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 (15 years, 4 months ago) by gezelter
File size:	8909 byte(s)
Log Message:	Updating visitor architecture to something a bit more modern
#	Content
1	/*
2	* 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	*/
41
42	#include <iostream>
43	#include <fstream>
44	#include <string>
45
46	#include "applications/dump2Xyz/Dump2XYZCmd.h"
47	#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	#include "visitors/AtomVisitor.hpp"
53	#include "visitors/ReplacementVisitor.hpp"
54	#include "visitors/CompositeVisitor.hpp"
55	#include "visitors/RigidBodyVisitor.hpp"
56	#include "visitors/OtherVisitor.hpp"
57	#include "visitors/ZconsVisitor.hpp"
58	#include "selection/SelectionEvaluator.hpp"
59	#include "selection/SelectionManager.hpp"
60	#include "visitors/LipidTransVisitor.hpp"
61	#include "visitors/AtomNameVisitor.hpp"
62
63	using namespace OpenMD;
64
65	int main(int argc, char* argv[]){
66
67	//register force fields
68	registerForceFields();
69
70	gengetopt_args_info args_info;
71	std::string dumpFileName;
72	std::string xyzFileName;
73
74	//parse the command line option
75	if (cmdline_parser (argc, argv, &args_info) != 0) {
76	exit(1) ;
77	}
78
79	//get the dumpfile name and meta-data file name
80	if (args_info.input_given){
81	dumpFileName = args_info.input_arg;
82	} else {
83	std::cerr << "Does not have input file name" << std::endl;
84	exit(1);
85	}
86
87	if (args_info.output_given){
88	xyzFileName = args_info.output_arg;
89	} else {
90	xyzFileName = dumpFileName;
91	xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
92	}
93
94	//parse md file and set up the system
95	SimCreator creator;
96	SimInfo* info = creator.createSim(dumpFileName, false);
97
98	//create visitor list
99	CompositeVisitor* compositeVisitor = new CompositeVisitor();
100
101	//create RigidBody Visitor
102	if(args_info.rigidbody_flag){
103	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104	compositeVisitor->addVisitor(rbCOMVisitor, 900);
105	}
106
107	//create SSD atom visitor
108	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109	compositeVisitor->addVisitor(ssdVisitor, 800);
110
111	//create default atom visitor
112	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
113	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
114
115	// 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	}
123
124	if (args_info.basetype_flag) {
125	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
126	compositeVisitor->addVisitor(atomNameVisitor, 550);
127	std::cout << compositeVisitor->toString();
128	}
129
130	//create ZconsVisitor
131	if(args_info.zconstraint_flag){
132
133	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
134
135	if(zconsVisitor->haveZconsMol()) {
136	compositeVisitor->addVisitor(zconsVisitor, 500);
137	} else {
138	delete zconsVisitor;
139	}
140	}
141
142	//create wrapping visitor
143
144	//if(args_info.periodicBox_flag){
145	// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
146	// compositeVisitor->addVisitor(wrappingVisitor, 400);
147	//}
148
149	//create replicate visitor
150	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
151	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
152	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
153	compositeVisitor->addVisitor(replicateVisitor, 300);
154	}
155
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	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
162	exit(1);
163	}
164
165	//create xyzVisitor
166	XYZVisitor* xyzVisitor;
167
168	if (args_info.selection_given) {
169	xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
170	} else {
171	xyzVisitor = new XYZVisitor(info);
172	}
173
174	if(args_info.printPosOnly_flag){
175	bool posOnly = true;
176	xyzVisitor->setPosOnly(posOnly);
177	}
178
179	compositeVisitor->addVisitor(xyzVisitor, 200);
180
181	//create prepareVisitor
182	PrepareVisitor* prepareVisitor = new PrepareVisitor();
183
184	//open dump file
185	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
186	int nframes = dumpReader->getNFrames();
187
188
189	std::ofstream xyzStream(xyzFileName.c_str());
190
191	SimInfo::MoleculeIterator miter;
192	Molecule::IntegrableObjectIterator iiter;
193	Molecule::RigidBodyIterator rbIter;
194	Molecule* mol;
195	StuntDouble* integrableObject;
196	RigidBody* rb;
197	Vector3d molCom;
198	Vector3d newMolCom;
199	Vector3d displacement;
200	Mat3x3d hmat;
201	Snapshot* currentSnapshot;
202
203	for (int i = 0; i < nframes; i += args_info.frame_arg){
204	dumpReader->readFrame(i);
205
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	//update atoms of rigidbody
221	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
229	//prepare visit
230	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	//update visitor
238	compositeVisitor->update();
239
240
241	//visit stuntdouble
242	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	}
248
249	xyzVisitor->writeFrame(xyzStream);
250	xyzVisitor->clear();
251
252	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
253
254	xyzStream.close();
255	delete prepareVisitor;
256	delete compositeVisitor;
257	delete info;
258	}