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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 "brains/SimSetup.hpp" |
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#include "applications/dump2Xyz/Dump2XYZCmd.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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|
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using namespace std; |
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|
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int main(int argc, char* argv[]){ |
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gengetopt_args_info args_info; |
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string dumpFileName; |
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string mdFileName; |
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char inFileName[2002]; |
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string xyzFileName; |
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SimInfo* info; |
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SimSetup startMe; |
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DumpReader* dumpReader; |
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ofstream xyzStream; |
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int nframes; |
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Molecule* mol; |
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vector<StuntDouble*> integrableObjects; |
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vector<StuntDouble*>::iterator iter; |
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vector<RigidBody*> myRigidBodies; |
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vector<RigidBody*>::iterator rbIter; |
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|
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CompositeVisitor* compositeVisitor; |
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SSDAtomVisitor* ssdVisitor; |
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DefaultAtomVisitor* defaultAtomVisitor; |
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LipidHeadVisitor* lipidVisitor; |
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RBCOMVisitor* rbCOMVisitor; |
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ReplicateVisitor* replicateVisitor; |
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WrappingVisitor* wrappingVisitor; |
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IgnoreVisitor* ignoreVisitor; |
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XYZVisitor* xyzVisitor; |
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ZConsVisitor* zconsVisitor; |
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PrepareVisitor* prepareVisitor; |
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WaterTypeVisitor* waterTypeVisitor; |
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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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} |
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else{ |
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cerr << "Does not have input file name" << endl; |
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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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|
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if (args_info.output_given){ |
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xyzFileName = args_info.output_arg; |
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} |
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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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info = new SimInfo(); |
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startMe.setSimInfo(info ); |
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|
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strcpy(inFileName, mdFileName.c_str() ); |
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startMe.parseFile( inFileName ); |
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|
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startMe.createSim(); |
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|
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|
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//creat visitor list |
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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 = 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 = 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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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 = 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 = 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 = 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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//creat wrapping visitor |
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|
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if(args_info.periodicBox_flag){ |
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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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IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg); |
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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 = new XYZVisitor(info); |
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compositeVisitor->addVisitor(xyzVisitor, 200); |
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|
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cout << compositeVisitor->toString(); |
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|
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//creat prepareVisitor |
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prepareVisitor = new PrepareVisitor(); |
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|
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//open dump file |
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dumpReader = new DumpReader(dumpFileName.c_str()); |
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nframes = dumpReader->getNframes(); |
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|
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xyzStream .open(xyzFileName.c_str()); |
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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(info, i); |
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|
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mol = info->molecules; |
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|
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//update atoms of rigidbody |
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for(int j = 0; j < info->n_mol; j++){ |
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myRigidBodies = mol[j].getMyRigidBodies(); |
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|
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for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter) |
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(*rbIter)->updateAtoms(); |
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} |
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|
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|
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//prepare visit |
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for(int j = 0; j < info->n_mol; j++){ |
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integrableObjects = mol[j].getIntegrableObjects(); |
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|
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for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter) |
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(*iter)->accept(prepareVisitor); |
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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(int j = 0; j < info->n_mol; j++){ |
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integrableObjects = mol[j].getIntegrableObjects(); |
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|
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for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter) |
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(*iter)->accept(compositeVisitor); |
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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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|
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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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} |
