePolicy->update();
534 +  }  
535 +  zsys = calcZSys();
536 +  cout << "---------------------------------------------------------------------" <<endl;
537 +  cout << "current time: " << info->getTime() << endl;
538 +  cout << "center of mass at z: " << zsys << endl;    
539 +  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
540 +  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
541  
542 +  //cout <<  "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
543 +
544    //do zconstraint force;
545    if (haveFixedZMols())
546      this->doZconstraintForce();
547 <  
547 >    
548    //use harmonical poteintial to move the molecules to the specified positions
549    if (haveMovingZMols())
550 <    //this->doHarmonic();
551 <  
552 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
553 <      
550 >    this->doHarmonic();
551 >
552 >  //cout <<  "after doHarmonic, totalForce is " << calcTotalForce() << endl;
553 >
554 >  //write out forces and current positions of z-constraint molecules
555 >  if(info->getTime() >= curZconsTime){    
556 >   for(int i = 0; i < zconsMols.size(); i++){
557 >      zconsMols[i]->getCOM(COM);
558 >    curZPos[i] = COM[whichDirection];
559 >
560 >    //if the z-constraint molecule is still moving, just record its force
561 >    if(states[i] == zcsMoving){
562 >         fz[i] = 0;
563 >      Atom** movingZAtoms;
564 >      movingZAtoms = zconsMols[i]->getMyAtoms();
565 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
566 >           movingZAtoms[j]->getFrc(force);
567 >           fz[i] += force[whichDirection];
568 >      }
569 >     }
570 >   }
571 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
572 >   curZconsTime += zconsTime;
573 >  }
574 >  
575 >  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
576 >  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
577   }
578 +
579 +
580 + /**
581 + *
582 + */
583  
584   template<typename T> double ZConstraint<T>::calcZSys()
585   {
# Line 359 | Line 588 | template<typename T> double ZConstraint<T>::calcZSys()
588    double totalMass;
589    double totalMZ_local;
590    double totalMZ;
362 –  double massOfUncons_local;
591    double massOfCurMol;
592    double COM[3];
593    
594    totalMass_local = 0;
367 –  totalMass = 0;
595    totalMZ_local = 0;
369 –  totalMZ = 0;
370 –  massOfUncons_local = 0;
371 –    
596    
597    for(int i = 0; i < nMols; i++){
598      massOfCurMol = molecules[i].getTotalMass();
# Line 376 | Line 600 | template<typename T> double ZConstraint<T>::calcZSys()
600      
601      totalMass_local += massOfCurMol;
602      totalMZ_local += massOfCurMol * COM[whichDirection];
603 <    
380 <    if(isZConstraintMol(&molecules[i]) == -1){
381 <    
382 <      massOfUncons_local += massOfCurMol;
383 <    }  
384 <    
603 >
604    }
605 +
606    
387 –  
607   #ifdef IS_MPI  
608 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
609 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
610 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
611 < #else
608 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
609 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
610 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
611 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
612 > #else
613    totalMass = totalMass_local;
614    totalMZ = totalMZ_local;
615 <  totalMassOfUncons = massOfUncons_local;
396 < #endif  
615 > #endif  
616  
617    double zsys;
618    zsys = totalMZ / totalMass;
# Line 412 | Line 631 | template<typename T> void ZConstraint<T>::thermalize(
631  
632   /**
633   *
415 – *
416 – *
634   */
635  
636   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 421 | Line 638 | template<typename T> void ZConstraint<T>::zeroOutVel()
638    Atom** fixedZAtoms;  
639    double COMvel[3];
640    double vel[3];
641 <  
641 >  double zSysCOMVel;
642 >
643    //zero out the velocities of center of mass of fixed z-constrained molecules
644    
645    for(int i = 0; i < zconsMols.size(); i++){
646  
647 <    if (states[i] == zcsFixed){
647 >    if (states[i] == zcsFixed){
648  
649 <        zconsMols[i]->getCOMvel(COMvel);      
649 >     zconsMols[i]->getCOMvel(COMvel);      
650 >    //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
651 >
652        fixedZAtoms = zconsMols[i]->getMyAtoms();
653 <          
653 >    
654        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
655          fixedZAtoms[j]->getVel(vel);
656 <          vel[whichDirection] -= COMvel[whichDirection];
657 <          fixedZAtoms[j]->setVel(vel);
656 >       vel[whichDirection] -= COMvel[whichDirection];
657 >       fixedZAtoms[j]->setVel(vel);
658        }
659 <          
659 >
660 >    zconsMols[i]->getCOMvel(COMvel);
661 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
662      }
441 –        
442 –  }
663    
664 +  }
665 +
666 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
667 +
668 +  zSysCOMVel = calcSysCOMVel();
669 + #ifdef IS_MPI
670 +  if(worldRank == 0){
671 + #endif
672 +    cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
673 + #ifdef IS_MPI
674 +  }
675 + #endif
676 +      
677    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
678    double MVzOfMovingMols_local;
679    double MVzOfMovingMols;
# Line 455 | Line 688 | template<typename T> void ZConstraint<T>::zeroOutVel()
688      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
689    }
690  
691 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
459 <
691 >  for(int i = 0; i < zconsMols.size(); i++){
692      if (states[i] == zcsMoving){
693        zconsMols[i]->getCOMvel(COMvel);
694        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
695 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
695 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
696      }
697 <                
697 >    
698    }
699  
700   #ifndef IS_MPI
# Line 491 | Line 723 | template<typename T> void ZConstraint<T>::zeroOutVel()
723  
724    //modify the velocities of moving z-constrained molecuels
725    Atom** movingZAtoms;
726 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
726 >  for(int i = 0; i < zconsMols.size(); i++){
727  
728      if (states[i] ==zcsMoving){
729    
730        movingZAtoms = zconsMols[i]->getMyAtoms();
731 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
731 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
732          movingZAtoms[j]->getVel(vel);
733          vel[whichDirection] -= vzOfMovingMols;
734 <          movingZAtoms[j]->setVel(vel);
503 <        }
504 <          
734 >       movingZAtoms[j]->setVel(vel);
735      }
736 +    
737 +   }
738 +
739 + }
740  
741 +
742 +  zSysCOMVel = calcSysCOMVel();
743 + #ifdef IS_MPI
744 +  if(worldRank == 0){
745 + #endif
746 +    cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
747 + #ifdef IS_MPI
748    }
749 + #endif
750  
751   }
752  
753 + /**
754 + *
755 + */
756 +
757   template<typename T> void ZConstraint<T>::doZconstraintForce(){
758  
759    Atom** zconsAtoms;
# Line 516 | Line 762 | template<typename T> void ZConstraint<T>::doZconstrain
762    double COMvel[3];  
763    double COM[3];
764    double force[3];
519 –  double zsys;
765  
521 –  int nMovingZMols_local;
522 –  int nMovingZMols;
766  
524 –  //constrain the molecules which do not reach the specified positions  
767  
768 <   zsys = calcZSys();
527 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
768 >  //constrain the molecules which do not reach the specified positions  
769      
770    //Zero Out the force of z-contrained molecules    
771    totalFZ_local = 0;
772  
773    //calculate the total z-contrained force of fixed z-contrained molecules
774 +
775    for(int i = 0; i < zconsMols.size(); i++){
776 <                
776 >    
777      if (states[i] == zcsFixed){
778 <                
778 >      
779        zconsMols[i]->getCOM(COM);
780        zconsAtoms = zconsMols[i]->getMyAtoms();  
781  
# Line 541 | Line 783 | template<typename T> void ZConstraint<T>::doZconstrain
783        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
784          zconsAtoms[j]->getFrc(force);
785          fz[i] += force[whichDirection];      
786 <      }
786 >      }
787        totalFZ_local += fz[i];
788  
789 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
789 >      cout << "Fixed Molecule --\tindex: " << indexOfZConsMols[i]
790 >             <<"\tcurrent zpos: " << COM[whichDirection]
791 >             << "\tcurrent fz: " <<fz[i] << endl;
792  
793      }
794 <          
794 >    
795    }
796  
797 <  //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 <  }
797 >  //calculate total z-constraint force
798   #ifdef IS_MPI
799    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);
800   #else
801    totalFZ = totalFZ_local;
564 –  nMovingZMols = nMovingZMols_local;
802   #endif
803  
804 +  
805 +  // apply negative to fixed z-constrained molecues;
806    force[0]= 0;
807    force[1]= 0;
808    force[2]= 0;
570 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
809  
810 <  //modify the velocites of unconstrained molecules
810 >  for(int i = 0; i < zconsMols.size(); i++){
811 >
812 >    if (states[i] == zcsFixed){  
813 >  
814 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
815 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
816 >    
817 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
818 >      force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
819 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
820 >        zconsAtoms[j]->addFrc(force);
821 >      }
822 >    
823 >    }
824 >  
825 >  }
826 >
827 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
828 >  //       << "total force is " << calcTotalForce() << endl;
829 >
830 >  //calculate the number of atoms of moving z-constrained molecules
831 >  int nMovingZAtoms_local;
832 >  int nMovingZAtoms;
833 >  
834 >  nMovingZAtoms_local = 0;
835 >  for(int i = 0; i < zconsMols.size(); i++)
836 >    if(states[i] == zcsMoving)
837 >     nMovingZAtoms_local += zconsMols[i]->getNAtoms();
838 >  
839 > #ifdef IS_MPI
840 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1,
841 >                      MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
842 > #else
843 >  nMovingZAtoms = nMovingZAtoms_local;
844 > #endif
845 >
846 >  force[0]= 0;
847 >  force[1]= 0;
848 >  force[2]= 0;
849 >
850 >  //modify the forces of unconstrained molecules
851    for(int i = 0; i < unconsMols.size(); i++){
852      
853       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
854      
855 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
855 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
856 >       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
857 >       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
858         unconsAtoms[j]->addFrc(force);
859 +     }
860      
861    }      
862  
863 < //modify the velocities of moving z-constrained molecules
863 > //modify the forces of moving z-constrained molecules
864    for(int i = 0; i < zconsMols.size(); i++) {
865 <   if (states[i] == zcsMoving){
866 <                
867 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
865 >    if (states[i] == zcsMoving){
866 >    
867 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
868  
869 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
870 <       movingZAtoms[j]->addFrc(force);
871 <     }
869 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
870 >        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
871 >        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
872 >        movingZAtoms[j]->addFrc(force);
873 >      }
874 >    }
875    }
876  
877 <  // apply negative to fixed z-constrained molecues;
878 <  force[0]= 0;
595 <  force[1]= 0;
596 <  force[2]= 0;
877 >  //cout << "after substracting z-constraint force from moving molecuels "
878 >  //      << "total force is " << calcTotalForce()  << endl;
879  
880 <  for(int i = 0; i < zconsMols.size(); i++){
880 > }
881  
882 <    if (states[i] == zcsFixed){  
883 <        
884 <      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
885 <      zconsAtoms = zconsMols[i]->getMyAtoms();  
882 > /**
883 >  *
884 >  *
885 >  */
886 >
887 > template<typename T> void ZConstraint<T>::doHarmonic(){
888 >  double force[3];
889 >  double harmonicU;
890 >  double harmonicF;
891 >  double COM[3];
892 >  double diff;
893 >  double totalFZ_local;
894 >  double totalFZ;
895 >  
896 >  force[0] = 0;
897 >  force[1] = 0;
898 >  force[2] = 0;
899 >
900 >  totalFZ_local = 0;
901 >
902 >  for(int i = 0; i < zconsMols.size(); i++) {
903 >
904 >    if (states[i] == zcsMoving){
905 >      zconsMols[i]->getCOM(COM);
906 >      cout << "Moving Molecule --\tindex: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
907      
908 <      for(int j =0; j < nAtomOfCurZConsMol; j++) {
909 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
910 <        zconsAtoms[j]->addFrc(force);
911 <      }
912 <                
908 >    diff = COM[whichDirection] -zPos[i];
909 >    
910 >      harmonicU = 0.5 * kz[i] * diff * diff;  
911 >    info->lrPot += harmonicU;
912 >
913 >      harmonicF =  - kz[i] * diff;
914 >      totalFZ_local += harmonicF;
915 >
916 >       //adjust force
917 >    
918 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
919 >
920 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
921 >        force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
922 >         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
923 >         movingZAtoms[j]->addFrc(force);
924 >       }
925      }
611 –        
612 –  }
926  
927 +  }
928 +
929 + #ifndef IS_MPI
930 +  totalFZ = totalFZ_local;
931 + #else
932 +  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
933 + #endif
934 +
935 +  force[0]= 0;
936 +  force[1]= 0;
937 +  force[2]= 0;
938 +
939 +  //modify the forces of unconstrained molecules
940 +  for(int i = 0; i < unconsMols.size(); i++){
941 +    
942 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
943 +    
944 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
945 +       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
946 +       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
947 +       unconsAtoms[j]->addFrc(force);    
948 +     }
949 +  }  
950 +
951   }
952  
953 + /**
954 + *
955 + */
956 +
957   template<typename T> bool ZConstraint<T>::checkZConsState(){
958    double COM[3];
959    double diff;
960    
961 <  bool changed;
961 >  int changed_local;
962 >  int changed;
963    
964 <  changed = false;
964 >  changed_local = 0;
965    
966    for(int i =0; i < zconsMols.size(); i++){
967  
968      zconsMols[i]->getCOM(COM);
969 <    diff = fabs(COM[whichDirection] - ZPos[i]);  
970 <    if (  diff <= ztol && states[i] == zcsMoving){
969 >    diff = fabs(COM[whichDirection] - zPos[i]);  
970 >    if (  diff <= zconsTol && states[i] == zcsMoving){
971        states[i] = zcsFixed;
972 <        changed = true;
972 >     changed_local = 1;
973      }
974 <    else if ( diff > ztol && states[i] == zcsFixed){
974 >    else if ( diff > zconsTol && states[i] == zcsFixed){
975        states[i] = zcsMoving;
976 <        changed = true;  
976 >     changed_local = 1;  
977      }
978    
979    }
980  
981 <  return changed;
981 > #ifndef IS_MPI
982 >  changed =changed_local;
983 > #else
984 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
985 > #endif
986 >
987 >  return changed > 0 ? true : false;
988   }
989  
990   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
643 –  for(int i = 0; i < zconsMols.size(); i++)
644 –    if (states[i] == zcsFixed)
645 –      return true;
991  
992 <  return false;
992 >  int havingFixed_local;
993 >  int havingFixed;
994 >
995 >  havingFixed_local = 0;
996 >
997 >  for(int i = 0; i < zconsMols.size(); i++)
998 >    if (states[i] == zcsFixed){
999 >      havingFixed_local = 1;
1000 >    break;
1001 >    }
1002 >
1003 > #ifndef IS_MPI
1004 >  havingFixed = havingFixed_local;
1005 > #else
1006 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1007 > #endif
1008 >
1009 >  return havingFixed > 0 ? true : false;
1010   }
1011  
1012  
# Line 652 | Line 1014 | template<typename T> bool ZConstraint<T>::haveMovingZM
1014   *
1015   */
1016   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1017 +
1018 +  int havingMoving_local;
1019 +  int havingMoving;
1020 +
1021 +  havingMoving_local = 0;
1022 +
1023    for(int i = 0; i < zconsMols.size(); i++)
1024 <    if (states[i] == zcsMoving)
1025 <      return true;
1024 >    if (states[i] == zcsMoving){
1025 >      havingMoving_local = 1;
1026 >    break;
1027 >    }
1028  
1029 <  return false;
1029 > #ifndef IS_MPI
1030 >  havingMoving = havingMoving_local;
1031 > #else
1032 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1033 > #endif
1034 >
1035 >  return havingMoving > 0 ? true : false;
1036    
1037 < }
1037 > }
1038 >
1039 > /**
1040 > *
1041 > */
1042 >
1043 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1044 > {
1045 >  double MVzOfMovingMols_local;
1046 >  double MVzOfMovingMols;
1047 >  double totalMassOfMovingZMols_local;
1048 >  double totalMassOfMovingZMols;
1049 >  double COMvel[3];
1050 >      
1051 >  MVzOfMovingMols_local = 0;
1052 >  totalMassOfMovingZMols_local = 0;
1053 >
1054 >  for(int i =0; i < unconsMols.size(); i++){
1055 >    unconsMols[i]->getCOMvel(COMvel);
1056 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1057 >  }
1058 >
1059 >  for(int i = 0; i < zconsMols.size(); i++){
1060 >
1061 >    if (states[i] == zcsMoving){
1062 >      zconsMols[i]->getCOMvel(COMvel);
1063 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1064 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1065 >    }
1066 >    
1067 >  }
1068 >
1069 > #ifndef IS_MPI
1070 >  MVzOfMovingMols = MVzOfMovingMols_local;
1071 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1072 > #else
1073 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1075 > #endif
1076 >
1077 >  double vzOfMovingMols;
1078 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1079 >
1080 >  return vzOfMovingMols;
1081 > }
1082 >
1083 > /**
1084 > *
1085 > */
1086 >
1087 > template<typename T> double ZConstraint<T>::calcSysCOMVel()
1088 > {
1089 >  double COMvel[3];
1090 >  double tempMVz_local;
1091 >  double tempMVz;
1092 >  double massOfZCons_local;
1093 >  double massOfZCons;
1094 >
1095 >
1096 > tempMVz_local = 0;
1097 >
1098 >  for(int i =0 ; i < nMols; i++){
1099 >    molecules[i].getCOMvel(COMvel);
1100 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1101 >  }
1102 >
1103 >  massOfZCons_local = 0;
1104 >  
1105 >  for(int i = 0; i < massOfZConsMols.size(); i++){
1106 >    massOfZCons_local += massOfZConsMols[i];
1107 >  }
1108 > #ifndef IS_MPI
1109 >  massOfZCons = massOfZCons_local;
1110 >  tempMVz = tempMVz_local;
1111 > #else
1112 >  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1113 >  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114 > #endif
1115 >
1116 >  return tempMVz /(totalMassOfUncons + massOfZCons);
1117 > }
1118 >
1119 > /**
1120 > *
1121 > */
1122 >
1123 > template<typename T> double ZConstraint<T>::calcTotalForce(){
1124 >
1125 >  double force[3];  
1126 >  double totalForce_local;
1127 >  double totalForce;
1128 >
1129 >  totalForce_local = 0;
1130 >
1131 >  for(int i = 0; i < nAtoms; i++){
1132 >    atoms[i]->getFrc(force);
1133 >    totalForce_local += force[whichDirection];
1134 >  }
1135 >
1136 > #ifndef IS_MPI
1137 >  totalForce = totalForce_local;
1138 > #else
1139 >  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1140 > #endif
1141 >
1142 >  return totalForce;
1143 >
1144 > }
1145 >
1146 > /**
1147 > *
1148 > */
1149 >
1150 > template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1151 >  //calculate the number of atoms of moving z-constrained molecules
1152 >  int nMovingZAtoms_local;
1153 >  int nMovingZAtoms;
1154 >  
1155 >  nMovingZAtoms_local = 0;
1156 >  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1157 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1158 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1159 >  
1160 > #ifdef IS_MPI
1161 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1162 > #else
1163 >  nMovingZAtoms = nMovingZAtoms_local;
1164 > #endif
1165 >  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1166 > }
1167 >
1168 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1169 >  return totalForce / mol->getNAtoms();
1170 > }
1171 >
1172 > template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1173 >  return totalForce / totNumOfMovingAtoms;
1174 > }
1175 >
1176 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1177 >    return totalForce / mol->getNAtoms();
1178 > }
1179 >
1180 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1181 >  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1182 > }
1183 >
1184 > /**
1185 > *
1186 > */
1187 >
1188 > template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1189 >  //calculate the number of atoms of moving z-constrained molecules
1190 >  double massOfMovingZAtoms_local;
1191 >  double massOfMovingZAtoms;
1192 >  
1193 >  massOfMovingZAtoms_local = 0;
1194 >  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1195 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1196 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1197 >  
1198 > #ifdef IS_MPI
1199 >  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1200 > #else
1201 >  massOfMovingZAtoms = massOfMovingZAtoms_local;
1202 > #endif
1203 >  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1204 > }
1205 >
1206 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1207 >  return totalForce * atom->getMass() / mol->getTotalMass();
1208 > }
1209 >
1210 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1211 >    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1212 > }
1213 >
1214 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1215 >  return totalForce * atom->getMass() / mol->getTotalMass();
1216 > }
1217 >
1218 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1219 >    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1220 > }
1221 >

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