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/* |
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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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* 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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include "constraints/Rattle.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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namespace OpenMD { |
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|
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Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) { |
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> |
Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) { |
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|
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if (info_->getSimParams()->haveDt()) { |
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dt_ = info_->getSimParams()->getDt(); |
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if (info_->getNConstraints() > 0) |
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doRattle_ = true; |
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|
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Globals* simParams = info_->getSimParams(); |
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|
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if (simParams->haveDt()) { |
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dt_ = simParams->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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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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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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} |
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> |
if (simParams->haveConstraintTime()){ |
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constraintTime_ = simParams->getConstraintTime(); |
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} else { |
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constraintTime_ = simParams->getStatusTime(); |
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} |
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|
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void Rattle::constraintA() { |
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if (info_->getNConstraints() > 0) { |
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doConstraint(&Rattle::constraintPairA); |
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constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces"; |
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|
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// create ConstraintWriter |
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constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str()); |
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|
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if (!constraintWriter_){ |
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sprintf(painCave.errMsg, "Failed to create ConstraintWriter\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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void Rattle::constraintB() { |
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if (info_->getNConstraints() > 0) { |
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doConstraint(&Rattle::constraintPairB); |
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} |
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|
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void Rattle::constraintA() { |
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if (!doRattle_) return; |
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doConstraint(&Rattle::constraintPairA); |
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} |
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void Rattle::constraintB() { |
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if (!doRattle_) return; |
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doConstraint(&Rattle::constraintPairB); |
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|
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if (currentSnapshot_->getTime() >= currConstraintTime_){ |
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
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ConstraintPair* consPair; |
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Molecule::ConstraintPairIterator cpi; |
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std::list<ConstraintPair*> constraints; |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; |
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consPair = mol->nextConstraintPair(cpi)) { |
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|
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constraints.push_back(consPair); |
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} |
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} |
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|
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constraintWriter_->writeConstraintForces(constraints); |
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currConstraintTime_ += constraintTime_; |
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} |
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} |
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} |
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|
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void Rattle::doConstraint(ConstraintPairFuncPtr func) { |
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void Rattle::doConstraint(ConstraintPairFuncPtr func) { |
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if (!doRattle_) return; |
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|
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
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ConstraintElem* consElem; |
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ConstraintPair* consPair; |
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Molecule::ConstraintPairIterator cpi; |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) { |
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consElem->setMoved(true); |
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consElem->setMoving(false); |
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} |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (consElem = mol->beginConstraintElem(cei); consElem != NULL; |
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consElem = mol->nextConstraintElem(cei)) { |
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consElem->setMoved(true); |
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consElem->setMoving(false); |
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} |
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} |
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|
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//main loop of constraint algorithm |
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bool done = false; |
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int iteration = 0; |
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while(!done && iteration < maxConsIteration_){ |
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done = true; |
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> |
done = true; |
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|
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//loop over every constraint pair |
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> |
//loop over every constraint pair |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
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> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
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> |
mol = info_->nextMolecule(mi)) { |
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> |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; |
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> |
consPair = mol->nextConstraintPair(cpi)) { |
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|
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|
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//dispatch constraint algorithm |
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< |
if(consPair->isMoved()) { |
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int exeStatus = (this->*func)(consPair); |
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//dispatch constraint algorithm |
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if(consPair->isMoved()) { |
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int exeStatus = (this->*func)(consPair); |
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|
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switch(exeStatus){ |
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case consFail: |
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sprintf(painCave.errMsg, |
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"Constraint failure in Rattle::constrainA, Constraint Fail\n"); |
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painCave.isFatal = 1; |
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simError(); |
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switch(exeStatus){ |
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case consFail: |
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sprintf(painCave.errMsg, |
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"Constraint failure in Rattle::constrainA, " |
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"Constraint Fail\n"); |
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painCave.isFatal = 1; |
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simError(); |
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|
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< |
break; |
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case consSuccess: |
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//constrain the pair by moving two elements |
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done = false; |
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consPair->getConsElem1()->setMoving(true); |
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consPair->getConsElem2()->setMoving(true); |
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break; |
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case consAlready: |
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//current pair is already constrained, do not need to move the elements |
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break; |
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default: |
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sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status"); |
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painCave.isFatal = 1; |
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simError(); |
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break; |
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} |
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} |
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} |
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}//end for(iter->first()) |
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> |
break; |
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> |
case consSuccess: |
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> |
// constrain the pair by moving two elements |
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done = false; |
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consPair->getConsElem1()->setMoving(true); |
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consPair->getConsElem2()->setMoving(true); |
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break; |
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case consAlready: |
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// current pair is already constrained, do not need to |
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// move the elements |
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break; |
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default: |
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sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() " |
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"Error: unrecognized status"); |
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painCave.isFatal = 1; |
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simError(); |
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break; |
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> |
} |
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> |
} |
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> |
} |
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> |
}//end for(iter->first()) |
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|
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|
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< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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< |
for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) { |
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< |
consElem->setMoved(consElem->getMoving()); |
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< |
consElem->setMoving(false); |
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} |
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< |
} |
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> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
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> |
mol = info_->nextMolecule(mi)) { |
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> |
for (consElem = mol->beginConstraintElem(cei); consElem != NULL; |
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> |
consElem = mol->nextConstraintElem(cei)) { |
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> |
consElem->setMoved(consElem->getMoving()); |
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> |
consElem->setMoving(false); |
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> |
} |
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> |
} |
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|
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< |
iteration++; |
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> |
iteration++; |
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}//end while |
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|
|
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|
if (!done){ |
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sprintf(painCave.errMsg, |
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"Constraint failure in Rattle::constrainA, too many iterations: %d\n", |
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> |
"Constraint failure in Rattle::constrainA, " |
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> |
"too many iterations: %d\n", |
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iteration); |
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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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< |
int Rattle::constraintPairA(ConstraintPair* consPair){ |
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< |
ConstraintElem* consElem1 = consPair->getConsElem1(); |
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< |
ConstraintElem* consElem2 = consPair->getConsElem2(); |
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> |
int Rattle::constraintPairA(ConstraintPair* consPair){ |
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|
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< |
Vector3d posA = consElem1->getPos(); |
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< |
Vector3d posB = consElem2->getPos(); |
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> |
ConstraintElem* consElem1 = consPair->getConsElem1(); |
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> |
ConstraintElem* consElem2 = consPair->getConsElem2(); |
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|
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< |
Vector3d pab = posA -posB; |
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> |
Vector3d posA = consElem1->getPos(); |
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> |
Vector3d posB = consElem2->getPos(); |
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|
|
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< |
//periodic boundary condition |
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> |
Vector3d pab = posA -posB; |
| 209 |
|
|
| 210 |
< |
currentSnapshot_->wrapVector(pab); |
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> |
//periodic boundary condition |
| 211 |
|
|
| 212 |
< |
double pabsq = pab.lengthSquare(); |
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> |
currentSnapshot_->wrapVector(pab); |
| 213 |
|
|
| 214 |
< |
double rabsq = consPair->getConsDistSquare(); |
| 166 |
< |
double diffsq = rabsq - pabsq; |
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> |
RealType pabsq = pab.lengthSquare(); |
| 215 |
|
|
| 216 |
< |
// the original rattle code from alan tidesley |
| 217 |
< |
if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){ |
| 216 |
> |
RealType rabsq = consPair->getConsDistSquare(); |
| 217 |
> |
RealType diffsq = rabsq - pabsq; |
| 218 |
> |
|
| 219 |
> |
// the original rattle code from alan tidesley |
| 220 |
> |
if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){ |
| 221 |
|
|
| 222 |
< |
Vector3d oldPosA = consElem1->getPrevPos(); |
| 223 |
< |
Vector3d oldPosB = consElem2->getPrevPos(); |
| 222 |
> |
Vector3d oldPosA = consElem1->getPrevPos(); |
| 223 |
> |
Vector3d oldPosB = consElem2->getPrevPos(); |
| 224 |
|
|
| 225 |
< |
Vector3d rab = oldPosA - oldPosB; |
| 225 |
> |
Vector3d rab = oldPosA - oldPosB; |
| 226 |
|
|
| 227 |
< |
currentSnapshot_->wrapVector(rab); |
| 227 |
> |
currentSnapshot_->wrapVector(rab); |
| 228 |
|
|
| 229 |
< |
double rpab = dot(rab, pab); |
| 230 |
< |
double rpabsq = rpab * rpab; |
| 229 |
> |
RealType rpab = dot(rab, pab); |
| 230 |
> |
RealType rpabsq = rpab * rpab; |
| 231 |
|
|
| 232 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
| 233 |
< |
return consFail; |
| 234 |
< |
} |
| 232 |
> |
if (rpabsq < (rabsq * -diffsq)){ |
| 233 |
> |
return consFail; |
| 234 |
> |
} |
| 235 |
|
|
| 236 |
< |
double rma = 1.0 / consElem1->getMass(); |
| 237 |
< |
double rmb = 1.0 / consElem2->getMass(); |
| 236 |
> |
RealType rma = 1.0 / consElem1->getMass(); |
| 237 |
> |
RealType rmb = 1.0 / consElem2->getMass(); |
| 238 |
|
|
| 239 |
< |
double gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 239 |
> |
RealType gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 240 |
|
|
| 241 |
< |
Vector3d delta = rab * gab; |
| 241 |
> |
Vector3d delta = rab * gab; |
| 242 |
|
|
| 243 |
< |
//set atom1's position |
| 244 |
< |
posA += rma * delta; |
| 245 |
< |
consElem1->setPos(posA); |
| 243 |
> |
//set atom1's position |
| 244 |
> |
posA += rma * delta; |
| 245 |
> |
consElem1->setPos(posA); |
| 246 |
|
|
| 247 |
< |
//set atom2's position |
| 248 |
< |
posB -= rmb * delta; |
| 249 |
< |
consElem2->setPos(posB); |
| 247 |
> |
//set atom2's position |
| 248 |
> |
posB -= rmb * delta; |
| 249 |
> |
consElem2->setPos(posB); |
| 250 |
|
|
| 251 |
< |
delta /= dt_; |
| 251 |
> |
delta /= dt_; |
| 252 |
|
|
| 253 |
< |
//set atom1's velocity |
| 254 |
< |
Vector3d velA = consElem1->getVel(); |
| 255 |
< |
velA += rma * delta; |
| 256 |
< |
consElem1->setVel(velA); |
| 253 |
> |
//set atom1's velocity |
| 254 |
> |
Vector3d velA = consElem1->getVel(); |
| 255 |
> |
velA += rma * delta; |
| 256 |
> |
consElem1->setVel(velA); |
| 257 |
|
|
| 258 |
< |
//set atom2's velocity |
| 259 |
< |
Vector3d velB = consElem2->getVel(); |
| 260 |
< |
velB -= rmb * delta; |
| 261 |
< |
consElem2->setVel(velB); |
| 262 |
< |
|
| 263 |
< |
return consSuccess; |
| 264 |
< |
} |
| 265 |
< |
else |
| 266 |
< |
return consAlready; |
| 258 |
> |
//set atom2's velocity |
| 259 |
> |
Vector3d velB = consElem2->getVel(); |
| 260 |
> |
velB -= rmb * delta; |
| 261 |
> |
consElem2->setVel(velB); |
| 262 |
> |
|
| 263 |
> |
// report the constraint force back to the constraint pair: |
| 264 |
> |
consPair->setConstraintForce(gab); |
| 265 |
> |
return consSuccess; |
| 266 |
> |
} |
| 267 |
> |
else |
| 268 |
> |
return consAlready; |
| 269 |
|
|
| 270 |
< |
} |
| 270 |
> |
} |
| 271 |
|
|
| 272 |
|
|
| 273 |
< |
int Rattle::constraintPairB(ConstraintPair* consPair){ |
| 273 |
> |
int Rattle::constraintPairB(ConstraintPair* consPair){ |
| 274 |
|
ConstraintElem* consElem1 = consPair->getConsElem1(); |
| 275 |
|
ConstraintElem* consElem2 = consPair->getConsElem2(); |
| 276 |
|
|
| 287 |
|
|
| 288 |
|
currentSnapshot_->wrapVector(rab); |
| 289 |
|
|
| 290 |
< |
double rma = 1.0 / consElem1->getMass(); |
| 291 |
< |
double rmb = 1.0 / consElem2->getMass(); |
| 290 |
> |
RealType rma = 1.0 / consElem1->getMass(); |
| 291 |
> |
RealType rmb = 1.0 / consElem2->getMass(); |
| 292 |
|
|
| 293 |
< |
double rvab = dot(rab, dv); |
| 293 |
> |
RealType rvab = dot(rab, dv); |
| 294 |
|
|
| 295 |
< |
double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
| 295 |
> |
RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
| 296 |
|
|
| 297 |
|
if (fabs(gab) > consTolerance_){ |
| 298 |
|
Vector3d delta = rab * gab; |
| 303 |
|
velB -= rmb * delta; |
| 304 |
|
consElem2->setVel(velB); |
| 305 |
|
|
| 306 |
+ |
// report the constraint force back to the constraint pair: |
| 307 |
+ |
consPair->setConstraintForce(gab); |
| 308 |
|
return consSuccess; |
| 309 |
|
} |
| 310 |
|
else |
| 311 |
|
return consAlready; |
| 312 |
|
|
| 313 |
< |
} |
| 313 |
> |
} |
| 314 |
|
|
| 315 |
|
} |
