src/constraints/ZConstraint.cpp

#include "integrators/Integrator.hpp"

#include "utils/simError.h"

#include <math.h>


const double INFINITE_TIME = 10e30;

template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo,

                                                 ForceFields* the_ff): T(theInfo, the_ff),

                                                                       fzOut(NULL),

                                                                       curZconsTime(0),

                                                                       forcePolicy(NULL),

                                                                       usingSMD(false),

                                                                       hasZConsGap(false){

  //get properties from SimInfo

  GenericData* data;

  ZConsParaData* zConsParaData;

  DoubleGenericData* sampleTime;

  DoubleGenericData* tolerance;

  DoubleGenericData* gap;

  DoubleGenericData* fixtime;

  StringGenericData* policy;

  StringGenericData* filename; 

  IntGenericData* smdFlag;

  double COM[3];


  //by default, the direction of constraint is z

  // 0 --> x

  // 1 --> y

  // 2 --> z

  whichDirection = 2;


  //estimate the force constant of harmonical potential

  double Kb = 1.986E-3 ; //in kcal/K


  double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /

                            2;

  zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox);


  //creat force Subtraction policy

  data = info->getPropertyByName(ZCONSFORCEPOLICY_ID);

  if (!data){

    sprintf(painCave.errMsg,

            "ZConstraint Warning: User does not set force Subtraction policy, "

            "PolicyByMass is used\n");

    painCave.isFatal = 0;

    simError();      


    forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);

  }

  else{

    policy = dynamic_cast<StringGenericData*>(data);


    if (!policy){

      sprintf(painCave.errMsg,

              "ZConstraint Error: Convertion from GenericData to StringGenericData failure, "

              "PolicyByMass is used\n");

      painCave.isFatal = 0;

      simError();      


      forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);

    }

    else{

      if (policy->getData() == "BYNUMBER")

        forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this);

      else if (policy->getData() == "BYMASS")

        forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);

      else{

        sprintf(painCave.errMsg,

                "ZConstraint Warning: unknown force Subtraction policy, "

                "PolicyByMass is used\n");

        painCave.isFatal = 0;

        simError();      

        forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);

      }

    }

  }


  //retrieve sample time of z-contraint 

  data = info->getPropertyByName(ZCONSTIME_ID);


  if (!data){

    sprintf(painCave.errMsg,

            "ZConstraint error: If you use an ZConstraint\n"

            " , you must set sample time.\n");

    painCave.isFatal = 1;

    simError();

  }

  else{

    sampleTime = dynamic_cast<DoubleGenericData*>(data);


    if (!sampleTime){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get property from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      this->zconsTime = sampleTime->getData();

    }

  }


  //retrieve output filename of z force

  data = info->getPropertyByName(ZCONSFILENAME_ID);

  if (!data){

    sprintf(painCave.errMsg,

            "ZConstraint error: If you use an ZConstraint\n"

            " , you must set output filename of z-force.\n");

    painCave.isFatal = 1;

    simError();

  }

  else{

    filename = dynamic_cast<StringGenericData*>(data);


    if (!filename){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get property from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      this->zconsOutput = filename->getData();

    }

  }


  //retrieve tolerance for z-constraint molecuels

  data = info->getPropertyByName(ZCONSTOL_ID);


  if (!data){

    sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n");

    painCave.isFatal = 1;

    simError();

  }

  else{

    tolerance = dynamic_cast<DoubleGenericData*>(data);


    if (!tolerance){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get property from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      this->zconsTol = tolerance->getData();

    }

  }


  //quick hack here

  data = info->getPropertyByName(ZCONSGAP_ID);


  if (data){

    gap = dynamic_cast<DoubleGenericData*>(data);


    if (!gap){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get property from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      this->hasZConsGap = true;

      this->zconsGap = gap->getData();

    }

  }


  data = info->getPropertyByName(ZCONSFIXTIME_ID);


  if (data){

    fixtime = dynamic_cast<DoubleGenericData*>(data);

    if (!fixtime){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get zconsFixTime from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      this->zconsFixTime = fixtime->getData();

    }

  }

  else if(hasZConsGap){

      sprintf(painCave.errMsg,

              "ZConstraint error: must set fixtime if already set zconsGap\n");

      painCave.isFatal = 1;

      simError();

  }


  data = info->getPropertyByName(ZCONSUSINGSMD_ID);


  if (data){

    smdFlag = dynamic_cast<IntGenericData*>(data);


    if (!smdFlag){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get property from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      this->usingSMD= smdFlag->getData() ? true : false;

    }


  }


  //retrieve index of z-constraint molecules

  data = info->getPropertyByName(ZCONSPARADATA_ID);

  if (!data){

    sprintf(painCave.errMsg,

            "ZConstraint error: If you use an ZConstraint\n"

            " , you must set index of z-constraint molecules.\n");

    painCave.isFatal = 1;

    simError();

  }

  else{

    zConsParaData = dynamic_cast<ZConsParaData*>(data);


    if (!zConsParaData){

      sprintf(painCave.errMsg,

              "ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");

      painCave.isFatal = 1;

      simError();

    }

    else{

      parameters = zConsParaData->getData();


      //check the range of zconsIndex

      //and the minimum value of index is the first one (we already sorted the data)

      //the maximum value of index is the last one


      int maxIndex;

      int minIndex;

      int totalNumMol;


      minIndex = (*parameters)[0].zconsIndex;

      if (minIndex < 0){

        sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");

        painCave.isFatal = 1;

        simError();

      }


      maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;


#ifndef IS_MPI

      totalNumMol = nMols;

#else

      totalNumMol = mpiSim->getNMolGlobal();   

#endif      


      if (maxIndex > totalNumMol - 1){

        sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");

        painCave.isFatal = 1;

        simError();

      }


      //if user does not specify the zpos for the zconstraint molecule

      //its initial z coordinate  will be used as default

      for (int i = 0; i < (int) (parameters->size()); i++){

        if (!(*parameters)[i].havingZPos){

#ifndef IS_MPI

          for (int j = 0; j < nMols; j++){

            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){

              molecules[j].getCOM(COM);

              break;

            }

          }

#else

          //query which processor current zconstraint molecule belongs to

          int* MolToProcMap;

          int whichNode;


          MolToProcMap = mpiSim->getMolToProcMap();

          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];


          //broadcast the zpos of current z-contraint molecule

          //the node which contain this 


          if (worldRank == whichNode){

            for (int j = 0; j < nMols; j++)

              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){

                molecules[j].getCOM(COM);

                break;

              }

          }


          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode,

                    MPI_COMM_WORLD);        

#endif


          (*parameters)[i].zPos = COM[whichDirection];


          sprintf(painCave.errMsg,

                  "ZConstraint warning: Does not specify zpos for z-constraint molecule "

                  "initial z coornidate will be used \n");

          painCave.isFatal = 0;

          simError();

        }

      }

    }//end if (!zConsParaData)


  }//end  if (!data)


  //  

#ifdef IS_MPI

  update(); 

#else  

  int searchResult;


  for (int i = 0; i < nMols; i++){

    searchResult = isZConstraintMol(&molecules[i]); 


    if (searchResult > -1){

      zconsMols.push_back(&molecules[i]);      

      massOfZConsMols.push_back(molecules[i].getTotalMass());  


      zPos.push_back((*parameters)[searchResult].zPos);

      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);

      
      if(usingSMD)

        cantVel.push_back((*parameters)[searchResult].cantVel);


    }

    else{

      unconsMols.push_back(&molecules[i]);

      massOfUnconsMols.push_back(molecules[i].getTotalMass());

    }

  }


  fz.resize(zconsMols.size());

  curZPos.resize(zconsMols.size());

  indexOfZConsMols.resize(zconsMols.size());  


  //determine the states of z-constraint molecules

  for (size_t i = 0; i < zconsMols.size(); i++){

    indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();


    zconsMols[i]->getCOM(COM);

    
    if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){

      states.push_back(zcsFixed);


      if (hasZConsGap)

        endFixTime.push_back(info->getTime() + zconsFixTime);

    }

    else{

      states.push_back(zcsMoving);


      if (hasZConsGap)

        endFixTime.push_back(INFINITE_TIME);

    }


    if(usingSMD)

      cantPos.push_back(COM[whichDirection]);    

  }


  if(usingSMD)

    prevCantPos = cantPos;

#endif 


  //get total masss of unconstraint molecules

  double totalMassOfUncons_local;

  totalMassOfUncons_local = 0;


  for (size_t i = 0; i < unconsMols.size(); i++)

    totalMassOfUncons_local += unconsMols[i]->getTotalMass();


#ifndef IS_MPI

  totalMassOfUncons = totalMassOfUncons_local;

#else

  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,

                MPI_SUM, MPI_COMM_WORLD);  

#endif


  //get total number of unconstrained atoms

  int nUnconsAtoms_local;

  nUnconsAtoms_local = 0;

  for (int i = 0; i < (int) (unconsMols.size()); i++)

    nUnconsAtoms_local += unconsMols[i]->getNAtoms();


#ifndef IS_MPI

  totNumOfUnconsAtoms = nUnconsAtoms_local;

#else

  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM,

                MPI_COMM_WORLD);  

#endif  


  forcePolicy->update();

}


template<typename T> ZConstraint<T>::~ZConstraint(){


  if (fzOut){

    delete fzOut;

  }


  if (forcePolicy){

    delete forcePolicy;

  }

}


/**

 * 

 */


#ifdef IS_MPI

template<typename T> void ZConstraint<T>::update(){

  double COM[3];

  int index;


  zconsMols.clear();

  massOfZConsMols.clear();

  zPos.clear();

  kz.clear();

  cantPos.clear();

  cantVel.clear();


  unconsMols.clear();

  massOfUnconsMols.clear();


  //creat zconsMol and unconsMol lists

  for (int i = 0; i < nMols; i++){

    index = isZConstraintMol(&molecules[i]); 


    if (index > -1){

      zconsMols.push_back(&molecules[i]);      

      zPos.push_back((*parameters)[index].zPos);

      kz.push_back((*parameters)[index].kRatio * zForceConst);

      massOfZConsMols.push_back(molecules[i].getTotalMass());

      
      if(usingSMD)

        cantVel.push_back((*parameters)[index].cantVel);


    }

    else{

      unconsMols.push_back(&molecules[i]);

      massOfUnconsMols.push_back(molecules[i].getTotalMass());

    }

  }


  fz.resize(zconsMols.size());

  curZPos.resize(zconsMols.size());

  indexOfZConsMols.resize(zconsMols.size());  

 
  for (size_t i = 0; i < zconsMols.size(); i++){

    indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();

  }

    
  //determine the states of z-constraint molecules

  for (int i = 0; i < (int) (zconsMols.size()); i++){


    zconsMols[i]->getCOM(COM);

    
    if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){

      states.push_back(zcsFixed);


      if (hasZConsGap)

        endFixTime.push_back(info->getTime() + zconsFixTime);

    }

    else{

      states.push_back(zcsMoving);


      if (hasZConsGap)

        endFixTime.push_back(INFINITE_TIME);

    }


    if(usingSMD)

      cantPos.push_back(COM[whichDirection]);        

  } 


  if(usingSMD)

  prevCantPos = cantPos;


  forcePolicy->update();

}


#endif


/**

 *  Function Name: isZConstraintMol

 *  Parameter

 *    Molecule* mol

 *  Return value:

 *    -1, if the molecule is not z-constraint molecule, 

 *    other non-negative values, its index in indexOfAllZConsMols vector

 */


template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){

  int index;

  int low;

  int high;

  int mid;


  index = mol->getGlobalIndex();


  low = 0;

  high = parameters->size() - 1;


  //Binary Search (we have sorted the array)  

  while (low <= high){

    mid = (low + high) / 2;

    if ((*parameters)[mid].zconsIndex == index)

      return mid;

    else if ((*parameters)[mid].zconsIndex > index)

      high = mid - 1;

    else

      low = mid + 1;

  }


  return -1;

}


template<typename T> void ZConstraint<T>::integrate(){

  // creat zconsWriter  

  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);   


  if (!fzOut){

    sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");

    painCave.isFatal = 1;

    simError();

  }


  //zero out the velocities of center of mass of unconstrained molecules 

  //and the velocities of center of mass of every single z-constrained molecueles

  zeroOutVel();


  curZconsTime = zconsTime + info->getTime();


  T::integrate();

}


template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){

  double zsys;

  double COM[3];

  double force[3];

  double zSysCOMVel;


  T::calcForce(calcPot, calcStress);


  if (hasZConsGap){

    updateZPos();

  }


  if (checkZConsState()){

    zeroOutVel();    

    forcePolicy->update();

  }  


  zsys = calcZSys();

  zSysCOMVel = calcSysCOMVel();

#ifdef IS_MPI

  if (worldRank == 0){

#endif


#ifdef IS_MPI

  }

#endif


  //do zconstraint force; 

  if (haveFixedZMols()){

    this->doZconstraintForce();

  }


  //use external force to move the molecules to the specified positions

  if (haveMovingZMols()){

    if (usingSMD)

      this->doHarmonic(cantPos);

    else

      this->doHarmonic(zPos);      

  }


  //write out forces and current positions of z-constraint molecules

  if (info->getTime() >= curZconsTime){

    for (int i = 0; i < (int) (zconsMols.size()); i++){

      zconsMols[i]->getCOM(COM);

      curZPos[i] = COM[whichDirection];


      //if the z-constraint molecule is still moving, just record its force

      if (states[i] == zcsMoving){

        fz[i] = 0;

        Atom** movingZAtoms;

        movingZAtoms = zconsMols[i]->getMyAtoms();

        for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){

          movingZAtoms[j]->getFrc(force);

          fz[i] += force[whichDirection];

        }

      }

    }

    fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],

                   &curZPos[0], &zPos[0]);

    curZconsTime += zconsTime;

  }


  zSysCOMVel = calcSysCOMVel();  

#ifdef IS_MPI

  if (worldRank == 0){

#endif

#ifdef IS_MPI

  }

#endif

}


template<typename T> double ZConstraint<T>::calcZSys(){

  //calculate reference z coordinate for z-constraint molecules

  double totalMass_local;

  double totalMass;

  double totalMZ_local;

  double totalMZ;

  double massOfCurMol;

  double COM[3];


  totalMass_local = 0;

  totalMZ_local = 0;


  for (int i = 0; i < nMols; i++){

    massOfCurMol = molecules[i].getTotalMass(); 

    molecules[i].getCOM(COM); 


    totalMass_local += massOfCurMol;

    totalMZ_local += massOfCurMol * COM[whichDirection];

  }


#ifdef IS_MPI  

  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,

                MPI_COMM_WORLD);

  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  

#else

  totalMass = totalMass_local;

  totalMZ = totalMZ_local;

#endif  


  double zsys;

  zsys = totalMZ / totalMass;


  return zsys;

}


template<typename T> void ZConstraint<T>::thermalize(void){

  T::thermalize();

  zeroOutVel();

}


template<typename T> void ZConstraint<T>::zeroOutVel(){

  Atom** fixedZAtoms;  

  double COMvel[3];

  double vel[3];

  double zSysCOMVel;


  //zero out the velocities of center of mass of fixed z-constrained molecules


  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsFixed){

      zconsMols[i]->getCOMvel(COMvel);      

      //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << std::endl;


      fixedZAtoms = zconsMols[i]->getMyAtoms(); 


      for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){

        vel = fixedZAtoms[j]->getVel();

        vel[whichDirection] -= COMvel[whichDirection];

        fixedZAtoms[j]->setVel(vel);

      }


      zconsMols[i]->getCOMvel(COMvel);

    }

  }


  zSysCOMVel = calcSysCOMVel();

#ifdef IS_MPI

  if (worldRank == 0){

#endif

#ifdef IS_MPI

  }

#endif


  // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules

  double MVzOfMovingMols_local;

  double MVzOfMovingMols;

  double totalMassOfMovingZMols_local;

  double totalMassOfMovingZMols;


  MVzOfMovingMols_local = 0;

  totalMassOfMovingZMols_local = 0;


  for (int i = 0; i < (int) (unconsMols.size()); i++){

    unconsMols[i]->getCOMvel(COMvel);

    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];

  } 


  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsMoving){

      zconsMols[i]->getCOMvel(COMvel);

      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];   

      totalMassOfMovingZMols_local += massOfZConsMols[i];

    }

  }


#ifndef IS_MPI

  MVzOfMovingMols = MVzOfMovingMols_local;

  totalMassOfMovingZMols = totalMassOfMovingZMols_local;

#else

  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,

                MPI_SUM, MPI_COMM_WORLD);

  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,

                MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  

#endif


  double vzOfMovingMols;

  vzOfMovingMols = MVzOfMovingMols /

                   (totalMassOfUncons + totalMassOfMovingZMols);


  //modify the velocites of unconstrained molecules  

  Atom** unconsAtoms;

  for (int i = 0; i < (int) (unconsMols.size()); i++){

    unconsAtoms = unconsMols[i]->getMyAtoms();

    for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){

      vel = unconsAtoms[j]->getVel();

      vel[whichDirection] -= vzOfMovingMols;

      unconsAtoms[j]->setVel(vel);

    }

  }  


  //modify the velocities of moving z-constrained molecuels

  Atom** movingZAtoms;

  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsMoving){

      movingZAtoms = zconsMols[i]->getMyAtoms();

      for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){

        vel = movingZAtoms[j]->getVel();

        vel[whichDirection] -= vzOfMovingMols;

        movingZAtoms[j]->setVel(vel);

      }

    }

  }


  zSysCOMVel = calcSysCOMVel();

#ifdef IS_MPI

  if (worldRank == 0){

#endif

#ifdef IS_MPI

  }

#endif

}


template<typename T> void ZConstraint<T>::doZconstraintForce(){

  Atom** zconsAtoms;

  double totalFZ; 

  double totalFZ_local;

  double COM[3];

  double force[3];


  //constrain the molecules which do not reach the specified positions  


  //Zero Out the force of z-contrained molecules    

  totalFZ_local = 0;


  //calculate the total z-contrained force of fixed z-contrained molecules


  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsFixed){

      zconsMols[i]->getCOM(COM);

      zconsAtoms = zconsMols[i]->getMyAtoms();  


      fz[i] = 0;      

      for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){

        zconsAtoms[j]->getFrc(force);

        fz[i] += force[whichDirection];

      } 

      totalFZ_local += fz[i];


    }

  } 


  //calculate total z-constraint force

#ifdef IS_MPI

  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);

#else

  totalFZ = totalFZ_local;

#endif


  // apply negative to fixed z-constrained molecues;

  force[0] = 0;

  force[1] = 0;

  force[2] = 0;


  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsFixed){

      int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();

      zconsAtoms = zconsMols[i]->getMyAtoms();  


      for (int j = 0; j < nAtomOfCurZConsMol; j++){

        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;

        force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],

                                                                zconsAtoms[j],

                                                                fz[i]);

        zconsAtoms[j]->addFrc(force);

      }

    }

  } 


  force[0] = 0;

  force[1] = 0;

  force[2] = 0;


  //modify the forces of unconstrained molecules

  for (int i = 0; i < (int) (unconsMols.size()); i++){

    Atom** unconsAtoms = unconsMols[i]->getMyAtoms();


    for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){

      //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);

      force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],

                                                             totalFZ);

      unconsAtoms[j]->addFrc(force);

    }

  }      


  //modify the forces of moving z-constrained molecules

  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsMoving){

      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();     


      for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){

        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);

        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],

                                                               totalFZ);

        movingZAtoms[j]->addFrc(force);

      }

    }

  }

}


template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){

  double force[3];

  double harmonicU;

  double harmonicF;

  double COM[3];

  double diff;

  double totalFZ_local;

  double totalFZ;


  force[0] = 0;

  force[1] = 0;

  force[2] = 0;


  totalFZ_local = 0;


  for (int i = 0; i < (int) (zconsMols.size()); i++){

    if (states[i] == zcsMoving){

      zconsMols[i]->getCOM(COM);


      diff = COM[whichDirection] - resPos[i];


      harmonicU = 0.5 * kz[i] * diff * diff;  

      info->lrPot += harmonicU;


      harmonicF = -kz[i] * diff;

      totalFZ_local += harmonicF;


      //adjust force


      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();     


      for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){

        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],

                                                               movingZAtoms[j],

                                                               harmonicF);

        movingZAtoms[j]->addFrc(force);

      }

    }

  }


#ifndef IS_MPI

  totalFZ = totalFZ_local;

#else

  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  

#endif


  force[0] = 0;

  force[1] = 0;

  force[2] = 0;


  //modify the forces of unconstrained molecules

  for (int i = 0; i < (int) (unconsMols.size()); i++){

    Atom** unconsAtoms = unconsMols[i]->getMyAtoms();


    for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){

      //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;

      force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],

                                                              totalFZ);

      unconsAtoms[j]->addFrc(force);

    }

  }   


}


template<typename T> bool ZConstraint<T>::checkZConsState(){

  double COM[3];

  double diff;


  int changed_local;

  int changed;


  changed_local = 0;


  for (int i = 0; i < (int) (zconsMols.size()); i++){

    zconsMols[i]->getCOM(COM);

    diff = fabs(COM[whichDirection] - zPos[i]);  

    if (diff <= zconsTol && states[i] == zcsMoving){

      states[i] = zcsFixed;

      changed_local = 1;


      if(usingSMD)

        prevCantPos = cantPos;


      if (hasZConsGap)

        endFixTime[i] = info->getTime() + zconsFixTime;

    }

    else if (diff > zconsTol && states[i] == zcsFixed){

      states[i] = zcsMoving;

      changed_local = 1;   


      if(usingSMD)

         cantPos = prevCantPos;

      
      if (hasZConsGap)

        endFixTime[i] = INFINITE_TIME;

    }

  }


#ifndef IS_MPI

  changed = changed_local; 

#else

  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);

#endif


  return (changed > 0);

}


template<typename T> bool ZConstraint<T>::haveFixedZMols(){

  int havingFixed_local;

  int havingFixed;


  havingFixed_local = 0;


  for (int i = 0; i < (int) (zconsMols.size()); i++)

    if (states[i] == zcsFixed){

      havingFixed_local = 1;

      break;

    }


#ifndef IS_MPI

  havingFixed = havingFixed_local;

#else

  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,

                MPI_COMM_WORLD);

#endif


  return (havingFixed > 0);

}


template<typename T> bool ZConstraint<T>::haveMovingZMols(){

  int havingMoving_local;

  int havingMoving;


  havingMoving_local = 0;


  for (int i = 0; i < (int) (zconsMols.size()); i++)

    if (states[i] == zcsMoving){

      havingMoving_local = 1;

      break;

    }


#ifndef IS_MPI

  havingMoving = havingMoving_local;

#else

  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,

                MPI_COMM_WORLD);

#endif


  return (havingMoving > 0);

}


template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){

  double MVzOfMovingMols_local;

  double MVzOfMovingMols;

  double totalMassOfMovingZMols_local;

  double totalMassOfMovingZMols;

  double COMvel[3];


  MVzOfMovingMols_local = 0;

  totalMassOfMovingZMols_local = 0;


  for (int i = 0; i < unconsMols.size(); i++){

    unconsMols[i]->getCOMvel(COMvel);

    MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];

  } 


  for (int i = 0; i < zconsMols.size(); i++){

    if (states[i] == zcsMoving){

      zconsMols[i]->getCOMvel(COMvel);

      MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];   

      totalMassOfMovingZMols_local += massOfZConsMols[i];

    }

  }


#ifndef IS_MPI

  MVzOfMovingMols = MVzOfMovingMols_local;

  totalMassOfMovingZMols = totalMassOfMovingZMols_local;

#else

  MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,

                MPI_SUM, MPI_COMM_WORLD);

  MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,

                MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  

#endif


  double vzOfMovingMols;

  vzOfMovingMols = MVzOfMovingMols /

                   (totalMassOfUncons + totalMassOfMovingZMols);


  return vzOfMovingMols;

}


template<typename T> double ZConstraint<T>::calcSysCOMVel(){

  double COMvel[3];

  double tempMVz_local;

  double tempMVz;

  double massOfZCons_local;

  double massOfZCons;


  tempMVz_local = 0;


  for (int i = 0 ; i < nMols; i++){

    molecules[i].getCOMvel(COMvel);

    tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];

  }


  massOfZCons_local = 0;


  for (int i = 0; i < (int) (massOfZConsMols.size()); i++){

    massOfZCons_local += massOfZConsMols[i];

  }

#ifndef IS_MPI

  massOfZCons = massOfZCons_local;

  tempMVz = tempMVz_local;

#else

  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,

                MPI_COMM_WORLD);

  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);

#endif


  return tempMVz / (totalMassOfUncons + massOfZCons);

}


template<typename T> double ZConstraint<T>::calcTotalForce(){

  double force[3];  

  double totalForce_local;

  double totalForce;


  totalForce_local = 0;


  for (int i = 0; i < nAtoms; i++){

    atoms[i]->getFrc(force);

    totalForce_local += force[whichDirection];

  }


#ifndef IS_MPI

  totalForce = totalForce_local;

#else

  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,

                MPI_COMM_WORLD);

#endif


  return totalForce;

}


template<typename T> void ZConstraint<T>::PolicyByNumber::update(){

  //calculate the number of atoms of moving z-constrained molecules

  int nMovingZAtoms_local;

  int nMovingZAtoms;


  nMovingZAtoms_local = 0;

  for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)

    if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){

      nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();

    }


#ifdef IS_MPI

  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,

                MPI_COMM_WORLD);

#else

  nMovingZAtoms = nMovingZAtoms_local;

#endif

  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;

}


template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,

                                                                              Atom* atom,

                                                                              double totalForce){

  return totalForce / mol->getNAtoms();

}


template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,

                                                                              double totalForce){

  return totalForce / totNumOfMovingAtoms;

}


template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,

                                                                              Atom* atom,

                                                                              double totalForce){

  return totalForce / mol->getNAtoms();

}


template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,

                                                                              double totalForce){

  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;

}


template<typename T> void ZConstraint<T>::PolicyByMass::update(){

  //calculate the number of atoms of moving z-constrained molecules

  double massOfMovingZAtoms_local;

  double massOfMovingZAtoms;


  massOfMovingZAtoms_local = 0;

  for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)

    if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){

      massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();

    }


#ifdef IS_MPI

  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,

                MPI_SUM, MPI_COMM_WORLD);

#else

  massOfMovingZAtoms = massOfMovingZAtoms_local;

#endif

  totMassOfMovingAtoms = massOfMovingZAtoms +

                         zconsIntegrator->totalMassOfUncons;

}


template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,

                                                                            Atom* atom,

                                                                            double totalForce){

  return totalForce * atom->getMass() / mol->getTotalMass();

}


template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,

                                                                            double totalForce){

  return totalForce * atom->getMass() / totMassOfMovingAtoms;

}


template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,

                                                                            Atom* atom,

                                                                            double totalForce){

  return totalForce * atom->getMass() / mol->getTotalMass();

}


template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,

                                                                            double totalForce){

  return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;

}


template<typename T> void ZConstraint<T>::updateZPos(){

  double curTime;

  double COM[3];

  
  curTime = info->getTime();


  for (size_t i = 0; i < zconsMols.size(); i++){


    if (states[i] == zcsFixed && curTime >= endFixTime[i]){

      zPos[i] += zconsGap;


      if (usingSMD){

        zconsMols[i]->getCOM(COM);

        cantPos[i] = COM[whichDirection];

      }

      
    }

    
  }

  
}


template<typename T> void ZConstraint<T>::updateCantPos(){

  double curTime;

  double dt;


  curTime = info->getTime();

  dt = info->dt;


  for (size_t i = 0; i < zconsMols.size(); i++){

    if (states[i] == zcsMoving){

      cantPos[i] += cantVel[i] * dt;

    }

  }


}

Revision:	1830
Committed:	Thu Dec 2 05:17:10 2004 UTC (19 years, 9 months ago) by tim
File size:	34259 byte(s)
Log Message:	change endl to std::endl