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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 2052 by gezelter, Fri Jan 9 19:06:35 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;
78	<	return false;
75	>	error = true;
76	>	errorMessage = compiler.getErrorMessage();
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
86		pc = 0;
#	Line 75 | Line 92 | bool SelectionEvaluator::loadScript(const std::string&
92
93		isDynamic_ = false;
94		for (i = aatoken.begin(); i != aatoken.end(); ++i) {
95	<	if (containDynamicToken(*i)) {
96	<	isDynamic_ = true;
97	<	break;
98	<	}
95	>	if (containDynamicToken(*i)) {
96	>	isDynamic_ = true;
97	>	break;
98	>	}
99		}
100
101		isLoaded_ = true;
102		return true;
103	<	}
103	>	}
104
105	<	void SelectionEvaluator::clearState() {
89	<	//for (int i = scriptLevelMax; --i >= 0; )
90	<	//    stack[i].clear();
91	<	//scriptLevel = 0;
105	>	void SelectionEvaluator::clearState() {
106		error = false;
107		errorMessage = "";
108	<	}
108	>	}
109
110	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
110	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
111		clearState();
112		return loadScript("", script);
113	<	}
113	>	}
114
115	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
115	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
116		clearState();
117		return loadScriptFileInternal(filename);
118	<	}
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;
123	>	return false;
124		}
125	<
125	>
126		const int bufferSize = 65535;
127		char buffer[bufferSize];
128		std::string script;
129		while(ifs.getline(buffer, bufferSize)) {
130	<	script += buffer;
130	>	script += buffer;
131		}
132		return loadScript(filename, script);
133	<	}
134	<
135	<	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
133	>	}
134	>
135	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
136
137		while ( pc < aatoken.size()) {
138	<	statement = aatoken[pc++];
139	<	statementLength = statement.size();
140	<	Token token = statement[0];
141	<	switch (token.tok) {
142	<	case Token::define:
143	<	define();
144	<	break;
145	<	case Token::select:
146	<	select(bs);
147	<	break;
148	<	default:
149	<	unrecognizedCommand(token);
150	<	return;
151	<	}
138	>	statement = aatoken[pc++];
139	>	statementLength = statement.size();
140	>	Token token = statement[0];
141	>	switch (token.tok) {
142	>	case Token::define:
143	>	define();
144	>	break;
145	>	case Token::select:
146	>	select(bs);
147	>	break;
148	>	default:
149	>	unrecognizedCommand(token);
150	>	return;
151	>	}
152		}
153
154	<	}
154	>	}
155
156	<	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
143	<	BitSet bs;
144	<	std::stack<BitSet> 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 152 | Line 189 | void SelectionEvaluator::instructionDispatchLoop(BitSe
189		case Token::expressionEnd:
190		break;
191		case Token::all:
192	<	bs = BitSet(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 = BitSet(nStuntDouble);
267	>	bs = SelectionSet(nObjects);
268		stack.push(bs);
269		break;
270		case Token::opOr:
#	Line 174 | Line 281 | void SelectionEvaluator::instructionDispatchLoop(BitSe
281		stack.top().flip();
282		break;
283		case Token::within:
284	<
178	<	withinInstruction(instruction, stack.top());
284	>	withinInstruction(instruction, stack.top(), frame);
285		break;
286	<	//case Token::selected:
287	<	//  stack.push(getSelectionSet());
288	<	//  break;
286	>	case Token::hull:
287	>	stack.push(hull(frame));
288	>	break;
289	>	//case Token::selected:
290	>	//  stack.push(getSelectionSet());
291	>	//  break;
292		case Token::name:
293		stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
294		break;
#	Line 195 | Line 304 | void SelectionEvaluator::instructionDispatchLoop(BitSe
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 209 | Line 318 | void SelectionEvaluator::instructionDispatchLoop(BitSe
318
319
320
321	<	BitSet 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;
217	<	BitSet bs(nStuntDouble);
325	>	SelectionSet bs = createSelectionSets();
326		bs.clearAll();
327
328		SimInfo::MoleculeIterator mi;
#	Line 223 | Line 331 | BitSet SelectionEvaluator::comparatorInstruction(const
331		Atom* atom;
332		Molecule::RigidBodyIterator rbIter;
333		RigidBody* rb;
334	+
335	+	for (mol = info->beginMolecule(mi); mol != NULL;
336	+	mol = info->nextMolecule(mi)) {
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;
343	+	rb = mol->nextRigidBody(rbIter)) {
344	+	compareProperty(rb, bs, property, comparator, comparisonValue);
345	+	}
346	+	}
347	+
348	+	return bs;
349	+	}
350	+
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	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
358	>	SimInfo::MoleculeIterator mi;
359	>	Molecule* mol;
360	>	Molecule::AtomIterator ai;
361	>	Atom* atom;
362	>	Molecule::RigidBodyIterator rbIter;
363	>	RigidBody* rb;
364
365	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
366	<	compareProperty(atom, bs, property, comparator, comparisonValue);
367	<	}
368	<
369	<	//change the positions of atoms which belong to the rigidbodies
370	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
371	<	compareProperty(rb, bs, property, comparator, comparisonValue);
372	<	}
365	>	for (mol = info->beginMolecule(mi); mol != NULL;
366	>	mol = info->nextMolecule(mi)) {
367	>
368	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
369	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
370	>	}
371	>
372	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
373	>	rb = mol->nextRigidBody(rbIter)) {
374	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
375	>	}
376		}
377
378		return bs;
379	<	}
379	>	}
380
381	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
382	<	double propertyValue;
383	<	switch (property) {
384	<	case Token::mass:
385	<	propertyValue = sd->getMass();
386	<	break;
387	<	case Token::charge:
388	<	return;
389	<	//break;
390	<	case Token::dipole:
391	<	return;
392	<	//break;
393	<	default:
394	<	unrecognizedAtomProperty(property);
395	<	}
381	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
382	>	int property, int comparator,
383	>	float comparisonValue) {
384	>	RealType propertyValue = 0.0;
385	>	Vector3d pos;
386	>
387	>	switch (property) {
388	>	case Token::mass:
389	>	propertyValue = sd->getMass();
390	>	break;
391	>	case Token::charge:
392	>	if (sd->isAtom()){
393	>	Atom* atom = static_cast<Atom*>(sd);
394	>	propertyValue = getCharge(atom);
395	>	} else if (sd->isRigidBody()) {
396	>	RigidBody* rb = static_cast<RigidBody*>(sd);
397	>	RigidBody::AtomIterator ai;
398	>	Atom* atom;
399	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
400	>	propertyValue+=  getCharge(atom);
401	>	}
402	>	}
403	>	break;
404	>	case Token::x:
405	>	propertyValue = sd->getPos().x();
406	>	break;
407	>	case Token::y:
408	>	propertyValue = sd->getPos().y();
409	>	break;
410	>	case Token::z:
411	>	propertyValue = sd->getPos().z();
412	>	break;
413	>	case Token::wrappedX:
414	>	pos = sd->getPos();
415	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
416	>	propertyValue = pos.x();
417	>	break;
418	>	case Token::wrappedY:
419	>	pos = sd->getPos();
420	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
421	>	propertyValue = pos.y();
422	>	break;
423	>	case Token::wrappedZ:
424	>	pos = sd->getPos();
425	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
426	>	propertyValue = pos.z();
427	>	break;
428	>	case Token::r:
429	>	propertyValue = sd->getPos().length();
430	>	break;
431	>	default:
432	>	unrecognizedAtomProperty(property);
433	>	}
434
435	<	bool match = false;
436	<	switch (comparator) {
437	<	case Token::opLT:
438	<	match = propertyValue < comparisonValue;
439	<	break;
440	<	case Token::opLE:
441	<	match = propertyValue <= comparisonValue;
442	<	break;
443	<	case Token::opGE:
444	<	match = propertyValue >= comparisonValue;
445	<	break;
446	<	case Token::opGT:
447	<	match = propertyValue > comparisonValue;
448	<	break;
449	<	case Token::opEQ:
450	<	match = propertyValue == comparisonValue;
451	<	break;
452	<	case Token::opNE:
453	<	match = propertyValue != comparisonValue;
454	<	break;
455	<	}
279	<	if (match)
280	<	bs.setBitOn(sd->getGlobalIndex());
435	>	bool match = false;
436	>	switch (comparator) {
437	>	case Token::opLT:
438	>	match = propertyValue < comparisonValue;
439	>	break;
440	>	case Token::opLE:
441	>	match = propertyValue <= comparisonValue;
442	>	break;
443	>	case Token::opGE:
444	>	match = propertyValue >= comparisonValue;
445	>	break;
446	>	case Token::opGT:
447	>	match = propertyValue > comparisonValue;
448	>	break;
449	>	case Token::opEQ:
450	>	match = propertyValue == comparisonValue;
451	>	break;
452	>	case Token::opNE:
453	>	match = propertyValue != comparisonValue;
454	>	break;
455	>	}
456
457	<	}
457	>	if (match)
458	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
459
460	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
460	>
461	>	}
462	>
463	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
464	>	int property, int comparator,
465	>	float comparisonValue, int frame) {
466	>	RealType propertyValue = 0.0;
467	>	Vector3d pos;
468	>	switch (property) {
469	>	case Token::mass:
470	>	propertyValue = sd->getMass();
471	>	break;
472	>	case Token::charge:
473	>	if (sd->isAtom()){
474	>	Atom* atom = static_cast<Atom*>(sd);
475	>	propertyValue = getCharge(atom,frame);
476	>	} else if (sd->isRigidBody()) {
477	>	RigidBody* rb = static_cast<RigidBody*>(sd);
478	>	RigidBody::AtomIterator ai;
479	>	Atom* atom;
480	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
481	>	propertyValue+=  getCharge(atom,frame);
482	>	}
483	>	}
484	>	break;
485	>	case Token::x:
486	>	propertyValue = sd->getPos(frame).x();
487	>	break;
488	>	case Token::y:
489	>	propertyValue = sd->getPos(frame).y();
490	>	break;
491	>	case Token::z:
492	>	propertyValue = sd->getPos(frame).z();
493	>	break;
494	>	case Token::wrappedX:
495	>	pos = sd->getPos(frame);
496	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
497	>	propertyValue = pos.x();
498	>	break;
499	>	case Token::wrappedY:
500	>	pos = sd->getPos(frame);
501	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
502	>	propertyValue = pos.y();
503	>	break;
504	>	case Token::wrappedZ:
505	>	pos = sd->getPos(frame);
506	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
507	>	propertyValue = pos.z();
508	>	break;
509	>
510	>	case Token::r:
511	>	propertyValue = sd->getPos(frame).length();
512	>	break;
513	>	default:
514	>	unrecognizedAtomProperty(property);
515	>	}
516	>
517	>	bool match = false;
518	>	switch (comparator) {
519	>	case Token::opLT:
520	>	match = propertyValue < comparisonValue;
521	>	break;
522	>	case Token::opLE:
523	>	match = propertyValue <= comparisonValue;
524	>	break;
525	>	case Token::opGE:
526	>	match = propertyValue >= comparisonValue;
527	>	break;
528	>	case Token::opGT:
529	>	match = propertyValue > comparisonValue;
530	>	break;
531	>	case Token::opEQ:
532	>	match = propertyValue == comparisonValue;
533	>	break;
534	>	case Token::opNE:
535	>	match = propertyValue != comparisonValue;
536	>	break;
537	>	}
538	>	if (match)
539	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
540	>
541
542	+	}
543	+
544	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
545	+	SelectionSet& bs){
546	+
547		boost::any withinSpec = instruction.value;
548		float distance;
549		if (withinSpec.type() == typeid(float)){
550	<	distance = boost::any_cast<float>(withinSpec);
550	>	distance = boost::any_cast<float>(withinSpec);
551		} else if (withinSpec.type() == typeid(int)) {
552	<	distance = boost::any_cast<int>(withinSpec);
552	>	distance = boost::any_cast<int>(withinSpec);
553		} else {
554	<	evalError("casting error in withinInstruction");
555	<	bs.clearAll();
554	>	evalError("casting error in withinInstruction");
555	>	bs.clearAll();
556		}
557
558		bs = distanceFinder.find(bs, distance);
559	<	}
559	>	}
560
561	<	void SelectionEvaluator::define() {
561	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
562	>	SelectionSet& bs, int frame){
563	>
564	>	boost::any withinSpec = instruction.value;
565	>	float distance;
566	>	if (withinSpec.type() == typeid(float)){
567	>	distance = boost::any_cast<float>(withinSpec);
568	>	} else if (withinSpec.type() == typeid(int)) {
569	>	distance = boost::any_cast<int>(withinSpec);
570	>	} else {
571	>	evalError("casting error in withinInstruction");
572	>	bs.clearAll();
573	>	}
574	>
575	>	bs = distanceFinder.find(bs, distance, frame);
576	>	}
577	>
578	>	void SelectionEvaluator::define() {
579		assert(statement.size() >= 3);
580	<
580	>
581		std::string variable = boost::any_cast<std::string>(statement[1].value);
582	+
583	+	variables.insert(VariablesType::value_type(variable,
584	+	expression(statement, 2)));
585	+	}
586	+
587
588	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
589	<	}
590	<
308	<
309	<	/** @todo */
310	<	void SelectionEvaluator::predefine(const std::string& script) {
311	<
588	>	/** @todo */
589	>	void SelectionEvaluator::predefine(const std::string& script) {
590	>
591		if (compiler.compile("#predefine", script)) {
592	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
593	<	if (aatoken.size() != 1) {
594	<	evalError("predefinition does not have exactly 1 command:"
595	<	+ script);
596	<	return;
597	<	}
598	<	std::vector<Token> statement = aatoken[0];
599	<	if (statement.size() > 2) {
600	<	int tok = statement[1].tok;
601	<	if (tok == Token::identifier || (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	<
592	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
593	>	if (aatoken.size() != 1) {
594	>	evalError("predefinition does not have exactly 1 command:"
595	>	+ script);
596	>	return;
597	>	}
598	>	std::vector<Token> statement = aatoken[0];
599	>	if (statement.size() > 2) {
600	>	int tok = statement[1].tok;
601	>	if (tok == Token::identifier ||
602	>	(tok & Token::predefinedset) == Token::predefinedset) {
603	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
604	>	variables.insert(VariablesType::value_type(variable, statement));
605	>
606	>	} else {
607	>	evalError("invalid variable name:" + script);
608	>	}
609	>	}else {
610	>	evalError("bad predefinition length:" + script);
611	>	}
612
613		} else {
614	<	evalError("predefined set compile error:" + script +
615	<	"\ncompile error:" + compiler.getErrorMessage());
614	>	evalError("predefined set compile error:" + script +
615	>	"\ncompile error:" + compiler.getErrorMessage());
616		}
617	+	}
618
619	<	}
340	<
341	<	void SelectionEvaluator::select(BitSet& bs){
619	>	void SelectionEvaluator::select(SelectionSet& bs){
620		bs = expression(statement, 1);
621	<	}
621	>	}
622
623	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
624	<
625	<	BitSet bs(nStuntDouble);
623	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
624	>	bs = expression(statement, 1, frame);
625	>	}
626	>
627	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
628	>
629	>	SelectionSet bs = createSelectionSets();
630		std::map<std::string, boost::any>::iterator i = variables.find(variable);
631
632		if (i != variables.end()) {
633	<	if (i->second.type() == typeid(BitSet)) {
634	<	return boost::any_cast<BitSet>(i->second);
635	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
636	<	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
637	<	i->second =  bs; /**@todo fixme */
638	<	return bs;
639	<	}
633	>	if (i->second.type() == typeid(SelectionSet)) {
634	>	return boost::any_cast<SelectionSet>(i->second);
635	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
636	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
637	>	i->second =  bs; /**@todo fixme */
638	>	return bs;
639	>	}
640		} else {
641	<	unrecognizedIdentifier(variable);
641	>	unrecognizedIdentifier(variable);
642		}
643	<
643	>
644		return bs;
645	<	}
645	>	}
646	>
647	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
648	>	return nameFinder.match(name);
649	>	}
650
651	<	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){
651	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
652		std::vector<Token>::const_iterator i;
653		for (i = tokens.begin(); i != tokens.end(); ++i) {
654	<	if (i->tok & Token::dynamic) {
655	<	return true;
656	<	}
654	>	if (i->tok & Token::dynamic) {
655	>	return true;
656	>	}
657		}
658	<
658	>
659		return false;
660	<	}
660	>	}
661
662	<	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
662	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
663		variables.clear();
664		//load predefine
665		//predefine();
666	<	}
666	>	}
667
668	<	BitSet SelectionEvaluator::evaluate() {
669	<	BitSet bs(nStuntDouble);
668	>	SelectionSet SelectionEvaluator::createSelectionSets() {
669	>	SelectionSet ss(nObjects);
670	>	return ss;
671	>	}
672	>
673	>	SelectionSet SelectionEvaluator::evaluate() {
674	>	SelectionSet bs = createSelectionSets();
675		if (isLoaded_) {
676	<	pc = 0;
677	<	instructionDispatchLoop(bs);
676	>	pc = 0;
677	>	instructionDispatchLoop(bs);
678		}
679	+	return bs;
680	+	}
681
682	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
683	+	SelectionSet bs = createSelectionSets();
684	+	if (isLoaded_) {
685	+	pc = 0;
686	+	instructionDispatchLoop(bs, frame);
687	+	}
688		return bs;
689	<	}
689	>	}
690
691	<	BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
692	<	BitSet bs(nStuntDouble);
691	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
692	>	SelectionSet bs = createSelectionSets();
693
694		if (value.type() == typeid(int)) {
695	<	int index = boost::any_cast<int>(value);
696	<	if (index < 0 || index >= bs.size()) {
697	<	invalidIndex(index);
698	<	} else {
699	<	indexFinder.find(index);
700	<	}
695	>	int index = boost::any_cast<int>(value);
696	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
697	>	invalidIndex(index);
698	>	} else {
699	>	bs = indexFinder.find(index);
700	>	}
701		} else if (value.type() == typeid(std::pair<int, int>)) {
702	<	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
703	<	assert(indexRange.first <= indexRange.second);
704	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
705	<	invalidIndexRange(indexRange);
706	<	}else {
707	<	indexFinder.find(indexRange.first, indexRange.second);
708	<	}
702	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
703	>	assert(indexRange.first <= indexRange.second);
704	>	if (indexRange.first < 0 ||
705	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
706	>	invalidIndexRange(indexRange);
707	>	}else {
708	>	bs = indexFinder.find(indexRange.first, indexRange.second);
709	>	}
710		}
711
712		return bs;
713	<	}
713	>	}
714
715	+	SelectionSet SelectionEvaluator::allInstruction() {
716	+	SelectionSet ss = createSelectionSets();
717	+
718	+	SimInfo::MoleculeIterator mi;
719	+	Molecule::AtomIterator ai;
720	+	Molecule::RigidBodyIterator rbIter;
721	+	Molecule::BondIterator bondIter;
722	+	Molecule::BendIterator bendIter;
723	+	Molecule::TorsionIterator torsionIter;
724	+	Molecule::InversionIterator inversionIter;
725	+
726	+	Molecule* mol;
727	+	Atom* atom;
728	+	RigidBody* rb;
729	+	Bond* bond;
730	+	Bend* bend;
731	+	Torsion* torsion;
732	+	Inversion* inversion;
733	+
734	+	// Doing the loop insures that we're actually on this processor.
735	+
736	+	for (mol = info->beginMolecule(mi); mol != NULL;
737	+	mol = info->nextMolecule(mi)) {
738	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
739	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
740	+	}
741	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
742	+	rb = mol->nextRigidBody(rbIter)) {
743	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
744	+	}
745	+	for (bond = mol->beginBond(bondIter); bond != NULL;
746	+	bond = mol->nextBond(bondIter)) {
747	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
748	+	}
749	+	for (bend = mol->beginBend(bendIter); bend != NULL;
750	+	bend = mol->nextBend(bendIter)) {
751	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
752	+	}
753	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
754	+	torsion = mol->nextTorsion(torsionIter)) {
755	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
756	+	}
757	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
758	+	inversion = mol->nextInversion(inversionIter)) {
759	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
760	+	}
761	+	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
762	+	}
763	+
764	+	return ss;
765	+	}
766	+
767	+	SelectionSet SelectionEvaluator::hull() {
768	+	SelectionSet bs = createSelectionSets();
769	+
770	+	bs = hullFinder.findHull();
771	+	surfaceArea_ = hullFinder.getSurfaceArea();
772	+	hasSurfaceArea_ = true;
773	+	return bs;
774	+	}
775	+
776	+
777	+	SelectionSet SelectionEvaluator::hull(int frame) {
778	+	SelectionSet bs = createSelectionSets();
779	+
780	+	bs = hullFinder.findHull(frame);
781	+
782	+	return bs;
783	+	}
784	+
785	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
786	+	RealType charge = 0.0;
787	+	AtomType* atomType = atom->getAtomType();
788	+
789	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
790	+	if ( fca.isFixedCharge() ) {
791	+	charge = fca.getCharge();
792	+	}
793	+
794	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
795	+	if ( fqa.isFluctuatingCharge() ) {
796	+	charge += atom->getFlucQPos();
797	+	}
798	+	return charge;
799	+	}
800	+
801	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
802	+	RealType charge = 0.0;
803	+	AtomType* atomType = atom->getAtomType();
804	+
805	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
806	+	if ( fca.isFixedCharge() ) {
807	+	charge = fca.getCharge();
808	+	}
809	+
810	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
811	+	if ( fqa.isFluctuatingCharge() ) {
812	+	charge += atom->getFlucQPos(frame);
813	+	}
814	+	return charge;
815	+	}
816	+
817		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

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