3 |
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#include "integrators/Integrator.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
6 |
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6 |
> |
#include "utils/StringUtils.hpp" |
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namespace oopse { |
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ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info) { |
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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//set zcons gap |
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if (simParam->haveZConsGap()){ |
48 |
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usingZconsGap_ = true; |
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zconsGap_ = simParam->getZconsGap(); |
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}else { |
51 |
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zconsGap_ = false; |
51 |
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usingZconsGap_ = false; |
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zconsGap_ = 0.0; |
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} |
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|
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//set zcons fixtime |
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usingSMD_ =false; |
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} |
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|
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std::string zconsOutput = getPrefix(info_->getFinalConfigFileName()) + ".fz"; |
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> |
zconsOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".fz"; |
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|
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//estimate the force constant of harmonical potential |
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Mat3x3d hmat = currSnapshot_->getHmat(); |
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ZconstraintParam param; |
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int zmolIndex = stamp[i]->getMolIndex(); |
89 |
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if (stamp[i]->haveZpos()) { |
88 |
– |
param.zTargetPos = getZTargetPos(zmolIndex); |
89 |
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} else { |
90 |
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param.zTargetPos = stamp[i]->getZpos(); |
91 |
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} else { |
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param.zTargetPos = getZTargetPos(zmolIndex); |
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} |
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|
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param.kz = zforceConstant * stamp[i]->getKratio(); |
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#endif |
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// creat zconsWriter |
123 |
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fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
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> |
fzOut = new ZConsWriter(info_, zconsOutput_.c_str()); |
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|
125 |
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if (!fzOut){ |
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sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n"); |
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sprintf(painCave.errMsg, "Fail to create ZConsWriter\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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ZconstraintForceManager::~ZConstraint(){ |
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ZconstraintForceManager::~ZconstraintForceManager(){ |
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if (fzOut){ |
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delete fzOut; |
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fixedZMols_.clear(); |
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movingZMols_.clear(); |
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unzconsMols_.clear(); |
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146 |
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std::map<int, ZconstraintParam>::iterator i; |
145 |
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for (i = allZMolIndices_.begin(); i != allZMolIndices_.end(); ++i) { |
145 |
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|
146 |
> |
for (std::map<int, ZconstraintParam>::iterator i = allZMolIndices_.begin(); i != allZMolIndices_.end(); ++i) { |
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#ifdef IS_MPI |
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if (info_->getMolToProc(i->first) == worldRank) { |
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#endif |
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ZconstraintMol zmol; |
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zmol->mol = info_->getMoleculeByGlobalIndex(i->first); |
152 |
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assert(zmol->mol); |
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zmol->param = info_->getMoleculeByGlobalIndex(i->second); |
154 |
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zmol->cantPos = zmol->param->zTargetPos; /**@todo fixed me when zmol migrate, it is incorrect*/ |
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Vector3d com = zmol->mol->getCom(); |
156 |
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double diff = fabs(zmol->param->zTargetPos - com[whichDirection]); |
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zmol.mol = info_->getMoleculeByGlobalIndex(i->first); |
152 |
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assert(zmol.mol); |
153 |
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zmol.param = i->second; |
154 |
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zmol.cantPos = zmol.param.zTargetPos; /**@todo fixed me when zmol migrate, it is incorrect*/ |
155 |
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Vector3d com = zmol.mol->getCom(); |
156 |
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double diff = fabs(zmol.param.zTargetPos - com[whichDirection]); |
157 |
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if (diff < zconsTol_) { |
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fixedZMols_.push_back(zmol); |
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} else { |
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calcTotalMassMovingZMols(); |
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|
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std::set<int> zmolSet; |
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std::list<ZconstraintMol>::iterator i; |
171 |
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for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
171 |
> |
for (std::list<ZconstraintMol>::iterator i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
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zmolSet.insert(i->mol->getGlobalIndex()); |
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} |
174 |
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|
175 |
< |
for ( i = fixedZMols_.begin(); i != movingZMols_.end(); ++i) { |
175 |
> |
for (std::list<ZconstraintMol>::iterator i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
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zmolSet.insert(i->mol->getGlobalIndex()); |
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} |
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|
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SimInfo::MoleculeIterator mi; |
180 |
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Molecule* mol; |
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for(mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
182 |
< |
if (zmolSet->find(mol->getGlobalIndex()) == zmolSet.end()) { |
183 |
< |
unzconsMols_.push_back(zmolSet); |
182 |
> |
if (zmolSet.find(mol->getGlobalIndex()) == zmolSet.end()) { |
183 |
> |
unzconsMols_.push_back(mol); |
184 |
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} |
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} |
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|
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} |
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bool ZconstraintForceManager::isZMol(Molecule* mol){ |
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< |
return allZMolIndices.find(mol->getGlobalIndex()) == allZMolIndices_.end() ? false : true; |
190 |
> |
return allZMolIndices_.find(mol->getGlobalIndex()) == allZMolIndices_.end() ? false : true; |
191 |
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} |
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|
193 |
< |
void ZconstraintForceManager::integrate(){ |
193 |
> |
void ZconstraintForceManager::init(){ |
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|
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//zero out the velocities of center of mass of unconstrained molecules |
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//and the velocities of center of mass of every single z-constrained molecueles |
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zeroVelocity(); |
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|
199 |
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curZconsTime = zconsTime + info->getTime(); |
201 |
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|
202 |
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T::integrate(); |
199 |
> |
currZconsTime_ = currSnapshot_->getTime(); |
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} |
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< |
void ZconstraintForceManager::calcForce(bool needPotential, bool needStress){ |
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< |
ForceManager::calcForce(needPotential, needStress); |
202 |
> |
void ZconstraintForceManager::calcForces(bool needPotential, bool needStress){ |
203 |
> |
ForceManager::calcForces(needPotential, needStress); |
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|
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if (usingZconsGap_){ |
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updateZPos(); |
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|
209 |
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if (checkZConsState()){ |
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zeroVelocity(); |
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forcePolicy->update(); |
211 |
> |
calcTotalMassMovingZMols(); |
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} |
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//do zconstraint force; |
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} |
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|
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//write out forces and current positions of z-constraint molecules |
225 |
< |
if (currSnapshot_->getTime() >= curZconsTime_){ |
225 |
> |
if (currSnapshot_->getTime() >= currZconsTime_){ |
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std::list<ZconstraintMol>::iterator i; |
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Vector3d com; |
228 |
< |
for(i = fixedZMols_.begin(); i != fixedZMols_.end() ++i) { |
228 |
> |
for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
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com = i->mol->getCom(); |
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i->zpos = com[whichDirection]; |
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} |
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|
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fzOut->writeFZ(fixedZMols_); |
234 |
< |
curZconsTime_ += zconsTime_; |
234 |
> |
currZconsTime_ += zconsTime_; |
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} |
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} |
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|
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std::list<ZconstraintMol>::iterator i; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
245 |
< |
Molecule::IntegrableObjectIteraot ii; |
245 |
> |
Molecule::IntegrableObjectIterator ii; |
246 |
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|
247 |
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//zero out the velocities of center of mass of fixed z-constrained molecules |
248 |
< |
for(i = fixedZMols_.begin(); i != fixedZMols_.end() ++i) { |
248 |
> |
for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
249 |
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mol = i->mol; |
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comVel = mol->getComVel(); |
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for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
252 |
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integrableObject = mol->nextIntegrableObject(ii)) { |
253 |
+ |
vel = integrableObject->getVel(); |
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vel[whichDirection] -= comVel[whichDirection]; |
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integrableObject->setVel(vel); |
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} |
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|
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// calculate the vz of center of mass of moving molecules(include unconstrained molecules |
260 |
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// and moving z-constrained molecules) |
261 |
< |
double pzMovingMols_local; |
261 |
> |
double pzMovingMols_local = 0.0; |
262 |
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double pzMovingMols; |
263 |
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|
264 |
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for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
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std::vector<Molecule*>::iterator j; |
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for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) { |
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mol =*j; |
273 |
< |
comVel = mol->getCoMVel(); |
273 |
> |
comVel = mol->getComVel(); |
274 |
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pzMovingMols_local += mol->getMass() * comVel[whichDirection]; |
275 |
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} |
276 |
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|
281 |
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MPI_SUM, MPI_COMM_WORLD); |
282 |
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#endif |
283 |
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|
284 |
< |
double vzMovingMols = pzMovingMols / totMassMovingMols_; |
284 |
> |
double vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_); |
285 |
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|
286 |
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//modify the velocities of moving z-constrained molecuels |
287 |
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for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
290 |
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integrableObject = mol->nextIntegrableObject(ii)) { |
291 |
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|
292 |
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vel = integrableObject->getVel(); |
293 |
< |
vel[whichDirection] -= vzOfMovingMols; |
293 |
> |
vel[whichDirection] -= vzMovingMols; |
294 |
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integrableObject->setVel(vel); |
295 |
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} |
296 |
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} |
302 |
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integrableObject = mol->nextIntegrableObject(ii)) { |
303 |
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|
304 |
|
vel = integrableObject->getVel(); |
305 |
< |
vel[whichDirection] -= vzOfMovingMols; |
305 |
> |
vel[whichDirection] -= vzMovingMols; |
306 |
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integrableObject->setVel(vel); |
307 |
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} |
308 |
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} |
327 |
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std::list<ZconstraintMol>::iterator i; |
328 |
|
Molecule* mol; |
329 |
|
StuntDouble* integrableObject; |
330 |
< |
Molecule::IntegrableObjectIteraot ii; |
330 |
> |
Molecule::IntegrableObjectIterator ii; |
331 |
|
|
332 |
|
for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
333 |
|
mol = i->mol; |
336 |
– |
com = mol->getCom(); |
337 |
– |
|
334 |
|
i->fz = 0.0; |
339 |
– |
|
340 |
– |
totalFZ_local += harmonicF; |
341 |
– |
|
342 |
– |
//adjust force |
335 |
|
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
336 |
|
integrableObject = mol->nextIntegrableObject(ii)) { |
337 |
|
|
338 |
|
force = integrableObject->getFrc(); |
339 |
< |
i->fz += force[whichDirection] |
339 |
> |
i->fz += force[whichDirection]; |
340 |
|
} |
341 |
|
totalFZ_local += i->fz; |
342 |
|
} |
366 |
|
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
367 |
|
integrableObject = mol->nextIntegrableObject(ii)) { |
368 |
|
|
369 |
< |
force[whichDirection] = -getZFOfMovingMols(mol, integrableObject, totalFZ); |
369 |
> |
force[whichDirection] = -getZFOfMovingMols(mol,totalFZ); |
370 |
|
integrableObject->addFrc(force); |
371 |
|
} |
372 |
|
} |
378 |
|
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
379 |
|
integrableObject = mol->nextIntegrableObject(ii)) { |
380 |
|
|
381 |
< |
force[whichDirection] = -getZFOfMovingMols(mol, integrableObject, totalFZ); |
381 |
> |
force[whichDirection] = -getZFOfMovingMols(mol, totalFZ); |
382 |
|
integrableObject->addFrc(force); |
383 |
|
} |
384 |
|
} |
387 |
|
|
388 |
|
|
389 |
|
void ZconstraintForceManager::doHarmonic(){ |
398 |
– |
double harmonicU; |
399 |
– |
double harmonicF; |
400 |
– |
double diff; |
401 |
– |
double totalFZ_local; |
390 |
|
double totalFZ; |
403 |
– |
|
391 |
|
Vector3d force(0.0); |
392 |
|
Vector3d com; |
406 |
– |
|
393 |
|
double totalFZ_local = 0; |
408 |
– |
|
394 |
|
std::list<ZconstraintMol>::iterator i; |
395 |
+ |
StuntDouble* integrableObject; |
396 |
+ |
Molecule::IntegrableObjectIterator ii; |
397 |
|
Molecule* mol; |
411 |
– |
StuntDouble* integrableObject; |
412 |
– |
Molecule::IntegrableObjectIteraot ii; |
413 |
– |
|
398 |
|
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
399 |
|
mol = i->mol; |
400 |
< |
com = mol->getCom(); |
401 |
< |
diff = com[whichDirection] - resPos; |
402 |
< |
harmonicU = 0.5 * kz * diff * diff; |
403 |
< |
currSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU; |
404 |
< |
harmonicF = -kz * diff; |
400 |
> |
com = mol->getCom(); |
401 |
> |
double resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
402 |
> |
double diff = com[whichDirection] - resPos; |
403 |
> |
double harmonicU = 0.5 * i->param.kz * diff * diff; |
404 |
> |
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU; |
405 |
> |
double harmonicF = -i->param.kz * diff; |
406 |
|
totalFZ_local += harmonicF; |
407 |
|
|
408 |
|
//adjust force |
427 |
|
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
428 |
|
integrableObject = mol->nextIntegrableObject(ii)) { |
429 |
|
|
430 |
< |
force[whichDirection] = getHFOfUnconsMols(mol, harmonicF); |
430 |
> |
force[whichDirection] = getHFOfUnconsMols(mol, totalFZ); |
431 |
|
integrableObject->addFrc(force); |
432 |
|
} |
433 |
|
} |
447 |
|
com = i->mol->getCom(); |
448 |
|
diff = fabs(com[whichDirection] - i->param.zTargetPos); |
449 |
|
if (diff > zconsTol_) { |
465 |
– |
//this fixed zconstraint molecule is about to moving |
466 |
– |
//moved this molecule to |
467 |
– |
j = i++; |
468 |
– |
newMovingZMols.push_back(fixedZMols_.erase(j)); |
450 |
|
if (usingZconsGap_) { |
451 |
|
i->endFixingTime = infiniteTime; |
452 |
|
} |
453 |
+ |
j = i++; |
454 |
+ |
newMovingZMols.push_back(*j); |
455 |
+ |
fixedZMols_.erase(j); |
456 |
+ |
|
457 |
|
changed_local = 1; |
458 |
|
}else { |
459 |
|
++i; |
465 |
|
com = i->mol->getCom(); |
466 |
|
diff = fabs(com[whichDirection] - i->param.zTargetPos); |
467 |
|
if (diff <= zconsTol_) { |
483 |
– |
//this moving zconstraint molecule is about to fixed |
484 |
– |
//moved this molecule to |
485 |
– |
j = i++; |
486 |
– |
newFixedZMols.push_back(movingZMols_.erase(j)); |
468 |
|
if (usingZconsGap_) { |
469 |
|
i->endFixingTime = currSnapshot_->getTime() + zconsFixingTime_; |
470 |
|
} |
471 |
+ |
//this moving zconstraint molecule is about to fixed |
472 |
+ |
//moved this molecule to |
473 |
+ |
j = i++; |
474 |
+ |
newFixedZMols.push_back(*j); |
475 |
+ |
movingZMols_.erase(j); |
476 |
|
changed_local = 1; |
477 |
|
}else { |
478 |
|
++i; |
480 |
|
} |
481 |
|
|
482 |
|
//merge the lists |
483 |
< |
fixedZMols_.merge(newFixedZMols); |
484 |
< |
movingZMols_.merge(newFixedZMols); |
483 |
> |
fixedZMols_.insert(fixedZMols_.end(), newFixedZMols.begin(), newFixedZMols.end()); |
484 |
> |
movingZMols_.insert(movingZMols_.end(), newMovingZMols.begin(), newMovingZMols.end()); |
485 |
|
|
486 |
|
int changed; |
487 |
|
#ifndef IS_MPI |
536 |
|
MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_DOUBLE, |
537 |
|
MPI_SUM, MPI_COMM_WORLD); |
538 |
|
#else |
539 |
< |
totMassMovingZMols_ = massOfMovingZAtoms_local; |
539 |
> |
totMassMovingZMols_ = totMassMovingZMols_local; |
540 |
|
#endif |
541 |
|
|
542 |
|
} |
545 |
|
return totalForce * sd->getMass() / mol->getMass(); |
546 |
|
} |
547 |
|
|
548 |
< |
double ZconstraintForceManager::getZFOfMovingMols(StuntDouble*sd, double totalForce){ |
549 |
< |
return totalForce * sd->getMass() / (totMassUnconsMols_ + totMassMovingZMols_); |
548 |
> |
double ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, double totalForce){ |
549 |
> |
return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_); |
550 |
|
} |
551 |
|
|
552 |
|
double ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, double totalForce){ |
553 |
|
return totalForce * sd->getMass() / mol->getMass(); |
554 |
|
} |
555 |
|
|
556 |
< |
double ZconstraintForceManager::getHFOfUnconsMols(StuntDouble*sd, double totalForce){ |
557 |
< |
return totalForce * sd->getMass() / totMassUnconsMols_; |
556 |
> |
double ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, double totalForce){ |
557 |
> |
return totalForce * mol->getMass() / totMassUnconsMols_; |
558 |
|
} |
559 |
|
|
560 |
|
void ZconstraintForceManager::updateZPos(){ |
576 |
|
double zTargetPos; |
577 |
|
#ifndef IS_MPI |
578 |
|
Molecule* mol = info_->getMoleculeByGlobalIndex(index); |
579 |
< |
assert(!mol); |
579 |
> |
assert(mol); |
580 |
|
Vector3d com = mol->getCom(); |
581 |
|
zTargetPos = com[whichDirection]; |
582 |
|
#else |