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"
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);
  
  
  
  //creat visitor list
  CompositeVisitor* compositeVisitor = new CompositeVisitor();
  
  //creat ignore visitor
  if(args_info.ignore_given ||args_info.water_flag){
    
    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
    
    for(int i = 0; i < args_info.ignore_given; i++)
      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
    
    //ignore water 
    if(args_info.water_flag){
      ignoreVisitor->addIgnoreType("SSD");
      ignoreVisitor->addIgnoreType("SSD1");
      ignoreVisitor->addIgnoreType("SSD_E");
      ignoreVisitor->addIgnoreType("SSD_RF");
      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
      ignoreVisitor->addIgnoreType("DPD_RB_0");
    }
    
    compositeVisitor->addVisitor(ignoreVisitor, 1000);
  }
  
  //creat RigidBody Visitor
  if(args_info.rigidbody_flag){
    RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
    compositeVisitor->addVisitor(rbCOMVisitor, 900);
  }
  
  //compositeVisitor->addVisitor(lipidVisitor, 900);
  
  //creat SSD atom visitor
  SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
  compositeVisitor->addVisitor(ssdVisitor, 800);
  
  LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
  compositeVisitor->addVisitor(linearVisitor, 750);
  
  //creat default atom visitor
  DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
  compositeVisitor->addVisitor(defaultAtomVisitor, 700);
  
  //creat waterType visitor
  if(args_info.watertype_flag){
    WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
    compositeVisitor->addVisitor(waterTypeVisitor, 600);
  }
  
  //create ZconsVisitor
  if(args_info.zconstraint_flag){

    ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
    
    if(zconsVisitor->haveZconsMol()) {
      compositeVisitor->addVisitor(zconsVisitor, 500);
    } else {
      delete zconsVisitor;
    }
  }
  
  //creat wrapping visitor
  
  if(args_info.periodicBox_flag){
    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
    compositeVisitor->addVisitor(wrappingVisitor, 400);
  }
  
  //creat 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);
  }
  
  //creat xyzVisitor
  XYZVisitor* xyzVisitor = new XYZVisitor(info);
  compositeVisitor->addVisitor(xyzVisitor, 200);
  
  std::cout << compositeVisitor->toString();
  
  //creat 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 compositeVisitor;
  delete info;
   
}
Revision:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	8104 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	User	Rev	Content
1	gezelter	1930	/*
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	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	gezelter	1930	using namespace oopse;
58	tim	1501
59			int main(int argc, char* argv[]){
60	gezelter	1930
61			//register force fields
62			registerForceFields();
63
64	tim	1501	gengetopt_args_info args_info;
65	gezelter	1930	std::string dumpFileName;
66			std::string mdFileName;
67			std::string xyzFileName;
68	tim	1501
69	gezelter	1930	//parse the command line option
70			if (cmdline_parser (argc, argv, &args_info) != 0) {
71			exit(1) ;
72			}
73	tim	1501
74			//get the dumpfile name and meta-data file name
75			if (args_info.input_given){
76			dumpFileName = args_info.input_arg;
77	gezelter	1930	} else {
78			std::cerr << "Does not have input file name" << std::endl;
79	tim	1501	exit(1);
80			}
81	gezelter	1930
82	tim	1501	mdFileName = dumpFileName;
83			mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
84	tim	1957
85	tim	1501	if (args_info.output_given){
86			xyzFileName = args_info.output_arg;
87	gezelter	1930	} else {
88	tim	1501	xyzFileName = dumpFileName;
89			xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
90			}
91	gezelter	1930
92	tim	1501	//parse md file and set up the system
93	gezelter	1930	SimCreator creator;
94	tim	1957	SimInfo* info = creator.createSim(mdFileName, false);
95	tim	1501
96	gezelter	1930
97
98	tim	1501	//creat visitor list
99	gezelter	1930	CompositeVisitor* compositeVisitor = new CompositeVisitor();
100
101	tim	1501	//creat ignore visitor
102			if(args_info.ignore_given \|\|args_info.water_flag){
103
104	gezelter	1930	IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
105
106	tim	1501	for(int i = 0; i < args_info.ignore_given; i++)
107			ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
108	gezelter	1930
109	tim	1501	//ignore water
110			if(args_info.water_flag){
111			ignoreVisitor->addIgnoreType("SSD");
112			ignoreVisitor->addIgnoreType("SSD1");
113			ignoreVisitor->addIgnoreType("SSD_E");
114			ignoreVisitor->addIgnoreType("SSD_RF");
115			ignoreVisitor->addIgnoreType("TIP3P_RB_0");
116			ignoreVisitor->addIgnoreType("TIP4P_RB_0");
117			ignoreVisitor->addIgnoreType("TIP5P_RB_0");
118			ignoreVisitor->addIgnoreType("SPCE_RB_0");
119			ignoreVisitor->addIgnoreType("DPD_RB_0");
120			}
121	gezelter	1930
122			compositeVisitor->addVisitor(ignoreVisitor, 1000);
123	tim	1501	}
124	gezelter	1930
125	tim	1501	//creat RigidBody Visitor
126			if(args_info.rigidbody_flag){
127	gezelter	1930	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
128	tim	1501	compositeVisitor->addVisitor(rbCOMVisitor, 900);
129			}
130	gezelter	1930
131	tim	1501	//compositeVisitor->addVisitor(lipidVisitor, 900);
132	gezelter	1930
133	tim	1501	//creat SSD atom visitor
134	gezelter	1930	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
135	tim	1501	compositeVisitor->addVisitor(ssdVisitor, 800);
136	gezelter	1930
137	tim	1934	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
138	chrisfen	1718	compositeVisitor->addVisitor(linearVisitor, 750);
139	gezelter	1930
140	tim	1501	//creat default atom visitor
141	gezelter	1930	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
142	tim	1501	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
143	gezelter	1930
144	tim	1501	//creat waterType visitor
145			if(args_info.watertype_flag){
146	gezelter	1930	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
147	tim	1501	compositeVisitor->addVisitor(waterTypeVisitor, 600);
148			}
149	gezelter	1930
150	tim	1501	//create ZconsVisitor
151			if(args_info.zconstraint_flag){
152	gezelter	1930
153			ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
154	tim	1501
155	gezelter	1930	if(zconsVisitor->haveZconsMol()) {
156	tim	1501	compositeVisitor->addVisitor(zconsVisitor, 500);
157	gezelter	1930	} else {
158	tim	1501	delete zconsVisitor;
159	gezelter	1930	}
160	tim	1501	}
161	gezelter	1930
162	tim	1501	//creat wrapping visitor
163	gezelter	1930
164	tim	1501	if(args_info.periodicBox_flag){
165	gezelter	1930	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
166	tim	1501	compositeVisitor->addVisitor(wrappingVisitor, 400);
167			}
168
169			//creat replicate visitor
170			if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
171	gezelter	1930	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
172			ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
173	tim	1501	compositeVisitor->addVisitor(replicateVisitor, 300);
174			}
175	gezelter	1930
176	tim	1501	//creat xyzVisitor
177	gezelter	1930	XYZVisitor* xyzVisitor = new XYZVisitor(info);
178	tim	1501	compositeVisitor->addVisitor(xyzVisitor, 200);
179	gezelter	1930
180			std::cout << compositeVisitor->toString();
181
182	tim	1501	//creat prepareVisitor
183	gezelter	1930	PrepareVisitor* prepareVisitor = new PrepareVisitor();
184
185	tim	1501	//open dump file
186	gezelter	1930	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
187			int nframes = dumpReader->getNFrames();
188
189
190			std::ofstream xyzStream;
191	tim	1501	xyzStream .open(xyzFileName.c_str());
192
193	gezelter	1930
194			SimInfo::MoleculeIterator miter;
195			Molecule::IntegrableObjectIterator iiter;
196			Molecule::RigidBodyIterator rbIter;
197			Molecule* mol;
198			StuntDouble* integrableObject;
199			RigidBody* rb;
200
201	tim	1501	for (int i = 0; i < nframes; i += args_info.frame_arg){
202	gezelter	1930	dumpReader->readFrame(i);
203
204	tim	1501	//update atoms of rigidbody
205	gezelter	1930	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
206
207			//change the positions of atoms which belong to the rigidbodies
208			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
209			rb->updateAtoms();
210			}
211			}
212	tim	1501
213			//prepare visit
214	gezelter	1930	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
215			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
216			integrableObject = mol->nextIntegrableObject(iiter)) {
217			integrableObject->accept(prepareVisitor);
218			}
219			}
220
221	tim	1501	//update visitor
222			compositeVisitor->update();
223
224			//visit stuntdouble
225	gezelter	1930	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
226			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
227			integrableObject = mol->nextIntegrableObject(iiter)) {
228			integrableObject->accept(compositeVisitor);
229			}
230	tim	1501	}
231	gezelter	1930
232	tim	1501	xyzVisitor->writeFrame(xyzStream);
233			xyzVisitor->clear();
234
235			}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
236	gezelter	1930
237	tim	1501	xyzStream.close();
238	gezelter	1930
239
240	tim	1501	delete compositeVisitor;
241			delete info;
242	gezelter	1930
243	tim	1501	}