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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 1931 by gezelter, Mon Aug 19 19:20:32 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 204 | Line 228 | namespace OpenMD {
228		case Token::opEQ:
229		case Token::opNE:
230		stack.push(comparatorInstruction(instruction));
231	+	break;
232	+	default:
233	+	unrecognizedExpression();
234	+	}
235	+	}
236	+	if (stack.size() != 1)
237	+	evalError("atom expression compiler error - stack over/underflow");
238	+
239	+	return stack.top();
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		}
#	Line 221 | Line 316 | namespace OpenMD {
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	+
381		switch (property) {
382		case Token::mass:
383		propertyValue = sd->getMass();
#	Line 278 | Line 404 | namespace OpenMD {
404		case Token::z:
405		propertyValue = sd->getPos().z();
406		break;
407	+	case Token::wrappedX:
408	+	pos = sd->getPos();
409	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
410	+	propertyValue = pos.x();
411	+	break;
412	+	case Token::wrappedY:
413	+	pos = sd->getPos();
414	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
415	+	propertyValue = pos.y();
416	+	break;
417	+	case Token::wrappedZ:
418	+	pos = sd->getPos();
419	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	+	propertyValue = pos.z();
421	+	break;
422	+	case Token::r:
423	+	propertyValue = sd->getPos().length();
424	+	break;
425		default:
426		unrecognizedAtomProperty(property);
427		}
#	Line 303 | Line 447 | namespace OpenMD {
447		match = propertyValue != comparisonValue;
448		break;
449		}
450	<	if (match)
450	>
451	>	if (match)
452		bs.setBitOn(sd->getGlobalIndex());
453	+
454
455		}
456
457	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
458	+	int property, int comparator,
459	+	float comparisonValue, int frame) {
460	+	RealType propertyValue = 0.0;
461	+	Vector3d pos;
462	+	switch (property) {
463	+	case Token::mass:
464	+	propertyValue = sd->getMass();
465	+	break;
466	+	case Token::charge:
467	+	if (sd->isAtom()){
468	+	Atom* atom = static_cast<Atom*>(sd);
469	+	propertyValue = getCharge(atom,frame);
470	+	} else if (sd->isRigidBody()) {
471	+	RigidBody* rb = static_cast<RigidBody*>(sd);
472	+	RigidBody::AtomIterator ai;
473	+	Atom* atom;
474	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
475	+	propertyValue+=  getCharge(atom,frame);
476	+	}
477	+	}
478	+	break;
479	+	case Token::x:
480	+	propertyValue = sd->getPos(frame).x();
481	+	break;
482	+	case Token::y:
483	+	propertyValue = sd->getPos(frame).y();
484	+	break;
485	+	case Token::z:
486	+	propertyValue = sd->getPos(frame).z();
487	+	break;
488	+	case Token::wrappedX:
489	+	pos = sd->getPos(frame);
490	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
491	+	propertyValue = pos.x();
492	+	break;
493	+	case Token::wrappedY:
494	+	pos = sd->getPos(frame);
495	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
496	+	propertyValue = pos.y();
497	+	break;
498	+	case Token::wrappedZ:
499	+	pos = sd->getPos(frame);
500	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
501	+	propertyValue = pos.z();
502	+	break;
503	+
504	+	case Token::r:
505	+	propertyValue = sd->getPos(frame).length();
506	+	break;
507	+	default:
508	+	unrecognizedAtomProperty(property);
509	+	}
510	+
511	+	bool match = false;
512	+	switch (comparator) {
513	+	case Token::opLT:
514	+	match = propertyValue < comparisonValue;
515	+	break;
516	+	case Token::opLE:
517	+	match = propertyValue <= comparisonValue;
518	+	break;
519	+	case Token::opGE:
520	+	match = propertyValue >= comparisonValue;
521	+	break;
522	+	case Token::opGT:
523	+	match = propertyValue > comparisonValue;
524	+	break;
525	+	case Token::opEQ:
526	+	match = propertyValue == comparisonValue;
527	+	break;
528	+	case Token::opNE:
529	+	match = propertyValue != comparisonValue;
530	+	break;
531	+	}
532	+	if (match)
533	+	bs.setBitOn(sd->getGlobalIndex());
534	+
535	+
536	+	}
537	+
538		void SelectionEvaluator::withinInstruction(const Token& instruction,
539		OpenMDBitSet& bs){
540
#	Line 324 | Line 551 | namespace OpenMD {
551
552		bs = distanceFinder.find(bs, distance);
553		}
554	+
555	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
556	+	OpenMDBitSet& bs, int frame){
557	+
558	+	boost::any withinSpec = instruction.value;
559	+	float distance;
560	+	if (withinSpec.type() == typeid(float)){
561	+	distance = boost::any_cast<float>(withinSpec);
562	+	} else if (withinSpec.type() == typeid(int)) {
563	+	distance = boost::any_cast<int>(withinSpec);
564	+	} else {
565	+	evalError("casting error in withinInstruction");
566	+	bs.clearAll();
567	+	}
568	+
569	+	bs = distanceFinder.find(bs, distance, frame);
570	+	}
571
572		void SelectionEvaluator::define() {
573		assert(statement.size() >= 3);
#	Line 369 | Line 613 | namespace OpenMD {
613		void SelectionEvaluator::select(OpenMDBitSet& bs){
614		bs = expression(statement, 1);
615		}
616	+
617	+	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
618	+	bs = expression(statement, 1, frame);
619	+	}
620
621		OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
622
#	Line 417 | Line 665 | namespace OpenMD {
665		pc = 0;
666		instructionDispatchLoop(bs);
667		}
668	+	return bs;
669	+	}
670
671	+	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
672	+	OpenMDBitSet bs(nStuntDouble);
673	+	if (isLoaded_) {
674	+	pc = 0;
675	+	instructionDispatchLoop(bs, frame);
676	+	}
677		return bs;
678		}
679
#	Line 444 | Line 700 | namespace OpenMD {
700		return bs;
701		}
702
703	+	OpenMDBitSet SelectionEvaluator::allInstruction() {
704	+	OpenMDBitSet bs(nStuntDouble);
705
706	+	SimInfo::MoleculeIterator mi;
707	+	Molecule* mol;
708	+	Molecule::AtomIterator ai;
709	+	Atom* atom;
710	+	Molecule::RigidBodyIterator rbIter;
711	+	RigidBody* rb;
712	+
713	+	// Doing the loop insures that we're actually on this processor.
714	+
715	+	for (mol = info->beginMolecule(mi); mol != NULL;
716	+	mol = info->nextMolecule(mi)) {
717	+
718	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	+	bs.setBitOn(atom->getGlobalIndex());
720	+	}
721	+
722	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
723	+	rb = mol->nextRigidBody(rbIter)) {
724	+	bs.setBitOn(rb->getGlobalIndex());
725	+	}
726	+	}
727	+
728	+	return bs;
729	+	}
730	+
731		OpenMDBitSet SelectionEvaluator::hull() {
732		OpenMDBitSet bs(nStuntDouble);
733
734		bs = hullFinder.findHull();
735	<
735	>	surfaceArea_ = hullFinder.getSurfaceArea();
736	>	hasSurfaceArea_ = true;
737		return bs;
738		}
739
740
741	+	OpenMDBitSet SelectionEvaluator::hull(int frame) {
742	+	OpenMDBitSet bs(nStuntDouble);
743	+
744	+	bs = hullFinder.findHull(frame);
745
746	+	return bs;
747	+	}
748	+
749		RealType SelectionEvaluator::getCharge(Atom* atom) {
750	<	RealType charge =0.0;
750	>	RealType charge = 0.0;
751		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);
752
753	<	if (doubleData != NULL) {
754	<	charge = doubleData->getData();
755	<
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	<	}
753	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
754	>	if ( fca.isFixedCharge() ) {
755	>	charge = fca.getCharge();
756		}
757	+
758	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
759	+	if ( fqa.isFluctuatingCharge() ) {
760	+	charge += atom->getFlucQPos();
761	+	}
762	+	return charge;
763	+	}
764
765	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
766	+	RealType charge = 0.0;
767	+	AtomType* atomType = atom->getAtomType();
768	+
769	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
770	+	if ( fca.isFixedCharge() ) {
771	+	charge = fca.getCharge();
772	+	}
773	+
774	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
775	+	if ( fqa.isFluctuatingCharge() ) {
776	+	charge += atom->getFlucQPos(frame);
777	+	}
778		return charge;
779		}
780

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 1412 by gezelter, Mon Mar 22 18:45:39 2010 UTC vs.
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC

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

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