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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#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/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 oopse;

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);
  
  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
  compositeVisitor->addVisitor(linearVisitor, 750);
  if (args_info.gb_given) {
    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
  }
  
  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
  compositeVisitor->addVisitor(gbLipidVisitor, 740);

  Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
  compositeVisitor->addVisitor(ring5Visitor, 730);

  HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
  compositeVisitor->addVisitor(headVisitor, 720);

  //create default atom visitor
  DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
  compositeVisitor->addVisitor(defaultAtomVisitor, 700);
  
  //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);

  }
  
  //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);
  
  std::cout << compositeVisitor->toString();
  
  //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)
 
  delete xyzVisitor; 
  xyzStream.close();
  delete prepareVisitor; 
  delete compositeVisitor;
  delete info;
}
Revision:	1282
Committed:	Wed Jul 30 18:11:19 2008 UTC (16 years, 9 months ago) by gezelter
Original Path:	*trunk/src/applications/dump2Xyz/Dump2XYZ.cpp*
File size:	9306 byte(s)
Log Message:	Many fixes
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
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			#include "visitors/CompositeVisitor.hpp"
54			#include "visitors/RigidBodyVisitor.hpp"
55			#include "visitors/OtherVisitor.hpp"
56			#include "visitors/ZconsVisitor.hpp"
57	tim	291	#include "selection/SelectionEvaluator.hpp"
58	tim	324	#include "selection/SelectionManager.hpp"
59	tim	369	#include "visitors/LipidTransVisitor.hpp"
60	tim	543	#include "visitors/AtomNameVisitor.hpp"
61	tim	369
62	gezelter	246	using namespace oopse;
63	tim	12
64			int main(int argc, char* argv[]){
65	gezelter	246
66			//register force fields
67			registerForceFields();
68
69	tim	12	gengetopt_args_info args_info;
70	gezelter	246	std::string dumpFileName;
71			std::string xyzFileName;
72	tim	12
73	gezelter	246	//parse the command line option
74			if (cmdline_parser (argc, argv, &args_info) != 0) {
75			exit(1) ;
76			}
77	tim	12
78			//get the dumpfile name and meta-data file name
79			if (args_info.input_given){
80			dumpFileName = args_info.input_arg;
81	gezelter	246	} else {
82			std::cerr << "Does not have input file name" << std::endl;
83	tim	12	exit(1);
84			}
85	gezelter	246
86	tim	12	if (args_info.output_given){
87			xyzFileName = args_info.output_arg;
88	gezelter	246	} else {
89	tim	12	xyzFileName = dumpFileName;
90			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
91			}
92	gezelter	246
93	tim	12	//parse md file and set up the system
94	gezelter	246	SimCreator creator;
95	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
96	tim	12
97	gezelter	1026
98	chrisfen	527	//create visitor list
99	gezelter	246	CompositeVisitor* compositeVisitor = new CompositeVisitor();
100	tim	12
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	tim	250	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112	chrisfen	211	compositeVisitor->addVisitor(linearVisitor, 750);
113	tim	954	if (args_info.gb_given) {
114			linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115			}
116	gezelter	246
117	xsun	881	GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118			compositeVisitor->addVisitor(gbLipidVisitor, 740);
119
120	xsun	1212	Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
121			compositeVisitor->addVisitor(ring5Visitor, 730);
122
123			HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
124			compositeVisitor->addVisitor(headVisitor, 720);
125
126	chrisfen	527	//create default atom visitor
127	gezelter	246	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128	tim	12	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129	gezelter	246
130	chrisfen	527	//create waterType visitor
131	tim	12	if(args_info.watertype_flag){
132	gezelter	246	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133	tim	12	compositeVisitor->addVisitor(waterTypeVisitor, 600);
134			}
135	tim	543
136			if (args_info.basetype_flag) {
137			AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
138			compositeVisitor->addVisitor(atomNameVisitor, 550);
139
140			}
141	gezelter	246
142	tim	12	//create ZconsVisitor
143			if(args_info.zconstraint_flag){
144	gezelter	246
145			ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
146	tim	12
147	gezelter	246	if(zconsVisitor->haveZconsMol()) {
148	tim	12	compositeVisitor->addVisitor(zconsVisitor, 500);
149	gezelter	246	} else {
150	tim	12	delete zconsVisitor;
151	gezelter	246	}
152	tim	12	}
153	gezelter	246
154	chrisfen	527	//create wrapping visitor
155	gezelter	246
156	tim	968	//if(args_info.periodicBox_flag){
157			// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
158			// compositeVisitor->addVisitor(wrappingVisitor, 400);
159			//}
160	tim	369
161	chrisfen	527	//create replicate visitor
162	tim	12	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
163	gezelter	246	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
164			ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
165	tim	12	compositeVisitor->addVisitor(replicateVisitor, 300);
166			}
167	tim	369
168
169			//create rotation visitor
170			if (args_info.refsele_given&& args_info.originsele_given) {
171			compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
172			} else if (args_info.refsele_given \|\| args_info.originsele_given) {
173	tim	381	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
174	tim	369	exit(1);
175			}
176
177	chrisfen	527	//create xyzVisitor
178	tim	413	XYZVisitor* xyzVisitor;
179	chuckv	1117
180	tim	413	if (args_info.selection_given) {
181			xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
182			} else {
183			xyzVisitor = new XYZVisitor(info);
184			}
185	chuckv	1117
186			if(args_info.printPosOnly_flag){
187			bool posOnly = true;
188			xyzVisitor->setPosOnly(posOnly);
189			}
190
191	tim	12	compositeVisitor->addVisitor(xyzVisitor, 200);
192	gezelter	246
193			std::cout << compositeVisitor->toString();
194
195	chrisfen	527	//create prepareVisitor
196	gezelter	246	PrepareVisitor* prepareVisitor = new PrepareVisitor();
197
198	tim	12	//open dump file
199	gezelter	246	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
200			int nframes = dumpReader->getNFrames();
201
202
203	gezelter	1282	std::ofstream xyzStream(xyzFileName.c_str());
204	tim	12
205	gezelter	246	SimInfo::MoleculeIterator miter;
206			Molecule::IntegrableObjectIterator iiter;
207			Molecule::RigidBodyIterator rbIter;
208			Molecule* mol;
209			StuntDouble* integrableObject;
210			RigidBody* rb;
211	tim	968	Vector3d molCom;
212			Vector3d newMolCom;
213			Vector3d displacement;
214			Mat3x3d hmat;
215			Snapshot* currentSnapshot;
216	tim	413
217	tim	12	for (int i = 0; i < nframes; i += args_info.frame_arg){
218	gezelter	246	dumpReader->readFrame(i);
219	tim	968
220			//wrapping the molecule
221			if(args_info.periodicBox_flag) {
222			currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
223			for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
224			molCom = mol->getCom();
225			newMolCom = molCom;
226			currentSnapshot->wrapVector(newMolCom);
227			displacement = newMolCom - molCom;
228			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
229			integrableObject = mol->nextIntegrableObject(iiter)) {
230			integrableObject->setPos(integrableObject->getPos() + displacement);
231			}
232			}
233			}
234	tim	12	//update atoms of rigidbody
235	gezelter	246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
236
237			//change the positions of atoms which belong to the rigidbodies
238			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
239			rb->updateAtoms();
240			}
241			}
242	tim	12
243			//prepare visit
244	gezelter	246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
245			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
246			integrableObject = mol->nextIntegrableObject(iiter)) {
247			integrableObject->accept(prepareVisitor);
248			}
249			}
250
251	tim	12	//update visitor
252			compositeVisitor->update();
253	tim	291
254	tim	413
255	tim	12	//visit stuntdouble
256	gezelter	246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
257			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
258			integrableObject = mol->nextIntegrableObject(iiter)) {
259			integrableObject->accept(compositeVisitor);
260			}
261	tim	12	}
262	gezelter	246
263	tim	12	xyzVisitor->writeFrame(xyzStream);
264			xyzVisitor->clear();
265
266			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
267	gezelter	1282
268			delete xyzVisitor;
269	tim	12	xyzStream.close();
270	tim	466	delete prepareVisitor;
271	tim	12	delete compositeVisitor;
272			delete info;
273			}