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;    
  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:	3321
Committed:	Wed Jan 23 21:21:13 2008 UTC (16 years, 5 months ago) by xsun
File size:	9318 byte(s)
Log Message:	Added a few visitors
#	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. 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	#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/CompositeVisitor.hpp"
54	#include "visitors/RigidBodyVisitor.hpp"
55	#include "visitors/OtherVisitor.hpp"
56	#include "visitors/ZconsVisitor.hpp"
57	#include "selection/SelectionEvaluator.hpp"
58	#include "selection/SelectionManager.hpp"
59	#include "visitors/LipidTransVisitor.hpp"
60	#include "visitors/AtomNameVisitor.hpp"
61
62	using namespace oopse;
63
64	int main(int argc, char* argv[]){
65
66	//register force fields
67	registerForceFields();
68
69	gengetopt_args_info args_info;
70	std::string dumpFileName;
71	std::string xyzFileName;
72
73	//parse the command line option
74	if (cmdline_parser (argc, argv, &args_info) != 0) {
75	exit(1) ;
76	}
77
78	//get the dumpfile name and meta-data file name
79	if (args_info.input_given){
80	dumpFileName = args_info.input_arg;
81	} else {
82	std::cerr << "Does not have input file name" << std::endl;
83	exit(1);
84	}
85
86	if (args_info.output_given){
87	xyzFileName = args_info.output_arg;
88	} else {
89	xyzFileName = dumpFileName;
90	xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
91	}
92
93	//parse md file and set up the system
94	SimCreator creator;
95	SimInfo* info = creator.createSim(dumpFileName, false);
96
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	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112	compositeVisitor->addVisitor(linearVisitor, 750);
113	if (args_info.gb_given) {
114	linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115	}
116
117	GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118	compositeVisitor->addVisitor(gbLipidVisitor, 740);
119
120	Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
121	compositeVisitor->addVisitor(ring5Visitor, 730);
122
123	HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
124	compositeVisitor->addVisitor(headVisitor, 720);
125
126	//create default atom visitor
127	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129
130	//create waterType visitor
131	if(args_info.watertype_flag){
132	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133	compositeVisitor->addVisitor(waterTypeVisitor, 600);
134	}
135
136	if (args_info.basetype_flag) {
137	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
138	compositeVisitor->addVisitor(atomNameVisitor, 550);
139
140	}
141
142	//create ZconsVisitor
143	if(args_info.zconstraint_flag){
144
145	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
146
147	if(zconsVisitor->haveZconsMol()) {
148	compositeVisitor->addVisitor(zconsVisitor, 500);
149	} else {
150	delete zconsVisitor;
151	}
152	}
153
154	//create wrapping visitor
155
156	//if(args_info.periodicBox_flag){
157	// WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
158	// compositeVisitor->addVisitor(wrappingVisitor, 400);
159	//}
160
161	//create replicate visitor
162	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
163	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
164	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
165	compositeVisitor->addVisitor(replicateVisitor, 300);
166	}
167
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	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
174	exit(1);
175	}
176
177	//create xyzVisitor
178	XYZVisitor* xyzVisitor;
179
180	if (args_info.selection_given) {
181	xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
182	} else {
183	xyzVisitor = new XYZVisitor(info);
184	}
185
186	if(args_info.printPosOnly_flag){
187	bool posOnly = true;
188	xyzVisitor->setPosOnly(posOnly);
189	}
190
191	compositeVisitor->addVisitor(xyzVisitor, 200);
192
193	std::cout << compositeVisitor->toString();
194
195	//create prepareVisitor
196	PrepareVisitor* prepareVisitor = new PrepareVisitor();
197
198	//open dump file
199	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
200	int nframes = dumpReader->getNFrames();
201
202
203	std::ofstream xyzStream;
204	xyzStream .open(xyzFileName.c_str());
205
206
207	SimInfo::MoleculeIterator miter;
208	Molecule::IntegrableObjectIterator iiter;
209	Molecule::RigidBodyIterator rbIter;
210	Molecule* mol;
211	StuntDouble* integrableObject;
212	RigidBody* rb;
213	Vector3d molCom;
214	Vector3d newMolCom;
215	Vector3d displacement;
216	Mat3x3d hmat;
217	Snapshot* currentSnapshot;
218
219	for (int i = 0; i < nframes; i += args_info.frame_arg){
220	dumpReader->readFrame(i);
221
222	//wrapping the molecule
223	if(args_info.periodicBox_flag) {
224	currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
225	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
226	molCom = mol->getCom();
227	newMolCom = molCom;
228	currentSnapshot->wrapVector(newMolCom);
229	displacement = newMolCom - molCom;
230	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
231	integrableObject = mol->nextIntegrableObject(iiter)) {
232	integrableObject->setPos(integrableObject->getPos() + displacement);
233	}
234	}
235	}
236	//update atoms of rigidbody
237	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
238
239	//change the positions of atoms which belong to the rigidbodies
240	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
241	rb->updateAtoms();
242	}
243	}
244
245	//prepare visit
246	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
247	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
248	integrableObject = mol->nextIntegrableObject(iiter)) {
249	integrableObject->accept(prepareVisitor);
250	}
251	}
252
253	//update visitor
254	compositeVisitor->update();
255
256
257	//visit stuntdouble
258	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
259	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
260	integrableObject = mol->nextIntegrableObject(iiter)) {
261	integrableObject->accept(compositeVisitor);
262	}
263	}
264
265	xyzVisitor->writeFrame(xyzStream);
266	xyzVisitor->clear();
267
268	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
269
270	xyzStream.close();
271
272	delete prepareVisitor;
273	delete compositeVisitor;
274	delete info;
275
276	}