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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. 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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* 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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* 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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|
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#include <cmath> |
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#include "visitors/ZconsVisitor.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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|
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ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){ |
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|
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visitorName = "ZConsVisitor"; |
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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->haveZconstraintTime()){ |
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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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"\tOOPSE 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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int nZconstraints = simParam->getNzConstraints(); |
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ZconStamp** stamp = simParam->getZconStamp(); |
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for (int i = 0; i < nZconstraints; i++){ |
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int zmolIndex = stamp[i]->getMolIndex(); |
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zmolStates_.insert(std::make_pair(zmolIndex, zsMoving)); |
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} |
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|
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|
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//fill zatomToZmol_ array |
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/** @todo only works for single version now*/ |
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std::map<int, ZConsState>::iterator j; |
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for (j = zmolStates_.begin(); j != zmolStates_.end(); ++j) { |
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Molecule* mol = info_->getMoleculeByGlobalIndex(j->first); |
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assert(mol != NULL); |
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Molecule::AtomIterator ai; |
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Atom* at; |
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for (at = mol->beginAtom(ai); at != NULL; at = mol->nextAtom(ai)) { |
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zatomToZmol_.insert(std::make_pair(at->getGlobalIndex(), mol->getGlobalIndex())); |
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} |
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} |
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|
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zconsFilename_ = getPrefix(info_->getFinalConfigFileName()) + ".fz"; |
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|
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zconsReader_ = new ZConsReader(info); |
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|
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if (zconsReader_->hasNextFrame()) |
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zconsReader_->readNextFrame(); |
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|
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} |
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|
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ZConsVisitor::~ZConsVisitor(){ |
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if(!zconsReader_) |
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delete zconsReader_; |
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|
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} |
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|
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void ZConsVisitor::visit(Atom* atom){ |
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std::string prefix; |
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if(isZconstraint(atom->getGlobalIndex(), prefix)) |
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internalVisit(atom, prefix); |
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} |
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|
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void ZConsVisitor::visit(DirectionalAtom* datom){ |
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std::string prefix; |
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|
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if(isZconstraint(datom->getGlobalIndex(), prefix)) |
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internalVisit(datom, prefix); |
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} |
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|
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void ZConsVisitor::visit(RigidBody* rb){ |
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std::string prefix; |
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std::vector<Atom*> atoms; |
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|
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atoms = rb->getAtoms(); |
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|
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if(isZconstraint(atoms[0]->getGlobalIndex(), prefix)) |
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internalVisit(rb, prefix); |
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} |
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|
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void ZConsVisitor::update(){ |
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Molecule* mol; |
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Vector3d com; |
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ZConsState state; |
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std::map<int, ZConsState>::iterator i; |
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for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) { |
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i->second = zsMoving; |
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} |
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|
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readZconsFile(currSnapshot_->getTime()); |
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|
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const std::vector<ZconsData>& fixedZmolData = zconsReader_->getFixedZMolData(); |
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std::vector<ZconsData>::const_iterator j; |
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for (j = fixedZmolData.begin(); j != fixedZmolData.end(); ++j) { |
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std::map<int, ZConsState>::iterator k = zmolStates_.find(j->zmolIndex); |
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assert(k != zmolStates_.end()); |
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k->second = zsFixed; |
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} |
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|
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} |
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|
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void ZConsVisitor::readZconsFile(double time) { |
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double tempTime; |
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while(zconsReader_->hasNextFrame()){ |
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tempTime = zconsReader_->getCurTime(); |
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if(tempTime >= time) { |
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return; |
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} |
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|
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zconsReader_->readNextFrame(); |
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} |
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} |
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|
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void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){ |
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GenericData* data; |
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AtomData* atomData; |
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AtomInfo* atomInfo; |
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std::vector<AtomInfo*>::iterator iter; |
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|
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//if there is not atom data, just skip it |
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data = sd->getPropertyByName("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL) |
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return; |
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} |
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else |
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return; |
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|
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for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter)) |
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(atomInfo->atomTypeName).insert(0, prefix); |
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} |
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|
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|
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bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){ |
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std::string prefixString[] = {"ZF", "ZM"}; |
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std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex); |
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if (i == zatomToZmol_.end() ){ |
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prefix = ""; |
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return false; |
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} else { |
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|
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std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second); |
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assert(j !=zmolStates_.end()); |
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prefix = prefixString[j->second]; |
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return true; |
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} |
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} |
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|
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const std::string ZConsVisitor::toString(){ |
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char buffer[65535]; |
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std::string result; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size()); |
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result += buffer; |
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|
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sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_); |
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result += buffer; |
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|
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sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_); |
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result += buffer; |
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|
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sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str()); |
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result += buffer; |
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|
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std::map<int, ZConsState>::iterator i; |
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int j = 0; |
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for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) { |
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sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first); |
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result += buffer; |
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} |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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|
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|
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}//namespace oopse |
