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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 282 by tim, Thu Feb 3 14:04:59 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>
44		#include "selection/SelectionEvaluator.hpp"
45	<	namespace oopse {
45	>	#include "primitives/Atom.hpp"
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
53
54	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
54	>	namespace OpenMD {
55	>
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	<	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;
85		aatoken = compiler.getAatokenCompiled();
86		linenumbers = compiler.getLineNumbers();
87		lineIndices = compiler.getLineIndices();
88	+
89	+	std::vector<std::vector<Token> >::const_iterator i;
90	+
91	+	isDynamic_ = false;
92	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
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() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i].clear();
65	<	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  string & filename) {
118	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
119	>	ifstrstream ifs(filename.c_str());
120	>	if (!ifs.is_open()) {
121	>	return false;
122	>	}
123	>
124	>	const int bufferSize = 65535;
125	>	char buffer[bufferSize];
126	>	std::string script;
127	>	while(ifs.getline(buffer, bufferSize)) {
128	>	script += buffer;
129	>	}
130	>	return loadScript(filename, script);
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	>	}
150	>	}
151
152	<	}
152	>	}
153
154	<	void SelectionEvaluator::instructionDispatchLoop(){
155	<
154	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
155	>
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();
166	<	break;
167	<	default:
168	<	unrecognizedCommand(token);
169	<	return;
170	<	}
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		}
102	–	}
172
173	<	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
105	<	int numberOfAtoms = viewer.getAtomCount();
106	<	BitSet bs;
107	<	BitSet[] stack = new BitSet[10];
108	<	int sp = 0;
173	>	}
174
175	<	for (int pc = pcStart; ; ++pc) {
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 116 | Line 187 | void SelectionEvaluator::instructionDispatchLoop(){
187		case Token::expressionEnd:
188		break;
189		case Token::all:
190	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
191	<	for (int i = numberOfAtoms; --i >= 0; )
121	<	bs.set(i);
190	>	bs = allInstruction();
191	>	stack.push(bs);
192		break;
193		case Token::none:
194	<	stack[sp++] = new BitSet();
194	>	bs = createSelectionSets();
195	>	stack.push(bs);
196		break;
197		case Token::opOr:
198	<	bs = stack[--sp];
199	<	stack[sp-1].or(bs);
198	>	bs= stack.top();
199	>	stack.pop();
200	>	stack.top() |= bs;
201		break;
202		case Token::opAnd:
203	<	bs = stack[--sp];
204	<	stack[sp-1].and(bs);
203	>	bs = stack.top();
204	>	stack.pop();
205	>	stack.top() &= bs;
206		break;
207		case Token::opNot:
208	<	bs = stack[sp - 1];
136	<	notSet(bs);
208	>	stack.top().flip();
209		break;
210		case Token::within:
211	<	bs = stack[sp - 1];
140	<	stack[sp - 1] = new BitSet();
141	<	withinInstruction(instruction, bs, stack[sp - 1]);
211	>	withinInstruction(instruction, stack.top());
212		break;
213	<	case Token::selected:
214	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
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	<
220	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
221		break;
222	<	case  Token::index:
223	<
222	>	case Token::index:
223	>	stack.push(indexInstruction(instruction.value));
224		break;
152	–	case Token::molname:
153	–
154	–	break;
155	–	case Token::molindex:
156	–	break;
225		case Token::identifier:
226	<	stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
226	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
227		break;
228		case Token::opLT:
229		case Token::opLE:
#	Line 163 | Line 231 | void SelectionEvaluator::instructionDispatchLoop(){
231		case Token::opGT:
232		case Token::opEQ:
233		case Token::opNE:
234	<	bs = stack[sp++] = new BitSet();
167	<	comparatorInstruction(instruction, bs);
234	>	stack.push(comparatorInstruction(instruction));
235		break;
236		default:
237		unrecognizedExpression();
238		}
239		}
240	<	if (sp != 1)
240	>	if (stack.size() != 1)
241		evalError("atom expression compiler error - stack over/underflow");
242	<	return stack[0];
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	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
256	<	int comparator = instruction.tok;
182	<	int property = instruction.intValue;
183	<	float propertyValue = 0; // just for temperature
184	<	int comparisonValue = ((Integer)instruction.value).intValue();
185	<	int numberOfAtoms = viewer.getAtomCount();
186	<	Frame frame = viewer.getFrame();
187	<	for (int i = 0; i < numberOfAtoms; ++i) {
188	<	Atom atom = frame.getAtomAt(i);
189	<	switch (property) {
190	<	case Token::mass:
191	<	//propertyValue = atom.getAtomNumber();
255	>	switch (instruction.tok) {
256	>	case Token::expressionBegin:
257		break;
258	<	case Token::charge:
194	<
258	>	case Token::expressionEnd:
259		break;
260	<	case Token::dipole:
261	<
262	<	break;
199	<	default:
200	<	unrecognizedAtomProperty(property);
201	<	}
202	<	bool match = false;
203	<	switch (comparator) {
204	<	case Token::opLT:
205	<	match = propertyValue < comparisonValue;
260	>	case Token::all:
261	>	bs = allInstruction();
262	>	stack.push(bs);
263		break;
264	<	case Token::opLE:
265	<	match = propertyValue <= comparisonValue;
264	>	case Token::none:
265	>	bs = SelectionSet(nObjects);
266	>	stack.push(bs);
267		break;
268	<	case Token::opGE:
269	<	match = propertyValue >= comparisonValue;
268	>	case Token::opOr:
269	>	bs = stack.top();
270	>	stack.pop();
271	>	stack.top() |= bs;
272		break;
273	<	case Token::opGT:
274	<	match = propertyValue > comparisonValue;
273	>	case Token::opAnd:
274	>	bs = stack.top();
275	>	stack.pop();
276	>	stack.top() &= bs;
277		break;
278	<	case Token::opEQ:
279	<	match = propertyValue == comparisonValue;
278	>	case Token::opNot:
279	>	stack.top().flip();
280		break;
281	+	case Token::within:
282	+	withinInstruction(instruction, stack.top(), frame);
283	+	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;
293	+	case Token::index:
294	+	stack.push(indexInstruction(instruction.value));
295	+	break;
296	+	case Token::identifier:
297	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
298	+	break;
299	+	case Token::opLT:
300	+	case Token::opLE:
301	+	case Token::opGE:
302	+	case Token::opGT:
303	+	case Token::opEQ:
304		case Token::opNE:
305	<	match = propertyValue != comparisonValue;
305	>	stack.push(comparatorInstruction(instruction, frame));
306		break;
307	+	default:
308	+	unrecognizedExpression();
309		}
223	–	if (match)
224	–	bs.set(i);
310		}
311	+	if (stack.size() != 1)
312	+	evalError("atom expression compiler error - stack over/underflow");
313	+
314	+	return stack.top();
315		}
316
228	–	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
317
318	<	boost::any withinSpec = instruction.value;
319	<	if (withinSpec.type() == typeid(float)){
320	<	withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
321	<	return;
322	<	}
318	>
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	>	SelectionSet bs = createSelectionSets();
324	>	bs.clearAll();
325
326	<	evalError("Unrecognized within parameter:" + withinSpec);
327	<	}
326	>	SimInfo::MoleculeIterator mi;
327	>	Molecule* mol;
328	>	Molecule::AtomIterator ai;
329	>	Atom* atom;
330	>	Molecule::RigidBodyIterator rbIter;
331	>	RigidBody* rb;
332
333	<	void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
334	<	Frame frame = viewer.getFrame();
335	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
336	<	if (bs.get(i)) {
337	<	Atom atom = frame.getAtomAt(i);
338	<	AtomIterator iterWithin =
339	<	frame.getWithinIterator(atom, distance);
246	<	while (iterWithin.hasNext())
247	<	bsResult.set(iterWithin.next().getAtomIndex());
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		}
350
351	<	void SelectionEvaluator::define() {
352	<	assert(statement.size() >= 3);
353	<
354	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
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	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
359	<	}
360	<	}
358	>	SimInfo::MoleculeIterator mi;
359	>	Molecule* mol;
360	>	Molecule::AtomIterator ai;
361	>	Atom* atom;
362	>	Molecule::RigidBodyIterator rbIter;
363	>	RigidBody* rb;
364
365	<	/** @todo */
366	<	void SelectionEvaluator::predefine(const std::string& script) {
365	>	for (mol = info->beginMolecule(mi); mol != NULL;
366	>	mol = info->nextMolecule(mi)) {
367
368	<	if (compiler.compile("#predefine", script)) {
265	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
266	<	if (aatoken.size() != 1) {
267	<	evalError("predefinition does not have exactly 1 command:"
268	<	+ script);
269	<	return;
270	<	}
271	<	std::vector<Token> statement = aatoken[0];
272	<	if (statement.size() > 2) {
273	<	int tok = statement[1].tok;
274	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
275	<	std::string variable = (std::string)statement[1].value;
276	<	variables.insert(std::make_pair(variable, statement));
368	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
369
370	<	} else {
371	<	evalError("invalid variable name:" + script);
372	<	}
373	<	}else {
374	<	evalError("bad predefinition length:" + script);
375	<	}
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	>	}
379
380	+	return bs;
381	+	}
382	+
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	+	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	<	} else {
438	<	evalError("predefined set compile error:" + script +
439	<	"\ncompile error:" + compiler.getErrorMessage());
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	<	}
459	>	if (match)
460	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
461
462	<	void SelectionEvaluator::select(){
463	<	viewer.setSelectionSet(expression(statement, 1));
295	<	}
462	>
463	>	}
464
465	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
466	<
467	<	std::map<std::string, boost::any>::iterator i = variables.find(variable);
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	<	if (i != variables.end()) {
472	<	if (i->second.type() == typeid(BitSet)) {
473	<	return boost::any_cast<BitSet>(i->second);
474	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
475	<	BitSet bs = expression(boost::any_cast(i->second), 2);
476	<	i->second =  bs; /**@todo fixme */
477	<	return bs;
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	+	}
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	<	}
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("casting error in withinInstruction");
710	>	bs.clearAll();
711	>	}
712	>
713	>	bs = distanceFinder.find(bs, distance);
714	>	}
715	>
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	+	/** @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	+	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(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);
797	+	}
798	+
799	+	return bs;
800	+	}
801	+
802	+	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
803	+	return nameFinder.match(name);
804	+	}
805	+
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	+	}
812	+	}
813	+
814	+	return false;
815	+	}
816	+
817	+	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
818	+	variables.clear();
819	+	//load predefine
820	+	//predefine();
821	+	}
822	+
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);
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	+	}
845	+
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.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 ||
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	+	}
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 282 by tim, Thu Feb 3 14:04:59 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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