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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 1903 by gezelter, Tue Jul 16 18:58:08 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
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		}
#	Line 144 | Line 148 | namespace OpenMD {
148
149		}
150
151	+	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs, int frame){
152	+
153	+	while ( pc < aatoken.size()) {
154	+	statement = aatoken[pc++];
155	+	statementLength = statement.size();
156	+	Token token = statement[0];
157	+	switch (token.tok) {
158	+	case Token::define:
159	+	define();
160	+	break;
161	+	case Token::select:
162	+	select(bs, frame);
163	+	break;
164	+	default:
165	+	unrecognizedCommand(token);
166	+	return;
167	+	}
168	+	}
169	+
170	+	}
171	+
172		OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
173		int pcStart) {
174		OpenMDBitSet bs;
175		std::stack<OpenMDBitSet> stack;
176
177	<	for (int pc = pcStart; pc < code.size(); ++pc) {
177	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
178		Token instruction = code[pc];
179
180		switch (instruction.tok) {
#	Line 158 | Line 183 | namespace OpenMD {
183		case Token::expressionEnd:
184		break;
185		case Token::all:
186	<	bs = OpenMDBitSet(nStuntDouble);
162	<	bs.setAll();
186	>	bs = allInstruction();
187		stack.push(bs);
188		break;
189		case Token::none:
#	Line 216 | Line 240 | namespace OpenMD {
240		}
241
242
243	+	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
244	+	int pcStart, int frame) {
245	+	OpenMDBitSet bs;
246	+	std::stack<OpenMDBitSet> stack;
247	+
248	+	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
249	+	Token instruction = code[pc];
250
251	+	switch (instruction.tok) {
252	+	case Token::expressionBegin:
253	+	break;
254	+	case Token::expressionEnd:
255	+	break;
256	+	case Token::all:
257	+	bs = allInstruction();
258	+	stack.push(bs);
259	+	break;
260	+	case Token::none:
261	+	bs = OpenMDBitSet(nStuntDouble);
262	+	stack.push(bs);
263	+	break;
264	+	case Token::opOr:
265	+	bs = stack.top();
266	+	stack.pop();
267	+	stack.top() |= bs;
268	+	break;
269	+	case Token::opAnd:
270	+	bs = stack.top();
271	+	stack.pop();
272	+	stack.top() &= bs;
273	+	break;
274	+	case Token::opNot:
275	+	stack.top().flip();
276	+	break;
277	+	case Token::within:
278	+	withinInstruction(instruction, stack.top(), frame);
279	+	break;
280	+	case Token::hull:
281	+	stack.push(hull(frame));
282	+	break;
283	+	//case Token::selected:
284	+	//  stack.push(getSelectionSet());
285	+	//  break;
286	+	case Token::name:
287	+	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
288	+	break;
289	+	case Token::index:
290	+	stack.push(indexInstruction(instruction.value));
291	+	break;
292	+	case Token::identifier:
293	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
294	+	break;
295	+	case Token::opLT:
296	+	case Token::opLE:
297	+	case Token::opGE:
298	+	case Token::opGT:
299	+	case Token::opEQ:
300	+	case Token::opNE:
301	+	stack.push(comparatorInstruction(instruction, frame));
302	+	break;
303	+	default:
304	+	unrecognizedExpression();
305	+	}
306	+	}
307	+	if (stack.size() != 1)
308	+	evalError("atom expression compiler error - stack over/underflow");
309	+
310	+	return stack.top();
311	+	}
312	+
313	+
314	+
315		OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
316		int comparator = instruction.tok;
317		int property = instruction.intValue;
318		float comparisonValue = boost::any_cast<float>(instruction.value);
224	–	float propertyValue;
319		OpenMDBitSet bs(nStuntDouble);
320		bs.clearAll();
321
#	Line 248 | Line 342 | namespace OpenMD {
342		return bs;
343		}
344
345	+	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
346	+	int comparator = instruction.tok;
347	+	int property = instruction.intValue;
348	+	float comparisonValue = boost::any_cast<float>(instruction.value);
349	+	OpenMDBitSet bs(nStuntDouble);
350	+	bs.clearAll();
351	+
352	+	SimInfo::MoleculeIterator mi;
353	+	Molecule* mol;
354	+	Molecule::AtomIterator ai;
355	+	Atom* atom;
356	+	Molecule::RigidBodyIterator rbIter;
357	+	RigidBody* rb;
358	+
359	+	for (mol = info->beginMolecule(mi); mol != NULL;
360	+	mol = info->nextMolecule(mi)) {
361	+
362	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
363	+	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
364	+	}
365	+
366	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
367	+	rb = mol->nextRigidBody(rbIter)) {
368	+	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
369	+	}
370	+	}
371	+
372	+	return bs;
373	+	}
374	+
375		void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
376		int property, int comparator,
377		float comparisonValue) {
378		RealType propertyValue = 0.0;
379	+	Vector3d pos;
380		switch (property) {
381		case Token::mass:
382		propertyValue = sd->getMass();
#	Line 278 | Line 403 | namespace OpenMD {
403		case Token::z:
404		propertyValue = sd->getPos().z();
405		break;
406	+	case Token::wrappedX:
407	+	pos = sd->getPos();
408	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
409	+	propertyValue = pos.x();
410	+	break;
411	+	case Token::wrappedY:
412	+	pos = sd->getPos();
413	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
414	+	propertyValue = pos.y();
415	+	break;
416	+	case Token::wrappedZ:
417	+	pos = sd->getPos();
418	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
419	+	propertyValue = pos.z();
420	+	break;
421	+	case Token::r:
422	+	propertyValue = sd->getPos().length();
423	+	break;
424		default:
425		unrecognizedAtomProperty(property);
426		}
#	Line 303 | Line 446 | namespace OpenMD {
446		match = propertyValue != comparisonValue;
447		break;
448		}
449	<	if (match)
449	>	if (match)
450		bs.setBitOn(sd->getGlobalIndex());
451	+
452
453		}
454
455	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
456	+	int property, int comparator,
457	+	float comparisonValue, int frame) {
458	+	RealType propertyValue = 0.0;
459	+	Vector3d pos;
460	+	switch (property) {
461	+	case Token::mass:
462	+	propertyValue = sd->getMass();
463	+	break;
464	+	case Token::charge:
465	+	if (sd->isAtom()){
466	+	Atom* atom = static_cast<Atom*>(sd);
467	+	propertyValue = getCharge(atom,frame);
468	+	} else if (sd->isRigidBody()) {
469	+	RigidBody* rb = static_cast<RigidBody*>(sd);
470	+	RigidBody::AtomIterator ai;
471	+	Atom* atom;
472	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
473	+	propertyValue+=  getCharge(atom,frame);
474	+	}
475	+	}
476	+	break;
477	+	case Token::x:
478	+	propertyValue = sd->getPos(frame).x();
479	+	break;
480	+	case Token::y:
481	+	propertyValue = sd->getPos(frame).y();
482	+	break;
483	+	case Token::z:
484	+	propertyValue = sd->getPos(frame).z();
485	+	break;
486	+	case Token::wrappedX:
487	+	pos = sd->getPos(frame);
488	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
489	+	propertyValue = pos.x();
490	+	break;
491	+	case Token::wrappedY:
492	+	pos = sd->getPos(frame);
493	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
494	+	propertyValue = pos.y();
495	+	break;
496	+	case Token::wrappedZ:
497	+	pos = sd->getPos(frame);
498	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
499	+	propertyValue = pos.z();
500	+	break;
501	+
502	+	case Token::r:
503	+	propertyValue = sd->getPos(frame).length();
504	+	break;
505	+	default:
506	+	unrecognizedAtomProperty(property);
507	+	}
508	+
509	+	bool match = false;
510	+	switch (comparator) {
511	+	case Token::opLT:
512	+	match = propertyValue < comparisonValue;
513	+	break;
514	+	case Token::opLE:
515	+	match = propertyValue <= comparisonValue;
516	+	break;
517	+	case Token::opGE:
518	+	match = propertyValue >= comparisonValue;
519	+	break;
520	+	case Token::opGT:
521	+	match = propertyValue > comparisonValue;
522	+	break;
523	+	case Token::opEQ:
524	+	match = propertyValue == comparisonValue;
525	+	break;
526	+	case Token::opNE:
527	+	match = propertyValue != comparisonValue;
528	+	break;
529	+	}
530	+	if (match)
531	+	bs.setBitOn(sd->getGlobalIndex());
532	+
533	+
534	+	}
535	+
536		void SelectionEvaluator::withinInstruction(const Token& instruction,
537		OpenMDBitSet& bs){
538
#	Line 324 | Line 549 | namespace OpenMD {
549
550		bs = distanceFinder.find(bs, distance);
551		}
552	+
553	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
554	+	OpenMDBitSet& bs, int frame){
555	+
556	+	boost::any withinSpec = instruction.value;
557	+	float distance;
558	+	if (withinSpec.type() == typeid(float)){
559	+	distance = boost::any_cast<float>(withinSpec);
560	+	} else if (withinSpec.type() == typeid(int)) {
561	+	distance = boost::any_cast<int>(withinSpec);
562	+	} else {
563	+	evalError("casting error in withinInstruction");
564	+	bs.clearAll();
565	+	}
566	+
567	+	bs = distanceFinder.find(bs, distance, frame);
568	+	}
569
570		void SelectionEvaluator::define() {
571		assert(statement.size() >= 3);
#	Line 369 | Line 611 | namespace OpenMD {
611		void SelectionEvaluator::select(OpenMDBitSet& bs){
612		bs = expression(statement, 1);
613		}
614	+
615	+	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
616	+	bs = expression(statement, 1, frame);
617	+	}
618
619		OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
620
#	Line 417 | Line 663 | namespace OpenMD {
663		pc = 0;
664		instructionDispatchLoop(bs);
665		}
666	+	return bs;
667	+	}
668
669	+	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
670	+	OpenMDBitSet bs(nStuntDouble);
671	+	if (isLoaded_) {
672	+	pc = 0;
673	+	instructionDispatchLoop(bs, frame);
674	+	}
675		return bs;
676		}
677
#	Line 444 | Line 698 | namespace OpenMD {
698		return bs;
699		}
700
701	+	OpenMDBitSet SelectionEvaluator::allInstruction() {
702	+	OpenMDBitSet bs(nStuntDouble);
703
704	+	SimInfo::MoleculeIterator mi;
705	+	Molecule* mol;
706	+	Molecule::AtomIterator ai;
707	+	Atom* atom;
708	+	Molecule::RigidBodyIterator rbIter;
709	+	RigidBody* rb;
710	+
711	+	// Doing the loop insures that we're actually on this processor.
712	+
713	+	for (mol = info->beginMolecule(mi); mol != NULL;
714	+	mol = info->nextMolecule(mi)) {
715	+
716	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
717	+	bs.setBitOn(atom->getGlobalIndex());
718	+	}
719	+
720	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
721	+	rb = mol->nextRigidBody(rbIter)) {
722	+	bs.setBitOn(rb->getGlobalIndex());
723	+	}
724	+	}
725	+
726	+	return bs;
727	+	}
728	+
729		OpenMDBitSet SelectionEvaluator::hull() {
730		OpenMDBitSet bs(nStuntDouble);
731
732		bs = hullFinder.findHull();
733	<
733	>	surfaceArea_ = hullFinder.getSurfaceArea();
734	>	hasSurfaceArea_ = true;
735		return bs;
736		}
737
738
739	+	OpenMDBitSet SelectionEvaluator::hull(int frame) {
740	+	OpenMDBitSet bs(nStuntDouble);
741	+
742	+	bs = hullFinder.findHull(frame);
743
744	+	return bs;
745	+	}
746	+
747		RealType SelectionEvaluator::getCharge(Atom* atom) {
748	<	RealType charge =0.0;
748	>	RealType charge = 0.0;
749		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);
750
751	<	if (doubleData != NULL) {
752	<	charge = doubleData->getData();
753	<
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	<	}
751	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
752	>	if ( fca.isFixedCharge() ) {
753	>	charge = fca.getCharge();
754		}
755	+
756	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
757	+	if ( fqa.isFluctuatingCharge() ) {
758	+	charge += atom->getFlucQPos();
759	+	}
760	+	return charge;
761	+	}
762
763	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
764	+	RealType charge = 0.0;
765	+	AtomType* atomType = atom->getAtomType();
766	+
767	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
768	+	if ( fca.isFixedCharge() ) {
769	+	charge = fca.getCharge();
770	+	}
771	+
772	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
773	+	if ( fqa.isFluctuatingCharge() ) {
774	+	charge += atom->getFlucQPos(frame);
775	+	}
776		return charge;
777		}
778

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 UTC

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

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