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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 1875 by gezelter, Fri May 17 14:41:42 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 114 | Line 121 | namespace OpenMD {
121		//----------------------------------------------------------------------------//
122
123		ReplicateVisitor::ReplicateVisitor(SimInfo *info, Vector3i opt) :
124	<	BaseVisitor() {
124	>	BaseVisitor(), replicateOpt(opt) {
125		this->info = info;
126		visitorName = "ReplicateVisitor";
120	–	this->replicateOpt = opt;
127
128		//generate the replicate directions
129		for( int i = 0; i <= replicateOpt[0]; i++ ) {
#	Line 178 | Line 184 | namespace OpenMD {
184		std::vector<AtomInfo *>::iterator i;
185
186		for( dirIter = dir.begin(); dirIter != dir.end(); ++dirIter ) {
187	<	for( i = infoList.begin(); i != infoList.end(); i++ ) {
187	>	for( i = infoList.begin(); i != infoList.end(); ++i ) {
188		newAtomInfo = new AtomInfo();
189		*newAtomInfo = *(*i);
190
#	Line 193 | Line 199 | namespace OpenMD {
199		const std::string ReplicateVisitor::toString() {
200		char                            buffer[65535];
201		std::string                     result;
196	–	std::set<std::string>::iterator i;
202
203	+
204		sprintf(buffer,
205	<	"------------------------------------------------------------------\n");
205	>	"--------------------------------------------------------------\n");
206		result += buffer;
207
208		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
#	Line 217 | Line 223 | namespace OpenMD {
223		result += buffer;
224
225		sprintf(buffer,
226	<	"------------------------------------------------------------------\n");
226	>	"--------------------------------------------------------------\n");
227		result += buffer;
228
229		return result;
230		}
231
232	<	//----------------------------------------------------------------------------//
232	>	//------------------------------------------------------------------------//
233
234	<	XYZVisitor::XYZVisitor(SimInfo *info) :
235	<	BaseVisitor(), seleMan(info), evaluator(info){
236	<	this->info = info;
237	<	visitorName = "XYZVisitor";
238	<
239	<	evaluator.loadScriptString("select all");
240	<
241	<	if (!evaluator.isDynamic()) {
242	<	seleMan.setSelectionSet(evaluator.evaluate());
243	<	}
244	<	posOnly_ = false;
234	>	XYZVisitor::XYZVisitor(SimInfo *info) : BaseVisitor(), seleMan(info),
235	>	evaluator(info), doPositions_(true),
236	>	doVelocities_(false),
237	>	doForces_(false), doVectors_(false),
238	>	doCharges_(false),
239	>	doElectricFields_(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	<
249	<	XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
250	<	BaseVisitor(), seleMan(info), evaluator(info) {
251	<	this->info = info;
252	<	visitorName = "XYZVisitor";
253	<
254	<	evaluator.loadScriptString(script);
255	<
256	<	if (!evaluator.isDynamic()) {
257	<	seleMan.setSelectionSet(evaluator.evaluate());
258	<	}
259	<	posOnly_ = false;
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), doElectricFields_(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	>	if (doElectricFields_ && atomInfo->hasElectricField) {
337	>	sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->eField[0],
338	>	atomInfo->eField[1], atomInfo->eField[2]);
339	>	line += buffer;
340	>	}
341	>	frame.push_back(line);
342	>	}
343		}
344
345		bool XYZVisitor::isSelected(StuntDouble *sd) {
#	Line 352 | Line 349 | namespace OpenMD {
349		void XYZVisitor::writeFrame(std::ostream &outStream) {
350		std::vector<std::string>::iterator i;
351		char buffer[1024];
352	<
353	<	if (frame.size() == 0)
352	>
353	>	if (frame.empty())
354		std::cerr << "Current Frame does not contain any atoms" << std::endl;
355	<
355	>
356		//total number of atoms
357		outStream << frame.size() << std::endl;
358	<
358	>
359		//write comment line
360		Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
361		Mat3x3d box = currSnapshot->getHmat();
#	Line 369 | Line 366 | namespace OpenMD {
366		box(0, 0), box(0, 1), box(0, 2),
367		box(1, 0), box(1, 1), box(1, 2),
368		box(2, 0), box(2, 1), box(2, 2));
369	<
369	>
370		outStream << buffer << std::endl;
371	<
371	>
372		for( i = frame.begin(); i != frame.end(); ++i )
373		outStream << *i << std::endl;
374		}
375	<
375	>
376		std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {
377		return atomTypeName.substr(0, atomTypeName.find('-'));
378		}
379	<
383	<	std::string XYZVisitor::baseTypeName(AtomType* at) {
384	<	std::vector<AtomType*> ayb = at->allYourBase();
385	<	return ayb[ayb.size()-1]->getName();
386	<	}
387	<
379	>
380		const std::string XYZVisitor::toString() {
381		char        buffer[65535];
382		std::string result;
383	<
383	>
384		sprintf(buffer,
385		"------------------------------------------------------------------\n");
386		result += buffer;
387	<
387	>
388		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
389		result += buffer;
390	<
390	>
391		sprintf(buffer,
392		"Visitor Description: assemble the atom data and output xyz file\n");
393		result += buffer;
#	Line 403 | Line 395 | namespace OpenMD {
395		sprintf(buffer,
396		"------------------------------------------------------------------\n");
397		result += buffer;
398	<
398	>
399		return result;
400		}
401	<
401	>
402		//----------------------------------------------------------------------------//
403	<
403	>
404		void PrepareVisitor::internalVisit(Atom *atom) {
405		GenericData *data;
406	<	AtomData *   atomData;
415	<
406	>
407		//if visited property is  existed, remove it
408		data = atom->getPropertyByName("VISITED");
409	<
409	>
410		if (data != NULL) {
411		atom->removeProperty("VISITED");
412		}
413	<
413	>
414		//remove atomdata
415		data = atom->getPropertyByName("ATOMDATA");
416
417		if (data != NULL) {
418	<	atomData = dynamic_cast<AtomData *>(data);
418	>	AtomData* atomData = dynamic_cast<AtomData *>(data);
419
420		if (atomData != NULL)
421		atom->removeProperty("ATOMDATA");
#	Line 488 | Line 479 | namespace OpenMD {
479		visitorName = "WaterTypeVisitor";
480		waterTypeList.insert("TIP3P_RB_0");
481		waterTypeList.insert("TIP4P_RB_0");
482	+	waterTypeList.insert("TIP4P-Ew_RB_0");
483		waterTypeList.insert("TIP5P_RB_0");
484	+	waterTypeList.insert("TIP5P-E_RB_0");
485		waterTypeList.insert("SPCE_RB_0");
486	+	waterTypeList.insert("SPC_RB_0");
487		}
488
489		void WaterTypeVisitor::visit(RigidBody *rb) {
490		std::string rbName;
491		std::vector<Atom *> myAtoms;
492		std::vector<Atom *>::iterator atomIter;
499	–	GenericData* data;
500	–	AtomData* atomData;
501	–	AtomInfo* atomInfo;
493		std::vector<AtomInfo *>::iterator i;
494	+	AtomData* atomData;
495
496		rbName = rb->getType();
497	<
497	>
498		if (waterTypeList.find(rbName) != waterTypeList.end()) {
499		myAtoms = rb->getAtoms();
500	<
500	>
501		for( atomIter = myAtoms.begin(); atomIter != myAtoms.end();
502		++atomIter ) {
503	<	data = (*atomIter)->getPropertyByName("ATOMDATA");
504	<
503	>	GenericData* data = (*atomIter)->getPropertyByName("ATOMDATA");
504	>
505		if (data != NULL) {
506		atomData = dynamic_cast<AtomData *>(data);
507	<
507	>
508		if (atomData == NULL)
509		continue;
510		} else
511		continue;
512	<
513	<	for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
512	>
513	>	for( AtomInfo* atomInfo = atomData->beginAtomInfo(i); atomInfo;
514		atomInfo = atomData->nextAtomInfo(i) ) {
515		atomInfo->atomTypeName = trimmedName(atomInfo->atomTypeName);
516	<	} //end for(atomInfo)
517	<	}     //end for(atomIter)
518	<	}         //end if (waterTypeList.find(rbName) != waterTypeList.end())
516	>	}
517	>	}
518	>	}
519		}
520
521		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 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

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

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