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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <cmath> |
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#include "constraints/ZconstraintForceManager.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "utils/simError.h" |
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#include "utils/PhysicalConstants.hpp" |
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#include "utils/StringUtils.hpp" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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namespace OpenMD { |
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ZconstraintForceManager::ZconstraintForceManager(SimInfo* info): ForceManager(info), infiniteTime(1e31) { |
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Globals* simParam = info_->getSimParams(); |
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|
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if (simParam->haveDt()){ |
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dt_ = simParam->getDt(); |
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} else { |
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sprintf(painCave.errMsg, |
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"Integrator Error: dt is not set\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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if (simParam->haveZconsTime()){ |
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zconsTime_ = simParam->getZconsTime(); |
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} |
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else{ |
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sprintf(painCave.errMsg, |
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"ZConstraint error: If you use a ZConstraint,\n" |
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"\tyou must set zconsTime.\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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if (simParam->haveZconsTol()){ |
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zconsTol_ = simParam->getZconsTol(); |
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} |
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else{ |
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zconsTol_ = 0.01; |
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sprintf(painCave.errMsg, |
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"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
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"\tOpenMD will use a default value of %f.\n" |
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"\tTo set the tolerance, use the zconsTol variable.\n", |
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zconsTol_); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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//set zcons gap |
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if (simParam->haveZconsGap()){ |
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usingZconsGap_ = true; |
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zconsGap_ = simParam->getZconsGap(); |
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}else { |
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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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if (simParam->haveZconsFixtime()){ |
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zconsFixingTime_ = simParam->getZconsFixtime(); |
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} else { |
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zconsFixingTime_ = infiniteTime; |
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} |
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|
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//set zconsUsingSMD |
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if (simParam->haveZconsUsingSMD()){ |
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usingSMD_ = simParam->getZconsUsingSMD(); |
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}else { |
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usingSMD_ =false; |
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} |
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|
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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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RealType halfOfLargestBox = std::max(hmat(0, 0), std::max(hmat(1, 1), hmat(2, 2))) /2; |
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RealType targetTemp; |
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if (simParam->haveTargetTemp()) { |
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targetTemp = simParam->getTargetTemp(); |
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} else { |
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targetTemp = 298.0; |
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} |
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RealType zforceConstant = PhysicalConstants::kb * targetTemp / (halfOfLargestBox * halfOfLargestBox); |
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|
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int nZconstraints = simParam->getNZconsStamps(); |
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std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
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// |
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for (int i = 0; i < nZconstraints; i++){ |
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|
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ZconstraintParam param; |
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int zmolIndex = stamp[i]->getMolIndex(); |
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if (stamp[i]->haveZpos()) { |
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param.zTargetPos = stamp[i]->getZpos(); |
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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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|
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if (stamp[i]->haveCantVel()) { |
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param.cantVel = stamp[i]->getCantVel(); |
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} else { |
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param.cantVel = 0.0; |
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} |
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|
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allZMolIndices_.insert(std::make_pair(zmolIndex, param)); |
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} |
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|
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//create fixedMols_, movingMols_ and unconsMols lists |
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update(); |
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|
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//calculate masss of unconstraint molecules in the whole system (never change during the simulation) |
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RealType totMassUnconsMols_local = 0.0; |
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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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totMassUnconsMols_local += (*j)->getMass(); |
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} |
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#ifndef IS_MPI |
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totMassUnconsMols_ = totMassUnconsMols_local; |
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#else |
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MPI_Allreduce(&totMassUnconsMols_local, &totMassUnconsMols_, 1, MPI_REALTYPE, |
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MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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|
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// creat zconsWriter |
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fzOut = new ZConsWriter(info_, zconsOutput_.c_str()); |
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|
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if (!fzOut){ |
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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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} |
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|
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ZconstraintForceManager::~ZconstraintForceManager(){ |
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|
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if (fzOut){ |
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delete fzOut; |
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} |
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|
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} |
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|
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void ZconstraintForceManager::update(){ |
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fixedZMols_.clear(); |
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movingZMols_.clear(); |
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unzconsMols_.clear(); |
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|
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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); |
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assert(zmol.mol); |
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zmol.param = i->second; |
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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(); |
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RealType diff = fabs(zmol.param.zTargetPos - com[whichDirection]); |
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if (diff < zconsTol_) { |
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fixedZMols_.push_back(zmol); |
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} else { |
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movingZMols_.push_back(zmol); |
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} |
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|
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#ifdef IS_MPI |
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} |
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#endif |
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} |
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|
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calcTotalMassMovingZMols(); |
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|
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std::set<int> zmolSet; |
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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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} |
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|
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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; |
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Molecule* mol; |
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for(mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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if (zmolSet.find(mol->getGlobalIndex()) == zmolSet.end()) { |
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unzconsMols_.push_back(mol); |
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} |
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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; |
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} |
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|
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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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|
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currZconsTime_ = currSnapshot_->getTime(); |
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} |
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|
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void ZconstraintForceManager::calcForces(){ |
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ForceManager::calcForces(); |
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|
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if (usingZconsGap_){ |
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updateZPos(); |
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} |
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|
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if (checkZConsState()){ |
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zeroVelocity(); |
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calcTotalMassMovingZMols(); |
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} |
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|
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//do zconstraint force; |
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if (haveFixedZMols()){ |
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doZconstraintForce(); |
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} |
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|
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//use external force to move the molecules to the specified positions |
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if (haveMovingZMols()){ |
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doHarmonic(); |
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} |
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|
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//write out forces and current positions of z-constraint molecules |
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if (currSnapshot_->getTime() >= currZconsTime_){ |
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std::list<ZconstraintMol>::iterator i; |
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Vector3d com; |
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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_); |
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currZconsTime_ += zconsTime_; |
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} |
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} |
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|
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void ZconstraintForceManager::zeroVelocity(){ |
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|
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Vector3d comVel; |
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Vector3d vel; |
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std::list<ZconstraintMol>::iterator i; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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Molecule::IntegrableObjectIterator ii; |
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|
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//zero out the velocities of center of mass of fixed z-constrained molecules |
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for(i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
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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; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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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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|
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// calculate the vz of center of mass of moving molecules(include unconstrained molecules |
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// and moving z-constrained molecules) |
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RealType pzMovingMols_local = 0.0; |
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RealType pzMovingMols; |
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|
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for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
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mol = i->mol; |
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comVel = mol->getComVel(); |
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pzMovingMols_local += mol->getMass() * comVel[whichDirection]; |
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} |
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|
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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; |
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comVel = mol->getComVel(); |
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pzMovingMols_local += mol->getMass() * comVel[whichDirection]; |
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} |
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|
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#ifndef IS_MPI |
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pzMovingMols = pzMovingMols_local; |
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#else |
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MPI_Allreduce(&pzMovingMols_local, &pzMovingMols, 1, MPI_REALTYPE, |
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MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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|
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RealType vzMovingMols = pzMovingMols / (totMassMovingZMols_ + totMassUnconsMols_); |
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|
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//modify the velocities of moving z-constrained molecuels |
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for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
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mol = i->mol; |
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for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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vel = integrableObject->getVel(); |
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vel[whichDirection] -= vzMovingMols; |
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integrableObject->setVel(vel); |
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} |
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} |
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|
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//modify the velocites of unconstrained molecules |
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for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) { |
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mol =*j; |
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for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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vel = integrableObject->getVel(); |
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vel[whichDirection] -= vzMovingMols; |
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integrableObject->setVel(vel); |
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} |
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} |
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|
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} |
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|
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|
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void ZconstraintForceManager::doZconstraintForce(){ |
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RealType totalFZ; |
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RealType totalFZ_local; |
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Vector3d com; |
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Vector3d force(0.0); |
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|
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//constrain the molecules which do not reach the specified positions |
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|
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//Zero Out the force of z-contrained molecules |
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totalFZ_local = 0; |
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|
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|
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//calculate the total z-contrained force of fixed z-contrained molecules |
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std::list<ZconstraintMol>::iterator i; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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Molecule::IntegrableObjectIterator ii; |
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|
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for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
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mol = i->mol; |
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i->fz = 0.0; |
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for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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force = integrableObject->getFrc(); |
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i->fz += force[whichDirection]; |
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} |
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totalFZ_local += i->fz; |
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} |
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|
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//calculate total z-constraint force |
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#ifdef IS_MPI |
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MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
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#else |
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totalFZ = totalFZ_local; |
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#endif |
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|
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|
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// apply negative to fixed z-constrained molecues; |
| 397 |
for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
| 398 |
mol = i->mol; |
| 399 |
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 400 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 401 |
|
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force[whichDirection] = -getZFOfFixedZMols(mol, integrableObject, i->fz); |
| 403 |
integrableObject->addFrc(force); |
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} |
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} |
| 406 |
|
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//modify the forces of moving z-constrained molecules |
| 408 |
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 409 |
mol = i->mol; |
| 410 |
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 411 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 412 |
|
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force[whichDirection] = -getZFOfMovingMols(mol,totalFZ); |
| 414 |
integrableObject->addFrc(force); |
| 415 |
} |
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} |
| 417 |
|
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//modify the forces of unconstrained molecules |
| 419 |
std::vector<Molecule*>::iterator j; |
| 420 |
for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) { |
| 421 |
mol =*j; |
| 422 |
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 423 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 424 |
|
| 425 |
force[whichDirection] = -getZFOfMovingMols(mol, totalFZ); |
| 426 |
integrableObject->addFrc(force); |
| 427 |
} |
| 428 |
} |
| 429 |
|
| 430 |
} |
| 431 |
|
| 432 |
|
| 433 |
void ZconstraintForceManager::doHarmonic(){ |
| 434 |
RealType totalFZ; |
| 435 |
Vector3d force(0.0); |
| 436 |
Vector3d com; |
| 437 |
RealType totalFZ_local = 0; |
| 438 |
std::list<ZconstraintMol>::iterator i; |
| 439 |
StuntDouble* integrableObject; |
| 440 |
Molecule::IntegrableObjectIterator ii; |
| 441 |
Molecule* mol; |
| 442 |
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 443 |
mol = i->mol; |
| 444 |
com = mol->getCom(); |
| 445 |
RealType resPos = usingSMD_? i->cantPos : i->param.zTargetPos; |
| 446 |
RealType diff = com[whichDirection] - resPos; |
| 447 |
RealType harmonicU = 0.5 * i->param.kz * diff * diff; |
| 448 |
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += harmonicU; |
| 449 |
RealType harmonicF = -i->param.kz * diff; |
| 450 |
totalFZ_local += harmonicF; |
| 451 |
|
| 452 |
//adjust force |
| 453 |
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 454 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 455 |
|
| 456 |
force[whichDirection] = getHFOfFixedZMols(mol, integrableObject, harmonicF); |
| 457 |
integrableObject->addFrc(force); |
| 458 |
} |
| 459 |
} |
| 460 |
|
| 461 |
#ifndef IS_MPI |
| 462 |
totalFZ = totalFZ_local; |
| 463 |
#else |
| 464 |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 465 |
#endif |
| 466 |
|
| 467 |
//modify the forces of unconstrained molecules |
| 468 |
std::vector<Molecule*>::iterator j; |
| 469 |
for ( j = unzconsMols_.begin(); j != unzconsMols_.end(); ++j) { |
| 470 |
mol = *j; |
| 471 |
for(integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 472 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 473 |
|
| 474 |
force[whichDirection] = getHFOfUnconsMols(mol, totalFZ); |
| 475 |
integrableObject->addFrc(force); |
| 476 |
} |
| 477 |
} |
| 478 |
|
| 479 |
} |
| 480 |
|
| 481 |
bool ZconstraintForceManager::checkZConsState(){ |
| 482 |
Vector3d com; |
| 483 |
RealType diff; |
| 484 |
int changed_local = 0; |
| 485 |
|
| 486 |
std::list<ZconstraintMol>::iterator i; |
| 487 |
std::list<ZconstraintMol>::iterator j; |
| 488 |
|
| 489 |
std::list<ZconstraintMol> newMovingZMols; |
| 490 |
for ( i = fixedZMols_.begin(); i != fixedZMols_.end();) { |
| 491 |
com = i->mol->getCom(); |
| 492 |
diff = fabs(com[whichDirection] - i->param.zTargetPos); |
| 493 |
if (diff > zconsTol_) { |
| 494 |
if (usingZconsGap_) { |
| 495 |
i->endFixingTime = infiniteTime; |
| 496 |
} |
| 497 |
j = i++; |
| 498 |
newMovingZMols.push_back(*j); |
| 499 |
fixedZMols_.erase(j); |
| 500 |
|
| 501 |
changed_local = 1; |
| 502 |
}else { |
| 503 |
++i; |
| 504 |
} |
| 505 |
} |
| 506 |
|
| 507 |
std::list<ZconstraintMol> newFixedZMols; |
| 508 |
for ( i = movingZMols_.begin(); i != movingZMols_.end();) { |
| 509 |
com = i->mol->getCom(); |
| 510 |
diff = fabs(com[whichDirection] - i->param.zTargetPos); |
| 511 |
if (diff <= zconsTol_) { |
| 512 |
if (usingZconsGap_) { |
| 513 |
i->endFixingTime = currSnapshot_->getTime() + zconsFixingTime_; |
| 514 |
} |
| 515 |
//this moving zconstraint molecule is about to fixed |
| 516 |
//moved this molecule to |
| 517 |
j = i++; |
| 518 |
newFixedZMols.push_back(*j); |
| 519 |
movingZMols_.erase(j); |
| 520 |
changed_local = 1; |
| 521 |
}else { |
| 522 |
++i; |
| 523 |
} |
| 524 |
} |
| 525 |
|
| 526 |
//merge the lists |
| 527 |
fixedZMols_.insert(fixedZMols_.end(), newFixedZMols.begin(), newFixedZMols.end()); |
| 528 |
movingZMols_.insert(movingZMols_.end(), newMovingZMols.begin(), newMovingZMols.end()); |
| 529 |
|
| 530 |
int changed; |
| 531 |
#ifndef IS_MPI |
| 532 |
changed = changed_local; |
| 533 |
#else |
| 534 |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 535 |
#endif |
| 536 |
|
| 537 |
return (changed > 0); |
| 538 |
} |
| 539 |
|
| 540 |
bool ZconstraintForceManager::haveFixedZMols(){ |
| 541 |
int havingFixed; |
| 542 |
int havingFixed_local = fixedZMols_.empty() ? 0 : 1; |
| 543 |
|
| 544 |
#ifndef IS_MPI |
| 545 |
havingFixed = havingFixed_local; |
| 546 |
#else |
| 547 |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM, |
| 548 |
MPI_COMM_WORLD); |
| 549 |
#endif |
| 550 |
|
| 551 |
return havingFixed > 0; |
| 552 |
} |
| 553 |
|
| 554 |
|
| 555 |
bool ZconstraintForceManager::haveMovingZMols(){ |
| 556 |
int havingMoving_local; |
| 557 |
int havingMoving; |
| 558 |
|
| 559 |
havingMoving_local = movingZMols_.empty()? 0 : 1; |
| 560 |
|
| 561 |
#ifndef IS_MPI |
| 562 |
havingMoving = havingMoving_local; |
| 563 |
#else |
| 564 |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM, |
| 565 |
MPI_COMM_WORLD); |
| 566 |
#endif |
| 567 |
|
| 568 |
return havingMoving > 0; |
| 569 |
} |
| 570 |
|
| 571 |
void ZconstraintForceManager::calcTotalMassMovingZMols(){ |
| 572 |
|
| 573 |
RealType totMassMovingZMols_local = 0.0; |
| 574 |
std::list<ZconstraintMol>::iterator i; |
| 575 |
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 576 |
totMassMovingZMols_local += i->mol->getMass(); |
| 577 |
} |
| 578 |
|
| 579 |
#ifdef IS_MPI |
| 580 |
MPI_Allreduce(&totMassMovingZMols_local, &totMassMovingZMols_, 1, MPI_REALTYPE, |
| 581 |
MPI_SUM, MPI_COMM_WORLD); |
| 582 |
#else |
| 583 |
totMassMovingZMols_ = totMassMovingZMols_local; |
| 584 |
#endif |
| 585 |
|
| 586 |
} |
| 587 |
|
| 588 |
RealType ZconstraintForceManager::getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce){ |
| 589 |
return totalForce * sd->getMass() / mol->getMass(); |
| 590 |
} |
| 591 |
|
| 592 |
RealType ZconstraintForceManager::getZFOfMovingMols(Molecule* mol, RealType totalForce){ |
| 593 |
return totalForce * mol->getMass() / (totMassUnconsMols_ + totMassMovingZMols_); |
| 594 |
} |
| 595 |
|
| 596 |
RealType ZconstraintForceManager::getHFOfFixedZMols(Molecule* mol, StuntDouble*sd, RealType totalForce){ |
| 597 |
return totalForce * sd->getMass() / mol->getMass(); |
| 598 |
} |
| 599 |
|
| 600 |
RealType ZconstraintForceManager::getHFOfUnconsMols(Molecule* mol, RealType totalForce){ |
| 601 |
return totalForce * mol->getMass() / totMassUnconsMols_; |
| 602 |
} |
| 603 |
|
| 604 |
void ZconstraintForceManager::updateZPos(){ |
| 605 |
RealType curTime = currSnapshot_->getTime(); |
| 606 |
std::list<ZconstraintMol>::iterator i; |
| 607 |
for ( i = fixedZMols_.begin(); i != fixedZMols_.end(); ++i) { |
| 608 |
i->param.zTargetPos += zconsGap_; |
| 609 |
} |
| 610 |
} |
| 611 |
|
| 612 |
void ZconstraintForceManager::updateCantPos(){ |
| 613 |
std::list<ZconstraintMol>::iterator i; |
| 614 |
for ( i = movingZMols_.begin(); i != movingZMols_.end(); ++i) { |
| 615 |
i->cantPos += i->param.cantVel * dt_; |
| 616 |
} |
| 617 |
} |
| 618 |
|
| 619 |
RealType ZconstraintForceManager::getZTargetPos(int index){ |
| 620 |
RealType zTargetPos; |
| 621 |
#ifndef IS_MPI |
| 622 |
Molecule* mol = info_->getMoleculeByGlobalIndex(index); |
| 623 |
assert(mol); |
| 624 |
Vector3d com = mol->getCom(); |
| 625 |
zTargetPos = com[whichDirection]; |
| 626 |
#else |
| 627 |
int whicProc = info_->getMolToProc(index); |
| 628 |
MPI_Bcast(&zTargetPos, 1, MPI_REALTYPE, whicProc, MPI_COMM_WORLD); |
| 629 |
#endif |
| 630 |
return zTargetPos; |
| 631 |
} |
| 632 |
|
| 633 |
} |
