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;
       
  for (int i = 0; i < nframes; i += args_info.frame_arg){
    dumpReader->readFrame(i);
    
    //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:	2749
Committed:	Wed May 10 01:44:48 2006 UTC (18 years, 2 months ago) by tim
File size:	8331 byte(s)
Log Message:	adding a gay-berne switch to Dump2XYZ
#	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 mdFileName;
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	mdFileName = dumpFileName;
88	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
89
90	if (args_info.output_given){
91	xyzFileName = args_info.output_arg;
92	} else {
93	xyzFileName = dumpFileName;
94	xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
95	}
96
97	//parse md file and set up the system
98	SimCreator creator;
99	SimInfo* info = creator.createSim(mdFileName, false);
100
101
102
103	//create visitor list
104	CompositeVisitor* compositeVisitor = new CompositeVisitor();
105
106	//create RigidBody Visitor
107	if(args_info.rigidbody_flag){
108	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
109	compositeVisitor->addVisitor(rbCOMVisitor, 900);
110	}
111
112	//create SSD atom visitor
113	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
114	compositeVisitor->addVisitor(ssdVisitor, 800);
115
116	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
117	compositeVisitor->addVisitor(linearVisitor, 750);
118	if (args_info.gb_given) {
119	linearVisitor->addGayBerneAtomType(args_info.gb_arg);
120	}
121
122	GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
123	compositeVisitor->addVisitor(gbLipidVisitor, 740);
124
125	//create default atom visitor
126	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
127	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
128
129	//create waterType visitor
130	if(args_info.watertype_flag){
131	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
132	compositeVisitor->addVisitor(waterTypeVisitor, 600);
133	}
134
135	if (args_info.basetype_flag) {
136	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
137	compositeVisitor->addVisitor(atomNameVisitor, 550);
138
139	}
140
141	//create ZconsVisitor
142	if(args_info.zconstraint_flag){
143
144	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
145
146	if(zconsVisitor->haveZconsMol()) {
147	compositeVisitor->addVisitor(zconsVisitor, 500);
148	} else {
149	delete zconsVisitor;
150	}
151	}
152
153	//create wrapping visitor
154
155	if(args_info.periodicBox_flag){
156	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
157	compositeVisitor->addVisitor(wrappingVisitor, 400);
158	}
159
160	//create replicate visitor
161	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
162	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
163	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
164	compositeVisitor->addVisitor(replicateVisitor, 300);
165	}
166
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	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
173	exit(1);
174	}
175
176	//create xyzVisitor
177	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	compositeVisitor->addVisitor(xyzVisitor, 200);
184
185	std::cout << compositeVisitor->toString();
186
187	//create prepareVisitor
188	PrepareVisitor* prepareVisitor = new PrepareVisitor();
189
190	//open dump file
191	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
192	int nframes = dumpReader->getNFrames();
193
194
195	std::ofstream xyzStream;
196	xyzStream .open(xyzFileName.c_str());
197
198
199	SimInfo::MoleculeIterator miter;
200	Molecule::IntegrableObjectIterator iiter;
201	Molecule::RigidBodyIterator rbIter;
202	Molecule* mol;
203	StuntDouble* integrableObject;
204	RigidBody* rb;
205
206	for (int i = 0; i < nframes; i += args_info.frame_arg){
207	dumpReader->readFrame(i);
208
209	//update atoms of rigidbody
210	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
211
212	//change the positions of atoms which belong to the rigidbodies
213	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
214	rb->updateAtoms();
215	}
216	}
217
218	//prepare visit
219	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
220	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
221	integrableObject = mol->nextIntegrableObject(iiter)) {
222	integrableObject->accept(prepareVisitor);
223	}
224	}
225
226	//update visitor
227	compositeVisitor->update();
228
229
230	//visit stuntdouble
231	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
232	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
233	integrableObject = mol->nextIntegrableObject(iiter)) {
234	integrableObject->accept(compositeVisitor);
235	}
236	}
237
238	xyzVisitor->writeFrame(xyzStream);
239	xyzVisitor->clear();
240
241	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
242
243	xyzStream.close();
244
245	delete prepareVisitor;
246	delete compositeVisitor;
247	delete info;
248
249	}