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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 12 by tim, Tue Sep 28 23:24:25 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 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>
44		#include <fstream>
45		#include <string>
46
5	–	#include "brains/SimSetup.hpp"
47		#include "applications/dump2Xyz/Dump2XYZCmd.h"
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"
59		#include "visitors/ZconsVisitor.hpp"
60	+	#include "selection/SelectionEvaluator.hpp"
61	+	#include "selection/SelectionManager.hpp"
62	+	#include "visitors/LipidTransVisitor.hpp"
63	+	#include "visitors/AtomNameVisitor.hpp"
64
65	<	using namespace std;
65	>	using namespace OpenMD;
66
67	+	using namespace std;
68		int main(int argc, char* argv[]){
69	+
70		gengetopt_args_info args_info;
71		string dumpFileName;
18	–	string mdFileName;
19	–	char inFileName[2002];
72		string xyzFileName;
73	<	SimInfo* info;
74	<	SimSetup startMe;
75	<	DumpReader* dumpReader;
76	<	ofstream xyzStream;
77	<	int nframes;
78	<	Molecule* mol;
27	<	vector<StuntDouble*> integrableObjects;
28	<	vector<StuntDouble*>::iterator iter;
29	<	vector<RigidBody*> myRigidBodies;
30	<	vector<RigidBody*>::iterator rbIter;
73	>
74	>	bool printVel(false);
75	>	bool printFrc(false);
76	>	bool printVec(false);
77	>	bool printChrg(false);
78	>	bool printField(false);
79
32	–	CompositeVisitor* compositeVisitor;
33	–	SSDAtomVisitor* ssdVisitor;
34	–	DefaultAtomVisitor* defaultAtomVisitor;
35	–	LipidHeadVisitor* lipidVisitor;
36	–	RBCOMVisitor* rbCOMVisitor;
37	–	ReplicateVisitor* replicateVisitor;
38	–	WrappingVisitor* wrappingVisitor;
39	–	IgnoreVisitor* ignoreVisitor;
40	–	XYZVisitor* xyzVisitor;
41	–	ZConsVisitor* zconsVisitor;
42	–	PrepareVisitor* prepareVisitor;
43	–	WaterTypeVisitor* waterTypeVisitor;
44	–
80		//parse the command line option
81	<	if (cmdline_parser (argc, argv, &args_info) != 0)
82	<	exit(1) ;
83	<
84	<
81	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
82	>	exit(1) ;
83	>	}
84	>
85		//get the dumpfile name and meta-data file name
86		if (args_info.input_given){
87		dumpFileName = args_info.input_arg;
88	<	}
54	<	else{
88	>	} else {
89		cerr << "Does not have input file name" << endl;
90		exit(1);
91		}
92	<	mdFileName = dumpFileName;
59	<	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
60	<
92	>
93		if (args_info.output_given){
94		xyzFileName = args_info.output_arg;
95	<	}
64	<	else{
95	>	} else {
96		xyzFileName = dumpFileName;
97		xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
98		}
99	<
99	>
100		//parse md file and set up the system
101	<	info = new SimInfo();
102	<	startMe.setSimInfo(info );
103	<
73	<	strcpy(inFileName, mdFileName.c_str() );
74	<	startMe.parseFile( inFileName );
75	<
76	<	startMe.createSim();
77	<
101	>	SimCreator creator;
102	>	SimInfo* info = creator.createSim(dumpFileName, false);
103	>	ForceManager* forceMan = new ForceManager(info);
104
105	<	//creat visitor list
106	<	compositeVisitor = new CompositeVisitor();
107	<
108	<	//creat ignore visitor
83	<	if(args_info.ignore_given ||args_info.water_flag){
84	<
85	<	ignoreVisitor = new IgnoreVisitor();
86	<
87	<	for(int i = 0; i < args_info.ignore_given; i++)
88	<	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
89	<
90	<	//ignore water
91	<	if(args_info.water_flag){
92	<	ignoreVisitor->addIgnoreType("SSD");
93	<	ignoreVisitor->addIgnoreType("SSD1");
94	<	ignoreVisitor->addIgnoreType("SSD_E");
95	<	ignoreVisitor->addIgnoreType("SSD_RF");
96	<	ignoreVisitor->addIgnoreType("TIP3P_RB_0");
97	<	ignoreVisitor->addIgnoreType("TIP4P_RB_0");
98	<	ignoreVisitor->addIgnoreType("TIP5P_RB_0");
99	<	ignoreVisitor->addIgnoreType("SPCE_RB_0");
100	<	ignoreVisitor->addIgnoreType("DPD_RB_0");
101	<	}
102	<
103	<	compositeVisitor->addVisitor(ignoreVisitor, 1000);
104	<	}
105	<
106	<	//creat RigidBody Visitor
105	>	//create visitor list
106	>	CompositeVisitor* compositeVisitor = new CompositeVisitor();
107	>
108	>	//create RigidBody Visitor
109		if(args_info.rigidbody_flag){
110	<	rbCOMVisitor = new RBCOMVisitor(info);
110	>	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
111		compositeVisitor->addVisitor(rbCOMVisitor, 900);
112		}
113	<
114	<	//compositeVisitor->addVisitor(lipidVisitor, 900);
115	<
114	<	//creat SSD atom visitor
115	<	ssdVisitor = new SSDAtomVisitor(info);
113	>
114	>	//create SSD atom visitor
115	>	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
116		compositeVisitor->addVisitor(ssdVisitor, 800);
117
118	<	//creat default atom visitor
119	<	defaultAtomVisitor = new DefaultAtomVisitor(info);
120	<	compositeVisitor->addVisitor(defaultAtomVisitor, 700);
118	>	//create GBtail atom visitor
119	>	GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
120	>	compositeVisitor->addVisitor(gbtVisitor, 790);
121
122	<	//creat waterType visitor
123	<	if(args_info.watertype_flag){
124	<	waterTypeVisitor = new WaterTypeVisitor;
125	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
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	>	// 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	>	cout << compositeVisitor->toString();
143		}
144	<
144	>
145		//create ZconsVisitor
146		if(args_info.zconstraint_flag){
130	–
131	–	zconsVisitor = new ZConsVisitor(info);
147
148	<	if(zconsVisitor->haveZconsMol())
148	>	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
149	>
150	>	if(zconsVisitor->haveZconsMol()) {
151		compositeVisitor->addVisitor(zconsVisitor, 500);
152	<	else
152	>	} else {
153		delete zconsVisitor;
154	+	}
155		}
138	–
139	–	//creat wrapping visitor
140	–
141	–	if(args_info.periodicBox_flag){
142	–	wrappingVisitor = new WrappingVisitor(info);
143	–	compositeVisitor->addVisitor(wrappingVisitor, 400);
144	–	}
156
157	<	//creat replicate visitor
158	<	if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
159	<	IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
160	<	replicateVisitor = new ReplicateVisitor(info, replicateOpt);
157	>	//create wrapping visitor
158	>
159	>	//if(args_info.periodicBox_flag){
160	>	//  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
161	>	//  compositeVisitor->addVisitor(wrappingVisitor, 400);
162	>	//}
163	>
164	>	//create replicate visitor
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
153	–	//creat xyzVisitor
154	–	xyzVisitor = new XYZVisitor(info);
155	–	compositeVisitor->addVisitor(xyzVisitor, 200);
176
177	<	cout << compositeVisitor->toString();
177	>	//create rotation visitor
178	>	if (args_info.refsele_given&& args_info.originsele_given) {
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	>	cerr << "Both of --refsele and --originsele should appear by pair"
185	>	<< endl;
186	>	exit(1);
187	>	}
188	>
189	>	//create xyzVisitor
190	>	XYZVisitor* xyzVisitor;
191
192	<	//creat prepareVisitor
193	<	prepareVisitor = new PrepareVisitor();
192	>	if (args_info.selection_given) {
193	>	xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
194	>	} else {
195	>	xyzVisitor = new XYZVisitor(info);
196	>	}
197
198	+	if(args_info.velocities_flag){
199	+	printVel = true;
200	+	xyzVisitor->doVelocities(printVel);
201	+	}
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	+	compositeVisitor->addVisitor(xyzVisitor, 200);
220	+
221	+	//create prepareVisitor
222	+	PrepareVisitor* prepareVisitor = new PrepareVisitor();
223	+
224		//open dump file
225	<	dumpReader = new DumpReader(dumpFileName.c_str());
226	<	nframes = dumpReader->getNframes();
165	<
166	<	xyzStream .open(xyzFileName.c_str());
225	>	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
226	>	int nframes = dumpReader->getNFrames();
227
228	+	ofstream xyzStream(xyzFileName.c_str());
229	+
230	+	SimInfo::MoleculeIterator miter;
231	+	Molecule::IntegrableObjectIterator  iiter;
232	+	Molecule::RigidBodyIterator rbIter;
233	+	Molecule* mol;
234	+	StuntDouble* sd;
235	+	RigidBody* rb;
236	+	Vector3d molCom;
237	+	Vector3d newMolCom;
238	+	Vector3d displacement;
239	+	Mat3x3d hmat;
240	+	Snapshot* currentSnapshot;
241	+
242		for (int i = 0; i < nframes; i += args_info.frame_arg){
243	<	dumpReader->readFrame(info, i);
243	>	dumpReader->readFrame(i);
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;
251	>	mol = info->nextMolecule(miter)) {
252	>
253	>	molCom = mol->getCom();
254	>	newMolCom = molCom;
255	>	currentSnapshot->wrapVector(newMolCom);
256	>	displacement = newMolCom - molCom;
257
258	<	mol = info->molecules;
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(int j = 0; j < info->n_mol; j++){
269	<	myRigidBodies = mol[j].getMyRigidBodies();
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;
273	>	rb = mol->nextRigidBody(rbIter)) {
274
275	<	for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
276	<	(*rbIter)->updateAtoms();
179	<	}
275	>	rb->updateAtoms();
276	>	if (printVel) rb->updateAtomVel();
277
278	+	}
279	+	}
280
281		//prepare visit
282	<	for(int j = 0; j < info->n_mol; j++){
283	<	integrableObjects = mol[j].getIntegrableObjects();
282	>	for (mol = info->beginMolecule(miter); mol != NULL;
283	>	mol = info->nextMolecule(miter)) {
284
285	<	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
286	<	(*iter)->accept(prepareVisitor);
188	<	}
285	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
286	>	sd = mol->nextIntegrableObject(iiter)) {
287
288	+	sd->accept(prepareVisitor);
289	+
290	+	}
291	+	}
292	+
293		//update visitor
294		compositeVisitor->update();
295	<
295	>
296	>
297		//visit stuntdouble
298	<	for(int j = 0; j < info->n_mol; j++){
299	<	integrableObjects = mol[j].getIntegrableObjects();
298	>	for (mol = info->beginMolecule(miter); mol != NULL;
299	>	mol = info->nextMolecule(miter)) {
300
301	<	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
302	<	(*iter)->accept(compositeVisitor);
199	<	}
301	>	for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
302	>	sd = mol->nextIntegrableObject(iiter)) {
303
304	+	sd->accept(compositeVisitor);
305	+
306	+	}
307	+	}
308	+
309		xyzVisitor->writeFrame(xyzStream);
310		xyzVisitor->clear();
311
312		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
313	<
313	>
314		xyzStream.close();
315	<
208	<
315	>	delete prepareVisitor;
316		delete compositeVisitor;
317		delete info;
211	–
212	–
318		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 12 by tim, Tue Sep 28 23:24:25 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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