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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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#include "visitors/RigidBodyVisitor.hpp" |
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#include "visitors/OtherVisitor.hpp" |
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#include "visitors/ZconsVisitor.hpp" |
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#include "selection/SelectionEvaluator.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include "visitors/LipidTransVisitor.hpp" |
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#include "visitors/AtomNameVisitor.hpp" |
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using namespace oopse; |
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int main(int argc, char* argv[]){ |
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gengetopt_args_info args_info; |
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std::string dumpFileName; |
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std::string mdFileName; |
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std::string xyzFileName; |
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//parse the command line option |
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exit(1); |
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} |
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mdFileName = dumpFileName; |
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mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
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if (args_info.output_given){ |
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xyzFileName = args_info.output_arg; |
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} else { |
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//parse md file and set up the system |
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SimCreator creator; |
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SimInfo* info = creator.createSim(mdFileName, false); |
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SimInfo* info = creator.createSim(dumpFileName, false); |
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//creat visitor list |
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//create visitor list |
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CompositeVisitor* compositeVisitor = new CompositeVisitor(); |
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//creat ignore visitor |
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if(args_info.ignore_given ||args_info.water_flag){ |
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IgnoreVisitor* ignoreVisitor = new IgnoreVisitor(); |
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for(int i = 0; i < args_info.ignore_given; i++) |
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ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]); |
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//ignore water |
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if(args_info.water_flag){ |
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ignoreVisitor->addIgnoreType("SSD"); |
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ignoreVisitor->addIgnoreType("SSD1"); |
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ignoreVisitor->addIgnoreType("SSD_E"); |
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ignoreVisitor->addIgnoreType("SSD_RF"); |
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ignoreVisitor->addIgnoreType("TIP3P_RB_0"); |
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ignoreVisitor->addIgnoreType("TIP4P_RB_0"); |
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ignoreVisitor->addIgnoreType("TIP5P_RB_0"); |
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ignoreVisitor->addIgnoreType("SPCE_RB_0"); |
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ignoreVisitor->addIgnoreType("DPD_RB_0"); |
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} |
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compositeVisitor->addVisitor(ignoreVisitor, 1000); |
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} |
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//creat RigidBody Visitor |
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//create RigidBody Visitor |
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if(args_info.rigidbody_flag){ |
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RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info); |
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compositeVisitor->addVisitor(rbCOMVisitor, 900); |
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} |
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//compositeVisitor->addVisitor(lipidVisitor, 900); |
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//creat SSD atom visitor |
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//create SSD atom visitor |
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SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info); |
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compositeVisitor->addVisitor(ssdVisitor, 800); |
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LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info); |
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compositeVisitor->addVisitor(linearVisitor, 750); |
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if (args_info.gb_given) { |
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linearVisitor->addGayBerneAtomType(args_info.gb_arg); |
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} |
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//creat default atom visitor |
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GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info); |
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compositeVisitor->addVisitor(gbLipidVisitor, 740); |
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Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info); |
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compositeVisitor->addVisitor(ring5Visitor, 730); |
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HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info); |
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compositeVisitor->addVisitor(headVisitor, 720); |
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//create default atom visitor |
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DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info); |
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compositeVisitor->addVisitor(defaultAtomVisitor, 700); |
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//creat waterType visitor |
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if(args_info.watertype_flag){ |
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WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
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compositeVisitor->addVisitor(waterTypeVisitor, 600); |
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// if we gave the -w option, we want to skip the waters: |
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std::cerr << "-w flag was set to:" << args_info.water_given << "\n"; |
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if (!args_info.water_given) { |
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//create waterType visitor |
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if(args_info.watertype_flag){ |
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WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
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compositeVisitor->addVisitor(waterTypeVisitor, 600); |
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} |
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} |
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if (args_info.basetype_flag) { |
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AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info); |
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compositeVisitor->addVisitor(atomNameVisitor, 550); |
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} |
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//create ZconsVisitor |
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if(args_info.zconstraint_flag){ |
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} |
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} |
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//creat wrapping visitor |
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//create wrapping visitor |
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if(args_info.periodicBox_flag){ |
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WrappingVisitor* wrappingVisitor = new WrappingVisitor(info); |
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compositeVisitor->addVisitor(wrappingVisitor, 400); |
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} |
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//creat replicate visitor |
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//if(args_info.periodicBox_flag){ |
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// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info); |
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// compositeVisitor->addVisitor(wrappingVisitor, 400); |
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//} |
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//create replicate visitor |
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if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){ |
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Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg); |
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ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt); |
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compositeVisitor->addVisitor(replicateVisitor, 300); |
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} |
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//creat xyzVisitor |
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XYZVisitor* xyzVisitor = new XYZVisitor(info); |
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//create rotation visitor |
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if (args_info.refsele_given&& args_info.originsele_given) { |
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compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250); |
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} else if (args_info.refsele_given || args_info.originsele_given) { |
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std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl; |
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exit(1); |
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} |
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//create xyzVisitor |
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XYZVisitor* xyzVisitor; |
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if (args_info.selection_given) { |
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xyzVisitor = new XYZVisitor(info, args_info.selection_arg); |
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} else { |
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xyzVisitor = new XYZVisitor(info); |
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} |
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if(args_info.printPosOnly_flag){ |
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bool posOnly = true; |
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xyzVisitor->setPosOnly(posOnly); |
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} |
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compositeVisitor->addVisitor(xyzVisitor, 200); |
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std::cout << compositeVisitor->toString(); |
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//creat prepareVisitor |
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//create prepareVisitor |
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PrepareVisitor* prepareVisitor = new PrepareVisitor(); |
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//open dump file |
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int nframes = dumpReader->getNFrames(); |
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std::ofstream xyzStream; |
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xyzStream .open(xyzFileName.c_str()); |
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std::ofstream xyzStream(xyzFileName.c_str()); |
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SimInfo::MoleculeIterator miter; |
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Molecule::IntegrableObjectIterator iiter; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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RigidBody* rb; |
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Vector3d molCom; |
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Vector3d newMolCom; |
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Vector3d displacement; |
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Mat3x3d hmat; |
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Snapshot* currentSnapshot; |
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for (int i = 0; i < nframes; i += args_info.frame_arg){ |
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dumpReader->readFrame(i); |
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//wrapping the molecule |
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if(args_info.periodicBox_flag) { |
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currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
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for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
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molCom = mol->getCom(); |
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newMolCom = molCom; |
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currentSnapshot->wrapVector(newMolCom); |
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displacement = newMolCom - molCom; |
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for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(iiter)) { |
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integrableObject->setPos(integrableObject->getPos() + displacement); |
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} |
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} |
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} |
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//update atoms of rigidbody |
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for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
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//update visitor |
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compositeVisitor->update(); |
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//visit stuntdouble |
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for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
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for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
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xyzVisitor->clear(); |
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}//end for (int i = 0; i < nframes; i += args_info.frame_arg) |
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xyzStream.close(); |
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delete prepareVisitor; |
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delete compositeVisitor; |
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delete info; |
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} |
