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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 281 by tim, Wed Feb 2 23:13:11 2005 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 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	>
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	<	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;
87		aatoken = compiler.getAatokenCompiled();
88		linenumbers = compiler.getLineNumbers();
89		lineIndices = compiler.getLineIndices();
90	+
91	+	std::vector<std::vector<Token> >::const_iterator i;
92	+
93	+	isDynamic_ = false;
94	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
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() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i].clear();
65	<	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	<
121	<	void SelectionEvaluator::instructionDispatchLoop(){
122	<
120	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
121	>	ifstrstream ifs(filename.c_str());
122	>	if (!ifs.is_open()) {
123	>	return false;
124	>	}
125	>
126	>	const int bufferSize = 65535;
127	>	char buffer[bufferSize];
128	>	std::string script;
129	>	while(ifs.getline(buffer, bufferSize)) {
130	>	script += buffer;
131	>	}
132	>	return loadScript(filename, script);
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();
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		}
99	–	}
153
154	<	void SelectionEvaluator::predefine(const std::string& script) {
102	<	if (compiler.compile("#predefine", script)) {
103	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
104	<	if (aatoken.size() != 1) {
105	<	viewer.scriptStatus("predefinition does not have exactly 1 command:"
106	<	+ script);
107	<	return;
108	<	}
154	>	}
155
156	<	std::vector<Token> statement = aatoken[0];
157	<
158	<	if (statement.size() > 2) {
159	<	int tok = statement[1].tok;
160	<	if (tok == Token::identifier ||
161	<	(tok & Token::predefinedset) == Token::predefinedset) {
162	<	std::string variable = (std::string)statement[1].value;
163	<	variables.put(variable, statement);
164	<	} else {
165	<	viewer.scriptStatus("invalid variable name:" + script);
166	<	}
167	<	} else {
168	<	viewer.scriptStatus("bad predefinition length:" + script);
156	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
157	>
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		}
124	–	} else {
125	–	viewer.scriptStatus("predefined set compile error:" + script +
126	–	"\ncompile error:" + compiler.getErrorMessage());
173		}
174	+
175		}
176
177	<
178	<
179	<	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
180	<	int numberOfAtoms = viewer.getAtomCount();
181	<	BitSet bs;
182	<	BitSet[] stack = new BitSet[10];
183	<	int sp = 0;
137	<
138	<	for (int pc = pcStart; ; ++pc) {
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	<	if (logMessages)
141	<	viewer.scriptStatus("instruction=" + instruction);
185	>
186		switch (instruction.tok) {
187		case Token::expressionBegin:
188		break;
189		case Token::expressionEnd:
190	<	break expression_loop;
190	>	break;
191		case Token::all:
192	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
193	<	for (int i = numberOfAtoms; --i >= 0; )
150	<	bs.set(i);
192	>	bs = allInstruction();
193	>	stack.push(bs);
194		break;
195		case Token::none:
196	<	stack[sp++] = new BitSet();
196	>	bs = createSelectionSets();
197	>	stack.push(bs);
198		break;
199		case Token::opOr:
200	<	bs = stack[--sp];
201	<	stack[sp-1].or(bs);
200	>	bs= stack.top();
201	>	stack.pop();
202	>	stack.top() |= bs;
203		break;
204		case Token::opAnd:
205	<	bs = stack[--sp];
206	<	stack[sp-1].and(bs);
205	>	bs = stack.top();
206	>	stack.pop();
207	>	stack.top() &= bs;
208		break;
209		case Token::opNot:
210	<	bs = stack[sp - 1];
165	<	notSet(bs);
210	>	stack.top().flip();
211		break;
212		case Token::within:
213	<	bs = stack[sp - 1];
169	<	stack[sp - 1] = new BitSet();
170	<	withinInstruction(instruction, bs, stack[sp - 1]);
213	>	withinInstruction(instruction, stack.top());
214		break;
215	<	case Token::selected:
216	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
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	<
222	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
223		break;
224	<	case  Token::index:
225	<
224	>	case Token::index:
225	>	stack.push(indexInstruction(instruction.value));
226		break;
181	–	case Token::molname:
182	–
183	–	break;
184	–	case Token::molindex:
185	–	break;
227		case Token::identifier:
228	<	stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
228	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
229		break;
230		case Token::opLT:
231		case Token::opLE:
#	Line 192 | Line 233 | void SelectionEvaluator::instructionDispatchLoop(){
233		case Token::opGT:
234		case Token::opEQ:
235		case Token::opNE:
236	<	bs = stack[sp++] = new BitSet();
196	<	comparatorInstruction(instruction, bs);
236	>	stack.push(comparatorInstruction(instruction));
237		break;
238		default:
239		unrecognizedExpression();
240		}
241		}
242	<	if (sp != 1)
242	>	if (stack.size() != 1)
243		evalError("atom expression compiler error - stack over/underflow");
244	<	return stack[0];
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	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
258	<	int comparator = instruction.tok;
211	<	int property = instruction.intValue;
212	<	float propertyValue = 0; // just for temperature
213	<	int comparisonValue = ((Integer)instruction.value).intValue();
214	<	int numberOfAtoms = viewer.getAtomCount();
215	<	Frame frame = viewer.getFrame();
216	<	for (int i = 0; i < numberOfAtoms; ++i) {
217	<	Atom atom = frame.getAtomAt(i);
218	<	switch (property) {
219	<	case Token::mass:
220	<	//propertyValue = atom.getAtomNumber();
257	>	switch (instruction.tok) {
258	>	case Token::expressionBegin:
259		break;
260	<	case Token::charge:
223	<
260	>	case Token::expressionEnd:
261		break;
262	<	case Token::dipole:
263	<
264	<	break;
228	<	default:
229	<	unrecognizedAtomProperty(property);
230	<	}
231	<	bool match = false;
232	<	switch (comparator) {
233	<	case Token::opLT:
234	<	match = propertyValue < comparisonValue;
262	>	case Token::all:
263	>	bs = allInstruction();
264	>	stack.push(bs);
265		break;
266	<	case Token::opLE:
267	<	match = propertyValue <= comparisonValue;
266	>	case Token::none:
267	>	bs = SelectionSet(nObjects);
268	>	stack.push(bs);
269		break;
270	<	case Token::opGE:
271	<	match = propertyValue >= comparisonValue;
270	>	case Token::opOr:
271	>	bs = stack.top();
272	>	stack.pop();
273	>	stack.top() |= bs;
274		break;
275	<	case Token::opGT:
276	<	match = propertyValue > comparisonValue;
275	>	case Token::opAnd:
276	>	bs = stack.top();
277	>	stack.pop();
278	>	stack.top() &= bs;
279		break;
280	<	case Token::opEQ:
281	<	match = propertyValue == comparisonValue;
280	>	case Token::opNot:
281	>	stack.top().flip();
282		break;
283	+	case Token::within:
284	+	withinInstruction(instruction, stack.top(), frame);
285	+	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;
295	+	case Token::index:
296	+	stack.push(indexInstruction(instruction.value));
297	+	break;
298	+	case Token::identifier:
299	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
300	+	break;
301	+	case Token::opLT:
302	+	case Token::opLE:
303	+	case Token::opGE:
304	+	case Token::opGT:
305	+	case Token::opEQ:
306		case Token::opNE:
307	<	match = propertyValue != comparisonValue;
307	>	stack.push(comparatorInstruction(instruction, frame));
308		break;
309	+	default:
310	+	unrecognizedExpression();
311		}
252	–	if (match)
253	–	bs.set(i);
312		}
313	+	if (stack.size() != 1)
314	+	evalError("atom expression compiler error - stack over/underflow");
315	+
316	+	return stack.top();
317		}
318
257	–	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
319
259	–	boost::any withinSpec = instruction.value;
260	–	if (withinSpec instanceof Float) {
261	–	withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
262	–	return;
263	–	}
264	–	evalError("Unrecognized within parameter:" + withinSpec);
265	–	}
320
321	<	void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
322	<	Frame frame = viewer.getFrame();
323	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
324	<	if (bs.get(i)) {
325	<	Atom atom = frame.getAtomAt(i);
326	<	AtomIterator iterWithin =
327	<	frame.getWithinIterator(atom, distance);
328	<	while (iterWithin.hasNext())
329	<	bsResult.set(iterWithin.next().getAtomIndex());
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	>	SelectionSet bs = createSelectionSets();
326	>	bs.clearAll();
327	>
328	>	SimInfo::MoleculeIterator mi;
329	>	Molecule* mol;
330	>	Molecule::AtomIterator ai;
331	>	Atom* atom;
332	>	Molecule::RigidBodyIterator rbIter;
333	>	RigidBody* rb;
334	>
335	>	for (mol = info->beginMolecule(mi); mol != NULL;
336	>	mol = info->nextMolecule(mi)) {
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		}
278	–	}
347
348	<	void SelectionEvaluator::define() {
281	<	std::string variable = (std::string)statement[1].value;
282	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
348	>	return bs;
349		}
284	–	}
350
351	<	void SelectionEvaluator::predefine(Token[] statement) {
352	<	std::string variable = (std::string)statement[1].value;
353	<	variables.put(variable, statement);
351	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
352	>	int comparator = instruction.tok;
353	>	int property = instruction.intValue;
354	>	float comparisonValue = boost::any_cast<float>(instruction.value);
355	>	SelectionSet bs = createSelectionSets();
356	>	bs.clearAll();
357	>
358	>	SimInfo::MoleculeIterator mi;
359	>	Molecule* mol;
360	>	Molecule::AtomIterator ai;
361	>	Atom* atom;
362	>	Molecule::RigidBodyIterator rbIter;
363	>	RigidBody* rb;
364	>
365	>	for (mol = info->beginMolecule(mi); mol != NULL;
366	>	mol = info->nextMolecule(mi)) {
367	>
368	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
369	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
370	>	}
371	>
372	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
373	>	rb = mol->nextRigidBody(rbIter)) {
374	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
375	>	}
376	>	}
377	>
378	>	return bs;
379		}
380
381	<	void SelectionEvaluator::select(){
382	<	viewer.setSelectionSet(expression(statement, 1));
381	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
382	>	int property, int comparator,
383	>	float comparisonValue) {
384	>	RealType propertyValue = 0.0;
385	>	Vector3d pos;
386	>
387	>	switch (property) {
388	>	case Token::mass:
389	>	propertyValue = sd->getMass();
390	>	break;
391	>	case Token::charge:
392	>	if (sd->isAtom()){
393	>	Atom* atom = static_cast<Atom*>(sd);
394	>	propertyValue = getCharge(atom);
395	>	} else if (sd->isRigidBody()) {
396	>	RigidBody* rb = static_cast<RigidBody*>(sd);
397	>	RigidBody::AtomIterator ai;
398	>	Atom* atom;
399	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
400	>	propertyValue+=  getCharge(atom);
401	>	}
402	>	}
403	>	break;
404	>	case Token::x:
405	>	propertyValue = sd->getPos().x();
406	>	break;
407	>	case Token::y:
408	>	propertyValue = sd->getPos().y();
409	>	break;
410	>	case Token::z:
411	>	propertyValue = sd->getPos().z();
412	>	break;
413	>	case Token::wrappedX:
414	>	pos = sd->getPos();
415	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
416	>	propertyValue = pos.x();
417	>	break;
418	>	case Token::wrappedY:
419	>	pos = sd->getPos();
420	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
421	>	propertyValue = pos.y();
422	>	break;
423	>	case Token::wrappedZ:
424	>	pos = sd->getPos();
425	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
426	>	propertyValue = pos.z();
427	>	break;
428	>	case Token::r:
429	>	propertyValue = sd->getPos().length();
430	>	break;
431	>	default:
432	>	unrecognizedAtomProperty(property);
433	>	}
434	>
435	>	bool match = false;
436	>	switch (comparator) {
437	>	case Token::opLT:
438	>	match = propertyValue < comparisonValue;
439	>	break;
440	>	case Token::opLE:
441	>	match = propertyValue <= comparisonValue;
442	>	break;
443	>	case Token::opGE:
444	>	match = propertyValue >= comparisonValue;
445	>	break;
446	>	case Token::opGT:
447	>	match = propertyValue > comparisonValue;
448	>	break;
449	>	case Token::opEQ:
450	>	match = propertyValue == comparisonValue;
451	>	break;
452	>	case Token::opNE:
453	>	match = propertyValue != comparisonValue;
454	>	break;
455	>	}
456	>
457	>	if (match)
458	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
459	>
460	>
461		}
462	+
463	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
464	+	int property, int comparator,
465	+	float comparisonValue, int frame) {
466	+	RealType propertyValue = 0.0;
467	+	Vector3d pos;
468	+	switch (property) {
469	+	case Token::mass:
470	+	propertyValue = sd->getMass();
471	+	break;
472	+	case Token::charge:
473	+	if (sd->isAtom()){
474	+	Atom* atom = static_cast<Atom*>(sd);
475	+	propertyValue = getCharge(atom,frame);
476	+	} else if (sd->isRigidBody()) {
477	+	RigidBody* rb = static_cast<RigidBody*>(sd);
478	+	RigidBody::AtomIterator ai;
479	+	Atom* atom;
480	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
481	+	propertyValue+=  getCharge(atom,frame);
482	+	}
483	+	}
484	+	break;
485	+	case Token::x:
486	+	propertyValue = sd->getPos(frame).x();
487	+	break;
488	+	case Token::y:
489	+	propertyValue = sd->getPos(frame).y();
490	+	break;
491	+	case Token::z:
492	+	propertyValue = sd->getPos(frame).z();
493	+	break;
494	+	case Token::wrappedX:
495	+	pos = sd->getPos(frame);
496	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
497	+	propertyValue = pos.x();
498	+	break;
499	+	case Token::wrappedY:
500	+	pos = sd->getPos(frame);
501	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
502	+	propertyValue = pos.y();
503	+	break;
504	+	case Token::wrappedZ:
505	+	pos = sd->getPos(frame);
506	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
507	+	propertyValue = pos.z();
508	+	break;
509	+
510	+	case Token::r:
511	+	propertyValue = sd->getPos(frame).length();
512	+	break;
513	+	default:
514	+	unrecognizedAtomProperty(property);
515	+	}
516	+
517	+	bool match = false;
518	+	switch (comparator) {
519	+	case Token::opLT:
520	+	match = propertyValue < comparisonValue;
521	+	break;
522	+	case Token::opLE:
523	+	match = propertyValue <= comparisonValue;
524	+	break;
525	+	case Token::opGE:
526	+	match = propertyValue >= comparisonValue;
527	+	break;
528	+	case Token::opGT:
529	+	match = propertyValue > comparisonValue;
530	+	break;
531	+	case Token::opEQ:
532	+	match = propertyValue == comparisonValue;
533	+	break;
534	+	case Token::opNE:
535	+	match = propertyValue != comparisonValue;
536	+	break;
537	+	}
538	+	if (match)
539	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
540	+
541	+
542	+	}
543	+
544	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
545	+	SelectionSet& bs){
546	+
547	+	boost::any withinSpec = instruction.value;
548	+	float distance;
549	+	if (withinSpec.type() == typeid(float)){
550	+	distance = boost::any_cast<float>(withinSpec);
551	+	} else if (withinSpec.type() == typeid(int)) {
552	+	distance = boost::any_cast<int>(withinSpec);
553	+	} else {
554	+	evalError("casting error in withinInstruction");
555	+	bs.clearAll();
556	+	}
557	+
558	+	bs = distanceFinder.find(bs, distance);
559	+	}
560	+
561	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
562	+	SelectionSet& bs, int frame){
563	+
564	+	boost::any withinSpec = instruction.value;
565	+	float distance;
566	+	if (withinSpec.type() == typeid(float)){
567	+	distance = boost::any_cast<float>(withinSpec);
568	+	} else if (withinSpec.type() == typeid(int)) {
569	+	distance = boost::any_cast<int>(withinSpec);
570	+	} else {
571	+	evalError("casting error in withinInstruction");
572	+	bs.clearAll();
573	+	}
574	+
575	+	bs = distanceFinder.find(bs, distance, frame);
576	+	}
577
578	<	}
578	>	void SelectionEvaluator::define() {
579	>	assert(statement.size() >= 3);
580	>
581	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
582	>
583	>	variables.insert(VariablesType::value_type(variable,
584	>	expression(statement, 2)));
585	>	}
586	>
587	>
588	>	/** @todo */
589	>	void SelectionEvaluator::predefine(const std::string& script) {
590	>
591	>	if (compiler.compile("#predefine", script)) {
592	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
593	>	if (aatoken.size() != 1) {
594	>	evalError("predefinition does not have exactly 1 command:"
595	>	+ script);
596	>	return;
597	>	}
598	>	std::vector<Token> statement = aatoken[0];
599	>	if (statement.size() > 2) {
600	>	int tok = statement[1].tok;
601	>	if (tok == Token::identifier ||
602	>	(tok & Token::predefinedset) == Token::predefinedset) {
603	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
604	>	variables.insert(VariablesType::value_type(variable, statement));
605	>
606	>	} else {
607	>	evalError("invalid variable name:" + script);
608	>	}
609	>	}else {
610	>	evalError("bad predefinition length:" + script);
611	>	}
612	>
613	>	} else {
614	>	evalError("predefined set compile error:" + script +
615	>	"\ncompile error:" + compiler.getErrorMessage());
616	>	}
617	>	}
618	>
619	>	void SelectionEvaluator::select(SelectionSet& bs){
620	>	bs = expression(statement, 1);
621	>	}
622	>
623	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
624	>	bs = expression(statement, 1, frame);
625	>	}
626	>
627	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
628	>
629	>	SelectionSet bs = createSelectionSets();
630	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
631	>
632	>	if (i != variables.end()) {
633	>	if (i->second.type() == typeid(SelectionSet)) {
634	>	return boost::any_cast<SelectionSet>(i->second);
635	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
636	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
637	>	i->second =  bs; /**@todo fixme */
638	>	return bs;
639	>	}
640	>	} else {
641	>	unrecognizedIdentifier(variable);
642	>	}
643	>
644	>	return bs;
645	>	}
646	>
647	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
648	>	return nameFinder.match(name);
649	>	}
650	>
651	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
652	>	std::vector<Token>::const_iterator i;
653	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
654	>	if (i->tok & Token::dynamic) {
655	>	return true;
656	>	}
657	>	}
658	>
659	>	return false;
660	>	}
661	>
662	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
663	>	variables.clear();
664	>	//load predefine
665	>	//predefine();
666	>	}
667	>
668	>	SelectionSet SelectionEvaluator::createSelectionSets() {
669	>	SelectionSet ss(nObjects);
670	>	return ss;
671	>	}
672	>
673	>	SelectionSet SelectionEvaluator::evaluate() {
674	>	SelectionSet bs = createSelectionSets();
675	>	if (isLoaded_) {
676	>	pc = 0;
677	>	instructionDispatchLoop(bs);
678	>	}
679	>	return bs;
680	>	}
681	>
682	>	SelectionSet SelectionEvaluator::evaluate(int frame) {
683	>	SelectionSet bs = createSelectionSets();
684	>	if (isLoaded_) {
685	>	pc = 0;
686	>	instructionDispatchLoop(bs, frame);
687	>	}
688	>	return bs;
689	>	}
690	>
691	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
692	>	SelectionSet bs = createSelectionSets();
693	>
694	>	if (value.type() == typeid(int)) {
695	>	int index = boost::any_cast<int>(value);
696	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
697	>	invalidIndex(index);
698	>	} else {
699	>	bs = indexFinder.find(index);
700	>	}
701	>	} else if (value.type() == typeid(std::pair<int, int>)) {
702	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
703	>	assert(indexRange.first <= indexRange.second);
704	>	if (indexRange.first < 0 ||
705	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
706	>	invalidIndexRange(indexRange);
707	>	}else {
708	>	bs = indexFinder.find(indexRange.first, indexRange.second);
709	>	}
710	>	}
711	>
712	>	return bs;
713	>	}
714	>
715	>	SelectionSet SelectionEvaluator::allInstruction() {
716	>	SelectionSet ss = createSelectionSets();
717	>
718	>	SimInfo::MoleculeIterator mi;
719	>	Molecule::AtomIterator ai;
720	>	Molecule::RigidBodyIterator rbIter;
721	>	Molecule::BondIterator bondIter;
722	>	Molecule::BendIterator bendIter;
723	>	Molecule::TorsionIterator torsionIter;
724	>	Molecule::InversionIterator inversionIter;
725	>
726	>	Molecule* mol;
727	>	Atom* atom;
728	>	RigidBody* rb;
729	>	Bond* bond;
730	>	Bend* bend;
731	>	Torsion* torsion;
732	>	Inversion* inversion;
733	>
734	>	// Doing the loop insures that we're actually on this processor.
735	>
736	>	for (mol = info->beginMolecule(mi); mol != NULL;
737	>	mol = info->nextMolecule(mi)) {
738	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
739	>	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
740	>	}
741	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
742	>	rb = mol->nextRigidBody(rbIter)) {
743	>	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
744	>	}
745	>	for (bond = mol->beginBond(bondIter); bond != NULL;
746	>	bond = mol->nextBond(bondIter)) {
747	>	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
748	>	}
749	>	for (bend = mol->beginBend(bendIter); bend != NULL;
750	>	bend = mol->nextBend(bendIter)) {
751	>	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
752	>	}
753	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
754	>	torsion = mol->nextTorsion(torsionIter)) {
755	>	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
756	>	}
757	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
758	>	inversion = mol->nextInversion(inversionIter)) {
759	>	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
760	>	}
761	>	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
762	>	}
763	>
764	>	return ss;
765	>	}
766	>
767	>	SelectionSet SelectionEvaluator::hull() {
768	>	SelectionSet bs = createSelectionSets();
769	>
770	>	bs = hullFinder.findHull();
771	>	surfaceArea_ = hullFinder.getSurfaceArea();
772	>	hasSurfaceArea_ = true;
773	>	return bs;
774	>	}
775	>
776	>
777	>	SelectionSet SelectionEvaluator::hull(int frame) {
778	>	SelectionSet bs = createSelectionSets();
779	>
780	>	bs = hullFinder.findHull(frame);
781	>
782	>	return bs;
783	>	}
784	>
785	>	RealType SelectionEvaluator::getCharge(Atom* atom) {
786	>	RealType charge = 0.0;
787	>	AtomType* atomType = atom->getAtomType();
788	>
789	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
790	>	if ( fca.isFixedCharge() ) {
791	>	charge = fca.getCharge();
792	>	}
793	>
794	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
795	>	if ( fqa.isFluctuatingCharge() ) {
796	>	charge += atom->getFlucQPos();
797	>	}
798	>	return charge;
799	>	}
800	>
801	>	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
802	>	RealType charge = 0.0;
803	>	AtomType* atomType = atom->getAtomType();
804	>
805	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
806	>	if ( fca.isFixedCharge() ) {
807	>	charge = fca.getCharge();
808	>	}
809	>
810	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
811	>	if ( fqa.isFluctuatingCharge() ) {
812	>	charge += atom->getFlucQPos(frame);
813	>	}
814	>	return charge;
815	>	}
816	>
817	>	}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 281 by tim, Wed Feb 2 23:13:11 2005 UTC vs.
Revision 2052 by gezelter, Fri Jan 9 19:06:35 2015 UTC

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