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

Comparing:
trunk/src/visitors/OtherVisitor.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 223 | Line 223 | namespace OpenMD {
223		return result;
224		}
225
226	<	//----------------------------------------------------------------------------//
226	>	//------------------------------------------------------------------------//
227
228	<	XYZVisitor::XYZVisitor(SimInfo *info) :
229	<	BaseVisitor(), seleMan(info), evaluator(info){
230	<	this->info = info;
231	<	visitorName = "XYZVisitor";
232	<
233	<	evaluator.loadScriptString("select all");
234	<
235	<	if (!evaluator.isDynamic()) {
236	<	seleMan.setSelectionSet(evaluator.evaluate());
237	<	}
238	<	posOnly_ = false;
228	>	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
229	>	evaluator(info), doPositions_(true),
230	>	doVelocities_(false),
231	>	doForces_(false), doVectors_(false),
232	>	doCharges_(false) {
233	>	this->info = info;
234	>	visitorName = "XYZVisitor";
235	>
236	>	evaluator.loadScriptString("select all");
237	>
238	>	if (!evaluator.isDynamic()) {
239	>	seleMan.setSelectionSet(evaluator.evaluate());
240		}
241	<
241	>	}
242	>
243		XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
244	<	BaseVisitor(), seleMan(info), evaluator(info) {
245	<	this->info = info;
246	<	visitorName = "XYZVisitor";
247	<
248	<	evaluator.loadScriptString(script);
249	<
250	<	if (!evaluator.isDynamic()) {
251	<	seleMan.setSelectionSet(evaluator.evaluate());
252	<	}
253	<	posOnly_ = false;
244	>	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
245	>	doVelocities_(false), doForces_(false), doVectors_(false),
246	>	doCharges_(false) {
247	>
248	>	this->info = info;
249	>	visitorName = "XYZVisitor";
250	>
251	>	evaluator.loadScriptString(script);
252	>
253	>	if (!evaluator.isDynamic()) {
254	>	seleMan.setSelectionSet(evaluator.evaluate());
255		}
256	+	}
257
258		void XYZVisitor::visit(Atom *atom) {
259		if (isSelected(atom))
#	Line 260 | Line 264 | namespace OpenMD {
264		if (isSelected(datom))
265		internalVisit(datom);
266		}
267	<
267	>
268		void XYZVisitor::visit(RigidBody *rb) {
269		if (isSelected(rb))
270		internalVisit(rb);
271		}
272	<
272	>
273		void XYZVisitor::update() {
274		//if dynamic, we need to re-evaluate the selection
275		if (evaluator.isDynamic()) {
276		seleMan.setSelectionSet(evaluator.evaluate());
277		}
278		}
279	<
279	>
280		void XYZVisitor::internalVisit(StuntDouble *sd) {
281		GenericData *                     data;
282		AtomData *                        atomData;
283		AtomInfo *                        atomInfo;
284		std::vector<AtomInfo *>::iterator i;
285		char                              buffer[1024];
286	<
286	>
287		//if there is not atom data, just skip it
288		data = sd->getPropertyByName("ATOMDATA");
289	<
289	>
290		if (data != NULL) {
291		atomData = dynamic_cast<AtomData *>(data);
292	<
292	>
293		if (atomData == NULL)
294		return;
295		} else
296		return;
297
298	<	AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
299	<	std::string bn = baseTypeName(at);
300	<
301	<	if (posOnly_){
302	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
303	<	atomInfo = atomData->nextAtomInfo(i) ) {
304	<	if (atomInfo->hasCharge) {
305	<	sprintf(buffer,
306	<	"%s%15.8f%15.8f%15.8f%15.8f",
307	<	bn.c_str(),
308	<	atomInfo->pos[0],
309	<	atomInfo->pos[1],
310	<	atomInfo->pos[2],
311	<	atomInfo->charge);
312	<	} else {
309	<	sprintf(buffer,
310	<	"%s%15.8f%15.8f%15.8f",
311	<	bn.c_str(),
312	<	atomInfo->pos[0],
313	<	atomInfo->pos[1],
314	<	atomInfo->pos[2]);
315	<	}
316	<	frame.push_back(buffer);
298	>	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
299	>	atomInfo = atomData->nextAtomInfo(i) ) {
300	>
301	>	std::string line;
302	>	sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
303	>	line += buffer;
304	>
305	>	if (doPositions_){
306	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
307	>	atomInfo->pos[1], atomInfo->pos[2]);
308	>	line += buffer;
309	>	}
310	>	if (doCharges_ && atomInfo->hasCharge) {
311	>	sprintf(buffer, "%15.8f", atomInfo->charge);
312	>	line += buffer;
313		}
314	<	}else{
315	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
316	<	atomInfo = atomData->nextAtomInfo(i) ) {
317	<	if (atomInfo->hasCharge) {
322	<	sprintf(buffer,
323	<	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
324	<	bn.c_str(),
325	<	atomInfo->pos[0],
326	<	atomInfo->pos[1],
327	<	atomInfo->pos[2],
328	<	atomInfo->charge,
329	<	atomInfo->dipole[0],
330	<	atomInfo->dipole[1],
331	<	atomInfo->dipole[2]);
332	<	} else {
333	<	sprintf(buffer,
334	<	"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
335	<	bn.c_str(),
336	<	atomInfo->pos[0],
337	<	atomInfo->pos[1],
338	<	atomInfo->pos[2],
339	<	atomInfo->dipole[0],
340	<	atomInfo->dipole[1],
341	<	atomInfo->dipole[2]);
342	<	}
343	<	frame.push_back(buffer);
314	>	if (doVectors_ && atomInfo->hasVector) {
315	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
316	>	atomInfo->vec[1], atomInfo->vec[2]);
317	>	line += buffer;
318		}
319	<	}
319	>	if (doVelocities_ && atomInfo->hasVelocity) {
320	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
321	>	atomInfo->vel[1], atomInfo->vel[2]);
322	>	line += buffer;
323	>	}
324	>	if (doForces_ && atomInfo->hasForce) {
325	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
326	>	atomInfo->frc[1], atomInfo->frc[2]);
327	>	line += buffer;
328	>	}
329	>	frame.push_back(line);
330	>	}
331		}
332
333		bool XYZVisitor::isSelected(StuntDouble *sd) {
#	Line 352 | Line 337 | namespace OpenMD {
337		void XYZVisitor::writeFrame(std::ostream &outStream) {
338		std::vector<std::string>::iterator i;
339		char buffer[1024];
340	<
340	>
341		if (frame.size() == 0)
342		std::cerr << "Current Frame does not contain any atoms" << std::endl;
343	<
343	>
344		//total number of atoms
345		outStream << frame.size() << std::endl;
346	<
346	>
347		//write comment line
348		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
349		Mat3x3d box = currSnapshot->getHmat();
#	Line 369 | Line 354 | namespace OpenMD {
354		box(0, 0), box(0, 1), box(0, 2),
355		box(1, 0), box(1, 1), box(1, 2),
356		box(2, 0), box(2, 1), box(2, 2));
357	<
357	>
358		outStream << buffer << std::endl;
359	<
359	>
360		for( i = frame.begin(); i != frame.end(); ++i )
361		outStream << *i << std::endl;
362		}
363	<
363	>
364		std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
365		return atomTypeName.substr(0, atomTypeName.find('-'));
366		}
367	<
383	<	std::string XYZVisitor::baseTypeName(AtomType* at) {
384	<	std::vector<AtomType*> ayb = at->allYourBase();
385	<	return ayb[ayb.size()-1]->getName();
386	<	}
387	<
367	>
368		const std::string XYZVisitor::toString() {
369		char        buffer[65535];
370		std::string result;
371	<
371	>
372		sprintf(buffer,
373		"------------------------------------------------------------------\n");
374		result += buffer;
375	<
375	>
376		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
377		result += buffer;
378	<
378	>
379		sprintf(buffer,
380		"Visitor Description: assemble the atom data and output xyz file\n");
381		result += buffer;
#	Line 403 | Line 383 | namespace OpenMD {
383		sprintf(buffer,
384		"------------------------------------------------------------------\n");
385		result += buffer;
386	<
386	>
387		return result;
388		}
389	<
389	>
390		//----------------------------------------------------------------------------//
391	<
391	>
392		void PrepareVisitor::internalVisit(Atom *atom) {
393		GenericData *data;
394		AtomData *   atomData;
395	<
395	>
396		//if visited property is  existed, remove it
397		data = atom->getPropertyByName("VISITED");
398	<
398	>
399		if (data != NULL) {
400		atom->removeProperty("VISITED");
401		}
402	<
402	>
403		//remove atomdata
404		data = atom->getPropertyByName("ATOMDATA");
405
#	Line 488 | Line 468 | namespace OpenMD {
468		visitorName = "WaterTypeVisitor";
469		waterTypeList.insert("TIP3P_RB_0");
470		waterTypeList.insert("TIP4P_RB_0");
471	+	waterTypeList.insert("TIP4P-Ew_RB_0");
472		waterTypeList.insert("TIP5P_RB_0");
473	+	waterTypeList.insert("TIP5P-E_RB_0");
474		waterTypeList.insert("SPCE_RB_0");
475	+	waterTypeList.insert("SPC_RB_0");
476		}
477
478		void WaterTypeVisitor::visit(RigidBody *rb) {
#	Line 502 | Line 485 | namespace OpenMD {
485		std::vector<AtomInfo *>::iterator i;
486
487		rbName = rb->getType();
488	<
488	>
489		if (waterTypeList.find(rbName) != waterTypeList.end()) {
490		myAtoms = rb->getAtoms();
491
492		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
493		++atomIter ) {
494		data = (*atomIter)->getPropertyByName("ATOMDATA");
495	<
495	>
496		if (data != NULL) {
497		atomData = dynamic_cast<AtomData *>(data);
498	<
498	>
499		if (atomData == NULL)
500		continue;
501		} else
502		continue;
503	<
503	>
504		for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
505		atomInfo = atomData->nextAtomInfo(i) ) {
506		atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);

Comparing:
trunk/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/OtherVisitor.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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