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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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, 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
50	–	namespace oopse {
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), hasSurfaceArea_(false),
60		isLoaded_(false){
61		nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
62		}
#	Line 67 | Line 72 | namespace oopse {
72
73		sprintf( painCave.errMsg,
74		"SelectionCompiler Error: %s\n", errorMessage.c_str());
75	<	painCave.severity = OOPSE_ERROR;
75	>	painCave.severity = OPENMD_ERROR;
76		painCave.isFatal = 1;
77		simError();
78		return false;
#	Line 122 | Line 127 | namespace oopse {
127		return loadScript(filename, script);
128		}
129
130	<	void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
130	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
131
132		while ( pc < aatoken.size()) {
133		statement = aatoken[pc++];
#	Line 143 | Line 148 | namespace oopse {
148
149		}
150
151	<	OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
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	<	OOPSEBitSet bs;
175	<	std::stack<OOPSEBitSet> stack;
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 oopse {
183		case Token::expressionEnd:
184		break;
185		case Token::all:
186	<	bs = OOPSEBitSet(nStuntDouble);
161	<	bs.setAll();
186	>	bs = allInstruction();
187		stack.push(bs);
188		break;
189		case Token::none:
190	<	bs = OOPSEBitSet(nStuntDouble);
190	>	bs = OpenMDBitSet(nStuntDouble);
191		stack.push(bs);
192		break;
193		case Token::opOr:
#	Line 181 | Line 206 | namespace oopse {
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 oopse {
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	<	OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
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);
319	<	float propertyValue;
221	<	OOPSEBitSet bs(nStuntDouble);
319	>	OpenMDBitSet bs(nStuntDouble);
320		bs.clearAll();
321
322		SimInfo::MoleculeIterator mi;
#	Line 244 | Line 342 | namespace oopse {
342		return bs;
343		}
344
345	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs,
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 274 | Line 404 | namespace oopse {
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 299 | Line 447 | namespace oopse {
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::withinInstruction(const Token& instruction,
458	<	OOPSEBitSet& bs){
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	+
541		boost::any withinSpec = instruction.value;
542		float distance;
543		if (withinSpec.type() == typeid(float)){
#	Line 320 | Line 551 | namespace oopse {
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 362 | Line 610 | namespace oopse {
610		}
611		}
612
613	<	void SelectionEvaluator::select(OOPSEBitSet& bs){
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	<	OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){
621	>	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
622
623	<	OOPSEBitSet bs(nStuntDouble);
623	>	OpenMDBitSet bs(nStuntDouble);
624		std::map<std::string, boost::any>::iterator i = variables.find(variable);
625
626		if (i != variables.end()) {
627	<	if (i->second.type() == typeid(OOPSEBitSet)) {
628	<	return boost::any_cast<OOPSEBitSet>(i->second);
627	>	if (i->second.type() == typeid(OpenMDBitSet)) {
628	>	return boost::any_cast<OpenMDBitSet>(i->second);
629		} else if (i->second.type() ==  typeid(std::vector<Token>)){
630		bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
631		i->second =  bs; /**@todo fixme */
#	Line 386 | Line 638 | namespace oopse {
638		return bs;
639		}
640
641	<	OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){
641	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
642		return nameFinder.match(name);
643		}
644
#	Line 407 | Line 659 | namespace oopse {
659		//predefine();
660		}
661
662	<	OOPSEBitSet SelectionEvaluator::evaluate() {
663	<	OOPSEBitSet bs(nStuntDouble);
662	>	OpenMDBitSet SelectionEvaluator::evaluate() {
663	>	OpenMDBitSet bs(nStuntDouble);
664		if (isLoaded_) {
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
680	<	OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
681	<	OOPSEBitSet bs(nStuntDouble);
680	>	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
681	>	OpenMDBitSet bs(nStuntDouble);
682
683		if (value.type() == typeid(int)) {
684		int index = boost::any_cast<int>(value);
#	Line 440 | Line 700 | namespace oopse {
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	+	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();
447	–	if (atomType->isCharge()) {
448	–	GenericData* data = atomType->getPropertyByName("Charge");
449	–	if (data != NULL) {
450	–	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
752
753	<	if (doubleData != NULL) {
754	<	charge = doubleData->getData();
755	<
455	<	} else {
456	<	sprintf( painCave.errMsg,
457	<	"Can not cast GenericData to DoubleGenericData\n");
458	<	painCave.severity = OOPSE_ERROR;
459	<	painCave.isFatal = 1;
460	<	simError();
461	<	}
462	<	}
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 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC

#	Line 0 | Line 1
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