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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 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stack>
#	Line 45 | Line 46
46		#include "primitives/DirectionalAtom.hpp"
47		#include "primitives/RigidBody.hpp"
48		#include "primitives/Molecule.hpp"
49	+	#include "io/ifstrstream.hpp"
50	+	#include "types/FixedChargeAdapter.hpp"
51	+	#include "types/FluctuatingChargeAdapter.hpp"
52
49	–	namespace oopse {
53
54	+	namespace OpenMD {
55
56	<	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
57	<	: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
58	<
59	<	nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
60	<	}
61	<
62	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
56	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
57	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
58	>	indexFinder(info), isLoaded_(false), hasSurfaceArea_(false) {
59	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
60	>	nObjects.push_back(info->getNGlobalBonds());
61	>	nObjects.push_back(info->getNGlobalBends());
62	>	nObjects.push_back(info->getNGlobalTorsions());
63	>	nObjects.push_back(info->getNGlobalInversions());
64	>	nObjects.push_back(info->getNGlobalMolecules());
65	>	}
66	>
67	>	bool SelectionEvaluator::loadScript(const std::string& filename,
68	>	const std::string& script) {
69		clearDefinitionsAndLoadPredefined();
70		this->filename = filename;
71		this->script = script;
72		if (! compiler.compile(filename, script)) {
73	<	error = true;
74	<	errorMessage = compiler.getErrorMessage();
75	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
76	<	return false;
73	>	error = true;
74	>	errorMessage = compiler.getErrorMessage();
75	>
76	>	sprintf( painCave.errMsg,
77	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
78	>	painCave.severity = OPENMD_ERROR;
79	>	painCave.isFatal = 1;
80	>	simError();
81	>	return false;
82		}
83
84		pc = 0;
#	Line 75 | Line 90 | bool SelectionEvaluator::loadScript(const std::string&
90
91		isDynamic_ = false;
92		for (i = aatoken.begin(); i != aatoken.end(); ++i) {
93	<	if (containDynamicToken(*i)) {
94	<	isDynamic_ = true;
95	<	break;
96	<	}
93	>	if (containDynamicToken(*i)) {
94	>	isDynamic_ = true;
95	>	break;
96	>	}
97		}
98
99		isLoaded_ = true;
100		return true;
101	<	}
101	>	}
102
103	<	void SelectionEvaluator::clearState() {
89	<	//for (int i = scriptLevelMax; --i >= 0; )
90	<	//    stack[i].clear();
91	<	//scriptLevel = 0;
103	>	void SelectionEvaluator::clearState() {
104		error = false;
105		errorMessage = "";
106	<	}
106	>	}
107
108	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
108	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
109		clearState();
110		return loadScript("", script);
111	<	}
111	>	}
112
113	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
113	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
114		clearState();
115		return loadScriptFileInternal(filename);
116	<	}
116	>	}
117
118	<	bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
119	<	std::ifstream ifs(filename.c_str());
118	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
119	>	ifstrstream ifs(filename.c_str());
120		if (!ifs.is_open()) {
121	<	return false;
121	>	return false;
122		}
123	<
123	>
124		const int bufferSize = 65535;
125		char buffer[bufferSize];
126		std::string script;
127		while(ifs.getline(buffer, bufferSize)) {
128	<	script += buffer;
128	>	script += buffer;
129		}
130		return loadScript(filename, script);
131	<	}
132	<
133	<	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
131	>	}
132	>
133	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
134
135		while ( pc < aatoken.size()) {
136	<	statement = aatoken[pc++];
137	<	statementLength = statement.size();
138	<	Token token = statement[0];
139	<	switch (token.tok) {
140	<	case Token::define:
141	<	define();
142	<	break;
143	<	case Token::select:
144	<	select(bs);
145	<	break;
146	<	default:
147	<	unrecognizedCommand(token);
148	<	return;
149	<	}
136	>	statement = aatoken[pc++];
137	>	statementLength = statement.size();
138	>	Token token = statement[0];
139	>	switch (token.tok) {
140	>	case Token::define:
141	>	define();
142	>	break;
143	>	case Token::select:
144	>	select(bs);
145	>	break;
146	>	default:
147	>	unrecognizedCommand(token);
148	>	return;
149	>	}
150		}
151
152	<	}
153	<
154	<	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
143	<	BitSet bs;
144	<	std::stack<BitSet> stack;
152	>	}
153	>
154	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
155
156	<	for (int pc = pcStart; pc < code.size(); ++pc) {
156	>	while ( pc < aatoken.size()) {
157	>	statement = aatoken[pc++];
158	>	statementLength = statement.size();
159	>	Token token = statement[0];
160	>	switch (token.tok) {
161	>	case Token::define:
162	>	define();
163	>	break;
164	>	case Token::select:
165	>	select(bs, frame);
166	>	break;
167	>	default:
168	>	unrecognizedCommand(token);
169	>	return;
170	>	}
171	>	}
172	>
173	>	}
174	>
175	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
176	>	int pcStart) {
177	>	SelectionSet bs = createSelectionSets();
178	>	std::stack<SelectionSet> stack;
179	>	vector<int> bsSize = bs.size();
180	>
181	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
182		Token instruction = code[pc];
183
184		switch (instruction.tok) {
#	Line 152 | Line 187 | void SelectionEvaluator::instructionDispatchLoop(BitSe
187		case Token::expressionEnd:
188		break;
189		case Token::all:
190	<	bs = BitSet(nStuntDouble);
191	<	bs.setAll();
190	>	bs = allInstruction();
191	>	stack.push(bs);
192	>	break;
193	>	case Token::none:
194	>	bs = createSelectionSets();
195	>	stack.push(bs);
196	>	break;
197	>	case Token::opOr:
198	>	bs= stack.top();
199	>	stack.pop();
200	>	stack.top() |= bs;
201	>	break;
202	>	case Token::opAnd:
203	>	bs = stack.top();
204	>	stack.pop();
205	>	stack.top() &= bs;
206	>	break;
207	>	case Token::opNot:
208	>	stack.top().flip();
209	>	break;
210	>	case Token::within:
211	>	withinInstruction(instruction, stack.top());
212	>	break;
213	>	case Token::hull:
214	>	stack.push(hull());
215	>	break;
216	>	//case Token::selected:
217	>	//  stack.push(getSelectionSet());
218	>	//  break;
219	>	case Token::name:
220	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
221	>	break;
222	>	case Token::index:
223	>	stack.push(indexInstruction(instruction.value));
224	>	break;
225	>	case Token::identifier:
226	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
227	>	break;
228	>	case Token::opLT:
229	>	case Token::opLE:
230	>	case Token::opGE:
231	>	case Token::opGT:
232	>	case Token::opEQ:
233	>	case Token::opNE:
234	>	stack.push(comparatorInstruction(instruction));
235	>	break;
236	>	default:
237	>	unrecognizedExpression();
238	>	}
239	>	}
240	>	if (stack.size() != 1)
241	>	evalError("atom expression compiler error - stack over/underflow");
242	>
243	>	return stack.top();
244	>	}
245	>
246	>
247	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
248	>	int pcStart, int frame) {
249	>	SelectionSet bs = createSelectionSets();
250	>	std::stack<SelectionSet> stack;
251	>
252	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
253	>	Token instruction = code[pc];
254	>
255	>	switch (instruction.tok) {
256	>	case Token::expressionBegin:
257	>	break;
258	>	case Token::expressionEnd:
259	>	break;
260	>	case Token::all:
261	>	bs = allInstruction();
262		stack.push(bs);
263		break;
264		case Token::none:
265	<	bs = BitSet(nStuntDouble);
265	>	bs = SelectionSet(nObjects);
266		stack.push(bs);
267		break;
268		case Token::opOr:
#	Line 174 | Line 279 | void SelectionEvaluator::instructionDispatchLoop(BitSe
279		stack.top().flip();
280		break;
281		case Token::within:
282	<
178	<	withinInstruction(instruction, stack.top());
282	>	withinInstruction(instruction, stack.top(), frame);
283		break;
284	<	//case Token::selected:
285	<	//  stack.push(getSelectionSet());
286	<	//  break;
284	>	case Token::hull:
285	>	stack.push(hull(frame));
286	>	break;
287	>	//case Token::selected:
288	>	//  stack.push(getSelectionSet());
289	>	//  break;
290		case Token::name:
291		stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
292		break;
#	Line 195 | Line 302 | void SelectionEvaluator::instructionDispatchLoop(BitSe
302		case Token::opGT:
303		case Token::opEQ:
304		case Token::opNE:
305	<	stack.push(comparatorInstruction(instruction));
305	>	stack.push(comparatorInstruction(instruction, frame));
306		break;
307		default:
308		unrecognizedExpression();
#	Line 209 | Line 316 | void SelectionEvaluator::instructionDispatchLoop(BitSe
316
317
318
319	<	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
319	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
320		int comparator = instruction.tok;
321		int property = instruction.intValue;
322		float comparisonValue = boost::any_cast<float>(instruction.value);
323	<	float propertyValue;
217	<	BitSet bs(nStuntDouble);
323	>	SelectionSet bs = createSelectionSets();
324		bs.clearAll();
325
326		SimInfo::MoleculeIterator mi;
#	Line 223 | Line 329 | BitSet SelectionEvaluator::comparatorInstruction(const
329		Atom* atom;
330		Molecule::RigidBodyIterator rbIter;
331		RigidBody* rb;
226	–
227	–	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
332
333	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
334	<	compareProperty(atom, bs, property, comparator, comparisonValue);
335	<	}
336	<
337	<	//change the positions of atoms which belong to the rigidbodies
338	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
339	<	compareProperty(rb, bs, property, comparator, comparisonValue);
340	<	}
333	>	for (mol = info->beginMolecule(mi); mol != NULL;
334	>	mol = info->nextMolecule(mi)) {
335	>
336	>	compareProperty(mol, bs, property, comparator, comparisonValue);
337	>
338	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
339	>	compareProperty(atom, bs, property, comparator, comparisonValue);
340	>	}
341	>
342	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
343	>	rb = mol->nextRigidBody(rbIter)) {
344	>	compareProperty(rb, bs, property, comparator, comparisonValue);
345	>	}
346		}
347
348		return bs;
349	<	}
349	>	}
350
351	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
352	<	double propertyValue;
353	<	switch (property) {
354	<	case Token::mass:
355	<	propertyValue = sd->getMass();
356	<	break;
357	<	case Token::charge:
358	<	return;
359	<	//break;
360	<	case Token::dipole:
361	<	return;
362	<	//break;
363	<	default:
255	<	unrecognizedAtomProperty(property);
256	<	}
257	<
258	<	bool match = false;
259	<	switch (comparator) {
260	<	case Token::opLT:
261	<	match = propertyValue < comparisonValue;
262	<	break;
263	<	case Token::opLE:
264	<	match = propertyValue <= comparisonValue;
265	<	break;
266	<	case Token::opGE:
267	<	match = propertyValue >= comparisonValue;
268	<	break;
269	<	case Token::opGT:
270	<	match = propertyValue > comparisonValue;
271	<	break;
272	<	case Token::opEQ:
273	<	match = propertyValue == comparisonValue;
274	<	break;
275	<	case Token::opNE:
276	<	match = propertyValue != comparisonValue;
277	<	break;
278	<	}
279	<	if (match)
280	<	bs.setBitOn(sd->getGlobalIndex());
351	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
352	>	int comparator = instruction.tok;
353	>	int property = instruction.intValue;
354	>	float comparisonValue = boost::any_cast<float>(instruction.value);
355	>	SelectionSet bs = createSelectionSets();
356	>	bs.clearAll();
357	>
358	>	SimInfo::MoleculeIterator mi;
359	>	Molecule* mol;
360	>	Molecule::AtomIterator ai;
361	>	Atom* atom;
362	>	Molecule::RigidBodyIterator rbIter;
363	>	RigidBody* rb;
364
365	<	}
365	>	for (mol = info->beginMolecule(mi); mol != NULL;
366	>	mol = info->nextMolecule(mi)) {
367
368	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
369	<
370	<	boost::any withinSpec = instruction.value;
371	<	float distance;
372	<	if (withinSpec.type() == typeid(float)){
373	<	distance = boost::any_cast<float>(withinSpec);
374	<	} else if (withinSpec.type() == typeid(int)) {
375	<	distance = boost::any_cast<int>(withinSpec);
376	<	} else {
377	<	evalError("casting error in withinInstruction");
294	<	bs.clearAll();
368	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
369	>
370	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
371	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
372	>	}
373	>
374	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
375	>	rb = mol->nextRigidBody(rbIter)) {
376	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
377	>	}
378		}
296	–
297	–	bs = distanceFinder.find(bs, distance);
298	–	}
379
380	<	void SelectionEvaluator::define() {
381	<	assert(statement.size() >= 3);
380	>	return bs;
381	>	}
382
383	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
383	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
384	>	int property, int comparator,
385	>	float comparisonValue) {
386	>	RealType propertyValue = 0.0;
387	>	Vector3d pos;
388
389	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
390	<	}
389	>	switch (property) {
390	>	case Token::mass:
391	>	propertyValue = sd->getMass();
392	>	break;
393	>	case Token::charge:
394	>	if (sd->isAtom()){
395	>	Atom* atom = static_cast<Atom*>(sd);
396	>	propertyValue = getCharge(atom);
397	>	} else if (sd->isRigidBody()) {
398	>	RigidBody* rb = static_cast<RigidBody*>(sd);
399	>	RigidBody::AtomIterator ai;
400	>	Atom* atom;
401	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
402	>	propertyValue+=  getCharge(atom);
403	>	}
404	>	}
405	>	break;
406	>	case Token::x:
407	>	propertyValue = sd->getPos().x();
408	>	break;
409	>	case Token::y:
410	>	propertyValue = sd->getPos().y();
411	>	break;
412	>	case Token::z:
413	>	propertyValue = sd->getPos().z();
414	>	break;
415	>	case Token::wrappedX:
416	>	pos = sd->getPos();
417	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
418	>	propertyValue = pos.x();
419	>	break;
420	>	case Token::wrappedY:
421	>	pos = sd->getPos();
422	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
423	>	propertyValue = pos.y();
424	>	break;
425	>	case Token::wrappedZ:
426	>	pos = sd->getPos();
427	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
428	>	propertyValue = pos.z();
429	>	break;
430	>	case Token::r:
431	>	propertyValue = sd->getPos().length();
432	>	break;
433	>	default:
434	>	unrecognizedAtomProperty(property);
435	>	}
436	>
437	>	bool match = false;
438	>	switch (comparator) {
439	>	case Token::opLT:
440	>	match = propertyValue < comparisonValue;
441	>	break;
442	>	case Token::opLE:
443	>	match = propertyValue <= comparisonValue;
444	>	break;
445	>	case Token::opGE:
446	>	match = propertyValue >= comparisonValue;
447	>	break;
448	>	case Token::opGT:
449	>	match = propertyValue > comparisonValue;
450	>	break;
451	>	case Token::opEQ:
452	>	match = propertyValue == comparisonValue;
453	>	break;
454	>	case Token::opNE:
455	>	match = propertyValue != comparisonValue;
456	>	break;
457	>	}
458
459	+	if (match)
460	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
461
462	<	/** @todo */
463	<	void SelectionEvaluator::predefine(const std::string& script) {
462	>
463	>	}
464
465	<	if (compiler.compile("#predefine", script)) {
466	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
467	<	if (aatoken.size() != 1) {
468	<	evalError("predefinition does not have exactly 1 command:"
469	<	+ script);
470	<	return;
465	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
466	>	int property, int comparator,
467	>	float comparisonValue) {
468	>	RealType propertyValue = 0.0;
469	>	Vector3d pos;
470	>
471	>	switch (property) {
472	>	case Token::mass:
473	>	propertyValue = mol->getMass();
474	>	break;
475	>	case Token::charge:
476	>	{
477	>	Molecule::AtomIterator ai;
478	>	Atom* atom;
479	>	for (atom = mol->beginAtom(ai); atom != NULL;
480	>	atom = mol->nextAtom(ai)) {
481	>	propertyValue+=  getCharge(atom);
482		}
483	<	std::vector<Token> statement = aatoken[0];
484	<	if (statement.size() > 2) {
485	<	int tok = statement[1].tok;
486	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
487	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
488	<	variables.insert(VariablesType::value_type(variable, statement));
483	>	}
484	>	break;
485	>	case Token::x:
486	>	propertyValue = mol->getCom().x();
487	>	break;
488	>	case Token::y:
489	>	propertyValue = mol->getCom().y();
490	>	break;
491	>	case Token::z:
492	>	propertyValue = mol->getCom().z();
493	>	break;
494	>	case Token::wrappedX:
495	>	pos = mol->getCom();
496	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
497	>	propertyValue = pos.x();
498	>	break;
499	>	case Token::wrappedY:
500	>	pos = mol->getCom();
501	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
502	>	propertyValue = pos.y();
503	>	break;
504	>	case Token::wrappedZ:
505	>	pos = mol->getCom();
506	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
507	>	propertyValue = pos.z();
508	>	break;
509	>	case Token::r:
510	>	propertyValue = mol->getCom().length();
511	>	break;
512	>	default:
513	>	unrecognizedMoleculeProperty(property);
514	>	}
515	>
516	>	bool match = false;
517	>	switch (comparator) {
518	>	case Token::opLT:
519	>	match = propertyValue < comparisonValue;
520	>	break;
521	>	case Token::opLE:
522	>	match = propertyValue <= comparisonValue;
523	>	break;
524	>	case Token::opGE:
525	>	match = propertyValue >= comparisonValue;
526	>	break;
527	>	case Token::opGT:
528	>	match = propertyValue > comparisonValue;
529	>	break;
530	>	case Token::opEQ:
531	>	match = propertyValue == comparisonValue;
532	>	break;
533	>	case Token::opNE:
534	>	match = propertyValue != comparisonValue;
535	>	break;
536	>	}
537	>
538	>	if (match)
539	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
540	>	}
541
542	<	} else {
543	<	evalError("invalid variable name:" + script);
544	<	}
545	<	}else {
546	<	evalError("bad predefinition length:" + script);
542	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
543	>	int property, int comparator,
544	>	float comparisonValue, int frame) {
545	>	RealType propertyValue = 0.0;
546	>	Vector3d pos;
547	>	switch (property) {
548	>	case Token::mass:
549	>	propertyValue = mol->getMass();
550	>	break;
551	>	case Token::charge:
552	>	{
553	>	Molecule::AtomIterator ai;
554	>	Atom* atom;
555	>	for (atom = mol->beginAtom(ai); atom != NULL;
556	>	atom = mol->nextAtom(ai)) {
557	>	propertyValue+=  getCharge(atom,frame);
558		}
559	+	}
560	+	break;
561	+	case Token::x:
562	+	propertyValue = mol->getCom(frame).x();
563	+	break;
564	+	case Token::y:
565	+	propertyValue = mol->getCom(frame).y();
566	+	break;
567	+	case Token::z:
568	+	propertyValue = mol->getCom(frame).z();
569	+	break;
570	+	case Token::wrappedX:
571	+	pos = mol->getCom(frame);
572	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
573	+	propertyValue = pos.x();
574	+	break;
575	+	case Token::wrappedY:
576	+	pos = mol->getCom(frame);
577	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
578	+	propertyValue = pos.y();
579	+	break;
580	+	case Token::wrappedZ:
581	+	pos = mol->getCom(frame);
582	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
583	+	propertyValue = pos.z();
584	+	break;
585
586	+	case Token::r:
587	+	propertyValue = mol->getCom(frame).length();
588	+	break;
589	+	default:
590	+	unrecognizedMoleculeProperty(property);
591	+	}
592
593	+	bool match = false;
594	+	switch (comparator) {
595	+	case Token::opLT:
596	+	match = propertyValue < comparisonValue;
597	+	break;
598	+	case Token::opLE:
599	+	match = propertyValue <= comparisonValue;
600	+	break;
601	+	case Token::opGE:
602	+	match = propertyValue >= comparisonValue;
603	+	break;
604	+	case Token::opGT:
605	+	match = propertyValue > comparisonValue;
606	+	break;
607	+	case Token::opEQ:
608	+	match = propertyValue == comparisonValue;
609	+	break;
610	+	case Token::opNE:
611	+	match = propertyValue != comparisonValue;
612	+	break;
613	+	}
614	+	if (match)
615	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
616	+
617	+
618	+	}
619	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
620	+	int property, int comparator,
621	+	float comparisonValue, int frame) {
622	+	RealType propertyValue = 0.0;
623	+	Vector3d pos;
624	+	switch (property) {
625	+	case Token::mass:
626	+	propertyValue = sd->getMass();
627	+	break;
628	+	case Token::charge:
629	+	if (sd->isAtom()){
630	+	Atom* atom = static_cast<Atom*>(sd);
631	+	propertyValue = getCharge(atom,frame);
632	+	} else if (sd->isRigidBody()) {
633	+	RigidBody* rb = static_cast<RigidBody*>(sd);
634	+	RigidBody::AtomIterator ai;
635	+	Atom* atom;
636	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
637	+	propertyValue+=  getCharge(atom,frame);
638	+	}
639	+	}
640	+	break;
641	+	case Token::x:
642	+	propertyValue = sd->getPos(frame).x();
643	+	break;
644	+	case Token::y:
645	+	propertyValue = sd->getPos(frame).y();
646	+	break;
647	+	case Token::z:
648	+	propertyValue = sd->getPos(frame).z();
649	+	break;
650	+	case Token::wrappedX:
651	+	pos = sd->getPos(frame);
652	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
653	+	propertyValue = pos.x();
654	+	break;
655	+	case Token::wrappedY:
656	+	pos = sd->getPos(frame);
657	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
658	+	propertyValue = pos.y();
659	+	break;
660	+	case Token::wrappedZ:
661	+	pos = sd->getPos(frame);
662	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
663	+	propertyValue = pos.z();
664	+	break;
665	+
666	+	case Token::r:
667	+	propertyValue = sd->getPos(frame).length();
668	+	break;
669	+	default:
670	+	unrecognizedAtomProperty(property);
671	+	}
672	+
673	+	bool match = false;
674	+	switch (comparator) {
675	+	case Token::opLT:
676	+	match = propertyValue < comparisonValue;
677	+	break;
678	+	case Token::opLE:
679	+	match = propertyValue <= comparisonValue;
680	+	break;
681	+	case Token::opGE:
682	+	match = propertyValue >= comparisonValue;
683	+	break;
684	+	case Token::opGT:
685	+	match = propertyValue > comparisonValue;
686	+	break;
687	+	case Token::opEQ:
688	+	match = propertyValue == comparisonValue;
689	+	break;
690	+	case Token::opNE:
691	+	match = propertyValue != comparisonValue;
692	+	break;
693	+	}
694	+	if (match)
695	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
696	+	}
697	+
698	+
699	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
700	+	SelectionSet& bs){
701	+
702	+	boost::any withinSpec = instruction.value;
703	+	float distance;
704	+	if (withinSpec.type() == typeid(float)){
705	+	distance = boost::any_cast<float>(withinSpec);
706	+	} else if (withinSpec.type() == typeid(int)) {
707	+	distance = boost::any_cast<int>(withinSpec);
708		} else {
709	<	evalError("predefined set compile error:" + script +
710	<	"\ncompile error:" + compiler.getErrorMessage());
709	>	evalError("casting error in withinInstruction");
710	>	bs.clearAll();
711		}
712	+
713	+	bs = distanceFinder.find(bs, distance);
714	+	}
715
716	<	}
716	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
717	>	SelectionSet& bs, int frame){
718	>
719	>	boost::any withinSpec = instruction.value;
720	>	float distance;
721	>	if (withinSpec.type() == typeid(float)){
722	>	distance = boost::any_cast<float>(withinSpec);
723	>	} else if (withinSpec.type() == typeid(int)) {
724	>	distance = boost::any_cast<int>(withinSpec);
725	>	} else {
726	>	evalError("casting error in withinInstruction");
727	>	bs.clearAll();
728	>	}
729	>
730	>	bs = distanceFinder.find(bs, distance, frame);
731	>	}
732	>
733	>	void SelectionEvaluator::define() {
734	>	assert(statement.size() >= 3);
735	>
736	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
737	>
738	>	variables.insert(VariablesType::value_type(variable,
739	>	expression(statement, 2)));
740	>	}
741	>
742
743	<	void SelectionEvaluator::select(BitSet& bs){
744	<	bs = expression(statement, 1);
745	<	}
746	<
747	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
743	>	/** @todo */
744	>	void SelectionEvaluator::predefine(const std::string& script) {
745	>
746	>	if (compiler.compile("#predefine", script)) {
747	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
748	>	if (aatoken.size() != 1) {
749	>	evalError("predefinition does not have exactly 1 command:"
750	>	+ script);
751	>	return;
752	>	}
753	>	std::vector<Token> statement = aatoken[0];
754	>	if (statement.size() > 2) {
755	>	int tok = statement[1].tok;
756	>	if (tok == Token::identifier ||
757	>	(tok & Token::predefinedset) == Token::predefinedset) {
758	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
759	>	variables.insert(VariablesType::value_type(variable, statement));
760	>
761	>	} else {
762	>	evalError("invalid variable name:" + script);
763	>	}
764	>	}else {
765	>	evalError("bad predefinition length:" + script);
766	>	}
767	>
768	>	} else {
769	>	evalError("predefined set compile error:" + script +
770	>	"\ncompile error:" + compiler.getErrorMessage());
771	>	}
772	>	}
773
774	<	BitSet bs(nStuntDouble);
774	>	void SelectionEvaluator::select(SelectionSet& bs){
775	>	bs = expression(statement, 1);
776	>	}
777	>
778	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
779	>	bs = expression(statement, 1, frame);
780	>	}
781	>
782	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
783	>
784	>	SelectionSet bs = createSelectionSets();
785		std::map<std::string, boost::any>::iterator i = variables.find(variable);
786
787		if (i != variables.end()) {
788	<	if (i->second.type() == typeid(BitSet)) {
789	<	return boost::any_cast<BitSet>(i->second);
790	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
791	<	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
792	<	i->second =  bs; /**@todo fixme */
793	<	return bs;
794	<	}
788	>	if (i->second.type() == typeid(SelectionSet)) {
789	>	return boost::any_cast<SelectionSet>(i->second);
790	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
791	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
792	>	i->second =  bs; /**@todo fixme */
793	>	return bs;
794	>	}
795		} else {
796	<	unrecognizedIdentifier(variable);
796	>	unrecognizedIdentifier(variable);
797		}
798	<
798	>
799		return bs;
800	<	}
800	>	}
801	>
802	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
803	>	return nameFinder.match(name);
804	>	}
805
806	<	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){
806	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
807		std::vector<Token>::const_iterator i;
808		for (i = tokens.begin(); i != tokens.end(); ++i) {
809	<	if (i->tok & Token::dynamic) {
810	<	return true;
811	<	}
809	>	if (i->tok & Token::dynamic) {
810	>	return true;
811	>	}
812		}
813	<
813	>
814		return false;
815	<	}
815	>	}
816
817	<	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
817	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
818		variables.clear();
819		//load predefine
820		//predefine();
821	<	}
821	>	}
822
823	<	BitSet SelectionEvaluator::evaluate() {
824	<	BitSet bs(nStuntDouble);
823	>	SelectionSet SelectionEvaluator::createSelectionSets() {
824	>	SelectionSet ss(nObjects);
825	>	return ss;
826	>	}
827	>
828	>	SelectionSet SelectionEvaluator::evaluate() {
829	>	SelectionSet bs = createSelectionSets();
830		if (isLoaded_) {
831	<	pc = 0;
832	<	instructionDispatchLoop(bs);
831	>	pc = 0;
832	>	instructionDispatchLoop(bs);
833		}
834	+	return bs;
835	+	}
836
837	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
838	+	SelectionSet bs = createSelectionSets();
839	+	if (isLoaded_) {
840	+	pc = 0;
841	+	instructionDispatchLoop(bs, frame);
842	+	}
843		return bs;
844	<	}
844	>	}
845
846	<	BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
847	<	BitSet bs(nStuntDouble);
846	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
847	>	SelectionSet bs = createSelectionSets();
848
849		if (value.type() == typeid(int)) {
850	<	int index = boost::any_cast<int>(value);
851	<	if (index < 0 || index >= bs.size()) {
852	<	invalidIndex(index);
853	<	} else {
854	<	indexFinder.find(index);
855	<	}
850	>	int index = boost::any_cast<int>(value);
851	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
852	>	invalidIndex(index);
853	>	} else {
854	>	bs = indexFinder.find(index);
855	>	}
856		} else if (value.type() == typeid(std::pair<int, int>)) {
857	<	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
858	<	assert(indexRange.first <= indexRange.second);
859	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
860	<	invalidIndexRange(indexRange);
861	<	}else {
862	<	indexFinder.find(indexRange.first, indexRange.second);
863	<	}
857	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
858	>	assert(indexRange.first <= indexRange.second);
859	>	if (indexRange.first < 0 ||
860	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
861	>	invalidIndexRange(indexRange);
862	>	}else {
863	>	bs = indexFinder.find(indexRange.first, indexRange.second);
864	>	}
865		}
866
867		return bs;
868	<	}
868	>	}
869
870	+	SelectionSet SelectionEvaluator::allInstruction() {
871	+	SelectionSet ss = createSelectionSets();
872	+
873	+	SimInfo::MoleculeIterator mi;
874	+	Molecule::AtomIterator ai;
875	+	Molecule::RigidBodyIterator rbIter;
876	+	Molecule::BondIterator bondIter;
877	+	Molecule::BendIterator bendIter;
878	+	Molecule::TorsionIterator torsionIter;
879	+	Molecule::InversionIterator inversionIter;
880	+
881	+	Molecule* mol;
882	+	Atom* atom;
883	+	RigidBody* rb;
884	+	Bond* bond;
885	+	Bend* bend;
886	+	Torsion* torsion;
887	+	Inversion* inversion;
888	+
889	+	// Doing the loop insures that we're actually on this processor.
890	+
891	+	for (mol = info->beginMolecule(mi); mol != NULL;
892	+	mol = info->nextMolecule(mi)) {
893	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
894	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
895	+	}
896	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
897	+	rb = mol->nextRigidBody(rbIter)) {
898	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
899	+	}
900	+	for (bond = mol->beginBond(bondIter); bond != NULL;
901	+	bond = mol->nextBond(bondIter)) {
902	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
903	+	}
904	+	for (bend = mol->beginBend(bendIter); bend != NULL;
905	+	bend = mol->nextBend(bendIter)) {
906	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
907	+	}
908	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
909	+	torsion = mol->nextTorsion(torsionIter)) {
910	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
911	+	}
912	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
913	+	inversion = mol->nextInversion(inversionIter)) {
914	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
915	+	}
916	+	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
917	+	}
918	+
919	+	return ss;
920	+	}
921	+
922	+	SelectionSet SelectionEvaluator::hull() {
923	+	SelectionSet bs = createSelectionSets();
924	+
925	+	bs = hullFinder.findHull();
926	+	surfaceArea_ = hullFinder.getSurfaceArea();
927	+	hasSurfaceArea_ = true;
928	+	return bs;
929	+	}
930	+
931	+
932	+	SelectionSet SelectionEvaluator::hull(int frame) {
933	+	SelectionSet bs = createSelectionSets();
934	+
935	+	bs = hullFinder.findHull(frame);
936	+
937	+	return bs;
938	+	}
939	+
940	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
941	+	RealType charge = 0.0;
942	+	AtomType* atomType = atom->getAtomType();
943	+
944	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
945	+	if ( fca.isFixedCharge() ) {
946	+	charge = fca.getCharge();
947	+	}
948	+
949	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
950	+	if ( fqa.isFluctuatingCharge() ) {
951	+	charge += atom->getFlucQPos();
952	+	}
953	+	return charge;
954	+	}
955	+
956	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
957	+	RealType charge = 0.0;
958	+	AtomType* atomType = atom->getAtomType();
959	+
960	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
961	+	if ( fca.isFixedCharge() ) {
962	+	charge = fca.getCharge();
963	+	}
964	+
965	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
966	+	if ( fqa.isFluctuatingCharge() ) {
967	+	charge += atom->getFlucQPos(frame);
968	+	}
969	+	return charge;
970	+	}
971	+
972		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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