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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.
branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  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		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;
68
69	<	CompositeVisitor* compositeVisitor;
70	<	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;
69	>	//register force fields
70	>	registerForceFields();
71
72	+	gengetopt_args_info args_info;
73	+	std::string dumpFileName;
74	+	std::string xyzFileName;
75	+	bool printVel;
76	+	bool printFrc;
77	+	bool printVec;
78	+	bool printChrg;
79	+
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	<	}
89	<	else{
55	<	cerr << "Does not have input file name" << endl;
88	>	} else {
89	>	std::cerr << "Does not have input file name" << std::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);
117	>
118	>	//create GBtail atom visitor
119	>	GBtailVisitor* gbtVisitor = new GBtailVisitor(info);
120	>	compositeVisitor->addVisitor(gbtVisitor, 790);
121	>
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	<	//creat waterType visitor
131	<	if(args_info.watertype_flag){
132	<	waterTypeVisitor = new WaterTypeVisitor;
133	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
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	>	std::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.repeatY_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	>	std::cerr << "Both of --refsele and --originsele should appear by pair"
185	>	<< std::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	+
215	+	compositeVisitor->addVisitor(xyzVisitor, 200);
216	+
217	+	//create prepareVisitor
218	+	PrepareVisitor* prepareVisitor = new PrepareVisitor();
219	+
220		//open dump file
221	<	dumpReader = new DumpReader(dumpFileName.c_str());
222	<	nframes = dumpReader->getNframes();
165	<
166	<	xyzStream .open(xyzFileName.c_str());
221	>	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
222	>	int nframes = dumpReader->getNFrames();
223
224	+	std::ofstream xyzStream(xyzFileName.c_str());
225	+
226	+	SimInfo::MoleculeIterator miter;
227	+	Molecule::IntegrableObjectIterator  iiter;
228	+	Molecule::RigidBodyIterator rbIter;
229	+	Molecule* mol;
230	+	StuntDouble* integrableObject;
231	+	RigidBody* rb;
232	+	Vector3d molCom;
233	+	Vector3d newMolCom;
234	+	Vector3d displacement;
235	+	Mat3x3d hmat;
236	+	Snapshot* currentSnapshot;
237	+
238		for (int i = 0; i < nframes; i += args_info.frame_arg){
239	<	dumpReader->readFrame(info, i);
240	<
241	<	mol = info->molecules;
242	<
239	>	dumpReader->readFrame(i);
240	>
241	>	if (printFrc) forceMan->calcForces();
242	>
243	>	//wrapping the molecule
244	>	if(args_info.periodicBox_flag) {
245	>	currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
246	>	for (mol = info->beginMolecule(miter); mol != NULL;
247	>	mol = info->nextMolecule(miter)) {
248	>	molCom = mol->getCom();
249	>	newMolCom = molCom;
250	>	currentSnapshot->wrapVector(newMolCom);
251	>	displacement = newMolCom - molCom;
252	>	for (integrableObject = mol->beginIntegrableObject(iiter);
253	>	integrableObject != NULL;
254	>	integrableObject = mol->nextIntegrableObject(iiter)) {
255	>	integrableObject->setPos(integrableObject->getPos() + displacement);
256	>	}
257	>	}
258	>	}
259		//update atoms of rigidbody
260	<	for(int j = 0; j < info->n_mol; j++){
261	<	myRigidBodies = mol[j].getMyRigidBodies();
262	<
263	<	for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
264	<	(*rbIter)->updateAtoms();
265	<	}
266	<
260	>	for (mol = info->beginMolecule(miter); mol != NULL;
261	>	mol = info->nextMolecule(miter)) {
262	>
263	>	//change the positions of atoms which belong to the rigidbodies
264	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
265	>	rb = mol->nextRigidBody(rbIter)) {
266	>	rb->updateAtoms();
267	>	if (printVel) rb->updateAtomVel();
268	>	}
269	>	}
270
271		//prepare visit
272	<	for(int j = 0; j < info->n_mol; j++){
273	<	integrableObjects = mol[j].getIntegrableObjects();
274	<
275	<	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
276	<	(*iter)->accept(prepareVisitor);
277	<	}
278	<
272	>	for (mol = info->beginMolecule(miter); mol != NULL;
273	>	mol = info->nextMolecule(miter)) {
274	>	for (integrableObject = mol->beginIntegrableObject(iiter);
275	>	integrableObject != NULL;
276	>	integrableObject = mol->nextIntegrableObject(iiter)) {
277	>	integrableObject->accept(prepareVisitor);
278	>	}
279	>	}
280	>
281		//update visitor
282		compositeVisitor->update();
192	–
193	–	//visit stuntdouble
194	–	for(int j = 0; j < info->n_mol; j++){
195	–	integrableObjects = mol[j].getIntegrableObjects();
283
197	–	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
198	–	(*iter)->accept(compositeVisitor);
199	–	}
284
285	+	//visit stuntdouble
286	+	for (mol = info->beginMolecule(miter); mol != NULL;
287	+	mol = info->nextMolecule(miter)) {
288	+	for (integrableObject = mol->beginIntegrableObject(iiter);
289	+	integrableObject != NULL;
290	+	integrableObject = mol->nextIntegrableObject(iiter)) {
291	+	integrableObject->accept(compositeVisitor);
292	+	}
293	+	}
294	+
295		xyzVisitor->writeFrame(xyzStream);
296		xyzVisitor->clear();
297
298		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
299	<
299	>
300		xyzStream.close();
301	<
208	<
301	>	delete prepareVisitor;
302		delete compositeVisitor;
303		delete info;
211	–
212	–
304		}

Comparing:
trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords), Revision 12 by tim, Tue Sep 28 23:24:25 2004 UTC vs.
branches/development/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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