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root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 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
43		#include <stack>
#	Line 45 | Line 46
46		#include "primitives/DirectionalAtom.hpp"
47		#include "primitives/RigidBody.hpp"
48		#include "primitives/Molecule.hpp"
49	<	#include "io/basic_ifstrstream.hpp"
49	>	#include "io/ifstrstream.hpp"
50	>	#include "types/FixedChargeAdapter.hpp"
51	>	#include "types/FluctuatingChargeAdapter.hpp"
52
53	+
54		namespace OpenMD {
55
56
57		SelectionEvaluator::SelectionEvaluator(SimInfo* si)
58		: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	<	indexFinder(info),
59	>	indexFinder(info), hasSurfaceArea_(false),
60		isLoaded_(false){
61	<	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
62	<	}
63	<
61	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
62	>	nObjects.push_back(info->getNGlobalBonds());
63	>	nObjects.push_back(info->getNGlobalBends());
64	>	nObjects.push_back(info->getNGlobalTorsions());
65	>	nObjects.push_back(info->getNGlobalInversions());
66	>	nObjects.push_back(info->getNGlobalMolecules());
67	>	}
68	>
69		bool SelectionEvaluator::loadScript(const std::string& filename,
70		const std::string& script) {
71		clearDefinitionsAndLoadPredefined();
#	Line 123 | Line 132 | namespace OpenMD {
132		return loadScript(filename, script);
133		}
134
135	<	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
135	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
136
137		while ( pc < aatoken.size()) {
138		statement = aatoken[pc++];
#	Line 144 | Line 153 | namespace OpenMD {
153
154		}
155
156	<	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
156	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
157	>
158	>	while ( pc < aatoken.size()) {
159	>	statement = aatoken[pc++];
160	>	statementLength = statement.size();
161	>	Token token = statement[0];
162	>	switch (token.tok) {
163	>	case Token::define:
164	>	define();
165	>	break;
166	>	case Token::select:
167	>	select(bs, frame);
168	>	break;
169	>	default:
170	>	unrecognizedCommand(token);
171	>	return;
172	>	}
173	>	}
174	>
175	>	}
176	>
177	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
178		int pcStart) {
179	<	OpenMDBitSet bs;
180	<	std::stack<OpenMDBitSet> stack;
179	>	SelectionSet bs = createSelectionSets();
180	>	std::stack<SelectionSet> stack;
181	>	vector<int> bsSize = bs.size();
182
183	<	for (int pc = pcStart; pc < code.size(); ++pc) {
183	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
184		Token instruction = code[pc];
185
186		switch (instruction.tok) {
#	Line 158 | Line 189 | namespace OpenMD {
189		case Token::expressionEnd:
190		break;
191		case Token::all:
192	<	bs = OpenMDBitSet(nStuntDouble);
193	<	bs.setAll();
192	>	bs = allInstruction();
193	>	stack.push(bs);
194	>	break;
195	>	case Token::none:
196	>	bs = createSelectionSets();
197	>	stack.push(bs);
198	>	break;
199	>	case Token::opOr:
200	>	bs= stack.top();
201	>	stack.pop();
202	>	stack.top() |= bs;
203	>	break;
204	>	case Token::opAnd:
205	>	bs = stack.top();
206	>	stack.pop();
207	>	stack.top() &= bs;
208	>	break;
209	>	case Token::opNot:
210	>	stack.top().flip();
211	>	break;
212	>	case Token::within:
213	>	withinInstruction(instruction, stack.top());
214	>	break;
215	>	case Token::hull:
216	>	stack.push(hull());
217	>	break;
218	>	//case Token::selected:
219	>	//  stack.push(getSelectionSet());
220	>	//  break;
221	>	case Token::name:
222	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
223	>	break;
224	>	case Token::index:
225	>	stack.push(indexInstruction(instruction.value));
226	>	break;
227	>	case Token::identifier:
228	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
229	>	break;
230	>	case Token::opLT:
231	>	case Token::opLE:
232	>	case Token::opGE:
233	>	case Token::opGT:
234	>	case Token::opEQ:
235	>	case Token::opNE:
236	>	stack.push(comparatorInstruction(instruction));
237	>	break;
238	>	default:
239	>	unrecognizedExpression();
240	>	}
241	>	}
242	>	if (stack.size() != 1)
243	>	evalError("atom expression compiler error - stack over/underflow");
244	>
245	>	return stack.top();
246	>	}
247	>
248	>
249	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
250	>	int pcStart, int frame) {
251	>	SelectionSet bs = createSelectionSets();
252	>	std::stack<SelectionSet> stack;
253	>
254	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
255	>	Token instruction = code[pc];
256	>
257	>	switch (instruction.tok) {
258	>	case Token::expressionBegin:
259	>	break;
260	>	case Token::expressionEnd:
261	>	break;
262	>	case Token::all:
263	>	bs = allInstruction();
264		stack.push(bs);
265		break;
266		case Token::none:
267	<	bs = OpenMDBitSet(nStuntDouble);
267	>	bs = SelectionSet(nObjects);
268		stack.push(bs);
269		break;
270		case Token::opOr:
#	Line 180 | Line 281 | namespace OpenMD {
281		stack.top().flip();
282		break;
283		case Token::within:
284	<	withinInstruction(instruction, stack.top());
284	>	withinInstruction(instruction, stack.top(), frame);
285		break;
286		case Token::hull:
287	<	stack.push(hull());
287	>	stack.push(hull(frame));
288		break;
289		//case Token::selected:
290		//  stack.push(getSelectionSet());
#	Line 203 | Line 304 | namespace OpenMD {
304		case Token::opGT:
305		case Token::opEQ:
306		case Token::opNE:
307	<	stack.push(comparatorInstruction(instruction));
307	>	stack.push(comparatorInstruction(instruction, frame));
308		break;
309		default:
310		unrecognizedExpression();
#	Line 217 | Line 318 | namespace OpenMD {
318
319
320
321	<	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
321	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
322		int comparator = instruction.tok;
323		int property = instruction.intValue;
324		float comparisonValue = boost::any_cast<float>(instruction.value);
325	<	float propertyValue;
225	<	OpenMDBitSet bs(nStuntDouble);
325	>	SelectionSet bs = createSelectionSets();
326		bs.clearAll();
327
328		SimInfo::MoleculeIterator mi;
#	Line 235 | Line 335 | namespace OpenMD {
335		for (mol = info->beginMolecule(mi); mol != NULL;
336		mol = info->nextMolecule(mi)) {
337
338	+	compareProperty(mol, bs, property, comparator, comparisonValue);
339	+
340		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
341		compareProperty(atom, bs, property, comparator, comparisonValue);
342		}
#	Line 248 | Line 350 | namespace OpenMD {
350		return bs;
351		}
352
353	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
353	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
354	>	int comparator = instruction.tok;
355	>	int property = instruction.intValue;
356	>	float comparisonValue = boost::any_cast<float>(instruction.value);
357	>	SelectionSet bs = createSelectionSets();
358	>	bs.clearAll();
359	>
360	>	SimInfo::MoleculeIterator mi;
361	>	Molecule* mol;
362	>	Molecule::AtomIterator ai;
363	>	Atom* atom;
364	>	Molecule::RigidBodyIterator rbIter;
365	>	RigidBody* rb;
366	>
367	>	for (mol = info->beginMolecule(mi); mol != NULL;
368	>	mol = info->nextMolecule(mi)) {
369	>
370	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
371	>
372	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
373	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
374	>	}
375	>
376	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
377	>	rb = mol->nextRigidBody(rbIter)) {
378	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
379	>	}
380	>	}
381	>
382	>	return bs;
383	>	}
384	>
385	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
386		int property, int comparator,
387		float comparisonValue) {
388		RealType propertyValue = 0.0;
389	+	Vector3d pos;
390	+
391		switch (property) {
392		case Token::mass:
393		propertyValue = sd->getMass();
#	Line 278 | Line 414 | namespace OpenMD {
414		case Token::z:
415		propertyValue = sd->getPos().z();
416		break;
417	+	case Token::wrappedX:
418	+	pos = sd->getPos();
419	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	+	propertyValue = pos.x();
421	+	break;
422	+	case Token::wrappedY:
423	+	pos = sd->getPos();
424	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	+	propertyValue = pos.y();
426	+	break;
427	+	case Token::wrappedZ:
428	+	pos = sd->getPos();
429	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
430	+	propertyValue = pos.z();
431	+	break;
432	+	case Token::r:
433	+	propertyValue = sd->getPos().length();
434	+	break;
435		default:
436		unrecognizedAtomProperty(property);
437		}
#	Line 303 | Line 457 | namespace OpenMD {
457		match = propertyValue != comparisonValue;
458		break;
459		}
460	<	if (match)
461	<	bs.setBitOn(sd->getGlobalIndex());
460	>
461	>	if (match)
462	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
463	>
464
465		}
466
467	<	void SelectionEvaluator::withinInstruction(const Token& instruction,
468	<	OpenMDBitSet& bs){
467	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
468	>	int property, int comparator,
469	>	float comparisonValue) {
470	>	RealType propertyValue = 0.0;
471	>	Vector3d pos;
472	>
473	>	switch (property) {
474	>	case Token::mass:
475	>	propertyValue = mol->getMass();
476	>	break;
477	>	case Token::charge:
478	>	{
479	>	Molecule::AtomIterator ai;
480	>	Atom* atom;
481	>	for (atom = mol->beginAtom(ai); atom != NULL;
482	>	atom = mol->nextAtom(ai)) {
483	>	propertyValue+=  getCharge(atom);
484	>	}
485	>	}
486	>	break;
487	>	case Token::x:
488	>	propertyValue = mol->getCom().x();
489	>	break;
490	>	case Token::y:
491	>	propertyValue = mol->getCom().y();
492	>	break;
493	>	case Token::z:
494	>	propertyValue = mol->getCom().z();
495	>	break;
496	>	case Token::wrappedX:
497	>	pos = mol->getCom();
498	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
499	>	propertyValue = pos.x();
500	>	break;
501	>	case Token::wrappedY:
502	>	pos = mol->getCom();
503	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
504	>	propertyValue = pos.y();
505	>	break;
506	>	case Token::wrappedZ:
507	>	pos = mol->getCom();
508	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
509	>	propertyValue = pos.z();
510	>	break;
511	>	case Token::r:
512	>	propertyValue = mol->getCom().length();
513	>	break;
514	>	default:
515	>	unrecognizedMoleculeProperty(property);
516	>	}
517	>
518	>	bool match = false;
519	>	switch (comparator) {
520	>	case Token::opLT:
521	>	match = propertyValue < comparisonValue;
522	>	break;
523	>	case Token::opLE:
524	>	match = propertyValue <= comparisonValue;
525	>	break;
526	>	case Token::opGE:
527	>	match = propertyValue >= comparisonValue;
528	>	break;
529	>	case Token::opGT:
530	>	match = propertyValue > comparisonValue;
531	>	break;
532	>	case Token::opEQ:
533	>	match = propertyValue == comparisonValue;
534	>	break;
535	>	case Token::opNE:
536	>	match = propertyValue != comparisonValue;
537	>	break;
538	>	}
539	>
540	>	if (match)
541	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
542	>	}
543	>
544	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
545	>	int property, int comparator,
546	>	float comparisonValue, int frame) {
547	>	RealType propertyValue = 0.0;
548	>	Vector3d pos;
549	>	switch (property) {
550	>	case Token::mass:
551	>	propertyValue = mol->getMass();
552	>	break;
553	>	case Token::charge:
554	>	{
555	>	Molecule::AtomIterator ai;
556	>	Atom* atom;
557	>	for (atom = mol->beginAtom(ai); atom != NULL;
558	>	atom = mol->nextAtom(ai)) {
559	>	propertyValue+=  getCharge(atom,frame);
560	>	}
561	>	}
562	>	break;
563	>	case Token::x:
564	>	propertyValue = mol->getCom(frame).x();
565	>	break;
566	>	case Token::y:
567	>	propertyValue = mol->getCom(frame).y();
568	>	break;
569	>	case Token::z:
570	>	propertyValue = mol->getCom(frame).z();
571	>	break;
572	>	case Token::wrappedX:
573	>	pos = mol->getCom(frame);
574	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
575	>	propertyValue = pos.x();
576	>	break;
577	>	case Token::wrappedY:
578	>	pos = mol->getCom(frame);
579	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
580	>	propertyValue = pos.y();
581	>	break;
582	>	case Token::wrappedZ:
583	>	pos = mol->getCom(frame);
584	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
585	>	propertyValue = pos.z();
586	>	break;
587	>
588	>	case Token::r:
589	>	propertyValue = mol->getCom(frame).length();
590	>	break;
591	>	default:
592	>	unrecognizedMoleculeProperty(property);
593	>	}
594	>
595	>	bool match = false;
596	>	switch (comparator) {
597	>	case Token::opLT:
598	>	match = propertyValue < comparisonValue;
599	>	break;
600	>	case Token::opLE:
601	>	match = propertyValue <= comparisonValue;
602	>	break;
603	>	case Token::opGE:
604	>	match = propertyValue >= comparisonValue;
605	>	break;
606	>	case Token::opGT:
607	>	match = propertyValue > comparisonValue;
608	>	break;
609	>	case Token::opEQ:
610	>	match = propertyValue == comparisonValue;
611	>	break;
612	>	case Token::opNE:
613	>	match = propertyValue != comparisonValue;
614	>	break;
615	>	}
616	>	if (match)
617	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
618
619	+
620	+	}
621	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
622	+	int property, int comparator,
623	+	float comparisonValue, int frame) {
624	+	RealType propertyValue = 0.0;
625	+	Vector3d pos;
626	+	switch (property) {
627	+	case Token::mass:
628	+	propertyValue = sd->getMass();
629	+	break;
630	+	case Token::charge:
631	+	if (sd->isAtom()){
632	+	Atom* atom = static_cast<Atom*>(sd);
633	+	propertyValue = getCharge(atom,frame);
634	+	} else if (sd->isRigidBody()) {
635	+	RigidBody* rb = static_cast<RigidBody*>(sd);
636	+	RigidBody::AtomIterator ai;
637	+	Atom* atom;
638	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
639	+	propertyValue+=  getCharge(atom,frame);
640	+	}
641	+	}
642	+	break;
643	+	case Token::x:
644	+	propertyValue = sd->getPos(frame).x();
645	+	break;
646	+	case Token::y:
647	+	propertyValue = sd->getPos(frame).y();
648	+	break;
649	+	case Token::z:
650	+	propertyValue = sd->getPos(frame).z();
651	+	break;
652	+	case Token::wrappedX:
653	+	pos = sd->getPos(frame);
654	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
655	+	propertyValue = pos.x();
656	+	break;
657	+	case Token::wrappedY:
658	+	pos = sd->getPos(frame);
659	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
660	+	propertyValue = pos.y();
661	+	break;
662	+	case Token::wrappedZ:
663	+	pos = sd->getPos(frame);
664	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
665	+	propertyValue = pos.z();
666	+	break;
667	+
668	+	case Token::r:
669	+	propertyValue = sd->getPos(frame).length();
670	+	break;
671	+	default:
672	+	unrecognizedAtomProperty(property);
673	+	}
674	+
675	+	bool match = false;
676	+	switch (comparator) {
677	+	case Token::opLT:
678	+	match = propertyValue < comparisonValue;
679	+	break;
680	+	case Token::opLE:
681	+	match = propertyValue <= comparisonValue;
682	+	break;
683	+	case Token::opGE:
684	+	match = propertyValue >= comparisonValue;
685	+	break;
686	+	case Token::opGT:
687	+	match = propertyValue > comparisonValue;
688	+	break;
689	+	case Token::opEQ:
690	+	match = propertyValue == comparisonValue;
691	+	break;
692	+	case Token::opNE:
693	+	match = propertyValue != comparisonValue;
694	+	break;
695	+	}
696	+	if (match)
697	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
698	+
699	+
700	+	}
701	+
702	+
703	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
704	+	SelectionSet& bs){
705	+
706		boost::any withinSpec = instruction.value;
707		float distance;
708		if (withinSpec.type() == typeid(float)){
#	Line 324 | Line 716 | namespace OpenMD {
716
717		bs = distanceFinder.find(bs, distance);
718		}
719	+
720	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
721	+	SelectionSet& bs, int frame){
722	+
723	+	boost::any withinSpec = instruction.value;
724	+	float distance;
725	+	if (withinSpec.type() == typeid(float)){
726	+	distance = boost::any_cast<float>(withinSpec);
727	+	} else if (withinSpec.type() == typeid(int)) {
728	+	distance = boost::any_cast<int>(withinSpec);
729	+	} else {
730	+	evalError("casting error in withinInstruction");
731	+	bs.clearAll();
732	+	}
733	+
734	+	bs = distanceFinder.find(bs, distance, frame);
735	+	}
736
737		void SelectionEvaluator::define() {
738		assert(statement.size() >= 3);
#	Line 366 | Line 775 | namespace OpenMD {
775		}
776		}
777
778	<	void SelectionEvaluator::select(OpenMDBitSet& bs){
778	>	void SelectionEvaluator::select(SelectionSet& bs){
779		bs = expression(statement, 1);
780		}
781	+
782	+	void SelectionEvaluator::select(SelectionSet& bs, int frame){
783	+	bs = expression(statement, 1, frame);
784	+	}
785
786	<	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
786	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
787
788	<	OpenMDBitSet bs(nStuntDouble);
788	>	SelectionSet bs = createSelectionSets();
789		std::map<std::string, boost::any>::iterator i = variables.find(variable);
790
791		if (i != variables.end()) {
792	<	if (i->second.type() == typeid(OpenMDBitSet)) {
793	<	return boost::any_cast<OpenMDBitSet>(i->second);
792	>	if (i->second.type() == typeid(SelectionSet)) {
793	>	return boost::any_cast<SelectionSet>(i->second);
794		} else if (i->second.type() ==  typeid(std::vector<Token>)){
795		bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
796		i->second =  bs; /**@todo fixme */
#	Line 390 | Line 803 | namespace OpenMD {
803		return bs;
804		}
805
806	<	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
806	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
807		return nameFinder.match(name);
808		}
809
#	Line 411 | Line 824 | namespace OpenMD {
824		//predefine();
825		}
826
827	<	OpenMDBitSet SelectionEvaluator::evaluate() {
828	<	OpenMDBitSet bs(nStuntDouble);
827	>	SelectionSet SelectionEvaluator::createSelectionSets() {
828	>	SelectionSet ss(nObjects);
829	>	return ss;
830	>	}
831	>
832	>	SelectionSet SelectionEvaluator::evaluate() {
833	>	SelectionSet bs = createSelectionSets();
834		if (isLoaded_) {
835		pc = 0;
836		instructionDispatchLoop(bs);
837		}
838	+	return bs;
839	+	}
840
841	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
842	+	SelectionSet bs = createSelectionSets();
843	+	if (isLoaded_) {
844	+	pc = 0;
845	+	instructionDispatchLoop(bs, frame);
846	+	}
847		return bs;
848		}
849
850	<	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	<	OpenMDBitSet bs(nStuntDouble);
850	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	>	SelectionSet bs = createSelectionSets();
852
853		if (value.type() == typeid(int)) {
854		int index = boost::any_cast<int>(value);
855	<	if (index < 0 || index >= bs.size()) {
855	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
856		invalidIndex(index);
857		} else {
858		bs = indexFinder.find(index);
#	Line 434 | Line 860 | namespace OpenMD {
860		} else if (value.type() == typeid(std::pair<int, int>)) {
861		std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
862		assert(indexRange.first <= indexRange.second);
863	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
863	>	if (indexRange.first < 0 ||
864	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
865		invalidIndexRange(indexRange);
866		}else {
867		bs = indexFinder.find(indexRange.first, indexRange.second);
#	Line 444 | Line 871 | namespace OpenMD {
871		return bs;
872		}
873
874	+	SelectionSet SelectionEvaluator::allInstruction() {
875	+	SelectionSet ss = createSelectionSets();
876
877	<	OpenMDBitSet SelectionEvaluator::hull() {
878	<	OpenMDBitSet bs(nStuntDouble);
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule::AtomIterator ai;
879	>	Molecule::RigidBodyIterator rbIter;
880	>	Molecule::BondIterator bondIter;
881	>	Molecule::BendIterator bendIter;
882	>	Molecule::TorsionIterator torsionIter;
883	>	Molecule::InversionIterator inversionIter;
884	>
885	>	Molecule* mol;
886	>	Atom* atom;
887	>	RigidBody* rb;
888	>	Bond* bond;
889	>	Bend* bend;
890	>	Torsion* torsion;
891	>	Inversion* inversion;
892	>
893	>	// Doing the loop insures that we're actually on this processor.
894	>
895	>	for (mol = info->beginMolecule(mi); mol != NULL;
896	>	mol = info->nextMolecule(mi)) {
897	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
898	>	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
899	>	}
900	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
901	>	rb = mol->nextRigidBody(rbIter)) {
902	>	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
903	>	}
904	>	for (bond = mol->beginBond(bondIter); bond != NULL;
905	>	bond = mol->nextBond(bondIter)) {
906	>	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
907	>	}
908	>	for (bend = mol->beginBend(bendIter); bend != NULL;
909	>	bend = mol->nextBend(bendIter)) {
910	>	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
911	>	}
912	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
913	>	torsion = mol->nextTorsion(torsionIter)) {
914	>	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
915	>	}
916	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
917	>	inversion = mol->nextInversion(inversionIter)) {
918	>	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
919	>	}
920	>	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
921	>	}
922	>
923	>	return ss;
924	>	}
925	>
926	>	SelectionSet SelectionEvaluator::hull() {
927	>	SelectionSet bs = createSelectionSets();
928
929		bs = hullFinder.findHull();
930	<
930	>	surfaceArea_ = hullFinder.getSurfaceArea();
931	>	hasSurfaceArea_ = true;
932		return bs;
933		}
934
935
936	+	SelectionSet SelectionEvaluator::hull(int frame) {
937	+	SelectionSet bs = createSelectionSets();
938	+
939	+	bs = hullFinder.findHull(frame);
940
941	+	return bs;
942	+	}
943	+
944		RealType SelectionEvaluator::getCharge(Atom* atom) {
945	<	RealType charge =0.0;
945	>	RealType charge = 0.0;
946		AtomType* atomType = atom->getAtomType();
461	–	if (atomType->isCharge()) {
462	–	GenericData* data = atomType->getPropertyByName("Charge");
463	–	if (data != NULL) {
464	–	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
947
948	<	if (doubleData != NULL) {
949	<	charge = doubleData->getData();
950	<
469	<	} else {
470	<	sprintf( painCave.errMsg,
471	<	"Can not cast GenericData to DoubleGenericData\n");
472	<	painCave.severity = OPENMD_ERROR;
473	<	painCave.isFatal = 1;
474	<	simError();
475	<	}
476	<	}
948	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
949	>	if ( fca.isFixedCharge() ) {
950	>	charge = fca.getCharge();
951		}
952	+
953	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
954	+	if ( fqa.isFluctuatingCharge() ) {
955	+	charge += atom->getFlucQPos();
956	+	}
957	+	return charge;
958	+	}
959
960	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
961	+	RealType charge = 0.0;
962	+	AtomType* atomType = atom->getAtomType();
963	+
964	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
965	+	if ( fca.isFixedCharge() ) {
966	+	charge = fca.getCharge();
967	+	}
968	+
969	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
970	+	if ( fqa.isFluctuatingCharge() ) {
971	+	charge += atom->getFlucQPos(frame);
972	+	}
973		return charge;
974		}
975

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

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