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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "applications/dump2Xyz/Dump2XYZCmd.h"
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "brains/ForceManager.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;

using namespace std;
int main(int argc, char* argv[]){
  
  //register force fields
  registerForceFields();
  
  gengetopt_args_info args_info;
  string dumpFileName;
  string xyzFileName;

  bool printVel(false);
  bool printFrc(false);
  bool printVec(false);
  bool printChrg(false);
  
  //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 {
    cerr << "Does not have input file name" << 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);
  ForceManager* forceMan = new ForceManager(info);
  
  //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 GBtail atom visitor
  GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
  compositeVisitor->addVisitor(gbtVisitor, 790);
  
  //create GBhead atom visitor
  GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
  compositeVisitor->addVisitor(gbhVisitor, 789);
  
  //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);    
    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) {
    cerr << "Both of --refsele and --originsele should appear by pair" 
              << 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.velocities_flag){
    printVel = true;
    xyzVisitor->doVelocities(printVel);
  }
  if(args_info.forces_flag){
    printFrc = true;
    xyzVisitor->doForces(printFrc);
  }
  if(args_info.vectors_flag){
    printVec = true;
    xyzVisitor->doVectors(printVec);
  }
  if(args_info.charges_flag){
    printChrg = true;
    xyzVisitor->doCharges(printChrg);
  }
  
  compositeVisitor->addVisitor(xyzVisitor, 200); 
  
  //create prepareVisitor
  PrepareVisitor* prepareVisitor = new PrepareVisitor();
  
  //open dump file
  DumpReader* dumpReader = new DumpReader(info, dumpFileName);
  int nframes = dumpReader->getNFrames();
  
  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);
    
    if (printFrc) forceMan->calcForces();
    
    //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();
        if (printVel) rb->updateAtomVel();
      }
    }
    
    //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:	1706
Committed:	Fri Apr 27 20:44:16 2012 UTC (13 years, 6 months ago) by gezelter
File size:	10163 byte(s)
Log Message:	fixed an initialization bug in Dump2XYZ
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	tim	12	#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "applications/dump2Xyz/Dump2XYZCmd.h"
48	gezelter	246	#include "brains/Register.hpp"
49			#include "brains/SimCreator.hpp"
50			#include "brains/SimInfo.hpp"
51	gezelter	1456	#include "brains/ForceManager.hpp"
52	gezelter	246	#include "io/DumpReader.hpp"
53			#include "utils/simError.h"
54	tim	12	#include "visitors/AtomVisitor.hpp"
55	gezelter	1455	#include "visitors/ReplacementVisitor.hpp"
56	tim	12	#include "visitors/CompositeVisitor.hpp"
57			#include "visitors/RigidBodyVisitor.hpp"
58			#include "visitors/OtherVisitor.hpp"
59			#include "visitors/ZconsVisitor.hpp"
60	tim	291	#include "selection/SelectionEvaluator.hpp"
61	tim	324	#include "selection/SelectionManager.hpp"
62	tim	369	#include "visitors/LipidTransVisitor.hpp"
63	tim	543	#include "visitors/AtomNameVisitor.hpp"
64	tim	369
65	gezelter	1390	using namespace OpenMD;
66	tim	12
67	gezelter	1706	using namespace std;
68	tim	12	int main(int argc, char* argv[]){
69	gezelter	246
70			//register force fields
71			registerForceFields();
72
73	tim	12	gengetopt_args_info args_info;
74	gezelter	1706	string dumpFileName;
75			string xyzFileName;
76
77			bool printVel(false);
78			bool printFrc(false);
79			bool printVec(false);
80			bool printChrg(false);
81	tim	12
82	gezelter	246	//parse the command line option
83			if (cmdline_parser (argc, argv, &args_info) != 0) {
84			exit(1) ;
85			}
86	tim	12
87			//get the dumpfile name and meta-data file name
88			if (args_info.input_given){
89			dumpFileName = args_info.input_arg;
90	gezelter	246	} else {
91	gezelter	1706	cerr << "Does not have input file name" << endl;
92	tim	12	exit(1);
93			}
94	gezelter	246
95	tim	12	if (args_info.output_given){
96			xyzFileName = args_info.output_arg;
97	gezelter	246	} else {
98	tim	12	xyzFileName = dumpFileName;
99			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
100			}
101	gezelter	246
102	tim	12	//parse md file and set up the system
103	gezelter	246	SimCreator creator;
104	gezelter	1026	SimInfo* info = creator.createSim(dumpFileName, false);
105	gezelter	1456	ForceManager* forceMan = new ForceManager(info);
106	tim	12
107	chrisfen	527	//create visitor list
108	gezelter	246	CompositeVisitor* compositeVisitor = new CompositeVisitor();
109	gezelter	1455
110	chrisfen	527	//create RigidBody Visitor
111	tim	12	if(args_info.rigidbody_flag){
112	gezelter	246	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
113	tim	12	compositeVisitor->addVisitor(rbCOMVisitor, 900);
114			}
115	gezelter	246
116	chrisfen	527	//create SSD atom visitor
117	gezelter	246	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
118	tim	12	compositeVisitor->addVisitor(ssdVisitor, 800);
119	gezelter	246
120	gezelter	1629	//create GBtail atom visitor
121			GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
122			compositeVisitor->addVisitor(gbtVisitor, 790);
123
124			//create GBhead atom visitor
125			GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
126			compositeVisitor->addVisitor(gbhVisitor, 789);
127
128	chrisfen	527	//create default atom visitor
129	gezelter	246	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
130	tim	12	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
131	gezelter	246
132	cli2	1303	// if we gave the -w option, we want to skip the waters:
133			if (!args_info.water_given) {
134			//create waterType visitor
135			if(args_info.watertype_flag){
136			WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
137			compositeVisitor->addVisitor(waterTypeVisitor, 600);
138			}
139	gezelter	1455	}
140
141	tim	543	if (args_info.basetype_flag) {
142	gezelter	1455	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
143			compositeVisitor->addVisitor(atomNameVisitor, 550);
144	gezelter	1706	cout << compositeVisitor->toString();
145	tim	543	}
146	gezelter	246
147	tim	12	//create ZconsVisitor
148			if(args_info.zconstraint_flag){
149	gezelter	246
150			ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
151	tim	12
152	gezelter	246	if(zconsVisitor->haveZconsMol()) {
153	tim	12	compositeVisitor->addVisitor(zconsVisitor, 500);
154	gezelter	246	} else {
155	tim	12	delete zconsVisitor;
156	gezelter	246	}
157	tim	12	}
158	gezelter	246
159	chrisfen	527	//create wrapping visitor
160	gezelter	246
161	tim	968	//if(args_info.periodicBox_flag){
162			// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
163			// compositeVisitor->addVisitor(wrappingVisitor, 400);
164			//}
165	tim	369
166	chrisfen	527	//create replicate visitor
167	gezelter	1456	if(args_info.repeatX_given > 0 \|\|
168			args_info.repeatY_given > 0 \|\|
169			args_info.repeatY_given > 0) {
170			Vector3i replicateOpt(args_info.repeatX_arg,
171			args_info.repeatY_arg,
172			args_info.repeatZ_arg);
173			ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
174			replicateOpt);
175	tim	12	compositeVisitor->addVisitor(replicateVisitor, 300);
176			}
177	tim	369
178
179			//create rotation visitor
180			if (args_info.refsele_given&& args_info.originsele_given) {
181	gezelter	1456	compositeVisitor->addVisitor(new LipidTransVisitor(info,
182			args_info.originsele_arg,
183			args_info.refsele_arg),
184			250);
185	tim	369	} else if (args_info.refsele_given \|\| args_info.originsele_given) {
186	gezelter	1706	cerr << "Both of --refsele and --originsele should appear by pair"
187			<< endl;
188	tim	369	exit(1);
189			}
190	gezelter	1456
191	chrisfen	527	//create xyzVisitor
192	tim	413	XYZVisitor* xyzVisitor;
193	chuckv	1117
194	tim	413	if (args_info.selection_given) {
195			xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
196			} else {
197			xyzVisitor = new XYZVisitor(info);
198			}
199	chuckv	1117
200	gezelter	1456	if(args_info.velocities_flag){
201			printVel = true;
202			xyzVisitor->doVelocities(printVel);
203	chuckv	1117	}
204	gezelter	1456	if(args_info.forces_flag){
205			printFrc = true;
206			xyzVisitor->doForces(printFrc);
207			}
208			if(args_info.vectors_flag){
209			printVec = true;
210			xyzVisitor->doVectors(printVec);
211			}
212			if(args_info.charges_flag){
213			printChrg = true;
214			xyzVisitor->doCharges(printChrg);
215			}
216
217	gezelter	1455	compositeVisitor->addVisitor(xyzVisitor, 200);
218	gezelter	246
219	chrisfen	527	//create prepareVisitor
220	gezelter	246	PrepareVisitor* prepareVisitor = new PrepareVisitor();
221
222	tim	12	//open dump file
223	gezelter	246	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
224			int nframes = dumpReader->getNFrames();
225
226	gezelter	1706	ofstream xyzStream(xyzFileName.c_str());
227	tim	12
228	gezelter	246	SimInfo::MoleculeIterator miter;
229			Molecule::IntegrableObjectIterator iiter;
230			Molecule::RigidBodyIterator rbIter;
231			Molecule* mol;
232			StuntDouble* integrableObject;
233			RigidBody* rb;
234	tim	968	Vector3d molCom;
235			Vector3d newMolCom;
236			Vector3d displacement;
237			Mat3x3d hmat;
238			Snapshot* currentSnapshot;
239	tim	413
240	tim	12	for (int i = 0; i < nframes; i += args_info.frame_arg){
241	gezelter	246	dumpReader->readFrame(i);
242	gezelter	1456
243	gezelter	1464	if (printFrc) forceMan->calcForces();
244	gezelter	1456
245	tim	968	//wrapping the molecule
246			if(args_info.periodicBox_flag) {
247			currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
248	gezelter	1456	for (mol = info->beginMolecule(miter); mol != NULL;
249			mol = info->nextMolecule(miter)) {
250	tim	968	molCom = mol->getCom();
251			newMolCom = molCom;
252			currentSnapshot->wrapVector(newMolCom);
253			displacement = newMolCom - molCom;
254	gezelter	1456	for (integrableObject = mol->beginIntegrableObject(iiter);
255			integrableObject != NULL;
256	tim	968	integrableObject = mol->nextIntegrableObject(iiter)) {
257			integrableObject->setPos(integrableObject->getPos() + displacement);
258			}
259			}
260			}
261	tim	12	//update atoms of rigidbody
262	gezelter	1456	for (mol = info->beginMolecule(miter); mol != NULL;
263			mol = info->nextMolecule(miter)) {
264	gezelter	246
265			//change the positions of atoms which belong to the rigidbodies
266	gezelter	1456	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
267			rb = mol->nextRigidBody(rbIter)) {
268	gezelter	246	rb->updateAtoms();
269	gezelter	1456	if (printVel) rb->updateAtomVel();
270	gezelter	246	}
271			}
272	tim	12
273			//prepare visit
274	gezelter	1456	for (mol = info->beginMolecule(miter); mol != NULL;
275			mol = info->nextMolecule(miter)) {
276			for (integrableObject = mol->beginIntegrableObject(iiter);
277			integrableObject != NULL;
278	gezelter	246	integrableObject = mol->nextIntegrableObject(iiter)) {
279			integrableObject->accept(prepareVisitor);
280			}
281			}
282
283	tim	12	//update visitor
284			compositeVisitor->update();
285	tim	291
286	tim	413
287	tim	12	//visit stuntdouble
288	gezelter	1456	for (mol = info->beginMolecule(miter); mol != NULL;
289			mol = info->nextMolecule(miter)) {
290			for (integrableObject = mol->beginIntegrableObject(iiter);
291			integrableObject != NULL;
292	gezelter	246	integrableObject = mol->nextIntegrableObject(iiter)) {
293			integrableObject->accept(compositeVisitor);
294			}
295	tim	12	}
296	gezelter	246
297	tim	12	xyzVisitor->writeFrame(xyzStream);
298			xyzVisitor->clear();
299
300			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
301	gezelter	1282
302	tim	12	xyzStream.close();
303	tim	466	delete prepareVisitor;
304	tim	12	delete compositeVisitor;
305			delete info;
306			}