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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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/ifstrstream.hpp"
50	+	#include "types/FixedChargeAdapter.hpp"
51	+	#include "types/FluctuatingChargeAdapter.hpp"
52
49	–	namespace oopse {
53
54	+	namespace OpenMD {
55
56		SelectionEvaluator::SelectionEvaluator(SimInfo* si)
57	<	: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
58	<
59	<	nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
60	<	}
61	<
62	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
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();
70		this->filename = filename;
71		this->script = script;
72		if (! compiler.compile(filename, script)) {
73		error = true;
74		errorMessage = compiler.getErrorMessage();
75	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
75	>
76	>	sprintf( painCave.errMsg,
77	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
78	>	painCave.severity = OPENMD_ERROR;
79	>	painCave.isFatal = 1;
80	>	simError();
81		return false;
82		}
83
#	Line 100 | Line 115 | namespace oopse {
115		return loadScriptFileInternal(filename);
116		}
117
118	<	bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
119	<	std::ifstream ifs(filename.c_str());
118	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
119	>	ifstrstream ifs(filename.c_str());
120		if (!ifs.is_open()) {
121		return false;
122		}
123	<
123	>
124		const int bufferSize = 65535;
125		char buffer[bufferSize];
126		std::string script;
#	Line 114 | Line 129 | namespace oopse {
129		}
130		return loadScript(filename, script);
131		}
132	<
133	<	void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
132	>
133	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
134
135		while ( pc < aatoken.size()) {
136		statement = aatoken[pc++];
#	Line 136 | Line 151 | namespace oopse {
151
152		}
153
154	<	OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
140	<	OOPSEBitSet bs;
141	<	std::stack<OOPSEBitSet> stack;
154	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
155
156	<	for (int pc = pcStart; pc < code.size(); ++pc) {
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	>	SelectionSet bs = createSelectionSets();
178	>	std::stack<SelectionSet> stack;
179	>	vector<int> bsSize = bs.size();
180	>
181	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
182		Token instruction = code[pc];
183
184		switch (instruction.tok) {
#	Line 149 | Line 187 | namespace oopse {
187		case Token::expressionEnd:
188		break;
189		case Token::all:
190	<	bs = OOPSEBitSet(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 = OOPSEBitSet(nStuntDouble);
265	>	bs = SelectionSet(nObjects);
266		stack.push(bs);
267		break;
268		case Token::opOr:
#	Line 171 | Line 279 | namespace oopse {
279		stack.top().flip();
280		break;
281		case Token::within:
282	<
175	<	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 192 | Line 302 | namespace oopse {
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 206 | Line 316 | namespace oopse {
316
317
318
319	<	OOPSEBitSet 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;
214	<	OOPSEBitSet bs(nStuntDouble);
323	>	SelectionSet bs = createSelectionSets();
324		bs.clearAll();
325
326		SimInfo::MoleculeIterator mi;
#	Line 220 | Line 329 | namespace oopse {
329		Atom* atom;
330		Molecule::RigidBodyIterator rbIter;
331		RigidBody* rb;
223	–
224	–	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
332
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		}
341	<
342	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
343	<	compareProperty(rb, bs, property, comparator, comparisonValue);
344	<	}
341	>
342	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
343	>	rb = mol->nextRigidBody(rbIter)) {
344	>	compareProperty(rb, bs, property, comparator, comparisonValue);
345	>	}
346		}
347
348		return bs;
349		}
350
351	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue) {
352	<	double propertyValue = 0.0;
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 254 | Line 403 | namespace oopse {
403		}
404		}
405		break;
406	+	case Token::x:
407	+	propertyValue = sd->getPos().x();
408	+	break;
409	+	case Token::y:
410	+	propertyValue = sd->getPos().y();
411	+	break;
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 279 | Line 455 | namespace oopse {
455		match = propertyValue != comparisonValue;
456		break;
457		}
282	–	if (match)
283	–	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, OOPSEBitSet& 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 300 | Line 713 | namespace oopse {
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);
735	<
735	>
736		std::string variable = boost::any_cast<std::string>(statement[1].value);
737	<
738	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
737	>
738	>	variables.insert(VariablesType::value_type(variable,
739	>	expression(statement, 2)));
740		}
741	+
742
311	–
743		/** @todo */
744		void SelectionEvaluator::predefine(const std::string& script) {
745	<
745	>
746		if (compiler.compile("#predefine", script)) {
747		std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
748		if (aatoken.size() != 1) {
#	Line 322 | Line 753 | namespace oopse {
753		std::vector<Token> statement = aatoken[0];
754		if (statement.size() > 2) {
755		int tok = statement[1].tok;
756	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
756	>	if (tok == Token::identifier ||
757	>	(tok & Token::predefinedset) == Token::predefinedset) {
758		std::string variable = boost::any_cast<std::string>(statement[1].value);
759		variables.insert(VariablesType::value_type(variable, statement));
760	<
760	>
761		} else {
762		evalError("invalid variable name:" + script);
763		}
764		}else {
765		evalError("bad predefinition length:" + script);
766	<	}
335	<
766	>	}
767
768		} else {
769		evalError("predefined set compile error:" + script +
770		"\ncompile error:" + compiler.getErrorMessage());
771		}
341	–
772		}
773
774	<	void SelectionEvaluator::select(OOPSEBitSet& bs){
774	>	void SelectionEvaluator::select(SelectionSet& bs){
775		bs = expression(statement, 1);
776		}
777
778	<	OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){
779	<
780	<	OOPSEBitSet bs(nStuntDouble);
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	>	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(OOPSEBitSet)) {
789	<	return boost::any_cast<OOPSEBitSet>(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 361 | Line 795 | namespace oopse {
795		} else {
796		unrecognizedIdentifier(variable);
797		}
798	<
798	>
799		return bs;
800		}
801	<
802	<	OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){
803	<
370	<	return nameFinder.match(name);
371	<
801	>
802	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
803	>	return nameFinder.match(name);
804		}
805
806		bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
#	Line 378 | Line 810 | namespace oopse {
810		return true;
811		}
812		}
813	<
813	>
814		return false;
815		}
816
#	Line 388 | Line 820 | namespace oopse {
820		//predefine();
821		}
822
823	<	OOPSEBitSet SelectionEvaluator::evaluate() {
824	<	OOPSEBitSet 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	<	OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
847	<	OOPSEBitSet 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 411 | Line 856 | namespace oopse {
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 421 | Line 867 | namespace oopse {
867		return bs;
868		}
869
870	+	SelectionSet SelectionEvaluator::allInstruction() {
871	+	SelectionSet ss = createSelectionSets();
872
873	<	double SelectionEvaluator::getCharge(Atom* atom) {
874	<	double charge =0.0;
875	<	AtomType* atomType = atom->getAtomType();
876	<	if (atomType->isCharge()) {
877	<	GenericData* data = atomType->getPropertyByName("Charge");
878	<	if (data != NULL) {
879	<	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
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	<	if (doubleData != NULL) {
882	<	charge = doubleData->getData();
881	>	Molecule* mol;
882	>	Atom* atom;
883	>	RigidBody* rb;
884	>	Bond* bond;
885	>	Bend* bend;
886	>	Torsion* torsion;
887	>	Inversion* inversion;
888
889	<	} else {
890	<	sprintf( painCave.errMsg,
891	<	"Can not cast GenericData to DoubleGenericData\n");
892	<	painCave.severity = OOPSE_ERROR;
893	<	painCave.isFatal = 1;
894	<	simError();
895	<	}
896	<	}
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;
942	+	AtomType* atomType = atom->getAtomType();
943	+
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	+
972		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
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