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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 1816 by gezelter, Fri Dec 7 18:33:33 2012 UTC

#	Line 36 | Line 36
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).
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), indexFinder(info),
58	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	>	indexFinder(info),
60		isLoaded_(false){
61		nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
62		}
#	Line 143 | 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 157 | Line 183 | namespace OpenMD {
183		case Token::expressionEnd:
184		break;
185		case Token::all:
186	<	bs = OpenMDBitSet(nStuntDouble);
161	<	bs.setAll();
186	>	bs = allInstruction();
187		stack.push(bs);
188		break;
189		case Token::none:
#	Line 181 | Line 206 | namespace OpenMD {
206		case Token::within:
207		withinInstruction(instruction, stack.top());
208		break;
209	+	case Token::hull:
210	+	stack.push(hull());
211	+	break;
212		//case Token::selected:
213		//  stack.push(getSelectionSet());
214		//  break;
#	Line 212 | 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);
220	–	float propertyValue;
319		OpenMDBitSet bs(nStuntDouble);
320		bs.clearAll();
321
#	Line 244 | 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) {
#	Line 274 | Line 402 | namespace OpenMD {
402		case Token::z:
403		propertyValue = sd->getPos().z();
404		break;
405	+	case Token::r:
406	+	propertyValue = sd->getPos().length();
407	+	break;
408		default:
409		unrecognizedAtomProperty(property);
410		}
#	Line 299 | Line 430 | namespace OpenMD {
430		match = propertyValue != comparisonValue;
431		break;
432		}
433	<	if (match)
433	>	if (match)
434		bs.setBitOn(sd->getGlobalIndex());
435	+
436
437		}
438
439	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
440	+	int property, int comparator,
441	+	float comparisonValue, int frame) {
442	+	RealType propertyValue = 0.0;
443	+	switch (property) {
444	+	case Token::mass:
445	+	propertyValue = sd->getMass();
446	+	break;
447	+	case Token::charge:
448	+	if (sd->isAtom()){
449	+	Atom* atom = static_cast<Atom*>(sd);
450	+	propertyValue = getCharge(atom,frame);
451	+	} else if (sd->isRigidBody()) {
452	+	RigidBody* rb = static_cast<RigidBody*>(sd);
453	+	RigidBody::AtomIterator ai;
454	+	Atom* atom;
455	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
456	+	propertyValue+=  getCharge(atom,frame);
457	+	}
458	+	}
459	+	break;
460	+	case Token::x:
461	+	propertyValue = sd->getPos(frame).x();
462	+	break;
463	+	case Token::y:
464	+	propertyValue = sd->getPos(frame).y();
465	+	break;
466	+	case Token::z:
467	+	propertyValue = sd->getPos(frame).z();
468	+	break;
469	+	case Token::r:
470	+	propertyValue = sd->getPos(frame).length();
471	+	break;
472	+	default:
473	+	unrecognizedAtomProperty(property);
474	+	}
475	+
476	+	bool match = false;
477	+	switch (comparator) {
478	+	case Token::opLT:
479	+	match = propertyValue < comparisonValue;
480	+	break;
481	+	case Token::opLE:
482	+	match = propertyValue <= comparisonValue;
483	+	break;
484	+	case Token::opGE:
485	+	match = propertyValue >= comparisonValue;
486	+	break;
487	+	case Token::opGT:
488	+	match = propertyValue > comparisonValue;
489	+	break;
490	+	case Token::opEQ:
491	+	match = propertyValue == comparisonValue;
492	+	break;
493	+	case Token::opNE:
494	+	match = propertyValue != comparisonValue;
495	+	break;
496	+	}
497	+	if (match)
498	+	bs.setBitOn(sd->getGlobalIndex());
499	+
500	+
501	+	}
502	+
503		void SelectionEvaluator::withinInstruction(const Token& instruction,
504		OpenMDBitSet& bs){
505
#	Line 320 | Line 516 | namespace OpenMD {
516
517		bs = distanceFinder.find(bs, distance);
518		}
519	+
520	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
521	+	OpenMDBitSet& bs, int frame){
522	+
523	+	boost::any withinSpec = instruction.value;
524	+	float distance;
525	+	if (withinSpec.type() == typeid(float)){
526	+	distance = boost::any_cast<float>(withinSpec);
527	+	} else if (withinSpec.type() == typeid(int)) {
528	+	distance = boost::any_cast<int>(withinSpec);
529	+	} else {
530	+	evalError("casting error in withinInstruction");
531	+	bs.clearAll();
532	+	}
533	+
534	+	bs = distanceFinder.find(bs, distance, frame);
535	+	}
536
537		void SelectionEvaluator::define() {
538		assert(statement.size() >= 3);
#	Line 365 | Line 578 | namespace OpenMD {
578		void SelectionEvaluator::select(OpenMDBitSet& bs){
579		bs = expression(statement, 1);
580		}
581	+
582	+	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
583	+	bs = expression(statement, 1, frame);
584	+	}
585
586		OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
587
#	Line 413 | Line 630 | namespace OpenMD {
630		pc = 0;
631		instructionDispatchLoop(bs);
632		}
633	+	return bs;
634	+	}
635
636	+	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
637	+	OpenMDBitSet bs(nStuntDouble);
638	+	if (isLoaded_) {
639	+	pc = 0;
640	+	instructionDispatchLoop(bs, frame);
641	+	}
642		return bs;
643		}
644
#	Line 440 | Line 665 | namespace OpenMD {
665		return bs;
666		}
667
668	+	OpenMDBitSet SelectionEvaluator::allInstruction() {
669	+	OpenMDBitSet bs(nStuntDouble);
670
671	+	SimInfo::MoleculeIterator mi;
672	+	Molecule* mol;
673	+	Molecule::AtomIterator ai;
674	+	Atom* atom;
675	+	Molecule::RigidBodyIterator rbIter;
676	+	RigidBody* rb;
677	+
678	+	// Doing the loop insures that we're actually on this processor.
679	+
680	+	for (mol = info->beginMolecule(mi); mol != NULL;
681	+	mol = info->nextMolecule(mi)) {
682	+
683	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
684	+	bs.setBitOn(atom->getGlobalIndex());
685	+	}
686	+
687	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
688	+	rb = mol->nextRigidBody(rbIter)) {
689	+	bs.setBitOn(rb->getGlobalIndex());
690	+	}
691	+	}
692	+
693	+	return bs;
694	+	}
695	+
696	+	OpenMDBitSet SelectionEvaluator::hull() {
697	+	OpenMDBitSet bs(nStuntDouble);
698	+
699	+	bs = hullFinder.findHull();
700	+
701	+	return bs;
702	+	}
703	+
704	+
705	+	OpenMDBitSet SelectionEvaluator::hull(int frame) {
706	+	OpenMDBitSet bs(nStuntDouble);
707	+
708	+	bs = hullFinder.findHull(frame);
709	+
710	+	return bs;
711	+	}
712	+
713		RealType SelectionEvaluator::getCharge(Atom* atom) {
714	<	RealType charge =0.0;
714	>	RealType charge = 0.0;
715		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);
716
717	<	if (doubleData != NULL) {
718	<	charge = doubleData->getData();
719	<
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	<	}
717	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
718	>	if ( fca.isFixedCharge() ) {
719	>	charge = fca.getCharge();
720		}
721	+
722	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
723	+	if ( fqa.isFluctuatingCharge() ) {
724	+	charge += atom->getFlucQPos();
725	+	}
726	+	return charge;
727	+	}
728
729	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
730	+	RealType charge = 0.0;
731	+	AtomType* atomType = atom->getAtomType();
732	+
733	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
734	+	if ( fca.isFixedCharge() ) {
735	+	charge = fca.getCharge();
736	+	}
737	+
738	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
739	+	if ( fqa.isFluctuatingCharge() ) {
740	+	charge += atom->getFlucQPos(frame);
741	+	}
742		return charge;
743		}
744

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1816 by gezelter, Fri Dec 7 18:33:33 2012 UTC

#	Line 0 | Line 1
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