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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 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stack>
#	Line 45 | Line 46
46		#include "primitives/DirectionalAtom.hpp"
47		#include "primitives/RigidBody.hpp"
48		#include "primitives/Molecule.hpp"
49	+	#include "io/ifstrstream.hpp"
50	+	#include "types/FixedChargeAdapter.hpp"
51	+	#include "types/FluctuatingChargeAdapter.hpp"
52
49	–	namespace oopse {
53
54	+	namespace OpenMD {
55
52	–	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
53	–	: info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
54	–
55	–	nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
56	–	}
56
57	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
57	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
58	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	>	indexFinder(info), hasSurfaceArea_(false),
60	>	isLoaded_(false){
61	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
62	>	nObjects.push_back(info->getNGlobalBonds());
63	>	nObjects.push_back(info->getNGlobalBends());
64	>	nObjects.push_back(info->getNGlobalTorsions());
65	>	nObjects.push_back(info->getNGlobalInversions());
66	>	nObjects.push_back(info->getNGlobalMolecules());
67	>	}
68	>
69	>	bool SelectionEvaluator::loadScript(const std::string& filename,
70	>	const std::string& script) {
71		clearDefinitionsAndLoadPredefined();
72		this->filename = filename;
73		this->script = script;
74		if (! compiler.compile(filename, script)) {
75	<	error = true;
76	<	errorMessage = compiler.getErrorMessage();
77	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
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;
226	–
227	–	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
334
335	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
336	<	compareProperty(atom, bs, property, comparator, comparisonValue);
337	<	}
338	<
339	<	//change the positions of atoms which belong to the rigidbodies
340	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
341	<	compareProperty(rb, bs, property, comparator, comparisonValue);
342	<	}
335	>	for (mol = info->beginMolecule(mi); mol != NULL;
336	>	mol = info->nextMolecule(mi)) {
337	>
338	>	compareProperty(mol, bs, property, comparator, comparisonValue);
339	>
340	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
341	>	compareProperty(atom, bs, property, comparator, comparisonValue);
342	>	}
343	>
344	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345	>	rb = mol->nextRigidBody(rbIter)) {
346	>	compareProperty(rb, bs, property, comparator, comparisonValue);
347	>	}
348		}
349
350		return bs;
351	<	}
351	>	}
352
353	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
354	<	double propertyValue;
355	<	switch (property) {
356	<	case Token::mass:
357	<	propertyValue = sd->getMass();
358	<	break;
359	<	case Token::charge:
360	<	return;
361	<	//break;
362	<	case Token::dipole:
363	<	return;
364	<	//break;
365	<	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());
353	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
354	>	int comparator = instruction.tok;
355	>	int property = instruction.intValue;
356	>	float comparisonValue = boost::any_cast<float>(instruction.value);
357	>	SelectionSet bs = createSelectionSets();
358	>	bs.clearAll();
359	>
360	>	SimInfo::MoleculeIterator mi;
361	>	Molecule* mol;
362	>	Molecule::AtomIterator ai;
363	>	Atom* atom;
364	>	Molecule::RigidBodyIterator rbIter;
365	>	RigidBody* rb;
366
367	<	}
367	>	for (mol = info->beginMolecule(mi); mol != NULL;
368	>	mol = info->nextMolecule(mi)) {
369
370	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
371	<
372	<	boost::any withinSpec = instruction.value;
373	<	float distance;
374	<	if (withinSpec.type() == typeid(float)){
375	<	distance = boost::any_cast<float>(withinSpec);
376	<	} else if (withinSpec.type() == typeid(int)) {
377	<	distance = boost::any_cast<int>(withinSpec);
378	<	} else {
379	<	evalError("casting error in withinInstruction");
294	<	bs.clearAll();
370	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
371	>
372	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
373	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
374	>	}
375	>
376	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
377	>	rb = mol->nextRigidBody(rbIter)) {
378	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
379	>	}
380		}
296	–
297	–	bs = distanceFinder.find(bs, distance);
298	–	}
381
382	<	void SelectionEvaluator::define() {
383	<	assert(statement.size() >= 3);
382	>	return bs;
383	>	}
384
385	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
385	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
386	>	int property, int comparator,
387	>	float comparisonValue) {
388	>	RealType propertyValue = 0.0;
389	>	Vector3d pos;
390
391	<	variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
392	<	}
391	>	switch (property) {
392	>	case Token::mass:
393	>	propertyValue = sd->getMass();
394	>	break;
395	>	case Token::charge:
396	>	if (sd->isAtom()){
397	>	Atom* atom = static_cast<Atom*>(sd);
398	>	propertyValue = getCharge(atom);
399	>	} else if (sd->isRigidBody()) {
400	>	RigidBody* rb = static_cast<RigidBody*>(sd);
401	>	RigidBody::AtomIterator ai;
402	>	Atom* atom;
403	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
404	>	propertyValue+=  getCharge(atom);
405	>	}
406	>	}
407	>	break;
408	>	case Token::x:
409	>	propertyValue = sd->getPos().x();
410	>	break;
411	>	case Token::y:
412	>	propertyValue = sd->getPos().y();
413	>	break;
414	>	case Token::z:
415	>	propertyValue = sd->getPos().z();
416	>	break;
417	>	case Token::wrappedX:
418	>	pos = sd->getPos();
419	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	>	propertyValue = pos.x();
421	>	break;
422	>	case Token::wrappedY:
423	>	pos = sd->getPos();
424	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	>	propertyValue = pos.y();
426	>	break;
427	>	case Token::wrappedZ:
428	>	pos = sd->getPos();
429	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
430	>	propertyValue = pos.z();
431	>	break;
432	>	case Token::r:
433	>	propertyValue = sd->getPos().length();
434	>	break;
435	>	default:
436	>	unrecognizedAtomProperty(property);
437	>	}
438	>
439	>	bool match = false;
440	>	switch (comparator) {
441	>	case Token::opLT:
442	>	match = propertyValue < comparisonValue;
443	>	break;
444	>	case Token::opLE:
445	>	match = propertyValue <= comparisonValue;
446	>	break;
447	>	case Token::opGE:
448	>	match = propertyValue >= comparisonValue;
449	>	break;
450	>	case Token::opGT:
451	>	match = propertyValue > comparisonValue;
452	>	break;
453	>	case Token::opEQ:
454	>	match = propertyValue == comparisonValue;
455	>	break;
456	>	case Token::opNE:
457	>	match = propertyValue != comparisonValue;
458	>	break;
459	>	}
460
461	+	if (match)
462	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
463
464	<	/** @todo */
465	<	void SelectionEvaluator::predefine(const std::string& script) {
464	>
465	>	}
466
467	<	if (compiler.compile("#predefine", script)) {
468	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
469	<	if (aatoken.size() != 1) {
470	<	evalError("predefinition does not have exactly 1 command:"
471	<	+ script);
472	<	return;
467	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
468	>	int property, int comparator,
469	>	float comparisonValue) {
470	>	RealType propertyValue = 0.0;
471	>	Vector3d pos;
472	>
473	>	switch (property) {
474	>	case Token::mass:
475	>	propertyValue = mol->getMass();
476	>	break;
477	>	case Token::charge:
478	>	{
479	>	Molecule::AtomIterator ai;
480	>	Atom* atom;
481	>	for (atom = mol->beginAtom(ai); atom != NULL;
482	>	atom = mol->nextAtom(ai)) {
483	>	propertyValue+=  getCharge(atom);
484		}
485	<	std::vector<Token> statement = aatoken[0];
486	<	if (statement.size() > 2) {
487	<	int tok = statement[1].tok;
488	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
489	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
490	<	variables.insert(VariablesType::value_type(variable, statement));
485	>	}
486	>	break;
487	>	case Token::x:
488	>	propertyValue = mol->getCom().x();
489	>	break;
490	>	case Token::y:
491	>	propertyValue = mol->getCom().y();
492	>	break;
493	>	case Token::z:
494	>	propertyValue = mol->getCom().z();
495	>	break;
496	>	case Token::wrappedX:
497	>	pos = mol->getCom();
498	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
499	>	propertyValue = pos.x();
500	>	break;
501	>	case Token::wrappedY:
502	>	pos = mol->getCom();
503	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
504	>	propertyValue = pos.y();
505	>	break;
506	>	case Token::wrappedZ:
507	>	pos = mol->getCom();
508	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
509	>	propertyValue = pos.z();
510	>	break;
511	>	case Token::r:
512	>	propertyValue = mol->getCom().length();
513	>	break;
514	>	default:
515	>	unrecognizedMoleculeProperty(property);
516	>	}
517	>
518	>	bool match = false;
519	>	switch (comparator) {
520	>	case Token::opLT:
521	>	match = propertyValue < comparisonValue;
522	>	break;
523	>	case Token::opLE:
524	>	match = propertyValue <= comparisonValue;
525	>	break;
526	>	case Token::opGE:
527	>	match = propertyValue >= comparisonValue;
528	>	break;
529	>	case Token::opGT:
530	>	match = propertyValue > comparisonValue;
531	>	break;
532	>	case Token::opEQ:
533	>	match = propertyValue == comparisonValue;
534	>	break;
535	>	case Token::opNE:
536	>	match = propertyValue != comparisonValue;
537	>	break;
538	>	}
539	>
540	>	if (match)
541	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
542	>	}
543
544	<	} else {
545	<	evalError("invalid variable name:" + script);
546	<	}
547	<	}else {
548	<	evalError("bad predefinition length:" + script);
544	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
545	>	int property, int comparator,
546	>	float comparisonValue, int frame) {
547	>	RealType propertyValue = 0.0;
548	>	Vector3d pos;
549	>	switch (property) {
550	>	case Token::mass:
551	>	propertyValue = mol->getMass();
552	>	break;
553	>	case Token::charge:
554	>	{
555	>	Molecule::AtomIterator ai;
556	>	Atom* atom;
557	>	for (atom = mol->beginAtom(ai); atom != NULL;
558	>	atom = mol->nextAtom(ai)) {
559	>	propertyValue+=  getCharge(atom,frame);
560		}
561	+	}
562	+	break;
563	+	case Token::x:
564	+	propertyValue = mol->getCom(frame).x();
565	+	break;
566	+	case Token::y:
567	+	propertyValue = mol->getCom(frame).y();
568	+	break;
569	+	case Token::z:
570	+	propertyValue = mol->getCom(frame).z();
571	+	break;
572	+	case Token::wrappedX:
573	+	pos = mol->getCom(frame);
574	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
575	+	propertyValue = pos.x();
576	+	break;
577	+	case Token::wrappedY:
578	+	pos = mol->getCom(frame);
579	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
580	+	propertyValue = pos.y();
581	+	break;
582	+	case Token::wrappedZ:
583	+	pos = mol->getCom(frame);
584	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
585	+	propertyValue = pos.z();
586	+	break;
587
588	+	case Token::r:
589	+	propertyValue = mol->getCom(frame).length();
590	+	break;
591	+	default:
592	+	unrecognizedMoleculeProperty(property);
593	+	}
594
595	<	} else {
596	<	evalError("predefined set compile error:" + script +
597	<	"\ncompile error:" + compiler.getErrorMessage());
595	>	bool match = false;
596	>	switch (comparator) {
597	>	case Token::opLT:
598	>	match = propertyValue < comparisonValue;
599	>	break;
600	>	case Token::opLE:
601	>	match = propertyValue <= comparisonValue;
602	>	break;
603	>	case Token::opGE:
604	>	match = propertyValue >= comparisonValue;
605	>	break;
606	>	case Token::opGT:
607	>	match = propertyValue > comparisonValue;
608	>	break;
609	>	case Token::opEQ:
610	>	match = propertyValue == comparisonValue;
611	>	break;
612	>	case Token::opNE:
613	>	match = propertyValue != comparisonValue;
614	>	break;
615		}
616	+	if (match)
617	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
618	+
619	+
620	+	}
621	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
622	+	int property, int comparator,
623	+	float comparisonValue, int frame) {
624	+	RealType propertyValue = 0.0;
625	+	Vector3d pos;
626	+	switch (property) {
627	+	case Token::mass:
628	+	propertyValue = sd->getMass();
629	+	break;
630	+	case Token::charge:
631	+	if (sd->isAtom()){
632	+	Atom* atom = static_cast<Atom*>(sd);
633	+	propertyValue = getCharge(atom,frame);
634	+	} else if (sd->isRigidBody()) {
635	+	RigidBody* rb = static_cast<RigidBody*>(sd);
636	+	RigidBody::AtomIterator ai;
637	+	Atom* atom;
638	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
639	+	propertyValue+=  getCharge(atom,frame);
640	+	}
641	+	}
642	+	break;
643	+	case Token::x:
644	+	propertyValue = sd->getPos(frame).x();
645	+	break;
646	+	case Token::y:
647	+	propertyValue = sd->getPos(frame).y();
648	+	break;
649	+	case Token::z:
650	+	propertyValue = sd->getPos(frame).z();
651	+	break;
652	+	case Token::wrappedX:
653	+	pos = sd->getPos(frame);
654	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
655	+	propertyValue = pos.x();
656	+	break;
657	+	case Token::wrappedY:
658	+	pos = sd->getPos(frame);
659	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
660	+	propertyValue = pos.y();
661	+	break;
662	+	case Token::wrappedZ:
663	+	pos = sd->getPos(frame);
664	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
665	+	propertyValue = pos.z();
666	+	break;
667
668	<	}
668	>	case Token::r:
669	>	propertyValue = sd->getPos(frame).length();
670	>	break;
671	>	default:
672	>	unrecognizedAtomProperty(property);
673	>	}
674	>
675	>	bool match = false;
676	>	switch (comparator) {
677	>	case Token::opLT:
678	>	match = propertyValue < comparisonValue;
679	>	break;
680	>	case Token::opLE:
681	>	match = propertyValue <= comparisonValue;
682	>	break;
683	>	case Token::opGE:
684	>	match = propertyValue >= comparisonValue;
685	>	break;
686	>	case Token::opGT:
687	>	match = propertyValue > comparisonValue;
688	>	break;
689	>	case Token::opEQ:
690	>	match = propertyValue == comparisonValue;
691	>	break;
692	>	case Token::opNE:
693	>	match = propertyValue != comparisonValue;
694	>	break;
695	>	}
696	>	if (match)
697	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
698
699	<	void SelectionEvaluator::select(BitSet& bs){
700	<	bs = expression(statement, 1);
343	<	}
699	>
700	>	}
701
702	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
703	<
704	<	BitSet bs(nStuntDouble);
348	<	std::map<std::string, boost::any>::iterator i = variables.find(variable);
702	>
703	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
704	>	SelectionSet& bs){
705
706	<	if (i != variables.end()) {
707	<	if (i->second.type() == typeid(BitSet)) {
708	<	return boost::any_cast<BitSet>(i->second);
709	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
710	<	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
711	<	i->second =  bs; /**@todo fixme */
356	<	return bs;
357	<	}
706	>	boost::any withinSpec = instruction.value;
707	>	float distance;
708	>	if (withinSpec.type() == typeid(float)){
709	>	distance = boost::any_cast<float>(withinSpec);
710	>	} else if (withinSpec.type() == typeid(int)) {
711	>	distance = boost::any_cast<int>(withinSpec);
712		} else {
713	<	unrecognizedIdentifier(variable);
713	>	evalError("casting error in withinInstruction");
714	>	bs.clearAll();
715		}
716	+
717	+	bs = distanceFinder.find(bs, distance);
718	+	}
719
720	<	return bs;
721	<	}
364	<
365	<	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
720	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
721	>	SelectionSet& bs, int frame){
722
723	<	return nameFinder.match(name);
723	>	boost::any withinSpec = instruction.value;
724	>	float distance;
725	>	if (withinSpec.type() == typeid(float)){
726	>	distance = boost::any_cast<float>(withinSpec);
727	>	} else if (withinSpec.type() == typeid(int)) {
728	>	distance = boost::any_cast<int>(withinSpec);
729	>	} else {
730	>	evalError("casting error in withinInstruction");
731	>	bs.clearAll();
732	>	}
733	>
734	>	bs = distanceFinder.find(bs, distance, frame);
735	>	}
736	>
737	>	void SelectionEvaluator::define() {
738	>	assert(statement.size() >= 3);
739	>
740	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
741	>
742	>	variables.insert(VariablesType::value_type(variable,
743	>	expression(statement, 2)));
744	>	}
745	>
746
747	<	}
747	>	/** @todo */
748	>	void SelectionEvaluator::predefine(const std::string& script) {
749	>
750	>	if (compiler.compile("#predefine", script)) {
751	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
752	>	if (aatoken.size() != 1) {
753	>	evalError("predefinition does not have exactly 1 command:"
754	>	+ script);
755	>	return;
756	>	}
757	>	std::vector<Token> statement = aatoken[0];
758	>	if (statement.size() > 2) {
759	>	int tok = statement[1].tok;
760	>	if (tok == Token::identifier ||
761	>	(tok & Token::predefinedset) == Token::predefinedset) {
762	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
763	>	variables.insert(VariablesType::value_type(variable, statement));
764	>
765	>	} else {
766	>	evalError("invalid variable name:" + script);
767	>	}
768	>	}else {
769	>	evalError("bad predefinition length:" + script);
770	>	}
771	>
772	>	} else {
773	>	evalError("predefined set compile error:" + script +
774	>	"\ncompile error:" + compiler.getErrorMessage());
775	>	}
776	>	}
777
778	<	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
778	>	void SelectionEvaluator::select(SelectionSet& bs){
779	>	bs = expression(statement, 1);
780	>	}
781	>
782	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
783	>	bs = expression(statement, 1, frame);
784	>	}
785	>
786	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
787	>
788	>	SelectionSet bs = createSelectionSets();
789	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
790	>
791	>	if (i != variables.end()) {
792	>	if (i->second.type() == typeid(SelectionSet)) {
793	>	return boost::any_cast<SelectionSet>(i->second);
794	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
795	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
796	>	i->second =  bs; /**@todo fixme */
797	>	return bs;
798	>	}
799	>	} else {
800	>	unrecognizedIdentifier(variable);
801	>	}
802	>
803	>	return bs;
804	>	}
805	>
806	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
807	>	return nameFinder.match(name);
808	>	}
809	>
810	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
811		std::vector<Token>::const_iterator i;
812		for (i = tokens.begin(); i != tokens.end(); ++i) {
813	<	if (i->tok & Token::dynamic) {
814	<	return true;
815	<	}
813	>	if (i->tok & Token::dynamic) {
814	>	return true;
815	>	}
816		}
817	<
817	>
818		return false;
819	<	}
819	>	}
820
821	<	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
821	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
822		variables.clear();
823		//load predefine
824		//predefine();
825	<	}
825	>	}
826
827	<	BitSet SelectionEvaluator::evaluate() {
828	<	BitSet bs(nStuntDouble);
827	>	SelectionSet SelectionEvaluator::createSelectionSets() {
828	>	SelectionSet ss(nObjects);
829	>	return ss;
830	>	}
831	>
832	>	SelectionSet SelectionEvaluator::evaluate() {
833	>	SelectionSet bs = createSelectionSets();
834		if (isLoaded_) {
835	<	pc = 0;
836	<	instructionDispatchLoop(bs);
835	>	pc = 0;
836	>	instructionDispatchLoop(bs);
837		}
838	+	return bs;
839	+	}
840
841	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
842	+	SelectionSet bs = createSelectionSets();
843	+	if (isLoaded_) {
844	+	pc = 0;
845	+	instructionDispatchLoop(bs, frame);
846	+	}
847		return bs;
848	<	}
848	>	}
849
850	<	BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	<	BitSet bs(nStuntDouble);
850	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	>	SelectionSet bs = createSelectionSets();
852
853		if (value.type() == typeid(int)) {
854	<	int index = boost::any_cast<int>(value);
855	<	if (index < 0 || index >= bs.size()) {
856	<	invalidIndex(index);
857	<	} else {
858	<	indexFinder.find(index);
859	<	}
854	>	int index = boost::any_cast<int>(value);
855	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
856	>	invalidIndex(index);
857	>	} else {
858	>	bs = indexFinder.find(index);
859	>	}
860		} else if (value.type() == typeid(std::pair<int, int>)) {
861	<	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
862	<	assert(indexRange.first <= indexRange.second);
863	<	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
864	<	invalidIndexRange(indexRange);
865	<	}else {
866	<	indexFinder.find(indexRange.first, indexRange.second);
867	<	}
861	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
862	>	assert(indexRange.first <= indexRange.second);
863	>	if (indexRange.first < 0 ||
864	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
865	>	invalidIndexRange(indexRange);
866	>	}else {
867	>	bs = indexFinder.find(indexRange.first, indexRange.second);
868	>	}
869		}
870
871		return bs;
872	<	}
872	>	}
873
874	+	SelectionSet SelectionEvaluator::allInstruction() {
875	+	SelectionSet ss = createSelectionSets();
876	+
877	+	SimInfo::MoleculeIterator mi;
878	+	Molecule::AtomIterator ai;
879	+	Molecule::RigidBodyIterator rbIter;
880	+	Molecule::BondIterator bondIter;
881	+	Molecule::BendIterator bendIter;
882	+	Molecule::TorsionIterator torsionIter;
883	+	Molecule::InversionIterator inversionIter;
884	+
885	+	Molecule* mol;
886	+	Atom* atom;
887	+	RigidBody* rb;
888	+	Bond* bond;
889	+	Bend* bend;
890	+	Torsion* torsion;
891	+	Inversion* inversion;
892	+
893	+	// Doing the loop insures that we're actually on this processor.
894	+
895	+	for (mol = info->beginMolecule(mi); mol != NULL;
896	+	mol = info->nextMolecule(mi)) {
897	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
898	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
899	+	}
900	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
901	+	rb = mol->nextRigidBody(rbIter)) {
902	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
903	+	}
904	+	for (bond = mol->beginBond(bondIter); bond != NULL;
905	+	bond = mol->nextBond(bondIter)) {
906	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
907	+	}
908	+	for (bend = mol->beginBend(bendIter); bend != NULL;
909	+	bend = mol->nextBend(bendIter)) {
910	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
911	+	}
912	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
913	+	torsion = mol->nextTorsion(torsionIter)) {
914	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
915	+	}
916	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
917	+	inversion = mol->nextInversion(inversionIter)) {
918	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
919	+	}
920	+	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
921	+	}
922	+
923	+	return ss;
924	+	}
925	+
926	+	SelectionSet SelectionEvaluator::hull() {
927	+	SelectionSet bs = createSelectionSets();
928	+
929	+	bs = hullFinder.findHull();
930	+	surfaceArea_ = hullFinder.getSurfaceArea();
931	+	hasSurfaceArea_ = true;
932	+	return bs;
933	+	}
934	+
935	+
936	+	SelectionSet SelectionEvaluator::hull(int frame) {
937	+	SelectionSet bs = createSelectionSets();
938	+
939	+	bs = hullFinder.findHull(frame);
940	+
941	+	return bs;
942	+	}
943	+
944	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
945	+	RealType charge = 0.0;
946	+	AtomType* atomType = atom->getAtomType();
947	+
948	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
949	+	if ( fca.isFixedCharge() ) {
950	+	charge = fca.getCharge();
951	+	}
952	+
953	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
954	+	if ( fqa.isFluctuatingCharge() ) {
955	+	charge += atom->getFlucQPos();
956	+	}
957	+	return charge;
958	+	}
959	+
960	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
961	+	RealType charge = 0.0;
962	+	AtomType* atomType = atom->getAtomType();
963	+
964	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
965	+	if ( fca.isFixedCharge() ) {
966	+	charge = fca.getCharge();
967	+	}
968	+
969	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
970	+	if ( fqa.isFluctuatingCharge() ) {
971	+	charge += atom->getFlucQPos(frame);
972	+	}
973	+	return charge;
974	+	}
975	+
976		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

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