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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 1 | Line 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
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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>
43		#include <fstream>
44		#include <string>
45
5	–	#include "brains/SimSetup.hpp"
46		#include "applications/dump2Xyz/Dump2XYZCmd.h"
47	+	#include "brains/Register.hpp"
48	+	#include "brains/SimCreator.hpp"
49	+	#include "brains/SimInfo.hpp"
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"
57		#include "visitors/ZconsVisitor.hpp"
58	+	#include "selection/SelectionEvaluator.hpp"
59	+	#include "selection/SelectionManager.hpp"
60	+	#include "visitors/LipidTransVisitor.hpp"
61	+	#include "visitors/AtomNameVisitor.hpp"
62
63	<	using namespace std;
63	>	using namespace OpenMD;
64
65		int main(int argc, char* argv[]){
16	–	gengetopt_args_info args_info;
17	–	string dumpFileName;
18	–	string mdFileName;
19	–	char inFileName[2002];
20	–	string xyzFileName;
21	–	SimInfo* info;
22	–	SimSetup startMe;
23	–	DumpReader* dumpReader;
24	–	ofstream xyzStream;
25	–	int nframes;
26	–	Molecule* mol;
27	–	vector<StuntDouble*> integrableObjects;
28	–	vector<StuntDouble*>::iterator iter;
29	–	vector<RigidBody*> myRigidBodies;
30	–	vector<RigidBody*>::iterator rbIter;
66
67	<	CompositeVisitor* compositeVisitor;
68	<	SSDAtomVisitor* ssdVisitor;
34	<	LinearAtomVisitor* linearVisitor;
35	<	DefaultAtomVisitor* defaultAtomVisitor;
36	<	LipidHeadVisitor* lipidVisitor;
37	<	RBCOMVisitor* rbCOMVisitor;
38	<	ReplicateVisitor* replicateVisitor;
39	<	WrappingVisitor* wrappingVisitor;
40	<	IgnoreVisitor* ignoreVisitor;
41	<	XYZVisitor* xyzVisitor;
42	<	ZConsVisitor* zconsVisitor;
43	<	PrepareVisitor* prepareVisitor;
44	<	WaterTypeVisitor* waterTypeVisitor;
67	>	//register force fields
68	>	registerForceFields();
69
70	+	gengetopt_args_info args_info;
71	+	std::string dumpFileName;
72	+	std::string xyzFileName;
73	+
74		//parse the command line option
75	<	if (cmdline_parser (argc, argv, &args_info) != 0)
76	<	exit(1) ;
77	<
78	<
75	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
76	>	exit(1) ;
77	>	}
78	>
79		//get the dumpfile name and meta-data file name
80		if (args_info.input_given){
81		dumpFileName = args_info.input_arg;
82	<	}
83	<	else{
56	<	cerr << "Does not have input file name" << endl;
82	>	} else {
83	>	std::cerr << "Does not have input file name" << std::endl;
84		exit(1);
85		}
86	<	mdFileName = dumpFileName;
60	<	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
61	<
86	>
87		if (args_info.output_given){
88		xyzFileName = args_info.output_arg;
89	<	}
65	<	else{
89	>	} else {
90		xyzFileName = dumpFileName;
91		xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
92		}
93	<
93	>
94		//parse md file and set up the system
95	<	info = new SimInfo();
96	<	startMe.setSimInfo(info );
73	<
74	<	strcpy(inFileName, mdFileName.c_str() );
75	<	startMe.parseFile( inFileName );
76	<
77	<	startMe.createSim();
78	<
95	>	SimCreator creator;
96	>	SimInfo* info = creator.createSim(dumpFileName, false);
97
98	<	//creat visitor list
99	<	compositeVisitor = new CompositeVisitor();
100	<
101	<	//creat ignore visitor
84	<	if(args_info.ignore_given ||args_info.water_flag){
85	<
86	<	ignoreVisitor = new IgnoreVisitor();
87	<
88	<	for(int i = 0; i < args_info.ignore_given; i++)
89	<	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
90	<
91	<	//ignore water
92	<	if(args_info.water_flag){
93	<	ignoreVisitor->addIgnoreType("SSD");
94	<	ignoreVisitor->addIgnoreType("SSD1");
95	<	ignoreVisitor->addIgnoreType("SSD_E");
96	<	ignoreVisitor->addIgnoreType("SSD_RF");
97	<	ignoreVisitor->addIgnoreType("TIP3P_RB_0");
98	<	ignoreVisitor->addIgnoreType("TIP4P_RB_0");
99	<	ignoreVisitor->addIgnoreType("TIP5P_RB_0");
100	<	ignoreVisitor->addIgnoreType("SPCE_RB_0");
101	<	ignoreVisitor->addIgnoreType("DPD_RB_0");
102	<	}
103	<
104	<	compositeVisitor->addVisitor(ignoreVisitor, 1000);
105	<	}
106	<
107	<	//creat RigidBody Visitor
98	>	//create visitor list
99	>	CompositeVisitor* compositeVisitor = new CompositeVisitor();
100	>
101	>	//create RigidBody Visitor
102		if(args_info.rigidbody_flag){
103	<	rbCOMVisitor = new RBCOMVisitor(info);
103	>	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
104		compositeVisitor->addVisitor(rbCOMVisitor, 900);
105		}
106	<
107	<	//compositeVisitor->addVisitor(lipidVisitor, 900);
108	<
115	<	//creat SSD atom visitor
116	<	ssdVisitor = new SSDAtomVisitor(info);
106	>
107	>	//create SSD atom visitor
108	>	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
109		compositeVisitor->addVisitor(ssdVisitor, 800);
110	<	linearVisitor = new LinearAtomVisitor(info);
111	<	compositeVisitor->addVisitor(linearVisitor, 750);
112	<
121	<	//creat default atom visitor
122	<	defaultAtomVisitor = new DefaultAtomVisitor(info);
110	>
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 = new WaterTypeVisitor;
118	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
114	>
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	<
129	>
130		//create ZconsVisitor
131		if(args_info.zconstraint_flag){
133	–
134	–	zconsVisitor = new ZConsVisitor(info);
132
133	<	if(zconsVisitor->haveZconsMol())
133	>	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
134	>
135	>	if(zconsVisitor->haveZconsMol()) {
136		compositeVisitor->addVisitor(zconsVisitor, 500);
137	<	else
137	>	} else {
138		delete zconsVisitor;
139	+	}
140		}
141	–
142	–	//creat wrapping visitor
143	–
144	–	if(args_info.periodicBox_flag){
145	–	wrappingVisitor = new WrappingVisitor(info);
146	–	compositeVisitor->addVisitor(wrappingVisitor, 400);
147	–	}
141
142	<	//creat replicate visitor
142	>	//create wrapping visitor
143	>
144	>	//if(args_info.periodicBox_flag){
145	>	//  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
146	>	//  compositeVisitor->addVisitor(wrappingVisitor, 400);
147	>	//}
148	>
149	>	//create replicate visitor
150		if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
151	<	IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
152	<	replicateVisitor = new ReplicateVisitor(info, replicateOpt);
151	>	Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
152	>	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
153		compositeVisitor->addVisitor(replicateVisitor, 300);
154		}
155
156	–	//creat xyzVisitor
157	–	xyzVisitor = new XYZVisitor(info);
158	–	compositeVisitor->addVisitor(xyzVisitor, 200);
156
157	<	cout << compositeVisitor->toString();
157	>	//create rotation visitor
158	>	if (args_info.refsele_given&& args_info.originsele_given) {
159	>	compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250);
160	>	} else if (args_info.refsele_given || args_info.originsele_given) {
161	>	std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
162	>	exit(1);
163	>	}
164	>
165	>	//create xyzVisitor
166	>	XYZVisitor* xyzVisitor;
167
168	<	//creat prepareVisitor
169	<	prepareVisitor = new PrepareVisitor();
168	>	if (args_info.selection_given) {
169	>	xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
170	>	} else {
171	>	xyzVisitor = new XYZVisitor(info);
172	>	}
173
174	<	//open dump file
175	<	dumpReader = new DumpReader(dumpFileName.c_str());
176	<	nframes = dumpReader->getNframes();
174	>	if(args_info.printPosOnly_flag){
175	>	bool posOnly = true;
176	>	xyzVisitor->setPosOnly(posOnly);
177	>	}
178
179	<	xyzStream .open(xyzFileName.c_str());
179	>	compositeVisitor->addVisitor(xyzVisitor, 200);
180
181	+	//create prepareVisitor
182	+	PrepareVisitor* prepareVisitor = new PrepareVisitor();
183	+
184	+	//open dump file
185	+	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
186	+	int nframes = dumpReader->getNFrames();
187	+
188	+
189	+	std::ofstream xyzStream(xyzFileName.c_str());
190	+
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(info, i);
204	>	dumpReader->readFrame(i);
205
206	<	mol = info->molecules;
207	<
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(int j = 0; j < info->n_mol; j++){
222	<	myRigidBodies = mol[j].getMyRigidBodies();
223	<
224	<	for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
225	<	(*rbIter)->updateAtoms();
226	<	}
227	<
221	>	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
222	>
223	>	//change the positions of atoms which belong to the rigidbodies
224	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
225	>	rb->updateAtoms();
226	>	}
227	>	}
228
229		//prepare visit
230	<	for(int j = 0; j < info->n_mol; j++){
231	<	integrableObjects = mol[j].getIntegrableObjects();
232	<
233	<	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
234	<	(*iter)->accept(prepareVisitor);
235	<	}
236	<
230	>	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
231	>	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
232	>	integrableObject = mol->nextIntegrableObject(iiter)) {
233	>	integrableObject->accept(prepareVisitor);
234	>	}
235	>	}
236	>
237		//update visitor
238		compositeVisitor->update();
195	–
196	–	//visit stuntdouble
197	–	for(int j = 0; j < info->n_mol; j++){
198	–	integrableObjects = mol[j].getIntegrableObjects();
239
200	–	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
201	–	(*iter)->accept(compositeVisitor);
202	–	}
240
241	+	//visit stuntdouble
242	+	for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
243	+	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
244	+	integrableObject = mol->nextIntegrableObject(iiter)) {
245	+	integrableObject->accept(compositeVisitor);
246	+	}
247	+	}
248	+
249		xyzVisitor->writeFrame(xyzStream);
250		xyzVisitor->clear();
251
252		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
253	<
253	>
254		xyzStream.close();
255	<
211	<
255	>	delete prepareVisitor;
256		delete compositeVisitor;
257		delete info;
214	–
215	–
258		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 0 | Line 1
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