ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp

Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents), Revision 1706 by gezelter, Fri Apr 27 20:44:16 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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]  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 57 | Line 60
60		#include "selection/SelectionEvaluator.hpp"
61		#include "selection/SelectionManager.hpp"
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
70		//register force fields
71		registerForceFields();
72
73		gengetopt_args_info args_info;
74	<	std::string dumpFileName;
75	<	std::string mdFileName;
76	<	std::string xyzFileName;
74	>	string dumpFileName;
75	>	string xyzFileName;
76	>
77	>	bool printVel(false);
78	>	bool printFrc(false);
79	>	bool printVec(false);
80	>	bool printChrg(false);
81
82		//parse the command line option
83		if (cmdline_parser (argc, argv, &args_info) != 0) {
#	Line 79 | Line 88 | int main(int argc, char* argv[]){
88		if (args_info.input_given){
89		dumpFileName = args_info.input_arg;
90		} else {
91	<	std::cerr << "Does not have input file name" << std::endl;
91	>	cerr << "Does not have input file name" << endl;
92		exit(1);
93		}
94
86	–	mdFileName = dumpFileName;
87	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
88	–
95		if (args_info.output_given){
96		xyzFileName = args_info.output_arg;
97		} else {
#	Line 95 | Line 101 | int main(int argc, char* argv[]){
101
102		//parse md file and set up the system
103		SimCreator creator;
104	<	SimInfo* info = creator.createSim(mdFileName, false);
104	>	SimInfo* info = creator.createSim(dumpFileName, false);
105	>	ForceManager* forceMan = new ForceManager(info);
106
107	<
101	<
102	<	//creat visitor list
107	>	//create visitor list
108		CompositeVisitor* compositeVisitor = new CompositeVisitor();
109	<
110	<	//creat RigidBody Visitor
109	>
110	>	//create RigidBody Visitor
111		if(args_info.rigidbody_flag){
112		RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
113		compositeVisitor->addVisitor(rbCOMVisitor, 900);
114		}
115
116	<	//creat SSD atom visitor
116	>	//create SSD atom visitor
117		SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
118		compositeVisitor->addVisitor(ssdVisitor, 800);
119
120	<	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
121	<	compositeVisitor->addVisitor(linearVisitor, 750);
120	>	//create GBtail atom visitor
121	>	GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
122	>	compositeVisitor->addVisitor(gbtVisitor, 790);
123
124	<	//creat default atom visitor
124	>	//create GBhead atom visitor
125	>	GBheadVisitor* gbhVisitor = new GBheadVisitor(info);
126	>	compositeVisitor->addVisitor(gbhVisitor, 789);
127	>
128	>	//create default atom visitor
129		DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
130		compositeVisitor->addVisitor(defaultAtomVisitor, 700);
131
132	<	//creat waterType visitor
133	<	if(args_info.watertype_flag){
134	<	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
135	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
132	>	// if we gave the -w option, we want to skip the waters:
133	>	if (!args_info.water_given) {
134	>	//create waterType visitor
135	>	if(args_info.watertype_flag){
136	>	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
137	>	compositeVisitor->addVisitor(waterTypeVisitor, 600);
138	>	}
139	>	}
140	>
141	>	if (args_info.basetype_flag) {
142	>	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
143	>	compositeVisitor->addVisitor(atomNameVisitor, 550);
144	>	cout << compositeVisitor->toString();
145		}
146
147		//create ZconsVisitor
#	Line 137 | Line 156 | int main(int argc, char* argv[]){
156		}
157		}
158
159	<	//creat wrapping visitor
159	>	//create wrapping visitor
160
161	<	if(args_info.periodicBox_flag){
162	<	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
163	<	compositeVisitor->addVisitor(wrappingVisitor, 400);
164	<	}
161	>	//if(args_info.periodicBox_flag){
162	>	//  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
163	>	//  compositeVisitor->addVisitor(wrappingVisitor, 400);
164	>	//}
165
166	<	//creat replicate visitor
167	<	if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
168	<	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
169	<	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
166	>	//create replicate visitor
167	>	if(args_info.repeatX_given > 0 ||
168	>	args_info.repeatY_given > 0 ||
169	>	args_info.repeatY_given > 0) {
170	>	Vector3i replicateOpt(args_info.repeatX_arg,
171	>	args_info.repeatY_arg,
172	>	args_info.repeatZ_arg);
173	>	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
174	>	replicateOpt);
175		compositeVisitor->addVisitor(replicateVisitor, 300);
176		}
177
178
179		//create rotation visitor
180		if (args_info.refsele_given&& args_info.originsele_given) {
181	<	compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
181	>	compositeVisitor->addVisitor(new LipidTransVisitor(info,
182	>	args_info.originsele_arg,
183	>	args_info.refsele_arg),
184	>	250);
185		} else if (args_info.refsele_given || args_info.originsele_given) {
186	<	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
186	>	cerr << "Both of --refsele and --originsele should appear by pair"
187	>	<< endl;
188		exit(1);
189		}
190	<
191	<	//creat xyzVisitor
190	>
191	>	//create xyzVisitor
192		XYZVisitor* xyzVisitor;
193	+
194		if (args_info.selection_given) {
195		xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
196		} else {
197		xyzVisitor = new XYZVisitor(info);
198		}
199	<	compositeVisitor->addVisitor(xyzVisitor, 200);
199	>
200	>	if(args_info.velocities_flag){
201	>	printVel = true;
202	>	xyzVisitor->doVelocities(printVel);
203	>	}
204	>	if(args_info.forces_flag){
205	>	printFrc = true;
206	>	xyzVisitor->doForces(printFrc);
207	>	}
208	>	if(args_info.vectors_flag){
209	>	printVec = true;
210	>	xyzVisitor->doVectors(printVec);
211	>	}
212	>	if(args_info.charges_flag){
213	>	printChrg = true;
214	>	xyzVisitor->doCharges(printChrg);
215	>	}
216
217	<	std::cout << compositeVisitor->toString();
217	>	compositeVisitor->addVisitor(xyzVisitor, 200);
218
219	<	//creat prepareVisitor
219	>	//create prepareVisitor
220		PrepareVisitor* prepareVisitor = new PrepareVisitor();
221
222		//open dump file
223		DumpReader* dumpReader = new DumpReader(info, dumpFileName);
224		int nframes = dumpReader->getNFrames();
225
226	+	ofstream xyzStream(xyzFileName.c_str());
227
182	–	std::ofstream xyzStream;
183	–	xyzStream .open(xyzFileName.c_str());
184	–
185	–
228		SimInfo::MoleculeIterator miter;
229		Molecule::IntegrableObjectIterator  iiter;
230		Molecule::RigidBodyIterator rbIter;
231		Molecule* mol;
232		StuntDouble* integrableObject;
233		RigidBody* rb;
234	+	Vector3d molCom;
235	+	Vector3d newMolCom;
236	+	Vector3d displacement;
237	+	Mat3x3d hmat;
238	+	Snapshot* currentSnapshot;
239
240		for (int i = 0; i < nframes; i += args_info.frame_arg){
241		dumpReader->readFrame(i);
242
243	+	if (printFrc) forceMan->calcForces();
244	+
245	+	//wrapping the molecule
246	+	if(args_info.periodicBox_flag) {
247	+	currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
248	+	for (mol = info->beginMolecule(miter); mol != NULL;
249	+	mol = info->nextMolecule(miter)) {
250	+	molCom = mol->getCom();
251	+	newMolCom = molCom;
252	+	currentSnapshot->wrapVector(newMolCom);
253	+	displacement = newMolCom - molCom;
254	+	for (integrableObject = mol->beginIntegrableObject(iiter);
255	+	integrableObject != NULL;
256	+	integrableObject = mol->nextIntegrableObject(iiter)) {
257	+	integrableObject->setPos(integrableObject->getPos() + displacement);
258	+	}
259	+	}
260	+	}
261		//update atoms of rigidbody
262	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
262	>	for (mol = info->beginMolecule(miter); mol != NULL;
263	>	mol = info->nextMolecule(miter)) {
264
265		//change the positions of atoms which belong to the rigidbodies
266	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
266	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
267	>	rb = mol->nextRigidBody(rbIter)) {
268		rb->updateAtoms();
269	+	if (printVel) rb->updateAtomVel();
270		}
271		}
272
273		//prepare visit
274	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
275	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
274	>	for (mol = info->beginMolecule(miter); mol != NULL;
275	>	mol = info->nextMolecule(miter)) {
276	>	for (integrableObject = mol->beginIntegrableObject(iiter);
277	>	integrableObject != NULL;
278		integrableObject = mol->nextIntegrableObject(iiter)) {
279		integrableObject->accept(prepareVisitor);
280		}
#	Line 215 | Line 285 | int main(int argc, char* argv[]){
285
286
287		//visit stuntdouble
288	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
289	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
288	>	for (mol = info->beginMolecule(miter); mol != NULL;
289	>	mol = info->nextMolecule(miter)) {
290	>	for (integrableObject = mol->beginIntegrableObject(iiter);
291	>	integrableObject != NULL;
292		integrableObject = mol->nextIntegrableObject(iiter)) {
293		integrableObject->accept(compositeVisitor);
294		}
#	Line 226 | Line 298 | int main(int argc, char* argv[]){
298		xyzVisitor->clear();
299
300		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
301	<
301	>
302		xyzStream.close();
303	<
232	<
303	>	delete prepareVisitor;
304		delete compositeVisitor;
305		delete info;
235	–
306		}

Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords), Revision 1706 by gezelter, Fri Apr 27 20:44:16 2012 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines