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#include "visitors/ZconsVisitor.hpp" |
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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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|
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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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#include "types/ZconsStamp.hpp" |
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namespace oopse { |
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|
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ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), zconsReader(NULL){ |
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GenericData* data; |
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DoubleGenericData* tolerance; |
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ZConsParaData* zConsParaData; |
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StringGenericData* filename; |
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DoubleGenericData* sampleTime; |
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vector<ZConsParaItem>* parameters; |
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ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){ |
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|
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this->info = info; |
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visitorName = "ZConsVisitor"; |
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|
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//retrieve tolerance for z-constraint molecuels |
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data = info->getProperty(ZCONSTOL_ID); |
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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 (!data){ |
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cerr << "Can not get zconstraint tolerance from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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} |
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else{ |
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tolerance = dynamic_cast<DoubleGenericData*>(data); |
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|
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if (!tolerance){ |
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cerr << "Can not get zconstraint tolerance from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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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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zconsTol = tolerance->getData(); |
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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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|
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//retrieve sample time of z-contraint |
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data = info->getProperty(ZCONSTIME_ID); |
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|
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if (!data){ |
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cerr << "Can not get zcons time from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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} |
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else{ |
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sampleTime = dynamic_cast<DoubleGenericData*>(data); |
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|
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if (!sampleTime){ |
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cerr << "Can not get zcons time from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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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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zconsTime = sampleTime->getData(); |
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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->getNZconsStamps(); |
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std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
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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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//retrieve index of z-constraint molecules |
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data = info->getProperty(ZCONSPARADATA_ID); |
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if (!data){ |
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cerr << "Can not get index of z-constraint molecules from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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} |
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else{ |
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zConsParaData = dynamic_cast<ZConsParaData*>(data); |
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|
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if (!zConsParaData){ |
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cerr << "Can not get index of z-constraint molecules from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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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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else{ |
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vector<ZConsParaItem>::iterator i; |
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Molecule* mol; |
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|
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parameters = zConsParaData->getData(); |
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for(i = parameters->begin(); i != parameters->end(); ++i){ |
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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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mol = findZconsMol(i->zconsIndex); |
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if(mol != NULL) |
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zconsMol.push_back(mol); |
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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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} |
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|
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if(zconsMol.size() < 1){ |
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cerr << "number of zconstraint molecules is less than one" << endl; |
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< |
haveZcons = false; |
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return; |
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} |
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|
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}//end if (!zConsParaData) |
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|
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}//end if (!data |
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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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//retrieve output filename of z force |
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data = info->getProperty(ZCONSFILENAME_ID); |
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if (!data){ |
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cerr << "Can not get filename of z-constraint output from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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|
} |
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else{ |
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filename = dynamic_cast<StringGenericData*>(data); |
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|
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if (!filename){ |
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cerr << "Can not get filename of z-constraint output from SimInfo" << endl; |
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haveZcons = false; |
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return; |
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} |
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else{ |
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zconsFilename = filename->getData(); |
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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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zconsReader = new ZConsReader(info); |
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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 (zconsReader->hasNextFrame()) |
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zconsReader->readNextFrame(); |
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|
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haveZcons = true; |
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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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< |
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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> |
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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< |
void ZConsVisitor::visit(Atom* atom){ |
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string prefix; |
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if(isZconstraint(atom->getIndex(), prefix)) |
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internalVisit(atom, prefix); |
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} |
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atoms = rb->getAtoms(); |
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|
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< |
void ZConsVisitor::visit(DirectionalAtom* datom){ |
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< |
string prefix; |
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< |
|
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< |
if(isZconstraint(datom->getIndex(), prefix)) |
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internalVisit(datom, prefix); |
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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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> |
} |
| 138 |
|
|
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< |
void ZConsVisitor::visit(RigidBody* rb){ |
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< |
string prefix; |
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< |
vector<Atom*> atoms; |
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< |
|
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< |
atoms = rb->getAtoms(); |
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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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> |
} |
| 157 |
|
|
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< |
if(isZconstraint(atoms[0]->getIndex(), prefix)) |
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< |
internalVisit(rb, prefix); |
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< |
} |
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> |
} |
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|
|
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< |
Molecule* ZConsVisitor::findZconsMol(int index){ |
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< |
Molecule* mols; |
| 162 |
< |
mols = info->molecules; |
| 163 |
< |
for(int i =0; i < info->n_mol; i++) |
| 164 |
< |
if(index == mols[i].getMyIndex()) |
| 165 |
< |
return &mols[i]; |
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> |
void ZConsVisitor::readZconsFile(RealType time) { |
| 161 |
> |
RealType tempTime; |
| 162 |
> |
while(zconsReader_->hasNextFrame()){ |
| 163 |
> |
tempTime = zconsReader_->getCurTime(); |
| 164 |
> |
if(tempTime >= time) { |
| 165 |
> |
return; |
| 166 |
> |
} |
| 167 |
> |
|
| 168 |
> |
zconsReader_->readNextFrame(); |
| 169 |
> |
} |
| 170 |
> |
} |
| 171 |
|
|
| 172 |
< |
return NULL; |
| 173 |
< |
} |
| 172 |
> |
void ZConsVisitor::internalVisit(StuntDouble* sd, const std::string& prefix){ |
| 173 |
> |
GenericData* data; |
| 174 |
> |
AtomData* atomData; |
| 175 |
> |
AtomInfo* atomInfo; |
| 176 |
> |
std::vector<AtomInfo*>::iterator iter; |
| 177 |
|
|
| 178 |
< |
void ZConsVisitor::update(){ |
| 179 |
< |
Molecule* mol; |
| 180 |
< |
double com[3]; |
| 181 |
< |
ZConsState state; |
| 182 |
< |
Atom** atoms; |
| 183 |
< |
int natoms; |
| 184 |
< |
|
| 171 |
< |
getZconsPos(info->currentTime); |
| 172 |
< |
|
| 173 |
< |
for(size_t i = 0; i < zconsMol.size(); i++){ |
| 174 |
< |
zconsMol[i]->getCOM(com); |
| 175 |
< |
|
| 176 |
< |
if(fabs(com[2] - zconsPos[i]) < zconsTol) |
| 177 |
< |
state = zsFixed; |
| 178 |
> |
//if there is not atom data, just skip it |
| 179 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
| 180 |
> |
if(data != NULL){ |
| 181 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 182 |
> |
if(atomData == NULL) |
| 183 |
> |
return; |
| 184 |
> |
} |
| 185 |
|
else |
| 186 |
< |
state = zsMoving; |
| 186 |
> |
return; |
| 187 |
|
|
| 188 |
< |
//update the state of zconstraint atom |
| 189 |
< |
natoms = zconsMol[i]->getNAtoms(); |
| 183 |
< |
atoms = zconsMol[i]->getMyAtoms(); |
| 184 |
< |
for(int j =0; j < natoms; j++) |
| 185 |
< |
zconsState[atoms[j]->getIndex()] = state; |
| 188 |
> |
for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter)) |
| 189 |
> |
(atomInfo->atomTypeName).insert(0, prefix); |
| 190 |
|
} |
| 187 |
– |
|
| 188 |
– |
} |
| 191 |
|
|
| 190 |
– |
void ZConsVisitor::getZconsPos(double time){ |
| 192 |
|
|
| 193 |
< |
vector<double> tempPos; |
| 194 |
< |
vector<double> prevPos; |
| 195 |
< |
double tempTime; |
| 193 |
> |
bool ZConsVisitor::isZconstraint(int atomIndex, std::string& prefix){ |
| 194 |
> |
std::string prefixString[] = {"ZF", "ZM"}; |
| 195 |
> |
std::map<int, int>::iterator i = zatomToZmol_.find(atomIndex); |
| 196 |
> |
if (i == zatomToZmol_.end() ){ |
| 197 |
> |
prefix = ""; |
| 198 |
> |
return false; |
| 199 |
> |
} else { |
| 200 |
|
|
| 201 |
< |
while(true){ |
| 202 |
< |
tempTime = zconsReader->getCurTime(); |
| 203 |
< |
|
| 204 |
< |
zconsPos = zconsReader->getZConsPos(); |
| 205 |
< |
|
| 201 |
< |
if(tempTime >= time) |
| 202 |
< |
return; |
| 203 |
< |
|
| 204 |
< |
zconsReader->readNextFrame(); |
| 205 |
< |
|
| 206 |
< |
} |
| 207 |
< |
|
| 208 |
< |
} |
| 209 |
< |
|
| 210 |
< |
void ZConsVisitor::internalVisit(StuntDouble* sd, const string& prefix){ |
| 211 |
< |
GenericData* data; |
| 212 |
< |
AtomData* atomData; |
| 213 |
< |
AtomInfo* atomInfo; |
| 214 |
< |
vector<AtomInfo*>::iterator iter; |
| 215 |
< |
|
| 216 |
< |
|
| 217 |
< |
//if there is not atom data, just skip it |
| 218 |
< |
data = sd->getProperty("ATOMDATA"); |
| 219 |
< |
if(data != NULL){ |
| 220 |
< |
atomData = dynamic_cast<AtomData*>(data); |
| 221 |
< |
if(atomData == NULL) |
| 222 |
< |
return; |
| 201 |
> |
std::map<int, ZConsState>::iterator j = zmolStates_.find(i->second); |
| 202 |
> |
assert(j !=zmolStates_.end()); |
| 203 |
> |
prefix = prefixString[j->second]; |
| 204 |
> |
return true; |
| 205 |
> |
} |
| 206 |
|
} |
| 224 |
– |
else |
| 225 |
– |
return; |
| 207 |
|
|
| 208 |
< |
for(atomInfo = atomData->beginAtomInfo(iter); atomInfo; atomInfo = atomData->nextAtomInfo(iter)) |
| 209 |
< |
(atomInfo->AtomType).insert(0, prefix); |
| 210 |
< |
} |
| 208 |
> |
const std::string ZConsVisitor::toString(){ |
| 209 |
> |
char buffer[65535]; |
| 210 |
> |
std::string result; |
| 211 |
|
|
| 212 |
+ |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 213 |
+ |
result += buffer; |
| 214 |
|
|
| 215 |
< |
bool ZConsVisitor::isZconstraint(int index, string& prefix){ |
| 216 |
< |
map<int, ZConsState>::iterator i; |
| 234 |
< |
string prefixString[] = {"ZF", "ZM"}; |
| 235 |
< |
|
| 236 |
< |
i = zconsState.find(index); |
| 237 |
< |
if(i !=zconsState.end()){ |
| 238 |
< |
prefix = prefixString[(*i).second]; |
| 239 |
< |
return true; |
| 240 |
< |
} |
| 241 |
< |
else{ |
| 242 |
< |
prefix = ""; |
| 243 |
< |
return false; |
| 244 |
< |
} |
| 245 |
< |
} |
| 215 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 216 |
> |
result += buffer; |
| 217 |
|
|
| 218 |
< |
const string ZConsVisitor::toString(){ |
| 219 |
< |
char buffer[65535]; |
| 249 |
< |
string result; |
| 250 |
< |
|
| 251 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 252 |
< |
result += buffer; |
| 218 |
> |
sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size()); |
| 219 |
> |
result += buffer; |
| 220 |
|
|
| 221 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 222 |
< |
result += buffer; |
| 256 |
< |
|
| 257 |
< |
sprintf(buffer , "number of zconstraint molecule: %d\n", zconsMol.size()); |
| 258 |
< |
result += buffer; |
| 221 |
> |
sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_); |
| 222 |
> |
result += buffer; |
| 223 |
|
|
| 224 |
< |
sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol); |
| 225 |
< |
result += buffer; |
| 224 |
> |
sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime_); |
| 225 |
> |
result += buffer; |
| 226 |
|
|
| 227 |
< |
sprintf(buffer , "zconstraint sample time = %lf\n", zconsTime); |
| 228 |
< |
result += buffer; |
| 227 |
> |
sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename_.c_str()); |
| 228 |
> |
result += buffer; |
| 229 |
|
|
| 230 |
< |
sprintf(buffer , "zconstraint output filename = %s\n", zconsFilename.c_str()); |
| 231 |
< |
result += buffer; |
| 230 |
> |
std::map<int, ZConsState>::iterator i; |
| 231 |
> |
int j = 0; |
| 232 |
> |
for ( i = zmolStates_.begin(); i != zmolStates_.end(); ++i) { |
| 233 |
> |
sprintf(buffer ,"zconstraint molecule[%d] = %d\n", j++, i->first); |
| 234 |
> |
result += buffer; |
| 235 |
> |
} |
| 236 |
|
|
| 237 |
< |
for(size_t i = 0; i < zconsMol.size(); ++i){ |
| 270 |
< |
sprintf(buffer ,"zconstraint molecule[%d] = %d\n", i, zconsMol[i]->getMyIndex()); |
| 237 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 238 |
|
result += buffer; |
| 239 |
|
|
| 240 |
+ |
return result; |
| 241 |
|
} |
| 242 |
|
|
| 275 |
– |
|
| 276 |
– |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 277 |
– |
result += buffer; |
| 243 |
|
|
| 279 |
– |
return result; |
| 280 |
– |
} |
| 281 |
– |
|
| 282 |
– |
|
| 244 |
|
}//namespace oopse |
