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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <iostream>
#	Line 47 | Line 47
47		#include "brains/Register.hpp"
48		#include "brains/SimCreator.hpp"
49		#include "brains/SimInfo.hpp"
50	+	#include "brains/ForceManager.hpp"
51		#include "io/DumpReader.hpp"
52		#include "utils/simError.h"
53		#include "visitors/AtomVisitor.hpp"
54	+	#include "visitors/ReplacementVisitor.hpp"
55		#include "visitors/CompositeVisitor.hpp"
56		#include "visitors/RigidBodyVisitor.hpp"
57		#include "visitors/OtherVisitor.hpp"
58		#include "visitors/ZconsVisitor.hpp"
59	<	using namespace oopse;
59	>	#include "selection/SelectionEvaluator.hpp"
60	>	#include "selection/SelectionManager.hpp"
61	>	#include "visitors/LipidTransVisitor.hpp"
62	>	#include "visitors/AtomNameVisitor.hpp"
63
64	+	using namespace OpenMD;
65	+
66		int main(int argc, char* argv[]){
67
68		//register force fields
#	Line 63 | Line 70 | int main(int argc, char* argv[]){
70
71		gengetopt_args_info args_info;
72		std::string dumpFileName;
66	–	std::string mdFileName;
73		std::string xyzFileName;
74	+	bool printVel;
75	+	bool printFrc;
76	+	bool printVec;
77	+	bool printChrg;
78
79		//parse the command line option
80		if (cmdline_parser (argc, argv, &args_info) != 0) {
#	Line 79 | Line 89 | int main(int argc, char* argv[]){
89		exit(1);
90		}
91
82	–	mdFileName = dumpFileName;
83	–	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
84	–
92		if (args_info.output_given){
93		xyzFileName = args_info.output_arg;
94		} else {
#	Line 91 | Line 98 | int main(int argc, char* argv[]){
98
99		//parse md file and set up the system
100		SimCreator creator;
101	<	SimInfo* info = creator.createSim(mdFileName, false);
101	>	SimInfo* info = creator.createSim(dumpFileName, false);
102	>	ForceManager* forceMan = new ForceManager(info);
103
104	<
97	<
98	<	//creat visitor list
104	>	//create visitor list
105		CompositeVisitor* compositeVisitor = new CompositeVisitor();
106
107	<	//creat ignore visitor
102	<	if(args_info.ignore_given ||args_info.water_flag){
103	<
104	<	IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
105	<
106	<	for(int i = 0; i < args_info.ignore_given; i++)
107	<	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
108	<
109	<	//ignore water
110	<	if(args_info.water_flag){
111	<	ignoreVisitor->addIgnoreType("SSD");
112	<	ignoreVisitor->addIgnoreType("SSD1");
113	<	ignoreVisitor->addIgnoreType("SSD_E");
114	<	ignoreVisitor->addIgnoreType("SSD_RF");
115	<	ignoreVisitor->addIgnoreType("TIP3P_RB_0");
116	<	ignoreVisitor->addIgnoreType("TIP4P_RB_0");
117	<	ignoreVisitor->addIgnoreType("TIP5P_RB_0");
118	<	ignoreVisitor->addIgnoreType("SPCE_RB_0");
119	<	ignoreVisitor->addIgnoreType("DPD_RB_0");
120	<	}
121	<
122	<	compositeVisitor->addVisitor(ignoreVisitor, 1000);
123	<	}
124	<
125	<	//creat RigidBody Visitor
107	>	//create RigidBody Visitor
108		if(args_info.rigidbody_flag){
109		RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
110		compositeVisitor->addVisitor(rbCOMVisitor, 900);
111		}
112
113	<	//compositeVisitor->addVisitor(lipidVisitor, 900);
132	<
133	<	//creat SSD atom visitor
113	>	//create SSD atom visitor
114		SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
115		compositeVisitor->addVisitor(ssdVisitor, 800);
116
117	<	LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
138	<	compositeVisitor->addVisitor(linearVisitor, 750);
139	<
140	<	//creat default atom visitor
117	>	//create default atom visitor
118		DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
119		compositeVisitor->addVisitor(defaultAtomVisitor, 700);
120
121	<	//creat waterType visitor
122	<	if(args_info.watertype_flag){
123	<	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
124	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
121	>	// if we gave the -w option, we want to skip the waters:
122	>	if (!args_info.water_given) {
123	>	//create waterType visitor
124	>	if(args_info.watertype_flag){
125	>	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
126	>	compositeVisitor->addVisitor(waterTypeVisitor, 600);
127	>	}
128	>	}
129	>
130	>	if (args_info.basetype_flag) {
131	>	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
132	>	compositeVisitor->addVisitor(atomNameVisitor, 550);
133	>	std::cout << compositeVisitor->toString();
134		}
135
136		//create ZconsVisitor
#	Line 159 | Line 145 | int main(int argc, char* argv[]){
145		}
146		}
147
148	<	//creat wrapping visitor
148	>	//create wrapping visitor
149
150	<	if(args_info.periodicBox_flag){
151	<	WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152	<	compositeVisitor->addVisitor(wrappingVisitor, 400);
150	>	//if(args_info.periodicBox_flag){
151	>	//  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152	>	//  compositeVisitor->addVisitor(wrappingVisitor, 400);
153	>	//}
154	>
155	>	//create replicate visitor
156	>	if(args_info.repeatX_given > 0 ||
157	>	args_info.repeatY_given > 0 ||
158	>	args_info.repeatY_given > 0) {
159	>	Vector3i replicateOpt(args_info.repeatX_arg,
160	>	args_info.repeatY_arg,
161	>	args_info.repeatZ_arg);
162	>	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
163	>	replicateOpt);
164	>	compositeVisitor->addVisitor(replicateVisitor, 300);
165		}
166	+
167	+
168	+	//create rotation visitor
169	+	if (args_info.refsele_given&& args_info.originsele_given) {
170	+	compositeVisitor->addVisitor(new LipidTransVisitor(info,
171	+	args_info.originsele_arg,
172	+	args_info.refsele_arg),
173	+	250);
174	+	} else if (args_info.refsele_given || args_info.originsele_given) {
175	+	std::cerr << "Both of --refsele and --originsele should appear by pair"
176	+	<< std::endl;
177	+	exit(1);
178	+	}
179
180	<	//creat replicate visitor
181	<	if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
182	<	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
183	<	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
184	<	compositeVisitor->addVisitor(replicateVisitor, 300);
180	>	//create xyzVisitor
181	>	XYZVisitor* xyzVisitor;
182	>
183	>	if (args_info.selection_given) {
184	>	xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
185	>	} else {
186	>	xyzVisitor = new XYZVisitor(info);
187		}
188	+
189	+	if(args_info.velocities_flag){
190	+	printVel = true;
191	+	xyzVisitor->doVelocities(printVel);
192	+	}
193	+	if(args_info.forces_flag){
194	+	printFrc = true;
195	+	xyzVisitor->doForces(printFrc);
196	+	}
197	+	if(args_info.vectors_flag){
198	+	printVec = true;
199	+	xyzVisitor->doVectors(printVec);
200	+	}
201	+	if(args_info.charges_flag){
202	+	printChrg = true;
203	+	xyzVisitor->doCharges(printChrg);
204	+	}
205
206	<	//creat xyzVisitor
177	<	XYZVisitor* xyzVisitor = new XYZVisitor(info);
178	<	compositeVisitor->addVisitor(xyzVisitor, 200);
206	>	compositeVisitor->addVisitor(xyzVisitor, 200);
207
208	<	std::cout << compositeVisitor->toString();
181	<
182	<	//creat prepareVisitor
208	>	//create prepareVisitor
209		PrepareVisitor* prepareVisitor = new PrepareVisitor();
210
211		//open dump file
212		DumpReader* dumpReader = new DumpReader(info, dumpFileName);
213		int nframes = dumpReader->getNFrames();
214
215	+	std::ofstream xyzStream(xyzFileName.c_str());
216
190	–	std::ofstream xyzStream;
191	–	xyzStream .open(xyzFileName.c_str());
192	–
193	–
217		SimInfo::MoleculeIterator miter;
218		Molecule::IntegrableObjectIterator  iiter;
219		Molecule::RigidBodyIterator rbIter;
220		Molecule* mol;
221		StuntDouble* integrableObject;
222		RigidBody* rb;
223	<
223	>	Vector3d molCom;
224	>	Vector3d newMolCom;
225	>	Vector3d displacement;
226	>	Mat3x3d hmat;
227	>	Snapshot* currentSnapshot;
228	>
229		for (int i = 0; i < nframes; i += args_info.frame_arg){
230		dumpReader->readFrame(i);
231
232	+	if (printFrc) forceMan->calcForces();
233	+
234	+	//wrapping the molecule
235	+	if(args_info.periodicBox_flag) {
236	+	currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
237	+	for (mol = info->beginMolecule(miter); mol != NULL;
238	+	mol = info->nextMolecule(miter)) {
239	+	molCom = mol->getCom();
240	+	newMolCom = molCom;
241	+	currentSnapshot->wrapVector(newMolCom);
242	+	displacement = newMolCom - molCom;
243	+	for (integrableObject = mol->beginIntegrableObject(iiter);
244	+	integrableObject != NULL;
245	+	integrableObject = mol->nextIntegrableObject(iiter)) {
246	+	integrableObject->setPos(integrableObject->getPos() + displacement);
247	+	}
248	+	}
249	+	}
250		//update atoms of rigidbody
251	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
251	>	for (mol = info->beginMolecule(miter); mol != NULL;
252	>	mol = info->nextMolecule(miter)) {
253
254		//change the positions of atoms which belong to the rigidbodies
255	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
255	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
256	>	rb = mol->nextRigidBody(rbIter)) {
257		rb->updateAtoms();
258	+	if (printVel) rb->updateAtomVel();
259		}
260		}
261
262		//prepare visit
263	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
264	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
263	>	for (mol = info->beginMolecule(miter); mol != NULL;
264	>	mol = info->nextMolecule(miter)) {
265	>	for (integrableObject = mol->beginIntegrableObject(iiter);
266	>	integrableObject != NULL;
267		integrableObject = mol->nextIntegrableObject(iiter)) {
268		integrableObject->accept(prepareVisitor);
269		}
#	Line 220 | Line 271 | int main(int argc, char* argv[]){
271
272		//update visitor
273		compositeVisitor->update();
274	<
274	>
275	>
276		//visit stuntdouble
277	<	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
278	<	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
277	>	for (mol = info->beginMolecule(miter); mol != NULL;
278	>	mol = info->nextMolecule(miter)) {
279	>	for (integrableObject = mol->beginIntegrableObject(iiter);
280	>	integrableObject != NULL;
281		integrableObject = mol->nextIntegrableObject(iiter)) {
282		integrableObject->accept(compositeVisitor);
283		}
#	Line 233 | Line 287 | int main(int argc, char* argv[]){
287		xyzVisitor->clear();
288
289		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
290	<
290	>
291		xyzStream.close();
292	<
239	<
292	>	delete prepareVisitor;
293		delete compositeVisitor;
294		delete info;
242	–
295		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC

#	Line 0 | Line 1
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