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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 968 by tim, Tue May 23 18:46:11 2006 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 59 | Line 60
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 68 | Line 69 | int main(int argc, char* argv[]){
69
70		gengetopt_args_info args_info;
71		std::string dumpFileName;
71	–	std::string mdFileName;
72		std::string xyzFileName;
73
74		//parse the command line option
#	Line 84 | Line 84 | int main(int argc, char* argv[]){
84		exit(1);
85		}
86
87	–	mdFileName = dumpFileName;
88	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
89	–
87		if (args_info.output_given){
88		xyzFileName = args_info.output_arg;
89		} else {
#	Line 96 | 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
101	–
102	–
98		//create visitor list
99		CompositeVisitor* compositeVisitor = new CompositeVisitor();
100	<
100	>
101		//create RigidBody Visitor
102		if(args_info.rigidbody_flag){
103		RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
#	Line 113 | Line 108 | int main(int argc, char* argv[]){
108		SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109		compositeVisitor->addVisitor(ssdVisitor, 800);
110
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	–
111		//create default atom visitor
112		DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
113		compositeVisitor->addVisitor(defaultAtomVisitor, 700);
114
115	<	//create waterType visitor
116	<	if(args_info.watertype_flag){
117	<	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
118	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
119	<	}
120	<
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	<
125	>	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
126	>	compositeVisitor->addVisitor(atomNameVisitor, 550);
127	>	std::cout << compositeVisitor->toString();
128		}
129
130		//create ZconsVisitor
#	Line 175 | Line 164 | int main(int argc, char* argv[]){
164
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
185	–	std::cout << compositeVisitor->toString();
186	–
181		//create prepareVisitor
182		PrepareVisitor* prepareVisitor = new PrepareVisitor();
183
#	Line 192 | Line 186 | int main(int argc, char* argv[]){
186		int nframes = dumpReader->getNFrames();
187
188
189	<	std::ofstream xyzStream;
196	<	xyzStream .open(xyzFileName.c_str());
189	>	std::ofstream xyzStream(xyzFileName.c_str());
190
198	–
191		SimInfo::MoleculeIterator miter;
192		Molecule::IntegrableObjectIterator  iiter;
193		Molecule::RigidBodyIterator rbIter;
#	Line 258 | 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();
263	–
255		delete prepareVisitor;
256		delete compositeVisitor;
257		delete info;
267	–
258		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 968 by tim, Tue May 23 18:46:11 2006 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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