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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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>
#	Line 50 | Line 50
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"
#	Line 57 | Line 58
58		#include "selection/SelectionEvaluator.hpp"
59		#include "selection/SelectionManager.hpp"
60		#include "visitors/LipidTransVisitor.hpp"
61	+	#include "visitors/AtomNameVisitor.hpp"
62
63	<	using namespace oopse;
63	>	using namespace OpenMD;
64
65		int main(int argc, char* argv[]){
66
#	Line 67 | Line 69 | int main(int argc, char* argv[]){
69
70		gengetopt_args_info args_info;
71		std::string dumpFileName;
70	–	std::string mdFileName;
72		std::string xyzFileName;
73
74		//parse the command line option
#	Line 83 | Line 84 | int main(int argc, char* argv[]){
84		exit(1);
85		}
86
86	–	mdFileName = dumpFileName;
87	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88	–
87		if (args_info.output_given){
88		xyzFileName = args_info.output_arg;
89		} else {
#	Line 95 | Line 93 | int main(int argc, char* argv[]){
93
94		//parse md file and set up the system
95		SimCreator creator;
96	<	SimInfo* info = creator.createSim(mdFileName, false);
96	>	SimInfo* info = creator.createSim(dumpFileName, false);
97
98	<
101	<
102	<	//creat visitor list
98	>	//create visitor list
99		CompositeVisitor* compositeVisitor = new CompositeVisitor();
100	<
101	<	//creat RigidBody Visitor
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	<	//creat SSD atom visitor
107	>	//create SSD atom visitor
108		SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109		compositeVisitor->addVisitor(ssdVisitor, 800);
110
111	<	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
116	<	compositeVisitor->addVisitor(linearVisitor, 750);
117	<
118	<	//creat default atom visitor
111	>	//create default atom visitor
112		DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
113		compositeVisitor->addVisitor(defaultAtomVisitor, 700);
114
115	<	//creat waterType visitor
116	<	if(args_info.watertype_flag){
117	<	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
118	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
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
#	Line 137 | Line 139 | int main(int argc, char* argv[]){
139		}
140		}
141
142	<	//creat wrapping visitor
142	>	//create wrapping visitor
143
144	<	if(args_info.periodicBox_flag){
145	<	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
146	<	compositeVisitor->addVisitor(wrappingVisitor, 400);
147	<	}
144	>	//if(args_info.periodicBox_flag){
145	>	//  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
146	>	//  compositeVisitor->addVisitor(wrappingVisitor, 400);
147	>	//}
148
149	<	//creat replicate visitor
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);
#	Line 160 | Line 162 | int main(int argc, char* argv[]){
162		exit(1);
163		}
164
165	<	//creat xyzVisitor
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	<	compositeVisitor->addVisitor(xyzVisitor, 200);
173	>
174	>	if(args_info.printPosOnly_flag){
175	>	bool posOnly = true;
176	>	xyzVisitor->setPosOnly(posOnly);
177	>	}
178	>
179	>	compositeVisitor->addVisitor(xyzVisitor, 200);
180
181	<	std::cout << compositeVisitor->toString();
173	<
174	<	//creat prepareVisitor
181	>	//create prepareVisitor
182		PrepareVisitor* prepareVisitor = new PrepareVisitor();
183
184		//open dump file
#	Line 179 | Line 186 | int main(int argc, char* argv[]){
186		int nframes = dumpReader->getNFrames();
187
188
189	<	std::ofstream xyzStream;
183	<	xyzStream .open(xyzFileName.c_str());
189	>	std::ofstream xyzStream(xyzFileName.c_str());
190
185	–
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	<
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
#	Line 226 | Line 250 | int main(int argc, char* argv[]){
250		xyzVisitor->clear();
251
252		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
253	<
253	>
254		xyzStream.close();
231	–
255		delete prepareVisitor;
256		delete compositeVisitor;
257		delete info;
235	–
258		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 0 | Line 1
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