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

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <stack>
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	<	bool SelectionEvaluator::loadScriptFileInternal(const  string & filename) {
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(bs);
147	>	break;
148	>	default:
149	>	unrecognizedCommand(token);
150	>	return;
151	>	}
152	>	}
153
154	<	}
154	>	}
155
156	<	void SelectionEvaluator::instructionDispatchLoop(){
157	<
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();
168	<	break;
169	<	default:
170	<	unrecognizedCommand(token);
171	<	return;
172	<	}
159	>	statement = aatoken[pc++];
160	>	statementLength = statement.size();
161	>	Token token = statement[0];
162	>	switch (token.tok) {
163	>	case Token::define:
164	>	define();
165	>	break;
166	>	case Token::select:
167	>	select(bs, frame);
168	>	break;
169	>	default:
170	>	unrecognizedCommand(token);
171	>	return;
172	>	}
173		}
102	–	}
174
175	<	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;
175	>	}
176
177	<	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
186		switch (instruction.tok) {
#	Line 116 | Line 189 | void SelectionEvaluator::instructionDispatchLoop(){
189		case Token::expressionEnd:
190		break;
191		case Token::all:
192	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
193	<	for (int i = numberOfAtoms; --i >= 0; )
121	<	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];
136	<	notSet(bs);
210	>	stack.top().flip();
211		break;
212		case Token::within:
213	<	bs = stack[sp - 1];
140	<	stack[sp - 1] = new BitSet();
141	<	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;
152	–	case Token::molname:
153	–
154	–	break;
155	–	case Token::molindex:
156	–	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 163 | Line 233 | void SelectionEvaluator::instructionDispatchLoop(){
233		case Token::opGT:
234		case Token::opEQ:
235		case Token::opNE:
236	<	bs = stack[sp++] = new BitSet();
167	<	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;
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();
257	>	switch (instruction.tok) {
258	>	case Token::expressionBegin:
259		break;
260	<	case Token::charge:
194	<
260	>	case Token::expressionEnd:
261		break;
262	<	case Token::dipole:
263	<
264	<	break;
199	<	default:
200	<	unrecognizedAtomProperty(property);
201	<	}
202	<	bool match = false;
203	<	switch (comparator) {
204	<	case Token::opLT:
205	<	match = propertyValue < comparisonValue;
262	>	case Token::all:
263	>	bs = allInstruction();
264	>	stack.push(bs);
265		break;
266	<	case Token::opLE:
267	<	match = propertyValue <= comparisonValue;
268	<	break;
210	<	case Token::opGE:
211	<	match = propertyValue >= comparisonValue;
266	>	case Token::none:
267	>	bs = SelectionSet(nObjects);
268	>	stack.push(bs);
269		break;
270	<	case Token::opGT:
271	<	match = propertyValue > comparisonValue;
270	>	case Token::opOr:
271	>	bs = stack.top();
272	>	stack.pop();
273	>	stack.top() |= bs;
274		break;
275	<	case Token::opEQ:
276	<	match = propertyValue == comparisonValue;
275	>	case Token::opAnd:
276	>	bs = stack.top();
277	>	stack.pop();
278	>	stack.top() &= bs;
279		break;
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		}
223	–	if (match)
224	–	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
228	–	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
319
320	<	boost::any withinSpec = instruction.value;
321	<	if (withinSpec.type() == typeid(float)){
322	<	withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
323	<	return;
324	<	}
320	>
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	<	evalError("Unrecognized within parameter:" + withinSpec);
329	<	}
328	>	SimInfo::MoleculeIterator mi;
329	>	Molecule* mol;
330	>	Molecule::AtomIterator ai;
331	>	Atom* atom;
332	>	Molecule::RigidBodyIterator rbIter;
333	>	RigidBody* rb;
334
335	<	void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
336	<	Frame frame = viewer.getFrame();
337	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
338	<	if (bs.get(i)) {
339	<	Atom atom = frame.getAtomAt(i);
340	<	AtomIterator iterWithin =
341	<	frame.getWithinIterator(atom, distance);
246	<	while (iterWithin.hasNext())
247	<	bsResult.set(iterWithin.next().getAtomIndex());
335	>	for (mol = info->beginMolecule(mi); mol != NULL;
336	>	mol = info->nextMolecule(mi)) {
337	>
338	>	compareProperty(mol, bs, property, comparator, comparisonValue);
339	>
340	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
341	>	compareProperty(atom, bs, property, comparator, comparisonValue);
342		}
343	+
344	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345	+	rb = mol->nextRigidBody(rbIter)) {
346	+	compareProperty(rb, bs, property, comparator, comparisonValue);
347	+	}
348		}
349	+
350	+	return bs;
351		}
352
353	<	void SelectionEvaluator::define() {
354	<	assert(statement.size() >= 3);
355	<
356	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
353	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
354	>	int comparator = instruction.tok;
355	>	int property = instruction.intValue;
356	>	float comparisonValue = boost::any_cast<float>(instruction.value);
357	>	SelectionSet bs = createSelectionSets();
358	>	bs.clearAll();
359
360	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
361	<	}
362	<	}
360	>	SimInfo::MoleculeIterator mi;
361	>	Molecule* mol;
362	>	Molecule::AtomIterator ai;
363	>	Atom* atom;
364	>	Molecule::RigidBodyIterator rbIter;
365	>	RigidBody* rb;
366
367	<	/** @todo */
368	<	void SelectionEvaluator::predefine(const std::string& script) {
367	>	for (mol = info->beginMolecule(mi); mol != NULL;
368	>	mol = info->nextMolecule(mi)) {
369
370	<	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));
370	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
371
372	<	} else {
373	<	evalError("invalid variable name:" + script);
374	<	}
375	<	}else {
376	<	evalError("bad predefinition length:" + script);
377	<	}
372	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
373	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
374	>	}
375	>
376	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
377	>	rb = mol->nextRigidBody(rbIter)) {
378	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
379	>	}
380	>	}
381
382	+	return bs;
383	+	}
384	+
385	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
386	+	int property, int comparator,
387	+	float comparisonValue) {
388	+	RealType propertyValue = 0.0;
389	+	Vector3d pos;
390	+
391	+	switch (property) {
392	+	case Token::mass:
393	+	propertyValue = sd->getMass();
394	+	break;
395	+	case Token::charge:
396	+	if (sd->isAtom()){
397	+	Atom* atom = static_cast<Atom*>(sd);
398	+	propertyValue = getCharge(atom);
399	+	} else if (sd->isRigidBody()) {
400	+	RigidBody* rb = static_cast<RigidBody*>(sd);
401	+	RigidBody::AtomIterator ai;
402	+	Atom* atom;
403	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
404	+	propertyValue+=  getCharge(atom);
405	+	}
406	+	}
407	+	break;
408	+	case Token::x:
409	+	propertyValue = sd->getPos().x();
410	+	break;
411	+	case Token::y:
412	+	propertyValue = sd->getPos().y();
413	+	break;
414	+	case Token::z:
415	+	propertyValue = sd->getPos().z();
416	+	break;
417	+	case Token::wrappedX:
418	+	pos = sd->getPos();
419	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	+	propertyValue = pos.x();
421	+	break;
422	+	case Token::wrappedY:
423	+	pos = sd->getPos();
424	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	+	propertyValue = pos.y();
426	+	break;
427	+	case Token::wrappedZ:
428	+	pos = sd->getPos();
429	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
430	+	propertyValue = pos.z();
431	+	break;
432	+	case Token::r:
433	+	propertyValue = sd->getPos().length();
434	+	break;
435	+	default:
436	+	unrecognizedAtomProperty(property);
437	+	}
438
439	<	} else {
440	<	evalError("predefined set compile error:" + script +
441	<	"\ncompile error:" + compiler.getErrorMessage());
439	>	bool match = false;
440	>	switch (comparator) {
441	>	case Token::opLT:
442	>	match = propertyValue < comparisonValue;
443	>	break;
444	>	case Token::opLE:
445	>	match = propertyValue <= comparisonValue;
446	>	break;
447	>	case Token::opGE:
448	>	match = propertyValue >= comparisonValue;
449	>	break;
450	>	case Token::opGT:
451	>	match = propertyValue > comparisonValue;
452	>	break;
453	>	case Token::opEQ:
454	>	match = propertyValue == comparisonValue;
455	>	break;
456	>	case Token::opNE:
457	>	match = propertyValue != comparisonValue;
458	>	break;
459		}
460
461	<	}
461	>	if (match)
462	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
463
464	<	void SelectionEvaluator::select(){
465	<	viewer.setSelectionSet(expression(statement, 1));
295	<	}
464	>
465	>	}
466
467	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
468	<
469	<	std::map<std::string, boost::any>::iterator i = variables.find(variable);
467	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
468	>	int property, int comparator,
469	>	float comparisonValue) {
470	>	RealType propertyValue = 0.0;
471	>	Vector3d pos;
472
473	<	if (i != variables.end()) {
474	<	if (i->second.type() == typeid(BitSet)) {
475	<	return boost::any_cast<BitSet>(i->second);
476	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
477	<	BitSet bs = expression(boost::any_cast(i->second), 2);
478	<	i->second =  bs; /**@todo fixme */
479	<	return bs;
473	>	switch (property) {
474	>	case Token::mass:
475	>	propertyValue = mol->getMass();
476	>	break;
477	>	case Token::charge:
478	>	{
479	>	Molecule::AtomIterator ai;
480	>	Atom* atom;
481	>	for (atom = mol->beginAtom(ai); atom != NULL;
482	>	atom = mol->nextAtom(ai)) {
483	>	propertyValue+=  getCharge(atom);
484		}
485	+	}
486	+	break;
487	+	case Token::x:
488	+	propertyValue = mol->getCom().x();
489	+	break;
490	+	case Token::y:
491	+	propertyValue = mol->getCom().y();
492	+	break;
493	+	case Token::z:
494	+	propertyValue = mol->getCom().z();
495	+	break;
496	+	case Token::wrappedX:
497	+	pos = mol->getCom();
498	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
499	+	propertyValue = pos.x();
500	+	break;
501	+	case Token::wrappedY:
502	+	pos = mol->getCom();
503	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
504	+	propertyValue = pos.y();
505	+	break;
506	+	case Token::wrappedZ:
507	+	pos = mol->getCom();
508	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
509	+	propertyValue = pos.z();
510	+	break;
511	+	case Token::r:
512	+	propertyValue = mol->getCom().length();
513	+	break;
514	+	default:
515	+	unrecognizedMoleculeProperty(property);
516		}
517	+
518	+	bool match = false;
519	+	switch (comparator) {
520	+	case Token::opLT:
521	+	match = propertyValue < comparisonValue;
522	+	break;
523	+	case Token::opLE:
524	+	match = propertyValue <= comparisonValue;
525	+	break;
526	+	case Token::opGE:
527	+	match = propertyValue >= comparisonValue;
528	+	break;
529	+	case Token::opGT:
530	+	match = propertyValue > comparisonValue;
531	+	break;
532	+	case Token::opEQ:
533	+	match = propertyValue == comparisonValue;
534	+	break;
535	+	case Token::opNE:
536	+	match = propertyValue != comparisonValue;
537	+	break;
538	+	}
539	+
540	+	if (match)
541	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
542	+	}
543
544	<	}
544	>	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
545	>	int property, int comparator,
546	>	float comparisonValue, int frame) {
547	>	RealType propertyValue = 0.0;
548	>	Vector3d pos;
549	>	switch (property) {
550	>	case Token::mass:
551	>	propertyValue = mol->getMass();
552	>	break;
553	>	case Token::charge:
554	>	{
555	>	Molecule::AtomIterator ai;
556	>	Atom* atom;
557	>	for (atom = mol->beginAtom(ai); atom != NULL;
558	>	atom = mol->nextAtom(ai)) {
559	>	propertyValue+=  getCharge(atom,frame);
560	>	}
561	>	}
562	>	break;
563	>	case Token::x:
564	>	propertyValue = mol->getCom(frame).x();
565	>	break;
566	>	case Token::y:
567	>	propertyValue = mol->getCom(frame).y();
568	>	break;
569	>	case Token::z:
570	>	propertyValue = mol->getCom(frame).z();
571	>	break;
572	>	case Token::wrappedX:
573	>	pos = mol->getCom(frame);
574	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
575	>	propertyValue = pos.x();
576	>	break;
577	>	case Token::wrappedY:
578	>	pos = mol->getCom(frame);
579	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
580	>	propertyValue = pos.y();
581	>	break;
582	>	case Token::wrappedZ:
583	>	pos = mol->getCom(frame);
584	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
585	>	propertyValue = pos.z();
586	>	break;
587	>
588	>	case Token::r:
589	>	propertyValue = mol->getCom(frame).length();
590	>	break;
591	>	default:
592	>	unrecognizedMoleculeProperty(property);
593	>	}
594	>
595	>	bool match = false;
596	>	switch (comparator) {
597	>	case Token::opLT:
598	>	match = propertyValue < comparisonValue;
599	>	break;
600	>	case Token::opLE:
601	>	match = propertyValue <= comparisonValue;
602	>	break;
603	>	case Token::opGE:
604	>	match = propertyValue >= comparisonValue;
605	>	break;
606	>	case Token::opGT:
607	>	match = propertyValue > comparisonValue;
608	>	break;
609	>	case Token::opEQ:
610	>	match = propertyValue == comparisonValue;
611	>	break;
612	>	case Token::opNE:
613	>	match = propertyValue != comparisonValue;
614	>	break;
615	>	}
616	>	if (match)
617	>	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
618	>
619	>
620	>	}
621	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
622	>	int property, int comparator,
623	>	float comparisonValue, int frame) {
624	>	RealType propertyValue = 0.0;
625	>	Vector3d pos;
626	>	switch (property) {
627	>	case Token::mass:
628	>	propertyValue = sd->getMass();
629	>	break;
630	>	case Token::charge:
631	>	if (sd->isAtom()){
632	>	Atom* atom = static_cast<Atom*>(sd);
633	>	propertyValue = getCharge(atom,frame);
634	>	} else if (sd->isRigidBody()) {
635	>	RigidBody* rb = static_cast<RigidBody*>(sd);
636	>	RigidBody::AtomIterator ai;
637	>	Atom* atom;
638	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
639	>	propertyValue+=  getCharge(atom,frame);
640	>	}
641	>	}
642	>	break;
643	>	case Token::x:
644	>	propertyValue = sd->getPos(frame).x();
645	>	break;
646	>	case Token::y:
647	>	propertyValue = sd->getPos(frame).y();
648	>	break;
649	>	case Token::z:
650	>	propertyValue = sd->getPos(frame).z();
651	>	break;
652	>	case Token::wrappedX:
653	>	pos = sd->getPos(frame);
654	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
655	>	propertyValue = pos.x();
656	>	break;
657	>	case Token::wrappedY:
658	>	pos = sd->getPos(frame);
659	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
660	>	propertyValue = pos.y();
661	>	break;
662	>	case Token::wrappedZ:
663	>	pos = sd->getPos(frame);
664	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
665	>	propertyValue = pos.z();
666	>	break;
667	>
668	>	case Token::r:
669	>	propertyValue = sd->getPos(frame).length();
670	>	break;
671	>	default:
672	>	unrecognizedAtomProperty(property);
673	>	}
674	>
675	>	bool match = false;
676	>	switch (comparator) {
677	>	case Token::opLT:
678	>	match = propertyValue < comparisonValue;
679	>	break;
680	>	case Token::opLE:
681	>	match = propertyValue <= comparisonValue;
682	>	break;
683	>	case Token::opGE:
684	>	match = propertyValue >= comparisonValue;
685	>	break;
686	>	case Token::opGT:
687	>	match = propertyValue > comparisonValue;
688	>	break;
689	>	case Token::opEQ:
690	>	match = propertyValue == comparisonValue;
691	>	break;
692	>	case Token::opNE:
693	>	match = propertyValue != comparisonValue;
694	>	break;
695	>	}
696	>	if (match)
697	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
698	>
699	>
700	>	}
701	>
702	>
703	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
704	>	SelectionSet& bs){
705	>
706	>	boost::any withinSpec = instruction.value;
707	>	float distance;
708	>	if (withinSpec.type() == typeid(float)){
709	>	distance = boost::any_cast<float>(withinSpec);
710	>	} else if (withinSpec.type() == typeid(int)) {
711	>	distance = boost::any_cast<int>(withinSpec);
712	>	} else {
713	>	evalError("casting error in withinInstruction");
714	>	bs.clearAll();
715	>	}
716	>
717	>	bs = distanceFinder.find(bs, distance);
718	>	}
719	>
720	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
721	>	SelectionSet& bs, int frame){
722	>
723	>	boost::any withinSpec = instruction.value;
724	>	float distance;
725	>	if (withinSpec.type() == typeid(float)){
726	>	distance = boost::any_cast<float>(withinSpec);
727	>	} else if (withinSpec.type() == typeid(int)) {
728	>	distance = boost::any_cast<int>(withinSpec);
729	>	} else {
730	>	evalError("casting error in withinInstruction");
731	>	bs.clearAll();
732	>	}
733	>
734	>	bs = distanceFinder.find(bs, distance, frame);
735	>	}
736	>
737	>	void SelectionEvaluator::define() {
738	>	assert(statement.size() >= 3);
739	>
740	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
741	>
742	>	variables.insert(VariablesType::value_type(variable,
743	>	expression(statement, 2)));
744	>	}
745	>
746
747	+	/** @todo */
748	+	void SelectionEvaluator::predefine(const std::string& script) {
749	+
750	+	if (compiler.compile("#predefine", script)) {
751	+	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
752	+	if (aatoken.size() != 1) {
753	+	evalError("predefinition does not have exactly 1 command:"
754	+	+ script);
755	+	return;
756	+	}
757	+	std::vector<Token> statement = aatoken[0];
758	+	if (statement.size() > 2) {
759	+	int tok = statement[1].tok;
760	+	if (tok == Token::identifier ||
761	+	(tok & Token::predefinedset) == Token::predefinedset) {
762	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
763	+	variables.insert(VariablesType::value_type(variable, statement));
764	+
765	+	} else {
766	+	evalError("invalid variable name:" + script);
767	+	}
768	+	}else {
769	+	evalError("bad predefinition length:" + script);
770	+	}
771	+
772	+	} else {
773	+	evalError("predefined set compile error:" + script +
774	+	"\ncompile error:" + compiler.getErrorMessage());
775	+	}
776	+	}
777	+
778	+	void SelectionEvaluator::select(SelectionSet& bs){
779	+	bs = expression(statement, 1);
780	+	}
781	+
782	+	void SelectionEvaluator::select(SelectionSet& bs, int frame){
783	+	bs = expression(statement, 1, frame);
784	+	}
785	+
786	+	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
787	+
788	+	SelectionSet bs = createSelectionSets();
789	+	std::map<std::string, boost::any>::iterator i = variables.find(variable);
790	+
791	+	if (i != variables.end()) {
792	+	if (i->second.type() == typeid(SelectionSet)) {
793	+	return boost::any_cast<SelectionSet>(i->second);
794	+	} else if (i->second.type() ==  typeid(std::vector<Token>)){
795	+	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
796	+	i->second =  bs; /**@todo fixme */
797	+	return bs;
798	+	}
799	+	} else {
800	+	unrecognizedIdentifier(variable);
801	+	}
802	+
803	+	return bs;
804	+	}
805	+
806	+	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
807	+	return nameFinder.match(name);
808	+	}
809	+
810	+	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
811	+	std::vector<Token>::const_iterator i;
812	+	for (i = tokens.begin(); i != tokens.end(); ++i) {
813	+	if (i->tok & Token::dynamic) {
814	+	return true;
815	+	}
816	+	}
817	+
818	+	return false;
819	+	}
820	+
821	+	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
822	+	variables.clear();
823	+	//load predefine
824	+	//predefine();
825	+	}
826	+
827	+	SelectionSet SelectionEvaluator::createSelectionSets() {
828	+	SelectionSet ss(nObjects);
829	+	return ss;
830	+	}
831	+
832	+	SelectionSet SelectionEvaluator::evaluate() {
833	+	SelectionSet bs = createSelectionSets();
834	+	if (isLoaded_) {
835	+	pc = 0;
836	+	instructionDispatchLoop(bs);
837	+	}
838	+	return bs;
839	+	}
840	+
841	+	SelectionSet SelectionEvaluator::evaluate(int frame) {
842	+	SelectionSet bs = createSelectionSets();
843	+	if (isLoaded_) {
844	+	pc = 0;
845	+	instructionDispatchLoop(bs, frame);
846	+	}
847	+	return bs;
848	+	}
849	+
850	+	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	+	SelectionSet bs = createSelectionSets();
852	+
853	+	if (value.type() == typeid(int)) {
854	+	int index = boost::any_cast<int>(value);
855	+	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
856	+	invalidIndex(index);
857	+	} else {
858	+	bs = indexFinder.find(index);
859	+	}
860	+	} else if (value.type() == typeid(std::pair<int, int>)) {
861	+	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
862	+	assert(indexRange.first <= indexRange.second);
863	+	if (indexRange.first < 0 ||
864	+	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
865	+	invalidIndexRange(indexRange);
866	+	}else {
867	+	bs = indexFinder.find(indexRange.first, indexRange.second);
868	+	}
869	+	}
870	+
871	+	return bs;
872	+	}
873	+
874	+	SelectionSet SelectionEvaluator::allInstruction() {
875	+	SelectionSet ss = createSelectionSets();
876	+
877	+	SimInfo::MoleculeIterator mi;
878	+	Molecule::AtomIterator ai;
879	+	Molecule::RigidBodyIterator rbIter;
880	+	Molecule::BondIterator bondIter;
881	+	Molecule::BendIterator bendIter;
882	+	Molecule::TorsionIterator torsionIter;
883	+	Molecule::InversionIterator inversionIter;
884	+
885	+	Molecule* mol;
886	+	Atom* atom;
887	+	RigidBody* rb;
888	+	Bond* bond;
889	+	Bend* bend;
890	+	Torsion* torsion;
891	+	Inversion* inversion;
892	+
893	+	// Doing the loop insures that we're actually on this processor.
894	+
895	+	for (mol = info->beginMolecule(mi); mol != NULL;
896	+	mol = info->nextMolecule(mi)) {
897	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
898	+	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
899	+	}
900	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
901	+	rb = mol->nextRigidBody(rbIter)) {
902	+	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
903	+	}
904	+	for (bond = mol->beginBond(bondIter); bond != NULL;
905	+	bond = mol->nextBond(bondIter)) {
906	+	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
907	+	}
908	+	for (bend = mol->beginBend(bendIter); bend != NULL;
909	+	bend = mol->nextBend(bendIter)) {
910	+	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
911	+	}
912	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
913	+	torsion = mol->nextTorsion(torsionIter)) {
914	+	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
915	+	}
916	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
917	+	inversion = mol->nextInversion(inversionIter)) {
918	+	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
919	+	}
920	+	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
921	+	}
922	+
923	+	return ss;
924	+	}
925	+
926	+	SelectionSet SelectionEvaluator::hull() {
927	+	SelectionSet bs = createSelectionSets();
928	+
929	+	bs = hullFinder.findHull();
930	+	surfaceArea_ = hullFinder.getSurfaceArea();
931	+	hasSurfaceArea_ = true;
932	+	return bs;
933	+	}
934	+
935	+
936	+	SelectionSet SelectionEvaluator::hull(int frame) {
937	+	SelectionSet bs = createSelectionSets();
938	+
939	+	bs = hullFinder.findHull(frame);
940	+
941	+	return bs;
942	+	}
943	+
944	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
945	+	RealType charge = 0.0;
946	+	AtomType* atomType = atom->getAtomType();
947	+
948	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
949	+	if ( fca.isFixedCharge() ) {
950	+	charge = fca.getCharge();
951	+	}
952	+
953	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
954	+	if ( fqa.isFluctuatingCharge() ) {
955	+	charge += atom->getFlucQPos();
956	+	}
957	+	return charge;
958	+	}
959	+
960	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
961	+	RealType charge = 0.0;
962	+	AtomType* atomType = atom->getAtomType();
963	+
964	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
965	+	if ( fca.isFixedCharge() ) {
966	+	charge = fca.getCharge();
967	+	}
968	+
969	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
970	+	if ( fqa.isFluctuatingCharge() ) {
971	+	charge += atom->getFlucQPos(frame);
972	+	}
973	+	return charge;
974	+	}
975	+
976		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 282 by tim, Thu Feb 3 14:04:59 2005 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

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