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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 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
52	–	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
53	–	: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
54	–
55	–	nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
56	–	}
56
57	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
57	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
58	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	>	indexFinder(info), hasSurfaceArea_(false),
60	>	isLoaded_(false){
61	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
62	>	nObjects.push_back(info->getNGlobalBonds());
63	>	nObjects.push_back(info->getNGlobalBends());
64	>	nObjects.push_back(info->getNGlobalTorsions());
65	>	nObjects.push_back(info->getNGlobalInversions());
66	>	nObjects.push_back(info->getNGlobalMolecules());
67	>	}
68	>
69	>	bool SelectionEvaluator::loadScript(const std::string& filename,
70	>	const std::string& script) {
71		clearDefinitionsAndLoadPredefined();
72		this->filename = filename;
73		this->script = script;
74		if (! compiler.compile(filename, script)) {
75		error = true;
76		errorMessage = compiler.getErrorMessage();
77	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
77	>
78	>	sprintf( painCave.errMsg,
79	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
80	>	painCave.severity = OPENMD_ERROR;
81	>	painCave.isFatal = 1;
82	>	simError();
83		return false;
84		}
85
#	Line 100 | Line 117 | namespace oopse {
117		return loadScriptFileInternal(filename);
118		}
119
120	<	bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
121	<	std::ifstream ifs(filename.c_str());
120	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
121	>	ifstrstream ifs(filename.c_str());
122		if (!ifs.is_open()) {
123		return false;
124		}
125	<
125	>
126		const int bufferSize = 65535;
127		char buffer[bufferSize];
128		std::string script;
#	Line 114 | Line 131 | namespace oopse {
131		}
132		return loadScript(filename, script);
133		}
134	<
135	<	void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
134	>
135	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
136
137		while ( pc < aatoken.size()) {
138		statement = aatoken[pc++];
#	Line 136 | Line 153 | namespace oopse {
153
154		}
155
156	<	OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
140	<	OOPSEBitSet bs;
141	<	std::stack<OOPSEBitSet> stack;
156	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
157
158	<	for (int pc = pcStart; pc < code.size(); ++pc) {
158	>	while ( pc < aatoken.size()) {
159	>	statement = aatoken[pc++];
160	>	statementLength = statement.size();
161	>	Token token = statement[0];
162	>	switch (token.tok) {
163	>	case Token::define:
164	>	define();
165	>	break;
166	>	case Token::select:
167	>	select(bs, frame);
168	>	break;
169	>	default:
170	>	unrecognizedCommand(token);
171	>	return;
172	>	}
173	>	}
174	>
175	>	}
176	>
177	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
178	>	int pcStart) {
179	>	SelectionSet bs = createSelectionSets();
180	>	std::stack<SelectionSet> stack;
181	>	vector<int> bsSize = bs.size();
182	>
183	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
184		Token instruction = code[pc];
185
186		switch (instruction.tok) {
#	Line 149 | Line 189 | namespace oopse {
189		case Token::expressionEnd:
190		break;
191		case Token::all:
192	<	bs = OOPSEBitSet(nStuntDouble);
193	<	bs.setAll();
192	>	bs = allInstruction();
193	>	stack.push(bs);
194	>	break;
195	>	case Token::none:
196	>	bs = createSelectionSets();
197	>	stack.push(bs);
198	>	break;
199	>	case Token::opOr:
200	>	bs= stack.top();
201	>	stack.pop();
202	>	stack.top() |= bs;
203	>	break;
204	>	case Token::opAnd:
205	>	bs = stack.top();
206	>	stack.pop();
207	>	stack.top() &= bs;
208	>	break;
209	>	case Token::opNot:
210	>	stack.top().flip();
211	>	break;
212	>	case Token::within:
213	>	withinInstruction(instruction, stack.top());
214	>	break;
215	>	case Token::hull:
216	>	stack.push(hull());
217	>	break;
218	>	//case Token::selected:
219	>	//  stack.push(getSelectionSet());
220	>	//  break;
221	>	case Token::name:
222	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
223	>	break;
224	>	case Token::index:
225	>	stack.push(indexInstruction(instruction.value));
226	>	break;
227	>	case Token::identifier:
228	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
229	>	break;
230	>	case Token::opLT:
231	>	case Token::opLE:
232	>	case Token::opGE:
233	>	case Token::opGT:
234	>	case Token::opEQ:
235	>	case Token::opNE:
236	>	stack.push(comparatorInstruction(instruction));
237	>	break;
238	>	default:
239	>	unrecognizedExpression();
240	>	}
241	>	}
242	>	if (stack.size() != 1)
243	>	evalError("atom expression compiler error - stack over/underflow");
244	>
245	>	return stack.top();
246	>	}
247	>
248	>
249	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
250	>	int pcStart, int frame) {
251	>	SelectionSet bs = createSelectionSets();
252	>	std::stack<SelectionSet> stack;
253	>
254	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
255	>	Token instruction = code[pc];
256	>
257	>	switch (instruction.tok) {
258	>	case Token::expressionBegin:
259	>	break;
260	>	case Token::expressionEnd:
261	>	break;
262	>	case Token::all:
263	>	bs = allInstruction();
264		stack.push(bs);
265		break;
266		case Token::none:
267	<	bs = OOPSEBitSet(nStuntDouble);
267	>	bs = SelectionSet(nObjects);
268		stack.push(bs);
269		break;
270		case Token::opOr:
#	Line 171 | Line 281 | namespace oopse {
281		stack.top().flip();
282		break;
283		case Token::within:
284	<
175	<	withinInstruction(instruction, stack.top());
284	>	withinInstruction(instruction, stack.top(), frame);
285		break;
286	+	case Token::hull:
287	+	stack.push(hull(frame));
288	+	break;
289		//case Token::selected:
290		//  stack.push(getSelectionSet());
291		//  break;
#	Line 192 | Line 304 | namespace oopse {
304		case Token::opGT:
305		case Token::opEQ:
306		case Token::opNE:
307	<	stack.push(comparatorInstruction(instruction));
307	>	stack.push(comparatorInstruction(instruction, frame));
308		break;
309		default:
310		unrecognizedExpression();
#	Line 206 | Line 318 | namespace oopse {
318
319
320
321	<	OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
321	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
322		int comparator = instruction.tok;
323		int property = instruction.intValue;
324		float comparisonValue = boost::any_cast<float>(instruction.value);
325	<	float propertyValue;
214	<	OOPSEBitSet bs(nStuntDouble);
325	>	SelectionSet bs = createSelectionSets();
326		bs.clearAll();
327
328		SimInfo::MoleculeIterator mi;
#	Line 220 | Line 331 | namespace oopse {
331		Atom* atom;
332		Molecule::RigidBodyIterator rbIter;
333		RigidBody* rb;
223	–
224	–	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
334
335	+	for (mol = info->beginMolecule(mi); mol != NULL;
336	+	mol = info->nextMolecule(mi)) {
337	+
338	+	compareProperty(mol, bs, property, comparator, comparisonValue);
339	+
340		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
341		compareProperty(atom, bs, property, comparator, comparisonValue);
342		}
343	<
344	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
345	<	compareProperty(rb, bs, property, comparator, comparisonValue);
346	<	}
343	>
344	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345	>	rb = mol->nextRigidBody(rbIter)) {
346	>	compareProperty(rb, bs, property, comparator, comparisonValue);
347	>	}
348		}
349
350		return bs;
351		}
352
353	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue) {
353	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
354	>	int comparator = instruction.tok;
355	>	int property = instruction.intValue;
356	>	float comparisonValue = boost::any_cast<float>(instruction.value);
357	>	SelectionSet bs = createSelectionSets();
358	>	bs.clearAll();
359	>
360	>	SimInfo::MoleculeIterator mi;
361	>	Molecule* mol;
362	>	Molecule::AtomIterator ai;
363	>	Atom* atom;
364	>	Molecule::RigidBodyIterator rbIter;
365	>	RigidBody* rb;
366	>
367	>	for (mol = info->beginMolecule(mi); mol != NULL;
368	>	mol = info->nextMolecule(mi)) {
369	>
370	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
371	>
372	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
373	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
374	>	}
375	>
376	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
377	>	rb = mol->nextRigidBody(rbIter)) {
378	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
379	>	}
380	>	}
381	>
382	>	return bs;
383	>	}
384	>
385	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
386	>	int property, int comparator,
387	>	float comparisonValue) {
388		RealType propertyValue = 0.0;
389	+	Vector3d pos;
390	+
391		switch (property) {
392		case Token::mass:
393		propertyValue = sd->getMass();
#	Line 254 | Line 405 | namespace oopse {
405		}
406		}
407		break;
408	+	case Token::x:
409	+	propertyValue = sd->getPos().x();
410	+	break;
411	+	case Token::y:
412	+	propertyValue = sd->getPos().y();
413	+	break;
414	+	case Token::z:
415	+	propertyValue = sd->getPos().z();
416	+	break;
417	+	case Token::wrappedX:
418	+	pos = sd->getPos();
419	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	+	propertyValue = pos.x();
421	+	break;
422	+	case Token::wrappedY:
423	+	pos = sd->getPos();
424	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	+	propertyValue = pos.y();
426	+	break;
427	+	case Token::wrappedZ:
428	+	pos = sd->getPos();
429	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
430	+	propertyValue = pos.z();
431	+	break;
432	+	case Token::r:
433	+	propertyValue = sd->getPos().length();
434	+	break;
435		default:
436		unrecognizedAtomProperty(property);
437		}
#	Line 279 | Line 457 | namespace oopse {
457		match = propertyValue != comparisonValue;
458		break;
459		}
282	–	if (match)
283	–	bs.setBitOn(sd->getGlobalIndex());
460
461	+	if (match)
462	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
463	+
464	+
465		}
466
467	<	void SelectionEvaluator::withinInstruction(const Token& instruction, OOPSEBitSet& bs){
467	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
468	>	int property, int comparator,
469	>	float comparisonValue) {
470	>	RealType propertyValue = 0.0;
471	>	Vector3d pos;
472	>
473	>	switch (property) {
474	>	case Token::mass:
475	>	propertyValue = mol->getMass();
476	>	break;
477	>	case Token::charge:
478	>	{
479	>	Molecule::AtomIterator ai;
480	>	Atom* atom;
481	>	for (atom = mol->beginAtom(ai); atom != NULL;
482	>	atom = mol->nextAtom(ai)) {
483	>	propertyValue+=  getCharge(atom);
484	>	}
485	>	}
486	>	break;
487	>	case Token::x:
488	>	propertyValue = mol->getCom().x();
489	>	break;
490	>	case Token::y:
491	>	propertyValue = mol->getCom().y();
492	>	break;
493	>	case Token::z:
494	>	propertyValue = mol->getCom().z();
495	>	break;
496	>	case Token::wrappedX:
497	>	pos = mol->getCom();
498	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
499	>	propertyValue = pos.x();
500	>	break;
501	>	case Token::wrappedY:
502	>	pos = mol->getCom();
503	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
504	>	propertyValue = pos.y();
505	>	break;
506	>	case Token::wrappedZ:
507	>	pos = mol->getCom();
508	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
509	>	propertyValue = pos.z();
510	>	break;
511	>	case Token::r:
512	>	propertyValue = mol->getCom().length();
513	>	break;
514	>	default:
515	>	unrecognizedMoleculeProperty(property);
516	>	}
517
518	+	bool match = false;
519	+	switch (comparator) {
520	+	case Token::opLT:
521	+	match = propertyValue < comparisonValue;
522	+	break;
523	+	case Token::opLE:
524	+	match = propertyValue <= comparisonValue;
525	+	break;
526	+	case Token::opGE:
527	+	match = propertyValue >= comparisonValue;
528	+	break;
529	+	case Token::opGT:
530	+	match = propertyValue > comparisonValue;
531	+	break;
532	+	case Token::opEQ:
533	+	match = propertyValue == comparisonValue;
534	+	break;
535	+	case Token::opNE:
536	+	match = propertyValue != comparisonValue;
537	+	break;
538	+	}
539	+
540	+	if (match)
541	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
542	+	}
543	+
544	+	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
545	+	int property, int comparator,
546	+	float comparisonValue, int frame) {
547	+	RealType propertyValue = 0.0;
548	+	Vector3d pos;
549	+	switch (property) {
550	+	case Token::mass:
551	+	propertyValue = mol->getMass();
552	+	break;
553	+	case Token::charge:
554	+	{
555	+	Molecule::AtomIterator ai;
556	+	Atom* atom;
557	+	for (atom = mol->beginAtom(ai); atom != NULL;
558	+	atom = mol->nextAtom(ai)) {
559	+	propertyValue+=  getCharge(atom,frame);
560	+	}
561	+	}
562	+	break;
563	+	case Token::x:
564	+	propertyValue = mol->getCom(frame).x();
565	+	break;
566	+	case Token::y:
567	+	propertyValue = mol->getCom(frame).y();
568	+	break;
569	+	case Token::z:
570	+	propertyValue = mol->getCom(frame).z();
571	+	break;
572	+	case Token::wrappedX:
573	+	pos = mol->getCom(frame);
574	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
575	+	propertyValue = pos.x();
576	+	break;
577	+	case Token::wrappedY:
578	+	pos = mol->getCom(frame);
579	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
580	+	propertyValue = pos.y();
581	+	break;
582	+	case Token::wrappedZ:
583	+	pos = mol->getCom(frame);
584	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
585	+	propertyValue = pos.z();
586	+	break;
587	+
588	+	case Token::r:
589	+	propertyValue = mol->getCom(frame).length();
590	+	break;
591	+	default:
592	+	unrecognizedMoleculeProperty(property);
593	+	}
594	+
595	+	bool match = false;
596	+	switch (comparator) {
597	+	case Token::opLT:
598	+	match = propertyValue < comparisonValue;
599	+	break;
600	+	case Token::opLE:
601	+	match = propertyValue <= comparisonValue;
602	+	break;
603	+	case Token::opGE:
604	+	match = propertyValue >= comparisonValue;
605	+	break;
606	+	case Token::opGT:
607	+	match = propertyValue > comparisonValue;
608	+	break;
609	+	case Token::opEQ:
610	+	match = propertyValue == comparisonValue;
611	+	break;
612	+	case Token::opNE:
613	+	match = propertyValue != comparisonValue;
614	+	break;
615	+	}
616	+	if (match)
617	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
618	+
619	+
620	+	}
621	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
622	+	int property, int comparator,
623	+	float comparisonValue, int frame) {
624	+	RealType propertyValue = 0.0;
625	+	Vector3d pos;
626	+	switch (property) {
627	+	case Token::mass:
628	+	propertyValue = sd->getMass();
629	+	break;
630	+	case Token::charge:
631	+	if (sd->isAtom()){
632	+	Atom* atom = static_cast<Atom*>(sd);
633	+	propertyValue = getCharge(atom,frame);
634	+	} else if (sd->isRigidBody()) {
635	+	RigidBody* rb = static_cast<RigidBody*>(sd);
636	+	RigidBody::AtomIterator ai;
637	+	Atom* atom;
638	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
639	+	propertyValue+=  getCharge(atom,frame);
640	+	}
641	+	}
642	+	break;
643	+	case Token::x:
644	+	propertyValue = sd->getPos(frame).x();
645	+	break;
646	+	case Token::y:
647	+	propertyValue = sd->getPos(frame).y();
648	+	break;
649	+	case Token::z:
650	+	propertyValue = sd->getPos(frame).z();
651	+	break;
652	+	case Token::wrappedX:
653	+	pos = sd->getPos(frame);
654	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
655	+	propertyValue = pos.x();
656	+	break;
657	+	case Token::wrappedY:
658	+	pos = sd->getPos(frame);
659	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
660	+	propertyValue = pos.y();
661	+	break;
662	+	case Token::wrappedZ:
663	+	pos = sd->getPos(frame);
664	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
665	+	propertyValue = pos.z();
666	+	break;
667	+
668	+	case Token::r:
669	+	propertyValue = sd->getPos(frame).length();
670	+	break;
671	+	default:
672	+	unrecognizedAtomProperty(property);
673	+	}
674	+
675	+	bool match = false;
676	+	switch (comparator) {
677	+	case Token::opLT:
678	+	match = propertyValue < comparisonValue;
679	+	break;
680	+	case Token::opLE:
681	+	match = propertyValue <= comparisonValue;
682	+	break;
683	+	case Token::opGE:
684	+	match = propertyValue >= comparisonValue;
685	+	break;
686	+	case Token::opGT:
687	+	match = propertyValue > comparisonValue;
688	+	break;
689	+	case Token::opEQ:
690	+	match = propertyValue == comparisonValue;
691	+	break;
692	+	case Token::opNE:
693	+	match = propertyValue != comparisonValue;
694	+	break;
695	+	}
696	+	if (match)
697	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
698	+
699	+
700	+	}
701	+
702	+
703	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
704	+	SelectionSet& bs){
705	+
706		boost::any withinSpec = instruction.value;
707		float distance;
708		if (withinSpec.type() == typeid(float)){
#	Line 300 | Line 717 | namespace oopse {
717		bs = distanceFinder.find(bs, distance);
718		}
719
720	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
721	+	SelectionSet& bs, int frame){
722	+
723	+	boost::any withinSpec = instruction.value;
724	+	float distance;
725	+	if (withinSpec.type() == typeid(float)){
726	+	distance = boost::any_cast<float>(withinSpec);
727	+	} else if (withinSpec.type() == typeid(int)) {
728	+	distance = boost::any_cast<int>(withinSpec);
729	+	} else {
730	+	evalError("casting error in withinInstruction");
731	+	bs.clearAll();
732	+	}
733	+
734	+	bs = distanceFinder.find(bs, distance, frame);
735	+	}
736	+
737		void SelectionEvaluator::define() {
738		assert(statement.size() >= 3);
739	<
739	>
740		std::string variable = boost::any_cast<std::string>(statement[1].value);
741	<
742	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
741	>
742	>	variables.insert(VariablesType::value_type(variable,
743	>	expression(statement, 2)));
744		}
745	+
746
311	–
747		/** @todo */
748		void SelectionEvaluator::predefine(const std::string& script) {
749	<
749	>
750		if (compiler.compile("#predefine", script)) {
751		std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
752		if (aatoken.size() != 1) {
#	Line 322 | Line 757 | namespace oopse {
757		std::vector<Token> statement = aatoken[0];
758		if (statement.size() > 2) {
759		int tok = statement[1].tok;
760	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
760	>	if (tok == Token::identifier ||
761	>	(tok & Token::predefinedset) == Token::predefinedset) {
762		std::string variable = boost::any_cast<std::string>(statement[1].value);
763		variables.insert(VariablesType::value_type(variable, statement));
764	<
764	>
765		} else {
766		evalError("invalid variable name:" + script);
767		}
768		}else {
769		evalError("bad predefinition length:" + script);
770	<	}
335	<
770	>	}
771
772		} else {
773		evalError("predefined set compile error:" + script +
774		"\ncompile error:" + compiler.getErrorMessage());
775		}
341	–
776		}
777
778	<	void SelectionEvaluator::select(OOPSEBitSet& bs){
778	>	void SelectionEvaluator::select(SelectionSet& bs){
779		bs = expression(statement, 1);
780		}
781
782	<	OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){
783	<
784	<	OOPSEBitSet bs(nStuntDouble);
782	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
783	>	bs = expression(statement, 1, frame);
784	>	}
785	>
786	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
787	>
788	>	SelectionSet bs = createSelectionSets();
789		std::map<std::string, boost::any>::iterator i = variables.find(variable);
790
791		if (i != variables.end()) {
792	<	if (i->second.type() == typeid(OOPSEBitSet)) {
793	<	return boost::any_cast<OOPSEBitSet>(i->second);
792	>	if (i->second.type() == typeid(SelectionSet)) {
793	>	return boost::any_cast<SelectionSet>(i->second);
794		} else if (i->second.type() ==  typeid(std::vector<Token>)){
795		bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
796		i->second =  bs; /**@todo fixme */
#	Line 361 | Line 799 | namespace oopse {
799		} else {
800		unrecognizedIdentifier(variable);
801		}
802	<
802	>
803		return bs;
804		}
805	<
806	<	OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){
807	<
370	<	return nameFinder.match(name);
371	<
805	>
806	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
807	>	return nameFinder.match(name);
808		}
809
810		bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
#	Line 378 | Line 814 | namespace oopse {
814		return true;
815		}
816		}
817	<
817	>
818		return false;
819		}
820
#	Line 388 | Line 824 | namespace oopse {
824		//predefine();
825		}
826
827	<	OOPSEBitSet SelectionEvaluator::evaluate() {
828	<	OOPSEBitSet bs(nStuntDouble);
827	>	SelectionSet SelectionEvaluator::createSelectionSets() {
828	>	SelectionSet ss(nObjects);
829	>	return ss;
830	>	}
831	>
832	>	SelectionSet SelectionEvaluator::evaluate() {
833	>	SelectionSet bs = createSelectionSets();
834		if (isLoaded_) {
835		pc = 0;
836		instructionDispatchLoop(bs);
837		}
838	+	return bs;
839	+	}
840
841	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
842	+	SelectionSet bs = createSelectionSets();
843	+	if (isLoaded_) {
844	+	pc = 0;
845	+	instructionDispatchLoop(bs, frame);
846	+	}
847		return bs;
848		}
849
850	<	OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	<	OOPSEBitSet bs(nStuntDouble);
850	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	>	SelectionSet bs = createSelectionSets();
852
853		if (value.type() == typeid(int)) {
854		int index = boost::any_cast<int>(value);
855	<	if (index < 0 || index >= bs.size()) {
855	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
856		invalidIndex(index);
857		} else {
858		bs = indexFinder.find(index);
#	Line 411 | Line 860 | namespace oopse {
860		} else if (value.type() == typeid(std::pair<int, int>)) {
861		std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
862		assert(indexRange.first <= indexRange.second);
863	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
863	>	if (indexRange.first < 0 ||
864	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
865		invalidIndexRange(indexRange);
866		}else {
867		bs = indexFinder.find(indexRange.first, indexRange.second);
#	Line 421 | Line 871 | namespace oopse {
871		return bs;
872		}
873
874	+	SelectionSet SelectionEvaluator::allInstruction() {
875	+	SelectionSet ss = createSelectionSets();
876
877	+	SimInfo::MoleculeIterator mi;
878	+	Molecule::AtomIterator ai;
879	+	Molecule::RigidBodyIterator rbIter;
880	+	Molecule::BondIterator bondIter;
881	+	Molecule::BendIterator bendIter;
882	+	Molecule::TorsionIterator torsionIter;
883	+	Molecule::InversionIterator inversionIter;
884	+
885	+	Molecule* mol;
886	+	Atom* atom;
887	+	RigidBody* rb;
888	+	Bond* bond;
889	+	Bend* bend;
890	+	Torsion* torsion;
891	+	Inversion* inversion;
892	+
893	+	// Doing the loop insures that we're actually on this processor.
894	+
895	+	for (mol = info->beginMolecule(mi); mol != NULL;
896	+	mol = info->nextMolecule(mi)) {
897	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
898	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
899	+	}
900	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
901	+	rb = mol->nextRigidBody(rbIter)) {
902	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
903	+	}
904	+	for (bond = mol->beginBond(bondIter); bond != NULL;
905	+	bond = mol->nextBond(bondIter)) {
906	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
907	+	}
908	+	for (bend = mol->beginBend(bendIter); bend != NULL;
909	+	bend = mol->nextBend(bendIter)) {
910	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
911	+	}
912	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
913	+	torsion = mol->nextTorsion(torsionIter)) {
914	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
915	+	}
916	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
917	+	inversion = mol->nextInversion(inversionIter)) {
918	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
919	+	}
920	+	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
921	+	}
922	+
923	+	return ss;
924	+	}
925	+
926	+	SelectionSet SelectionEvaluator::hull() {
927	+	SelectionSet bs = createSelectionSets();
928	+
929	+	bs = hullFinder.findHull();
930	+	surfaceArea_ = hullFinder.getSurfaceArea();
931	+	hasSurfaceArea_ = true;
932	+	return bs;
933	+	}
934	+
935	+
936	+	SelectionSet SelectionEvaluator::hull(int frame) {
937	+	SelectionSet bs = createSelectionSets();
938	+
939	+	bs = hullFinder.findHull(frame);
940	+
941	+	return bs;
942	+	}
943	+
944		RealType SelectionEvaluator::getCharge(Atom* atom) {
945	<	RealType charge =0.0;
945	>	RealType charge = 0.0;
946		AtomType* atomType = atom->getAtomType();
428	–	if (atomType->isCharge()) {
429	–	GenericData* data = atomType->getPropertyByName("Charge");
430	–	if (data != NULL) {
431	–	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
947
948	<	if (doubleData != NULL) {
949	<	charge = doubleData->getData();
950	<
436	<	} else {
437	<	sprintf( painCave.errMsg,
438	<	"Can not cast GenericData to DoubleGenericData\n");
439	<	painCave.severity = OOPSE_ERROR;
440	<	painCave.isFatal = 1;
441	<	simError();
442	<	}
443	<	}
948	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
949	>	if ( fca.isFixedCharge() ) {
950	>	charge = fca.getCharge();
951		}
952	+
953	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
954	+	if ( fqa.isFluctuatingCharge() ) {
955	+	charge += atom->getFlucQPos();
956	+	}
957	+	return charge;
958	+	}
959
960	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
961	+	RealType charge = 0.0;
962	+	AtomType* atomType = atom->getAtomType();
963	+
964	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
965	+	if ( fca.isFixedCharge() ) {
966	+	charge = fca.getCharge();
967	+	}
968	+
969	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
970	+	if ( fqa.isFluctuatingCharge() ) {
971	+	charge += atom->getFlucQPos(frame);
972	+	}
973		return charge;
974		}
975

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

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