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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 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1   #include "Integrator.hpp"
2   #include "simError.h"
3 < #include <cmath>
3 > #include <math.h>
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), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL),
6 >                                      fzOut(NULL), curZconsTime(0), forcePolicy(NULL)
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 Subtraction 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 Subtraction policy, "
35 >               "PolicyByMass is used\n");
36 >    painCave.isFatal = 0;
37 >    simError();      
38 >
39 >    forcePolicy = (ForceSubtractionPolicy*) 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 = (ForceSubtractionPolicy*) 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 = (ForceSubtractionPolicy*) new PolicyByNumber(this);
56 >      else if(policy->getData() == "BYMASS")
57 >        forcePolicy = (ForceSubtractionPolicy*) 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 <          
65 <      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 Subtraction policy, "
61 >                  "PolicyByMass is used\n");
62 >        painCave.isFatal = 0;
63 >        simError();      
64 >        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
65 >      }  
66      }
70 –        
67    }
68    
69 +  
70    //retrieve sample time of z-contraint
71 <  data = info->getProperty("zconstime");
71 >  data = info->getProperty(ZCONSTIME_ID);
72    
73    if(!data) {
74        
# Line 99 | Line 96 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
96  
97    }
98    
102 –  
99    //retrieve output filename of z force
100 <  data = info->getProperty("zconsfilename");
100 >  data = info->getProperty(ZCONSFILENAME_ID);
101    if(!data) {
102  
103        
# Line 114 | Line 110 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
110    }
111    else{
112  
113 <     filename = dynamic_cast<StringData*>(data);
113 >    filename = dynamic_cast<StringData*>(data);
114      
115      if(!filename){
116  
# Line 128 | Line 124 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
124        this->zconsOutput = filename->getData();
125      }
126      
127 +  }
128  
129 +  //retrieve tolerance for z-constraint molecuels
130 +  data = info->getProperty(ZCONSTOL_ID);
131 +  
132 +  if(!data) {
133 +      
134 +    sprintf( painCave.errMsg,
135 +               "ZConstraint error: can not get tolerance \n");
136 +    painCave.isFatal = 1;
137 +    simError();      
138    }
139 +  else{
140    
141 +    tolerance = dynamic_cast<DoubleData*>(data);
142 +    
143 +    if(!tolerance){
144 +
145 +      sprintf( painCave.errMsg,
146 +                 "ZConstraint error: Can not get property from SimInfo\n");
147 +      painCave.isFatal = 1;
148 +      simError();  
149 +      
150 +    }
151 +    else{
152 +      this->zconsTol = tolerance->getData();
153 +    }
154 +
155 +  }
156 +  
157 +  //retrieve index of z-constraint molecules
158 +  data = info->getProperty(ZCONSPARADATA_ID);
159 +  if(!data) {
160 +
161 +    sprintf( painCave.errMsg,
162 +               "ZConstraint error: If you use an ZConstraint\n"
163 +               " , you must set index of z-constraint molecules.\n");
164 +    painCave.isFatal = 1;
165 +    simError();  
166 +  }
167 +  else{
168 +  
169 +    zConsParaData = dynamic_cast<ZConsParaData*>(data);
170 +    
171 +    if(!zConsParaData){
172 +
173 +      sprintf( painCave.errMsg,
174 +                 "ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
175 +      painCave.isFatal = 1;
176 +      simError();  
177 +    
178 +    }
179 +    else{
180 +      
181 +      parameters = zConsParaData->getData();
182 +
183 +      //check the range of zconsIndex
184 +      //and the minimum value of index is the first one (we already sorted the data)
185 +      //the maximum value of index is the last one
186 +
187 +      int maxIndex;
188 +      int minIndex;
189 +      int totalNumMol;
190 +
191 +      minIndex = (*parameters)[0].zconsIndex;
192 +      if(minIndex < 0){
193 +        sprintf( painCave.errMsg,
194 +               "ZConstraint error: index is out of range\n");
195 +        painCave.isFatal = 1;
196 +        simError();
197 +        }
198 +
199 +      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
200 +
201 + #ifndef IS_MPI
202 +      totalNumMol = nMols;
203 + #else
204 +      totalNumMol = mpiSim->getTotNmol();  
205 + #endif      
206 +      
207 +      if(maxIndex > totalNumMol - 1){
208 +        sprintf( painCave.errMsg,
209 +               "ZConstraint error: index is out of range\n");
210 +        painCave.isFatal = 1;
211 +        simError();                  
212 +      }
213 +
214 +      //if user does not specify the zpos for the zconstraint molecule
215 +      //its initial z coordinate  will be used as default
216 +      for(int i = 0; i < (int)(parameters->size()); i++){
217 +
218 +        if(!(*parameters)[i].havingZPos){
219 + #ifndef IS_MPI
220 +          for(int j = 0; j < nMols; j++){
221 +            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
222 +              molecules[j].getCOM(COM);
223 +        break;
224 +            }
225 +          }
226 + #else
227 +            //query which processor current zconstraint molecule belongs to
228 +          int *MolToProcMap;
229 +          int whichNode;
230 +          
231 +          MolToProcMap = mpiSim->getMolToProcMap();
232 +          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
233 +        
234 +          //broadcast the zpos of current z-contraint molecule
235 +          //the node which contain this
236 +          
237 +          if (worldRank == whichNode ){
238 +            
239 +            for(int j = 0; j < nMols; j++)
240 +              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
241 +                molecules[j].getCOM(COM);
242 +          break;
243 +              }
244 +        
245 +          }
246 +
247 +          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
248 + #endif
249 +            
250 +          (*parameters)[i].zPos = COM[whichDirection];
251 +
252 +          sprintf( painCave.errMsg,
253 +                     "ZConstraint warning: Does not specify zpos for z-constraint molecule "
254 +                     "initial z coornidate will be used \n");
255 +           painCave.isFatal = 0;
256 +           simError();  
257 +    
258 +  }
259 +      }
260 +      
261 +    }//end if (!zConsParaData)
262 +  }//end  if (!data)
263 +            
264 + //  
265   #ifdef IS_MPI
266    update();
267   #else  
268    int searchResult;
138 –  double COM[3];
269        
270    for(int i = 0; i < nMols; i++){
271      
# Line 145 | Line 275 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
275      
276        zconsMols.push_back(&molecules[i]);      
277        massOfZConsMols.push_back(molecules[i].getTotalMass());  
278 +
279 +      zPos.push_back((*parameters)[searchResult].zPos);
280 + //       cout << "index: "<< (*parameters)[searchResult].zconsIndex
281 + //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
282        
283 +      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        molecules[i].getCOM(COM);
285      }
286      else
# Line 158 | Line 293 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
293    }
294  
295    fz = new double[zconsMols.size()];
296 +  curZPos = new double[zconsMols.size()];
297    indexOfZConsMols = new int [zconsMols.size()];
298  
299 <  if(!fz || !indexOfZConsMols){
299 >  if(!fz || !curZPos || !indexOfZConsMols){
300      sprintf( painCave.errMsg,
301               "Memory allocation failure in class Zconstraint\n");
302      painCave.isFatal = 1;
303      simError();
304    }
305  
306 <  for(int i = 0; i < zconsMols.size(); i++)
306 >  //determine the states of z-constraint molecules
307 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
308      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
309 +
310 +    zconsMols[i]->getCOM(COM);
311 +    if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
312 +      states.push_back(zcsFixed);
313 +    else
314 +      states.push_back(zcsMoving);
315 +  }
316    
317   #endif
318 +
319 +  //get total masss of unconstraint molecules
320 +  double totalMassOfUncons_local;
321 +  totalMassOfUncons_local = 0;
322 +  
323 +  for(int i = 0; i < (int)(unconsMols.size()); i++)
324 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
325 +    
326 + #ifndef IS_MPI
327 +  totalMassOfUncons = totalMassOfUncons_local;
328 + #else
329 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
330 +                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331 + #endif
332  
333    //get total number of unconstrained atoms
334    int nUnconsAtoms_local;
335    nUnconsAtoms_local = 0;
336 <  for(int i = 0; i < unconsMols.size(); i++)
336 >  for(int i = 0; i < (int)(unconsMols.size()); i++)
337      nUnconsAtoms_local += unconsMols[i]->getNAtoms();
338      
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 <
188 <  
189 <  fzOut = new ZConsWriter(zconsOutput.c_str());  
190 <  
191 <  if(!fzOut){
192 <    sprintf( painCave.errMsg,
193 <             "Memory allocation failure in class Zconstraint\n");
194 <    painCave.isFatal = 1;
195 <    simError();
196 <  }
197 <  
346 >  forcePolicy->update();
347   }
348  
349   template<typename T> ZConstraint<T>::~ZConstraint()
350   {
351    if(fz)
352      delete[] fz;
353 +
354 +  if(curZPos)
355 +    delete[] curZPos;
356    
357    if(indexOfZConsMols)
358      delete[] indexOfZConsMols;
359    
360    if(fzOut)
361      delete fzOut;
362 +  
363 +  if(forcePolicy)
364 +    delete forcePolicy;
365   }
366  
367 +
368 + /**
369 + *
370 + */
371 +
372   #ifdef IS_MPI
373   template<typename T> void ZConstraint<T>::update()
374   {
# Line 217 | Line 377 | template<typename T> void ZConstraint<T>::update()
377    
378    zconsMols.clear();
379    massOfZConsMols.clear();
380 +  zPos.clear();
381 +  kz.clear();
382    
383    unconsMols.clear();
384    massOfUnconsMols.clear();
# Line 230 | Line 392 | template<typename T> void ZConstraint<T>::update()
392      if(index > -1){
393      
394        zconsMols.push_back(&molecules[i]);      
395 +      zPos.push_back((*parameters)[index].zPos);
396 +      kz.push_back((*parameters)[index].kRatio * zForceConst);
397        massOfZConsMols.push_back(molecules[i].getTotalMass());  
398        
399        molecules[i].getCOM(COM);
# Line 242 | Line 406 | template<typename T> void ZConstraint<T>::update()
406  
407      }
408    }
409 +
410 +  //determine the states of z-constraint molecules
411 +  for(int i = 0; i < (int)(zconsMols.size()); i++){
412 +     zconsMols[i]->getCOM(COM);
413 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
414 +      states.push_back(zcsFixed);
415 +     else
416 +      states.push_back(zcsMoving);
417 +  }
418 +
419      
420    //The reason to declare fz and indexOfZconsMols as pointer to array is
421    // that we want to make the MPI communication simple
422    if(fz)
423      delete[] fz;
424 +  
425 +  if(curZPos)
426 +    delete[] curZPos;
427      
428    if(indexOfZConsMols)
429      delete[] indexOfZConsMols;
430      
431    if (zconsMols.size() > 0){
432      fz = new double[zconsMols.size()];
433 +   curZPos = new double[zconsMols.size()];
434      indexOfZConsMols =  new int[zconsMols.size()];
435      
436 <    if(!fz || !indexOfZConsMols){
436 >    if(!fz || !curZPos || !indexOfZConsMols){
437        sprintf( painCave.errMsg,
438                 "Memory allocation failure in class Zconstraint\n");
439        painCave.isFatal = 1;
440        simError();
441      }
442          
443 <    for(int i = 0; i < zconsMols.size(); i++){
443 >    for(int i = 0; i < (int)(zconsMols.size()); i++){
444        indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
445      }
446  
447    }
448    else{
449      fz = NULL;
450 +   curZPos = NULL;
451      indexOfZConsMols = NULL;
452    }
453    
454 +  //
455 +  forcePolicy->update();
456 +  
457   }
458  
459   #endif
460  
461 < /**  Function Name: isZConstraintMol
462 < **  Parameter
463 < **    Molecule* mol
464 < **  Return value:
465 < **    -1, if the molecule is not z-constraint molecule,
466 < **    other non-negative values, its index in indexOfAllZConsMols vector
461 > /**
462 > *  Function Name: isZConstraintMol
463 > *  Parameter
464 > *    Molecule* mol
465 > *  Return value:
466 > *    -1, if the molecule is not z-constraint molecule,
467 > *    other non-negative values, its index in indexOfAllZConsMols vector
468   */
469  
470   template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
# Line 294 | Line 477 | template<typename T> int ZConstraint<T>::isZConstraint
477    index = mol->getGlobalIndex();
478    
479    low = 0;
480 <  high = indexOfAllZConsMols.size() - 1;
480 >  high = parameters->size() - 1;
481    
482    //Binary Search (we have sorted the array)  
483    while(low <= high){
484      mid = (low + high) /2;
485 <    if (indexOfAllZConsMols[mid] == index)
485 >    if ((*parameters)[mid].zconsIndex == index)
486        return mid;
487 <    else if (indexOfAllZConsMols[mid] > index )
487 >    else if ((*parameters)[mid].zconsIndex > index )
488         high = mid -1;
489      else    
490        low = mid + 1;
# Line 310 | Line 493 | template<typename T> int ZConstraint<T>::isZConstraint
493    return -1;
494   }
495  
313 – /**
314 – * Description:
315 – *  Reset the z coordinates
316 – */
496   template<typename T> void ZConstraint<T>::integrate(){
497 +
498 +  // creat zconsWriter  
499 +  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);  
500    
501 +  if(!fzOut){
502 +    sprintf( painCave.errMsg,
503 +             "Memory allocation failure in class Zconstraint\n");
504 +    painCave.isFatal = 1;
505 +    simError();
506 +  }
507 +  
508    //zero out the velocities of center of mass of unconstrained molecules
509    //and the velocities of center of mass of every single z-constrained molecueles
510    zeroOutVel();
511 +
512 +  curZconsTime = zconsTime + info->getTime();
513    
514    T::integrate();
515  
# Line 330 | Line 521 | template<typename T> void ZConstraint<T>::integrate(){
521   *
522   *
523   *
524 < */
334 <
335 <
524 > */
525   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
526 +  double zsys;
527 +  double COM[3];
528 +  double force[3];
529 +  double zSysCOMVel;
530  
531    T::calcForce(calcPot, calcStress);
532  
533 <  if (checkZConsState())
534 <    zeroOutVel();
533 >  if (checkZConsState()){    
534 >    zeroOutVel();    
535 >    forcePolicy->update();
536 >  }  
537 >  
538 >  zsys = calcZSys();
539 >  zSysCOMVel = calcSysCOMVel();
540 > #ifdef IS_MPI
541 >  if(worldRank == 0){
542 > #endif
543 >     //cout << "---------------------------------------------------------------------" <<endl;
544 >     //cout << "current time: " << info->getTime() << endl;
545 >     //cout << "center of mass at z: " << zsys << endl;    
546 >     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
547  
548 + #ifdef IS_MPI
549 +  }
550 + #endif
551 +
552    //do zconstraint force;
553    if (haveFixedZMols())
554      this->doZconstraintForce();
555 <  
555 >
556    //use harmonical poteintial to move the molecules to the specified positions
557    if (haveMovingZMols())
558 <    //this->doHarmonic();
559 <  
560 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
561 <      
558 >    this->doHarmonic();
559 >
560 >  //write out forces and current positions of z-constraint molecules
561 >  if(info->getTime() >= curZconsTime){    
562 >   for(int i = 0; i < (int)(zconsMols.size()); i++){
563 >      zconsMols[i]->getCOM(COM);
564 >    curZPos[i] = COM[whichDirection];
565 >
566 >    //if the z-constraint molecule is still moving, just record its force
567 >    if(states[i] == zcsMoving){
568 >         fz[i] = 0;
569 >      Atom** movingZAtoms;
570 >      movingZAtoms = zconsMols[i]->getMyAtoms();
571 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
572 >           movingZAtoms[j]->getFrc(force);
573 >           fz[i] += force[whichDirection];
574 >      }
575 >     }
576 >   }
577 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
578 >   curZconsTime += zconsTime;
579 >  }
580 >
581 >  zSysCOMVel = calcSysCOMVel();  
582 > #ifdef IS_MPI
583 >  if(worldRank == 0){
584 > #endif
585 >     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
586 > #ifdef IS_MPI
587 >  }
588 > #endif
589   }
590 +
591 +
592 + /**
593 + *
594 + */
595  
596   template<typename T> double ZConstraint<T>::calcZSys()
597   {
# Line 359 | Line 600 | template<typename T> double ZConstraint<T>::calcZSys()
600    double totalMass;
601    double totalMZ_local;
602    double totalMZ;
362 –  double massOfUncons_local;
603    double massOfCurMol;
604    double COM[3];
605    
606    totalMass_local = 0;
367 –  totalMass = 0;
607    totalMZ_local = 0;
369 –  totalMZ = 0;
370 –  massOfUncons_local = 0;
371 –    
608    
609    for(int i = 0; i < nMols; i++){
610      massOfCurMol = molecules[i].getTotalMass();
# Line 376 | Line 612 | template<typename T> double ZConstraint<T>::calcZSys()
612      
613      totalMass_local += massOfCurMol;
614      totalMZ_local += massOfCurMol * COM[whichDirection];
615 <    
380 <    if(isZConstraintMol(&molecules[i]) == -1){
381 <    
382 <      massOfUncons_local += massOfCurMol;
383 <    }  
384 <    
615 >
616    }
617 +
618    
387 –  
619   #ifdef IS_MPI  
620 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
621 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
622 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
623 < #else
620 >  MPI_Allreduce(&totalMass_local, &totalMass, 1,
621 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
622 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
623 >                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
624 > #else
625    totalMass = totalMass_local;
626    totalMZ = totalMZ_local;
627 <  totalMassOfUncons = massOfUncons_local;
396 < #endif  
627 > #endif  
628  
629    double zsys;
630    zsys = totalMZ / totalMass;
# Line 412 | Line 643 | template<typename T> void ZConstraint<T>::thermalize(
643  
644   /**
645   *
415 – *
416 – *
646   */
647  
648   template<typename T> void ZConstraint<T>::zeroOutVel(){
# Line 421 | Line 650 | template<typename T> void ZConstraint<T>::zeroOutVel()
650    Atom** fixedZAtoms;  
651    double COMvel[3];
652    double vel[3];
653 <  
653 >  double zSysCOMVel;
654 >
655    //zero out the velocities of center of mass of fixed z-constrained molecules
656    
657 <  for(int i = 0; i < zconsMols.size(); i++){
657 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
658  
659 <    if (states[i] == zcsFixed){
659 >    if (states[i] == zcsFixed){
660  
661 <        zconsMols[i]->getCOMvel(COMvel);      
661 >     zconsMols[i]->getCOMvel(COMvel);      
662 >     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663 >
664        fixedZAtoms = zconsMols[i]->getMyAtoms();
665 <          
665 >    
666        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
667          fixedZAtoms[j]->getVel(vel);
668 <          vel[whichDirection] -= COMvel[whichDirection];
669 <          fixedZAtoms[j]->setVel(vel);
668 >       vel[whichDirection] -= COMvel[whichDirection];
669 >       fixedZAtoms[j]->setVel(vel);
670        }
671 <          
671 >
672 >    zconsMols[i]->getCOMvel(COMvel);
673 >    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
674      }
441 –        
442 –  }
675    
676 +  }
677 +
678 +    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
679 +
680 +  zSysCOMVel = calcSysCOMVel();
681 + #ifdef IS_MPI
682 +  if(worldRank == 0){
683 + #endif
684 +     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
685 + #ifdef IS_MPI
686 +  }
687 + #endif
688 +      
689    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
690    double MVzOfMovingMols_local;
691    double MVzOfMovingMols;
# Line 450 | Line 695 | template<typename T> void ZConstraint<T>::zeroOutVel()
695    MVzOfMovingMols_local = 0;
696    totalMassOfMovingZMols_local = 0;
697  
698 <  for(int i =0; i < unconsMols.size(); i++){
698 >  for(int i =0; i < (int)(unconsMols.size()); i++){
699      unconsMols[i]->getCOMvel(COMvel);
700      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
701    }
702  
703 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
459 <
703 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
704      if (states[i] == zcsMoving){
705        zconsMols[i]->getCOMvel(COMvel);
706        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
707 <      totalMassOfMovingZMols_local += massOfZConsMols[i];              
707 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
708      }
709 <                
709 >    
710    }
711  
712   #ifndef IS_MPI
# Line 478 | Line 722 | template<typename T> void ZConstraint<T>::zeroOutVel()
722  
723    //modify the velocites of unconstrained molecules  
724    Atom** unconsAtoms;
725 <  for(int i = 0; i < unconsMols.size(); i++){
725 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
726    
727      unconsAtoms = unconsMols[i]->getMyAtoms();
728      for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
# Line 491 | Line 735 | template<typename T> void ZConstraint<T>::zeroOutVel()
735  
736    //modify the velocities of moving z-constrained molecuels
737    Atom** movingZAtoms;
738 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
738 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
739  
740      if (states[i] ==zcsMoving){
741    
742        movingZAtoms = zconsMols[i]->getMyAtoms();
743 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
743 >     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
744          movingZAtoms[j]->getVel(vel);
745          vel[whichDirection] -= vzOfMovingMols;
746 <          movingZAtoms[j]->setVel(vel);
503 <        }
504 <          
746 >       movingZAtoms[j]->setVel(vel);
747      }
748 +    
749 +   }
750  
751 + }
752 +
753 +
754 +  zSysCOMVel = calcSysCOMVel();
755 + #ifdef IS_MPI
756 +  if(worldRank == 0){
757 + #endif
758 +     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
759 + #ifdef IS_MPI
760    }
761 + #endif
762  
763   }
764  
765 + /**
766 + *
767 + */
768 +
769   template<typename T> void ZConstraint<T>::doZconstraintForce(){
770  
771    Atom** zconsAtoms;
772    double totalFZ;
773    double totalFZ_local;
516 –  double COMvel[3];  
774    double COM[3];
775    double force[3];
519 –  double zsys;
776  
777 <  int nMovingZMols_local;
522 <  int nMovingZMols;
523 <
524 <  //constrain the molecules which do not reach the specified positions  
525 <
526 <   zsys = calcZSys();
527 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
777 >  //constrain the molecules which do not reach the specified positions  
778      
779    //Zero Out the force of z-contrained molecules    
780    totalFZ_local = 0;
781  
782    //calculate the total z-contrained force of fixed z-contrained molecules
783 <  for(int i = 0; i < zconsMols.size(); i++){
784 <                
783 >  
784 >  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
785 >  //       << "total force is " << calcTotalForce() << endl;
786 >
787 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
788 >    
789      if (states[i] == zcsFixed){
790 <                
790 >      
791        zconsMols[i]->getCOM(COM);
792        zconsAtoms = zconsMols[i]->getMyAtoms();  
793  
# Line 541 | Line 795 | template<typename T> void ZConstraint<T>::doZconstrain
795        for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
796          zconsAtoms[j]->getFrc(force);
797          fz[i] += force[whichDirection];      
798 <      }
798 >      }
799        totalFZ_local += fz[i];
800  
801 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
801 >      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
802 >      //      <<"\tcurrent zpos: " << COM[whichDirection]
803 >      //      << "\tcurrent fz: " <<fz[i] << endl;
804  
805 +
806      }
807 <          
807 >    
808    }
809  
810 <  //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 <  }
810 >  //calculate total z-constraint force
811   #ifdef IS_MPI
812    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);
813   #else
814    totalFZ = totalFZ_local;
564 –  nMovingZMols = nMovingZMols_local;
815   #endif
816  
817 +  
818 +  // apply negative to fixed z-constrained molecues;
819    force[0]= 0;
820    force[1]= 0;
821    force[2]= 0;
570 –  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
822  
823 <  //modify the velocites of unconstrained molecules
824 <  for(int i = 0; i < unconsMols.size(); i++){
823 >  for(int i = 0; i < (int)(zconsMols.size()); i++){
824 >
825 >    if (states[i] == zcsFixed){  
826 >  
827 >      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
828 >      zconsAtoms = zconsMols[i]->getMyAtoms();  
829 >    
830 >      for(int j =0; j < nAtomOfCurZConsMol; j++) {
831 >        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
832 >        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
833 >        zconsAtoms[j]->addFrc(force);
834 >      }
835 >    
836 >    }
837 >  
838 >  }
839 >
840 >  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
841 >  //      << "total force is " << calcTotalForce() << endl;
842 >  
843 >
844 >  force[0]= 0;
845 >  force[1]= 0;
846 >  force[2]= 0;
847 >
848 >  //modify the forces of unconstrained molecules
849 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
850      
851       Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
852      
853 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
853 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
854 >       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
855 >       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
856         unconsAtoms[j]->addFrc(force);
857 +     }
858      
859    }      
860  
861 < //modify the velocities of moving z-constrained molecules
862 <  for(int i = 0; i < zconsMols.size(); i++) {
863 <   if (states[i] == zcsMoving){
864 <                
865 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
861 > //modify the forces of moving z-constrained molecules
862 >  for(int i = 0; i < (int)(zconsMols.size()); i++) {
863 >    if (states[i] == zcsMoving){
864 >    
865 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
866  
867 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
868 <       movingZAtoms[j]->addFrc(force);
869 <     }
867 >      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
868 >        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
869 >        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
870 >        movingZAtoms[j]->addFrc(force);
871 >      }
872 >    }
873    }
874 + //  cout << "after substracting z-constraint force from moving molecuels "
875 + //        << "total force is " << calcTotalForce()  << endl;
876  
877 <  // apply negative to fixed z-constrained molecues;
877 > }
878 >
879 > /**
880 >  *
881 >  *
882 >  */
883 >
884 > template<typename T> void ZConstraint<T>::doHarmonic(){
885 >  double force[3];
886 >  double harmonicU;
887 >  double harmonicF;
888 >  double COM[3];
889 >  double diff;
890 >  double totalFZ_local;
891 >  double totalFZ;
892 >  
893 >  force[0] = 0;
894 >  force[1] = 0;
895 >  force[2] = 0;
896 >
897 >  totalFZ_local = 0;
898 >
899 >  for(int i = 0; i < (int)(zconsMols.size()); i++) {
900 >
901 >    if (states[i] == zcsMoving){
902 >      zconsMols[i]->getCOM(COM);
903 > //       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
904 > //         << "\tcurrent zpos: " << COM[whichDirection] << endl;
905 >
906 >      diff = COM[whichDirection] -zPos[i];
907 >    
908 >      harmonicU = 0.5 * kz[i] * diff * diff;  
909 >      info->lrPot += harmonicU;
910 >
911 >      harmonicF =  - kz[i] * diff;
912 >      totalFZ_local += harmonicF;
913 >
914 >       //adjust force
915 >    
916 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
917 >
918 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
919 >        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
920 >        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
921 >         movingZAtoms[j]->addFrc(force);
922 >       }
923 >    }
924 >
925 >  }
926 >
927 > #ifndef IS_MPI
928 >  totalFZ = totalFZ_local;
929 > #else
930 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
931 > #endif
932 >
933 >  //cout << "before substracting harmonic force from moving molecuels "
934 >  //      << "total force is " << calcTotalForce()  << endl;
935 >
936    force[0]= 0;
937    force[1]= 0;
938    force[2]= 0;
939  
940 <  for(int i = 0; i < zconsMols.size(); i++){
940 >  //modify the forces of unconstrained molecules
941 >  for(int i = 0; i < (int)(unconsMols.size()); i++){
942 >    
943 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
944 >    
945 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
946 >       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
947 >       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
948 >       unconsAtoms[j]->addFrc(force);    
949 >     }
950 >  }  
951  
952 <    if (states[i] == zcsFixed){  
953 <        
602 <      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
603 <      zconsAtoms = zconsMols[i]->getMyAtoms();  
604 <    
605 <      for(int j =0; j < nAtomOfCurZConsMol; j++) {
606 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
607 <        zconsAtoms[j]->addFrc(force);
608 <      }
609 <                
610 <    }
611 <        
612 <  }
952 >  //cout << "after substracting harmonic force from moving molecuels "
953 >  //      << "total force is " << calcTotalForce()  << endl;
954  
955   }
956  
957 + /**
958 + *
959 + */
960 +
961   template<typename T> bool ZConstraint<T>::checkZConsState(){
962    double COM[3];
963    double diff;
964    
965 <  bool changed;
965 >  int changed_local;
966 >  int changed;
967    
968 <  changed = false;
968 >  changed_local = 0;
969    
970 <  for(int i =0; i < zconsMols.size(); i++){
970 >  for(int i =0; i < (int)(zconsMols.size()); i++){
971  
972      zconsMols[i]->getCOM(COM);
973 <    diff = fabs(COM[whichDirection] - ZPos[i]);  
974 <    if (  diff <= ztol && states[i] == zcsMoving){
973 >    diff = fabs(COM[whichDirection] - zPos[i]);  
974 >    if (  diff <= zconsTol && states[i] == zcsMoving){
975        states[i] = zcsFixed;
976 <        changed = true;
976 >     changed_local = 1;
977      }
978 <    else if ( diff > ztol && states[i] == zcsFixed){
978 >    else if ( diff > zconsTol && states[i] == zcsFixed){
979        states[i] = zcsMoving;
980 <        changed = true;  
980 >     changed_local = 1;  
981      }
982    
983    }
984  
985 <  return changed;
985 > #ifndef IS_MPI
986 >  changed =changed_local;
987 > #else
988 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
989 > #endif
990 >
991 >  return (changed > 0);
992 >
993   }
994  
995   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
643 –  for(int i = 0; i < zconsMols.size(); i++)
644 –    if (states[i] == zcsFixed)
645 –      return true;
996  
997 <  return false;
997 >  int havingFixed_local;
998 >  int havingFixed;
999 >
1000 >  havingFixed_local = 0;
1001 >
1002 >  for(int i = 0; i < (int)(zconsMols.size()); i++)
1003 >    if (states[i] == zcsFixed){
1004 >      havingFixed_local = 1;
1005 >    break;
1006 >    }
1007 >
1008 > #ifndef IS_MPI
1009 >  havingFixed = havingFixed_local;
1010 > #else
1011 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1012 > #endif
1013 >
1014 >  return (havingFixed > 0);
1015   }
1016  
1017  
# Line 652 | Line 1019 | template<typename T> bool ZConstraint<T>::haveMovingZM
1019   *
1020   */
1021   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
655 –  for(int i = 0; i < zconsMols.size(); i++)
656 –    if (states[i] == zcsMoving)
657 –      return true;
1022  
1023 <  return false;
1023 >  int havingMoving_local;
1024 >  int havingMoving;
1025 >
1026 >  havingMoving_local = 0;
1027 >
1028 >  for(int i = 0; i < (int)(zconsMols.size()); i++)
1029 >    if (states[i] == zcsMoving){
1030 >      havingMoving_local = 1;
1031 >    break;
1032 >    }
1033 >
1034 > #ifndef IS_MPI
1035 >  havingMoving = havingMoving_local;
1036 > #else
1037 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
1038 > #endif
1039 >
1040 >  return (havingMoving > 0);
1041    
1042 < }
1042 > }
1043 >
1044 > /**
1045 > *
1046 > */
1047 >
1048 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1049 > {
1050 >  double MVzOfMovingMols_local;
1051 >  double MVzOfMovingMols;
1052 >  double totalMassOfMovingZMols_local;
1053 >  double totalMassOfMovingZMols;
1054 >  double COMvel[3];
1055 >      
1056 >  MVzOfMovingMols_local = 0;
1057 >  totalMassOfMovingZMols_local = 0;
1058 >
1059 >  for(int i =0; i < unconsMols.size(); i++){
1060 >    unconsMols[i]->getCOMvel(COMvel);
1061 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1062 >  }
1063 >
1064 >  for(int i = 0; i < zconsMols.size(); i++){
1065 >
1066 >    if (states[i] == zcsMoving){
1067 >      zconsMols[i]->getCOMvel(COMvel);
1068 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1069 >      totalMassOfMovingZMols_local += massOfZConsMols[i];      
1070 >    }
1071 >    
1072 >  }
1073 >
1074 > #ifndef IS_MPI
1075 >  MVzOfMovingMols = MVzOfMovingMols_local;
1076 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1077 > #else
1078 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1080 > #endif
1081 >
1082 >  double vzOfMovingMols;
1083 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1084 >
1085 >  return vzOfMovingMols;
1086 > }
1087 >
1088 > /**
1089 > *
1090 > */
1091 >
1092 > template<typename T> double ZConstraint<T>::calcSysCOMVel()
1093 > {
1094 >  double COMvel[3];
1095 >  double tempMVz_local;
1096 >  double tempMVz;
1097 >  double massOfZCons_local;
1098 >  double massOfZCons;
1099 >
1100 >
1101 > tempMVz_local = 0;
1102 >
1103 >  for(int i =0 ; i < nMols; i++){
1104 >    molecules[i].getCOMvel(COMvel);
1105 >   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1106 >  }
1107 >
1108 >  massOfZCons_local = 0;
1109 >  
1110 >  for(int i = 0; i < (int)(massOfZConsMols.size()); i++){
1111 >    massOfZCons_local += massOfZConsMols[i];
1112 >  }
1113 > #ifndef IS_MPI
1114 >  massOfZCons = massOfZCons_local;
1115 >  tempMVz = tempMVz_local;
1116 > #else
1117 >  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1118 >  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1119 > #endif
1120 >
1121 >  return tempMVz /(totalMassOfUncons + massOfZCons);
1122 > }
1123 >
1124 > /**
1125 > *
1126 > */
1127 >
1128 > template<typename T> double ZConstraint<T>::calcTotalForce(){
1129 >
1130 >  double force[3];  
1131 >  double totalForce_local;
1132 >  double totalForce;
1133 >
1134 >  totalForce_local = 0;
1135 >
1136 >  for(int i = 0; i < nAtoms; i++){
1137 >    atoms[i]->getFrc(force);
1138 >    totalForce_local += force[whichDirection];
1139 >  }
1140 >
1141 > #ifndef IS_MPI
1142 >  totalForce = totalForce_local;
1143 > #else
1144 >  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1145 > #endif
1146 >
1147 >  return totalForce;
1148 >
1149 > }
1150 >
1151 > /**
1152 > *
1153 > */
1154 >
1155 > template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1156 >  //calculate the number of atoms of moving z-constrained molecules
1157 >  int nMovingZAtoms_local;
1158 >  int nMovingZAtoms;
1159 >  
1160 >  nMovingZAtoms_local = 0;
1161 >  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1162 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1163 >     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1164 >  
1165 > #ifdef IS_MPI
1166 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1167 > #else
1168 >  nMovingZAtoms = nMovingZAtoms_local;
1169 > #endif
1170 >  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1171 > }
1172 >
1173 > template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1174 >  return totalForce / mol->getNAtoms();
1175 > }
1176 >
1177 > template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1178 >  return totalForce / totNumOfMovingAtoms;
1179 > }
1180 >
1181 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1182 >    return totalForce / mol->getNAtoms();
1183 > }
1184 >
1185 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1186 >  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1187 > }
1188 >
1189 > /**
1190 > *
1191 > */
1192 >
1193 > template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1194 >  //calculate the number of atoms of moving z-constrained molecules
1195 >  double massOfMovingZAtoms_local;
1196 >  double massOfMovingZAtoms;
1197 >  
1198 >  massOfMovingZAtoms_local = 0;
1199 >  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
1200 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1201 >     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1202 >  
1203 > #ifdef IS_MPI
1204 >  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1205 > #else
1206 >  massOfMovingZAtoms = massOfMovingZAtoms_local;
1207 > #endif
1208 >  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
1209 > }
1210 >
1211 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1212 >  return totalForce * atom->getMass() / mol->getTotalMass();
1213 > }
1214 >
1215 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1216 >    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1217 > }
1218 >
1219 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1220 >  return totalForce * atom->getMass() / mol->getTotalMass();
1221 > }
1222 >
1223 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1224 >    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1225 > }
1226 >

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