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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 1212 by xsun, Wed Jan 23 21:21:13 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <iostream>
#	Line 47 | Line 48
48		#include "brains/Register.hpp"
49		#include "brains/SimCreator.hpp"
50		#include "brains/SimInfo.hpp"
51	+	#include "brains/ForceManager.hpp"
52		#include "io/DumpReader.hpp"
53		#include "utils/simError.h"
54		#include "visitors/AtomVisitor.hpp"
55	+	#include "visitors/ReplacementVisitor.hpp"
56		#include "visitors/CompositeVisitor.hpp"
57		#include "visitors/RigidBodyVisitor.hpp"
58		#include "visitors/OtherVisitor.hpp"
#	Line 59 | Line 62
62		#include "visitors/LipidTransVisitor.hpp"
63		#include "visitors/AtomNameVisitor.hpp"
64
65	<	using namespace oopse;
65	>	using namespace OpenMD;
66
67	+	using namespace std;
68		int main(int argc, char* argv[]){
69
66	–	//register force fields
67	–	registerForceFields();
68	–
70		gengetopt_args_info args_info;
71	<	std::string dumpFileName;
72	<	std::string xyzFileName;
71	>	string dumpFileName;
72	>	string xyzFileName;
73	>
74	>	bool printVel(false);
75	>	bool printFrc(false);
76	>	bool printVec(false);
77	>	bool printChrg(false);
78	>	bool printField(false);
79
80		//parse the command line option
81		if (cmdline_parser (argc, argv, &args_info) != 0) {
#	Line 79 | Line 86 | int main(int argc, char* argv[]){
86		if (args_info.input_given){
87		dumpFileName = args_info.input_arg;
88		} else {
89	<	std::cerr << "Does not have input file name" << std::endl;
89	>	cerr << "Does not have input file name" << endl;
90		exit(1);
91		}
92
#	Line 93 | Line 100 | int main(int argc, char* argv[]){
100		//parse md file and set up the system
101		SimCreator creator;
102		SimInfo* info = creator.createSim(dumpFileName, false);
103	+	ForceManager* forceMan = new ForceManager(info);
104
97	–
105		//create visitor list
106		CompositeVisitor* compositeVisitor = new CompositeVisitor();
107	<
107	>
108		//create RigidBody Visitor
109		if(args_info.rigidbody_flag){
110		RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
#	Line 107 | Line 114 | int main(int argc, char* argv[]){
114		//create SSD atom visitor
115		SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
116		compositeVisitor->addVisitor(ssdVisitor, 800);
110	–
111	–	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
112	–	compositeVisitor->addVisitor(linearVisitor, 750);
113	–	if (args_info.gb_given) {
114	–	linearVisitor->addGayBerneAtomType(args_info.gb_arg);
115	–	}
116	–
117	–	GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
118	–	compositeVisitor->addVisitor(gbLipidVisitor, 740);
117
118	<	Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info);
119	<	compositeVisitor->addVisitor(ring5Visitor, 730);
118	>	//create GBtail atom visitor
119	>	GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
120	>	compositeVisitor->addVisitor(gbtVisitor, 790);
121
122	<	HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info);
123	<	compositeVisitor->addVisitor(headVisitor, 720);
124	<
122	>	//create GBhead atom visitor
123	>	GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
124	>	compositeVisitor->addVisitor(gbhVisitor, 789);
125	>
126		//create default atom visitor
127		DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
128		compositeVisitor->addVisitor(defaultAtomVisitor, 700);
129
130	<	//create waterType visitor
131	<	if(args_info.watertype_flag){
132	<	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
133	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
134	<	}
135	<
130	>	// if we gave the -w option, we want to skip the waters:
131	>	if (!args_info.water_given) {
132	>	//create waterType visitor
133	>	if(args_info.watertype_flag){
134	>	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
135	>	compositeVisitor->addVisitor(waterTypeVisitor, 600);
136	>	}
137	>	}
138	>
139		if (args_info.basetype_flag) {
140	<	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
141	<	compositeVisitor->addVisitor(atomNameVisitor, 550);
142	<
140	>	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
141	>	compositeVisitor->addVisitor(atomNameVisitor, 550);
142	>	cout << compositeVisitor->toString();
143		}
144
145		//create ZconsVisitor
#	Line 159 | Line 162 | int main(int argc, char* argv[]){
162		//}
163
164		//create replicate visitor
165	<	if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
166	<	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
167	<	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
165	>	if(args_info.repeatX_given > 0 ||
166	>	args_info.repeatY_given > 0 ||
167	>	args_info.repeatZ_given > 0) {
168	>	Vector3i replicateOpt(args_info.repeatX_arg,
169	>	args_info.repeatY_arg,
170	>	args_info.repeatZ_arg);
171	>	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
172	>	replicateOpt);
173		compositeVisitor->addVisitor(replicateVisitor, 300);
174		}
175
176
177		//create rotation visitor
178		if (args_info.refsele_given&& args_info.originsele_given) {
179	<	compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
179	>	compositeVisitor->addVisitor(new LipidTransVisitor(info,
180	>	args_info.originsele_arg,
181	>	args_info.refsele_arg),
182	>	250);
183		} else if (args_info.refsele_given || args_info.originsele_given) {
184	<	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
184	>	cerr << "Both of --refsele and --originsele should appear by pair"
185	>	<< endl;
186		exit(1);
187		}
188	<
188	>
189		//create xyzVisitor
190		XYZVisitor* xyzVisitor;
191
#	Line 183 | Line 195 | int main(int argc, char* argv[]){
195		xyzVisitor = new XYZVisitor(info);
196		}
197
198	<	if(args_info.printPosOnly_flag){
199	<	bool posOnly = true;
200	<	xyzVisitor->setPosOnly(posOnly);
198	>	if(args_info.velocities_flag){
199	>	printVel = true;
200	>	xyzVisitor->doVelocities(printVel);
201		}
202	<
203	<	compositeVisitor->addVisitor(xyzVisitor, 200);
202	>	if(args_info.forces_flag){
203	>	printFrc = true;
204	>	xyzVisitor->doForces(printFrc);
205	>	}
206	>	if(args_info.vectors_flag){
207	>	printVec = true;
208	>	xyzVisitor->doVectors(printVec);
209	>	}
210	>	if(args_info.charges_flag){
211	>	printChrg = true;
212	>	xyzVisitor->doCharges(printChrg);
213	>	}
214	>	if(args_info.efield_flag){
215	>	printField = true;
216	>	xyzVisitor->doElectricFields(printField);
217	>	}
218
219	<	std::cout << compositeVisitor->toString();
219	>	compositeVisitor->addVisitor(xyzVisitor, 200);
220
221		//create prepareVisitor
222		PrepareVisitor* prepareVisitor = new PrepareVisitor();
#	Line 199 | Line 225 | int main(int argc, char* argv[]){
225		DumpReader* dumpReader = new DumpReader(info, dumpFileName);
226		int nframes = dumpReader->getNFrames();
227
228	+	ofstream xyzStream(xyzFileName.c_str());
229
203	–	std::ofstream xyzStream;
204	–	xyzStream .open(xyzFileName.c_str());
205	–
206	–
230		SimInfo::MoleculeIterator miter;
231		Molecule::IntegrableObjectIterator  iiter;
232		Molecule::RigidBodyIterator rbIter;
233		Molecule* mol;
234	<	StuntDouble* integrableObject;
234	>	StuntDouble* sd;
235		RigidBody* rb;
236		Vector3d molCom;
237		Vector3d newMolCom;
#	Line 218 | Line 241 | int main(int argc, char* argv[]){
241
242		for (int i = 0; i < nframes; i += args_info.frame_arg){
243		dumpReader->readFrame(i);
244	<
244	>
245	>	if (printFrc) forceMan->calcForces();
246	>
247		//wrapping the molecule
248		if(args_info.periodicBox_flag) {
249		currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
250	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
251	<	molCom = mol->getCom();
252	<	newMolCom = molCom;
253	<	currentSnapshot->wrapVector(newMolCom);
254	<	displacement = newMolCom - molCom;
255	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
256	<	integrableObject = mol->nextIntegrableObject(iiter)) {
257	<	integrableObject->setPos(integrableObject->getPos() + displacement);
250	>	for (mol = info->beginMolecule(miter); mol != NULL;
251	>	mol = info->nextMolecule(miter)) {
252	>
253	>	molCom = mol->getCom();
254	>	newMolCom = molCom;
255	>	currentSnapshot->wrapVector(newMolCom);
256	>	displacement = newMolCom - molCom;
257	>
258	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
259	>	sd = mol->nextIntegrableObject(iiter)) {
260	>
261	>	sd->setPos(sd->getPos() + displacement);
262	>
263		}
264		}
265		}
266	+
267		//update atoms of rigidbody
268	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
268	>	for (mol = info->beginMolecule(miter); mol != NULL;
269	>	mol = info->nextMolecule(miter)) {
270
271		//change the positions of atoms which belong to the rigidbodies
272	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
272	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
273	>	rb = mol->nextRigidBody(rbIter)) {
274	>
275		rb->updateAtoms();
276	+	if (printVel) rb->updateAtomVel();
277	+
278		}
279		}
280
281		//prepare visit
282	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
283	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
284	<	integrableObject = mol->nextIntegrableObject(iiter)) {
285	<	integrableObject->accept(prepareVisitor);
282	>	for (mol = info->beginMolecule(miter); mol != NULL;
283	>	mol = info->nextMolecule(miter)) {
284	>
285	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
286	>	sd = mol->nextIntegrableObject(iiter)) {
287	>
288	>	sd->accept(prepareVisitor);
289	>
290		}
291		}
292
#	Line 255 | Line 295 | int main(int argc, char* argv[]){
295
296
297		//visit stuntdouble
298	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
299	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
300	<	integrableObject = mol->nextIntegrableObject(iiter)) {
301	<	integrableObject->accept(compositeVisitor);
298	>	for (mol = info->beginMolecule(miter); mol != NULL;
299	>	mol = info->nextMolecule(miter)) {
300	>
301	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
302	>	sd = mol->nextIntegrableObject(iiter)) {
303	>
304	>	sd->accept(compositeVisitor);
305	>
306		}
307		}
308
#	Line 266 | Line 310 | int main(int argc, char* argv[]){
310		xyzVisitor->clear();
311
312		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
313	<
313	>
314		xyzStream.close();
271	–
315		delete prepareVisitor;
316		delete compositeVisitor;
317		delete info;
275	–
318		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 1212 by xsun, Wed Jan 23 21:21:13 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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