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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 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
52	–
56		SelectionEvaluator::SelectionEvaluator(SimInfo* si)
57	<	: info(si), nameFinder(info), distanceFinder(info), indexFinder(info),
58	<	isLoaded_(false){
59	<	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
60	<	}
61	<
57	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
58	>	indexFinder(info), isLoaded_(false), hasSurfaceArea_(false) {
59	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
60	>	nObjects.push_back(info->getNGlobalBonds());
61	>	nObjects.push_back(info->getNGlobalBends());
62	>	nObjects.push_back(info->getNGlobalTorsions());
63	>	nObjects.push_back(info->getNGlobalInversions());
64	>	nObjects.push_back(info->getNGlobalMolecules());
65	>	}
66	>
67		bool SelectionEvaluator::loadScript(const std::string& filename,
68		const std::string& script) {
69		clearDefinitionsAndLoadPredefined();
#	Line 122 | Line 130 | namespace OpenMD {
130		return loadScript(filename, script);
131		}
132
133	<	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
133	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
134
135		while ( pc < aatoken.size()) {
136		statement = aatoken[pc++];
#	Line 143 | Line 151 | namespace OpenMD {
151
152		}
153
154	<	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
154	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
155	>
156	>	while ( pc < aatoken.size()) {
157	>	statement = aatoken[pc++];
158	>	statementLength = statement.size();
159	>	Token token = statement[0];
160	>	switch (token.tok) {
161	>	case Token::define:
162	>	define();
163	>	break;
164	>	case Token::select:
165	>	select(bs, frame);
166	>	break;
167	>	default:
168	>	unrecognizedCommand(token);
169	>	return;
170	>	}
171	>	}
172	>
173	>	}
174	>
175	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
176		int pcStart) {
177	<	OpenMDBitSet bs;
178	<	std::stack<OpenMDBitSet> stack;
177	>	SelectionSet bs = createSelectionSets();
178	>	std::stack<SelectionSet> stack;
179	>	vector<int> bsSize = bs.size();
180
181	<	for (int pc = pcStart; pc < code.size(); ++pc) {
181	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
182		Token instruction = code[pc];
183
184		switch (instruction.tok) {
#	Line 157 | Line 187 | namespace OpenMD {
187		case Token::expressionEnd:
188		break;
189		case Token::all:
190	<	bs = OpenMDBitSet(nStuntDouble);
191	<	bs.setAll();
190	>	bs = allInstruction();
191	>	stack.push(bs);
192	>	break;
193	>	case Token::none:
194	>	bs = createSelectionSets();
195	>	stack.push(bs);
196	>	break;
197	>	case Token::opOr:
198	>	bs= stack.top();
199	>	stack.pop();
200	>	stack.top() |= bs;
201	>	break;
202	>	case Token::opAnd:
203	>	bs = stack.top();
204	>	stack.pop();
205	>	stack.top() &= bs;
206	>	break;
207	>	case Token::opNot:
208	>	stack.top().flip();
209	>	break;
210	>	case Token::within:
211	>	withinInstruction(instruction, stack.top());
212	>	break;
213	>	case Token::hull:
214	>	stack.push(hull());
215	>	break;
216	>	//case Token::selected:
217	>	//  stack.push(getSelectionSet());
218	>	//  break;
219	>	case Token::name:
220	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
221	>	break;
222	>	case Token::index:
223	>	stack.push(indexInstruction(instruction.value));
224	>	break;
225	>	case Token::identifier:
226	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
227	>	break;
228	>	case Token::opLT:
229	>	case Token::opLE:
230	>	case Token::opGE:
231	>	case Token::opGT:
232	>	case Token::opEQ:
233	>	case Token::opNE:
234	>	stack.push(comparatorInstruction(instruction));
235	>	break;
236	>	default:
237	>	unrecognizedExpression();
238	>	}
239	>	}
240	>	if (stack.size() != 1)
241	>	evalError("atom expression compiler error - stack over/underflow");
242	>
243	>	return stack.top();
244	>	}
245	>
246	>
247	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
248	>	int pcStart, int frame) {
249	>	SelectionSet bs = createSelectionSets();
250	>	std::stack<SelectionSet> stack;
251	>
252	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
253	>	Token instruction = code[pc];
254	>
255	>	switch (instruction.tok) {
256	>	case Token::expressionBegin:
257	>	break;
258	>	case Token::expressionEnd:
259	>	break;
260	>	case Token::all:
261	>	bs = allInstruction();
262		stack.push(bs);
263		break;
264		case Token::none:
265	<	bs = OpenMDBitSet(nStuntDouble);
265	>	bs = SelectionSet(nObjects);
266		stack.push(bs);
267		break;
268		case Token::opOr:
#	Line 179 | Line 279 | namespace OpenMD {
279		stack.top().flip();
280		break;
281		case Token::within:
282	<	withinInstruction(instruction, stack.top());
282	>	withinInstruction(instruction, stack.top(), frame);
283		break;
284	+	case Token::hull:
285	+	stack.push(hull(frame));
286	+	break;
287		//case Token::selected:
288		//  stack.push(getSelectionSet());
289		//  break;
#	Line 199 | Line 302 | namespace OpenMD {
302		case Token::opGT:
303		case Token::opEQ:
304		case Token::opNE:
305	<	stack.push(comparatorInstruction(instruction));
305	>	stack.push(comparatorInstruction(instruction, frame));
306		break;
307		default:
308		unrecognizedExpression();
#	Line 213 | Line 316 | namespace OpenMD {
316
317
318
319	<	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
319	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
320		int comparator = instruction.tok;
321		int property = instruction.intValue;
322		float comparisonValue = boost::any_cast<float>(instruction.value);
323	<	float propertyValue;
221	<	OpenMDBitSet bs(nStuntDouble);
323	>	SelectionSet bs = createSelectionSets();
324		bs.clearAll();
325
326		SimInfo::MoleculeIterator mi;
#	Line 231 | Line 333 | namespace OpenMD {
333		for (mol = info->beginMolecule(mi); mol != NULL;
334		mol = info->nextMolecule(mi)) {
335
336	+	compareProperty(mol, bs, property, comparator, comparisonValue);
337	+
338		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
339		compareProperty(atom, bs, property, comparator, comparisonValue);
340		}
#	Line 244 | Line 348 | namespace OpenMD {
348		return bs;
349		}
350
351	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
351	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
352	>	int comparator = instruction.tok;
353	>	int property = instruction.intValue;
354	>	float comparisonValue = boost::any_cast<float>(instruction.value);
355	>	SelectionSet bs = createSelectionSets();
356	>	bs.clearAll();
357	>
358	>	SimInfo::MoleculeIterator mi;
359	>	Molecule* mol;
360	>	Molecule::AtomIterator ai;
361	>	Atom* atom;
362	>	Molecule::RigidBodyIterator rbIter;
363	>	RigidBody* rb;
364	>
365	>	for (mol = info->beginMolecule(mi); mol != NULL;
366	>	mol = info->nextMolecule(mi)) {
367	>
368	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
369	>
370	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
371	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
372	>	}
373	>
374	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
375	>	rb = mol->nextRigidBody(rbIter)) {
376	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
377	>	}
378	>	}
379	>
380	>	return bs;
381	>	}
382	>
383	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
384		int property, int comparator,
385		float comparisonValue) {
386		RealType propertyValue = 0.0;
387	+	Vector3d pos;
388	+
389		switch (property) {
390		case Token::mass:
391		propertyValue = sd->getMass();
#	Line 274 | Line 412 | namespace OpenMD {
412		case Token::z:
413		propertyValue = sd->getPos().z();
414		break;
415	+	case Token::wrappedX:
416	+	pos = sd->getPos();
417	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
418	+	propertyValue = pos.x();
419	+	break;
420	+	case Token::wrappedY:
421	+	pos = sd->getPos();
422	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
423	+	propertyValue = pos.y();
424	+	break;
425	+	case Token::wrappedZ:
426	+	pos = sd->getPos();
427	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
428	+	propertyValue = pos.z();
429	+	break;
430	+	case Token::r:
431	+	propertyValue = sd->getPos().length();
432	+	break;
433		default:
434		unrecognizedAtomProperty(property);
435		}
#	Line 299 | Line 455 | namespace OpenMD {
455		match = propertyValue != comparisonValue;
456		break;
457		}
458	<	if (match)
459	<	bs.setBitOn(sd->getGlobalIndex());
458	>
459	>	if (match)
460	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
461	>
462
463		}
464
465	<	void SelectionEvaluator::withinInstruction(const Token& instruction,
466	<	OpenMDBitSet& bs){
465	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
466	>	int property, int comparator,
467	>	float comparisonValue) {
468	>	RealType propertyValue = 0.0;
469	>	Vector3d pos;
470	>
471	>	switch (property) {
472	>	case Token::mass:
473	>	propertyValue = mol->getMass();
474	>	break;
475	>	case Token::charge:
476	>	{
477	>	Molecule::AtomIterator ai;
478	>	Atom* atom;
479	>	for (atom = mol->beginAtom(ai); atom != NULL;
480	>	atom = mol->nextAtom(ai)) {
481	>	propertyValue+=  getCharge(atom);
482	>	}
483	>	}
484	>	break;
485	>	case Token::x:
486	>	propertyValue = mol->getCom().x();
487	>	break;
488	>	case Token::y:
489	>	propertyValue = mol->getCom().y();
490	>	break;
491	>	case Token::z:
492	>	propertyValue = mol->getCom().z();
493	>	break;
494	>	case Token::wrappedX:
495	>	pos = mol->getCom();
496	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
497	>	propertyValue = pos.x();
498	>	break;
499	>	case Token::wrappedY:
500	>	pos = mol->getCom();
501	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
502	>	propertyValue = pos.y();
503	>	break;
504	>	case Token::wrappedZ:
505	>	pos = mol->getCom();
506	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
507	>	propertyValue = pos.z();
508	>	break;
509	>	case Token::r:
510	>	propertyValue = mol->getCom().length();
511	>	break;
512	>	default:
513	>	unrecognizedMoleculeProperty(property);
514	>	}
515	>
516	>	bool match = false;
517	>	switch (comparator) {
518	>	case Token::opLT:
519	>	match = propertyValue < comparisonValue;
520	>	break;
521	>	case Token::opLE:
522	>	match = propertyValue <= comparisonValue;
523	>	break;
524	>	case Token::opGE:
525	>	match = propertyValue >= comparisonValue;
526	>	break;
527	>	case Token::opGT:
528	>	match = propertyValue > comparisonValue;
529	>	break;
530	>	case Token::opEQ:
531	>	match = propertyValue == comparisonValue;
532	>	break;
533	>	case Token::opNE:
534	>	match = propertyValue != comparisonValue;
535	>	break;
536	>	}
537	>
538	>	if (match)
539	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
540	>	}
541	>
542	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
543	>	int property, int comparator,
544	>	float comparisonValue, int frame) {
545	>	RealType propertyValue = 0.0;
546	>	Vector3d pos;
547	>	switch (property) {
548	>	case Token::mass:
549	>	propertyValue = mol->getMass();
550	>	break;
551	>	case Token::charge:
552	>	{
553	>	Molecule::AtomIterator ai;
554	>	Atom* atom;
555	>	for (atom = mol->beginAtom(ai); atom != NULL;
556	>	atom = mol->nextAtom(ai)) {
557	>	propertyValue+=  getCharge(atom,frame);
558	>	}
559	>	}
560	>	break;
561	>	case Token::x:
562	>	propertyValue = mol->getCom(frame).x();
563	>	break;
564	>	case Token::y:
565	>	propertyValue = mol->getCom(frame).y();
566	>	break;
567	>	case Token::z:
568	>	propertyValue = mol->getCom(frame).z();
569	>	break;
570	>	case Token::wrappedX:
571	>	pos = mol->getCom(frame);
572	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
573	>	propertyValue = pos.x();
574	>	break;
575	>	case Token::wrappedY:
576	>	pos = mol->getCom(frame);
577	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
578	>	propertyValue = pos.y();
579	>	break;
580	>	case Token::wrappedZ:
581	>	pos = mol->getCom(frame);
582	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
583	>	propertyValue = pos.z();
584	>	break;
585	>
586	>	case Token::r:
587	>	propertyValue = mol->getCom(frame).length();
588	>	break;
589	>	default:
590	>	unrecognizedMoleculeProperty(property);
591	>	}
592	>
593	>	bool match = false;
594	>	switch (comparator) {
595	>	case Token::opLT:
596	>	match = propertyValue < comparisonValue;
597	>	break;
598	>	case Token::opLE:
599	>	match = propertyValue <= comparisonValue;
600	>	break;
601	>	case Token::opGE:
602	>	match = propertyValue >= comparisonValue;
603	>	break;
604	>	case Token::opGT:
605	>	match = propertyValue > comparisonValue;
606	>	break;
607	>	case Token::opEQ:
608	>	match = propertyValue == comparisonValue;
609	>	break;
610	>	case Token::opNE:
611	>	match = propertyValue != comparisonValue;
612	>	break;
613	>	}
614	>	if (match)
615	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
616
617	+
618	+	}
619	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
620	+	int property, int comparator,
621	+	float comparisonValue, int frame) {
622	+	RealType propertyValue = 0.0;
623	+	Vector3d pos;
624	+	switch (property) {
625	+	case Token::mass:
626	+	propertyValue = sd->getMass();
627	+	break;
628	+	case Token::charge:
629	+	if (sd->isAtom()){
630	+	Atom* atom = static_cast<Atom*>(sd);
631	+	propertyValue = getCharge(atom,frame);
632	+	} else if (sd->isRigidBody()) {
633	+	RigidBody* rb = static_cast<RigidBody*>(sd);
634	+	RigidBody::AtomIterator ai;
635	+	Atom* atom;
636	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
637	+	propertyValue+=  getCharge(atom,frame);
638	+	}
639	+	}
640	+	break;
641	+	case Token::x:
642	+	propertyValue = sd->getPos(frame).x();
643	+	break;
644	+	case Token::y:
645	+	propertyValue = sd->getPos(frame).y();
646	+	break;
647	+	case Token::z:
648	+	propertyValue = sd->getPos(frame).z();
649	+	break;
650	+	case Token::wrappedX:
651	+	pos = sd->getPos(frame);
652	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
653	+	propertyValue = pos.x();
654	+	break;
655	+	case Token::wrappedY:
656	+	pos = sd->getPos(frame);
657	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
658	+	propertyValue = pos.y();
659	+	break;
660	+	case Token::wrappedZ:
661	+	pos = sd->getPos(frame);
662	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
663	+	propertyValue = pos.z();
664	+	break;
665	+
666	+	case Token::r:
667	+	propertyValue = sd->getPos(frame).length();
668	+	break;
669	+	default:
670	+	unrecognizedAtomProperty(property);
671	+	}
672	+
673	+	bool match = false;
674	+	switch (comparator) {
675	+	case Token::opLT:
676	+	match = propertyValue < comparisonValue;
677	+	break;
678	+	case Token::opLE:
679	+	match = propertyValue <= comparisonValue;
680	+	break;
681	+	case Token::opGE:
682	+	match = propertyValue >= comparisonValue;
683	+	break;
684	+	case Token::opGT:
685	+	match = propertyValue > comparisonValue;
686	+	break;
687	+	case Token::opEQ:
688	+	match = propertyValue == comparisonValue;
689	+	break;
690	+	case Token::opNE:
691	+	match = propertyValue != comparisonValue;
692	+	break;
693	+	}
694	+	if (match)
695	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
696	+	}
697	+
698	+
699	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
700	+	SelectionSet& bs){
701	+
702		boost::any withinSpec = instruction.value;
703		float distance;
704		if (withinSpec.type() == typeid(float)){
#	Line 320 | Line 712 | namespace OpenMD {
712
713		bs = distanceFinder.find(bs, distance);
714		}
715	+
716	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
717	+	SelectionSet& bs, int frame){
718	+
719	+	boost::any withinSpec = instruction.value;
720	+	float distance;
721	+	if (withinSpec.type() == typeid(float)){
722	+	distance = boost::any_cast<float>(withinSpec);
723	+	} else if (withinSpec.type() == typeid(int)) {
724	+	distance = boost::any_cast<int>(withinSpec);
725	+	} else {
726	+	evalError("casting error in withinInstruction");
727	+	bs.clearAll();
728	+	}
729	+
730	+	bs = distanceFinder.find(bs, distance, frame);
731	+	}
732
733		void SelectionEvaluator::define() {
734		assert(statement.size() >= 3);
#	Line 362 | Line 771 | namespace OpenMD {
771		}
772		}
773
774	<	void SelectionEvaluator::select(OpenMDBitSet& bs){
774	>	void SelectionEvaluator::select(SelectionSet& bs){
775		bs = expression(statement, 1);
776		}
777	<
778	<	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
777	>
778	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
779	>	bs = expression(statement, 1, frame);
780	>	}
781	>
782	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
783
784	<	OpenMDBitSet bs(nStuntDouble);
784	>	SelectionSet bs = createSelectionSets();
785		std::map<std::string, boost::any>::iterator i = variables.find(variable);
786
787		if (i != variables.end()) {
788	<	if (i->second.type() == typeid(OpenMDBitSet)) {
789	<	return boost::any_cast<OpenMDBitSet>(i->second);
788	>	if (i->second.type() == typeid(SelectionSet)) {
789	>	return boost::any_cast<SelectionSet>(i->second);
790		} else if (i->second.type() ==  typeid(std::vector<Token>)){
791		bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
792		i->second =  bs; /**@todo fixme */
#	Line 386 | Line 799 | namespace OpenMD {
799		return bs;
800		}
801
802	<	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
802	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
803		return nameFinder.match(name);
804		}
805
#	Line 407 | Line 820 | namespace OpenMD {
820		//predefine();
821		}
822
823	<	OpenMDBitSet SelectionEvaluator::evaluate() {
824	<	OpenMDBitSet bs(nStuntDouble);
823	>	SelectionSet SelectionEvaluator::createSelectionSets() {
824	>	SelectionSet ss(nObjects);
825	>	return ss;
826	>	}
827	>
828	>	SelectionSet SelectionEvaluator::evaluate() {
829	>	SelectionSet bs = createSelectionSets();
830		if (isLoaded_) {
831		pc = 0;
832		instructionDispatchLoop(bs);
833		}
834	+	return bs;
835	+	}
836
837	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
838	+	SelectionSet bs = createSelectionSets();
839	+	if (isLoaded_) {
840	+	pc = 0;
841	+	instructionDispatchLoop(bs, frame);
842	+	}
843		return bs;
844		}
845
846	<	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
847	<	OpenMDBitSet bs(nStuntDouble);
846	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
847	>	SelectionSet bs = createSelectionSets();
848
849		if (value.type() == typeid(int)) {
850		int index = boost::any_cast<int>(value);
851	<	if (index < 0 || index >= bs.size()) {
851	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
852		invalidIndex(index);
853		} else {
854		bs = indexFinder.find(index);
#	Line 430 | Line 856 | namespace OpenMD {
856		} else if (value.type() == typeid(std::pair<int, int>)) {
857		std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
858		assert(indexRange.first <= indexRange.second);
859	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
859	>	if (indexRange.first < 0 ||
860	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
861		invalidIndexRange(indexRange);
862		}else {
863		bs = indexFinder.find(indexRange.first, indexRange.second);
#	Line 440 | Line 867 | namespace OpenMD {
867		return bs;
868		}
869
870	+	SelectionSet SelectionEvaluator::allInstruction() {
871	+	SelectionSet ss = createSelectionSets();
872
873	+	SimInfo::MoleculeIterator mi;
874	+	Molecule::AtomIterator ai;
875	+	Molecule::RigidBodyIterator rbIter;
876	+	Molecule::BondIterator bondIter;
877	+	Molecule::BendIterator bendIter;
878	+	Molecule::TorsionIterator torsionIter;
879	+	Molecule::InversionIterator inversionIter;
880	+
881	+	Molecule* mol;
882	+	Atom* atom;
883	+	RigidBody* rb;
884	+	Bond* bond;
885	+	Bend* bend;
886	+	Torsion* torsion;
887	+	Inversion* inversion;
888	+
889	+	// Doing the loop insures that we're actually on this processor.
890	+
891	+	for (mol = info->beginMolecule(mi); mol != NULL;
892	+	mol = info->nextMolecule(mi)) {
893	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
894	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
895	+	}
896	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
897	+	rb = mol->nextRigidBody(rbIter)) {
898	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
899	+	}
900	+	for (bond = mol->beginBond(bondIter); bond != NULL;
901	+	bond = mol->nextBond(bondIter)) {
902	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
903	+	}
904	+	for (bend = mol->beginBend(bendIter); bend != NULL;
905	+	bend = mol->nextBend(bendIter)) {
906	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
907	+	}
908	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
909	+	torsion = mol->nextTorsion(torsionIter)) {
910	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
911	+	}
912	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
913	+	inversion = mol->nextInversion(inversionIter)) {
914	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
915	+	}
916	+	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
917	+	}
918	+
919	+	return ss;
920	+	}
921	+
922	+	SelectionSet SelectionEvaluator::hull() {
923	+	SelectionSet bs = createSelectionSets();
924	+
925	+	bs = hullFinder.findHull();
926	+	surfaceArea_ = hullFinder.getSurfaceArea();
927	+	hasSurfaceArea_ = true;
928	+	return bs;
929	+	}
930	+
931	+
932	+	SelectionSet SelectionEvaluator::hull(int frame) {
933	+	SelectionSet bs = createSelectionSets();
934	+
935	+	bs = hullFinder.findHull(frame);
936	+
937	+	return bs;
938	+	}
939	+
940		RealType SelectionEvaluator::getCharge(Atom* atom) {
941	<	RealType charge =0.0;
941	>	RealType charge = 0.0;
942		AtomType* atomType = atom->getAtomType();
447	–	if (atomType->isCharge()) {
448	–	GenericData* data = atomType->getPropertyByName("Charge");
449	–	if (data != NULL) {
450	–	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
943
944	<	if (doubleData != NULL) {
945	<	charge = doubleData->getData();
946	<
455	<	} else {
456	<	sprintf( painCave.errMsg,
457	<	"Can not cast GenericData to DoubleGenericData\n");
458	<	painCave.severity = OPENMD_ERROR;
459	<	painCave.isFatal = 1;
460	<	simError();
461	<	}
462	<	}
944	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
945	>	if ( fca.isFixedCharge() ) {
946	>	charge = fca.getCharge();
947		}
948	+
949	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
950	+	if ( fqa.isFluctuatingCharge() ) {
951	+	charge += atom->getFlucQPos();
952	+	}
953	+	return charge;
954	+	}
955
956	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
957	+	RealType charge = 0.0;
958	+	AtomType* atomType = atom->getAtomType();
959	+
960	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
961	+	if ( fca.isFixedCharge() ) {
962	+	charge = fca.getCharge();
963	+	}
964	+
965	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
966	+	if ( fqa.isFluctuatingCharge() ) {
967	+	charge += atom->getFlucQPos(frame);
968	+	}
969		return charge;
970		}
971

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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