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"

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(info);
    
    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);
  }
  
  //create selection visitor
  //if (args_info.selection_given){
  //  SelectionVisitor* selectionVisitor = new SelectionVisitor(info, args_info.selection_arg);
  //  compositeVisitor->addVisitor(selectionVisitor, 850);
  //}

  SelectionEvaluator* evaluator = NULL;
  if (args_info.selection_given) {
    evaluator = new SelectionEvaluator(info);
    assert(evaluator);
    evaluator->loadScriptString( args_info.selection_arg);
          
  }
  
  //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);
  }


  //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 --originselc should appear by pair" << std::endl;
    exit(1);
  }
    
  //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;

  if (evaluator && !evaluator->isDynamic()) {
    info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
  }
  
  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();

    //if dynamic, we need to re-evaluate the selection
    if (evaluator && evaluator->isDynamic()) {
      info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
    }
    
    //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:	369
Committed:	Fri Feb 18 23:07:32 2005 UTC (20 years, 8 months ago) by tim
File size:	9324 byte(s)
Log Message:	adding LipidTransVisitor, GofXyz is working now
#	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
61	using namespace oopse;
62
63	int main(int argc, char* argv[]){
64
65	//register force fields
66	registerForceFields();
67
68	gengetopt_args_info args_info;
69	std::string dumpFileName;
70	std::string mdFileName;
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	mdFileName = dumpFileName;
87	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88
89	if (args_info.output_given){
90	xyzFileName = args_info.output_arg;
91	} else {
92	xyzFileName = dumpFileName;
93	xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
94	}
95
96	//parse md file and set up the system
97	SimCreator creator;
98	SimInfo* info = creator.createSim(mdFileName, false);
99
100
101
102	//creat visitor list
103	CompositeVisitor* compositeVisitor = new CompositeVisitor();
104
105	//creat ignore visitor
106	if(args_info.ignore_given \|\|args_info.water_flag){
107
108	IgnoreVisitor* ignoreVisitor = new IgnoreVisitor(info);
109
110	for(int i = 0; i < args_info.ignore_given; i++)
111	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
112
113	//ignore water
114	if(args_info.water_flag){
115	ignoreVisitor->addIgnoreType("SSD");
116	ignoreVisitor->addIgnoreType("SSD1");
117	ignoreVisitor->addIgnoreType("SSD_E");
118	ignoreVisitor->addIgnoreType("SSD_RF");
119	ignoreVisitor->addIgnoreType("TIP3P_RB_0");
120	ignoreVisitor->addIgnoreType("TIP4P_RB_0");
121	ignoreVisitor->addIgnoreType("TIP5P_RB_0");
122	ignoreVisitor->addIgnoreType("SPCE_RB_0");
123	ignoreVisitor->addIgnoreType("DPD_RB_0");
124	}
125
126	compositeVisitor->addVisitor(ignoreVisitor, 1000);
127	}
128
129	//creat RigidBody Visitor
130	if(args_info.rigidbody_flag){
131	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
132	compositeVisitor->addVisitor(rbCOMVisitor, 900);
133	}
134
135	//create selection visitor
136	//if (args_info.selection_given){
137	// SelectionVisitor* selectionVisitor = new SelectionVisitor(info, args_info.selection_arg);
138	// compositeVisitor->addVisitor(selectionVisitor, 850);
139	//}
140
141	SelectionEvaluator* evaluator = NULL;
142	if (args_info.selection_given) {
143	evaluator = new SelectionEvaluator(info);
144	assert(evaluator);
145	evaluator->loadScriptString( args_info.selection_arg);
146
147	}
148
149	//creat SSD atom visitor
150	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
151	compositeVisitor->addVisitor(ssdVisitor, 800);
152
153	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
154	compositeVisitor->addVisitor(linearVisitor, 750);
155
156	//creat default atom visitor
157	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
158	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
159
160	//creat waterType visitor
161	if(args_info.watertype_flag){
162	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
163	compositeVisitor->addVisitor(waterTypeVisitor, 600);
164	}
165
166	//create ZconsVisitor
167	if(args_info.zconstraint_flag){
168
169	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
170
171	if(zconsVisitor->haveZconsMol()) {
172	compositeVisitor->addVisitor(zconsVisitor, 500);
173	} else {
174	delete zconsVisitor;
175	}
176	}
177
178	//creat wrapping visitor
179
180	if(args_info.periodicBox_flag){
181	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
182	compositeVisitor->addVisitor(wrappingVisitor, 400);
183	}
184
185	//creat replicate visitor
186	if(args_info.repeatX_given > 0 \|\| args_info.repeatY_given > 0 \|\|args_info.repeatY_given > 0){
187	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
188	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
189	compositeVisitor->addVisitor(replicateVisitor, 300);
190	}
191
192
193	//create rotation visitor
194	if (args_info.refsele_given&& args_info.originsele_given) {
195	compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
196	} else if (args_info.refsele_given \|\| args_info.originsele_given) {
197	std::cerr << "Both of --refsele and --originselc should appear by pair" << std::endl;
198	exit(1);
199	}
200
201	//creat xyzVisitor
202	XYZVisitor* xyzVisitor = new XYZVisitor(info);
203	compositeVisitor->addVisitor(xyzVisitor, 200);
204
205	std::cout << compositeVisitor->toString();
206
207	//creat prepareVisitor
208	PrepareVisitor* prepareVisitor = new PrepareVisitor();
209
210	//open dump file
211	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
212	int nframes = dumpReader->getNFrames();
213
214
215	std::ofstream xyzStream;
216	xyzStream .open(xyzFileName.c_str());
217
218
219	SimInfo::MoleculeIterator miter;
220	Molecule::IntegrableObjectIterator iiter;
221	Molecule::RigidBodyIterator rbIter;
222	Molecule* mol;
223	StuntDouble* integrableObject;
224	RigidBody* rb;
225
226	if (evaluator && !evaluator->isDynamic()) {
227	info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
228	}
229
230	for (int i = 0; i < nframes; i += args_info.frame_arg){
231	dumpReader->readFrame(i);
232
233	//update atoms of rigidbody
234	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
235
236	//change the positions of atoms which belong to the rigidbodies
237	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
238	rb->updateAtoms();
239	}
240	}
241
242	//prepare visit
243	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
244	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
245	integrableObject = mol->nextIntegrableObject(iiter)) {
246	integrableObject->accept(prepareVisitor);
247	}
248	}
249
250	//update visitor
251	compositeVisitor->update();
252
253	//if dynamic, we need to re-evaluate the selection
254	if (evaluator && evaluator->isDynamic()) {
255	info->getSelectionManager()->setSelectionSet(evaluator->evaluate());
256	}
257
258	//visit stuntdouble
259	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
260	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
261	integrableObject = mol->nextIntegrableObject(iiter)) {
262	integrableObject->accept(compositeVisitor);
263	}
264	}
265
266	xyzVisitor->writeFrame(xyzStream);
267	xyzVisitor->clear();
268
269	}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
270
271	xyzStream.close();
272
273
274	delete compositeVisitor;
275	delete info;
276
277	}