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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 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/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	>	}
67	>
68	>	bool SelectionEvaluator::loadScript(const std::string& filename,
69	>	const std::string& script) {
70		clearDefinitionsAndLoadPredefined();
71		this->filename = filename;
72		this->script = script;
73		if (! compiler.compile(filename, script)) {
74	<	error = true;
75	<	errorMessage = compiler.getErrorMessage();
76	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
77	<	return false;
74	>	error = true;
75	>	errorMessage = compiler.getErrorMessage();
76	>
77	>	sprintf( painCave.errMsg,
78	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
79	>	painCave.severity = OPENMD_ERROR;
80	>	painCave.isFatal = 1;
81	>	simError();
82	>	return false;
83		}
84
85		pc = 0;
#	Line 75 | Line 91 | bool SelectionEvaluator::loadScript(const std::string&
91
92		isDynamic_ = false;
93		for (i = aatoken.begin(); i != aatoken.end(); ++i) {
94	<	if (containDynamicToken(*i)) {
95	<	isDynamic_ = true;
96	<	break;
97	<	}
94	>	if (containDynamicToken(*i)) {
95	>	isDynamic_ = true;
96	>	break;
97	>	}
98		}
99
100		isLoaded_ = true;
101		return true;
102	<	}
102	>	}
103
104	<	void SelectionEvaluator::clearState() {
89	<	//for (int i = scriptLevelMax; --i >= 0; )
90	<	//    stack[i].clear();
91	<	//scriptLevel = 0;
104	>	void SelectionEvaluator::clearState() {
105		error = false;
106		errorMessage = "";
107	<	}
107	>	}
108
109	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
109	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
110		clearState();
111		return loadScript("", script);
112	<	}
112	>	}
113
114	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
114	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
115		clearState();
116		return loadScriptFileInternal(filename);
117	<	}
117	>	}
118
119	<	bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
120	<	std::ifstream ifs(filename.c_str());
119	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
120	>	ifstrstream ifs(filename.c_str());
121		if (!ifs.is_open()) {
122	<	return false;
122	>	return false;
123		}
124	<
124	>
125		const int bufferSize = 65535;
126		char buffer[bufferSize];
127		std::string script;
128		while(ifs.getline(buffer, bufferSize)) {
129	<	script += buffer;
129	>	script += buffer;
130		}
131		return loadScript(filename, script);
132	<	}
133	<
134	<	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
132	>	}
133	>
134	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
135
136		while ( pc < aatoken.size()) {
137	<	statement = aatoken[pc++];
138	<	statementLength = statement.size();
139	<	Token token = statement[0];
140	<	switch (token.tok) {
141	<	case Token::define:
142	<	define();
143	<	break;
144	<	case Token::select:
145	<	select(bs);
146	<	break;
147	<	default:
148	<	unrecognizedCommand(token);
149	<	return;
150	<	}
137	>	statement = aatoken[pc++];
138	>	statementLength = statement.size();
139	>	Token token = statement[0];
140	>	switch (token.tok) {
141	>	case Token::define:
142	>	define();
143	>	break;
144	>	case Token::select:
145	>	select(bs);
146	>	break;
147	>	default:
148	>	unrecognizedCommand(token);
149	>	return;
150	>	}
151		}
152
153	<	}
153	>	}
154
155	<	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
143	<	BitSet bs;
144	<	std::stack<BitSet> stack;
155	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
156
157	<	for (int pc = pcStart; pc < code.size(); ++pc) {
157	>	while ( pc < aatoken.size()) {
158	>	statement = aatoken[pc++];
159	>	statementLength = statement.size();
160	>	Token token = statement[0];
161	>	switch (token.tok) {
162	>	case Token::define:
163	>	define();
164	>	break;
165	>	case Token::select:
166	>	select(bs, frame);
167	>	break;
168	>	default:
169	>	unrecognizedCommand(token);
170	>	return;
171	>	}
172	>	}
173	>
174	>	}
175	>
176	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
177	>	int pcStart) {
178	>	SelectionSet bs = createSelectionSets();
179	>	std::stack<SelectionSet> stack;
180	>	vector<int> bsSize = bs.size();
181	>
182	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
183		Token instruction = code[pc];
184
185		switch (instruction.tok) {
#	Line 152 | Line 188 | void SelectionEvaluator::instructionDispatchLoop(BitSe
188		case Token::expressionEnd:
189		break;
190		case Token::all:
191	<	bs = BitSet(nStuntDouble);
192	<	bs.setAll();
191	>	bs = allInstruction();
192	>	stack.push(bs);
193	>	break;
194	>	case Token::none:
195	>	bs = createSelectionSets();
196	>	stack.push(bs);
197	>	break;
198	>	case Token::opOr:
199	>	bs= stack.top();
200	>	stack.pop();
201	>	stack.top() |= bs;
202	>	break;
203	>	case Token::opAnd:
204	>	bs = stack.top();
205	>	stack.pop();
206	>	stack.top() &= bs;
207	>	break;
208	>	case Token::opNot:
209	>	stack.top().flip();
210	>	break;
211	>	case Token::within:
212	>	withinInstruction(instruction, stack.top());
213	>	break;
214	>	case Token::hull:
215	>	stack.push(hull());
216	>	break;
217	>	//case Token::selected:
218	>	//  stack.push(getSelectionSet());
219	>	//  break;
220	>	case Token::name:
221	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
222	>	break;
223	>	case Token::index:
224	>	stack.push(indexInstruction(instruction.value));
225	>	break;
226	>	case Token::identifier:
227	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
228	>	break;
229	>	case Token::opLT:
230	>	case Token::opLE:
231	>	case Token::opGE:
232	>	case Token::opGT:
233	>	case Token::opEQ:
234	>	case Token::opNE:
235	>	stack.push(comparatorInstruction(instruction));
236	>	break;
237	>	default:
238	>	unrecognizedExpression();
239	>	}
240	>	}
241	>	if (stack.size() != 1)
242	>	evalError("atom expression compiler error - stack over/underflow");
243	>
244	>	return stack.top();
245	>	}
246	>
247	>
248	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
249	>	int pcStart, int frame) {
250	>	SelectionSet bs = createSelectionSets();
251	>	std::stack<SelectionSet> stack;
252	>
253	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
254	>	Token instruction = code[pc];
255	>
256	>	switch (instruction.tok) {
257	>	case Token::expressionBegin:
258	>	break;
259	>	case Token::expressionEnd:
260	>	break;
261	>	case Token::all:
262	>	bs = allInstruction();
263		stack.push(bs);
264		break;
265		case Token::none:
266	<	bs = BitSet(nStuntDouble);
266	>	bs = SelectionSet(nObjects);
267		stack.push(bs);
268		break;
269		case Token::opOr:
#	Line 174 | Line 280 | void SelectionEvaluator::instructionDispatchLoop(BitSe
280		stack.top().flip();
281		break;
282		case Token::within:
283	<
178	<	withinInstruction(instruction, stack.top());
283	>	withinInstruction(instruction, stack.top(), frame);
284		break;
285	<	//case Token::selected:
286	<	//  stack.push(getSelectionSet());
287	<	//  break;
285	>	case Token::hull:
286	>	stack.push(hull(frame));
287	>	break;
288	>	//case Token::selected:
289	>	//  stack.push(getSelectionSet());
290	>	//  break;
291		case Token::name:
292		stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
293		break;
#	Line 195 | Line 303 | void SelectionEvaluator::instructionDispatchLoop(BitSe
303		case Token::opGT:
304		case Token::opEQ:
305		case Token::opNE:
306	<	stack.push(comparatorInstruction(instruction));
306	>	stack.push(comparatorInstruction(instruction, frame));
307		break;
308		default:
309		unrecognizedExpression();
#	Line 209 | Line 317 | void SelectionEvaluator::instructionDispatchLoop(BitSe
317
318
319
320	<	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
320	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
321		int comparator = instruction.tok;
322		int property = instruction.intValue;
323		float comparisonValue = boost::any_cast<float>(instruction.value);
324	<	float propertyValue;
217	<	BitSet bs(nStuntDouble);
324	>	SelectionSet bs = createSelectionSets();
325		bs.clearAll();
326
327		SimInfo::MoleculeIterator mi;
#	Line 223 | Line 330 | BitSet SelectionEvaluator::comparatorInstruction(const
330		Atom* atom;
331		Molecule::RigidBodyIterator rbIter;
332		RigidBody* rb;
333	+
334	+	for (mol = info->beginMolecule(mi); mol != NULL;
335	+	mol = info->nextMolecule(mi)) {
336	+
337	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
338	+	compareProperty(atom, bs, property, comparator, comparisonValue);
339	+	}
340	+
341	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
342	+	rb = mol->nextRigidBody(rbIter)) {
343	+	compareProperty(rb, bs, property, comparator, comparisonValue);
344	+	}
345	+	}
346	+
347	+	return bs;
348	+	}
349	+
350	+	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
351	+	int comparator = instruction.tok;
352	+	int property = instruction.intValue;
353	+	float comparisonValue = boost::any_cast<float>(instruction.value);
354	+	SelectionSet bs = createSelectionSets();
355	+	bs.clearAll();
356
357	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
357	>	SimInfo::MoleculeIterator mi;
358	>	Molecule* mol;
359	>	Molecule::AtomIterator ai;
360	>	Atom* atom;
361	>	Molecule::RigidBodyIterator rbIter;
362	>	RigidBody* rb;
363
364	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
365	<	compareProperty(atom, bs, property, comparator, comparisonValue);
366	<	}
367	<
368	<	//change the positions of atoms which belong to the rigidbodies
369	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
370	<	compareProperty(rb, bs, property, comparator, comparisonValue);
371	<	}
364	>	for (mol = info->beginMolecule(mi); mol != NULL;
365	>	mol = info->nextMolecule(mi)) {
366	>
367	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
368	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
369	>	}
370	>
371	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
372	>	rb = mol->nextRigidBody(rbIter)) {
373	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
374	>	}
375		}
376
377		return bs;
378	<	}
378	>	}
379
380	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
381	<	double propertyValue;
382	<	switch (property) {
383	<	case Token::mass:
384	<	propertyValue = sd->getMass();
385	<	break;
386	<	case Token::charge:
387	<	return;
388	<	//break;
389	<	case Token::dipole:
390	<	return;
391	<	//break;
392	<	default:
393	<	unrecognizedAtomProperty(property);
394	<	}
380	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
381	>	int property, int comparator,
382	>	float comparisonValue) {
383	>	RealType propertyValue = 0.0;
384	>	Vector3d pos;
385	>
386	>	switch (property) {
387	>	case Token::mass:
388	>	propertyValue = sd->getMass();
389	>	break;
390	>	case Token::charge:
391	>	if (sd->isAtom()){
392	>	Atom* atom = static_cast<Atom*>(sd);
393	>	propertyValue = getCharge(atom);
394	>	} else if (sd->isRigidBody()) {
395	>	RigidBody* rb = static_cast<RigidBody*>(sd);
396	>	RigidBody::AtomIterator ai;
397	>	Atom* atom;
398	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
399	>	propertyValue+=  getCharge(atom);
400	>	}
401	>	}
402	>	break;
403	>	case Token::x:
404	>	propertyValue = sd->getPos().x();
405	>	break;
406	>	case Token::y:
407	>	propertyValue = sd->getPos().y();
408	>	break;
409	>	case Token::z:
410	>	propertyValue = sd->getPos().z();
411	>	break;
412	>	case Token::wrappedX:
413	>	pos = sd->getPos();
414	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
415	>	propertyValue = pos.x();
416	>	break;
417	>	case Token::wrappedY:
418	>	pos = sd->getPos();
419	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	>	propertyValue = pos.y();
421	>	break;
422	>	case Token::wrappedZ:
423	>	pos = sd->getPos();
424	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	>	propertyValue = pos.z();
426	>	break;
427	>	case Token::r:
428	>	propertyValue = sd->getPos().length();
429	>	break;
430	>	default:
431	>	unrecognizedAtomProperty(property);
432	>	}
433
434	<	bool match = false;
435	<	switch (comparator) {
436	<	case Token::opLT:
437	<	match = propertyValue < comparisonValue;
438	<	break;
439	<	case Token::opLE:
440	<	match = propertyValue <= comparisonValue;
441	<	break;
442	<	case Token::opGE:
443	<	match = propertyValue >= comparisonValue;
444	<	break;
445	<	case Token::opGT:
446	<	match = propertyValue > comparisonValue;
447	<	break;
448	<	case Token::opEQ:
449	<	match = propertyValue == comparisonValue;
450	<	break;
451	<	case Token::opNE:
452	<	match = propertyValue != comparisonValue;
453	<	break;
454	<	}
279	<	if (match)
280	<	bs.setBitOn(sd->getGlobalIndex());
434	>	bool match = false;
435	>	switch (comparator) {
436	>	case Token::opLT:
437	>	match = propertyValue < comparisonValue;
438	>	break;
439	>	case Token::opLE:
440	>	match = propertyValue <= comparisonValue;
441	>	break;
442	>	case Token::opGE:
443	>	match = propertyValue >= comparisonValue;
444	>	break;
445	>	case Token::opGT:
446	>	match = propertyValue > comparisonValue;
447	>	break;
448	>	case Token::opEQ:
449	>	match = propertyValue == comparisonValue;
450	>	break;
451	>	case Token::opNE:
452	>	match = propertyValue != comparisonValue;
453	>	break;
454	>	}
455
456	<	}
456	>	if (match)
457	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
458
459	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
459	>
460	>	}
461	>
462	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
463	>	int property, int comparator,
464	>	float comparisonValue, int frame) {
465	>	RealType propertyValue = 0.0;
466	>	Vector3d pos;
467	>	switch (property) {
468	>	case Token::mass:
469	>	propertyValue = sd->getMass();
470	>	break;
471	>	case Token::charge:
472	>	if (sd->isAtom()){
473	>	Atom* atom = static_cast<Atom*>(sd);
474	>	propertyValue = getCharge(atom,frame);
475	>	} else if (sd->isRigidBody()) {
476	>	RigidBody* rb = static_cast<RigidBody*>(sd);
477	>	RigidBody::AtomIterator ai;
478	>	Atom* atom;
479	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
480	>	propertyValue+=  getCharge(atom,frame);
481	>	}
482	>	}
483	>	break;
484	>	case Token::x:
485	>	propertyValue = sd->getPos(frame).x();
486	>	break;
487	>	case Token::y:
488	>	propertyValue = sd->getPos(frame).y();
489	>	break;
490	>	case Token::z:
491	>	propertyValue = sd->getPos(frame).z();
492	>	break;
493	>	case Token::wrappedX:
494	>	pos = sd->getPos(frame);
495	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
496	>	propertyValue = pos.x();
497	>	break;
498	>	case Token::wrappedY:
499	>	pos = sd->getPos(frame);
500	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
501	>	propertyValue = pos.y();
502	>	break;
503	>	case Token::wrappedZ:
504	>	pos = sd->getPos(frame);
505	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
506	>	propertyValue = pos.z();
507	>	break;
508	>
509	>	case Token::r:
510	>	propertyValue = sd->getPos(frame).length();
511	>	break;
512	>	default:
513	>	unrecognizedAtomProperty(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	>	if (match)
538	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
539	>
540
541	+	}
542	+
543	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
544	+	SelectionSet& bs){
545	+
546		boost::any withinSpec = instruction.value;
547		float distance;
548		if (withinSpec.type() == typeid(float)){
549	<	distance = boost::any_cast<float>(withinSpec);
549	>	distance = boost::any_cast<float>(withinSpec);
550		} else if (withinSpec.type() == typeid(int)) {
551	<	distance = boost::any_cast<int>(withinSpec);
551	>	distance = boost::any_cast<int>(withinSpec);
552		} else {
553	<	evalError("casting error in withinInstruction");
554	<	bs.clearAll();
553	>	evalError("casting error in withinInstruction");
554	>	bs.clearAll();
555		}
556
557		bs = distanceFinder.find(bs, distance);
558	<	}
558	>	}
559
560	<	void SelectionEvaluator::define() {
560	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
561	>	SelectionSet& bs, int frame){
562	>
563	>	boost::any withinSpec = instruction.value;
564	>	float distance;
565	>	if (withinSpec.type() == typeid(float)){
566	>	distance = boost::any_cast<float>(withinSpec);
567	>	} else if (withinSpec.type() == typeid(int)) {
568	>	distance = boost::any_cast<int>(withinSpec);
569	>	} else {
570	>	evalError("casting error in withinInstruction");
571	>	bs.clearAll();
572	>	}
573	>
574	>	bs = distanceFinder.find(bs, distance, frame);
575	>	}
576	>
577	>	void SelectionEvaluator::define() {
578		assert(statement.size() >= 3);
579	<
579	>
580		std::string variable = boost::any_cast<std::string>(statement[1].value);
581	+
582	+	variables.insert(VariablesType::value_type(variable,
583	+	expression(statement, 2)));
584	+	}
585	+
586
587	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
588	<	}
589	<
308	<
309	<	/** @todo */
310	<	void SelectionEvaluator::predefine(const std::string& script) {
311	<
587	>	/** @todo */
588	>	void SelectionEvaluator::predefine(const std::string& script) {
589	>
590		if (compiler.compile("#predefine", script)) {
591	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
592	<	if (aatoken.size() != 1) {
593	<	evalError("predefinition does not have exactly 1 command:"
594	<	+ script);
595	<	return;
596	<	}
597	<	std::vector<Token> statement = aatoken[0];
598	<	if (statement.size() > 2) {
599	<	int tok = statement[1].tok;
600	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
601	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
602	<	variables.insert(VariablesType::value_type(variable, statement));
603	<
604	<	} else {
605	<	evalError("invalid variable name:" + script);
606	<	}
607	<	}else {
608	<	evalError("bad predefinition length:" + script);
609	<	}
610	<
591	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
592	>	if (aatoken.size() != 1) {
593	>	evalError("predefinition does not have exactly 1 command:"
594	>	+ script);
595	>	return;
596	>	}
597	>	std::vector<Token> statement = aatoken[0];
598	>	if (statement.size() > 2) {
599	>	int tok = statement[1].tok;
600	>	if (tok == Token::identifier ||
601	>	(tok & Token::predefinedset) == Token::predefinedset) {
602	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
603	>	variables.insert(VariablesType::value_type(variable, statement));
604	>
605	>	} else {
606	>	evalError("invalid variable name:" + script);
607	>	}
608	>	}else {
609	>	evalError("bad predefinition length:" + script);
610	>	}
611
612		} else {
613	<	evalError("predefined set compile error:" + script +
614	<	"\ncompile error:" + compiler.getErrorMessage());
613	>	evalError("predefined set compile error:" + script +
614	>	"\ncompile error:" + compiler.getErrorMessage());
615		}
616	+	}
617
618	<	}
340	<
341	<	void SelectionEvaluator::select(BitSet& bs){
618	>	void SelectionEvaluator::select(SelectionSet& bs){
619		bs = expression(statement, 1);
620	<	}
620	>	}
621
622	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
623	<
624	<	BitSet bs(nStuntDouble);
622	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
623	>	bs = expression(statement, 1, frame);
624	>	}
625	>
626	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
627	>
628	>	SelectionSet bs = createSelectionSets();
629		std::map<std::string, boost::any>::iterator i = variables.find(variable);
630
631		if (i != variables.end()) {
632	<	if (i->second.type() == typeid(BitSet)) {
633	<	return boost::any_cast<BitSet>(i->second);
634	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
635	<	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
636	<	i->second =  bs; /**@todo fixme */
637	<	return bs;
638	<	}
632	>	if (i->second.type() == typeid(SelectionSet)) {
633	>	return boost::any_cast<SelectionSet>(i->second);
634	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
635	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
636	>	i->second =  bs; /**@todo fixme */
637	>	return bs;
638	>	}
639		} else {
640	<	unrecognizedIdentifier(variable);
640	>	unrecognizedIdentifier(variable);
641		}
642	<
642	>
643		return bs;
644	<	}
644	>	}
645	>
646	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
647	>	return nameFinder.match(name);
648	>	}
649
650	<	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
366	<
367	<	return nameFinder.match(name);
368	<
369	<	}
370	<
371	<	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
650	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
651		std::vector<Token>::const_iterator i;
652		for (i = tokens.begin(); i != tokens.end(); ++i) {
653	<	if (i->tok & Token::dynamic) {
654	<	return true;
655	<	}
653	>	if (i->tok & Token::dynamic) {
654	>	return true;
655	>	}
656		}
657	<
657	>
658		return false;
659	<	}
659	>	}
660
661	<	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
661	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
662		variables.clear();
663		//load predefine
664		//predefine();
665	<	}
665	>	}
666
667	<	BitSet SelectionEvaluator::evaluate() {
668	<	BitSet bs(nStuntDouble);
667	>	SelectionSet SelectionEvaluator::createSelectionSets() {
668	>	SelectionSet ss(nObjects);
669	>	return ss;
670	>	}
671	>
672	>	SelectionSet SelectionEvaluator::evaluate() {
673	>	SelectionSet bs = createSelectionSets();
674		if (isLoaded_) {
675	<	pc = 0;
676	<	instructionDispatchLoop(bs);
675	>	pc = 0;
676	>	instructionDispatchLoop(bs);
677		}
678	+	return bs;
679	+	}
680
681	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
682	+	SelectionSet bs = createSelectionSets();
683	+	if (isLoaded_) {
684	+	pc = 0;
685	+	instructionDispatchLoop(bs, frame);
686	+	}
687		return bs;
688	<	}
688	>	}
689
690	<	BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
691	<	BitSet bs(nStuntDouble);
690	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
691	>	SelectionSet bs = createSelectionSets();
692
693		if (value.type() == typeid(int)) {
694	<	int index = boost::any_cast<int>(value);
695	<	if (index < 0 || index >= bs.size()) {
696	<	invalidIndex(index);
697	<	} else {
698	<	indexFinder.find(index);
699	<	}
694	>	int index = boost::any_cast<int>(value);
695	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
696	>	invalidIndex(index);
697	>	} else {
698	>	bs = indexFinder.find(index);
699	>	}
700		} else if (value.type() == typeid(std::pair<int, int>)) {
701	<	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
702	<	assert(indexRange.first <= indexRange.second);
703	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
704	<	invalidIndexRange(indexRange);
705	<	}else {
706	<	indexFinder.find(indexRange.first, indexRange.second);
707	<	}
701	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
702	>	assert(indexRange.first <= indexRange.second);
703	>	if (indexRange.first < 0 ||
704	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
705	>	invalidIndexRange(indexRange);
706	>	}else {
707	>	bs = indexFinder.find(indexRange.first, indexRange.second);
708	>	}
709		}
710
711		return bs;
712	<	}
712	>	}
713
714	+	SelectionSet SelectionEvaluator::allInstruction() {
715	+	SelectionSet ss = createSelectionSets();
716	+
717	+	SimInfo::MoleculeIterator mi;
718	+	Molecule::AtomIterator ai;
719	+	Molecule::RigidBodyIterator rbIter;
720	+	Molecule::BondIterator bondIter;
721	+	Molecule::BendIterator bendIter;
722	+	Molecule::TorsionIterator torsionIter;
723	+	Molecule::InversionIterator inversionIter;
724	+
725	+	Molecule* mol;
726	+	Atom* atom;
727	+	RigidBody* rb;
728	+	Bond* bond;
729	+	Bend* bend;
730	+	Torsion* torsion;
731	+	Inversion* inversion;
732	+
733	+	// Doing the loop insures that we're actually on this processor.
734	+
735	+	for (mol = info->beginMolecule(mi); mol != NULL;
736	+	mol = info->nextMolecule(mi)) {
737	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
738	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
739	+	}
740	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
741	+	rb = mol->nextRigidBody(rbIter)) {
742	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
743	+	}
744	+	for (bond = mol->beginBond(bondIter); bond != NULL;
745	+	bond = mol->nextBond(bondIter)) {
746	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
747	+	}
748	+	for (bend = mol->beginBend(bendIter); bend != NULL;
749	+	bend = mol->nextBend(bendIter)) {
750	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
751	+	}
752	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
753	+	torsion = mol->nextTorsion(torsionIter)) {
754	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
755	+	}
756	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
757	+	inversion = mol->nextInversion(inversionIter)) {
758	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
759	+	}
760	+	}
761	+
762	+	return ss;
763	+	}
764	+
765	+	SelectionSet SelectionEvaluator::hull() {
766	+	SelectionSet bs = createSelectionSets();
767	+
768	+	bs = hullFinder.findHull();
769	+	surfaceArea_ = hullFinder.getSurfaceArea();
770	+	hasSurfaceArea_ = true;
771	+	return bs;
772	+	}
773	+
774	+
775	+	SelectionSet SelectionEvaluator::hull(int frame) {
776	+	SelectionSet bs = createSelectionSets();
777	+
778	+	bs = hullFinder.findHull(frame);
779	+
780	+	return bs;
781	+	}
782	+
783	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
784	+	RealType charge = 0.0;
785	+	AtomType* atomType = atom->getAtomType();
786	+
787	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
788	+	if ( fca.isFixedCharge() ) {
789	+	charge = fca.getCharge();
790	+	}
791	+
792	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
793	+	if ( fqa.isFluctuatingCharge() ) {
794	+	charge += atom->getFlucQPos();
795	+	}
796	+	return charge;
797	+	}
798	+
799	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
800	+	RealType charge = 0.0;
801	+	AtomType* atomType = atom->getAtomType();
802	+
803	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
804	+	if ( fca.isFixedCharge() ) {
805	+	charge = fca.getCharge();
806	+	}
807	+
808	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
809	+	if ( fqa.isFluctuatingCharge() ) {
810	+	charge += atom->getFlucQPos(frame);
811	+	}
812	+	return charge;
813	+	}
814	+
815		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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