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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 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <stack>
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	>
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	>	}
67	>
68	>	bool SelectionEvaluator::loadScript(const std::string& filename,
69	>	const std::string& script) {
70	>	clearDefinitionsAndLoadPredefined();
71		this->filename = filename;
72		this->script = script;
73		if (! compiler.compile(filename, script)) {
74	<	error = true;
75	<	errorMessage = compiler.getErrorMessage();
76	<	return false;
74	>	error = true;
75	>	errorMessage = compiler.getErrorMessage();
76	>
77	>	sprintf( painCave.errMsg,
78	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
79	>	painCave.severity = OPENMD_ERROR;
80	>	painCave.isFatal = 1;
81	>	simError();
82	>	return false;
83		}
84
85		pc = 0;
86		aatoken = compiler.getAatokenCompiled();
87		linenumbers = compiler.getLineNumbers();
88		lineIndices = compiler.getLineIndices();
89	+
90	+	std::vector<std::vector<Token> >::const_iterator i;
91	+
92	+	isDynamic_ = false;
93	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
94	+	if (containDynamicToken(*i)) {
95	+	isDynamic_ = true;
96	+	break;
97	+	}
98	+	}
99	+
100	+	isLoaded_ = true;
101		return true;
102	<	}
102	>	}
103
104	<	void SelectionEvaluator::clearState() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i].clear();
65	<	scriptLevel = 0;
104	>	void SelectionEvaluator::clearState() {
105		error = false;
106		errorMessage = "";
107	<	}
107	>	}
108
109	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
109	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
110		clearState();
111		return loadScript("", script);
112	<	}
112	>	}
113
114	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
114	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
115		clearState();
116		return loadScriptFileInternal(filename);
117	<	}
117	>	}
118
119	<	bool SelectionEvaluator::loadScriptFileInternal(const  string & filename) {
119	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
120	>	ifstrstream ifs(filename.c_str());
121	>	if (!ifs.is_open()) {
122	>	return false;
123	>	}
124	>
125	>	const int bufferSize = 65535;
126	>	char buffer[bufferSize];
127	>	std::string script;
128	>	while(ifs.getline(buffer, bufferSize)) {
129	>	script += buffer;
130	>	}
131	>	return loadScript(filename, script);
132	>	}
133	>
134	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
135	>
136	>	while ( pc < aatoken.size()) {
137	>	statement = aatoken[pc++];
138	>	statementLength = statement.size();
139	>	Token token = statement[0];
140	>	switch (token.tok) {
141	>	case Token::define:
142	>	define();
143	>	break;
144	>	case Token::select:
145	>	select(bs);
146	>	break;
147	>	default:
148	>	unrecognizedCommand(token);
149	>	return;
150	>	}
151	>	}
152
153	<	}
153	>	}
154
155	<	void SelectionEvaluator::instructionDispatchLoop(){
156	<
155	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
156	>
157		while ( pc < aatoken.size()) {
158	<	statement = aatoken[pc++];
159	<	statementLength = statement.size();
160	<	Token token = statement[0];
161	<	switch (token.tok) {
162	<	case Token::define:
163	<	define();
164	<	break;
165	<	case Token::select:
166	<	select();
167	<	break;
168	<	default:
169	<	unrecognizedCommand(token);
170	<	return;
171	<	}
158	>	statement = aatoken[pc++];
159	>	statementLength = statement.size();
160	>	Token token = statement[0];
161	>	switch (token.tok) {
162	>	case Token::define:
163	>	define();
164	>	break;
165	>	case Token::select:
166	>	select(bs, frame);
167	>	break;
168	>	default:
169	>	unrecognizedCommand(token);
170	>	return;
171	>	}
172		}
102	–	}
173
174	<	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;
174	>	}
175
176	<	for (int pc = pcStart; ; ++pc) {
176	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
177	>	int pcStart) {
178	>	SelectionSet bs = createSelectionSets();
179	>	std::stack<SelectionSet> stack;
180	>	vector<int> bsSize = bs.size();
181	>
182	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
183		Token instruction = code[pc];
184
185		switch (instruction.tok) {
#	Line 116 | Line 188 | void SelectionEvaluator::instructionDispatchLoop(){
188		case Token::expressionEnd:
189		break;
190		case Token::all:
191	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
192	<	for (int i = numberOfAtoms; --i >= 0; )
121	<	bs.set(i);
191	>	bs = allInstruction();
192	>	stack.push(bs);
193		break;
194		case Token::none:
195	<	stack[sp++] = new BitSet();
195	>	bs = createSelectionSets();
196	>	stack.push(bs);
197		break;
198		case Token::opOr:
199	<	bs = stack[--sp];
200	<	stack[sp-1].or(bs);
199	>	bs= stack.top();
200	>	stack.pop();
201	>	stack.top() |= bs;
202		break;
203		case Token::opAnd:
204	<	bs = stack[--sp];
205	<	stack[sp-1].and(bs);
204	>	bs = stack.top();
205	>	stack.pop();
206	>	stack.top() &= bs;
207		break;
208		case Token::opNot:
209	<	bs = stack[sp - 1];
136	<	notSet(bs);
209	>	stack.top().flip();
210		break;
211		case Token::within:
212	<	bs = stack[sp - 1];
140	<	stack[sp - 1] = new BitSet();
141	<	withinInstruction(instruction, bs, stack[sp - 1]);
212	>	withinInstruction(instruction, stack.top());
213		break;
214	<	case Token::selected:
215	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
214	>	case Token::hull:
215	>	stack.push(hull());
216		break;
217	+	//case Token::selected:
218	+	//  stack.push(getSelectionSet());
219	+	//  break;
220		case Token::name:
221	<
221	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
222		break;
223	<	case  Token::index:
224	<
223	>	case Token::index:
224	>	stack.push(indexInstruction(instruction.value));
225		break;
152	–	case Token::molname:
153	–
154	–	break;
155	–	case Token::molindex:
156	–	break;
226		case Token::identifier:
227	<	stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
227	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
228		break;
229		case Token::opLT:
230		case Token::opLE:
#	Line 163 | Line 232 | void SelectionEvaluator::instructionDispatchLoop(){
232		case Token::opGT:
233		case Token::opEQ:
234		case Token::opNE:
235	<	bs = stack[sp++] = new BitSet();
167	<	comparatorInstruction(instruction, bs);
235	>	stack.push(comparatorInstruction(instruction));
236		break;
237		default:
238		unrecognizedExpression();
239		}
240		}
241	<	if (sp != 1)
241	>	if (stack.size() != 1)
242		evalError("atom expression compiler error - stack over/underflow");
243	<	return stack[0];
243	>
244	>	return stack.top();
245		}
246
247
248	+	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
249	+	int pcStart, int frame) {
250	+	SelectionSet bs = createSelectionSets();
251	+	std::stack<SelectionSet> stack;
252	+
253	+	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
254	+	Token instruction = code[pc];
255
256	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
257	<	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();
256	>	switch (instruction.tok) {
257	>	case Token::expressionBegin:
258		break;
259	<	case Token::charge:
194	<
259	>	case Token::expressionEnd:
260		break;
261	<	case Token::dipole:
262	<
263	<	break;
199	<	default:
200	<	unrecognizedAtomProperty(property);
201	<	}
202	<	bool match = false;
203	<	switch (comparator) {
204	<	case Token::opLT:
205	<	match = propertyValue < comparisonValue;
261	>	case Token::all:
262	>	bs = allInstruction();
263	>	stack.push(bs);
264		break;
265	<	case Token::opLE:
266	<	match = propertyValue <= comparisonValue;
265	>	case Token::none:
266	>	bs = SelectionSet(nObjects);
267	>	stack.push(bs);
268		break;
269	<	case Token::opGE:
270	<	match = propertyValue >= comparisonValue;
269	>	case Token::opOr:
270	>	bs = stack.top();
271	>	stack.pop();
272	>	stack.top() |= bs;
273		break;
274	<	case Token::opGT:
275	<	match = propertyValue > comparisonValue;
274	>	case Token::opAnd:
275	>	bs = stack.top();
276	>	stack.pop();
277	>	stack.top() &= bs;
278		break;
279	<	case Token::opEQ:
280	<	match = propertyValue == comparisonValue;
279	>	case Token::opNot:
280	>	stack.top().flip();
281		break;
282	+	case Token::within:
283	+	withinInstruction(instruction, stack.top(), frame);
284	+	break;
285	+	case Token::hull:
286	+	stack.push(hull(frame));
287	+	break;
288	+	//case Token::selected:
289	+	//  stack.push(getSelectionSet());
290	+	//  break;
291	+	case Token::name:
292	+	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
293	+	break;
294	+	case Token::index:
295	+	stack.push(indexInstruction(instruction.value));
296	+	break;
297	+	case Token::identifier:
298	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
299	+	break;
300	+	case Token::opLT:
301	+	case Token::opLE:
302	+	case Token::opGE:
303	+	case Token::opGT:
304	+	case Token::opEQ:
305		case Token::opNE:
306	<	match = propertyValue != comparisonValue;
306	>	stack.push(comparatorInstruction(instruction, frame));
307		break;
308	+	default:
309	+	unrecognizedExpression();
310		}
223	–	if (match)
224	–	bs.set(i);
311		}
312	+	if (stack.size() != 1)
313	+	evalError("atom expression compiler error - stack over/underflow");
314	+
315	+	return stack.top();
316		}
317
228	–	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
318
319	<	boost::any withinSpec = instruction.value;
320	<	if (withinSpec.type() == typeid(float)){
321	<	withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
322	<	return;
323	<	}
319	>
320	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
321	>	int comparator = instruction.tok;
322	>	int property = instruction.intValue;
323	>	float comparisonValue = boost::any_cast<float>(instruction.value);
324	>	SelectionSet bs = createSelectionSets();
325	>	bs.clearAll();
326
327	<	evalError("Unrecognized within parameter:" + withinSpec);
328	<	}
327	>	SimInfo::MoleculeIterator mi;
328	>	Molecule* mol;
329	>	Molecule::AtomIterator ai;
330	>	Atom* atom;
331	>	Molecule::RigidBodyIterator rbIter;
332	>	RigidBody* rb;
333
334	<	void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
335	<	Frame frame = viewer.getFrame();
336	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
337	<	if (bs.get(i)) {
338	<	Atom atom = frame.getAtomAt(i);
244	<	AtomIterator iterWithin =
245	<	frame.getWithinIterator(atom, distance);
246	<	while (iterWithin.hasNext())
247	<	bsResult.set(iterWithin.next().getAtomIndex());
334	>	for (mol = info->beginMolecule(mi); mol != NULL;
335	>	mol = info->nextMolecule(mi)) {
336	>
337	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
338	>	compareProperty(atom, bs, property, comparator, comparisonValue);
339		}
340	+
341	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
342	+	rb = mol->nextRigidBody(rbIter)) {
343	+	compareProperty(rb, bs, property, comparator, comparisonValue);
344	+	}
345		}
346	+
347	+	return bs;
348		}
349
350	<	void SelectionEvaluator::define() {
351	<	assert(statement.size() >= 3);
352	<
353	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
350	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
351	>	int comparator = instruction.tok;
352	>	int property = instruction.intValue;
353	>	float comparisonValue = boost::any_cast<float>(instruction.value);
354	>	SelectionSet bs = createSelectionSets();
355	>	bs.clearAll();
356
357	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
358	<	}
359	<	}
357	>	SimInfo::MoleculeIterator mi;
358	>	Molecule* mol;
359	>	Molecule::AtomIterator ai;
360	>	Atom* atom;
361	>	Molecule::RigidBodyIterator rbIter;
362	>	RigidBody* rb;
363
364	<	/** @todo */
365	<	void SelectionEvaluator::predefine(const std::string& script) {
364	>	for (mol = info->beginMolecule(mi); mol != NULL;
365	>	mol = info->nextMolecule(mi)) {
366
367	<	if (compiler.compile("#predefine", script)) {
368	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
369	<	if (aatoken.size() != 1) {
370	<	evalError("predefinition does not have exactly 1 command:"
371	<	+ script);
372	<	return;
373	<	}
374	<	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));
277	<
278	<	} else {
279	<	evalError("invalid variable name:" + script);
280	<	}
281	<	}else {
282	<	evalError("bad predefinition length:" + script);
283	<	}
284	<
285	<
286	<	} else {
287	<	evalError("predefined set compile error:" + script +
288	<	"\ncompile error:" + compiler.getErrorMessage());
367	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
368	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
369	>	}
370	>
371	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
372	>	rb = mol->nextRigidBody(rbIter)) {
373	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
374	>	}
375		}
376
377	<	}
377	>	return bs;
378	>	}
379
380	<	void SelectionEvaluator::select(){
381	<	viewer.setSelectionSet(expression(statement, 1));
382	<	}
380	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
381	>	int property, int comparator,
382	>	float comparisonValue) {
383	>	RealType propertyValue = 0.0;
384	>	Vector3d pos;
385
386	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
386	>	switch (property) {
387	>	case Token::mass:
388	>	propertyValue = sd->getMass();
389	>	break;
390	>	case Token::charge:
391	>	if (sd->isAtom()){
392	>	Atom* atom = static_cast<Atom*>(sd);
393	>	propertyValue = getCharge(atom);
394	>	} else if (sd->isRigidBody()) {
395	>	RigidBody* rb = static_cast<RigidBody*>(sd);
396	>	RigidBody::AtomIterator ai;
397	>	Atom* atom;
398	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
399	>	propertyValue+=  getCharge(atom);
400	>	}
401	>	}
402	>	break;
403	>	case Token::x:
404	>	propertyValue = sd->getPos().x();
405	>	break;
406	>	case Token::y:
407	>	propertyValue = sd->getPos().y();
408	>	break;
409	>	case Token::z:
410	>	propertyValue = sd->getPos().z();
411	>	break;
412	>	case Token::wrappedX:
413	>	pos = sd->getPos();
414	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
415	>	propertyValue = pos.x();
416	>	break;
417	>	case Token::wrappedY:
418	>	pos = sd->getPos();
419	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	>	propertyValue = pos.y();
421	>	break;
422	>	case Token::wrappedZ:
423	>	pos = sd->getPos();
424	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	>	propertyValue = pos.z();
426	>	break;
427	>	case Token::r:
428	>	propertyValue = sd->getPos().length();
429	>	break;
430	>	default:
431	>	unrecognizedAtomProperty(property);
432	>	}
433	>
434	>	bool match = false;
435	>	switch (comparator) {
436	>	case Token::opLT:
437	>	match = propertyValue < comparisonValue;
438	>	break;
439	>	case Token::opLE:
440	>	match = propertyValue <= comparisonValue;
441	>	break;
442	>	case Token::opGE:
443	>	match = propertyValue >= comparisonValue;
444	>	break;
445	>	case Token::opGT:
446	>	match = propertyValue > comparisonValue;
447	>	break;
448	>	case Token::opEQ:
449	>	match = propertyValue == comparisonValue;
450	>	break;
451	>	case Token::opNE:
452	>	match = propertyValue != comparisonValue;
453	>	break;
454	>	}
455
456	<	std::map<std::string, boost::any>::iterator i = variables.find(variable);
456	>	if (match)
457	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
458
459	+
460	+	}
461	+
462	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
463	+	int property, int comparator,
464	+	float comparisonValue, int frame) {
465	+	RealType propertyValue = 0.0;
466	+	Vector3d pos;
467	+	switch (property) {
468	+	case Token::mass:
469	+	propertyValue = sd->getMass();
470	+	break;
471	+	case Token::charge:
472	+	if (sd->isAtom()){
473	+	Atom* atom = static_cast<Atom*>(sd);
474	+	propertyValue = getCharge(atom,frame);
475	+	} else if (sd->isRigidBody()) {
476	+	RigidBody* rb = static_cast<RigidBody*>(sd);
477	+	RigidBody::AtomIterator ai;
478	+	Atom* atom;
479	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
480	+	propertyValue+=  getCharge(atom,frame);
481	+	}
482	+	}
483	+	break;
484	+	case Token::x:
485	+	propertyValue = sd->getPos(frame).x();
486	+	break;
487	+	case Token::y:
488	+	propertyValue = sd->getPos(frame).y();
489	+	break;
490	+	case Token::z:
491	+	propertyValue = sd->getPos(frame).z();
492	+	break;
493	+	case Token::wrappedX:
494	+	pos = sd->getPos(frame);
495	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
496	+	propertyValue = pos.x();
497	+	break;
498	+	case Token::wrappedY:
499	+	pos = sd->getPos(frame);
500	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
501	+	propertyValue = pos.y();
502	+	break;
503	+	case Token::wrappedZ:
504	+	pos = sd->getPos(frame);
505	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
506	+	propertyValue = pos.z();
507	+	break;
508	+
509	+	case Token::r:
510	+	propertyValue = sd->getPos(frame).length();
511	+	break;
512	+	default:
513	+	unrecognizedAtomProperty(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	+	if (match)
538	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
539	+
540	+
541	+	}
542	+
543	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
544	+	SelectionSet& bs){
545	+
546	+	boost::any withinSpec = instruction.value;
547	+	float distance;
548	+	if (withinSpec.type() == typeid(float)){
549	+	distance = boost::any_cast<float>(withinSpec);
550	+	} else if (withinSpec.type() == typeid(int)) {
551	+	distance = boost::any_cast<int>(withinSpec);
552	+	} else {
553	+	evalError("casting error in withinInstruction");
554	+	bs.clearAll();
555	+	}
556	+
557	+	bs = distanceFinder.find(bs, distance);
558	+	}
559	+
560	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
561	+	SelectionSet& bs, int frame){
562	+
563	+	boost::any withinSpec = instruction.value;
564	+	float distance;
565	+	if (withinSpec.type() == typeid(float)){
566	+	distance = boost::any_cast<float>(withinSpec);
567	+	} else if (withinSpec.type() == typeid(int)) {
568	+	distance = boost::any_cast<int>(withinSpec);
569	+	} else {
570	+	evalError("casting error in withinInstruction");
571	+	bs.clearAll();
572	+	}
573	+
574	+	bs = distanceFinder.find(bs, distance, frame);
575	+	}
576	+
577	+	void SelectionEvaluator::define() {
578	+	assert(statement.size() >= 3);
579	+
580	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
581	+
582	+	variables.insert(VariablesType::value_type(variable,
583	+	expression(statement, 2)));
584	+	}
585	+
586	+
587	+	/** @todo */
588	+	void SelectionEvaluator::predefine(const std::string& script) {
589	+
590	+	if (compiler.compile("#predefine", script)) {
591	+	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
592	+	if (aatoken.size() != 1) {
593	+	evalError("predefinition does not have exactly 1 command:"
594	+	+ script);
595	+	return;
596	+	}
597	+	std::vector<Token> statement = aatoken[0];
598	+	if (statement.size() > 2) {
599	+	int tok = statement[1].tok;
600	+	if (tok == Token::identifier ||
601	+	(tok & Token::predefinedset) == Token::predefinedset) {
602	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
603	+	variables.insert(VariablesType::value_type(variable, statement));
604	+
605	+	} else {
606	+	evalError("invalid variable name:" + script);
607	+	}
608	+	}else {
609	+	evalError("bad predefinition length:" + script);
610	+	}
611	+
612	+	} else {
613	+	evalError("predefined set compile error:" + script +
614	+	"\ncompile error:" + compiler.getErrorMessage());
615	+	}
616	+	}
617	+
618	+	void SelectionEvaluator::select(SelectionSet& bs){
619	+	bs = expression(statement, 1);
620	+	}
621	+
622	+	void SelectionEvaluator::select(SelectionSet& bs, int frame){
623	+	bs = expression(statement, 1, frame);
624	+	}
625	+
626	+	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
627	+
628	+	SelectionSet bs = createSelectionSets();
629	+	std::map<std::string, boost::any>::iterator i = variables.find(variable);
630	+
631		if (i != variables.end()) {
632	<	if (i->second.type() == typeid(BitSet)) {
633	<	return boost::any_cast<BitSet>(i->second);
634	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
635	<	BitSet bs = expression(boost::any_cast(i->second), 2);
636	<	i->second =  bs; /**@todo fixme */
637	<	return bs;
638	<	}
632	>	if (i->second.type() == typeid(SelectionSet)) {
633	>	return boost::any_cast<SelectionSet>(i->second);
634	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
635	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
636	>	i->second =  bs; /**@todo fixme */
637	>	return bs;
638	>	}
639	>	} else {
640	>	unrecognizedIdentifier(variable);
641		}
642	+
643	+	return bs;
644	+	}
645	+
646	+	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
647	+	return nameFinder.match(name);
648	+	}
649
650	<	}
650	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
651	>	std::vector<Token>::const_iterator i;
652	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
653	>	if (i->tok & Token::dynamic) {
654	>	return true;
655	>	}
656	>	}
657	>
658	>	return false;
659	>	}
660
661	+	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
662	+	variables.clear();
663	+	//load predefine
664	+	//predefine();
665	+	}
666	+
667	+	SelectionSet SelectionEvaluator::createSelectionSets() {
668	+	SelectionSet ss(nObjects);
669	+	return ss;
670	+	}
671	+
672	+	SelectionSet SelectionEvaluator::evaluate() {
673	+	SelectionSet bs = createSelectionSets();
674	+	if (isLoaded_) {
675	+	pc = 0;
676	+	instructionDispatchLoop(bs);
677	+	}
678	+	return bs;
679	+	}
680	+
681	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
682	+	SelectionSet bs = createSelectionSets();
683	+	if (isLoaded_) {
684	+	pc = 0;
685	+	instructionDispatchLoop(bs, frame);
686	+	}
687	+	return bs;
688	+	}
689	+
690	+	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
691	+	SelectionSet bs = createSelectionSets();
692	+
693	+	if (value.type() == typeid(int)) {
694	+	int index = boost::any_cast<int>(value);
695	+	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
696	+	invalidIndex(index);
697	+	} else {
698	+	bs = indexFinder.find(index);
699	+	}
700	+	} else if (value.type() == typeid(std::pair<int, int>)) {
701	+	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
702	+	assert(indexRange.first <= indexRange.second);
703	+	if (indexRange.first < 0 ||
704	+	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
705	+	invalidIndexRange(indexRange);
706	+	}else {
707	+	bs = indexFinder.find(indexRange.first, indexRange.second);
708	+	}
709	+	}
710	+
711	+	return bs;
712	+	}
713	+
714	+	SelectionSet SelectionEvaluator::allInstruction() {
715	+	SelectionSet ss = createSelectionSets();
716	+
717	+	SimInfo::MoleculeIterator mi;
718	+	Molecule::AtomIterator ai;
719	+	Molecule::RigidBodyIterator rbIter;
720	+	Molecule::BondIterator bondIter;
721	+	Molecule::BendIterator bendIter;
722	+	Molecule::TorsionIterator torsionIter;
723	+	Molecule::InversionIterator inversionIter;
724	+
725	+	Molecule* mol;
726	+	Atom* atom;
727	+	RigidBody* rb;
728	+	Bond* bond;
729	+	Bend* bend;
730	+	Torsion* torsion;
731	+	Inversion* inversion;
732	+
733	+	// Doing the loop insures that we're actually on this processor.
734	+
735	+	for (mol = info->beginMolecule(mi); mol != NULL;
736	+	mol = info->nextMolecule(mi)) {
737	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
738	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
739	+	}
740	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
741	+	rb = mol->nextRigidBody(rbIter)) {
742	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
743	+	}
744	+	for (bond = mol->beginBond(bondIter); bond != NULL;
745	+	bond = mol->nextBond(bondIter)) {
746	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
747	+	}
748	+	for (bend = mol->beginBend(bendIter); bend != NULL;
749	+	bend = mol->nextBend(bendIter)) {
750	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
751	+	}
752	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
753	+	torsion = mol->nextTorsion(torsionIter)) {
754	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
755	+	}
756	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
757	+	inversion = mol->nextInversion(inversionIter)) {
758	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
759	+	}
760	+	}
761	+
762	+	return ss;
763	+	}
764	+
765	+	SelectionSet SelectionEvaluator::hull() {
766	+	SelectionSet bs = createSelectionSets();
767	+
768	+	bs = hullFinder.findHull();
769	+	surfaceArea_ = hullFinder.getSurfaceArea();
770	+	hasSurfaceArea_ = true;
771	+	return bs;
772	+	}
773	+
774	+
775	+	SelectionSet SelectionEvaluator::hull(int frame) {
776	+	SelectionSet bs = createSelectionSets();
777	+
778	+	bs = hullFinder.findHull(frame);
779	+
780	+	return bs;
781	+	}
782	+
783	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
784	+	RealType charge = 0.0;
785	+	AtomType* atomType = atom->getAtomType();
786	+
787	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
788	+	if ( fca.isFixedCharge() ) {
789	+	charge = fca.getCharge();
790	+	}
791	+
792	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
793	+	if ( fqa.isFluctuatingCharge() ) {
794	+	charge += atom->getFlucQPos();
795	+	}
796	+	return charge;
797	+	}
798	+
799	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
800	+	RealType charge = 0.0;
801	+	AtomType* atomType = atom->getAtomType();
802	+
803	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
804	+	if ( fca.isFixedCharge() ) {
805	+	charge = fca.getCharge();
806	+	}
807	+
808	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
809	+	if ( fqa.isFluctuatingCharge() ) {
810	+	charge += atom->getFlucQPos(frame);
811	+	}
812	+	return charge;
813	+	}
814	+
815		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 282 by tim, Thu Feb 3 14:04:59 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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