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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 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

#	Line 36 | Line 36
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).
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 223 | Line 230 | namespace OpenMD {
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	>	this->info = info;
241	>	visitorName = "XYZVisitor";
242	>
243	>	evaluator.loadScriptString("select all");
244	>
245	>	if (!evaluator.isDynamic()) {
246	>	seleMan.setSelectionSet(evaluator.evaluate());
247		}
248	<
248	>	}
249	>
250		XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
251	<	BaseVisitor(), seleMan(info), evaluator(info) {
252	<	this->info = info;
253	<	visitorName = "XYZVisitor";
254	<
255	<	evaluator.loadScriptString(script);
256	<
257	<	if (!evaluator.isDynamic()) {
258	<	seleMan.setSelectionSet(evaluator.evaluate());
259	<	}
260	<	posOnly_ = false;
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	>
258	>	evaluator.loadScriptString(script);
259	>
260	>	if (!evaluator.isDynamic()) {
261	>	seleMan.setSelectionSet(evaluator.evaluate());
262		}
263	+	}
264
265		void XYZVisitor::visit(Atom *atom) {
266		if (isSelected(atom))
#	Line 260 | Line 271 | namespace OpenMD {
271		if (isSelected(datom))
272		internalVisit(datom);
273		}
274	<
274	>
275		void XYZVisitor::visit(RigidBody *rb) {
276		if (isSelected(rb))
277		internalVisit(rb);
278		}
279	<
279	>
280		void XYZVisitor::update() {
281		//if dynamic, we need to re-evaluate the selection
282		if (evaluator.isDynamic()) {
283		seleMan.setSelectionSet(evaluator.evaluate());
284		}
285		}
286	<
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	<
299	>
300		if (atomData == NULL)
301		return;
302		} else
303		return;
304
305	<	AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
306	<	std::string bn = baseTypeName(at);
307	<
308	<	if (posOnly_){
309	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
310	<	atomInfo = atomData->nextAtomInfo(i) ) {
311	<	if (atomInfo->hasCharge) {
312	<	sprintf(buffer,
313	<	"%s%15.8f%15.8f%15.8f%15.8f",
314	<	bn.c_str(),
315	<	atomInfo->pos[0],
316	<	atomInfo->pos[1],
317	<	atomInfo->pos[2],
318	<	atomInfo->charge);
319	<	} 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);
305	>	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
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	<	}else{
322	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
323	<	atomInfo = atomData->nextAtomInfo(i) ) {
324	<	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);
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	<	}
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) {
#	Line 352 | Line 344 | namespace OpenMD {
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	<
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 369 | Line 361 | namespace OpenMD {
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	<
370	>
371		std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
372		return atomTypeName.substr(0, atomTypeName.find('-'));
373		}
374	<
383	<	std::string XYZVisitor::baseTypeName(AtomType* at) {
384	<	std::vector<AtomType*> ayb = at->allYourBase();
385	<	return ayb[ayb.size()-1]->getName();
386	<	}
387	<
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 403 | Line 390 | namespace OpenMD {
390		sprintf(buffer,
391		"------------------------------------------------------------------\n");
392		result += buffer;
393	<
393	>
394		return result;
395		}
396	<
396	>
397		//----------------------------------------------------------------------------//
398	<
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");
408		}
409	<
409	>
410		//remove atomdata
411		data = atom->getPropertyByName("ATOMDATA");
412
#	Line 488 | Line 475 | namespace OpenMD {
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	+	waterTypeList.insert("SPC_RB_0");
483		}
484
485		void WaterTypeVisitor::visit(RigidBody *rb) {
#	Line 502 | Line 492 | namespace OpenMD {
492		std::vector<AtomInfo *>::iterator i;
493
494		rbName = rb->getType();
495	<
495	>
496		if (waterTypeList.find(rbName) != waterTypeList.end()) {
497		myAtoms = rb->getAtoms();
498
499		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
500		++atomIter ) {
501		data = (*atomIter)->getPropertyByName("ATOMDATA");
502	<
502	>
503		if (data != NULL) {
504		atomData = dynamic_cast<AtomData *>(data);
505	<
505	>
506		if (atomData == NULL)
507		continue;
508		} else
509		continue;
510	<
510	>
511		for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
512		atomInfo = atomData->nextAtomInfo(i) ) {
513		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 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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

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