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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 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

#	Line 35 | Line 35
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).
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		#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	+	#include "brains/Thermo.hpp"
49	+
50		namespace OpenMD {
51
52		void WrappingVisitor::visit(Atom *atom) {
#	Line 76 | Line 79 | namespace OpenMD {
79
80		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
81
82	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
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		}
91
92		void WrappingVisitor::update() {
93		if (useCom_){
94	<	origin_ = info->getCom();
94	>	Thermo thermo(info);
95	>	origin_ = thermo.getCom();
96		}
97		}
98
#	Line 178 | Line 185 | namespace OpenMD {
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++ ) {
188	>	for( i = infoList.begin(); i != infoList.end(); ++i ) {
189		newAtomInfo = new AtomInfo();
190		*newAtomInfo = *(*i);
191
#	Line 193 | Line 200 | namespace OpenMD {
200		const std::string ReplicateVisitor::toString() {
201		char                            buffer[65535];
202		std::string                     result;
196	–	std::set<std::string>::iterator i;
203
204	+
205		sprintf(buffer,
206	<	"------------------------------------------------------------------\n");
206	>	"--------------------------------------------------------------\n");
207		result += buffer;
208
209		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
#	Line 217 | Line 224 | namespace OpenMD {
224		result += buffer;
225
226		sprintf(buffer,
227	<	"------------------------------------------------------------------\n");
227	>	"--------------------------------------------------------------\n");
228		result += buffer;
229
230		return result;
231		}
232
233	<	//----------------------------------------------------------------------------//
233	>	//------------------------------------------------------------------------//
234
235	<	XYZVisitor::XYZVisitor(SimInfo *info) :
236	<	BaseVisitor(), seleMan(info), evaluator(info){
237	<	this->info = info;
238	<	visitorName = "XYZVisitor";
239	<
240	<	evaluator.loadScriptString("select all");
241	<
242	<	if (!evaluator.isDynamic()) {
243	<	seleMan.setSelectionSet(evaluator.evaluate());
244	<	}
245	<	posOnly_ = false;
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	>	doElectricFields_(false) {
241	>	this->info = info;
242	>	visitorName = "XYZVisitor";
243	>
244	>	evaluator.loadScriptString("select all");
245	>
246	>	if (!evaluator.isDynamic()) {
247	>	seleMan.setSelectionSet(evaluator.evaluate());
248		}
249	<
249	>	}
250	>
251		XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
252	<	BaseVisitor(), seleMan(info), evaluator(info) {
253	<	this->info = info;
254	<	visitorName = "XYZVisitor";
255	<
256	<	evaluator.loadScriptString(script);
257	<
258	<	if (!evaluator.isDynamic()) {
259	<	seleMan.setSelectionSet(evaluator.evaluate());
260	<	}
261	<	posOnly_ = false;
252	>	BaseVisitor(), seleMan(info), evaluator(info), doPositions_(true),
253	>	doVelocities_(false), doForces_(false), doVectors_(false),
254	>	doCharges_(false), doElectricFields_(false) {
255	>
256	>	this->info = info;
257	>	visitorName = "XYZVisitor";
258	>
259	>	evaluator.loadScriptString(script);
260	>
261	>	if (!evaluator.isDynamic()) {
262	>	seleMan.setSelectionSet(evaluator.evaluate());
263		}
264	+	}
265
266		void XYZVisitor::visit(Atom *atom) {
267		if (isSelected(atom))
#	Line 260 | Line 272 | namespace OpenMD {
272		if (isSelected(datom))
273		internalVisit(datom);
274		}
275	<
275	>
276		void XYZVisitor::visit(RigidBody *rb) {
277		if (isSelected(rb))
278		internalVisit(rb);
279		}
280	<
280	>
281		void XYZVisitor::update() {
282		//if dynamic, we need to re-evaluate the selection
283		if (evaluator.isDynamic()) {
284		seleMan.setSelectionSet(evaluator.evaluate());
285		}
286		}
287	<
287	>
288		void XYZVisitor::internalVisit(StuntDouble *sd) {
289		GenericData *                     data;
290		AtomData *                        atomData;
291		AtomInfo *                        atomInfo;
292		std::vector<AtomInfo *>::iterator i;
293		char                              buffer[1024];
294	<
294	>
295		//if there is not atom data, just skip it
296		data = sd->getPropertyByName("ATOMDATA");
297	<
297	>
298		if (data != NULL) {
299		atomData = dynamic_cast<AtomData *>(data);
300	<
300	>
301		if (atomData == NULL)
302		return;
303		} else
304		return;
305
306	<	AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
307	<	std::string bn = baseTypeName(at);
308	<
309	<	if (posOnly_){
310	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
311	<	atomInfo = atomData->nextAtomInfo(i) ) {
312	<	if (atomInfo->hasCharge) {
313	<	sprintf(buffer,
314	<	"%s%15.8f%15.8f%15.8f%15.8f",
315	<	bn.c_str(),
316	<	atomInfo->pos[0],
317	<	atomInfo->pos[1],
318	<	atomInfo->pos[2],
319	<	atomInfo->charge);
320	<	} 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);
306	>	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
307	>	atomInfo = atomData->nextAtomInfo(i) ) {
308	>
309	>	std::string line;
310	>	sprintf(buffer, "%s", atomInfo->atomTypeName.c_str());
311	>	line += buffer;
312	>
313	>	if (doPositions_){
314	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->pos[0],
315	>	atomInfo->pos[1], atomInfo->pos[2]);
316	>	line += buffer;
317	>	}
318	>	if (doCharges_ && atomInfo->hasCharge) {
319	>	sprintf(buffer, "%15.8f", atomInfo->charge);
320	>	line += buffer;
321		}
322	<	}else{
323	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
324	<	atomInfo = atomData->nextAtomInfo(i) ) {
325	<	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);
322	>	if (doVectors_ && atomInfo->hasVector) {
323	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vec[0],
324	>	atomInfo->vec[1], atomInfo->vec[2]);
325	>	line += buffer;
326		}
327	<	}
327	>	if (doVelocities_ && atomInfo->hasVelocity) {
328	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->vel[0],
329	>	atomInfo->vel[1], atomInfo->vel[2]);
330	>	line += buffer;
331	>	}
332	>	if (doForces_ && atomInfo->hasForce) {
333	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->frc[0],
334	>	atomInfo->frc[1], atomInfo->frc[2]);
335	>	line += buffer;
336	>	}
337	>	if (doElectricFields_ && atomInfo->hasElectricField) {
338	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->eField[0],
339	>	atomInfo->eField[1], atomInfo->eField[2]);
340	>	line += buffer;
341	>	}
342	>	frame.push_back(line);
343	>	}
344		}
345
346		bool XYZVisitor::isSelected(StuntDouble *sd) {
#	Line 352 | Line 350 | namespace OpenMD {
350		void XYZVisitor::writeFrame(std::ostream &outStream) {
351		std::vector<std::string>::iterator i;
352		char buffer[1024];
353	<
354	<	if (frame.size() == 0)
353	>
354	>	if (frame.empty())
355		std::cerr << "Current Frame does not contain any atoms" << std::endl;
356	<
356	>
357		//total number of atoms
358		outStream << frame.size() << std::endl;
359	<
359	>
360		//write comment line
361		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
362		Mat3x3d box = currSnapshot->getHmat();
#	Line 369 | Line 367 | namespace OpenMD {
367		box(0, 0), box(0, 1), box(0, 2),
368		box(1, 0), box(1, 1), box(1, 2),
369		box(2, 0), box(2, 1), box(2, 2));
370	<
370	>
371		outStream << buffer << std::endl;
372	<
372	>
373		for( i = frame.begin(); i != frame.end(); ++i )
374		outStream << *i << std::endl;
375		}
376	<
376	>
377		std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
378		return atomTypeName.substr(0, atomTypeName.find('-'));
379		}
380	<
383	<	std::string XYZVisitor::baseTypeName(AtomType* at) {
384	<	std::vector<AtomType*> ayb = at->allYourBase();
385	<	return ayb[ayb.size()-1]->getName();
386	<	}
387	<
380	>
381		const std::string XYZVisitor::toString() {
382		char        buffer[65535];
383		std::string result;
384	<
384	>
385		sprintf(buffer,
386		"------------------------------------------------------------------\n");
387		result += buffer;
388	<
388	>
389		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
390		result += buffer;
391	<
391	>
392		sprintf(buffer,
393		"Visitor Description: assemble the atom data and output xyz file\n");
394		result += buffer;
#	Line 403 | Line 396 | namespace OpenMD {
396		sprintf(buffer,
397		"------------------------------------------------------------------\n");
398		result += buffer;
399	<
399	>
400		return result;
401		}
402	<
402	>
403		//----------------------------------------------------------------------------//
404	<
404	>
405		void PrepareVisitor::internalVisit(Atom *atom) {
406		GenericData *data;
407	<	AtomData *   atomData;
415	<
407	>
408		//if visited property is  existed, remove it
409		data = atom->getPropertyByName("VISITED");
410	<
410	>
411		if (data != NULL) {
412		atom->removeProperty("VISITED");
413		}
414	<
414	>
415		//remove atomdata
416		data = atom->getPropertyByName("ATOMDATA");
417
418		if (data != NULL) {
419	<	atomData = dynamic_cast<AtomData *>(data);
419	>	AtomData* atomData = dynamic_cast<AtomData *>(data);
420
421		if (atomData != NULL)
422		atom->removeProperty("ATOMDATA");
#	Line 488 | Line 480 | namespace OpenMD {
480		visitorName = "WaterTypeVisitor";
481		waterTypeList.insert("TIP3P_RB_0");
482		waterTypeList.insert("TIP4P_RB_0");
483	+	waterTypeList.insert("TIP4P-Ew_RB_0");
484		waterTypeList.insert("TIP5P_RB_0");
485	+	waterTypeList.insert("TIP5P-E_RB_0");
486		waterTypeList.insert("SPCE_RB_0");
487	+	waterTypeList.insert("SPC_RB_0");
488		}
489
490		void WaterTypeVisitor::visit(RigidBody *rb) {
491		std::string rbName;
492		std::vector<Atom *> myAtoms;
493		std::vector<Atom *>::iterator atomIter;
499	–	GenericData* data;
500	–	AtomData* atomData;
501	–	AtomInfo* atomInfo;
494		std::vector<AtomInfo *>::iterator i;
495	+	AtomData* atomData;
496
497		rbName = rb->getType();
498	<
498	>
499		if (waterTypeList.find(rbName) != waterTypeList.end()) {
500		myAtoms = rb->getAtoms();
501	<
501	>
502		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
503		++atomIter ) {
504	<	data = (*atomIter)->getPropertyByName("ATOMDATA");
505	<
504	>	GenericData* data = (*atomIter)->getPropertyByName("ATOMDATA");
505	>
506		if (data != NULL) {
507		atomData = dynamic_cast<AtomData *>(data);
508	<
508	>
509		if (atomData == NULL)
510		continue;
511		} else
512		continue;
513	<
514	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
513	>
514	>	for( AtomInfo* atomInfo = atomData->beginAtomInfo(i); atomInfo;
515		atomInfo = atomData->nextAtomInfo(i) ) {
516		atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
517	<	} //end for(atomInfo)
518	<	}     //end for(atomIter)
519	<	}         //end if (waterTypeList.find(rbName) != waterTypeList.end())
517	>	}
518	>	}
519	>	}
520		}
521
522		std::string WaterTypeVisitor::trimmedName(const std::string&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 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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