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root/OpenMD/branches/development/src/visitors/OtherVisitor.cpp

Comparing:
trunk/src/visitors/OtherVisitor.cpp (file contents), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	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		#include "selection/SelectionManager.hpp"
43		#include "visitors/OtherVisitor.hpp"
#	Line 44 | Line 45
45		#include "primitives/RigidBody.hpp"
46		#include "primitives/Molecule.hpp"
47		#include "brains/SimInfo.hpp"
48	<	namespace oopse {
48	>	#include "brains/Thermo.hpp"
49
50	<	void WrappingVisitor::visit(Atom *atom) {
50	<	internalVisit(atom);
51	<	}
50	>	namespace OpenMD {
51
52	<	void WrappingVisitor::visit(DirectionalAtom *datom) {
53	<	internalVisit(datom);
54	<	}
52	>	void WrappingVisitor::visit(Atom *atom) {
53	>	internalVisit(atom);
54	>	}
55
56	<	void WrappingVisitor::visit(RigidBody *rb) {
57	<	internalVisit(rb);
58	<	}
56	>	void WrappingVisitor::visit(DirectionalAtom *datom) {
57	>	internalVisit(datom);
58	>	}
59
60	<	void WrappingVisitor::internalVisit(StuntDouble *sd) {
60	>	void WrappingVisitor::visit(RigidBody *rb) {
61	>	internalVisit(rb);
62	>	}
63	>
64	>	void WrappingVisitor::internalVisit(StuntDouble *sd) {
65		GenericData *                     data;
66		AtomData *                        atomData;
67		AtomInfo *                        atomInfo;
#	Line 67 | Line 70 | void WrappingVisitor::internalVisit(StuntDouble *sd) {
70		data = sd->getPropertyByName("ATOMDATA");
71
72		if (data != NULL) {
73	<	atomData = dynamic_cast<AtomData *>(data);
73	>	atomData = dynamic_cast<AtomData *>(data);
74
75	<	if (atomData == NULL)
76	<	return;
75	>	if (atomData == NULL)
76	>	return;
77		} else
78	<	return;
78	>	return;
79
80		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
81
82	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
83	<	currSnapshot->wrapVector(atomInfo->pos);
82	>	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
83	>	atomInfo = atomData->nextAtomInfo(i) ) {
84	>
85	>	Vector3d newPos = atomInfo->pos - origin_;
86	>	currSnapshot->wrapVector(newPos);
87	>	atomInfo->pos = newPos;
88	>
89		}
90	<	}
90	>	}
91
92	<	const std::string WrappingVisitor::toString() {
92	>	void WrappingVisitor::update() {
93	>	if (useCom_){
94	>	Thermo thermo(info);
95	>	origin_ = thermo.getCom();
96	>	}
97	>	}
98	>
99	>	const std::string WrappingVisitor::toString() {
100		char        buffer[65535];
101		std::string result;
102
#	Line 101 | Line 116 | const std::string WrappingVisitor::toString() {
116		result += buffer;
117
118		return result;
119	<	}
119	>	}
120
121	<	//----------------------------------------------------------------------------//
121	>	//----------------------------------------------------------------------------//
122
123	<	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
123	>	ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
124		BaseVisitor() {
125	<	this->info = info;
126	<	visitorName = "ReplicateVisitor";
127	<	this->replicateOpt = opt;
125	>	this->info = info;
126	>	visitorName = "ReplicateVisitor";
127	>	this->replicateOpt = opt;
128
129	<	//generate the replicate directions
130	<	for( int i = 0; i <= replicateOpt[0]; i++ ) {
129	>	//generate the replicate directions
130	>	for( int i = 0; i <= replicateOpt[0]; i++ ) {
131		for( int j = 0; j <= replicateOpt[1]; j++ ) {
132	<	for( int k = 0; k <= replicateOpt[2]; k++ ) {
133	<	//skip original frame
134	<	if (i == 0 && j == 0 && k == 0) {
135	<	continue;
136	<	} else {
137	<	dir.push_back(Vector3i(i, j, k));
138	<	}
139	<	}
132	>	for( int k = 0; k <= replicateOpt[2]; k++ ) {
133	>	//skip original frame
134	>	if (i == 0 && j == 0 && k == 0) {
135	>	continue;
136	>	} else {
137	>	dir.push_back(Vector3i(i, j, k));
138	>	}
139	>	}
140		}
141	<	}
141	>	}
142
143	<	}
143	>	}
144
145	<	void ReplicateVisitor::visit(Atom *atom) {
146	<	internalVisit(atom);
147	<	}
145	>	void ReplicateVisitor::visit(Atom *atom) {
146	>	internalVisit(atom);
147	>	}
148
149	<	void ReplicateVisitor::visit(DirectionalAtom *datom) {
150	<	internalVisit(datom);
151	<	}
149	>	void ReplicateVisitor::visit(DirectionalAtom *datom) {
150	>	internalVisit(datom);
151	>	}
152
153	<	void ReplicateVisitor::visit(RigidBody *rb) {
154	<	internalVisit(rb);
155	<	}
153	>	void ReplicateVisitor::visit(RigidBody *rb) {
154	>	internalVisit(rb);
155	>	}
156
157	<	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
157	>	void ReplicateVisitor::internalVisit(StuntDouble *sd) {
158		GenericData *          data;
159		AtomData *             atomData;
160
#	Line 147 | Line 162 | void ReplicateVisitor::internalVisit(StuntDouble *sd)
162		data = sd->getPropertyByName("ATOMDATA");
163
164		if (data != NULL) {
165	<	atomData = dynamic_cast<AtomData *>(data);
165	>	atomData = dynamic_cast<AtomData *>(data);
166
167	<	if (atomData == NULL) {
168	<	return;
169	<	}
167	>	if (atomData == NULL) {
168	>	return;
169	>	}
170		} else {
171	<	return;
171	>	return;
172		}
173
174		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
#	Line 162 | Line 177 | void ReplicateVisitor::internalVisit(StuntDouble *sd)
177		std::vector<AtomInfo *> atomInfoList = atomData->getData();
178
179		replicate(atomInfoList, atomData, box);
180	<	}
180	>	}
181
182	<	void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) {
182	>	void ReplicateVisitor::replicate(std::vector<AtomInfo *>&infoList, AtomData *data, const Mat3x3d& box) {
183		AtomInfo* newAtomInfo;
184		std::vector<Vector3i>::iterator dirIter;
185		std::vector<AtomInfo *>::iterator i;
186
187		for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
188	<	for( i = infoList.begin(); i != infoList.end(); i++ ) {
189	<	newAtomInfo = new AtomInfo();
190	<	*newAtomInfo = *(*i);
188	>	for( i = infoList.begin(); i != infoList.end(); i++ ) {
189	>	newAtomInfo = new AtomInfo();
190	>	*newAtomInfo = *(*i);
191
192	<	for( int j = 0; j < 3; j++ )
193	<	newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2);
192	>	for( int j = 0; j < 3; j++ )
193	>	newAtomInfo->pos[j] += (*dirIter)[0]*box(j, 0) + (*dirIter)[1]*box(j, 1) + (*dirIter)[2]*box(j, 2);
194
195	<	data->addAtomInfo(newAtomInfo);
196	<	}
195	>	data->addAtomInfo(newAtomInfo);
196	>	}
197		} // end for(dirIter)
198	<	}
198	>	}
199
200	<	const std::string ReplicateVisitor::toString() {
200	>	const std::string ReplicateVisitor::toString() {
201		char                            buffer[65535];
202		std::string                     result;
203		std::set<std::string>::iterator i;
#	Line 213 | Line 228 | const std::string ReplicateVisitor::toString() {
228		result += buffer;
229
230		return result;
231	<	}
231	>	}
232
233	<	//----------------------------------------------------------------------------//
233	>	//------------------------------------------------------------------------//
234
235	<	XYZVisitor::XYZVisitor(SimInfo *info) :
236	<	BaseVisitor(), seleMan(info), evaluator(info){
235	>	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
236	>	evaluator(info), doPositions_(true),
237	>	doVelocities_(false),
238	>	doForces_(false), doVectors_(false),
239	>	doCharges_(false) {
240		this->info = info;
241		visitorName = "XYZVisitor";
242	<
242	>
243		evaluator.loadScriptString("select all");
244	<
244	>
245		if (!evaluator.isDynamic()) {
246	<	seleMan.setSelectionSet(evaluator.evaluate());
246	>	seleMan.setSelectionSet(evaluator.evaluate());
247		}
248	<
249	<	}
250	<
251	<	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
252	<	BaseVisitor(), seleMan(info), evaluator(info) {
248	>	}
249	>
250	>	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
251	>	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
252	>	doVelocities_(false), doForces_(false), doVectors_(false),
253	>	doCharges_(false) {
254	>
255		this->info = info;
256		visitorName = "XYZVisitor";
257	<
257	>
258		evaluator.loadScriptString(script);
259	<
259	>
260		if (!evaluator.isDynamic()) {
261	<	seleMan.setSelectionSet(evaluator.evaluate());
261	>	seleMan.setSelectionSet(evaluator.evaluate());
262		}
263	<
244	<	}
263	>	}
264
265	<	void XYZVisitor::visit(Atom *atom) {
265	>	void XYZVisitor::visit(Atom *atom) {
266		if (isSelected(atom))
267	<	internalVisit(atom);
268	<	}
267	>	internalVisit(atom);
268	>	}
269
270	<	void XYZVisitor::visit(DirectionalAtom *datom) {
270	>	void XYZVisitor::visit(DirectionalAtom *datom) {
271		if (isSelected(datom))
272	<	internalVisit(datom);
273	<	}
274	<
275	<	void XYZVisitor::visit(RigidBody *rb) {
272	>	internalVisit(datom);
273	>	}
274	>
275	>	void XYZVisitor::visit(RigidBody *rb) {
276		if (isSelected(rb))
277	<	internalVisit(rb);
278	<	}
279	<
280	<	void XYZVisitor::update() {
277	>	internalVisit(rb);
278	>	}
279	>
280	>	void XYZVisitor::update() {
281		//if dynamic, we need to re-evaluate the selection
282		if (evaluator.isDynamic()) {
283	<	seleMan.setSelectionSet(evaluator.evaluate());
283	>	seleMan.setSelectionSet(evaluator.evaluate());
284		}
285	<	}
286	<
287	<	void XYZVisitor::internalVisit(StuntDouble *sd) {
285	>	}
286	>
287	>	void XYZVisitor::internalVisit(StuntDouble *sd) {
288		GenericData *                     data;
289		AtomData *                        atomData;
290		AtomInfo *                        atomInfo;
291		std::vector<AtomInfo *>::iterator i;
292		char                              buffer[1024];
293	<
293	>
294		//if there is not atom data, just skip it
295		data = sd->getPropertyByName("ATOMDATA");
296	<
296	>
297		if (data != NULL) {
298	<	atomData = dynamic_cast<AtomData *>(data);
299	<
300	<	if (atomData == NULL)
301	<	return;
298	>	atomData = dynamic_cast<AtomData *>(data);
299	>
300	>	if (atomData == NULL)
301	>	return;
302		} else
303	<	return;
303	>	return;
304
305		for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
306	<	atomInfo = atomData->nextAtomInfo(i) ) {
307	<	sprintf(buffer,
308	<	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
309	<	atomInfo->atomTypeName.c_str(),
310	<	atomInfo->pos[0],
311	<	atomInfo->pos[1],
312	<	atomInfo->pos[2],
313	<	atomInfo->dipole[0],
314	<	atomInfo->dipole[1],
315	<	atomInfo->dipole[2]);
316	<	frame.push_back(buffer);
317	<	}
318	<	}
306	>	atomInfo = atomData->nextAtomInfo(i) ) {
307	>
308	>	std::string line;
309	>	sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
310	>	line += buffer;
311	>
312	>	if (doPositions_){
313	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
314	>	atomInfo->pos[1], atomInfo->pos[2]);
315	>	line += buffer;
316	>	}
317	>	if (doCharges_ && atomInfo->hasCharge) {
318	>	sprintf(buffer, "%15.8f", atomInfo->charge);
319	>	line += buffer;
320	>	}
321	>	if (doVectors_ && atomInfo->hasVector) {
322	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
323	>	atomInfo->vec[1], atomInfo->vec[2]);
324	>	line += buffer;
325	>	}
326	>	if (doVelocities_ && atomInfo->hasVelocity) {
327	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
328	>	atomInfo->vel[1], atomInfo->vel[2]);
329	>	line += buffer;
330	>	}
331	>	if (doForces_ && atomInfo->hasForce) {
332	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
333	>	atomInfo->frc[1], atomInfo->frc[2]);
334	>	line += buffer;
335	>	}
336	>	frame.push_back(line);
337	>	}
338	>	}
339
340	<	bool XYZVisitor::isSelected(StuntDouble *sd) {
340	>	bool XYZVisitor::isSelected(StuntDouble *sd) {
341		return seleMan.isSelected(sd);
342	<	}
342	>	}
343
344	<	void XYZVisitor::writeFrame(std::ostream &outStream) {
344	>	void XYZVisitor::writeFrame(std::ostream &outStream) {
345		std::vector<std::string>::iterator i;
346		char buffer[1024];
347	<
347	>
348		if (frame.size() == 0)
349	<	std::cerr << "Current Frame does not contain any atoms" << std::endl;
350	<
349	>	std::cerr << "Current Frame does not contain any atoms" << std::endl;
350	>
351		//total number of atoms
352		outStream << frame.size() << std::endl;
353	<
353	>
354		//write comment line
355		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
356		Mat3x3d box = currSnapshot->getHmat();
#	Line 322 | Line 361 | void XYZVisitor::writeFrame(std::ostream &outStream) {
361		box(0, 0), box(0, 1), box(0, 2),
362		box(1, 0), box(1, 1), box(1, 2),
363		box(2, 0), box(2, 1), box(2, 2));
364	<
364	>
365		outStream << buffer << std::endl;
366	<
366	>
367		for( i = frame.begin(); i != frame.end(); ++i )
368	<	outStream << *i << std::endl;
369	<	}
370	<
371	<	const std::string XYZVisitor::toString() {
368	>	outStream << *i << std::endl;
369	>	}
370	>
371	>	std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
372	>	return atomTypeName.substr(0, atomTypeName.find('-'));
373	>	}
374	>
375	>	const std::string XYZVisitor::toString() {
376		char        buffer[65535];
377		std::string result;
378	<
378	>
379		sprintf(buffer,
380		"------------------------------------------------------------------\n");
381		result += buffer;
382	<
382	>
383		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
384		result += buffer;
385	<
385	>
386		sprintf(buffer,
387		"Visitor Description: assemble the atom data and output xyz file\n");
388		result += buffer;
#	Line 347 | Line 390 | const std::string XYZVisitor::toString() {
390		sprintf(buffer,
391		"------------------------------------------------------------------\n");
392		result += buffer;
393	<
393	>
394		return result;
395	<	}
396	<
397	<	//----------------------------------------------------------------------------//
398	<
399	<	void PrepareVisitor::internalVisit(Atom *atom) {
395	>	}
396	>
397	>	//----------------------------------------------------------------------------//
398	>
399	>	void PrepareVisitor::internalVisit(Atom *atom) {
400		GenericData *data;
401		AtomData *   atomData;
402	<
402	>
403		//if visited property is  existed, remove it
404		data = atom->getPropertyByName("VISITED");
405	<
405	>
406		if (data != NULL) {
407	<	atom->removeProperty("VISITED");
407	>	atom->removeProperty("VISITED");
408		}
409	<
409	>
410		//remove atomdata
411		data = atom->getPropertyByName("ATOMDATA");
412
413		if (data != NULL) {
414	<	atomData = dynamic_cast<AtomData *>(data);
414	>	atomData = dynamic_cast<AtomData *>(data);
415
416	<	if (atomData != NULL)
417	<	atom->removeProperty("ATOMDATA");
416	>	if (atomData != NULL)
417	>	atom->removeProperty("ATOMDATA");
418		}
419	<	}
419	>	}
420
421	<	void PrepareVisitor::internalVisit(RigidBody *rb) {
421	>	void PrepareVisitor::internalVisit(RigidBody *rb) {
422		GenericData* data;
423		AtomData* atomData;
424		std::vector<Atom *> myAtoms;
#	Line 385 | Line 428 | void PrepareVisitor::internalVisit(RigidBody *rb) {
428		data = rb->getPropertyByName("VISITED");
429
430		if (data != NULL) {
431	<	rb->removeProperty("VISITED");
431	>	rb->removeProperty("VISITED");
432		}
433
434		//remove atomdata
435		data = rb->getPropertyByName("ATOMDATA");
436
437		if (data != NULL) {
438	<	atomData = dynamic_cast<AtomData *>(data);
438	>	atomData = dynamic_cast<AtomData *>(data);
439
440	<	if (atomData != NULL)
441	<	rb->removeProperty("ATOMDATA");
440	>	if (atomData != NULL)
441	>	rb->removeProperty("ATOMDATA");
442		}
443
444		myAtoms = rb->getAtoms();
445
446		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter )
447	<	internalVisit(*atomIter);
448	<	}
447	>	internalVisit(*atomIter);
448	>	}
449
450	<	const std::string PrepareVisitor::toString() {
451	<	char buffer[65535];
452	<	std::string result;
450	>	const std::string PrepareVisitor::toString() {
451	>	char buffer[65535];
452	>	std::string result;
453
454	<	sprintf(buffer,
455	<	"------------------------------------------------------------------\n");
456	<	result += buffer;
454	>	sprintf(buffer,
455	>	"------------------------------------------------------------------\n");
456	>	result += buffer;
457
458	<	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
459	<	result += buffer;
458	>	sprintf(buffer, "Visitor name: %s", visitorName.c_str());
459	>	result += buffer;
460
461	<	sprintf(buffer,
462	<	"Visitor Description: prepare for operation of other vistors\n");
463	<	result += buffer;
461	>	sprintf(buffer,
462	>	"Visitor Description: prepare for operation of other vistors\n");
463	>	result += buffer;
464
465	<	sprintf(buffer,
466	<	"------------------------------------------------------------------\n");
467	<	result += buffer;
465	>	sprintf(buffer,
466	>	"------------------------------------------------------------------\n");
467	>	result += buffer;
468
469	<	return result;
470	<	}
469	>	return result;
470	>	}
471
472	<	//----------------------------------------------------------------------------//
472	>	//----------------------------------------------------------------------------//
473
474	<	WaterTypeVisitor::WaterTypeVisitor() {
474	>	WaterTypeVisitor::WaterTypeVisitor() {
475		visitorName = "WaterTypeVisitor";
476		waterTypeList.insert("TIP3P_RB_0");
477		waterTypeList.insert("TIP4P_RB_0");
478	+	waterTypeList.insert("TIP4P-Ew_RB_0");
479		waterTypeList.insert("TIP5P_RB_0");
480	+	waterTypeList.insert("TIP5P-E_RB_0");
481		waterTypeList.insert("SPCE_RB_0");
482	<	}
482	>	waterTypeList.insert("SPC_RB_0");
483	>	}
484
485	<	void WaterTypeVisitor::visit(RigidBody *rb) {
485	>	void WaterTypeVisitor::visit(RigidBody *rb) {
486		std::string rbName;
487		std::vector<Atom *> myAtoms;
488		std::vector<Atom *>::iterator atomIter;
#	Line 446 | Line 492 | void WaterTypeVisitor::visit(RigidBody *rb) {
492		std::vector<AtomInfo *>::iterator i;
493
494		rbName = rb->getType();
495	<
495	>
496		if (waterTypeList.find(rbName) != waterTypeList.end()) {
497	<	myAtoms = rb->getAtoms();
497	>	myAtoms = rb->getAtoms();
498
499	<	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
500	<	++atomIter ) {
501	<	data = (*atomIter)->getPropertyByName("ATOMDATA");
502	<
503	<	if (data != NULL) {
504	<	atomData = dynamic_cast<AtomData *>(data);
505	<
506	<	if (atomData == NULL)
507	<	continue;
508	<	} else
509	<	continue;
510	<
511	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
512	<	atomInfo = atomData->nextAtomInfo(i) ) {
513	<	atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
514	<	} //end for(atomInfo)
515	<	}     //end for(atomIter)
499	>	for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
500	>	++atomIter ) {
501	>	data = (*atomIter)->getPropertyByName("ATOMDATA");
502	>
503	>	if (data != NULL) {
504	>	atomData = dynamic_cast<AtomData *>(data);
505	>
506	>	if (atomData == NULL)
507	>	continue;
508	>	} else
509	>	continue;
510	>
511	>	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
512	>	atomInfo = atomData->nextAtomInfo(i) ) {
513	>	atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
514	>	} //end for(atomInfo)
515	>	}     //end for(atomIter)
516		}         //end if (waterTypeList.find(rbName) != waterTypeList.end())
517	<	}
517	>	}
518
519		std::string WaterTypeVisitor::trimmedName(const std::string&atomTypeName) {
520		return atomTypeName.substr(0, atomTypeName.find('_'));
521		}
522
523	<	const std::string WaterTypeVisitor::toString() {
523	>	const std::string WaterTypeVisitor::toString() {
524		char buffer[65535];
525		std::string result;
526
#	Line 494 | Line 540 | const std::string WaterTypeVisitor::toString() {
540		result += buffer;
541
542		return result;
543	<	}
543	>	}
544
545	<	} //namespace oopse
545	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 0 | Line 1
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