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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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#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 "brains/ForceManager.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/ReplacementVisitor.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 OpenMD; |
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|
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using namespace std; |
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int main(int argc, char* argv[]){ |
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|
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gengetopt_args_info args_info; |
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string dumpFileName; |
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string xyzFileName; |
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|
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bool printVel(false); |
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bool printFrc(false); |
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bool printVec(false); |
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bool printChrg(false); |
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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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cerr << "Does not have input file name" << endl; |
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exit(1); |
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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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} 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(dumpFileName, false); |
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ForceManager* forceMan = new ForceManager(info); |
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|
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//create visitor list |
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CompositeVisitor* compositeVisitor = new CompositeVisitor(); |
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|
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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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|
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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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//create GBtail atom visitor |
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GBtailVisitor* gbtVisitor = new GBtailVisitor(info); |
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compositeVisitor->addVisitor(gbtVisitor, 790); |
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|
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//create GBhead atom visitor |
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GBheadVisitor* gbhVisitor = new GBheadVisitor(info); |
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compositeVisitor->addVisitor(gbhVisitor, 789); |
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|
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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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// if we gave the -w option, we want to skip the waters: |
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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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|
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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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cout << compositeVisitor->toString(); |
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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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//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 || |
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args_info.repeatY_given > 0 || |
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args_info.repeatY_given > 0) { |
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Vector3i replicateOpt(args_info.repeatX_arg, |
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args_info.repeatY_arg, |
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args_info.repeatZ_arg); |
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ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, |
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replicateOpt); |
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compositeVisitor->addVisitor(replicateVisitor, 300); |
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} |
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|
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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, |
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args_info.originsele_arg, |
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args_info.refsele_arg), |
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250); |
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} else if (args_info.refsele_given || args_info.originsele_given) { |
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cerr << "Both of --refsele and --originsele should appear by pair" |
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<< endl; |
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exit(1); |
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} |
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|
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//create xyzVisitor |
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XYZVisitor* xyzVisitor; |
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|
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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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|
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if(args_info.velocities_flag){ |
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printVel = true; |
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xyzVisitor->doVelocities(printVel); |
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} |
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if(args_info.forces_flag){ |
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printFrc = true; |
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xyzVisitor->doForces(printFrc); |
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} |
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if(args_info.vectors_flag){ |
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printVec = true; |
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xyzVisitor->doVectors(printVec); |
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} |
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if(args_info.charges_flag){ |
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printChrg = true; |
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xyzVisitor->doCharges(printChrg); |
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} |
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|
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compositeVisitor->addVisitor(xyzVisitor, 200); |
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|
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//create 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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ofstream xyzStream(xyzFileName.c_str()); |
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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* sd; |
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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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|
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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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if (printFrc) forceMan->calcForces(); |
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|
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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; |
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mol = info->nextMolecule(miter)) { |
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|
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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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|
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for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
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sd = mol->nextIntegrableObject(iiter)) { |
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|
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sd->setPos(sd->getPos() + displacement); |
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|
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} |
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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; |
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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; |
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rb = mol->nextRigidBody(rbIter)) { |
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|
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rb->updateAtoms(); |
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if (printVel) rb->updateAtomVel(); |
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|
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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; |
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mol = info->nextMolecule(miter)) { |
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|
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for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
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sd = mol->nextIntegrableObject(iiter)) { |
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|
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sd->accept(prepareVisitor); |
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|
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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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|
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//visit stuntdouble |
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for (mol = info->beginMolecule(miter); mol != NULL; |
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mol = info->nextMolecule(miter)) { |
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|
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for (sd = mol->beginIntegrableObject(iiter); sd != NULL; |
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sd = mol->nextIntegrableObject(iiter)) { |
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|
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sd->accept(compositeVisitor); |
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|
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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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|
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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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} |
