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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 699 by tim, Fri Aug 15 19:24:13 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);
43 <    
44 <    if(!index){
29 <
42 >    policy = dynamic_cast<StringData*>(data);
43 >                
44 >         if(!policy){
45        sprintf( painCave.errMsg,
46 <                 "ZConstraint error: Can not get property from SimInfo\n");
47 <      painCave.isFatal = 1;
48 <      simError();  
49 <    
35 <    }
36 <    else{
37 <          
38 <      indexOfAllZConsMols = index->getIndexData();
39 <      
40 <      //the maximum value of index is the last one(we sorted the index data in SimSetup.cpp)
41 <      int maxIndex;
42 <        int minIndex;
43 <      int totalNumMol;
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 <      minIndex = indexOfAllZConsMols[0];
52 <      if(minIndex < 0){
51 >      forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this);
52 >         }
53 >         else{
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 <          
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 <      
69 <    }
70 <        
60 >                  "ZConstraint Warning: unknown force substraction policy, "
61 >                  "average force substraction policy is used\n");
62 >        painCave.isFatal = 0;
63 >        simError();      
64 >           }            
65 >         }
66    }
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 130 | Line 126 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
126      
127  
128    }
129 +
130 +  //retrieve tolerance for z-constraint molecuels
131 +  data = info->getProperty(ZCONSTOL_ID);
132    
133 +  if(!data) {
134 +      
135 +    sprintf( painCave.errMsg,
136 +               "ZConstraint error: can not get tolerance \n");
137 +    painCave.isFatal = 1;
138 +    simError();      
139 +  }
140 +  else{
141 +  
142 +    tolerance = dynamic_cast<DoubleData*>(data);
143 +    
144 +    if(!tolerance){
145 +
146 +      sprintf( painCave.errMsg,
147 +                 "ZConstraint error: Can not get property from SimInfo\n");
148 +      painCave.isFatal = 1;
149 +      simError();  
150 +      
151 +    }
152 +    else{
153 +      this->zconsTol = tolerance->getData();
154 +    }
155 +
156 +  }
157 +        
158 +  //retrieve index of z-constraint molecules
159 +  data = info->getProperty(ZCONSPARADATA_ID);
160 +  if(!data) {
161 +
162 +    sprintf( painCave.errMsg,
163 +               "ZConstraint error: If you use an ZConstraint\n"
164 +               " , you must set index of z-constraint molecules.\n");
165 +    painCave.isFatal = 1;
166 +    simError();  
167 +  }
168 +  else{
169 +  
170 +    zConsParaData = dynamic_cast<ZConsParaData*>(data);
171 +    
172 +    if(!zConsParaData){
173 +
174 +      sprintf( painCave.errMsg,
175 +                 "ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
176 +      painCave.isFatal = 1;
177 +      simError();  
178 +    
179 +    }
180 +    else{
181 +      
182 +      parameters = zConsParaData->getData();
183 +
184 +      //check the range of zconsIndex
185 +      //and the minimum value of index is the first one (we already sorted the data)
186 +      //the maximum value of index is the last one
187 +
188 +      int maxIndex;
189 +      int minIndex;
190 +      int totalNumMol;
191 +
192 +      minIndex = (*parameters)[0].zconsIndex;
193 +      if(minIndex < 0){
194 +        sprintf( painCave.errMsg,
195 +               "ZConstraint error: index is out of range\n");
196 +        painCave.isFatal = 1;
197 +        simError();
198 +        }
199 +
200 +      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
201 +
202 + #ifndef IS_MPI
203 +      totalNumMol = nMols;
204 + #else
205 +      totalNumMol = mpiSim->getTotNmol();  
206 + #endif      
207 +      
208 +      if(maxIndex > totalNumMol - 1){
209 +        sprintf( painCave.errMsg,
210 +               "ZConstraint error: index is out of range\n");
211 +        painCave.isFatal = 1;
212 +        simError();                  
213 +      }
214 +
215 +      //if user does not specify the zpos for the zconstraint molecule
216 +      //its initial z coordinate  will be used as default
217 +      for(int i = 0; i < parameters->size(); i++){
218 +
219 +              if(!(*parameters)[i].havingZPos){
220 +
221 + #ifndef IS_MPI
222 +            for(int j = 0; j < nMols; j++){
223 +              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
224 +                 molecules[j].getCOM(COM);
225 +                          break;
226 +              }
227 +            }
228 + #else
229 +            //query which processor current zconstraint molecule belongs to
230 +           int *MolToProcMap;
231 +           int whichNode;
232 +                         double initZPos;
233 +           MolToProcMap = mpiSim->getMolToProcMap();
234 +           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
235 +                          
236 +           //broadcast the zpos of current z-contraint molecule
237 +           //the node which contain this
238 +          
239 +           if (worldRank == whichNode ){
240 +                                                
241 +             for(int j = 0; j < nMols; j++)
242 +               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
243 +                 molecules[j].getCOM(COM);
244 +                                         break;
245 +               }
246 +                                
247 +           }
248 +
249 +            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);                          
250 + #endif
251 +            
252 +                 (*parameters)[i].zPos = COM[whichDirection];
253 +
254 +            sprintf( painCave.errMsg,
255 +                     "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
256 +                     "initial z coornidate will be used \n");
257 +            painCave.isFatal = 0;
258 +            simError();  
259 +          
260 +              }
261 +            }
262 +                        
263 +    }//end if (!zConsParaData)
264 +  }//end  if (!data)
265 +            
266 + //  
267   #ifdef IS_MPI
268    update();
269   #else  
270    int searchResult;
138 –  double COM[3];
271        
272    for(int i = 0; i < nMols; i++){
273      
# Line 145 | Line 277 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
277      
278        zconsMols.push_back(&molecules[i]);      
279        massOfZConsMols.push_back(molecules[i].getTotalMass());  
280 +
281 +      zPos.push_back((*parameters)[searchResult].zPos);
282 +                cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl;
283 +           kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
284        
285        molecules[i].getCOM(COM);
286      }
# Line 158 | Line 294 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
294    }
295  
296    fz = new double[zconsMols.size()];
297 +  curZPos = new double[zconsMols.size()];
298    indexOfZConsMols = new int [zconsMols.size()];
299  
300 <  if(!fz || !indexOfZConsMols){
300 >  if(!fz || !curZPos || !indexOfZConsMols){
301      sprintf( painCave.errMsg,
302               "Memory allocation failure in class Zconstraint\n");
303      painCave.isFatal = 1;
304      simError();
305    }
306  
307 <  for(int i = 0; i < zconsMols.size(); i++)
307 >  //determine the states of z-constraint molecules
308 >  for(int i = 0; i < zconsMols.size(); i++){
309      indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
310 +
311 +         zconsMols[i]->getCOM(COM);
312 +    if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
313 +                states.push_back(zcsFixed);
314 +         else
315 +                states.push_back(zcsMoving);
316 +  }
317    
318   #endif
319  
320 +  //get total masss of unconstraint molecules
321 +  double totalMassOfUncons_local;
322 +  totalMassOfUncons_local = 0;
323 +  
324 +  for(int i = 0; i < unconsMols.size(); i++)
325 +    totalMassOfUncons_local += unconsMols[i]->getTotalMass();
326 +    
327 + #ifndef IS_MPI
328 +  totalMassOfUncons = totalMassOfUncons_local;
329 + #else
330 +  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
331 + #endif
332 +
333 +
334    //get total number of unconstrained atoms
335    int nUnconsAtoms_local;
336    nUnconsAtoms_local = 0;
# Line 181 | Line 340 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
340   #ifndef IS_MPI
341    totNumOfUnconsAtoms = nUnconsAtoms_local;
342   #else
343 <  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
344 < #endif
343 >  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, 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   #ifdef IS_MPI
# Line 217 | Line 382 | template<typename T> void ZConstraint<T>::update()
382    
383    zconsMols.clear();
384    massOfZConsMols.clear();
385 +  zPos.clear();
386 +  kz.clear();
387    
388    unconsMols.clear();
389    massOfUnconsMols.clear();
# Line 230 | Line 397 | template<typename T> void ZConstraint<T>::update()
397      if(index > -1){
398      
399        zconsMols.push_back(&molecules[i]);      
400 +      zPos.push_back((*parameters)[index].zPos);
401 +        kz.push_back((*parameters)[index].kRatio * zForceConst);
402 +                        
403        massOfZConsMols.push_back(molecules[i].getTotalMass());  
404        
405        molecules[i].getCOM(COM);
# Line 242 | Line 412 | template<typename T> void ZConstraint<T>::update()
412  
413      }
414    }
415 +
416 +  //determine the states of z-constraint molecules
417 +  for(int i = 0; i < zconsMols.size(); i++){
418 +           zconsMols[i]->getCOM(COM);
419 +      if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
420 +                  states.push_back(zcsFixed);
421 +           else
422 +                  states.push_back(zcsMoving);
423 +  }
424 +
425      
426    //The reason to declare fz and indexOfZconsMols as pointer to array is
427    // that we want to make the MPI communication simple
428    if(fz)
429      delete[] fz;
430 +        
431 +  if(curZPos)
432 +    delete[] curZPos;
433      
434    if(indexOfZConsMols)
435      delete[] indexOfZConsMols;
436      
437    if (zconsMols.size() > 0){
438      fz = new double[zconsMols.size()];
439 +         curZPos = new double[zconsMols.size()];
440      indexOfZConsMols =  new int[zconsMols.size()];
441      
442 <    if(!fz || !indexOfZConsMols){
442 >    if(!fz || !curZPos || !indexOfZConsMols){
443        sprintf( painCave.errMsg,
444                 "Memory allocation failure in class Zconstraint\n");
445        painCave.isFatal = 1;
# Line 269 | Line 453 | template<typename T> void ZConstraint<T>::update()
453    }
454    else{
455      fz = NULL;
456 +         curZPos = NULL;
457      indexOfZConsMols = NULL;
458    }
459 +        
460 +  //
461 +  forcePolicy->update();
462    
463   }
464  
# Line 294 | Line 482 | template<typename T> int ZConstraint<T>::isZConstraint
482    index = mol->getGlobalIndex();
483    
484    low = 0;
485 <  high = indexOfAllZConsMols.size() - 1;
485 >  high = parameters->size() - 1;
486    
487    //Binary Search (we have sorted the array)  
488    while(low <= high){
489      mid = (low + high) /2;
490 <    if (indexOfAllZConsMols[mid] == index)
490 >    if ((*parameters)[mid].zconsIndex == index)
491        return mid;
492 <    else if (indexOfAllZConsMols[mid] > index )
492 >    else if ((*parameters)[mid].zconsIndex > index )
493         high = mid -1;
494      else    
495        low = mid + 1;
# Line 310 | Line 498 | template<typename T> int ZConstraint<T>::isZConstraint
498    return -1;
499   }
500  
313 – /**
314 – * Description:
315 – *  Reset the z coordinates
316 – */
501   template<typename T> void ZConstraint<T>::integrate(){
502    
503    //zero out the velocities of center of mass of unconstrained molecules
# Line 330 | Line 514 | template<typename T> void ZConstraint<T>::integrate(){
514   *
515   *
516   *
517 < */
334 <
335 <
517 > */
518   template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
519 +  double zsys;
520 +  double COM[3];
521 +  double force[3];
522  
523    T::calcForce(calcPot, calcStress);
524  
525 <  if (checkZConsState())
525 >  if (checkZConsState()){
526      zeroOutVel();
527 +         forcePolicy->update();
528 +  }  
529 +  zsys = calcZSys();
530 +  cout << "---------------------------------------------------------------------" <<endl;
531 +  cout << "current time: " << info->getTime() << endl;
532 +  cout << "center of mass at z: " << zsys << endl;      
533 +  //cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
534 +  cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
535  
536 +  //cout <<      "before doZConstraintForce, totalForce is " << calcTotalForce() << endl;
537 +
538    //do zconstraint force;
539    if (haveFixedZMols())
540      this->doZconstraintForce();
541 <  
541 >    
542    //use harmonical poteintial to move the molecules to the specified positions
543    if (haveMovingZMols())
544 <    //this->doHarmonic();
545 <  
546 <  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
547 <      
544 >    this->doHarmonic();
545 >
546 >  //cout <<      "after doHarmonic, totalForce is " << calcTotalForce() << endl;
547 >
548 >  //write out forces and current positions of z-constraint molecules
549 >  if(info->getTime() >= curZconsTime){          
550 >         for(int i = 0; i < zconsMols.size(); i++){
551 >      zconsMols[i]->getCOM(COM);
552 >                curZPos[i] = COM[whichDirection];
553 >
554 >                //if the z-constraint molecule is still moving, just record its force
555 >                if(states[i] == zcsMoving){
556 >         fz[i] = 0;
557 >                  Atom** movingZAtoms;
558 >                  movingZAtoms = zconsMols[i]->getMyAtoms();
559 >                  for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
560 >           movingZAtoms[j]->getFrc(force);
561 >           fz[i] += force[whichDirection];
562 >                  }
563 >           }
564 >         }
565 >    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
566 >         curZconsTime += zconsTime;
567 >  }
568 >        
569 >  //cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
570 >  cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl;
571   }
572  
573   template<typename T> double ZConstraint<T>::calcZSys()
# Line 359 | Line 577 | template<typename T> double ZConstraint<T>::calcZSys()
577    double totalMass;
578    double totalMZ_local;
579    double totalMZ;
362 –  double massOfUncons_local;
580    double massOfCurMol;
581    double COM[3];
582 <  
582 >        
583    totalMass_local = 0;
367 –  totalMass = 0;
584    totalMZ_local = 0;
369 –  totalMZ = 0;
370 –  massOfUncons_local = 0;
371 –    
585    
586    for(int i = 0; i < nMols; i++){
587      massOfCurMol = molecules[i].getTotalMass();
# Line 376 | Line 589 | template<typename T> double ZConstraint<T>::calcZSys()
589      
590      totalMass_local += massOfCurMol;
591      totalMZ_local += massOfCurMol * COM[whichDirection];
592 <    
380 <    if(isZConstraintMol(&molecules[i]) == -1){
381 <    
382 <      massOfUncons_local += massOfCurMol;
383 <    }  
384 <    
592 >
593    }
594 +
595    
387 –  
596   #ifdef IS_MPI  
597 <  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
598 <  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
599 <  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
392 < #else
597 >  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
598 >  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
599 > #else
600    totalMass = totalMass_local;
601    totalMZ = totalMZ_local;
602 <  totalMassOfUncons = massOfUncons_local;
396 < #endif  
602 > #endif  
603  
604    double zsys;
605    zsys = totalMZ / totalMass;
# Line 421 | Line 627 | template<typename T> void ZConstraint<T>::zeroOutVel()
627    Atom** fixedZAtoms;  
628    double COMvel[3];
629    double vel[3];
630 <  
630 >
631    //zero out the velocities of center of mass of fixed z-constrained molecules
632    
633    for(int i = 0; i < zconsMols.size(); i++){
634  
635      if (states[i] == zcsFixed){
636  
637 <        zconsMols[i]->getCOMvel(COMvel);      
637 >           zconsMols[i]->getCOMvel(COMvel);      
638 >                //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
639 >
640        fixedZAtoms = zconsMols[i]->getMyAtoms();
641            
642        for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
643          fixedZAtoms[j]->getVel(vel);
644 <          vel[whichDirection] -= COMvel[whichDirection];
645 <          fixedZAtoms[j]->setVel(vel);
644 >             vel[whichDirection] -= COMvel[whichDirection];
645 >             fixedZAtoms[j]->setVel(vel);
646        }
647 <          
647 >
648 >                zconsMols[i]->getCOMvel(COMvel);
649 >                //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
650      }
651          
652    }
653 <  
653 >
654 >        //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;      
655 >
656 > #ifdef IS_MPI
657 >  if (worldRank == 0){
658 > #endif
659 >    cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl;      
660 > #ifdef IS_MPI
661 >  }
662 > #endif
663 >                  
664    // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
665    double MVzOfMovingMols_local;
666    double MVzOfMovingMols;
# Line 455 | Line 675 | template<typename T> void ZConstraint<T>::zeroOutVel()
675      MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
676    }
677  
678 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
459 <
678 >  for(int i = 0; i < zconsMols.size(); i++){
679      if (states[i] == zcsMoving){
680        zconsMols[i]->getCOMvel(COMvel);
681        MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
# Line 491 | Line 710 | template<typename T> void ZConstraint<T>::zeroOutVel()
710  
711    //modify the velocities of moving z-constrained molecuels
712    Atom** movingZAtoms;
713 <  for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){
713 >  for(int i = 0; i < zconsMols.size(); i++){
714  
715      if (states[i] ==zcsMoving){
716    
717        movingZAtoms = zconsMols[i]->getMyAtoms();
718 <        for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
718 >           for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
719          movingZAtoms[j]->getVel(vel);
720          vel[whichDirection] -= vzOfMovingMols;
721 <          movingZAtoms[j]->setVel(vel);
722 <        }
721 >             movingZAtoms[j]->setVel(vel);
722 >          }
723            
724 <    }
724 >   }
725 >
726 > }
727  
728 + #ifdef IS_MPI
729 +  if (worldRank == 0){
730 + #endif
731 +        cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl;
732 + #ifdef IS_MPI
733    }
734 + #endif
735  
736   }
737  
# Line 516 | Line 743 | template<typename T> void ZConstraint<T>::doZconstrain
743    double COMvel[3];  
744    double COM[3];
745    double force[3];
519 –  double zsys;
746  
521 –  int nMovingZMols_local;
522 –  int nMovingZMols;
747  
524 –  //constrain the molecules which do not reach the specified positions  
748  
749 <   zsys = calcZSys();
527 <   cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;  
749 >  //constrain the molecules which do not reach the specified positions  
750      
751    //Zero Out the force of z-contrained molecules    
752    totalFZ_local = 0;
753  
754    //calculate the total z-contrained force of fixed z-contrained molecules
755 +
756 + #ifdef IS_MPI
757 +  if (worldRank == 0){
758 + #endif
759 +    cout << "Fixed Molecules" << endl;
760 + #ifdef IS_MPI
761 +  }
762 + #endif
763 +
764    for(int i = 0; i < zconsMols.size(); i++){
765                  
766      if (states[i] == zcsFixed){
# Line 544 | Line 775 | template<typename T> void ZConstraint<T>::doZconstrain
775        }
776        totalFZ_local += fz[i];
777  
778 <      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
778 >      cout << "index: " << indexOfZConsMols[i]
779 >                                <<"\tcurrent zpos: " << COM[whichDirection]
780 >                                << "\tcurrent fz: " <<fz[i] << endl;
781  
782      }
783            
784    }
785  
786 <  //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 <  }
786 >  //calculate total z-constraint force
787   #ifdef IS_MPI
788    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);
789   #else
790    totalFZ = totalFZ_local;
564 –  nMovingZMols = nMovingZMols_local;
791   #endif
792  
793 <  force[0]= 0;
568 <  force[1]= 0;
569 <  force[2]= 0;
570 <  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
571 <
572 <  //modify the velocites of unconstrained molecules
573 <  for(int i = 0; i < unconsMols.size(); i++){
574 <    
575 <     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
576 <    
577 <     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
578 <       unconsAtoms[j]->addFrc(force);
579 <    
580 <  }      
581 <
582 < //modify the velocities of moving z-constrained molecules
583 <  for(int i = 0; i < zconsMols.size(); i++) {
584 <   if (states[i] == zcsMoving){
585 <                
586 <     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
587 <
588 <     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
589 <       movingZAtoms[j]->addFrc(force);
590 <     }
591 <  }
592 <
793 >        
794    // apply negative to fixed z-constrained molecues;
795    force[0]= 0;
796    force[1]= 0;
# Line 603 | Line 804 | template<typename T> void ZConstraint<T>::doZconstrain
804        zconsAtoms = zconsMols[i]->getMyAtoms();  
805      
806        for(int j =0; j < nAtomOfCurZConsMol; j++) {
807 <        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
807 >                  force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
808 >        //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
809          zconsAtoms[j]->addFrc(force);
810        }
811                  
# Line 611 | Line 813 | template<typename T> void ZConstraint<T>::doZconstrain
813          
814    }
815  
816 +  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
817 +  //               << "total force is " << calcTotalForce() << endl;
818 +
819 +  //calculate the number of atoms of moving z-constrained molecules
820 +  int nMovingZAtoms_local;
821 +  int nMovingZAtoms;
822 +        
823 +  nMovingZAtoms_local = 0;
824 +  for(int i = 0; i < zconsMols.size(); i++)
825 +    if(states[i] == zcsMoving)
826 +           nMovingZAtoms_local += zconsMols[i]->getNAtoms();
827 +  
828 + #ifdef IS_MPI
829 +  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
830 + #else
831 +  nMovingZAtoms = nMovingZAtoms_local;
832 + #endif
833 +
834 +  force[0]= 0;
835 +  force[1]= 0;
836 +  force[2]= 0;
837 +
838 +  //modify the forces of unconstrained molecules
839 +  for(int i = 0; i < unconsMols.size(); i++){
840 +    
841 +     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
842 +    
843 +     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
844 +       force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
845 +       //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
846 +       unconsAtoms[j]->addFrc(force);
847 +     }
848 +    
849 +  }      
850 +
851 + //modify the forces of moving z-constrained molecules
852 +  for(int i = 0; i < zconsMols.size(); i++) {
853 +    if (states[i] == zcsMoving){
854 +                
855 +      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
856 +
857 +      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
858 +        force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
859 +        //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
860 +        movingZAtoms[j]->addFrc(force);
861 +      }
862 +    }
863 +  }
864 +
865 +  //cout << "after substracting z-constraint force from moving molecuels "
866 +  //              << "total force is " << calcTotalForce()  << endl;
867 +
868   }
869  
870   template<typename T> bool ZConstraint<T>::checkZConsState(){
871    double COM[3];
872    double diff;
873    
874 <  bool changed;
874 >  int changed_local;
875 >  int changed;
876 >        
877 >  changed_local = 0;
878    
622 –  changed = false;
623 –  
879    for(int i =0; i < zconsMols.size(); i++){
880  
881      zconsMols[i]->getCOM(COM);
882 <    diff = fabs(COM[whichDirection] - ZPos[i]);  
883 <    if (  diff <= ztol && states[i] == zcsMoving){
882 >    diff = fabs(COM[whichDirection] - zPos[i]);  
883 >    if (  diff <= zconsTol && states[i] == zcsMoving){
884        states[i] = zcsFixed;
885 <        changed = true;
885 >           changed_local = 1;
886      }
887 <    else if ( diff > ztol && states[i] == zcsFixed){
887 >    else if ( diff > zconsTol && states[i] == zcsFixed){
888        states[i] = zcsMoving;
889 <        changed = true;  
889 >           changed_local = 1;    
890      }
891    
892    }
893  
894 <  return changed;
894 > #ifndef IS_MPI
895 >  changed =changed_local;
896 > #else
897 >  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
898 > #endif
899 >
900 >  return changed > 0 ? true : false;
901   }
902  
903   template<typename T> bool ZConstraint<T>::haveFixedZMols(){
904 +
905 +  int havingFixed_local;
906 +  int havingFixed;
907 +
908 +  havingFixed_local = 0;
909 +
910    for(int i = 0; i < zconsMols.size(); i++)
911 <    if (states[i] == zcsFixed)
912 <      return true;
911 >    if (states[i] == zcsFixed){
912 >      havingFixed_local = 1;
913 >                break;
914 >    }
915  
916 <  return false;
916 > #ifndef IS_MPI
917 >  havingFixed = havingFixed_local;
918 > #else
919 >  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
920 > #endif
921 >
922 >  return havingFixed > 0 ? true : false;
923   }
924  
925  
# Line 652 | Line 927 | template<typename T> bool ZConstraint<T>::haveMovingZM
927   *
928   */
929   template<typename T> bool ZConstraint<T>::haveMovingZMols(){
930 +
931 +  int havingMoving_local;
932 +  int havingMoving;
933 +
934 +  havingMoving_local = 0;
935 +
936    for(int i = 0; i < zconsMols.size(); i++)
937 <    if (states[i] == zcsMoving)
938 <      return true;
937 >    if (states[i] == zcsMoving){
938 >      havingMoving_local = 1;
939 >                break;
940 >    }
941  
942 <  return false;
942 > #ifndef IS_MPI
943 >  havingMoving = havingMoving_local;
944 > #else
945 >  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
946 > #endif
947 >
948 >  return havingMoving > 0 ? true : false;
949    
950 < }
950 > }
951 >
952 > /**
953 >  *
954 >  *
955 >  */
956 >
957 > template<typename T> void ZConstraint<T>::doHarmonic(){
958 >  double force[3];
959 >  double harmonicU;
960 >  double harmonicF;
961 >  double COM[3];
962 >  double diff;
963 >  double totalFZ_local;
964 >  double totalFZ;
965 >        
966 >  force[0] = 0;
967 >  force[1] = 0;
968 >  force[2] = 0;
969 >
970 >  totalFZ_local = 0;
971 >
972 > #ifdef IS_MPI
973 >  if (worldRank == 0){
974 > #endif
975 >    cout << "Moving Molecules" << endl;
976 > #ifdef IS_MPI
977 >  }
978 > #endif
979 >
980 >
981 >  for(int i = 0; i < zconsMols.size(); i++) {
982 >
983 >    if (states[i] == zcsMoving){
984 >      zconsMols[i]->getCOM(COM);
985 >      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
986 >                
987 >                diff = COM[whichDirection] -zPos[i];
988 >                
989 >      harmonicU = 0.5 * kz[i] * diff * diff;  
990 >                info->lrPot += harmonicU;
991 >
992 >      harmonicF =  - kz[i] * diff;
993 >      totalFZ_local += harmonicF;
994 >
995 >       //adjust force
996 >                
997 >      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();    
998 >
999 >       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
1000 >                  force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
1001 >         //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
1002 >         movingZAtoms[j]->addFrc(force);
1003 >       }
1004 >    }
1005 >
1006 >  }
1007 >
1008 > #ifndef IS_MPI
1009 >  totalFZ = totalFZ_local;
1010 > #else
1011 >  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1012 > #endif
1013 >
1014 >  force[0]= 0;
1015 >  force[1]= 0;
1016 >  force[2]= 0;
1017 >
1018 >  //modify the forces of unconstrained molecules
1019 >  for(int i = 0; i < unconsMols.size(); i++){
1020 >    
1021 >     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
1022 >    
1023 >     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
1024 >       force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
1025 >       //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
1026 >       unconsAtoms[j]->addFrc(force);    
1027 >     }
1028 >  }  
1029 >
1030 > }
1031 >
1032 > template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
1033 > {
1034 >  double MVzOfMovingMols_local;
1035 >  double MVzOfMovingMols;
1036 >  double totalMassOfMovingZMols_local;
1037 >  double totalMassOfMovingZMols;
1038 >  double COMvel[3];
1039 >      
1040 >  MVzOfMovingMols_local = 0;
1041 >  totalMassOfMovingZMols_local = 0;
1042 >
1043 >  for(int i =0; i < unconsMols.size(); i++){
1044 >    unconsMols[i]->getCOMvel(COMvel);
1045 >    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
1046 >  }
1047 >
1048 >  for(int i = 0; i < zconsMols.size(); i++){
1049 >
1050 >    if (states[i] == zcsMoving){
1051 >      zconsMols[i]->getCOMvel(COMvel);
1052 >      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];  
1053 >      totalMassOfMovingZMols_local += massOfZConsMols[i];              
1054 >    }
1055 >                
1056 >  }
1057 >
1058 > #ifndef IS_MPI
1059 >  MVzOfMovingMols = MVzOfMovingMols_local;
1060 >  totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1061 > #else
1062 >  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1063 >  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
1064 > #endif
1065 >
1066 >  double vzOfMovingMols;
1067 >  vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1068 >
1069 >  return vzOfMovingMols;
1070 > }
1071 >
1072 >
1073 > template<typename T> double ZConstraint<T>::calcSysCOMVel()
1074 > {
1075 >  double COMvel[3];
1076 >  double tempMVz_local;
1077 >  double tempMVz;
1078 >  double massOfZCons_local;
1079 >  double massOfZCons;
1080 >
1081 >
1082 > tempMVz_local = 0;
1083 >
1084 >  for(int i =0 ; i < nMols; i++){
1085 >    molecules[i].getCOMvel(COMvel);
1086 >         tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
1087 >  }
1088 >
1089 >  massOfZCons_local = 0;
1090 >        
1091 >  for(int i = 0; i < massOfZConsMols.size(); i++){
1092 >    massOfZCons_local += massOfZConsMols[i];
1093 >  }
1094 > #ifndef IS_MPI
1095 >  massOfZCons = massOfZCons_local;
1096 >  tempMVz = tempMVz_local;
1097 > #else
1098 >  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1099 >  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1100 > #endif
1101 >
1102 >  return tempMVz /(totalMassOfUncons + massOfZCons);
1103 > }
1104 >
1105 > template<typename T> double ZConstraint<T>::calcTotalForce(){
1106 >
1107 >  double force[3];  
1108 >  double totalForce_local;
1109 >  double totalForce;
1110 >
1111 >  totalForce_local = 0;
1112 >
1113 >  for(int i = 0; i < nAtoms; i++){
1114 >    atoms[i]->getFrc(force);
1115 >    totalForce_local += force[whichDirection];
1116 >  }
1117 >
1118 > #ifndef IS_MPI
1119 >  totalForce = totalForce_local;
1120 > #else
1121 >  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1122 > #endif
1123 >
1124 >  return totalForce;
1125 >
1126 > }
1127 >
1128 > /**
1129 > *
1130 > */
1131 >
1132 > template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1133 >  //calculate the number of atoms of moving z-constrained molecules
1134 >  int nMovingZAtoms_local;
1135 >  int nMovingZAtoms;
1136 >        
1137 >  nMovingZAtoms_local = 0;
1138 >  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1139 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1140 >           nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1141 >  
1142 > #ifdef IS_MPI
1143 >  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1144 > #else
1145 >  nMovingZAtoms = nMovingZAtoms_local;
1146 > #endif
1147 >  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1148 > }
1149 >
1150 > template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1151 >  return totalForce / mol->getNAtoms();
1152 > }
1153 >
1154 > template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
1155 >  return totalForce / totNumOfMovingAtoms;
1156 > }
1157 >
1158 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1159 >    return totalForce / mol->getNAtoms();
1160 > }
1161 >
1162 > template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
1163 >  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1164 > }
1165 >
1166 > /**
1167 > *
1168 > */
1169 >
1170 > template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1171 >  //calculate the number of atoms of moving z-constrained molecules
1172 >  double massOfMovingZAtoms_local;
1173 >  double massOfMovingZAtoms;
1174 >        
1175 >  massOfMovingZAtoms_local = 0;
1176 >  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
1177 >    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
1178 >           massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1179 >  
1180 > #ifdef IS_MPI
1181 >  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1182 > #else
1183 >  massOfMovingZAtoms = massOfMovingZAtoms_local;
1184 > #endif
1185 >  totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons;
1186 > }
1187 >
1188 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1189 >  return totalForce * atom->getMass() / mol->getTotalMass();
1190 > }
1191 >
1192 > template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
1193 >    return totalForce * atom->getMass() / totMassOfMovingAtoms;
1194 > }
1195 >
1196 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
1197 >  return totalForce * atom->getMass() / mol->getTotalMass();
1198 > }
1199 >
1200 > template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
1201 >    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1202 > }
1203 >

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