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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 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stack>
#	Line 45 | Line 46
46		#include "primitives/DirectionalAtom.hpp"
47		#include "primitives/RigidBody.hpp"
48		#include "primitives/Molecule.hpp"
49	+	#include "io/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	>	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
62	>	}
63	>
64	>	bool SelectionEvaluator::loadScript(const std::string& filename,
65	>	const std::string& script) {
66		clearDefinitionsAndLoadPredefined();
67		this->filename = filename;
68		this->script = script;
69		if (! compiler.compile(filename, script)) {
70	<	error = true;
71	<	errorMessage = compiler.getErrorMessage();
72	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
73	<	return false;
70	>	error = true;
71	>	errorMessage = compiler.getErrorMessage();
72	>
73	>	sprintf( painCave.errMsg,
74	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
75	>	painCave.severity = OPENMD_ERROR;
76	>	painCave.isFatal = 1;
77	>	simError();
78	>	return false;
79		}
80
81		pc = 0;
#	Line 75 | Line 87 | bool SelectionEvaluator::loadScript(const std::string&
87
88		isDynamic_ = false;
89		for (i = aatoken.begin(); i != aatoken.end(); ++i) {
90	<	if (containDynamicToken(*i)) {
91	<	isDynamic_ = true;
92	<	break;
93	<	}
90	>	if (containDynamicToken(*i)) {
91	>	isDynamic_ = true;
92	>	break;
93	>	}
94		}
95
96		isLoaded_ = true;
97		return true;
98	<	}
98	>	}
99
100	<	void SelectionEvaluator::clearState() {
89	<	//for (int i = scriptLevelMax; --i >= 0; )
90	<	//    stack[i].clear();
91	<	//scriptLevel = 0;
100	>	void SelectionEvaluator::clearState() {
101		error = false;
102		errorMessage = "";
103	<	}
103	>	}
104
105	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
105	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
106		clearState();
107		return loadScript("", script);
108	<	}
108	>	}
109
110	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
110	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
111		clearState();
112		return loadScriptFileInternal(filename);
113	<	}
113	>	}
114
115	<	bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
116	<	std::ifstream ifs(filename.c_str());
115	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
116	>	ifstrstream ifs(filename.c_str());
117		if (!ifs.is_open()) {
118	<	return false;
118	>	return false;
119		}
120	<
120	>
121		const int bufferSize = 65535;
122		char buffer[bufferSize];
123		std::string script;
124		while(ifs.getline(buffer, bufferSize)) {
125	<	script += buffer;
125	>	script += buffer;
126		}
127		return loadScript(filename, script);
128	<	}
129	<
130	<	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
128	>	}
129	>
130	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
131
132		while ( pc < aatoken.size()) {
133	<	statement = aatoken[pc++];
134	<	statementLength = statement.size();
135	<	Token token = statement[0];
136	<	switch (token.tok) {
137	<	case Token::define:
138	<	define();
139	<	break;
140	<	case Token::select:
141	<	select(bs);
142	<	break;
143	<	default:
144	<	unrecognizedCommand(token);
145	<	return;
146	<	}
133	>	statement = aatoken[pc++];
134	>	statementLength = statement.size();
135	>	Token token = statement[0];
136	>	switch (token.tok) {
137	>	case Token::define:
138	>	define();
139	>	break;
140	>	case Token::select:
141	>	select(bs);
142	>	break;
143	>	default:
144	>	unrecognizedCommand(token);
145	>	return;
146	>	}
147		}
148
149	<	}
149	>	}
150
151	<	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
143	<	BitSet bs;
144	<	std::stack<BitSet> stack;
151	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs, int frame){
152
153	<	for (int pc = pcStart; pc < code.size(); ++pc) {
153	>	while ( pc < aatoken.size()) {
154	>	statement = aatoken[pc++];
155	>	statementLength = statement.size();
156	>	Token token = statement[0];
157	>	switch (token.tok) {
158	>	case Token::define:
159	>	define();
160	>	break;
161	>	case Token::select:
162	>	select(bs, frame);
163	>	break;
164	>	default:
165	>	unrecognizedCommand(token);
166	>	return;
167	>	}
168	>	}
169	>
170	>	}
171	>
172	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
173	>	int pcStart) {
174	>	OpenMDBitSet bs;
175	>	std::stack<OpenMDBitSet> stack;
176	>
177	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
178		Token instruction = code[pc];
179
180		switch (instruction.tok) {
#	Line 152 | Line 183 | void SelectionEvaluator::instructionDispatchLoop(BitSe
183		case Token::expressionEnd:
184		break;
185		case Token::all:
186	<	bs = BitSet(nStuntDouble);
156	<	bs.setAll();
186	>	bs = allInstruction();
187		stack.push(bs);
188		break;
189		case Token::none:
190	<	bs = BitSet(nStuntDouble);
190	>	bs = OpenMDBitSet(nStuntDouble);
191		stack.push(bs);
192		break;
193		case Token::opOr:
#	Line 174 | Line 204 | void SelectionEvaluator::instructionDispatchLoop(BitSe
204		stack.top().flip();
205		break;
206		case Token::within:
177	–
207		withinInstruction(instruction, stack.top());
208		break;
209	<	//case Token::selected:
210	<	//  stack.push(getSelectionSet());
211	<	//  break;
209	>	case Token::hull:
210	>	stack.push(hull());
211	>	break;
212	>	//case Token::selected:
213	>	//  stack.push(getSelectionSet());
214	>	//  break;
215		case Token::name:
216		stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
217		break;
#	Line 208 | Line 240 | void SelectionEvaluator::instructionDispatchLoop(BitSe
240		}
241
242
243	+	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
244	+	int pcStart, int frame) {
245	+	OpenMDBitSet bs;
246	+	std::stack<OpenMDBitSet> stack;
247	+
248	+	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
249	+	Token instruction = code[pc];
250
251	<	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
251	>	switch (instruction.tok) {
252	>	case Token::expressionBegin:
253	>	break;
254	>	case Token::expressionEnd:
255	>	break;
256	>	case Token::all:
257	>	bs = allInstruction();
258	>	stack.push(bs);
259	>	break;
260	>	case Token::none:
261	>	bs = OpenMDBitSet(nStuntDouble);
262	>	stack.push(bs);
263	>	break;
264	>	case Token::opOr:
265	>	bs = stack.top();
266	>	stack.pop();
267	>	stack.top() |= bs;
268	>	break;
269	>	case Token::opAnd:
270	>	bs = stack.top();
271	>	stack.pop();
272	>	stack.top() &= bs;
273	>	break;
274	>	case Token::opNot:
275	>	stack.top().flip();
276	>	break;
277	>	case Token::within:
278	>	withinInstruction(instruction, stack.top(), frame);
279	>	break;
280	>	case Token::hull:
281	>	stack.push(hull(frame));
282	>	break;
283	>	//case Token::selected:
284	>	//  stack.push(getSelectionSet());
285	>	//  break;
286	>	case Token::name:
287	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
288	>	break;
289	>	case Token::index:
290	>	stack.push(indexInstruction(instruction.value));
291	>	break;
292	>	case Token::identifier:
293	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
294	>	break;
295	>	case Token::opLT:
296	>	case Token::opLE:
297	>	case Token::opGE:
298	>	case Token::opGT:
299	>	case Token::opEQ:
300	>	case Token::opNE:
301	>	stack.push(comparatorInstruction(instruction, frame));
302	>	break;
303	>	default:
304	>	unrecognizedExpression();
305	>	}
306	>	}
307	>	if (stack.size() != 1)
308	>	evalError("atom expression compiler error - stack over/underflow");
309	>
310	>	return stack.top();
311	>	}
312	>
313	>
314	>
315	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
316		int comparator = instruction.tok;
317		int property = instruction.intValue;
318		float comparisonValue = boost::any_cast<float>(instruction.value);
319	<	float propertyValue;
217	<	BitSet bs(nStuntDouble);
319	>	OpenMDBitSet bs(nStuntDouble);
320		bs.clearAll();
321
322		SimInfo::MoleculeIterator mi;
#	Line 223 | Line 325 | BitSet SelectionEvaluator::comparatorInstruction(const
325		Atom* atom;
326		Molecule::RigidBodyIterator rbIter;
327		RigidBody* rb;
328	+
329	+	for (mol = info->beginMolecule(mi); mol != NULL;
330	+	mol = info->nextMolecule(mi)) {
331	+
332	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
333	+	compareProperty(atom, bs, property, comparator, comparisonValue);
334	+	}
335	+
336	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
337	+	rb = mol->nextRigidBody(rbIter)) {
338	+	compareProperty(rb, bs, property, comparator, comparisonValue);
339	+	}
340	+	}
341	+
342	+	return bs;
343	+	}
344	+
345	+	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
346	+	int comparator = instruction.tok;
347	+	int property = instruction.intValue;
348	+	float comparisonValue = boost::any_cast<float>(instruction.value);
349	+	OpenMDBitSet bs(nStuntDouble);
350	+	bs.clearAll();
351
352	<	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
352	>	SimInfo::MoleculeIterator mi;
353	>	Molecule* mol;
354	>	Molecule::AtomIterator ai;
355	>	Atom* atom;
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358
359	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
360	<	compareProperty(atom, bs, property, comparator, comparisonValue);
361	<	}
362	<
363	<	//change the positions of atoms which belong to the rigidbodies
364	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
365	<	compareProperty(rb, bs, property, comparator, comparisonValue);
366	<	}
359	>	for (mol = info->beginMolecule(mi); mol != NULL;
360	>	mol = info->nextMolecule(mi)) {
361	>
362	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
363	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
364	>	}
365	>
366	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
367	>	rb = mol->nextRigidBody(rbIter)) {
368	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
369	>	}
370		}
371
372		return bs;
373	<	}
373	>	}
374
375	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
376	<	double propertyValue;
377	<	switch (property) {
378	<	case Token::mass:
379	<	propertyValue = sd->getMass();
380	<	break;
381	<	case Token::charge:
382	<	return;
383	<	//break;
384	<	case Token::dipole:
385	<	return;
386	<	//break;
387	<	default:
388	<	unrecognizedAtomProperty(property);
389	<	}
375	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
376	>	int property, int comparator,
377	>	float comparisonValue) {
378	>	RealType propertyValue = 0.0;
379	>	Vector3d pos;
380	>
381	>	switch (property) {
382	>	case Token::mass:
383	>	propertyValue = sd->getMass();
384	>	break;
385	>	case Token::charge:
386	>	if (sd->isAtom()){
387	>	Atom* atom = static_cast<Atom*>(sd);
388	>	propertyValue = getCharge(atom);
389	>	} else if (sd->isRigidBody()) {
390	>	RigidBody* rb = static_cast<RigidBody*>(sd);
391	>	RigidBody::AtomIterator ai;
392	>	Atom* atom;
393	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
394	>	propertyValue+=  getCharge(atom);
395	>	}
396	>	}
397	>	break;
398	>	case Token::x:
399	>	propertyValue = sd->getPos().x();
400	>	break;
401	>	case Token::y:
402	>	propertyValue = sd->getPos().y();
403	>	break;
404	>	case Token::z:
405	>	propertyValue = sd->getPos().z();
406	>	break;
407	>	case Token::wrappedX:
408	>	pos = sd->getPos();
409	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
410	>	propertyValue = pos.x();
411	>	break;
412	>	case Token::wrappedY:
413	>	pos = sd->getPos();
414	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
415	>	propertyValue = pos.y();
416	>	break;
417	>	case Token::wrappedZ:
418	>	pos = sd->getPos();
419	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	>	propertyValue = pos.z();
421	>	break;
422	>	case Token::r:
423	>	propertyValue = sd->getPos().length();
424	>	break;
425	>	default:
426	>	unrecognizedAtomProperty(property);
427	>	}
428
429	<	bool match = false;
430	<	switch (comparator) {
431	<	case Token::opLT:
432	<	match = propertyValue < comparisonValue;
433	<	break;
434	<	case Token::opLE:
435	<	match = propertyValue <= comparisonValue;
436	<	break;
437	<	case Token::opGE:
438	<	match = propertyValue >= comparisonValue;
439	<	break;
440	<	case Token::opGT:
441	<	match = propertyValue > comparisonValue;
442	<	break;
443	<	case Token::opEQ:
444	<	match = propertyValue == comparisonValue;
445	<	break;
446	<	case Token::opNE:
447	<	match = propertyValue != comparisonValue;
448	<	break;
449	<	}
279	<	if (match)
280	<	bs.setBitOn(sd->getGlobalIndex());
429	>	bool match = false;
430	>	switch (comparator) {
431	>	case Token::opLT:
432	>	match = propertyValue < comparisonValue;
433	>	break;
434	>	case Token::opLE:
435	>	match = propertyValue <= comparisonValue;
436	>	break;
437	>	case Token::opGE:
438	>	match = propertyValue >= comparisonValue;
439	>	break;
440	>	case Token::opGT:
441	>	match = propertyValue > comparisonValue;
442	>	break;
443	>	case Token::opEQ:
444	>	match = propertyValue == comparisonValue;
445	>	break;
446	>	case Token::opNE:
447	>	match = propertyValue != comparisonValue;
448	>	break;
449	>	}
450
451	<	}
451	>	if (match)
452	>	bs.setBitOn(sd->getGlobalIndex());
453	>
454	>
455	>	}
456
457	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
457	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
458	>	int property, int comparator,
459	>	float comparisonValue, int frame) {
460	>	RealType propertyValue = 0.0;
461	>	Vector3d pos;
462	>	switch (property) {
463	>	case Token::mass:
464	>	propertyValue = sd->getMass();
465	>	break;
466	>	case Token::charge:
467	>	if (sd->isAtom()){
468	>	Atom* atom = static_cast<Atom*>(sd);
469	>	propertyValue = getCharge(atom,frame);
470	>	} else if (sd->isRigidBody()) {
471	>	RigidBody* rb = static_cast<RigidBody*>(sd);
472	>	RigidBody::AtomIterator ai;
473	>	Atom* atom;
474	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
475	>	propertyValue+=  getCharge(atom,frame);
476	>	}
477	>	}
478	>	break;
479	>	case Token::x:
480	>	propertyValue = sd->getPos(frame).x();
481	>	break;
482	>	case Token::y:
483	>	propertyValue = sd->getPos(frame).y();
484	>	break;
485	>	case Token::z:
486	>	propertyValue = sd->getPos(frame).z();
487	>	break;
488	>	case Token::wrappedX:
489	>	pos = sd->getPos(frame);
490	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
491	>	propertyValue = pos.x();
492	>	break;
493	>	case Token::wrappedY:
494	>	pos = sd->getPos(frame);
495	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
496	>	propertyValue = pos.y();
497	>	break;
498	>	case Token::wrappedZ:
499	>	pos = sd->getPos(frame);
500	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
501	>	propertyValue = pos.z();
502	>	break;
503	>
504	>	case Token::r:
505	>	propertyValue = sd->getPos(frame).length();
506	>	break;
507	>	default:
508	>	unrecognizedAtomProperty(property);
509	>	}
510	>
511	>	bool match = false;
512	>	switch (comparator) {
513	>	case Token::opLT:
514	>	match = propertyValue < comparisonValue;
515	>	break;
516	>	case Token::opLE:
517	>	match = propertyValue <= comparisonValue;
518	>	break;
519	>	case Token::opGE:
520	>	match = propertyValue >= comparisonValue;
521	>	break;
522	>	case Token::opGT:
523	>	match = propertyValue > comparisonValue;
524	>	break;
525	>	case Token::opEQ:
526	>	match = propertyValue == comparisonValue;
527	>	break;
528	>	case Token::opNE:
529	>	match = propertyValue != comparisonValue;
530	>	break;
531	>	}
532	>	if (match)
533	>	bs.setBitOn(sd->getGlobalIndex());
534	>
535
536	+	}
537	+
538	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
539	+	OpenMDBitSet& bs){
540	+
541		boost::any withinSpec = instruction.value;
542		float distance;
543		if (withinSpec.type() == typeid(float)){
544	<	distance = boost::any_cast<float>(withinSpec);
544	>	distance = boost::any_cast<float>(withinSpec);
545		} else if (withinSpec.type() == typeid(int)) {
546	<	distance = boost::any_cast<int>(withinSpec);
546	>	distance = boost::any_cast<int>(withinSpec);
547		} else {
548	<	evalError("casting error in withinInstruction");
549	<	bs.clearAll();
548	>	evalError("casting error in withinInstruction");
549	>	bs.clearAll();
550		}
551
552		bs = distanceFinder.find(bs, distance);
553	<	}
553	>	}
554
555	<	void SelectionEvaluator::define() {
555	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
556	>	OpenMDBitSet& bs, int frame){
557	>
558	>	boost::any withinSpec = instruction.value;
559	>	float distance;
560	>	if (withinSpec.type() == typeid(float)){
561	>	distance = boost::any_cast<float>(withinSpec);
562	>	} else if (withinSpec.type() == typeid(int)) {
563	>	distance = boost::any_cast<int>(withinSpec);
564	>	} else {
565	>	evalError("casting error in withinInstruction");
566	>	bs.clearAll();
567	>	}
568	>
569	>	bs = distanceFinder.find(bs, distance, frame);
570	>	}
571	>
572	>	void SelectionEvaluator::define() {
573		assert(statement.size() >= 3);
574	<
574	>
575		std::string variable = boost::any_cast<std::string>(statement[1].value);
576	+
577	+	variables.insert(VariablesType::value_type(variable,
578	+	expression(statement, 2)));
579	+	}
580	+
581
582	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
583	<	}
584	<
308	<
309	<	/** @todo */
310	<	void SelectionEvaluator::predefine(const std::string& script) {
311	<
582	>	/** @todo */
583	>	void SelectionEvaluator::predefine(const std::string& script) {
584	>
585		if (compiler.compile("#predefine", script)) {
586	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
587	<	if (aatoken.size() != 1) {
588	<	evalError("predefinition does not have exactly 1 command:"
589	<	+ script);
590	<	return;
591	<	}
592	<	std::vector<Token> statement = aatoken[0];
593	<	if (statement.size() > 2) {
594	<	int tok = statement[1].tok;
595	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
596	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
597	<	variables.insert(VariablesType::value_type(variable, statement));
598	<
599	<	} else {
600	<	evalError("invalid variable name:" + script);
601	<	}
602	<	}else {
603	<	evalError("bad predefinition length:" + script);
604	<	}
605	<
586	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
587	>	if (aatoken.size() != 1) {
588	>	evalError("predefinition does not have exactly 1 command:"
589	>	+ script);
590	>	return;
591	>	}
592	>	std::vector<Token> statement = aatoken[0];
593	>	if (statement.size() > 2) {
594	>	int tok = statement[1].tok;
595	>	if (tok == Token::identifier ||
596	>	(tok & Token::predefinedset) == Token::predefinedset) {
597	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
598	>	variables.insert(VariablesType::value_type(variable, statement));
599	>
600	>	} else {
601	>	evalError("invalid variable name:" + script);
602	>	}
603	>	}else {
604	>	evalError("bad predefinition length:" + script);
605	>	}
606
607		} else {
608	<	evalError("predefined set compile error:" + script +
609	<	"\ncompile error:" + compiler.getErrorMessage());
608	>	evalError("predefined set compile error:" + script +
609	>	"\ncompile error:" + compiler.getErrorMessage());
610		}
611	+	}
612
613	<	}
340	<
341	<	void SelectionEvaluator::select(BitSet& bs){
613	>	void SelectionEvaluator::select(OpenMDBitSet& bs){
614		bs = expression(statement, 1);
615	<	}
615	>	}
616
617	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
618	<
619	<	BitSet bs(nStuntDouble);
617	>	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
618	>	bs = expression(statement, 1, frame);
619	>	}
620	>
621	>	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
622	>
623	>	OpenMDBitSet bs(nStuntDouble);
624		std::map<std::string, boost::any>::iterator i = variables.find(variable);
625
626		if (i != variables.end()) {
627	<	if (i->second.type() == typeid(BitSet)) {
628	<	return boost::any_cast<BitSet>(i->second);
629	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
630	<	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
631	<	i->second =  bs; /**@todo fixme */
632	<	return bs;
633	<	}
627	>	if (i->second.type() == typeid(OpenMDBitSet)) {
628	>	return boost::any_cast<OpenMDBitSet>(i->second);
629	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
630	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
631	>	i->second =  bs; /**@todo fixme */
632	>	return bs;
633	>	}
634		} else {
635	<	unrecognizedIdentifier(variable);
635	>	unrecognizedIdentifier(variable);
636		}
637	<
637	>
638		return bs;
639	<	}
639	>	}
640	>
641	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
642	>	return nameFinder.match(name);
643	>	}
644
645	<	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){
645	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
646		std::vector<Token>::const_iterator i;
647		for (i = tokens.begin(); i != tokens.end(); ++i) {
648	<	if (i->tok & Token::dynamic) {
649	<	return true;
650	<	}
648	>	if (i->tok & Token::dynamic) {
649	>	return true;
650	>	}
651		}
652	<
652	>
653		return false;
654	<	}
654	>	}
655
656	<	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
656	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
657		variables.clear();
658		//load predefine
659		//predefine();
660	<	}
660	>	}
661
662	<	BitSet SelectionEvaluator::evaluate() {
663	<	BitSet bs(nStuntDouble);
662	>	OpenMDBitSet SelectionEvaluator::evaluate() {
663	>	OpenMDBitSet bs(nStuntDouble);
664		if (isLoaded_) {
665	<	pc = 0;
666	<	instructionDispatchLoop(bs);
665	>	pc = 0;
666	>	instructionDispatchLoop(bs);
667		}
668	+	return bs;
669	+	}
670
671	+	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
672	+	OpenMDBitSet bs(nStuntDouble);
673	+	if (isLoaded_) {
674	+	pc = 0;
675	+	instructionDispatchLoop(bs, frame);
676	+	}
677		return bs;
678	<	}
678	>	}
679
680	<	BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
681	<	BitSet bs(nStuntDouble);
680	>	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
681	>	OpenMDBitSet bs(nStuntDouble);
682
683		if (value.type() == typeid(int)) {
684	<	int index = boost::any_cast<int>(value);
685	<	if (index < 0 || index >= bs.size()) {
686	<	invalidIndex(index);
687	<	} else {
688	<	indexFinder.find(index);
689	<	}
684	>	int index = boost::any_cast<int>(value);
685	>	if (index < 0 || index >= bs.size()) {
686	>	invalidIndex(index);
687	>	} else {
688	>	bs = indexFinder.find(index);
689	>	}
690		} else if (value.type() == typeid(std::pair<int, int>)) {
691	<	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
692	<	assert(indexRange.first <= indexRange.second);
693	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
694	<	invalidIndexRange(indexRange);
695	<	}else {
696	<	indexFinder.find(indexRange.first, indexRange.second);
697	<	}
691	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
692	>	assert(indexRange.first <= indexRange.second);
693	>	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
694	>	invalidIndexRange(indexRange);
695	>	}else {
696	>	bs = indexFinder.find(indexRange.first, indexRange.second);
697	>	}
698		}
699
700		return bs;
701	<	}
701	>	}
702
703	+	OpenMDBitSet SelectionEvaluator::allInstruction() {
704	+	OpenMDBitSet bs(nStuntDouble);
705	+
706	+	SimInfo::MoleculeIterator mi;
707	+	Molecule* mol;
708	+	Molecule::AtomIterator ai;
709	+	Atom* atom;
710	+	Molecule::RigidBodyIterator rbIter;
711	+	RigidBody* rb;
712	+
713	+	// Doing the loop insures that we're actually on this processor.
714	+
715	+	for (mol = info->beginMolecule(mi); mol != NULL;
716	+	mol = info->nextMolecule(mi)) {
717	+
718	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	+	bs.setBitOn(atom->getGlobalIndex());
720	+	}
721	+
722	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
723	+	rb = mol->nextRigidBody(rbIter)) {
724	+	bs.setBitOn(rb->getGlobalIndex());
725	+	}
726	+	}
727	+
728	+	return bs;
729	+	}
730	+
731	+	OpenMDBitSet SelectionEvaluator::hull() {
732	+	OpenMDBitSet bs(nStuntDouble);
733	+
734	+	bs = hullFinder.findHull();
735	+	surfaceArea_ = hullFinder.getSurfaceArea();
736	+	hasSurfaceArea_ = true;
737	+	return bs;
738	+	}
739	+
740	+
741	+	OpenMDBitSet SelectionEvaluator::hull(int frame) {
742	+	OpenMDBitSet bs(nStuntDouble);
743	+
744	+	bs = hullFinder.findHull(frame);
745	+
746	+	return bs;
747	+	}
748	+
749	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
750	+	RealType charge = 0.0;
751	+	AtomType* atomType = atom->getAtomType();
752	+
753	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
754	+	if ( fca.isFixedCharge() ) {
755	+	charge = fca.getCharge();
756	+	}
757	+
758	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
759	+	if ( fqa.isFluctuatingCharge() ) {
760	+	charge += atom->getFlucQPos();
761	+	}
762	+	return charge;
763	+	}
764	+
765	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
766	+	RealType charge = 0.0;
767	+	AtomType* atomType = atom->getAtomType();
768	+
769	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
770	+	if ( fca.isFixedCharge() ) {
771	+	charge = fca.getCharge();
772	+	}
773	+
774	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
775	+	if ( fqa.isFluctuatingCharge() ) {
776	+	charge += atom->getFlucQPos(frame);
777	+	}
778	+	return charge;
779	+	}
780	+
781		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC

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