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 mdFileName;
  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);
  }
  
  mdFileName = dumpFileName;
  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";

  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(mdFileName, 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);

  //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);
  }
  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;    
  xyzStream .open(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:	2764
Committed:	Tue May 23 18:46:11 2006 UTC (18 years, 2 months ago) by tim
File size:	9111 byte(s)
Log Message:	wrapping back to PBC by molecule instead of by individual atom
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	1501	#include <iostream>
43			#include <fstream>
44			#include <string>
45
46			#include "applications/dump2Xyz/Dump2XYZCmd.h"
47	gezelter	1930	#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	1501	#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	1975	#include "selection/SelectionEvaluator.hpp"
58	tim	2008	#include "selection/SelectionManager.hpp"
59	tim	2053	#include "visitors/LipidTransVisitor.hpp"
60	tim	2240	#include "visitors/AtomNameVisitor.hpp"
61	tim	2053
62	gezelter	1930	using namespace oopse;
63	tim	1501
64			int main(int argc, char* argv[]){
65	gezelter	1930
66			//register force fields
67			registerForceFields();
68
69	tim	1501	gengetopt_args_info args_info;
70	gezelter	1930	std::string dumpFileName;
71			std::string mdFileName;
72			std::string xyzFileName;
73	tim	1501
74	gezelter	1930	//parse the command line option
75			if (cmdline_parser (argc, argv, &args_info) != 0) {
76			exit(1) ;
77			}
78	tim	1501
79			//get the dumpfile name and meta-data file name
80			if (args_info.input_given){
81			dumpFileName = args_info.input_arg;
82	gezelter	1930	} else {
83			std::cerr << "Does not have input file name" << std::endl;
84	tim	1501	exit(1);
85			}
86	gezelter	1930
87	tim	1501	mdFileName = dumpFileName;
88			mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
89	tim	1957
90	tim	1501	if (args_info.output_given){
91			xyzFileName = args_info.output_arg;
92	gezelter	1930	} else {
93	tim	1501	xyzFileName = dumpFileName;
94			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
95			}
96	gezelter	1930
97	tim	1501	//parse md file and set up the system
98	gezelter	1930	SimCreator creator;
99	tim	1957	SimInfo* info = creator.createSim(mdFileName, false);
100	tim	1501
101	gezelter	1930
102
103	chrisfen	2224	//create visitor list
104	gezelter	1930	CompositeVisitor* compositeVisitor = new CompositeVisitor();
105	tim	1501
106	chrisfen	2224	//create RigidBody Visitor
107	tim	1501	if(args_info.rigidbody_flag){
108	gezelter	1930	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
109	tim	1501	compositeVisitor->addVisitor(rbCOMVisitor, 900);
110			}
111	gezelter	1930
112	chrisfen	2224	//create SSD atom visitor
113	gezelter	1930	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
114	tim	1501	compositeVisitor->addVisitor(ssdVisitor, 800);
115	gezelter	1930
116	tim	1934	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
117	chrisfen	1718	compositeVisitor->addVisitor(linearVisitor, 750);
118	tim	2749	if (args_info.gb_given) {
119			linearVisitor->addGayBerneAtomType(args_info.gb_arg);
120			}
121	gezelter	1930
122	xsun	2581	GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
123			compositeVisitor->addVisitor(gbLipidVisitor, 740);
124
125	chrisfen	2224	//create default atom visitor
126	gezelter	1930	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
127	tim	1501	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
128	gezelter	1930
129	chrisfen	2224	//create waterType visitor
130	tim	1501	if(args_info.watertype_flag){
131	gezelter	1930	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
132	tim	1501	compositeVisitor->addVisitor(waterTypeVisitor, 600);
133			}
134	tim	2240
135			if (args_info.basetype_flag) {
136			AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
137			compositeVisitor->addVisitor(atomNameVisitor, 550);
138
139			}
140	gezelter	1930
141	tim	1501	//create ZconsVisitor
142			if(args_info.zconstraint_flag){
143	gezelter	1930
144			ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
145	tim	1501
146	gezelter	1930	if(zconsVisitor->haveZconsMol()) {
147	tim	1501	compositeVisitor->addVisitor(zconsVisitor, 500);
148	gezelter	1930	} else {
149	tim	1501	delete zconsVisitor;
150	gezelter	1930	}
151	tim	1501	}
152	gezelter	1930
153	chrisfen	2224	//create wrapping visitor
154	gezelter	1930
155	tim	2764	//if(args_info.periodicBox_flag){
156			// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
157			// compositeVisitor->addVisitor(wrappingVisitor, 400);
158			//}
159	tim	2053
160	chrisfen	2224	//create replicate visitor
161	tim	1501	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
162	gezelter	1930	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
163			ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
164	tim	1501	compositeVisitor->addVisitor(replicateVisitor, 300);
165			}
166	tim	2053
167
168			//create rotation visitor
169			if (args_info.refsele_given&& args_info.originsele_given) {
170			compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
171			} else if (args_info.refsele_given \|\| args_info.originsele_given) {
172	tim	2065	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
173	tim	2053	exit(1);
174			}
175
176	chrisfen	2224	//create xyzVisitor
177	tim	2097	XYZVisitor* xyzVisitor;
178			if (args_info.selection_given) {
179			xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
180			} else {
181			xyzVisitor = new XYZVisitor(info);
182			}
183	tim	1501	compositeVisitor->addVisitor(xyzVisitor, 200);
184	gezelter	1930
185			std::cout << compositeVisitor->toString();
186
187	chrisfen	2224	//create prepareVisitor
188	gezelter	1930	PrepareVisitor* prepareVisitor = new PrepareVisitor();
189
190	tim	1501	//open dump file
191	gezelter	1930	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
192			int nframes = dumpReader->getNFrames();
193
194
195			std::ofstream xyzStream;
196	tim	1501	xyzStream .open(xyzFileName.c_str());
197
198	gezelter	1930
199			SimInfo::MoleculeIterator miter;
200			Molecule::IntegrableObjectIterator iiter;
201			Molecule::RigidBodyIterator rbIter;
202			Molecule* mol;
203			StuntDouble* integrableObject;
204			RigidBody* rb;
205	tim	2764	Vector3d molCom;
206			Vector3d newMolCom;
207			Vector3d displacement;
208			Mat3x3d hmat;
209			Snapshot* currentSnapshot;
210	tim	2097
211	tim	1501	for (int i = 0; i < nframes; i += args_info.frame_arg){
212	gezelter	1930	dumpReader->readFrame(i);
213	tim	2764
214			//wrapping the molecule
215			if(args_info.periodicBox_flag) {
216			currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
217			for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
218			molCom = mol->getCom();
219			newMolCom = molCom;
220			currentSnapshot->wrapVector(newMolCom);
221			displacement = newMolCom - molCom;
222			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
223			integrableObject = mol->nextIntegrableObject(iiter)) {
224			integrableObject->setPos(integrableObject->getPos() + displacement);
225			}
226			}
227			}
228	tim	1501	//update atoms of rigidbody
229	gezelter	1930	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
230
231			//change the positions of atoms which belong to the rigidbodies
232			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
233			rb->updateAtoms();
234			}
235			}
236	tim	1501
237			//prepare visit
238	gezelter	1930	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
239			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
240			integrableObject = mol->nextIntegrableObject(iiter)) {
241			integrableObject->accept(prepareVisitor);
242			}
243			}
244
245	tim	1501	//update visitor
246			compositeVisitor->update();
247	tim	1975
248	tim	2097
249	tim	1501	//visit stuntdouble
250	gezelter	1930	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
251			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
252			integrableObject = mol->nextIntegrableObject(iiter)) {
253			integrableObject->accept(compositeVisitor);
254			}
255	tim	1501	}
256	gezelter	1930
257	tim	1501	xyzVisitor->writeFrame(xyzStream);
258			xyzVisitor->clear();
259
260			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
261	gezelter	1930
262	tim	1501	xyzStream.close();
263	gezelter	1930
264	tim	2163	delete prepareVisitor;
265	tim	1501	delete compositeVisitor;
266			delete info;
267	gezelter	1930
268	tim	1501	}