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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 <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 "brains/Register.hpp" |
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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 "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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#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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|
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< |
using namespace std; |
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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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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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//register force fields |
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registerForceFields(); |
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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 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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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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} 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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mdFileName = dumpFileName; |
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mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
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|
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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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} 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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|
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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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SimCreator creator; |
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SimInfo* info = creator.createSim(dumpFileName, false); |
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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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//create visitor list |
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CompositeVisitor* compositeVisitor = new CompositeVisitor(); |
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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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//create RigidBody Visitor |
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if(args_info.rigidbody_flag){ |
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rbCOMVisitor = new RBCOMVisitor(info); |
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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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ssdVisitor = new SSDAtomVisitor(info); |
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|
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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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|
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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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|
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GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info); |
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compositeVisitor->addVisitor(gbLipidVisitor, 740); |
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|
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//creat default atom visitor |
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defaultAtomVisitor = new DefaultAtomVisitor(info); |
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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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|
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//creat waterType visitor |
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|
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//create waterType visitor |
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if(args_info.watertype_flag){ |
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waterTypeVisitor = new WaterTypeVisitor; |
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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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} |
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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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> |
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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> |
} 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 = 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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> |
//create 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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> |
//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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< |
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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> |
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 = 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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> |
//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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> |
} |
| 170 |
> |
|
| 171 |
> |
//create xyzVisitor |
| 172 |
> |
XYZVisitor* xyzVisitor; |
| 173 |
> |
if (args_info.selection_given) { |
| 174 |
> |
xyzVisitor = new XYZVisitor(info, args_info.selection_arg); |
| 175 |
> |
} else { |
| 176 |
> |
xyzVisitor = new XYZVisitor(info); |
| 177 |
> |
} |
| 178 |
> |
compositeVisitor->addVisitor(xyzVisitor, 200); |
| 179 |
> |
|
| 180 |
> |
std::cout << compositeVisitor->toString(); |
| 181 |
> |
|
| 182 |
> |
//create prepareVisitor |
| 183 |
> |
PrepareVisitor* prepareVisitor = new PrepareVisitor(); |
| 184 |
> |
|
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|
//open dump file |
| 186 |
< |
dumpReader = new DumpReader(dumpFileName.c_str()); |
| 187 |
< |
nframes = dumpReader->getNframes(); |
| 188 |
< |
|
| 186 |
> |
DumpReader* dumpReader = new DumpReader(info, dumpFileName); |
| 187 |
> |
int nframes = dumpReader->getNFrames(); |
| 188 |
> |
|
| 189 |
> |
|
| 190 |
> |
std::ofstream xyzStream; |
| 191 |
|
xyzStream .open(xyzFileName.c_str()); |
| 192 |
|
|
| 193 |
+ |
|
| 194 |
+ |
SimInfo::MoleculeIterator miter; |
| 195 |
+ |
Molecule::IntegrableObjectIterator iiter; |
| 196 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 197 |
+ |
Molecule* mol; |
| 198 |
+ |
StuntDouble* integrableObject; |
| 199 |
+ |
RigidBody* rb; |
| 200 |
+ |
Vector3d molCom; |
| 201 |
+ |
Vector3d newMolCom; |
| 202 |
+ |
Vector3d displacement; |
| 203 |
+ |
Mat3x3d hmat; |
| 204 |
+ |
Snapshot* currentSnapshot; |
| 205 |
+ |
|
| 206 |
|
for (int i = 0; i < nframes; i += args_info.frame_arg){ |
| 207 |
< |
dumpReader->readFrame(info, i); |
| 207 |
> |
dumpReader->readFrame(i); |
| 208 |
|
|
| 209 |
< |
mol = info->molecules; |
| 210 |
< |
|
| 209 |
> |
//wrapping the molecule |
| 210 |
> |
if(args_info.periodicBox_flag) { |
| 211 |
> |
currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 212 |
> |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 213 |
> |
molCom = mol->getCom(); |
| 214 |
> |
newMolCom = molCom; |
| 215 |
> |
currentSnapshot->wrapVector(newMolCom); |
| 216 |
> |
displacement = newMolCom - molCom; |
| 217 |
> |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 218 |
> |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 219 |
> |
integrableObject->setPos(integrableObject->getPos() + displacement); |
| 220 |
> |
} |
| 221 |
> |
} |
| 222 |
> |
} |
| 223 |
|
//update atoms of rigidbody |
| 224 |
< |
for(int j = 0; j < info->n_mol; j++){ |
| 225 |
< |
myRigidBodies = mol[j].getMyRigidBodies(); |
| 226 |
< |
|
| 227 |
< |
for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter) |
| 228 |
< |
(*rbIter)->updateAtoms(); |
| 229 |
< |
} |
| 230 |
< |
|
| 224 |
> |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 225 |
> |
|
| 226 |
> |
//change the positions of atoms which belong to the rigidbodies |
| 227 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 228 |
> |
rb->updateAtoms(); |
| 229 |
> |
} |
| 230 |
> |
} |
| 231 |
|
|
| 232 |
|
//prepare visit |
| 233 |
< |
for(int j = 0; j < info->n_mol; j++){ |
| 234 |
< |
integrableObjects = mol[j].getIntegrableObjects(); |
| 235 |
< |
|
| 236 |
< |
for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter) |
| 237 |
< |
(*iter)->accept(prepareVisitor); |
| 238 |
< |
} |
| 239 |
< |
|
| 233 |
> |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 234 |
> |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 235 |
> |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 236 |
> |
integrableObject->accept(prepareVisitor); |
| 237 |
> |
} |
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
|
//update visitor |
| 241 |
|
compositeVisitor->update(); |
| 192 |
– |
|
| 193 |
– |
//visit stuntdouble |
| 194 |
– |
for(int j = 0; j < info->n_mol; j++){ |
| 195 |
– |
integrableObjects = mol[j].getIntegrableObjects(); |
| 242 |
|
|
| 197 |
– |
for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter) |
| 198 |
– |
(*iter)->accept(compositeVisitor); |
| 199 |
– |
} |
| 243 |
|
|
| 244 |
+ |
//visit stuntdouble |
| 245 |
+ |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 246 |
+ |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 247 |
+ |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 248 |
+ |
integrableObject->accept(compositeVisitor); |
| 249 |
+ |
} |
| 250 |
+ |
} |
| 251 |
+ |
|
| 252 |
|
xyzVisitor->writeFrame(xyzStream); |
| 253 |
|
xyzVisitor->clear(); |
| 254 |
|
|
| 255 |
|
}//end for (int i = 0; i < nframes; i += args_info.frame_arg) |
| 256 |
< |
|
| 256 |
> |
|
| 257 |
|
xyzStream.close(); |
| 258 |
< |
|
| 259 |
< |
|
| 258 |
> |
|
| 259 |
> |
delete prepareVisitor; |
| 260 |
|
delete compositeVisitor; |
| 261 |
|
delete info; |
| 262 |
< |
|
| 212 |
< |
|
| 262 |
> |
|
| 263 |
|
} |
