src/constraints/ZconstraintForceManager.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <cmath>
#include "constraints/ZconstraintForceManager.hpp"
#include "integrators/Integrator.hpp"
#include "utils/simError.h"
#include "utils/OOPSEConstant.hpp"
#include "utils/StringUtils.hpp"
namespace oopse {
ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) {
    currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    Globals* simParam = info_->getSimParams();

    if (simParam->haveDt()){
        dt_ = simParam->getDt();
    } else {
        sprintf(painCave.errMsg,
                "Integrator Error: dt is not set\n");
        painCave.isFatal = 1;
        simError();    
    }

    if (simParam->haveZconstraintTime()){
        zconsTime_ = simParam->getZconsTime();
    }
    else{
        sprintf(painCave.errMsg,
        "ZConstraint error: If you use a ZConstraint,\n"
        "\tyou must set zconsTime.\n");
        painCave.isFatal = 1;
        simError();
    }

    if (simParam->haveZconsTol()){
        zconsTol_ = simParam->getZconsTol();
    }
    else{
        zconsTol_ = 0.01;
        sprintf(painCave.errMsg,
            "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
            "\tOOPSE will use a default value of %f.\n"
            "\tTo set the tolerance, use the zconsTol variable.\n",
            zconsTol_);
        painCave.isFatal = 0;
        simError();      
    }

    //set zcons gap
    if (simParam->haveZConsGap()){
        usingZconsGap_ = true;
        zconsGap_ = simParam->getZconsGap();
    }else {
        usingZconsGap_ = false;
        zconsGap_ = 0.0;
    }

    //set zcons fixtime
    if (simParam->haveZConsFixTime()){
        zconsFixingTime_ = simParam->getZconsFixtime();
    } else {
        zconsFixingTime_ = infiniteTime;
    }

    //set zconsUsingSMD
    if (simParam->haveZConsUsingSMD()){
        usingSMD_ = simParam->getZconsUsingSMD();
    }else {
        usingSMD_ =false;
    }
    
    zconsOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";

    //estimate the force constant of harmonical potential
    Mat3x3d hmat = currSnapshot_->getHmat();
    double halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2;        
    double targetTemp;
    if (simParam->haveTargetTemp()) {
        targetTemp = simParam->getTargetTemp();
    } else {
        targetTemp = 298.0;
    }
    double zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox);
         
    int nZconstraints = simParam->getNzConstraints();
    ZconStamp** stamp = simParam->getZconStamp();
    //
    for (int i = 0; i < nZconstraints; i++){

        ZconstraintParam param;
        int zmolIndex = stamp[i]->getMolIndex();
        if (stamp[i]->haveZpos()) {
            param.zTargetPos = stamp[i]->getZpos();
        } else {
            param.zTargetPos = getZTargetPos(zmolIndex);
        }

        param.kz = zforceConstant * stamp[i]->getKratio();

        if (stamp[i]->haveCantVel()) {
            param.cantVel = stamp[i]->getCantVel();
        } else {
            param.cantVel = 0.0;
        }

        allZMolIndices_.insert(std::make_pair(zmolIndex, param));
    }

    //create fixedMols_, movingMols_ and unconsMols lists 
    update();
    
    //calculate masss of unconstraint molecules in the whole system (never change during the simulation)
    double totMassUnconsMols_local = 0.0;    
    std::vector<Molecule*>::iterator j;
    for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
        totMassUnconsMols_local += (*j)->getMass();
    }    
#ifndef IS_MPI
    totMassUnconsMols_ = totMassUnconsMols_local;
#else
    MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_DOUBLE,
        MPI_SUM, MPI_COMM_WORLD);  
#endif

    // creat zconsWriter  
    fzOut = new ZConsWriter(info_, zconsOutput_.c_str());   

    if (!fzOut){
      sprintf(painCave.errMsg, "Fail to create ZConsWriter\n");
      painCave.isFatal = 1;
      simError();
    }

}

ZconstraintForceManager::~ZconstraintForceManager(){

  if (fzOut){
    delete fzOut;
  }

}

void ZconstraintForceManager::update(){
    fixedZMols_.clear();
    movingZMols_.clear();
    unzconsMols_.clear();

    for (std::map<int, ZconstraintParam>::iterator i = allZMolIndices_.begin(); i != allZMolIndices_.end(); ++i) {
#ifdef IS_MPI
        if (info_->getMolToProc(i->first) == worldRank) {
#endif
            ZconstraintMol zmol;
            zmol.mol = info_->getMoleculeByGlobalIndex(i->first);
            assert(zmol.mol);
            zmol.param = i->second;
            zmol.cantPos = zmol.param.zTargetPos; /**@todo fixed me when zmol migrate, it is incorrect*/
            Vector3d com = zmol.mol->getCom();
            double diff = fabs(zmol.param.zTargetPos - com[whichDirection]);
            if (diff < zconsTol_) {
                fixedZMols_.push_back(zmol);
            } else {
                movingZMols_.push_back(zmol);            
            }

#ifdef IS_MPI
        }
#endif
    }

    calcTotalMassMovingZMols();

    std::set<int> zmolSet;
    for (std::list<ZconstraintMol>::iterator i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        zmolSet.insert(i->mol->getGlobalIndex());
    }    

    for (std::list<ZconstraintMol>::iterator i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
        zmolSet.insert(i->mol->getGlobalIndex());
    }

    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    for(mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
        if (zmolSet.find(mol->getGlobalIndex()) == zmolSet.end()) {
            unzconsMols_.push_back(mol);
        }
    }

}

bool ZconstraintForceManager::isZMol(Molecule* mol){
    return allZMolIndices_.find(mol->getGlobalIndex()) == allZMolIndices_.end() ? false : true;
}

void ZconstraintForceManager::init(){

  //zero out the velocities of center of mass of unconstrained molecules 
  //and the velocities of center of mass of every single z-constrained molecueles
  zeroVelocity();

  currZconsTime_ = currSnapshot_->getTime();
}

void ZconstraintForceManager::calcForces(bool needPotential, bool needStress){
    ForceManager::calcForces(needPotential, needStress);
    
    if (usingZconsGap_){
        updateZPos();
    }

    if (checkZConsState()){
        zeroVelocity();    
        calcTotalMassMovingZMols();
    }  

    //do zconstraint force; 
    if (haveFixedZMols()){
        doZconstraintForce();
    }

    //use external force to move the molecules to the specified positions
    if (haveMovingZMols()){
        doHarmonic();
    }

    //write out forces and current positions of z-constraint molecules    
    if (currSnapshot_->getTime() >= currZconsTime_){
        std::list<ZconstraintMol>::iterator i;
        Vector3d com;
        for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
            com = i->mol->getCom();
            i->zpos = com[whichDirection];
        }
        
        fzOut->writeFZ(fixedZMols_);
        currZconsTime_ += zconsTime_;
    }
}

void ZconstraintForceManager::zeroVelocity(){

    Vector3d comVel;
    Vector3d vel;
    std::list<ZconstraintMol>::iterator i;
    Molecule* mol;
    StuntDouble* integrableObject;
    Molecule::IntegrableObjectIterator ii;

    //zero out the velocities of center of mass of fixed z-constrained molecules
    for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
        mol = i->mol;
        comVel = mol->getComVel();
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {
            vel = integrableObject->getVel();  
            vel[whichDirection] -= comVel[whichDirection];
            integrableObject->setVel(vel);
        }
    }

    // calculate the vz of center of mass of moving molecules(include unconstrained molecules 
    // and moving z-constrained molecules)  
    double pzMovingMols_local = 0.0;
    double pzMovingMols;
    
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        mol = i->mol;        
        comVel = mol->getComVel();
        pzMovingMols_local +=  mol->getMass() * comVel[whichDirection];   
    }

    std::vector<Molecule*>::iterator j;
    for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
        mol =*j;
        comVel = mol->getComVel();
        pzMovingMols_local += mol->getMass() * comVel[whichDirection];
    }
    
#ifndef IS_MPI
    pzMovingMols = pzMovingMols_local;
#else
    MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_DOUBLE,
        MPI_SUM, MPI_COMM_WORLD);
#endif

    double vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_);

    //modify the velocities of moving z-constrained molecuels
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        mol = i->mol;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            vel = integrableObject->getVel();
            vel[whichDirection] -= vzMovingMols;
            integrableObject->setVel(vel); 
        }
    }

    //modify the velocites of unconstrained molecules  
    for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
        mol =*j;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            vel = integrableObject->getVel();
            vel[whichDirection] -= vzMovingMols;
            integrableObject->setVel(vel); 
        }
    }
    
}


void ZconstraintForceManager::doZconstraintForce(){
  double totalFZ; 
  double totalFZ_local;
  Vector3d com;
  Vector3d force(0.0);

  //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
    std::list<ZconstraintMol>::iterator i;
    Molecule* mol;
    StuntDouble* integrableObject;
    Molecule::IntegrableObjectIterator ii;

    for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
        mol = i->mol;
        i->fz = 0.0;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            force = integrableObject->getFrc();    
            i->fz += force[whichDirection]; 
        }
         totalFZ_local += i->fz;
    }

  //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;
    for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
        mol = i->mol;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            force[whichDirection] = -getZFOfFixedZMols(mol, integrableObject, i->fz);
            integrableObject->addFrc(force);
        }
    }

  //modify the forces of moving z-constrained molecules
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        mol = i->mol;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            force[whichDirection] = -getZFOfMovingMols(mol,totalFZ);
            integrableObject->addFrc(force);
        }
    }

  //modify the forces of unconstrained molecules
    std::vector<Molecule*>::iterator j;
    for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
        mol =*j;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            force[whichDirection] = -getZFOfMovingMols(mol, totalFZ);
            integrableObject->addFrc(force);
        }
    }

}


void ZconstraintForceManager::doHarmonic(){
    double totalFZ;
    Vector3d force(0.0);
    Vector3d com;
    double totalFZ_local = 0;
    std::list<ZconstraintMol>::iterator i;
    StuntDouble* integrableObject;
    Molecule::IntegrableObjectIterator ii;
    Molecule* mol;
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        mol = i->mol;
        com = mol->getCom();   
        double resPos = usingSMD_? i->cantPos : i->param.zTargetPos;
        double diff = com[whichDirection] - resPos; 
        double harmonicU = 0.5 * i->param.kz * diff * diff;
        currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU;
        double harmonicF = -i->param.kz * diff;
        totalFZ_local += harmonicF;

        //adjust force
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            force[whichDirection] = getHFOfFixedZMols(mol, integrableObject, harmonicF);
            integrableObject->addFrc(force);            
        }
    }

#ifndef IS_MPI
  totalFZ = totalFZ_local;
#else
  MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
#endif

    //modify the forces of unconstrained molecules
    std::vector<Molecule*>::iterator j;
    for ( j = unzconsMols_.begin(); j !=  unzconsMols_.end(); ++j) {
        mol = *j;
        for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) {

            force[whichDirection] = getHFOfUnconsMols(mol, totalFZ);
            integrableObject->addFrc(force);            
        }
    }

}

bool ZconstraintForceManager::checkZConsState(){
    Vector3d com;
    double diff;
    int changed_local = 0;

    std::list<ZconstraintMol>::iterator i;
    std::list<ZconstraintMol>::iterator j;
    
    std::list<ZconstraintMol> newMovingZMols;
    for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end();) {
        com = i->mol->getCom();
        diff = fabs(com[whichDirection] - i->param.zTargetPos);
        if (diff > zconsTol_) {
            if (usingZconsGap_) {
                i->endFixingTime = infiniteTime;
            }
            j = i++;
            newMovingZMols.push_back(*j);
            fixedZMols_.erase(j);
            
            changed_local = 1;            
        }else {
            ++i;
        }
    }  

    std::list<ZconstraintMol> newFixedZMols;
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end();) {
        com = i->mol->getCom();
        diff = fabs(com[whichDirection] - i->param.zTargetPos);
        if (diff <= zconsTol_) {
            if (usingZconsGap_) {
                i->endFixingTime = currSnapshot_->getTime() + zconsFixingTime_;
            }
            //this moving zconstraint molecule is about to fixed
            //moved this molecule to
            j = i++;
            newFixedZMols.push_back(*j);
            movingZMols_.erase(j);
            changed_local = 1;            
        }else {
            ++i;
        }
    }     

    //merge the lists
    fixedZMols_.insert(fixedZMols_.end(), newFixedZMols.begin(), newFixedZMols.end());
    movingZMols_.insert(movingZMols_.end(), newMovingZMols.begin(), newMovingZMols.end());

    int changed;
#ifndef IS_MPI
    changed = changed_local; 
#else
    MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#endif

    return (changed > 0);
}

bool ZconstraintForceManager::haveFixedZMols(){
  int havingFixed;
  int havingFixed_local = fixedZMols_.empty() ? 0 : 1;

#ifndef IS_MPI
  havingFixed = havingFixed_local;
#else
  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
                MPI_COMM_WORLD);
#endif

  return havingFixed > 0;
}


bool ZconstraintForceManager::haveMovingZMols(){
  int havingMoving_local;
  int havingMoving;

  havingMoving_local = movingZMols_.empty()? 0 : 1;

#ifndef IS_MPI
  havingMoving = havingMoving_local;
#else
  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
                MPI_COMM_WORLD);
#endif

  return havingMoving > 0;
}

void ZconstraintForceManager::calcTotalMassMovingZMols(){

    double totMassMovingZMols_local = 0.0;
    std::list<ZconstraintMol>::iterator i;
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        totMassMovingZMols_local += i->mol->getMass();
    }
    
#ifdef IS_MPI
    MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_DOUBLE,
                MPI_SUM, MPI_COMM_WORLD);
#else
    totMassMovingZMols_ = totMassMovingZMols_local;
#endif

}

double ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce){
  return totalForce * sd->getMass() / mol->getMass();
}

double ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, double totalForce){
  return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_);
}

double ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, double totalForce){
  return totalForce * sd->getMass() / mol->getMass();
}

double ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, double totalForce){
  return totalForce * mol->getMass() / totMassUnconsMols_;
}

void ZconstraintForceManager::updateZPos(){
    double curTime = currSnapshot_->getTime();
    std::list<ZconstraintMol>::iterator i;
    for ( i = fixedZMols_.begin(); i !=  fixedZMols_.end(); ++i) {
        i->param.zTargetPos += zconsGap_;     
    }  
}

void ZconstraintForceManager::updateCantPos(){
    std::list<ZconstraintMol>::iterator i;
    for ( i = movingZMols_.begin(); i !=  movingZMols_.end(); ++i) {
        i->cantPos += i->param.cantVel * dt_;
    }
}

double ZconstraintForceManager::getZTargetPos(int index){
    double zTargetPos;
#ifndef IS_MPI    
    Molecule* mol = info_->getMoleculeByGlobalIndex(index);
    assert(mol);
    Vector3d com = mol->getCom();
    zTargetPos = com[whichDirection];
#else
    int whicProc = info_->getMolToProc(index);
    MPI_Bcast(&zTargetPos, 1, MPI_DOUBLE, whicProc, MPI_COMM_WORLD);
#endif
    return zTargetPos;
}

}
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	20309 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#include <cmath>
43	#include "constraints/ZconstraintForceManager.hpp"
44	#include "integrators/Integrator.hpp"
45	#include "utils/simError.h"
46	#include "utils/OOPSEConstant.hpp"
47	#include "utils/StringUtils.hpp"
48	namespace oopse {
49	ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) {
50	currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
51	Globals* simParam = info_->getSimParams();
52
53	if (simParam->haveDt()){
54	dt_ = simParam->getDt();
55	} else {
56	sprintf(painCave.errMsg,
57	"Integrator Error: dt is not set\n");
58	painCave.isFatal = 1;
59	simError();
60	}
61
62	if (simParam->haveZconstraintTime()){
63	zconsTime_ = simParam->getZconsTime();
64	}
65	else{
66	sprintf(painCave.errMsg,
67	"ZConstraint error: If you use a ZConstraint,\n"
68	"\tyou must set zconsTime.\n");
69	painCave.isFatal = 1;
70	simError();
71	}
72
73	if (simParam->haveZconsTol()){
74	zconsTol_ = simParam->getZconsTol();
75	}
76	else{
77	zconsTol_ = 0.01;
78	sprintf(painCave.errMsg,
79	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
80	"\tOOPSE will use a default value of %f.\n"
81	"\tTo set the tolerance, use the zconsTol variable.\n",
82	zconsTol_);
83	painCave.isFatal = 0;
84	simError();
85	}
86
87	//set zcons gap
88	if (simParam->haveZConsGap()){
89	usingZconsGap_ = true;
90	zconsGap_ = simParam->getZconsGap();
91	}else {
92	usingZconsGap_ = false;
93	zconsGap_ = 0.0;
94	}
95
96	//set zcons fixtime
97	if (simParam->haveZConsFixTime()){
98	zconsFixingTime_ = simParam->getZconsFixtime();
99	} else {
100	zconsFixingTime_ = infiniteTime;
101	}
102
103	//set zconsUsingSMD
104	if (simParam->haveZConsUsingSMD()){
105	usingSMD_ = simParam->getZconsUsingSMD();
106	}else {
107	usingSMD_ =false;
108	}
109
110	zconsOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
111
112	//estimate the force constant of harmonical potential
113	Mat3x3d hmat = currSnapshot_->getHmat();
114	double halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2;
115	double targetTemp;
116	if (simParam->haveTargetTemp()) {
117	targetTemp = simParam->getTargetTemp();
118	} else {
119	targetTemp = 298.0;
120	}
121	double zforceConstant = OOPSEConstant::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox);
122
123	int nZconstraints = simParam->getNzConstraints();
124	ZconStamp** stamp = simParam->getZconStamp();
125	//
126	for (int i = 0; i < nZconstraints; i++){
127
128	ZconstraintParam param;
129	int zmolIndex = stamp[i]->getMolIndex();
130	if (stamp[i]->haveZpos()) {
131	param.zTargetPos = stamp[i]->getZpos();
132	} else {
133	param.zTargetPos = getZTargetPos(zmolIndex);
134	}
135
136	param.kz = zforceConstant * stamp[i]->getKratio();
137
138	if (stamp[i]->haveCantVel()) {
139	param.cantVel = stamp[i]->getCantVel();
140	} else {
141	param.cantVel = 0.0;
142	}
143
144	allZMolIndices_.insert(std::make_pair(zmolIndex, param));
145	}
146
147	//create fixedMols_, movingMols_ and unconsMols lists
148	update();
149
150	//calculate masss of unconstraint molecules in the whole system (never change during the simulation)
151	double totMassUnconsMols_local = 0.0;
152	std::vector<Molecule*>::iterator j;
153	for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) {
154	totMassUnconsMols_local += (*j)->getMass();
155	}
156	#ifndef IS_MPI
157	totMassUnconsMols_ = totMassUnconsMols_local;
158	#else
159	MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_DOUBLE,
160	MPI_SUM, MPI_COMM_WORLD);
161	#endif
162
163	// creat zconsWriter
164	fzOut = new ZConsWriter(info_, zconsOutput_.c_str());
165
166	if (!fzOut){
167	sprintf(painCave.errMsg, "Fail to create ZConsWriter\n");
168	painCave.isFatal = 1;
169	simError();
170	}
171
172	}
173
174	ZconstraintForceManager::~ZconstraintForceManager(){
175
176	if (fzOut){
177	delete fzOut;
178	}
179
180	}
181
182	void ZconstraintForceManager::update(){
183	fixedZMols_.clear();
184	movingZMols_.clear();
185	unzconsMols_.clear();
186
187	for (std::map<int, ZconstraintParam>::iterator i = allZMolIndices_.begin(); i != allZMolIndices_.end(); ++i) {
188	#ifdef IS_MPI
189	if (info_->getMolToProc(i->first) == worldRank) {
190	#endif
191	ZconstraintMol zmol;
192	zmol.mol = info_->getMoleculeByGlobalIndex(i->first);
193	assert(zmol.mol);
194	zmol.param = i->second;
195	zmol.cantPos = zmol.param.zTargetPos; /*@todo fixed me when zmol migrate, it is incorrect/
196	Vector3d com = zmol.mol->getCom();
197	double diff = fabs(zmol.param.zTargetPos - com[whichDirection]);
198	if (diff < zconsTol_) {
199	fixedZMols_.push_back(zmol);
200	} else {
201	movingZMols_.push_back(zmol);
202	}
203
204	#ifdef IS_MPI
205	}
206	#endif
207	}
208
209	calcTotalMassMovingZMols();
210
211	std::set<int> zmolSet;
212	for (std::list<ZconstraintMol>::iterator i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
213	zmolSet.insert(i->mol->getGlobalIndex());
214	}
215
216	for (std::list<ZconstraintMol>::iterator i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
217	zmolSet.insert(i->mol->getGlobalIndex());
218	}
219
220	SimInfo::MoleculeIterator mi;
221	Molecule* mol;
222	for(mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
223	if (zmolSet.find(mol->getGlobalIndex()) == zmolSet.end()) {
224	unzconsMols_.push_back(mol);
225	}
226	}
227
228	}
229
230	bool ZconstraintForceManager::isZMol(Molecule* mol){
231	return allZMolIndices_.find(mol->getGlobalIndex()) == allZMolIndices_.end() ? false : true;
232	}
233
234	void ZconstraintForceManager::init(){
235
236	//zero out the velocities of center of mass of unconstrained molecules
237	//and the velocities of center of mass of every single z-constrained molecueles
238	zeroVelocity();
239
240	currZconsTime_ = currSnapshot_->getTime();
241	}
242
243	void ZconstraintForceManager::calcForces(bool needPotential, bool needStress){
244	ForceManager::calcForces(needPotential, needStress);
245
246	if (usingZconsGap_){
247	updateZPos();
248	}
249
250	if (checkZConsState()){
251	zeroVelocity();
252	calcTotalMassMovingZMols();
253	}
254
255	//do zconstraint force;
256	if (haveFixedZMols()){
257	doZconstraintForce();
258	}
259
260	//use external force to move the molecules to the specified positions
261	if (haveMovingZMols()){
262	doHarmonic();
263	}
264
265	//write out forces and current positions of z-constraint molecules
266	if (currSnapshot_->getTime() >= currZconsTime_){
267	std::list<ZconstraintMol>::iterator i;
268	Vector3d com;
269	for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
270	com = i->mol->getCom();
271	i->zpos = com[whichDirection];
272	}
273
274	fzOut->writeFZ(fixedZMols_);
275	currZconsTime_ += zconsTime_;
276	}
277	}
278
279	void ZconstraintForceManager::zeroVelocity(){
280
281	Vector3d comVel;
282	Vector3d vel;
283	std::list<ZconstraintMol>::iterator i;
284	Molecule* mol;
285	StuntDouble* integrableObject;
286	Molecule::IntegrableObjectIterator ii;
287
288	//zero out the velocities of center of mass of fixed z-constrained molecules
289	for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
290	mol = i->mol;
291	comVel = mol->getComVel();
292	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
293	integrableObject = mol->nextIntegrableObject(ii)) {
294	vel = integrableObject->getVel();
295	vel[whichDirection] -= comVel[whichDirection];
296	integrableObject->setVel(vel);
297	}
298	}
299
300	// calculate the vz of center of mass of moving molecules(include unconstrained molecules
301	// and moving z-constrained molecules)
302	double pzMovingMols_local = 0.0;
303	double pzMovingMols;
304
305	for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
306	mol = i->mol;
307	comVel = mol->getComVel();
308	pzMovingMols_local += mol->getMass() * comVel[whichDirection];
309	}
310
311	std::vector<Molecule*>::iterator j;
312	for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) {
313	mol =*j;
314	comVel = mol->getComVel();
315	pzMovingMols_local += mol->getMass() * comVel[whichDirection];
316	}
317
318	#ifndef IS_MPI
319	pzMovingMols = pzMovingMols_local;
320	#else
321	MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_DOUBLE,
322	MPI_SUM, MPI_COMM_WORLD);
323	#endif
324
325	double vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_);
326
327	//modify the velocities of moving z-constrained molecuels
328	for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
329	mol = i->mol;
330	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
331	integrableObject = mol->nextIntegrableObject(ii)) {
332
333	vel = integrableObject->getVel();
334	vel[whichDirection] -= vzMovingMols;
335	integrableObject->setVel(vel);
336	}
337	}
338
339	//modify the velocites of unconstrained molecules
340	for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) {
341	mol =*j;
342	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
343	integrableObject = mol->nextIntegrableObject(ii)) {
344
345	vel = integrableObject->getVel();
346	vel[whichDirection] -= vzMovingMols;
347	integrableObject->setVel(vel);
348	}
349	}
350
351	}
352
353
354	void ZconstraintForceManager::doZconstraintForce(){
355	double totalFZ;
356	double totalFZ_local;
357	Vector3d com;
358	Vector3d force(0.0);
359
360	//constrain the molecules which do not reach the specified positions
361
362	//Zero Out the force of z-contrained molecules
363	totalFZ_local = 0;
364
365
366	//calculate the total z-contrained force of fixed z-contrained molecules
367	std::list<ZconstraintMol>::iterator i;
368	Molecule* mol;
369	StuntDouble* integrableObject;
370	Molecule::IntegrableObjectIterator ii;
371
372	for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
373	mol = i->mol;
374	i->fz = 0.0;
375	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376	integrableObject = mol->nextIntegrableObject(ii)) {
377
378	force = integrableObject->getFrc();
379	i->fz += force[whichDirection];
380	}
381	totalFZ_local += i->fz;
382	}
383
384	//calculate total z-constraint force
385	#ifdef IS_MPI
386	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
387	#else
388	totalFZ = totalFZ_local;
389	#endif
390
391
392	// apply negative to fixed z-constrained molecues;
393	for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
394	mol = i->mol;
395	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
396	integrableObject = mol->nextIntegrableObject(ii)) {
397
398	force[whichDirection] = -getZFOfFixedZMols(mol, integrableObject, i->fz);
399	integrableObject->addFrc(force);
400	}
401	}
402
403	//modify the forces of moving z-constrained molecules
404	for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
405	mol = i->mol;
406	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
407	integrableObject = mol->nextIntegrableObject(ii)) {
408
409	force[whichDirection] = -getZFOfMovingMols(mol,totalFZ);
410	integrableObject->addFrc(force);
411	}
412	}
413
414	//modify the forces of unconstrained molecules
415	std::vector<Molecule*>::iterator j;
416	for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) {
417	mol =*j;
418	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
419	integrableObject = mol->nextIntegrableObject(ii)) {
420
421	force[whichDirection] = -getZFOfMovingMols(mol, totalFZ);
422	integrableObject->addFrc(force);
423	}
424	}
425
426	}
427
428
429	void ZconstraintForceManager::doHarmonic(){
430	double totalFZ;
431	Vector3d force(0.0);
432	Vector3d com;
433	double totalFZ_local = 0;
434	std::list<ZconstraintMol>::iterator i;
435	StuntDouble* integrableObject;
436	Molecule::IntegrableObjectIterator ii;
437	Molecule* mol;
438	for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
439	mol = i->mol;
440	com = mol->getCom();
441	double resPos = usingSMD_? i->cantPos : i->param.zTargetPos;
442	double diff = com[whichDirection] - resPos;
443	double harmonicU = 0.5 * i->param.kz * diff * diff;
444	currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU;
445	double harmonicF = -i->param.kz * diff;
446	totalFZ_local += harmonicF;
447
448	//adjust force
449	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
450	integrableObject = mol->nextIntegrableObject(ii)) {
451
452	force[whichDirection] = getHFOfFixedZMols(mol, integrableObject, harmonicF);
453	integrableObject->addFrc(force);
454	}
455	}
456
457	#ifndef IS_MPI
458	totalFZ = totalFZ_local;
459	#else
460	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
461	#endif
462
463	//modify the forces of unconstrained molecules
464	std::vector<Molecule*>::iterator j;
465	for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) {
466	mol = *j;
467	for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
468	integrableObject = mol->nextIntegrableObject(ii)) {
469
470	force[whichDirection] = getHFOfUnconsMols(mol, totalFZ);
471	integrableObject->addFrc(force);
472	}
473	}
474
475	}
476
477	bool ZconstraintForceManager::checkZConsState(){
478	Vector3d com;
479	double diff;
480	int changed_local = 0;
481
482	std::list<ZconstraintMol>::iterator i;
483	std::list<ZconstraintMol>::iterator j;
484
485	std::list<ZconstraintMol> newMovingZMols;
486	for ( i = fixedZMols_.begin(); i != fixedZMols_.end();) {
487	com = i->mol->getCom();
488	diff = fabs(com[whichDirection] - i->param.zTargetPos);
489	if (diff > zconsTol_) {
490	if (usingZconsGap_) {
491	i->endFixingTime = infiniteTime;
492	}
493	j = i++;
494	newMovingZMols.push_back(*j);
495	fixedZMols_.erase(j);
496
497	changed_local = 1;
498	}else {
499	++i;
500	}
501	}
502
503	std::list<ZconstraintMol> newFixedZMols;
504	for ( i = movingZMols_.begin(); i != movingZMols_.end();) {
505	com = i->mol->getCom();
506	diff = fabs(com[whichDirection] - i->param.zTargetPos);
507	if (diff <= zconsTol_) {
508	if (usingZconsGap_) {
509	i->endFixingTime = currSnapshot_->getTime() + zconsFixingTime_;
510	}
511	//this moving zconstraint molecule is about to fixed
512	//moved this molecule to
513	j = i++;
514	newFixedZMols.push_back(*j);
515	movingZMols_.erase(j);
516	changed_local = 1;
517	}else {
518	++i;
519	}
520	}
521
522	//merge the lists
523	fixedZMols_.insert(fixedZMols_.end(), newFixedZMols.begin(), newFixedZMols.end());
524	movingZMols_.insert(movingZMols_.end(), newMovingZMols.begin(), newMovingZMols.end());
525
526	int changed;
527	#ifndef IS_MPI
528	changed = changed_local;
529	#else
530	MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
531	#endif
532
533	return (changed > 0);
534	}
535
536	bool ZconstraintForceManager::haveFixedZMols(){
537	int havingFixed;
538	int havingFixed_local = fixedZMols_.empty() ? 0 : 1;
539
540	#ifndef IS_MPI
541	havingFixed = havingFixed_local;
542	#else
543	MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
544	MPI_COMM_WORLD);
545	#endif
546
547	return havingFixed > 0;
548	}
549
550
551	bool ZconstraintForceManager::haveMovingZMols(){
552	int havingMoving_local;
553	int havingMoving;
554
555	havingMoving_local = movingZMols_.empty()? 0 : 1;
556
557	#ifndef IS_MPI
558	havingMoving = havingMoving_local;
559	#else
560	MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
561	MPI_COMM_WORLD);
562	#endif
563
564	return havingMoving > 0;
565	}
566
567	void ZconstraintForceManager::calcTotalMassMovingZMols(){
568
569	double totMassMovingZMols_local = 0.0;
570	std::list<ZconstraintMol>::iterator i;
571	for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
572	totMassMovingZMols_local += i->mol->getMass();
573	}
574
575	#ifdef IS_MPI
576	MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_DOUBLE,
577	MPI_SUM, MPI_COMM_WORLD);
578	#else
579	totMassMovingZMols_ = totMassMovingZMols_local;
580	#endif
581
582	}
583
584	double ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce){
585	return totalForce * sd->getMass() / mol->getMass();
586	}
587
588	double ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, double totalForce){
589	return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_);
590	}
591
592	double ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, double totalForce){
593	return totalForce * sd->getMass() / mol->getMass();
594	}
595
596	double ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, double totalForce){
597	return totalForce * mol->getMass() / totMassUnconsMols_;
598	}
599
600	void ZconstraintForceManager::updateZPos(){
601	double curTime = currSnapshot_->getTime();
602	std::list<ZconstraintMol>::iterator i;
603	for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) {
604	i->param.zTargetPos += zconsGap_;
605	}
606	}
607
608	void ZconstraintForceManager::updateCantPos(){
609	std::list<ZconstraintMol>::iterator i;
610	for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) {
611	i->cantPos += i->param.cantVel * dt_;
612	}
613	}
614
615	double ZconstraintForceManager::getZTargetPos(int index){
616	double zTargetPos;
617	#ifndef IS_MPI
618	Molecule* mol = info_->getMoleculeByGlobalIndex(index);
619	assert(mol);
620	Vector3d com = mol->getCom();
621	zTargetPos = com[whichDirection];
622	#else
623	int whicProc = info_->getMolToProc(index);
624	MPI_Bcast(&zTargetPos, 1, MPI_DOUBLE, whicProc, MPI_COMM_WORLD);
625	#endif
626	return zTargetPos;
627	}
628
629	}