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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 1782 by gezelter, Wed Aug 22 02:28:28 2012 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, 24107 (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
51	+	namespace OpenMD {
52
53	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
53	>
54	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
55	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
56	>	indexFinder(info),
57	>	isLoaded_(false){
58	>	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
59	>	}
60	>
61	>	bool SelectionEvaluator::loadScript(const std::string& filename,
62	>	const std::string& script) {
63	>	clearDefinitionsAndLoadPredefined();
64		this->filename = filename;
65		this->script = script;
66		if (! compiler.compile(filename, script)) {
67	<	error = true;
68	<	errorMessage = compiler.getErrorMessage();
69	<	return false;
67	>	error = true;
68	>	errorMessage = compiler.getErrorMessage();
69	>
70	>	sprintf( painCave.errMsg,
71	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
72	>	painCave.severity = OPENMD_ERROR;
73	>	painCave.isFatal = 1;
74	>	simError();
75	>	return false;
76		}
77
78		pc = 0;
79		aatoken = compiler.getAatokenCompiled();
80		linenumbers = compiler.getLineNumbers();
81		lineIndices = compiler.getLineIndices();
82	+
83	+	std::vector<std::vector<Token> >::const_iterator i;
84	+
85	+	isDynamic_ = false;
86	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
87	+	if (containDynamicToken(*i)) {
88	+	isDynamic_ = true;
89	+	break;
90	+	}
91	+	}
92	+
93	+	isLoaded_ = true;
94		return true;
95	<	}
95	>	}
96
97	<	void SelectionEvaluator::clearState() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i].clear();
65	<	scriptLevel = 0;
97	>	void SelectionEvaluator::clearState() {
98		error = false;
99		errorMessage = "";
100	<	}
100	>	}
101
102	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
102	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
103		clearState();
104		return loadScript("", script);
105	<	}
105	>	}
106
107	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
107	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
108		clearState();
109		return loadScriptFileInternal(filename);
110	<	}
110	>	}
111
112	<	bool SelectionEvaluator::loadScriptFileInternal(const  string & filename) {
113	<
114	<	}
115	<
116	<	void SelectionEvaluator::instructionDispatchLoop(){
117	<
112	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
113	>	ifstrstream ifs(filename.c_str());
114	>	if (!ifs.is_open()) {
115	>	return false;
116	>	}
117	>
118	>	const int bufferSize = 65535;
119	>	char buffer[bufferSize];
120	>	std::string script;
121	>	while(ifs.getline(buffer, bufferSize)) {
122	>	script += buffer;
123	>	}
124	>	return loadScript(filename, script);
125	>	}
126	>
127	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
128	>
129		while ( pc < aatoken.size()) {
130	<	statement = aatoken[pc++];
131	<	statementLength = statement.size();
132	<	Token token = statement[0];
133	<	switch (token.tok) {
134	<	case Token::define:
135	<	define();
136	<	break;
137	<	case Token::select:
138	<	select();
139	<	break;
140	<	default:
141	<	unrecognizedCommand(token);
142	<	return;
143	<	}
130	>	statement = aatoken[pc++];
131	>	statementLength = statement.size();
132	>	Token token = statement[0];
133	>	switch (token.tok) {
134	>	case Token::define:
135	>	define();
136	>	break;
137	>	case Token::select:
138	>	select(bs);
139	>	break;
140	>	default:
141	>	unrecognizedCommand(token);
142	>	return;
143	>	}
144		}
102	–	}
145
146	<	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;
146	>	}
147
148	<	for (int pc = pcStart; ; ++pc) {
148	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
149	>	int pcStart) {
150	>	OpenMDBitSet bs;
151	>	std::stack<OpenMDBitSet> stack;
152	>
153	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
154		Token instruction = code[pc];
155
156		switch (instruction.tok) {
#	Line 116 | Line 159 | void SelectionEvaluator::instructionDispatchLoop(){
159		case Token::expressionEnd:
160		break;
161		case Token::all:
162	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
163	<	for (int i = numberOfAtoms; --i >= 0; )
164	<	bs.set(i);
162	>	bs = OpenMDBitSet(nStuntDouble);
163	>	bs.setAll();
164	>	stack.push(bs);
165		break;
166		case Token::none:
167	<	stack[sp++] = new BitSet();
167	>	bs = OpenMDBitSet(nStuntDouble);
168	>	stack.push(bs);
169		break;
170		case Token::opOr:
171	<	bs = stack[--sp];
172	<	stack[sp-1].or(bs);
171	>	bs = stack.top();
172	>	stack.pop();
173	>	stack.top() |= bs;
174		break;
175		case Token::opAnd:
176	<	bs = stack[--sp];
177	<	stack[sp-1].and(bs);
176	>	bs = stack.top();
177	>	stack.pop();
178	>	stack.top() &= bs;
179		break;
180		case Token::opNot:
181	<	bs = stack[sp - 1];
136	<	notSet(bs);
181	>	stack.top().flip();
182		break;
183		case Token::within:
184	<	bs = stack[sp - 1];
140	<	stack[sp - 1] = new BitSet();
141	<	withinInstruction(instruction, bs, stack[sp - 1]);
184	>	withinInstruction(instruction, stack.top());
185		break;
186	<	case Token::selected:
187	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
186	>	case Token::hull:
187	>	stack.push(hull());
188		break;
189	+	//case Token::selected:
190	+	//  stack.push(getSelectionSet());
191	+	//  break;
192		case Token::name:
193	<
193	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
194		break;
195	<	case  Token::index:
196	<
195	>	case Token::index:
196	>	stack.push(indexInstruction(instruction.value));
197		break;
152	–	case Token::molname:
153	–
154	–	break;
155	–	case Token::molindex:
156	–	break;
198		case Token::identifier:
199	<	stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
199	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
200		break;
201		case Token::opLT:
202		case Token::opLE:
#	Line 163 | Line 204 | void SelectionEvaluator::instructionDispatchLoop(){
204		case Token::opGT:
205		case Token::opEQ:
206		case Token::opNE:
207	<	bs = stack[sp++] = new BitSet();
167	<	comparatorInstruction(instruction, bs);
207	>	stack.push(comparatorInstruction(instruction));
208		break;
209		default:
210		unrecognizedExpression();
211		}
212		}
213	<	if (sp != 1)
213	>	if (stack.size() != 1)
214		evalError("atom expression compiler error - stack over/underflow");
215	<	return stack[0];
215	>
216	>	return stack.top();
217		}
218
219
220
221	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
221	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
222		int comparator = instruction.tok;
223		int property = instruction.intValue;
224	<	float propertyValue = 0; // just for temperature
225	<	int comparisonValue = ((Integer)instruction.value).intValue();
226	<	int numberOfAtoms = viewer.getAtomCount();
227	<	Frame frame = viewer.getFrame();
228	<	for (int i = 0; i < numberOfAtoms; ++i) {
229	<	Atom atom = frame.getAtomAt(i);
230	<	switch (property) {
231	<	case Token::mass:
232	<	//propertyValue = atom.getAtomNumber();
233	<	break;
193	<	case Token::charge:
224	>	float comparisonValue = boost::any_cast<float>(instruction.value);
225	>	OpenMDBitSet bs(nStuntDouble);
226	>	bs.clearAll();
227	>
228	>	SimInfo::MoleculeIterator mi;
229	>	Molecule* mol;
230	>	Molecule::AtomIterator ai;
231	>	Atom* atom;
232	>	Molecule::RigidBodyIterator rbIter;
233	>	RigidBody* rb;
234
235	<	break;
236	<	case Token::dipole:
235	>	for (mol = info->beginMolecule(mi); mol != NULL;
236	>	mol = info->nextMolecule(mi)) {
237
238	<	break;
239	<	default:
200	<	unrecognizedAtomProperty(property);
238	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
239	>	compareProperty(atom, bs, property, comparator, comparisonValue);
240		}
241	<	bool match = false;
242	<	switch (comparator) {
243	<	case Token::opLT:
244	<	match = propertyValue < comparisonValue;
206	<	break;
207	<	case Token::opLE:
208	<	match = propertyValue <= comparisonValue;
209	<	break;
210	<	case Token::opGE:
211	<	match = propertyValue >= comparisonValue;
212	<	break;
213	<	case Token::opGT:
214	<	match = propertyValue > comparisonValue;
215	<	break;
216	<	case Token::opEQ:
217	<	match = propertyValue == comparisonValue;
218	<	break;
219	<	case Token::opNE:
220	<	match = propertyValue != comparisonValue;
221	<	break;
241	>
242	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
243	>	rb = mol->nextRigidBody(rbIter)) {
244	>	compareProperty(rb, bs, property, comparator, comparisonValue);
245		}
223	–	if (match)
224	–	bs.set(i);
246		}
247	+
248	+	return bs;
249		}
250
251	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
252	<
253	<	boost::any withinSpec = instruction.value;
254	<	if (withinSpec.type() == typeid(float)){
255	<	withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
256	<	return;
257	<	}
258	<
259	<	evalError("Unrecognized within parameter:" + withinSpec);
260	<	}
261	<
262	<	void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
263	<	Frame frame = viewer.getFrame();
264	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
265	<	if (bs.get(i)) {
266	<	Atom atom = frame.getAtomAt(i);
267	<	AtomIterator iterWithin =
268	<	frame.getWithinIterator(atom, distance);
269	<	while (iterWithin.hasNext())
247	<	bsResult.set(iterWithin.next().getAtomIndex());
251	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
252	>	int property, int comparator,
253	>	float comparisonValue) {
254	>	RealType propertyValue = 0.0;
255	>	switch (property) {
256	>	case Token::mass:
257	>	propertyValue = sd->getMass();
258	>	break;
259	>	case Token::charge:
260	>	if (sd->isAtom()){
261	>	Atom* atom = static_cast<Atom*>(sd);
262	>	propertyValue = getCharge(atom);
263	>	} else if (sd->isRigidBody()) {
264	>	RigidBody* rb = static_cast<RigidBody*>(sd);
265	>	RigidBody::AtomIterator ai;
266	>	Atom* atom;
267	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
268	>	propertyValue+=  getCharge(atom);
269	>	}
270		}
271	+	break;
272	+	case Token::x:
273	+	propertyValue = sd->getPos().x();
274	+	break;
275	+	case Token::y:
276	+	propertyValue = sd->getPos().y();
277	+	break;
278	+	case Token::z:
279	+	propertyValue = sd->getPos().z();
280	+	break;
281	+	case Token::r:
282	+	propertyValue = sd->getPos().length();
283	+	break;
284	+	default:
285	+	unrecognizedAtomProperty(property);
286		}
287	+
288	+	bool match = false;
289	+	switch (comparator) {
290	+	case Token::opLT:
291	+	match = propertyValue < comparisonValue;
292	+	break;
293	+	case Token::opLE:
294	+	match = propertyValue <= comparisonValue;
295	+	break;
296	+	case Token::opGE:
297	+	match = propertyValue >= comparisonValue;
298	+	break;
299	+	case Token::opGT:
300	+	match = propertyValue > comparisonValue;
301	+	break;
302	+	case Token::opEQ:
303	+	match = propertyValue == comparisonValue;
304	+	break;
305	+	case Token::opNE:
306	+	match = propertyValue != comparisonValue;
307	+	break;
308	+	}
309	+	if (match)
310	+	bs.setBitOn(sd->getGlobalIndex());
311	+
312		}
313
314	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
315	+	OpenMDBitSet& bs){
316	+
317	+	boost::any withinSpec = instruction.value;
318	+	float distance;
319	+	if (withinSpec.type() == typeid(float)){
320	+	distance = boost::any_cast<float>(withinSpec);
321	+	} else if (withinSpec.type() == typeid(int)) {
322	+	distance = boost::any_cast<int>(withinSpec);
323	+	} else {
324	+	evalError("casting error in withinInstruction");
325	+	bs.clearAll();
326	+	}
327	+
328	+	bs = distanceFinder.find(bs, distance);
329	+	}
330	+
331		void SelectionEvaluator::define() {
332		assert(statement.size() >= 3);
333	<
333	>
334		std::string variable = boost::any_cast<std::string>(statement[1].value);
335
336	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
336	>	variables.insert(VariablesType::value_type(variable,
337	>	expression(statement, 2)));
338		}
339	<	}
339	>
340
341	<	/** @todo */
342	<	void SelectionEvaluator::predefine(const std::string& script) {
343	<
341	>	/** @todo */
342	>	void SelectionEvaluator::predefine(const std::string& script) {
343	>
344		if (compiler.compile("#predefine", script)) {
345	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
346	<	if (aatoken.size() != 1) {
347	<	evalError("predefinition does not have exactly 1 command:"
348	<	+ script);
349	<	return;
350	<	}
351	<	std::vector<Token> statement = aatoken[0];
352	<	if (statement.size() > 2) {
353	<	int tok = statement[1].tok;
354	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
355	<	std::string variable = (std::string)statement[1].value;
356	<	variables.insert(std::make_pair(variable, statement));
357	<
358	<	} else {
359	<	evalError("invalid variable name:" + script);
360	<	}
361	<	}else {
362	<	evalError("bad predefinition length:" + script);
363	<	}
364	<
345	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
346	>	if (aatoken.size() != 1) {
347	>	evalError("predefinition does not have exactly 1 command:"
348	>	+ script);
349	>	return;
350	>	}
351	>	std::vector<Token> statement = aatoken[0];
352	>	if (statement.size() > 2) {
353	>	int tok = statement[1].tok;
354	>	if (tok == Token::identifier ||
355	>	(tok & Token::predefinedset) == Token::predefinedset) {
356	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
357	>	variables.insert(VariablesType::value_type(variable, statement));
358	>
359	>	} else {
360	>	evalError("invalid variable name:" + script);
361	>	}
362	>	}else {
363	>	evalError("bad predefinition length:" + script);
364	>	}
365
366		} else {
367	<	evalError("predefined set compile error:" + script +
368	<	"\ncompile error:" + compiler.getErrorMessage());
367	>	evalError("predefined set compile error:" + script +
368	>	"\ncompile error:" + compiler.getErrorMessage());
369		}
370	+	}
371
372	<	}
372	>	void SelectionEvaluator::select(OpenMDBitSet& bs){
373	>	bs = expression(statement, 1);
374	>	}
375	>
376	>	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
377	>
378	>	OpenMDBitSet bs(nStuntDouble);
379	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
380	>
381	>	if (i != variables.end()) {
382	>	if (i->second.type() == typeid(OpenMDBitSet)) {
383	>	return boost::any_cast<OpenMDBitSet>(i->second);
384	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
385	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
386	>	i->second =  bs; /**@todo fixme */
387	>	return bs;
388	>	}
389	>	} else {
390	>	unrecognizedIdentifier(variable);
391	>	}
392	>
393	>	return bs;
394	>	}
395	>
396	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
397	>	return nameFinder.match(name);
398	>	}
399
400	<	void SelectionEvaluator::select(){
401	<	viewer.setSelectionSet(expression(statement, 1));
402	<	}
400	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
401	>	std::vector<Token>::const_iterator i;
402	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
403	>	if (i->tok & Token::dynamic) {
404	>	return true;
405	>	}
406	>	}
407	>
408	>	return false;
409	>	}
410
411	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
411	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
412	>	variables.clear();
413	>	//load predefine
414	>	//predefine();
415	>	}
416
417	<	std::map<std::string, boost::any>::iterator i = variables.find(variable);
417	>	OpenMDBitSet SelectionEvaluator::evaluate() {
418	>	OpenMDBitSet bs(nStuntDouble);
419	>	if (isLoaded_) {
420	>	pc = 0;
421	>	instructionDispatchLoop(bs);
422	>	}
423
424	<	if (i != variables.end()) {
425	<	if (i->second.type() == typeid(BitSet)) {
426	<	return boost::any_cast<BitSet>(i->second);
427	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
428	<	BitSet bs = expression(boost::any_cast(i->second), 2);
429	<	i->second =  bs; /**@todo fixme */
430	<	return bs;
431	<	}
424	>	return bs;
425	>	}
426	>
427	>	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
428	>	OpenMDBitSet bs(nStuntDouble);
429	>
430	>	if (value.type() == typeid(int)) {
431	>	int index = boost::any_cast<int>(value);
432	>	if (index < 0 || index >= bs.size()) {
433	>	invalidIndex(index);
434	>	} else {
435	>	bs = indexFinder.find(index);
436	>	}
437	>	} else if (value.type() == typeid(std::pair<int, int>)) {
438	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
439	>	assert(indexRange.first <= indexRange.second);
440	>	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
441	>	invalidIndexRange(indexRange);
442	>	}else {
443	>	bs = indexFinder.find(indexRange.first, indexRange.second);
444	>	}
445		}
446
447	<	}
447	>	return bs;
448	>	}
449
450	+
451	+	OpenMDBitSet SelectionEvaluator::hull() {
452	+	OpenMDBitSet bs(nStuntDouble);
453	+
454	+	bs = hullFinder.findHull();
455	+
456	+	return bs;
457	+	}
458	+
459	+
460	+
461	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
462	+	RealType charge =0.0;
463	+	AtomType* atomType = atom->getAtomType();
464	+	if (atomType->isCharge()) {
465	+	GenericData* data = atomType->getPropertyByName("Charge");
466	+	if (data != NULL) {
467	+	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
468	+
469	+	if (doubleData != NULL) {
470	+	charge = doubleData->getData();
471	+
472	+	} else {
473	+	sprintf( painCave.errMsg,
474	+	"Can not cast GenericData to DoubleGenericData\n");
475	+	painCave.severity = OPENMD_ERROR;
476	+	painCave.isFatal = 1;
477	+	simError();
478	+	}
479	+	}
480	+	}
481	+
482	+	return charge;
483	+	}
484	+
485		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 282 by tim, Thu Feb 3 14:04:59 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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