applications/dump2Xyz/Dump2XYZ.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "applications/dump2Xyz/Dump2XYZCmd.h"
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"
#include "utils/simError.h"
#include "visitors/AtomVisitor.hpp"
#include "visitors/ReplacementVisitor.hpp"
#include "visitors/CompositeVisitor.hpp"
#include "visitors/RigidBodyVisitor.hpp"
#include "visitors/OtherVisitor.hpp"
#include "visitors/ZconsVisitor.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "visitors/LipidTransVisitor.hpp"
#include "visitors/AtomNameVisitor.hpp"

using namespace OpenMD;

int main(int argc, char* argv[]){
  
  //register force fields
  registerForceFields();
  
  gengetopt_args_info args_info;
  std::string dumpFileName;
  std::string xyzFileName;
  
  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }
  
  //get the dumpfile name and meta-data file name
  if (args_info.input_given){
    dumpFileName = args_info.input_arg;
  } else {
    std::cerr << "Does not have input file name" << std::endl;
    exit(1);
  }
  
  if (args_info.output_given){
    xyzFileName = args_info.output_arg;
  } else {
    xyzFileName = dumpFileName;
    xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
  }
  
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName, false);
  
  //create visitor list
  CompositeVisitor* compositeVisitor = new CompositeVisitor();
  
  //create RigidBody Visitor
  if(args_info.rigidbody_flag){
    RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
    compositeVisitor->addVisitor(rbCOMVisitor, 900);
  }
  
  //create SSD atom visitor
  SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
  compositeVisitor->addVisitor(ssdVisitor, 800);
  
  //create default atom visitor
  DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
  compositeVisitor->addVisitor(defaultAtomVisitor, 700);
  
  // if we gave the -w option, we want to skip the waters:
  if (!args_info.water_given) {
    //create waterType visitor
    if(args_info.watertype_flag){
      WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
      compositeVisitor->addVisitor(waterTypeVisitor, 600);
    }
  } 
  
  if (args_info.basetype_flag) {
    AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
    compositeVisitor->addVisitor(atomNameVisitor, 550);    
    std::cout << compositeVisitor->toString();
  }
  
  //create ZconsVisitor
  if(args_info.zconstraint_flag){

    ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
    
    if(zconsVisitor->haveZconsMol()) {
      compositeVisitor->addVisitor(zconsVisitor, 500);
    } else {
      delete zconsVisitor;
    }
  }
  
  //create wrapping visitor
  
  //if(args_info.periodicBox_flag){
  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
  //}

  //create replicate visitor
  if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
    Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
    ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
    compositeVisitor->addVisitor(replicateVisitor, 300);
  }


  //create rotation visitor
  if (args_info.refsele_given&& args_info.originsele_given) {
    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250); 
  } else if (args_info.refsele_given || args_info.originsele_given) {
    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
    exit(1);
  }
    
  //create xyzVisitor
  XYZVisitor* xyzVisitor;

  if (args_info.selection_given) {
    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
  } else {
    xyzVisitor = new XYZVisitor(info);
  }

  if(args_info.printPosOnly_flag){
    bool posOnly = true;
    xyzVisitor->setPosOnly(posOnly);
  }

  compositeVisitor->addVisitor(xyzVisitor, 200); 
  
  //create prepareVisitor
  PrepareVisitor* prepareVisitor = new PrepareVisitor();
  
  //open dump file
  DumpReader* dumpReader = new DumpReader(info, dumpFileName);
  int nframes = dumpReader->getNFrames();
  
  
  std::ofstream xyzStream(xyzFileName.c_str());
  
  SimInfo::MoleculeIterator miter;
  Molecule::IntegrableObjectIterator  iiter;
  Molecule::RigidBodyIterator rbIter;
  Molecule* mol;
  StuntDouble* integrableObject;
  RigidBody* rb;
  Vector3d molCom;
  Vector3d newMolCom;
  Vector3d displacement;
  Mat3x3d hmat;
  Snapshot* currentSnapshot;
       
  for (int i = 0; i < nframes; i += args_info.frame_arg){
    dumpReader->readFrame(i);

    //wrapping the molecule
    if(args_info.periodicBox_flag) {
      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
          molCom = mol->getCom();
          newMolCom = molCom;
          currentSnapshot->wrapVector(newMolCom);
          displacement = newMolCom - molCom;
        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
             integrableObject = mol->nextIntegrableObject(iiter)) {  
          integrableObject->setPos(integrableObject->getPos() + displacement);
        }
      }    
    }
    //update atoms of rigidbody
    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
      
      //change the positions of atoms which belong to the rigidbodies
      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
        rb->updateAtoms();
      }
    }
    
    //prepare visit
    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(iiter)) {
        integrableObject->accept(prepareVisitor);
      }
    }
    
    //update visitor
    compositeVisitor->update();


    //visit stuntdouble
    for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(iiter)) {
        integrableObject->accept(compositeVisitor);
      }
    }
    
    xyzVisitor->writeFrame(xyzStream);
    xyzVisitor->clear();
    
  }//end for (int i = 0; i < nframes; i += args_info.frame_arg)
 
  xyzStream.close();
  delete prepareVisitor; 
  delete compositeVisitor;
  delete info;
}
Revision:	1455
Committed:	Thu Jun 24 20:44:18 2010 UTC (14 years, 11 months ago) by gezelter
Original Path:	*trunk/src/applications/dump2Xyz/Dump2XYZ.cpp*
File size:	8909 byte(s)
Log Message:	Updating visitor architecture to something a bit more modern
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	tim	12	#include <iostream>
43			#include <fstream>
44			#include <string>
45
46			#include "applications/dump2Xyz/Dump2XYZCmd.h"
47	gezelter	246	#include "brains/Register.hpp"
48			#include "brains/SimCreator.hpp"
49			#include "brains/SimInfo.hpp"
50			#include "io/DumpReader.hpp"
51			#include "utils/simError.h"
52	tim	12	#include "visitors/AtomVisitor.hpp"
53	gezelter	1455	#include "visitors/ReplacementVisitor.hpp"
54	tim	12	#include "visitors/CompositeVisitor.hpp"
55			#include "visitors/RigidBodyVisitor.hpp"
56			#include "visitors/OtherVisitor.hpp"
57			#include "visitors/ZconsVisitor.hpp"
58	tim	291	#include "selection/SelectionEvaluator.hpp"
59	tim	324	#include "selection/SelectionManager.hpp"
60	tim	369	#include "visitors/LipidTransVisitor.hpp"
61	tim	543	#include "visitors/AtomNameVisitor.hpp"
62	tim	369
63	gezelter	1390	using namespace OpenMD;
64	tim	12
65			int main(int argc, char* argv[]){
66	gezelter	246
67			//register force fields
68			registerForceFields();
69
70	tim	12	gengetopt_args_info args_info;
71	gezelter	246	std::string dumpFileName;
72			std::string xyzFileName;
73	tim	12
74	gezelter	246	//parse the command line option
75			if (cmdline_parser (argc, argv, &args_info) != 0) {
76			exit(1) ;
77			}
78	tim	12
79			//get the dumpfile name and meta-data file name
80			if (args_info.input_given){
81			dumpFileName = args_info.input_arg;
82	gezelter	246	} else {
83			std::cerr << "Does not have input file name" << std::endl;
84	tim	12	exit(1);
85			}
86	gezelter	246
87	tim	12	if (args_info.output_given){
88			xyzFileName = args_info.output_arg;
89	gezelter	246	} else {
90	tim	12	xyzFileName = dumpFileName;
91			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
92			}
93	gezelter	246
94	tim	12	//parse md file and set up the system
95	gezelter	246	SimCreator creator;
96	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
97	tim	12
98	chrisfen	527	//create visitor list
99	gezelter	246	CompositeVisitor* compositeVisitor = new CompositeVisitor();
100	gezelter	1455
101	chrisfen	527	//create RigidBody Visitor
102	tim	12	if(args_info.rigidbody_flag){
103	gezelter	246	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104	tim	12	compositeVisitor->addVisitor(rbCOMVisitor, 900);
105			}
106	gezelter	246
107	chrisfen	527	//create SSD atom visitor
108	gezelter	246	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109	tim	12	compositeVisitor->addVisitor(ssdVisitor, 800);
110	gezelter	246
111	chrisfen	527	//create default atom visitor
112	gezelter	246	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
113	tim	12	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
114	gezelter	246
115	cli2	1303	// if we gave the -w option, we want to skip the waters:
116			if (!args_info.water_given) {
117			//create waterType visitor
118			if(args_info.watertype_flag){
119			WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
120			compositeVisitor->addVisitor(waterTypeVisitor, 600);
121			}
122	gezelter	1455	}
123
124	tim	543	if (args_info.basetype_flag) {
125	gezelter	1455	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
126			compositeVisitor->addVisitor(atomNameVisitor, 550);
127			std::cout << compositeVisitor->toString();
128	tim	543	}
129	gezelter	246
130	tim	12	//create ZconsVisitor
131			if(args_info.zconstraint_flag){
132	gezelter	246
133			ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
134	tim	12
135	gezelter	246	if(zconsVisitor->haveZconsMol()) {
136	tim	12	compositeVisitor->addVisitor(zconsVisitor, 500);
137	gezelter	246	} else {
138	tim	12	delete zconsVisitor;
139	gezelter	246	}
140	tim	12	}
141	gezelter	246
142	chrisfen	527	//create wrapping visitor
143	gezelter	246
144	tim	968	//if(args_info.periodicBox_flag){
145			// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
146			// compositeVisitor->addVisitor(wrappingVisitor, 400);
147			//}
148	tim	369
149	chrisfen	527	//create replicate visitor
150	tim	12	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
151	gezelter	246	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
152			ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
153	tim	12	compositeVisitor->addVisitor(replicateVisitor, 300);
154			}
155	tim	369
156
157			//create rotation visitor
158			if (args_info.refsele_given&& args_info.originsele_given) {
159			compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
160			} else if (args_info.refsele_given \|\| args_info.originsele_given) {
161	tim	381	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
162	tim	369	exit(1);
163			}
164
165	chrisfen	527	//create xyzVisitor
166	tim	413	XYZVisitor* xyzVisitor;
167	chuckv	1117
168	tim	413	if (args_info.selection_given) {
169			xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
170			} else {
171			xyzVisitor = new XYZVisitor(info);
172			}
173	chuckv	1117
174			if(args_info.printPosOnly_flag){
175			bool posOnly = true;
176			xyzVisitor->setPosOnly(posOnly);
177			}
178
179	gezelter	1455	compositeVisitor->addVisitor(xyzVisitor, 200);
180	gezelter	246
181	chrisfen	527	//create prepareVisitor
182	gezelter	246	PrepareVisitor* prepareVisitor = new PrepareVisitor();
183
184	tim	12	//open dump file
185	gezelter	246	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
186			int nframes = dumpReader->getNFrames();
187
188
189	gezelter	1282	std::ofstream xyzStream(xyzFileName.c_str());
190	tim	12
191	gezelter	246	SimInfo::MoleculeIterator miter;
192			Molecule::IntegrableObjectIterator iiter;
193			Molecule::RigidBodyIterator rbIter;
194			Molecule* mol;
195			StuntDouble* integrableObject;
196			RigidBody* rb;
197	tim	968	Vector3d molCom;
198			Vector3d newMolCom;
199			Vector3d displacement;
200			Mat3x3d hmat;
201			Snapshot* currentSnapshot;
202	tim	413
203	tim	12	for (int i = 0; i < nframes; i += args_info.frame_arg){
204	gezelter	246	dumpReader->readFrame(i);
205	tim	968
206			//wrapping the molecule
207			if(args_info.periodicBox_flag) {
208			currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
209			for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
210			molCom = mol->getCom();
211			newMolCom = molCom;
212			currentSnapshot->wrapVector(newMolCom);
213			displacement = newMolCom - molCom;
214			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
215			integrableObject = mol->nextIntegrableObject(iiter)) {
216			integrableObject->setPos(integrableObject->getPos() + displacement);
217			}
218			}
219			}
220	tim	12	//update atoms of rigidbody
221	gezelter	246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
222
223			//change the positions of atoms which belong to the rigidbodies
224			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
225			rb->updateAtoms();
226			}
227			}
228	tim	12
229			//prepare visit
230	gezelter	246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
231			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
232			integrableObject = mol->nextIntegrableObject(iiter)) {
233			integrableObject->accept(prepareVisitor);
234			}
235			}
236
237	tim	12	//update visitor
238			compositeVisitor->update();
239	tim	291
240	tim	413
241	tim	12	//visit stuntdouble
242	gezelter	246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
243			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
244			integrableObject = mol->nextIntegrableObject(iiter)) {
245			integrableObject->accept(compositeVisitor);
246			}
247	tim	12	}
248	gezelter	246
249	tim	12	xyzVisitor->writeFrame(xyzStream);
250			xyzVisitor->clear();
251
252			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
253	gezelter	1282
254	tim	12	xyzStream.close();
255	tim	466	delete prepareVisitor;
256	tim	12	delete compositeVisitor;
257			delete info;
258			}