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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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#include <iostream> |
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#include <fstream> |
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#include <string> |
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|
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#include "applications/dump2Xyz/Dump2XYZCmd.h" |
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|
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "io/DumpReader.hpp" |
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#include "minimizers/MinimizerFactory.hpp" |
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#include "minimizers/MinimizerCreator.hpp" |
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#include "minimizers/PRCG.hpp" |
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#include "minimizers/SDMinimizer.hpp" |
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#include "UseTheForce/DUFF.hpp" |
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#include "UseTheForce/EAM.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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#include "utils/simError.h" |
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#include "visitors/AtomVisitor.hpp" |
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#include "visitors/CompositeVisitor.hpp" |
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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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using namespace oopse; |
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|
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int main(int argc, char* argv[]){ |
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|
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//DUFF, WATER and LJ are merged into one force field |
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ForceFieldBuilder<DUFF> DUFFCreator("DUFF"); |
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ForceFieldBuilder<DUFF> WATERCreator("WATER"); |
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ForceFieldBuilder<DUFF> LJCreator("LJ"); |
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//in theory, EAM can also be merged |
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ForceFieldBuilder<EAM> EAMCreator("EAM"); |
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|
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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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|
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//parse the command line option |
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if (cmdline_parser (argc, argv, &args_info) != 0) { |
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exit(1) ; |
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} |
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|
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//get the dumpfile name and meta-data file name |
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if (args_info.input_given){ |
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dumpFileName = args_info.input_arg; |
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} else { |
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std::cerr << "Does not have input file name" << std::endl; |
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exit(1); |
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} |
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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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|
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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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xyzFileName = dumpFileName; |
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xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz"; |
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} |
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|
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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); |
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|
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|
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|
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//creat visitor list |
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CompositeVisitor* compositeVisitor = new CompositeVisitor(); |
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|
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//creat ignore visitor |
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if(args_info.ignore_given ||args_info.water_flag){ |
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|
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IgnoreVisitor* ignoreVisitor = new IgnoreVisitor(); |
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|
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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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|
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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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|
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compositeVisitor->addVisitor(ignoreVisitor, 1000); |
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} |
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|
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//creat 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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|
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//compositeVisitor->addVisitor(lipidVisitor, 900); |
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|
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//creat SSD atom visitor |
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SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info); |
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compositeVisitor->addVisitor(ssdVisitor, 800); |
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|
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//creat default atom visitor |
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DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info); |
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compositeVisitor->addVisitor(defaultAtomVisitor, 700); |
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|
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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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} |
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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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ZConsVisitor* zconsVisitor = new ZConsVisitor(info); |
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|
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if(zconsVisitor->haveZconsMol()) { |
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compositeVisitor->addVisitor(zconsVisitor, 500); |
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} else { |
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delete zconsVisitor; |
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} |
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} |
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|
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//creat wrapping visitor |
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|
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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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|
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//creat 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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|
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//creat xyzVisitor |
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XYZVisitor* xyzVisitor = new XYZVisitor(info); |
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compositeVisitor->addVisitor(xyzVisitor, 200); |
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|
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std::cout << compositeVisitor->toString(); |
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|
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//creat prepareVisitor |
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PrepareVisitor* prepareVisitor = new PrepareVisitor(); |
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|
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//open dump file |
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DumpReader* dumpReader = new DumpReader(info, dumpFileName); |
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int nframes = dumpReader->getNFrames(); |
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|
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|
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std::ofstream xyzStream; |
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xyzStream .open(xyzFileName.c_str()); |
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|
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|
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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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|
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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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|
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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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|
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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//prepare visit |
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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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integrableObject = mol->nextIntegrableObject(iiter)) { |
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integrableObject->accept(prepareVisitor); |
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} |
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} |
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|
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//update visitor |
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compositeVisitor->update(); |
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|
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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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integrableObject = mol->nextIntegrableObject(iiter)) { |
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integrableObject->accept(compositeVisitor); |
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} |
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} |
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|
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xyzVisitor->writeFrame(xyzStream); |
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xyzVisitor->clear(); |
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|
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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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|
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|
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delete compositeVisitor; |
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delete info; |
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|
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|
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} |
