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root/OpenMD/branches/development/src/selection/SelectionEvaluator.cpp

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trunk/src/selection/SelectionEvaluator.cpp (file contents), Revision 288 by tim, Fri Feb 4 22:39:26 2005 UTC vs.
branches/development/src/selection/SelectionEvaluator.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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>
#	Line 45 | Line 46
46		#include "primitives/DirectionalAtom.hpp"
47		#include "primitives/RigidBody.hpp"
48		#include "primitives/Molecule.hpp"
49	+	#include "io/ifstrstream.hpp"
50
51	<	namespace oopse {
51	>	namespace OpenMD {
52
53
54	<	SelectionEvaluator::SelectionEvaluator(SimInfo* si) : info(si), finder(info), isLoaded_(false){
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	<	}
62	<
56	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
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	<	std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
70	<	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;
#	Line 73 | Line 84 | bool SelectionEvaluator::loadScript(const std::string&
84
85		isDynamic_ = false;
86		for (i = aatoken.begin(); i != aatoken.end(); ++i) {
87	<	if (containDynamicToken(*i)) {
88	<	isDynamic_ = true;
89	<	break;
90	<	}
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() {
87	<	//for (int i = scriptLevelMax; --i >= 0; )
88	<	//    stack[i].clear();
89	<	//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  std::string & filename) {
113	<	ifstream ifs(filename.c_str());
112	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
113	>	ifstrstream ifs(filename.c_str());
114		if (!ifs.is_open()) {
115	<	return false;
115	>	return false;
116		}
117	<
117	>
118		const int bufferSize = 65535;
119		char buffer[bufferSize];
120		std::string script;
121		while(ifs.getline(buffer, bufferSize)) {
122	<	script += buffer;
122	>	script += buffer;
123		}
124		return loadScript(filename, script);
125	<	}
126	<
127	<	void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
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(bs);
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		}
145
146	<	}
146	>	}
147
148	<	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
149	<	BitSet bs;
150	<	std::stack<BitSet> stack;
151	<
148	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
149	>	int pcStart) {
150	>	OpenMDBitSet bs;
151	>	std::stack<OpenMDBitSet> stack;
152	>
153		for (int pc = pcStart; pc < code.size(); ++pc) {
154		Token instruction = code[pc];
155
#	Line 150 | Line 159 | void SelectionEvaluator::instructionDispatchLoop(BitSe
159		case Token::expressionEnd:
160		break;
161		case Token::all:
162	<	bs = BitSet(nStuntDouble);
162	>	bs = OpenMDBitSet(nStuntDouble);
163		bs.setAll();
164		stack.push(bs);
165		break;
166		case Token::none:
167	<	bs = BitSet(nStuntDouble);
167	>	bs = OpenMDBitSet(nStuntDouble);
168		stack.push(bs);
169		break;
170		case Token::opOr:
#	Line 172 | Line 181 | void SelectionEvaluator::instructionDispatchLoop(BitSe
181		stack.top().flip();
182		break;
183		case Token::within:
175	–
184		withinInstruction(instruction, stack.top());
185		break;
186	<	//case Token::selected:
187	<	//  stack.push(getSelectionSet());
188	<	//  break;
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		stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
194		break;
195	+	case Token::index:
196	+	stack.push(indexInstruction(instruction.value));
197		break;
198		case Token::identifier:
199		stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
#	Line 205 | Line 218 | void SelectionEvaluator::instructionDispatchLoop(BitSe
218
219
220
221	<	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
221	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
222		int comparator = instruction.tok;
223		int property = instruction.intValue;
224		float comparisonValue = boost::any_cast<float>(instruction.value);
225		float propertyValue;
226	<	BitSet bs(nStuntDouble);
226	>	OpenMDBitSet bs(nStuntDouble);
227	>	bs.clearAll();
228
229		SimInfo::MoleculeIterator mi;
230		Molecule* mol;
#	Line 218 | Line 232 | BitSet SelectionEvaluator::comparatorInstruction(const
232		Atom* atom;
233		Molecule::RigidBodyIterator rbIter;
234		RigidBody* rb;
221	–
222	–	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
235
236	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
237	<	compareProperty(atom, bs, property, comparator, comparisonValue);
238	<	}
239	<
240	<	//change the positions of atoms which belong to the rigidbodies
241	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
242	<	compareProperty(rb, bs, property, comparator, comparisonValue);
243	<	}
236	>	for (mol = info->beginMolecule(mi); mol != NULL;
237	>	mol = info->nextMolecule(mi)) {
238	>
239	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
240	>	compareProperty(atom, bs, property, comparator, comparisonValue);
241	>	}
242	>
243	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
244	>	rb = mol->nextRigidBody(rbIter)) {
245	>	compareProperty(rb, bs, property, comparator, comparisonValue);
246	>	}
247		}
248
249		return bs;
250	<	}
250	>	}
251
252	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
253	<	double propertyValue;
254	<	switch (property) {
255	<	case Token::mass:
256	<	propertyValue = sd->getMass();
257	<	break;
258	<	case Token::charge:
259	<	return;
260	<	//break;
261	<	case Token::dipole:
262	<	return;
263	<	//break;
264	<	default:
265	<	unrecognizedAtomProperty(property);
266	<	}
252	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
253	>	int property, int comparator,
254	>	float comparisonValue) {
255	>	RealType propertyValue = 0.0;
256	>	switch (property) {
257	>	case Token::mass:
258	>	propertyValue = sd->getMass();
259	>	break;
260	>	case Token::charge:
261	>	if (sd->isAtom()){
262	>	Atom* atom = static_cast<Atom*>(sd);
263	>	propertyValue = getCharge(atom);
264	>	} else if (sd->isRigidBody()) {
265	>	RigidBody* rb = static_cast<RigidBody*>(sd);
266	>	RigidBody::AtomIterator ai;
267	>	Atom* atom;
268	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
269	>	propertyValue+=  getCharge(atom);
270	>	}
271	>	}
272	>	break;
273	>	case Token::x:
274	>	propertyValue = sd->getPos().x();
275	>	break;
276	>	case Token::y:
277	>	propertyValue = sd->getPos().y();
278	>	break;
279	>	case Token::z:
280	>	propertyValue = sd->getPos().z();
281	>	break;
282	>	case Token::r:
283	>	propertyValue = sd->getPos().length();
284	>	break;
285	>	default:
286	>	unrecognizedAtomProperty(property);
287	>	}
288
289	<	bool match = false;
290	<	switch (comparator) {
291	<	case Token::opLT:
292	<	match = propertyValue < comparisonValue;
293	<	break;
294	<	case Token::opLE:
295	<	match = propertyValue <= comparisonValue;
296	<	break;
297	<	case Token::opGE:
298	<	match = propertyValue >= comparisonValue;
299	<	break;
300	<	case Token::opGT:
301	<	match = propertyValue > comparisonValue;
302	<	break;
303	<	case Token::opEQ:
304	<	match = propertyValue == comparisonValue;
305	<	break;
306	<	case Token::opNE:
307	<	match = propertyValue != comparisonValue;
308	<	break;
309	<	}
310	<	if (match)
311	<	bs.setBitOn(sd->getGlobalIndex());
312	<
313	<	}
278	<
279	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
289	>	bool match = false;
290	>	switch (comparator) {
291	>	case Token::opLT:
292	>	match = propertyValue < comparisonValue;
293	>	break;
294	>	case Token::opLE:
295	>	match = propertyValue <= comparisonValue;
296	>	break;
297	>	case Token::opGE:
298	>	match = propertyValue >= comparisonValue;
299	>	break;
300	>	case Token::opGT:
301	>	match = propertyValue > comparisonValue;
302	>	break;
303	>	case Token::opEQ:
304	>	match = propertyValue == comparisonValue;
305	>	break;
306	>	case Token::opNE:
307	>	match = propertyValue != comparisonValue;
308	>	break;
309	>	}
310	>	if (match)
311	>	bs.setBitOn(sd->getGlobalIndex());
312	>
313	>	}
314
315	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
316	+	OpenMDBitSet& bs){
317	+
318		boost::any withinSpec = instruction.value;
319	+	float distance;
320		if (withinSpec.type() == typeid(float)){
321	<	//
322	<	return;
321	>	distance = boost::any_cast<float>(withinSpec);
322	>	} else if (withinSpec.type() == typeid(int)) {
323	>	distance = boost::any_cast<int>(withinSpec);
324	>	} else {
325	>	evalError("casting error in withinInstruction");
326	>	bs.clearAll();
327		}
328
329	<	evalError("Unrecognized within parameter");
330	<	}
331	<
332	<	void SelectionEvaluator::define() {
329	>	bs = distanceFinder.find(bs, distance);
330	>	}
331	>
332	>	void SelectionEvaluator::define() {
333		assert(statement.size() >= 3);
334	<
334	>
335		std::string variable = boost::any_cast<std::string>(statement[1].value);
336	+
337	+	variables.insert(VariablesType::value_type(variable,
338	+	expression(statement, 2)));
339	+	}
340	+
341
342	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
343	<	}
344	<
298	<
299	<	/** @todo */
300	<	void SelectionEvaluator::predefine(const std::string& script) {
301	<
342	>	/** @todo */
343	>	void SelectionEvaluator::predefine(const std::string& script) {
344	>
345		if (compiler.compile("#predefine", script)) {
346	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
347	<	if (aatoken.size() != 1) {
348	<	evalError("predefinition does not have exactly 1 command:"
349	<	+ script);
350	<	return;
351	<	}
352	<	std::vector<Token> statement = aatoken[0];
353	<	if (statement.size() > 2) {
354	<	int tok = statement[1].tok;
355	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
356	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
357	<	variables.insert(std::make_pair(variable, statement));
358	<
359	<	} else {
360	<	evalError("invalid variable name:" + script);
361	<	}
362	<	}else {
363	<	evalError("bad predefinition length:" + script);
364	<	}
365	<
346	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
347	>	if (aatoken.size() != 1) {
348	>	evalError("predefinition does not have exactly 1 command:"
349	>	+ script);
350	>	return;
351	>	}
352	>	std::vector<Token> statement = aatoken[0];
353	>	if (statement.size() > 2) {
354	>	int tok = statement[1].tok;
355	>	if (tok == Token::identifier ||
356	>	(tok & Token::predefinedset) == Token::predefinedset) {
357	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
358	>	variables.insert(VariablesType::value_type(variable, statement));
359	>
360	>	} else {
361	>	evalError("invalid variable name:" + script);
362	>	}
363	>	}else {
364	>	evalError("bad predefinition length:" + script);
365	>	}
366
367		} else {
368	<	evalError("predefined set compile error:" + script +
369	<	"\ncompile error:" + compiler.getErrorMessage());
368	>	evalError("predefined set compile error:" + script +
369	>	"\ncompile error:" + compiler.getErrorMessage());
370		}
371	+	}
372
373	<	}
330	<
331	<	void SelectionEvaluator::select(BitSet& bs){
373	>	void SelectionEvaluator::select(OpenMDBitSet& bs){
374		bs = expression(statement, 1);
375	<	}
376	<
377	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
378	<
375	>	}
376	>
377	>	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
378	>
379	>	OpenMDBitSet bs(nStuntDouble);
380		std::map<std::string, boost::any>::iterator i = variables.find(variable);
381	<
381	>
382		if (i != variables.end()) {
383	<	if (i->second.type() == typeid(BitSet)) {
384	<	return boost::any_cast<BitSet>(i->second);
385	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
386	<	BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
387	<	i->second =  bs; /**@todo fixme */
388	<	return bs;
389	<	}
383	>	if (i->second.type() == typeid(OpenMDBitSet)) {
384	>	return boost::any_cast<OpenMDBitSet>(i->second);
385	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
386	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
387	>	i->second =  bs; /**@todo fixme */
388	>	return bs;
389	>	}
390		} else {
391	<	unrecognizedIdentifier(variable);
391	>	unrecognizedIdentifier(variable);
392		}
350	–	}
351	–
352	–	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
393
394	<	return finder.match(name);
394	>	return bs;
395	>	}
396	>
397	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
398	>	return nameFinder.match(name);
399	>	}
400
401	<	}
357	<
358	<	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
401	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
402		std::vector<Token>::const_iterator i;
403		for (i = tokens.begin(); i != tokens.end(); ++i) {
404	<	if (i->tok & Token::dynamic) {
405	<	return true;
406	<	}
404	>	if (i->tok & Token::dynamic) {
405	>	return true;
406	>	}
407		}
408	<
408	>
409		return false;
410	<	}
410	>	}
411
412	<	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
412	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
413		variables.clear();
414		//load predefine
415		//predefine();
416	<	}
416	>	}
417
418	<	BitSet SelectionEvaluator::evaluate() {
419	<	BitSet bs(nStuntDouble);
418	>	OpenMDBitSet SelectionEvaluator::evaluate() {
419	>	OpenMDBitSet bs(nStuntDouble);
420		if (isLoaded_) {
421	<	instructionDispatchLoop(bs);
421	>	pc = 0;
422	>	instructionDispatchLoop(bs);
423		}
424
425		return bs;
426	<	}
383	<
384	<	//BitSet SelectionEvaluator::evaluate(int frameNo) {
385	<	//
386	<	//}
426	>	}
427
428	+	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
429	+	OpenMDBitSet bs(nStuntDouble);
430	+
431	+	if (value.type() == typeid(int)) {
432	+	int index = boost::any_cast<int>(value);
433	+	if (index < 0 || index >= bs.size()) {
434	+	invalidIndex(index);
435	+	} else {
436	+	bs = indexFinder.find(index);
437	+	}
438	+	} else if (value.type() == typeid(std::pair<int, int>)) {
439	+	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
440	+	assert(indexRange.first <= indexRange.second);
441	+	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
442	+	invalidIndexRange(indexRange);
443	+	}else {
444	+	bs = indexFinder.find(indexRange.first, indexRange.second);
445	+	}
446	+	}
447	+
448	+	return bs;
449	+	}
450	+
451	+
452	+	OpenMDBitSet SelectionEvaluator::hull() {
453	+	OpenMDBitSet bs(nStuntDouble);
454	+
455	+	bs = hullFinder.findHull();
456	+
457	+	return bs;
458	+	}
459	+
460	+
461	+
462	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
463	+	RealType charge =0.0;
464	+	AtomType* atomType = atom->getAtomType();
465	+	if (atomType->isCharge()) {
466	+	GenericData* data = atomType->getPropertyByName("Charge");
467	+	if (data != NULL) {
468	+	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
469	+
470	+	if (doubleData != NULL) {
471	+	charge = doubleData->getData();
472	+
473	+	} else {
474	+	sprintf( painCave.errMsg,
475	+	"Can not cast GenericData to DoubleGenericData\n");
476	+	painCave.severity = OPENMD_ERROR;
477	+	painCave.isFatal = 1;
478	+	simError();
479	+	}
480	+	}
481	+	}
482	+
483	+	return charge;
484	+	}
485	+
486		}

Comparing:
trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords), Revision 288 by tim, Fri Feb 4 22:39:26 2005 UTC vs.
branches/development/src/selection/SelectionEvaluator.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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